# List of top-scoring protein chains for T0334.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 2aqjA 538 1.87e-58 1dob 394 1.09e-11 1pbe c.3.1.2,d.16.1.2 30362,37893 1pxb 394 1.17e-11 1pbe c.3.1.2,d.16.1.2 30367,37898 1k0iA 394 1.21e-11 c.3.1.2,d.16.1.2 67942,67943 1iut 394 1.26e-11 1pbe c.3.1.2,d.16.1.2 30355,37886 1pxc 394 1.26e-11 1pbe c.3.1.2,d.16.1.2 30361,37892 1pbe 394 1.36e-11 1pbe c.3.1.2,d.16.1.2 30338,37869 1ykjA 394 1.38e-11 1cj3A 392 1.56e-11 1pbe c.3.1.2,d.16.1.2 30347,37878 1bgj 394 1.58e-11 1pbe c.3.1.2,d.16.1.2 30352,37883 1cj2A 391 1.79e-11 1pbe c.3.1.2,d.16.1.2 30351,37882 1pbd 394 1.89e-11 1pbe c.3.1.2,d.16.1.2 30342,37873 1bf3 394 1.96e-11 1pbe c.3.1.2,d.16.1.2 30346,37877 1pxa 394 2.00e-11 1pbe c.3.1.2,d.16.1.2 30366,37897 1cj4A 392 2.03e-11 1pbe c.3.1.2,d.16.1.2 30345,37876 1pbf 394 2.07e-11 1pbe c.3.1.2,d.16.1.2 30349,37880 1bgn 394 2.20e-11 1pbe c.3.1.2,d.16.1.2 30339,37870 1cc6A 394 2.29e-11 1pbe c.3.1.2,d.16.1.2 30344,37875 1bkwA 394 2.35e-11 1pbe c.3.1.2,d.16.1.2 30343,37874 1cc4A 394 5.46e-11 1pbe c.3.1.2,d.16.1.2 30340,37871 1pj5A 830 1.34e-10 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1d4cA 572 8.35e-10 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19698,30435,42318 1d4dA 572 8.38e-10 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19702,30439,42322 1y56B 382 1.13e-09 1pn0A 665 1.45e-09 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1fohA 664 2.06e-09 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1x31B 404 2.52e-09 1ng4A 390 3.19e-09 c.3.1.2,d.16.1.3 85666,85667 1ryiA 382 3.65e-09 1l9cA 389 2.28e-08 c.3.1.2,d.16.1.3 77815,77816 1el5A 389 3.27e-08 1b3mA c.3.1.2,d.16.1.3 30369,37937 1c0pA 363 3.39e-08 1an9A c.4.1.2,d.16.1.3 30647,37934 1q9iA 571 1.19e-07 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 2b7sA 571 1.37e-07 1jryA 571 1.38e-07 a.138.1.3,c.3.1.4,d.168.1.1 67199,67200,67201 1jrzA 571 1.41e-07 a.138.1.3,c.3.1.4,d.168.1.1 67205,67206,67207 2b7rA 571 1.42e-07 1y0pA 571 1.44e-07 1p2eA 571 1.44e-07 a.138.1.3,c.3.1.4,d.168.1.1 93926,93927,93928 1e39A 571 1.44e-07 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1jrxA 571 1.45e-07 a.138.1.3,c.3.1.4,d.168.1.1 67193,67194,67195 1p2hA 571 1.47e-07 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1ksuA 571 1.47e-07 a.138.1.3,c.3.1.4,d.168.1.1 72931,72932,72933 1kssA 571 1.47e-07 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1m64A 571 1.49e-07 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1lj1A 571 1.49e-07 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1ojt 482 9.67e-07 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30581,30582,40212 1bhy 482 9.77e-07 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30583,30584,40213 1lvl 458 1.23e-06 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1qo8A 566 1.44e-06 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1jnrA 643 2.16e-06 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1s3eA 520 2.32e-06 c.3.1.2,d.16.1.5 98426,98427 2c73A 520 2.34e-06 2c76A 520 2.37e-06 2c72A 520 2.39e-06 2c75A 520 2.46e-06 2gqfA 401 2.55e-06 2bk5A 520 2.67e-06 2cvjA 180 2.81e-06 2a87A 335 2.87e-06 2fjbA 643 2.89e-06 1zovA 386 3.71e-06 1f8rA 498 5.94e-06 1f8rA c.3.1.2,d.16.1.5 30410,37974 1onfA 500 9.04e-06 c.3.1.5,c.3.1.5,d.87.1.1 87141,87142,87143 1w4xA 542 9.57e-06 c.3.1.5,c.3.1.5 109171,109172 1ebdA 455 3.55e-05 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1an9A 340 3.61e-05 1an9A c.4.1.2,d.16.1.3 30617,37904 1ve9A 347 3.63e-05 c.4.1.2,d.16.1.3 100571,100572 1xdiA 499 4.84e-05 1yy5A 513 5.02e-05 1rsgA 516 5.02e-05 2bxrA 527 5.54e-05 1dxlA 470 6.56e-05 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30585,30586,40214 2a8xA 464 9.55e-05 1xhcA 367 1.13e-04 1m6iA 493 1.38e-04 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1gv4A 528 1.71e-04 c.3.1.5,c.3.1.5,d.87.1.1 70589,70590,70591 1f8wA 447 1.78e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30561,30562,40202 1npx 447 1.79e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30557,30558,40200 1nhp 447 1.82e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1nhq 447 1.82e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30551,30552,40197 1nhr 447 1.85e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30553,30554,40198 1nhs 447 1.87e-04 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1tdf 316 2.07e-04 1trb c.3.1.5,c.3.1.5 30533,30534 1trb 320 2.07e-04 1trb c.3.1.5,c.3.1.5 30529,30530 1tde 316 2.31e-04 1trb c.3.1.5,c.3.1.5 30531,30532 1cl0A 320 2.32e-04 1trb c.3.1.5,c.3.1.5 30535,30536 1v59A 478 2.47e-04 1rp0A 284 2.48e-04 1o5wA 534 2.49e-04 c.3.1.2,d.16.1.5 92520,92521 1f6mA 320 2.54e-04 1trb c.3.1.5,c.3.1.5 30537,30538 2bryA 497 3.14e-04 2braA 484 4.83e-04 1fcdA 401 6.62e-04 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1q1rA 431 6.68e-04 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1zk7A 467 6.69e-04 1y56A 493 7.29e-04 1lpfA 477 7.40e-04 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30569,30570,40206 1d7yA 408 1.00e-03 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1x31A 964 1.03e-03 1kdgA 546 1.44e-03 c.3.1.2,d.16.1.1 77337,77338 1naaA 541 1.59e-03 c.3.1.2,d.16.1.1 80365,80366 1zy8A 474 2.06e-03 1reoA 486 2.43e-03 c.3.1.2,d.16.1.5 97325,97326 3ladA 476 2.58e-03 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1ju2A 536 2.94e-03 c.3.1.2,d.16.1.1 77169,77170 1zmdA 474 2.96e-03 1ps9A 671 3.01e-03 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1sezA 504 3.38e-03 c.3.1.2,d.16.1.5 98822,98823 1k4qA 461 4.63e-03 c.3.1.5,c.3.1.5,d.87.1.1 68140,68141,68142 1xan 461 5.66e-03 3grs c.3.1.5,c.3.1.5,d.87.1.1 30449,30450,40156 3grs 478 5.67e-03 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 2aaqA 479 5.67e-03 2bi7A 384 6.31e-03 1wamA 384 6.52e-03 1i8tA 367 7.41e-03 c.4.1.3,d.16.1.7 66094,66095 1gesA 450 9.50e-03 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 5grt 461 1.12e-02 3grs c.3.1.5,c.3.1.5,d.87.1.1 30465,30466,40164 1grt 478 1.13e-02 3grs c.3.1.5,c.3.1.5,d.87.1.1 30467,30468,40165 1cf3A 583 1.14e-02 1gpeA c.3.1.2,d.16.1.1 30385,37949 1gerA 450 1.22e-02 3grs c.3.1.5,c.3.1.5,d.87.1.1 30477,30478,40170 1fl2A 310 1.23e-02 1hyuA c.3.1.5,c.3.1.5 59869,59870 1vqwA 457 1.34e-02 1h6vA 499 1.62e-02 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1yvvA 336 1.78e-02 2cfyA 521 2.17e-02 2ew2A 316 2.84e-02 1chuA 540 3.95e-02 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1knrA 540 3.99e-02 a.7.3.1,c.3.1.4,d.168.1.1 72788,72789,72790 1hyuA 521 4.24e-02 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1vdc 333 5.02e-02 1trb c.3.1.5,c.3.1.5 30545,30546 1qlaA 656 6.72e-02 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 2culA 232 7.07e-02 1tt0A 623 7.77e-02 1tzlA 622 7.84e-02 2g1uA 155 8.10e-02 1qzzA 374 8.25e-02 a.4.5.29,c.66.1.12 96719,96720 2bs3A 656 8.43e-02 1e7pG 655 8.43e-02 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 59359,59360,59361 1qrrA 394 1.06e-01 1qrrA c.2.1.2 29824 1cjcA 460 1.34e-01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1i2cA 404 1.50e-01 c.2.1.2 83666 1i24A 404 1.55e-01 c.2.1.2 83663 1gpeA 587 1.59e-01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1b5qA 472 1.60e-01 1b37B c.3.1.2,d.16.1.5 30404,37968 1h7xA 1025 1.71e-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 1gteA 1025 1.71e-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 1kf6A 602 1.72e-01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1ur5A 309 1.78e-01 c.2.1.5,d.162.1.1 99807,99808 1uxgA 309 1.80e-01 c.2.1.5,d.162.1.1 108100,108101 1uxkA 309 1.82e-01 c.2.1.5,d.162.1.1 108116,108117 1uxjA 309 1.84e-01 c.2.1.5,d.162.1.1 108112,108113 2b2cA 314 1.94e-01 2b76A 602 2.13e-01 2avnA 260 2.40e-01 2b9wA 424 2.47e-01 1djqA 729 2.65e-01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1o94A 729 2.67e-01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1gxfA 492 3.20e-01 c.3.1.5,c.3.1.5,d.87.1.1 90527,90528,90529 3hdhA 302 4.54e-01 2hdhA a.100.1.3,c.2.1.6 18805,30209 3hadA 308 5.53e-01 2hdhA a.100.1.3,c.2.1.6 18799,30203 1lsjA 302 5.57e-01 a.100.1.3,c.2.1.6 91116,91117 2hdhA 293 5.89e-01 2hdhA a.100.1.3,c.2.1.6 18795,30199 1lsoA 302 6.01e-01 a.100.1.3,c.2.1.6 91120,91121 1il0A 302 6.52e-01 a.100.1.3,c.2.1.6 66189,66190 1m75A 302 6.52e-01 a.100.1.3,c.2.1.6 91212,91213 1f0yA 302 6.72e-01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1f17A 310 7.21e-01 2hdhA a.100.1.3,c.2.1.6 18797,30201 1y6jA 318 7.42e-01 1m76A 302 7.82e-01 a.100.1.3,c.2.1.6 91216,91217 1lssA 140 9.24e-01 c.2.1.9 74246 1zkqA 517 9.63e-01 1a5z 319 1.06e+00 1ceqA c.2.1.5,d.162.1.1 30181,42148 1pjcA 361 1.12e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1ldnA 316 1.20e+00 1hyhA c.2.1.5,d.162.1.1 30166,42133 1ldbA 317 1.20e+00 2cmd 312 1.27e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1v6sA 390 1.30e+00 c.86.1.1 100424 1zoyA 622 1.34e+00 1bzlA 486 1.44e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30521,30522,40192 1ndaA 491 1.54e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30525,30526,40194 1ib6A 312 1.59e+00 c.2.1.5,d.162.1.1 62146,62147 1y7lA 316 1.65e+00 1aogA 485 1.91e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1nekA 588 1.99e+00 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1lqtA 456 2.08e+00 c.3.1.1,c.4.1.1 74198,74199 1mo9A 523 2.21e+00 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1v0jA 399 2.97e+00 2fbwA 621 3.09e+00 1jw9B 249 3.11e+00 c.111.1.1 67377 1t3qB 788 3.58e+00 d.41.1.1,d.133.1.1 106369,106370 3cox 507 3.68e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1smaA 588 3.94e+00 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21854,27781,28768 3sqcA 631 4.17e+00 2sqcA a.102.4.2,a.102.4.2 18860,18861 1lwdA 413 4.29e+00 c.77.1.1 78265 1j0hA 588 4.79e+00 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 2cdcA 366 4.85e+00 2cd9A 366 5.05e+00 2sqcA 631 5.14e+00 2sqcA a.102.4.2,a.102.4.2 18854,18855 1lldA 319 5.35e+00 3ldh c.2.1.5,d.162.1.1 30177,42144 1ts9A 102 5.63e+00 1np3A 338 6.25e+00 a.100.1.2,c.2.1.6 85946,85947 1v1aA 309 6.40e+00 c.72.1.1 100249 1gviA 588 6.40e+00 b.1.18.2,b.71.1.1,c.1.8.1 70604,70605,70606 1j0jA 588 6.49e+00 b.1.18.2,b.71.1.1,c.1.8.1 77039,77040,77041 1ydeA 270 6.98e+00 1u7zA 226 7.76e+00 1rpmA 278 8.26e+00 2shpA c.45.1.2 32679 1guzA 310 9.18e+00 c.2.1.5,d.162.1.1 65586,65587 1gv0A 310 9.56e+00 c.2.1.5,d.162.1.1 65594,65595 1ez4A 318 9.64e+00 c.2.1.5,d.162.1.1 64917,64918 1dwqA 262 9.80e+00 1qj4A c.69.1.20 34808 1x0vA 354 9.94e+00 1luaA 287 9.98e+00 c.2.1.7,c.58.1.4 78216,78217 1pc0A 61 1.04e+01 b.137.1.1 94426 1d2fA 390 1.07e+01 1d2fA c.67.1.3 34411 2aaoA 166 1.09e+01 1gpmA 525 1.16e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1wpqA 349 1.20e+01 1tw3A 360 1.23e+01 a.4.5.29,c.66.1.12 107373,107374 1zud1 251 1.28e+01 1zfnA 253 1.28e+01 2d5cA 263 1.32e+01 1r43A 463 1.37e+01 c.56.5.4,d.58.19.1 96969,96970 1r3nA 462 1.37e+01 c.56.5.4,d.58.19.1 96945,96946 1gpjA 404 1.47e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1b25A 619 1.50e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2ghsA 326 1.62e+01 1dwoA 262 1.65e+01 1qj4A c.69.1.20 34804 1zcjA 463 1.70e+01 1ub7A 322 1.73e+01 c.95.1.2,c.95.1.2 88402,88403 1preA 470 1.76e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1mjfA 281 1.80e+01 c.66.1.17 79198 1z52A 470 1.81e+01 1vpe 398 1.84e+01 16pk c.86.1.1 35453 1e89A 262 1.84e+01 1qj4A c.69.1.20 59375 1tt5B 434 1.87e+01 c.111.1.2 107292 1yovB 444 1.90e+01 1inlA 296 1.92e+01 c.66.1.17 66220 1iqpA 327 1.93e+01 a.80.1.1,c.37.1.20 62649,62650 1q7gA 359 2.01e+01 c.2.1.3,d.81.1.2 96038,96039 1r4mB 431 2.01e+01 c.111.1.2 97000 1v9lA 421 2.11e+01 1vrmA 325 2.13e+01 1zdzA 302 2.17e+01 1z10A 476 2.19e+01 1a0cA 438 2.26e+01 1a0cA c.1.15.3 29529 1c7gA 456 2.28e+01 c.67.1.2 90415 1kb9G 125 2.33e+01 f.27.1.1 77322 1kyoG 126 2.35e+01 f.27.1.1 73259 1hm5A 558 2.38e+01 c.80.1.2 76717 1kojA 557 2.39e+01 c.80.1.2 72821 1vmeA 410 2.40e+01 c.23.5.1,d.157.1.3 108893,108894 1n8tA 557 2.44e+01 c.80.1.2 85454 1zemA 262 2.54e+01 1k8tA 510 2.56e+01 e.41.1.1 68316 1tueA 212 2.69e+01 c.37.1.20 107323 2g5cA 281 2.69e+01 1zt2A 330 2.74e+01 1n11A 437 2.76e+01 d.211.1.1 79778 1kveA 63 2.76e+01 1kveA d.70.1.2 39590 2czrA 226 2.81e+01 1sh7A 284 2.85e+01 1we0A 187 2.87e+01 1pk0A 507 2.93e+01 e.41.1.1 94795 1d5tA 433 3.03e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1oen 540 3.13e+01 1ayl c.91.1.1,c.109.1.1 64750,64751 1gnd 447 3.15e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 1lv0A 449 3.17e+01 c.3.1.3,d.16.1.6 91130,91131 2crwA 149 3.19e+01 1nulA 152 3.24e+01 1nulA c.61.1.1 34011 1wcv1 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