# List of top-scoring protein chains for t2k-80-60-80-str2+near-backbone-11-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.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 1exmA 405 2.11e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1eft 405 2.48e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1ha3A 405 3.51e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1efcA 393 3.57e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1d2eA 397 7.19e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2c78A 405 7.26e-01 2g1lA 104 1.20e+00 1yloA 348 1.94e+00 1aipE 405 2.13e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 2c5qA 240 3.06e+00 1m5sA 297 3.40e+00 d.58.33.1,d.58.33.1 74511,74512 1efuA 385 4.78e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1cid 177 5.19e+00 1cid b.1.1.1,b.1.1.3 19740,21679 1w99A 558 5.76e+00 2a7yA 83 5.93e+00 1ux6A 350 7.31e+00 b.29.1.16,g.75.1.1 100145,100146 1jjeA 222 7.56e+00 1a7tA d.157.1.1 63117 1aipA 405 7.82e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1cf9A 753 8.16e+00 1cf9A c.23.16.3,e.5.1.1 31441,42815 1p80A 753 8.88e+00 c.23.16.3,e.5.1.1 94337,94338 1r9gA 216 1.01e+01 c.23.16.1 97258 1g38A 393 1.02e+01 2admA c.66.1.27 60235 1yukB 120 1.20e+01 1uebA 184 1.20e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1vcbC 160 1.21e+01 1vcbC b.3.3.1 22535 1fx7A 230 1.21e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1drw 273 1.22e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1nbfA 353 1.23e+01 d.3.1.9 80387 1z9lA 128 1.33e+01 1dih 273 1.33e+01 1drw c.2.1.3,d.81.1.3 30056,39971 1z6bA 154 1.34e+01 1r6vA 671 1.37e+01 2abwA 227 1.39e+01 1z4xA 532 1.44e+01 1kk1A 410 1.49e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1ftrA 296 1.53e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1zpuA 534 1.54e+01 1xauA 122 1.57e+01 1g65K 211 1.65e+01 d.153.1.4 41907 1yrkA 126 1.66e+01 1lqbC 162 1.66e+01 b.3.3.1 74186 1imvA 398 1.66e+01 e.1.1.1 62591 1hd7A 318 1.71e+01 1bix d.151.1.1 41780 2azeA 155 1.76e+01 1v04A 355 1.78e+01 b.68.6.2 100240 1zd7A 159 1.90e+01 1xodA 118 1.91e+01 1bmc 221 1.92e+01 1a7tA d.157.1.1 42038 1ukfA 188 1.95e+01 d.3.1.10 99488 1whi 122 1.96e+01 1whi b.39.1.1 24810 1am2 199 1.98e+01 1am2 b.86.1.2 28381 1m2xA 223 2.00e+01 d.157.1.1 84764 1lm8V 160 2.04e+01 b.3.3.1 74035 2mspA 126 2.05e+01 1mspA b.1.11.2 22335 2a7mA 250 2.10e+01 2fhxA 246 2.17e+01 1i1qB 192 2.18e+01 1qdlB c.23.16.1 61544 1n99A 166 2.18e+01 b.36.1.1,b.36.1.1 85459,85460 2an1A 292 2.22e+01 4sli 679 2.24e+01 2sli b.29.1.9,b.68.1.1 24275,27612 2furA 209 2.26e+01 1udzA 182 2.29e+01 b.51.1.1 99239 1i7qB 193 2.32e+01 1qdlB c.23.16.1 61902 1nb8A 353 2.35e+01 d.3.1.9 80385 1v0eA 666 2.36e+01 2gaiA 633 2.45e+01 1cr1A 296 2.47e+01 1cr1A c.37.1.11 32286 1wkrA 340 2.48e+01 b.50.1.2 109395 1ah9 71 2.50e+01 1ah9 b.40.4.5 25330 1neu 124 2.50e+01 1neu b.1.1.1 19704 1s1dA 331 2.51e+01 b.67.3.1 98344 1jg1A 235 2.52e+01 c.66.1.7 66661 1qpxA 218 2.58e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1w61A 414 2.60e+01 1cqkA 101 2.62e+01 1cqkA b.1.1.2 21547 1cqxA 403 2.65e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1rhoC 145 2.67e+01 1rhoA b.1.18.8 21901 1t77A 414 2.67e+01 1x11A 172 2.69e+01 1x11A b.55.1.2 26985 2sli 679 2.79e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1wk8A 194 2.83e+01 1zo0A 126 2.93e+01 1hkvA 453 2.97e+01 b.49.2.3,c.1.6.1 83559,83560 2fytA 340 2.98e+01 1dgfA 497 2.99e+01 1cf9A e.5.1.1 42782 1of5A 221 2.99e+01 d.17.4.2 86933 1d7kA 421 3.10e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 2cw8A 537 3.14e+01 1jjtA 228 3.14e+01 1a7tA d.157.1.1 63139 1f60A 458 3.15e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1ofzA 312 3.28e+01 b.68.8.1 86978 1efnA 59 3.32e+01 1bbzA b.34.2.1 24465 1yhpA 212 3.33e+01 1i4uA 181 3.33e+01 b.60.1.1 61732 1pkp 150 3.36e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1grwA 126 3.36e+01 b.1.11.2 70391 1z4vA 532 3.39e+01 1dghB 498 3.43e+01 1cf9A e.5.1.1 42791 1hfuA 503 3.48e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1xp8A 366 3.56e+01 1dd6A 228 3.60e+01 1a7tA d.157.1.1 42054 1ym5A 300 3.67e+01 1uypA 432 3.69e+01 b.29.1.19,b.67.2.3 100176,100177 1yhfA 115 3.74e+01 1w2tA 432 3.74e+01 1gvhA 396 3.76e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1jfmA 174 3.76e+01 d.19.1.1 66640 1eylA 186 3.88e+01 1wba b.42.4.1 25593 1fr3A 67 3.93e+01 1fr3A b.40.6.1 25436 1e69B 322 3.97e+01 1e69B c.37.1.12 32377 1svr 114 4.01e+01 1svy d.109.1.1 40833 1dlc 584 4.02e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 2a6sA 84 4.03e+01 1zvyA 136 4.11e+01 1sr9A 644 4.26e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1wnyA 186 4.29e+01 1ofuA 320 4.32e+01 c.32.1.1,d.79.2.1 86972,86973 1gg4A 452 4.34e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1b0fA 218 4.40e+01 1a7s b.47.1.2 26237 1ni5A 433 4.46e+01 c.26.2.5,d.229.1.1 80533,80534 1rhoA 145 4.50e+01 1rhoA b.1.18.8 21899 1ytaA 180 4.55e+01 1a65A 504 4.59e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1eb0A 147 4.63e+01 b.107.1.1,d.58.38.1 64890,64891 1m07A 111 4.69e+01 d.5.1.1 78328 2d1eA 248 4.70e+01 1b8kA 119 4.75e+01 1bndA g.17.1.3 44795 1vqoA 240 4.79e+01 2eifA 136 4.79e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 2alaA 391 4.80e+01 1bqsA 209 4.83e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1eur 365 4.93e+01 1eut b.68.1.1 27607 1zkpA 268 4.97e+01 1e8uA 454 4.98e+01 1e8tA b.68.1.1 59389 1gsmA 210 5.20e+01 b.1.1.4,b.1.1.4 65535,65536 2mev1 277 5.20e+01 2mev1 1fujA 221 5.20e+01 1a7s b.47.1.2 26349 1gikA 261 5.20e+01 d.165.1.1 90513 2bc2B 227 5.21e+01 1a7tA d.157.1.1 42032 1cr0A 296 5.33e+01 1cr1A c.37.1.11 32287 1ktjA 129 5.36e+01 b.1.18.7 72974 1n0lA 224 5.40e+01 b.1.11.1,b.7.2.1 79744,79745 1fsoA 139 5.43e+01 1rhoA b.1.18.8 60007 1aqcA 172 5.52e+01 1x11A b.55.1.2 26983 1kmtA 141 5.58e+01 b.1.18.8 77442 1umzA 278 5.59e+01 b.29.1.2 99639 1bmg 98 5.60e+01 1agdB b.1.1.2 20667 1utiA 58 5.66e+01 b.34.2.1 99962 1hn0A 1021 5.71e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1ifrA 121 5.81e+01 b.1.16.1 71203 2sfa 191 5.83e+01 1qq4A b.47.1.1 25815 1bbzA 58 5.86e+01 1bbzA b.34.2.1 24477 2av9A 147 5.92e+01 1xkpC 143 5.94e+01 1t6cA 315 5.98e+01 c.55.1.8,c.55.1.8 106558,106559 2bhuA 602 6.05e+01 1nteA 82 6.22e+01 b.36.1.1 86163 1ciy 590 6.23e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1npeA 267 6.27e+01 b.68.5.1 92032 1y9qA 192 6.35e+01 1h54A 754 6.36e+01 a.102.1.4,b.30.5.3 60634,60635 1gxuA 91 6.38e+01 d.58.10.1 76378 1bix 287 6.41e+01 1bix d.151.1.1 41781 2as9A 210 6.46e+01 1ji6A 589 6.53e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1a1rA 198 6.55e+01 1jxpA b.47.1.3 26406 1earA 147 6.61e+01 b.107.1.1,d.58.38.1 64875,64876 1oxsC 353 6.70e+01 b.40.6.3,c.37.1.12 87519,87520 1l3iA 192 6.78e+01 c.66.1.22 77676 1vctA 205 6.82e+01 1yb3A 175 6.85e+01 1z47A 355 6.86e+01 1khbA 625 6.88e+01 c.91.1.1,c.109.1.1 68606,68607 1ypqA 135 6.88e+01 1ihvA 52 6.88e+01 1ihvA b.34.7.1 24629 1vzyA 291 6.91e+01 1u7zA 226 6.91e+01 1b07A 59 6.93e+01 1ckaA b.34.2.1 24461 1jt8A 102 7.10e+01 b.40.4.5 63279 1wqsA 173 7.14e+01 1h91A 180 7.15e+01 b.60.1.1 60805 1itwA 741 7.28e+01 c.77.1.2 76793 2biwA 490 7.31e+01 1dj7B 75 7.31e+01 1dj7B b.34.4.3 24598 1bbzE 58 7.32e+01 1bbzA b.34.2.1 24479 1svy 114 7.33e+01 1svy d.109.1.1 40831 1h0bA 256 7.34e+01 b.29.1.11 83422 1twfH 146 7.37e+01 2bvyA 475 7.38e+01 1q1rA 431 7.40e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1fnlA 175 7.58e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 2b5eA 504 7.59e+01 1mkaA 171 7.62e+01 1mkaA d.38.1.2 38543 1r9fA 136 7.77e+01 d.255.1.1 97257 3pyp 125 7.78e+01 3pyp d.110.3.1 40897 1llwA 1520 7.79e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 7odcA 424 7.86e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1tbuA 118 7.97e+01 1uq5A 263 7.98e+01 d.165.1.1 99778 1bndB 119 8.02e+01 1bndA g.17.1.3 44794 1a6x 87 8.08e+01 1bdo b.84.1.1 28215 2bw8A 227 8.12e+01 1sr4B 261 8.14e+01 d.151.1.1 105949 1x8hA 228 8.23e+01 1qniA 581 8.34e+01 1qniA b.6.1.4,b.69.3.1 23042,27642 1gpl 432 8.45e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1q8iA 783 8.52e+01 c.55.3.5,e.8.1.1 96208,96209 1mspA 126 8.58e+01 1mspA b.1.11.2 22333 1w9hA 427 8.61e+01 2cvhA 220 8.71e+01 1y1oA 203 8.72e+01 1aqt 138 8.72e+01 1aqt a.2.10.1,b.93.1.1 15718,28435 1ztcA 221 8.74e+01 1a2yB 116 8.76e+01 1gc1H b.1.1.1 19927 2blkA 122 8.78e+01 1e7uA 961 8.81e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1umhA 184 8.85e+01 b.18.1.21 99605 1q7rA 219 8.91e+01 c.23.16.1 96054 1zbtA 371 8.91e+01