(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:
-
- T0382 APC6185, Rhodopseudomonas palustris CGA009, 123 res
-
- gi|39934958|ref|NP_947234.1|_1:123 hypothetical protein RPA1889 [Rhodopseudomonas palustris CGA009]
- gi|39648809|emb|CAE27330.1| hypothetical protein [Rhodopseudomonas palustris CGA009]
-
- gi|78492586|ref|ZP_00844822.1|_38:157 hypothetical protein RPCDRAFT_3982 [Rhodopseudomonas palustris BisB18]
-
- gi|90423317|ref|YP_531687.1|_11:130 hypothetical protein RPC_1809 [Rhodopseudomonas palustris BisB18]
- gi|90105331|gb|ABD87368.1| hypothetical protein RPC_1809 [Rhodopseudomonas palustris BisB18]
-
- gi|90423316|ref|YP_531686.1|_1:122 hypothetical protein RPC_1808 [Rhodopseudomonas palustris BisB18]
- gi|90105330|gb|ABD87367.1| conserved hypothetical protein [Rhodopseudomonas palustris BisB18]
- gi|78492585|ref|ZP_00844821.1| conserved hypothetical protein [Rhodopseudomonas palustris BisB18]
-
- gi|85716634|ref|ZP_01047604.1|_5:124 hypothetical protein NB311A_12297 [Nitrobacter sp. Nb-311A]
- gi|85696635|gb|EAQ34523.1| hypothetical protein NB311A_12297 [Nitrobacter sp. Nb-311A]
-
- gi|68193765|gb|EAN08417.1|_5:123 conserved hypothetical protein [Mesorhizobium sp. BNC1]
- gi|69275325|ref|ZP_00611237.1| conserved hypothetical protein [Mesorhizobium sp. BNC1]
-
- gi|74420232|gb|ABA04431.1|_1:122 conserved hypothetical protein [Nitrobacter winogradskyi Nb-255]
- gi|75675362|ref|YP_317783.1| hypothetical protein Nwi_1169 [Nitrobacter winogradskyi Nb-255]
-
- gi|77742580|ref|ZP_00811057.1|_1:119 conserved hypothetical protein [Rhodopseudomonas palustris BisA53]
- gi|77697687|gb|EAO88847.1| conserved hypothetical protein [Rhodopseudomonas palustris BisA53]
-
- gi|108762430|ref|YP_632654.1|_25:141 hypothetical protein MXAN_4485 [Myxococcus xanthus DK 1622]
- gi|108466310|gb|ABF91495.1| hypothetical protein MXAN_4485 [Myxococcus xanthus DK 1622]
-
- gi|49022455|dbj|BAD23986.1|_1:111 orf116 [Myxococcus xanthus]
-
- gi|68193764|gb|EAN08416.1|_2:80 conserved hypothetical protein [Mesorhizobium sp. BNC1]
- gi|69275324|ref|ZP_00611236.1| conserved hypothetical protein [Mesorhizobium sp. BNC1]
-
- gi|74420233|gb|ABA04432.1|_10:79 hypothetical protein Nwi_1170 [Nitrobacter winogradskyi Nb-255]
- gi|75675363|ref|YP_317784.1| hypothetical protein Nwi_1170 [Nitrobacter winogradskyi Nb-255]
10 20 30 40 50 60
| | | | | |
1 MSKLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSL
2 MSKLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSL
3 --GEDLQQMSVEGLVKRLVEIGVAQDAALLGAEYAKFNRLFDRMQQVSAELKRRDGDQRRALLAL
4 --GEDLQQMSVEGLVKRLVEIGVAQDAALLGAEYAKFNRLFDRMQQVSAELKRRDGDQRRALLAL
5 MKRTNLVEMSTPALVMRFAHMGIAQDEAMLQGDTAKFSRLFVQMDLISKELKRRDGDQRRALMTL
6 --KIRLDAMPVDQLVGRFAAITAAQDDALLGHELTKFNRLFDRMMEVSNELKGRPGDQRRALMAL
7 ---QNLARFTSEHLVMRFAEIGIEQDNALLRNEIGSFNKLYDEKAAILAELKSREGDQRTLLLRL
8 MTPVQSDGARVQGLIARFAEIGMAQYDAIYVINTIKYNRLYAEMKRVWTELKEMPGDQRTALLPL
9 MSGTSNSTMTAGELLDRYIELSIQQGTAIDLSDGSQINRLGSKIFRINDELKSRSGDQRRILFGL
10 --REGALVMKLEDLVEQFAQNVAGQNEAILRGDAKIGNKHARKYGAAVDKLLANGNAGRDALAVL
11 --------MKLEDLVEQFAQNVAGQNEAILRGDAKIGNKHARKYGAAVDKLLANGNAGRDALAVL
12 --------------------------------------------MIISDELKRRPGDHRRYLSSL
13 ----------VKNLVAQFVEIGVAQYDAINVIDNAMYNRLYKKMERIRAELRKMPGDQRRALLPL
70 80 90 100 110 120
| | | | | |
1 FEYPNMQVRLQAAKLTLAVAPVKAREQLEAIVSSKWFPQAGDAGMCLDLLDDGTFKPK
2 FEYPNMQVRLQAAKLTLAVAPVKAREQLEAIVSSKWFPQAGDAGMCLDLLDDGTFKPK
3 YDHPNMQVRLKAAKHTLAVAPVEARQQLEAIAGSKWFPQAGDAGMSLWNLDRGVFKP-
4 YDHPNMQVRLKAAKHTLAVAPVEARQQLEAIAGSKWFPQAGDAGMSLWNLDRGVFKP-
5 YDHPNMQVRLKAAKHTLAVASAEARQQLEAIAESKWFPQAGDAGMSLWNLERGVFKP-
6 YHHPNMQAQLQAAKLTLAVAPDEARKKIEAIASSRWLPQSGDAGMCLINLDRGIFKP-
7 YSHPNMQVRLNAAKATLAIEPNEARKQLEAIAASGQGPQAGDAGMSLWTLDEGIFKP-
8 LSHTNVQVRLMAAHSLLALYPGLARRTLETIRDSGIEPQNGSAANAIRRLDEGSYVP-
9 LSHQNPYVRYNAATSLIRIFPVEARNVLQTIADSKWYPLAGHAGMYLHMLDTRI----
10 LKHERLDVRVMAAAHLLRYRTDGAKAVLEEAAKGQGLAPFGAQQALKRWEEGTW----
11 LKHERLDVRVMAAAHLLRYRTDGAKAVLEEAAKGQGLAPFGAQQALKRWEEGTW----
12 YQHPNTKVRAKAAIHTLAVLPEEARKVLEEVGSLKGYSGPMDARGILRALDEGTYVPE
13 LSHPNVQVRLKAAHS-------------------------------------------