# List of top-scoring protein chains for t2k-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 1wolA 122 3.15e-19 1ufbA 127 1.24e-15 a.24.16.3 99331 1o3uA 135 2.26e-13 a.24.16.3 86615 1h1wA 289 9.50e-02 d.144.1.7 83460 1uu3A 310 2.11e-01 d.144.1.7 99999 1a17 166 1.44e+00 1a17 a.118.8.1 19206 1d4aA 273 2.46e+00 1d4aA c.23.5.3 31219 1kbqA 273 2.52e+00 c.23.5.3 68391 1qbgA 272 2.63e+00 1d4aA c.23.5.3 31227 1xrhA 351 2.70e+00 1wwpA 119 2.75e+00 3grx 82 2.76e+00 1aba c.47.1.1 32769 1khoA 370 2.80e+00 a.124.1.1,b.12.1.3 72489,72490 1gs5A 258 3.02e+00 c.73.1.2 70395 1n5dA 288 3.04e+00 c.2.1.2 80030 1hu4A 288 3.04e+00 1hu4A 1na3A 91 3.15e+00 k.38.1.1 85481 2cfuA 658 3.26e+00 2anxA 146 3.56e+00 1knzA 164 3.77e+00 e.34.1.1 68709 1v3wA 173 4.04e+00 b.81.1.5 100291 2frvB 536 4.15e+00 1h2rL e.18.1.1 43291 2e2aA 105 4.42e+00 a.7.2.1 88499 1e2aA 105 4.42e+00 1e2aA a.7.2.1 16322 2evrA 246 4.60e+00 1frvB 536 4.63e+00 1h2rL e.18.1.1 43296 1dlc 584 5.21e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1b8aA 438 5.24e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ca1 370 5.35e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 2avpA 70 5.36e+00 16vpA 366 5.59e+00 16vpA d.180.1.1 42601 1q0sA 259 6.25e+00 c.66.1.28 95509 1eg7A 557 6.52e+00 1eg7A c.37.1.10 32241 1wkbA 810 6.54e+00 1ji6A 589 7.12e+00 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1yf3A 259 7.26e+00 1elwA 118 7.28e+00 1a17 a.118.8.1 19207 1yn9A 169 8.22e+00 1wtyA 119 8.38e+00 1zq4A 693 9.24e+00 1y21A 282 9.64e+00 1u5dA 108 9.70e+00 1qhdA 398 9.86e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1si6X 282 1.06e+01 2ag5A 246 1.06e+01 1ntfA 282 1.08e+01 d.151.1.2 92104 1k47A 337 1.13e+01 d.14.1.5,d.58.26.4 72040,72041 1tzvA 142 1.16e+01 a.79.1.1 107526 1v7nV 163 1.26e+01 a.26.1.2 100476 1usmA 80 1.33e+01 d.74.1.1 99876 1uwkA 557 1.34e+01 e.51.1.1 108065 1gtxA 472 1.37e+01 1gtxA 1s5lE 84 1.38e+01 2axtE 84 1.45e+01 1p4xA 250 1.47e+01 a.4.5.28,a.4.5.28 87784,87785 2g0qA 173 1.48e+01 1hhsA 664 1.56e+01 1hi0P e.8.1.6 61045 1uvjA 664 1.60e+01 e.8.1.6 100045 1x92A 199 1.64e+01 2a61A 145 1.67e+01 1mwwA 128 1.69e+01 d.80.1.4 91483 1ohvA 472 1.74e+01 c.67.1.4 93031 1wcrA 103 1.74e+01 2crbA 97 1.79e+01 1v52A 133 1.80e+01 1tph1 247 1.82e+01 1amk 2djkA 133 1.84e+01 1hzdA 272 1.85e+01 c.14.1.3 65969 1xdfA 157 1.87e+01 2chgA 226 1.90e+01 3thiA 371 1.93e+01 2thiA c.94.1.1 35792 1w3iA 293 1.97e+01 c.1.10.1 109152 1hi0P 664 2.01e+01 1hi0P e.8.1.6 61051 1tueB 218 2.02e+01 b.91.1.1 107324 1o7fA 469 2.02e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1siqA 392 2.05e+01 a.29.3.1,e.6.1.1 105585,105586 2g03A 194 2.12e+01 2c31A 568 2.13e+01 2eshA 118 2.16e+01 1zrzA 364 2.17e+01 1qcrF 103 2.18e+01 1be3F f.27.1.1 43676 1kamA 194 2.20e+01 c.26.1.3 72254 1wmaA 276 2.22e+01 4pfk 319 2.24e+01 3pfk c.89.1.1 35582 1pmzA 86 2.27e+01 a.39.1.10 104195 1d7mA 101 2.30e+01 1d7mA h.1.10.1 45628 1mvoA 136 2.36e+01 c.23.1.1 79513 1kr7A 110 2.38e+01 a.1.1.4 72890 2fsrA 195 2.40e+01 1am9A 82 2.40e+01 1am9A a.38.1.1 17140 1lox 662 2.40e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1yc9A 442 2.46e+01 3pfk 319 2.46e+01 3pfk c.89.1.1 35581 1ppjF 110 2.50e+01 f.27.1.1 104262 1mo0A 275 2.50e+01 c.1.1.1 79329 2thiA 379 2.51e+01 2thiA c.94.1.1 35794 1jx6A 342 2.52e+01 c.93.1.1 67406 1cw0A 155 2.55e+01 1vsrA c.52.1.15 33333 1xg2B 153 2.56e+01 1l7bA 92 2.59e+01 c.15.1.2 91053 1sflA 238 2.59e+01 1azo 232 2.60e+01 1azo c.52.1.14 33329 1a8y 367 2.62e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2bf9A 36 2.64e+01 1rljA 139 2.73e+01 c.23.5.7 104983 1x6vA 630 2.73e+01 1dd5A 185 2.75e+01 1dd5A d.67.3.1 39564 1e8yA 966 2.78e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1f16A 192 2.80e+01 1f16A f.1.4.1 43400 1a6r 471 2.86e+01 3gcb d.3.1.1 37033 2b0jA 358 2.87e+01 3gcb 470 2.93e+01 3gcb d.3.1.1 37032 1anv 356 2.95e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17890,45365,45371 1j30A 144 2.97e+01 a.25.1.1 90806 1senA 164 3.04e+01 c.47.1.1 105465 1hh1A 143 3.05e+01 1gefA c.52.1.18 61036 1d7kA 421 3.09e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1qwiA 143 3.10e+01 d.227.1.1 96474 1uklC 61 3.16e+01 a.38.1.1 99495 1e7uA 961 3.16e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1ymtA 246 3.17e+01 1w5cE 84 3.19e+01 1ppt 36 3.23e+01 1ppt j.6.1.1 46089 1i5pA 633 3.25e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1izmA 184 3.28e+01 a.199.1.1 90725 1r2rA 248 3.36e+01 c.1.1.1 96875 1adt 356 3.40e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17887,45362,45368 2ftzA 284 3.40e+01 1dmmA 131 3.47e+01 1opy d.17.4.3 38114 1be3F 110 3.50e+01 1be3F f.27.1.1 43668 1jcdA 52 3.53e+01 h.1.16.1 84157 1vzjA 40 3.58e+01 1s3cA 141 3.60e+01 1i60A 278 3.68e+01 c.1.15.4 71118 1om2A 95 3.75e+01 1om2A a.23.4.1 16520 1o5hA 214 3.75e+01 a.191.1.1 92497 2pgd 482 3.80e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1wbeA 209 3.85e+01 1gcb 454 3.92e+01 3gcb d.3.1.1 37034 1n3lA 372 3.92e+01 c.26.1.1 79966 1jagA 241 3.95e+01 c.37.1.1 66463 1t7pA 698 3.95e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1kmiZ 214 4.00e+01 h.4.11.1 72752 1fz1C 389 4.02e+01 1mtyB a.25.1.2 16746 1is1A 185 4.03e+01 d.67.3.1 83704 1o1xA 155 4.07e+01 c.121.1.1 86553 1sfjA 238 4.08e+01 1qysA 106 4.10e+01 k.41.1.1 96603 1u60A 310 4.11e+01 e.3.1.2 107692 1bxkA 355 4.14e+01 1bxkA c.2.1.2 29803 1j9bA 141 4.16e+01 c.47.1.12 66459 1opy 131 4.23e+01 1opy d.17.4.3 38113 1huxA 270 4.26e+01 1huxA c.55.1.5 61278 1tfjA 219 4.29e+01 1cjcA 460 4.42e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1wd6A 123 4.43e+01 1vpqA 273 4.46e+01 2cq2A 114 4.56e+01 1rkbA 173 4.58e+01 2arkA 188 4.68e+01 1ea2A 131 4.72e+01 d.17.4.3 64860 1ihgA 370 4.84e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1ti6A 875 4.85e+01 b.52.2.2,c.81.1.1 106974,106975 1e19A 314 5.00e+01 1b7bA c.73.1.1 34967 1qo0D 196 5.04e+01 1qo0D c.23.1.3 31125 1ireB 228 5.05e+01 b.34.4.4 76770 1atg 231 5.09e+01 1atg c.94.1.1 35834 1e8xA 961 5.12e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1mldA 314 5.24e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1np6A 174 5.26e+01 c.37.1.10 85954 1i36A 264 5.27e+01 a.100.1.8,c.2.1.6 71108,71109 3mdeA 385 5.28e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 1d3yA 301 5.28e+01 1d3yA e.12.1.1 43252 1wt4A 73 5.29e+01 2a7kA 250 5.31e+01 1hfuA 503 5.32e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1ooeA 236 5.33e+01 c.2.1.2 87196 1ugpB 226 5.35e+01 b.34.4.4 107832 1a65A 504 5.35e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1io7A 368 5.45e+01 1f4tA a.104.1.1 18971 1qq9A 284 5.46e+01 1xjo c.56.5.4 33841 2cyjA 118 5.47e+01 1liaA 164 5.53e+01 1cpcA a.1.1.3 15661 1e3aA 260 5.54e+01 1ajqA d.153.1.2 41838 1womA 271 5.56e+01 1b8oA 284 5.58e+01 1b8oA c.56.2.1 33762 1iioA 84 5.59e+01 a.39.4.1 66150 1tkjA 284 5.67e+01 1f1eA 154 5.70e+01 a.22.1.2 64927 1rcy 151 5.76e+01 1rcy b.6.1.1 23018 1a3z 155 5.87e+01 1rcy b.6.1.1 23019 1swxA 209 5.93e+01 a.224.1.1 106075 2b2hA 399 5.93e+01 1x9mA 698 5.94e+01 1xjo 284 5.97e+01 1xjo c.56.5.4 33843 1myt 146 6.05e+01 1a6m a.1.1.2 15207 1ltlA 279 6.07e+01 b.40.4.11 84701 2genA 197 6.11e+01 1wdtA 665 6.14e+01 1np8A 159 6.14e+01 a.39.1.8 92022 1tf9A 284 6.20e+01 1iujA 106 6.20e+01 d.58.4.5 90701 2b5eA 504 6.25e+01 1c1gA 284 6.29e+01 1c1gA h.1.5.1 45573 1jfgA 374 6.33e+01 a.128.1.5 66636 1ev7A 317 6.34e+01 1ev7B c.52.1.9 33315 1qnxA 209 6.39e+01 1qnxA d.111.1.1 40914 1pprM 312 6.46e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1ajqA 209 6.46e+01 1ajqA d.153.1.2 41840 1c1gC 284 6.49e+01 1c1gA h.1.5.1 45575 1gz5A 456 6.49e+01 c.87.1.6 76406 1xmaA 145 6.58e+01 1krhA 338 6.68e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1fjkA 52 6.69e+01 1fjkA j.37.1.1 46288 1zxxA 319 6.75e+01 1ii2A 524 6.77e+01 c.91.1.1,c.109.1.1 66146,66147 1jfaA 374 6.88e+01 a.128.1.5 66622 1x79B 112 6.92e+01 1puc 105 6.93e+01 1puc d.97.1.1 40675 2g7gA 213 7.00e+01 1c1gD 284 7.00e+01 1c1gA h.1.5.1 45576 163l 164 7.04e+01 1l92 d.2.1.3 36658 1ouvA 273 7.04e+01 a.118.18.1 93570 1oshA 232 7.11e+01 a.123.1.1 93496 1mmoB 384 7.19e+01 1mtyB a.25.1.2 16768 1ah7 245 7.20e+01 1ah7 a.124.1.1 19339 1x6mA 196 7.22e+01 1c1gB 284 7.25e+01 1c1gB h.1.5.1 45574 1b8dA 164 7.32e+01 1cpcA a.1.1.3 15665 1uqtA 482 7.38e+01 c.87.1.6 99794 1p5zB 263 7.40e+01 c.37.1.1 87815 1mngA 203 7.42e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1weuA 91 7.48e+01 2f6sA 201 7.51e+01 1xsnA 335 7.51e+01 1enp 312 7.53e+01 1enp c.2.1.2 29906 1lxjA 104 7.53e+01 d.58.48.1 84736 1evsA 187 7.54e+01 1evsA a.26.1.1 16845 1adeA 431 7.55e+01 1adeA c.37.1.10 32213 1ci4A 89 7.56e+01 1qckA a.60.5.1 17970 1sjiA 350 7.59e+01 1t46A 313 7.62e+01 d.144.1.7 106397 1wn0A 145 7.64e+01 1d4oA 184 7.64e+01 1d4oA c.31.1.4 31748 1mopA 300 7.66e+01 c.26.1.4 85035 1uquA 482 7.67e+01 c.87.1.6 99796 2fymA 431 7.72e+01 1eno 312 7.73e+01 1enp c.2.1.2 29905 1qxoA 388 7.75e+01 d.258.1.1 96539 1z8oA 404 7.77e+01 2aorA 223 7.79e+01 1n2eA 300 7.82e+01 c.26.1.4 85268 1yyqA 374 7.84e+01 1ag9A 175 7.86e+01 1rcf c.23.5.1 31178 2agyA 361 7.91e+01 1s3jA 155 7.97e+01 a.4.5.28 98437 1sceA 112 7.98e+01 1puc d.97.1.1 40676 2fsp 124 8.23e+01 1dz3A c.23.1.1 31119 1d7oA 297 8.25e+01 1enp c.2.1.2 29907 1mtyB 384 8.27e+01 1mtyB a.25.1.2 16740 1tc5A 194 8.28e+01 c.110.1.1 106752 2ftuA 118 8.48e+01 2gcc 70 8.54e+01 2gcc d.10.1.2 37484 1wjgA 137 8.56e+01 1cpt 412 8.61e+01 1cpt a.104.1.1 18968 1gw5S 142 8.62e+01 d.110.4.2 70633 1gm7A 209 8.62e+01 d.153.1.2 65302 1qx2A 76 8.73e+01 a.39.1.1 104622 1e7wA 291 8.73e+01 c.2.1.2 59373 1k1xA 659 8.78e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1kfnA 56 8.80e+01 h.1.16.1 72422 1t8qA 336 8.81e+01 c.1.18.3 106669 1w9yA 319 8.87e+01 1n6zA 105 8.92e+01 d.263.1.1 85369 1pinA 163 8.96e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1ai7A 209 8.97e+01 1ajqA d.153.1.2 41845