# List of top-scoring protein chains for t04-100-30-alpha-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 1oa4A 222 2.44e-01 b.29.1.11 86731 1a65A 504 2.54e-01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1rvaA 244 2.63e-01 1rvaA c.52.1.2 33240 1hfuA 503 3.30e-01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 2b0mA 393 4.87e-01 1zclA 180 5.28e-01 1d3gA 367 6.25e-01 1d3gA c.1.4.1 28600 1yvvA 336 6.40e-01 1y71A 130 7.55e-01 1sx5A 244 7.73e-01 c.52.1.2 99023 1vqqA 646 9.01e-01 1bpyA 335 9.98e-01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1twyA 290 1.02e+00 1qwtA 255 1.04e+00 b.26.1.3 96501 1uumA 372 1.22e+00 c.1.4.1 100010 1rztA 331 1.40e+00 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1md6A 154 1.78e+00 b.42.1.2 91242 1nt0A 286 1.94e+00 b.23.1.1,b.23.1.1,g.3.11.1 86143,86144,86145 1wsrA 375 2.14e+00 1wtaA 275 2.34e+00 1pm4A 119 2.35e+00 b.135.1.1 94891 1tv9A 335 2.43e+00 2fe5A 94 2.46e+00 1e3aB 560 2.58e+00 1ajqB 1cpo 299 2.67e+00 1cpo a.39.3.1,a.39.3.1 17390,17391 2tmdA 729 2.73e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 2fmpA 335 2.74e+00 1o94A 729 2.87e+00 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1gk9B 557 2.96e+00 1e0cA 271 3.08e+00 1e0cA c.46.1.2,c.46.1.2 32717,32718 1u2fA 90 3.23e+00 1u2fA d.58.7.1 39168 1gttA 429 3.26e+00 d.177.1.1,d.177.1.1 70529,70530 2cqeA 98 3.34e+00 1u3oA 82 3.42e+00 1yrrA 382 3.43e+00 1wocA 103 3.43e+00 1rf6A 427 3.66e+00 d.68.2.2 97366 1djqA 729 3.74e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1c1lA 136 3.75e+00 1c1lA b.29.1.3 24219 1xsnA 335 3.78e+00 1djnA 729 3.79e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1i7oA 429 3.93e+00 1i7oA d.177.1.1,d.177.1.1 61893,61894 1rxdA 159 4.02e+00 1tueA 212 5.55e+00 c.37.1.20 107323 1txyA 104 5.57e+00 1eonA 245 5.86e+00 1rvaA c.52.1.2 33238 1m8uA 173 6.71e+00 b.11.1.1,b.11.1.1 91233,91234 1p1cA 199 6.91e+00 c.66.1.16 87669 2bcqA 335 6.94e+00 1pvxA 194 7.50e+00 1axkA b.29.1.11 24341 1is3A 135 7.52e+00 b.29.1.3 76773 1yge 839 7.56e+00 1yge a.119.1.1,b.12.1.1 19234,23634 1tr7A 164 7.60e+00 1gqzA 274 7.71e+00 d.21.1.1,d.21.1.1 83311,83312 1sqjA 789 7.96e+00 b.69.13.1,b.69.13.1 105918,105919 1oh0A 131 8.02e+00 d.17.4.3 87004 2gkeA 274 8.27e+00 1kcfA 258 8.46e+00 a.140.2.1,c.55.3.7 68434,68435 1na6A 404 8.46e+00 b.142.1.1,c.52.1.22 91748,91749 1eu8A 409 8.72e+00 1eu8A c.94.1.1 59502 1paz 123 9.01e+00 1bqk b.6.1.1 22878 1lo6A 223 9.31e+00 b.47.1.2 74143 1o6dA 163 9.34e+00 c.116.1.3 92567 1v5vA 401 9.37e+00 1cskA 71 9.48e+00 1ckaA b.34.2.1 24513 1bf5A 545 9.64e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1uwfA 158 9.83e+00 1x24A 180 1.06e+01 1wk2A 121 1.06e+01 4ubpB 126 1.11e+01 1ubpB b.85.3.1 28345 1wyxA 69 1.12e+01 1l6pA 125 1.12e+01 b.1.17.1 73626 1sxvA 172 1.15e+01 1bwzA 274 1.15e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 2nlrA 234 1.18e+01 2nlrA b.29.1.11 24344 1g0xA 197 1.23e+01 1nkr b.1.1.4,b.1.1.4 21805,21806 1qunB 279 1.26e+01 b.2.3.2,b.2.3.2 22411,22412 2adgA 214 1.35e+01 1kutA 230 1.36e+01 d.143.1.1 73017 1q33A 292 1.44e+01 d.113.1.1 95657 2ahmE 203 1.46e+01 1xmkA 79 1.51e+01 2b4wA 315 1.52e+01 1qfoA 119 1.52e+01 1qfoA b.1.1.1 19708 2bjfA 329 1.53e+01 1zckA 154 1.69e+01 1nb9A 147 1.73e+01 b.43.5.1 85515 1u6zA 513 1.74e+01 1spjA 238 1.76e+01 1h6zA 913 1.78e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1v0jA 399 1.81e+01 2dp5A 332 1.84e+01 1ukmB 128 1.85e+01 d.169.1.1 99500 1lkqA 21 1.86e+01 1q45A 391 1.86e+01 c.1.4.1 95780 1fi8A 228 1.87e+01 5ptp b.47.1.2 26374 1klfB 279 1.88e+01 b.2.3.2,b.2.3.2 72684,72685 1ov3A 138 1.94e+01 b.34.2.1,b.34.2.1 87451,87452 1v1qA 134 1.99e+01 2az4A 429 2.00e+01 1ko3A 230 2.06e+01 d.157.1.1 90974 1pidA 21 2.07e+01 1r4pA 297 2.10e+01 d.165.1.2 97025 1wojA 214 2.11e+01 1q4vA 21 2.12e+01 1xe1A 116 2.13e+01 b.43.3.1 109571 1cmiA 85 2.19e+01 1cmiA d.39.1.1 38551 1opy 131 2.22e+01 1opy d.17.4.3 38113 1b06A 210 2.24e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1wlpB 138 2.25e+01 1zy1B 197 2.25e+01 1lktA 104 2.33e+01 1lktA b.90.1.1 28398 1qqp4 85 2.36e+01 1qqp4 1v7pB 128 2.36e+01 d.169.1.1 108407 1jcaA 21 2.43e+01 1yh6A 179 2.45e+01 1bs0A 384 2.46e+01 1bs0A c.67.1.4 34490 1iohA 21 2.51e+01 1i8kA 107 2.55e+01 b.1.1.1 71130 2gcfA 73 2.55e+01 1oqvA 192 2.56e+01 d.24.1.2 87320 1g7aA 21 2.57e+01 1xclA 235 2.60e+01 1w0nA 131 2.62e+01 1dmmA 131 2.62e+01 1opy d.17.4.3 38114 1rweA 21 2.64e+01 1rdfA 267 2.64e+01 c.108.1.3 104884 2bjhA 260 2.87e+01 1nlnA 204 2.90e+01 d.3.1.7 91962 1msoA 21 2.92e+01 1yna 194 2.94e+01 1axkA b.29.1.11 24335 1x3eA 165 2.97e+01 1cjaA 342 2.98e+01 1cjaA d.144.1.3 41708 2aegA 268 3.07e+01 1evxA 162 3.07e+01 1a73A d.4.1.3 37149 1s1hM 132 3.12e+01 i.1.1.1 105165 2evrA 246 3.12e+01 1vqb 87 3.20e+01 1gvp b.40.4.7 25370 1wj9A 211 3.22e+01 1zxzA 197 3.24e+01 1xw7A 21 3.26e+01 1e0gA 48 3.27e+01 1e01A d.7.1.1 37325 1fonA 240 3.30e+01 5ptp b.47.1.2 26231 1xypA 190 3.34e+01 1axkA b.29.1.11 24327 2csoA 127 3.35e+01 1w6vA 141 3.37e+01 1l7dA 384 3.37e+01 c.2.1.4,c.23.12.2 77774,77775 1mqeA 207 3.41e+01 d.113.1.1 91394 5reqA 727 3.41e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1j55A 95 3.43e+01 a.39.1.2 77078 1uwcA 261 3.44e+01 c.69.1.17 100101 2bydA 323 3.47e+01 1gcb 454 3.55e+01 3gcb d.3.1.1 37034 1lk9A 448 3.57e+01 c.67.1.1 78057 1j2gA 319 3.57e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 2g1lA 104 3.70e+01 1se8A 301 3.70e+01 b.40.4.3 105448 1tit 98 3.73e+01 1tit b.1.1.4 21716 1fezA 256 3.73e+01 1fezA c.108.1.3 43343 1k3mA 21 3.74e+01 1fo4A 1332 3.75e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1jjzA 29 3.79e+01 g.3.3.1 71699 1pc3A 350 3.80e+01 c.94.1.1 104102 1v97A 1332 3.82e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1ema 236 3.85e+01 1ema d.22.1.1 38339 1qlaA 656 3.86e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 3gcb 470 3.86e+01 3gcb d.3.1.1 37032 2bs3A 656 3.87e+01 1xjuA 163 3.87e+01 2hlcA 230 3.92e+01 5ptp b.47.1.2 26074 1m6dA 214 3.94e+01 d.3.1.1 84849 1reoA 486 4.02e+01 c.3.1.2,d.16.1.5 97325,97326 1a8p 258 4.12e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1ng2A 193 4.22e+01 b.34.2.1,b.34.2.1 85660,85661 2covD 104 4.23e+01 2fauA 341 4.23e+01 1kk1A 410 4.24e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1a73A 163 4.25e+01 1a73A d.4.1.3 37145 1el5A 389 4.26e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 2a74C 343 4.31e+01 1swvA 267 4.35e+01 1jhnA 424 4.35e+01 b.104.1.1,b.29.1.12 66722,70060 1q2yA 140 4.35e+01 d.108.1.1 95655 1eajA 126 4.37e+01 1f5wA b.1.1.1 59401 1qwnA 1045 4.41e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1wmxA 205 4.46e+01 b.18.1.24 109418 1fmb 104 4.59e+01 1fmb b.50.1.1 26777 2rn2 155 4.68e+01 2rn2 c.55.3.1 33551 1p5hA 428 4.72e+01 c.123.1.1 87802 1ireB 228 4.72e+01 b.34.4.4 76770 1a70 97 4.72e+01 1awd d.15.4.1 37678 1hdfA 102 4.72e+01 1ag4 b.11.1.1 23627 1q9jA 422 4.78e+01 c.43.1.2,c.43.1.2 104590,104591 1mo9A 523 4.79e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2bcmA 165 4.80e+01 1yjdC 140 4.83e+01 1rvkA 382 4.85e+01 c.1.11.2,d.54.1.1 97928,97929 1cb0A 283 4.86e+01 1cb0A c.56.2.1 33790 1avpA 204 4.91e+01 1avpA d.3.1.7 37132 1gpc 218 4.97e+01 1gpc b.40.4.7 25393 1vkpA 383 5.01e+01 d.126.1.6 108686 1dp4A 435 5.01e+01 1dp4A c.93.1.1 35710 2rslA 140 5.13e+01 2rslA c.53.1.1 33345 2aq5A 402 5.18e+01 2gzqA 200 5.20e+01 1reqA 727 5.26e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1xvsA 126 5.27e+01 1u5dA 108 5.27e+01 1ahsA 126 5.30e+01 1ahsA b.19.1.1 23794 1tjyA 316 5.31e+01 c.93.1.1 107062 2fdbM 164 5.34e+01 2a1vA 144 5.44e+01 1gvp 87 5.48e+01 1gvp b.40.4.7 25369 2crbA 97 5.48e+01 1bw0A 416 5.53e+01 1bw0A c.67.1.1 34385 1l2lA 457 5.64e+01 c.72.1.3 77656 1eaf 243 5.72e+01 1eaf c.43.1.1 32617 1htyA 1015 5.77e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 2ajuL 216 5.79e+01 1ztxE 108 5.80e+01 1ppn 212 5.81e+01 1cs8A d.3.1.1 37004 1c3cA 429 5.89e+01 1c3cA a.127.1.1 19425 1flcB 175 5.91e+01 1flcB h.3.1.1 45716 1wzzA 334 5.95e+01 1os8A 223 5.96e+01 b.47.1.1 93481 1eazA 125 5.98e+01 b.55.1.1 70113 1yo3A 102 6.02e+01 1ifrA 121 6.02e+01 b.1.16.1 71203 1faoA 126 6.04e+01 1faoA b.55.1.1 26974 1zx0A 236 6.07e+01 1ncwH 222 6.09e+01 b.1.1.1,b.1.1.2 85555,85556 2c43A 323 6.13e+01 1m40A 263 6.15e+01 e.3.1.1 74437 1ogaD 215 6.15e+01 b.1.1.1,b.1.1.2 86990,86991 1agjA 242 6.15e+01 1agjA b.47.1.1 25827 1hn3A 40 6.18e+01 j.91.1.1 65892 1wznA 252 6.20e+01 1yt8A 539 6.21e+01 1bb9 115 6.22e+01 1bb9 b.34.2.1 24554 1ermA 263 6.25e+01 1btl e.3.1.1 42690 1sd4A 126 6.31e+01 a.4.5.39 105428 1xg8A 111 6.40e+01 1vi6A 208 6.41e+01 c.23.15.1 100736 1m9zA 111 6.42e+01 g.7.1.3 78881 1ilr1 152 6.43e+01 1irp 1umgA 362 6.49e+01 d.280.1.1 107956 1i0lA 221 6.53e+01 c.61.1.1 71096 1sgt 223 6.59e+01 5ptp b.47.1.1 25814 1btl 263 6.61e+01 1btl e.3.1.1 42691 2bbhA 269 6.71e+01 1khqA 212 6.73e+01 d.3.1.1 90964 1gxrA 337 6.73e+01 b.69.4.1 70722 2bkaA 242 6.80e+01 1lvwA 295 6.82e+01 c.68.1.6 84723 1elvA 333 6.83e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1i6pA 220 6.83e+01 1ddzA c.53.2.1 61848 1uisA 231 6.86e+01 d.22.1.1 99431 1a53 247 6.88e+01 1a53 c.1.2.4 28564 1upiA 225 6.96e+01 b.82.1.1 99757 2cioA 212 6.97e+01 2d3jA 157 7.00e+01 2fneA 117 7.05e+01 2cb5A 453 7.09e+01 3gcb d.3.1.1 37035 1y7bA 542 7.10e+01 1n08A 163 7.10e+01 b.43.5.1 79730 2bn3A 21 7.15e+01 1kn6A 90 7.15e+01 d.58.3.3 72770 1oyc 400 7.15e+01 1oyc c.1.4.1 28603 1oxdA 227 7.24e+01 d.22.1.1 93687 1uwsA 489 7.26e+01 c.1.8.4 108073 1lf2A 331 7.27e+01 b.50.1.2 77914 1sgoA 139 7.27e+01 d.82.3.1 98857 2a8yA 270 7.28e+01 1gvhA 396 7.34e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1yqzA 438 7.35e+01 1dro 122 7.41e+01 1btn b.55.1.1 26954 1vjvA 415 7.42e+01 d.3.1.9 108632 1eemA 241 7.45e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1zirA 173 7.46e+01 1rovA 857 7.58e+01 a.119.1.1,b.12.1.1 97674,97675 1qmyA 167 7.59e+01 1qmyA d.3.1.2 37094 1vm6A 228 7.60e+01 c.2.1.3,d.81.1.3 108876,108877 1vp6A 138 7.69e+01 1iogA 21 7.70e+01 1ugpB 226 7.72e+01 b.34.4.4 107832 2g6yA 217 7.87e+01 1r1gA 31 7.89e+01 g.3.7.2 96816 2a74A 643 7.92e+01 2azwA 148 7.93e+01 1rw2A 152 7.93e+01 a.118.19.1 97961 1ngzA 213 7.95e+01 b.1.1.1,b.1.1.2 80500,80501 1h8gA 95 8.06e+01 b.109.1.1 65735 1nw1A 429 8.10e+01 d.144.1.8 86286 1tksA 204 8.15e+01 d.115.1.2 107114 1dleA 298 8.16e+01 1dleA b.47.1.2 26312 1neu 124 8.23e+01 1neu b.1.1.1 19704 1bqyA 234 8.36e+01 5ptp b.47.1.2 26332 1zpuA 534 8.38e+01 1h2bA 359 8.40e+01 b.35.1.2,c.2.1.1 90543,90544 1cghA 224 8.44e+01 1a7s b.47.1.2 26290 1usuB 170 8.48e+01 d.83.2.1 99886 2g3aA 152 8.52e+01 1fzoA 274 8.56e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1pwhA 327 8.61e+01 c.79.1.1 95224 1g31A 111 8.66e+01 1g31A b.35.1.1 24656 1y96A 86 8.67e+01 2atvA 196 8.68e+01 1xa0A 328 8.70e+01 1rqlA 267 8.80e+01 c.108.1.3 97750 1ztcA 221 8.83e+01 1f8rA 498 8.84e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1v88A 130 8.87e+01 b.55.1.1 108423 2bmeA 186 8.87e+01 1mtyD 512 8.90e+01 1mhyD a.25.1.2 16742