(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|49238829|emb|CAF28110.1|_1:75 Putative cell filamentation protein [Bartonella henselae str. Houston-1]
- gi|56368455|emb|CAD89506.1| BepA protein [Bartonella henselae]
- gi|49476021|ref|YP_034062.1| Putative cell filamentation protein [Bartonella henselae str. Houston-1]
-
- gi|24940342|emb|CAD37389.1|_25:99 putative cell filamentation protein [Bartonella tribocorum]
-
- gi|49238831|emb|CAF28112.1|_2:73 hypothetical protein [Bartonella henselae str. Houston-1]
- gi|56368457|emb|CAD89508.1| BepB protein [Bartonella henselae]
- gi|49476023|ref|YP_034064.1| hypothetical protein BH13390 [Bartonella henselae str. Houston-1]
-
- gi|49238832|emb|CAF28113.1|_4:62 Putative cell filamentation protein [Bartonella henselae str. Houston-1]
- gi|56368458|emb|CAD89509.1| BepC protein [Bartonella henselae]
- gi|49476024|ref|YP_034065.1| Putative cell filamentation protein [Bartonella henselae str. Houston-1]
-
- gi|49240093|emb|CAF26532.1|_4:62 Putative cell filamentation protein [Bartonella quintana str. Toulouse]
- gi|49474589|ref|YP_032631.1| Putative cell filamentation protein [Bartonella quintana str. Toulouse]
-
- gi|77956649|ref|ZP_00820734.1|_10:67 COG2184: Protein involved in cell division [Yersinia bercovieri ATCC 43970]
-
- gi|77963620|ref|ZP_00827428.1|_10:67 COG2184: Protein involved in cell division [Yersinia mollaretii ATCC 43969]
-
- gi|110595546|ref|ZP_01383876.1|_7:63 Filamentation induced by cAMP protein Fic [Acidovorax sp. JS42]
- gi|110335071|gb|EAT54807.1| Filamentation induced by cAMP protein Fic [Acidovorax sp. JS42]
-
- gi|87133401|gb|ABD24311.1|_7:61 Fic protein family [Bacillus thuringiensis]
10 20 30 40 50 60
| | | | | |
1 MPKAKAKTKNTEIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAMINLREESLPEYFDT
2 MPKAKAKTKNTEIISPHHYVYPNTTTLKNKYGIKNLNAFLEKCSHDTAKAMINLREESLPEYFDT
3 MPKAKEKTKNIETSSPHHYVYPNTTTLKNKYGITNFDAFTAKYTHDTAKAIVNLREAPLPEKFDS
4 ---PKAKAKNISTASPHNYIYPGTQILKNKYGETDLKLLLEKCLHDREQAMMNLRAESLPEYFDC
5 ----------------HNYLYKNSNTLKNKYGIKDPQRLYERCAHDTAREVMNLRFEPPPQRFGL
6 ----------------HNYFYKNSATLKNKHGIKNPRKLYERCAHETAREAVNFRLEPPPGKFDA
7 ---------------PDPYTYPNSQVLINKFGITDDDQFIEMEKDFSELAIMEIEFSPPP--YDL
8 ---------------PDPYTYPNSQVLINKLSITDDVQFIEMEKDFSELAIMDIEFSPPP--YNL
9 ------------------YTYPGTHVLKNKADIRDLAALQRFERGATAVRIQELRENPVRGEYDL
10 ------------------YTYDGTDVLKNKFGIKDQAELEELEKLITTAKIAELEIKPIQGNFDL
70
|
1 AYLCHIHQQL
2 AYLCHIHQQL
3 SYLCSIHHQL
4 AYLCYIHQQL
5 AYLKLIHWTL
6 AYLRTIHWCL
7 LYWRSLHQAL
8 RYWCSLHQAL
9 AHLQAIHKQV
10 DHLKKIHK--