(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:
-
- T0385 Rv2844, Mycobacterium tuberculosis, 162 res
-
- gi|13882684|gb|AAK47236.1|_4:162 hypothetical protein MT2910 [Mycobacterium tuberculosis CDC1551]
- gi|31794021|ref|NP_856514.1| CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN [Mycobacterium bovis AF2122/97]
- gi|31619615|emb|CAD95054.1| CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN [Mycobacterium bovis AF2122/97]
- gi|2078015|emb|CAB08446.1| CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN [Mycobacterium tuberculosis H37Rv]
- gi|15609981|ref|NP_217360.1| CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN [Mycobacterium tuberculosis H37Rv]
- gi|15842385|ref|NP_337422.1| hypothetical protein MT2910 [Mycobacterium tuberculosis CDC1551]
- gi|76783319|ref|ZP_00770511.1| hypothetical protein MtubF_01002930 [Mycobacterium tuberculosis F11]
- gi|81253091|ref|ZP_00877654.1| hypothetical protein MtubC_01002712 [Mycobacterium tuberculosis C]
-
- gi|41409010|ref|NP_961846.1|_5:148 hypothetical protein MAP2912 [Mycobacterium avium subsp. paratuberculosis K-10]
- gi|41397369|gb|AAS05229.1| hypothetical protein MAP_2912 [Mycobacterium avium subsp. paratuberculosis K-10]
-
- gi|89341890|ref|ZP_01194131.1|_14:161 conserved hypothetical alanine rich protein [Mycobacterium flavescens PYR-GCK]
- gi|89317928|gb|EAS09426.1| conserved hypothetical alanine rich protein [Mycobacterium flavescens PYR-GCK]
-
- gi|13093374|emb|CAC30512.1|_6:165 conserved hypothetical protein [Mycobacterium leprae]
- gi|4455673|emb|CAB36565.1| hypothetical protein MLCB596.09c [Mycobacterium leprae]
- gi|15827822|ref|NP_302085.1| hypothetical protein ML1561 [Mycobacterium leprae TN]
-
- gi|90205349|ref|ZP_01207989.1|_180:334 hypothetical protein MvanDRAFT_1273 [Mycobacterium vanbaalenii PYR-1]
- gi|90195673|gb|EAS22438.1| hypothetical protein MvanDRAFT_1273 [Mycobacterium vanbaalenii PYR-1]
-
- gi|108799044|ref|YP_639241.1|_8:156 conserved hypothetical alanine rich protein [Mycobacterium sp. MCS]
- gi|108769463|gb|ABG08185.1| conserved hypothetical alanine rich protein [Mycobacterium sp. MCS]
- gi|92915719|ref|ZP_01284341.1| conserved hypothetical alanine rich protein [Mycobacterium sp. KMS]
- gi|92907210|ref|ZP_01275990.1| conserved hypothetical alanine rich protein [Mycobacterium sp. JLS]
- gi|92439917|gb|EAS97762.1| conserved hypothetical alanine rich protein [Mycobacterium sp. KMS]
- gi|92435510|gb|EAS94841.1| conserved hypothetical alanine rich protein [Mycobacterium sp. JLS]
-
- gi|41326167|emb|CAF20330.1|_132:270 putative secreted protein [Corynebacterium glutamicum ATCC 13032]
- gi|62390829|ref|YP_226231.1| putative secreted protein [Corynebacterium glutamicum ATCC 13032]
-
- gi|21324759|dbj|BAB99382.1|_278:415 Hypothetical protein [Corynebacterium glutamicum ATCC 13032]
-
- gi|19553193|ref|NP_601195.1|_132:269 hypothetical protein NCgl1914 [Corynebacterium glutamicum ATCC 13032]
-
- gi|29829098|ref|NP_823732.1|_8:151 hypothetical protein SAV2556 [Streptomyces avermitilis MA-4680]
- gi|29606204|dbj|BAC70267.1| hypothetical protein [Streptomyces avermitilis MA-4680]
-
- gi|21224050|ref|NP_629829.1|_8:144 hypothetical protein SCO5701 [Streptomyces coelicolor A3(2)]
- gi|7801273|emb|CAB91137.1| hypothetical protein SC5H4.25c [Streptomyces coelicolor A3(2)]
-
- gi|56314941|emb|CAI09586.1|_37:190 conserved hypothetical protein,putatively exported via twin-arginine system [Azoarcus sp. EbN1]
- gi|56478898|ref|YP_160487.1| conserved hypothetical protein, putatively exported via twin-arginine system [Azoarcus sp. EbN1]
-
- gi|38200324|emb|CAE50009.1|_160:299 Putative secreted protein [Corynebacterium diphtheriae]
- gi|38234062|ref|NP_939829.1| Putative secreted protein [Corynebacterium diphtheriae NCTC 13129]
-
- gi|54017550|dbj|BAD58920.1|_4:132 hypothetical protein [Nocardia farcinica IFM 10152]
- gi|54026042|ref|YP_120284.1| hypothetical protein nfa40710 [Nocardia farcinica IFM 10152]
-
- gi|23493723|dbj|BAC18692.1|_147:286 hypothetical protein [Corynebacterium efficiens YS-314]
- gi|25028438|ref|NP_738492.1| hypothetical protein CE1882 [Corynebacterium efficiens YS-314]
-
- gi|66964181|ref|ZP_00411751.1|_230:378 hypothetical protein ArthDRAFT_2941 [Arthrobacter sp. FB24]
- gi|66869708|gb|EAL97074.1| hypothetical protein ArthDRAFT_2941 [Arthrobacter sp. FB24]
-
- gi|71368363|ref|ZP_00658864.1|_3:139 Conserved hypothetical protein [Nocardioides sp. JS614]
- gi|71155931|gb|EAO06357.1| Conserved hypothetical protein [Nocardioides sp. JS614]
-
- gi|71914909|gb|AAZ54811.1|_7:147 conserved hypothetical protein [Thermobifida fusca YX]
- gi|72161177|ref|YP_288834.1| hypothetical protein Tfu_0773 [Thermobifida fusca YX]
-
- gi|86742248|ref|YP_482648.1|_15:161 hypothetical protein Francci3_3567 [Frankia sp. CcI3]
- gi|86569110|gb|ABD12919.1| conserved hypothetical protein [Frankia sp. CcI3]
10 20 30 40 50
| | | | |
1 MTSSEPAHGATPKRSPSEGSADNAALCDALAVEHATI..YGYGIVSALSP....P.....GVNFL
2 ---SEPAHGATPKRSPSEGSADNAALCDALAVEHATI..YGYGIVSALSP....P.....GVNFL
3 ------------------KDADNAALCDALAIEHSTI..YGYGIVSAMSP....P.....SVNDM
4 --------------PTRPEDAAAGALFDALAAEHATI..YGYGVVSAHST....P.....ELNYL
5 --PSAPTPVATPKRTPVSQDSDNAGLSEALVVEHSTI..YGYGIVLALSP....P.....NANSL
6 -------TAPDQGMPSRPDDAADGALFDAIATEHATI..YGYGLVSAHST....P.....DVNYL
7 -------------PPARPADSADGALYDAIATEHAAI..YGYGLVSAHST....P.....EVNWL
8 --EFAEGSEVSVPVDLELTEAELAAAKDLADREFSAA..WSLGVALAQLP....E.....TDREE
9 --EFAEGSEVSVPVDLELTEAELAAAKDLADREFSAA..WSLGVALAQLP....E.....TDREE
10 --EFAEGSEVSVPVDLELTEAELAAAKDLADREFSAA..WSLGVALAQLP....E.....TDREE
11 ---------TGTPKAESTESAELRALQAALGAEHAAV..YGYGVVGGKIG....Q.....ARRAD
12 ---------------------RLDALQAALAAEHAAV..YGYGVVGGRIA....E.....DRRAE
13 ------ALAAQADTRQGDPAADARILNTALAAEHEAIaaYQLGAGSGLLR....A.....PMRDL
14 --QLNPRNEINKGTSKDDLIHDRESLKKALDWEYSAI..YGLGVALAHSP....A.....GTRTA
15 --------------------AERQALLDALRAEYAAV..YAYGVIAAYAS....P.....ERAGL
16 ----PPPEEITIPEDLSLKGEDLTRAQDLLAGEYAAT..WALGVALAYVS....P.....DLTDA
17 --ESSCPPAPAASGPAAGSATTATALAMTVKTEAETV..YGYQVALARLD....G.....AAAGS
18 ---------------------ELDALQIALAAEHAAV..YVYGALGGRTSrsatP.....ELFAS
19 ------------PTPSGEAGAATAALRDALLAEHAAV..YGYSFAAAHTD....A.....DLRSL
20 -------PTESTAATEHPDPAGVAALVTMLTATHAAV..YATAAAGGAVA....Plg6aaQAREL
60 70 80 90 100 110
| | | | | |
1 VADALKQHRHRRDDVIVMLSARGVTAP.IAAAGYQLPM....QVSSAADAARLAVRMENDGATAW
2 VADALKQHRHRRDDVIVMLSARGVTAP.IAAAGYQLPM....QVSSAADAARLAVRMENDGATAW
3 VVEALEQHRQRRDDVIAMLTARKVTAP.VAAAGYQLPL....VVGSPADAARLAARMENDGAGAW
4 VSAAIAEHRARREAAIALCEQQGVDPA.VPEAGYQMPF....EVDTPADATNLAVQMEEDAAEAW
5 VVDALIQHRQRRDDIIVMLTARRVSPP.VAASGYQLPM....LVGSAADAARLAVRMENDGATAW
6 VSEAMAEHRARREAAIALLAEQGAEAP.LPAAGYQLPM....EVDTPAEAVDLAVRMEEDAAVAW
7 VSASIAEHRERREAAIALLEQRQVAAP.LPAAGYQVPM....RVDDPRDAAKLAVRMEEDGAAAW
8 VETAISNHHDRASQLQIITSGTTPAPG.YVSE----LP....DPTDETSARSNIETVENNVTQAW
9 VETAISNHHDRASQLQIITSGTTPAPG.YVSE----LP....DPTDETSARSNIETVENNVTQAW
10 VETAISNHHDRASQLQIITSGTTPAPG.YVSE----LP....DPTDETSARSNIETVENNVTQAW
11 ARAAYDAHRARRDELARSVRDLGGTPQ.AAAAGYALPF....AVPDATAAVRLAAELEERVAGVY
12 ARTAYDAHRARRDALAREVRDLGGEPV.AAAAGYALPF....SVPDSAAAVRLAAELEDRLAGVY
13 ALQFQGHHKAHVDLLAQTVTKLGGKPA.ESRQKYDFPVa...TLKAEADVLRFASGLEQGAVSAY
14 VSDAITAHRDRVELLESSFAESFPNET.IPRPEAAYEFsgypEPHDAQSSRAFFDSLEADSAAWW
15 IAEHTAAHRARRDATADALRAAGADVP.SPDAAYGVPF....PVQDPVAAARLAETVETDATVAW
16 TQDAIDRHREYAAVLRTTITPFADTAPsEPGYDLAGLT....EPTDPDSALTLIREVQDNAVTSW
17 ASQLLARHESVLAEAEALSRAQCVDIP.PREAGYTLGP....LF--LESPAAGLGSLEAGTLPVY
18 VVRAYDAHRARRDRLTATILDEGAEPV.AAEPAYELP-....RLDTPAQVDRAALAVERACAATY
19 CLSHLEKHRAWRDTLHSALVARDAVPP.GGEDAYQLP-....EHTGPEELRSFAAGLEETTAQAY
20 ARLSCLAHQALRDDLITAIRARGGDAP.PALPAYRLPV....APEGIGAALALLARIEDACAMAA
120 130 140 150 160
| | | | |
1 RAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE
2 RAVVEHAETADDRVFASTALTESAVMATRWNRVLGAWPITAAFPGGDE
3 RVVAEHAETGDDRAFAATALVQSAVMAARWNRVLGAWPITTSFPGGND
4 RAVVEQATDPGVRAFGVTALTECAVTAAQWRAVRGDTTVTVAFPGGSE
5 RAVAEHAETADDRTFAAMALAQSAVMAARWNKMLGAWPITTTFPGSNE
6 RAVVEQAADQAVRAFGVTALTECALTAARWRAVRGDSTVTVAFPGGSE
7 RAVVEQATGTEDRTFGLTALTESAVAAARWTQIAGTDPVTVAFPGGNE
8 HAAASAATTDAWRVFCAHIAGDTARELTLID-----------------
9 HAAASAATTDAWRVFCAHIAGDTARELTLI------------------
10 HAAASAATTDAWRVFCAHIAGDTARELTLI------------------
11 SDLVRAG-TGARRRSAAEALREAAVRAVRWSGESVAFPGL--------
12 SDLVRAAE-GGGRTSAAGALREAAVRAVRWRGGSVAFPGLAERVG---
13 LGAVPLFANPDLAKAAASILGDEAMHWAILRQALGEDPVPSAF-----
14 LHALSESHSATWRALCASLAAQSA------------------------
15 RAVVEQGDSEATRRLGVEALTEAALRLAAWQAILG-------------
16 HNAASVATDPGWRILASRIAGATARDTVT-------------------
17 GDLVALS-DGGIRQWAIAGLLAAANRAAQWGADSGPLPGI--------
18 AYLVEHTV-GEQRRSAVGALNEAAVRELVFRGTPEMFPGRDE------
19 LELAAVP-DAGLRDLAGRALGEATLRMLALGGQLSAFPGF---P----
20 HDAVAVLV-GDVRALALDALTGTAVRAQRARIAAG-------------