# 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 1jfaA 374 2.79e-01 a.128.1.5 66622 3gcb 470 3.46e-01 3gcb d.3.1.1 37032 1rcwA 231 3.55e-01 a.132.1.4 97299 1a6r 471 3.86e-01 3gcb d.3.1.1 37033 1gcb 454 4.19e-01 3gcb d.3.1.1 37034 1jfgA 374 4.92e-01 a.128.1.5 66636 1yyqA 374 6.61e-01 1de4C 640 7.19e-01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 2aelA 374 8.69e-01 1f45B 197 9.95e-01 1f45B a.26.1.1 59642 1wn0A 145 1.20e+00 1kiyA 374 1.53e+00 a.128.1.5 72555 1f4tA 368 1.60e+00 1f4tA a.104.1.1 18973 1ffkB 338 2.14e+00 1ffkB b.43.3.2 25719 1gw5B 591 2.89e+00 a.118.1.10 70630 1cx8B 639 3.07e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 1y1xA 191 4.27e+00 1au1A 166 4.37e+00 1ifa a.26.1.3 16889 2grrB 170 4.65e+00 1bjwA 382 4.83e+00 1bjwA c.67.1.1 34349 1b5pA 385 5.07e+00 c.67.1.1 90403 1q8fA 313 5.09e+00 c.70.1.1 96203 1w33A 181 6.08e+00 1jfbA 404 6.55e+00 a.104.1.1 66624 1cx8A 639 7.11e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 1dq3A 454 7.63e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1ciy 590 7.68e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1hqvA 191 7.70e+00 1hqvA a.39.1.8 61160 145l 164 8.21e+00 1l92 d.2.1.3 36860 1cmnA 402 8.50e+00 1rom a.104.1.1 18958 1z5hA 780 8.99e+00 1c3cA 429 9.23e+00 1c3cA a.127.1.1 19425 1wusA 180 9.24e+00 1zejA 293 9.34e+00 1f24A 402 9.41e+00 1rom a.104.1.1 18953 2beqA 38 9.46e+00 1ll2A 333 9.55e+00 c.68.1.14 74005 144l 164 9.73e+00 1l92 d.2.1.3 36893 173l 164 1.01e+01 1l92 d.2.1.3 36728 1ecmA 109 1.02e+01 1ecmA a.130.1.1 19492 1hz4A 373 1.07e+01 a.118.8.2 65960 2fx0A 201 1.10e+01 1gumA 222 1.12e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 152l 164 1.17e+01 1l92 d.2.1.3 36904 1t56A 216 1.19e+01 a.4.1.9,a.121.1.1 106428,106429 172l 164 1.22e+01 1l92 d.2.1.3 36905 156l 164 1.25e+01 1l92 d.2.1.3 36709 1rom 403 1.26e+01 1rom a.104.1.1 18963 170l 164 1.27e+01 1l92 d.2.1.3 36968 1ry6A 360 1.28e+01 c.37.1.9 98090 1rtwA 220 1.33e+01 a.132.1.3 97823 123l 164 1.35e+01 1l92 d.2.1.3 36697 1dhpA 292 1.35e+01 1dhpA c.1.10.1 29097 2a11A 242 1.36e+01 155l 164 1.37e+01 1l92 d.2.1.3 36762 166l 164 1.37e+01 1l92 d.2.1.3 36681 1g7oA 215 1.41e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1gulA 222 1.41e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 2azqA 311 1.45e+01 5eat 548 1.45e+01 5eat a.102.4.1,a.128.1.3 18853,19445 113l 164 1.45e+01 1l92 d.2.1.3 36678 1uc2A 481 1.47e+01 d.261.1.1 99161 160l 164 1.47e+01 1l92 d.2.1.3 36748 1l58 164 1.47e+01 1l92 d.2.1.3 36635 2c12A 439 1.49e+01 118l 164 1.50e+01 1l92 d.2.1.3 36642 138l 164 1.51e+01 1l92 d.2.1.3 36679 143l 164 1.56e+01 1l92 d.2.1.3 36857 111l 164 1.59e+01 1l92 d.2.1.3 36661 177l 164 1.59e+01 1l92 d.2.1.3 36958 190l 164 1.62e+01 1l92 d.2.1.3 36892 119l 164 1.62e+01 1l92 d.2.1.3 36622 146l 164 1.62e+01 1l92 d.2.1.3 36763 1nx8A 273 1.63e+01 b.82.2.8 86374 1keyA 235 1.64e+01 a.118.16.1 72389 149l 164 1.66e+01 1l92 d.2.1.3 36959 130l 164 1.67e+01 1l92 d.2.1.3 36638 129l 164 1.68e+01 1l92 d.2.1.3 36660 1huxA 270 1.68e+01 1huxA c.55.1.5 61278 1qgrA 876 1.70e+01 1qgrA a.118.1.1 19119 137lA 164 1.73e+01 1l92 d.2.1.3 36791 114l 164 1.74e+01 1l92 d.2.1.3 36663 180lA 164 1.75e+01 1l92 d.2.1.3 36867 109l 164 1.75e+01 1l92 d.2.1.3 36781 107l 164 1.77e+01 1l92 d.2.1.3 36690 112l 164 1.78e+01 1l92 d.2.1.3 36677 2thiA 379 1.78e+01 2thiA c.94.1.1 35794 120l 164 1.78e+01 1l92 d.2.1.3 36720 165l 164 1.78e+01 1l92 d.2.1.3 36680 104lA 166 1.79e+01 1l92 d.2.1.3 36969 1jalA 363 1.79e+01 c.37.1.8,d.15.10.2 84138,84139 131l 164 1.82e+01 1l92 d.2.1.3 36685 110l 164 1.85e+01 1l92 d.2.1.3 36684 1v4eA 299 1.87e+01 a.128.1.1 100296 1b9uA 34 1.91e+01 1b9uA j.35.1.1 46260 158l 164 1.93e+01 1l92 d.2.1.3 36747 1b6iA 164 1.96e+01 1l92 d.2.1.3 36945 108l 164 1.97e+01 1l92 d.2.1.3 36669 115l 164 1.97e+01 1l92 d.2.1.3 36700 102l 165 1.98e+01 1l92 d.2.1.3 36724 142l 164 1.98e+01 1l92 d.2.1.3 36874 192l 164 1.99e+01 1l92 d.2.1.3 36815 1l92 164 2.00e+01 1l92 d.2.1.3 36629 167lA 164 2.01e+01 1l92 d.2.1.3 36937 1p36A 164 2.01e+01 d.2.1.3 93978 176lA 164 2.02e+01 1l92 d.2.1.3 36942 125l 164 2.04e+01 1l92 d.2.1.3 36672 103l 167 2.04e+01 1l92 d.2.1.3 36870 1v71A 323 2.06e+01 1asx 159 2.11e+01 1a6dA c.8.5.2 30821 195l 164 2.12e+01 1l92 d.2.1.3 36841 1po5A 476 2.17e+01 a.104.1.1 94963 1rxqA 178 2.19e+01 a.213.1.1 105118 1lw9A 164 2.21e+01 d.2.1.3 84727 164l 164 2.31e+01 1l92 d.2.1.3 36714 174lA 164 2.32e+01 1l92 d.2.1.3 36956 1oyzA 280 2.33e+01 a.118.1.16 93775 189l 164 2.33e+01 1l92 d.2.1.3 36960 175lA 164 2.33e+01 1l92 d.2.1.3 36924 1fs1B 141 2.34e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1g5gB 481 2.34e+01 f.12.1.1,h.3.2.1 65157,65158 2ahqA 76 2.36e+01 2astA 159 2.38e+01 197l 164 2.40e+01 1l92 d.2.1.3 36911 147l 164 2.42e+01 1l92 d.2.1.3 36864 163l 164 2.47e+01 1l92 d.2.1.3 36658 191l 164 2.50e+01 1l92 d.2.1.3 36826 1hyp 80 2.52e+01 1hyp a.52.1.1 17806 1en7A 157 2.54e+01 1en7A a.140.4.1,d.4.1.5 64733,64734 1etpA 190 2.61e+01 1etpA a.3.1.4,a.3.1.4 15962,15963 139l 164 2.61e+01 1l92 d.2.1.3 36643 2ex0A 399 2.62e+01 1ass 159 2.64e+01 1a6dA c.8.5.2 30818 3thiA 371 2.69e+01 2thiA c.94.1.1 35792 1zcdA 388 2.70e+01 126l 164 2.70e+01 1l92 d.2.1.3 36699 162l 164 2.76e+01 1l92 d.2.1.3 36749 196l 164 2.78e+01 1l92 d.2.1.3 36927 1ej5A 107 2.78e+01 1ej5A a.68.1.1 18268 1e7lA 157 2.82e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 2u2fA 85 2.85e+01 2u2fA d.58.7.1 39167 159l 164 2.88e+01 1l92 d.2.1.3 36682 1e5rA 290 2.89e+01 1e5rA b.82.2.4 59276 2d2mD 145 2.90e+01 1xv5A 401 2.93e+01 1htjF 210 2.94e+01 1htjF a.91.1.1 61254 1rw6A 210 2.95e+01 a.47.4.1 105113 1jmeA 455 3.01e+01 a.104.1.1 66885 2ap3A 199 3.04e+01 1uok 558 3.14e+01 1uok b.71.1.1,c.1.8.1 27801,28788 198l 164 3.14e+01 1l92 d.2.1.3 36785 122l 164 3.14e+01 1l92 d.2.1.3 36667 1wdgA 94 3.20e+01 h.3.3.1 109248 2fbnA 198 3.29e+01 128l 164 3.36e+01 1l92 d.2.1.3 36634 140l 164 3.40e+01 1l92 d.2.1.3 36891 1m32A 366 3.42e+01 c.67.1.3 78508 2b7aA 293 3.46e+01 1foeA 377 3.57e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1l8rA 101 3.68e+01 a.6.1.4 73700 1hu3A 260 3.75e+01 1hu3A a.118.1.14 19137 171l 164 3.75e+01 1l92 d.2.1.3 36962 199l 164 3.80e+01 1l92 d.2.1.3 36855 1vkeA 133 3.83e+01 a.152.1.2 108650 1qq8A 214 3.84e+01 1qq8A 1dxeA 256 3.87e+01 1dxeA c.1.12.5 29310 1vqrA 297 3.88e+01 141l 164 3.89e+01 1l92 d.2.1.3 36863 1w9cA 321 3.90e+01 2bptA 861 3.96e+01 1tcvA 287 4.03e+01 161l 164 4.05e+01 1l92 d.2.1.3 36636 1vf7A 369 4.08e+01 f.46.1.1 108557 1vg5A 73 4.11e+01 1aueA 100 4.12e+01 1nsgB a.24.7.1 16615 1ug3A 339 4.15e+01 1kpsB 171 4.21e+01 a.118.12.1 68787 1aab 83 4.26e+01 1cktA a.21.1.1 16420 1zs3A 182 4.29e+01 1zmbA 290 4.30e+01 2prd 174 4.41e+01 2prd b.40.5.1 25435 1x79B 112 4.44e+01 3fapB 94 4.49e+01 1nsgB a.24.7.1 16612 1jnyA 435 4.50e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1av1A 201 4.56e+01 1av1A h.5.1.1 45796 151l 164 4.58e+01 1l92 d.2.1.3 36944 168lA 164 4.61e+01 1l92 d.2.1.3 36975 1emy 153 4.62e+01 1a6m a.1.1.2 15204 2gnoA 305 4.62e+01 1s9pA 227 4.69e+01 a.123.1.1 105384 1paqA 189 4.72e+01 a.118.1.14 94413 1h5zA 455 4.73e+01 a.104.1.1 90622 1e2xA 243 4.73e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1lqtA 456 4.82e+01 c.3.1.1,c.4.1.1 74198,74199 1sctB 151 4.83e+01 3sdhA a.1.1.2 15003 1yhlA 362 4.83e+01 2db0A 253 4.86e+01 1yoyA 175 4.91e+01 1x92A 199 4.97e+01 1g5gA 481 4.97e+01 f.12.1.1,h.3.2.1 65155,65156 1gdoB 240 4.97e+01 1gdoA 1jsxA 207 4.99e+01 c.66.1.20 71846 1ow4A 129 5.00e+01 a.39.2.1 93628 1o5kA 306 5.13e+01 c.1.10.1 92504 1x9gA 200 5.15e+01 c.33.1.3 109527 2cp8A 54 5.22e+01 1r4gA 53 5.25e+01 a.8.5.1 96996 1b8dA 164 5.27e+01 1cpcA a.1.1.3 15665 2bmhA 455 5.32e+01 1bu7A a.104.1.1 18941 1ox3A 109 5.33e+01 h.1.17.1 93668 127l 164 5.37e+01 d.2.1.3 36745 1hw1A 239 5.46e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 157l 164 5.47e+01 1l92 d.2.1.3 36717 1je8A 82 5.50e+01 a.4.6.2 77108 1n45A 233 5.58e+01 a.132.1.1 79981 1su0B 159 5.58e+01 d.224.1.2 106015 1hybA 181 5.58e+01 1f9aA c.26.1.3 61399 1abbA 828 5.58e+01 1a8i c.87.1.4 35536 1syyA 346 5.66e+01 a.25.1.2 106126 1cktA 71 5.68e+01 1cktA a.21.1.1 16417 1t5eA 360 5.75e+01 f.46.1.1 106436 1ltlA 279 5.81e+01 b.40.4.11 84701 1t3wA 148 5.81e+01 2polA 366 5.82e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1ds6B 180 5.88e+01 1rhoA b.1.18.8 21898 1zl8A 53 5.94e+01 1ll0A 339 6.01e+01 c.68.1.14 73995 2br9A 234 6.03e+01 1u13A 455 6.05e+01 a.104.1.1 107578 1fs7A 485 6.07e+01 1qdbA a.138.1.3 19691 1gk4D 84 6.08e+01 h.1.20.1 70206 2hdhA 293 6.08e+01 2hdhA a.100.1.3,c.2.1.6 18795,30199 1gntA 553 6.12e+01 e.26.1.1 70290 1w5fA 353 6.15e+01 1kn1B 161 6.18e+01 a.1.1.3 77456 1ss9A 311 6.21e+01 c.68.1.4 105978 1x3kA 152 6.21e+01 1b33B 161 6.28e+01 1qgwC a.1.1.3 15650 2gyqA 175 6.32e+01 1zw0A 66 6.35e+01 1dowA 205 6.35e+01 1dovA a.24.9.1 16626 1dp4A 435 6.36e+01 1dp4A c.93.1.1 35710 1a9t 284 6.38e+01 1b8oA c.56.2.1 33765 1bvoA 175 6.40e+01 1a3qA b.2.5.3 22457 1jbgA 109 6.41e+01 a.6.1.3 66480 1jilA 420 6.47e+01 c.26.1.1 66745 1ql1A 46 6.47e+01 1ql1A h.1.4.1 45564 2a6nA 292 6.48e+01 2a6lA 292 6.48e+01 1e2uA 553 6.48e+01 1e1dA e.26.1.1 43362 1oglA 283 6.50e+01 a.204.1.1 92922 1fc4A 401 6.53e+01 1bs0A c.67.1.4 59760 1yrbA 262 6.55e+01 1esmA 316 6.55e+01 1esmA c.37.1.6 31953 1x1nA 524 6.59e+01 1nc5A 373 6.60e+01 a.102.1.6 85548 1y74A 57 6.71e+01 1fapB 95 6.81e+01 1nsgB a.24.7.1 16618 1s35A 214 6.83e+01 a.7.1.1,a.7.1.1 98420,98421 1gk4A 84 6.84e+01 h.1.20.1 70203 1lniA 96 6.91e+01 d.1.1.2 74046 1g60A 260 6.92e+01 c.66.1.11 70151 1sig 339 6.97e+01 1sig a.177.1.1 19068 1yfsA 465 6.97e+01 1jpzA 473 6.98e+01 a.104.1.1 67069 1g9rA 311 7.01e+01 1ga8A c.68.1.4 34517 1w36B 1180 7.01e+01 2ez6A 221 7.05e+01 1jysA 242 7.06e+01 c.56.2.1 77216 1x8vA 455 7.07e+01 1ga8A 311 7.11e+01 1ga8A c.68.1.4 34516 1px5A 349 7.20e+01 a.160.1.2,d.218.1.6 95277,95278 1ju3A 583 7.22e+01 b.18.1.13,c.69.1.21 67300,67301 2dfkA 402 7.28e+01 169lA 164 7.29e+01 1l92 d.2.1.3 36963 1lmzA 187 7.33e+01 a.96.1.4 74037 1m8jA 181 7.35e+01 c.26.1.3 84875 1vkmA 297 7.39e+01 c.138.1.1 108670 1xqrA 296 7.39e+01 1io7A 368 7.41e+01 1f4tA a.104.1.1 18971 1j3mA 129 7.43e+01 d.129.7.1 103836 1vf6C 72 7.43e+01 a.194.1.1 100602 1pbn 289 7.51e+01 1b8oA c.56.2.1 33771 1vgoA 253 7.51e+01 1o70A 324 7.55e+01 b.118.1.1,b.118.1.1 81115,81116 1myt 146 7.57e+01 1a6m a.1.1.2 15207 1winA 143 7.67e+01 1ifm 46 7.67e+01 1ql1A h.1.4.1 45557 1mmiA 366 7.68e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1pv9A 348 7.72e+01 c.55.2.1,d.127.1.1 95157,95158 1dkzA 219 7.76e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1xkgA 312 7.79e+01 1ewqA 765 7.79e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1w2wA 211 7.80e+01 c.124.1.5 109130 2etsA 128 7.89e+01 1rgeA 96 7.93e+01 1rgeA d.1.1.2 36028 1gmpA 96 7.95e+01 1rgeA d.1.1.2 36036 1i8vA 96 7.98e+01 d.1.1.2 61985 1f60A 458 8.00e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1dguA 183 8.02e+01 1dguA a.39.1.5 17333 1cpcA 162 8.03e+01 1cpcA a.1.1.3 15643 1a9r 282 8.05e+01 1b8oA c.56.2.1 33767 1wy1A 172 8.24e+01 2d8dA 90 8.26e+01 1nsgB 94 8.43e+01 1nsgB a.24.7.1 16613 1q1lA 401 8.44e+01 d.258.1.1 95591 1e1dA 553 8.53e+01 1e1dA e.26.1.1 43363 1yxcA 292 8.60e+01 1cb2A 365 8.61e+01 1bvwA c.6.1.1 30661 1ctqA 166 8.65e+01 1ctqA c.37.1.8 31965 1xffA 240 8.67e+01 d.153.1.1 109580 1sfcA 96 8.68e+01 1sfcA h.1.15.1 45643 1h3nA 878 8.68e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1o5iA 249 8.70e+01 c.2.1.2 92499 1a9s 289 8.72e+01 1b8oA c.56.2.1 33768 1riqA 465 8.75e+01 a.203.1.1,d.104.1.1 97516,97517 2rslA 140 8.76e+01 2rslA c.53.1.1 33345 1j8yF 297 8.88e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1v7bA 185 8.90e+01 1jqjC 343 8.91e+01 a.80.1.1,c.37.1.20 67097,67098