# 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 1y14B 171 6.36e-02 1dhn 121 1.23e-01 1dhn d.96.1.3 40663 1zq1A 438 2.53e-01 1fr3A 67 4.45e-01 1fr3A b.40.6.1 25436 2d9rA 104 4.60e-01 1ofdA 1520 5.91e-01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2basA 431 6.01e-01 1ie7C 570 7.98e-01 1ubpC b.92.1.1,c.1.9.2 62315,62316 4ubpC 570 7.98e-01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1l2mA 118 9.26e-01 d.89.1.4 77657 2h6lA 146 1.01e+00 1ubpC 570 1.04e+00 1ubpC b.92.1.1,c.1.9.2 28432,29054 1h2kA 349 1.05e+00 b.82.2.6 76572 1mzeA 351 1.09e+00 b.82.2.6 79694 1khoA 370 1.12e+00 a.124.1.1,b.12.1.3 72489,72490 1yfuA 174 1.20e+00 1llwA 1520 1.24e+00 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1c9oA 66 1.55e+00 1mjc b.40.4.5 25325 2occB 227 1.81e+00 2occB b.6.1.2,f.17.2.1 23027,43519 1smvA 260 2.29e+00 1smvA b.121.4.7 23288 1fdr 248 2.72e+00 1fdr b.43.4.2,c.25.1.1 25653,31543 1aszB 490 2.98e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 2fb7A 95 3.30e+00 1ea0A 1479 3.44e+00 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1a8vA 121 3.44e+00 1a62 a.140.3.1,b.40.4.5 64712,64713 1ca1 370 3.57e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 1csp 67 4.04e+00 1mjc b.40.4.5 25321 1wjnA 97 4.13e+00 1usuA 260 4.26e+00 d.14.1.8 99885 2pcfB 250 4.54e+00 1hcz i.4.1.1 45911 1ha3A 405 4.56e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1v54B 227 4.65e+00 b.6.1.2,f.17.2.1 100322,100323 1c20A 128 4.78e+00 1c20A a.4.3.1 16079 1s5aA 150 5.94e+00 d.17.4.10 98525 1hcz 252 6.52e+00 1hcz b.2.6.1,b.84.2.2 22464,28250 1am2 199 7.04e+00 1am2 b.86.1.2 28381 1jv1A 505 7.26e+00 c.68.1.5 71892 1bia 321 7.47e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1mqoA 227 7.75e+00 d.157.1.1 103846 1zkdA 387 7.88e+00 1eft 405 8.13e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1a8p 258 8.22e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 2bc2A 227 8.29e+00 1a7tA d.157.1.1 42031 2aynA 404 8.39e+00 1gutA 68 8.46e+00 b.40.6.1 65576 1exmA 405 8.63e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1cbf 285 8.66e+00 1cbf c.90.1.1 35587 1kq1A 77 8.84e+00 b.38.1.2 72848 1l3iA 192 9.12e+00 c.66.1.22 77676 1dk4A 252 9.26e+00 1dk4A e.7.1.1 42970 2bszA 278 9.39e+00 2c78A 405 9.50e+00 2bc2B 227 9.70e+00 1a7tA d.157.1.1 42032 2cbf 234 9.72e+00 1cbf c.90.1.1 35588 1yavA 159 9.81e+00 1asyA 490 1.01e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1kk1A 410 1.10e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1qqcA 773 1.13e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1v8gA 329 1.14e+01 a.46.2.1,c.27.1.1 100505,100506 1a62 130 1.24e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1jacA 133 1.26e+01 1jotA 2fwkA 121 1.29e+01 1x36A 237 1.31e+01 1h8eA 510 1.32e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2fcfA 103 1.34e+01 1yezA 68 1.38e+01 1aipE 405 1.41e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1yphE 97 1.43e+01 4sbvA 261 1.44e+01 1smvA b.121.4.7 23299 1ab9C 97 1.46e+01 5ptp 1ihjA 98 1.50e+01 1pdr b.36.1.1 62382 1j5wA 298 1.52e+01 d.104.1.1 71589 1afqC 96 1.52e+01 5ptp 1gg6C 97 1.52e+01 5ptp 1b6fA 159 1.55e+01 1bv1 d.129.3.1 41316 1u0mA 382 1.57e+01 c.95.1.2,c.95.1.2 107557,107558 1mtnC 97 1.58e+01 5ptp 1xxqA 161 1.59e+01 1vquA 374 1.65e+01 2ck3A 510 1.66e+01 1p4kA 295 1.67e+01 d.153.1.5 87772 1e79A 510 1.67e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1x33A 268 1.68e+01 1xw4X 110 1.68e+01 1m26A 133 1.70e+01 1vrbA 342 1.72e+01 9gafA 295 1.73e+01 1apyA d.153.1.5 42008 1i6pA 220 1.76e+01 1ddzA c.53.2.1 61848 2cwpA 112 1.79e+01 1bmfA 510 1.80e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1bib 321 1.80e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1jacC 133 1.82e+01 1jotA 1iz0A 302 1.83e+01 b.35.1.2,c.2.1.1 83821,83822 1q6hA 224 1.84e+01 d.26.1.1 95975 1aipA 405 1.85e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1x35A 268 1.91e+01 1a0lA 244 1.92e+01 5ptp b.47.1.2 26286 1hk9A 74 1.94e+01 b.38.1.2 83541 2cspA 130 1.94e+01 1a63 130 1.94e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1dfcA 493 1.94e+01 1dfcA b.42.5.1,b.42.5.1,b.42.5.1,b.42.5.1 25616,25617,25618,25619 1zd7A 159 1.98e+01 1vj0A 380 1.99e+01 b.35.1.2,c.2.1.1 100786,100787 1zkpA 268 2.01e+01 1qmrA 159 2.01e+01 1bv1 d.129.3.1 41314 2aacA 177 2.02e+01 2arcA b.82.4.1 28150 1ku8A 133 2.04e+01 1yloA 348 2.06e+01 2akrA 285 2.10e+01 1h10A 125 2.11e+01 b.55.1.1 83446 1unqA 125 2.11e+01 b.55.1.1 107968 2arcA 164 2.13e+01 2arcA b.82.4.1 28148 2arcB 164 2.14e+01 2arcA b.82.4.1 28149 1ne9A 335 2.15e+01 d.108.1.4,d.108.1.4 91839,91840 1bv1 159 2.19e+01 1bv1 d.129.3.1 41313 1vm8A 534 2.21e+01 1cjwA 166 2.23e+01 1cjwA d.108.1.1 40818 1xw3A 110 2.26e+01 1j6wA 175 2.28e+01 1j98A d.185.1.2 62663 2f4nA 273 2.30e+01 1t3cA 421 2.32e+01 d.92.1.7 106343 1kuxA 207 2.32e+01 d.108.1.1 73021 1kqqA 139 2.33e+01 a.4.3.1 72885 1zx8A 136 2.35e+01 1obbA 480 2.36e+01 c.2.1.5,d.162.1.2 86760,86761 1jotA 133 2.40e+01 1jotA 2azeA 155 2.42e+01 1yb3A 175 2.44e+01 2aj6A 159 2.48e+01 1b6bA 174 2.53e+01 1cjwA d.108.1.1 40819 1dl2A 511 2.54e+01 1dl2A a.102.2.1 18844 1zybA 232 2.55e+01 2cs7A 55 2.58e+01 1bvsB 203 2.61e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1vmeA 410 2.66e+01 c.23.5.1,d.157.1.3 108893,108894 2gfaA 119 2.77e+01 1b8aA 438 2.89e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1dxkA 227 2.90e+01 1a7tA d.157.1.1 42036 1vq2A 193 2.91e+01 1vkkA 154 2.92e+01 d.109.1.2 108669 1g0hA 252 3.00e+01 1dk4A e.7.1.1 60171 1dgsA 667 3.03e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1kzlA 208 3.07e+01 b.43.4.3,b.43.4.3 77635,77636 1lqsR 214 3.08e+01 b.1.2.1,b.1.2.1 74194,74195 1klqA 197 3.11e+01 d.135.1.1 68689 1qd6C 240 3.13e+01 1qd5A 1xubA 298 3.15e+01 2cxaA 256 3.16e+01 1yzsA 121 3.19e+01 1pms 136 3.22e+01 1awe b.55.1.1 26966 1tgoA 773 3.29e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1qnjA 240 3.29e+01 5ptp b.47.1.2 26238 1bmc 221 3.34e+01 1a7tA d.157.1.1 42038 1mjc 69 3.34e+01 1mjc b.40.4.5 25319 1btu 240 3.42e+01 5ptp b.47.1.2 26241 1e0gA 48 3.43e+01 1e01A d.7.1.1 37325 1ugxA 133 3.46e+01 1gj7B 253 3.50e+01 1gvkB 240 3.54e+01 b.47.1.2 70610 1uwzA 136 3.54e+01 c.97.1.1 108081 1jtkA 136 3.56e+01 c.97.1.1 71862 1ah9 71 3.57e+01 1ah9 b.40.4.5 25330 1dfx 125 3.61e+01 1dfx b.1.13.1,g.41.5.2 22367,45255 2gu2A 312 3.64e+01 1llnA 262 3.81e+01 d.165.1.1 84625 1c5yB 253 3.82e+01 5ptp 1rkd 309 3.96e+01 1rkd c.72.1.1 34928 1oqvA 192 3.97e+01 d.24.1.2 87320 1cd1A 315 3.98e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1ci8A 392 4.04e+01 e.3.1.1 64765 1xe0A 114 4.11e+01 1ixmA 192 4.16e+01 1ixmA d.123.1.1 41114 1x47A 98 4.18e+01 2cgaA 245 4.21e+01 5ptp b.47.1.2 26028 1fehA 574 4.22e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1em8B 112 4.25e+01 c.126.1.1 90458 1i6xA 209 4.28e+01 a.4.5.4,b.82.3.2 83673,83674 1gajA 257 4.35e+01 1gajA c.37.1.12 60416 1e01A 48 4.35e+01 1e01A 1k8tA 510 4.45e+01 e.41.1.1 68316 1vctA 205 4.46e+01 1ts9A 102 4.50e+01 2gzvA 114 4.60e+01 1vphA 149 4.60e+01 1e3dB 542 4.64e+01 1h2rL e.18.1.1 59189 1u1wA 298 4.65e+01 1f3aA 222 4.66e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1f37A 110 4.72e+01 1f37A c.47.1.11 33088 1ci9A 392 4.73e+01 e.3.1.1 64767 1kngA 156 4.86e+01 c.47.1.10 72777 1g291 372 4.92e+01 1g291 2cu3A 64 4.94e+01 1xy7A 166 4.97e+01 1liuA 528 5.02e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 3fruA 269 5.05e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 1z1yA 186 5.08e+01 1umuA 116 5.09e+01 1umuA b.87.1.1 28382 1fm4A 159 5.11e+01 1bv1 d.129.3.1 76186 1k2fA 190 5.17e+01 b.8.1.2 68054 1nz6A 101 5.21e+01 a.2.3.1 86441 2cgpA 210 5.27e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 2fgtA 417 5.31e+01 1h9jA 145 5.38e+01 1h9jA b.40.6.2,b.40.6.2 60829,60830 1xrtA 467 5.40e+01 1k3yA 221 5.40e+01 a.45.1.1,c.47.1.5 77245,77246 1nykA 165 5.44e+01 b.33.1.1 86408 1mz5A 638 5.53e+01 b.29.1.15,b.68.1.1 79679,79680 1db3A 372 5.59e+01 1db3A c.2.1.2 29813 1umuB 116 5.64e+01 1umuA b.87.1.1 28383 1dl5A 317 5.66e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1pz4A 116 5.74e+01 d.106.1.1 95400 2fdiA 211 5.74e+01 1vr9A 213 5.82e+01 1ltoA 245 5.84e+01 b.47.1.2 84707 1qd5A 275 5.85e+01 1qd5A f.4.2.1 43748 1uspA 139 5.86e+01 d.227.1.1 99879 1sefA 274 5.89e+01 b.82.1.11 105452 1u1sA 82 5.90e+01 1tuhA 156 6.03e+01 d.17.4.11 107345 1qwrA 319 6.08e+01 b.82.1.3 96491 1nz0A 118 6.10e+01 d.14.1.2 86433 1gpiA 431 6.10e+01 b.29.1.10 65450 1k2i1 245 6.22e+01 1j7vR 214 6.25e+01 b.1.2.1,b.1.2.1 62705,62706 1c8nA 276 6.26e+01 1smvA b.121.4.7 23308 1qxoA 388 6.29e+01 d.258.1.1 96539 1e2wA 251 6.30e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1n1tA 641 6.31e+01 b.29.1.15,b.68.1.1 79821,79822 1h9mA 145 6.35e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1rf6A 427 6.36e+01 d.68.2.2 97366 1pls 113 6.36e+01 1pls b.55.1.1 26965 1mjfA 281 6.36e+01 c.66.1.17 79198 1u1tA 82 6.36e+01 1sb2A 133 6.43e+01 1zczA 464 6.47e+01 1zmaA 118 6.48e+01 1zupA 315 6.51e+01 1qhtA 775 6.56e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1efuA 385 6.60e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1drw 273 6.63e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1i18A 97 6.65e+01 b.43.4.3 61520 1dih 273 6.67e+01 1drw c.2.1.3,d.81.1.3 30056,39971 1gseA 221 6.69e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 2gokA 429 6.71e+01 5abp 306 6.72e+01 8abp c.93.1.1 35651 1k3lA 221 6.73e+01 a.45.1.1,c.47.1.5 77229,77230 1c3oB 382 6.88e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 1c30B 382 6.93e+01 c.8.3.1,c.23.16.1 30736,31413 2dekA 265 7.07e+01 1cs0B 382 7.22e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1bdmB 327 7.27e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 1qhlA 227 7.27e+01 1qhlA c.37.1.12 32382 2fikA 287 7.31e+01 1jfuA 186 7.34e+01 c.47.1.10 62940 1z4eA 153 7.45e+01 1k1tA 99 7.45e+01 b.50.1.1 71995 1es6A 296 7.48e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1vjnA 220 7.48e+01 d.157.1.4 100825 1go4A 205 7.59e+01 d.135.1.1 70292 1smd 496 7.66e+01 1smd b.71.1.1,c.1.8.1 27768,28755 2a8kA 108 7.67e+01 2fhzB 108 7.70e+01 2fz0A 149 7.70e+01 1jpzA 473 7.72e+01 a.104.1.1 67069 2a5zA 262 7.74e+01 1vmfA 145 7.74e+01 1lopA 164 7.77e+01 2cpl b.62.1.1 27510 1vjkA 98 7.78e+01 d.15.3.1 108631 1ylxA 103 7.82e+01 1a9xB 379 7.97e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1auyA 189 7.99e+01 1auyA b.121.4.6 23311 2f1kA 279 8.00e+01 1c9fA 90 8.08e+01 1c9fA d.15.2.1 37639 1wqaA 455 8.19e+01 2f9nA 245 8.21e+01 1krhA 338 8.28e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1ne2A 200 8.34e+01 c.66.1.32 85586 1m2aA 110 8.34e+01 c.47.1.11 78472 1h9sA 140 8.37e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1e4eA 343 8.37e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1q6uA 245 8.39e+01 d.26.1.1 95998 1g6nA 210 8.51e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1elt 236 8.58e+01 5ptp b.47.1.2 26281 1bdmA 327 8.59e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1wzoA 246 8.59e+01 1bmdA 327 8.67e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1y7tA 327 8.69e+01 1ht6A 405 8.72e+01 b.71.1.1,c.1.8.1 83629,83630 2cjaA 522 8.72e+01 1gyzA 60 8.77e+01 a.144.2.1 70793 1axkA 394 8.85e+01 1axkA b.29.1.2,b.29.1.11 24181,24315 1eps 427 8.91e+01 1eps d.68.2.2 39586 2fug5 207 8.92e+01 2bbhA 269 8.95e+01 1x3lA 440 8.97e+01