# List of top-scoring protein chains for t04-100-30-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 2f4qA 346 4.70e-02 1m93C 41 2.40e-01 2a2pA 129 6.96e-01 1yaxA 153 1.13e+00 1u0tA 307 1.18e+00 e.52.1.1 107567 1lktA 104 1.68e+00 1lktA b.90.1.1 28398 1kllA 130 1.73e+00 d.32.1.2 72720 2fh5A 185 1.95e+00 2fa8A 105 2.44e+00 1tp6A 128 2.72e+00 d.17.4.12 107184 1vq2A 193 2.77e+00 1sqeA 109 2.90e+00 d.58.4.5 105908 1w9hA 427 3.25e+00 2c3vA 102 3.35e+00 3nul 130 3.54e+00 3nul d.110.1.1 40891 1iscA 192 3.59e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1m7xA 617 3.86e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 16pk 415 3.97e+00 16pk c.86.1.1 35454 1zkdA 387 4.14e+00 1huxA 270 4.97e+00 1huxA c.55.1.5 61278 1ui0A 205 5.31e+00 c.18.1.2 99411 1l6rA 227 5.60e+00 c.108.1.10 77768 1vjfA 180 5.60e+00 d.116.1.1 100809 1lq9A 112 5.72e+00 d.58.4.3 78129 2cr5A 109 6.03e+00 1a8q 274 6.11e+00 1brt c.69.1.12 34702 1qhoA 686 6.20e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1z0wA 207 6.26e+00 1vetA 124 6.46e+00 d.110.7.1 108553 1v74A 107 6.56e+00 d.243.1.1 100442 2dg5B 190 6.83e+00 1yx1A 264 7.38e+00 1cqyA 99 7.65e+00 1b9zA b.3.1.1 22527 1mtpB 43 7.76e+00 1xvqA 175 7.86e+00 1jtkA 136 8.29e+00 c.97.1.1 71862 1skoA 143 8.47e+00 d.110.7.1 105676 1xc3A 302 8.49e+00 1p6oA 161 8.74e+00 c.97.1.2 94185 1q0qA 406 1.01e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1uwzA 136 1.02e+01 c.97.1.1 108081 2gcc 70 1.03e+01 2gcc d.10.1.2 37484 1uhvA 500 1.08e+01 b.71.1.2,c.1.8.3 99402,99403 1lrzA 426 1.11e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1wi1A 126 1.12e+01 1tqzA 133 1.14e+01 2bjfA 329 1.14e+01 1vr9A 213 1.17e+01 1qauA 112 1.18e+01 1qauA b.36.1.1 24779 1jvsA 400 1.19e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1pqzA 238 1.20e+01 b.1.1.2,d.19.1.1 104297,104298 2fv7A 331 1.20e+01 1xfsA 178 1.21e+01 d.129.3.5 109589 1bu6O 501 1.22e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1iow 306 1.22e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1u58A 253 1.23e+01 3ezmA 101 1.23e+01 3ezmA b.89.1.1 28395 1dcjA 81 1.24e+01 1dcjA d.68.3.3 59115 1w6sA 599 1.25e+01 2pil 159 1.25e+01 2pil d.24.1.1 38376 1txkA 498 1.26e+01 b.1.18.2,b.30.5.9 107425,107426 1nqcA 217 1.27e+01 d.3.1.1 86024 2akrA 285 1.28e+01 2bs9A 503 1.28e+01 1jv4A 162 1.28e+01 b.60.1.1 67343 1j5pA 253 1.29e+01 d.81.1.3,c.2.1.3 71577,83092 2fq9A 225 1.32e+01 1h4rA 314 1.32e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 2a6aA 218 1.34e+01 1qmvA 197 1.38e+01 1qq2A c.47.1.10 33066 1zndA 174 1.40e+01 1cdq 77 1.41e+01 1cds g.7.1.3 44459 1lwdA 413 1.42e+01 c.77.1.1 78265 1lrwA 600 1.45e+01 b.70.1.1 91111 1y9wA 140 1.47e+01 1ttzA 87 1.47e+01 c.47.1.1 107309 1uasA 362 1.48e+01 b.71.1.1,c.1.8.1 88388,88389 2bfgA 503 1.57e+01 1ffyA 917 1.58e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1z5lA 285 1.62e+01 1am2 199 1.65e+01 1am2 b.86.1.2 28381 1iujA 106 1.66e+01 d.58.4.5 90701 1bywA 110 1.68e+01 1bywA d.110.3.6 40912 1qy1A 174 1.68e+01 b.60.1.1 96568 2dcnA 311 1.69e+01 1i05A 180 1.70e+01 1mup b.60.1.1 27130 1nrlA 316 1.70e+01 a.123.1.1 92091 1pm1X 180 1.75e+01 b.60.1.1 104189 1vcdA 126 1.76e+01 1j79A 347 1.81e+01 1j79A c.1.9.4 62675 2ap1A 327 1.82e+01 1xqaA 113 1.88e+01 1y0pA 571 1.92e+01 1p2hA 571 1.92e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1q9iA 571 1.92e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1pufB 73 1.92e+01 a.4.1.1 95132 1tyv 542 1.94e+01 1tyv b.80.1.6 28038 1e39A 571 1.97e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1i06A 180 1.97e+01 1mup b.60.1.1 27131 2dg5A 366 1.98e+01 1kssA 571 1.99e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1zyeA 220 1.99e+01 1wm3A 72 2.00e+01 1z2mA 155 2.00e+01 1w44A 331 2.03e+01 1ka9H 200 2.03e+01 c.23.16.1 77308 1xf1A 926 2.06e+01 1pylA 97 2.07e+01 d.1.1.2 104391 1mdwA 328 2.09e+01 d.3.1.3 84934 1wrvA 308 2.11e+01 1b9wA 89 2.17e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1m65A 245 2.19e+01 c.6.3.1 84847 1cv8 174 2.21e+01 1cv8 d.3.1.1 37089 2fikA 287 2.23e+01 1rvkA 382 2.32e+01 c.1.11.2,d.54.1.1 97928,97929 1b72B 87 2.34e+01 1akhA a.4.1.1 16001 1icxA 155 2.36e+01 d.129.3.1 71191 1icpA 376 2.39e+01 1oyc c.1.4.1 62270 1ywlA 96 2.40e+01 1y88A 199 2.40e+01 1vjlA 164 2.41e+01 d.257.1.1 100822 1jofA 365 2.43e+01 b.69.10.1 71775 1u6mA 199 2.44e+01 1psdA 409 2.44e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1c96A 753 2.50e+01 1amj c.8.2.1,c.83.1.1 30727,35403 2basA 431 2.59e+01 1kb0A 677 2.60e+01 a.3.1.6,b.70.1.1 68378,68379 1tiyA 164 2.63e+01 c.97.1.2 107012 1gv3A 248 2.65e+01 a.2.11.1,d.44.1.1 70585,70586 1mup 166 2.67e+01 1mup b.60.1.1 27133 2be1A 339 2.68e+01 1rewC 135 2.69e+01 g.7.1.3 97336 1h80A 464 2.73e+01 b.80.1.8 65714 1gw5S 142 2.73e+01 d.110.4.2 70633 1c44A 123 2.77e+01 1qndA d.106.1.1 40795 2a15A 139 2.79e+01 1xrkA 124 2.80e+01 1voqa 90 2.81e+01 2fhxA 246 2.82e+01 1th8A 145 2.86e+01 d.122.1.3 106908 1a7cA 379 2.91e+01 1sek e.1.1.1 42660 1bx1A 314 2.91e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1e25A 282 2.94e+01 1e25A e.3.1.1 42731 1ro5A 201 2.97e+01 d.108.1.3 105023 1sgvA 316 2.99e+01 b.122.1.1,d.265.1.2 98858,98859 1ifqA 138 3.04e+01 1ifqA d.110.4.1 62350 1hw6A 278 3.06e+01 1frb c.1.7.1 61296 8acn 754 3.10e+01 1amj c.8.2.1,c.83.1.1 30724,35400 1kv9A 668 3.11e+01 a.3.1.6,b.70.1.1 73056,73057 2ghrA 302 3.13e+01 1h3qA 140 3.16e+01 d.110.4.3 76652 1gpeA 587 3.20e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 2gaiA 633 3.25e+01 1xkiA 162 3.27e+01 1obr 326 3.39e+01 1aye c.56.5.2 33828 2c7xA 436 3.43e+01 1h6hA 143 3.44e+01 d.189.1.1 65681 2a8eA 220 3.46e+01 1vemA 516 3.46e+01 1rkd 309 3.46e+01 1rkd c.72.1.1 34928 1sc6A 404 3.55e+01 1vecA 206 3.55e+01 c.37.1.19 100575 1e2wA 251 3.55e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1um5H 217 3.55e+01 1gqzA 274 3.56e+01 d.21.1.1,d.21.1.1 83311,83312 2b5nA 323 3.58e+01 1fnd 314 3.59e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 2crvA 120 3.61e+01 1uh6A 100 3.62e+01 d.15.1.1 99394 1x6oA 174 3.67e+01 b.34.5.2,b.40.4.5 109493,109494 1qnnA 191 3.67e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1pvmA 184 3.67e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1fm2B 520 3.67e+01 1fm2B 1kay 381 3.67e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2h3bA 494 3.67e+01 1wdvA 152 3.70e+01 1lfdA 87 3.72e+01 1lfdA d.15.1.5 37622 1or0B 528 3.72e+01 1pswA 348 3.73e+01 c.87.1.7 88287 1itcA 516 3.76e+01 b.3.1.1,c.1.8.1 83705,83706 1vjvA 415 3.81e+01 d.3.1.9 108632 2go8A 122 3.82e+01 1sq9A 397 3.82e+01 b.69.4.1 105889 2ae5B 528 3.83e+01 2a2lA 145 3.86e+01 1uesA 191 3.87e+01 a.2.11.1,d.44.1.1 107798,107799 1wkqA 164 3.90e+01 c.97.1.2 109393 1g72A 573 3.94e+01 4aahA b.70.1.1 27680 2bgiA 272 3.97e+01 1bupA 386 3.97e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2f9zC 159 4.00e+01 1zg2A 107 4.01e+01 2cl1A 279 4.06e+01 1n3gA 113 4.10e+01 d.204.1.1 79962 1xvsA 126 4.13e+01 2a25A 193 4.16e+01 1x54A 434 4.18e+01 1h9oA 112 4.21e+01 1qadA d.93.1.1 60837 1glcG 501 4.22e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1itbB 315 4.22e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1qqp1 213 4.28e+01 1qqp1 1k7jA 206 4.29e+01 d.115.1.1 72103 1e1aA 314 4.30e+01 1e1aA b.68.6.1 59155 1a79A 171 4.34e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1peeA 180 4.38e+01 b.60.1.1 104126 1vkcA 158 4.39e+01 1fjgP 88 4.41e+01 1emwA d.27.1.1 38444 1ijqA 316 4.43e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1p3dA 475 4.43e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1mkeA 152 4.46e+01 b.55.1.4 79231 1w4tA 299 4.47e+01 1r13A 148 4.47e+01 d.169.1.1,h.1.1.1 96782,96783 1xubA 298 4.50e+01 1hd2A 161 4.50e+01 c.47.1.10 60962 1l6sA 323 4.50e+01 c.1.10.3 73627 1ri9A 102 4.51e+01 b.34.2.1 97506 1kngA 156 4.53e+01 c.47.1.10 72777 1g2rA 100 4.55e+01 1g2rA d.192.1.1 60231 1bbt1 213 4.55e+01 1qqp1 1zceA 155 4.57e+01 2bf6A 449 4.58e+01 2c82A 413 4.59e+01 1zbsA 291 4.59e+01 1omiA 248 4.63e+01 b.82.3.3,a.4.5.4 87079,87080 1op3H 225 4.74e+01 b.1.1.1,b.1.1.2 87208,87209 2gfoA 396 4.79e+01 1xt9A 212 4.83e+01 1b77A 228 4.86e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2hayA 224 4.90e+01 1m7jA 484 4.97e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1pjxA 314 4.97e+01 b.68.6.1 104167 2ga9D 469 5.01e+01 1zq1A 438 5.03e+01 1te7A 103 5.05e+01 1wwrA 171 5.06e+01 1i0cA 60 5.08e+01 1aojA b.34.2.1 61485 1n13A 52 5.09e+01 d.155.1.2 85248 2cu3A 64 5.10e+01 2a4vA 159 5.11e+01 1xxqA 161 5.14e+01 1rk6A 496 5.20e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1xkgA 312 5.20e+01 1llnA 262 5.28e+01 d.165.1.1 84625 1njkA 156 5.32e+01 d.38.1.1 85818 1oe8A 211 5.40e+01 a.45.1.1,c.47.1.5 86905,86906 2cw9A 194 5.41e+01 1npsA 88 5.41e+01 1prs b.11.1.1 23622 1m22A 503 5.62e+01 c.117.1.1 78464 1b8aA 438 5.63e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1qb5D 99 5.69e+01 b.40.2.1 88357 1wlsA 328 5.72e+01 2gk3A 256 5.72e+01 1q45A 391 5.76e+01 c.1.4.1 95780 1w41A 101 5.86e+01 1gt1A 159 5.86e+01 b.60.1.1 90515 1hn2A 159 5.86e+01 b.60.1.1 65890 1s4uX 407 5.89e+01 1xniA 118 5.93e+01 1kyhA 276 5.94e+01 c.72.1.4 73222 1tzaA 134 5.94e+01 b.1.23.1 107468 1bco 327 5.96e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1brt 277 6.00e+01 1brt c.69.1.12 34699 1fnc 314 6.09e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1qjpA 171 6.09e+01 1bxwA f.4.1.1 43742 2he7A 283 6.11e+01 1tiiD 99 6.12e+01 1tiiD b.40.2.1 24965 1broA 277 6.14e+01 1brt c.69.1.12 34700 1obpA 159 6.15e+01 1obpA b.60.1.1 27092 1lgpA 116 6.17e+01 b.26.1.2 73890 1qlaA 656 6.18e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1r4pB 70 6.21e+01 b.40.2.1 97026 1c4zA 358 6.23e+01 1c4zA d.148.1.1 41766 1xgyH 219 6.27e+01 1s9jA 341 6.33e+01 2bs6A 90 6.37e+01 1ex1A 605 6.40e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1hjrA 158 6.42e+01 1hjrA c.55.3.6 33727 1pzxA 289 6.43e+01 c.119.1.1 95484 1k55A 246 6.44e+01 e.3.1.1 68156 1gmuA 143 6.49e+01 b.107.1.1,d.58.38.1 65335,65336 1eajA 126 6.57e+01 1f5wA b.1.1.1 59401 1h7mA 102 6.59e+01 d.79.3.1 83485 1ndh 272 6.59e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1i07A 60 6.66e+01 1aojA b.34.2.1 61477 1dmhA 311 6.68e+01 1dmhA b.3.6.1 22633 2bt9A 90 6.71e+01 1ny1A 240 6.73e+01 c.6.2.3 86395 1m9sA 605 6.76e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1vqoS 85 6.81e+01 1xyiA 66 6.83e+01 2ftwA 521 6.84e+01 1p4kA 295 6.85e+01 d.153.1.5 87772 1s72S 85 6.86e+01 d.12.1.1 105338 1jj2R 84 6.86e+01 1ffkP d.12.1.1 63103 2b7kA 200 6.86e+01 1pmhX 185 6.87e+01 b.18.1.18 104193 4ubpC 570 6.90e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1iwdA 215 6.91e+01 d.3.1.1 83756 1o7iA 119 6.94e+01 b.40.4.3 86642 1zm8A 259 6.99e+01 2bs3A 656 6.99e+01 2a5hA 416 7.00e+01 1e3uA 246 7.07e+01 1fofA e.3.1.1 42755 2cwzA 141 7.13e+01 1mkiA 330 7.14e+01 e.3.1.2 84994 1o6aA 96 7.20e+01 b.139.1.1 92562 1mqeA 207 7.30e+01 d.113.1.1 91394 1qgoA 264 7.32e+01 1qgoA c.92.1.2 35596 1khbA 625 7.34e+01 c.91.1.1,c.109.1.1 68606,68607 1ro7A 259 7.36e+01 c.130.1.1 97667 1wz9A 375 7.36e+01 1ayaA 101 7.41e+01 1qadA d.93.1.1 40460 1v8hA 107 7.47e+01 2sli 679 7.47e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1lkkA 105 7.51e+01 1lckA d.93.1.1 40412 1wnfA 328 7.58e+01 1ospO 257 7.58e+01 1ospO b.76.1.1 27971 1f00I 282 7.59e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1wejH 223 7.65e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1u9tA 354 7.65e+01 1qx4A 274 7.65e+01 b.43.4.2,c.25.1.1 104624,104625 2f4nA 273 7.66e+01 1tqxA 227 7.66e+01 1pj5A 830 7.68e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 2b59B 172 7.69e+01 1r77A 103 7.72e+01 1s68A 249 7.74e+01 d.142.2.4 98591 1u1wA 298 7.75e+01 1fecA 490 7.79e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1r26A 125 7.82e+01 c.47.1.1 96847 1o7zA 77 7.85e+01 d.9.1.1 86660 1d4tA 104 7.88e+01 1d4tA d.93.1.1 40537 1qhvA 195 7.91e+01 1qhvA b.21.1.1 23842 1z5yE 149 7.92e+01 2c26A 260 7.95e+01 1ru3A 732 8.04e+01 e.26.1.3 97835 1g5aA 628 8.05e+01 b.71.1.1,c.1.8.1 65152,65153 1u14A 172 8.08e+01 c.51.4.3 107579 1aisA 182 8.09e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1vggA 161 8.12e+01 1azpA 66 8.16e+01 1azpA b.34.13.1 37467 2dchX 216 8.21e+01 1a9xA 1058 8.25e+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 18550,31479,31657,31658,41502,41503 1jtdB 273 8.28e+01 b.69.5.2 67265 2gupA 292 8.28e+01 1vl2A 421 8.35e+01 c.26.2.1,d.210.1.1 108708,108709 1ryaA 160 8.38e+01 d.113.1.5 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