# List of top-scoring protein chains for 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.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 1vaeA 111 3.82e-13 b.36.1.1 108466 2omjA 89 7.11e-13 1tp5A 119 9.57e-13 b.36.1.1 119305 2he2A 102 1.12e-12 1be9A 119 1.12e-12 1pdr b.36.1.1 24774 1um7A 113 1.62e-12 b.36.1.1 99579 1g9oA 91 2.15e-12 1pdr b.36.1.1 60400 1gq5A 91 2.20e-12 b.36.1.1 76274 2he4A 90 2.24e-12 1i92A 91 2.28e-12 1pdr b.36.1.1 61990 1gq4A 90 2.53e-12 b.36.1.1 70340 2r4hA 112 2.58e-12 2dlsA 93 3.05e-12 2ozfA 92 3.92e-12 2dkrA 93 4.31e-12 2ocsA 88 4.49e-12 1wi2A 104 4.61e-12 b.36.1.1 114659 2jilA 97 6.31e-12 1pdrA 99 9.31e-12 b.36.1.1 24771 2iwqA 123 9.77e-12 1uf1A 128 1.46e-11 b.36.1.1 99288 1uezA 101 1.55e-11 b.36.1.1 99286 2d90A 102 1.58e-11 2f5yA 91 1.74e-11 b.36.1.1 133015 2fneA 117 1.87e-11 b.36.1.1 133813 2i0iA 85 2.10e-11 b.36.1.1 136953 1x5qA 110 2.23e-11 b.36.1.1 121717 1whdA 100 2.27e-11 b.36.1.1 114641 1q3oA 109 2.30e-11 b.36.1.1 95700 1wfvA 103 2.31e-11 b.36.1.1 114594 2dm8A 116 2.62e-11 2pktA 91 2.82e-11 2dc2A 103 2.91e-11 2fcfA 103 3.17e-11 b.36.1.1 133267 2bygA 117 3.34e-11 b.36.1.1 129480 2enoA 120 4.32e-11 1w9eA 166 5.08e-11 b.36.1.1 120779 b.36.1.1 120780 2jikA 101 5.60e-11 2dluA 111 5.89e-11 2v90A 96 6.08e-11 2jinA 102 6.26e-11 2edzA 114 6.33e-11 1rgrA 99 7.39e-11 b.36.1.1 104931 1whaA 105 7.63e-11 b.36.1.1 114638 1kefA 93 8.07e-11 b.36.1.1 72369 1iu0A 91 8.85e-11 b.36.1.1 83707 2vrfA 95 1.10e-10 1zokA 93 1.19e-10 b.36.1.1 125451 2eeiA 106 1.36e-10 2eejA 96 1.70e-10 2opgA 98 2.74e-10 2i1nA 102 2.83e-10 2iwoA 120 2.87e-10 1qavA 90 3.24e-10 1qauA b.36.1.1 24777 1uewA 114 3.79e-10 b.36.1.1 99281 2q3gA 89 3.80e-10 1vj6A 102 3.91e-10 b.36.1.1 120064 1d5gA 96 4.00e-10 b.36.1.1 70080 1z87A 263 4.12e-10 2uzcA 88 4.18e-10 1uhpA 107 4.31e-10 b.36.1.1 99400 1z86A 87 4.67e-10 b.36.1.1 124690 2pdzA 86 4.75e-10 1pdr b.36.1.1 24778 2fe5A 94 5.19e-10 b.36.1.1 133323 2v1wA 90 6.02e-10 1gm1A 94 6.28e-10 b.36.1.1 70271 2awxA 105 6.36e-10 2eegA 94 6.59e-10 2oqsA 97 6.78e-10 1ujuA 111 7.20e-10 b.36.1.1 99469 2djtA 104 7.55e-10 1x5rA 112 8.00e-10 b.36.1.1 121718 2yuyA 126 8.15e-10 1rgwA 85 8.17e-10 b.36.1.1 97455 2g2lA 105 8.27e-10 1wjlA 90 8.29e-10 b.36.1.1 114701 1x5nA 114 8.53e-10 b.36.1.1 121714 1ueqA 123 8.94e-10 b.36.1.1 99271 1uitA 117 9.02e-10 b.36.1.1 99433 2awwA 105 9.21e-10 2awuA 105 9.60e-10 1x6dA 119 9.92e-10 b.36.1.2 121739 1v5lA 103 1.05e-09 b.36.1.1 108378 2ogpA 97 1.05e-09 2eehA 100 1.35e-09 1vb7A 94 1.46e-09 b.36.1.1 108474 1wf7A 103 1.47e-09 b.36.1.1 114577 2q9vA 90 1.91e-09 1um1A 110 2.02e-09 b.36.1.1 99578 1ihjA 98 2.15e-09 1pdr b.36.1.1 62382 2egkA 101 2.16e-09 2i0lA 84 2.27e-09 2ehrA 117 2.34e-09 1q7xA 108 2.62e-09 b.36.1.1 96059 2pntA 98 2.68e-09 2egoA 96 2.71e-09 1n7eA 97 2.73e-09 b.36.1.1 91691 1v5qA 122 2.76e-09 b.36.1.1 108383 1qlcA 95 2.77e-09 1qauA b.36.1.1 24776 1p1eA 101 2.93e-09 b.36.1.1 93898 2qg1A 92 3.22e-09 2pa1A 87 3.33e-09 2o2tA 117 3.59e-09 1m5zA 91 3.74e-09 b.36.1.1 78676 2dazA 124 4.13e-09 3b76A 118 4.61e-09 1wf8A 107 4.91e-09 b.36.1.1 120967 1p1dA 196 5.46e-09 b.36.1.1 93896 b.36.1.1 93897 2dmzA 129 5.67e-09 2fn5A 94 6.37e-09 1oziA 99 7.17e-09 b.36.1.1 93845 1ry4A 128 7.45e-09 b.36.1.1 98085 2gzvA 114 7.57e-09 2i04A 85 1.03e-08 1b8qA 127 1.10e-08 1qauA b.36.1.1 24781 1qavB 115 1.19e-08 1qauA b.36.1.1 24780 1x8sA 102 1.22e-08 b.36.1.1 114967 2cs5A 119 1.33e-08 b.36.1.1 130747 1rzxA 98 1.35e-08 b.36.1.1 98236 1qauA 112 1.37e-08 1qauA b.36.1.1 24779 1nf3C 128 1.43e-08 b.36.1.1 85596 2vphA 100 1.45e-08 2g5mB 113 1.53e-08 1xz9A 101 1.55e-08 b.36.1.1 122471 1t2mA 101 1.78e-08 b.36.1.1 119133 2ainA 93 1.81e-08 2h3lA 103 2.56e-08 b.36.1.1 136046 1mfgA 95 2.66e-08 b.36.1.1 79043 1uepA 103 3.12e-08 b.36.1.1 99270 1r6jA 82 3.44e-08 b.36.1.1 97151 1obxA 79 4.16e-08 b.36.1.1 86783 1wh1A 124 4.94e-08 b.36.1.1 114629 1va8A 113 5.04e-08 b.36.1.1 119903 2iwnA 97 5.82e-08 2d92A 108 5.93e-08 2cssA 121 7.28e-08 b.36.1.1 130780 2csjA 117 7.32e-08 b.36.1.1 130771 2pkuA 87 7.78e-08 2qbwA 195 7.84e-08 1wi4A 109 8.55e-08 b.36.1.1 120973 1fc6A 388 9.40e-08 1fc6A b.36.1.3 64738 c.14.1.2 64739 2jweA 88 9.97e-08 2db5A 128 1.00e-07 1ujdA 117 1.01e-07 b.36.1.1 99454 1fc9A 388 1.16e-07 1fc6A b.36.1.3 64742 c.14.1.2 64743 1ufxA 103 1.17e-07 b.36.1.1 99359 1zubA 114 1.17e-07 b.36.1.1 125665 1y7nA 90 1.33e-07 b.36.1.1 122700 2rczA 81 1.42e-07 1i16A 130 1.46e-07 b.36.1.2 24787 1wg6A 127 1.50e-07 b.36.1.1 114603 1u3bA 185 1.51e-07 b.36.1.1 119508 b.36.1.1 119509 2edvA 96 1.58e-07 1u39A 80 1.60e-07 b.36.1.1 119503 1ujvA 96 2.14e-07 b.36.1.1 99470 3bpuA 88 2.54e-07 2edpA 100 3.11e-07 2yt8A 94 3.20e-07 2osgA 83 3.24e-07 1kwaA 88 3.38e-07 1kwaA b.36.1.1 24772 1l6oA 95 3.39e-07 b.36.1.1 84534 2f0aA 98 3.53e-07 b.36.1.1 132661 2reyA 100 3.64e-07 2eaqA 90 3.83e-07 1v62A 117 3.94e-07 b.36.1.1 108390 2ev8A 97 5.22e-07 1wfgA 131 7.37e-07 b.36.1.1 114581 1mc7A 95 8.44e-07 b.36.1.1 91241 2ejyA 97 9.37e-07 2h2cA 107 1.13e-06 2h2bA 107 1.13e-06 2h3mA 97 1.20e-06 1v6bA 118 1.65e-06 b.36.1.1 108394 2joaA 105 2.56e-06 2ytwA 118 2.60e-06 1u37A 89 4.58e-06 b.36.1.1 119501 1x45A 98 4.67e-06 b.36.1.1 121679 1wifA 126 7.48e-06 b.36.1.1 114669 2pzdA 113 8.98e-06 2yt7A 101 1.29e-05 2d8iA 114 1.89e-05 2p3wA 112 2.25e-05 2e7kA 91 3.47e-05 1lcyA 325 4.26e-05 b.36.1.4 73834 b.47.1.1 73835 2yubA 118 6.93e-05 1ky9A 448 1.26e-04 b.36.1.4 73198 b.47.1.1 73199 1sozA 314 2.35e-04 b.36.1.4 105859 b.47.1.1 105860 1te0A 318 2.35e-04 b.36.1.4 112400 b.47.1.1 112401 1sotA 320 2.36e-04 b.36.1.4 105852 b.47.1.1 105853 2qktA 90 4.31e-04 2qkvA 96 5.27e-04 2hgaA 125 4.72e-03 1y8tA 324 6.14e-03 b.36.1.4 122763 b.47.1.1 122764 2j3tD 219 1.72e-01 2i4sA 105 3.67e-01 2dy0A 190 6.14e-01 2bh4X 134 9.62e-01 2bgvX 134 9.76e-01 1db3A 372 9.92e-01 1db3A c.2.1.2 29813 2i6vA 87 1.06e+00 1ao0A 459 1.40e+00 1ecfB c.61.1.1 34049 d.153.1.1 41816 1gph1 465 1.41e+00 1ecfB 1hvyA 288 1.96e+00 1bkpA d.117.1.1 41049 1hzwA 290 1.97e+00 1bkpA d.117.1.1 61464 1hw3A 313 2.05e+00 1bkpA d.117.1.1 41053 1ju6A 313 2.09e+00 d.117.1.1 63289 1hw4A 355 2.24e+00 1bkpA d.117.1.1 41054 1ypvA 313 2.27e+00 1lnzA 342 2.41e+00 b.117.1.1 78112 c.37.1.8 78113 1qgc4 438 2.86e+00 1igtB 155cA 134 3.07e+00 a.3.1.1 15900 1figH 216 3.37e+00 1igtB b.1.1.1 19923 b.1.1.2 21017 1cotA 129 3.45e+00 a.3.1.1 15899 2retB 175 4.20e+00 1sw2A 275 4.55e+00 c.94.1.1 106064 1sw5A 275 4.55e+00 c.94.1.1 106069 1sw5B 275 4.55e+00 c.94.1.1 106070 2d7uA 339 4.66e+00 1d7aA 161 5.03e+00 1qczA c.23.8.1 31277 2yxoA 267 5.12e+00 1qczA 169 5.18e+00 1qczA c.23.8.1 31276 1wkvA 389 5.25e+00 c.79.1.1 120989 2nshA 169 5.49e+00 1yb2A 275 5.70e+00 c.66.1.13 122868 2nslA 169 5.81e+00 1o88A 353 6.08e+00 b.80.1.1 81178 2eweA 353 6.08e+00 2tsrA 307 6.24e+00 1bkpA d.117.1.1 41043 1e6vC 258 7.28e+00 1mroC d.58.31.1 39439 2o8bB 1022 7.29e+00 1nw9B 277 8.24e+00 c.17.1.1 86294 1jxqA 284 8.37e+00 c.17.1.1 67426 1uzlA 247 9.10e+00 c.2.1.2 119809 2g3fA 421 9.59e+00 1h3gA 601 9.66e+00 b.1.18.2 90594 b.71.1.1 90595 c.1.8.1 90596 2ntnA 267 1.04e+01 1dl6A 58 1.10e+01 1dl6A g.41.3.1 45207 1rlyA 60 1.10e+01 g.41.3.1 104988 1vl8A 267 1.12e+01 c.2.1.2 108733 1fp8A 500 1.13e+01 c.1.8.1 90498 1eswA 500 1.13e+01 1cwyA c.1.8.1 59500 1cwyA 500 1.13e+01 1cwyA c.1.8.1 28789 1l1dA 152 1.15e+01 b.88.1.3 73452 1uzmA 247 1.18e+01 c.2.1.2 119811 1iruC 261 1.19e+01 d.153.1.4 71354 2owcA 502 1.20e+01 2yxyA 115 1.20e+01 3colA 196 1.20e+01 1zz1A 369 1.28e+01 2vcgA 375 1.29e+01 1kaeA 434 1.31e+01 c.82.1.2 72247 1k75A 434 1.31e+01 c.82.1.2 68253 2eguA 308 1.32e+01 1ot1A 686 1.39e+01 b.1.18.2 87392 b.3.1.1 87393 b.71.1.1 87394 c.1.8.1 87395 1ot2A 686 1.39e+01 b.1.18.2 87396 b.3.1.1 87397 b.71.1.1 87398 c.1.8.1 87399 2p0iA 456 1.43e+01 1eo5A 686 1.46e+01 1cxlA b.1.18.2 21828 b.3.1.1 22497 b.71.1.1 27735 c.1.8.1 28722 1d3cA 686 1.51e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1dtuA 686 1.51e+01 1cxlA b.1.18.2 21840 b.3.1.1 22509 b.71.1.1 27747 c.1.8.1 28734 1bxoA 323 1.52e+01 2er7E b.50.1.2 26805 1tisA 286 1.52e+01 d.117.1.1 41040 1kclA 686 1.52e+01 b.1.18.2 68445 b.3.1.1 68446 b.71.1.1 68447 c.1.8.1 68448 1cgwA 686 1.52e+01 b.1.18.2 21822 b.3.1.1 22491 b.71.1.1 27729 c.1.8.1 28716 1cgyA 686 1.53e+01 b.1.18.2 21823 b.3.1.1 22492 b.71.1.1 27730 c.1.8.1 28717 1tcmA 686 1.53e+01 1cxlA b.1.18.2 21833 b.3.1.1 22502 b.71.1.1 27740 c.1.8.1 28727 1cgvA 686 1.53e+01 b.1.18.2 21820 b.3.1.1 22489 b.71.1.1 27727 c.1.8.1 28714 1pj9A 686 1.53e+01 b.1.18.2 94754 b.3.1.1 94755 b.71.1.1 94756 c.1.8.1 94757 1cdgA 686 1.53e+01 b.1.18.2 21816 b.3.1.1 22485 b.71.1.1 27723 c.1.8.1 28710 1kckA 686 1.53e+01 b.1.18.2 68441 b.3.1.1 68442 b.71.1.1 68443 c.1.8.1 68444 1cgxA 686 1.53e+01 b.1.18.2 21832 b.3.1.1 22501 b.71.1.1 27739 c.1.8.1 28726 1cxlA 686 1.53e+01 1cxlA b.1.18.2 21829 b.3.1.1 22498 b.71.1.1 27736 c.1.8.1 28723 2dicA 105 1.58e+01 b.1.18.10 131528 1pezA 686 1.58e+01 b.1.18.2 94600 b.3.1.1 94601 b.71.1.1 94602 c.1.8.1 94603 2o3lA 85 1.60e+01 2plnA 137 1.66e+01 2ywvA 244 1.82e+01 1fdrA 248 1.82e+01 b.43.4.2 25653 c.25.1.1 31543 2v40A 459 1.86e+01 1p99A 295 1.88e+01 c.94.1.1 94384 2irpA 208 1.89e+01 2ps1A 226 1.90e+01 3bs5B 80 1.93e+01 2cw9A 194 1.96e+01 d.17.4.13 130920 1ksiA 642 1.96e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1ksiB 642 1.96e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1w2zA 649 1.97e+01 b.30.2.1 114106 d.17.2.1 114107 d.17.2.1 114108 1nulA 152 2.11e+01 1nulA c.61.1.1 34011 2h2qA 521 2.12e+01 1mzvA 235 2.19e+01 c.61.1.1 91502 1nkqA 259 2.21e+01 d.177.1.1 103862 1nvjA 140 2.23e+01 d.41.5.1 86243 3biiE 149 2.31e+01 2ar9A 278 2.32e+01 1fm0E 150 2.32e+01 1fmaE d.41.5.1 38629 1a97A 148 2.41e+01 1nulA c.61.1.1 34023 1koeA 172 2.41e+01 d.169.1.5 42448 1n7kA 234 2.47e+01 c.1.10.1 85374 1dy1A 188 2.51e+01 1koe d.169.1.5 42450 1a98A 152 2.52e+01 1nulA c.61.1.1 34021 2fa5A 162 2.58e+01 3cegA 323 2.58e+01 2hqoA 123 2.62e+01 2p5iA 288 2.75e+01 2eanA 83 2.88e+01 2hc1A 291 2.88e+01 1kcrH 218 2.89e+01 b.1.1.1 72303 b.1.1.2 72304 1ik6A 369 2.99e+01 c.36.1.7 66174 c.48.1.2 66175 1qb7A 236 3.14e+01 1qb7A c.61.1.1 34087 2fyqA 194 3.15e+01 2bngA 149 3.18e+01 1hkvA 453 3.24e+01 b.49.2.3 83559 c.1.6.1 83560 1zn8A 180 3.24e+01 c.61.1.1 125376 1nsnH 210 3.28e+01 1igtB b.1.1.1 20071 b.1.1.2 21103 2o0tA 467 3.38e+01 1hd0A 75 3.47e+01 1ha1 d.58.7.1 39188 1bnlA 178 3.48e+01 1koe d.169.1.5 42444 1wi9A 72 3.55e+01 a.4.5.47 114663 1jx1A 222 3.55e+01 d.36.1.1 71925 1vsqC 165 3.68e+01 1jx0A 222 3.70e+01 d.36.1.1 71923 2adoA 196 3.71e+01 2o3bA 241 3.74e+01 1eyqA 222 3.76e+01 1eypA d.36.1.1 38534 2bh8A 101 3.78e+01 1mkmA 249 3.81e+01 a.4.5.33 79242 d.110.2.2 79243 2azmA 207 3.82e+01 1ri9A 102 3.86e+01 b.34.2.1 97506 2etxA 209 3.87e+01 1hz9A 66 3.88e+01 b.40.4.5 65961 1jmhA 316 3.89e+01 d.117.1.1 41009 1zm8A 259 3.89e+01 2ge9A 125 3.92e+01 1m54A 363 4.00e+01 c.79.1.1 74463