# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 3cghA 516 5.77e-33 a.118.8.6 156618 3gzsA 515 1.79e-31 3ejnA 474 1.27e-30 a.118.8.6 158180 3ehmA 532 2.51e-28 3fdhA 499 3.70e-25 3i4gA 528 8.10e-23 3jq1A 481 2.30e-22 3kezA 461 3.08e-22 3jq0A 493 6.10e-21 3l22A 441 5.50e-20 3ihvA 535 1.83e-19 3lewA 495 2.37e-19 3iv0A 481 7.81e-19 3jysA 499 1.44e-18 3hdxA 478 3.42e-18 3ckcA 527 3.77e-17 a.118.8.6 156736 2e01A 457 3.48e-01 1muwA 386 1.13e+00 c.1.15.3 79495 1lkxA 697 1.21e+00 c.37.1.9 73981 1gcb 454 1.47e+00 3gcb 1hh8A 213 1.52e+00 1e96B a.118.8.1 61042 1nxcA 478 1.53e+00 a.102.2.1 92293 2pmvA 399 1.58e+00 3gcb 470 1.65e+00 3gcb 3gcbA 470 1.65e+00 d.3.1.1 37032 1wm5A 208 1.88e+00 a.118.8.1 121028 3gnxA 387 2.03e+00 1gw9A 388 2.04e+00 c.1.15.3 70658 1e96B 203 2.22e+00 1e96B a.118.8.1 19211 2x6hA 696 2.62e+00 3xis 387 2.64e+00 4xis 4xis 387 2.65e+00 4xis 3ls8A 614 2.85e+00 3a6pA 1204 2.91e+00 1wuiL 534 3.27e+00 e.18.1.1 121289 3kq5A 393 3.61e+00 3ihyA 600 3.79e+00 1h2rL 534 3.79e+00 1h2rL e.18.1.1 43298 3e3pA 360 3.85e+00 3d64A 494 3.89e+00 1c4oA 664 4.01e+00 1d2mA c.37.1.19,c.37.1.19 32415,32416 4xiaA 393 4.12e+00 4xis c.1.15.3 29439 2i6lA 320 4.34e+00 2f4qA 346 4.38e+00 3efzA 268 5.19e+00 a.118.7.1 158144 2b9hA 353 5.49e+00 1miwA 404 5.73e+00 a.173.1.1,d.218.1.4 79162,79163 1i84S 1184 5.78e+00 1lvk i.15.1.1 61940 1jpnA 296 6.18e+00 a.24.13.1,c.37.1.10 67039,67040 2hr2A 159 6.30e+00 a.118.8.8 147369 2wqhA 125 6.62e+00 1tz7A 505 6.83e+00 c.1.8.1 119394 1ubkL 534 6.92e+00 e.18.1.1 88422 1h2aL 567 7.21e+00 1h2rL e.18.1.1 43299 16vpA 366 7.59e+00 16vpA d.180.1.1 42601 1wq3A 322 7.64e+00 1a0cA 438 7.65e+00 1a0cA c.1.15.3 29529 1um0A 365 7.84e+00 d.258.1.1 107942 1i0lA 221 8.14e+00 c.61.1.1 71096 1q41A 424 8.53e+00 d.144.1.7 95774 3ibvA 980 8.93e+00 1fo3A 460 9.13e+00 1dl2A a.102.2.1 18845 2o11A 407 9.16e+00 2a97A 439 9.39e+00 3c96A 415 9.60e+00 c.3.1.2,d.16.1.2 156122,156123 1j1bA 420 9.84e+00 d.144.1.7 90758 1ayx 492 9.90e+00 1ayx 2yxnA 322 1.01e+01 1a6dB 543 1.04e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 3kq4A 393 1.06e+01 1i0aA 466 1.07e+01 1auwA a.127.1.1 61479 3kczA 368 1.09e+01 1zq9A 285 1.14e+01 c.66.1.24 125505 2r3iA 298 1.16e+01 2a8aA 439 1.17e+01 2qhfA 407 1.24e+01 1hz4A 373 1.26e+01 a.118.8.2 65960 3e1tA 512 1.30e+01 3e1sA 574 1.37e+01 1ywrA 360 1.38e+01 1o5zA 442 1.41e+01 c.59.1.2,c.72.2.2 92530,92531 3iegA 359 1.43e+01 1z57A 339 1.47e+01 2cqsA 842 1.48e+01 1q1lA 401 1.50e+01 d.258.1.1 95591 3lw1A 253 1.51e+01 2e4uA 555 1.52e+01 3kjdA 368 1.52e+01 1f82A 424 1.53e+01 1f82A d.92.1.7 40307 1t3cA 421 1.56e+01 d.92.1.7 106343 1bj4A 470 1.62e+01 1bj4A c.67.1.4 34479 3lvtA 899 1.62e+01 1cm7A 363 1.62e+01 1cnzA c.77.1.1 35063 2gz6A 388 1.64e+01 1sqgA 429 1.66e+01 a.79.1.3,c.66.1.38 105912,105913 1ldjA 760 1.66e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 2zygA 480 1.68e+01 2jdxA 385 1.69e+01 1jdw d.126.1.2 41139 1w0dA 337 1.71e+01 c.77.1.1 114060 1tc1A 220 1.71e+01 1tc1A c.61.1.1 34083 1lldA 319 1.74e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1wkuA 254 1.75e+01 1ezfA 340 1.75e+01 1ezfA a.128.1.2 19440 1tqnA 486 1.78e+01 a.104.1.1 107238 2ij2A 470 1.82e+01 a.104.1.1 137449 1qtqA 553 1.83e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1hcl 298 1.86e+01 1hcl 1cb8A 678 1.90e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 2o02A 230 1.91e+01 a.118.7.1 148541 2pth 193 1.94e+01 2pth 2pthA 193 1.94e+01 c.56.3.1 33793 1iznA 286 1.99e+01 e.43.1.1 83847 2ia7A 134 2.01e+01 d.373.1.1 147585 2hgsA 474 2.07e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 1gz8A 299 2.11e+01 d.144.1.7 83405 1aosA 464 2.11e+01 1auwA a.127.1.1 19414 1g8xA 1010 2.14e+01 1lvk k.1.1.1 46378 2f7fA 494 2.15e+01 c.1.17.1,d.41.2.1 133088,133089 2dtxA 264 2.17e+01 2frvB 536 2.19e+01 1h2rL e.18.1.1 43291 3hhsA 694 2.19e+01 2c2xA 281 2.23e+01 1z2cB 383 2.24e+01 a.118.1.23 124377 1hy0A 466 2.25e+01 1auwA a.127.1.1 61392 2ebfX 746 2.25e+01 a.296.1.1,c.150.1.2,d.3.1.17 146766,146767,146768 2b1eA 564 2.29e+01 1n4qB 377 2.30e+01 a.102.4.3 91636 3iam5 207 2.33e+01 2zy5A 546 2.42e+01 1oqyA 368 2.44e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1aua 296 2.44e+01 1aua 1auaA 296 2.44e+01 a.5.3.1,c.13.1.1 16290,30882 1ls1A 295 2.44e+01 a.24.13.1,c.37.1.10 78170,78171 2qmiA 447 2.47e+01 3ioyA 319 2.47e+01 3c4hA 357 2.48e+01 3hf2A 482 2.48e+01 2pidA 356 2.50e+01 1obbA 480 2.51e+01 c.2.1.5,d.162.1.2 86760,86761 1gtrA 553 2.53e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1onrA 316 2.54e+01 1onrA c.1.10.1 29169 2b05A 246 2.57e+01 2hz7A 851 2.57e+01 3eljA 369 2.61e+01 1gln 468 2.62e+01 1gln 3draB 390 2.65e+01 2ohcA 289 2.66e+01 2ph7A 246 2.67e+01 2cb5A 453 2.68e+01 3gcb d.3.1.1 37035 2bnxA 386 2.69e+01 a.118.1.23 128861 3glqA 494 2.71e+01 1c4zA 358 2.73e+01 1c4zA d.148.1.1 41766 3gc8A 370 2.73e+01 1ng1 294 2.73e+01 1ng1 3gjwA 350 2.76e+01 3co8A 380 2.80e+01 2gpyA 233 2.81e+01 2zzrA 397 2.82e+01 1xnfA 275 2.84e+01 a.118.8.1 115580 1khoA 370 2.84e+01 a.124.1.1,b.12.1.3 72489,72490 3hrbA 359 2.85e+01 1frvB 536 2.85e+01 1h2rL e.18.1.1 43296 3kofA 337 2.89e+01 1jpzA 473 2.92e+01 a.104.1.1 67069 2fbaA 492 2.95e+01 a.102.1.1 133239 2j5aA 110 2.98e+01 d.58.14.1 147886 2vc7A 314 2.98e+01 1ybdA 239 2.99e+01 c.73.1.3 122884 1aru 344 2.99e+01 1arv 1eetB 427 3.03e+01 1rthA e.8.1.2 43079 1tu5A 746 3.06e+01 1dofA 403 3.06e+01 1c3cA a.127.1.1 19429 3losA 543 3.10e+01 1y8qB 640 3.10e+01 3fp3A 537 3.10e+01 1wbsA 360 3.15e+01 d.144.1.7 120860 3fddA 533 3.15e+01 1d5rA 324 3.21e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1nw3A 416 3.22e+01 c.66.1.31 86288 1kvkA 395 3.24e+01 d.14.1.5,d.58.26.3 73060,73061 2a19B 284 3.28e+01 2zxrA 666 3.30e+01 3a1yG 284 3.30e+01 3fnrA 464 3.31e+01 1nu5A 370 3.32e+01 c.1.11.2,d.54.1.1 92183,92184 1arv 344 3.37e+01 1arv 2q9fA 456 3.39e+01 1x9dA 538 3.41e+01 a.102.2.1 121810 1mkmA 249 3.43e+01 a.4.5.33,d.110.2.2 79242,79243 1td2A 287 3.43e+01 c.72.1.5 106765 1t4hA 290 3.46e+01 d.144.1.7 106420 3euhC 234 3.49e+01 1mswD 883 3.50e+01 e.8.1.3 79427 3cp2A 649 3.52e+01 2wzxA 371 3.52e+01 2zxiA 637 3.52e+01 3hmmA 303 3.53e+01 3k8tA 888 3.53e+01 2zdtA 364 3.55e+01 d.144.1.7 154400 1ufaA 520 3.58e+01 a.8.3.3,c.6.2.4 99329,99330 1blxA 326 3.58e+01 1hcl d.144.1.7 41596 3edtB 283 3.64e+01 1bucA 383 3.65e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851 1rom 403 3.80e+01 1rom 3gc7A 366 3.82e+01 1rv3A 483 3.91e+01 c.67.1.4 105101 3g7rA 221 3.94e+01 3ip0A 158 3.94e+01 2ofkA 183 3.98e+01 3m9vA 439 4.01e+01 1mo9A 523 4.02e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1f1uA 323 4.02e+01 d.32.1.3,d.32.1.3 83200,83201 3kk1B 452 4.04e+01 1qlpA 394 4.07e+01 1ovaA e.1.1.1 42628 3fpqA 290 4.11e+01 3llqA 256 4.12e+01 3ituA 345 4.13e+01 3bu8A 235 4.16e+01 a.146.1.1 155595 1p0yA 444 4.18e+01 a.166.1.1,b.85.7.3 87654,87655 1ecrA 309 4.18e+01 1ecrA e.2.1.1 42678 3kycB 660 4.18e+01 1vi9A 299 4.20e+01 c.72.1.5 100750 2q8xA 331 4.22e+01 1dosA 358 4.23e+01 1dosA c.1.10.2 29175 3dmqA 968 4.29e+01 2wn6A 463 4.32e+01 1f9yA 158 4.35e+01 d.58.30.1 83249 3g6iA 204 4.35e+01 1pmnA 364 4.36e+01 d.144.1.7 94907 2ga9A 297 4.38e+01 c.66.1.25 134885 2br9A 234 4.40e+01 3h4aA 158 4.41e+01 1dnpA 471 4.43e+01 1qnf a.99.1.1,c.28.1.1 18775,31630 3hoyC 347 4.44e+01 2ou6A 190 4.44e+01 a.213.1.2 149020 1g59A 468 4.45e+01 a.97.1.1,c.26.1.1 60257,60258 1h6pA 203 4.46e+01 a.146.1.1 60690 1bmlC 362 4.47e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 3isnD 427 4.48e+01 1pb1A 416 4.52e+01 c.77.1.1 88014 2jbrA 422 4.54e+01 3hucA 360 4.57e+01 1izoA 417 4.58e+01 a.104.1.1 83851 1oc0A 379 4.58e+01 e.1.1.1 86790 3fyfA 176 4.64e+01 3lhxA 319 4.64e+01 1vrmA 325 4.64e+01 d.96.2.1 120472 2wa7A 245 4.64e+01 3k1qB 1027 4.67e+01 2h21A 440 4.68e+01 a.166.1.1,b.85.7.3 135976,135977 3bujA 397 4.75e+01 1r45A 204 4.79e+01 d.166.1.1 111683 1zo4A 473 4.80e+01 1j77A 209 4.83e+01 1j77A a.132.1.2 62674 2qxfA 482 4.83e+01 c.55.3.5 151455 2bifA 469 4.84e+01 1bif c.37.1.7,c.60.1.4 31963,34009 2w5qA 424 4.87e+01 1uhvA 500 4.90e+01 b.71.1.2,c.1.8.3 99402,99403 1i2oA 316 4.91e+01 1onrA c.1.10.1 61574 3bzcA 785 4.92e+01 a.60.2.6,a.60.2.6,a.294.1.1,b.40.4.5,c.55.3.13 155752,155753,155754,155755,155756 1ovnA 248 4.94e+01 a.71.1.1,c.47.1.7 93602,93603 1o57A 291 4.94e+01 a.4.5.40,c.61.1.1 92483,92484 1na3A 91 4.97e+01 k.38.1.1 85481 1vjyA 303 4.99e+01 d.144.1.7 108633 1qpbA 563 5.01e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 2cmwA 310 5.01e+01 2j6vA 301 5.01e+01 1gw5A 621 5.06e+01 a.118.1.10 70629 2w40A 503 5.07e+01 1fxxA 482 5.09e+01 1fxxA c.55.3.5 33726 3eqcA 360 5.17e+01 1zelA 298 5.28e+01 a.4.5.83,d.377.1.1 145994,145995 1dbfA 127 5.28e+01 2chsA d.79.1.2 39761 2dsjA 423 5.30e+01 3kl4A 433 5.33e+01 1cnzA 363 5.43e+01 1cnzA c.77.1.1 35061 2qg7A 458 5.48e+01 1d4aA 273 5.54e+01 1d4aA c.23.5.3 31219 2e0cA 409 5.55e+01 2ousA 331 5.55e+01 1e6pA 499 5.56e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1siqA 392 5.65e+01 a.29.3.1,e.6.1.1 105585,105586 1n82A 331 5.67e+01 c.1.8.3 91703 2wwwA 349 5.67e+01 2vq7A 461 5.67e+01 2g8lA 299 5.67e+01 e.50.1.1 134775 1ejdA 419 5.69e+01 1uae d.68.2.2 39576 1bu7A 455 5.70e+01 1bu7A a.104.1.1 18937 2c1nA 258 5.71e+01 a.118.7.1 129640 1pydA 556 5.72e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1t06A 235 5.73e+01 a.118.1.17 106194 1e3dB 542 5.73e+01 1h2rL e.18.1.1 59189 3danA 473 5.74e+01 3cwnA 337 5.74e+01 3hoaA 509 5.79e+01 1n7zA 334 5.81e+01 b.127.1.1 85380 1j09A 468 5.82e+01 a.97.1.1,c.26.1.1 77025,77026 2ve7C 250 5.83e+01 2vouA 397 5.85e+01 c.3.1.2,d.16.1.2 153389,153390 3bs5A 106 5.86e+01 1p57A 114 5.88e+01 d.170.1.2 94125 2b1pA 355 5.88e+01 d.144.1.7 127672 1k7jA 206 5.89e+01 d.115.1.1 72103 3gs6A 340 5.91e+01 1e4fT 419 5.91e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1bllE 488 5.92e+01 1lam c.50.1.1,c.56.5.3 33170,33833 2carA 196 5.97e+01 c.51.4.1 130161 2i71A 400 6.02e+01 e.72.1.1 147531 3gc9A 370 6.04e+01 1goiA 499 6.05e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 2fnaA 357 6.06e+01 a.4.5.11,c.37.1.20 133809,133810 1byb 495 6.07e+01 1byb 1fuiA 591 6.09e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 3a9iA 376 6.12e+01 1zzlA 351 6.12e+01 d.144.1.7 125910 1ek9A 428 6.13e+01 1ek9A f.5.1.1 43809 1tffA 234 6.14e+01 d.3.1.11 106854 2wotA 306 6.14e+01 3fy4A 537 6.15e+01 1pvdA 537 6.15e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 2dm9A 198 6.17e+01 d.81.4.1 146544 3hazA 1001 6.18e+01 2cyaA 364 6.21e+01 2brxA 244 6.27e+01 c.73.1.3 129028 3c0qA 301 6.27e+01 1qbgA 272 6.30e+01 1d4aA c.23.5.3 31227 1v02A 565 6.30e+01 c.1.8.4 108194 1f1xA 322 6.31e+01 d.32.1.3,d.32.1.3 83208,83209 1li5A 461 6.32e+01 a.27.1.1,c.26.1.1 73912,73913 2bfgA 503 6.32e+01 b.71.1.2,c.1.8.3 128423,128424 3gb2A 353 6.41e+01 3i3kA 461 6.53e+01 1lfwA 470 6.53e+01 c.56.5.4,d.58.19.1 77942,77943 1j27A 102 6.54e+01 d.58.50.1 90778 1reqA 727 6.58e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1u16A 472 6.61e+01 a.127.1.1 112952 2q01A 497 6.64e+01 2hd1A 326 6.66e+01 a.211.1.2 136338 3ferA 262 6.68e+01 3lg6A 235 6.70e+01 1dboA 506 6.75e+01 1dbgA b.80.1.4 28034 1h4pA 408 6.81e+01 c.1.8.3 90617 2yxlA 450 6.89e+01 3dfhA 394 6.94e+01 1twfC 318 6.96e+01 d.74.3.1,d.181.1.1 112727,112728 3dhiA 500 6.97e+01 3ge3A 500 6.98e+01 1dbgA 506 6.99e+01 1dbgA b.80.1.4 28033 1s7zA 117 7.02e+01 a.159.3.1 98715 1xwfA 431 7.02e+01 c.2.1.4,c.23.12.3 122392,122393 2e3bA 344 7.04e+01 a.93.1.1 132024 1o69A 394 7.06e+01 c.67.1.4 92560 1zy4A 303 7.08e+01 1o6zA 303 7.08e+01 c.2.1.5,d.162.1.1 81107,81108 1cbgA 490 7.09e+01 c.1.8.4 28933 3kkjA 336 7.10e+01 1cmnA 402 7.14e+01 1rom a.104.1.1 18958 2a6hC 1119 7.16e+01 e.29.1.1 126264 2zy4A 546 7.18e+01 2qugA 394 7.23e+01 3icaA 213 7.23e+01 2vdeA 460 7.25e+01 1zbmA 280 7.25e+01 c.94.1.1 124858 3ffrA 362 7.27e+01 1hyuA 521 7.27e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1uu1A 335 7.29e+01 c.67.1.1 99993 1g6q2 328 7.35e+01 1g6q2 3d19A 283 7.39e+01 a.29.13.1,a.29.13.1 157176,157177 1dik 874 7.41e+01 1dik 3hhpA 312 7.45e+01 1w9cA 321 7.46e+01 a.118.1.19 114410 1b3rA 431 7.46e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1ofdA 1520 7.47e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1o9dA 260 7.52e+01 a.118.7.1 86689 1wyuA 438 7.53e+01 c.67.1.7 121452 1bif 469 7.54e+01 1bif 1bifA 469 7.54e+01 c.37.1.7,c.60.1.4 31961,34003 1qgrA 876 7.62e+01 1qgrA a.118.1.1 19119 3bs7A 78 7.63e+01 3bmxA 642 7.63e+01 3czgA 644 7.64e+01 2qp2A 511 7.65e+01 1lj5A 379 7.66e+01 e.1.1.1 73928 2welA 327 7.72e+01 3gzdA 440 7.72e+01 1t33A 224 7.76e+01 a.4.1.9,a.121.1.1 106295,106296 1a4iA 301 7.77e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1kk9A 221 7.79e+01 d.115.1.1 77432 1imvA 398 7.79e+01 e.1.1.1 62591 1iuqA 367 7.81e+01 c.112.1.1 90703 3czbA 351 7.81e+01 1xvlA 321 7.83e+01 c.92.2.2 122380 2w01A 208 7.83e+01 1nu7D 282 7.90e+01 a.8.6.1,a.8.6.1 92191,92192 2gk9A 426 7.91e+01 1bf5A 545 7.92e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1jnyA 435 7.97e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1jxhA 288 7.99e+01 c.72.1.2 67415