# List of top-scoring protein chains for t2k-100-30-bys-scores 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 1dvoA 152 5.95e-18 1dvoA a.136.1.1 19623 1x8bA 289 3.10e-01 1cv2A 296 3.94e-01 1bn6A c.69.1.8 34680 1iz7A 295 4.50e-01 c.69.1.8 76982 1mj5A 302 4.59e-01 c.69.1.8 91285 1jj2C 246 1.67e+00 1ffkC c.22.1.1 63087 1s72C 246 1.67e+00 c.22.1.1 105321 2ga1A 106 1.91e+00 1ge9A 184 1.93e+00 1dd5A d.67.3.1 60463 1jksA 294 2.28e+00 d.144.1.7 71710 1yr2A 741 2.56e+00 1a26 361 2.59e+00 1a26 a.41.1.1,d.166.1.2 17412,42274 1z1dA 103 2.66e+00 2anuA 255 2.84e+00 1vqoC 246 2.91e+00 1an7A 136 3.00e+00 1seiA d.140.1.1 41465 1dszB 85 3.13e+00 2nllB g.39.1.2 45108 1vgjA 184 3.78e+00 1pmzA 86 3.80e+00 a.39.1.10 104195 2gyqA 175 3.95e+00 2ffsA 157 4.04e+00 1efyA 350 4.17e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1kqfC 217 4.23e+00 f.21.1.1 72874 1by4A 82 4.36e+00 2nllB g.39.1.2 45110 1jr3D 343 5.02e+00 a.80.1.1,c.37.1.20 63251,63252 1ryp1 222 5.34e+00 1ryp1 1svfB 38 5.50e+00 1svfB h.3.2.1 45764 1r6vA 671 5.77e+00 1dpuA 99 5.81e+00 1dpuA a.4.5.16 16150 1uby 367 6.07e+00 1uby a.128.1.1 19435 1vdxA 184 6.08e+00 1qkrA 188 7.88e+00 1qkrA a.24.9.1 16628 2a6sA 84 8.10e+00 2flsA 132 8.21e+00 1tgoA 773 8.52e+00 1tgoA c.55.3.5,e.8.1.1 33721,43010 1mzbA 136 9.43e+00 a.4.5.42 91497 1pbjA 125 9.60e+00 d.37.1.1,d.37.1.1 94414,94415 1k9uA 78 1.00e+01 a.39.1.10 84348 1is1A 185 1.02e+01 d.67.3.1 83704 1v7cA 351 1.08e+01 c.79.1.1 100446 1pvmA 184 1.12e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1f53A 84 1.13e+01 1f53A b.11.1.4 23632 1bg1A 722 1.13e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1pme 380 1.14e+01 1hcl d.144.1.7 41653 1jqjC 343 1.15e+01 a.80.1.1,c.37.1.20 67097,67098 1tvoA 368 1.16e+01 1lcyA 325 1.18e+01 b.36.1.4,b.47.1.1 73834,73835 1o9gA 250 1.19e+01 c.66.1.29 86692 1td6A 306 1.21e+01 1i7qB 193 1.25e+01 1qdlB c.23.16.1 61902 2gwxA 267 1.25e+01 2prgA a.123.1.1 19323 2a74B 188 1.32e+01 2c8mA 262 1.34e+01 1ud0A 113 1.37e+01 a.8.4.1 99198 1hw1A 239 1.39e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1hg2A 289 1.39e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1hf8A 289 1.40e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2fswA 107 1.40e+01 1hg5A 289 1.42e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1k3rA 268 1.48e+01 b.40.4.10,c.116.1.2 72018,72019 1usyA 275 1.48e+01 1p4fA 293 1.50e+01 d.144.1.7 104063 1kzyC 259 1.50e+01 c.15.1.4,c.15.1.4 73383,73384 2ci9A 102 1.51e+01 1e2xA 243 1.52e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1qc7A 101 1.52e+01 1qc7A a.118.14.1 18456 1hqvA 191 1.52e+01 1hqvA a.39.1.8 61160 1ht9A 76 1.53e+01 4icb a.39.1.1 61252 1wraA 308 1.57e+01 1wmiA 90 1.59e+01 2bitX 165 1.64e+01 1q5dA 419 1.66e+01 a.104.1.1 95891 1a78A 134 1.67e+01 1c1lA b.29.1.3 24212 1kgnA 329 1.68e+01 a.25.1.2 68584 1lfo 128 1.70e+01 1hmt b.60.1.2 27223 2b7aA 293 1.72e+01 1yllA 200 1.73e+01 1xxqA 161 1.73e+01 1fgkA 310 1.76e+01 1fgkA d.144.1.7 41693 1w61A 414 1.76e+01 1xclA 235 1.84e+01 2bibA 547 1.95e+01 1r2fA 319 1.97e+01 1r2fA a.25.1.2 16800 1a2q 275 1.97e+01 1gci c.41.1.1 32512 3erk 364 1.98e+01 1hcl d.144.1.7 41654 1b43A 340 1.99e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1ak9 275 1.99e+01 1gci c.41.1.1 32517 1sup 275 2.01e+01 1gci c.41.1.1 32510 1aqn 275 2.13e+01 1gci c.41.1.1 32514 1u2zA 433 2.15e+01 c.66.1.31 107626 1lw6E 281 2.20e+01 c.41.1.1 74293 1vm7A 311 2.22e+01 c.72.1.1 108884 1g4yR 148 2.28e+01 1cll a.39.1.5 60252 1isaA 192 2.28e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1p1cA 199 2.31e+01 c.66.1.16 87669 1i1qB 192 2.31e+01 1qdlB c.23.16.1 61544 1jo0A 98 2.33e+01 d.68.4.1 77140 1ej6A 1289 2.36e+01 i.7.1.1 45967 1b63A 333 2.38e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 2cybA 323 2.46e+01 1to2E 281 2.47e+01 1j1bA 420 2.51e+01 d.144.1.7 90758 1v3wA 173 2.56e+01 b.81.1.5 100291 1ufbA 127 2.58e+01 a.24.16.3 99331 1iscA 192 2.59e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1gdc 72 2.59e+01 2nllB g.39.1.2 45127 2erbA 125 2.61e+01 1fps 348 2.61e+01 1uby a.128.1.1 19436 1erd 40 2.63e+01 1erd a.10.1.1 16362 2ff4A 388 2.65e+01 1wwiA 148 2.70e+01 1zelA 298 2.70e+01 1tbmA 326 2.73e+01 a.211.1.2 106744 2fneA 117 2.74e+01 1lj9A 144 2.76e+01 a.4.5.28 78035 2bl0C 142 2.81e+01 2bjqA 345 2.81e+01 1khhA 198 2.84e+01 c.66.1.16 68615 1brwA 433 2.85e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1jv1A 505 2.88e+01 c.68.1.5 71892 1ve3A 227 2.93e+01 1ffkC 246 2.94e+01 1ffkC c.22.1.1 31037 1y9zA 441 2.98e+01 1opc 110 2.99e+01 1opc a.4.6.1 16231 1gluA 81 3.00e+01 2nllB g.39.1.2 45124 1v6cA 441 3.01e+01 2ae2A 260 3.03e+01 1bdb c.2.1.2 29945 1yumA 242 3.04e+01 2fkbA 180 3.07e+01 2nllA 66 3.09e+01 2nllB g.39.1.2 45109 1khvA 516 3.09e+01 e.8.1.4 68627 1tdpA 111 3.11e+01 a.29.8.1 106781 1b1gA 75 3.11e+01 1psrA a.39.1.1 17151 1jgcA 161 3.11e+01 a.25.1.1 66673 1e4eA 343 3.13e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1kk8B 139 3.14e+01 a.39.1.5 77430 1ea7A 310 3.24e+01 c.41.1.1 70086 1m1hA 248 3.26e+01 b.114.1.1,d.58.42.1 78415,78416 1riqA 465 3.27e+01 a.203.1.1,d.104.1.1 97516,97517 1g0uL 241 3.28e+01 d.153.1.4 41894 1zx0A 236 3.28e+01 1o50A 157 3.28e+01 d.37.1.1,d.37.1.1 92478,92479 2ciaA 102 3.29e+01 1sgwA 214 3.34e+01 c.37.1.12 105541 1fhvA 323 3.41e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1wdcB 156 3.41e+01 1wdcB a.39.1.5 17302 1s01 283 3.43e+01 1gci c.41.1.1 32511 1o5iA 249 3.45e+01 c.2.1.2 92499 1tlqA 189 3.45e+01 a.195.1.1 107134 1te2A 226 3.48e+01 c.108.1.6 106792 1y6nL 145 3.53e+01 2cx5A 158 3.53e+01 1h0jA 60 3.53e+01 g.7.1.1 83432 1ujnA 348 3.60e+01 e.22.1.1 99460 1ov9A 50 3.62e+01 a.155.1.1 93591 1bc8C 93 3.62e+01 1awcA a.4.5.21 16168 1r6wA 322 3.67e+01 c.1.11.2,d.54.1.1 97165,97166 1gvnA 90 3.75e+01 a.8.2.1 76353 1g71A 347 3.75e+01 1g71A d.264.1.1 43268 1g2yA 32 3.75e+01 a.34.2.1 17003 1wyuB 474 3.86e+01 1jotA 133 3.89e+01 1jotA 1gw5B 591 3.90e+01 a.118.1.10 70630 1jpyB 137 3.92e+01 g.17.1.6 67066 1llfA 534 3.96e+01 c.69.1.17 78094 1thg 544 3.97e+01 1thg c.69.1.17 34763 1t06A 235 4.05e+01 a.118.1.17 106194 1lkvX 232 4.11e+01 a.118.14.1 73980 1tu5A 746 4.14e+01 1ucrA 78 4.15e+01 a.4.5.45 99188 1ialA 453 4.17e+01 1bk5A a.118.1.1 19116 1njrA 284 4.19e+01 c.50.1.2 103858 1z5hA 780 4.24e+01 1vloA 381 4.26e+01 b.44.2.1,d.250.1.1 108838,108839 1odd 118 4.30e+01 1opc a.4.6.1 16232 1uujA 88 4.36e+01 a.221.1.1 108046 1z9bA 135 4.36e+01 1t0qB 330 4.36e+01 a.25.1.2 106221 1ufaA 520 4.38e+01 a.8.3.3,c.6.2.4 99329,99330 1rykA 69 4.40e+01 a.60.11.1 98105 2arsA 262 4.41e+01 1q41A 424 4.45e+01 d.144.1.7 95774 1rxr 83 4.48e+01 2nllB g.39.1.2 45114 1bcfA 158 4.50e+01 1bcfA a.25.1.1 16648 1t3wA 148 4.51e+01 1ot5A 477 4.55e+01 b.18.1.20,c.41.1.1 87409,87410 1jajA 174 4.57e+01 d.218.1.2 66471 1gp4A 356 4.59e+01 b.82.2.1 65439 1glv 303 4.60e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1btu 240 4.62e+01 5ptp b.47.1.2 26241 1s9kD 53 4.68e+01 1vl6A 388 4.71e+01 c.2.1.7,c.58.1.3 108724,108725 1y9iA 178 4.72e+01 1ppjC 379 4.74e+01 f.32.1.1,f.21.1.2 104256,104257 2bzoB 79 4.81e+01 12asA 330 4.82e+01 12asA d.104.1.1 40783 1d3uB 201 4.89e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1rq6A 62 4.89e+01 1z6fA 363 4.89e+01 2feaA 236 4.92e+01 1wm3A 72 4.93e+01 1ugxA 133 4.98e+01 1yueA 427 5.01e+01 1f93E 32 5.03e+01 1f93E a.34.2.1 17013 1awqA 164 5.05e+01 2cpl b.62.1.1 27461 1b62A 349 5.05e+01 1b63A d.14.1.3,d.122.1.2 37567,41108 2ghsA 326 5.07e+01 1v8cA 168 5.08e+01 d.15.3.1,d.129.5.1 100495,100496 1nzoA 363 5.09e+01 b.105.1.1,e.3.1.1 92383,92384 1awsA 164 5.17e+01 2cpl b.62.1.1 27431 1gp6A 356 5.19e+01 b.82.2.1 65441 1kjwA 295 5.25e+01 b.34.2.1,c.37.1.1 68643,68644 1jacC 133 5.25e+01 1jotA 1usmA 80 5.30e+01 d.74.1.1 99876 1cwoA 165 5.35e+01 2cpl b.62.1.1 27445 1i7gA 287 5.38e+01 a.123.1.1 71121 1vdnA 162 5.39e+01 1kv9A 668 5.40e+01 a.3.1.6,b.70.1.1 73056,73057 1tca 317 5.41e+01 1tca c.69.1.17 34726 1tueA 212 5.44e+01 c.37.1.20 107323 1xauA 122 5.45e+01 1cleA 534 5.46e+01 1thg c.69.1.17 34771 1qvbA 481 5.50e+01 1qvbA c.1.8.4 28983 1qfoC 119 5.58e+01 1qfoA b.1.1.1 19710 2nllB 103 5.60e+01 2nllB g.39.1.2 45115 1v4aA 440 5.60e+01 a.24.16.4,d.218.1.9 108350,108351 1i50F 155 5.64e+01 a.143.1.2 61760 1rtxA 123 5.65e+01 a.1.1.1 97827 1m5yA 408 5.66e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1vkeA 133 5.68e+01 a.152.1.2 108650 1m26A 133 5.72e+01 1hr6B 443 5.78e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1s69A 124 5.84e+01 a.1.1.1 105305 1s6dA 103 5.86e+01 a.52.1.3 105307 1hbxG 157 5.88e+01 1awcA a.4.5.21 60934 1dazC 99 5.93e+01 1hvc b.50.1.1 26501 1v8yA 170 5.93e+01 2gsfA 373 5.94e+01 1scmB 145 5.96e+01 1wdcB a.39.1.5 17304 1hd8A 363 5.98e+01 b.105.1.1,e.3.1.1 65803,65804 1y0mA 61 5.99e+01 1pdnC 128 6.00e+01 6paxA a.4.1.5 16047 1um0A 365 6.00e+01 d.258.1.1 107942 1b0nB 57 6.02e+01 1b0nB a.34.1.1 17002 2f31B 20 6.02e+01 1ncg 110 6.06e+01 1edhA b.1.6.1 22193 1yc5A 246 6.15e+01 1jacA 133 6.17e+01 1jotA 1vcbB 112 6.17e+01 1vcbB d.42.1.1 38633 1c9bA 207 6.22e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1qfoA 119 6.23e+01 1qfoA b.1.1.1 19708 1vm8A 534 6.24e+01 1nj4A 363 6.26e+01 b.105.1.1,e.3.1.1 80545,80546 1qgtA 149 6.38e+01 1qgtA a.62.1.1 18135 2cosA 54 6.39e+01 1f1uA 323 6.41e+01 d.32.1.3,d.32.1.3 83200,83201 1ps1A 337 6.43e+01 1ps1A a.128.1.4 19450 1zs4A 83 6.45e+01 1rxxA 421 6.46e+01 d.126.1.4 98061 1fdo 715 6.53e+01 2napA b.52.2.2,c.81.1.1 26917,35325 1x2iA 75 6.54e+01 2bh8A 101 6.59e+01 1s7oA 113 6.60e+01 a.4.13.3 105354 1ku8A 133 6.60e+01 1a6aA 176 6.62e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 1fd9A 213 6.62e+01 1fd9A d.26.1.1 59771 2cpl 165 6.66e+01 2cpl b.62.1.1 27420 1n5nA 180 6.67e+01 d.167.1.1 85336 1be3C 379 6.67e+01 1be3C f.32.1.1,f.21.1.2 75805,75806 1fneA 192 6.68e+01 1iakA b.1.1.2,d.19.1.1 59896,59897 1yndA 165 6.72e+01 2a8mA 420 6.83e+01 2fhzB 108 6.85e+01 1yruB 74 6.87e+01 2fnjC 96 6.90e+01 1kgsA 225 6.91e+01 a.4.6.1,c.23.1.1 68596,68597 2comA 124 6.98e+01 1f1xA 322 6.99e+01 d.32.1.3,d.32.1.3 83208,83209 2bwnA 401 7.00e+01 1qydA 313 7.01e+01 c.2.1.2 96583 1ywpA 64 7.05e+01 1xneA 113 7.07e+01 1n00A 321 7.15e+01 a.65.1.1 85241 1p6pA 125 7.18e+01 b.60.1.2 87839 1mkaA 171 7.25e+01 1mkaA d.38.1.2 38543 1ieaA 192 7.26e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 1ug4A 60 7.32e+01 1duxC 94 7.39e+01 1awcA a.4.5.21 16170 1latA 82 7.41e+01 2nllB g.39.1.2 45122 1nciA 110 7.44e+01 1edhA b.1.6.1 22191 1quqB 121 7.45e+01 1quqB b.40.4.3 25305 1ig5A 75 7.45e+01 4icb a.39.1.1 62363 2azqA 311 7.49e+01 1b67A 68 7.51e+01 1a7w a.22.1.2 16474 1xuqA 212 7.57e+01 1rfzA 168 7.57e+01 a.195.1.1 97411 1cx0A 95 7.58e+01 1urnA d.58.7.1 39158 1qp8A 303 7.58e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 2fp7B 172 7.61e+01 1a58 177 7.63e+01 2cpl b.62.1.1 27495 1hta 69 7.64e+01 1a7w a.22.1.2 16476 1qhtA 775 7.64e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1bd3A 243 7.68e+01 1bd3A c.61.1.1 34098 1twfF 155 7.68e+01 1jxmA 301 7.69e+01 b.34.2.1,c.37.1.1 67420,67421 3lynA 136 7.70e+01 1lis a.19.1.1 16413 1jpaA 312 7.70e+01 d.144.1.7 67011 1xvaA 292 7.70e+01 1xvaA c.66.1.5 34183 2av5A 120 7.75e+01 1ihgA 370 7.79e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2a8kA 108 7.81e+01 1rm6C 161 7.83e+01 2ftbA 125 7.86e+01 2b5gA 171 7.91e+01 1wosA 364 8.00e+01 b.44.2.1,d.250.1.1 109468,109469 1dmhA 311 8.00e+01 1dmhA b.3.6.1 22633 1bkb 136 8.00e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 4icb 76 8.02e+01 4icb a.39.1.1 17145 1yv5A 374 8.04e+01 1hyt 316 8.06e+01 1hyt d.92.1.2 59005 2tmp 127 8.08e+01 1br9 b.40.3.1 25236 1qk8A 146 8.08e+01 1ewxA c.47.1.10 33061 2bapC 56 8.08e+01 1fngA 192 8.12e+01 1iakA b.1.1.2,d.19.1.1 59904,59905 1l1dA 152 8.14e+01 b.88.1.3 73452 1zvdA 380 8.14e+01 2bo4A 397 8.14e+01 1qu9A 128 8.16e+01 1qu9A d.79.1.1 39755 1qu9C 128 8.16e+01 1qu9A d.79.1.1 39757 1mldA 314 8.17e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1p8cA 145 8.18e+01 a.152.1.2 94354 1a9nB 96 8.18e+01 1urnA d.58.7.1 39165 2b1xA 470 8.22e+01 1b65A 375 8.23e+01 1b65A d.154.1.1 42020 1xwrA 97 8.32e+01 1audA 101 8.32e+01 1urnA d.58.7.1 39156 1ys1X 320 8.33e+01 2c1vA 338 8.37e+01 1sr8A 298 8.51e+01 e.54.1.1 105959 1zgyA 272 8.51e+01 1m2oB 190 8.54e+01 c.37.1.8 78485 1d2gA 292 8.60e+01 1xvaA c.66.1.5 34187 1jpyA 137 8.60e+01 g.17.1.6 67065 1e0cA 271 8.60e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1aqdA 192 8.61e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1pvaA 110 8.63e+01 1a75A a.39.1.4 17207 1nct 106 8.63e+01 1wit b.1.1.4 21708 1uw4A 91 8.67e+01 d.58.7.4 100071 1gvkB 240 8.68e+01 b.47.1.2 70610 1yf3A 259 8.85e+01 1g5gA 481 8.86e+01 f.12.1.1,h.3.2.1 65155,65156 1v4xB 146 8.87e+01 a.1.1.2 108364 2a9gA 418 8.88e+01 1woqA 267 8.90e+01 c.55.1.10,c.55.1.10 109462,109463 2be4A 272 8.91e+01 1vpbA 451 8.92e+01 1rz4A 226 8.96e+01 a.4.5.53,a.118.1.18 105131,105132 1bouB 302 8.97e+01 1bouB c.56.6.1 33859 1pjhA 280 8.99e+01 c.14.1.3 94761 1awcA 110 9.00e+01 1awcA a.4.5.21 16167