# 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 1jgsA 138 5.62e-14 a.4.5.28 66683 1b1bA 140 1.52e-06 1bi0 a.4.5.24 16215 a.76.1.1 18421 1fx7A 230 1.76e-06 1bi0 a.4.5.24 60088 a.76.1.1 60089 b.34.1.2 60090 1hsjA 487 1.79e-06 4mbp a.4.5.28 61237 c.94.1.1 61238 1f5tA 121 1.15e-05 1bi0 a.4.5.24 16203 a.76.1.1 18409 1bi0 226 1.55e-05 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1ddnA 226 1.57e-05 1bi0 a.4.5.24 16207 a.76.1.1 18413 2dtr 226 1.58e-05 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1g3tA 226 1.58e-05 a.4.5.24 65127 a.76.1.1 65128 b.34.1.2 65129 1c0wB 225 1.65e-05 1bi0 a.4.5.24 16212 a.76.1.1 18418 b.34.1.2 24454 1g3yA 226 2.03e-05 a.4.5.24 65136 a.76.1.1 65137 b.34.1.2 65138 1fwzA 226 2.13e-05 a.4.5.24 60077 a.76.1.1 60078 b.34.1.2 60079 1fzpB 123 6.23e-05 1fznD a.4.5.28 19008 1jmrA 249 5.53e-04 1i1gA 141 3.52e-03 a.4.5.32 65982 d.58.37.1 65983 1ft9A 222 6.89e-03 1ft9A a.4.5.4 16107 b.82.3.1 28131 1db9A 200 3.19e-02 a.4.5.4 64782 b.82.3.2 64783 1dpuA 99 3.32e-02 1dpuA a.4.5.16 16150 1db7A 200 4.67e-02 a.4.5.4 64778 b.82.3.2 64779 1bw6A 56 4.69e-02 1bw6A a.4.1.7 16052 1hw5A 210 5.28e-02 2cgpA a.4.5.4 16098 b.82.3.2 28137 1cgpA 205 5.54e-02 a.4.5.4 16096 b.82.3.2 28135 1runA 209 5.59e-02 2cgpA a.4.5.4 16103 b.82.3.2 28142 2cgpA 210 5.63e-02 2cgpA a.4.5.4 16102 b.82.3.2 28141 1smtB 122 5.98e-02 1smtA a.4.5.5 16110 1smtA 122 5.98e-02 1smtA a.4.5.5 16109 1hlvA 131 8.20e-02 a.4.1.7 65854 a.4.1.7 65855 1e2xA 243 9.75e-02 1e2xA a.4.5.6 16113 a.78.1.1 18443 1hw1A 239 1.05e-01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1ruoB 209 1.11e-01 2cgpA a.4.5.4 16106 b.82.3.2 28145 1j75A 67 1.85e-01 a.4.5.19 62673 1i1sA 96 1.87e-01 1bjaA a.4.5.9 16124 1bjaA 95 1.89e-01 1bjaA a.4.5.9 16122 1qgpA 77 2.49e-01 1qbjA a.4.5.19 16158 1qbjA 81 2.64e-01 1qbjA a.4.5.19 16155 1ldkB 366 5.09e-01 1c8bA 371 6.27e-01 1c8bA c.56.1.2 59082 1lccA 51 7.51e-01 1pru a.35.1.5 17110 1lcdA 51 7.51e-01 1pru a.35.1.5 17111 1ge9A 184 7.53e-01 1dd5A d.67.3.1 60463 1lqc 56 8.33e-01 1pru a.35.1.5 17109 1a04A 215 8.80e-01 1a04A a.4.6.2 16234 c.23.1.1 31089 1l1mA 62 9.54e-01 1cjgA 62 9.64e-01 1pru a.35.1.5 17112 1lea 84 1.32e+00 1lea a.4.5.2 16085 1cqjB 385 1.61e+00 2scuB c.23.4.1 31143 d.142.1.4 41564 1qpiA 203 1.61e+00 2tct a.4.1.9 16072 a.121.1.1 19249 2scuB 388 1.62e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1jllB 388 1.62e+00 c.23.4.1 66853 d.142.1.4 66854 1bjyA 207 1.64e+00 2tct a.4.1.9 16069 a.121.1.1 19246 2tct 207 1.64e+00 2tct a.4.1.9 16063 a.121.1.1 19240 1ldjA 760 1.68e+00 2trt 217 1.74e+00 2tct a.4.1.9 16064 a.121.1.1 19241 1a6i 217 1.95e+00 2tct a.4.1.9 16066 a.121.1.1 19243 1jhhA 202 2.08e+00 a.4.5.2 63060 b.87.1.1 63061 1jhfA 202 2.10e+00 a.4.5.2 63057 b.87.1.1 63058 6paxA 133 2.41e+00 6paxA a.4.1.5 64758 a.4.1.5 64759 1h8aC 128 3.04e+00 a.4.1.3 65731 a.4.1.3 65732 1k78A 149 3.12e+00 a.4.1.5 68255 a.4.1.5 68256 1bdg 451 3.35e+00 1qhaA c.55.1.3 33461 c.55.1.3 33462 1pdnC 128 4.89e+00 6paxA a.4.1.5 16047 1erg 70 5.36e+00 1cds g.7.1.3 44462 1b24A 188 5.58e+00 1b24A d.95.2.1 40573 d.95.2.1 40574 1qktA 248 5.63e+00 3erdA a.123.1.1 19295 1b0nA 111 5.63e+00 1b0nA a.34.1.1 17001 a.35.1.3 17064 1g50A 247 5.64e+00 a.123.1.1 65149 1qkuA 250 5.65e+00 3erdA a.123.1.1 19306 1ereA 253 5.70e+00 3erdA a.123.1.1 19300 1a52A 258 5.76e+00 3erdA a.123.1.1 19296 3ertA 261 5.76e+00 3erdA a.123.1.1 19292 3erdA 261 5.76e+00 3erdA a.123.1.1 19293 1cds 77 5.79e+00 1cds g.7.1.3 44461 1cdq 77 5.79e+00 1cds g.7.1.3 44459 1opc 110 5.91e+00 1opc a.4.6.1 16231 1l2iA 261 6.00e+00 1odd 118 6.05e+00 1opc a.4.6.1 16232 1al3 324 6.11e+00 1al3 c.94.1.1 35835 1efaB 333 6.15e+00 1tlfA a.35.1.5 17107 c.93.1.1 35692 1jyfA 349 6.36e+00 c.93.1.1 67456 1jyeA 349 6.37e+00 c.93.1.1 67455 1b9nA 265 6.39e+00 1b9mA a.4.5.8 16120 b.40.6.2 58942 b.40.6.2 58943 1g91A 77 6.39e+00 1b3aA d.9.1.1 60389 1pru 56 6.54e+00 1pru a.35.1.5 17104 1lbiA 360 6.61e+00 1tlfA c.93.1.1 35694 1jhgA 101 6.79e+00 1jhgA a.107.1.1 19009 1res 43 6.99e+00 1ret a.4.1.2 16023 1ret 43 6.99e+00 1ret a.4.1.2 16024 1lliA 92 7.74e+00 1lmb3 a.35.1.2 17025 2hcc 66 8.28e+00 1b3aA d.9.1.1 37457 1zncA 266 9.23e+00 2cba b.74.1.1 27955 1c75A 71 9.58e+00 451c a.3.1.1 15796 1k3gA 71 9.60e+00 a.3.1.1 68111 1gs5A 258 1.00e+01 1dhjB 159 1.05e+01 1vdrA c.71.1.1 34834 1gsjA 258 1.10e+01 1j7kA 334 1.16e+01 1hqcA a.4.5.11 62695 c.37.1.13 62696 1in6A 334 1.18e+01 1hqcA a.4.5.11 62601 c.37.1.13 62602 1in4A 334 1.19e+01 1hqcA a.4.5.11 62597 c.37.1.13 62598 1in8A 334 1.19e+01 1hqcA a.4.5.11 62605 c.37.1.13 62606 1in5A 334 1.19e+01 1hqcA a.4.5.11 62599 c.37.1.13 62600 1in7A 334 1.19e+01 1hqcA a.4.5.11 62603 c.37.1.13 62604 1eblA 317 1.22e+01 1hn9A c.95.1.1 35973 c.95.1.1 35974 1eblB 317 1.22e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1hnhA 317 1.37e+01 1hn9A c.95.1.1 35983 c.95.1.1 35984 1ddgA 374 1.37e+01 1amoA b.43.4.1 25671 c.25.1.4 31559 1rcsA 105 1.41e+01 1jhgA a.107.1.1 19025 1a5j 110 1.41e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 2wrpR 107 1.42e+01 1jhgA a.107.1.1 19010 3wrp 108 1.43e+01 1jhgA a.107.1.1 19015 1trrA 107 1.43e+01 1jhgA a.107.1.1 19017 1troA 108 1.45e+01 1jhgA a.107.1.1 19011 1b9mA 265 1.45e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1a0rB 340 1.50e+01 1tbgA b.69.4.1 27658 1gotB 340 1.50e+01 1tbgA b.69.4.1 27648 1tbgA 340 1.51e+01 1tbgA b.69.4.1 27649 1tdrB 159 1.52e+01 1vdrA c.71.1.1 34866 1bia 321 1.52e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1bib 321 1.52e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1ddrB 159 1.54e+01 1vdrA c.71.1.1 34857 1jygA 69 1.55e+01 a.60.11.1 67457 2drcB 159 1.57e+01 1vdrA c.71.1.1 34849 1g2hA 61 1.57e+01 1g2hA a.4.1.10 60224 1ra9 159 1.57e+01 1vdrA c.71.1.1 34820 6dfr 159 1.57e+01 1vdrA c.71.1.1 34874 1draA 159 1.58e+01 1vdrA c.71.1.1 34831 1dhiB 159 1.58e+01 1vdrA c.71.1.1 34845 1drbB 159 1.60e+01 1vdrA c.71.1.1 34829 2mllA 241 1.61e+01 1mrj d.165.1.1 42195 1ce7A 241 1.62e+01 1mrj d.165.1.1 42194 1gof 639 1.63e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 1.63e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1k3iA 656 1.68e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1mseC 105 1.73e+01 1a5j a.4.1.3 16039 a.4.1.3 16040 1iawA 317 1.76e+01 c.52.1.9 62126 1ev7A 317 1.76e+01 1ev7B c.52.1.9 33315 1ev7B 317 1.76e+01 1ev7B c.52.1.9 33316 1eyqA 222 1.83e+01 1eypA d.36.1.1 38534 1jepA 222 1.83e+01 d.36.1.1 66612 1eypA 222 1.83e+01 1eypA d.36.1.1 38536 1nhkL 144 1.89e+01 1npk d.58.6.1 39142 1a58 177 1.99e+01 2cpl b.62.1.1 27495 1bed 181 2.11e+01 1fvkA a.44.1.1 17514 c.47.1.4 32808 1dwaM 499 2.12e+01 1e70M c.1.8.4 28928 1e4mM 501 2.13e+01 1e70M c.1.8.4 59226 1e6qM 501 2.13e+01 1e70M c.1.8.4 28920 1e70M 501 2.13e+01 1e70M c.1.8.4 28926 1uxd 65 2.14e+01 1uxc a.35.1.5 17118 1uxc 65 2.14e+01 1uxc a.35.1.5 17119 1a25A 149 2.18e+01 1rsy b.7.1.2 23197 1gdtA 183 2.21e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1hfgA 71 2.22e+01 1b3aA d.9.1.1 37409 1vmpA 71 2.23e+01 1b3aA d.9.1.1 37407 1g82A 160 2.23e+01 1bfg b.42.1.1 60337 1dl5A 317 2.24e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1kc6A 257 2.31e+01 c.52.1.19 68419 1jpdX 324 2.33e+01 c.1.11.2 67014 d.54.1.1 67015 1mspA 126 2.41e+01 1mspA b.1.11.2 22333 1ihkA 174 2.41e+01 1bfg b.42.1.1 62384 1qipA 183 2.50e+01 1qipA d.32.1.1 38470 1cm9A 74 2.56e+01 1b3aA d.9.1.1 37405 1g6uA 48 2.57e+01 1g6uA k.9.1.1 46425 1j7nA 776 2.64e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1myr 501 2.65e+01 1e70M c.1.8.4 28925 1bh5A 183 2.68e+01 1qipA d.32.1.1 38476 1qjjA 200 2.68e+01 1iae d.92.1.8 40313 1iab 200 2.70e+01 1iae d.92.1.8 40312 1ast 200 2.70e+01 1iae d.92.1.8 40310 1iae 200 2.70e+01 1iae d.92.1.8 40311 2rslA 140 2.92e+01 2rslA c.53.1.1 33345 1qg8A 255 2.98e+01 1qg8A c.68.1.1 34505 1fseA 74 3.02e+01 1fseA a.4.6.2 60000 1gkuB 1054 3.21e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1gl9B 1054 3.26e+01 c.37.1.16 65291 c.37.1.16 65292 e.10.1.1 65293 1qc7A 101 3.31e+01 1qc7A a.82.1.1 18456 1k44A 136 3.32e+01 1f3lA 321 3.41e+01 1g6q2 c.66.1.6 59630 1nsj 205 3.55e+01 1nsj c.1.2.4 28560 1tn4 159 3.58e+01 1ncx a.39.1.5 17248 1g3uA 214 3.68e+01 c.37.1.1 65132 1gtvA 214 3.68e+01 1c9fA 90 3.76e+01 1c9fA d.15.2.1 37639 1f2rC 87 3.79e+01 1c9fA d.15.2.1 37640 1le8A 53 3.93e+01 1vie 62 3.95e+01 1vie b.34.4.1 24592 1vif 62 3.95e+01 1vie b.34.4.1 24593 2dln 306 3.97e+01 1iow c.30.1.2 31715 d.142.1.1 41483 1iow 306 3.99e+01 1iow c.30.1.2 31713 d.142.1.1 41481