# List of top-scoring protein chains for t04-100-30-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.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 2fgqX 332 1.05e-22 f.4.3.1 133439 1e54A 332 1.09e-22 1e54A f.4.3.1 59258 2omf 340 2.12e-22 2omf 1hxxA 340 2.78e-22 2omf f.4.3.1 61385 2j1nA 346 3.33e-22 2por 301 1.95e-07 2por 2porA 301 1.95e-07 f.4.3.1 43759 3prn 289 3.32e-05 3prn 3prnA 289 3.32e-05 f.4.3.1 43761 1prn 289 8.06e-05 3prn 2o4vA 411 1.03e-04 1p4tA 155 7.10e-03 f.4.1.1 87779 1a0tP 413 1.22e-02 1a0tP f.4.3.2 43794 1qd6C 240 1.61e-02 1qd5A 2gufA 594 2.70e-02 f.4.3.3 135736 2odjA 428 3.81e-02 1qd5A 275 3.96e-02 1qd5A f.4.2.1 43748 1nqeA 594 7.14e-02 f.4.3.3 86027 2jqyA 280 1.08e-01 2qv3A 457 1.11e-01 2mprA 421 1.34e-01 2mprA f.4.3.2 43788 1i78A 297 1.93e-01 f.4.4.1 66046 2iwvA 281 2.76e-01 2icrA 237 3.40e-01 1t16A 427 3.71e-01 f.4.3.4 106242 2bjqA 345 4.62e-01 b.169.1.1,b.169.1.1 128626,128627 3bo5A 290 5.27e-01 2hpwA 233 5.30e-01 2f1cX 286 5.74e-01 2iciA 227 8.22e-01 1po0A 751 1.09e+00 f.4.3.3 94960 2f1vA 197 1.26e+00 2bjrA 368 1.29e+00 b.169.1.1,b.169.1.1 128628,128629 1kmoA 774 1.31e+00 f.4.3.3 72753 2b3rA 134 1.56e+00 1qjpA 171 2.12e+00 1bxwA f.4.1.1 43742 2hr7A 486 2.50e+00 1m93B 245 2.54e+00 1a8d 452 2.72e+00 1a8d 1a8dA 452 2.72e+00 b.29.1.6,b.42.4.2 24262,25607 2a9dA 372 2.90e+00 b.1.18.6,d.176.1.1 126431,126432 2v43A 303 3.01e+00 1soxA 466 3.02e+00 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1tv8A 340 3.24e+00 c.1.28.3 107352 1f0cA 305 3.54e+00 1c8oA e.1.1.1 42676 2fbeA 201 3.82e+00 b.29.1.22 133241 1itbB 315 4.17e+00 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1bkzA 135 4.24e+00 1a3k b.29.1.3 24202 1yqfA 203 4.29e+00 d.25.1.1 123880 2mev1 277 4.31e+00 2mev1 1y4wA 518 4.47e+00 b.29.1.19,b.67.2.3 116470,116471 2zaiA 497 4.51e+00 2qdrA 303 4.81e+00 1mkfA 382 5.04e+00 b.116.1.1 79232 2ogrA 229 5.38e+00 1cb8A 678 5.39e+00 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 2a6hA 315 5.81e+00 d.74.3.1,d.181.1.1 126260,126261 1qfgA 725 5.88e+00 1by5A f.4.3.3 43803 3psgA 370 6.04e+00 b.50.1.2 26841 1txnA 328 6.17e+00 d.248.1.1 112779 1jmxA 494 6.32e+00 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 3cla 213 6.47e+00 3cla 3claA 213 6.47e+00 c.43.1.1 32610 1wdiA 345 6.61e+00 e.53.1.1 114535 2p0wA 324 6.83e+00 1enfA 212 6.91e+00 3seb b.40.2.2,d.15.6.1 25198,37787 1tyv 542 7.01e+00 1tyv 1tyvA 554 7.03e+00 b.80.1.6 28038 1lkeA 184 7.30e+00 b.60.1.1 84622 1y43B 173 7.36e+00 2fb2A 340 7.55e+00 1upsA 420 7.60e+00 b.29.1.2,b.42.2.3 113394,113395 1olrA 224 7.70e+00 b.29.1.11 93330 1h5rA 293 7.79e+00 c.68.1.6 65623 3bh7B 352 7.85e+00 2oxaA 600 8.04e+00 2fp8A 322 8.08e+00 1o6vA 466 8.16e+00 b.1.18.15,c.10.2.1 81099,81100 2hkjA 469 8.40e+00 a.156.1.3,d.14.1.3,d.122.1.2 136553,136554,136555 2d6mA 159 8.56e+00 1k2eA 156 8.65e+00 d.113.1.1 72010 1vcaA 202 8.72e+00 1vcaA b.1.1.3,b.1.1.4 21649,21685 2hx0A 154 9.31e+00 d.290.1.3 136830 2p4bA 295 9.43e+00 2qn6A 414 9.46e+00 1mu5A 471 9.77e+00 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 2qntA 141 1.01e+01 1qhoA 686 1.03e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1ukgA 252 1.04e+01 b.29.1.1 99489 1uxtA 501 1.05e+01 c.82.1.1 108125 2dekA 265 1.05e+01 c.90.1.1 131430 1mq7A 154 1.06e+01 b.85.4.1 79404 2qxlA 658 1.07e+01 2z6rA 265 1.12e+01 2bx6A 350 1.14e+01 1n12A 138 1.22e+01 b.2.3.2 79779 2ahoA 414 1.23e+01 b.43.3.1,b.44.1.1,c.37.1.8 126767,126768,126769 1w9hA 427 1.24e+01 c.55.3.10 120785 2re9A 181 1.26e+01 2eh6A 375 1.26e+01 2dj0A 137 1.26e+01 1xw3A 110 1.28e+01 2hft 218 1.30e+01 1boy 2hftA 218 1.30e+01 b.1.2.1,b.1.2.1 21951,21952 1q40B 219 1.31e+01 d.17.4.2 95771 1a1x 108 1.31e+01 1a1x 1a1xA 108 1.31e+01 b.63.1.1 27514 1mx0A 472 1.32e+01 a.156.1.3,d.14.1.3,d.122.1.2 79618,79619,79620 2odiA 238 1.33e+01 2iepA 192 1.34e+01 1hnf 182 1.35e+01 1qa9A 1hnfA 182 1.35e+01 b.1.1.1,b.1.1.3 19741,21680 1xezA 721 1.36e+01 2h5uA 499 1.39e+01 2ac1A 541 1.48e+01 1jhjA 171 1.48e+01 b.18.1.9 66714 2ol2A 395 1.53e+01 2aioA 269 1.55e+01 d.157.1.1 126829 1zh8A 340 1.57e+01 c.2.1.3,d.81.1.5 125077,125078 2qk0A 74 1.60e+01 3b9fI 395 1.61e+01 1u5rA 348 1.61e+01 d.144.1.7 113050 1aym1 285 1.62e+01 1aym1 1kxoA 184 1.62e+01 b.60.1.1 84475 1smlA 269 1.63e+01 1smlA d.157.1.1 42053 1h54A 754 1.64e+01 a.102.1.4,b.30.5.3 60634,60635 1hleA 345 1.64e+01 1ovaA e.1.1.1 42618 1mjc 69 1.66e+01 1mjc 1mjcA 69 1.66e+01 b.40.4.5 25319 1bbpA 173 1.66e+01 1bbpA b.60.1.1 27147 1cqqA 180 1.66e+01 1cqqA b.47.1.4 26422 1c1lA 136 1.66e+01 1c1lA b.29.1.3 24219 2ogtA 498 1.70e+01 1umzA 278 1.72e+01 b.29.1.2 99639 1acc 735 1.74e+01 1acc 1accA 735 1.74e+01 f.11.1.1 43828 1kshB 152 1.78e+01 b.1.18.8 72915 2rhsB 800 1.80e+01 1ryaA 160 1.84e+01 d.113.1.5 105122 2f6eA 127 1.85e+01 1yzsA 121 1.88e+01 1w18A 493 1.88e+01 1hq0A 295 1.90e+01 1hzgA d.194.1.1 61122 1r1a1 287 1.92e+01 1aym1 1kopA 223 1.93e+01 2cba b.74.1.1 27966 1ukcA 522 1.94e+01 c.69.1.17 107911 1qcsA 211 1.98e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1lmiA 131 2.01e+01 b.1.19.1 78098 1tk1A 260 2.08e+01 d.248.1.1 107066 1cpnA 208 2.10e+01 b.29.1.2 24175 2g6yA 217 2.11e+01 2a6zA 222 2.11e+01 b.29.1.13 126319 2b59A 187 2.11e+01 b.2.2.2 127879 2r7dA 469 2.11e+01 2fs2A 151 2.13e+01 d.38.1.5 134003 2yueA 168 2.19e+01 2jubA 76 2.19e+01 1mp4A 292 2.22e+01 c.68.1.6 79376 2cu9A 161 2.23e+01 2bm3A 166 2.24e+01 b.2.2.2 128762 1hn0A 1021 2.26e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1g6hA 257 2.26e+01 1gajA c.37.1.12 60318 1fnlA 175 2.26e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 2jh2A 148 2.32e+01 1ajoA 214 2.34e+01 1axkA b.29.1.2 24179 2jerA 389 2.34e+01 1nr0A 611 2.34e+01 b.69.4.1,b.69.4.1 86078,86079 1c8cA 64 2.37e+01 1azpA b.34.13.1 59084 2c2iA 151 2.42e+01 d.38.1.4 129670 1uliA 460 2.48e+01 b.33.1.2,d.129.3.3 107921,107922 2yv8A 164 2.48e+01 1qe3A 489 2.50e+01 2bce c.69.1.1 34630 1vhwA 253 2.53e+01 c.56.2.1 100706 2xatA 212 2.54e+01 b.81.1.3 28058 1a65A 504 2.55e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1wckA 220 2.55e+01 1sixA 174 2.55e+01 b.85.4.1 98892 2ahdA 165 2.56e+01 d.159.1.7 126752 1gbg 214 2.58e+01 1axkA 1gbgA 214 2.58e+01 b.29.1.2 24171 2hdiA 639 2.62e+01 1fx5A 242 2.63e+01 1led b.29.1.1 24135 1q67A 231 2.63e+01 b.55.1.7 95960 1khoA 370 2.70e+01 a.124.1.1,b.12.1.3 72489,72490 1lvwA 295 2.73e+01 c.68.1.6 84723 1gzcA 239 2.73e+01 b.29.1.1 70803 2egxA 269 2.74e+01 1psuA 140 2.77e+01 d.38.1.5 88285 1xhcA 367 2.77e+01 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 2blfA 373 2.85e+01 2ek8A 421 2.86e+01 1p57B 255 2.86e+01 b.47.1.2 94126 2hrgA 496 2.94e+01 1gppA 237 2.96e+01 b.86.1.2 76262 2o62A 270 2.96e+01 1ytqA 204 3.01e+01 b.11.1.1,b.11.1.1 124012,124013 1f5jA 199 3.06e+01 1axkA b.29.1.11 24342 2b9uA 176 3.10e+01 2qt6A 498 3.10e+01 2oggA 152 3.16e+01 2ekdA 207 3.20e+01 2qkiB 188 3.24e+01 1ryp2 233 3.24e+01 1ryp2 1vi4A 174 3.26e+01 c.8.7.1 100731 1upiA 225 3.26e+01 b.82.1.1 99757 1who 96 3.27e+01 1who 1whoA 96 3.27e+01 b.7.3.1 23215 1ajkA 214 3.31e+01 1axkA b.29.1.2 24176 1qlpA 394 3.33e+01 1ovaA e.1.1.1 42628 2olnA 397 3.35e+01 1n7vA 555 3.37e+01 b.126.1.1 85377 1avbA 226 3.43e+01 1led b.29.1.1 24158 2oz4A 265 3.43e+01 1h2kA 349 3.44e+01 b.82.2.6 76572 1ea5A 537 3.44e+01 2bce c.69.1.1 34592 3b9cA 144 3.48e+01 1j5wA 298 3.49e+01 d.104.1.1 71589 3c8wA 255 3.56e+01 1zmyA 142 3.61e+01 1y7wA 291 3.62e+01 3cswA 285 3.64e+01 2g8sA 353 3.65e+01 1p9qC 256 3.70e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2dc4A 165 3.75e+01 1idk 359 3.79e+01 1qcxA 1idkA 359 3.79e+01 b.80.1.2 28025 2aexA 346 3.81e+01 1z8gA 372 3.85e+01 b.47.1.2,d.170.1.2 124697,124698 2hwkA 320 3.85e+01 1jv2A 957 3.87e+01 b.1.15.1,b.1.15.1,b.1.15.1,b.69.8.1 67334,67335,67336,67337 1wbiA 129 3.91e+01 2b3nA 159 3.92e+01 d.38.1.4 127792 1hfuA 503 3.96e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 2h7cA 542 3.98e+01 c.69.1.1 136207 1ejxC 567 3.98e+01 b.92.1.1,c.1.9.2 83184,83185 2c1iA 431 4.00e+01 c.6.2.3,d.341.1.1 129636,129637 1ys5A 164 4.01e+01 f.4.1.3 123956 2f9cA 334 4.01e+01 b.81.1.7 133158 2pigA 334 4.02e+01 2rdgA 196 4.09e+01 1pn0A 665 4.09e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1iamA 185 4.12e+01 b.1.1.3,b.1.1.4 21653,21689 2g19A 244 4.14e+01 1ca1 370 4.15e+01 1ca1 1ca1A 370 4.15e+01 a.124.1.1,b.12.1.3 19340,23648 2vg9A 217 4.16e+01 2a74B 188 4.17e+01 1tq5A 242 4.19e+01 b.82.1.12 119311 2ownA 262 4.31e+01 1xkwA 665 4.33e+01 1lurA 339 4.39e+01 b.30.5.4 84717 2rikA 284 4.39e+01 1o4yA 288 4.44e+01 b.29.1.2 92473 2bb2 181 4.44e+01 2bb2 2pil 159 4.45e+01 2pil 1yllA 200 4.49e+01 b.82.1.17 123653 1f60A 458 4.52e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1fepA 724 4.52e+01 1fepA f.4.3.3 43808 2bjfA 329 4.53e+01 1yxaA 398 4.53e+01 1z6jT 211 4.58e+01 b.1.2.1,b.1.2.1 124527,124528 1mveA 243 4.59e+01 b.29.1.2 85140 2qjtA 352 4.60e+01 1iqyA 638 4.63e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1ut7A 171 4.66e+01 b.143.1.1 99906 2ayuA 417 4.71e+01 d.305.1.1 127571 3b4tA 262 4.80e+01 1f8rA 498 4.83e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1reoA 486 4.85e+01 c.3.1.2,d.16.1.5 97325,97326 2obdA 476 4.85e+01 2qxvA 361 4.93e+01 1w9zA 283 4.95e+01 2volB 180 4.98e+01 2hbtA 247 5.03e+01 2iidA 498 5.06e+01 c.3.1.2,d.16.1.5 137426,137427 1wcdJ 441 5.13e+01 b.121.4.9 120887 1uok 558 5.15e+01 1uok 1uokA 558 5.15e+01 b.71.1.1,c.1.8.1 27801,28788 1pamA 686 5.17e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 2rk9A 145 5.18e+01 1rmg 422 5.18e+01 1rmg 1rmgA 422 5.18e+01 b.80.1.3 28029 2b5tI 432 5.19e+01 e.1.1.1 127905 1zgkA 308 5.27e+01 2j04B 524 5.30e+01 2v5iA 559 5.37e+01 2vngA 180 5.40e+01 2vokA 188 5.49e+01 2df7A 458 5.52e+01 b.121.4.9 131449 2nr8A 358 5.52e+01 1z52A 470 5.54e+01 d.169.1.2,f.8.1.1 124445,124446 1kyfA 247 5.54e+01 b.1.10.1,d.105.1.1 73220,73221 1u2xA 474 5.55e+01 c.72.1.3 107622 3brgC 427 5.58e+01 1bec 238 5.62e+01 1bec 1becA 238 5.62e+01 b.1.1.1,b.1.1.2 20627,21561 1oixA 191 5.68e+01 c.37.1.8 118710 2alaA 391 5.69e+01 b.1.18.4,f.10.1.1 126973,126974 3butA 136 5.71e+01 1t95A 240 5.71e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 2ia1A 178 5.73e+01 3bn8A 128 5.76e+01 2cmwA 310 5.76e+01 1k1xA 659 5.78e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2il5A 171 5.81e+01 2c1gA 431 5.87e+01 c.6.2.3,d.341.1.1 129632,129633 1xeuA 263 5.87e+01 2cb4A 291 5.90e+01 1ovaA 386 5.93e+01 1ovaA e.1.1.1 42619 2bmzA 141 5.94e+01 2c1fA 234 5.96e+01 1pguA 615 5.98e+01 b.69.4.1,b.69.4.1 88069,88070 1s4cA 155 6.00e+01 b.82.2.7 118860 2p9wA 334 6.01e+01 1hxs3 237 6.03e+01 1fnuA 221 6.05e+01 3seb b.40.2.2,d.15.6.1 25212,37801 2hr0A 645 6.05e+01 1uy4A 145 6.06e+01 b.18.1.10 108131 1vyqA 173 6.08e+01 b.85.4.1 120548 1ei5A 520 6.09e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1st0A 337 6.11e+01 d.13.1.3,d.246.1.1 98979,98980 2bqxA 173 6.15e+01 2hi2A 158 6.21e+01 2pqsA 159 6.22e+01 1qtsA 247 6.27e+01 1qtsA b.1.10.1,d.105.1.1 22313,40789 2psbA 320 6.28e+01 1vjnA 220 6.33e+01 d.157.1.4 100825 1nvtA 287 6.35e+01 c.2.1.7,c.58.1.5 86270,86271 1vefA 395 6.36e+01 c.67.1.4 120018 2yu1A 451 6.36e+01 2c0cA 362 6.40e+01 1l5aA 436 6.42e+01 c.43.1.2,c.43.1.2 75923,75924 1iwmA 186 6.42e+01 b.125.1.2 83758 1wmxA 205 6.50e+01 b.18.1.24 109418 2vj8A 611 6.52e+01 1tetL 216 6.54e+01 32c2A b.1.1.1,b.1.1.2 19902,20996 1xnzA 264 6.55e+01 d.127.1.1 115673 2b7aA 293 6.59e+01 1b6a 478 6.61e+01 1bn5 1b6aA 478 6.61e+01 a.4.5.25,d.127.1.1 16223,41160 1cqxA 403 6.61e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1usyA 275 6.66e+01 d.104.1.1 113422 1dg6A 191 6.68e+01 1d4vB b.22.1.1 23883 2pjsA 119 6.72e+01 9wgaA 171 6.73e+01 9wgaA g.3.1.1,g.3.1.1,g.3.1.1,g.3.1.1 44000,44001,44002,44003 2pmlX 348 6.74e+01 2hjvA 163 6.77e+01 1c8uA 285 6.78e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 2okxA 956 6.80e+01 1f00I 282 6.87e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1l3iA 192 6.88e+01 c.66.1.22 77676 2i8tA 167 6.91e+01 1ua4A 455 6.91e+01 c.72.1.3 99128 2bc4A 211 6.92e+01 1s8eA 333 6.95e+01 d.159.1.4 105368 1v3wA 173 7.01e+01 b.81.1.5 100291 1q32A 544 7.01e+01 d.136.1.3,d.136.1.3 104507,104508 1ty0A 211 7.06e+01 b.40.2.2,d.15.6.1 107440,107441 1c24A 263 7.10e+01 1c24A d.127.1.1 41148 3bjeA 349 7.15e+01 1r0vA 305 7.16e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1mtpA 323 7.23e+01 e.1.1.1 85107 1jmoA 480 7.26e+01 e.1.1.1 77138 1xgsA 295 7.35e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1d6mA 653 7.37e+01 1d6mA e.10.1.1 43248 1budA 197 7.47e+01 1atlA d.92.1.9 40328 1xn5A 146 7.49e+01 d.129.3.5 115574 3choA 610 7.53e+01 2gtqA 867 7.54e+01 1ywhA 313 7.55e+01 2e4tA 519 7.62e+01 1tu1A 148 7.72e+01 d.107.1.3 107316 1ii7A 333 7.73e+01 1ii7A d.159.1.4 62415 1ac5 483 7.74e+01 1ac5 1ac5A 483 7.74e+01 c.69.1.5 34653 1v8dA 235 7.84e+01 c.140.1.1 108425 2zb6A 481 7.85e+01 1w6nA 134 7.86e+01 b.29.1.3 114275 1so9A 164 7.88e+01 b.146.1.1 105842 1thqA 170 7.88e+01 f.4.1.2 106920 1g1kA 143 7.92e+01 1aohA b.2.2.2 22404 2rdeA 251 7.98e+01 2gk6A 624 7.98e+01