# List of top-scoring protein chains for t2k-w0.5 hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 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. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 2pgd 482 7.57e-01 2pgd a.100.1.1 18778 c.2.1.6 30190 1jb0F 164 1.79e+00 1jb0F f.2.1.12 62825 1xze 214 2.04e+00 1cex c.23.9.1 31310 9gacA 295 2.28e+00 1apyA d.153.1.5 42010 1cue 197 2.34e+00 1cex c.23.9.1 31322 9gaaA 295 2.50e+00 1apyA d.153.1.5 42014 9gafA 295 2.78e+00 1apyA d.153.1.5 42008 2cut 198 2.83e+00 1cex c.23.9.1 31315 1xzf 214 2.85e+00 1cex c.23.9.1 31291 1cui 214 3.00e+00 1cex c.23.9.1 31323 1agy 200 3.02e+00 1cex c.23.9.1 31286 1xzd 214 3.03e+00 1cex c.23.9.1 31321 1cus 200 3.09e+00 1cex c.23.9.1 31287 1ffe 214 3.14e+00 1cex c.23.9.1 31288 1cua 214 3.16e+00 1cex c.23.9.1 31313 1cuz 214 3.17e+00 1cex c.23.9.1 31314 1cub 214 3.18e+00 1cex c.23.9.1 31304 1ffb 214 3.18e+00 1cex c.23.9.1 31305 1xzj 214 3.20e+00 1cex c.23.9.1 31299 1cug 214 3.21e+00 1cex c.23.9.1 31308 1cuj 214 3.22e+00 1cex c.23.9.1 31294 1cex 214 3.23e+00 1cex c.23.9.1 31285 1xzl 214 3.24e+00 1cex c.23.9.1 31295 1cuy 214 3.25e+00 1cex c.23.9.1 31302 1cuh 214 3.26e+00 1cex c.23.9.1 31311 1ffa 214 3.27e+00 1cex c.23.9.1 31289 1xzh 214 3.27e+00 1cex c.23.9.1 31293 1cuu 214 3.30e+00 1cex c.23.9.1 31309 1xzg 214 3.35e+00 1cex c.23.9.1 31292 1cux 214 3.35e+00 1cex c.23.9.1 31306 1ffd 214 3.37e+00 1cex c.23.9.1 31290 1cuwA 214 3.42e+00 1cex c.23.9.1 31324 1cuv 214 3.43e+00 1cex c.23.9.1 31318 1ffc 214 3.43e+00 1cex c.23.9.1 31296 1xzi 214 3.97e+00 1cex c.23.9.1 31297 1htbA 374 5.05e+00 2ohxA b.35.1.2 24715 c.2.1.1 29731 1eg0B 148 5.26e+00 1pkp i.1.1.1 45808 1xzb 214 5.42e+00 1cex c.23.9.1 31303 1pkp 150 5.43e+00 1pkp d.14.1.1 37551 d.50.1.2 38787 1hdyA 374 5.54e+00 2ohxA b.35.1.2 24723 c.2.1.1 29739 1dv4E 145 5.55e+00 i.1.1.3 45875 1hdzA 374 5.55e+00 2ohxA b.35.1.2 24725 c.2.1.1 29741 1dehA 374 5.65e+00 2ohxA b.35.1.2 24713 c.2.1.1 29729 1ja9A 274 6.48e+00 c.2.1.2 62817 1jwtA 305 7.33e+00 b.47.1.2 67398 1cuf 214 7.36e+00 1cex c.23.9.1 31301 2gacB 144 7.36e+00 1apyB 1ayyD 144 7.48e+00 1apyB 1ht0A 374 8.66e+00 2ohxA b.35.1.2 24709 c.2.1.1 29725 1ji1A 637 9.06e+00 1jt2A 268 9.37e+00 1bqk 124 1.02e+01 1bqk b.6.1.1 22889 1jjfA 268 1.02e+01 c.69.1.2 66765 1adwA 123 1.04e+01 1bqk b.6.1.1 22893 1ucyE 109 1.22e+01 1ucyE 1ee2A 373 1.37e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1ee2B 373 1.37e+01 2ohxA b.35.1.2 24664 c.2.1.1 29680 1a71A 374 1.44e+01 2ohxA b.35.1.2 24673 c.2.1.1 29689 1axgA 374 1.45e+01 2ohxA b.35.1.2 24691 c.2.1.1 29707 1ju9A 374 1.47e+01 b.35.1.2 63293 c.2.1.1 63294 1axeA 374 1.48e+01 2ohxA b.35.1.2 24681 c.2.1.1 29697 1hetA 374 1.48e+01 2ohxA b.35.1.2 60975 c.2.1.1 60976 1heuA 374 1.48e+01 2ohxA b.35.1.2 60979 c.2.1.1 60980 2ohxA 374 1.48e+01 2ohxA b.35.1.2 24669 c.2.1.1 29685 8adh 374 1.48e+01 2ohxA b.35.1.2 24690 c.2.1.1 29706 1bhxF 105 1.50e+01 1ucyE 1qlhA 374 1.59e+01 2ohxA b.35.1.2 24685 c.2.1.1 29701 1c7hA 131 1.64e+01 1opy d.17.4.3 38117 1cz8V 94 1.66e+01 1vpfA g.17.1.1 44765 1fltV 98 1.68e+01 1vpfA g.17.1.1 44751 1ayg 80 1.74e+01 451c a.3.1.1 15831 1bf6A 291 1.75e+01 1pscA c.1.9.3 29065 1hnjA 317 1.77e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1hn9A 317 1.77e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1g97A 459 1.80e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1h65A 270 1.82e+01 c.37.1.8 65640 1hm9A 468 1.82e+01 b.81.1.4 65866 c.68.1.5 65867 1ej9A 563 1.88e+01 1a36A d.163.1.2 42172 e.15.1.1 43265 1hvxA 515 1.93e+01 1bli b.71.1.1 27721 c.1.8.1 28708 1a35A 538 1.95e+01 1a36A d.163.1.2 42171 e.15.1.1 43264 1a31A 538 1.98e+01 1a36A d.163.1.2 42170 e.15.1.1 43263 1esp 317 1.99e+01 1hyt d.92.1.2 58979 1d1tA 373 2.00e+01 2ohxA b.35.1.2 24719 c.2.1.1 29735 1agnA 373 2.00e+01 2ohxA b.35.1.2 24737 c.2.1.1 29753 1gsn 478 2.03e+01 3grs c.3.1.5 30445 c.3.1.5 30446 d.87.1.1 40154 1cvjB 190 2.03e+01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1a36A 592 2.09e+01 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1vppV 102 2.11e+01 1vpfA g.17.1.1 44753 1vpfA 102 2.11e+01 1vpfA g.17.1.1 44767 1bdg 451 2.15e+01 1qhaA c.55.1.3 33461 c.55.1.3 33462 1go3E 187 2.15e+01 b.40.4.5 65406 1h7xB 1025 2.15e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h7xC 1025 2.15e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xD 1025 2.15e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1h7xA 1025 2.15e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1gthA 1025 2.16e+01 1gthD 1025 2.16e+01 1h7wD 1025 2.16e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1h7wB 1025 2.16e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1gt8A 1025 2.16e+01 1h7wA 1025 2.16e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gthC 1025 2.16e+01 1gteD 1025 2.16e+01 1gthB 1025 2.16e+01 1gt8D 1025 2.16e+01 1gt8B 1025 2.16e+01 1gt8C 1025 2.16e+01 1gteA 1025 2.16e+01 1e97A 131 2.23e+01 d.17.4.3 64803 1dmnA 131 2.37e+01 1opy d.17.4.3 38115 1lwhA 441 2.44e+01 1qdlA 422 2.46e+01 1qdlA d.161.1.1 42088 1hms 132 2.54e+01 1hmt b.60.1.2 27168 1hmt 132 2.54e+01 1hmt b.60.1.2 27169 1xan 461 2.59e+01 3grs c.3.1.5 30449 c.3.1.5 30450 d.87.1.1 40156 1dnc 478 2.59e+01 3grs c.3.1.5 30443 c.3.1.5 30444 d.87.1.1 40153 2ng1 293 2.60e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 3grs 478 2.61e+01 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 4gr1 478 2.61e+01 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 5grt 461 2.61e+01 3grs c.3.1.5 30465 c.3.1.5 30466 d.87.1.1 40164 1ffh 294 2.62e+01 1ng1 a.24.13.1 16960 c.37.1.10 32271 1h9cA 106 2.64e+01 1iibA c.44.2.1 60820 1grt 478 2.65e+01 3grs c.3.1.5 30467 c.3.1.5 30468 d.87.1.1 40165 1ng1 294 2.65e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1hu3A 260 2.67e+01 1hu3A a.118.1.2 19137 1jpnA 296 2.69e+01 a.24.13.1 67039 c.37.1.10 67040 1iibA 106 2.72e+01 1iibA c.44.2.1 32648 1e2b 106 2.72e+01 1iibA c.44.2.1 32650 1bwyA 132 2.73e+01 1hmt b.60.1.2 27172 1npc 317 2.73e+01 1hyt d.92.1.2 59012 1dusA 194 2.78e+01 1dusA c.66.1.4 34182 1jg8A 347 2.78e+01 1jg8A c.67.1.1 62946 1fjxA 327 2.81e+01 6mhtA c.66.1.10 34228 1dmmA 131 2.86e+01 1opy d.17.4.3 38114 1imjA 210 2.88e+01 1jriG 85 3.02e+01 b.38.1.1 67127 1eyrA 228 3.08e+01 1eyrA c.68.1.3 34514 1eziA 228 3.08e+01 1eyrA c.68.1.3 34512 1hnhA 317 3.08e+01 1hn9A c.95.1.1 35983 c.95.1.1 35984 1ucyK 259 3.10e+01 1ucyE 1dmqA 131 3.14e+01 1opy d.17.4.3 38116 1d1nA 99 3.17e+01 1d1nA b.43.3.1 25718 1mkp 144 3.34e+01 1vhrA c.45.1.1 32654 1bthH 259 3.35e+01 5ptp 1k4qA 463 3.36e+01 c.3.1.5 68140 c.3.1.5 68141 d.87.1.1 68142 1i81A 83 3.37e+01 1d3bB b.38.1.1 61930 1h8iH 253 3.38e+01 1ucyE 1g71A 347 3.39e+01 1g71A e.16.1.1 43268 1f3oA 235 3.40e+01 1b0uA c.37.1.12 59631 1eblA 317 3.43e+01 1hn9A c.95.1.1 35973 c.95.1.1 35974 1eblB 317 3.43e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1jouB 259 3.44e+01 1ucyE 1dm4B 260 3.44e+01 1ucyE 1g0sA 209 3.46e+01 1g0sA d.113.1.1 60187 1c5lH 259 3.47e+01 5ptp 1ahtH 259 3.47e+01 5ptp 8kme2 259 3.47e+01 1ucyE 1ea2A 131 3.54e+01 d.17.4.3 64860 1lid 131 3.55e+01 1hmt b.60.1.2 27184 1lkfA 299 3.55e+01 1pvl f.6.1.1 43821 1b7xB 259 3.55e+01 1ucyE 2mjpA 193 3.57e+01 1b78A c.51.4.1 33223 1b78A 193 3.57e+01 1b78A c.51.4.1 33221 1mkxK 308 3.57e+01 5ptp b.47.1.2 26204 1dx5M 259 3.59e+01 1ucyE 6mhtA 327 3.59e+01 6mhtA c.66.1.10 34226 1hmy 327 3.59e+01 6mhtA c.66.1.10 34229 3mhtA 327 3.59e+01 6mhtA c.66.1.10 34234 1hxeH 251 3.63e+01 5ptp 1b5l 172 3.63e+01 1b5l a.26.1.3 16900 1a2dA 131 3.66e+01 1hmt b.60.1.2 27193 1ehwA 162 3.71e+01 1npk d.58.6.1 39088 1hagE 295 3.71e+01 1ucyE b.47.1.2 26135 1qsjA 277 3.77e+01 1c3d a.102.4.4 18876 1qqfA 277 3.77e+01 1c3d a.102.4.4 18875 4tsuA 130 3.77e+01 1opy d.17.4.3 38118 1opy 131 3.78e+01 1opy d.17.4.3 38113 1culC 380 3.81e+01 1cipA a.66.1.1 18204 c.37.1.8 32087 1e3rA 131 3.83e+01 1opy d.17.4.3 59199 1e7tA 59 3.84e+01 h.1.20.1 59371 1aztB 388 3.92e+01 1cipA a.66.1.1 18202 c.37.1.8 32085