# List of top-scoring protein chains for t2k-100-30-n_notor2-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 2ait 74 1.30e+00 1hoe b.5.1.1 22837 1s4iA 175 1.52e+00 1id0A 152 1.58e+00 d.122.1.3 66111 1txkA 498 1.67e+00 b.1.18.2,b.30.5.9 107425,107426 2bg9A 370 1.94e+00 1c1lA 136 2.04e+00 1c1lA b.29.1.3 24219 1kgcD 206 2.10e+00 b.1.1.1,b.1.1.2 77384,77385 1v0eA 666 2.55e+00 1abrB 267 2.85e+00 1abrB b.42.2.1,b.42.2.1 25563,25564 1kqfB 294 3.03e+00 d.58.1.5,f.23.22.1 75900,75901 1azcA 129 3.08e+00 1nwpA b.6.1.1 22899 2fimA 276 3.16e+00 2giyA 191 3.31e+00 1xtmA 175 3.92e+00 1amk 251 4.45e+00 1amk c.1.1.1 28503 1oaqL 120 4.63e+00 b.1.1.1 92708 1mfa 247 4.73e+00 1mfa b.1.1.1,b.1.1.1 19888,19889 1uh4A 637 5.46e+00 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1zn8A 180 5.52e+00 1o9wA 177 5.74e+00 b.2.3.5 86713 1ji1A 637 5.80e+00 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1b09A 206 5.82e+00 1sacA b.29.1.5 24247 1ui7A 638 5.87e+00 b.30.2.1,d.17.2.1,d.17.2.1 99413,99414,99415 1g7vA 284 6.57e+00 1d9eA c.1.10.4 60335 2bspA 420 7.91e+00 1pcl b.80.1.1 28023 1kmoA 774 8.17e+00 f.4.3.3 72753 1ok0A 74 8.98e+00 b.5.1.1 93191 1yhfA 115 9.08e+00 1a6vL 110 9.32e+00 1mfa b.1.1.1 20256 2fazA 78 9.50e+00 2fbjL 213 9.53e+00 8fabA b.1.1.1,b.1.1.2 19850,20954 3bamA 213 1.03e+01 1bam c.52.1.3 33288 1psuA 140 1.06e+01 d.38.1.5 88285 5er2E 330 1.10e+01 2er7E b.50.1.2 26783 1ck7A 631 1.13e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1hoe 74 1.15e+01 1hoe b.5.1.1 22833 2blnA 305 1.18e+01 3ait 74 1.19e+01 1hoe b.5.1.1 22835 1mwsA 646 1.23e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1wdkC 390 1.23e+01 c.95.1.1,c.95.1.1 109258,109259 1euwA 152 1.25e+01 1dupA b.85.4.1 28349 1fecA 490 1.32e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1gt8D 1025 1.32e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1xx9A 238 1.32e+01 1lml 478 1.38e+01 1lml d.92.1.3 40295 1v6fA 151 1.39e+01 d.109.1.2 108395 8fabB 224 1.40e+01 1igtB b.1.1.1,b.1.1.2 19773,20883 1lyxA 248 1.45e+01 c.1.1.1 78304 1hzdA 272 1.51e+01 c.14.1.3 65969 1oewA 329 1.53e+01 b.50.1.2 86924 1efuA 385 1.54e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1gvuA 329 1.58e+01 b.50.1.2 70619 1lg2A 365 1.62e+01 c.1.8.5,d.26.3.1 77950,77951 2c78A 405 1.63e+01 1d3cA 686 1.65e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1ze3C 205 1.69e+01 1ton 235 1.79e+01 5ptp b.47.1.2 26307 2fs2A 151 1.81e+01 1c3mA 147 1.81e+01 1jotA b.77.3.1 27983 1qhdA 398 1.82e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1pamA 686 1.84e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1a1vA 476 1.84e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1ll7A 392 1.85e+01 c.1.8.5,d.26.3.1 78085,78086 1zhpA 238 1.87e+01 1exmA 405 1.88e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1uiuA 502 1.91e+01 c.94.1.1 99434 1l1qA 186 1.96e+01 c.61.1.1 77653 2gpzA 111 1.98e+01 1rsgA 516 2.02e+01 2cn3A 737 2.08e+01 1wh0A 134 2.12e+01 1a7lA 389 2.16e+01 4mbp c.94.1.1 35787 1liuA 528 2.20e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 1pixA 587 2.20e+01 c.14.1.4 94708 1ha3A 405 2.27e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1d2pA 373 2.30e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1d2oA 187 2.31e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1s31A 273 2.32e+01 1fil 139 2.34e+01 1pne d.110.1.1 40869 1cb0A 283 2.37e+01 1cb0A c.56.2.1 33790 1cxlA 686 2.40e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1lba 146 2.44e+01 1lba d.118.1.1 41062 1gctA 245 2.47e+01 5ptp b.47.1.2 26021 1ejhA 190 2.47e+01 1ejhA d.86.1.1 40147 2a74A 643 2.49e+01 2fomB 185 2.65e+01 1d2kA 392 2.69e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1rlmA 271 2.74e+01 1hkbA 917 2.79e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 1pv1A 299 2.81e+01 1as8A 343 2.84e+01 1nif b.6.1.3,b.6.1.3 23074,23075 1h8eA 510 2.92e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1xtlA 175 2.97e+01 1ecfB 504 2.97e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1w9pA 433 2.99e+01 1keeC 1073 3.02e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 1flcA 432 3.06e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 2b5eA 504 3.10e+01 1uebA 184 3.11e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1pedA 351 3.13e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1fr7A 260 3.14e+01 2cba b.74.1.1 27828 1c5lH 259 3.17e+01 5ptp 1j05A 111 3.19e+01 b.1.1.1 90735 1i8aA 189 3.21e+01 1i82A b.1.9.2 61951 1hkkA 364 3.21e+01 c.1.8.5,d.26.3.1 90634,90635 1xezA 721 3.35e+01 1xx0A 127 3.37e+01 1itvA 195 3.38e+01 b.66.1.1 76791 1ig8A 486 3.40e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1vkpA 383 3.42e+01 d.126.1.6 108686 1yo1A 260 3.42e+01 1po0A 751 3.43e+01 f.4.3.3 94960 1wkrA 340 3.43e+01 b.50.1.2 109395 1yuwA 554 3.44e+01 1awiA 138 3.51e+01 1pne d.110.1.1 40871 1vckA 115 3.54e+01 1hzmA 154 3.56e+01 c.46.1.1 65975 1lxtA 561 3.61e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35432,35433,35434,41309 2gq1A 332 3.61e+01 1azvA 153 3.61e+01 1mfmA b.1.8.1 22247 1ecfA 504 3.61e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1ot1A 686 3.65e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1k4vA 289 3.74e+01 c.68.1.9 72066 1jjiA 311 3.80e+01 c.69.1.2 66766 2ck3A 510 3.86e+01 12ca 260 3.86e+01 2cba b.74.1.1 27942 1fs0E 138 3.89e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1nddD 76 3.93e+01 1ubi d.15.1.1 37602 1y7rA 133 3.94e+01 2avtA 378 4.04e+01 1nbaA 264 4.10e+01 1nbaA c.33.1.3 31753 1z6bA 154 4.11e+01 1ftrA 296 4.14e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1wb0A 445 4.15e+01 2bjfA 329 4.17e+01 1ojqA 212 4.18e+01 d.166.1.1 93146 1sc6A 404 4.19e+01 1ayrB 363 4.22e+01 1cf1A b.1.18.11,b.1.18.11 21917,21918 1earA 147 4.23e+01 b.107.1.1,d.58.38.1 64875,64876 1y7mA 164 4.27e+01 1vlyA 338 4.31e+01 b.44.2.1,d.250.1.1 108871,108872 2rmcA 182 4.37e+01 2cpl b.62.1.1 27491 1kblA 873 4.38e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1x05A 129 4.41e+01 1a39 402 4.45e+01 1celA b.29.1.10 24305 1ifrA 121 4.51e+01 b.1.16.1 71203 1o9yA 84 4.55e+01 b.139.1.1 92692 1i60A 278 4.65e+01 c.1.15.4 71118 1gof 639 4.66e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1jq5A 370 4.67e+01 e.22.1.2 67084 1obbA 480 4.68e+01 c.2.1.5,d.162.1.2 86760,86761 2cb2A 318 4.69e+01 1j8wB 273 4.70e+01 1gwcA 230 4.77e+01 a.45.1.1,c.47.1.5 70660,70661 1xhdA 173 4.79e+01 1bpoA 494 4.79e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1e0tA 470 4.81e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1cfyA 143 4.84e+01 1cof d.109.1.2 40858 1ijqA 316 4.91e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1qx4A 274 4.98e+01 b.43.4.2,c.25.1.1 104624,104625 1mua 256 5.06e+01 2cba b.74.1.1 27831 8kme2 259 5.10e+01 1ucyE 2fpqA 444 5.10e+01 1zlqA 502 5.11e+01 1wljA 189 5.14e+01 1i82A 189 5.14e+01 1i82A b.1.9.2 61937 1cdwA 179 5.18e+01 1ytbA d.129.1.1,d.129.1.1 41212,41213 1uaiA 224 5.22e+01 b.29.1.18 107761 1mt6A 280 5.23e+01 b.76.2.1,b.85.7.1 79446,79447 1aszB 490 5.29e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2fhxA 246 5.39e+01 2bdrA 175 5.40e+01 1yrtA 364 5.44e+01 2f9nA 245 5.49e+01 1yz1A 174 5.51e+01 1j6pA 418 5.55e+01 b.92.1.4,c.1.9.9 77089,77090 1f1gA 154 5.60e+01 b.1.8.1 76153 1eexA 554 5.64e+01 1dioA c.1.19.3 29650 2gjgA 248 5.65e+01 2asuB 234 5.66e+01 1w1oA 534 5.71e+01 d.58.32.4,d.145.1.1 109071,109072 1b8rA 108 5.79e+01 1a75A a.39.1.4 17201 1j2aA 166 5.80e+01 b.62.1.1 90779 1jcv 153 5.98e+01 1mfmA b.1.8.1 22279 1cgt 684 6.02e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21815,22484,27722,28709 1fdd 106 6.04e+01 1a6l d.58.1.2 38960 1f15B 218 6.04e+01 1f15B b.121.4.5 23321 1b65A 375 6.05e+01 1b65A d.154.1.1 42020 1aohB 147 6.10e+01 1aohA b.2.2.2 22402 1attA 421 6.13e+01 1ovaA e.1.1.1 42638 1e8xA 961 6.15e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1nfdA 203 6.16e+01 1tcrA b.1.1.1,b.1.1.2 20612,21550 1m8aA 70 6.19e+01 d.9.1.1 74579 1yg9A 330 6.21e+01 1kapP 479 6.21e+01 1sat b.80.7.1,d.92.1.6 28012,40298 1v70A 105 6.27e+01 1ea1A 455 6.28e+01 1ea1A a.104.1.1 18970 1qbkB 890 6.28e+01 1qbkB a.118.1.1 19127 1anu 138 6.30e+01 1aohA b.2.2.2 22403 1dqgA 135 6.30e+01 1dqgA b.42.2.2 25579 1fcjA 322 6.35e+01 1oasA c.79.1.1 35289 1g3kA 174 6.36e+01 1nedA d.153.1.4 41989 1kwhA 492 6.54e+01 c.94.1.1 68876 1g8kA 825 6.55e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1nszA 347 6.56e+01 b.30.5.4 80724 2fymA 431 6.57e+01 1a45 173 6.62e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1agjA 242 6.70e+01 1agjA b.47.1.1 25827 1ykfA 352 6.70e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1gt8B 1025 6.78e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1914 232 6.84e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1yzyA 413 6.85e+01 1w9zA 283 6.86e+01 1yhpA 212 6.86e+01 1gtfA 74 6.94e+01 b.82.5.1 70460 1owqA 361 6.95e+01 c.1.8.5,d.26.3.1 104041,104042 1f5mB 180 6.99e+01 1f5mB d.110.2.1 40896 1who 96 7.00e+01 1who b.7.3.1 23215 1qba 858 7.01e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1z6jT 211 7.02e+01 1ts3A 194 7.02e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 2polA 366 7.02e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1kvs 338 7.04e+01 1xel c.2.1.2 29799 3lck 271 7.04e+01 1fmk d.144.1.7 41686 1pg4A 652 7.08e+01 e.23.1.1 88067 1fnb 314 7.08e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1dmtA 696 7.09e+01 1dmtA d.92.1.4 40296 1ku0A 388 7.11e+01 c.69.1.18 72994 2pec 353 7.17e+01 1air b.80.1.1 28019 1m5q1 130 7.27e+01 1a31A 538 7.29e+01 1a36A d.163.1.2,e.15.1.1 42170,43263 1lu4A 136 7.31e+01 c.47.1.10 91124 1hbq 183 7.32e+01 1aqb b.60.1.1 27078 2a5zA 262 7.34e+01 1yaiA 151 7.35e+01 1yaiA b.1.8.1 22289 1mpyA 307 7.36e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1am1 213 7.38e+01 1yer d.122.1.1 41095 1a0sP 413 7.39e+01 1a0tP f.4.3.2 43797 1mjc 69 7.40e+01 1mjc b.40.4.5 25319 1o88A 353 7.46e+01 b.80.1.1 81178 1amw 214 7.47e+01 1yer d.122.1.1 41093 1ndh 272 7.47e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1o70A 324 7.51e+01 b.118.1.1,b.118.1.1 81115,81116 2d0oA 610 7.62e+01 1oa2A 218 7.62e+01 b.29.1.11 86721 1wapA 75 7.73e+01 1wapA b.82.5.1 28153 1ltoA 245 7.81e+01 b.47.1.2 84707 1v8eA 224 7.89e+01 1ea9C 583 7.90e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1dst 228 7.92e+01 1a7s b.47.1.2 26318 1yruA 364 8.02e+01 1xn5A 146 8.05e+01 1lkxA 697 8.05e+01 c.37.1.9 73981 1fujA 221 8.08e+01 1a7s b.47.1.2 26349 1nekA 588 8.11e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1wkcA 184 8.15e+01 1o66A 275 8.20e+01 c.1.12.8 92547 1sz6B 263 8.24e+01 1ukgA 252 8.31e+01 b.29.1.1 99489 1v9tA 166 8.32e+01 b.62.1.1 108451 1ipcA 217 8.37e+01 d.86.1.1 71257 1zm0A 114 8.39e+01 1e8oA 85 8.47e+01 1914 d.49.1.1 38773 1nbfD 76 8.48e+01 d.15.1.1 80390 1b2wH 220 8.53e+01 1igtB b.1.1.1,b.1.1.2 20307,21299 1pfl 139 8.56e+01 1pne d.110.1.1 40877 1aohA 147 8.56e+01 1aohA b.2.2.2 22401 1wrjA 156 8.58e+01 1a4h 230 8.58e+01 1yer d.122.1.1 41099 1r1hA 696 8.58e+01 d.92.1.4 104756 1mal 421 8.58e+01 2mprA f.4.3.2 43784 1q87A 221 8.60e+01 e.47.1.1 96192 1keeE 1073 8.60e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1a16 440 8.66e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 4cpv 109 8.67e+01 1a75A a.39.1.4 17198 1k32A 1045 8.72e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 2aeeA 211 8.72e+01 2gfaA 119 8.75e+01 1en2A 89 8.80e+01 1hev g.3.1.1,g.3.1.1 44048,44049 1j1lA 290 8.83e+01 b.82.1.12 90766 1oalA 151 8.88e+01 b.1.8.1 86739 1n6eA 1071 8.89e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1barA 140 8.93e+01 1bfg b.42.1.1 25504 1ncwH 222 8.98e+01 b.1.1.1,b.1.1.2 85555,85556 15c8L 213 8.98e+01 8fabA b.1.1.1,b.1.1.2 20300,21292