# List of top-scoring protein chains for t2k-100-30-str2-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 2ap1A 327 6.57e-02 1rypA 243 2.71e-01 1pmaA d.153.1.4 41932 1wzvA 155 3.17e-01 1g0uG 252 3.96e-01 d.153.1.4 41952 1yrvA 169 4.49e-01 1kxoA 184 9.30e-01 b.60.1.1 84475 2ahqA 76 9.85e-01 1fseA 74 1.10e+00 1fseA a.4.6.2 60000 1xawA 140 1.39e+00 2b20A 403 1.57e+00 1qhbA 596 1.58e+00 1qhbA a.111.1.2 19055 1f1sA 814 2.09e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1z8uA 102 2.98e+00 1wxcB 134 2.99e+00 2g0uA 92 3.13e+00 1ahr 146 3.14e+00 1cll a.39.1.5 17287 1q2hA 69 3.29e+00 a.34.4.1 104498 1u9aA 160 3.50e+00 1u9aA d.20.1.1 38333 1a3s 160 3.86e+00 1u9aA d.20.1.1 38335 1xttA 216 3.87e+00 1ej8A 140 3.94e+00 1qupA b.1.8.1 22300 2db9A 149 4.29e+00 1o7fA 469 4.42e+00 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1ufiA 64 4.65e+00 a.30.4.1 99336 1u7kA 131 4.74e+00 1wgxA 73 4.84e+00 1emwA 88 4.84e+00 1emwA d.27.1.1 38448 1q02A 52 5.05e+00 a.5.2.1 95490 1osa 148 5.53e+00 1cll a.39.1.5 17300 1up8A 598 5.59e+00 a.111.1.2 99710 1bbpA 173 5.68e+00 1bbpA b.60.1.1 27147 1fzyA 149 5.79e+00 d.20.1.1 65072 1xkpA 246 6.06e+00 1veaA 148 6.21e+00 d.275.1.1 108529 1yx1A 264 6.27e+00 3proC 166 6.35e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1cll 148 6.51e+00 1cll a.39.1.5 17263 1jsdA 319 6.68e+00 b.19.1.2 63258 1uzbA 516 7.17e+00 c.82.1.1 100220 1zd9A 188 7.42e+00 1tn4 159 7.44e+00 1ncx a.39.1.5 17248 1lkkA 105 7.70e+00 1lckA d.93.1.1 40412 2grrA 161 7.86e+00 1wf9A 107 8.07e+00 1wqgA 185 8.13e+00 1xqaA 113 8.18e+00 2bjkA 516 8.20e+00 2a19A 175 8.25e+00 1wpaA 114 8.39e+00 1y01A 102 8.59e+00 1g9uA 454 8.76e+00 c.10.2.6 65172 1jl5A 454 9.42e+00 c.10.2.6 66830 1vcvA 226 9.50e+00 1a8y 367 9.71e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1keiA 316 9.75e+00 d.92.1.2 77349 4bcl 366 9.98e+00 4bcl b.75.1.1 27968 2dgkA 452 1.00e+01 1cxpC 466 1.01e+01 1mhlC 1mhlC 466 1.03e+01 1mhlC 1d2vC 466 1.11e+01 1mhlC 3cln 148 1.12e+01 1cll a.39.1.5 17286 1k4nA 192 1.12e+01 d.32.1.5 72059 2fjlA 150 1.13e+01 1ggzA 148 1.20e+01 a.39.1.5 70176 1diwA 441 1.22e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1pmmA 466 1.24e+01 c.67.1.6 94901 1z52A 470 1.25e+01 1ztpA 251 1.25e+01 1um8A 376 1.28e+01 c.37.1.20 99580 1hp0A 339 1.39e+01 c.70.1.1 65900 1hyt 316 1.40e+01 1hyt d.92.1.2 59005 1hozA 339 1.43e+01 c.70.1.1 65898 1fxtA 149 1.45e+01 d.20.1.1 65055 1w0bA 102 1.47e+01 a.7.11.1 108985 1qupA 222 1.50e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1bjwA 382 1.51e+01 1bjwA c.67.1.1 34349 1d0hA 469 1.51e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1t6cA 315 1.56e+01 c.55.1.8,c.55.1.8 106558,106559 6tmnE 316 1.60e+01 1hyt d.92.1.2 59071 2aegA 268 1.61e+01 1b5pA 385 1.62e+01 c.67.1.1 90403 1lcjA 109 1.62e+01 1qadA d.93.1.1 40414 2fi9A 128 1.67e+01 1o04A 500 1.68e+01 c.82.1.1 86508 2ajrA 331 1.69e+01 1cuk 203 1.72e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1hfoA 113 1.73e+01 d.80.1.3 61006 2tmnE 316 1.76e+01 1hyt d.92.1.2 59055 1sseB 86 1.79e+01 1jy2O 56 1.80e+01 h.1.8.1 67441 1jy3O 56 1.80e+01 h.1.8.1 67447 1preA 470 1.82e+01 1preA d.169.1.2,f.8.1.1 42437,43824 8tlnE 316 1.82e+01 1hyt d.92.1.2 59075 1z5yE 149 1.83e+01 1zoyC 140 1.88e+01 1h0hA 977 1.89e+01 b.52.2.2,c.81.1.1 76435,76436 2c43A 323 1.92e+01 1fjgP 88 1.94e+01 1emwA d.27.1.1 38444 1hynP 379 1.97e+01 1hynP d.112.1.2 61408 2bydA 323 1.99e+01 1kq4A 232 2.01e+01 d.207.1.1 68791 1a8d 452 2.05e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1g4yR 148 2.09e+01 1cll a.39.1.5 60252 1zfpE 98 2.11e+01 1griA d.93.1.1 40465 1ytw 306 2.12e+01 1ytw c.45.1.2 32689 3proD 166 2.12e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1u2eA 289 2.15e+01 1exrA 148 2.16e+01 1cll a.39.1.5 17299 2cglA 489 2.17e+01 2f3yA 148 2.17e+01 1fgyA 127 2.18e+01 1faoA b.55.1.1 26976 1yh6A 179 2.18e+01 1ffkI 194 2.22e+01 1ffkI d.12.1.2 37494 1zg2A 107 2.23e+01 1q1lA 401 2.24e+01 d.258.1.1 95591 1szoA 257 2.24e+01 c.14.1.3 106164 1ayzA 169 2.27e+01 1u9aA d.20.1.1 38326 1xi7A 61 2.32e+01 1lckA 175 2.35e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1x1iA 752 2.35e+01 1uuhA 159 2.35e+01 d.169.1.4 100008 1ag8A 499 2.40e+01 1bpwA c.82.1.1 35341 1vjeA 166 2.40e+01 d.185.1.2 100807 1v54E 109 2.40e+01 a.118.11.1 100326 1innA 166 2.43e+01 1j98A d.185.1.2 62608 1i42A 89 2.44e+01 1jruA d.15.1.2 61651 1eqfA 280 2.45e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1top 162 2.46e+01 1ncx a.39.1.5 17223 1xzzA 246 2.47e+01 1k1fA 72 2.47e+01 a.147.1.1 68007 1brwA 433 2.60e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1sxjE 354 2.65e+01 a.80.1.1,c.37.1.20 106089,106090 1r0pA 312 2.66e+01 d.144.1.7 96734 1o26A 232 2.71e+01 d.207.1.1 86566 1jf4A 147 2.75e+01 a.1.1.2 71643 1lre 81 2.77e+01 1lre a.13.1.1 16376 2occE 109 2.80e+01 2occE a.118.11.1 19224 1ois 223 2.87e+01 1a36A e.15.1.1 43267 1jruA 89 2.89e+01 1jruA d.15.1.2 63257 1nrjA 158 2.96e+01 d.110.4.4 86124 1yts 278 3.02e+01 1ytw c.45.1.2 32690 1tf1A 198 3.09e+01 d.110.2.2 106826 1ncx 162 3.12e+01 1ncx a.39.1.5 17222 1z2lA 423 3.13e+01 1pysA 350 3.15e+01 1pysA d.104.1.1 40775 1sjiA 350 3.16e+01 1j98A 157 3.17e+01 1j98A d.185.1.2 62755 1zr6A 503 3.19e+01 2fm9A 215 3.19e+01 1q15A 503 3.27e+01 c.26.2.1,d.153.1.1 95538,95539 1jj2L 194 3.31e+01 1ffkI d.12.1.2 63097 1preB 470 3.32e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1ov2A 99 3.33e+01 a.13.1.1 93580 1p27B 106 3.33e+01 d.58.7.1 93908 1fvrA 327 3.34e+01 d.144.1.7 60047 1ytn 306 3.42e+01 1ytw c.45.1.2 32688 2ddrA 306 3.43e+01 2gupA 292 3.44e+01 1zhxA 438 3.47e+01 1u08A 386 3.53e+01 c.67.1.1 107543 1dd5A 185 3.53e+01 1dd5A d.67.3.1 39564 1a49A 530 3.56e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1f7lA 121 3.65e+01 1f7lA d.150.1.2 59666 1o8uA 257 3.71e+01 c.14.1.3 81194 1hjp 203 3.71e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1a93A 34 3.72e+01 1a93A h.1.3.1 45543 1gqeA 365 3.72e+01 e.38.1.1 70351 1s3sG 127 3.73e+01 d.15.1.2 98457 2b0tA 738 3.79e+01 1q5yA 85 3.85e+01 d.58.18.4 95950 1yua 122 3.86e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1gd2I 70 3.86e+01 1gd2I h.1.3.1 45532 1rp0A 284 3.87e+01 1hgeA 328 3.90e+01 1hgeA b.19.1.2 23816 1oxwA 373 3.93e+01 c.19.1.3 87539 1k9dA 679 3.94e+01 c.1.8.10,d.92.2.2 77292,77293 1ufoA 238 3.98e+01 c.69.1.27 99344 1lmeA 176 4.00e+01 d.167.1.1 84629 1xn9A 101 4.01e+01 2h88C 140 4.03e+01 1o9iA 266 4.11e+01 a.25.1.3 92671 1jkvA 266 4.13e+01 a.25.1.3 71719 2aobA 99 4.13e+01 1h8gA 95 4.23e+01 b.109.1.1 65735 1gg3A 279 4.26e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1pq4A 291 4.28e+01 c.92.2.2 94995 1zpuA 534 4.29e+01 1op1A 82 4.30e+01 a.13.1.1 93396 1k24A 253 4.30e+01 f.4.4.2 72002 1pkn 530 4.31e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1h2kA 349 4.31e+01 b.82.2.6 76572 1m7yA 435 4.31e+01 c.67.1.4 78761 1onwA 390 4.32e+01 b.92.1.7,c.1.9.13 87172,87173 1ywlA 96 4.34e+01 1gvjA 146 4.35e+01 a.4.5.21 90525 1z6oA 212 4.41e+01 1otkA 249 4.46e+01 a.25.1.2 93521 1v0wA 506 4.56e+01 d.136.1.2,d.136.1.2 108220,108221 1yptA 305 4.56e+01 1ytw c.45.1.2 32686 1p4kA 295 4.62e+01 d.153.1.5 87772 1bs0A 384 4.65e+01 1bs0A c.67.1.4 34490 1lyvA 306 4.67e+01 c.45.1.2 74348 1l8dA 112 4.67e+01 h.4.12.1 73687 2ftxB 64 4.75e+01 1ynuA 473 4.77e+01 1r31A 428 4.77e+01 d.58.20.1,d.179.1.1 96897,96898 1q1vA 70 4.80e+01 a.159.4.1 104479 2fbwC 141 4.82e+01 1w7lA 422 4.83e+01 c.67.1.1 109226 2a3qA 170 4.84e+01 2fp1A 166 4.90e+01 2f6lA 166 4.90e+01 1hylA 230 4.94e+01 5ptp b.47.1.2 26076 1v64A 108 4.97e+01 a.21.1.1 108392 1b8gA 429 5.01e+01 1b8gA c.67.1.4 34499 1l8nA 679 5.01e+01 c.1.8.10,d.92.2.2 84564,84565 1ybxA 143 5.02e+01 1jf3A 147 5.13e+01 a.1.1.2 71642 1ofgA 381 5.13e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1qaxA 428 5.15e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 2fulA 178 5.18e+01 1f7tA 122 5.22e+01 1f7lA d.150.1.2 59667 1c4zD 154 5.22e+01 1u9aA d.20.1.1 38331 1zbtA 371 5.25e+01 1pzlA 237 5.31e+01 a.123.1.1 104393 2gokA 429 5.39e+01 1h6dA 433 5.39e+01 c.2.1.3,d.81.1.5 65656,65657 1j0mA 752 5.40e+01 a.102.3.2,b.24.1.1,b.30.5.2 83910,83911,83912 1td6A 306 5.46e+01 2b8iA 77 5.59e+01 1yh2A 175 5.59e+01 1vreA 147 5.65e+01 2hbg a.1.1.2 15017 1nxcA 478 5.69e+01 a.102.2.1 92293 2g50A 530 5.70e+01 2av5A 120 5.75e+01 1twjA 84 5.79e+01 d.284.1.1 107407 1nrkA 328 5.80e+01 b.44.2.1,d.250.1.1 92089,92090 1efnA 59 5.80e+01 1bbzA b.34.2.1 24465 2h03A 291 5.84e+01 1tiiD 99 5.86e+01 1tiiD b.40.2.1 24965 1i2oA 316 6.01e+01 1onrA c.1.10.1 61574 1gvfA 286 6.04e+01 c.1.10.2 70599 1onrA 316 6.08e+01 1onrA c.1.10.1 29169 1gd8A 118 6.09e+01 d.188.1.1 60445 1ofdA 1520 6.10e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 3hmgA 328 6.11e+01 1hgeA b.19.1.2 23825 1z21A 112 6.13e+01 2gl5A 410 6.14e+01 1tzeE 98 6.15e+01 1griA d.93.1.1 40468 1jyrA 96 6.15e+01 d.93.1.1 71969 1gvmA 136 6.15e+01 b.109.1.1 70612 1sfkA 76 6.24e+01 a.190.1.1 105488 1shfA 59 6.28e+01 1bbzA b.34.2.1 24462 1l1jA 239 6.32e+01 b.47.1.1 84516 9gafA 295 6.35e+01 1apyA d.153.1.5 42008 1zymA 258 6.42e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1qb5D 99 6.43e+01 b.40.2.1 88357 1avsA 90 6.45e+01 1cll a.39.1.5 17226 2bfxA 284 6.49e+01 1wsrA 375 6.53e+01 1tgoA 773 6.54e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1wp5A 323 6.72e+01 1kpkA 473 6.73e+01 f.20.1.1 68776 1vlyA 338 6.79e+01 b.44.2.1,d.250.1.1 108871,108872 1wguA 136 6.85e+01 1t4nA 94 6.86e+01 d.50.1.1 106424 1xsjA 778 6.90e+01 1mioA 534 6.95e+01 1qguA c.92.2.3 35601 1d9uA 154 6.96e+01 1am7A d.2.1.4 59111 1ucpA 91 6.96e+01 a.77.1.5 99186 1t3jA 96 6.99e+01 h.4.16.1 106356 1ni5A 433 6.99e+01 c.26.2.5,d.229.1.1 80533,80534 1f20A 435 7.00e+01 b.43.4.1,c.25.1.4 64932,64933 1hcxA 127 7.04e+01 b.109.1.1 65800 2sttA 96 7.12e+01 1awcA a.4.5.21 16163 1azgB 67 7.13e+01 1bbzA b.34.2.1 24471 1ux8A 132 7.17e+01 1p4oA 322 7.20e+01 d.144.1.7 87775 1jqeA 292 7.22e+01 c.66.1.19 71789 1hmpA 217 7.22e+01 1qk3A c.61.1.1 34075 2hlcA 230 7.22e+01 5ptp b.47.1.2 26074 1a0nB 69 7.30e+01 1bbzA b.34.2.1 24469 2arpF 152 7.34e+01 1a2xA 159 7.43e+01 1ncx a.39.1.5 17251 1b7yA 350 7.44e+01 1pysA d.104.1.1 40776 1nkpA 88 7.46e+01 a.38.1.1 80573 1pl5A 142 7.50e+01 h.1.23.1 104186 1z7gA 217 7.52e+01 1qayA 428 7.57e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1yrnB 83 7.61e+01 1akhB a.4.1.1 15986 1zac 90 7.61e+01 1ncx a.39.1.5 17236 1azwA 313 7.62e+01 1qtrA c.69.1.7 34658 1hz4A 373 7.71e+01 a.118.8.2 65960 1kvdB 77 7.71e+01 1kveB 1kveB 77 7.71e+01 1kveB 1s4kA 120 7.81e+01 a.35.1.6 105254 2avdA 219 7.87e+01 1akhB 83 7.92e+01 1akhB a.4.1.1 15985 1q18A 332 7.92e+01 c.55.1.7,c.55.1.7 104470,104471 1s28A 132 7.97e+01 d.198.1.1 105223 1pkm 530 8.01e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1v74A 107 8.09e+01 d.243.1.1 100442 1w9yA 319 8.15e+01 1fa0B 537 8.17e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1u5uA 374 8.23e+01 2scuB 388 8.23e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1szhA 161 8.27e+01 a.226.1.1 106157 1quvA 578 8.31e+01 1quvA e.8.1.4 43119 2gkpA 167 8.35e+01 1msk 331 8.36e+01 1msk d.173.1.1 42495 1lwjA 441 8.36e+01 b.71.1.1,c.1.8.1 74303,74304 1vhnA 318 8.50e+01 c.1.4.1 100693 1gu7A 364 8.50e+01 b.35.1.2,c.2.1.1 83321,83322 1s62A 106 8.52e+01 1stzA 338 8.62e+01 a.4.5.51,d.110.2.3 106009,106010 2cohA 202 8.81e+01 1bmbA 123 8.82e+01 1griA d.93.1.1 40466 1dk5A 322 8.89e+01 1dk5A a.65.1.1 18192 1fa0A 537 8.92e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 2ae0X 345 8.94e+01