# 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 1nxmA 197 9.61e-02 b.82.1.1 86385 1vqoW 154 9.28e-01 1jj2V 154 1.15e+00 1ffkT d.59.1.1 63107 1s72W 154 1.15e+00 d.59.1.1 105342 1ark 60 1.41e+00 1bb9 b.34.2.1 24473 1z90A 469 2.36e+00 1pk6A 133 2.79e+00 b.22.1.1 94801 1fxzA 476 2.92e+00 b.82.1.2,b.82.1.2 65059,65060 1svpA 161 3.17e+00 1svpA b.47.1.3 26384 1d7yA 408 3.71e+00 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1mt6A 280 4.10e+00 b.76.2.1,b.85.7.1 79446,79447 1m98A 317 4.64e+00 a.175.1.1,d.17.4.6 78866,78867 3nul 130 4.85e+00 3nul d.110.1.1 40891 1f9zA 135 4.96e+00 1qipA d.32.1.1 38484 2fcr 173 5.08e+00 1rcf c.23.5.1 31151 1q8bA 105 5.47e+00 d.58.4.6 96201 1lxdA 100 5.49e+00 1lfdA d.15.1.5 37624 1fa8A 135 6.15e+00 1qipA d.32.1.1 38486 1jlnA 297 6.33e+00 1pty c.45.1.2 63172 1ih7A 903 6.57e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1zgkA 308 6.66e+00 1cqa 133 6.82e+00 3nul d.110.1.1 40890 1ld4A 264 7.07e+00 i.6.1.1 77886 1ps2 60 7.23e+00 2pspA g.16.1.1 44746 1u6dX 308 7.29e+00 1a0k 131 7.63e+00 3nul d.110.1.1 40892 1pm3A 78 7.70e+00 b.41.1.2 94889 1jtdB 273 7.70e+00 b.69.5.2 67265 2fp8A 322 7.92e+00 2awaA 390 8.15e+00 1h8gA 95 8.28e+00 b.109.1.1 65735 1oboA 169 8.44e+00 c.23.5.1 86776 1qipA 183 8.48e+00 1qipA d.32.1.1 38470 1h1iD 350 8.85e+00 b.82.1.5 76472 1h1iB 350 9.03e+00 b.82.1.5 76470 2ghsA 326 9.16e+00 2bepA 159 9.34e+00 1el4A 195 9.40e+00 1ej3A a.39.1.5 59453 1qv1A 195 9.55e+00 a.39.1.5 96347 1o5uA 101 9.88e+00 b.82.1.8 92518 1gvmA 136 1.00e+01 b.109.1.1 70612 2bryA 497 1.02e+01 1h1iC 350 1.06e+01 b.82.1.5 76471 1y6iA 233 1.07e+01 1juhA 350 1.10e+01 b.82.1.5 71884 1wwrA 171 1.11e+01 1rcf 169 1.11e+01 1rcf c.23.5.1 31170 1s4iA 175 1.12e+01 1prs 173 1.16e+01 1prs b.11.1.1,b.11.1.1 23625,23626 1ywfA 296 1.18e+01 1prr 173 1.18e+01 1prs b.11.1.1,b.11.1.1 23623,23624 2fqpA 97 1.19e+01 1nziA 159 1.20e+01 b.23.1.1,g.3.11.1 86449,86450 1wkqA 164 1.23e+01 c.97.1.2 109393 1khdA 345 1.28e+01 a.46.2.1,c.27.1.1 77400,77401 1xtmA 175 1.30e+01 1gmeA 151 1.32e+01 b.15.1.1 65305 1khiA 176 1.38e+01 b.34.5.2,b.40.4.5 77408,77409 1oneA 436 1.39e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1cc1L 498 1.44e+01 1h2rL e.18.1.1 43301 1jf2A 195 1.49e+01 1ej3A a.39.1.5 62930 1jf0A 195 1.52e+01 1ej3A a.39.1.5 62926 2f5tX 233 1.54e+01 1u2cA 246 1.55e+01 b.1.6.2,d.272.1.1 107610,107611 1xtlA 175 1.55e+01 1o12A 376 1.63e+01 b.92.1.5,c.1.9.10 80758,80759 1bh5A 183 1.64e+01 1qipA d.32.1.1 38476 1gmmA 133 1.66e+01 b.18.1.10 65314 1p5zB 263 1.69e+01 c.37.1.1 87815 2al1A 436 1.71e+01 1m1fA 110 1.73e+01 b.34.6.2 78401 1hcxA 127 1.75e+01 b.109.1.1 65800 1qyaA 307 1.75e+01 d.21.1.2,d.21.1.2 104653,104654 1ww9A 392 1.80e+01 2ge3A 170 1.86e+01 1npsA 88 1.88e+01 1prs b.11.1.1 23622 1c4rA 182 1.88e+01 1c4rA b.29.1.4 24229 1bnr 110 1.90e+01 1b20A d.1.1.2 36206 1pot 325 1.93e+01 1pot c.94.1.1 35807 1ahjA 207 1.93e+01 2ahjA d.149.1.1 41774 1syxB 86 1.95e+01 1eo1A 124 1.96e+01 1eo1A c.55.5.1 33739 2oneA 436 1.99e+01 4enl c.1.11.1,d.54.1.1 29203,38847 1q8fA 313 2.00e+01 c.70.1.1 96203 4enl 436 2.02e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1z4rA 168 2.04e+01 1bngA 110 2.07e+01 1b20A d.1.1.2 36184 1eur 365 2.09e+01 1eut b.68.1.1 27607 1vp4A 425 2.20e+01 1yr0A 175 2.28e+01 1brhA 110 2.28e+01 1b20A d.1.1.2 36151 1lfdA 87 2.29e+01 1lfdA d.15.1.5 37622 1ne8A 117 2.34e+01 b.34.6.2 80424 1baoA 110 2.36e+01 1b20A d.1.1.2 36187 1yhfA 115 2.38e+01 2ahjA 206 2.40e+01 2ahjA d.149.1.1 41772 1rzhH 260 2.45e+01 b.41.1.1,f.23.10.1 98162,98163 1qovH 260 2.52e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1aijH 260 2.52e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 1uaqA 158 2.52e+01 c.97.1.2 88386 2rgf 97 2.63e+01 1lfdA d.15.1.5 37627 1df7A 159 2.64e+01 3dfr c.71.1.1 34885 1p1mA 406 2.64e+01 b.92.1.4,c.1.9.9 87696,87697 1j71A 334 2.67e+01 1eagA b.50.1.2 62669 1woqA 267 2.68e+01 c.55.1.10,c.55.1.10 109462,109463 1o97C 264 2.72e+01 c.26.2.3 81232 1p6oA 161 2.75e+01 c.97.1.2 94185 1zq1A 438 2.75e+01 2ahjC 206 2.79e+01 2ahjA d.149.1.1 41773 1noyA 388 2.89e+01 1clqA c.55.3.5 33713 1vquA 374 2.90e+01 1jv1A 505 2.93e+01 c.68.1.5 71892 1urrA 102 2.94e+01 d.58.10.1 107998 1b20A 110 2.95e+01 1b20A d.1.1.2 36207 1b2zA 110 2.96e+01 1b20A d.1.1.2 36216 1k6wA 426 3.06e+01 b.92.1.2,c.1.9.5 68236,68237 1raxA 115 3.07e+01 1lfdA d.15.1.5 37626 1xfsA 178 3.12e+01 d.129.3.5 109589 1ycsA 199 3.18e+01 1tupA b.2.5.2 22433 1b3sA 110 3.18e+01 1b20A d.1.1.2 36229 1r26A 125 3.19e+01 c.47.1.1 96847 2gupA 292 3.20e+01 1ra0A 430 3.22e+01 1egxA 115 3.30e+01 1evhA b.55.1.4 27000 1gyfA 62 3.31e+01 1gyfA d.76.1.1 39749 2al2A 436 3.32e+01 1frrA 95 3.33e+01 1awd d.15.4.1 37674 1vkdA 338 3.38e+01 b.67.2.4 108644 1xe7A 203 3.40e+01 1tw7A 99 3.42e+01 1rb9 53 3.47e+01 1rb9 g.41.5.1 45214 2cz1A 206 3.48e+01 2fvgA 340 3.54e+01 2c4bA 143 3.54e+01 8rxnA 52 3.54e+01 1rb9 g.41.5.1 45215 1b2sA 110 3.56e+01 1b20A d.1.1.2 36213 1pcfA 66 3.56e+01 1pcfA d.18.1.1 38142 1ew0A 130 3.61e+01 1drmA d.110.3.2 40905 1u9aA 160 3.72e+01 1u9aA d.20.1.1 38333 1uzkA 162 3.74e+01 1t2wA 145 3.77e+01 b.100.1.1 106289 1ctt 294 3.79e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1d06A 130 3.79e+01 1drmA d.110.3.2 40906 2as0A 396 3.80e+01 1f5sA 211 3.85e+01 1f5sA c.108.1.4 59656 1fd9A 213 3.87e+01 1fd9A d.26.1.1 59771 1ojqA 212 3.92e+01 d.166.1.1 93146 1kblA 873 3.93e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1o6jA 150 3.97e+01 c.47.1.10 81089 1uzpA 162 4.00e+01 g.3.11.1,g.3.11.1,g.23.1.1 100232,100233,100234 2grrA 161 4.06e+01 1yopA 83 4.07e+01 1eut 605 4.11e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1rnbA 110 4.16e+01 1b20A d.1.1.2 36196 1s4bP 674 4.19e+01 d.92.1.5 105252 1cv8 174 4.20e+01 1cv8 d.3.1.1 37089 1erzA 303 4.25e+01 1erzA d.160.1.2 59498 1uf5A 303 4.31e+01 d.160.1.2 107808 1h91A 180 4.32e+01 b.60.1.1 60805 1w8oA 601 4.32e+01 1euu 605 4.34e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1lvoA 302 4.36e+01 b.47.1.4 74284 1i4uA 181 4.48e+01 b.60.1.1 61732 1banA 110 4.48e+01 1b20A d.1.1.2 36197 1yfuA 174 4.61e+01 1v04A 355 4.64e+01 b.68.6.2 100240 1lcyA 325 4.65e+01 b.36.1.4,b.47.1.1 73834,73835 1j6pA 418 4.74e+01 b.92.1.4,c.1.9.9 77089,77090 1wba 175 4.74e+01 1wba b.42.4.1 25591 1m4uA 206 4.75e+01 g.17.1.7 78625 2fa8A 105 4.81e+01 1umgA 362 4.92e+01 d.280.1.1 107956 1ecsA 126 4.99e+01 1ecsA d.32.1.2 59407 2f1lA 187 5.06e+01 2fuvA 549 5.19e+01 1tiyA 164 5.21e+01 c.97.1.2 107012 1dik 874 5.26e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1kzkA 99 5.31e+01 b.50.1.1 73371 1sffA 426 5.33e+01 c.67.1.4 105482 1zn6A 227 5.52e+01 1kjvA 284 5.53e+01 b.1.1.2,d.19.1.1 77421,77422 1b9vA 390 5.59e+01 2qwc b.68.1.1 27603 2biqA 219 5.59e+01 1ufkA 254 5.62e+01 c.66.1.39 99340 1tupA 219 5.62e+01 1tupA b.2.5.2 22434 1mpyA 307 5.77e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 2ampA 304 5.81e+01 1dx5I 118 5.81e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 1qwkA 317 5.82e+01 c.1.7.1 96482 2gwdA 449 5.87e+01 1r45A 204 5.90e+01 1axaA 99 6.01e+01 1hvc b.50.1.1 26633 1tsrA 219 6.06e+01 1tupA b.2.5.2 22437 2amdA 311 6.18e+01 1bcpC 199 6.18e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1d4tA 104 6.25e+01 1d4tA d.93.1.1 40537 1lqsR 214 6.27e+01 b.1.2.1,b.1.2.1 74194,74195 1e44B 96 6.28e+01 1e44B b.101.1.1 59220 1ri6A 343 6.28e+01 b.69.11.1 97503 1a2pA 110 6.47e+01 1b20A d.1.1.2 36140 2ffsA 157 6.51e+01 1brnL 110 6.55e+01 1b20A d.1.1.2 36143 1vzwA 244 6.66e+01 1zn8A 180 6.69e+01 1l7mA 211 6.72e+01 c.108.1.4 73664 1zhhB 242 6.76e+01 1fxtA 149 6.76e+01 d.20.1.1 65055 1nw3A 416 6.79e+01 c.66.1.31 86288 1j97A 211 6.89e+01 1f5sA c.108.1.4 62753 1lcjA 109 6.92e+01 1qadA d.93.1.1 40414 1a3s 160 6.93e+01 1u9aA d.20.1.1 38335 1wcqA 601 6.96e+01 1uolA 219 6.98e+01 b.2.5.2 99695 1xygD 359 7.01e+01 1u69A 163 7.04e+01 d.32.1.7 107699 2fymA 431 7.13e+01 1yh6A 179 7.14e+01 1vgjA 184 7.18e+01 2b59A 187 7.25e+01 2c7xA 436 7.26e+01 3fruA 269 7.29e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 1o22A 170 7.36e+01 d.238.1.1 86557 2f0aA 98 7.39e+01 1wr2A 238 7.41e+01 1vdxA 184 7.43e+01 1qz8A 113 7.43e+01 b.140.1.1 96619 2cw8A 537 7.58e+01 1g7pA 274 7.64e+01 b.1.1.2,d.19.1.1 70153,70154 1n3yA 198 7.68e+01 c.62.1.1 79976 1lvmA 229 7.68e+01 b.47.1.3 78243 1b21A 110 7.71e+01 1b20A d.1.1.2 36219 1svvA 359 7.75e+01 c.67.1.1 106054 1k0hA 117 7.75e+01 b.106.1.2 71975 2f4wA 187 7.80e+01 1xs1A 193 7.85e+01 1ca1 370 7.92e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1bxoA 323 7.93e+01 2er7E b.50.1.2 26805 1evhA 112 8.05e+01 1evhA b.55.1.4 26997 1ewxA 146 8.20e+01 1ewxA c.47.1.10 33062 1lyvA 306 8.20e+01 c.45.1.2 74348 1i1qA 520 8.24e+01 1qdlA d.161.1.1 61543 1lj2C 28 8.25e+01 1kjkA 64 8.31e+01 d.10.1.4 72613 2a5kA 307 8.33e+01 1culA 217 8.45e+01 1azsA d.58.29.1 39417 1olzA 663 8.50e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1xrtA 467 8.64e+01 1b8pA 329 8.65e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1q2wA 308 8.71e+01 b.47.1.4 88355 1l3lA 234 8.71e+01 a.4.6.2,d.110.5.1 73541,73542 2c9wA 169 8.77e+01 1txkA 498 8.79e+01 b.1.18.2,b.30.5.9 107425,107426 1vplA 256 8.84e+01 1kn0A 212 8.92e+01 d.50.1.3 77444 1vbkA 307 8.94e+01 1uv4A 293 8.95e+01 2ftwA 521 8.97e+01