# List of top-scoring protein chains for t04-100-30-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 2a72A 146 3.39e-24 2bt2A 161 4.23e-24 1fqiA 147 4.44e-24 1agrE a.91.1.1 18542 1dk8A 147 7.17e-20 1agrE a.91.1.1 18548 1omwA 689 1.47e-13 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1htjF 210 4.65e-09 1htjF a.91.1.1 61254 1iapA 211 3.75e-04 a.91.1.1 62119 1y3nA 490 1.13e-01 1xx4A 261 1.15e-01 1eljA 381 2.21e-01 4mbp c.94.1.1 35791 1wixA 164 3.29e-01 1h5uA 842 3.31e-01 1a8i c.87.1.4 60655 1j1nA 492 3.41e-01 c.94.1.1 83978 1mnaA 298 3.52e-01 c.69.1.22 79322 1a8i 842 4.19e-01 1a8i c.87.1.4 35490 1x3kA 152 4.97e-01 1eca 136 5.06e-01 1flp a.1.1.2 15209 1ibrB 462 7.73e-01 1qgrA a.118.1.1 19120 1wa5B 530 1.19e+00 2lhb 149 1.20e+00 2fal a.1.1.2 15597 1alu 186 1.22e+00 1alu a.26.1.1 16826 2azjA 289 1.82e+00 1ee4A 423 1.89e+00 1ee4A a.118.1.1 19128 1edg 380 2.25e+00 1edg c.1.8.3 28807 1k3yA 221 2.43e+00 a.45.1.1,c.47.1.5 77245,77246 1ngnA 155 3.22e+00 a.96.1.2 85697 1t46A 313 3.33e+00 d.144.1.7 106397 1geqA 248 3.45e+00 2tysA c.1.2.4 28589 1syyA 346 3.55e+00 a.25.1.2 106126 1d5tA 433 3.61e+00 1gnd c.3.1.3,d.16.1.6 30422,37986 1ayl 541 4.19e+00 1ayl c.91.1.1,c.109.1.1 64718,64719 1p32A 209 4.40e+00 1p32A d.25.1.1 38379 1f3aA 222 4.50e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1qgrA 876 4.66e+00 1qgrA a.118.1.1 19119 1z1lA 345 4.71e+00 1mhyB 395 4.79e+00 1mtyB a.25.1.2 16781 1pvtA 238 4.82e+00 c.74.1.1 95189 1k8kG 151 5.19e+00 a.118.13.1 68313 1n9dA 199 5.28e+00 a.26.1.1 85464 1xsm 390 5.30e+00 1xsm a.25.1.2 16804 1lrrA 131 5.36e+00 d.228.1.1 78165 1txuA 273 5.52e+00 a.222.1.1 107439 1c3cA 429 5.84e+00 1c3cA a.127.1.1 19425 1ug3A 339 6.48e+00 1sazA 381 6.75e+00 1zpdA 568 6.82e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1yz7A 188 7.23e+00 2an9A 207 7.40e+00 1ja1A 622 7.78e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 2cb5A 453 7.84e+00 3gcb d.3.1.1 37035 1hx0A 496 7.90e+00 b.71.1.1,c.1.8.1 61346,61347 1ykuA 136 8.15e+00 1xjeA 644 8.27e+00 2ffeA 311 8.55e+00 1qhfA 240 8.58e+00 1qhfA c.60.1.1 33960 1xjjA 644 8.62e+00 1n5uA 585 8.85e+00 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1n08A 163 9.13e+00 b.43.5.1 79730 1b25A 619 9.80e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1qjbA 245 9.87e+00 1qjaA a.118.7.1 19202 1n8vA 112 1.04e+01 a.118.21.1 85457 1nznA 126 1.07e+01 a.118.8.1 92382 1v77A 212 1.08e+01 c.6.3.2 108402 1w68A 390 1.08e+01 a.25.1.2 109216 1sg4A 260 1.09e+01 1ruxA 951 1.13e+01 1dhx 1oxjA 173 1.14e+01 a.60.1.2,a.118.1.13 87517,87518 1smd 496 1.20e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1yyqA 374 1.20e+01 1f2dA 341 1.22e+01 1f2dA c.79.1.1 35298 2csbA 519 1.24e+01 2bxkA 585 1.29e+01 1wozA 177 1.31e+01 1gnd 447 1.31e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 1i2sA 282 1.32e+01 e.3.1.1 71104 1j0dA 341 1.33e+01 c.79.1.1 83902 1jk0A 419 1.33e+01 a.25.1.2 63142 1h7sA 365 1.35e+01 d.14.1.3,d.122.1.2 65705,65706 1aisB 200 1.35e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1p30A 952 1.37e+01 b.121.2.2,b.121.2.2 93964,93965 1k0mA 241 1.41e+01 a.45.1.1,c.47.1.5 67949,67950 1p2fA 220 1.42e+01 a.4.6.1,c.23.1.1 87720,87721 6mhtA 327 1.47e+01 6mhtA c.66.1.26 34226 2aw5A 541 1.48e+01 1de4C 640 1.49e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1ash 150 1.50e+01 1ash a.1.1.2 15622 1ir3A 306 1.50e+01 1fmk d.144.1.7 41702 1h0oA 390 1.52e+01 a.25.1.2 70845 1a7tA 232 1.55e+01 1a7tA d.157.1.1 42041 1ovnA 248 1.56e+01 a.71.1.1,c.47.1.7 93602,93603 1rvgA 305 1.57e+01 c.1.10.2 97920 1p2zA 968 1.58e+01 b.121.2.2,b.121.2.2 93962,93963 1r0pA 312 1.59e+01 d.144.1.7 96734 1vf1A 229 1.60e+01 1ush 550 1.62e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1lj2A 110 1.63e+01 h.1.13.2 73926 1fezA 256 1.64e+01 1fezA c.108.1.3 43343 1s3eA 520 1.65e+01 c.3.1.2,d.16.1.5 98426,98427 1v9sA 208 1.67e+01 1p99A 295 1.68e+01 c.94.1.1 94384 1yozA 116 1.69e+01 1e7aA 585 1.69e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19360,19361,19362 1ojaA 520 1.76e+01 c.3.1.2,d.16.1.5 93096,93097 1ct9A 553 1.79e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 2fbmA 291 1.81e+01 1t1vA 93 1.89e+01 c.47.1.14 106278 1g5hA 454 1.89e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 2f2gA 221 1.91e+01 4blmA 265 1.94e+01 1btl e.3.1.1 42721 1q4mA 221 1.94e+01 a.132.1.3 95805 1qlaA 656 1.96e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1ylhA 560 1.97e+01 2c2hA 192 2.02e+01 3pviA 157 2.03e+01 3pviA c.52.1.6 33300 1qb7A 236 2.04e+01 1qb7A c.61.1.1 34087 1uj2A 252 2.05e+01 c.37.1.6 99452 1uf2C 421 2.06e+01 a.115.1.3,b.19.1.1 99291,99292 1xewY 172 2.06e+01 1xocA 520 2.07e+01 1eswA 500 2.10e+01 1cwyA c.1.8.1 59500 2pviA 157 2.11e+01 3pviA c.52.1.6 33302 1ne9A 335 2.11e+01 d.108.1.4,d.108.1.4 91839,91840 1z5vA 474 2.14e+01 1hp1A 516 2.15e+01 d.114.1.1,d.159.1.2 70976,70977 1h8mA 140 2.17e+01 1h8mA d.110.4.1 60782 1s96A 219 2.28e+01 c.37.1.1 98740 1r9kA 172 2.30e+01 a.168.1.1 104869 1jv1A 505 2.31e+01 c.68.1.5 71892 1ylmA 144 2.31e+01 1wkuA 254 2.34e+01 1td6A 306 2.36e+01 1xm8A 254 2.42e+01 1qgiA 259 2.44e+01 1qgiA d.2.1.7 37001 1ltqA 301 2.45e+01 c.108.1.9,c.37.1.1 78208,78209 2f7fA 494 2.45e+01 2b0jA 358 2.47e+01 2fueA 262 2.48e+01 1eg3A 261 2.50e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1fs7A 485 2.50e+01 1qdbA a.138.1.3 19691 1a41 234 2.59e+01 1a41 d.163.1.2 42174 1pmzA 86 2.61e+01 a.39.1.10 104195 1g94A 448 2.64e+01 b.71.1.1,c.1.8.1 65169,65170 2bs3A 656 2.64e+01 1ile 821 2.65e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1ln1A 214 2.65e+01 d.129.3.2 74038 1bdfA 235 2.70e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2c7pA 327 2.72e+01 1f3lA 321 2.74e+01 1g6q2 c.66.1.6 59630 1ffyA 917 2.77e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1m2tA 254 2.80e+01 d.165.1.1 84761 2occA 514 2.82e+01 2occA f.24.1.1 43518 1ywnA 316 2.83e+01 1v54A 514 2.89e+01 f.24.1.1 100321 2d0tA 406 2.93e+01 1rqjA 299 3.00e+01 a.128.1.1 97744 1em8B 112 3.02e+01 c.126.1.1 90458 2fqxA 318 3.07e+01 1qtoA 122 3.07e+01 1bylA d.32.1.2 38494 1vjyA 303 3.10e+01 d.144.1.7 108633 1h4lD 147 3.11e+01 a.74.1.1 70873 1jixA 351 3.11e+01 1c3jA c.87.1.1 63081 1dv1A 449 3.12e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1ez3A 127 3.12e+01 1dn1B a.47.2.1 17768 1kmqA 184 3.12e+01 c.37.1.8 84412 1jkvA 266 3.14e+01 a.25.1.3 71719 1tx4B 178 3.14e+01 1ctqA c.37.1.8 32045 1kiyA 374 3.14e+01 a.128.1.5 72555 1qpaA 345 3.19e+01 1arv a.93.1.1 18585 1o9iA 266 3.19e+01 a.25.1.3 92671 1rlr 761 3.23e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 2d29A 387 3.25e+01 1obdA 306 3.25e+01 d.143.1.1 86767 1o5oA 221 3.26e+01 c.61.1.1 92509 1a48 306 3.31e+01 1a48 d.143.1.1 41590 1nxuA 333 3.33e+01 c.122.1.1 86389 1s7zA 117 3.37e+01 a.159.3.1 98715 1uxjA 309 3.38e+01 c.2.1.5,d.162.1.1 108112,108113 1s58A 554 3.38e+01 b.121.5.2 105262 1aqm 453 3.39e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1nf3A 195 3.40e+01 c.37.1.8 85594 1swvA 267 3.42e+01 2fw2A 260 3.44e+01 1y6nL 145 3.50e+01 1w2wA 211 3.51e+01 c.124.1.5 109130 1eueA 86 3.53e+01 1cyo d.120.1.1 59504 2kfnA 605 3.54e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1qrrA 394 3.56e+01 1qrrA c.2.1.2 29824 1y6iA 233 3.62e+01 1qh8B 519 3.63e+01 1qguB c.92.2.3 35634 1utxA 66 3.64e+01 a.35.1.3 108034 1p8kZ 254 3.65e+01 d.95.2.1,d.95.2.1 94361,94362 2cx9A 387 3.71e+01 1x6mA 196 3.75e+01 1am9A 82 3.79e+01 1am9A a.38.1.1 17140 1qzmA 94 3.83e+01 c.37.1.20 96651 2a0mA 316 3.84e+01 1xrjA 261 3.84e+01 1szqA 483 3.86e+01 e.44.1.1 99045 1jqeA 292 3.90e+01 c.66.1.19 71789 1pv9A 348 3.90e+01 c.55.2.1,d.127.1.1 95157,95158 1ws9A 387 3.92e+01 1m98A 317 3.95e+01 a.175.1.1,d.17.4.6 78866,78867 2bcgG 453 3.96e+01 1s6cA 183 3.96e+01 a.39.1.5 98594 1i24A 404 3.98e+01 c.2.1.2 83663 1jk0B 345 3.98e+01 a.25.1.2 63143 1bueA 265 3.99e+01 1btl e.3.1.1 42727 1qlaC 256 4.02e+01 1qlaC f.21.2.1 43722 1omrA 201 4.02e+01 a.39.1.5 93349 1dcfA 136 4.05e+01 1dcfA c.23.1.2 31124 2fiyA 309 4.12e+01 1mq4A 272 4.13e+01 d.144.1.7 91391 2bs3C 256 4.21e+01 2ilk 160 4.22e+01 2ilk a.26.1.3 16885 2f8mA 244 4.25e+01 2aeuA 374 4.27e+01 1va6A 518 4.29e+01 1ieaB 228 4.32e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1qsaA 618 4.33e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 2fflA 756 4.41e+01 1j0fA 100 4.41e+01 c.47.1.14 90739 1ib2A 349 4.41e+01 1ib2A a.118.1.8 62141 1unlD 208 4.53e+01 1auiB 169 4.55e+01 1auiB a.39.1.5 17325 1ukvG 453 4.56e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1kl7A 514 4.69e+01 c.79.1.1 72678 1sz6A 249 4.74e+01 1dciA 275 4.76e+01 1dciA c.14.1.3 30918 1o0sA 605 4.88e+01 c.2.1.7,c.58.1.3 86540,86541 1u7nA 336 4.93e+01 c.77.1.4 107726 1d8cA 723 4.94e+01 1d8cA c.1.13.1 29325 1wvfA 520 4.98e+01 8tlnE 316 5.04e+01 1hyt d.92.1.2 59075 2aelA 374 5.07e+01 1j2jB 45 5.14e+01 a.7.8.1 84017 1es5A 262 5.22e+01 1skf e.3.1.1 42679 1ur5A 309 5.24e+01 c.2.1.5,d.162.1.1 99807,99808 1szhA 161 5.24e+01 a.226.1.1 106157 1vrtA 560 5.25e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1ufkA 254 5.25e+01 c.66.1.39 99340 2tmnE 316 5.26e+01 1hyt d.92.1.2 59055 1pytA 94 5.30e+01 1pytA d.58.3.1 39064 2al6A 375 5.31e+01 1o17A 345 5.37e+01 a.46.2.1,c.27.1.1 80765,80766 2evaA 307 5.38e+01 1kdxA 81 5.42e+01 1kdxA a.12.1.1 16375 1ooeA 236 5.42e+01 c.2.1.2 87196 1ctj 89 5.44e+01 1ctj a.3.1.1 15798 1x72A 334 5.51e+01 d.126.1.6 109495 1v37A 177 5.54e+01 1imbA 277 5.56e+01 1imbA e.7.1.1 42957 1ufaA 520 5.59e+01 a.8.3.3,c.6.2.4 99329,99330 1xvxA 312 5.63e+01 1g6aA 271 5.67e+01 1btl e.3.1.1 42704 1x9bA 53 5.70e+01 1lbkA 208 5.71e+01 a.45.1.1,c.47.1.5 73809,73810 1p7tA 731 5.72e+01 c.1.13.1 94319 1hzoA 271 5.73e+01 e.3.1.1 71092 1cy9A 264 5.76e+01 1ecl e.10.1.1 43236 1bjt 793 5.88e+01 1bjt e.11.1.1 43249 1r2fA 319 5.92e+01 1r2fA a.25.1.2 16800 1lj8A 493 5.98e+01 a.100.1.9,c.2.1.6 90392,90393 1rec 201 6.01e+01 1rec a.39.1.5 17326 1dceA 567 6.02e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 2aotA 292 6.02e+01 1j4nA 271 6.02e+01 f.19.1.1 71510 2ghjA 118 6.08e+01 1eu8A 409 6.13e+01 1eu8A c.94.1.1 59502 1lwjA 441 6.15e+01 b.71.1.1,c.1.8.1 74303,74304 1ugmA 125 6.18e+01 d.15.1.3 107827 2aehA 369 6.21e+01 1eyhA 144 6.22e+01 1eduA a.118.9.1 19214 1lqvA 193 6.22e+01 d.19.1.1 74206 1khbA 625 6.23e+01 c.91.1.1,c.109.1.1 68606,68607 2c5qA 240 6.25e+01 1jae 471 6.30e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1fpoA 171 6.39e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 1oyjA 231 6.39e+01 a.45.1.1,c.47.1.5 87597,87598 1l5xA 280 6.40e+01 c.106.1.1 77718 1hulA 108 6.42e+01 1hulA a.26.1.2 16865 2f6mB 109 6.49e+01 2gtrA 261 6.56e+01 1rgyA 360 6.69e+01 e.3.1.1 97456 1b9hA 388 6.72e+01 1b9hA c.67.1.4 34488 1it2A 146 6.73e+01 a.1.1.2 66365 1h1yA 228 6.78e+01 c.1.2.2 76506 1zkjA 359 6.78e+01 1dbhA 354 6.89e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1h6dA 433 6.91e+01 c.2.1.3,d.81.1.5 65656,65657 1t7lA 766 6.95e+01 2fe7A 166 6.96e+01 1fr2B 134 6.98e+01 d.4.1.1 83257 1f2tB 148 7.01e+01 1f2tB 1aq5A 47 7.02e+01 1aq5A h.1.6.1 45577 1c3jA 351 7.04e+01 1c3jA c.87.1.1 35459 1hyeA 313 7.08e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1w9gA 104 7.20e+01 2gwhA 298 7.21e+01 1gnuA 117 7.21e+01 d.15.1.3 65403 1gzsB 165 7.24e+01 a.168.1.1 76425 1tvlA 454 7.34e+01 c.1.16.4 107366 1urvA 190 7.36e+01 1ut0A 190 7.36e+01 a.1.1.2 108012 1vm8A 534 7.44e+01 1v9dA 340 7.46e+01 a.207.1.1 100535 2c12A 439 7.47e+01 1vqzA 341 7.50e+01 4tmkA 213 7.53e+01 5tmpA c.37.1.1 31930 1ltzA 297 7.55e+01 d.178.1.1 74254 1gqaA 130 7.56e+01 a.24.3.2 76275 1gjwA 637 7.58e+01 b.71.1.1,c.1.8.1 60582,60583 1n35A 1267 7.60e+01 e.8.1.4 79935 1ntyA 311 7.60e+01 a.87.1.1,b.55.1.1 103873,103874 1dvjA 246 7.65e+01 1dvjA c.1.2.3 28546 1xrxA 50 7.76e+01 1qopA 268 7.78e+01 2tysA c.1.2.4 28570 1ylqA 96 7.80e+01 2eulA 156 7.80e+01 1tmxA 293 7.82e+01 2bfxA 284 7.88e+01 1octC 156 7.92e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1hzyA 332 7.92e+01 1pscA c.1.9.3 61468 2a6tA 271 7.93e+01 1i0dA 332 7.93e+01 1pscA c.1.9.3 61487 1gr0A 367 7.99e+01 c.2.1.3,d.81.1.3 70379,70380 1ignA 246 8.03e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 4icb 76 8.07e+01 4icb a.39.1.1 17145 1pgtA 210 8.10e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 2cvzA 289 8.14e+01 2g8yA 385 8.15e+01 1m4iA 181 8.16e+01 d.108.1.1 74457 1zklA 353 8.19e+01 2a6hA 315 8.32e+01 2be4A 272 8.34e+01 1rqlA 267 8.59e+01 c.108.1.3 97750 2d68A 82 8.60e+01 1ae9A 179 8.62e+01 1ae9A d.163.1.1 42153 1mw9X 592 8.62e+01 e.10.1.1 91480 1vqoX 92 8.65e+01 1w77A 228 8.66e+01 1vr8A 142 8.66e+01 2fytA 340 8.75e+01 2d00A 109 8.77e+01 1hu3A 260 8.78e+01 1hu3A a.118.1.14 19137 1v93A 296 8.87e+01 c.1.23.1 100532 1r6uA 437 8.94e+01 c.26.1.1 97163 1wz7A 111 8.99e+01