# List of top-scoring protein chains for t2k-100-30-str2 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 1mrzA 293 2.18e-01 b.43.5.1 -4048 c.26.1.3 -6616 1fd8A 73 4.33e-01 1cc8A d.58.17.1 59770 1se0A 116 6.57e-01 g.52.1.1 -12841 1cc8A 73 1.13e+00 1cc8A d.58.17.1 39343 1v95A 130 1.13e+00 1ejdA 419 1.23e+00 1uae d.68.2.2 39576 1omhA 293 1.51e+00 unknown_sccs -10527 1uae 419 1.92e+00 1uae d.68.2.2 39574 1lfpA 249 2.28e+00 e.39.1.1 73885 1fzrA 138 2.39e+00 1fzrA c.52.1.17 33336 1rvgA 305 2.41e+00 c.1.10.2 -5500 1qavA 90 2.52e+00 1qauA b.36.1.1 24777 1g73C 121 2.55e+00 1g3fA g.52.1.1 45375 1i8xA 30 2.63e+00 g.3.16.1 71132 1gmxA 108 2.73e+00 c.46.1.3 65355 1odkA 235 2.88e+00 c.56.2.1 86863 1qftA 175 2.94e+00 1qftA b.60.1.1 27151 1mvfD 82 3.04e+00 b.129.1.1 85143 1atiB 505 3.13e+00 1atiA c.51.1.1 33197 d.104.1.1 40746 1atiA 505 3.19e+00 1atiA c.51.1.1 33196 d.104.1.1 40745 1fokA 568 3.24e+00 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1xyzA 347 3.25e+00 1taxA c.1.8.3 28804 1ica 40 3.34e+00 1ica g.3.7.4 44173 1npiA 61 3.70e+00 g.3.7.1 80685 1gn0A 108 3.77e+00 c.46.1.3 65358 1vj7A 393 3.87e+00 unknown_sccs -1265 unknown_sccs -9814 1scy 32 4.02e+00 1pnh g.3.7.2 44155 1b7dA 61 4.23e+00 1aho g.3.7.1 44139 1hwxA 501 4.34e+00 1hwyA c.2.1.7 30250 c.58.1.1 33898 1hwyA 501 4.43e+00 1hwyA c.2.1.7 30262 c.58.1.1 33910 1m0dA 138 4.43e+00 c.52.1.17 74354 2fokA 579 4.58e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1prgA 270 4.62e+00 2prgA a.123.1.1 19314 1g6sA 427 4.73e+00 1eps d.68.2.2 39584 1g3fA 117 4.73e+00 1g3fA g.52.1.1 45378 1eblB 317 4.78e+00 1hn9A c.95.1.1 35975 c.95.1.1 35976 1bjaA 95 4.79e+00 1bjaA a.4.5.9 16122 1hn9A 317 4.86e+00 1hn9A c.95.1.1 35977 c.95.1.1 35978 1g57A 217 4.88e+00 1g57A d.115.1.2 60253 1nf2A 268 4.96e+00 c.108.1.10 -6842 2wsyA 268 5.02e+00 2tysA c.1.2.4 28588 1hnjA 317 5.09e+00 1hn9A c.95.1.1 35969 c.95.1.1 35970 1geqA 248 5.30e+00 2tysA c.1.2.4 28589 1qgmA 30 5.43e+00 g.3.16.1 44380 1eblA 317 5.50e+00 1hn9A c.95.1.1 35973 c.95.1.1 35974 1mb3A 124 5.75e+00 c.23.1.1 78907 1i1qB 192 5.77e+00 1qdlB c.23.16.1 61544 1c9qA 117 5.80e+00 1c9qA g.52.1.1 45377 1l6rA 227 5.86e+00 c.108.1.10 77768 1im5A 180 6.00e+00 unknown_sccs 66211 1f8fA 371 6.02e+00 b.35.1.2 83246 c.2.1.1 83247 1eps 427 6.03e+00 1eps d.68.2.2 39586 1lvl 458 6.06e+00 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1rf6A 427 6.16e+00 d.68.2.2 -10314 1qopA 268 6.35e+00 2tysA c.1.2.4 28570 1pht 85 6.36e+00 1ckaA b.34.2.1 24483 1oi7A 288 6.43e+00 c.2.1.8 87049 c.23.4.1 87050 1f37A 110 6.53e+00 1f37A c.47.1.11 33088 1o6aA 96 6.61e+00 unknown_sccs -4101 1bj4A 470 6.73e+00 1bj4A c.67.1.4 34479 7reqB 637 6.74e+00 1reqB c.1.19.1 29617 c.23.6.1 31244 1ixkA 315 6.89e+00 unknown_sccs -8099 1dbtA 239 6.95e+00 1dbtA c.1.2.3 28539 2tysA 268 7.01e+00 2tysA c.1.2.4 28572 1bksA 268 7.32e+00 2tysA c.1.2.4 28585 2occB 227 7.45e+00 2occB b.6.1.2 23027 f.17.2.1 43519 1har 216 7.66e+00 1rthA e.8.1.2 43025 1pkn 530 7.75e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1okrA 123 8.16e+00 unknown_sccs -235 1ufkA 254 8.17e+00 unknown_sccs -8103 1giqA 413 8.72e+00 d.166.1.1 76224 d.166.1.1 76225 1reqD 637 8.73e+00 1reqB c.1.19.1 29623 c.23.6.1 31250 1m2aA 110 8.75e+00 c.47.1.11 78472 1kafA 108 8.82e+00 d.199.1.1 68372 1m2bA 110 8.99e+00 c.47.1.11 78474 1lg7A 182 9.03e+00 d.213.1.1 73888 1m2dA 110 9.06e+00 c.47.1.11 78476 1j1yA 136 9.10e+00 d.38.1.5 -9671 1cv8 174 9.29e+00 1cv8 d.3.1.1 37089 1liiA 363 9.90e+00 c.72.1.1 73921 1fltV 98 1.00e+01 1vpfA g.17.1.1 44751 1kgsA 225 1.00e+01 a.4.6.1 68596 c.23.1.1 68597 1m6dA 214 1.03e+01 d.3.1.1 84849 1qwgA 251 1.04e+01 unknown_sccs -5678 1jmmA 377 1.04e+01 b.30.6.1 71749 1fm9D 272 1.08e+01 2prgA a.123.1.1 19313 1ygs 234 1.10e+01 1ygs b.26.1.1 23907 1veaA 148 1.11e+01 1a49A 530 1.11e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 2prgA 271 1.11e+01 2prgA a.123.1.1 19311 1e0tA 470 1.12e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 4bp2 130 1.12e+01 1poa a.133.1.2 19584 1ko7A 314 1.16e+01 c.98.2.1 72797 c.91.1.2 72798 2rslA 140 1.17e+01 2rslA c.53.1.1 33345 1kyaA 499 1.17e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1k7jA 206 1.19e+01 d.115.1.1 72103 1kk9A 221 1.24e+01 d.115.1.1 77432 1f9mA 112 1.24e+01 1erv c.47.1.1 32736 1i60A 278 1.27e+01 c.1.15.4 71118 1uc7A 125 1.33e+01 c.47.1.1 -7414 1aj6 219 1.33e+01 1aj6 d.122.1.2 41106 1jd5A 124 1.33e+01 g.52.1.1 66544 1etc 110 1.34e+01 1awcA a.4.5.21 16162 1mgrA 99 1.39e+01 d.1.1.2 79106 1reqB 637 1.40e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1faaA 124 1.42e+01 1erv c.47.1.1 32738 1eucB 396 1.42e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1plq 258 1.43e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1gmeA 151 1.51e+01 b.15.1.1 65305 1vjqA 79 1.59e+01 unknown_sccs -13478 1tqnA 486 1.62e+01 1n99A 166 1.64e+01 b.36.1.1 85459 b.36.1.1 85460 1eudB 396 1.64e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1ti6B 274 1.64e+01 1k6wA 426 1.65e+01 b.92.1.2 68236 c.1.9.5 68237 1r5rA 119 1.65e+01 a.39.2.1 -893 1l6oA 95 1.66e+01 b.36.1.1 84534 1euhA 475 1.67e+01 1euhA c.82.1.1 35369 1dgmA 363 1.67e+01 1bx4A c.72.1.1 34936 1qniA 581 1.69e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1dcfA 136 1.69e+01 1dcfA c.23.1.2 31124 1dv2A 452 1.72e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1jj2Y 73 1.72e+01 1ffkW g.41.8.1 63110 1nw2A 105 1.74e+01 c.47.1.1 -7380 1jroB 777 1.75e+01 d.41.1.1 67141 d.133.1.1 67142 1g2iA 166 1.76e+01 1g2iA c.23.16.2 31438 1ffkC 246 1.80e+01 1ffkC c.22.1.1 31037 1li5A 461 1.81e+01 a.27.1.1 73912 c.26.1.1 73913 1pydA 556 1.82e+01 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1bi0 226 1.84e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1ae7 119 1.86e+01 1poa a.133.1.2 19553 1b7bA 310 1.87e+01 1b7bA c.73.1.1 34963 2napA 723 1.91e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1ro0A 216 1.92e+01 unknown_sccs -11390 1pytA 94 1.94e+01 1pytA d.58.3.1 39064 1dciA 275 1.95e+01 1dciA c.14.1.3 30918 1ju5A 109 1.97e+01 d.93.1.1 77173 1amuA 563 1.97e+01 1amuA e.23.1.1 43351 1iezA 217 1.98e+01 d.115.1.2 66129 1qpbA 563 1.98e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1qhoA 686 2.03e+01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1sd4A 126 2.03e+01 1f3uB 171 2.03e+01 1f3uB b.65.1.1 27525 1i12A 160 2.04e+01 1i21A d.108.1.1 61515 1r13A 148 2.10e+01 d.169.1.1 -11646 h.1.1.1 -12895 1l5zA 155 2.12e+01 c.23.1.1 77722 1dmlB 36 2.12e+01 1dmlB 1b7gO 340 2.14e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1upaA 573 2.16e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1nbaA 264 2.17e+01 1nbaA unknown_sccs 31753 1mk0A 97 2.18e+01 d.226.1.1 79216 2dtr 226 2.20e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1ivyA 452 2.24e+01 1ivyA c.69.1.5 34654 1jg5A 83 2.25e+01 d.205.1.1 66666 1qkkA 155 2.26e+01 1dbwA c.23.1.1 31104 1oyc 400 2.27e+01 1oyc c.1.4.1 28603 1g26A 31 2.28e+01 1g26A g.3.16.1 44381 1m5tA 124 2.29e+01 c.23.1.1 78660 1lvaA 258 2.30e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1itzA 675 2.31e+01 c.36.1.6 76798 c.36.1.10 76797 c.48.1.1 76799 1iba 101 2.32e+01 1iba d.95.1.1 40567 1jb1A 205 2.33e+01 1jb1A c.91.1.2 62832 1psuA 140 2.34e+01 d.38.1.5 88285 1rl6A 177 2.35e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1pvdA 537 2.38e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1f7dA 136 2.39e+01 1dun b.85.4.1 28353 1rv3A 483 2.41e+01 1p32A 209 2.41e+01 1p32A d.25.1.1 38379 1kvoA 124 2.44e+01 1poa a.133.1.2 19564 1sh0A 510 2.45e+01 e.8.1.4 -11949 1qapA 296 2.45e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 2scuB 388 2.46e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1i7qB 193 2.47e+01 1qdlB c.23.16.1 61902 1bncA 449 2.48e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1nmoA 247 2.52e+01 unknown_sccs -8746 1j6pA 418 2.53e+01 b.92.1.4 77089 c.1.9.9 77090 1h77A 605 2.53e+01 1qumA 285 2.54e+01 1qumA c.1.15.1 29393 1g4iA 123 2.54e+01 1poa a.133.1.2 60241 1gx1A 160 2.55e+01 d.79.5.1 70675 1dfuP 94 2.58e+01 1dfuP b.53.1.1 26936 1e19A 314 2.59e+01 1b7bA c.73.1.1 34967 1oya 400 2.61e+01 1oyc c.1.4.1 28604 1ve9A 347 2.64e+01 c.4.1.2 -6056 d.16.1.3 -9214 1mbxC 106 2.65e+01 d.45.1.2 78929 1mku 123 2.68e+01 1poa a.133.1.2 19590 1pvuA 154 2.75e+01 3pviA c.52.1.6 33306 1ro2A 216 2.76e+01 unknown_sccs -11391 1kwgA 645 2.77e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1kwkA 645 2.77e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1udxA 416 2.83e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1dfeA 37 2.86e+01 1dfeA g.42.1.1 45318 1q35A 320 2.96e+01 c.94.1.1 -8658 1oqjA 97 3.01e+01 d.217.1.1 -9412 1qv9A 283 3.02e+01 unknown_sccs -6888 1qz9A 416 3.02e+01 c.67.1.3 -8180 1p1mA 406 3.02e+01 b.92.1.4 87696 c.1.9.9 87697 1qamA 244 3.05e+01 2ercA c.66.1.24 34220 1i16 130 3.09e+01 1i16 b.36.1.2 24787 1qi6A 475 3.11e+01 1euhA c.82.1.1 35373 1ojxA 263 3.13e+01 c.1.10.1 -5445 3mag 307 3.18e+01 3mag c.66.1.25 34205 1aa8A 347 3.21e+01 1an9A 1gmiA 136 3.21e+01 b.7.1.1 65309 1q9uA 130 3.26e+01 unknown_sccs -11025 1mvoA 136 3.31e+01 c.23.1.1 79513 1o5zA 442 3.34e+01 c.59.1.2 -7939 c.72.2.2 -8418 1ako 268 3.42e+01 1ako d.151.1.1 41779 1une 123 3.43e+01 1poa a.133.1.2 19583 1p5zB 263 3.44e+01 c.37.1.1 87815 1jy8A 159 3.45e+01 d.79.5.1 67452 1v39 322 3.45e+01 3mag c.66.1.25 34206 1vp9 322 3.45e+01 3mag c.66.1.25 34210 1pxwA 128 3.46e+01 d.79.3.1 -10406 1e0zA 128 3.50e+01 1awd d.15.4.1 59153 1rcuA 195 3.51e+01 unknown_sccs -7279 1gtkA 313 3.51e+01 c.94.1.1 76346 d.50.2.1 76347 1gvjA 146 3.51e+01 a.4.5.21 -293 1yacA 208 3.52e+01 1yacA unknown_sccs 31757 2hhmA 276 3.65e+01 1imbA e.7.1.1 42955 1dfoA 417 3.66e+01 1bj4A c.67.1.4 34480 5croA 66 3.68e+01 1orc a.35.1.2 17044 1gln 468 3.69e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1s29A 92 3.71e+01 unknown_sccs -315 1lrrA 131 3.71e+01 d.228.1.1 78165 1eljA 381 3.72e+01 4mbp c.94.1.1 35791 1k8hA 133 3.74e+01 b.111.1.1 72176 1tiqA 180 3.74e+01 1i0rA 169 3.74e+01 1i0rA b.45.1.2 61489 1i0sA 169 3.74e+01 1i0rA b.45.1.2 61491 1pda 315 3.76e+01 1pda c.94.1.1 35751 d.50.2.1 38794 1dl0A 37 3.78e+01 1dl0A g.3.6.2 44112 487dL 133 3.78e+01 1mmsA i.1.1.2 45839 2pspA 106 3.84e+01 2pspA g.16.1.1 44730 g.16.1.1 44731 1iow 306 3.91e+01 1iow c.30.1.2 31713 d.142.1.1 41481 1v2dA 381 3.92e+01 1vid 221 3.99e+01 1vid c.66.1.1 34178