# List of top-scoring protein chains for T0376.t2k-w0.5 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 1xkyA 301 2.52e-40 1o5kA 306 4.95e-40 c.1.10.1 92504 1yxcA 292 4.33e-39 2a6nA 292 6.38e-39 1s5vA 292 6.92e-39 c.1.10.1 98581 1s5tA 292 7.07e-39 c.1.10.1 98571 2a6lA 292 7.58e-39 1s5wA 292 8.79e-39 c.1.10.1 98583 1xxxA 303 3.27e-35 1hl2A 297 2.29e-33 c.1.10.1 83581 1fdyA 297 3.68e-33 1nal3 c.1.10.1 29071 1nal1 297 3.70e-33 1nal3 1f74A 293 3.78e-29 1nal3 c.1.10.1 29079 1w37A 294 2.35e-27 c.1.10.1 109142 1w3iA 293 2.41e-27 c.1.10.1 109152 1y0eA 223 2.38e-01 1mzhA 225 3.28e-01 c.1.10.1 79698 1xo5A 183 3.97e-01 2chqA 319 7.63e-01 1h5yA 253 8.23e-01 c.1.2.1 65638 1izlB 472 1.06e+00 i.5.1.1 76995 2fnjB 118 1.16e+00 1tx2A 297 1.21e+00 c.1.21.1 107420 1jflA 228 1.99e+00 c.78.2.1,c.78.2.1 71656,71657 1lm8B 118 2.24e+00 d.15.1.1 74033 2axtB 510 2.45e+00 1w9hA 427 2.76e+00 1ep3A 311 3.10e+00 2dorA c.1.4.1 28597 1s1mA 545 3.22e+00 c.23.16.1,c.37.1.10 105201,105202 1ulzA 451 3.40e+00 b.84.2.1,c.30.1.1,d.142.1.2 99575,99576,99577 1pn3A 404 3.88e+00 c.87.1.5 94938 1jfsA 340 4.23e+00 a.35.1.5,c.93.1.1 66650,66651 1s2uA 295 4.23e+00 c.1.12.7 98401 1s2wA 295 4.28e+00 c.1.12.7 98407 1qqbA 340 4.37e+00 1qpzA a.35.1.5,c.93.1.1 17099,35674 1jh9A 340 4.95e+00 a.35.1.5,c.93.1.1 66710,66711 1qpzA 340 5.00e+00 1qpzA a.35.1.5,c.93.1.1 17097,35673 2pugA 340 5.06e+00 1qpzA a.35.1.5,c.93.1.1 17088,35683 1jhzA 289 5.08e+00 c.93.1.1 66731 1jftA 340 5.11e+00 a.35.1.5,c.93.1.1 66652,66653 2pucA 340 5.11e+00 1qpzA a.35.1.5,c.93.1.1 17094,35684 1ub3A 220 5.16e+00 c.1.10.1 88395 2czdA 208 5.31e+00 2cqyA 108 5.55e+00 1vpwA 340 5.83e+00 1qpzA a.35.1.5,c.93.1.1 17087,35680 1dbqA 289 6.07e+00 1qpzA c.93.1.1 35666 1tygA 253 6.57e+00 c.1.31.1 107454 1vkyA 347 6.68e+00 e.53.1.1 108696 1xm3A 264 6.78e+00 1oypA 245 6.97e+00 d.14.1.4,d.101.1.1 93734,93735 1b74A 254 8.08e+00 1b74A c.78.2.1,c.78.2.1 35264,35265 1zlpA 318 8.30e+00 1ka9F 252 9.50e+00 c.1.2.1 77307 1oysA 245 9.70e+00 d.14.1.4,d.101.1.1 93758,93759 2c76A 520 9.90e+00 1xgwA 176 9.96e+00 1e6vA 553 1.02e+01 1mroA a.89.1.1,d.58.31.2 18527,39445 2bk5A 520 1.09e+01 2c73A 520 1.09e+01 1s3eA 520 1.09e+01 c.3.1.2,d.16.1.5 98426,98427 2c72A 520 1.09e+01 2c75A 520 1.10e+01 1ylvA 342 1.10e+01 1b4kA c.1.10.3 29180 3ldh 330 1.18e+01 3ldh i.12.1.1 46015 1zoiA 276 1.19e+01 1m1nB 522 1.21e+01 c.92.2.3 78418 1g20B 523 1.22e+01 1qguB c.92.2.3 35614 1yixA 265 1.22e+01 1xg5A 279 1.27e+01 2avyT 86 1.27e+01 2a0nA 265 1.31e+01 2b4gA 317 1.32e+01 1vrdA 494 1.32e+01 1vh7A 265 1.37e+01 c.1.2.1 100646 1ezwA 349 1.38e+01 1ezwA c.1.16.3 29558 1aoa 275 1.55e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1mumA 295 1.56e+01 c.1.12.7 85108 1uqvA 85 1.59e+01 a.60.1.2 99798 1vs1A 276 1.61e+01 1gpwA 253 1.62e+01 c.1.2.1 65460 1zxoA 291 1.63e+01 1zq1A 438 1.63e+01 1gp0A 143 1.65e+01 b.64.1.1 70300 1xuuA 349 1.71e+01 2c8uA 211 1.72e+01 1oe8A 211 1.72e+01 a.45.1.1,c.47.1.5 86905,86906 2f8fA 211 1.72e+01 2caqA 211 1.74e+01 1z1vA 80 1.74e+01 1zfjA 491 1.74e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1rrqA 369 1.76e+01 a.96.1.2,d.113.1.3 97798,97799 1navA 263 1.80e+01 a.123.1.1 85500 1mioB 458 1.80e+01 1qguB c.92.2.3 35602 1cs4C 394 1.91e+01 1cipA a.66.1.1,c.37.1.8 18205,32088 1hdhA 536 1.91e+01 c.76.1.2 65805 1azsC 402 1.94e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1bw0A 416 1.98e+01 1bw0A c.67.1.1 34385 1zvvA 332 2.02e+01 1xjdA 345 2.02e+01 1taq 832 2.02e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1z0sA 278 2.02e+01 1bgxT 832 2.02e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18083,33353,33699,42992 1p0fA 373 2.06e+01 b.35.1.2,c.2.1.1 87642,87643 1oy5A 257 2.07e+01 c.116.1.4 93718 1qwgA 251 2.08e+01 c.1.27.1 96473 1thfD 253 2.09e+01 1thfD c.1.2.1 28535 1x1oA 286 2.11e+01 1p9lA 245 2.26e+01 c.2.1.3,d.81.1.3 94393,94394 1rpxA 230 2.32e+01 1rpxA c.1.2.2 28536 1yl7A 245 2.33e+01 1yl5A 247 2.36e+01 1xg4A 295 2.42e+01 1rrsA 369 2.44e+01 a.96.1.2,d.113.1.3 97800,97801 1pg5A 299 2.50e+01 c.78.1.1,c.78.1.1 104146,104147 1p1xA 260 2.53e+01 c.1.10.1 104060 1h7nA 340 2.53e+01 1b4kA c.1.10.3 60726 1h7oA 341 2.53e+01 c.1.10.3 60727 1y4jA 284 2.53e+01 1ohlA 342 2.54e+01 c.1.10.3 87035 1jcjA 260 2.55e+01 c.1.10.1 66499 1ktnA 250 2.59e+01 c.1.10.1 72988 1sxrA 183 2.63e+01 d.118.1.1 106101 1sjwA 144 2.82e+01 d.17.4.9 98899 1t8uA 272 2.89e+01 c.37.1.5 106687 1t8tA 271 2.89e+01 c.37.1.5 106685 1ri7A 171 2.93e+01 a.4.5.32,d.58.4.2 97504,97505 1s2jA 209 2.94e+01 d.118.1.1 105227 1hwuA 112 2.96e+01 d.58.5.1 83633 1nuoA 261 2.96e+01 a.123.1.1 86198 1xzxX 281 2.98e+01 1gzkA 315 3.13e+01 d.144.1.7 83406 1w5fA 353 3.13e+01 6xia 387 3.17e+01 4xis c.1.15.3 29406 2gp5A 349 3.18e+01 1o6lA 337 3.22e+01 d.144.1.7 81092 1gznA 335 3.24e+01 d.144.1.7 83407 1o6kA 336 3.25e+01 d.144.1.7 81091 1mryA 339 3.36e+01 d.144.1.7 91451 1s7eA 147 3.38e+01 1r6gA 259 3.39e+01 1vlhA 173 3.42e+01 c.26.1.3 108824 1n46A 258 3.48e+01 a.123.1.1 85315 1bsxA 260 3.48e+01 2lbd a.123.1.1 19330 1nq0A 263 3.49e+01 a.123.1.1 86005 1naxA 252 3.51e+01 a.123.1.1 85501 1nq1A 263 3.51e+01 a.123.1.1 86006 1q4xA 253 3.53e+01 a.123.1.1 95833 1sxgA 280 3.54e+01 2cg5A 319 3.57e+01 2c43A 323 3.58e+01 1vpxA 230 3.61e+01 1jlwA 219 3.64e+01 a.45.1.1,c.47.1.5 71741,71742 1rzrA 332 3.73e+01 1mpgA 282 3.94e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 2bdqA 224 3.95e+01 1g8sA 230 3.96e+01 c.66.1.3 90507 1nq2A 264 4.06e+01 a.123.1.1 86007 1ukwA 379 4.14e+01 1b4eA 323 4.18e+01 1b4kA c.1.10.3 29186 1vzyA 291 4.24e+01 1dquA 538 4.25e+01 1dquA c.1.12.7 29314 1ql6A 298 4.26e+01 1cdkA d.144.1.7 41636 1b4jL 214 4.29e+01 8fabA b.1.1.1,b.1.1.2 20308,21300 1l6sA 323 4.30e+01 c.1.10.3 73627 1a76 326 4.32e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 2phkA 277 4.35e+01 1cdkA d.144.1.7 41637 1phk 298 4.37e+01 1cdkA d.144.1.7 41635 1c9kA 180 4.38e+01 1c9kB c.37.1.11 32363 1iwgA 1053 4.49e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1oyeA 1049 4.49e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1t9xA 1049 4.49e+01 1px5A 349 4.50e+01 a.160.1.2,d.218.1.6 95277,95278 1vflA 356 4.51e+01 1ae1A 273 4.64e+01 1bdb c.2.1.2 29943 1vq0A 302 4.77e+01 1wekA 217 4.79e+01 1iu9A 111 4.83e+01 c.78.2.1 90694 1qopA 268 4.88e+01 2tysA c.1.2.4 28570 1t3fA 214 4.89e+01 1kfcA 268 4.96e+01 c.1.2.4 77371 1xcfA 268 4.97e+01 1vizA 240 5.04e+01 c.1.4.1 100784 1szeA 511 5.07e+01 c.1.4.1 106151 1kbiA 511 5.08e+01 c.1.4.1,d.120.1.1 72277,72278 1lcoA 511 5.08e+01 1gox c.1.4.1,d.120.1.1 28624,41088 1xqsC 191 5.10e+01 1ltdA 506 5.11e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1szfA 511 5.13e+01 c.1.4.1 106153 1pnsT 99 5.25e+01 i.1.1.1 88187 1fjgT 106 5.46e+01 1fjfT a.7.6.1 16338 1uweL 213 5.46e+01 b.1.1.1,b.1.1.2 100105,100106 1n0xL 215 5.60e+01 b.1.1.1,b.1.1.2 91532,91533 1owlA 484 5.61e+01 a.99.1.1,c.28.1.1 93647,93648 1vhnA 318 5.62e+01 c.1.4.1 100693 2drwA 363 5.68e+01 2fcwB 80 5.69e+01 1xrsB 262 5.69e+01 1n83A 270 5.70e+01 a.123.1.1 80276 1i94T 105 5.77e+01 1fjfT a.7.6.1 62011 1xmqT 106 5.80e+01 1zcoA 262 5.88e+01 1wq5A 268 5.95e+01 1wyuB 474 6.19e+01 2cw6A 298 6.23e+01 1w4xA 542 6.29e+01 c.3.1.5,c.3.1.5 109171,109172 1tezA 474 6.36e+01 1etzB 228 6.45e+01 1igtB b.1.1.1,b.1.1.2 20481,21445 1ugpB 226 6.50e+01 b.34.4.4 107832 1sr2A 116 6.52e+01 1gnkA 112 6.54e+01 2pii d.58.5.1 39073 1za6A 220 6.58e+01 1ireB 228 6.69e+01 b.34.4.4 76770 1o6bA 169 6.71e+01 c.26.1.3 92564 1ad1A 266 6.72e+01 1aj2 c.1.21.1 29668 1wznA 252 6.85e+01 1na0A 125 6.92e+01 k.38.1.1 85479 1rt8A 513 6.93e+01 a.40.1.1 105095 1nmoA 247 6.98e+01 c.135.1.1 91980 1nhzA 280 6.98e+01 a.123.1.1 85727 2bdeA 470 6.99e+01 1u6aL 215 7.11e+01 1zrzA 364 7.13e+01 1u2eA 289 7.21e+01 1aw5 340 7.24e+01 1b4kA c.1.10.3 29181 1j3nA 408 7.26e+01 c.95.1.1,c.95.1.1 84074,84075 1rzfL 213 7.37e+01 b.1.1.1,b.1.1.2 98152,98153 1tjpA 268 7.38e+01 1w1mA 560 7.43e+01 d.58.32.1,d.145.1.1 109067,109068 1kkqA 269 7.47e+01 a.123.1.1 68679 1kfbA 268 7.54e+01 c.1.2.4 77369 1bbjA 211 7.58e+01 1tziA 214 7.63e+01 b.1.1.1,b.1.1.2 107487,107488 1iwlA 182 7.72e+01 b.125.1.1 83757 1bnlA 178 7.73e+01 1koe d.169.1.5 42444 1w8xP 117 7.78e+01 1x8iA 227 7.79e+01 1x8hA 228 7.80e+01 1c5cL 214 7.80e+01 32c2A b.1.1.1,b.1.1.2 20474,21438 1yymL 214 7.81e+01 1gc1L 213 7.83e+01 8fabA b.1.1.1,b.1.1.2 20264,21264 1l7iL 214 7.84e+01 b.1.1.1,b.1.1.2 73658,73659 2tpsA 227 7.85e+01 2tpsA c.1.3.1 28591 1i7gA 287 7.87e+01 a.123.1.1 71121 1vgeL 214 7.94e+01 8fabA b.1.1.1,b.1.1.2 20094,21126 1p8rA 308 7.94e+01 c.42.1.1 87977 1uwgL 213 7.98e+01 b.1.1.1,b.1.1.2 100117,100118 1um5L 219 7.99e+01 1a4kA 217 8.00e+01 8fabA b.1.1.1,b.1.1.2 20236,21248 2rcsL 214 8.02e+01 8fabA b.1.1.1,b.1.1.2 20086,21118 1z6tA 591 8.03e+01 1vb9A 585 8.04e+01 1gafL 214 8.05e+01 8fabA b.1.1.1,b.1.1.2 20082,21114 1ad0A 213 8.07e+01 8fabA b.1.1.1,b.1.1.2 20124,21154 1f76A 336 8.09e+01 c.1.4.1 76160 1vfoA 585 8.09e+01 1iqdA 211 8.10e+01 32c2A b.1.1.1,b.1.1.2 62644,62645 1gu9A 177 8.11e+01 a.152.1.1 65540 1tzhA 213 8.11e+01 b.1.1.1,b.1.1.2 107477,107478 1rhhA 215 8.15e+01 b.1.1.1,b.1.1.2 97473,97474 1me5A 177 8.15e+01 a.152.1.1 79024 1p2fA 220 8.15e+01 a.4.6.1,c.23.1.1 87720,87721 3fctA 213 8.17e+01 8fabA b.1.1.1,b.1.1.2 20374,21366 1ngyA 213 8.19e+01 b.1.1.1,b.1.1.2 80496,80497 1vaoA 560 8.22e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 2fj0A 551 8.22e+01 2btqB 426 8.24e+01 2atrA 138 8.25e+01 1w1lA 560 8.26e+01 d.58.32.1,d.145.1.1 109063,109064 1ngxA 213 8.26e+01 b.1.1.1,b.1.1.2 85702,85703 1ngzA 213 8.28e+01 b.1.1.1,b.1.1.2 80500,80501 1pq3A 306 8.31e+01 c.42.1.1 94989 1mimL 210 8.33e+01 8fabA b.1.1.1,b.1.1.2 20128,21158 1rziA 212 8.35e+01 b.1.1.1,b.1.1.2 98166,98167 1w1jA 560 8.36e+01 d.58.32.1,d.145.1.1 109055,109056 1mtoA 319 8.37e+01 c.89.1.1 79458 1rz7L 212 8.48e+01 b.1.1.1,b.1.1.2 98135,98136 1za3A 213 8.56e+01 1y34I 64 8.60e+01 2ashA 381 8.62e+01 2fjfA 214 8.64e+01 2xinA 393 8.65e+01 4xis c.1.15.3 29493 1lw1A 177 8.67e+01 a.152.1.1 74290 1tzgL 214 8.70e+01 1op3K 212 8.72e+01 b.1.1.1,b.1.1.2 87210,87211 1zlsL 211 8.73e+01 1p32A 209 8.75e+01 1p32A d.25.1.1 38379 1uf3A 228 8.78e+01 d.159.1.6 99317 1nf7A 514 8.81e+01 c.1.5.1,d.37.1.1,d.37.1.1 91852,91853,91854 1jcnA 514 8.83e+01 c.1.5.1,d.37.1.1,d.37.1.1 84160,84161,84162 1to3A 304 8.86e+01 c.1.10.1 107161 1gkzA 388 8.86e+01 a.29.5.1,d.122.1.4 65268,65269 1deeA 214 8.87e+01 32c2A b.1.1.1,b.1.1.2 20442,21408 1k7lA 288 8.87e+01 a.123.1.1 68268 1hezA 214 8.87e+01 32c2A b.1.1.1,b.1.1.2 60983,60984 1n8zA 214 8.92e+01 b.1.1.1,b.1.1.2 80318,80319 1beuA 268 8.93e+01 2tysA c.1.2.4 28574 1oadA 388 8.99e+01 c.1.15.3 81253