SEQIO -- A Package for Sequence File I/O

FMTSEQ Big Alignment Example


The following big alignment was produced by first running the following FASTA command

  fasta -q -d 30 mgmstm1.aa s > fasta_out.30
where "mgmstm1.aa" is one of the example sequences from the FASTA distribution and "s" is the FASTLIBS entry for the Swiss-Prot database (Version 30). Then, the following fmtseq command was executed:
  fmtseq fasta_out.30 -fpretty -nametop -nameleft=11 -width=60 -idprefix=sp
         -nocolspace -interline=3 '-gapout= ' -otemp
where the actual command was give on a single line containing all of the options.

  1. sp:GT8.7 transl. of pa875.con, 19 to 675, 243 aa.
  2. sp:GTB1_MOUSE GLUTATHIONE S-TRANSFERASE GT8.7 (EC 2.5.1.1, 243 aa.
  3. sp:GTB1_RAT GLUTATHIONE S-TRANSFERASE YB1 (EC 2.5.1.18), 243 aa.
  4. sp:GTB1_CRILO GLUTATHIONE S-TRANSFERASE Y1 (EC 2.5.1.18), 243 aa.
  5. sp:GTB3_MOUSE GLUTATHIONE S-TRANSFERASE GT9.3 (EC 2.5.1.1, 243 aa.
  6. sp:GTB2_MOUSE GLUTATHIONE S-TRANSFERASE 5 (EC 2.5.1.18) (, 243 aa.
  7. sp:GTB2_RAT GLUTATHIONE S-TRANSFERASE YB2 (EC 2.5.1.18), 243 aa.
  8. sp:GTB_CAVPO GLUTATHIONE S-TRANSFERASE B (EC 2.5.1.18) (, 243 aa.
  9. sp:GTM1_HUMAN GLUTATHIONE S-TRANSFERASE HB SUBUNIT 4 (EC, 243 aa.
 10. sp:GTMU_MESAU GLUTATHIONE S-TRANSFERASE (EC 2.5.1.18) (CL, 243 aa.
 11. sp:GTM4_HUMAN GLUTATHIONE S-TRANSFERASE MUSCLE (EC 2.5.1, 243 aa.
 12. sp:GTB3_RAT GLUTATHIONE S-TRANSFERASE YB3 (EC 2.5.1.18), 243 aa.
 13. sp:GTM5_HUMAN GLUTATHIONE S-TRANSFERASE TESTIS/BRAIN (EC, 243 aa.
 14. sp:GT2_CHICK GLUTATHIONE S-TRANSFERASE 2 (EC 2.5.1.18) (, 243 aa.
 15. sp:GT26_FASHE GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 16. sp:GT27_FASHE GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 17. sp:GT28_FASHE GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 18. sp:GT27_SCHMA GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 19. sp:GT26_SCHJA GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 20. sp:GT26_SCHMA GLUTATHIONE S-TRANSFERASE 26 KD (EC 2.5.1.1, 243 aa.
 21. sp:GTP_BOVIN GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (, 243 aa.
 22. sp:GTP_MOUSE GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (, 243 aa.
 23. sp:GTP_HUMAN GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (, 243 aa.
 24. sp:GTP_RAT GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (, 243 aa.
 25. sp:GTP_CAEEL GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18), 243 aa.
 26. sp:GTP_PIG GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (, 243 aa.
 27. sp:GTA1_RAT GLUTATHIONE S-TRANSFERASE YA (EC 2.5.1.18), 243 aa.
 28. sp:GTA2_MOUSE GLUTATHIONE S-TRANSFERASE YA CHAIN (EC 2.5, 243 aa.
 29. sp:GTA2_RAT GLUTATHIONE S-TRANSFERASE YA (EC 2.5.1.18), 243 aa.
 30. sp:GTA1_MOUSE GLUTATHIONE S-TRANSFERASE GT41A (EC 2.5.1.1, 243 aa.

GT8.7        PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL  G LDFP 
GTB1_MOUSE   PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL  G LDFP 
GTB1_RAT     PMILGYWNVRGLTHPIRLLLEYTDSSYEEKRYAMGDAPDYDRSQWLNEKFKL  G LDFP 
GTB1_CRILO   PMILGYWNVRGLTNPIRLLLEYTDSSYEEKKYTMGDAPDSDRSQWLNEKFKL  G LDFP 
GTB3_MOUSE   PMTLGYWNTRGLTHSIRLLLEYTDSSYEEKRYVMGDAPNFDRSQWLSEKFNL  G LDFP 
GTB2_MOUSE   PMTLGYWDIRGLAHAIRLLLEYTDTSYEDKKYTMGDAPDYDRSQWLSEKFKL  G LDFP 
GTB2_RAT     PMTLGYWDIRGLAHAIRLFLEYTDTSYEDKKYSMGDAPDYDRSQWLSEKFKL  G LDFP 
GTB_CAVPO    PMTLGYWNIRGLTHPIRLILEYTNSGYEEKRYNMGDAPDYDRSQWLNEKFKL  G LDFP 
GTM1_HUMAN   PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKL  G LDFP 
GTMU_MESAU   PVTLGYWDIRGLAHAIRLLLEYTDTSYEEKKYTMGDAPNFDRSQWLNEKFKL  G LDFP 
GTM4_HUMAN   PMTLGYWNIRGLAHSIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKL  G LDFP 
GTB3_RAT     PMTLGYWDIRGLAHAIRLLLEYTDSSYEEKRYTMGDAPDFDRSQWLNEKFKL  G LDFP 
GTM5_HUMAN    MVLGYWDIRGLAHAIRLLLEFTDTSYEEKRYTCGEAPDYDRSQWLDVKFKL  D LDFP 
GT2_CHICK       LGYWDIRGLAHAIRLLLEYTETPYQERRYKAGPAPDFDPSDWTNEKEKL  G LDFP 
GT26_FASHE   PAKLGYWKIRGLQQPVRLLLEYLGEEYEEHLY    GRD DREKWFGDKFNM  G LDLP 
GT27_FASHE         WKLRGLAQPVRLFLEYLGEEYEEHLY    GRD DREKWMSEKFNM  G LDLP 
GT28_FASHE           IRGLQQPVRLFLEYLGEEYEEHLYGRND     REKWLGDKFNM  G LDLP 
GT27_SCHMA      LGYWKIKGLVQPTRLLLEYLGERYEERLY   DRNDGDV  WRNEKFKL  G LDFP 
GT26_SCHJA     ILGYWKIKGLVQPTRLLLEYLEEKYEEHLYER DEGD    KWRNKKFEL  G LEFP 
GT26_SCHMA      FGYWKVKGLVQPTRLLLEHLEETYEERAY   DRNEID  AWSNDKFKL  G LEFP 
GTP_BOVIN    PYTIVYFPVQGRCEAMRMLLADQGQSWKEEVVAM        QSWLQGPLKA  S CLYG 
GTP_MOUSE    PYTIVYFPVRGRCEAMRMLLADQGQSWKEEVVTI        DTWMQGLLKP  T CLYG 
GTP_HUMAN    PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTV        ETWQEGSLKA  S CLYG 
GTP_RAT      PYTIVYFPVRGRCEATRMLLADQGQSWKEEVVTI DV       WLQGSLKS  T CLYG 
GTP_CAEEL       LTYFDIHGLAEPIRLLLADKQVAYEDHRVTY        EQWADIKPKM     IFG 
GTP_PIG      PYTITYFPVRGRCEAMRMLLADQDQSWKEEVVTMETWPPL          KP  S CLFR 
GTA1_RAT       VLHYFNARGRMECIRWLLAAAGVEFDEK         FIQSPEDLEKLKKDGN LMFD 
GTA2_MOUSE     VLHYFNARGRMECIRWLLAAAGVEFEEK         FIQSPEDLEKLKKDGN LMFD 
GTA2_RAT       VLHYFNARGRMECIRWLLAAAGVEFEEK  LIQSPEDLEKLK      KD  GNLMFD 
GTA1_MOUSE     VLHYFNARGRMECIRWLLAAAGVEFEEK         FIQSPEDLEKLKKDGN LMFD 



GT8.7        NLPYL IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD TRM  QLIML 
GTB1_MOUSE   NLPYL IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD TRM  QLIML 
GTB1_RAT     NLPYL IDGSRKITQSNAIMRYLARKHHLCGETEEERIRADIVENQVMD NRM  QLIML 
GTB1_CRILO   NLPYL IDGSHKITQSNAILRYIARKHNLCGETEEERIRVDIVENQAMD TRM  QLIML 
GTB3_MOUSE   NLPYL IDGSHKVTQSNAILRYLGRKHNLCGETEEERIRVDTLENQVMD TRI  QLMIV 
GTB2_MOUSE   NLPYL IDGSHKITQSNAILRYLARKHNLCGETEEERIRVDILENQAMD TRI  QLAMV 
GTB2_RAT     NLPYL IDGSHKITQSNAILRYLGRKHNLCGETEEERIRVDVLENQAMD TRL  QLAMV 
GTB_CAVPO    NLPYL IDGTHKLTQSNAILRYIARKHNLCGVTEEETIRMDILENQVMD IRM  QLIML 
GTM1_HUMAN   NLPYL IDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMD NHM  QLGMI 
GTMU_MESAU   NLPYL IDGSHKITQSNAILRYIARKHDLCGETEEERIQLDILENQAMD TRM  QLAMV 
GTM4_HUMAN   NLPYL IDGTHKITQSNAILRYIARKHNLCGESEKEQIREDILENQFMD SRM  QLAKL 
GTB3_RAT     NLPYL IDGSHKITQSNAILRYLGRKHNLCGETEEERIRVDILENQLMD NRM  VLARL 
GTM5_HUMAN   NLPYL LDGKNKITQSNAILRYIARKHNMCGETEEEKIRVDIIENQVMD FRT  QLIRL 
GT2_CHICK    NLPYL IDGDVKLTQSNAILRYIARKHNMCGETEVEKQRVDVLENHLMD LRM  AFARL 
GT26_FASHE   NLPYY IDDKCKLTQSVAIMRYIADKHGMLGTTPEERARISMIEGAAMD LRM  GFVRV 
GT27_FASHE   NLPYY IDDKCKLTQSVAIMRYIADKHGMLGTTPEERARISMIEGAAMD LRI  GFGRV 
GT28_FASHE   NLPYY IDDKCKLTQSVAIMRYIADKHGMLGSTPEERARISMIEGAAMD LRI  GFGLT 
GT27_SCHMA   NLPYY IDGDVKLTQSMAILRYIADKHNMLGGCPKERAEISMLEGAILD IRY  GVSRI 
GT26_SCHJA   NLPYY IDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLD IRY  GVSRI 
GT26_SCHMA   NLPYY IDGDFKLTQSMAIIRYIADKHNMLGACPKERAEISMLEGAVLD IRM  GVLRI 
GTP_BOVIN    QLPKF QDGDLTLYQSNAILRHLGRTLGLYGKDQQEAALVDMVNDGVED LRC  KYVSL 
GTP_MOUSE    QLPKF EDGDLTLYQSNAILRHLGRSLGLYGKNQREAAQMDMVNDGVED LRG  KYVTL 
GTP_HUMAN    QLPKF QDGDLTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVED LRC  KYISL 
GTP_RAT      QLPKF EDGDLTLYQSNAILRHLGRSLGLYGKDQKEAALVDMVNDGVED LRC  KYGTL 
GTP_CAEEL    QVPCL LSGDEEIVQSGAIIRHLARLNGLNGSNETETTFIDMFYEGLRD LHT  KYTTM 
GTP_PIG      QLPKF QDGDLTLYQSNAILRHLGRSFGLYGKDQKEAALVDMVNDGVED LRC  KYATL 
GTA1_RAT     QVPMVEIDG MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEM  IMQLV 
GTA2_MOUSE   QVPMVEIDG MKLAQTRAILNYIATKYDLYGKDMKERALIDMYSEGILDLTEMIGQLV L 
GTA2_RAT     QVPMVEIDG MKLAQTRAILNYIATKYDLYGKDMKERALIDMYSEGILD LTE  MIIQL 
GTA1_MOUSE   QVPMVEIDG MKLVQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIGQLV L 



GT8.7          CYNPDFEKQKPEFLK  TI PEKM    K    LYSEFL    GK  RPWFAGDKVTY 
GTB1_MOUSE     CYNPDFEKQKPEFLK  TI PEKM    K    LYSEFL    GK  RPWFAGDKVTY 
GTB1_RAT       CYNPDFEKQKPEFLK  TI PEKM    K    LYSEFL    GK  RPWFAGDKVTY 
GTB1_CRILO     CYNPDFEKQKPEFLK  TI PEKM    K    MYSEFL    GK  RPWFAGDKVTL 
GTB3_MOUSE     CCSPDFEKQKPEFLK  AI PEKM    K    LYSEFL    GK  RPWFAGDKVTY 
GTB2_MOUSE     CYSPDFEKKKPEYLE  GL PEKM    K    LYSEFL    GK  QPWFAGNKVTY 
GTB2_RAT       CYSPDFERKKPEYLE  GL PEKM    K    LYSEFL    GK  QPWFAGNKITY 
GTB_CAVPO      CYSPDFEQKKAEFLE  GI PDKM    K    LFSQFL    GK  LPWFAGNKLTY 
GTM1_HUMAN     CYNPEFEKLKPKYLE  EL PEKL    K    LYSEFL    GK  RPWFAGNKITF 
GTMU_MESAU     CYSPDFEKRKPEYLE  GL PEKM    K    LYSEFL    GK  RSWFAGDKITY 
GTM4_HUMAN     CYDPDFEKLKPEYLQ  AL PEML    K    LYSQFL    GK  QPWFLGDKITF 
GTB3_RAT       CYNPDFEKLKPGYLE  QL PGMM    R    LYSEFL    GK  RPWFAGDKITF 
GTM5_HUMAN     CYSSDHEKLKPQYLE  EL PGQL    K    QFSMFL    WK  FSWFAGEKLTF 
GT2_CHICK      CYSPDFEKLKPAYLE  LL PGKL    R    QLSRFL    GS  RSWFVGDKLTF 
GT26_FASHE     CYNPKFEEVKGDYLK  EL PTTL    K    MWSNFL    GD  RHYLTGSPVSH 
GT27_FASHE     CYNPKFEEVKEEYVK  EL PKTL    K    MWSDFL    GD  RHYLTGSSVSH 
GT28_FASHE     CYNPKFEELKGDYLK  GL PTTL    K    MWSDFL    GD  RQYLIGSSVSH 
GT27_SCHMA     AYNKEFETLKVDFLN  QL PGML    K    MFEDRL    SH  NTYLNGDKVTH 
GT26_SCHJA     AYSKDFETLKVDFLS  KL PEML    K    MFEDRL    CH  KTYLNGDHVTH 
GT26_SCHMA     AYNKEYETLKVDFLN  KL PGRL    K    MFEDRL    SN  KTYLNGNCVTH 
GTP_BOVIN      IYT NYEAGKEDYVK  AL PQHL    K    PFETLLSQNKGG  QAFIVGDQISF 
GTP_MOUSE      IYT NYENGKNDYVK  AL PGHL    KPFETLLSQNQ    GG  KAFIVGDQISF 
GTP_HUMAN      IYT NYEAGKDDYVK  AL PGQL    KPFETLLSQNQ    GG  KTFIVGDQISF 
GTP_RAT        IYT NYENGKDDYVK  AL PGHL    KPFETLLSQNQ    GG  KAFIVGNQISF 
GTP_CAEEL      IYR NYEDGKAPYIK  DVLPGELARLEK    LFHTYK    NG  EHYVIGDKESY 
GTP_PIG        IYT NYEAGKEKYVK  EL PEHL    KPFETLLSQNQ    GG  QAFVVGSQISF 
GTA1_RAT       ICPPDQKEAKTALAKDRTK NRYL    P    AFEKVL    KSHGQDYLVGNKLTR 
GTA2_MOUSE     C PPDQREAKTALAKDRTK NRYL    P    AFEKVL    KSHGQDYLVGNRLTR 
GTA2_RAT     VIC PPDQREAKTALAKDRTK NRYL    P    AFEKVL    KSHGQDYLVGNRLTR 
GTA1_MOUSE     C PPDQREAKTALAKDRTK NRYL    P    AFEKVL    KSHGQDYLVGNRLTR 



GT8.7        VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW 
GTB1_MOUSE   VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHW 
GTB1_RAT     VDFLAYDILDQYHIFEPKCLDAFPNLKDFLARFEGLKKISAYMKSSRYLSTPIFSKLAQW 
GTB1_CRILO   CGFLAYDVLDQYQMFEPKCLDPFPNLKDFLARFEGLKKISAYMKTSRFLRRPIFSKMAQW 
GTB3_MOUSE   VDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRFLPRPVFTKIAQW 
GTB2_MOUSE   VDFLVYDVLDQHRIFEPKCLDAFPNLKDFMGRFEGLKKISDYMKSSRFLSKPIFAKMAFW 
GTB2_RAT     VDFLVYDVLDQHRIFEPKCLDAFPNLKDFVARFEGLKKISDYMKSGRFLSKPIFAKMAFW 
GTB_CAVPO    VDFLAYDVLDQYRMLEPKCLEAFPNLKDFISRFEGLEKISSYMKSSRFLPKPLFSKFAFW 
GTM1_HUMAN   VDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVW 
GTMU_MESAU   VDFLIYDVLDQHRIFAPKCLDAFPNLKDFLARFEGLKKISDYMKSSRFSCKQIFAKMAVW 
GTM4_HUMAN   VDFIAYDVLERNQVFEPSCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFTKMAVW 
GTB3_RAT     VDFIAYDVLERNQVFEATCLDAFPNLKDFIARFEGLKKISDYMKSSRFLPRPLFTKMAIW 
GTM5_HUMAN   VDFLTYDILDQNRIFDPKCLDEFPNLKAFMCRFEALEKIAAYLQSDQFCKMPINNKMAQW 
GT2_CHICK    VDFLAYDVLDQQRMFVPDCPELQGNLSQFLQRFEALEKISAYMRSGRFMKAPIFWYTALW 
GT26_FASHE   VDFMVYEALDCIRYLAPQCLEDFPKLKEFKSRIEDLPKIKAYMESEKFIKWPLNSWIA   
GT27_FASHE   VDFMLYETLDSIRYLAPHCLDEFPKLKEFKSRIEALPKIKAYMESKRFIKWPL        
GT28_FASHE   VDFMVYEALDCIRYLAPQCLDDFPKLKEFKSRIEDLPKIKEYMKSERFIKWPLHS      
GT27_SCHMA   PDFMLYDALDVVLYMDPKCLDNFPKLISFKQRIENLPPIKNYLNSNRYIKWPL        
GT26_SCHJA   PDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPL        
GT26_SCHMA   PDFMLYDALDVVLYMDSQCLNEFPKLVSFKKCIEDLPQIKNYLNSSRYIKWPL        
GTP_BOVIN    ADYNLLDLLRIHQVLAPSCLDSFPLLSAYVARLNSRPKLKAFLASPEHMNRPI        
GTP_MOUSE    ADYNLLDLLLIHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPEHVNRPI        
GTP_HUMAN    ADYNLLDLLLIHEVLAPGCLDAFPLLSAYVGRLSARPKLKAFLASPEYVNLPI        
GTP_RAT      ADYNLLDLLLVHQVLAPGCLDNFPLLSAYVARLSARPKIKAFLSSPDHLNRPI        
GTP_CAEEL    ADYVLFEELDIHLILTPNALDGVPALKKFHERFAERPNIKAYLNKRAAINPPV        
GTP_PIG      ADYNLLDLLRIHQVLNPSCLDAFPLLSAYVARLSARPKIKAFLASPEHVNRPI        
GTA1_RAT     VDIHLLELLLYVEEFDASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPMDAKQIEE 
GTA2_MOUSE   VDIHLLEVLLYVEEFDASLLTPFPLLKAFKSRISSLPNVKKFLQPGSQRKPPMDAKQIQE 
GTA2_RAT     VDIHLLELLLYVEEFDASLLTSFPLLKAFKSRISSLPNVKKFLQ                 
GTA1_MOUSE   VDVHLLELLLYVEELDASLLTPFPLLKAFKSRISSLPNVKKFLQPGSQRKPPLDAKQIEE 



GT8.7        SNK                                                          
GTB1_MOUSE   SNK                                                          
GTB1_RAT     SNK                                                          
GTB1_CRILO   SNK                                                          
GTB3_MOUSE   G                                                            
GTB2_MOUSE   NPK                                                          
GTB2_RAT     NPK                                                          
GTB_CAVPO    NNK                                                          
GTM1_HUMAN   GNK                                                          
GTMU_MESAU   NSK                                                          
GTM4_HUMAN   GNK                                                          
GTB3_RAT     GSK                                                          
GTM5_HUMAN   GNK                                                          
GT2_CHICK    NNK                                                          
GT26_FASHE                                                                
GT27_FASHE                                                                
GT28_FASHE                                                                
GT27_SCHMA                                                                
GT26_SCHJA                                                                
GT26_SCHMA                                                                
GTP_BOVIN                                                                 
GTP_MOUSE                                                                 
GTP_HUMAN                                                                 
GTP_RAT                                                                   
GTP_CAEEL                                                                 
GTP_PIG                                                                   
GTA1_RAT     ARK                                                          
GTA2_MOUSE   ARK                                                          
GTA2_RAT                                                                  
GTA1_MOUSE   ARK                                                          




James R. Knight, knight@cs.ucdavis.edu
March 25, 1996