(c) 1992-2000 Regents of the University of California, Santa Cruz
Sequence Alignment and Modeling Software System
http://www.cse.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:
-
- T0135 Boiling stable protein, P. tremula
-
- gi|13445204|emb|CAC34953.1|_1:108 (AJ276517) boiling stable protein A [Populus tremula]
-
- gi|7484771|pir||T09703_1:108 pop3 protein - western balsam poplar x cottonwood
- gi|169459|gb|AAC26526.1| (M18538) pop3 peptide [Populus balsamifera subsp. trichocarpa x Populus deltoides]
-
- gi|20805049|dbj|BAB92723.1|_6:105 (AP003562) contains EST AU092422(C50524)~unknown protein [Oryza sativa (japonica cultivar-group)]
-
- gi|629499|pir||S30515_9:113 wound-induced protein - western balsam poplar
- gi|20956|emb|CAA39082.1| (X55440) unnamed protein product [Populus balsamifera subsp. trichocarpa]
- gi|20965|emb|CAA40072.1| (X56752) unnamed protein product [Populus balsamifera subsp. trichocarpa x Populus deltoides]
-
- gi|18401423|ref|NP_566569.1|_6:102 (NM_112598) expressed protein [Arabidopsis thaliana]
- gi|11994536|dbj|BAB02723.1| (AB022216) gene_id:MGD8.2~unknown protein [Arabidopsis thaliana]
- gi|13877523|gb|AAK43839.1|AF370462_1 (AF370462) Unknown protein [Arabidopsis thaliana]
- gi|17978771|gb|AAL47379.1| (AY064673) unknown protein [Arabidopsis thaliana]
-
- gi|20804543|dbj|BAB92236.1|_6:290 (AP003202) contains ESTs AU092422(C50524),C26948(C50524)~unknown protein [Oryza sativa (japonica cultivar-group)]
- gi|20805047|dbj|BAB92721.1| (AP003562) contains ESTs AU092422(C50524),C26948(C50524)~unknown protein [Oryza sativa (japonica cultivar-group)]
-
- gi|15225120|ref|NP_180725.1|_42:142 (NM_128724) unknown protein [Arabidopsis thaliana]
- gi|4582460|gb|AAD24844.1| (AC007071) unknown protein [Arabidopsis thaliana]
-
- gi|15223825|ref|NP_175547.1|_2:100 (NM_104014) unknown protein [Arabidopsis thaliana]
- gi|4836945|gb|AAD30647.1|AC006085_20 (AC006085) Unknown protein [Arabidopsis thaliana]
-
- gi|14495314|gb|AAK64267.1|AF373840_27_9:101 (AF373840) ORF106 [Arthrobacter nicotinovorans]
-
- gi|18309835|ref|NP_561769.1|_1:98 (NC_003366) hypothetical protein [Clostridium perfringens]
- gi|18144513|dbj|BAB80559.1| (AP003188) hypothetical protein [Clostridium perfringens]
-
- gi|18420541|ref|NP_568422.1|_6:98 (NM_122164) expressed protein [Arabidopsis thaliana]
- gi|9758664|dbj|BAB09130.1| (AB012244) gene_id:MQJ16.12~unknown protein [Arabidopsis thaliana]
- gi|14190417|gb|AAK55689.1|AF378886_1 (AF378886) AT5g22580/MQJ16_12 [Arabidopsis thaliana]
- gi|15215901|gb|AAK91494.1| (AY050481) AT5g22580/MQJ16_12 [Arabidopsis thaliana]
-
- gi|14192878|gb|AAK55783.1|AC079038_17_41:148 (AC079038) Hypothetical protein [Oryza sativa]
-
- gi|13472687|ref|NP_104254.1|_1:90 (NC_002678) hypothetical protein [Mesorhizobium loti]
- gi|14023434|dbj|BAB50040.1| (AP003001) hypothetical protein [Mesorhizobium loti]
-
- gi|15225691|ref|NP_180809.1|_50:150 (NM_128809) hypothetical protein [Arabidopsis thaliana]
- gi|7487440|pir||T02549 hypothetical protein T26B15.6 - Arabidopsis thaliana
- gi|3298538|gb|AAC25932.1| (AC004681) hypothetical protein [Arabidopsis thaliana]
-
- gi|15888120|ref|NP_353801.1|_1:91 (NC_003062) AGR_C_1419p [Agrobacterium tumefaciens] [Agrobacterium tumefaciens str. C58 (Cereon)]
- gi|17934687|ref|NP_531477.1| (NC_003304) conserved hypothetical protein [Agrobacterium tumefaciens str. C58 (U. Washington)]
- gi|15155754|gb|AAK86586.1| (AE008011) AGR_C_1419p [Agrobacterium tumefaciens str. C58 (Cereon)]
- gi|17739148|gb|AAL41793.1| (AE009045) conserved hypothetical protein [Agrobacterium tumefaciens str. C58 (U. Washington)]
10 20 30 40 50
| | | | |
1 MATRTPKLVKHTLLTRFKDE....ITREQIDNYINDYTNLLDLIPSMKSFN.....WGTDLGMES
2 MATRTPKLVKHTLLTRFKDE....ITREQIDNYINDYTNLLDLIPSMKSFN.....WGTDLGMES
3 MATRTPKLVKHTLLTRFKDE....ITREQIDNYINDYTNLLDLIPTMKSFN.....WGTDLGMES
4 ---GSGGVVKHILLARFKED....VAPERLDQLIRGYAGLVDLVPSMKAFH.....WGTDVSIEN
5 -VLPGSKVLKHIVFVRFNDG....ITDEQIEKFIKDYAHVADVVEPVKGFG.....WGKNYPVQQ
6 ------GPVKHVLLASFKDG....VSPEKIEELIKGYANLVNLIEPMKAFH.....WGKDVSIEN
7 PAAGRSGVLKHIVLARFKEE....VTPERLDHLIRGFGGLVNLVPSMKAFNc182cWGTDVSIEN
8 -STPQSQIIEHIVLFKTKDD....ADSTKITSMINNLNALAYLDQVLHIST.....SPLHRISSA
9 -----SSIVEHVVLFKLNDDd...VDSGKINSMVNGINELVNLDQVLHLYC.....GSIHRLITT
10 --------VRHVFAWRVAEG....SNQEEIVEILNTLPPRLGFIQGWEIGT.....HSGDPGDNG
11 -------MIKHIVMWKLKDEaegnSKAENAKIIKNSLEDLKEKINEIVHLE.....VGIDVNKSE
12 --------FKHLVVVKFKED....---TKVDEILKGLENLVSQIDTVKSFE.....WGEDKESHD
13 PATAIAAPVEHIVLIKVRPEa...AASGAAAAMVSSLQALSSVVPGLSYIH.....VGPVLRLRS
14 -------MIRHCVFVRFRGD....VPESERAAIHADLEALRQVIDGMDTVH.....FSANVSPEP
15 -SNKTRKVVEHVCLLKAKEG....LSEEVEKDMLDYLYTTQYQMRGIVAIS.....VGCIGDRNN
16 -------MILHCVFLRFKAA....TASSEKHAVFEAIAALKDEIPGIVDVK.....YGQNISPEG
60 70 80 90 100
| | | | |
1 .AELNRGYTHAFESTFESKSGLQEYLDSAALAAF.AEGFLPTLSQRLVIDYFLY
2 .AELNRGYTHAFESTFESKSGLQEYLDSAALAAF.AEGFLPTLSQRLVIDYFLY
3 .AELNRGYTHAFESTFESKSGLQEYLDSAALAAF.AEGFLPTLSQRLVIDYFLY
4 .--MHQGFTHVFESTFESTEGVKEYIEHPAHVEF.ANEFLPVLEKTLIIDY---
5 .--LNHDYLYGFELSFDSQDAFNEYLQSPALTEF.HAKFLPACASRMIMDYYLF
6 .--LHQGYTHIFESTFESKEAVAEYIAHPAHVEF.ATIFLGSLDKVLVIDY---
7 .--MHHGFTHVFECTFESTEGVKEYIEHPAHLEF.AKEILLAMEKTLIIDY---
8 .----TAFTHVLHSRYESKEDLASYAAHPDHVRVvKESVLPICDDIMAVDW---
9 .--TASDFTHVLHSRYRSKEDLNAYAIHPDHVRV.VKESESIREDIMAVDW---
10 .----APWDGVLISDFASWADLDKYSTDPFHLEV.VATLMPMFADRAVVDY---
11 .----QAYDVVLYSTFNSLEDLDSYQKNPDHVKA.GYFVKKVASSRVVVDY---
12 .M-LRQGFTHAFSMTFENKDGYVAFTSHPLHVEF.SAAFTAVIDKIVLLDF---
13 pAAEALGPTHVLHSRYATKPDLAAYAAHPAHVAAvQGHVLPNALDTTAIDW---
14 .--FARGFSHGFTIDFRDAAARDAYLVHEAHQRA.GARLVAALEG---------
15 .----EYFTHALYMRFQKKEDLDKFYENPFFLKVlNEYVTPFCHGLTNVDY---
16 .--LNGGFVDGFIVTLESPEARDGYLAHPQHVEV.GERLVSLTDGG--------