(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|7388366|sp|O30181|Y055_ARCFU_78:132 UPF0107 protein AF_0055
- gi|11497675|ref|NP_068896.1| hypothetical protein AF0055 [Archaeoglobus fulgidus DSM 4304]
- gi|2650587|gb|AAB91166.1| conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
-
- gi|19914010|gb|AAM03697.1|_82:136 conserved hypothetical protein [Methanosarcina acetivorans C2A]
- gi|23822316|sp|Q8TU30|Y244_METAC UPF0107 protein MA_0244
- gi|20089142|ref|NP_615217.1| hypothetical protein MA0244 [Methanosarcina acetivorans C2A]
-
- gi|21227626|ref|NP_633548.1|_82:135 hypothetical protein MM1524 [Methanosarcina mazei Go1]
- gi|23822346|sp|Q8PWQ2|Y1524_METMA UPF0107 protein MM_1524
- gi|20906014|gb|AAM31220.1| conserved protein [Methanosarcina mazei Go1]
-
- gi|72395423|gb|AAZ69696.1|_82:135 conserved hypothetical protein [Methanosarcina barkeri str. fusaro]
- gi|73668261|ref|YP_304276.1| hypothetical protein Mbar_A0718 [Methanosarcina barkeri str. fusaro]
-
- gi|91773436|ref|YP_566128.1|_82:136 protein of unknown function DUF126 [Methanococcoides burtonii DSM 6242]
- gi|91712451|gb|ABE52378.1| protein of unknown function DUF126 [Methanococcoides burtonii DSM 6242]
-
- gi|57159507|dbj|BAD85437.1|_79:130 hypothetical protein, conserved, DUF126 family [Thermococcus kodakarensis KOD1]
- gi|57641183|ref|YP_183661.1| hypothetical protein TK1248 [Thermococcus kodakarensis KOD1]
-
- gi|1592056|gb|AAB99415.1|_78:127 conserved hypothetical protein [Methanocaldococcus jannaschii DSM 2661]
- gi|7388489|sp|Q58802|Y1407_METJA UPF0107 protein MJ1407
- gi|15669597|ref|NP_248410.1| hypothetical protein MJ1407 [Methanocaldococcus jannaschii DSM 2661]
-
- gi|84489053|ref|YP_447285.1|_81:127 hypothetical protein Msp_0225 [Methanosphaera stadtmanae DSM 3091]
- gi|84372372|gb|ABC56642.1| conserved hypothetical protein [Methanosphaera stadtmanae DSM 3091]
-
- gi|88951117|ref|ZP_01153691.1|_79:125 Protein of unknown function DUF126 [Methanosaeta thermophila PT]
- gi|88930316|gb|EAR49264.1| Protein of unknown function DUF126 [Methanosaeta thermophila PT]
10 20 30 40 50
| | | | |
1 PKAIINKKTETIIAVGAAMAEIPLVEVRDEKFFEAVKTGDRVVVNADEGYVELIE
2 PKAIINKKTETIIAVGAAMAEIPLVEVRDEKFFEAVKTGDRVVVNADEGYVELIE
3 PVAIINLETEPIVAVGAIISEIPLVDMLEKSPYESLKDGDVVQVNGSEGYIELIK
4 PAAIINLETEPIVAVGAIISEIPLVDMLEKDPYEFLKDGDTVLVNGSEGYIELL-
5 PAAIINLETEPIVAVGAIISEIPLVDMLEKNPYEVLNNGDLVLVNGSKGYIELF-
6 PAAMINIDSEPIVAVGAIISDIPLVDRLDKDPFTIFKNGDRVKVDSTSGFVELMD
7 PKAIIVGEAETIVATGAIISDIPMVDGVDV---SKLKTGMKVRVDADSGEVEILE
8 -KGIVNKECEPIVATGAILGGIPLVDKID---IEEIKTGDRIVVDGNTGVVKIL-
9 PRAIICQKAEPIIAIGAIISKIPMVDNPDVDIINTINTNDEITVDAD--------
10 PAAMINLKSEPIVAVGAIISDIPLVDRVPE-WILDVKDGTRVVVDARR-------