(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:
-
- T0138 KaiA N-terminal domain, S. elongatus
-
-
- gi|19352185|dbj|BAB85983.1|_3:131 (AB071375) circadian clock protein KaiA [Synechococcus elongatus]
-
- gi|16332220|ref|NP_442948.1|_1:134 (NC_000911) PCC7942 clock gene...ORFD [Synechocystis sp. PCC 6803]
- gi|7469768|pir||S76848 hypothetical protein - Synechocystis sp. (strain PCC 6803)
- gi|1653850|dbj|BAA18760.1| (D90917) ORF_ID:slr0756~PCC7942 clock gene...ORFD [Synechocystis sp. PCC 6803]
10 20 30 40 50 60
| | | | | |
1 MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRA
2 MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRA
3 QSTALTICGLVYSPAIGQELVRLHTSDIDELVYFSSEREFCNYLEARRNSIACLILEWGEGT-PQ
4 MQSPLSLCLFA-PEHVAHRLRSIFQGDRHYLSTFQALDDFCAFLEDKPERIDCLLVYYEANSLP-
70 80 90 100 110 120 1
| | | | | |
1 VVQQLCFEGVVVPAIVVGDRDS..EDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRL
2 VVQQLCFEGVVVPAIVVGDRDS..EDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRL
3 IITYLHHSATLLPAILIFP---..AAPAPPPAGPHYHIAEVILTTDQLDQLNRQIEEAITGFVKL
4 VLNRLYEQGRLLPIILLEPSPSalAKTTDEHPTIVYHNAEIHLPESQWSELPTVVDRAIAHYLHL
30
|
1 APVETMA
2 APVETMA
3 CPGCA--
4 GPICTL-