# List of top-scoring protein chains for t04-100-30-str2-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.soe.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 1gefA 123 9.46e-04 1gefA c.52.1.18 60465 2eo0A 147 2.72e-03 1hh1A 143 4.33e-03 1gefA c.52.1.18 61036 1ob8A 135 1.54e-02 c.52.1.18 111627 1y88A 199 3.32e-02 a.60.4.3,c.52.1.30 116560,116561 1sw2A 275 4.82e-01 c.94.1.1 106064 1cliA 345 5.92e-01 1cliA d.79.4.1,d.139.1.1 39816,41459 1gmlA 178 1.22e+00 c.8.5.2 70273 2j5vA 367 1.98e+00 1sw5B 275 2.01e+00 c.94.1.1 106070 1sw5A 275 2.28e+00 c.94.1.1 106069 2inbA 140 2.46e+00 1sx5A 244 2.59e+00 c.52.1.2 99023 1ohvA 472 2.62e+00 c.67.1.4 93031 1vrpA 381 2.82e+00 a.83.1.1,d.128.1.2 120473,120474 1m1lA 236 2.83e+00 d.260.1.1 91166 2btuA 346 3.09e+00 1eonA 245 3.10e+00 1rvaA c.52.1.2 33238 2okfA 140 3.53e+00 1w97L 246 3.82e+00 c.55.1.11,c.55.1.11 114406,114407 3bixA 574 3.87e+00 1f9yA 158 3.90e+00 d.58.30.1 83249 1o12A 376 4.15e+00 b.92.1.5,c.1.9.10 80758,80759 1nv8A 284 5.03e+00 c.66.1.30 86224 1qh4A 380 5.39e+00 1qh4A a.83.1.1,d.128.1.2 18462,41197 2gl6A 392 5.49e+00 1we0A 187 5.91e+00 c.47.1.10 120930 1aw9A 216 5.93e+00 a.45.1.1,c.47.1.5 17736,33030 1wohA 305 6.22e+00 c.42.1.1 109446 1gvfA 286 7.08e+00 c.1.10.2 70599 1jq5A 370 7.28e+00 e.22.1.2 67084 2j78A 468 7.55e+00 c.1.8.4 138099 1zmdA 474 7.64e+00 1w32A 348 7.67e+00 c.1.8.3 114120 2p14A 192 7.70e+00 5croA 66 7.89e+00 1orc a.35.1.2 17044 1vm7A 311 8.50e+00 c.72.1.1 108884 1j7nA 776 8.74e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1ka9H 200 8.81e+00 c.23.16.1 77308 1xmxA 385 9.28e+00 c.52.1.26 115568 2jroA 78 9.43e+00 1uv7A 110 9.58e+00 d.67.4.1 100040 1p3wA 404 1.04e+01 c.67.1.3 87752 2bycA 137 1.06e+01 d.58.10.2 129476 2jc5A 259 1.07e+01 1i1nA 226 1.08e+01 c.66.1.7 71102 2a8jA 420 1.14e+01 1u6rA 380 1.15e+01 a.83.1.1,d.128.1.2 119600,119601 2a8mA 420 1.20e+01 1to3A 304 1.21e+01 c.1.10.1 107161 1d7yA 408 1.24e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 2v9yA 334 1.25e+01 2ostA 151 1.27e+01 1sbp 310 1.29e+01 1sbp 1sbpA 310 1.29e+01 c.94.1.1 35760 2obaA 138 1.32e+01 1yrtA 364 1.33e+01 1c4kA 730 1.35e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1dosA 358 1.37e+01 1dosA c.1.10.2 29175 1f9zA 135 1.37e+01 1qipA d.32.1.1 38484 1fxoA 293 1.39e+01 1g0rA c.68.1.6 34524 1qmvA 197 1.41e+01 1qq2A c.47.1.10 33066 1y8cA 246 1.42e+01 c.66.1.43 116563 1o6dA 163 1.46e+01 c.116.1.3 92567 2e5vA 472 1.47e+01 2cjgA 449 1.48e+01 1zotA 358 1.54e+01 1zesA 125 1.55e+01 c.23.1.1 124994 1ea5A 537 1.57e+01 2bce c.69.1.1 34592 1b00A 127 1.57e+01 3chy c.23.1.1 31122 1ygyA 529 1.59e+01 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 1n8jA 186 1.61e+01 c.47.1.10 85401 1h5rA 293 1.62e+01 c.68.1.6 65623 2jesA 503 1.62e+01 2pzmA 330 1.64e+01 1fa8A 135 1.65e+01 1qipA d.32.1.1 38486 1lvwA 295 1.66e+01 c.68.1.6 84723 2aqjA 538 1.69e+01 2gqwA 408 1.72e+01 2a8lA 420 1.73e+01 2ex4A 241 1.73e+01 c.66.1.42 132516 2ggoA 401 1.74e+01 1vimA 200 1.76e+01 c.80.1.3 100758 2o14A 375 1.79e+01 2ganA 190 1.80e+01 d.108.1.1 134889 1mp4A 292 1.83e+01 c.68.1.6 79376 1tyyA 339 1.85e+01 c.72.1.1 112850 1of5B 184 1.86e+01 d.17.4.2 86934 1ty0A 211 1.87e+01 b.40.2.2,d.15.6.1 107440,107441 2j8gA 339 1.90e+01 2p3yA 491 1.94e+01 2a40B 260 1.98e+01 d.151.1.1 126139 1o0pA 104 1.99e+01 d.58.7.1 86535 2pvxA 54 2.01e+01 2ew2A 316 2.01e+01 2fa8A 105 2.01e+01 c.47.1.23 133185 3d02A 303 2.07e+01 1ml8A 134 2.07e+01 d.227.1.2 85013 1brfA 53 2.09e+01 1rb9 g.41.5.1 45236 2oodA 475 2.10e+01 2hstA 143 2.12e+01 1xfkA 336 2.12e+01 c.42.1.1 115264 1eg5A 384 2.14e+01 1ecxA c.67.1.3 34429 1qrrA 394 2.17e+01 1qrrA c.2.1.2 29824 1bq9A 54 2.19e+01 1rb9 g.41.5.1 45238 1y1pA 342 2.20e+01 c.2.1.2 122550 1yzfA 195 2.22e+01 c.23.10.5 124275 1irxA 523 2.25e+01 a.97.1.2,c.26.1.1 71378,71379 2pvqA 201 2.29e+01 2liv 344 2.32e+01 2liv 1yf5L 254 2.32e+01 c.55.1.11,c.55.1.11 123049,123050 1g0cA 364 2.33e+01 7a3hA c.1.8.3 60165 1i24A 404 2.35e+01 c.2.1.2 83663 1orc 71 2.36e+01 1orc 1orcA 71 2.36e+01 a.35.1.2 17054 1h09A 338 2.38e+01 b.109.1.1,c.1.8.8 83420,83421 2q7eA 291 2.39e+01 1yqyA 523 2.39e+01 d.92.1.14,d.166.1.1 123903,123904 2e4qA 109 2.40e+01 1z7dA 433 2.40e+01 c.67.1.4 124600 1z15A 344 2.44e+01 1tz9A 367 2.48e+01 c.1.15.6 107466 3cmgA 667 2.51e+01 1yk4A 52 2.54e+01 1i2cA 404 2.55e+01 c.2.1.2 83666 1a0gA 282 2.58e+01 1daaA e.17.1.1 43276 2h0eA 121 2.59e+01 1iroA 54 2.60e+01 g.41.5.1 45223 1b13A 54 2.60e+01 1rb9 g.41.5.1 45227 1y0kA 209 2.62e+01 c.52.1.31 122485 2pveA 54 2.63e+01 1x1nA 524 2.65e+01 c.1.8.1 121593 3cox 507 2.67e+01 1b8sA 3coxA 507 2.67e+01 c.3.1.2,d.16.1.1 30332,37863 1eg9A 449 2.79e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 2dsxA 52 2.80e+01 g.41.5.1 131699 1iow 306 2.80e+01 1iow 1iowA 306 2.80e+01 c.30.1.2,d.142.1.1 31713,41481 1g0uG 252 2.84e+01 d.153.1.4 41952 1vffA 423 2.87e+01 c.1.8.4 120033 1zjaA 557 2.89e+01 2gagB 405 2.90e+01 2gvkA 317 2.90e+01 d.58.4.14 135782 1kshA 186 2.98e+01 c.37.1.8 72914 3bhwA 209 3.03e+01 1r42A 615 3.06e+01 d.92.1.5 96968 1vp8A 201 3.07e+01 c.49.1.2 113947 1rypA 243 3.08e+01 1pmaA d.153.1.4 41932 2gm3A 175 3.08e+01 c.26.2.4 135354 6rxnA 45 3.09e+01 g.41.5.1 45222 2f9zC 159 3.14e+01 1wyuA 438 3.14e+01 c.67.1.7 121452 2jbaA 127 3.16e+01 1j3wA 163 3.17e+01 d.110.7.1 90833 1o7nA 449 3.18e+01 b.33.1.2,d.129.3.3 81162,81163 2eh6A 375 3.20e+01 2rgmA 481 3.29e+01 1kmkA 406 3.36e+01 c.67.1.3 68696 1wcgA 464 3.45e+01 c.1.8.4 120888 2f02A 323 3.48e+01 c.72.1.1 132649 2vhlA 396 3.52e+01 2jsoA 88 3.52e+01 2e52A 300 3.56e+01 1x31B 404 3.59e+01 2yydA 345 3.62e+01 2zodA 345 3.63e+01 2z5bA 151 3.64e+01 2dq6A 870 3.65e+01 3b34A 891 3.67e+01 1jeoA 180 3.69e+01 c.80.1.3 66611 1zaiA 363 3.70e+01 c.1.10.1 124828 2gsjA 271 3.71e+01 1adoA 363 3.72e+01 1fbaA c.1.10.1 29124 2it1A 362 3.78e+01 1uoyA 64 3.82e+01 g.3.19.1 99709 2ntoA 201 3.87e+01 1tf4A 605 3.87e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 2cvjA 180 3.88e+01 1wxxA 382 3.88e+01 b.122.1.9,c.66.1.51 121418,121419 2ywlA 180 3.90e+01 1eluA 390 3.92e+01 1elqA c.67.1.3 34434 1iukA 140 3.93e+01 c.2.1.8 83712 1jf9A 408 3.94e+01 1c0nA c.67.1.3 62931 2pmlX 348 3.94e+01 1elqA 390 3.94e+01 1elqA c.67.1.3 34436 1eceA 358 3.97e+01 1eceA c.1.8.3 28813 1q7fA 286 4.01e+01 b.68.9.1 96036 3cb2A 475 4.02e+01 2hl0A 143 4.11e+01 1jsxA 207 4.13e+01 c.66.1.20 71846 3daaA 277 4.14e+01 1daaA e.17.1.1 43272 1zp7A 206 4.14e+01 1u8tA 129 4.14e+01 c.23.1.1 113192 3bv4A 341 4.16e+01 1mkiA 330 4.18e+01 e.3.1.2 84994 2po1B 277 4.23e+01 2oasA 436 4.25e+01 1o1xA 155 4.26e+01 c.121.1.1 86553 2es9A 115 4.30e+01 a.247.1.1 132318 3bqxA 150 4.30e+01 1wj5A 120 4.30e+01 a.4.5.59 114692 2q8zA 342 4.36e+01 1y2qA 143 4.40e+01 2r4vA 247 4.46e+01 2pbyA 308 4.51e+01 2dnjA 260 4.57e+01 3dni d.151.1.1 41790 1e4eA 343 4.67e+01 1iow c.30.1.2,d.142.1.1 59221,59222 2ajfA 597 4.69e+01 d.92.1.5 126882 2epjA 434 4.75e+01 2icgA 160 4.77e+01 2ovgA 66 4.77e+01 3bbdA 205 4.77e+01 1jbeA 128 4.85e+01 3chy c.23.1.1 62845 1clxA 347 4.96e+01 1taxA c.1.8.3 28899 1g6hA 257 5.02e+01 1gajA c.37.1.12 60318 1nekA 588 5.03e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 2bcgG 453 5.03e+01 c.3.1.3,c.3.1.3,d.16.1.6 128282,128283,128284 1xdwA 331 5.03e+01 1opy 131 5.03e+01 1opy 2oz8A 389 5.09e+01 1dmmA 131 5.11e+01 1opy d.17.4.3 38114 1t92A 116 5.21e+01 d.24.1.3 112326 1m3sA 186 5.23e+01 c.80.1.3 78573 2pb2A 420 5.29e+01 2g5dA 422 5.34e+01 1oh0A 131 5.37e+01 d.17.4.3 87004 1vm6A 228 5.38e+01 d.81.1.3,c.2.1.3 108877,118631 1rznA 205 5.42e+01 c.52.1.28 111981 1hrdA 449 5.43e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1eokA 290 5.44e+01 1eokA c.1.8.5 28991 2orwA 184 5.47e+01 2jh1A 246 5.49e+01 8rucI 123 5.51e+01 1rboC d.73.1.1 39629 1iyeA 309 5.52e+01 e.17.1.1 83786 1xl7A 612 5.52e+01 c.43.1.3,c.43.1.3 115438,115439 1fp3A 402 5.53e+01 1fp3A a.102.1.3 18842 2evbA 74 5.53e+01 1ysjA 404 5.57e+01 c.56.5.4,d.58.19.1 123975,123976 2pltA 98 5.58e+01 b.6.1.1 22862 2qziA 103 5.58e+01 2qz7A 194 5.67e+01 2dj5A 133 5.67e+01 c.92.1.3 131536 1skoA 143 5.71e+01 d.110.7.1 105676 1xvsA 126 5.71e+01 b.1.23.1 116095 2iyeA 263 5.72e+01 1m15A 357 5.72e+01 a.83.1.1,d.128.1.2 78368,78369 1vplA 256 5.75e+01 c.37.1.12 113966 1xf1A 926 5.79e+01 2ae6A 166 5.85e+01 d.108.1.1 126600 1bli 483 5.86e+01 1bli 1ir6A 424 5.88e+01 c.107.1.2 71342 1o7fA 469 5.89e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1gqeA 365 5.90e+01 e.38.1.1 70351 2pn8A 211 5.93e+01 1rm8A 169 5.97e+01 d.92.1.11 97660 2zctA 249 5.99e+01 1rreA 200 6.01e+01 d.14.1.10 97791 1qipA 183 6.02e+01 1qipA d.32.1.1 38470 3c8xA 206 6.02e+01 1jofA 365 6.04e+01 b.69.10.1 71775 1j3nA 408 6.09e+01 c.95.1.1,c.95.1.1 84074,84075 3by4A 212 6.12e+01 2yquA 455 6.17e+01 2an1A 292 6.20e+01 2h4uA 145 6.23e+01 d.38.1.5 136082 1iibA 106 6.25e+01 1iibA c.44.2.1 32648 2oolA 337 6.26e+01 1wy7A 207 6.33e+01 c.66.1.32 121433 2gsaA 432 6.34e+01 2gsaA c.67.1.4 34446 1zq7A 207 6.35e+01 d.309.1.1 125501 3b8dA 363 6.37e+01 1xtoA 311 6.38e+01 d.157.1.6 116030 2g45A 129 6.46e+01 2rauA 354 6.48e+01 1pbgA 468 6.53e+01 1e70M c.1.8.4 28946 3dni 260 6.55e+01 3dni 1k2yX 463 6.55e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1iirA 415 6.56e+01 1iirA c.87.1.5 62453 3cneA 175 6.56e+01 1p5dX 463 6.61e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2b6hA 192 6.67e+01 c.37.1.8 127994 1hjrA 158 6.70e+01 1hjrA c.55.3.6 33727 2r2nA 425 6.71e+01 1p2fA 220 6.79e+01 a.4.6.1,c.23.1.1 87720,87721 2r76A 152 6.90e+01 1xvxA 312 6.92e+01 c.94.1.1 116097 1a4iA 301 6.94e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 2bmoA 447 6.95e+01 b.33.1.2,d.129.3.3 128804,128805 3b59A 310 6.99e+01 1wteA 272 7.05e+01 c.52.1.29 114876 2jf7A 532 7.05e+01 1qb5D 99 7.06e+01 b.40.2.1 88357 2hboA 158 7.06e+01 d.38.1.5 136319 1lrzA 426 7.10e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1vr8A 142 7.10e+01 d.312.1.1 120445 1vetA 124 7.13e+01 d.110.7.1 108553 1vqoU 66 7.20e+01 g.39.1.6 120382 2g0wA 296 7.24e+01 c.1.15.4 134503 2fv7A 331 7.27e+01 c.72.1.1 134197 1s3zA 165 7.28e+01 d.108.1.1 105250 2d2eA 250 7.30e+01 2iyaA 424 7.31e+01 1h8mA 140 7.31e+01 1h8mA d.110.4.1 60782 1xi3A 215 7.33e+01 c.1.3.1 109601 2nttA 217 7.36e+01 1sg0A 230 7.37e+01 c.23.5.3 118955 1d66A 66 7.39e+01 1d66A g.38.1.1,h.1.3.1 45076,45510 1atiA 505 7.43e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1nrjB 218 7.43e+01 c.37.1.8 86125 2i5tA 188 7.43e+01 1whzA 70 7.52e+01 d.50.3.2 114656 1ug6A 431 7.53e+01 c.1.8.4 88490 1zboA 210 7.56e+01 b.122.1.10 124859 1l2lA 457 7.57e+01 c.72.1.3 77656 2iswA 323 7.58e+01 2hc5A 117 7.59e+01 1senA 164 7.59e+01 c.47.1.1 105465 1xjdA 345 7.68e+01 d.144.1.7 115388 2obbA 142 7.69e+01 1fjgD 209 7.72e+01 1c05A d.66.1.2 39553 1y1oA 203 7.72e+01 c.52.1.28 116345 2grjA 192 7.83e+01 1lt3A 240 7.86e+01 1lt3A d.166.1.1 42230 1k8kF 168 7.89e+01 d.198.2.1 68312 2bx2L 517 7.93e+01 1rb9A 52 7.96e+01 g.41.5.1 45214