# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1gmuA 143 3.68e-01 b.107.1.1 65335 d.58.38.1 65336 1qpoA 284 7.12e-01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1gmwA 143 7.44e-01 b.107.1.1 65347 d.58.38.1 65348 1s1pA 331 8.30e-01 c.1.7.1 -5240 1g8lA 411 8.32e-01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1iw7C 1119 9.73e-01 e.29.1.1 71474 1j96A 323 1.10e+00 c.1.7.1 71616 1eb0A 147 1.32e+00 b.107.1.1 64890 d.58.38.1 64891 1o54A 277 1.38e+00 c.66.1.13 -8095 1gqoN 143 1.81e+00 c.23.13.1 76308 1gqoX 143 1.92e+00 c.23.13.1 76317 1gqoV 143 2.03e+00 c.23.13.1 76316 1cbf 285 2.04e+00 1cbf c.90.1.1 35587 1gqoK 143 2.35e+00 c.23.13.1 76305 1gaxA 862 2.56e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1earA 147 2.79e+00 b.107.1.1 64875 d.58.38.1 64876 1gvhA 396 3.42e+00 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1gmmA 133 3.47e+00 b.18.1.10 65314 1g0oA 283 3.67e+00 1ybvA c.2.1.2 60181 1uxxX 133 3.79e+00 b.18.1.10 -3107 1ujnA 348 3.79e+00 e.22.1.1 -11998 1gqoL 143 3.95e+00 c.23.13.1 76306 1edg 380 4.07e+00 1edg c.1.8.3 28807 1gqoD 143 4.20e+00 c.23.13.1 76298 1gqoE 143 4.25e+00 c.23.13.1 76299 1gqoS 143 4.25e+00 c.23.13.1 76313 2cbf 234 4.38e+00 1cbf c.90.1.1 35588 1qstA 160 4.44e+00 1yghA d.108.1.1 40804 1ybvA 283 4.44e+00 1ybvA c.2.1.2 29948 1ju3A 583 4.55e+00 b.18.1.13 67300 c.69.1.21 67301 1cz1A 394 4.55e+00 1cz1A c.1.8.3 28839 1eqcA 394 4.56e+00 1cz1A c.1.8.3 28811 1gqoO 143 4.61e+00 c.23.13.1 76309 1gqoT 143 4.61e+00 c.23.13.1 76314 1gqoR 143 4.73e+00 c.23.13.1 76312 1jvwA 167 4.82e+00 d.26.1.1 71907 1gqoH 143 4.84e+00 c.23.13.1 76302 1h3nA 878 5.23e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1drtA 324 5.30e+00 1drtA b.82.2.2 28130 1j0hA 588 5.34e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1lrzA 426 5.34e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1gqoU 143 5.39e+00 c.23.13.1 76315 1f20A 435 5.42e+00 b.43.4.1 64932 c.25.1.4 64933 1p3dA 475 5.49e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1gqoJ 143 6.01e+00 c.23.13.1 76304 1gqoC 143 6.28e+00 c.23.13.1 76297 1gqoI 143 6.51e+00 c.23.13.1 76303 1uz5A 402 6.54e+00 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1fjgQ 105 6.67e+00 1fjfQ b.40.4.5 25352 1aszB 490 6.76e+00 1b8aA b.40.4.1 25241 d.104.1.1 40762 1pqhA 143 7.38e+00 b.52.2.1 -4318 1d7kA 421 7.45e+00 7odcA b.49.2.3 26486 c.1.6.1 28648 1pil 112 7.47e+00 2pii d.58.5.1 39072 1gqoG 143 7.69e+00 c.23.13.1 76301 1gqoM 143 8.00e+00 c.23.13.1 76307 1o7iA 119 8.05e+00 b.40.4.3 86642 1vhcA 224 8.19e+00 c.1.10.1 -5488 1p2fA 220 8.35e+00 a.4.6.1 87720 c.23.1.1 87721 1h7wD 1025 9.59e+00 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1ffkK 186 9.67e+00 1ffkK c.55.4.1 33731 1gqoF 143 9.83e+00 c.23.13.1 76300 1ml9A 302 9.88e+00 b.85.7.1 79282 1rqpA 299 9.91e+00 unknown_sccs -4411 unknown_sccs -7908 1ekqA 272 1.01e+01 1c3qA c.72.1.2 34941 1gqoB 143 1.03e+01 c.23.13.1 76296 1gteA 1025 1.04e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1m1hA 248 1.04e+01 b.114.1.1 78415 d.58.42.1 78416 1h7wA 1025 1.04e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1h7wB 1025 1.04e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1gkpA 458 1.04e+01 b.92.1.3 70231 c.1.9.6 70232 1l5jA 865 1.05e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1pt1A 143 1.06e+01 b.52.2.1 -4322 1gqoQ 143 1.07e+01 c.23.13.1 76311 1przA 252 1.09e+01 unknown_sccs -10158 1oroA 213 1.10e+01 1opr c.61.1.1 34093 1h75A 81 1.11e+01 1h75A c.47.1.1 60716 1iqvA 218 1.12e+01 1rss a.75.1.1 62661 1gthD 1025 1.15e+01 a.1.2.2 70498 c.1.4.1 70499 c.3.1.1 70500 c.4.1.1 70501 d.58.1.5 70502 1d0nA 729 1.15e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1bkb 136 1.20e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1ds1A 324 1.22e+01 1drtA b.82.2.2 28127 1dryA 324 1.26e+01 1drtA b.82.2.2 28128 1h7xD 1025 1.26e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1h7xC 1025 1.31e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1h7xA 1025 1.35e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1h7xB 1025 1.35e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1gthA 1025 1.35e+01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1gthC 1025 1.35e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1jvnA 555 1.37e+01 c.1.2.1 67355 c.23.16.1 67356 1gqyA 475 1.37e+01 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1gteD 1025 1.38e+01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 7odcA 424 1.42e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1xxaA 78 1.45e+01 1xxaA d.74.2.1 39700 1dmhA 311 1.45e+01 1dmhA b.3.6.1 22633 1m5q1 130 1.49e+01 1fzkB 99 1.53e+01 1agdB b.1.1.2 60151 1gd7A 109 1.53e+01 b.40.4.4 60441 1tidB 119 1.54e+01 1vjrA 271 1.54e+01 unknown_sccs -6853 1i8dA 213 1.55e+01 b.43.4.3 61953 b.43.4.3 61954 1mhcB 99 1.55e+01 1agdB b.1.1.2 20832 1v9fA 325 1.61e+01 1nsj 205 1.65e+01 1nsj c.1.2.4 28560 1gthB 1025 1.66e+01 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 1gz6A 319 1.68e+01 c.2.1.2 76410 1f6yA 262 1.69e+01 1f6yA c.1.21.2 29673 1iz6A 138 1.70e+01 b.34.5.2 76976 b.40.4.5 76977 1a7s 221 1.72e+01 1a7s b.47.1.2 26284 1gt8A 1025 1.74e+01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1jxmA 301 1.75e+01 b.34.2.1 67420 c.37.1.1 67421 1asyA 490 1.77e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 1a49A 530 1.77e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 2pii 112 1.77e+01 2pii d.58.5.1 39071 1fzoB 99 1.80e+01 1agdB b.1.1.2 60157 1g7pB 99 1.80e+01 b.1.1.2 70155 1lk2B 99 1.80e+01 b.1.1.2 -2576 1omzA 293 1.80e+01 c.68.1.15 87093 1gt8D 1025 1.83e+01 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1opr 213 1.83e+01 1opr c.61.1.1 34091 1vhsA 175 1.84e+01 d.108.1.1 -10794 1gt8C 1025 1.88e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1crxA 322 1.93e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1k0hA 117 1.93e+01 b.106.1.2 71975 1r9hA 135 1.95e+01 d.26.1.1 -9482 1iv0A 98 1.97e+01 unknown_sccs -7667 1c0pA 363 2.05e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1mugA 168 2.09e+01 1mugA c.18.1.2 31030 1p4dA 330 2.13e+01 unknown_sccs -10522 4pgaA 337 2.13e+01 4pgaA c.88.1.1 35565 1iwmA 186 2.16e+01 b.125.1.2 83758 1geqA 248 2.32e+01 2tysA c.1.2.4 28589 1rl2A 137 2.36e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1l4zB 136 2.41e+01 d.15.5.1 77704 1pkn 530 2.50e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1k5wA 152 2.59e+01 b.7.1.2 68212 1fx4A 231 2.62e+01 1fx2A d.58.29.1 39431 1jj2A 239 2.64e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1ble 163 2.67e+01 1ble c.38.1.1 32475 1fjgB 256 2.69e+01 1fjfB c.23.15.1 31400 1hw6A 278 2.71e+01 1frb c.1.7.1 61296 1et7A 341 2.73e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1k8hA 133 2.76e+01 b.111.1.1 72176 1cawB 184 2.78e+01 1caxB b.82.1.2 28113 1kpuB 99 2.84e+01 b.1.1.2 84458 1iakA 199 2.87e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 5gcnA 166 2.88e+01 1yghA d.108.1.1 40807 1kjwA 295 2.89e+01 b.34.2.1 68643 c.37.1.1 68644 1d0vA 356 2.91e+01 1d0vA c.39.1.1 32476 1php 394 2.92e+01 16pk c.86.1.1 35452 1im5A 180 2.94e+01 unknown_sccs 66211 1c3jA 351 3.01e+01 1c3jA c.87.1.1 35459 1jr2A 286 3.03e+01 c.113.1.1 67111 1cjxA 357 3.05e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 1l6rA 227 3.05e+01 c.108.1.10 77768 1oi7A 288 3.06e+01 c.2.1.8 87049 c.23.4.1 87050 1gt8B 1025 3.06e+01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1cydA 244 3.08e+01 1cydA c.2.1.2 29825 1gqoY 143 3.09e+01 c.23.13.1 76318 1nzjA 298 3.13e+01 c.26.1.1 -6600 1ep3A 311 3.14e+01 2dorA c.1.4.1 28597 1l5oA 356 3.15e+01 c.39.1.1 77711 1f44A 324 3.18e+01 a.60.9.1 64982 d.163.1.1 64983 1g8aA 227 3.19e+01 c.66.1.3 -8049 1caxB 184 3.24e+01 1caxB b.82.1.2 28105 1v9kA 228 3.24e+01 1qwgA 251 3.29e+01 unknown_sccs -5678 1gqoP 143 3.37e+01 c.23.13.1 76310 1svr 114 3.42e+01 1svy d.109.1.1 40833 1op0A 234 3.45e+01 1lwdA 413 3.48e+01 c.77.1.1 78265 1lssA 140 3.61e+01 c.2.1.9 74246 1irxA 523 3.63e+01 a.97.1.2 71378 c.26.1.1 71379 1qlmA 316 3.66e+01 1qlmA d.147.1.1 41765 1sy6A 204 3.66e+01 1qg0A 308 3.67e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1uu1A 335 3.75e+01 c.67.1.1 -8146 1qk9A 92 3.76e+01 1qk9A d.10.1.3 37485 1a80 277 3.81e+01 1frb c.1.7.1 28700 1e4fT 419 3.87e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1uayA 242 3.87e+01 c.2.1.2 88390 1kjvB 100 3.89e+01 b.1.1.2 77423 1qopA 268 3.89e+01 2tysA c.1.2.4 28570 1yghA 164 3.94e+01 1yghA d.108.1.1 40802 1p0yA 444 3.97e+01 a.166.1.1 87654 b.85.7.3 87655 1lw1A 177 3.97e+01 a.152.1.1 74290