<owner_name="James Knight, knight@cs.ucdavis.edu">
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