# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1josA 128 9.33e-02 d.52.7.1 84191 1hw8A 467 1.61e-01 1dqaA d.58.20.1 61298 d.179.1.1 61299 1pa4A 116 2.53e-01 d.52.7.1 -9780 1dqaA 467 2.96e-01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1dqaC 467 4.23e-01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1r31A 428 4.97e-01 d.58.20.1 -10108 d.179.1.1 -11716 1qaxA 428 8.40e-01 1qaxA d.58.20.1 39376 d.179.1.1 42597 1i9bA 217 8.43e-01 1i9bA b.96.1.1 62084 1h2vZ 156 8.65e-01 d.58.7.1 76595 1h6kZ 98 9.11e-01 d.58.7.1 60686 1hcl 298 9.37e-01 1hcl d.144.1.7 41593 1uw6A 211 9.84e-01 b.96.1.1 -3077 1f3mC 297 1.20e+00 1hcl d.144.1.7 41677 1h6kX 97 1.25e+00 d.58.7.1 60684 1ge9A 184 1.28e+00 1dd5A d.67.3.1 60463 1qayA 428 1.30e+00 1qaxA d.58.20.1 39378 d.179.1.1 42599 1gz8A 299 1.42e+00 d.144.1.7 83405 1cx0A 95 1.87e+00 1urnA d.58.7.1 39158 1r3eA 309 2.16e+00 b.122.1.1 -5118 unknown_sccs -10146 1p27B 106 2.18e+00 d.58.7.1 -10020 1sqlA 146 2.25e+00 1a63 130 2.64e+00 1a62 a.140.3.1 64710 b.40.4.5 64711 1mw7A 240 2.70e+00 e.39.1.1 79557 1is1A 185 2.83e+00 d.67.3.1 83704 1jvpP 298 2.92e+00 d.144.1.7 67371 1cof 143 3.06e+00 1cof d.109.1.2 40860 1cfyA 143 3.11e+00 1cof d.109.1.2 40858 1j98A 157 3.14e+00 1j98A d.185.1.2 62755 1urnA 97 3.18e+00 1urnA d.58.7.1 39153 1o0pA 104 3.35e+00 d.58.7.1 86535 1b4vA 504 3.40e+00 1b8sA c.3.1.2 30334 d.16.1.1 37865 1e1xA 299 3.61e+00 1hcl d.144.1.7 59157 1b8sA 504 3.82e+00 1b8sA c.3.1.2 30335 d.16.1.1 37866 1c0aA 585 4.08e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1n1pA 504 4.18e+00 c.3.1.2 -5988 d.16.1.1 -9206 1cc8A 73 4.24e+00 1cc8A d.58.17.1 39343 1n16A 381 4.27e+00 a.83.1.1 79781 d.128.1.2 79782 1dd5A 185 4.27e+00 1dd5A d.67.3.1 39564 1jjgA 102 4.47e+00 b.40.4.5 71696 1n4wA 504 4.68e+00 c.3.1.2 -5991 d.16.1.1 -9209 1dhn 121 4.92e+00 1dhn d.96.1.3 40663 1mxtA 504 5.14e+00 c.3.1.2 79671 d.16.1.1 79672 1l0wA 580 5.22e+00 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1mk4A 157 5.24e+00 d.108.1.1 84979 1qh4A 380 5.32e+00 1qh4A a.83.1.1 18462 d.128.1.2 41197 1v7oA 165 5.45e+00 unknown_sccs -10249 1ea0A 1479 5.47e+00 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1s3zA 165 5.61e+00 1ksyA 154 5.61e+00 d.89.1.2 72948 1gudA 288 5.65e+00 c.93.1.1 83326 2e2c 156 5.78e+00 1u9aA d.20.1.1 38336 1i21A 159 6.23e+00 1i21A d.108.1.1 61549 3sxlA 184 6.35e+00 1b7fA d.58.7.1 39173 d.58.7.1 39174 1opjA 293 6.35e+00 d.144.1.7 87230 1lw9A 164 6.48e+00 d.2.1.3 84727 1nwwA 149 6.65e+00 d.17.4.8 86306 1k38A 254 6.76e+00 e.3.1.1 84303 1konA 249 6.88e+00 e.39.1.1 72823 1ijhA 504 6.88e+00 c.3.1.2 66161 d.16.1.1 66162 1k8hA 133 7.03e+00 b.111.1.1 72176 1p36A 164 7.23e+00 d.2.1.3 -8840 1i1dA 161 7.33e+00 1i21A d.108.1.1 61526 1b9mA 265 7.90e+00 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1rk8A 165 8.12e+00 d.58.7.1 -10018 1lxnA 99 8.14e+00 d.58.48.1 84737 1csn 298 8.18e+00 1csn d.144.1.7 41664 1kzlA 208 8.19e+00 b.43.4.3 77635 b.43.4.3 77636 1tf4A 605 8.38e+00 1tf4A a.102.1.2 18827 b.2.2.2 22393 1rpjA 288 8.43e+00 2dri c.93.1.1 35656 1oo0B 110 8.52e+00 d.58.7.1 87183 1i12A 160 8.60e+00 1i21A d.108.1.1 61515 1dppA 507 8.61e+00 1dpe c.94.1.1 35800 1a8vA 121 8.86e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1mq4A 272 8.95e+00 d.144.1.7 -11349 1jy8A 159 8.98e+00 d.79.5.1 67452 1nbwA 607 9.06e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1oxsC 353 9.46e+00 b.40.6.3 87519 c.37.1.12 87520 1qzgA 187 9.72e+00 b.40.4.3 -3920 1asyA 490 9.74e+00 1b8aA b.40.4.1 25242 d.104.1.1 40763 1ib8A 164 9.82e+00 b.38.2.1 71168 d.52.4.1 71169 1jmtA 104 9.85e+00 d.58.7.3 63180 1egaA 301 9.97e+00 1egaA c.37.1.8 32150 d.52.3.1 38836 1m5oC 100 1.01e+01 d.58.7.1 78654 1qupA 222 1.01e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1f7wA 144 1.03e+01 1f46A d.129.4.1 59679 1fxlA 167 1.03e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1oxxK 353 1.03e+01 b.40.6.3 -3969 c.37.1.12 -7187 1gx1A 160 1.07e+01 d.79.5.1 70675 1egr 85 1.09e+01 1kte c.47.1.1 32765 1v6fA 151 1.09e+01 1rro 108 1.14e+01 1a75A a.39.1.4 17195 1hd2A 161 1.15e+01 c.47.1.10 60962 1k3tA 359 1.16e+01 c.2.1.3 72022 d.81.1.1 72023 1fjcA 96 1.18e+01 1fjcA d.58.7.1 39212 1kpeA 126 1.19e+01 1kpf d.13.1.1 37508 1s71A 316 1.20e+01 1sgvA 316 1.20e+01 b.122.1.1 -5120 unknown_sccs -10148 1hl6A 165 1.23e+01 d.58.7.1 83609 1tx4B 178 1.23e+01 1ctqA c.37.1.8 32045 1usuA 260 1.23e+01 unknown_sccs -9045 1cnuA 137 1.23e+01 1cof d.109.1.2 40862 1bam 213 1.28e+01 1bam c.52.1.3 33285 1s14A 194 1.32e+01 d.122.1.2 -10973 1uc2A 481 1.32e+01 unknown_sccs -11725 1j08A 226 1.34e+01 c.47.1.2 83855 c.47.1.2 83856 1tfe 145 1.34e+01 1tfe d.43.1.1 38680 1lay 256 1.36e+01 1lay b.57.1.1 27014 1bxnA 485 1.38e+01 1burA c.1.14.1 29376 d.58.9.1 39282 1qrdA 273 1.40e+01 1d4aA c.23.5.3 31217 1j6wA 175 1.44e+01 1j98A d.185.1.2 62663 1k3sA 113 1.44e+01 d.198.1.1 68120 1gk8A 475 1.46e+01 c.1.14.1 65234 d.58.9.1 65235 1a8l 226 1.50e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1afi 72 1.53e+01 1aw0 d.58.17.1 39339 1ln1A 214 1.56e+01 d.129.3.2 74038 1ek0A 170 1.57e+01 1ctqA c.37.1.8 32076 1vioA 243 1.57e+01 unknown_sccs -10154 d.66.1.5 -10240 1gkuB 1054 1.61e+01 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1qfnA 85 1.66e+01 1qfnA c.47.1.1 32768 1nqcA 217 1.76e+01 d.3.1.1 86024 1quqA 129 1.79e+01 1quqA b.40.4.3 25303 119l 164 1.80e+01 1l92 d.2.1.3 36622 1oapA 109 1.82e+01 unknown_sccs -10428 1f08A 148 1.84e+01 1f08A d.89.1.2 59564 1j0wA 103 1.89e+01 b.55.1.2 -4364 1d4aA 273 1.90e+01 1d4aA c.23.5.3 31219 1l58 164 1.90e+01 1l92 d.2.1.3 36635 1gehA 444 1.91e+01 c.1.14.1 65181 d.58.9.1 65182 1a62 130 1.97e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1kobA 387 1.98e+01 1tkiA d.144.1.7 41640 1v8fA 276 1.98e+01 c.26.1.4 -6618 1bcpF 99 1.99e+01 1prtF b.40.2.1 25142 1m15A 357 2.01e+01 a.83.1.1 78368 d.128.1.2 78369 1l92 164 2.06e+01 1l92 d.2.1.3 36629 1ak1 310 2.06e+01 1ak1 c.92.1.1 35594 1dpe 507 2.19e+01 1dpe c.94.1.1 35799 1i1gA 141 2.29e+01 a.4.5.32 65982 d.58.4.2 65983 8rucA 475 2.35e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1osdA 72 2.36e+01 1gw5S 142 2.36e+01 d.110.4.2 70633 1t8hA 277 2.38e+01 1efuB 282 2.40e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 3bamA 213 2.41e+01 1bam c.52.1.3 33288 1ek8A 185 2.43e+01 1ek8A d.67.3.1 59444 1esgA 213 2.46e+01 1bam c.52.1.3 33286 1jksA 294 2.46e+01 d.144.1.7 71710 1oiaA 95 2.48e+01 d.58.7.1 87051 1vjeA 166 2.49e+01 d.185.1.2 -10261 1t95A 240 2.50e+01 1qk8A 146 2.55e+01 1ewxA c.47.1.10 33061 1blxA 326 2.60e+01 1hcl d.144.1.7 41596 1prxB 224 2.68e+01 1prxA c.47.1.10 33077 1qpsA 261 2.70e+01 1ckqA c.52.1.1 33234 1iqzA 81 2.73e+01 d.58.1.4 66281 1h7xD 1025 2.77e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1gt8C 1025 2.79e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1b8aA 438 2.81e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1kmqA 184 2.83e+01 c.37.1.8 84412 1huqA 164 2.88e+01 1byuA c.37.1.8 32020 1p4oA 322 2.89e+01 d.144.1.7 87775 1kbqA 273 2.90e+01 c.23.5.3 68391 1cvjB 190 2.95e+01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1dozA 309 2.95e+01 1ak1 c.92.1.1 35592 1qy5A 269 2.97e+01 d.122.1.1 -10958 1h7wB 1025 2.98e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1eriA 276 2.99e+01 1ckqA c.52.1.1 33231 1a48 306 3.01e+01 1a48 d.143.1.1 41590 1aqb 183 3.03e+01 1aqb b.60.1.1 27084 1l3iA 192 3.03e+01 c.66.1.22 77676 2fmr 65 3.03e+01 2fmr d.51.1.1 38808 1p9qC 256 3.05e+01 1ris 101 3.16e+01 1ris d.58.14.1 39314 1fzyA 149 3.19e+01 d.20.1.1 65072 1gteA 1025 3.19e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1h7wD 1025 3.20e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1psdA 409 3.20e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1gp0A 143 3.21e+01 b.64.1.1 70300 1llwA 1520 3.22e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 1innA 166 3.22e+01 1j98A d.185.1.2 62608 1qm9A 198 3.25e+01 1qm9A d.58.7.1 39207 d.58.7.1 39208 1qltA 560 3.26e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 2hqi 72 3.29e+01 1aw0 d.58.17.1 39340 1on0A 158 3.30e+01 d.108.1.1 87095 1h7xB 1025 3.33e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1kid 203 3.35e+01 1derA c.8.5.1 30771 1h1wA 289 3.35e+01 d.144.1.7 83460 1aym1 285 3.35e+01 1aym1 2gbp 309 3.37e+01 1gca c.93.1.1 35657 1gteD 1025 3.43e+01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1nu4A 97 3.44e+01 d.58.7.1 80731 1ofdA 1520 3.45e+01 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1qpzA 340 3.46e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1vhiA 142 3.49e+01 1b3tA d.58.8.1 39230 1n6hA 170 3.51e+01 c.37.1.8 80197 1trb 320 3.51e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1a3aC 148 3.53e+01 1a3aA d.112.1.1 40919 1shsA 147 3.54e+01 1shsA b.15.1.1 23675 1b9lA 120 3.54e+01 1b9lA d.96.1.3 40665 1jqhA 308 3.57e+01 d.144.1.7 71793 1vzoA 355 3.58e+01 1cpzA 68 3.59e+01 1aw0 d.58.17.1 39351 1fm0E 150 3.63e+01 1fmaE d.41.5.1 38629 1howA 373 3.64e+01 1hcl d.144.1.7 41679 1mwpA 96 3.64e+01 1mwpA d.170.2.1 42453 1b3tA 147 3.66e+01 1b3tA d.58.8.1 39228 1ha1 184 3.66e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1gthC 1025 3.67e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1prxA 224 3.69e+01 1prxA c.47.1.10 33076 1i88A 389 3.71e+01 c.95.1.2 66070 c.95.1.2 66071 3bamB 213 3.73e+01 1bam c.52.1.3 33289 1e8gA 560 3.78e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1cjxA 357 3.78e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1j6uA 469 3.80e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1h91A 180 3.81e+01 b.60.1.1 60805 1ep0A 185 3.83e+01 1dzrA b.82.1.1 28080 1h7wA 1025 3.88e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1wpoB 256 3.92e+01 1lay b.57.1.1 27013 1ks2A 219 3.94e+01 unknown_sccs 72908 d.58.40.1 72909 1fd8A 73 3.95e+01 1cc8A d.58.17.1 59770 1bovA 69 3.97e+01 2bosA b.40.2.1 25070 1fl2A 310 4.00e+01 1hyuA c.3.1.5 59869 c.3.1.5 59870