Differences

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--- finding_genes_of_interest_with_panther_hmms [2026/01/23 15:31] – [Do an hmmscan] 172.20.120.170
+++ finding_genes_of_interest_with_panther_hmms [2026/03/16 14:41] (current) – [Mitochondrial import] 172.20.54.200
@@ Line 73: / Line 73: @@
 </code>
-'hmmscan' can be very slow sometimes. In which case you'll want to use 'hmmsearch', which sometimes is more computationally efficient.
+''hmmscan'' can be very slow sometimes. In which case you'll want to use ''hmmsearch'', which sometimes is more computationally efficient.
 <code>
@@ Line 86: / Line 86: @@
 </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.
+''-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''.
@@ Line 137: / Line 137: @@
 <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
+This yields a file that looks like this (if you did hmmscan)
 <code>
@@ Line 310: / Line 314: @@
 <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) \
@@ Line 429: / Line 439: @@
 <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
@@ Line 634: / Line 646: @@
 <code>
-PROTEIN_IMPORT_AND_FOLDING  IMPORT  Tom40                          PTHR10802.mag.mod    MITOCHONDRIAL_IMPORT_RECEPTOR_SUBUNIT_TOM40                               PTHR10802.orig.30.pir
+TRANSLOCASE_OF_THE_OUTER_MEMBRANE  TOM  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
+TRANSLOCASE_OF_THE_OUTER_MEMBRANE  TOM  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
+SORTING_AND_ASSEMBLY_MACHINERY     SAM  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
+SORTING_AND_ASSEMBLY_MACHINERY     SAM  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
+MITOCHONDRIAL_IMPORT_AND_ASSEMBLY  MIA  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
+MITOCHONDRIAL_IMPORT_AND_ASSEMBLY  MIA  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
+TRANSLOCASE_OF_THE_INNER_MEMBRANE  TIM  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
@@ Line 699: / Line 711: @@
 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>
@@ Line 1005: / Line 1037: @@
 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>
-==== Polyadenylation machinery ====
+==== polyA machinary====
 <code>
-POLYA_MACHINERY CPSF    CPSF1/CPSF160   PTHR10644.mag.mod       DNA REPAIR/RNA PROCESSING CPSF FAMILY
+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
+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
+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
+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
+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
+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
+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
+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
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF18.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF18.pir
-POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF24.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4       PTHR23102.SF24.pir
-POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.SF2.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1
+POLYA_MACHINERY CPSF    CPSF4/CPSF30    PTHR23102.SF19.mod      CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-LIKE PROTEIN-RELATED       PTHR23102.SF19.pir
-POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2
+POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.orig.30.pir
-POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.SF6.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2
+POLYA_MACHINERY CstF    CstF1/CstF50    PTHR44133.SF2.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 1   PTHR44133.SF2.pir
-POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.mag.mod       RNA CLEAVAGE STIMULATION FACTOR
+POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.mag.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.orig.30.pir
-POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.SF0.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 3
+POLYA_MACHINERY CstF    CstF2/CstF64    PTHR45735.SF6.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 2   PTHR45735.SF6.pir
-POLYA_MACHINERY other   Fip1    PTHR13484.mag.mod       FIP1-LIKE 1 PROTEIN
+POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.mag.mod       RNA CLEAVAGE STIMULATION FACTOR PTHR19980.orig.30.pir
-POLYA_MACHINERY other   Fip1    PTHR13484.SF9.mod       PRE-MRNA 3'-END-PROCESSING FACTOR FIP1
+POLYA_MACHINERY CstF    CstF3/CstF77    PTHR19980.SF0.mod       CLEAVAGE STIMULATION FACTOR SUBUNIT 3   PTHR19980.SF0.pir
-POLYA_MACHINERY other   WDR33   PTHR22836.mag.mod       WD40 REPEAT PROTEIN
+POLYA_MACHINERY other   Fip1    PTHR13484.mag.mod       FIP1-LIKE 1 PROTEIN     PTHR13484.orig.30.pir
-POLYA_MACHINERY other   WDR33   PTHR22836.SF0.mod       PRE-MRNA 3' END PROCESSING PROTEIN WDR33
+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
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