# List of top-scoring protein chains for t2k-100-30-o_sep-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 1bd8 156 9.14e-02 1bd8 d.211.1.1 19157 1ni3A 392 1.35e-01 c.37.1.8,d.15.10.2 80531,80532 1zd3A 555 1.50e-01 1ihp 438 1.86e-01 1ihp c.60.1.2 33993 1efcA 393 4.65e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1ufaA 520 5.04e-01 a.8.3.3,c.6.2.4 99329,99330 1vj5A 555 5.56e-01 c.108.1.2,c.69.1.11 100799,100800 1p4dA 330 7.16e-01 d.89.1.5 94101 2ccmA 191 8.05e-01 1zbfA 142 8.76e-01 1trrA 107 1.22e+00 1jhgA a.4.12.1 19017 1de6A 426 1.24e+00 1de5A c.1.15.2 29398 2furA 209 1.46e+00 1q18A 332 1.87e+00 c.55.1.7,c.55.1.7 104470,104471 1mzbA 136 1.88e+00 a.4.5.42 91497 2afwA 329 1.98e+00 1fgkA 310 2.40e+00 1fgkA d.144.1.7 41693 1cr6B 554 2.51e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 2fqmA 75 2.57e+00 1ad3A 452 2.59e+00 1ad3A c.82.1.1 35335 1jpaA 312 2.65e+00 d.144.1.7 67011 1inzA 148 2.79e+00 1eduA a.118.9.1 62610 2b7aA 293 2.82e+00 2fu4A 83 3.03e+00 1sz2A 332 3.06e+00 1fehA 574 3.21e+00 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1v1rA 400 3.22e+00 c.36.1.11 108272 1mun 225 3.29e+00 1mun a.96.1.2 18744 1tqyB 415 3.46e+00 c.95.1.1,c.95.1.1 107247,107248 2myo 118 3.47e+00 2myo d.211.1.1 19175 2wrpR 107 3.48e+00 1jhgA a.4.12.1 19010 1de5A 426 3.49e+00 1de5A c.1.15.2 29402 1y3nA 490 3.63e+00 1x6vA 630 3.86e+00 1j8mF 297 4.01e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1jhgA 101 4.10e+00 1jhgA a.4.12.1 19009 1d8wA 426 4.15e+00 1de5A c.1.15.2 29394 1yzxA 226 4.21e+00 1efuA 385 4.25e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1hfeL 421 4.32e+00 1fehA c.96.1.1,d.58.1.5 36018,39001 2gsvA 80 4.80e+00 1dckA 126 4.91e+00 1dbwA c.23.1.1 31097 1guxA 218 4.97e+00 1guxA a.74.1.3 18388 1i9gA 280 5.05e+00 c.66.1.13 62090 1j8yF 297 5.07e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 2fiyA 309 5.20e+00 2eiaB 206 5.24e+00 1eia a.28.3.1,a.73.1.1 16950,18330 1m6jA 261 5.24e+00 c.1.1.1 78693 1bp1 456 5.26e+00 1bp1 d.83.1.1,d.83.1.1 40026,40027 1v54H 85 5.31e+00 a.51.1.1 100329 1qrjB 199 5.60e+00 1qrjB a.28.3.1 16952 1qwoA 442 5.75e+00 c.60.1.2 104620 1yozA 116 5.78e+00 1qfxA 460 6.45e+00 1qfxA c.60.1.2 33994 1zv1A 65 6.46e+00 1whrA 124 6.55e+00 1im5A 180 6.64e+00 c.33.1.3 66211 1nd7A 374 6.82e+00 d.148.1.1 91817 1muyA 225 7.08e+00 1mun a.96.1.2 18745 1ewfA 456 7.31e+00 1bp1 d.83.1.1,d.83.1.1 40024,40025 1d5wC 126 7.48e+00 1dbwA c.23.1.1 31101 1zboA 210 7.54e+00 1hdiA 413 7.61e+00 16pk c.86.1.1 60964 1eia 207 7.71e+00 1eia a.28.3.1,a.73.1.1 16951,18331 1z2nX 324 8.00e+00 2esnA 310 8.01e+00 1x6iA 91 8.07e+00 1bh9B 89 8.12e+00 1bh9B a.22.1.3 16485 7atjA 308 8.17e+00 1bgp a.93.1.1 18673 2atjA 308 8.65e+00 1bgp a.93.1.1 18675 1z6gA 218 8.97e+00 1r4wA 226 9.02e+00 c.47.1.13 97050 1rkd 309 9.06e+00 1rkd c.72.1.1 34928 2fmcA 82 9.12e+00 1t92A 116 9.25e+00 1z6uA 150 9.63e+00 1myo 118 9.81e+00 2myo d.211.1.1 19174 1qd9A 124 9.94e+00 1qu9A d.79.1.1 39758 2g38B 198 1.00e+01 1gd9A 389 1.01e+01 c.67.1.1 60454 1gwuA 309 1.01e+01 a.93.1.1 83351 2f96A 224 1.02e+01 1h2vC 771 1.03e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1z3eB 73 1.03e+01 1kpsB 171 1.07e+01 a.118.12.1 68787 1adjA 421 1.10e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1zq9A 285 1.10e+01 1skf 262 1.11e+01 1skf e.3.1.1 42684 1x7yA 400 1.12e+01 1jcqA 382 1.13e+01 a.118.6.1 66504 1e08A 371 1.17e+01 i.4.1.1 45914 2fx0A 201 1.19e+01 1n0qA 93 1.21e+01 k.37.1.1 79754 1esiA 262 1.23e+01 1skf e.3.1.1 42682 1dbwA 126 1.24e+01 1dbwA c.23.1.1 31095 1h4vB 421 1.27e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1mgpA 313 1.27e+01 c.119.1.1 79098 1bpoA 494 1.29e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1sheA 103 1.29e+01 d.274.1.1 105551 1ycsB 239 1.32e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 2pf1 156 1.35e+01 5hpgA g.14.1.1,g.32.1.1 44652,44968 1gdeA 389 1.36e+01 c.67.1.1 60456 1h7xA 1025 1.36e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15687,28632,30328,30613,39011 1amf 233 1.36e+01 1wod c.94.1.1 35833 1es5A 262 1.36e+01 1skf e.3.1.1 42679 1gteD 1025 1.37e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 2mev2 256 1.40e+01 1aym2 1o5hA 214 1.42e+01 a.191.1.1 92497 2g3kA 94 1.44e+01 1ld8A 382 1.44e+01 a.118.6.1 73838 1kblA 873 1.47e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1nw3A 416 1.47e+01 c.66.1.31 86288 1h7xD 1025 1.47e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15690,28635,30331,30616,39014 2b1eA 564 1.47e+01 1u5dA 108 1.49e+01 2a7mA 250 1.53e+01 1xfsA 178 1.55e+01 d.129.3.5 109589 1y0uA 96 1.57e+01 2g62A 325 1.59e+01 1jmtB 28 1.59e+01 1gthD 1025 1.61e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70498,70499,70500,70501,70502 2b33A 140 1.64e+01 1tn6A 382 1.65e+01 1gt8C 1025 1.66e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 1h7wD 1025 1.68e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1ihbA 162 1.68e+01 1bd8 d.211.1.1 19161 1wod 233 1.69e+01 1wod c.94.1.1 35832 1kopA 223 1.69e+01 2cba b.74.1.1 27966 1rcb 129 1.71e+01 1rcb a.26.1.2 16854 1gthA 1025 1.71e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1kfd 605 1.72e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 2lefA 86 1.75e+01 2lefA a.21.1.1 16433 1h7wA 1025 1.76e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 1qu9A 128 1.79e+01 1qu9A d.79.1.1 39755 1qu9C 128 1.79e+01 1qu9A d.79.1.1 39757 1koqA 253 1.80e+01 2cba b.74.1.1 27964 1eu8A 409 1.80e+01 1eu8A c.94.1.1 59502 1ut7A 171 1.80e+01 b.143.1.1 99906 2f8mA 244 1.81e+01 1m93B 245 1.83e+01 1h7xC 1025 1.86e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1gteA 1025 1.87e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1h7xB 1025 1.88e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15688,28633,30329,30614,39012 1u9iA 519 1.88e+01 1jmxA 494 1.90e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1l4sA 112 1.92e+01 d.204.1.1 77693 1voqa 90 1.95e+01 1vjkA 98 1.95e+01 d.15.3.1 108631 1im8A 244 1.97e+01 c.66.1.14 66212 1mp8A 281 2.02e+01 d.144.1.7 91384 1es2A 262 2.03e+01 1skf e.3.1.1 42680 1g2fC 90 2.03e+01 k.12.1.1 60222 1sszA 34 2.04e+01 j.35.1.1 105999 1cqxA 403 2.04e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1c7nA 399 2.04e+01 1d2fA c.67.1.3 34413 2aheA 267 2.05e+01 1gqeA 365 2.08e+01 e.38.1.1 70351 1gt8D 1025 2.10e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70433,70434,70435,70436,70437 1wwrA 171 2.18e+01 1x74A 360 2.20e+01 2bemA 170 2.21e+01 1xqaA 113 2.23e+01 1h7wB 1025 2.24e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1gt8B 1025 2.25e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70423,70424,70425,70426,70427 1ia6A 441 2.25e+01 a.102.1.2 76738 1a1hA 90 2.27e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45004,45005,45006 1tbmA 326 2.28e+01 a.211.1.2 106744 1ssqA 267 2.29e+01 b.81.1.6 105993 1rcsA 105 2.29e+01 1jhgA a.4.12.1 19025 1esmA 316 2.32e+01 1esmA c.37.1.6 31953 1jb0I 38 2.35e+01 1jb0I f.23.17.1 62826 1ttzA 87 2.36e+01 c.47.1.1 107309 1m48A 133 2.37e+01 a.26.1.2 74443 2b1xA 470 2.39e+01 1d6gA 47 2.39e+01 1d6gA g.33.1.1 44976 1ireA 204 2.46e+01 d.149.1.1 76769 1alvA 173 2.46e+01 1alvA a.39.1.8 17370 6gsvA 217 2.47e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1t4bA 367 2.49e+01 c.2.1.3,d.81.1.1 106406,106407 1gthC 1025 2.51e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1uetA 437 2.51e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1euvA 221 2.52e+01 1euvA d.3.1.7 37133 1cjsA 219 2.52e+01 1cjsA e.24.1.1 43354 1a1gA 90 2.52e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45010,45011,45012 1a1iA 90 2.54e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1w1oA 534 2.54e+01 d.58.32.4,d.145.1.1 109071,109072 1huvA 380 2.55e+01 c.1.4.1 61277 1ml4A 308 2.55e+01 c.78.1.1,c.78.1.1 79255,79256 1a3c 181 2.56e+01 1a3c c.61.1.1 34095 1aayA 90 2.60e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45001,45002,45003 1iciA 256 2.62e+01 1iciA c.31.1.5 62266 2gboA 104 2.62e+01 1llmC 88 2.63e+01 g.37.1.1,g.37.1.1 91059,91060 1ugpA 203 2.65e+01 d.149.1.1 107831 1zaaC 87 2.65e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015 1oqcA 125 2.66e+01 a.24.15.1 87264 1jae 471 2.72e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1mg2D 155 2.72e+01 a.3.1.1 79062 1tkeA 224 2.73e+01 1kinA 366 2.75e+01 1tueA 212 2.76e+01 c.37.1.20 107323 1crkA 380 2.76e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1vjeA 166 2.76e+01 d.185.1.2 100807 1jfxA 217 2.77e+01 c.1.8.8 62943 1cf3A 583 2.77e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 2end 138 2.78e+01 2end a.18.1.1 16400 1imuA 107 2.78e+01 d.204.1.1 66218 1p4cA 380 2.81e+01 c.1.4.1 94100 3kinB 117 2.82e+01 3kinB 1yw0A 276 2.85e+01 2a61A 145 2.85e+01 1n2fA 142 2.89e+01 d.227.1.1 79853 1innA 166 2.90e+01 1j98A d.185.1.2 62608 2a10A 125 2.92e+01 1gal 583 2.92e+01 1gpeA c.3.1.2,d.16.1.1 30386,37950 1v96A 149 2.93e+01 1y82A 157 2.95e+01 1ewqA 765 2.98e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1jakA 512 3.01e+01 c.1.8.6,d.92.2.1 66472,66473 1t7rA 269 3.07e+01 a.123.1.1 106635 2f02A 323 3.08e+01 1gthB 1025 3.10e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70488,70489,70490,70491,70492 1hp5A 512 3.13e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1mp9A 198 3.15e+01 d.129.1.1,d.129.1.1 91385,91386 1m2kA 249 3.15e+01 c.31.1.5 84754 1qahA 136 3.17e+01 d.79.1.1 96338 1bku 33 3.22e+01 1bku j.6.1.1 46104 1f5qB 252 3.23e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1hp4A 512 3.24e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1xkmB 25 3.29e+01 2awdA 323 3.34e+01 1ngkA 128 3.36e+01 a.1.1.1 85673 1aquA 297 3.36e+01 1aquA c.37.1.5 31942 1aisA 182 3.36e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1wddS 128 3.37e+01 2b0jA 358 3.42e+01 1lkyA 77 3.43e+01 a.60.1.1 73985 1bj8 109 3.43e+01 1bquA b.1.2.1 22070 1f0cA 305 3.44e+01 1c8oA e.1.1.1 42676 1zzpA 130 3.46e+01 1regX 122 3.47e+01 1regX d.58.27.1 39406 1oniA 137 3.50e+01 d.79.1.1 87144 1paqA 189 3.53e+01 a.118.1.14 94413 1x91A 153 3.57e+01 1pczA 191 3.63e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1ji7A 89 3.67e+01 a.60.1.1 71682 1brmA 367 3.67e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1tx4A 198 3.67e+01 1tx4A a.116.1.1 19098 1apyA 162 3.77e+01 1apyA d.153.1.5 42004 1xw5A 217 3.78e+01 1o63A 219 3.78e+01 c.94.1.1 92540 1l8dA 112 3.79e+01 h.4.12.1 73687 1wmaA 276 3.80e+01 1cem 363 3.83e+01 1cem a.102.1.2 18826 2fh1A 344 3.83e+01 1r89A 437 3.86e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1ka9H 200 3.89e+01 c.23.16.1 77308 1iomA 377 3.91e+01 a.103.1.1 83698 1m2oA 768 3.92e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1p8xA 344 3.94e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1f44A 324 3.95e+01 a.60.9.1,d.163.1.1 64982,64983 2c4jA 218 3.95e+01 1m6kA 251 3.95e+01 e.3.1.1 78695 1z2uA 150 3.96e+01 1t8sA 484 3.99e+01 c.56.2.1 106679 1x54A 434 3.99e+01 1z0jA 170 4.00e+01 1h3nA 878 4.06e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1a22A 180 4.06e+01 1huw a.26.1.1 16833 1d8dA 377 4.08e+01 1ft1A a.118.6.1 19185 2ax9A 256 4.08e+01 1iy8A 267 4.09e+01 c.2.1.2 83774 1s0pA 176 4.09e+01 a.192.1.1 98300 1qbqA 333 4.09e+01 1ft1A a.118.6.1 19187 1sphA 88 4.10e+01 1ptf d.94.1.1 40544 1v73A 342 4.12e+01 1jd1A 129 4.13e+01 1qu9A d.79.1.1 62890 1hu4A 288 4.14e+01 1hu4A 1n5dA 288 4.15e+01 c.2.1.2 80030 2akrA 285 4.16e+01 1i1qA 520 4.17e+01 1qdlA d.161.1.1 61543 2ax6A 256 4.22e+01 1lngA 87 4.22e+01 d.201.1.1 74045 1ztsA 139 4.24e+01 1g3mA 294 4.31e+01 c.37.1.5 83268 1ujkA 147 4.35e+01 a.118.9.2 99457 1qs2A 401 4.39e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 3bdpA 580 4.40e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1j6rA 214 4.40e+01 d.173.1.2 71598 2int 129 4.41e+01 1rcb a.26.1.2 16855 1l0lK 56 4.42e+01 f.23.15.1 84497 1t3uA 104 4.44e+01 d.244.1.1 99120 1hy3A 294 4.49e+01 c.37.1.5 71090 1g5hA 454 4.49e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1xqiA 195 4.50e+01 1thg 544 4.50e+01 1thg c.69.1.17 34763 1gt8A 1025 4.51e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1vf6A 83 4.51e+01 a.194.1.1 100600 2gsfA 373 4.53e+01 3inkC 133 4.54e+01 3inkC a.26.1.2 16881 1wdeA 294 4.57e+01 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