# List of top-scoring protein chains for t04-100-30-str2-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 1wgzA 510 1.23e-01 1srvA 145 5.29e-01 1derA c.8.5.1 30817 1b8zA 90 5.48e-01 1huuA a.55.1.1 17902 1nd6A 354 7.78e-01 c.60.1.2 80407 2hpaA 342 1.02e+00 1cviA c.60.1.2 33985 1nox 205 1.23e+00 1nox d.90.1.1 40242 1tffA 234 1.27e+00 d.3.1.11 106854 1sheA 103 1.33e+00 d.274.1.1 105551 2fflA 756 1.49e+00 2fbwC 141 1.62e+00 1csn 298 1.92e+00 1csn d.144.1.7 41664 1swvA 267 2.07e+00 1kid 203 2.22e+00 1derA c.8.5.1 30771 1yz7A 188 2.89e+00 1dbhA 354 3.04e+00 1awe a.87.1.1,b.55.1.1 18514,26967 1vin 268 3.04e+00 1vin a.74.1.1,a.74.1.1 18354,18355 2aelA 374 3.41e+00 1qkrA 188 3.44e+00 1qkrA a.24.9.1 16628 1vpqA 273 3.86e+00 1fezA 256 4.30e+00 1fezA c.108.1.3 43343 1urvA 190 4.36e+00 1ut0A 190 4.36e+00 a.1.1.2 108012 1tx4A 198 4.51e+00 1tx4A a.116.1.1 19098 2anuA 255 5.06e+00 4pah 308 5.31e+00 4pah d.178.1.1 42576 1qc7A 101 5.50e+00 1qc7A a.118.14.1 18456 1j8uA 325 5.51e+00 d.178.1.1 71611 1evyA 366 5.67e+00 1evyA a.100.1.6,c.2.1.6 18811,30215 2ex3B 264 5.87e+00 1iq8A 582 6.20e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1dmtA 696 7.04e+00 1dmtA d.92.1.4 40296 1tq8A 163 7.09e+00 c.26.2.4 107204 1ay7B 89 7.34e+00 1ay7B c.9.1.1 30836 1rw6A 210 7.41e+00 a.47.4.1 105113 1e3aA 260 7.57e+00 1ajqA d.153.1.2 41838 1w2yA 229 7.77e+00 a.204.1.1 109140 1mojA 182 7.92e+00 a.25.1.1 91367 1tjoA 182 7.92e+00 1qs1A 462 8.02e+00 1qs1A d.166.1.1,d.166.1.1 42260,42261 1gk9A 260 8.14e+00 d.153.1.2 65246 1j34A 129 8.31e+00 d.169.1.1 84048 1rqlA 267 8.77e+00 c.108.1.3 97750 2mgg 154 8.79e+00 1a6m a.1.1.2 15069 1tufA 434 8.87e+00 b.49.2.3,c.1.6.1 107335,107336 1mroB 442 8.97e+00 1mroB a.89.1.1,d.58.31.2 18531,39449 1hbnB 442 9.01e+00 1mroB a.89.1.1,d.58.31.2 60900,60901 103m 154 9.14e+00 1a6m a.1.1.2 15124 1qojA 63 9.70e+00 1qojA a.2.9.1 15716 1wlsA 328 9.84e+00 1xqwA 293 9.86e+00 1mlo 154 9.86e+00 1a6m a.1.1.2 15085 1mll 154 9.90e+00 1a6m a.1.1.2 15057 1mod 154 9.95e+00 1a6m a.1.1.2 15107 1r2zA 274 1.01e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 2mgb 154 1.02e+01 1a6m a.1.1.2 15102 1mym 154 1.02e+01 1a6m a.1.1.2 15054 1colA 204 1.02e+01 1a87 f.1.1.1 43378 1yyqA 374 1.04e+01 1spgB 147 1.04e+01 1cg5B a.1.1.2 15588 1a6m 151 1.08e+01 1a6m a.1.1.2 15018 1mlg 154 1.09e+01 1a6m a.1.1.2 15104 1bzpA 153 1.10e+01 1a6m a.1.1.2 15020 1kiyA 374 1.10e+01 a.128.1.5 72555 1yt3A 375 1.12e+01 2spl 154 1.12e+01 1a6m a.1.1.2 15047 2ah5A 210 1.14e+01 1v6tA 255 1.16e+01 1l1zA 274 1.16e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1r1hA 696 1.17e+01 d.92.1.4 104756 1q4mA 221 1.19e+01 a.132.1.3 95805 1nm2A 317 1.22e+01 c.19.1.1,d.58.23.1 80654,80655 1z6aA 500 1.24e+01 1z4eA 153 1.25e+01 1v7pB 128 1.26e+01 d.169.1.1 108407 1rpa 342 1.26e+01 1cviA c.60.1.2 33983 1ukmB 128 1.26e+01 d.169.1.1 99500 1qghA 156 1.29e+01 1qghA a.25.1.1 16728 1nw2A 105 1.38e+01 c.47.1.1 92215 2bwvA 440 1.38e+01 1wl9A 440 1.40e+01 1az9 457 1.44e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1xewX 182 1.47e+01 1qddA 144 1.48e+01 1qddA d.169.1.1 42324 1w9cA 321 1.57e+01 2be4A 272 1.57e+01 1q0pA 223 1.59e+01 c.62.1.1 95507 2bx2L 517 1.61e+01 1mla 309 1.66e+01 1mla c.19.1.1,d.58.23.1 31031,39383 2bh9A 489 1.68e+01 1o08A 221 1.69e+01 c.108.1.6 86525 1z5zA 271 1.71e+01 1l9hA 349 1.73e+01 f.13.1.2 73720 1wm1A 317 1.74e+01 c.69.1.7 109405 1tk9A 188 1.75e+01 c.80.1.3 107082 1gpmA 525 1.76e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1em9A 154 1.78e+01 1d1dA a.73.1.1 18333 1z7aA 308 1.79e+01 1jmsA 381 1.79e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1mtzA 293 1.81e+01 c.69.1.7 79467 1vkhA 273 1.82e+01 c.69.1.32 108662 1z5bA 469 1.83e+01 1z63A 500 1.84e+01 1u19A 349 1.85e+01 1w0dA 337 1.86e+01 1dwtA 153 1.86e+01 1a6m a.1.1.2 15190 1wmiA 90 1.87e+01 1gjnA 153 1.89e+01 a.1.1.2 70191 1zoyC 140 1.95e+01 1huuA 90 1.97e+01 1huuA a.55.1.1 17897 1twiA 434 1.98e+01 b.49.2.3,c.1.6.1 107399,107400 2f2gA 221 2.00e+01 1v9dA 340 2.05e+01 a.207.1.1 100535 1q3eA 207 2.05e+01 b.82.3.2 95669 1vz6A 393 2.06e+01 d.154.1.2 108949 1rcwA 231 2.08e+01 a.132.1.4 97299 1ymqA 261 2.09e+01 1v98A 140 2.11e+01 1t9kA 347 2.12e+01 c.124.1.5 106721 1e94F 449 2.15e+01 1do0A c.37.1.20 32443 1wwpA 119 2.29e+01 2fd5A 180 2.30e+01 1u8vA 490 2.31e+01 1hzxA 349 2.38e+01 1f88A f.13.1.2 61466 1nrjB 218 2.44e+01 c.37.1.8 86125 2end 138 2.48e+01 2end a.18.1.1 16400 1qgrA 876 2.49e+01 1qgrA a.118.1.1 19119 1ld8A 382 2.54e+01 a.118.6.1 73838 1w33A 181 2.56e+01 1t6t1 118 2.56e+01 1ebmA 317 2.58e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1kz7A 353 2.60e+01 a.87.1.1,b.55.1.1 73333,73334 1tia 279 2.60e+01 3tgl c.69.1.17 34737 2fh5A 185 2.64e+01 2a14A 263 2.68e+01 1wyzA 242 2.68e+01 1rfyA 102 2.71e+01 2a2dA 478 2.72e+01 2dh4A 340 2.78e+01 2a2cA 478 2.79e+01 1fxxA 482 2.80e+01 1fxxA c.55.3.5 33726 1jq5A 370 2.80e+01 e.22.1.2 67084 1tn6A 382 2.81e+01 1khoA 370 2.84e+01 a.124.1.1,b.12.1.3 72489,72490 1na3A 91 2.84e+01 k.38.1.1 85481 1qtrA 317 2.89e+01 1qtrA c.69.1.7 34660 1nswA 105 2.89e+01 c.47.1.1 92097 1wr8A 231 2.89e+01 1rtxA 123 2.93e+01 a.1.1.1 97827 1uv0A 149 2.94e+01 d.169.1.1 100028 1w7jA 795 3.04e+01 1ydhA 216 3.04e+01 2cqnA 77 3.07e+01 1d2zB 153 3.09e+01 1d2zB a.77.1.2 18439 1ixcA 294 3.11e+01 a.4.5.37,c.94.1.1 83764,83765 1y9aA 360 3.14e+01 1y74A 57 3.15e+01 1kl1A 419 3.20e+01 c.67.1.4 72663 1chuA 540 3.20e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1hjzA 192 3.21e+01 c.50.1.2 83520 1d8dA 377 3.25e+01 1ft1A a.118.6.1 19185 1u2kA 309 3.27e+01 1ki1B 352 3.27e+01 a.87.1.1,b.55.1.1 72497,72498 1nzeA 149 3.28e+01 a.24.18.1 92374 1bh9B 89 3.34e+01 1bh9B a.22.1.3 16485 1nwzA 125 3.36e+01 d.110.3.1 86370 3pyp 125 3.36e+01 3pyp d.110.3.1 40897 1u7kA 131 3.37e+01 1tdzA 272 3.40e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1fmhB 33 3.44e+01 1fmhB k.6.1.1 46410 1nnjA 271 3.47e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1ne2A 200 3.47e+01 c.66.1.32 85586 1zq9A 285 3.48e+01 1aszB 490 3.50e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1omwA 689 3.52e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1vhuA 211 3.57e+01 c.50.1.2 100703 1w98B 283 3.57e+01 1akhA 61 3.60e+01 1akhA a.4.1.1 15980 2fvhA 120 3.68e+01 1fx8A 281 3.69e+01 f.19.1.1 43651 1ug3A 339 3.71e+01 1vqrA 297 3.72e+01 1v1rA 400 3.73e+01 c.36.1.11 108272 1owfA 99 3.74e+01 a.55.1.1 87487 1jk0B 345 3.76e+01 a.25.1.2 63143 2g38B 198 3.78e+01 1px5A 349 3.78e+01 a.160.1.2,d.218.1.6 95277,95278 1a41 234 3.82e+01 1a41 d.163.1.2 42174 1m1zA 513 3.82e+01 c.26.2.1,d.153.1.1 78457,78458 1azwA 313 3.83e+01 1qtrA c.69.1.7 34658 2gfhA 260 3.86e+01 1x6zA 123 3.86e+01 1ev7A 317 3.91e+01 1ev7B c.52.1.9 33315 2d0iA 333 3.99e+01 1txgA 335 4.00e+01 1dp3A 55 4.07e+01 1dp3A a.55.1.2 59128 1o5hA 214 4.12e+01 a.191.1.1 92497 1ush 550 4.16e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1pjjA 271 4.21e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1g5aA 628 4.22e+01 b.71.1.1,c.1.8.1 65152,65153 1u59A 287 4.22e+01 d.144.1.7 107681 1mw5A 187 4.23e+01 d.259.1.1 91477 1dzoA 123 4.28e+01 1dzoA d.24.1.1 38378 1pxvA 183 4.28e+01 d.3.1.1 95301 1y4hA 188 4.32e+01 1upkA 341 4.35e+01 a.118.1.15 99758 1qz5A 375 4.36e+01 c.55.1.1,c.55.1.1 96614,96615 1yjsA 419 4.41e+01 1f75A 249 4.49e+01 1f75A c.101.1.1 59662 7odcA 424 4.51e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1ywfA 296 4.58e+01 1wuaA 375 4.60e+01 1d4xA 375 4.65e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1miwA 404 4.65e+01 a.173.1.1,d.218.1.4 79162,79163 1k8kA 418 4.67e+01 c.55.1.1,c.55.1.1 68305,68306 2ahrA 259 4.68e+01 1t2bA 397 4.70e+01 2ax6A 256 4.71e+01 1or4A 178 4.76e+01 a.1.1.2 93447 1j6zA 376 4.77e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1hhsA 664 4.77e+01 1hi0P e.8.1.6 61045 2c1lA 358 4.81e+01 1rro 108 4.84e+01 1a75A a.39.1.4 17195 1l8wA 348 4.95e+01 a.154.1.1 73704 1jwiB 125 5.03e+01 d.169.1.1 67384 1jigA 146 5.06e+01 a.25.1.1 71685 2avpA 70 5.07e+01 1va6A 518 5.12e+01 2abqA 306 5.12e+01 1wu7A 434 5.14e+01 1o97D 320 5.15e+01 c.26.2.3,c.31.1.2 81233,81234 1wtyA 119 5.15e+01 1wovA 250 5.17e+01 2axtT 32 5.17e+01 1euhA 475 5.18e+01 1euhA c.82.1.1 35369 2fxuA 375 5.20e+01 1mlwA 301 5.23e+01 d.178.1.1 79289 1mngA 203 5.27e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1q8iA 783 5.31e+01 c.55.3.5,e.8.1.1 96208,96209 1jhsA 188 5.36e+01 d.107.1.1 84172 1f44A 324 5.40e+01 a.60.9.1,d.163.1.1 64982,64983 1nuuA 252 5.44e+01 c.26.1.3 86209 1vgmA 378 5.45e+01 1g1eB 89 5.46e+01 1g1eB a.59.1.1 17931 1xnfA 275 5.48e+01 1eq6A 189 5.50e+01 1eq6A d.107.1.1 40796 1ede 310 5.52e+01 1b6g c.69.1.8 34662 2c1vA 338 5.54e+01 1kshA 186 5.56e+01 c.37.1.8 72914 1ka2A 499 5.66e+01 d.92.1.5 77305 1dgaA 375 5.67e+01 1yagA 2b7oA 464 5.70e+01 1lldA 319 5.71e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 2aaoA 166 5.73e+01 1qu1A 155 5.73e+01 1qu1A h.3.1.1 45670 1v9sA 208 5.73e+01 1ni3A 392 5.73e+01 c.37.1.8,d.15.10.2 80531,80532 1uvjA 664 5.76e+01 e.8.1.6 100045 2g39A 497 5.80e+01 1uxtA 501 5.81e+01 c.82.1.1 108125 1ca1 370 5.82e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1x9bA 53 5.84e+01 1yb5A 351 5.84e+01 1z98A 281 5.85e+01 1wdcB 156 5.92e+01 1wdcB a.39.1.5 17302 2cxcA 144 5.94e+01 1w19A 160 6.00e+01 2gdzA 267 6.02e+01 1kk8B 139 6.05e+01 a.39.1.5 77430 1wnfA 328 6.05e+01 4crxA 322 6.07e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 2a0iA 330 6.09e+01 1e79G 272 6.13e+01 1e79G c.49.2.1 33158 1b6g 310 6.14e+01 1b6g c.69.1.8 34661 1yc9A 442 6.26e+01 1xk4A 93 6.34e+01 1ec7A 446 6.35e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2b8wA 328 6.43e+01 1x7yA 400 6.44e+01 1h8eG 272 6.47e+01 1e79G c.49.2.1 60756 1hziA 129 6.54e+01 1rcb a.26.1.2 61449 2b99A 156 6.57e+01 1ug7A 128 6.61e+01 a.24.24.1 107824 1rtwA 220 6.70e+01 a.132.1.3 97823 1lq7A 67 6.71e+01 k.9.1.1 74183 1mr8A 93 6.72e+01 1b4cA a.39.1.2 17186 1uptB 60 6.78e+01 a.193.1.1 99768 1u00A 227 6.81e+01 1zavA 180 6.85e+01 1dxeA 256 6.89e+01 1dxeA c.1.12.5 29310 2f5tX 233 6.91e+01 1q7sA 117 6.92e+01 c.131.1.1 96055 1sz9A 144 6.93e+01 a.118.9.4 106139 1t46A 313 6.94e+01 d.144.1.7 106397 1w0mA 226 6.96e+01 c.1.1.1 109027 1tz9A 367 6.98e+01 c.1.15.6 107466 1g291 372 6.98e+01 1g291 1buoA 121 7.01e+01 1buoA d.42.1.1 38631 1p5hA 428 7.04e+01 c.123.1.1 87802 1s8nA 205 7.09e+01 c.23.1.1 105374 1pe1A 267 7.18e+01 c.1.10.4 94591 1ezfA 340 7.18e+01 1ezfA a.128.1.2 19440 1rcb 129 7.18e+01 1rcb a.26.1.2 16854 2aa1B 146 7.20e+01 1w5rA 278 7.21e+01 1p7gA 222 7.21e+01 a.2.11.1,d.44.1.1 94223,94224 1fxqA 267 7.25e+01 1d9eA c.1.10.4 60108 1a5t 334 7.25e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1tqgA 105 7.30e+01 a.24.10.3 107224 1jcxA 267 7.32e+01 c.1.10.4 66510 1ash 150 7.43e+01 1ash a.1.1.2 15622 2a61A 145 7.45e+01 1hp1A 516 7.51e+01 d.114.1.1,d.159.1.2 70976,70977 1fwsA 267 7.53e+01 1d9eA c.1.10.4 60063 1uroA 367 7.53e+01 1uroA c.1.22.1 29675 2eboA 74 7.56e+01 2eboA h.3.2.1 45754 1gnwA 211 7.57e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1r3sA 367 7.61e+01 c.1.22.1 96963 1zhaA 267 7.61e+01 1uzeA 589 7.61e+01 d.92.1.5 108174 1v5xA 203 7.63e+01 c.1.2.4 100377 1on2A 142 7.68e+01 a.4.5.24,a.76.1.1 87103,87104 2es9A 115 7.68e+01 1t8xA 267 7.77e+01 4ubpA 101 7.78e+01 1ubpA d.8.1.1 37352 1nofA 383 7.78e+01 b.71.1.2,c.1.8.3 92020,92021 2bmoA 447 7.80e+01 1abrA 251 7.82e+01 1mrj d.165.1.1 42196 1o86A 589 7.88e+01 d.92.1.5 81177 1yewB 247 7.91e+01 2f4qA 346 7.93e+01 1s5lT 32 7.93e+01 1b0uA 262 7.94e+01 1b0uA c.37.1.12 32370 1tvzA 388 8.02e+01 c.95.1.2,c.95.1.2 107367,107368 1wryA 121 8.03e+01 1seiA 130 8.09e+01 1seiA d.140.1.1 41463 1us6A 102 8.12e+01 a.2.13.1 107999 1jr8A 117 8.16e+01 a.24.15.1 67115 1obbA 480 8.21e+01 c.2.1.5,d.162.1.2 86760,86761 2g7lA 243 8.25e+01 1k4mA 213 8.27e+01 c.26.1.3 77258 1vykA 149 8.27e+01 1vkmA 297 8.28e+01 c.138.1.1 108670 1f0iA 504 8.36e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1xm9A 457 8.39e+01 1hvyA 288 8.40e+01 1bkpA d.117.1.1 41049 1tfuA 157 8.43e+01 c.26.1.3 106859 1ku1A 230 8.49e+01 a.118.3.1 72996 1g2nA 264 8.55e+01 1lbd a.123.1.1 60227 1s69A 124 8.57e+01 a.1.1.1 105305 1xmkA 79 8.66e+01 1u61A 138 8.74e+01 a.149.1.1 107696 1ii7A 333 8.74e+01 1ii7A d.159.1.4 62415 1a0p 290 8.81e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1epuA 591 8.81e+01 1dn1A e.25.1.1 43358 1a05A 358 8.91e+01 1cnzA c.77.1.1 35059