1pamA - reference 3


Name                 cyclodextrin																

Number of sequences              19
Alignment Length                 605
Longest Sequence                 511
Shortest Sequence                404
Average Percent Identity         34
Maximum Percent Identity         78
Minimum Percent Identity         16

Sequence Name    SWISSPROT Accession
1pamA                P05618         
amy_bacci            P08137         
cdgt_bacli           P14014         
amy_thetu            P26827         
CDG2_PAEMA           P31835         
CDG1_PAEMA           P04830         
cdgt_bacst           P31797         
cdgt_bacs2           P31746         
amym_bacst           P19531         
cdgt_klepn           P08704         
2aaa                 P56271         
amyb_paepo           P21543         
amya_aspor           P10529         
amy1_deboc           P19269         
amy1_sacfi           P21567         
ydd2_schpo           Q10427         
amy1_schpo           Q09840         
1smd                 P04745         
1jdc                 P13507         

Family   1pamA amy_bacci cdgt_bacli amy_thetu CDG2_PAEMA CDG1_PAEMA cdgt_bacst cdgt_bacs2 amym_bacst cdgt_klepn
Family   2aaa amyb_paepo amya_aspor amy1_deboc amy1_sacfi ydd2_schpo amy1_schpo
Family   1smd
Family   1jdc


1pamA        1  .tDVIYQIFTdrfs..DGNPANnptgaa...fdgsct.nlrlYCGGDWQG
amy_bacci    1  .tDVIYQIVTdrfv..DGNTANnpagsa...ydatcstnlklYCGGDWQG
cdgt_bacli   1  .tDVIYQVFTdrfl..DGNPSNnptgaa...fdgtcs.nlklYCGGDWQG
amy_thetu    1  .tDVIYQIVTdrfv..DGNTSNnptgdl...ydptht.slkkYFGGDWQG
CDG2_PAEMA   1  .tDTVYQIVTdrfv..DGNSANnptgaa...fssdhs.nlklYFGGDWQG
CDG1_PAEMA   1  .tDVIYQIVTdrfa..DGDRTNnpagda...fsgdrs.nlklYFGGDWQG
cdgt_bacst   1  .sDVVYQIVVdrfv..DGNTSNnpsgal...fssgct.nlrkYCGGDWQG
cdgt_bacs2   1  .kDVIYQIVTdrfs..DGNPGNnpsgai...fsqnci.dlhkYCGGDWQG
amym_bacst   1  .gDVIYQIIIdrfy..DGDTTNnnpaksyglydptks.kwkmYWGGDLEG
cdgt_klepn   1  .kETIYFLFLdrfs..DGDPSNnagfns.atydpn...nlkkYTGGDLRG
2aaa         1  .tQSIYFLLTdrfgrtdns............ttatcntgneiYCGGSWQG
amyb_paepo   1  .kQSIYFIMTdrfsngdpsndnyg.......gfnsnnsdqrkWHGGDFQG
amya_aspor   1  .sQSIYFLLTdrfartdgs............ttatcntadqkYCGGTWQG
amy1_deboc   1  .dQSIYQIVTdrfarsdgs............ttadclvsdrkYCGGSYKG
amy1_sacfi   1  .sQSIYQIVTdrfartdgd............tsascntedrlYCGGSFQG
ydd2_schpo   1  .kQVIYQVLTdrfaldedn............fyakas..gnlYLGGTWKG
amy1_schpo   1  .rRSIYQIITdrfsleegat...........eripcdpvrfmYCGGTWNG
1smd         1  grTSIVHLFE...................................wrwvd
1jdc         1  gdEIILQGFHwnvvreap...........................ndwyn

1pamA       44  IINKIndgYLTGMGITAIWIs.qpveniysvinysgv.nntAYHGYWARD
amy_bacci   45  IMNKIndgYFTGMGITALWIs.qpveniysvinysgv.nntAYHGYWARD
cdgt_bacli  44  LVNKIndnYFSDLGVTALWIs.qpvenifatinysgv.tntAYHGYWARD
amy_thetu   44  IINKIndgYLTGMGVTAIWIs.qpveniyavlpdstfggstSYHGYWARD
CDG2_PAEMA  44  ITNKIndgYLTGMGITALWIs.qpvenitavinysgv.nntAYHGYWPRD
CDG1_PAEMA  44  IIDKIndgYLTGMGVTALWIs.qpvenitsvikysgv.nntSYHGYWARD
cdgt_bacst  44  IINKIndgYLTDMGVTAIWIs.qpvenvfsvmndasg..saSYHGYWARD
cdgt_bacs2  44  IIDKIndgYLTDLGITALWIs.qpvenvyalhpsg....ytSYHGYWARD
amym_bacst  47  VRQKL..pYLKQLGVTTIWLs.pvlnnldtlagtd....ntGYHGYWTRD
cdgt_klepn  44  LINKL..pYLKSLGVTSIWIt.ppidnvnntdaag....ntGYHGYWGRD
2aaa        38  IIDHLd..YIEGMGFTAIWIs.piteqlpqdtad.....geAYHGYWQQK
amyb_paepo  43  IINKLd..YIKNMGFTAIWIt.pvtmqkse..........yAYHGYHTYD
amya_aspor  38  IIDKLd..YIQGMGFTAIWIt.pvtaqlpqttay.....gdAYHGYWQQD
amy1_deboc  38  IIDKLd..YIQGMGFTAIWIs.pvveqipdntay.....gyAYHGYWMKN
amy1_sacfi  38  IIKKLd..YIKDMGFTAIWIs.pvvenipdntay.....gyAYHGYWMKN
ydd2_schpo  36  ITRNLd..YIKSLGCTAIWIs.pivknisettdc.....gqAYHGYWAQD
amy1_schpo  39  IRNHLd..YIQGMGFDAIWIs.pifenvegndid.....gsSYHGYWTTN
1smd        16  ialecer.YLAPKGFGGVQVs.ppnenvaihnp......frPWWERYQPV
1jdc        24  ilrqqaa.TIAADGFSAIWMpvpwrd..fsswsdgs..ksgggegyfwhd

1pamA       92  FKKTNPAYGTMQDFKNLIDTAhah..nIKVIIDFAPNHtspassddpsfa
amy_bacci   93  FKKTNPAFGSMTDFANLISAAhsr..nIKVVIDFAPNHtspametnasfg
cdgt_bacli  92  FKKTNPYFGTMTDFQNLVTTAhak..gIKIIIDFAPNHtspametdtsfa
amy_thetu   93  FKRTNPYFGSFTDFQNLINTAhah..nIKVIIDFAPNHtspasetdptya
CDG2_PAEMA  92  FKKTNAAFGSFTDFSNLIAAAhsh..nIKVVMDFAPNHtnpasstdpsfa
CDG1_PAEMA  92  FKQTNDAFGDFADFQNLIDTAhah..nIKVVIDFAPNHtspadrdnpgfa
cdgt_bacst  91  FKKPNPFFGTLSDFQRLVDAAhak..gIKVIIDFAPNHtspasetnpsym
cdgt_bacs2  89  YKKTNPYYGNFDDFDRLMSTAhsn..gIKVIMDFTPNHsspaletnpnyv
amym_bacst  90  FKQIEEHFGNWTTFDTLVNDAhqn..gIKVIVDFVPNHstpfkandstfa
cdgt_klepn  87  YFRIDEHFGNLDDFKELTSLMhspdynMKLVLDYAPNHsnanden.....
2aaa        80  IYDVNSNFGTADNLKSLSDALhar..gMYLMVDVVPDHmgyagn......
amyb_paepo  80  FYAVDGHLGTMDKLQELVRKAhdk..nIAVMVDVVVNHtgdf........
amya_aspor  80  IYSLNENYGTADDLKALSSALher..gMYLMVDVVANHmgydga......
amy1_deboc  80  IDELNTNFGTADELKQLASELhsr..sMLLMVDVVYNHyawngd......
amy1_sacfi  80  IYKINENFGTADDLKSLAQELhdr..dMLLMVDIVTNHygsdgs......
ydd2_schpo  78  MTQLNENFGTEEDLKELVNAIhek..nMLCMVDIVVNHmghags......
amy1_schpo  81  LYELNHHFGTKEEFMELIQELhkr..dIWILLDVAINSmaingp......
1smd        58  SYKLCTRSGNEDEFRNMVTRCnnv..gVRIYVDAVINHmcgnavsagtss
1jdc        69  fnk.ngrygsdaqlrqaasalgga..gVKVLYDVVPNHmnr.........

1pamA      140  engrlydngnll.ggytnd...tqNLFHHY.ggtd......fst....ie
amy_bacci  141  engklydngtll.ggytgd...tnGYFHHN.ggtd......fst....lk
cdgt_bacli 140  engklydngnlv.ggytnd...tnGYFHHN.ggsd......fst....le
amy_thetu  141  engrlydngtll.ggytnd...tnGYFHHY.ggtd......fss....ye
CDG2_PAEMA 140  engalynngtll.gkysnd...taGLFHHN.ggtd......fst....te
CDG1_PAEMA 140  enggmydngsll.gaysnd...taGLFHHN.ggtd......fst....ie
cdgt_bacst 139  engrlydngtll.ggytnd...anMYFHHN.ggtt......fss....le
cdgt_bacs2 137  engaiydngall.gnysnd...qqNLFHHN.ggtd......fss....ye
amym_bacst 138  eggalynngtym.gnyfdd..atkGYFHHN.gdis.....nwdd....ry
cdgt_klepn 132  efgalyrdgvfi.tdyptnvaantGWYHHN.ggvt.....nwnd......
2aaa       122  ..gndvdysvfd....pfd...ssSYFHPY.clit.....dwdn.....l
amyb_paepo 120  ..qpgngfaka.....pfd...kaDWYHHN.gdit...dgdyns......
amya_aspor 122  ..gssvdysvfk....pfs...sqDYFHPF.cfiq.....nyed..qtqv
amy1_deboc 122  ..gssvdyssft....pfn...qqSYFHDY.clit.....nynd..qtnv
amy1_sacfi 122  ..gdsidyseyt....pfn...dqKYFHNY.clis.....nydd..qaqv
ydd2_schpo 120  ...kpvnfllyq....pfn...sgKYYHNW.qfvq.....nydd..phet
amy1_schpo 123  ..leqmsfekvi....pfn...daSFFHPH.cwv......dyesndiesv
1smd       106  tcgsyfnpgsrdfpavpy....sgWDFNDGkcktgsgdienynd.....a
1jdc       107  .......gypdkeinlpa....gqGFWRND.cadpg....nypn.....d

1pamA      175  ngiykn.....lYDLADLNHNNSSVDVYLKDaikmwl.dlGVDGIRVDAV
amy_bacci  176  ngiykn.....lYDLADLNHNNSTIDTYFKNairlwl.dmGIDGIRVDAV
cdgt_bacli 175  ngiykn.....lYDLADLNHNNSTIDTYFKDaiklwl.dmGVDGIRVDAV
amy_thetu  176  dgiyrn.....lFDLADLNQQNSTIDSYLKSaikvwl.dmGIDGIRLDAV
CDG2_PAEMA 175  sgiykn.....lYDLADINQNNNTIDSYLKEsiqlwl.nlGVDGIRFDAV
CDG1_PAEMA 175  dgiykn.....lYDLADINHNNNAMDAYFKSaidlwl.gmGVDGIRFDAV
cdgt_bacst 174  dgiyrn.....lFDLADLNHQNPVIDRYLKDavkmwi.dmGIDGIRMDAV
cdgt_bacs2 172  dsiyrn.....lYDLADYDLNNTVMDQYLKEsikfwl.dkGIDGIRVDAV
amym_bacst 175  eaqwknftdpagFSLADLSQENGTIAQYLTDaav....qlVAHGLRIDAV
cdgt_klepn 169  ffqvknhn...lFNLSDLNQSNTDVYQYLLDgskfwi.daGVDAIRIDAI
2aaa       152  tmvedcwegdtiVSLPDLDTTETAVRTIWYDwvadlvsnySVDGLRIDSV
amyb_paepo 150  nnqwkiengd.vAGLDDLNHENPATANELKNwikwllnetGIDGLRLDTV
amya_aspor 155  edcwlgdn...tVSLPDLDTTKDVVKNEWYDwvgslvsnySIDGLRIDTV
amy1_deboc 155  edcwegdt...eVSLPDLSTEDNEVIGVFQTwvsdfvqnySIDGLRIDSA
amy1_sacfi 155  qscwegds...sVALPDLRTEDSDVASVFNSwvkdfvgnySIDGLRIDSA
ydd2_schpo 152  itgwlgds...hVNLPDIRTEKNEVRKFFQNwvsdlikryQFDGIRLDTA
amy1_schpo 157  qncwlgde...nLLLADVDTENEVVLSVLEKwiknvvqeyDIDGIRFDAI
1smd       147  tqvrdcr....lSGLLDLALGKDYVRSKIAEymnhli.diGVAGFRIDAS
1jdc       136  cddgdrf....iGGDADLNTGHPQVYGMFRDeftnlrsqyGAGGFRFDFV

1pamA      219  KHMPfgwqksfmatinnyk........pvFTFGEWFlgvnei........
amy_bacci  220  KHMPfgwqknwmssiysyk........pvFTFGEWFlgtnet........
cdgt_bacli 219  KHMPqgwqknwmssiyahk........pvFTFGEWFlgsaap........
amy_thetu  220  KHMPfgwqknfmdsilsyr........pvFTFGEWFlgtnei........
CDG2_PAEMA 219  KHMPqgwqksyvssiyssan.......pvFTFGEWFlgpdem........
CDG1_PAEMA 219  KHMPfgwqksfvssiyggdh.......pvFTFGEWYlgadqt........
cdgt_bacst 218  KHMPfgwqkslmdeidnyr........pvFTFGEWFlsenev........
cdgt_bacs2 216  KHMSegwqtslmseiyshk........pvFTFGEWFlgsgev........
amym_bacst 221  KHFNsgfsksladklyqkk........diFLVGEWYgddpgtan......
cdgt_klepn 215  KHMDksfiqkwtsdiydysksigre..gfFFFGEWFgasantttgv....
2aaa       202  LEVQpdffpgynkas............gvYCVGEIDng............
amyb_paepo 199  KHVPkgflkdfdqaa............ntFTMGEIFhg............
amya_aspor 202  KHVQkdfwpgynkaa............gvYCIGEVLdg............
amy1_deboc 202  KHVDtasltkfedas............gvYNLGEVYqg............
amy1_sacfi 202  KHVDqgffpdfvsas............gvYSVGEVFqg............
ydd2_schpo 199  KHVEksffptfieaa............nvFTTGEVFhg............
amy1_schpo 204  KHAPiefwlrmskaa............diFTIGEYFtg............
1smd       192  KHMWpgdikaildklhnlnsnwfpegskpFIYQEVIdlgg..........
1jdc       182  RGYApervnswmtdsa..........dnsFCVGQLWkgpseypnwdwrnt

1pamA      253  ..speyhq.fanesgmslldfrfaqkarqvfrdnt.dnmyglk.amlegs
amy_bacci  254  ..dannty.fanesgmslldfrfsqkvrqvfrdgs.dtmygld.smlsst
cdgt_bacli 253  ..dadntd.fanesgmslldfrfnsavrnvfrdnt.snmyald.smltat
amy_thetu  254  ..dvnnty.fanesgmslldfrfsqkvrqvfrdnt.dtmygld.smiqst
CDG2_PAEMA 254  ..tqdnin.fanqsgmhlldfafaqeirevfrdks.etmtdln.svisst
CDG1_PAEMA 254  ..dgdnik.fanesgmnlldfeyaqevrevfrdkt.etmkdly.evlast
cdgt_bacst 252  ..dannhy.fanesgmslldfrfgqklrqvlrnns.dnwygfn.qmiqdt
cdgt_bacs2 250  ..dpqnhh.fanesgmslldfqfgqtirnvlkdrt.snwydfn.emitst
amym_bacst 257  ..hlekvr.yannsgvnvldfdlntvirnvfgtft.qtmydln.nmvnqt
cdgt_klepn 259  ..dg.naidyantsgsalldfgfrdtlervlvgrsgntmktln.sylikr
2aaa       228  ..npasdcpyqk.vldgvlnypiywqllyafesss.gsisnly.nmiksv
amyb_paepo 225  ..dpayvgdytr.yldaaldfpmyytikdvfghd..qsmrkik.drysdd
amya_aspor 228  ..dpaytcpyqn.vmdgvlnypiyypllnafksts.gsmddly.nmintv
amy1_deboc 228  ..dptytcpyqn.ymkgvtnyplyypvyrffsdts.atsselt.smistl
amy1_sacfi 228  ..dpaytcpyqn.yipgvsnyplyypttrffkttd.sssselt.qmissv
ydd2_schpo 225  ..dpkvvgdyqk.ylpstlnfplffqlretfldpk.hsmfsfydkavldv
amy1_schpo 230  ..spaeacdyqnsgldsflnfplywpitwafnntg.lqceala.iainqi
1smd       232  ..epikssdyf..gngrvtefkygaklgtvirkwngekmsylk.nwgegw
1jdc       222  aswqqiikdwsdrakcpvfdfalkermqn.......gsiadwk.hglngn

1pamA      298  evdyaqvndqvTFIDNHDMERfht.....................sngdr
amy_bacci  299  aadyysvndqvTFLDNHDMDRfqv.....................sgang
cdgt_bacli 298  aadynqvndqvTFIDNHDMDRfkt.....................savnn
amy_thetu  299  asdynfindmvTFIDNHDMDRfy......................nggst
CDG2_PAEMA 299  gssynyinnmvTFIDNHDMDRfqq.....................agast
CDG1_PAEMA 299  esqydyinnmvTFIDNHDMDRfqv.....................agsgt
cdgt_bacst 297  asaydevldqvTFIDNHDMDRfmi.....................dggdp
cdgt_bacs2 295  ekeynevidqvTFIDNHDMSRfsv.....................gsssn
amym_bacst 302  gneykykenliTFIDNHDMSRfls.....................vnskn
cdgt_klepn 305  qtvftsddwqvVFMDNHDMARigtalrsnattfgpgnnetggsqseafaq
2aaa       273  asdcsdptllgNFIENHDNPRfak.....................ytsdy
amyb_paepo 269  r.yyrdaqtngVFIDNHDVKRflndasgkpga.............nydkw
amya_aspor 273  ksdcpdstllgTFVENHDNPRfas.....................ytndi
amy1_deboc 273  qsscsdvsllgNFIENHDQVRfps.....................vtsdt
amy1_sacfi 273  asscsdptlltNFVENHDNERfas.....................mtsdq
ydd2_schpo 271  rhyfkdvtvlcNFLENHDFPRffh.....................etkdi
amy1_schpo 276  neecndinvlgTFIGNHDLPRish.....................nntdq
1smd       277  g..fmpsdralVFVDNHDNQRghgaggasil..............tfwda
1jdc       264  pd.prwrevavTFVDNHDTGYspgqnggqhh..............walqd

1pamA      327  rkLEQALAFTLTSR.gvPAIYYgseqymsgg.........NDPDNRar..
amy_bacci  328  rkLEQALALTLTSR.gvPAIYYgteqymtg.........nGDPNNRakm.
cdgt_bacli 327  rrLEQALAFTLTSR.gvPAIYYgteqyltg.........nGDPDNRgkm.
amy_thetu  327  rpVEQALAFTLTSR.gvPAIYYgteqymtg.........nGDPYNRamm.
CDG2_PAEMA 328  rpTEQALAVTLTSR.gvPAIYYgteqymtg.........nGDPNNRgmm.
CDG1_PAEMA 328  raTEQALALTLTSR.gvPAIYYgteqymtg.........dGDPNNRamm.
cdgt_bacst 326  rkVDMALAVLLTSR.gvPNIYYgteqymtg.........nGDPNNRkmm.
cdgt_bacs2 324  rqTDMALAVLLTSR.gvPTIYYgteqyvtg.........gNDPENRkpl.
amym_bacst 331  kaNLHQRLLSFSLRgvrPPIYYgteqymag.........gNDPYNRgmm.
cdgt_klepn 355  krIDLGLVATMTVR.giPAIYYgtehyaanftsnsfgqvgSDPYNRekm.
2aaa       302  sqAKNVLSYIFLSD.giPIVYAgeeqhyagg.........KVPYNRea..
amyb_paepo 305  pqLKAALGFTLTSR.giPIIYQgteqgysg.........gDDPANRen..
amya_aspor 302  alAKNVAAFIILND.giPIIYAgqeqhyagg.........NDPANReat.
amy1_deboc 302  slIKNDMAFIILGD.giPIIYYgqeqglngg.........SDPANReal.
amy1_sacfi 302  slISNAIAFVLLGD.giPVIYYgqeqglsgk.........SDPNNReal.
ydd2_schpo 300  alALNALTALIFMD.giPIIYYgqeqmfdgg.........SDPDNRegl.
amy1_schpo 305  arIMNAITFVMMWD.giPIIYYgteqnfnsy.........HDPFNReal.
1smd       311  rlYKMAVGFMLAHPygfTRVMSsyrwpryfengkdvndwvgpp.ndngvt
1jdc       299  glIRQAYAYILTSP.gtpvvywdhmydwg.....................

1pamA      365  ...........lpsfsttttayQVIQKLAPLRKsn....paiaygsther
amy_bacci  367  ............ssfststtayNVISKLAPLRKsn....paiaygttqqr
cdgt_bacli 366  ............psfsksttafNVISKLAPLRKsn....paiaygstqqr
amy_thetu  366  ............tsfntsttayNVIKKLAPLRKsn....paiaygttqqr
CDG2_PAEMA 367  ............tgfdtnktayKVIKALAPLRKsn....palaygsttqr
CDG1_PAEMA 367  ............tsfntgttayKVIQALAPLRKsn....paiaygttter
cdgt_bacst 365  ............ssfnkntrayQVIQKLSSLRRnn....palaygdteqr
cdgt_bacs2 363  ............ktfdrstnsyQIISKLASLRQtn....salgygttter
amym_bacst 371  ............pafdttttafKEVSTLAGLRRnn....aaiqygtttqr
cdgt_klepn 403  ............pgfdteseafSIIKTLGDLRKss....paiqngtytel
2aaa       340  .........twlsgydtsaelyTWIATTNAIRKlaiaadsayityandaf
amyb_paepo 343  ............mnfnanhdlyQYIAKLNYVRNnh....palqngsqrek
amya_aspor 341  ..........wlsgyptdselyKLIASANAIRNyaiskdtgfvtyknwpi
amy1_deboc 341  ..........wlsgyntdseyyELISKLNQIRNqaikkdsaystykssvv
amy1_sacfi 341  ..........wlsgynkesdyyKLIAKANAARNaavyqdssyatsqlsvi
ydd2_schpo 339  ..........wkskyntsnpmfRHLSSMIRTRQnlvetypeftyvlsfql
amy1_schpo 344  ..........wlsnfdmenvyyKLIGILNRFRKsvqrqeenyvntrstil
1smd       360  kevtinpdttcgndwvceh.rwRQIRNMVNFRNvv........dgqpftn
1jdc       327  ....................ygDFIRQLIQVRRaa......gvradsais

1pamA      400  win..ndVIIYERkfgnnVAVVAINrn..mntpasitglvtslprgs...
amy_bacci  401  win..ndVYIYERkfgnnVAVVAINknl..tssysiaglntslpsgt...
cdgt_bacli 400  win..ndVYIYERkfgksVAVVAVNrnl..ttptsitnlntslpsgt...
amy_thetu  400  win..ndVYIYERkfgnnVALVAINrnl..stsynitglytalpagt...
CDG2_PAEMA 401  wvn..sdVYVYERkfgsnVALVAVNrss..ttaypisgaltalpngt...
CDG1_PAEMA 401  wvn..ndVLIIERkfgssAALVAINrns..saaypisgllsslpagt...
cdgt_bacst 399  win..gdVYVYERqfgkdVVLVAVNrss..ssnysitglftalpagt...
cdgt_bacs2 397  wln..edIYIYERtfgnsIVLTAVNss...nsnqtitnlntslpqgn...
amym_bacst 405  win..ndVYIYERkffndVVLVAINrnt..qssysisglqtalpngs...
cdgt_klepn 437  wvn..ddILVFERrsgndIVIVALNrg....eantinvkniavpngv...
2aaa       381  ytd..snTIAMAKgtsgsQVITVLSnkgssgssytltlsgsgytsgtk..
amyb_paepo 377  wvd..dsFYSFQRskngdEAIVFINnsw.nsqtrti.gnfdnlsngtr..
amya_aspor 381  ykd..dtTIAMRKgtdgsQIVTILSnkgasgdsytlslsgagytagqq..
amy1_deboc 381  sss..dhYIATRKgsdanQLISIFNnlgsngsq.ditvsntgyssgdk..
amy1_sacfi 381  fsn..dhVIATKRgs....VVSVFNnlgssgss.dvtisntgyssged..
ydd2_schpo 379  yid..dsVYVFTRpg....VIIAISnegs.tssfkveidlkehwkevpss
amy1_schpo 384  svk..ihHIVVQKln....VITVLNnygi.hneerlsivfkplgaspkdt
1smd       401  wydngsnQVAFGRg...nRGFIVFNnd...dwtfsltl.qtglpagt...
1jdc       351  fhsgysgLVATVSg...sQQTLVVAln......sdlgn.pgqvasgs...

1pamA      443  yndvlggiln.....gntltvgaggaasnftlap..ggtavwqyttdatt
amy_bacci  444  ytdvlanslsg.....nsitvgssgavntftlqa..ggea..........
cdgt_bacli 443  ytdvlggvlng.....nnits.sggnissftlaa..gatavwqytasett
amy_thetu  443  ytdvlggllng.....nsisvasdgsvtpftlsa..gevavwqyvsssns
CDG2_PAEMA 444  ytdvlggllng.....nsitv.nggtvsnftlaa..ggtavwqytttess
CDG1_PAEMA 444  ysdvlngllng.....nsitvgsggavtnftlaa..ggtavwqytapets
cdgt_bacst 442  ytdqlgglldg.....ntiqvgsngsvnafdlgp..gevgvwaysatest
cdgt_bacs2 439  ytdelqqrldg.....ntitvnangavnsfqlra..nsvavwqvsnpsts
amym_bacst 448  yadylsgllgg.....ngisvsngsva.sftlap..gavsvwqystsasa
cdgt_klepn 478  ypslign.........nsvsvankrtt..ltlmq..neavvirsqsd...
2aaa       427  lieaytc.........tsvtvdssgdi.pvpmas..glprvllpasvvds
amyb_paepo 421  ltnqlsn.........dsvqinngsit..vtlap..kevkvf........
amya_aspor 427  ltevigc.........ttvtvgsdgn...vpvpma.gglprvlyptekla
amy1_deboc 426  vidiisc.........nsvlagdsgs...lsvsis.ggmpqvyapssvls
amy1_sacfi 422  lvevltc.........stvs..gssd...lqvsiq.ggqpqifvpaky..
ydd2_schpo 422  ftdiltq.........ktipckdhk....lkiksk.sglpkiliss...d
amy1_schpo 427  ffdiinn.........qkyvvntdgt...lkvvit.ngfpivlyptskie
1smd       441  ycdvisgdkingnctgikiyvsddgka.hfsisnsaedpfiaihaeskl.
1jdc       388  fseavnasng.............................qvrvwrs....

1pamA      486  piign
amy_bacci  477  .....
cdgt_bacli 485  ptigh
amy_thetu  486  pligh
CDG2_PAEMA 486  piign
CDG1_PAEMA 487  paign
cdgt_bacst 485  piigh
cdgt_bacs2 482  pligq
amym_bacst 490  pqigs
cdgt_klepn 512  .....
2aaa       465  sslcg
amyb_paepo 450  .....
amya_aspor 464  gskic
amy1_deboc 463  gsgic
amy1_sacfi 455  asdic
ydd2_schpo 455  psfl.
amy1_schpo 464  ts...
1smd       489  .....
1jdc       405  .....

Key

alpha helix         RED
beta strand         GREEN
core blocks         UNDERSCORE

You can also look at the alignment in RSF format, or MSF format with a Feature Table

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