# List of top-scoring protein chains for t2k-100-30-alpha-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 1vj5A 555 1.77e-02 c.108.1.2,c.69.1.11 100799,100800 1zd3A 555 3.30e-02 1cr6B 554 4.58e-02 1cr6B c.69.1.11,c.108.1.2 34688,43338 1de5A 426 5.61e-02 1de5A c.1.15.2 29402 1de6A 426 8.77e-02 1de5A c.1.15.2 29398 1d8wA 426 1.01e-01 1de5A c.1.15.2 29394 1ihp 438 2.01e-01 1ihp c.60.1.2 33993 1h6zA 913 5.09e-01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1qrjB 199 6.61e-01 1qrjB a.28.3.1 16952 1ad3A 452 7.51e-01 1ad3A c.82.1.1 35335 1qfxA 460 8.87e-01 1qfxA c.60.1.2 33994 2myo 118 1.08e+00 2myo d.211.1.1 19175 2ccmA 191 1.41e+00 1trrA 107 1.71e+00 1jhgA a.4.12.1 19017 1tbmA 326 1.84e+00 a.211.1.2 106744 1rcsA 105 1.85e+00 1jhgA a.4.12.1 19025 1jpaA 312 1.95e+00 d.144.1.7 67011 1jhgA 101 2.06e+00 1jhgA a.4.12.1 19009 1zv1A 65 2.07e+00 1w07A 659 2.10e+00 1x7yA 400 2.13e+00 1fsu 492 2.19e+00 1auk c.76.1.2 35032 1wmmA 145 2.26e+00 2b1eA 564 2.27e+00 1w1oA 534 2.29e+00 d.58.32.4,d.145.1.1 109071,109072 2wrpR 107 2.50e+00 1jhgA a.4.12.1 19010 1myo 118 2.54e+00 2myo d.211.1.1 19174 1v1rA 400 2.58e+00 c.36.1.11 108272 1x6vA 630 2.74e+00 1xioA 261 3.39e+00 6gsvA 217 3.62e+00 1b8xA a.45.1.1,c.47.1.5 17633,32925 1bd8 156 3.65e+00 1bd8 d.211.1.1 19157 2mev2 256 3.86e+00 1aym2 1q18A 332 4.17e+00 c.55.1.7,c.55.1.7 104470,104471 2afwA 329 4.30e+00 1jb0I 38 4.42e+00 1jb0I f.23.17.1 62826 1sz2A 332 4.42e+00 1x1fA 149 4.70e+00 1llmC 88 4.87e+00 g.37.1.1,g.37.1.1 91059,91060 1m98A 317 4.97e+00 a.175.1.1,d.17.4.6 78866,78867 1z6uA 150 5.33e+00 1v96A 149 5.57e+00 2fqmA 75 5.70e+00 2furA 209 5.92e+00 1hzfA 367 6.01e+00 a.102.4.4 76731 1x91A 153 6.04e+00 1zq9A 285 6.56e+00 1hp4A 512 6.61e+00 1hp4A c.1.8.6,d.92.2.1 61111,61112 1z2nX 324 6.74e+00 1tqxA 227 6.95e+00 1hdiA 413 6.96e+00 16pk c.86.1.1 60964 1y3nA 490 6.96e+00 2db0A 253 7.09e+00 1jmtB 28 7.17e+00 1qd9A 124 7.38e+00 1qu9A d.79.1.1 39758 2mtaC 147 7.61e+00 2mtaC a.3.1.1 15908 1yzxA 226 7.64e+00 1bf5A 545 7.87e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2fb6A 117 8.42e+00 1r4wA 226 8.78e+00 c.47.1.13 97050 1sszA 34 8.84e+00 j.35.1.1 105999 2gsfA 373 8.96e+00 2aheA 267 9.01e+00 1jakA 512 9.49e+00 c.1.8.6,d.92.2.1 66472,66473 1i9gA 280 9.68e+00 c.66.1.13 62090 1kblA 873 9.97e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ufaA 520 1.00e+01 a.8.3.3,c.6.2.4 99329,99330 1jhdA 396 1.05e+01 b.122.1.3,c.26.1.5 66712,66713 1dik 874 1.05e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1n2fA 142 1.07e+01 d.227.1.1 79853 1ppjF 110 1.08e+01 f.27.1.1 104262 1u5tC 202 1.11e+01 a.4.5.54,a.4.5.54 107688,107689 1qcrF 103 1.12e+01 1be3F f.27.1.1 43676 1i2aA 219 1.13e+01 e.24.1.1 90660 1ewfA 456 1.15e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 1hp5A 512 1.16e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1v9jA 113 1.23e+01 d.52.6.1 100542 1mg2D 155 1.23e+01 a.3.1.1 79062 1vjkA 98 1.30e+01 d.15.3.1 108631 1iciA 256 1.35e+01 1iciA c.31.1.5 62266 2ctoA 93 1.39e+01 1x74A 360 1.39e+01 1m6jA 261 1.41e+01 c.1.1.1 78693 1im5A 180 1.42e+01 c.33.1.3 66211 1rzsA 61 1.49e+01 a.35.1.2 105139 1hfeL 421 1.51e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1es5A 262 1.51e+01 1skf e.3.1.1 42679 1xmeA 568 1.53e+01 1m48A 133 1.53e+01 a.26.1.2 74443 1mgpA 313 1.59e+01 c.119.1.1 79098 2fiyA 309 1.60e+01 1t92A 116 1.62e+01 1iuhA 198 1.62e+01 d.61.1.2 83711 1pa7A 130 1.63e+01 a.40.1.1 94410 1pdnC 128 1.64e+01 6paxA a.4.1.5 16047 1tqyB 415 1.65e+01 c.95.1.1,c.95.1.1 107247,107248 1alvA 173 1.69e+01 1alvA a.39.1.8 17370 1y82A 157 1.70e+01 1be3F 110 1.70e+01 1be3F f.27.1.1 43668 2gboA 104 1.72e+01 1cjsA 219 1.74e+01 1cjsA e.24.1.1 43354 2dg5A 366 1.82e+01 2fmcA 82 1.86e+01 1bp1 456 1.88e+01 1bp1 d.83.1.1,d.83.1.1 40026,40027 1o5hA 214 1.92e+01 a.191.1.1 92497 1bccF 109 1.96e+01 1be3F f.27.1.1 43700 1sphA 88 1.99e+01 1ptf d.94.1.1 40544 2b05A 246 1.99e+01 1h2vC 771 2.08e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1rmg 422 2.12e+01 1rmg b.80.1.3 28029 2c4jA 218 2.16e+01 2bfdA 400 2.17e+01 2c7pA 327 2.18e+01 2fikA 287 2.19e+01 2bemA 170 2.21e+01 1hz4A 373 2.22e+01 a.118.8.2 65960 1h3nA 878 2.26e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2a7mA 250 2.28e+01 1p2fA 220 2.31e+01 a.4.6.1,c.23.1.1 87720,87721 1skf 262 2.34e+01 1skf e.3.1.1 42684 1kfuS 184 2.36e+01 a.39.1.8 68574 1eciB 34 2.43e+01 1eciA a.33.1.1 17000 1esiA 262 2.43e+01 1skf e.3.1.1 42682 1whrA 124 2.46e+01 1m93B 245 2.52e+01 1cqzA 554 2.55e+01 1cr6B c.69.1.11,c.108.1.2 34689,43339 1qu9A 128 2.57e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.57e+01 1qu9A d.79.1.1 39757 1kplA 473 2.62e+01 f.20.1.1 68782 1kpsB 171 2.62e+01 a.118.12.1 68787 1wjgA 137 2.64e+01 1xw5A 217 2.64e+01 1ssqA 267 2.71e+01 b.81.1.6 105993 1b35A 260 2.72e+01 1b35A b.121.4.1 23333 1huvA 380 2.72e+01 c.1.4.1 61277 1fb6A 105 2.78e+01 1thx c.47.1.1 32739 1p4cA 380 2.85e+01 c.1.4.1 94100 2cqsA 842 2.87e+01 1fjxA 327 2.87e+01 6mhtA c.66.1.26 34228 3mhtA 327 2.91e+01 6mhtA c.66.1.26 34234 1z3eB 73 2.93e+01 1r6wA 322 2.96e+01 c.1.11.2,d.54.1.1 97165,97166 1hmy 327 2.96e+01 6mhtA c.66.1.26 34229 1uurA 473 3.00e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 2a9iA 113 3.01e+01 1fhvA 323 3.03e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 2b33A 140 3.05e+01 1mli 96 3.06e+01 1mli d.58.4.1 39070 1xb4A 202 3.06e+01 1adjA 421 3.06e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1kyqA 274 3.08e+01 c.2.1.11,e.37.1.1 73281,73282 1t8kA 77 3.10e+01 a.28.1.1 106666 2fgtA 417 3.10e+01 1n1jA 93 3.11e+01 a.22.1.3 79813 1rtwA 220 3.16e+01 a.132.1.3 97823 1yw0A 276 3.16e+01 1ituA 369 3.17e+01 c.1.9.7 71423 1p1mA 406 3.17e+01 b.92.1.4,c.1.9.9 87696,87697 1olsA 400 3.22e+01 c.36.1.11 93331 2akrA 285 3.23e+01 1z5lA 285 3.28e+01 2g3kA 94 3.30e+01 1qh4A 380 3.31e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 2bjqA 345 3.33e+01 1xqrA 296 3.37e+01 2eu8A 216 3.38e+01 1u5dA 108 3.40e+01 1nddA 76 3.41e+01 1ubi d.15.1.1 37599 1aj5A 173 3.45e+01 1alvA a.39.1.8 17367 1efuA 385 3.47e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1vzoA 355 3.47e+01 d.144.1.7 108971 1dfwA 25 3.54e+01 j.35.1.1 46255 2b7aA 293 3.57e+01 1ni3A 392 3.58e+01 c.37.1.8,d.15.10.2 80531,80532 1x6iA 91 3.65e+01 2f96A 224 3.67e+01 1jmxA 494 3.69e+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 1efcA 393 3.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1c7nA 399 3.85e+01 1d2fA c.67.1.3 34413 1vi0A 206 3.90e+01 a.4.1.9,a.121.1.1 100720,100721 1jae 471 3.93e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1ngzA 213 3.94e+01 b.1.1.1,b.1.1.2 80500,80501 1p3jA 217 3.95e+01 c.37.1.1,g.41.2.1 94022,94023 1ka9H 200 3.99e+01 c.23.16.1 77308 2fu4A 83 4.01e+01 1otsA 465 4.03e+01 f.20.1.1 87415 1rg9A 383 4.04e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1gdeA 389 4.04e+01 c.67.1.1 60456 1l0iA 78 4.05e+01 a.28.1.1 77643 1b4pA 217 4.05e+01 a.45.1.1,c.47.1.5 83158,83159 1ddzA 496 4.09e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1gd9A 389 4.10e+01 c.67.1.1 60454 1qwoA 442 4.11e+01 c.60.1.2 104620 1oaoC 729 4.13e+01 e.26.1.3 86746 1p4dA 330 4.18e+01 d.89.1.5 94101 1c5a 73 4.22e+01 1kjs a.50.1.1 17794 1b73A 254 4.32e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1cd1A 315 4.36e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1wr7A 41 4.37e+01 1zboA 210 4.40e+01 1x8vA 455 4.43e+01 1a1iA 90 4.48e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1l7iL 214 4.49e+01 b.1.1.1,b.1.1.2 73658,73659 2b4aA 138 4.49e+01 1zaaC 87 4.51e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015 1crkA 380 4.54e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 2aplA 157 4.60e+01 1a1hA 90 4.65e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45004,45005,45006 1h4vB 421 4.67e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1axsA 211 4.67e+01 8fabA b.1.1.1,b.1.1.2 20200,21216 1zy9A 564 4.68e+01 1gjjA 168 4.76e+01 a.140.1.1,a.140.1.1 83291,83292 1aayA 90 4.78e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45001,45002,45003 1eia 207 4.80e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1tueA 212 4.80e+01 c.37.1.20 107323 1z83A 196 4.84e+01 6mhtA 327 4.87e+01 6mhtA c.66.1.26 34226 1u6rA 380 4.87e+01 1eerA 166 4.88e+01 1eerA a.26.1.2 16846 1g2fC 90 4.89e+01 k.12.1.1 60222 2beiA 170 4.95e+01 1vqoI 162 5.01e+01 2gsvA 80 5.13e+01 1bs0A 384 5.14e+01 1bs0A c.67.1.4 34490 1rkd 309 5.19e+01 1rkd c.72.1.1 34928 1jy3N 53 5.20e+01 h.1.8.1 67446 2fx0A 201 5.22e+01 1ea1A 455 5.24e+01 1ea1A a.104.1.1 18970 2iu5A 195 5.25e+01 1zc6A 305 5.25e+01 1tkeA 224 5.25e+01 2ceyA 306 5.28e+01 3inkC 133 5.32e+01 3inkC a.26.1.2 16881 1t7rA 269 5.36e+01 a.123.1.1 106635 1u9iA 519 5.37e+01 1bquA 215 5.42e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 2aucA 126 5.44e+01 1buyA 166 5.58e+01 1eerA a.26.1.2 16848 1x6mA 196 5.60e+01 1y8oA 419 5.63e+01 1e9xA 455 5.65e+01 1ea1A a.104.1.1 18969 1thg 544 5.72e+01 1thg c.69.1.17 34763 1s9jA 341 5.73e+01 12e8L 214 5.75e+01 8fabA b.1.1.1,b.1.1.2 20268,21268 1aj0 282 5.75e+01 1aj2 c.1.21.1 29667 1n0xL 215 5.76e+01 b.1.1.1,b.1.1.2 91532,91533 1irzA 64 5.84e+01 a.4.1.11 76772 1cjcA 460 5.84e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1b0xA 94 5.85e+01 1b4fA a.60.1.2 17933 1h5zA 455 5.88e+01 a.104.1.1 90622 1qmzB 259 5.89e+01 1vin a.74.1.1,a.74.1.1 18338,18339 1mjgM 729 5.93e+01 e.26.1.3 79204 1um5L 219 5.94e+01 1acp 77 5.98e+01 1acp a.28.1.1 16931 1nd7A 374 6.00e+01 d.148.1.1 91817 1b2wL 214 6.02e+01 8fabA b.1.1.1,b.1.1.2 20306,21298 1a1gA 90 6.07e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45010,45011,45012 1pa2A 306 6.09e+01 1bgp a.93.1.1 18693 1ordA 730 6.18e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1amf 233 6.20e+01 1wod c.94.1.1 35833 2a2pA 129 6.21e+01 1u13A 455 6.23e+01 a.104.1.1 107578 1c8oA 300 6.23e+01 1c8oA e.1.1.1 42677 2bo9A 308 6.24e+01 1mxa 383 6.26e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41326,41327,41328 1xg2B 153 6.27e+01 1qo7A 394 6.31e+01 1qo7A c.69.1.11 34697 2bopA 85 6.32e+01 2bopA d.58.8.1 39217 1a4kA 217 6.35e+01 8fabA b.1.1.1,b.1.1.2 20236,21248 1nmtA 392 6.36e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1cfr 285 6.43e+01 1cfr c.52.1.7 33312 1hmvB 440 6.43e+01 1rthA e.8.1.2 43047 2ag9A 164 6.49e+01 1c5cL 214 6.49e+01 32c2A b.1.1.1,b.1.1.2 20474,21438 1w34A 304 6.54e+01 1r6uA 437 6.55e+01 c.26.1.1 97163 2eiaB 206 6.55e+01 1eia a.28.3.1,a.73.1.1 16950,18330 2dbgA 103 6.61e+01 1jem 87 6.64e+01 1ptf d.94.1.1 40548 1bj8 109 6.64e+01 1bquA b.1.2.1 22070 1zanL 214 6.71e+01 1wod 233 6.71e+01 1wod c.94.1.1 35832 1j6pA 418 6.77e+01 b.92.1.4,c.1.9.9 77089,77090 1g7oA 215 6.85e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1m2kA 249 6.92e+01 c.31.1.5 84754 1kpkA 473 7.00e+01 f.20.1.1 68776 1f0cA 305 7.03e+01 1c8oA e.1.1.1 42676 1rypH 205 7.04e+01 d.153.1.4 41876 1z6gA 218 7.07e+01 1n1fA 159 7.14e+01 a.26.1.3 79803 1jy2N 53 7.15e+01 h.1.8.1 67440 1b74A 254 7.18e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1xfsA 178 7.20e+01 d.129.3.5 109589 3kinB 117 7.22e+01 3kinB 1pv0A 46 7.28e+01 a.2.12.1 95141 1lghA 56 7.33e+01 1lghA f.3.1.1 43733 1jajA 174 7.36e+01 d.218.1.2 66471 1sheA 103 7.37e+01 d.274.1.1 105551 1ad0A 213 7.39e+01 8fabA b.1.1.1,b.1.1.2 20124,21154 1aj2 282 7.39e+01 1aj2 c.1.21.1 29665 2ag4A 164 7.40e+01 1a5fL 220 7.40e+01 8fabA b.1.1.1,b.1.1.2 20302,21294 2chnA 716 7.40e+01 2bmwA 304 7.48e+01 1phk 298 7.57e+01 1cdkA d.144.1.7 41635 1m7vA 363 7.57e+01 d.174.1.1 78748 1ogiA 303 7.63e+01 b.43.4.2,c.25.1.1 92914,92915 1ylqA 96 7.67e+01 1bavA 309 7.78e+01 1aye c.56.5.1 33806 2d2sA 235 7.78e+01 1hfx 123 7.82e+01 3lzt d.2.1.2 36600 2cchB 260 7.87e+01 1go2A 304 7.88e+01 b.43.4.2,c.25.1.1 76243,76244 1j2rA 199 7.95e+01 c.33.1.3 90788 1lkyA 77 7.96e+01 a.60.1.1 73985 1a0qL 212 8.00e+01 8fabA b.1.1.1,b.1.1.2 20286,21278 1har 216 8.06e+01 1rthA e.8.1.2 43025 1o8xA 146 8.14e+01 c.47.1.10 86681 1cn4C 166 8.18e+01 1eerA a.26.1.2 16847 1b4jL 214 8.26e+01 8fabA b.1.1.1,b.1.1.2 20308,21300 1x23A 155 8.28e+01 1qahA 136 8.34e+01 d.79.1.1 96338 1xikA 375 8.35e+01 1xikA a.25.1.2 16784 1cojA 212 8.37e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1pu5A 164 8.39e+01 b.95.1.1 104310 1yzyA 413 8.40e+01 1m65A 245 8.40e+01 c.6.3.1 84847 2dfkA 402 8.49e+01 1b2rA 304 8.67e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1mpyA 307 8.70e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 2choA 716 8.71e+01 1x31D 99 8.75e+01 1ae6L 219 8.80e+01 8fabA b.1.1.1,b.1.1.2 20210,21222 1ylxA 103 8.90e+01 1hlvA 131 8.90e+01 a.4.1.7,a.4.1.7 65854,65855 1que 303 8.94e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1yo3A 102 8.97e+01 1tetL 216 8.97e+01 32c2A b.1.1.1,b.1.1.2 19902,20996 1dckA 126 8.97e+01 1dbwA c.23.1.1 31097 1qh0A 295 8.99e+01 b.43.4.2,c.25.1.1 68891,68892