# List of top-scoring protein chains for t2k-100-30-bys-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 1bg2 325 1.54e-66 1bg2 c.37.1.9 32189 1i5sA 367 2.53e-63 1bg2 c.37.1.9 61822 1ii6A 368 3.45e-62 1bg2 c.37.1.9 62413 1i6iA 366 1.47e-61 1bg2 c.37.1.9 61844 1q0bA 367 1.34e-60 c.37.1.9 95502 1x88A 359 1.59e-60 1vfvA 366 1.70e-60 c.37.1.9 108592 3kar 346 9.94e-59 1bg2 c.37.1.9 32198 1cz7A 406 8.88e-58 1bg2 c.37.1.9 32194 1f9vA 347 1.76e-57 1bg2 c.37.1.9 59745 1ry6A 360 3.63e-53 c.37.1.9 98090 2kinA 238 2.90e-48 1bg2 c.37.1.9 32190 2kinB 100 1.56e-19 3kinB 3kinB 117 7.62e-19 3kinB 1odfA 290 2.00e-01 c.37.1.6 92782 1j8mF 297 2.51e-01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1l8qA 324 4.13e-01 a.4.12.2,c.37.1.20 77809,77810 1d2mA 665 4.15e-01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1um8A 376 4.24e-01 c.37.1.20 99580 1u9iA 519 5.82e-01 2azqA 311 8.17e-01 1yagG 125 9.78e-01 1d0nA d.109.1.1 40846 1wmhA 89 9.86e-01 2cdnA 201 1.11e+00 1dmhA 311 1.16e+00 1dmhA b.3.6.1 22633 1htjF 210 1.22e+00 1htjF a.91.1.1 61254 1c4oA 664 1.34e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 1zk7A 467 1.45e+00 1p9rA 418 1.50e+00 c.37.1.11 94399 1ex2A 189 1.50e+00 1ex2A c.51.4.2 33225 1oe9A 795 1.75e+00 b.34.3.1,c.37.1.9 92792,92793 1bueA 265 1.90e+00 1btl e.3.1.1 42727 1nm1G 125 1.90e+00 d.109.1.1 80653 1w7jA 795 1.98e+00 1xmrA 243 1.98e+00 1g6oA 330 2.04e+00 1g6oA c.37.1.11 32430 2a5yB 549 2.12e+00 1gvnB 287 2.16e+00 c.37.1.21 76354 1xwiA 322 2.43e+00 1f60A 458 2.44e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1g6q2 328 2.45e+00 1g6q2 1d4xG 126 2.87e+00 1d0nA d.109.1.1 59109 1vfrA 218 2.96e+00 1vfrA d.90.1.1 40247 1g291 372 3.05e+00 1g291 2f4nA 273 3.92e+00 1wdtA 665 4.26e+00 2bjvA 265 4.27e+00 1ji0A 240 4.32e+00 c.37.1.12 71665 1xkwA 665 4.50e+00 1lv7A 257 4.60e+00 c.37.1.20 78232 1ofhA 310 4.62e+00 c.37.1.20 86948 1vom 762 5.08e+00 1lvk b.34.3.1,c.37.1.9 24577,32174 1vns 609 5.17e+00 1vns a.111.1.3 19061 1w9iA 770 5.23e+00 5ukdA 194 5.53e+00 1zin c.37.1.1 31851 1lkxA 697 5.63e+00 c.37.1.9 73981 1br2A 791 6.03e+00 1lvk b.34.3.1,c.37.1.9 24558,32155 1nv8A 284 6.29e+00 c.66.1.30 86224 1bhjA 292 6.37e+00 1xvaA c.66.1.5 34189 2akaA 776 6.78e+00 1taq 832 6.95e+00 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1lvk 762 6.97e+00 1lvk b.34.3.1,c.37.1.9 24576,32173 1ofuA 320 7.47e+00 c.32.1.1,d.79.2.1 86972,86973 1ebdA 455 7.79e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1ryqA 69 8.03e+00 g.41.9.3 105126 1vnc 609 8.32e+00 1vns a.111.1.3 19065 2azeA 155 8.40e+00 1p27B 106 8.65e+00 d.58.7.1 93908 1ng1 294 8.97e+00 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ls1A 295 9.41e+00 a.24.13.1,c.37.1.10 78170,78171 1q5dA 419 9.60e+00 a.104.1.1 95891 2ghpA 292 9.84e+00 1ffh 294 9.90e+00 1ng1 a.24.13.1,c.37.1.10 16960,32271 1mr3F 181 9.93e+00 c.37.1.8 79422 1qf9A 194 9.99e+00 1zin c.37.1.1 31848 1d2gA 292 1.01e+01 1xvaA c.66.1.5 34187 1mnd 762 1.03e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 2bycA 137 1.10e+01 1gesA 450 1.10e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1fa0A 537 1.16e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1e94F 449 1.17e+01 1do0A c.37.1.20 32443 1a5z 319 1.17e+01 1ceqA c.2.1.5,d.162.1.1 30181,42148 1xvaA 292 1.21e+01 1xvaA c.66.1.5 34183 1dofA 403 1.27e+01 1c3cA a.127.1.1 19429 1tmxA 293 1.31e+01 1x0pA 143 1.31e+01 1thtA 305 1.31e+01 1thtA c.69.1.13 34711 1zj6A 187 1.34e+01 2c78A 405 1.37e+01 1tueA 212 1.40e+01 c.37.1.20 107323 1xw8A 252 1.42e+01 2aynA 404 1.43e+01 1e9rA 437 1.45e+01 c.37.1.11 64827 1ris 101 1.53e+01 1ris d.58.14.1 39314 2adcA 229 1.53e+01 1j90A 230 1.54e+01 c.37.1.1 66448 1u94A 356 1.57e+01 c.37.1.11,d.48.1.1 107743,107744 1u0jA 267 1.60e+01 c.37.1.20 107546 1m33A 258 1.61e+01 c.69.1.26 78514 1ddzA 496 1.64e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1qdeA 224 1.66e+01 1qvaA c.37.1.19 32410 1do0A 442 1.71e+01 1do0A c.37.1.20 32432 1ad3A 452 1.73e+01 1ad3A c.82.1.1 35335 1xkqA 280 1.74e+01 2cu5A 129 1.74e+01 1zu4A 320 1.76e+01 1exmA 405 1.80e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1z0jA 170 1.82e+01 1s7kA 182 1.82e+01 1h6kX 97 1.86e+01 d.58.7.1 60684 1fnnA 389 1.90e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1m2oB 190 1.92e+01 c.37.1.8 78485 1iqpA 327 1.93e+01 a.80.1.1,c.37.1.20 62649,62650 1h2vZ 156 1.95e+01 d.58.7.1 76595 1f42A 306 2.07e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1hv8A 367 2.09e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1f3aA 222 2.09e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1cfzA 162 2.09e+01 1cfzA c.56.1.1 33754 1vf1A 229 2.12e+01 1n7oA 721 2.15e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1uxtA 501 2.17e+01 c.82.1.1 108125 1vm8A 534 2.18e+01 1k3yA 221 2.20e+01 a.45.1.1,c.47.1.5 77245,77246 1z47A 355 2.25e+01 1xx6A 191 2.26e+01 1k3lA 221 2.27e+01 a.45.1.1,c.47.1.5 77229,77230 1h6kZ 98 2.28e+01 d.58.7.1 60686 1lxkA 721 2.28e+01 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 1ihuA 589 2.30e+01 c.37.1.10,c.37.1.10 62394,62395 1xx1A 285 2.31e+01 2ng1 293 2.34e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1ha3A 405 2.36e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1guiA 155 2.37e+01 b.18.1.14 76351 2db3A 434 2.38e+01 1eft 405 2.39e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1am2 199 2.40e+01 1am2 b.86.1.2 28381 2ch4A 320 2.48e+01 1eguA 731 2.49e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1y8cA 246 2.51e+01 2nllA 66 2.51e+01 2nllB g.39.1.2 45109 1ltqA 301 2.52e+01 c.108.1.9,c.37.1.1 78208,78209 1shkA 173 2.56e+01 1shkA c.37.1.2 31932 1fts 295 2.59e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1d0yA 761 2.60e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1tljA 213 2.60e+01 d.282.1.1 107126 1jpnA 296 2.65e+01 a.24.13.1,c.37.1.10 67039,67040 1cqmA 101 2.65e+01 1ris d.58.14.1 39321 1louA 101 2.66e+01 1ris d.58.14.1 39323 1w36B 1180 2.72e+01 1i58A 189 2.74e+01 1b3qA d.122.1.3 61773 5tmpA 213 2.79e+01 5tmpA c.37.1.1 31931 1i69A 219 2.83e+01 c.94.1.1 61825 1fjhB 257 2.91e+01 1fjhB c.2.1.2 29871 1wyzA 242 2.97e+01 1aj6 219 3.06e+01 1aj6 d.122.1.2 41106 1txkA 498 3.08e+01 b.1.18.2,b.30.5.9 107425,107426 1y44A 320 3.09e+01 1g8jA 825 3.14e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1fviA 297 3.14e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1f6bA 198 3.15e+01 c.37.1.8 64986 1knqA 175 3.18e+01 c.37.1.17 72786 2fhzA 109 3.26e+01 2fytA 340 3.27e+01 2b8tA 223 3.34e+01 3aig 202 3.36e+01 1atlA d.92.1.9 40321 1f48A 589 3.37e+01 1f48A c.37.1.10,c.37.1.10 32280,32281 1oe0A 230 3.38e+01 c.37.1.1 92788 1i6aA 219 3.39e+01 c.94.1.1 61827 2fsrA 195 3.40e+01 1o20A 427 3.40e+01 c.82.1.1 86556 1d5cA 162 3.44e+01 1ctqA c.37.1.8 32021 1esmA 316 3.58e+01 1esmA c.37.1.6 31953 1wznA 252 3.64e+01 1g6hA 257 3.66e+01 1gajA c.37.1.12 60318 1gadO 330 3.66e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1f2tA 149 3.66e+01 1f2tA c.37.1.12 32373 1gl4A 285 3.66e+01 d.22.1.2,g.3.11.5 65286,65287 1gseA 221 3.71e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1u35D 126 3.79e+01 1k1xA 659 3.79e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1yobA 179 3.80e+01 1e9cA 215 3.87e+01 c.37.1.1 64808 1g8pA 350 3.88e+01 1g8pA c.37.1.20 60376 1pzgA 331 3.92e+01 c.2.1.5,d.162.1.1 95425,95426 4tmkA 213 3.96e+01 5tmpA c.37.1.1 31930 1y14A 187 3.96e+01 1vraB 215 3.97e+01 3adk 195 3.98e+01 1zin c.37.1.1 31885 1bxsA 501 4.00e+01 1bpwA c.82.1.1 35357 1xrjA 261 4.02e+01 1kagA 173 4.11e+01 c.37.1.2 72249 2shkA 173 4.15e+01 1shkA c.37.1.2 31934 1sheA 103 4.15e+01 d.274.1.1 105551 1kkuA 279 4.16e+01 c.26.1.3 72661 1ohtA 215 4.17e+01 d.118.1.1 87036 1e58A 249 4.19e+01 1qhfA c.60.1.1 59262 1ck7A 631 4.25e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1nh2B 53 4.26e+01 a.32.1.1 91874 1r9cA 139 4.28e+01 d.32.1.2 97255 1im4A 221 4.31e+01 e.8.1.7 62581 1iexA 605 4.31e+01 c.1.8.7,c.23.11.1 66127,66128 1s3eA 520 4.32e+01 c.3.1.2,d.16.1.5 98426,98427 1i6pA 220 4.35e+01 1ddzA c.53.2.1 61848 1g5pA 289 4.36e+01 1cp2A c.37.1.10 32253 1by4A 82 4.37e+01 2nllB g.39.1.2 45110 1nipA 289 4.40e+01 1cp2A c.37.1.10 32263 1tzyB 126 4.40e+01 a.22.1.1 107531 1k3sA 113 4.50e+01 d.198.1.1 68120 1xw4X 110 4.50e+01 1fzaB 328 4.51e+01 3fib d.171.1.1,h.1.8.1 42480,45621 1in4A 334 4.51e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1fpxA 352 4.51e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 2a9sA 171 4.55e+01 2cbzA 237 4.60e+01 1p9gA 41 4.62e+01 g.3.1.1 104091 1u2eA 289 4.69e+01 1zm7A 230 4.71e+01 1nn5A 215 4.75e+01 c.37.1.1 85892 1hurA 180 4.77e+01 1hurA c.37.1.8 32052 1ucrA 78 4.77e+01 a.4.5.45 99188 1hq3B 126 4.78e+01 1aoiD a.22.1.1 16444 1h65A 270 4.81e+01 c.37.1.8 65640 1a8s 273 4.81e+01 1brt c.69.1.12 34710 1efaA 333 4.87e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1fyeA 229 4.89e+01 1fyeA c.23.16.4 31477 1kfiA 572 4.93e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1b3qA 379 4.95e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1l2tA 235 4.95e+01 c.37.1.12 73514 1sq5A 308 4.96e+01 c.37.1.6 105882 1z5zA 271 5.00e+01 1nrjB 218 5.05e+01 c.37.1.8 86125 1ojaA 520 5.08e+01 c.3.1.2,d.16.1.5 93096,93097 3bifA 468 5.10e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1ytfB 53 5.12e+01 1ytfB a.32.1.1 16997 1yzgA 179 5.12e+01 1ns5A 155 5.14e+01 c.116.1.3 80705 2b67A 204 5.16e+01 1c3wA 222 5.18e+01 1c3wA f.13.1.1 43405 1d0nA 729 5.18e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1dciA 275 5.22e+01 1dciA c.14.1.3 30918 1epuA 591 5.23e+01 1dn1A e.25.1.1 43358 1fjhA 257 5.25e+01 1fjhB c.2.1.2 29870 1fy2A 229 5.26e+01 1fyeA c.23.16.4 31478 1muhA 481 5.29e+01 c.55.3.4 79485 1rj9A 304 5.29e+01 a.24.13.1,c.37.1.10 97553,97554 1jwyB 315 5.32e+01 c.37.1.8 67401 2pia 321 5.38e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1nbfD 76 5.39e+01 d.15.1.1 80390 1ta8A 332 5.41e+01 2fqxA 318 5.45e+01 1vd2A 89 5.55e+01 d.15.2.2 108517 2ccjA 205 5.56e+01 1ex1A 605 5.64e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1efcA 393 5.65e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1air 353 5.66e+01 1air b.80.1.1 28018 1q0uA 219 5.73e+01 c.37.1.19 95512 1kqnA 279 5.80e+01 c.26.1.3 77492 1o5xA 248 5.80e+01 c.1.1.1 92528 1jb0D 138 5.87e+01 1jb0D d.187.1.1 62823 1uf5A 303 5.90e+01 d.160.1.2 107808 1fp2A 352 5.91e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 2cvhA 220 5.96e+01 1q5xA 161 6.05e+01 c.8.7.1 95947 2fpmA 322 6.09e+01 1xjcA 169 6.11e+01 1x38A 602 6.17e+01 1yumA 242 6.17e+01 2aq4A 434 6.22e+01 1fp6A 289 6.23e+01 1cp2A c.37.1.10 32243 1o4uA 285 6.27e+01 c.1.17.1,d.41.2.1 86624,86625 1e69B 322 6.27e+01 1e69B c.37.1.12 32377 2f1wA 158 6.30e+01 1ei1A 391 6.34e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1g8kA 825 6.38e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1e9eA 215 6.40e+01 c.37.1.1 64810 1r0wA 286 6.41e+01 c.37.1.12 96754 1m7gA 211 6.42e+01 c.37.1.4 78724 1jflA 228 6.48e+01 c.78.2.1,c.78.2.1 71656,71657 1wn2A 121 6.51e+01 1uj2A 252 6.55e+01 c.37.1.6 99452 2pec 353 6.57e+01 1air b.80.1.1 28019 1gajA 257 6.57e+01 1gajA c.37.1.12 60416 1ubq 76 6.57e+01 1ubi d.15.1.1 37585 1e2gA 215 6.61e+01 3tmkA c.37.1.1 59165 1wi6A 88 6.62e+01 2fuqA 747 6.65e+01 1wn5A 130 6.65e+01 1f0iA 504 6.68e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1xviA 275 6.68e+01 1wkyA 464 6.83e+01 2dg5B 190 6.85e+01 2aiqA 231 6.91e+01 1tkeA 224 6.99e+01 1lfpA 249 7.03e+01 e.39.1.1 73885 1ye8A 178 7.06e+01 1uptC 170 7.08e+01 c.37.1.8 99769 1yr0A 175 7.08e+01 1dbhA 354 7.15e+01 1awe a.87.1.1,b.55.1.1 18514,26967 2gk4A 232 7.21e+01 1d3zA 76 7.23e+01 1ubi d.15.1.1 37592 1ag8A 499 7.33e+01 1bpwA c.82.1.1 35341 1o88A 353 7.36e+01 b.80.1.1 81178 1bif 469 7.43e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1wvcA 259 7.43e+01 1v5vA 401 7.46e+01 1e2fA 215 7.51e+01 3tmkA c.37.1.1 59164 1ifrA 121 7.51e+01 b.1.16.1 71203 1vhzA 198 7.52e+01 d.113.1.1 100718 1efuA 385 7.54e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1yj1A 76 7.58e+01 2fnaA 357 7.61e+01 2bifA 469 7.63e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1tqmA 282 7.69e+01 a.4.5.56,d.144.1.9 107236,107237 1m0wA 491 7.88e+01 c.30.1.4,d.142.1.6 78363,78364 1e19A 314 7.92e+01 1b7bA c.73.1.1 34967 2akaB 299 7.94e+01 1yy6A 155 7.99e+01 1jvwA 167 8.07e+01 d.26.1.1 71907 2bdeA 470 8.27e+01 2bbdA 350 8.28e+01 1gt6A 269 8.29e+01 c.69.1.17 76342 1sek 378 8.30e+01 1sek e.1.1.1 42675 1viaA 175 8.33e+01 c.37.1.2 100754 1hcuA 503 8.33e+01 a.102.2.1 65796 2rveA 244 8.39e+01 1rvaA c.52.1.2 33283 1khoA 370 8.42e+01 a.124.1.1,b.12.1.3 72489,72490 1lyxA 248 8.54e+01 c.1.1.1 78304 1miwA 404 8.62e+01 a.173.1.1,d.218.1.4 79162,79163 1z83A 196 8.63e+01 1pmi 440 8.67e+01 1pmi b.82.1.3 28114 1ble 163 8.77e+01 1ble c.38.1.1 32475 1euhA 475 8.83e+01 1euhA c.82.1.1 35369 1nijA 318 8.83e+01 c.37.1.10,d.237.1.1 85741,85742 1yvoA 172 8.85e+01 1olmA 403 8.85e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1yghA 164 8.96e+01 1yghA d.108.1.1 40802