(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.soe.ucsc.edu/research/compbio/sam.html
Citations (SAM, SAM-T99, HMMs)
- R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
- K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
- A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
Sequence numbers correspond to the following labels:
-
-
- gi|84357610|ref|ZP_00982425.1|_95:202 COG4318: Uncharacterized protein conserved in bacteria [Burkholderia cenocepacia PC184]
-
- gi|84361624|ref|ZP_00986282.1|_95:202 COG4318: Uncharacterized protein conserved in bacteria [Burkholderia dolosa AUO158]
-
- gi|107022611|ref|YP_620938.1|_95:202 hypothetical protein Bcen_1058 [Burkholderia cenocepacia AU 1054]
- gi|105892800|gb|ABF75965.1| conserved hypothetical protein [Burkholderia cenocepacia AU 1054]
-
- gi|77966893|gb|ABB08273.1|_95:202 conserved hypothetical protein [Burkholderia sp. 383]
- gi|78066148|ref|YP_368917.1| hypothetical protein Bcep18194_A4678 [Burkholderia sp. 383]
-
- gi|52426916|gb|AAU47509.1|_95:202 conserved hypothetical protein [Burkholderia mallei ATCC 23344]
- gi|52209906|emb|CAH35878.1| conserved hypothetical protein [Burkholderia pseudomallei K96243]
- gi|53723493|ref|YP_102940.1| hypothetical protein BMA1271 [Burkholderia mallei ATCC 23344]
- gi|82534339|ref|ZP_00893379.1| hypothetical protein Bpse110_02004412 [Burkholderia pseudomallei 1106b]
- gi|90291316|ref|ZP_01210945.1| hypothetical protein Bpse17_02003972 [Burkholderia pseudomallei 1710a]
- gi|53719492|ref|YP_108478.1| hypothetical protein BPSL1879 [Burkholderia pseudomallei K96243]
- gi|100265766|ref|ZP_01340220.1| hypothetical protein Bmal2_03001924 [Burkholderia mallei 2002721280]
- gi|85064679|ref|ZP_01025532.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei 10229]
- gi|84522664|ref|ZP_01009800.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei SAVP1]
- gi|67737749|ref|ZP_00488481.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia pseudomallei 668]
- gi|67645217|ref|ZP_00443517.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei NCTC 10247]
- gi|67640286|ref|ZP_00439099.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei GB8 horse 4]
- gi|83625993|ref|ZP_00936220.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei JHU]
- gi|83617385|ref|ZP_00927895.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia mallei FMH]
- gi|100915980|ref|ZP_01344466.1| hypothetical protein Bmal10_03002754 [Burkholderia mallei 10399]
- gi|100233081|ref|ZP_01334195.1| hypothetical protein Bpse4_03003331 [Burkholderia pseudomallei 406e]
- gi|100060176|ref|ZP_01322269.1| hypothetical protein BpseP_03003967 [Burkholderia pseudomallei Pasteur]
- gi|82529037|ref|ZP_00888293.1| COG4318: Uncharacterized protein conserved in bacteria [Burkholderia pseudomallei 1106a]
-
- gi|99908493|ref|ZP_01316185.1|_50:157 hypothetical protein Bpse1_03004504 [Burkholderia pseudomallei 1655]
-
- gi|100121814|ref|ZP_01327722.1|_95:202 hypothetical protein BpseS_03004183 [Burkholderia pseudomallei S13]
-
- gi|76578754|gb|ABA48229.1|_330:437 conserved hypothetical protein [Burkholderia pseudomallei 1710b]
- gi|76809301|ref|YP_333359.1| hypothetical protein BURPS1710b_1961 [Burkholderia pseudomallei 1710b]
-
- gi|67549138|ref|ZP_00427011.1|_95:202 conserved hypothetical protein [Burkholderia vietnamiensis G4]
- gi|67529579|gb|EAM26441.1| conserved hypothetical protein [Burkholderia vietnamiensis G4]
-
- gi|83719811|ref|YP_443042.1|_95:202 hypothetical protein BTH_I2525 [Burkholderia thailandensis E264]
- gi|83653636|gb|ABC37699.1| conserved hypothetical protein [Burkholderia thailandensis E264]
-
- gi|78695829|ref|ZP_00860340.1|_96:204 conserved hypothetical protein [Bradyrhizobium sp. BTAi1]
- gi|78516392|gb|EAP29692.1| conserved hypothetical protein [Bradyrhizobium sp. BTAi1]
-
- gi|74015995|ref|ZP_00686622.1|_96:202 conserved hypothetical protein [Burkholderia ambifaria AMMD]
- gi|72611424|gb|EAO47369.1| conserved hypothetical protein [Burkholderia ambifaria AMMD]
-
- gi|39935093|ref|NP_947369.1|_95:203 hypothetical protein RPA2024 [Rhodopseudomonas palustris CGA009]
- gi|39648944|emb|CAE27465.1| conserved unknown protein [Rhodopseudomonas palustris CGA009]
-
- gi|86750462|ref|YP_486958.1|_95:203 hypothetical protein RPB_3351 [Rhodopseudomonas palustris HaA2]
- gi|86573490|gb|ABD08047.1| conserved hypothetical protein [Rhodopseudomonas palustris HaA2]
-
- gi|14021654|dbj|BAB48266.1|_96:204 mlr0735 [Mesorhizobium loti MAFF303099]
- gi|13470911|ref|NP_102480.1| hypothetical protein mlr0735 [Mesorhizobium loti MAFF303099]
-
- gi|27378923|ref|NP_770452.1|_381:488 hypothetical protein blr3812 [Bradyrhizobium japonicum USDA 110]
- gi|27352073|dbj|BAC49077.1| blr3812 [Bradyrhizobium japonicum USDA 110]
-
- gi|17935439|ref|NP_532229.1|_96:203 hypothetical protein Atu1540 [Agrobacterium tumefaciens str. C58]
- gi|17739967|gb|AAL42545.1| conserved hypothetical protein [Agrobacterium tumefaciens str. C58]
- gi|15156626|gb|AAK87328.1| AGR_C_2837p [Agrobacterium tumefaciens str. C58]
- gi|15888862|ref|NP_354543.1| hypothetical protein AGR_C_2837 [Agrobacterium tumefaciens str. C58]
-
- gi|56542820|gb|AAV88974.1|_96:202 conserved hypothetical protein [Zymomonas mobilis subsp. mobilis ZM4]
- gi|56551246|ref|YP_162085.1| hypothetical protein ZMO0350 [Zymomonas mobilis subsp. mobilis ZM4]
-
- gi|92116321|ref|YP_576050.1|_95:204 hypothetical protein Nham_0704 [Nitrobacter hamburgensis X14]
- gi|91799215|gb|ABE61590.1| conserved hypothetical protein [Nitrobacter hamburgensis X14]
-
- gi|17427717|emb|CAD14236.1|_112:217 conserved hypothetical protein [Ralstonia solanacearum]
- gi|17545425|ref|NP_518827.1| hypothetical protein RSc0706 [Ralstonia solanacearum GMI1000]
-
- gi|83746199|ref|ZP_00943253.1|_92:197 Hypothetical Protein RRSL_04237 [Ralstonia solanacearum UW551]
- gi|83727165|gb|EAP74289.1| Hypothetical Protein RRSL_04237 [Ralstonia solanacearum UW551]
-
- gi|33866069|ref|NP_897628.1|_107:218 hypothetical protein SYNW1535 [Synechococcus sp. WH 8102]
- gi|33639044|emb|CAE08050.1| conserved hypothetical protein [Synechococcus sp. WH 8102]
-
- gi|94311152|ref|YP_584362.1|_93:195 hypothetical protein Rmet_2214 [Ralstonia metallidurans CH34]
- gi|93355004|gb|ABF09093.1| conserved hypothetical protein [Ralstonia metallidurans CH34]
-
- gi|78196967|gb|ABB34732.1|_108:218 conserved hypothetical protein [Synechococcus sp. CC9605]
- gi|78212508|ref|YP_381287.1| hypothetical protein Syncc9605_0974 [Synechococcus sp. CC9605]
-
- gi|49081854|gb|AAT50327.1|_117:223 PA4384 [synthetic construct]
-
- gi|9950614|gb|AAG07772.1|_117:223 hypothetical protein PA4384 [Pseudomonas aeruginosa PAO1]
- gi|15599580|ref|NP_253074.1| hypothetical protein PA4384 [Pseudomonas aeruginosa PAO1]
- gi|84316905|ref|ZP_00965363.1| COG4318: Uncharacterized protein conserved in bacteria [Pseudomonas aeruginosa C3719]
-
- gi|107100031|ref|ZP_01363949.1|_117:223 hypothetical protein PaerPA_01001052 [Pseudomonas aeruginosa PACS2]
-
- gi|84323084|ref|ZP_00971161.1|_117:223 COG4318: Uncharacterized protein conserved in bacteria [Pseudomonas aeruginosa 2192]
-
- gi|32039599|ref|ZP_00137871.1|_117:223 COG4318: Uncharacterized protein conserved in bacteria [Pseudomonas aeruginosa UCBPP-PA14]
-
- gi|78168756|gb|ABB25853.1|_110:218 conserved hypothetical protein [Synechococcus sp. CC9902]
- gi|78184462|ref|YP_376897.1| hypothetical protein Syncc9902_0887 [Synechococcus sp. CC9902]
-
- gi|88807752|ref|ZP_01123264.1|_113:220 hypothetical protein WH7805_14413 [Synechococcus sp. WH 7805]
- gi|88788966|gb|EAR20121.1| hypothetical protein WH7805_14413 [Synechococcus sp. WH 7805]
-
- gi|94415498|ref|ZP_01295338.1|_117:223 hypothetical protein PaerP_01002661 [Pseudomonas aeruginosa PA7]
-
- gi|87123972|ref|ZP_01079822.1|_110:215 hypothetical protein RS9917_10191 [Synechococcus sp. RS9917]
- gi|86168541|gb|EAQ69798.1| hypothetical protein RS9917_10191 [Synechococcus sp. RS9917]
-
- gi|84518383|ref|ZP_01005732.1|_113:221 hypothetical protein P9211_06002 [Prochlorococcus marinus str. MIT 9211]
- gi|84513132|gb|EAQ09470.1| hypothetical protein P9211_06002 [Prochlorococcus marinus str. MIT 9211]
-
- gi|72121544|gb|AAZ63730.1|_107:213 conserved hypothetical protein [Ralstonia eutropha JMP134]
- gi|73538207|ref|YP_298574.1| hypothetical protein Reut_B4378 [Ralstonia eutropha JMP134]
-
- gi|72121540|gb|AAZ63726.1|_115:222 conserved hypothetical protein [Ralstonia eutropha JMP134]
- gi|73538203|ref|YP_298570.1| hypothetical protein Reut_B4374 [Ralstonia eutropha JMP134]
-
- gi|87301913|ref|ZP_01084747.1|_109:216 hypothetical protein WH5701_01270 [Synechococcus sp. WH 5701]
- gi|87283481|gb|EAQ75436.1| hypothetical protein WH5701_01270 [Synechococcus sp. WH 5701]
-
- gi|66827801|ref|XP_647255.1|_120:227 hypothetical protein DDB0189492 [Dictyostelium discoideum]
- gi|60475379|gb|EAL73314.1| hypothetical protein DDBDRAFT_0189492 [Dictyostelium discoideum AX4]
-
- gi|33863115|ref|NP_894675.1|_87:191 hypothetical protein PMT0843 [Prochlorococcus marinus str. MIT 9313]
- gi|33635032|emb|CAE21018.1| conserved hypothetical protein [Prochlorococcus marinus str. MIT 9313]
-
- gi|89359800|ref|ZP_01197620.1|_100:204 conserved hypothetical protein [Xanthobacter autotrophicus Py2]
- gi|89351349|gb|EAS16630.1| conserved hypothetical protein [Xanthobacter autotrophicus Py2]
-
- gi|87302308|ref|ZP_01085133.1|_108:207 hypothetical protein WH5701_08904 [Synechococcus sp. WH 5701]
- gi|87283233|gb|EAQ75189.1| hypothetical protein WH5701_08904 [Synechococcus sp. WH 5701]
10 20 30 40 50 60
| | | | | |
1 GKDEFWSVMDHRNLIYPFDAQGLR.RQSGDIPKNIHDLEDDPFRSLAGALRMAGGYA.KV.IIPF
2 DDTIFWRMMEHNQWVHPFGPDGSR.RDYAHLPKALTGLEDDPYRSLAGELRTAGGYA.KD.ATPF
3 DDTIFWRMMEHNQWVHPFDADGAR.RDYAELPKVLTALDDDPYRSLAGELRTAGGYA.KD.ATPF
4 DDTIFWRMMEHNQWVHPFGPDGSR.RDYAHLPKVLTGLEDDPYRSLAGELRTAGGYA.KD.ATPF
5 DETIFWRMMEHNQWVHPFGADGTR.RDYGNLPKALTGLVDDPYRSLAGELRTAGGYA.KD.ATPF
6 DETIFWRMMEHNQWVHPFGANGAR.HDYDHLPTSLVGLKDDPYRSLAGELRAAGGYA.KD.ATPF
7 DETIFWRMMEHNQWVHPFGANGAR.HDYDHLPTSLVGLKDDPYRSLAGELRAAGGYA.KD.ATPF
8 DETIFWRMMEHNQWVHPFGANGAR.HDYDHLPTSLVGLKDDPYRSLAGELRAAGGYA.KD.ATPF
9 DETIFWRMMEHNQWVHPFGANGAR.HDYDHLPTSLVGLKDDPYRSLAGELRAAGGYA.KD.ATPF
10 DDTIFWRIMEHNQWVHPFGPDGAR.REYAHLPQALTGLEDDPYRSLAGELRTAGGYA.KD.ATPF
11 DETLFWRMMEHNQWVHPFGANGAR.HDYDHLPTSLVGLKDDPYRSLAGELRTAGGYA.KD.AMPF
12 DRDGFWNVMDNKRWVYPYDAKGER.RHFKDLPKTVADLKDDPFRSLAGELRRAGGFA.KD.TTPF
13 -DTIFWRMMEHNQWVHPFGPDGSR.RDYANLPKVLTGLEDDPYRSLAGELRTAGGYA.KD.ATPF
14 DREAFWVVLDSRRWVYPYDAKGER.HHYREIPKTVAGLKDDPFRSLAGELRRVGGYA.KD.TTPF
15 DRDAFWVVLDSRRWVYPYDAKGER.HHYKDLPKTVAALKDDPFRSLAGELRRIGGYA.KD.TTPF
16 DKDTFLFVLDNRGWMHPFDESGRR.RDYSAIPKTIGELIDDPYRSMAGELRRMGGFA.KD.TTPF
17 -REAFWGVMDNKRWVYPYDSKGER.RPFRDLPKSVADLRDDPFRSLAGELRRLGGFA.KD.TTPF
18 -KDEFWSVMDHRNLIYPFDAQGLR.RQSGDIPKNIHDLEDDPFRSLAGALRMAGGYA.KV.IIPF
19 -KDHFWFVMDSQRWMHPFDEKGIR.RSYQDIPDSLTEMKDDPYRSLAGSLRRAGGYA.KD.VTPF
20 DKDAFLIVLDNRAWMHPFDASGRR.RPYNDLPKSVDKLVDDPFRSLAGEVRRLGGYA.KD.TTPF
21 --DDFWKAMDQNLWVHPLDEHGVR.HYYASIPKHLEKLVDDPYRSLAGYVRDAGGYD.KT.PTAF
22 --DDFWKAMDQNLWVHPLDEHGVR.HYYASIPDHLEKLVDDPYRSLAGYVRNAGGYD.KT.PTAF
23 DRSEVLRFLEQQGWLYLIDGRGAGpRQPMELPRTLLDLEDDPYRSLVWKLKKEGFIKpQP.QIPY
24 ---DFWGEMDKNQWVHPLDENGVR.HCYTLIPSHLEKLIDDPYRSLAGYVRDAGGYQ.KT.PTAF
25 -RSSVLTYLHNQGWLYLYDGRGNGpRPAEQLPMSLLGLDDDPYRSLVWKLKQEGWIKpQP.LIPY
26 --SDFWEKMQENHWVWLHDARGAE.IPPEALPDALAGLGDDPYRALAGYAEDENAFD.KDrQSYF
27 --SDFWEKMQENHWVWLHDARGAE.IPPEALPDALAGLGDDPYRALAGYAEDENAFD.KDrQSYF
28 --SDFWEKMQENHWVWLHDARGAE.IPPEALPNALAGLGDDPYRALAGYAEDENAFD.KDrQSYF
29 --SDFWEKMQENHWVWLHDARGAE.IPPEALPNALAGLGDDPYRALAGYAEDENAFD.KDrQSYF
30 --TDFWKKMQENHWVWLHDARGAE.IPPEALPDALAGLGDDPYRALAGYAEDENAFD.KDrQSYF
31 ---AAITYLQTQGWLYLYDSRGQGpRHPSELPRSLLTLEDDPYRSLVWKLKQEGLIKpQA.HIPY
32 ---SALEALQKRGWLYLFDGRGNGpKPATELPHTLLGLQDDPYRSLVWKLKKEGLIKpQP.LIPY
33 --SDFWEKMQENHWVWLHDAHGAP.IPPAALPDDLAGLGNDPYRALAGYAEDENAFD.KDrRSYF
34 ---ETLRELQSRGWLYLHDGRGQGpWPPEQLPTSLLDLQDDPYRSLVWKLKKEGVLRpQP.LIPY
35 --SHMLDFLDEQGWLYLYNSRGLGpHPTKYLKENLLELEDDPYRSLVWKLKQEGIIKaKP.LIPY
36 --TAFWKRMRALGFVHPYDELGQR.LGIDALPATVMGMRDDPYRSLAAFARQSGAYR.KP.PDAY
37 --QAFWEWMLDNHMVHPYDEHGRR.RPLSELPECIHAMRDDPYRSLEAFVQLAGGYR.KV.KQAY
38 -PSAALEALAQRGWLYLHDGRGQGpWPPERLPQSLLSLDDDPYRSLVWKLKQEKVISpAP.LIPF
39 -NSQFWNKMNSEKWVHPYNKNGEGpLDVNEIPKKVCELEDDVFRSIAAVVKIKGGFK.KS.FIPY
40 ----SLQLLADRGWLYLYNGRGHGpLLPQGLPKSLLMLEDDPYRSLAWKLKSEGLIRpEP.LIPY
41 --PTFWHRMESQGLCWPIDVDGNR.RPCIKIPGHISELTDNPWRTLARGVR-GDAYS.NL.DTPF
42 ---HCLEELNRRGWLYLRDGEGRGpLPPERLPMDLGGLEDDPFRSLVWKLKQEGLIRaQP.QVPF
70 80 90 100 110
| | | | |
1 SEFGWADFLRRRIDR.DLLS.DSFDDALAEAMKLAKSREARHLPGWCGVEE
2 SEFLWADYLRQHVSL.DQIR.KNFAKALDIALHRAHEQDARYLPGWSG---
3 SEFLWADYLRQHVSV.DQIR.KSFSKALDAALRRAHDQDARYLPGWSG---
4 SEFLWADYLRQHVSL.DQIR.KNFAKALDIALQRAHEQDARYLPGWSG---
5 SEFLWADYLRQHVSL.DQIR.KNFAKALDIALHRAHEQDARYLPGWSG---
6 SEFLWADFLRPRIAL.AQIR.KEFAKALEAALGYAHTQEARYLPGWSG---
7 SEFLWADFLRPRIAL.AQIR.KEFAKALEAALGYAHTQEARYLPGWSG---
8 SEFLWADFLRPRIAL.AQIR.KEFAKALEAALGYAHTQEARYLPGWSG---
9 SEFLWADFLRPRIAL.AQIR.KEFAKALEAALGYAHTQEARYLPGWSG---
10 SEFLWADYLRQHVSL.DQIR.KNFDKALDLSLRRAHDQDARYLPGWSG---
11 SEFLWADFLRTKIAL.TQIR.KEFAKALEAALGYAHTQEARYLPGWSG---
12 SEFLWADFLRRRVKR.KTVE.SHFAAAMEHALALAKSHDAVYLPGWCGP--
13 SEFLWADYLRQHVTL.DQIR.KNFSKALDLSLRRAHDQDARYLPGWSG---
14 SEFLWADFLRRRLSR.KSVT.ANFQNAAEKALALAKSKDAIYLPGWCGP--
15 SEFLWADFLRRRLSR.KSVD.ADFAKATELSLALAKSRDAIYLPGWCGP--
16 SEFIWADFLRRRIDR.NAVA.KNFDKAMKEALSLAKGKDADYLPGWCGP--
17 SEFLWADYLRRKLSR.KAVD.ANFDKALEKALSAAKSKDAIYLPGWCGP--
18 SEFGWADFLRRRIDR.DLLS.DSFDDALAEAMKLAKSREARHLPGWCGV--
19 SEFLWADYLRRQFNG.ADIA.HNFNDFLEKALILAHDKKASYLPGWCA---
20 AEFLWADFFRRRMDA.RGLE.DDFHKAATHALRLARQKSAGYLPGWSGPD-
21 AEFVWADFFRRSIPI.EDLL.ADFQAAVHAALPLAKSKFAKALPGYNG---
22 AEFVWADFFRRSIPI.EDLL.ADFQAAVRAALPLAKSKFAHALPGYNG---
23 HEFRWGAWLRRRPLP.PFSS.RQLQPALAPARRLVCSQAASTMAGWKGDK-
24 AEFVWADFFRRHIAV.EDLK.ADFQAAVKCAKVLAASKWASGLPGF-----
25 HEFRWGAWLRSRPLP.PFSS.RRLEPALAAARQLVCSAAAQDMPGWKGDK-
26 IEFHWARYFGERMHWrPISR.ATLPDDLKQALRLACEPAARELPGYR----
27 IEFHWARYFGERMHWrPISR.ATLPDDLKQALRLACEPAARELPGYR----
28 IEFHWARYFGERMHWrPISR.ATLPDDLKQALHLACEPAARELPGYR----
29 IEFHWARYFGERMHWrPISR.ATLPDDLKQALHLACEPAARELPGYR----
30 IEFHWARYFGERMHWrPISR.ATLPDDLKQALRLACEPAAKELPGYR----
31 HEFRWAAWLRQRPLP.PFSS.RQLEPALAPARRLVCSESARNMAGWKGEK-
32 HEFRWGSWLRTRPLP.PFSS.ARLEPALPAARCLARSAAARHLAGWRGG--
33 IEFHWARYFGERMHWrPISR.ASLPGDLEEALRLACEPAAKELPGYR----
34 HEFRWGAWLRRRPLP.PFHS.GCLEPALPTARRLARSPAALHLAGWK----
35 HEFRWAAWLRKRPLP.PFNS.RNLTPALTKARKFTTSQAASSLAGWTGD--
36 GDFRWAGFLRERIEE.DMGTiGGFALALSQAIRLARGSAARRLPGYCG---
37 PDFKWADFFRRHVEG.PLDSpEMFAAALVRAFQLAQSPKARGLPGFIEK--
38 HEFRWGAWLRSRCLP.PFSS.LCLEPALPAARALARSAAGSRLAGWR----
39 AEFQWANYFRSCFEN.KKVDdNNFDKVIDESLELAKNEEAKKLPGYI----
40 HEFRWGTWLRSRALP.PFSS.KYLEPALPAARSLVRSNAASHLDGWI----
41 QEFMWGNYYRSFMTT.RLLQ.SDIELAEKLAVKLSRLDEAQDLPGYLG---
42 LEFHWGSWLRHQNLP.AFGS.MDLSPALPEARRLVRGQVGL----------