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====== Finding genes of interest with PANTHER HMMs ======

By Joran Martijn (Sep 2023)

===== The PANTHER database =====

The [[https://www.pantherdb.org/|PANTHER]] (**P**rotein **AN**alysis **TH**rough **E**volutionary **R**elationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. The goal of PANTHER is to classify proteins by **function**.
 
The PANTHER initiative started in 1998 and was the first online database that included protein phylogenetic trees. Initially, very few species had whole genome sequences available but starting with version 6 (released in 2006), many more species were added. PANTHER16 (or 17?) included **142 fully sequenced genomes**, including 19 vertebrates, 15 invertebrates, 14 fungi, 40 plants, 11 other eukaryotes, 8 archaea and 35 bacteria. The list is thus fairly limited and, more focused towards non-protist eukaryotes.

In 2002, PANTHER3 had 271779 proteins over 6155 families. In 2020, PANTHER16 had 2063337 proteins over 15635 families.

PANTHER families are defined as clusters of related proteins for which a good multiple sequence alignment can be made (defined in their original [[https://genome.cshlp.org/content/13/9/2129.short|2003 paper]] ). The emphasis is thus not so much on trying to reconstruct exact, complete orthogroups, but rather groupings that are useful to predict protein function on new protein sequences.

A key aspect of the PANTHER database is the division of families into multiple **subfamilies**. PANTHER's focus is on function and to a lesser degree evolutionary history, hence they attempt to classify proteins with distinct functions into distinct subfamilies. The idea is thus that each different subfamily has a distinct function.

The splitting of families into subfamilies was initially I think mostly done manually by trained biologists. However, in the most recent versions, it seems to be a mostly automated process but with the results still curated by trained biologists. In the [[https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4218|2021 paper]] a subfamily is defined as follows

A subfamily roughly corresponds to a group of least diverged orthologs, 
  in that most members of each subfamily are mutually least diverged orthologs 
  of all other members of the subfamily

I find this definition a bit cryptic, but it becomes a bit clearer with the visual example that they provide in the 2021 paper.

Here, sequences from distinct subfamilies are given a different color (blue, red, brown, pink, green). Speciation events are marked with green circles, duplication events with orange circles. Triangles are collapsed nodes, and diamonds indicate the root nodes of distinct subfamilies.

What becomes immediately apparent is that subfamilies are not necessary monophyletic! For example, the blue subfamily are polyphyletic (or paraphyletic?).

This is because of a **duplication event** that happened in the bottom daughter of the global root node. Two branches flow from the duplication event: a shorter one and a longer one. In PANTHERs definition, the sequences emerging from the shorter one comprise the least diverged orthologs (orthologs relative to the DANRE/ORYLA lineage on the top of the figure), and thus they belong to the same subfamily as the DANRE/ORYLA proteins. The sequences emerging from the longer one are thus NOT the least diverged, and hence they belong to a distinct subfamily.

Thus, any time a duplication event happens, a new subfamily is spawned. The exception is when the duplication leads to in-paralogs, or technically more specifically, to within-genome paralogs. That is why the duplication to the ORYLA and ORNAN copies did not spawn new subfamilies. The implication here is thus that after a duplication, one of the copies evolves to assume a new functional role.

Each family and subfamily in the database has associated with it a MSA, a tree and an HMM. The HMMs are useful to detect orthologs of these families and subfamilies in your pet genome. It is also useful to compare the E-values / bit-scores between families and subfamilies. If a novel predicted protein from your pet genome scores more highly against a family than a subfamily, it may indicate that your protein represents a novel subfamily.

===== PANTHER on Perun =====

Currently, the PANTHER17 database is stored on Perun here ''/scratch3/rogerlab_databases/other_dbs/PANTHER17.0/''. It contains two subdirectories, ''books/'' and ''globals/''. The ''globals'' directory contains the actual database of HMMs, ''binHmm.*'' files, and ''names.tab'', a file containing the actual annotation of each family and subfamily. Let's take a closer look:

<code>
PTHR10000.mag.mod       PHOSPHOSERINE PHOSPHATASE
PTHR10000.SF55.mod      5-AMINO-6-(5-PHOSPHO-D-RIBITYLAMINO)URACIL PHOSPHATASE YCSE
PTHR10000.SF23.mod      5-AMINO-6-(5-PHOSPHO-D-RIBITYLAMINO)URACIL PHOSPHATASE YITU
PTHR10000.SF57.mod      KANOSAMINE-6-PHOSPHATE PHOSPHATASE
...                     ...
PTHR10000.SF56.mod      MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
PTHR10003.mag.mod       SUPEROXIDE DISMUTASE  CU-ZN -RELATED
PTHR10003.SF95.mod      SUPEROXIDE DISMUTASE [CU-ZN] 2, CHLOROPLASTIC
PTHR10003.SF82.mod      SOD_CU DOMAIN-CONTAINING PROTEIN
PTHR10003.SF94.mod      EXTRACELLULAR SUPEROXIDE DISMUTASE [CU-ZN] 3
PTHR10003.SF31.mod      SUPEROXIDE DISMUTASE [CU-ZN] 3
...                     ...
</code>

Those ending with ''.mag.mod'' are families, and those ending with ''.SF[number].mod'' are their respective subfamilies.

The ''Light_panther17.tsv'' file is a simple list of all families.

===== Searching your genome for PANTHER families homologs =====

==== Do an hmmscan or hmmsearch ====

Simply do an ''hmmscan'' from the HMMER3 package. hmmscan takes as a query a single or a list of protein sequences and compares them with a database of HMM profiles. Below, we are taking the entire PANTHER17 database of HMMs as a database.

<code>
hmmscan \
   -E 0.001 --incE 0.0001 \
   --domE 0.01 --incdomE 0.01 \
   --notextw --cpu 10 \
   --tblout ergo_vs_panther17.tblout --domtblout ergo_vs_panther17.domtblout
   binHmm Ergobibamus_cyprinoides_CL.proteins.fa
</code>

''hmmscan'' can be very slow sometimes. In which case you'll want to use ''hmmsearch'', which sometimes is more computationally efficient.

<code>
hmmsearch \
   -Z 140251 --domZ 140251 \
   -E 0.001 --incE 0.0001 \
   --domE 0.01 --incdomE 0.01 \
   --notextw --cpu 10 \
   --tblout ergo_vs_panther17.tblout \
   --domtblout ergo_vs_panther17.domtblout \
   binHmm_flat.hmm Ergobibamus_cyprinoides_CL.proteins.fa
</code>

''-Z'' and ''--domZ'' have to manually adjusted to be set to 140251, i.e. the number of profiles in the PANTHER17 profile database. Otherwise the E-value will be calculated using the number of proteins of the Ergobibamus proteome instead. We don't want that, it should be calculated with the size of the PANTHER17 database.

This will yield two outfiles, the ''ergo_vs_panther17.tblout'' and ''ergo_vs_panther17.domtblout''.

The ''.tblout'' file is a tabular output file where each line has a unique query (a protein sequence) and target (the HMM profile) combination. The overall E-value and score between HMM and sequence are reported ("full sequence"), as well as the segment of the protein that scored the highest with said HMM ("best 1 domain"), as well as a bunch of metrics for estimating the number of "domains".

<code>
#                                                                --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name         accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
# ------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
PTHR31752.SF18.pir    -          FUN_000001-T1        -            6.8e-23   83.9   5.0   3.3e-12   48.7   2.4   2.1   1   1   1   2   2   2   2 -
PTHR36838.orig.30.pir -          FUN_000001-T1        -            5.6e-22   81.0  13.0     7e-22   80.7   1.8   2.2   2   0   0   2   2   2   2 -
PTHR36838.SF1.pir     -          FUN_000001-T1        -            1.9e-19   72.8   4.4   1.9e-19   72.8   4.4   2.4   2   0   0   2   2   1   1 -
PTHR31752.orig.30.pir -          FUN_000001-T1        -            3.3e-16   62.0   4.6   2.6e-14   55.7   4.6   2.2   1   1   0   1   1   1   1 -
PTHR36838.SF3.pir     -          FUN_000001-T1        -            1.4e-12   50.3   3.7   2.6e-12   49.3   0.1   2.2   2   0   0   2   2   1   1 -
PTHR31752.SF40.pir    -          FUN_000001-T1        -            1.2e-11   47.3   0.0     2e-11   46.6   0.0   1.3   1   0   0   1   1   1   1 -
PTHR31752.SF2.pir     -          FUN_000001-T1        -            5.5e-09   38.3   0.0     7e-09   38.0   0.0   1.2   1   0   0   1   1   1   1 -
PTHR31752.SF49.pir    -          FUN_000001-T1        -            3.4e-08   35.9   0.0   5.9e-08   35.2   0.0   1.4   1   0   0   1   1   1   1 -
...
</code>

NOTE that the outfile uses the word "domain" because traditionally HMM profiles describe protein domains. The Pfam is a good example of a database of domain HMM profiles. PANTHER HMM describes entire proteins. Hence the term 'domain' is not very well suited here, and can be a bit confusing.

NOTE also that the names of the families are slightly different here. Instead of ending with ''.mag.mod'' or ''.SF[number].mod'', they end with ''.orig.30.pir'' and ''.SF[number].pir''.

A protein sequence may have multiple segments that each match well with a particular HMM profile independently. To see each of these alignments separately, we can inspect the ''.domtblout'' file:

<code>
#                                                                             --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
# target name         accession   tlen query name           accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
# ------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
PTHR31752.SF18.pir    -            418 FUN_000001-T1        -            412   6.8e-23   83.9   5.0   1   2   1.9e-16   3.3e-12   48.7   2.4     9   167    10   174     4   201 0.78 -
PTHR31752.SF18.pir    -            418 FUN_000001-T1        -            412   6.8e-23   83.9   5.0   2   2   1.4e-12   2.4e-08   35.9   0.0   261   369   210   350   182   404 0.72 -
PTHR36838.orig.30.pir -            308 FUN_000001-T1        -            412   5.6e-22   81.0  13.0   1   2     4e-26     7e-22   80.7   1.8    10   214    15   272     9   281 0.82 -
PTHR36838.orig.30.pir -            308 FUN_000001-T1        -            412   5.6e-22   81.0  13.0   2   2    0.0028        50    5.6   3.8   222   276   310   367   301   398 0.80 -
PTHR36838.SF1.pir     -            308 FUN_000001-T1        -            412   1.9e-19   72.8   4.4   1   1   1.1e-23   1.9e-19   72.8   4.4     9   211    14   269     8   276 0.82 -
PTHR31752.orig.30.pir -            405 FUN_000001-T1        -            412   3.3e-16   62.0   4.6   1   1   1.4e-18   2.6e-14   55.7   4.6    10   340    10   330     3   402 0.73 -
PTHR36838.SF3.pir     -            312 FUN_000001-T1        -            412   1.4e-12   50.3   3.7   1   1   1.5e-16   2.6e-12   49.3   0.1    10   216    16   272    10   279 0.77 -
PTHR31752.SF40.pir    -            360 FUN_000001-T1        -            412   1.2e-11   47.3   0.0   1   1   1.1e-15     2e-11   46.6   0.0    37   267    36   274     8   282 0.75 -
PTHR31752.SF2.pir     -            349 FUN_000001-T1        -            412   5.5e-09   38.3   0.0   1   1     4e-13     7e-09   38.0   0.0   103   284   105   332    60   400 0.70 -
...
</code>

Now, each line represents a unique "domain" (i.e. segment of a protein sequence) and HMM profile combination. The overall E-value and score between HMM and the full sequence is still reported, as well as the scores of the specific "domains" that were found for each sequence.

==== Add HMM profile coverage information ====

You may want to reduce the number of false positives (i.e. protein sequences that match with an HMM but are not really orthologs) by discarding queries that only have partial alignments with the HMM. With BLAST I like to use the fields ''qcovhsp'', ''qcovs'', which describe how much of the query was covered by the HSP (High scoring Segment Pair, or in simpler terms, the alignment between query and hit) (qcovhsp) or collection of alignments between the same query and hit (qcovs). For example, if an alignment covered less than, say 60% of the length of the query, I may consider it a false positive hit. Unfortunately, HMMER does not directly report such metrics, but it does report the metrics necessary to calculate them. I wrote a python script, ''extend_hmmer_domtblout.py'' that does exactly this:

<code>
# if you did hmmscan
python extend_hmmer_domtblout.py -m hmmscan -i ergo_vs_panther17.domtblout > ergo_vs_panther17.ext.domtblout

# if you did hmmsearch
python extend_hmmer_domtblout.py -m hmmsearch -i ergo_vs_panther17.domtblout > ergo_vs_panther17.ext.domtblout
</code>

This yields a file that looks like this (if you did hmmscan)

<code>
TargetName             TargetAcc  TargetLen  QueryName      QueryAcc  QueryLen  seq-E-value  seq-Score  seq-Bias  dom-No  dom-Count  dom-c-Evalue  dom-i-Evalue  dom-Score  dom-Bias  hmm-From  hmm-To  ali-From  ali-To  env-From  env-To  mean-PP  DescriptionOfTarget  qcovhsp  tcovhsp  qcovs  tcovs
PTHR31752.SF18.pir     -          418        FUN_000001-T1  -         412       6.8e-23      83.9       5.0       1       2          1.9e-16       3.3e-12       48.7       2.4       9         167     10        174     4         201     0.78     -                    0.40     0.38     0.74   0.64
PTHR31752.SF18.pir     -          418        FUN_000001-T1  -         412       6.8e-23      83.9       5.0       2       2          1.4e-12       2.4e-08       35.9       0.0       261       369     210       350     182       404     0.72     -                    0.34     0.26     0.74   0.64
PTHR36838.orig.30.pir  -          308        FUN_000001-T1  -         412       5.6e-22      81.0       13.0      1       2          4e-26         7e-22         80.7       1.8       10        214     15        272     9         281     0.82     -                    0.63     0.67     0.77   0.84
PTHR36838.orig.30.pir  -          308        FUN_000001-T1  -         412       5.6e-22      81.0       13.0      2       2          0.0028        50.0          5.6        3.8       222       276     310       367     301       398     0.8      -                    0.14     0.18     0.77   0.84
PTHR36838.SF1.pir      -          308        FUN_000001-T1  -         412       1.9e-19      72.8       4.4       1       1          1.1e-23       1.9e-19       72.8       4.4       9         211     14        269     8         276     0.82     -                    0.62     0.66     0.62   0.66
PTHR31752.orig.30.pir  -          405        FUN_000001-T1  -         412       3.3e-16      62.0       4.6       1       1          1.4e-18       2.6e-14       55.7       4.6       10        340     10        330     3         402     0.73     -                    0.78     0.82     0.78   0.82
PTHR36838.SF3.pir      -          312        FUN_000001-T1  -         412       1.4e-12      50.3       3.7       1       1          1.5e-16       2.6e-12       49.3       0.1       10        216     16        272     10        279     0.77     -                    0.62     0.66     0.62   0.66
PTHR31752.SF40.pir     -          360        FUN_000001-T1  -         412       1.2e-11      47.3       0.0       1       1          1.1e-15       2e-11         46.6       0.0       37        267     36        274     8         282     0.75     -                    0.58     0.64     0.58   0.64
PTHR31752.SF2.pir      -          349        FUN_000001-T1  -         412       5.5e-09      38.3       0.0       1       1          4e-13         7e-09         38.0       0.0       103       284     105       332     60        400     0.7      -                    0.55     0.52     0.55   0.52
PTHR31752.SF49.pir     -          358        FUN_000001-T1  -         412       3.4e-08      35.9       0.0       1       1          3.3e-12       5.9e-08       35.2       0.0       39        309     38        319     6         370     0.72     -                    0.68     0.76     0.68   0.76
PTHR31913.orig.30.pir  -          655        FUN_000003-T1  -         778       1e-54        189.4      0.0       1       1          7.2e-59       2e-54         188.4      0.0       203       649     350       776     296       778     0.83     -                    0.55     0.68     0.55   0.68
PTHR31913.SF0.pir      -          659        FUN_000003-T1  -         778       8e-54        186.4      0.0       1       1          5.1e-58       1.4e-53       185.6      0.0       313       653     441       776     332       778     0.88     -                    0.43     0.52     0.43   0.52
PTHR31913.SF7.pir      -          619        FUN_000003-T1  -         778       7.6e-15      57.4       0.0       1       1          4.9e-19       1.4e-14       56.6       0.0       325       551     516       730     506       739     0.85     -                    0.28     0.37     0.28   0.37
...
</code>

The script does a few things. It reformats the header line, and it makes the whole table tab delimited, which makes it easier to parse later on. Most importantly, it adds 4 new columns, ''qcovhsp'', ''tcovhsp'', ''qcovs'' and ''tcovs''.

<code>
qcovhsp        how much of the query (the protein sequence) is covered by the HMM:protein alignment
tcovhsp        how much of the target (the HMM profile) is covered by the HMM:protein alignment
qcovs          how much of the query (the protein sequence) is covered _in_total_ by all HMM:protein alignments between this HMM and this protein
tcovs          how much of the target (the HMM profile) is covered _in_total_ by all HMM:protein alignments between this HMM and this protein
</code>

The ''qcovs'' and ''tcovs'' metrics are particularly useful when working with PANTHER HMM-profiles because of the nature of these profiles. Since they describe entire proteins, and not just single domains, a true but distant ortholog of the PANTHER family may not align well over the entire profile. Poorly conserved regions, such as those in between conserved domains (i.e. 'linker' regions) tend to prematurely break the alignment between protein and profile. Thus, we'd get two significant hits, one with the first part of the profile, and one with the second part of the profile. The ''qcovs'' and ''tcovs'' thus take into account both alignments, whereas the ''qcovhsp'' and ''tcovhsp'' do not.
==== Add PANTHER annotation ====

Knowing which families and subfamilies had hits in your genome is nice and all, but it's just a bunch of unintelligible identifiers. I wrote another script that links these identifiers with their actual annotations (this linking information is found in ''names.tab'' and adds the actual annotations to the ''.domtblout'' file

<code>
add_pthr_annotation_to_hmmer_out.py -i ergo_vs_panther17.ext.domtblout -n names.tab > ergo_vs_panther17.annot.ext.domtblout
</code>

The output file will look something like this

<code>
TargetName             TargetAcc  TargetLen  QueryName      QueryAcc  QueryLen  seq-E-value  seq-Score  seq-Bias  dom-No  dom-Count  dom-c-Evalue  dom-i-Evalue  dom-Score  dom-Bias  hmm-From  hmm-To  ali-From  ali-To  env-From  env-To  mean-PP  DescriptionOfTarget  qcovhsp  tcovhsp  qcovs  tcovs    annotation
PTHR31752.SF18.pir     -          418        FUN_000001-T1  -         412       6.8e-23      83.9       5.0       1       2          1.9e-16       3.3e-12       48.7       2.4       9         167     10        174     4         201     0.78     -                    0.40     0.38     0.74   0.64     AUXIN_EFFLUX_CARRIER_COMPONENT_3A
PTHR31752.SF18.pir     -          418        FUN_000001-T1  -         412       6.8e-23      83.9       5.0       2       2          1.4e-12       2.4e-08       35.9       0.0       261       369     210       350     182       404     0.72     -                    0.34     0.26     0.74   0.64     AUXIN_EFFLUX_CARRIER_COMPONENT_3A
PTHR36838.orig.30.pir  -          308        FUN_000001-T1  -         412       5.6e-22      81.0       13.0      1       2          4e-26         7e-22         80.7       1.8       10        214     15        272     9         281     0.82     -                    0.63     0.67     0.77   0.84     AUXIN_EFFLUX_CARRIER_FAMILY_PROTEIN
PTHR36838.orig.30.pir  -          308        FUN_000001-T1  -         412       5.6e-22      81.0       13.0      2       2          0.0028        50.0          5.6        3.8       222       276     310       367     301       398     0.8      -                    0.14     0.18     0.77   0.84     AUXIN_EFFLUX_CARRIER_FAMILY_PROTEIN
PTHR36838.SF1.pir      -          308        FUN_000001-T1  -         412       1.9e-19      72.8       4.4       1       1          1.1e-23       1.9e-19       72.8       4.4       9         211     14        269     8         276     0.82     -                    0.62     0.66     0.62   0.66     SLR1864_PROTEIN
PTHR31752.orig.30.pir  -          405        FUN_000001-T1  -         412       3.3e-16      62.0       4.6       1       1          1.4e-18       2.6e-14       55.7       4.6       10        340     10        330     3         402     0.73     -                    0.78     0.82     0.78   0.82     AUXIN_EFFLUX_CARRIER_COMPONENT_1B-RELATED
PTHR36838.SF3.pir      -          312        FUN_000001-T1  -         412       1.4e-12      50.3       3.7       1       1          1.5e-16       2.6e-12       49.3       0.1       10        216     16        272     10        279     0.77     -                    0.62     0.66     0.62   0.66     AUXIN_EFFLUX_CARRIER_FAMILY_PROTEIN
PTHR31752.SF40.pir     -          360        FUN_000001-T1  -         412       1.2e-11      47.3       0.0       1       1          1.1e-15       2e-11         46.6       0.0       37        267     36        274     8         282     0.75     -                    0.58     0.64     0.58   0.64     AUXIN_EFFLUX_CARRIER_COMPONENT_8
PTHR31752.SF2.pir      -          349        FUN_000001-T1  -         412       5.5e-09      38.3       0.0       1       1          4e-13         7e-09         38.0       0.0       103       284     105       332     60        400     0.7      -                    0.55     0.52     0.55   0.52     AUXIN_EFFLUX_CARRIER_COMPONENT_5
PTHR31752.SF49.pir     -          358        FUN_000001-T1  -         412       3.4e-08      35.9       0.0       1       1          3.3e-12       5.9e-08       35.2       0.0       39        309     38        319     6         370     0.72     -                    0.68     0.76     0.68   0.76     AUXIN_EFFLUX_CARRIER_COMPONENT
PTHR31913.orig.30.pir  -          655        FUN_000003-T1  -         778       1e-54        189.4      0.0       1       1          7.2e-59       2e-54         188.4      0.0       203       649     350       776     296       778     0.83     -                    0.55     0.68     0.55   0.68     VACUOLAR_IMPORT_AND_DEGRADATION_PROTEIN_27
PTHR31913.SF0.pir      -          659        FUN_000003-T1  -         778       8e-54        186.4      0.0       1       1          5.1e-58       1.4e-53       185.6      0.0       313       653     441       776     332       778     0.88     -                    0.43     0.52     0.43   0.52     VACUOLAR_IMPORT_AND_DEGRADATION_PROTEIN_27
PTHR31913.SF7.pir      -          619        FUN_000003-T1  -         778       7.6e-15      57.4       0.0       1       1          4.9e-19       1.4e-14       56.6       0.0       325       551     516       730     506       739     0.85     -                    0.28     0.37     0.28   0.37     DEM_PROTEIN
PTHR31913.SF5.pir      -          613        FUN_000003-T1  -         778       2.3e-12      49.0       0.1       1       1          5.5e-16       1.5e-11       46.2       0.1       231       539     442       731     434       740     0.78     -                    0.37     0.50     0.37   0.50     VID27_DOMAIN-CONTAINING_PROTEIN
PTHR31913.SF2.pir      -          622        FUN_000003-T1  -         778       4.1e-08      35.1       0.0       1       1          1.4e-11       3.9e-07       31.9       0.0       325       553     516       729     506       738     0.77     -                    0.28     0.37     0.28   0.37     OS02G0789600_PROTEIN
PTHR23359.SF250.pir    -          270        FUN_000004-T1  -         520       7.6e-74      251.2      0.0       1       2          3.2e-74       7.2e-71       241.4      0.0       59        265     48        262     21        267     0.93     -                    0.41     0.77     0.45   0.77     KINASE,_PUTATIVE-RELATED
...
</code>

==== Filter by HMM profile coverage and composition bias ====

You may only want to keep proteins of your pet genome that are (nearly) fully covered by PANTHER (sub)families to reduce the number of false positives.

I did this by only keeping lines of the ''.domtblout'' where the ''tcovs'' (the coverage of the target accumulated over all protein:HMM-profile alignments; the 27th column) is at least 50% of the HMM-profile length, and the ''seq-Bias'' score (9th column) is less than 90% of the total bit ''seq-Score'' (8th column).

After that, the table is sorted by protein sequence identifier and only the best hit, according to seq-Score remains.

<code>
function body {
    IFS= read -r header
    printf '%s\n' "$header"
    "$@"
}

cat ergo_vs_panther17.annot.ext.domtblout \
    | body awk '$27>=0.50 && $9/$8<0.9' \
    | body sort -k4,4 -k8,8nr \
    | body sort -k4,4 -u \
    > ergo_vs_panther17.filt.ext.domtblout
</code>

The ''body'' function is a nifty trick to only apply your awk or sort operations on the body of the table and leave the header intact.

Our new file looks as follows:
<code>
TargetName             TargetAcc  TargetLen  QueryName      QueryAcc  QueryLen  seq-E-value  seq-Score  seq-Bias  dom-No  dom-Count  dom-c-Evalue  dom-i-Evalue  dom-Score  dom-Bias  hmm-From  hmm-To  ali-From  ali-To  env-From  env-To  mean-PP  DescriptionOfTarget  qcovhsp  tcovhsp  qcovs  tcovs    annotation
PTHR31752.SF18.pir     -          418        FUN_000001-T1  -         412       6.8e-23      83.9       5.0       1       2          1.9e-16       3.3e-12       48.7       2.4       9         167     10        174     4         201     0.78     -                    0.40     0.38     0.74   0.64     AUXIN_EFFLUX_CARRIER_COMPONENT_3A
PTHR31913.orig.30.pir  -          655        FUN_000003-T1  -         778       1e-54        189.4      0.0       1       1          7.2e-59       2e-54         188.4      0.0       203       649     350       776     296       778     0.83     -                    0.55     0.68     0.55   0.68     VACUOLAR_IMPORT_AND_DEGRADATION_PROTEIN_27
PTHR23359.SF250.pir    -          270        FUN_000004-T1  -         520       7.6e-74      251.2      0.0       1       2          3.2e-74       7.2e-71       241.4      0.0       59        265     48        262     21        267     0.93     -                    0.41     0.77     0.45   0.77     KINASE,_PUTATIVE-RELATED
PTHR45991.orig.30.pir  -          450        FUN_000005-T1  -         544       9.4e-99      334.2      0.0       1       1          2e-101        1.3e-98       333.8      0.0       32        438     18        505     11        520     0.86     -                    0.90     0.90     0.90   0.90     PACHYTENE_CHECKPOINT_PROTEIN_2
PTHR13563.orig.30.pir  -          346        FUN_000006-T1  -         343       8.1e-52      179.5      0.0       1       1          3.6e-56       1e-51         179.1      0.0       63        321     43        320     20        343     0.79     -                    0.81     0.75     0.81   0.75     TRNA_(GUANINE-9-)_METHYLTRANSFERASE
PTHR11685.SF436.pir    -          285        FUN_000007-T1  -         589       2.4e-19      72.8       8.5       1       1          5.8e-23       2.6e-19       72.6       8.5       76        240     241       491     132       578     0.7      -                    0.43     0.58     0.43   0.58     RBR-TYPE_E3_UBIQUITIN_TRANSFERASE
PTHR46233.orig.30.pir  -          231        FUN_000011-T1  -         208       1.7e-48      167.7      0.0       1       1          5.2e-52       2.1e-48       167.4      0.0       20        214     11        206     3         207     0.94     -                    0.94     0.84     0.94   0.84     HYDROXYACYLGLUTATHIONE_HYDROLASE_GLOC
PTHR23102.SF19.pir     -          206        FUN_000013-T1  -         233       1e-31        113.1      9.9       1       1          1.1e-35       1.3e-31       112.7      9.9       58        172     38        151     31        186     0.9      -                    0.49     0.56     0.49   0.56     CLEAVAGE_AND_POLYADENYLATION_SPECIFICITY_FACTOR_SUBUNIT_4-LIKE_PROTEIN-RELATED
PTHR47979.SF50.pir     -          216        FUN_000014-T1  -         206       1.6e-105     353.9      0.0       1       1          8.5e-108      1.9e-105      353.7      0.0       1         193     1         193     1         204     0.98     -                    0.94     0.89     0.94   0.89     RAS-RELATED_PROTEIN_RAB-2B
PTHR17605.orig.30.pir  -          732        FUN_000016-T1  -         712       4.8e-175     586.8      0.0       1       1          1e-177        6.9e-175      586.3      0.0       151       729     100       710     92        712     0.92     -                    0.86     0.79     0.86   0.79     RIBOSOME_BIOGENESIS_PROTEIN_BOP1__BLOCK_OF_PROLIFERATION_1_PROTEIN
...
</code>

Each of the protein queries in this list has a significant hit against a PANTHER family, and all the alignments between this protein and the HMM-profile cumulatively cover at least 50% of the HMM-profile.

==== Selecting (sub)families of interest ====

Until now we have considered all predicted proteins of our pet genome. But perhaps we are only particularly interested for whatever reason in a subset of them.

For example, we want to know what kind of energy conservation genes are present in our genome. From studying the literature, I've compiled in ''families_of_interest.ATP.upd.list'' the following list of PANTHER families that seem to be involved in ATP synthesis. The table is formatted like "category long name", "category short name", "gene or protein name", "PANTHER family identifier (names.tab)", "PANTHER family annotation", "PANTHER family identifier (binHmm database)".

<code>
ENERGY_CONSERVATION  ATP  ME                           PTHR23406.mag.mod    MALIC_ENZYME-RELATED                                                  PTHR23406.orig.30.pir
ENERGY_CONSERVATION  ATP  ME                           PTHR23406.SF32.mod   NADP-DEPENDENT_MALIC_ENZYME                                           PTHR23406.SF32.pir
ENERGY_CONSERVATION  ATP  PNO/PFO                      PTHR32154.mag.mod    PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED                            PTHR32154.orig.30.pir
ENERGY_CONSERVATION  ATP  PNO/PFO                      PTHR32154.SF0.mod    PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED                            PTHR32154.SF0.pir
ENERGY_CONSERVATION  ATP  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.mag.mod    FERREDOXIN/ADRENODOXIN                                                PTHR23426.orig.30.pir
ENERGY_CONSERVATION  ATP  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.SF65.mod   FERREDOXIN_1-RELATED                                                  PTHR23426.SF65.pir
ENERGY_CONSERVATION  ATP  FdxR/Arh1                    PTHR11938.mag.mod    FAD_NADPH_DEHYDROGENASE/OXIDOREDUCTASE                                PTHR11938.orig.30.pir
ENERGY_CONSERVATION  ATP  FdxR/Arh1                    PTHR11938.SF91.mod   NADPH:ADRENODOXIN_OXIDOREDUCTASE,_MITOCHONDRIAL                       PTHR11938.SF91.pir
ENERGY_CONSERVATION  ATP  HydA                         PTHR11615.mag.mod    NITRATE,_FORMATE,_IRON_DEHYDROGENASE                                  PTHR11615.orig.30.pir
ENERGY_CONSERVATION  ATP  HydA-1                       PTHR11615.SF345.mod  CATALYTIC_SUBUNIT_OF_IRON-ONLY_HYDROGENASE-RELATED                    PTHR11615.SF345.pir
ENERGY_CONSERVATION  ATP  HydA-4                       PTHR11615.SF304.mod  IRON_HYDROGENASE,_PUTATIVE-RELATED                                    PTHR11615.SF304.pir
ENERGY_CONSERVATION  ATP  HydE                         PTHR43726.mag.mod    3-METHYLORNITHINE_SYNTHASE                                            PTHR43726.orig.30.pir
ENERGY_CONSERVATION  ATP  HydE                         PTHR43726.SF1.mod    [FEFE]_HYDROGENASE_MATURASE_SUBUNIT_HYDE                              PTHR43726.SF1.pir
ENERGY_CONSERVATION  ATP  HydF                         PTHR42714.mag.mod    TRNA_MODIFICATION_GTPASE_GTPBP3                                       PTHR42714.orig.30.pir
ENERGY_CONSERVATION  ATP  HydF                         PTHR42714.SF6.mod    TRANSLATION_INITIATION_FACTOR_IF-2                                    PTHR42714.SF6.pir
ENERGY_CONSERVATION  ATP  HydG                         PTHR43583.mag.mod    2-IMINOACETATE_SYNTHASE                                               PTHR43583.orig.30.pir
ENERGY_CONSERVATION  ATP  HydG                         PTHR43583.SF2.mod    BIOTIN_AND_THIAMIN_SYNTHESIS_ASSOCIATED_DOMAIN_CONTAINING_PROTEIN     PTHR43583.SF2.pir
ENERGY_CONSERVATION  ATP  NuoF/Complex_I_51kDa         PTHR11780.mag.mod    NADH-UBIQUINONE_OXIDOREDUCTASE_FLAVOPROTEIN_1_NDUFV1                  PTHR11780.orig.30.pir
ENERGY_CONSERVATION  ATP  NuoF/Complex_I_51kDa         PTHR11780.SF10.mod   NADH_DEHYDROGENASE_[UBIQUINONE]_FLAVOPROTEIN_1,_MITOCHONDRIAL         PTHR11780.SF10.pir
ENERGY_CONSERVATION  ATP  NuoE/Complex_I_24kDa         PTHR10371.mag.mod    NADH_DEHYDROGENASE_UBIQUINONE_FLAVOPROTEIN_2,_MITOCHONDRIAL           PTHR10371.orig.30.pir
ENERGY_CONSERVATION  ATP  NuoE/Complex_I_24kDa         PTHR10371.SF3.mod    NADH_DEHYDROGENASE_[UBIQUINONE]_FLAVOPROTEIN_2,_MITOCHONDRIAL         PTHR10371.SF3.pir
ENERGY_CONSERVATION  ATP  ASCT-1B                      PTHR21432.mag.mod    ACETYL-COA_HYDROLASE-RELATED                                          PTHR21432.orig.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1B                      PTHR21432.SF20.mod   ACETYL-COA_DEACYLASE                                                  PTHR21432.SF20.pir
ENERGY_CONSERVATION  ATP  ASCT-1C                      PTHR43609.mag.mod    ACETYL-COA_HYDROLASE                                                  PTHR43609.orig.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1C                      PTHR43609.SF1.mod    ACETYL-COA_HYDROLASE                                                  PTHR43609.SF1.pir
ENERGY_CONSERVATION  ATP  SCSa/STKa                    PTHR11117.mag.mod    SUCCINYL-COA_LIGASE_SUBUNIT_ALPHA                                     PTHR11117.orig.30.pir
ENERGY_CONSERVATION  ATP  SCSa/STKa                    PTHR11117.SF2.mod    SUCCINATE--COA_LIGASE_[ADP/GDP-FORMING]_SUBUNIT_ALPHA,_MITOCHONDRIAL  PTHR11117.SF2.pir
ENERGY_CONSERVATION  ATP  SCSb/STKb                    PTHR11815.mag.mod    SUCCINYL-COA_SYNTHETASE_BETA_CHAIN                                    PTHR11815.orig.30.pir
ENERGY_CONSERVATION  ATP  SCSb/STKb                    PTHR11815.SF10.mod   SUCCINATE--COA_LIGASE_[GDP-FORMING]_SUBUNIT_BETA,_MITOCHONDRIAL       PTHR11815.SF10.pir
ENERGY_CONSERVATION  ATP  DLDH                         PTHR43716.mag.mod    D-2-HYDROXYGLUTARATE_DEHYDROGENASE,_MITOCHONDRIAL                     PTHR43716.orig.30.pir
ENERGY_CONSERVATION  ATP  DLDH                         PTHR43716.SF1.mod    D-2-HYDROXYGLUTARATE_DEHYDROGENASE,_MITOCHONDRIAL                     PTHR43716.SF1.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.mag.mod    NITRIC_OXIDE_SYNTHASE-RELATED                                         PTHR19384.orig.30.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.SF109.mod  SULFITE_REDUCTASE_[NADPH]_FLAVOPROTEIN_COMPONENT                      PTHR19384.SF109.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.SF17.mod   NADPH--CYTOCHROME_P450_REDUCTASE                                      PTHR19384.SF17.pir
ENERGY_CONSERVATION  ATP  PFL                          PTHR30191.mag.mod    FORMATE_ACETYLTRANSFERASE                                             PTHR30191.orig.30.pir
ENERGY_CONSERVATION  ATP  PFL                          PTHR30191.SF0.mod    FORMATE_ACETYLTRANSFERASE_1                                           PTHR30191.SF0.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR42793.mag.mod    COA_BINDING_DOMAIN_CONTAINING_PROTEIN                                 PTHR42793.orig.30.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR42793.SF1.mod    PEPTIDYL-LYSINE_N-ACETYLTRANSFERASE_PATZ                              PTHR42793.SF1.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR43334.mag.mod    ACETATE--COA_LIGASE_[ADP-FORMING]                                     PTHR43334.orig.30.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR43334.SF1.mod    ACETATE--COA_LIGASE_[ADP-FORMING]                                     PTHR43334.SF1.pir
ENERGY_CONSERVATION  ATP  MM-CoA-epimerase             PTHR43048.mag.mod    METHYLMALONYL-COA_EPIMERASE                                           PTHR43048.orig.30.pir
ENERGY_CONSERVATION  ATP  MM-CoA-epimerase             PTHR43048.SF3.mod    METHYLMALONYL-COA_EPIMERASE,_MITOCHONDRIAL                            PTHR43048.SF3.pir
ENERGY_CONSERVATION  ATP  MM-CoA-mutase                PTHR48101.SF4.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL                               PTHR48101.SF4.pir
ENERGY_CONSERVATION  ATP  MM-CoA-mutase                PTHR48101.mag.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL-RELATED                       PTHR48101.orig.30.pir
ENERGY_CONSERVATION  ATP  MMSA-dehydrogenase           PTHR43866.mag.mod    MALONATE-SEMIALDEHYDE_DEHYDROGENASE                                   PTHR43866.orig.30.pir
ENERGY_CONSERVATION  ATP  MMSA-dehydrogenase           PTHR43866.SF3.mod    METHYLMALONATE-SEMIALDEHYDE_DEHYDROGENASE_[ACYLATING],_MITOCHONDRIAL  PTHR43866.SF3.pir
ENERGY_CONSERVATION  ATP  PCCa                         PTHR18866.mag.mod    CARBOXYLASE:PYRUVATE/ACETYL-COA/PROPIONYL-COA_CARBOXYLASE             PTHR18866.orig.30.pir
ENERGY_CONSERVATION  ATP  PCCa                         PTHR18866.SF33.mod   METHYLCROTONOYL-COA_CARBOXYLASE_SUBUNIT_ALPHA,_MITOCHONDRIAL-RELATED  PTHR18866.SF33.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR43842.mag.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN                                  PTHR43842.orig.30.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR43842.SF2.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN-RELATED                          PTHR43842.SF2.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR45728.SF3.mod    ACETYL-COA_CARBOXYLASE                                                PTHR45728.SF3.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR45728.mag.mod    ACETYL-COA_CARBOXYLASE,_ISOFORM_A                                     PTHR45728.orig.30.pir
ENERGY_CONSERVATION  ATP  3HB-dehydrogenase            PTHR43060.mag.mod    3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED      PTHR43060.orig.30.pir
ENERGY_CONSERVATION  ATP  3HB-dehydrogenase            PTHR43060.SF15.mod   3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED      PTHR43060.SF15.pir
</code>

NOTE that I've included for every gene the family and the subfamily identifier.
So, which of these are in our genome?

<code>
function body {
    IFS= read -r header
    printf '%s\n' "$header"
    "$@"
}

cat ergo_vs_panther17.filt.ext.domtblout \
    | body rg -f <(cut -f 6 families_of_interest.ATP.upd.list) \
    | body sort -k28,28 \
    > ergo_vs_panther17.ATP.ext.domtblout
</code>

''rg'' is a modern unix tool that is very similar to the classic ''grep'' (it is literally called ripgrep) but its a lot faster, particularly with the ''-f'' option.

We now get the following file

<code>
TargetName             TargetAcc  TargetLen  QueryName      QueryAcc  QueryLen  seq-E-value  seq-Score  seq-Bias  dom-No  dom-Count  dom-c-Evalue  dom-i-Evalue  dom-Score  dom-Bias  hmm-From  hmm-To  ali-From  ali-To  env-From  env-To  mean-PP  DescriptionOfTarget  qcovhsp  tcovhsp  qcovs  tcovs    annotation
PTHR43726.orig.30.pir  -          384        FUN_005298-T1  -         390       7.1e-100     337.2      0.0       1       1          8.8e-104      8.9e-100      336.9      0.0       45        380     18        380     5         383     0.94     -                    0.93     0.88     0.93   0.88     3-METHYLORNITHINE_SYNTHASE
PTHR43334.orig.30.pir  -          705        FUN_004883-T1  -         761       1.1e-247     826.9      0.0       1       1          1.3e-251      1.4e-247      826.6      0.0       4         702     31        733     29        736     0.98     -                    0.92     0.99     0.92   0.99     ACETATE--COA_LIGASE_[ADP-FORMING]
PTHR43334.orig.30.pir  -          705        FUN_004897-T1  -         647       1.4e-224     750.4      0.0       1       1          1.7e-228      1.8e-224      750.1      0.0       1         630     12        643     12        646     0.98     -                    0.98     0.89     0.98   0.89     ACETATE--COA_LIGASE_[ADP-FORMING]
PTHR43583.SF2.pir      -          498        FUN_005007-T1  -         570       6e-189       631.4      0.0       1       1          5.7e-193      7.3e-189      631.1      0.0       19        498     58        570     31        570     0.97     -                    0.90     0.96     0.90   0.96     BIOTIN_AND_THIAMIN_SYNTHESIS_ASSOCIATED_DOMAIN_CONTAINING_PROTEIN
PTHR43583.SF2.pir      -          498        FUN_005031-T1  -         570       7.6e-189     631.1      0.0       1       1          7.2e-193      9.3e-189      630.8      0.0       19        498     58        570     31        570     0.97     -                    0.90     0.96     0.90   0.96     BIOTIN_AND_THIAMIN_SYNTHESIS_ASSOCIATED_DOMAIN_CONTAINING_PROTEIN
PTHR11615.SF345.pir    -          585        FUN_003250-T1  -         583       5.5e-167     559.9      0.2       1       1          1.1e-170      6.3e-167      559.7      0.2       6         581     5         579     1         582     0.94     -                    0.99     0.98     0.99   0.98     CATALYTIC_SUBUNIT_OF_IRON-ONLY_HYDROGENASE-RELATED
PTHR11615.SF345.pir    -          585        FUN_003742-T1  -         461       3.9e-127     428.3      1.4       1       1          5.8e-131      6.9e-127      427.5      1.4       139       580     31        460     4         461     0.92     -                    0.93     0.76     0.93   0.76     CATALYTIC_SUBUNIT_OF_IRON-ONLY_HYDROGENASE-RELATED
PTHR42793.orig.30.pir  -          472        FUN_000469-T1  -         843       1.5e-104     353.0      0.0       1       1          5.9e-109      1.7e-104      352.9      0.0       5         460     352       842     146       843     0.93     -                    0.58     0.97     0.58   0.97     COA_BINDING_DOMAIN_CONTAINING_PROTEIN
PTHR23426.SF65.pir     -          153        FUN_000689-T1  -         116       1.5e-13      54.3       0.0       1       1          1.7e-17       1.7e-13       54.1       0.0       57        142     28        109     14        115     0.87     -                    0.71     0.56     0.71   0.56     FERREDOXIN_1-RELATED
PTHR23426.SF65.pir     -          153        FUN_001937-T1  -         106       2.1e-13      53.8       0.1       1       1          1.9e-17       2.4e-13       53.6       0.1       46        139     8         99      3         105     0.81     -                    0.87     0.61     0.87   0.61     FERREDOXIN_1-RELATED
PTHR30191.SF0.pir      -          749        FUN_003588-T1  -         742       0.0          1182.9     0.1       1       1          0.0           0.0           1182.7     0.1       20        748     4         741     1         742     0.98     -                    0.99     0.97     0.99   0.97     FORMATE_ACETYLTRANSFERASE_1
PTHR30191.SF0.pir      -          749        FUN_004683-T1  -         779       0.0          1200.2     0.0       1       1          0.0           0.0           1199.9     0.0       15        748     36        778     26        779     0.98     -                    0.95     0.98     0.95   0.98     FORMATE_ACETYLTRANSFERASE_1
PTHR30191.SF0.pir      -          749        FUN_004725-T1  -         744       0.0          1199.6     0.0       1       1          0.0           0.0           1199.4     0.0       21        748     7         743     1         744     0.98     -                    0.99     0.97     0.99   0.97     FORMATE_ACETYLTRANSFERASE_1
PTHR30191.SF0.pir      -          749        FUN_004737-T1  -         744       0.0          1199.6     0.0       1       1          0.0           0.0           1199.4     0.0       21        748     7         743     1         744     0.98     -                    0.99     0.97     0.99   0.97     FORMATE_ACETYLTRANSFERASE_1
PTHR30191.SF0.pir      -          749        FUN_006165-T1  -         744       0.0          1196.1     0.0       1       1          0.0           0.0           1195.9     0.0       22        748     8         743     3         744     0.98     -                    0.99     0.97     0.99   0.97     FORMATE_ACETYLTRANSFERASE_1
PTHR11615.SF304.pir    -          431        FUN_004893-T1  -         1202      5.6e-80      272.2      0.0       1       2          0.0045        19.0          6.9        0.8       44        65      219       257     147       271     0.7      -                    0.03     0.05     0.63   0.89     IRON_HYDROGENASE,_PUTATIVE-RELATED
PTHR11615.SF304.pir    -          431        FUN_005208-T1  -         1444      5.2e-84      285.5      0.0       1       4          1.1e-06       0.0045        18.8       5.8       44        75      288       340     187       347     0.72     -                    0.04     0.07     0.38   0.86     IRON_HYDROGENASE,_PUTATIVE-RELATED
PTHR11780.SF10.pir     -          449        FUN_001132-T1  -         414       4.3e-83      282.2      0.0       1       2          1.8e-53       3.6e-49       170.4      0.0       67        210     2         180     1         194     0.97     -                    0.43     0.32     0.74   0.59     NADH_DEHYDROGENASE_[UBIQUINONE]_FLAVOPROTEIN_1,_MITOCHONDRIAL
PTHR10371.orig.30.pir  -          230        FUN_002223-T1  -         208       7.2e-51      175.7      0.0       1       1          2.6e-55       7.4e-51       175.7      0.0       29        183     8         166     2         208     0.88     -                    0.76     0.67     0.76   0.67     NADH_DEHYDROGENASE__UBIQUINONE__FLAVOPROTEIN_2,_MITOCHONDRIAL
PTHR11780.orig.30.pir  -          449        FUN_000599-T1  -         466       8.9e-152     508.6      0.0       1       1          7.2e-156      1.1e-151      508.2      0.0       14        430     38        456     29        464     0.95     -                    0.90     0.93     0.90   0.93     NADH-UBIQUINONE_OXIDOREDUCTASE_FLAVOPROTEIN_1__NDUFV1
PTHR23406.SF32.pir     -          596        FUN_001722-T1  -         585       2.8e-186     623.3      0.0       1       1          6.5e-190      3.4e-186      623.1      0.0       43        591     20        585     2         585     0.93     -                    0.97     0.92     0.97   0.92     NADP-DEPENDENT_MALIC_ENZYME
PTHR23406.SF32.pir     -          596        FUN_003026-T1  -         563       4.2e-195     652.5      0.0       1       1          9.7e-199      5.1e-195      652.2      0.0       39        593     11        552     2         555     0.96     -                    0.96     0.93     0.96   0.93     NADP-DEPENDENT_MALIC_ENZYME
PTHR23406.SF32.pir     -          596        FUN_003030-T1  -         563       4.2e-195     652.5      0.0       1       1          9.7e-199      5.1e-195      652.2      0.0       39        593     11        552     2         555     0.96     -                    0.96     0.93     0.96   0.93     NADP-DEPENDENT_MALIC_ENZYME
PTHR32154.SF0.pir      -          1159       FUN_000496-T1  -         1228      0.0          1568.0     0.0       1       1          0.0           0.0           1567.6     0.0       3         1156    51        1226    48        1227    0.98     -                    0.96     1.00     0.96   1.00     PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED
PTHR32154.SF0.pir      -          1159       FUN_000974-T1  -         1261      0.0          1402.3     0.0       1       1          0.0           0.0           1402.0     0.0       5         1154    81        1256    78        1261    0.97     -                    0.93     0.99     0.93   0.99     PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED
PTHR32154.SF0.pir      -          1159       FUN_003906-T1  -         1427      0.0          1268.7     0.0       1       1          0.0           0.0           1264.6     0.0       5         1156    101       1383    98        1394    0.95     -                    0.90     0.99     0.90   0.99     PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED
PTHR32154.SF0.pir      -          1159       FUN_004094-T1  -         1404      0.0          1481.8     0.0       1       1          0.0           0.0           1481.4     0.0       4         1154    3         1223    1         1228    0.96     -                    0.87     0.99     0.87   0.99     PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED
PTHR11117.SF2.pir      -          320        FUN_001614-T1  -         326       6.7e-140     468.5      4.9       1       1          1.1e-143      7.9e-140      468.2      4.9       21        318     25        319     6         321     0.96     -                    0.90     0.93     0.90   0.93     SUCCINATE--COA_LIGASE_[ADP/GDP-FORMING]_SUBUNIT_ALPHA,_MITOCHONDRIAL
PTHR11815.orig.30.pir  -          402        FUN_002952-T1  -         408       3.8e-159     532.8      0.0       1       1          3.9e-163      4.6e-159      532.5      0.0       5         399     7         405     4         408     0.98     -                    0.98     0.98     0.98   0.98     SUCCINYL-COA_SYNTHETASE_BETA_CHAIN
PTHR42714.SF6.pir      -          467        FUN_004742-T1  -         491       6.2e-29      104.5      0.0       1       1          5e-31         4.2e-27       98.5       0.0       70        441     18        413     15        434     0.71     -                    0.81     0.80     0.81   0.80     TRANSLATION_INITIATION_FACTOR_IF-2
</code>

To verify that each of these proteins are truly orthologs of the PANTHER families, we'd have to make trees, but this is a good starting point.

NOTE that we purposefully started by comparing our proteins to the entire PANTHER HMM-profile database, rather than starting out from a selection of HMM-profiles of gene families that we know we are interested in. This prevents false positive associations between our protein and and HMM profile:

Let's say that our genome doesn't have an ortholog of PANTHER family A, but it does have a distant paralog of that family (represented in the PANTHER database by family B). We are interested in A, but not in B. If we search with PANTHER family A, but not with family B, we may get a significant hit against family A, even though its not a true ortholog. If we were to include family B in our search as well, then we'd get significant hits against family A and B, but the score against B would be much better. It is thus clear that our protein is not a true ortholog of family A.

==== Premade categories of PANTHER families of interest ====

Mitochondria related
  
==== Energy conservation ====

<code>
ENERGY_CONSERVATION  ATP  ME                           PTHR23406.mag.mod    MALIC_ENZYME-RELATED                                                  PTHR23406.orig.30.pir
ENERGY_CONSERVATION  ATP  ME                           PTHR23406.SF32.mod   NADP-DEPENDENT_MALIC_ENZYME                                           PTHR23406.SF32.pir
ENERGY_CONSERVATION  ATP  PNO/PFO                      PTHR32154.mag.mod    PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED                            PTHR32154.orig.30.pir
ENERGY_CONSERVATION  ATP  PNO/PFO                      PTHR32154.SF0.mod    PYRUVATE-FLAVODOXIN_OXIDOREDUCTASE-RELATED                            PTHR32154.SF0.pir
ENERGY_CONSERVATION  ATP  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.mag.mod    FERREDOXIN/ADRENODOXIN                                                PTHR23426.orig.30.pir
ENERGY_CONSERVATION  ATP  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.SF65.mod   FERREDOXIN_1-RELATED                                                  PTHR23426.SF65.pir
ENERGY_CONSERVATION  ATP  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.SF63.mod   TRANSFER_PROTEIN,_PUTATIVE-RELATED                                    PTHR23426.SF63.pir
ENERGY_CONSERVATION  ATP  FdxR/Arh1                    PTHR11938.mag.mod    FAD_NADPH_DEHYDROGENASE/OXIDOREDUCTASE                                PTHR11938.orig.30.pir
ENERGY_CONSERVATION  ATP  FdxR/Arh1                    PTHR11938.SF91.mod   NADPH:ADRENODOXIN_OXIDOREDUCTASE,_MITOCHONDRIAL                       PTHR11938.SF91.pir
ENERGY_CONSERVATION  ATP  HydA                         PTHR11615.mag.mod    NITRATE,_FORMATE,_IRON_DEHYDROGENASE                                  PTHR11615.orig.30.pir
ENERGY_CONSERVATION  ATP  HydA-1                       PTHR11615.SF345.mod  CATALYTIC_SUBUNIT_OF_IRON-ONLY_HYDROGENASE-RELATED                    PTHR11615.SF345.pir
ENERGY_CONSERVATION  ATP  HydA-4                       PTHR11615.SF304.mod  IRON_HYDROGENASE,_PUTATIVE-RELATED                                    PTHR11615.SF304.pir
ENERGY_CONSERVATION  ATP  HydE                         PTHR43726.mag.mod    3-METHYLORNITHINE_SYNTHASE                                            PTHR43726.orig.30.pir
ENERGY_CONSERVATION  ATP  HydE                         PTHR43726.SF1.mod    [FEFE]_HYDROGENASE_MATURASE_SUBUNIT_HYDE                              PTHR43726.SF1.pir
ENERGY_CONSERVATION  ATP  HydF                         PTHR42714.mag.mod    TRNA_MODIFICATION_GTPASE_GTPBP3                                       PTHR42714.orig.30.pir
ENERGY_CONSERVATION  ATP  HydF                         PTHR42714.SF6.mod    TRANSLATION_INITIATION_FACTOR_IF-2                                    PTHR42714.SF6.pir
ENERGY_CONSERVATION  ATP  HydG                         PTHR43583.mag.mod    2-IMINOACETATE_SYNTHASE                                               PTHR43583.orig.30.pir
ENERGY_CONSERVATION  ATP  HydG                         PTHR43583.SF2.mod    BIOTIN_AND_THIAMIN_SYNTHESIS_ASSOCIATED_DOMAIN_CONTAINING_PROTEIN     PTHR43583.SF2.pir
ENERGY_CONSERVATION  ATP  NuoF/Complex_I_51kDa         PTHR11780.mag.mod    NADH-UBIQUINONE_OXIDOREDUCTASE_FLAVOPROTEIN_1_NDUFV1                  PTHR11780.orig.30.pir
ENERGY_CONSERVATION  ATP  NuoF/Complex_I_51kDa         PTHR11780.SF10.mod   NADH_DEHYDROGENASE_[UBIQUINONE]_FLAVOPROTEIN_1,_MITOCHONDRIAL         PTHR11780.SF10.pir
ENERGY_CONSERVATION  ATP  NuoE/Complex_I_24kDa         PTHR10371.mag.mod    NADH_DEHYDROGENASE_UBIQUINONE_FLAVOPROTEIN_2,_MITOCHONDRIAL           PTHR10371.orig.30.pir
ENERGY_CONSERVATION  ATP  NuoE/Complex_I_24kDa         PTHR10371.SF3.mod    NADH_DEHYDROGENASE_[UBIQUINONE]_FLAVOPROTEIN_2,_MITOCHONDRIAL         PTHR10371.SF3.pir
ENERGY_CONSERVATION  ATP  ASCT-1A                      PTHR13707.mag.mod    KETOACID-COENZYME_A_TRANSFERASE                                       PTHR13707.orig.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1A                      PTHR13707.SF23.mod   SUCCINYL-COA:3-KETOACID-COENZYME_A_TRANSFERASE                        PTHR13707.SF23.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1B                      PTHR21432.mag.mod    ACETYL-COA_HYDROLASE-RELATED                                          PTHR21432.orig.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1B                      PTHR21432.SF20.mod   ACETYL-COA_DEACYLASE                                                  PTHR21432.SF20.pir
ENERGY_CONSERVATION  ATP  ASCT-1C                      PTHR43609.mag.mod    ACETYL-COA_HYDROLASE                                                  PTHR43609.orig.30.pir
ENERGY_CONSERVATION  ATP  ASCT-1C                      PTHR43609.SF1.mod    ACETYL-COA_HYDROLASE                                                  PTHR43609.SF1.pir
ENERGY_CONSERVATION  ATP  SCSa/STKa                    PTHR11117.mag.mod    SUCCINYL-COA_LIGASE_SUBUNIT_ALPHA                                     PTHR11117.orig.30.pir
ENERGY_CONSERVATION  ATP  SCSa/STKa                    PTHR11117.SF2.mod    SUCCINATE--COA_LIGASE_[ADP/GDP-FORMING]_SUBUNIT_ALPHA,_MITOCHONDRIAL  PTHR11117.SF2.pir
ENERGY_CONSERVATION  ATP  SCSb/STKb                    PTHR11815.mag.mod    SUCCINYL-COA_SYNTHETASE_BETA_CHAIN                                    PTHR11815.orig.30.pir
ENERGY_CONSERVATION  ATP  SCSb/STKb                    PTHR11815.SF10.mod   SUCCINATE--COA_LIGASE_[GDP-FORMING]_SUBUNIT_BETA,_MITOCHONDRIAL       PTHR11815.SF10.pir
ENERGY_CONSERVATION  ATP  DLDH                         PTHR43716.mag.mod    D-2-HYDROXYGLUTARATE_DEHYDROGENASE,_MITOCHONDRIAL                     PTHR43716.orig.30.pir
ENERGY_CONSERVATION  ATP  DLDH                         PTHR43716.SF1.mod    D-2-HYDROXYGLUTARATE_DEHYDROGENASE,_MITOCHONDRIAL                     PTHR43716.SF1.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.mag.mod    NITRIC_OXIDE_SYNTHASE-RELATED                                         PTHR19384.orig.30.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.SF109.mod  SULFITE_REDUCTASE_[NADPH]_FLAVOPROTEIN_COMPONENT                      PTHR19384.SF109.pir
ENERGY_CONSERVATION  ATP  CysJ-fused_HydA              PTHR19384.SF17.mod   NADPH--CYTOCHROME_P450_REDUCTASE                                      PTHR19384.SF17.pir
ENERGY_CONSERVATION  ATP  PFL                          PTHR30191.mag.mod    FORMATE_ACETYLTRANSFERASE                                             PTHR30191.orig.30.pir
ENERGY_CONSERVATION  ATP  PFL                          PTHR30191.SF0.mod    FORMATE_ACETYLTRANSFERASE_1                                           PTHR30191.SF0.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR42793.mag.mod    COA_BINDING_DOMAIN_CONTAINING_PROTEIN                                 PTHR42793.orig.30.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR42793.SF1.mod    PEPTIDYL-LYSINE_N-ACETYLTRANSFERASE_PATZ                              PTHR42793.SF1.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR43334.mag.mod    ACETATE--COA_LIGASE_[ADP-FORMING]                                     PTHR43334.orig.30.pir
ENERGY_CONSERVATION  ATP  ACS                          PTHR43334.SF1.mod    ACETATE--COA_LIGASE_[ADP-FORMING]                                     PTHR43334.SF1.pir
ENERGY_CONSERVATION  ATP  MM-CoA-epimerase             PTHR43048.mag.mod    METHYLMALONYL-COA_EPIMERASE                                           PTHR43048.orig.30.pir
ENERGY_CONSERVATION  ATP  MM-CoA-epimerase             PTHR43048.SF3.mod    METHYLMALONYL-COA_EPIMERASE,_MITOCHONDRIAL                            PTHR43048.SF3.pir
ENERGY_CONSERVATION  ATP  MM-CoA-mutase                PTHR48101.SF4.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL                               PTHR48101.SF4.pir
ENERGY_CONSERVATION  ATP  MM-CoA-mutase                PTHR48101.mag.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL-RELATED                       PTHR48101.orig.30.pir
ENERGY_CONSERVATION  ATP  MMSA-dehydrogenase           PTHR43866.mag.mod    MALONATE-SEMIALDEHYDE_DEHYDROGENASE                                   PTHR43866.orig.30.pir
ENERGY_CONSERVATION  ATP  MMSA-dehydrogenase           PTHR43866.SF3.mod    METHYLMALONATE-SEMIALDEHYDE_DEHYDROGENASE_[ACYLATING],_MITOCHONDRIAL  PTHR43866.SF3.pir
ENERGY_CONSERVATION  ATP  PCCa                         PTHR18866.mag.mod    CARBOXYLASE:PYRUVATE/ACETYL-COA/PROPIONYL-COA_CARBOXYLASE             PTHR18866.orig.30.pir
ENERGY_CONSERVATION  ATP  PCCa                         PTHR18866.SF33.mod   METHYLCROTONOYL-COA_CARBOXYLASE_SUBUNIT_ALPHA,_MITOCHONDRIAL-RELATED  PTHR18866.SF33.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR43842.mag.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN                                  PTHR43842.orig.30.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR43842.SF2.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN-RELATED                          PTHR43842.SF2.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR45728.SF3.mod    ACETYL-COA_CARBOXYLASE                                                PTHR45728.SF3.pir
ENERGY_CONSERVATION  ATP  PCCb                         PTHR45728.mag.mod    ACETYL-COA_CARBOXYLASE,_ISOFORM_A                                     PTHR45728.orig.30.pir
ENERGY_CONSERVATION  ATP  3HB-dehydrogenase            PTHR43060.mag.mod    3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED      PTHR43060.orig.30.pir
ENERGY_CONSERVATION  ATP  3HB-dehydrogenase            PTHR43060.SF15.mod   3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED      PTHR43060.SF15.pir
</code>

==== Iron-Sulfur cluster biosynthesis ====

<code>
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Acp1                         PTHR20863.mag.mod    ACYL CARRIER PROTEIN                                            PTHR20863.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Acp1                         PTHR20863.SF28.mod   ACYL CARRIER PROTEIN, MITOCHONDRIAL                             PTHR20863.SF28.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Frataxin/FXN                 PTHR16821.mag.mod    FRATAXIN                                                        PTHR16821.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Frataxin/FXN                 PTHR16821.SF2.mod    FRATAXIN,_MITOCHONDRIAL                                         PTHR16821.SF2.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.mag.mod    FERREDOXIN/ADRENODOXIN                                          PTHR23426.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.SF65.mod   FERREDOXIN_1-RELATED                                            PTHR23426.SF65.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Adrenodoxin/Ferredoxin_Yah1  PTHR23426.SF63.mod   TRANSFER PROTEIN,_PUTATIVE-RELATED                              PTHR23426.SF63.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  FdxR/Arh1                    PTHR11938.mag.mod    FAD_NADPH_DEHYDROGENASE/OXIDOREDUCTASE                          PTHR11938.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  FdxR/Arh1                    PTHR11938.SF91.mod   NADPH:ADRENODOXIN_OXIDOREDUCTASE,_MITOCHONDRIAL                 PTHR11938.SF91.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscS/Nfs1                    PTHR11601.mag.mod    CYSTEINE_DESULFURYLASE_FAMILY_MEMBER                            PTHR11601.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscS/Nfs1                    PTHR11601.SF34.mod   CYSTEINE_DESULFURASE,_MITOCHONDRIAL                             PTHR11601.SF34.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Isd11                        PTHR13166.mag.mod    PROTEIN_C6ORF149                                                PTHR13166.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Isd11                        PTHR13166.SF7.mod    LYR_MOTIF-CONTAINING_PROTEIN_4                                  PTHR13166.SF7.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscU/NifU                    PTHR10093.mag.mod    IRON-SULFUR_CLUSTER_ASSEMBLY_ENZYME__NIFU_HOMOLOG               PTHR10093.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscU/NifU                    PTHR10093.SF8.mod    NIFU_N_DOMAIN-CONTAINING_PROTEIN                                PTHR10093.SF8.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  mtHsp70/SSQ1                 PTHR19375.mag.mod    HEAT_SHOCK_PROTEIN_70KDA                                        PTHR19375.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  mtHsp70/SSQ1                 PTHR19375.SF184.mod  STRESS-70_PROTEIN,_MITOCHONDRIAL                                PTHR19375.SF184.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  mtHsp70/SSQ1                 PTHR19375.SF197.mod  IRON-SULFUR_CLUSTER_BIOGENESIS_CHAPERONE,_MITOCHONDRIAL         PTHR19375.SF197.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  mtHsp70/SSQ1                 PTHR19375.SF510.mod  HEAT_SHOCK_70_KDA_PROTEIN,_MITOCHONDRIAL                        PTHR19375.SF510.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  GrpE1/Mge1                   PTHR21237.mag.mod    GRPE_PROTEIN                                                    PTHR21237.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  GrpE1/Mge1                   PTHR21237.SF23.mod   GRPE_PROTEIN_HOMOLOG,_MITOCHONDRIAL                             PTHR21237.SF23.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Glrx5                        PTHR10293.mag.mod    GLUTAREDOXIN_FAMILY_MEMBER                                      PTHR10293.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Glrx5                        PTHR10293.SF16.mod   GLUTAREDOXIN-RELATED_PROTEIN_5,_MITOCHONDRIAL                   PTHR10293.SF16.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Glrx5                        PTHR10293.SF72.mod   MONOTHIOL_GLUTAREDOXIN-S14,_CHLOROPLASTIC                       PTHR10293.SF72.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscA1                        PTHR10072.mag.mod    IRON-SULFUR_CLUSTER_ASSEMBLY_PROTEIN                            PTHR10072.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscA1                        PTHR10072.SF41.mod   IRON-SULFUR_CLUSTER_ASSEMBLY_1_HOMOLOG,_MITOCHONDRIAL           PTHR10072.SF41.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscA2                        PTHR43011.mag.mod    IRON-SULFUR_CLUSTER_ASSEMBLY_2_HOMOLOG,_MITOCHONDRIAL           PTHR43011.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IscA2                        PTHR43011.SF1.mod    IRON-SULFUR_CLUSTER_ASSEMBLY_2_HOMOLOG,_MITOCHONDRIAL           PTHR43011.SF1.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Nfu1                         PTHR11178.mag.mod    IRON-SULFUR_CLUSTER_SCAFFOLD_PROTEIN_NFU-RELATED                PTHR11178.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Nfu1                         PTHR11178.SF1.mod    NFU1_IRON-SULFUR_CLUSTER_SCAFFOLD_HOMOLOG,_MITOCHONDRIAL        PTHR11178.SF1.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IND1                         PTHR42961.mag.mod    IRON-SULFUR_PROTEIN_NUBPL                                       PTHR42961.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  IND1                         PTHR42961.SF2.mod    IRON-SULFUR_PROTEIN_NUBPL                                       PTHR42961.SF2.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  BolA1                        PTHR46230.mag.mod    FAMILY_NOT_NAMED                                                PTHR46230.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  BolA1                        PTHR46230.SF4.mod    BOLA-LIKE_PROTEIN_1                                             PTHR46230.SF4.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Jac1/HscB/Hsc20              PTHR14021.mag.mod    IRON-SULFUR_CLUSTER_CO-CHAPERONE_PROTEIN_HSCB                   PTHR14021.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Jac1/HscB/Hsc20              PTHR14021.SF15.mod   IRON-SULFUR_CLUSTER_CO-CHAPERONE_PROTEIN_HSCB                   PTHR14021.SF15.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Atm1                         PTHR24221.mag.mod    ATP-BINDING_CASSETTE_SUB-FAMILY_B                               PTHR24221.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Atm1                         PTHR24221.SF402.mod  IRON-SULFUR_CLUSTERS_TRANSPORTER_ABCB7,_MITOCHONDRIAL           PTHR24221.SF402.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Xxx1                         PTHR24089.mag.mod    SOLUTE_CARRIER_FAMILY_25                                        PTHR24089.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Xxx1                         PTHR24089.SF442.mod  MITOCHONDRIAL_SUBSTRATE_CARRIER_FAMILY_PROTEIN_A                PTHR24089.SF442.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Xxx2                         PTHR43687.mag.mod    ADENYLYLSULFATE_REDUCTASE,_BETA_SUBUNIT_                        PTHR43687.SF1.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Xxx2                         PTHR43687.SF1.mod    L-ASPARTATE_SEMIALDEHYDE_SULFURTRANSFERASE_IRON-SULFUR_SUBUNIT  PTHR43687.SF1.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Erv1                         PTHR12645.mag.mod    ALR/ERV                                                         PTHR12645.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  Erv1                         PTHR12645.SF0.mod    FAD-LINKED_SULFHYDRYL_OXIDASE_ALR                               PTHR12645.SF0.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  SufCB                        PTHR30508.mag.mod    FES_CLUSTER_ASSEMBLY_PROTEIN_SUF                                PTHR30508.orig.30.pir
IRON_SULFUR_CLUSTER_ASSEMBLY  FeS  SufCB                        PTHR30508.SF1.mod    UPF0051_PROTEIN_ABCI8,_CHLOROPLASTIC-RELATED                    PTHR30508.SF1.pir
</code>

==== Electron Transfer ====

<code>
Electron_transfer  CAT_SHORT_NAME  Alternative_oxidase              PTHR31803.mag.mod    ALTERNATIVE_OXIDASE                                                      PTHR31803.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  Alternative_oxidase              PTHR31803.SF3.mod    ALTERNATIVE_OXIDASE                                                      PTHR31803.SF3.pir
Electron_transfer  CAT_SHORT_NAME  ETF-alpha                        PTHR43153.mag.mod    ELECTRON_TRANSFER_FLAVOPROTEIN_ALPHA                                     PTHR43153.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  ETF-alpha                        PTHR43153.SF1.mod    ELECTRON_TRANSFER_FLAVOPROTEIN_SUBUNIT_ALPHA,_MITOCHONDRIAL              PTHR43153.SF1.pir
Electron_transfer  CAT_SHORT_NAME  ETF-beta                         PTHR21294.mag.mod    ELECTRON_TRANSFER_FLAVOPROTEIN_BETA-SUBUNIT                              PTHR21294.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  ETF-beta                         PTHR21294.SF8.mod    ELECTRON_TRANSFER_FLAVOPROTEIN_SUBUNIT_BETA                              PTHR21294.SF8.pir
Electron_transfer  CAT_SHORT_NAME  ETF-ubiquinone_oxidoreductase_1  PTHR10617.mag.mod    ELECTRON_TRANSFER_FLAVOPROTEIN-UBIQUINONE_OXIDOREDUCTASE                 PTHR10617.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  ETF-ubiquinone_oxidoreductase_1  PTHR10617.SF107.mod  ELECTRON_TRANSFER_FLAVOPROTEIN-UBIQUINONE_OXIDOREDUCTASE,_MITOCHONDRIAL  PTHR10617.SF107.pir
Electron_transfer  CAT_SHORT_NAME  ETF-ubiquinone_oxidoreductase_2  PTHR10617.mag.mod    ELECTRON_TRANSFER_FLAVOPROTEIN-UBIQUINONE_OXIDOREDUCTASE                 PTHR10617.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  ETF-ubiquinone_oxidoreductase_2  PTHR10617.SF107.mod  ELECTRON_TRANSFER_FLAVOPROTEIN-UBIQUINONE_OXIDOREDUCTASE,_MITOCHONDRIAL  PTHR10617.SF107.pir
Electron_transfer  CAT_SHORT_NAME  Glycerol-3-phosphate_DH          PTHR11985.mag.mod    GLYCEROL-3-PHOSPHATE_DEHYDROGENASE                                       PTHR11985.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  Glycerol-3-phosphate_DH          PTHR11985.SF15.mod   GLYCEROL-3-PHOSPHATE_DEHYDROGENASE,_MITOCHONDRIAL                        PTHR11985.SF15.pir
Electron_transfer  CAT_SHORT_NAME  cytosolic_flavoprotein_A         PTHR32145.mag.mod    DIFLAVIN_FLAVOPROTEIN_A_2-RELATED                                        PTHR32145.orig.30.pir
Electron_transfer  CAT_SHORT_NAME  cytosolic_flavoprotein_A         PTHR32145.SF11.mod   DIFLAVIN_FLAVOPROTEIN_A_2-RELATED                                        PTHR32145.SF11.pir

</code>

==== Amino acid metabolism ====

<code>
AMINO_ACID_METABOLISM  AA      GCS-L                                             PTHR22912.mag.mod    DISULFIDE_OXIDOREDUCTASE                                                                                    PTHR22912.orig.30.pir
AMINO_ACID_METABOLISM  AA      GCS-L                                             PTHR22912.SF151.mod  DIHYDROLIPOYL_DEHYDROGENASE,_MITOCHONDRIAL                                                                  PTHR22912.SF151.pir
AMINO_ACID_METABOLISM  AA      GCS-L                                             PTHR22912.SF211.mod  DIHYDROLIPOYL_DEHYDROGENASE_2,_MITOCHONDRIAL                                                                PTHR22912.SF211.pir
AMINO_ACID_METABOLISM  AA      GCS-L                                             PTHR22912.SF223.mod  DIHYDROLIPOYL_DEHYDROGENASE_1,_MITOCHONDRIAL                                                                PTHR22912.SF223.pir
AMINO_ACID_METABOLISM  AA      GCS-H                                             PTHR11715.mag.mod    GLYCINE_CLEAVAGE_SYSTEM_H_PROTEIN                                                                           PTHR11715.orig.30.pir
AMINO_ACID_METABOLISM  AA      GCS-H                                             PTHR11715.SF3.mod    GLYCINE_CLEAVAGE_SYSTEM_H_PROTEIN,_MITOCHONDRIAL                                                            PTHR11715.SF3.pir
AMINO_ACID_METABOLISM  AA      GCS-P1                                            PTHR42806.mag.mod    GLYCINE_CLEAVAGE_SYSTEM_P-PROTEIN                                                                           PTHR42806.orig.30.pir
AMINO_ACID_METABOLISM  AA      GCS-P1                                            PTHR42806.SF1.mod    GLYCINE_DEHYDROGENASE_(DECARBOXYLATING)                                                                     PTHR42806.SF1.pir
AMINO_ACID_METABOLISM  AA      GCS-P2                                            PTHR11773.mag.mod    GLYCINE_DEHYDROGENASE,_DECARBOXYLATING                                                                      PTHR11773.orig.30.pir
AMINO_ACID_METABOLISM  AA      GCS-P2                                            PTHR11773.SF1.mod    GLYCINE_DEHYDROGENASE_(DECARBOXYLATING),_MITOCHONDRIAL                                                      PTHR11773.SF1.pir
AMINO_ACID_METABOLISM  AA      GCS-P2                                            PTHR11773.SF12.mod   GLYCINE_CLEAVAGE_SYSTEM_P_PROTEIN                                                                           PTHR11773.SF12.pir
AMINO_ACID_METABOLISM  AA      GCS-T                                             PTHR43757.mag.mod    AMINOMETHYLTRANSFERASE                                                                                      PTHR43757.orig.30.pir
AMINO_ACID_METABOLISM  AA      GCS-T                                             PTHR43757.SF2.mod    AMINOMETHYLTRANSFERASE,_MITOCHONDRIAL                                                                       PTHR43757.SF2.pir
AMINO_ACID_METABOLISM  AA      SHMT                                              PTHR11680.mag.mod    SERINE_HYDROXYMETHYLTRANSFERASE                                                                             PTHR11680.orig.30.pir
AMINO_ACID_METABOLISM  AA      SHMT                                              PTHR11680.SF28.mod   SERINE_HYDROXYMETHYLTRANSFERASE,_MITOCHONDRIAL                                                              PTHR11680.SF28.pir
AMINO_ACID_METABOLISM  AA      ECH                                               PTHR43802.mag.mod    ENOYL-COA_HYDRATASE                                                                                         PTHR43802.orig.30.pir
AMINO_ACID_METABOLISM  AA      ECH                                               PTHR43802.SF1.mod    ZGC:101569                                                                                                  PTHR43802.SF1.pir
AMINO_ACID_METABOLISM  AA      ACAD                                              PTHR43884.mag.mod    ACYL-COA_DEHYDROGENASE                                                                                      PTHR43884.orig.30.pir
AMINO_ACID_METABOLISM  AA      ACAD                                              PTHR43884.SF1.mod    SHORT/BRANCHED_CHAIN_SPECIFIC_ACYL-COA_DEHYDROGENASE,_MITOCHONDRIAL                                         PTHR43884.SF1.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E1a                                         PTHR43380.mag.mod    2-OXOISOVALERATE_DEHYDROGENASE_SUBUNIT_ALPHA,_MITOCHONDRIAL                                                 PTHR43380.orig.30.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E1a                                         PTHR43380.SF1.mod    2-OXOISOVALERATE_DEHYDROGENASE_SUBUNIT_ALPHA,_MITOCHONDRIAL                                                 PTHR43380.SF1.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E1b                                         PTHR42980.mag.mod    2-OXOISOVALERATE_DEHYDROGENASE_SUBUNIT_BETA-RELATED                                                         PTHR42980.orig.30.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E1b                                         PTHR42980.SF1.mod    2-OXOISOVALERATE_DEHYDROGENASE_SUBUNIT_BETA,_MITOCHONDRIAL                                                  PTHR42980.SF1.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E2                                          PTHR43178.mag.mod    DIHYDROLIPOAMIDE_ACETYLTRANSFERASE_COMPONENT_OF_PYRUVATE_DEHYDROGENASE_COMPLEX                              PTHR43178.orig.30.pir
AMINO_ACID_METABOLISM  AA      BaKDH-E2                                          PTHR43178.SF5.mod    LIPOAMIDE_ACYLTRANSFERASE_COMPONENT_OF_BRANCHED-CHAIN_ALPHA-KETO_ACID_DEHYDROGENASE_COMPLEX,_MITOCHONDRIAL  PTHR43178.SF5.pir
AMINO_ACID_METABOLISM  AA      BCAAT                                             PTHR11825.mag.mod    SUBGROUP_IIII_AMINOTRANSFERASE                                                                              PTHR11825.orig.30.pir
AMINO_ACID_METABOLISM  AA      BCAAT                                             PTHR11825.SF44.mod   BRANCHED-CHAIN-AMINO-ACID_AMINOTRANSFERASE                                                                  PTHR11825.SF44.pir
AMINO_ACID_METABOLISM  AA      3HB-dehydrogenase                                 PTHR43060.mag.mod    3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED                                            PTHR43060.orig.30.pir
AMINO_ACID_METABOLISM  AA      3HB-dehydrogenase                                 PTHR43060.SF15.mod   3-HYDROXYISOBUTYRATE_DEHYDROGENASE-LIKE_1,_MITOCHONDRIAL-RELATED                                            PTHR43060.SF15.pir
AMINO_ACID_METABOLISM  AA      hydroxymethylglutaryl-CoA_synthase                PTHR43323.mag.mod    3-HYDROXY-3-METHYLGLUTARYL_COENZYME_A_SYNTHASE                                                              PTHR43323.orig.30.pir
AMINO_ACID_METABOLISM  AA      hydroxymethylglutaryl-CoA_synthase                PTHR43323.SF2.mod    3-HYDROXY-3-METHYLGLUTARYL_COENZYME_A_SYNTHASE                                                              PTHR43323.SF2.pir
AMINO_ACID_METABOLISM  AA      MMSA-dehydrogenase                                PTHR43866.mag.mod    MALONATE-SEMIALDEHYDE_DEHYDROGENASE                                                                         PTHR43866.orig.30.pir
AMINO_ACID_METABOLISM  AA      MMSA-dehydrogenase                                PTHR43866.SF3.mod    METHYLMALONATE-SEMIALDEHYDE_DEHYDROGENASE_[ACYLATING],_MITOCHONDRIAL                                        PTHR43866.SF3.pir
AMINO_ACID_METABOLISM  AA      PCCa                                              PTHR18866.mag.mod    CARBOXYLASE:PYRUVATE/ACETYL-COA/PROPIONYL-COA_CARBOXYLASE                                                   PTHR18866.orig.30.pir
AMINO_ACID_METABOLISM  AA      PCCa                                              PTHR18866.SF33.mod   METHYLCROTONOYL-COA_CARBOXYLASE_SUBUNIT_ALPHA,_MITOCHONDRIAL-RELATED                                        PTHR18866.SF33.pir
AMINO_ACID_METABOLISM  AA      PCCb                                              PTHR43842.mag.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN                                                                        PTHR43842.orig.30.pir
AMINO_ACID_METABOLISM  AA      PCCb                                              PTHR43842.SF2.mod    PROPIONYL-COA_CARBOXYLASE_BETA_CHAIN-RELATED                                                                PTHR43842.SF2.pir
AMINO_ACID_METABOLISM  AA      MM-CoA-epimerase                                  PTHR43048.mag.mod    METHYLMALONYL-COA_EPIMERASE                                                                                 PTHR43048.orig.30.pir
AMINO_ACID_METABOLISM  AA      MM-CoA-epimerase                                  PTHR43048.SF3.mod    METHYLMALONYL-COA_EPIMERASE,_MITOCHONDRIAL                                                                  PTHR43048.SF3.pir
AMINO_ACID_METABOLISM  AA      MM-CoA-mutase                                     PTHR48101.mag.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL-RELATED                                                             PTHR48101.orig.30.pir
AMINO_ACID_METABOLISM  AA      MM-CoA-mutase                                     PTHR48101.SF4.mod    METHYLMALONYL-COA_MUTASE,_MITOCHONDRIAL                                                                     PTHR48101.SF4.pir
AMINO_ACID_METABOLISM  AA      AGT                                               PTHR45688.mag.mod    -                                                                                                           PTHR45688.orig.30.pir
AMINO_ACID_METABOLISM  AA      AGT                                               PTHR45688.SF3.mod    ALANINE--GLYOXYLATE_AMINOTRANSFERASE_2,_MITOCHONDRIAL                                                       PTHR45688.SF3.pir
AMINO_ACID_METABOLISM  AA      AST                                               PTHR11879.mag.mod    ASPARTATE_AMINOTRANSFERASE                                                                                  PTHR11879.orig.30.pir
AMINO_ACID_METABOLISM  AA      AST                                               PTHR11879.SF22.mod   ASPARTATE_AMINOTRANSFERASE,_MITOCHONDRIAL                                                                   PTHR11879.SF22.pir
AMINO_ACID_METABOLISM  AA      AST                                               PTHR11879.SF55.mod   ASPARTATE_TRANSAMINASE                                                                                      PTHR11879.SF55.pir
AMINO_ACID_METABOLISM  AA      ALT                                               PTHR11751.mag.mod    ALANINE_AMINOTRANSFERASE                                                                                    PTHR11751.orig.30.pir
AMINO_ACID_METABOLISM  AA      ALT                                               PTHR11751.SF29.mod   AT04676P                                                                                                    PTHR11751.SF29.pir
AMINO_ACID_METABOLISM  AA      Cysteine_synthase?                                PTHR43797.mag.mod    HOMOCYSTEINE/CYSTEINE_SYNTHASE                                                                              PTHR43797.orig.30.pir
AMINO_ACID_METABOLISM  AA      Cysteine_synthase?                                PTHR43797.SF2.mod    HOMOCYSTEINE/CYSTEINE_SYNTHASE                                                                              PTHR43797.SF2.pir
AMINO_ACID_METABOLISM  AA      Pyrroline-5-carboxylate_reductase                 PTHR11645.mag.mod    PYRROLINE-5-CARBOXYLATE_REDUCTASE                                                                           PTHR11645.orig.30.pir
AMINO_ACID_METABOLISM  AA      Pyrroline-5-carboxylate_reductase                 PTHR11645.SF0.mod    PYRROLINE-5-CARBOXYLATE_REDUCTASE_3                                                                         PTHR11645.SF0.pir
AMINO_ACID_METABOLISM  AA      Delta-1-pyrroline-5-carboxylate_dehydrogenase     PTHR42862.mag.mod    DELTA-1-PYRROLINE-5-CARBOXYLATE_DEHYDROGENASE_1,_ISOFORM_A-RELATED                                          PTHR42862.orig.30.pir
AMINO_ACID_METABOLISM  AA      Delta-1-pyrroline-5-carboxylate_dehydrogenase     PTHR42862.SF1.mod    DELTA-1-PYRROLINE-5-CARBOXYLATE_DEHYDROGENASE_2,_ISOFORM_A-RELATED                                          PTHR42862.SF1.pir
AMINO_ACID_METABOLISM  AA      Citrate_Lyase                                     PTHR32308.mag.mod    LYASE_BETA_SUBUNIT,_PUTATIVE_(AFU_ORTHOLOGUE_AFUA_4G13030)-RELATED                                          PTHR32308.orig.30.pir
AMINO_ACID_METABOLISM  AA      Citrate_Lyase                                     PTHR32308.SF1.mod    HPCH_HPAI_DOMAIN-CONTAINING_PROTEIN                                                                         PTHR32308.SF1.pir
AMINO_ACID_METABOLISM  AA      Citrate_Lyase                                     PTHR32308.SF10.mod   CITRATE_LYASE_SUBUNIT_BETA                                                                                  PTHR32308.SF10.pir
AMINO_ACID_METABOLISM  AA      Citrate_Lyase                                     PTHR11105.mag.mod    CITRATE_LYASE_SUBUNIT_BETA-RELATED                                                                          PTHR11105.orig.30.pir
AMINO_ACID_METABOLISM  AA      Citrate_Lyase                                     PTHR11105.SF0.mod    CITRAMALYL-COA_LYASE,_MITOCHONDRIAL                                                                         PTHR11105.SF0.pir
AMINO_ACID_METABOLISM  AA      Glutamate_DH                                      PTHR11606.mag.mod    GLUTAMATE_DEHYDROGENASE                                                                                     PTHR11606.orig.30.pir
AMINO_ACID_METABOLISM  AA      Glutamate_DH                                      PTHR11606.SF13.mod   GLUTAMATE_DEHYDROGENASE_1,_MITOCHONDRIAL                                                                    PTHR11606.SF13.pir
AMINO_ACID_METABOLISM  AA      thiosulfate/3-mercaptopyruvate_sulfurtransferase  PTHR11364.mag.mod    THIOSULFATE_SULFERTANSFERASE                                                                                PTHR11364.orig.30.pir
AMINO_ACID_METABOLISM  AA      thiosulfate/3-mercaptopyruvate_sulfurtransferase  PTHR11364.SF27.mod   SULFURTRANSFERASE                                                                                           PTHR11364.SF27.pir
AMINO_ACID_METABOLISM  AA      ThrC_-_bussel_extension                           PTHR48078.mag.mod    THREONINE_DEHYDRATASE,_MITOCHONDRIAL-RELATED                                                                PTHR48078.orig.30.pir
AMINO_ACID_METABOLISM  AA      ThrC_-_bussel_extension                           PTHR48078.SF6.mod    ACT_DOMAIN-CONTAINING_PROTEIN                                                                               PTHR48078.SF6.pir
AMINO_ACID_METABOLISM  KETONE  ACAT                                              PTHR18919.mag.mod    ACETYL-COA_C-ACYLTRANSFERASE                                                                                PTHR18919.orig.30.pir
AMINO_ACID_METABOLISM  KETONE  ACAT                                              PTHR18919.SF156.mod  ACETYL-COA_ACETYLTRANSFERASE,_MITOCHONDRIAL                                                                 PTHR18919.SF156.pir
AMINO_ACID_METABOLISM  KETONE  SCOT                                              PTHR13707.mag.mod    KETOACID-COENZYME_A_TRANSFERASE                                                                             PTHR13707.orig.30.pir
AMINO_ACID_METABOLISM  KETONE  SCOT                                              PTHR13707.SF23.mod   SUCCINYL-COA:3-KETOACID-COENZYME_A_TRANSFERASE                                                              PTHR13707.SF23.pir
AMINO_ACID_METABOLISM  KETONE  Ketobutyrate_lyase                                PTHR13693.mag.mod    CLASS_II_AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE_SYNTHASE                                                   PTHR13693.orig.30.pir
AMINO_ACID_METABOLISM  KETONE  Ketobutyrate_lyase                                PTHR13693.SF102.mod  2-AMINO-3-KETOBUTYRATE_COENZYME_A_LIGASE,_MITOCHONDRIAL                                                     PTHR13693.SF102.pir

</code>

==== Fatty acid metabolism ====

<code>
FATTY_ACID_METABOLISM  FATTY_ACID  4-aminobutyrate_transaminase                    PTHR43206.SF1.mod   4-AMINOBUTYRATE_AMINOTRANSFERASE,_MITOCHONDRIAL                                                                           PTHR43206.SF1.pir
FATTY_ACID_METABOLISM  FATTY_ACID  4-aminobutyrate_transaminase                    PTHR43206.mag.mod   AMINOTRANSFERASE                                                                                                          PTHR43206.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  glutamate_dehydrogenase_(NADP)                  PTHR43571.mag.mod   NADP-SPECIFIC_GLUTAMATE_DEHYDROGENASE_1-RELATED                                                                           PTHR43571.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  glutamate_dehydrogenase_(NADP)                  PTHR43571.SF1.mod   NADP-SPECIFIC_GLUTAMATE_DEHYDROGENASE_1-RELATED                                                                           PTHR43571.SF1.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Succinate_semialdehyde_dehydrogenase_(NADP)     PTHR43217.mag.mod   SUCCINATE_SEMIALDEHYDE_DEHYDROGENASE_[NAD(P)+]_SAD                                                                        PTHR43217.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Succinate_semialdehyde_dehydrogenase_(NADP)     PTHR43217.SF1.mod   SUCCINATE_SEMIALDEHYDE_DEHYDROGENASE_[NAD(P)+]_SAD                                                                        PTHR43217.SF1.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E1_component      PTHR23152.mag.mod   2-OXOGLUTARATE_DEHYDROGENASE                                                                                              PTHR23152.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E1_component      PTHR23152.SF4.mod   2-OXOGLUTARATE_DEHYDROGENASE_E1_COMPONENT_DHKTD1,_MITOCHONDRIAL-RELATED                                                   PTHR23152.SF4.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E2_component      PTHR43416.SF5.mod   DIHYDROLIPOYLLYSINE-RESIDUE_SUCCINYLTRANSFERASE_COMPONENT_OF_2-OXOGLUTARATE_DEHYDROGENASE_COMPLEX,_MITOCHONDRIAL          PTHR43416.SF5.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E2_component      PTHR43416.mag.mod   DIHYDROLIPOYLLYSINE-RESIDUE_SUCCINYLTRANSFERASE_COMPONENT_OF_2-OXOGLUTARATE_DEHYDROGENASE_COMPLEX,_MITOCHONDRIAL-RELATED  PTHR43416.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E2_component      PTHR43416.SF5.mod   DIHYDROLIPOYLLYSINE-RESIDUE_SUCCINYLTRANSFERASE_COMPONENT_OF_2-OXOGLUTARATE_DEHYDROGENASE_COMPLEX,_MITOCHONDRIAL          PTHR43416.SF5.pir
FATTY_ACID_METABOLISM  FATTY_ACID  2-oxoglutarate_dehydrogenase,_E2_component      PTHR43416.mag.mod   DIHYDROLIPOYLLYSINE-RESIDUE_SUCCINYLTRANSFERASE_COMPONENT_OF_2-OXOGLUTARATE_DEHYDROGENASE_COMPLEX,_MITOCHONDRIAL-RELATED  PTHR43416.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  kynurenine/alpha-aminoadipate_aminotransferase  PTHR42790.mag.mod   AMINOTRANSFERASE                                                                                                          PTHR42790.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  kynurenine/alpha-aminoadipate_aminotransferase  PTHR42790.SF3.mod   KYNURENINE/ALPHA-AMINOADIPATE_AMINOTRANSFERASE,_MITOCHONDRIAL                                                             PTHR42790.SF3.pir
FATTY_ACID_METABOLISM  FATTY_ACID  tyrosine_aminotransferase                       PTHR45744.mag.mod   TYROSINE_AMINOTRANSFERASE                                                                                                 PTHR45744.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  tyrosine_aminotransferase                       PTHR45744.SF2.mod   TYROSINE_AMINOTRANSFERASE                                                                                                 PTHR45744.SF2.pir
FATTY_ACID_METABOLISM  FATTY_ACID  S-adenosylmethionine_synthetase                 PTHR11964.SF1.mod   S-ADENOSYLMETHIONINE_SYNTHASE                                                                                             PTHR11964.SF1.pir
FATTY_ACID_METABOLISM  FATTY_ACID  S-adenosylmethionine_synthetase                 PTHR11964.mag.mod   S-ADENOSYLMETHIONINE_SYNTHETASE                                                                                           PTHR11964.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Saccharopine_dehydrogenase                      PTHR11133.SF25.mod  ALPHA-AMINOADIPIC_SEMIALDEHYDE_SYNTHASE,_MITOCHONDRIAL                                                                    PTHR11133.SF25.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Saccharopine_dehydrogenase                      PTHR11133.mag.mod   SACCHAROPINE_DEHYDROGENASE                                                                                                PTHR11133.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Acyl-CoA_synthetase                             PTHR42793.mag.mod   COA_BINDING_DOMAIN_CONTAINING_PROTEIN                                                                                     PTHR42793.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Acyl-CoA_synthetase                             PTHR42793.SF1.mod   PEPTIDYL-LYSINE_N-ACETYLTRANSFERASE_PATZ                                                                                  PTHR42793.SF1.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Pyridine_nucleotide_disulphide_oxidoreductase   PTHR43429.SF3.mod   NITRITE_REDUCTASE_[NAD(P)H]                                                                                               PTHR43429.SF3.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Pyridine_nucleotide_disulphide_oxidoreductase   PTHR43429.mag.mod   PYRIDINE_NUCLEOTIDE-DISULFIDE_OXIDOREDUCTASE_DOMAIN-CONTAINING                                                            PTHR43429.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Delta-1-pyrroline-5-carboxylate_dehydrogenase   PTHR43521.mag.mod   ALPHA-AMINOADIPIC_SEMIALDEHYDE_DEHYDROGENASE                                                                              PTHR43521.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Delta-1-pyrroline-5-carboxylate_dehydrogenase   PTHR43521.SF7.mod   DELTA-1-PYRROLINE-5-CARBOXYLATE_DEHYDROGENASE_12A1,_MITOCHONDRIAL                                                         PTHR43521.SF7.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Acetyl-CoA_carboxylase                          PTHR45728.SF3.mod   ACETYL-COA_CARBOXYLASE                                                                                                    PTHR45728.SF3.pir
FATTY_ACID_METABOLISM  FATTY_ACID  Acetyl-CoA_carboxylase                          PTHR45728.mag.mod   ACETYL-COA_CARBOXYLASE,_ISOFORM_A                                                                                         PTHR45728.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  long-chain-fatty-acid-coA-ligase_(1)            PTHR43272.SF32.mod  AMP-BINDING_DOMAIN-CONTAINING_PROTEIN                                                                                     PTHR43272.SF32.pir
FATTY_ACID_METABOLISM  FATTY_ACID  long-chain-fatty-acid-coA-ligase_(1)            PTHR43272.mag.mod   LONG-CHAIN-FATTY-ACID--COA_LIGASE                                                                                         PTHR43272.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  long-chain-fatty-acid-coA-ligase_(2)            PTHR43272.SF32.mod  AMP-BINDING_DOMAIN-CONTAINING_PROTEIN                                                                                     PTHR43272.SF32.pir
FATTY_ACID_METABOLISM  FATTY_ACID  long-chain-fatty-acid-coA-ligase_(2)            PTHR43272.mag.mod   LONG-CHAIN-FATTY-ACID--COA_LIGASE                                                                                         PTHR43272.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  enoyl-[acyl-carrier-protein]_reductase          PTHR43981.mag.mod   ENOYL-[ACYL-CARRIER-PROTEIN]_REDUCTASE,_MITOCHONDRIAL                                                                     PTHR43981.orig.30.pir
FATTY_ACID_METABOLISM  FATTY_ACID  enoyl-[acyl-carrier-protein]_reductase          PTHR43981.SF2.mod   ENOYL-[ACYL-CARRIER-PROTEIN]_REDUCTASE,_MITOCHONDRIAL                                                                     PTHR43981.SF2.pir
FATTY_ACID_METABOLISM  FATTY_ACID  enoyl-[acyl-carrier-protein]_reductase          PTHR43981.SF9.mod   ENOYL-[ACYL-CARRIER-PROTEIN]_REDUCTASE,_MITOCHONDRIAL                                                                     PTHR43981.SF9.pir

</code>

==== Mitochondrial carriers ====

<code>
SOLUTE_CARRIERS  CARRIERS  arginine/ornithine_transport_system_ATPase  PTHR23408.mag.mod    METHYLMALONYL-COA_MUTASE                               PTHR23408.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  arginine/ornithine_transport_system_ATPase  PTHR23408.SF3.mod    METHYLMALONIC_ACIDURIA_TYPE_A_PROTEIN,_MITOCHONDRIAL   PTHR23408.SF3.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(1)    PTHR24089.mag.mod    SOLUTE_CARRIER_FAMILY_25                               PTHR24089.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(1)    PTHR24089.SF246.mod  SOLUTE_CARRIER_FAMILY_25_MEMBER_43                     PTHR24089.SF246.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(2)    PTHR46181.mag.mod    MITOCHONDRIAL_GLYCINE_TRANSPORTER                      PTHR46181.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(2)    PTHR46181.SF3.mod    MITOCHONDRIAL_GLYCINE_TRANSPORTER                      PTHR46181.SF3.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(3)    PTHR47567.mag.mod    MITOCHONDRIAL_SUBSTRATE/SOLUTE_CARRIER                 PTHR47567.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(3)    PTHR47567.SF1.mod    EPIMERASE_DOMAIN-CONTAINING_PROTEIN                    PTHR47567.SF1.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(4)    PTHR45635.mag.mod    ADP,ATP_CARRIER_PROTEIN_1-RELATED-RELATED              PTHR45635.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  Mitochondrial_carrier_family_protein_(4)    PTHR45635.SF14.mod   ADP/ATP_TRANSLOCASE                                    PTHR45635.SF14.pir
SOLUTE_CARRIERS  CARRIERS  Aralar_Asp/Glu_carrier                      PTHR45678.mag.mod    MITOCHONDRIAL_2-OXODICARBOXYLATE_CARRIER_1-RELATED     PTHR45678.orig.30.pir
SOLUTE_CARRIERS  CARRIERS  Aralar_Asp/Glu_carrier                      PTHR45678.SF9.mod    CALCIUM-BINDING_MITOCHONDRIAL_CARRIER_PROTEIN_ARALAR1  PTHR45678.SF9.pir

</code>

==== Mitochondrial import ====

<code>
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tom40                          PTHR10802.mag.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40                               PTHR10802.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tom40                          PTHR10802.SF2.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40_HOMOLOG_1-RELATED             PTHR10802.SF2.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Sam50                          PTHR12815.SF18.mod   SORTING_AND_ASSEMBLY_MACHINERY_COMPONENT_50_HOMOLOG                       PTHR12815.SF18.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Sam50                          PTHR12815.mag.mod    SORTING_AND_ASSEMBLY_MACHINERY_SAMM50_PROTEIN_FAMILY_MEMBER               PTHR12815.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mia40                          PTHR21622.SF0.mod    AU015836_PROTEIN-RELATED                                                  PTHR21622.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mia40                          PTHR21622.mag.mod    COILED-COIL-HELIX-COILED-COIL-HELIX_DOMAIN_CONTAINING_4                   PTHR21622.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.mag.mod    TRANSLOCASE_OF_INNER_MITOCHONDRIAL_MEMBRANE_13_HOMOLOG                    PTHR19338.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.SF1.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM8_A-B-RELATED  PTHR19338.SF1.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim8/Tim13                     PTHR19338.SF4.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT                   PTHR19338.SF4.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim9                           PTHR13172.SF5.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9              PTHR13172.SF5.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim9                           PTHR13172.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM9B             PTHR13172.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim10                          PTHR11038.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim10                          PTHR11038.SF16.mod   MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM10             PTHR11038.SF16.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim22                          PTHR14110.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim22                          PTHR14110.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM22             PTHR14110.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim23                          PTHR15371.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM23             PTHR15371.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim23                          PTHR15371.mag.mod    TIM23                                                                     PTHR15371.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam18/Tim14                    PTHR12763.mag.mod    UNCHARACTERIZED                                                           PTHR12763.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam18/Tim14                    PTHR12763.SF28.mod   GEO10507P1-RELATED                                                        PTHR12763.SF28.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam18/Tim14                    PTHR12763.SF42.mod   MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM14-3-LIKE      PTHR12763.SF42.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam16/Tim16                    PTHR12388.mag.mod    MITOCHONDRIA_ASSOCIATED_GRANULOCYTE_MACROPHAGE_CSF_SIGNALING_MOLECULE     PTHR12388.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam16/Tim16                    PTHR12388.SF0.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM16             PTHR12388.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam17                          PTHR28021.mag.mod    PRESEQUENCE_TRANSLOCATED-ASSOCIATED_MOTOR_SUBUNIT_PAM17,_MITOCHONDRIAL    PTHR28021.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Pam17                          PTHR28021.SF1.mod    PRESEQUENCE_TRANSLOCATED-ASSOCIATED_MOTOR_SUBUNIT_PAM17,_MITOCHONDRIAL    PTHR28021.SF1.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim17                          PTHR10485.SF0.mod    AT05822P-RELATED                                                          PTHR10485.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim17                          PTHR10485.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM-17            PTHR10485.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim44                          PTHR10721.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM44             PTHR10721.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim44                          PTHR10721.SF1.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM44             PTHR10721.SF1.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim44                          PTHR47652.mag.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM44             PTHR47652.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tim44                          PTHR47652.SF3.mod    MITOCHONDRIAL_IMPORT_INNER_MEMBRANE_TRANSLOCASE_SUBUNIT_TIM44             PTHR47652.SF3.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  mtHsp70/SSQ1                   PTHR19375.mag.mod    HEAT_SHOCK_PROTEIN_70KDA                                                  PTHR19375.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  mtHsp70/SSQ1                   PTHR19375.SF184.mod  STRESS-70_PROTEIN,_MITOCHONDRIAL                                          PTHR19375.SF184.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  mtHsp70/SSQ1                   PTHR19375.SF197.mod  IRON-SULFUR_CLUSTER_BIOGENESIS_CHAPERONE,_MITOCHONDRIAL                   PTHR19375.SF197.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  mtHsp70/SSQ1                   PTHR19375.SF510.mod  HEAT_SHOCK_70_KDA_PROTEIN,_MITOCHONDRIAL                                  PTHR19375.SF510.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  GrpE/Mge1                      PTHR21237.mag.mod    GRPE_PROTEIN                                                              PTHR21237.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  GrpE/Mge1                      PTHR21237.SF23.mod   GRPE_PROTEIN_HOMOLOG,_MITOCHONDRIAL                                       PTHR21237.SF23.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mitochondrial_chaperone_BCS-1  PTHR23070.mag.mod    BCS1_AAA-TYPE_ATPASE                                                      PTHR23070.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mitochondrial_chaperone_BCS-1  PTHR23070.SF144.mod  MITOCHONDRIAL_CHAPERONE_BCS1                                              PTHR23070.SF144.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  MPPa                           PTHR11851.mag.mod    METALLOPROTEASE                                                           PTHR11851.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  MPPa                           PTHR11851.SF49.mod   MITOCHONDRIAL-PROCESSING_PEPTIDASE_SUBUNIT_ALPHA                          PTHR11851.SF49.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  MPPb                           PTHR11851.SF149.mod  GH01077P                                                                  PTHR11851.SF149.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  MPPb                           PTHR11851.mag.mod    METALLOPROTEASE                                                           PTHR11851.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Cpn10                          PTHR10772.mag.mod    10_KDA_HEAT_SHOCK_PROTEIN                                                 PTHR10772.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Cpn10                          PTHR10772.SF0.mod    10_KDA_HEAT_SHOCK_PROTEIN,_MITOCHONDRIAL                                  PTHR10772.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Cpn60                          PTHR45633.mag.mod    60_KDA_HEAT_SHOCK_PROTEIN,_MITOCHONDRIAL                                  PTHR45633.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Cpn60                          PTHR45633.SF3.mod    60_KDA_HEAT_SHOCK_PROTEIN,_MITOCHONDRIAL                                  PTHR45633.SF3.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Metaxin                        PTHR12289.SF41.mod   FAILED_AXON_CONNECTIONS-RELATED                                           PTHR12289.SF41.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Metaxin                        PTHR12289.mag.mod    METAXIN_RELATED                                                           PTHR12289.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  UPS1                           PTHR11158.mag.mod    MSF1/PX19_RELATED                                                         PTHR11158.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  UPS1                           PTHR11158.SF17.mod   PROTEIN_SLOWMO                                                            PTHR11158.SF17.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  UPS2                           PTHR11158.mag.mod    MSF1/PX19_RELATED                                                         PTHR11158.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  UPS2                           PTHR11158.SF30.mod   PRELI/MSF1_DOMAIN-CONTAINING_PROTEIN                                      PTHR11158.SF30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mmp37/Tam41                    PTHR13619.SF0.mod    PHOSPHATIDATE_CYTIDYLYLTRANSFERASE,_MITOCHONDRIAL                         PTHR13619.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mmp37/Tam41                    PTHR13619.mag.mod    UNCHARACTERIZED                                                           PTHR13619.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Prohibitin                     PTHR23222.mag.mod    PROHIBITIN                                                                PTHR23222.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Prohibitin                     PTHR23222.SF0.mod    PROHIBITIN                                                                PTHR23222.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Presequence_protease           PTHR43016.mag.mod    PRESEQUENCE_PROTEASE                                                      PTHR43016.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Presequence_protease           PTHR43016.SF13.mod   PRESEQUENCE_PROTEASE,_MITOCHONDRIAL                                       PTHR43016.SF13.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Fumarate_reductase/Osm1        PTHR43400.SF7.mod    FAD_BINDING_2_DOMAIN-CONTAINING_PROTEIN                                   PTHR43400.SF7.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Fumarate_reductase/Osm1        PTHR43400.mag.mod    FUMARATE_REDUCTASE                                                        PTHR43400.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Fumarate_Hydratase             PTHR11444.SF1.mod    FUMARATE_HYDRATASE,_MITOCHONDRIAL                                         PTHR11444.SF1.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Fumarate_Hydratase             PTHR11444.SF22.mod   FUMARATE_HYDRATASE_CLASS_II                                               PTHR11444.SF22.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Fumarate_Hydratase             PTHR11444.mag.mod    ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE_LYASE                 PTHR11444.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Atp23                          PTHR21711.mag.mod    MITOCHONDRIAL_INNER_MEMBRANE_PROTEASE                                     PTHR21711.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Atp23                          PTHR21711.SF0.mod    MITOCHONDRIAL_INNER_MEMBRANE_PROTEASE_ATP23_HOMOLOG                       PTHR21711.SF0.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.mag.mod    PROTEASE FAMILY S26 MITOCHONDRIAL INNER MEMBRANE PROTEASE-RELATED         PTHR12383.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF16.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1                           PTHR12383.SF16.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF32.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT                             PTHR12383.SF32.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp1                           PTHR12383.SF33.mod   MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1                           PTHR12383.SF33.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.mag.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF1.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF1.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF2.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF2.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF3.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF3.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Imp2                           PTHR46041.SF4.mod    MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2                           PTHR46041.SF4.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.mag.mod       OXA1                                                                   PTHR12428.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF66.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1L                             PTHR12428.SF66.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF60.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-LIKE                         PTHR12428.SF60.pir 
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF63.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-2                            PTHR12428.SF63.pir   
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF34.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1                              PTHR12428.SF34.pir  
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF49.mod      OXAA/YIDC-LIKE MEMBRANE INSERTION PROTEIN                              PTHR12428.SF49.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Oxa1                           PTHR12428.SF64.mod      MITOCHONDRIAL INNER MEMBRANE PROTEIN OXA1-LIKE                         PTHR12428.SF64.pir

PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mdm10                          PTHR28035.mag.mod       MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 10                   PTHR28035.orig.30.pir
PROTEIN_IMPORT_AND_FOLDING  IMPORT  Mdm10                          PTHR28035.SF1.mod       MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 10                   PTHR28035.SF1.pir

</code>

==== Reactive Oxygen Species and Oxygen detoxification ====

<code>
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  flavoprotein_A_-_ferredoxin_fused_to_N-terminus                            PTHR43717.mag.mod   ANAEROBIC_NITRIC_OXIDE_REDUCTASE_FLAVORUBREDOXIN                PTHR43717.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  flavoprotein_A_-_ferredoxin_fused_to_N-terminus                            PTHR43717.SF1.mod   ANAEROBIC_NITRIC_OXIDE_REDUCTASE_FLAVORUBREDOXIN                PTHR43717.SF1.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  peroxiredoxin_V                                                            PTHR10430.mag.mod   PEROXIREDOXIN                                                   PTHR10430.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  peroxiredoxin_V                                                            PTHR10430.SF16.mod  PEROXIREDOXIN-5,_MITOCHONDRIAL                                  PTHR10430.SF16.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  thioredoxin_(1)                                                            PTHR45663.mag.mod   GEO12009P1                                                      PTHR45663.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  thioredoxin_(1)                                                            PTHR45663.SF11.mod  GEO12009P1                                                      PTHR45663.SF11.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  superoxide_dismutase                                                       PTHR42769.mag.mod   SUPEROXIDE_DISMUTASE                                            PTHR42769.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  superoxide_dismutase                                                       PTHR42769.SF3.mod   SUPEROXIDE_DISMUTASE_[FE]_2,_CHLOROPLASTIC                      PTHR42769.SF3.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  NADPH-dependent_thioredoxin_reductase_1_(selenoprotein)                    PTHR42737.mag.mod   GLUTATHIONE_REDUCTASE                                           PTHR42737.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  NADPH-dependent_thioredoxin_reductase_1_(selenoprotein)                    PTHR42737.SF3.mod   THIOREDOXIN-DISULFIDE_REDUCTASE                                 PTHR42737.SF3.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Amoebozoa-type';_FDP_fused_with_NADH_oxidase_domain                        PTHR32145.mag.mod   DIFLAVIN_FLAVOPROTEIN_A_2-RELATED                               PTHR32145.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Amoebozoa-type';_FDP_fused_with_NADH_oxidase_domain                        PTHR32145.SF11.mod  DIFLAVIN_FLAVOPROTEIN_A_2-RELATED                               PTHR32145.SF11.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Glutathione_repair__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402446/  PTHR23088.mag.mod   NITRILASE-RELATED                                               PTHR23088.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Glutathione_repair__https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402446/  PTHR23088.SF30.mod  OMEGA-AMIDASE_NIT2                                              PTHR23088.SF30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Nitroreductase                                                             PTHR43673.mag.mod   NAD(P)H_NITROREDUCTASE_YDGI-RELATED                             PTHR43673.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Nitroreductase                                                             PTHR43673.SF2.mod   NITROREDUCTASE_FAMILY_PROTEIN                                   PTHR43673.SF2.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  RBR                                                                        PTHR43865.mag.mod   RUBRERYTHRIN-RELATED                                            PTHR43865.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  RBR                                                                        PTHR43865.SF1.mod   RUBRERYTHRIN-RELATED                                            PTHR43865.SF1.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Glutaredoxin_                                                              PTHR10293.mag.mod   GLUTAREDOXIN_FAMILY_MEMBER                                      PTHR10293.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Glutaredoxin_                                                              PTHR10293.SF16.mod  GLUTAREDOXIN-RELATED_PROTEIN_5,_MITOCHONDRIAL                   PTHR10293.SF16.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  OsmC/Ohr                                                                   PTHR35368.mag.mod   HYDROPEROXIDE_REDUCTASE                                         PTHR35368.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  OsmC/Ohr                                                                   PTHR35368.SF1.mod   HYDROPEROXIDE_REDUCTASE                                         PTHR35368.SF1.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Thioredoxin                                                                PTHR43601.mag.mod   THIOREDOXIN,_MITOCHONDRIAL                                      PTHR43601.orig.30.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  Thioredoxin                                                                PTHR43601.SF3.mod   THIOREDOXIN,_MITOCHONDRIAL                                      PTHR43601.SF3.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  NADH_oxidase                                                               PTHR43429.SF1.mod   NAD(P)H_SULFUR_OXIDOREDUCTASE_(COA-DEPENDENT)                   PTHR43429.SF1.pir
ROS_AND_OXYGEN_DETOXIFICATION  ROS_O2  NADH_oxidase                                                               PTHR43429.mag.mod   PYRIDINE_NUCLEOTIDE-DISULFIDE_OXIDOREDUCTASE_DOMAIN-CONTAINING  PTHR43429.orig.30.pir

</code>

Cell division

==== Kinetochore ====

<code>
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Incenp     PTHR13142.mag.mod    INNER_CENTROMERE_PROTEIN                                                                   PTHR13142.orig.30.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Incenp     PTHR13142.SF1.mod    INNER_CENTROMERE_PROTEIN                                                                   PTHR13142.SF1.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Survivin   PTHR46771.mag.mod    DETERIN                                                                                    PTHR46771.orig.30.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Survivin   PTHR46771.SF5.mod    DETERIN                                                                                    PTHR46771.SF5.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Shugoshin  PTHR21577.mag.mod    SHUGOSHIN                                                                                  PTHR21577.orig.30.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Shugoshin  PTHR21577.SF3.mod    SHUGOSHIN_1-RELATED                                                                        PTHR21577.SF3.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Aurora     PTHR24350.mag.mod    SERINE/THREONINE-PROTEIN_KINASE_IAL-RELATED                                                PTHR24350.orig.30.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Aurora     PTHR24350.SF0.mod    AURORA_KINASE                                                                              PTHR24350.SF0.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Aurora     PTHR24350.SF5.mod    AURORA_KINASE_A                                                                            PTHR24350.SF5.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Aurora     PTHR24350.SF24.mod   AURORA_KINASE_B                                                                            PTHR24350.SF24.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Borealin   PTHR16040.mag.mod    AUSTRALIN,_ISOFORM_A-RELATED                                                               PTHR16040.orig.30.pir
CHROMOSOMAL_PASSENGER_COMPLEX               CPC                   Borealin   PTHR16040.SF6.mod    BOREALIN                                                                                   PTHR16040.SF6.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpA      PTHR45810.mag.mod    HISTONE_H3.2                                                                               PTHR45810.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpA      PTHR45810.SF14.mod   CENTROMERE_PROTEIN_A                                                                       PTHR45810.SF14.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpC      PTHR16684.mag.mod    CENTROMERE_PROTEIN_C                                                                       PTHR16684.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpC      PTHR16684.SF12.mod   CENTROMERE_PROTEIN_C                                                                       PTHR16684.SF12.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpH      PTHR48122.mag.mod    CENTROMERE_PROTEIN_H                                                                       PTHR48122.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpH      PTHR48122.SF1.mod    CENTROMERE_PROTEIN_H                                                                       PTHR48122.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpI      PTHR48208.mag.mod    CENTROMERE_PROTEIN_I                                                                       PTHR48208.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpI      PTHR48208.SF2.mod    CENTROMERE_PROTEIN_I                                                                       PTHR48208.SF2.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpK      PTHR14401.mag.mod    CENTROMERE_PROTEIN_K                                                                       PTHR14401.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpK      PTHR14401.SF6.mod    CENTROMERE_PROTEIN_K                                                                       PTHR14401.SF6.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpM      PTHR34436.mag.mod    CENTROMERE_PROTEIN_M                                                                       PTHR34436.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpM      PTHR34436.SF1.mod    CENTROMERE_PROTEIN_M                                                                       PTHR34436.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpL      PTHR31740.mag.mod    CENTROMERE_PROTEIN_L                                                                       PTHR31740.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpL      PTHR31740.SF2.mod    CENTROMERE_PROTEIN_L                                                                       PTHR31740.SF2.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpN      PTHR46790.mag.mod    CENTROMERE_PROTEIN_N                                                                       PTHR46790.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpN      PTHR46790.SF1.mod    CENTROMERE_PROTEIN_N                                                                       PTHR46790.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpO      PTHR14582.mag.mod    INNER_KINETOCHORE_SUBUNIT_MAL2                                                             PTHR14582.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpO      PTHR14582.SF1.mod    CENTROMERE_PROTEIN_O                                                                       PTHR14582.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpP      PTHR28577.mag.mod    CENTROMERE_PROTEIN_P                                                                       PTHR28577.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpP      PTHR28577.SF1.mod    CENTROMERE_PROTEIN_P                                                                       PTHR28577.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpQ      PTHR31345.mag.mod    CENTROMERE_PROTEIN_Q                                                                       PTHR31345.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpQ      PTHR31345.SF3.mod    CENTROMERE_PROTEIN_Q                                                                       PTHR31345.SF3.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpU      PTHR32222.mag.mod    CENTROMERE_PROTEIN_U                                                                       PTHR32222.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpU      PTHR32222.SF1.mod    CENTROMERE_PROTEIN_U                                                                       PTHR32222.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpT      PTHR46904.mag.mod    CENTROMERE_PROTEIN_T                                                                       PTHR46904.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpT      PTHR46904.SF1.mod    CENTROMERE_PROTEIN_T                                                                       PTHR46904.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpW      PTHR34832.mag.mod    CENTROMERE_PROTEIN_W                                                                       PTHR34832.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpW      PTHR34832.SF1.mod    CENTROMERE_PROTEIN_W                                                                       PTHR34832.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpX      PTHR28680.mag.mod    CENTROMERE_PROTEIN_X                                                                       PTHR28680.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpX      PTHR28680.SF1.mod    CENTROMERE_PROTEIN_X                                                                       PTHR28680.SF1.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpS      PTHR22980.mag.mod    CORTISTATIN                                                                                PTHR22980.orig.30.pir
CONSTITUTIVE_CENTROMERE_ASSOCIATED_NETWORK  CCAN                  CenpS      PTHR22980.SF0.mod    CENTROMERE_PROTEIN_S                                                                       PTHR22980.SF0.pir
LINKER                                      MIS12                 Mis12      PTHR14527.mag.mod    PROTEIN_MIS12_HOMOLOG                                                                      PTHR14527.orig.30.pir
LINKER                                      MIS12                 Mis12      PTHR14527.SF2.mod    PROTEIN_MIS12_HOMOLOG                                                                      PTHR14527.SF2.pir
LINKER                                      MIS12                 Nnf1       PTHR15459.mag.mod    POLYAMINE-MODULATED_FACTOR_1                                                               PTHR15459.orig.30.pir
LINKER                                      MIS12                 Nnf1       PTHR15459.SF3.mod    POLYAMINE-MODULATED_FACTOR_1                                                               PTHR15459.SF3.pir
LINKER                                      MIS12                 Dsn1       PTHR14778.mag.mod    KINETOCHORE-ASSOCIATED_PROTEIN_DSN1_HOMOLOG                                                PTHR14778.orig.30.pir
LINKER                                      MIS12                 Dsn1       PTHR14778.SF2.mod    KINETOCHORE-ASSOCIATED_PROTEIN_DSN1_HOMOLOG                                                PTHR14778.SF2.pir
LINKER                                      MIS12                 Csm1       PTHR28006.mag.mod    MONOPOLIN_COMPLEX_SUBUNIT_CSM1                                                             PTHR28006.orig.30.pir
LINKER                                      MIS12                 Csm1       PTHR28006.SF1.mod    MONOPOLIN_COMPLEX_SUBUNIT_PCS1                                                             PTHR28006.SF1.pir
NDC80_COMPLEX                               NDC80                 Ndc80      PTHR10643.mag.mod    KINETOCHORE_PROTEIN_NDC80                                                                  PTHR10643.orig.30.pir
NDC80_COMPLEX                               NDC80                 Ndc80      PTHR10643.SF2.mod    KINETOCHORE_PROTEIN_NDC80_HOMOLOG                                                          PTHR10643.SF2.pir
NDC80_COMPLEX                               NDC80                 Ndc80      PTHR46681.mag.mod    KINETOCHORE_PROTEIN_NDC80_HOMOLOG                                                          PTHR46681.orig.30.pir
NDC80_COMPLEX                               NDC80                 Ndc80      PTHR46681.SF1.mod    KINETOCHORE_PROTEIN_NDC80_HOMOLOG                                                          PTHR46681.SF1.pir
NDC80_COMPLEX                               NDC80                 Nuf2       PTHR21650.mag.mod    MEMBRALIN/KINETOCHORE_PROTEIN_NUF2                                                         PTHR21650.orig.30.pir
NDC80_COMPLEX                               NDC80                 Nuf2       PTHR21650.SF2.mod    KINETOCHORE_PROTEIN_NUF2                                                                   PTHR21650.SF2.pir
NDC80_COMPLEX                               NDC80                 Spc24      PTHR35730.mag.mod    KINETOCHORE_PROTEIN_SPC24_HOMOLOG-RELATED                                                  PTHR35730.orig.30.pir
NDC80_COMPLEX                               NDC80                 Spc24      PTHR35730.SF2.mod    KINETOCHORE_PROTEIN_SPC24_HOMOLOG-RELATED                                                  PTHR35730.SF2.pir
NDC80_COMPLEX                               NDC80                 Spc24      PTHR22142.mag.mod    UNCHARACTERIZED                                                                            PTHR22142.orig.30.pir
NDC80_COMPLEX                               NDC80                 Spc24      PTHR22142.SF2.mod    KINETOCHORE_PROTEIN_SPC24                                                                  PTHR22142.SF2.pir
NDC80_COMPLEX                               NDC80                 Spc25      PTHR14281.mag.mod    KINETOCHORE_PROTEIN_SPC25-RELATED                                                          PTHR14281.orig.30.pir
NDC80_COMPLEX                               NDC80                 Spc25      PTHR14281.SF0.mod    KINETOCHORE_PROTEIN_SPC25                                                                  PTHR14281.SF0.pir
NDC80_COMPLEX                               NDC80                 Spc25      PTHR14281.SF1.mod    KINETOCHORE_PROTEIN_SPC25                                                                  PTHR14281.SF1.pir
NDC80_COMPLEX                               NDC80                 Spc25      PTHR14281.SF2.mod    KINETOCHORE_PROTEIN_SPC25                                                                  PTHR14281.SF2.pir
NDC80_COMPLEX                               NDC80                 Spc25      PTHR14281.SF3.mod    KINETOCHORE_PROTEIN_SPC25                                                                  PTHR14281.SF3.pir
SKA_COMPLEX                                 SKA                   Ska1       PTHR28573.mag.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_1                                               PTHR28573.orig.30.pir
SKA_COMPLEX                                 SKA                   Ska1       PTHR28573.SF1.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_1                                               PTHR28573.SF1.pir
SKA_COMPLEX                                 SKA                   Ska2       PTHR32017.mag.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_2                                               PTHR32017.orig.30.pir
SKA_COMPLEX                                 SKA                   Ska2       PTHR32017.SF3.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_2                                               PTHR32017.SF3.pir
SKA_COMPLEX                                 SKA                   Ska3       PTHR48118.mag.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_3                                               PTHR48118.orig.30.pir
SKA_COMPLEX                                 SKA                   Ska3       PTHR48118.SF1.mod    SPINDLE_AND_KINETOCHORE-ASSOCIATED_PROTEIN_3                                               PTHR48118.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Dam1       PTHR28113.mag.mod    DASH_COMPLEX_SUBUNIT_DAM1                                                                  PTHR28113.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Dam1       PTHR28113.SF1.mod    DASH_COMPLEX_SUBUNIT_DAM1                                                                  PTHR28113.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Duo1       PTHR28216.mag.mod    DASH_COMPLEX_SUBUNIT_DUO1                                                                  PTHR28216.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Duo1       PTHR28216.SF1.mod    DASH_COMPLEX_SUBUNIT_DUO1                                                                  PTHR28216.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Hsk3       PTHR28289.mag.mod    DASH_COMPLEX_SUBUNIT_HSK3                                                                  PTHR28289.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Hsk3       PTHR28289.SF1.mod    DASH_COMPLEX_SUBUNIT_HSK3                                                                  PTHR28289.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Ask1       PTHR28200.mag.mod    DASH_COMPLEX_SUBUNIT_ASK1                                                                  PTHR28200.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Ask1       PTHR28200.SF1.mod    DASH_COMPLEX_SUBUNIT_ASK1                                                                  PTHR28200.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Spc19      PTHR28262.mag.mod    DASH_COMPLEX_SUBUNIT_SPC19                                                                 PTHR28262.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Spc19      PTHR28262.SF1.mod    DASH_COMPLEX_SUBUNIT_SPC19                                                                 PTHR28262.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Dad1       PTHR28025.mag.mod    DASH_COMPLEX_SUBUNIT_DAD1                                                                  PTHR28025.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Dad1       PTHR28025.SF1.mod    DASH_COMPLEX_SUBUNIT_DAD1                                                                  PTHR28025.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Dad2       PTHR28036.mag.mod    DASH_COMPLEX_SUBUNIT_DAD2                                                                  PTHR28036.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Dad2       PTHR28036.SF1.mod    DASH_COMPLEX_SUBUNIT_DAD2                                                                  PTHR28036.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Dad3       PTHR28017.mag.mod    DASH_COMPLEX_SUBUNIT_DAD3                                                                  PTHR28017.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Dad3       PTHR28017.SF1.mod    DASH_COMPLEX_SUBUNIT_DAD3                                                                  PTHR28017.SF1.pir
DAM_COMPLEX                                 DAM1-DASH             Dad4       PTHR28222.mag.mod    DASH_COMPLEX_SUBUNIT_DAD4                                                                  PTHR28222.orig.30.pir
DAM_COMPLEX                                 DAM1-DASH             Dad4       PTHR28222.SF1.mod    DASH_COMPLEX_SUBUNIT_DAD4                                                                  PTHR28222.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc1       PTHR12827.SF3.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_1                                                       PTHR12827.SF3.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc1       PTHR12827.SF5.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_1                                                       PTHR12827.SF5.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc4       PTHR13260.mag.mod    ANAPHASE_PROMOTING_COMPLEX_SUBUNIT_4__APC4                                                 PTHR13260.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc4       PTHR13260.SF0.mod    ANAPHASE_PROMOTING_COMPLEX_SUBUNIT_4__APC4                                                 PTHR13260.SF0.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc5       PTHR12830.mag.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_5                                                       PTHR12830.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc5       PTHR12830.SF9.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_5                                                       PTHR12830.SF9.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-platform        Apc15      PTHR22526.SF4.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_15                                                      PTHR22526.SF4.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc3       PTHR12558.SF13.mod   CELL_DIVISION_CYCLE_PROTEIN_27_HOMOLOG                                                     PTHR12558.SF13.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc6       PTHR12558.SF9.mod    CELL_DIVISION_CYCLE_PROTEIN_16_HOMOLOG                                                     PTHR12558.SF9.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc8       PTHR12558.SF10.mod   CELL_DIVISION_CYCLE_PROTEIN_23_HOMOLOG                                                     PTHR12558.SF10.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc12      PTHR28579.mag.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_CDC26                                                   PTHR28579.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc12      PTHR28579.SF1.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_CDC26                                                   PTHR28579.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc13      PTHR28672.mag.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_13                                                      PTHR28672.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-arc             Apc13      PTHR28672.SF1.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_13                                                      PTHR28672.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Apc2       PTHR45957.mag.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_2                                                       PTHR45957.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Apc2       PTHR45957.SF1.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_2                                                       PTHR45957.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Apc10      PTHR12936.mag.mod    ANAPHASE-PROMOTING_COMPLEX_10                                                              PTHR12936.orig.30.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Apc10      PTHR12936.SF0.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_10                                                      PTHR12936.SF0.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Apc11      PTHR11210.SF1.mod    ANAPHASE-PROMOTING_COMPLEX_SUBUNIT_11                                                      PTHR11210.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Ube2s      PTHR24068.SF126.mod  UBC_CORE_DOMAIN-CONTAINING_PROTEIN                                                         PTHR24068.SF126.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-catalytic_core  Ube2c      PTHR24067.SF338.mod  UBIQUITIN-CONJUGATING_ENZYME_E2C                                                           PTHR24067.SF338.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-co-activator    Cdh1       PTHR19918.SF1.mod    FIZZY-RELATED_PROTEIN_HOMOLOG                                                              PTHR19918.SF1.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-co-activator    Cdc20      PTHR19918.SF8.mod    WD_REPEAT-CONTAINING_PROTEIN_55_HOMOLOG                                                    PTHR19918.SF8.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-co-activator    Cdc20      PTHR19918.SF5.mod    MEIOSIS-SPECIFIC_APC-C_ACTIVATOR_PROTEIN_AMA1                                              PTHR19918.SF5.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-substrates      Cyclin_A   PTHR10177.SF472.mod  G2/MITOTIC-SPECIFIC_CYCLIN-3-RELATED                                                       PTHR10177.SF472.pir
ANAPHASE_PROMOTING_COMPLEX/CYCLOSOME        APC-C-substrates      Cyclin_B   PTHR10177.SF559.mod  G2/MITOTIC-SPECIFIC_CYCLIN-B                                                               PTHR10177.SF559.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Mad1       PTHR23168.mag.mod    MITOTIC_SPINDLE_ASSEMBLY_CHECKPOINT_PROTEIN_MAD1__MITOTIC_ARREST_DEFICIENT-LIKE_PROTEIN_1  PTHR23168.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Mad1       PTHR23168.SF0.mod    MITOTIC_SPINDLE_ASSEMBLY_CHECKPOINT_PROTEIN_MAD1__MITOTIC_ARREST_DEFICIENT-LIKE_PROTEIN_1  PTHR23168.SF0.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Mad2       PTHR11842.mag.mod    MITOTIC_SPINDLE_ASSEMBLY_CHECKPOINT_PROTEIN_MAD2                                           PTHR11842.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Mad2       PTHR11842.SF11.mod   MITOTIC_SPINDLE_ASSEMBLY_CHECKPOINT_PROTEIN_MAD2A                                          PTHR11842.SF11.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   MadBub     PTHR14030.mag.mod    MITOTIC_CHECKPOINT_SERINE/THREONINE-PROTEIN_KINASE_BUB1                                    PTHR14030.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   MadBub     PTHR14030.SF4.mod    BUB1-RELATED_KINASE                                                                        PTHR14030.SF4.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Mps1       PTHR22974.SF21.mod   DUAL_SPECIFICITY_PROTEIN_KINASE_TTK                                                        PTHR22974.SF21.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Plk        PTHR24345.SF92.mod   SERINE/THREONINE-PROTEIN_KINASE_PLK                                                        PTHR24345.SF92.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Bub3       PTHR10971.mag.mod    MRNA_EXPORT_FACTOR_AND_BUB3                                                                PTHR10971.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Bub3       PTHR10971.SF5.mod    MITOTIC_CHECKPOINT_PROTEIN_BUB3                                                            PTHR10971.SF5.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   BugZ       PTHR23215.mag.mod    ZINC_FINGER_PROTEIN_207                                                                    PTHR23215.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   BugZ       PTHR23215.SF1.mod    BUB3-INTERACTING_AND_GLEBS_MOTIF-CONTAINING_PROTEIN_ZNF207                                 PTHR23215.SF1.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Zwint-1    PTHR31504.mag.mod    ZW10_INTERACTOR_ZWINT                                                                      PTHR31504.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Zwint-1    PTHR31504.SF1.mod    ZW10_INTERACTOR                                                                            PTHR31504.SF1.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Knl1       PTHR16520.mag.mod    KINETOCHORE_SCAFFOLD_1                                                                     PTHR16520.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Knl1       PTHR16520.SF3.mod    KINETOCHORE_SCAFFOLD_1                                                                     PTHR16520.SF3.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   ZW10       PTHR12205.mag.mod    CENTROMERE/KINETOCHORE_PROTEIN_ZW10                                                        PTHR12205.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   ZW10       PTHR12205.SF0.mod    CENTROMERE/KINETOCHORE_PROTEIN_ZW10_HOMOLOG                                                PTHR12205.SF0.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Zwilch     PTHR15995.mag.mod    PROTEIN_ZWILCH_HOMOLOG                                                                     PTHR15995.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Zwilch     PTHR15995.SF1.mod    PROTEIN_ZWILCH_HOMOLOG                                                                     PTHR15995.SF1.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Rod        PTHR15688.mag.mod    KINETOCHORE-ASSOCIATED_PROTEIN_1                                                           PTHR15688.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Rod        PTHR15688.SF1.mod    KINETOCHORE-ASSOCIATED_PROTEIN_1                                                           PTHR15688.SF1.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Trip13     PTHR45991.mag.mod    PACHYTENE_CHECKPOINT_PROTEIN_2                                                             PTHR45991.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   Trip13     PTHR45991.SF1.mod    PACHYTENE_CHECKPOINT_PROTEIN_2_HOMOLOG                                                     PTHR45991.SF1.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   p31comet   PTHR15681.mag.mod    MAD2L1-BINDING_PROTEIN                                                                     PTHR15681.orig.30.pir
SPINDLE_ASSEMBLY_CHECKPOINT                 SAC                   p31comet   PTHR15681.SF1.mod    MAD2L1-BINDING_PROTEIN                                                                     PTHR15681.SF1.pir

</code>
  
==== Replisome ====

<code>
ORIGIN_RECOGNITION_COMPLEX          ORC       Cdc6-Orc1  PTHR10763.mag.mod    CELL_DIVISION_CONTROL_PROTEIN_6-RELATED                       PTHR10763.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Cdc6       PTHR10763.SF26.mod   CELL_DIVISION_CONTROL_PROTEIN_6_HOMOLOG                       PTHR10763.SF26.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc1       PTHR10763.SF23.mod   ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_1                          PTHR10763.SF23.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc2       PTHR14052.mag.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_2                          PTHR14052.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc2       PTHR14052.SF0.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_2                          PTHR14052.SF0.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc3       PTHR12748.mag.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_3                          PTHR12748.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc3       PTHR12748.SF0.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_3                          PTHR12748.SF0.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc3       PTHR12748.SF1.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_3                          PTHR12748.SF1.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc4       PTHR12087.mag.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_4                          PTHR12087.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc4       PTHR12087.SF0.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_4                          PTHR12087.SF0.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc5       PTHR12705.mag.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_5                          PTHR12705.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc5       PTHR12705.SF0.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_5                          PTHR12705.SF0.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc6       PTHR13394.mag.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_6                          PTHR13394.orig.30.pir
ORIGIN_RECOGNITION_COMPLEX          ORC       Orc6       PTHR13394.SF0.mod    ORIGIN_RECOGNITION_COMPLEX_SUBUNIT_6                          PTHR13394.SF0.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdt1       PTHR28637.mag.mod    DNA_REPLICATION_FACTOR_CDT1                                   PTHR28637.orig.30.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdt1       PTHR28637.SF1.mod    DNA_REPLICATION_FACTOR_CDT1                                   PTHR28637.SF1.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdt1       PTHR28637.SF10.mod   CDT1-LIKE_PROTEIN_B                                           PTHR28637.SF10.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdt1       PTHR28637.SF12.mod   CDT1_DOMAIN-CONTAINING_PROTEIN                                PTHR28637.SF12.pir
FIRING_ELONGATION_FACTORS           FIRE      Mcm10      PTHR13454.mag.mod    PROTEIN_MCM10_HOMOLOG                                         PTHR13454.orig.30.pir
FIRING_ELONGATION_FACTORS           FIRE      Mcm10      PTHR13454.SF11.mod   PROTEIN_MCM10_HOMOLOG                                         PTHR13454.SF11.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdc45      PTHR10507.mag.mod    CDC45-RELATED_PROTEIN                                         PTHR10507.orig.30.pir
FIRING_ELONGATION_FACTORS           FIRE      Cdc45      PTHR10507.SF0.mod    CELL_DIVISION_CONTROL_PROTEIN_45_HOMOLOG                      PTHR10507.SF0.pir
FIRING_ELONGATION_FACTORS           FIRE      GMNN       PTHR13372.mag.mod    GEMININ                                                       PTHR13372.orig.30.pir
FIRING_ELONGATION_FACTORS           FIRE      GMNN       PTHR13372.SF2.mod    GEMININ_COILED-COIL_DOMAIN-CONTAINING_PROTEIN_1               PTHR13372.SF2.pir
FIRING_ELONGATION_FACTORS           FIRE      GMNN       PTHR13372.SF5.mod    GEMININ                                                       PTHR13372.SF5.pir
FIRING_ELONGATION_FACTORS           FIRE      GMNN       PTHR13372.SF4.mod    GEMININ                                                       PTHR13372.SF4.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF1       PTHR12914.mag.mod    PARTNER_OF_SLD5                                               PTHR12914.orig.30.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF1       PTHR12914.SF2.mod    DNA_REPLICATION_COMPLEX_GINS_PROTEIN_PSF1                     PTHR12914.SF2.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF2       PTHR12772.mag.mod    DNA_REPLICATION_COMPLEX_GINS_PROTEIN_PSF2                     PTHR12772.orig.30.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF2       PTHR12772.SF0.mod    DNA_REPLICATION_COMPLEX_GINS_PROTEIN_PSF2                     PTHR12772.SF0.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF3       PTHR22768.mag.mod    UNCHARACTERIZED                                               PTHR22768.orig.30.pir
DNA_REPLICATION_COMPLEX_GINS        GINS      PSF3       PTHR22768.SF0.mod    DNA_REPLICATION_COMPLEX_GINS_PROTEIN_PSF3                     PTHR22768.SF0.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.mag.mod    PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.orig.30.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF0.mod    PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF0.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF5.mod    PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF5.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF6.mod    PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF6.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF8.mod    PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF8.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF10.mod   PROLIFERATING_CELL_NUCLEAR_ANTIGEN_FAMILY_PROTEIN             PTHR11352.SF10.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF11.mod   PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF11.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF12.mod   PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF12.pir
PROLIFERATING_CELL_NUCLEAR_ANTIGEN  PCNA      PCNA       PTHR11352.SF13.mod   PROLIFERATING_CELL_NUCLEAR_ANTIGEN                            PTHR11352.SF13.pir
MCM_HELICASE                        MCM       Mcm2-7     PTHR11630.mag.mod    DNA_REPLICATION_LICENSING_FACTOR_MCM_FAMILY_MEMBER            PTHR11630.orig.30.pir
MCM_HELICASE                        MCM       Mcm2       PTHR11630.SF101.mod  DNA_REPLICATION_LICENSING_FACTOR_MCM2                         PTHR11630.SF101.pir
MCM_HELICASE                        MCM       Mcm2       PTHR11630.SF44.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM2                         PTHR11630.SF44.pir
MCM_HELICASE                        MCM       Mcm3       PTHR11630.SF46.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM3                         PTHR11630.SF46.pir
MCM_HELICASE                        MCM       Mcm4       PTHR11630.SF66.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM4                         PTHR11630.SF66.pir
MCM_HELICASE                        MCM       Mcm5       PTHR11630.SF42.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM5                         PTHR11630.SF42.pir
MCM_HELICASE                        MCM       Mcm6       PTHR11630.SF43.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM6                         PTHR11630.SF43.pir
MCM_HELICASE                        MCM       Mcm6       PTHR11630.SF73.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM6                         PTHR11630.SF73.pir
MCM_HELICASE                        MCM       Mcm7       PTHR11630.SF105.mod  DNA_REPLICATION_LICENSING_FACTOR_MCM7                         PTHR11630.SF105.pir
MCM_HELICASE                        MCM       Mcm7       PTHR11630.SF26.mod   DNA_REPLICATION_LICENSING_FACTOR_MCM7                         PTHR11630.SF26.pir
CDC7_DB4                            CDC7_DB4  Cdc7       PTHR44167.mag.mod    OVARIAN-SPECIFIC_SERINE/THREONINE-PROTEIN_KINASE_LOK-RELATED  PTHR44167.orig.30.pir
CDC7_DB4                            CDC7_DB4  Cdc7       PTHR44167.SF23.mod   CDC7_KINASE,_ISOFORM_A-RELATED                                PTHR44167.SF23.pir
CDC7_DB4                            CDC7_DB4  Db4        PTHR15375.mag.mod    ACTIVATOR_OF_S-PHASE_KINASE-RELATED                           PTHR15375.orig.30.pir
CDC7_DB4                            CDC7_DB4  Db4a       PTHR15375.SF22.mod   PROTEIN_DBF4_HOMOLOG_A                                        PTHR15375.SF22.pir
CDC7_DB4                            CDC7_DB4  Db4b       PTHR15375.SF24.mod   PROTEIN_DBF4_HOMOLOG_B                                        PTHR15375.SF24.pir
REPLICATION_FACTOR_A                RFA       RFA1       PTHR23273.mag.mod    REPLICATION_FACTOR_A_1,_RFA1                                  PTHR23273.orig.30.pir
REPLICATION_FACTOR_A                RFA       RFA1       PTHR23273.SF47.mod   REPLICATION_PROTEIN_A_70_KDA_DNA-BINDING_SUBUNIT_A            PTHR23273.SF47.pir
REPLICATION_FACTOR_A                RFA       RFA2       PTHR13989.SF43.mod   REPLICATION_PROTEIN_A_30_KDA_SUBUNIT-RELATED                  PTHR13989.SF43.pir
REPLICATION_FACTOR_A                RFA       RFA3       PTHR47058.mag.mod    REPLICATION_PROTEIN_A_14_KDA_SUBUNIT_A-RELATED                PTHR47058.orig.30.pir
REPLICATION_FACTOR_A                RFA       RFA3       PTHR47058.SF3.mod    REPLICATION_PROTEIN_A_14_KDA_SUBUNIT_A-RELATED                PTHR47058.SF3.pir
REPLICATION_FACTOR_C                RFC       RFC1       PTHR23389.SF6.mod    REPLICATION_FACTOR_C_SUBUNIT_1                                PTHR23389.SF6.pir
REPLICATION_FACTOR_C                RFC       RFC2       PTHR11669.SF5.mod    REPLICATION_FACTOR_C_SUBUNIT_2                                PTHR11669.SF5.pir
REPLICATION_FACTOR_C                RFC       RFC3       PTHR11669.SF1.mod    REPLICATION_FACTOR_C_SUBUNIT_3                                PTHR11669.SF1.pir
REPLICATION_FACTOR_C                RFC       RFC4       PTHR11669.SF20.mod   REPLICATION_FACTOR_C_SUBUNIT_4                                PTHR11669.SF20.pir
REPLICATION_FACTOR_C                RFC       RFC5       PTHR11669.SF9.mod    REPLICATION_FACTOR_C_SUBUNIT_5                                PTHR11669.SF9.pir
DNA_POLYMERASE_ALPHA                POLA      PolA1      PTHR45861.mag.mod    DNA_POLYMERASE_ALPHA_CATALYTIC_SUBUNIT                        PTHR45861.orig.30.pir
DNA_POLYMERASE_ALPHA                POLA      PolA1      PTHR45861.SF1.mod    DNA_POLYMERASE_ALPHA_CATALYTIC_SUBUNIT                        PTHR45861.SF1.pir
DNA_POLYMERASE_ALPHA                POLA      PolA2      PTHR23061.mag.mod    DNA_POLYMERASE_2_ALPHA_70_KDA_SUBUNIT                         PTHR23061.orig.30.pir
DNA_POLYMERASE_ALPHA                POLA      PolA2      PTHR23061.SF12.mod   DNA_POLYMERASE_ALPHA_SUBUNIT_B                                PTHR23061.SF12.pir
DNA_PRIMASE                         PRIM      Prim1      PTHR10536.mag.mod    DNA_PRIMASE_SMALL_SUBUNIT                                     PTHR10536.orig.30.pir
DNA_PRIMASE                         PRIM      Prim1      PTHR10536.SF0.mod    DNA_PRIMASE_SMALL_SUBUNIT                                     PTHR10536.SF0.pir
DNA_PRIMASE                         PRIM      Prim2      PTHR10537.mag.mod    DNA_PRIMASE_LARGE_SUBUNIT                                     PTHR10537.orig.30.pir
DNA_PRIMASE                         PRIM      Prim2      PTHR10537.SF3.mod    DNA_PRIMASE_LARGE_SUBUNIT                                     PTHR10537.SF3.pir
DNA_PRIMASE                         PRIM      Prim2      PTHR10537.SF6.mod    DNA_PRIMASE_LARGE_SUBUNIT                                     PTHR10537.SF6.pir
DNA_POLYMERASE_DELTA                POLD      PolD1      PTHR10322.mag.mod    DNA_POLYMERASE_CATALYTIC_SUBUNIT                              PTHR10322.orig.30.pir
DNA_POLYMERASE_DELTA                POLD      PolD1      PTHR10322.SF23.mod   DNA_POLYMERASE_DELTA_CATALYTIC_SUBUNIT                        PTHR10322.SF23.pir
DNA_POLYMERASE_DELTA                POLD      PolD2      PTHR10416.mag.mod    DNA_POLYMERASE_DELTA_SUBUNIT_2                                PTHR10416.orig.30.pir
DNA_POLYMERASE_DELTA                POLD      PolD2      PTHR10416.SF0.mod    DNA_POLYMERASE_DELTA_SUBUNIT_2                                PTHR10416.SF0.pir
DNA_POLYMERASE_DELTA                POLD      PolD3      PTHR17598.mag.mod    DNA_POLYMERASE_DELTA_SUBUNIT_3                                PTHR17598.orig.30.pir
DNA_POLYMERASE_DELTA                POLD      PolD3      PTHR17598.SF13.mod   DNA_POLYMERASE_DELTA_SUBUNIT_3                                PTHR17598.SF13.pir
DNA_POLYMERASE_DELTA                POLD      PolD4      PTHR14303.mag.mod    DNA_POLYMERASE_DELTA_SUBUNIT_4                                PTHR14303.orig.30.pir
DNA_POLYMERASE_DELTA                POLD      PolD4      PTHR14303.SF0.mod    DNA_POLYMERASE_DELTA_SUBUNIT_4                                PTHR14303.SF0.pir
DNA_POLYMERASE_EPSILON              POLE      PolE1      PTHR10670.mag.mod    DNA_POLYMERASE_EPSILON_CATALYTIC_SUBUNIT_A                    PTHR10670.orig.30.pir
DNA_POLYMERASE_EPSILON              POLE      PolE1      PTHR10670.SF0.mod    DNA_POLYMERASE_EPSILON_CATALYTIC_SUBUNIT_A                    PTHR10670.SF0.pir
DNA_POLYMERASE_EPSILON              POLE      PolE2      PTHR12708.mag.mod    DNA_POLYMERASE_EPSILON_SUBUNIT_B                              PTHR12708.orig.30.pir
DNA_POLYMERASE_EPSILON              POLE      PolE3      PTHR46172.mag.mod    DNA_POLYMERASE_EPSILON_SUBUNIT_3                              PTHR46172.orig.30.pir
DNA_POLYMERASE_EPSILON              POLE      PolE3      PTHR46172.SF1.mod    DNA_POLYMERASE_EPSILON_SUBUNIT_3                              PTHR46172.SF1.pir
DNA_POLYMERASE_EPSILON              POLE      PolE4      PTHR10252.SF79.mod   DNA_POLYMERASE_EPSILON_SUBUNIT_4                              PTHR10252.SF79.pir

</code>

==== Sexual reproduction / Meiosis ? ====

<code>
CATSPER_COMPLEX                  CATSPER  CatSper-g  PTHR14327.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_GAMMA           PTHR14327.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-g  PTHR14327.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_GAMMA           PTHR14327.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-b  PTHR14705.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_BETA            PTHR14705.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-b  PTHR14705.SF0.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_BETA            PTHR14705.SF0.pir
CATSPER_COMPLEX                  CATSPER  CatSper-d  PTHR33722.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_DELTA-RELATED   PTHR33722.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-e  PTHR33722.SF3.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_EPSILON         PTHR33722.SF3.pir
CATSPER_COMPLEX                  CATSPER  CatSper-d  PTHR33722.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_DELTA           PTHR33722.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-z  PTHR42155.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_ZETA            PTHR42155.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-z  PTHR42155.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_SUBUNIT_ZETA            PTHR42155.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-2  PTHR46923.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_2                       PTHR46923.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-2  PTHR46923.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_2                       PTHR46923.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-4  PTHR47077.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_4                       PTHR47077.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-3  PTHR47131.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_3                       PTHR47131.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-3  PTHR47131.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_3                       PTHR47131.SF1.pir
CATSPER_COMPLEX                  CATSPER  CatSper-1  PTHR47193.mag.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_1                       PTHR47193.orig.30.pir
CATSPER_COMPLEX                  CATSPER  CatSper-1  PTHR47193.SF1.mod  CATION_CHANNEL_SPERM-ASSOCIATED_PROTEIN_1                       PTHR47193.SF1.pir
CAMP_SIGNALING_TMCB              TMCB     tmcB       PTHR31600.mag.mod  TINY_MACROCYSTS_PROTEIN_B-RELATED                               PTHR31600.orig.30.pir
CAMP_SIGNALING_TMCB              TMCB     tmcB       PTHR31600.SF2.mod  TINY_MACROCYSTS_PROTEIN_B-RELATED                               PTHR31600.SF2.pir
GAMETE_EXPRESSION                GEX1     gex1       PTHR33538.mag.mod  PROTEIN_GAMETE_EXPRESSED_1                                      PTHR33538.orig.30.pir
GAMETE_EXPRESSION                GEX1     gex1       PTHR33538.SF2.mod  PROTEIN_GAMETE_EXPRESSED_1                                      PTHR33538.SF2.pir
MEMBRANE_FUSION_BETWEEN_GAMETES  HAP2     hap2       PTHR31764.mag.mod  PROTEIN_HAPLESS_2                                               PTHR31764.orig.30.pir
MEMBRANE_FUSION_BETWEEN_GAMETES  HAP2     hap2       PTHR31764.SF0.mod  HAP2-GCS1_DOMAIN-CONTAINING_PROTEIN                             PTHR31764.SF0.pir
</code>

==== polyA machinary====

<code>
POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.mag.mod       DNA REPAIR/RNA PROCESSING CPSF FAMILY   PTHR10644.orig.30.pir
POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF2.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 1       PTHR10644.SF2.pir
POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.SF6.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR (CPSF) A SUBUNIT PROTEIN          PTHR10644.SF6.pir
POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2       PTHR45922.orig.30.pir
POLYA_MACHINERY CPSF    CPSF2/CPSF100   PTHR45922.SF1.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2       PTHR45922.SF1.pir
POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR FAMILY MEMBER   PTHR11203.orig.30.pir
POLYA_MACHINERY CPSF    CPSF3/CPSF73    PTHR11203.SF11.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 3       PTHR11203.SF11.pir
POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.mag.mod       CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-RELATED       PTHR23102.orig.30.pir
POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF18.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF18.pir
POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF24.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF24.pir
POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF19.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-LIKE PROTEIN-RELATED       PTHR23102.SF19.pir
POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.orig.30.pir
POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.SF2.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.SF2.pir
POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.orig.30.pir
POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.SF6.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.SF6.pir
POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.mag.mod       RNA CLEAVAGE STIMULATION FACTOR PTHR19980.orig.30.pir
POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.SF0.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 3   PTHR19980.SF0.pir
POLYA_MACHINERY other   Fip1    PTHR13484.mag.mod       FIP1-LIKE 1 PROTEIN     PTHR13484.orig.30.pir
POLYA_MACHINERY other   Fip1    PTHR13484.SF9.mod       PRE-MRNA 3'-END-PROCESSING FACTOR FIP1  PTHR13484.SF9.pir
POLYA_MACHINERY other   WDR33   PTHR22836.mag.mod       WD40 REPEAT PROTEIN     PTHR22836.orig.30.pir
POLYA_MACHINERY other   WDR33   PTHR22836.SF0.mod       PRE-MRNA 3' END PROCESSING PROTEIN WDR33        PTHR22836.SF0.pir
</code>

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