# List of top-scoring protein chains for t04-100-30-alpha 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 1tljA 213 2.09e-32 1ecfA 504 1.18e-01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1i1kA 309 1.71e-01 1daaA e.17.1.1 61533 1knwA 425 1.83e-01 b.49.2.3 -4274 c.1.6.1 -5229 1e8gA 560 2.05e-01 1qltA d.58.32.1 39455 d.145.1.1 41718 1hl2A 297 2.18e-01 c.1.10.1 83581 1mu5A 471 3.01e-01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1w1kA 560 4.42e-01 1gpjA 404 5.58e-01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1nb8A 353 6.60e-01 d.3.1.9 80385 1brwA 433 7.22e-01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1eqfA 280 8.17e-01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1iyeA 309 8.93e-01 e.17.1.1 83786 1j5yA 187 9.21e-01 a.4.5.1 71592 d.94.2.1 71593 1ftrA 296 1.25e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1pl5A 142 1.27e+00 1f0xA 571 1.49e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1rpjA 288 1.49e+00 2dri c.93.1.1 35656 1kl7A 514 1.62e+00 c.79.1.1 72678 1t7pA 698 1.76e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1gefA 123 1.87e+00 1gefA c.52.1.18 60465 1a04A 215 2.03e+00 1a04A a.4.6.2 16234 c.23.1.1 31089 1mszA 86 2.06e+00 d.68.7.1 79428 1b65A 375 2.07e+00 1b65A d.154.1.1 42020 1gudA 288 2.07e+00 c.93.1.1 83326 1nal1 297 2.08e+00 1nal3 1s1pA 331 2.09e+00 c.1.7.1 -5240 1vrtA 560 2.64e+00 1rthA c.55.3.1 33574 e.8.1.2 43023 1om4A 422 3.01e+00 d.174.1.1 87067 1oo0B 110 3.01e+00 d.58.7.1 87183 1vc4A 254 3.18e+00 c.1.2.4 -5172 1p5dX 463 3.22e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1izcA 339 3.29e+00 c.1.12.5 83838 1nyhA 166 3.32e+00 h.1.23.1 86403 1fjgJ 105 3.37e+00 1fjfJ d.58.15.1 39330 1rtm1 149 3.38e+00 1rtm1 1rk8A 165 3.72e+00 d.58.7.1 -10018 1f7uA 607 4.24e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1ofuX 119 4.30e+00 c.37.1.22 86976 1qysA 106 4.49e+00 unknown_sccs -13432 1afb1 154 4.56e+00 1rtm1 1vhwA 253 4.63e+00 c.56.2.1 -7765 1l1lA 739 4.64e+00 c.7.1.4 73470 1k47A 337 4.95e+00 d.14.1.5 72040 d.58.26.4 72041 1chmA 401 5.17e+00 1chmA c.55.2.1 33545 d.127.1.1 41142 2napA 723 5.27e+00 2napA b.52.2.2 26926 c.81.1.1 35334 1hh1A 143 5.35e+00 1gefA c.52.1.18 61036 1b8oA 284 5.43e+00 1b8oA c.56.2.1 33762 1j6oA 268 6.33e+00 c.1.9.12 77088 1agi 125 6.45e+00 7rsa d.5.1.1 37303 1j34B 123 6.67e+00 d.169.1.1 84049 1s98A 107 6.88e+00 1k2xA 177 6.94e+00 d.153.1.5 -11450 1kwgA 645 7.29e+00 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1jnyA 435 7.33e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1g6sA 427 7.51e+00 1eps d.68.2.2 39584 1qm4A 396 7.67e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 2sak 121 8.18e+00 2sak d.15.5.1 37711 1byi 224 8.18e+00 1byi c.37.1.10 32199 1sk4A 163 8.46e+00 1eudB 396 8.50e+00 2scuB c.23.4.1 31150 d.142.1.4 41571 3daaA 277 8.71e+00 1daaA e.17.1.1 43272 1p3wA 404 8.72e+00 c.67.1.3 87752 1is1A 185 8.85e+00 d.67.3.1 83704 1gox 370 8.96e+00 1gox c.1.4.1 28607 1dseA 292 9.00e+00 1ryc a.93.1.1 59130 1r94A 118 9.36e+00 b.124.1.1 -4402 1k2yX 463 9.73e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1bueA 265 9.79e+00 1btl e.3.1.1 42727 1gakA 141 9.94e+00 1gakA a.19.1.1 16415 1jdrA 294 9.95e+00 1ryc a.93.1.1 62908 1fc4A 401 1.01e+01 1bs0A c.67.1.4 59760 1k9sA 237 1.03e+01 c.56.2.1 68359 1j3mA 129 1.03e+01 1bvyF 191 1.03e+01 1bvyF c.23.5.1 31207 1ek8A 185 1.06e+01 1ek8A d.67.3.1 59444 1q7sA 117 1.08e+01 unknown_sccs -7522 1p4cA 380 1.10e+01 c.1.4.1 -5201 1i9sA 210 1.10e+01 1i9sA c.45.1.1 62099 1r72A 211 1.12e+01 unknown_sccs -215 unknown_sccs -5981 1r9cA 139 1.14e+01 d.32.1.2 -9557 1lx7A 253 1.17e+01 c.56.2.1 74329 1dp4A 435 1.19e+01 1dp4A c.93.1.1 35710 1oltA 457 1.19e+01 unknown_sccs -5688 1o0xA 262 1.20e+01 d.127.1.1 80755 1oz7A 131 1.21e+01 d.169.1.1 -11622 1i8jA 323 1.22e+01 1b4kA c.1.10.3 61968 1ff9A 450 1.26e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1vhh 162 1.26e+01 1vhh d.65.1.2 39550 1geqA 248 1.26e+01 2tysA c.1.2.4 28589 1sv6A 269 1.26e+01 1qtqA 553 1.31e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1ehiA 377 1.31e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1rthA 560 1.31e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1ecpA 238 1.32e+01 1ecpA c.56.2.1 33775 1dkzA 219 1.33e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1euaA 213 1.34e+01 1fwrA c.1.10.1 29155 1l6sA 323 1.36e+01 c.1.10.3 73627 1b4bA 71 1.36e+01 1b4aA d.74.2.1 39718 1n45A 233 1.37e+01 a.132.1.1 79981 1pe9A 361 1.38e+01 b.80.1.1 -4765 1vhoA 346 1.44e+01 unknown_sccs -4283 c.56.5.4 -7893 1hufA 140 1.45e+01 1hufA d.195.1.1 61272 8abp 306 1.45e+01 8abp c.93.1.1 35647 1mbxC 106 1.48e+01 d.45.1.2 78929 1igs 248 1.49e+01 1a53 c.1.2.4 28565 1qvbA 481 1.57e+01 1qvbA c.1.8.4 28983 1aky 221 1.57e+01 1zin c.37.1.1 31896 g.41.2.1 45197 1a53 247 1.59e+01 1a53 c.1.2.4 28564 1gowA 489 1.64e+01 1qvbA c.1.8.4 28981 1rlkA 117 1.65e+01 unknown_sccs -7526 1uwsA 489 1.66e+01 1c1lA 136 1.70e+01 1c1lA b.29.1.3 24219 1byb 495 1.74e+01 1byb c.1.8.1 28790 1cby 259 1.79e+01 1cby d.103.1.1 40705 1rxyA 253 1.79e+01 c.56.2.1 -7834 1ukz 203 1.80e+01 1zin c.37.1.1 31840 1fp2A 352 1.80e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1agjA 242 1.82e+01 1agjA b.47.1.1 25827 1nf2A 268 1.82e+01 c.108.1.10 -6842 1oj5A 132 1.82e+01 unknown_sccs -10848 1odkA 235 1.88e+01 c.56.2.1 86863 1ci9A 392 1.88e+01 e.3.1.1 64767 1ln4A 104 1.95e+01 d.68.4.1 74043 1qwdA 177 2.04e+01 b.60.1.1 -4455 1uuhA 159 2.07e+01 d.169.1.4 -11651 1rhs 296 2.10e+01 1rhs c.46.1.2 32703 c.46.1.2 32704 1k5nA 276 2.11e+01 b.1.1.2 77266 d.19.1.1 77267 2oatA 439 2.18e+01 2dkb c.67.1.4 34452 1gnlA 544 2.22e+01 e.26.1.1 70287 1jtaA 361 2.25e+01 b.80.1.1 71859 2dkb 433 2.25e+01 2dkb c.67.1.4 34438 1zmeC 70 2.27e+01 1zmeC g.38.1.1 45081 h.1.3.1 45514 1rfzA 168 2.27e+01 unknown_sccs -1206 1spgB 147 2.28e+01 1cg5B a.1.1.2 15588 1j96A 323 2.30e+01 c.1.7.1 71616 1qwiA 143 2.30e+01 d.227.1.1 -11183 1gntA 553 2.33e+01 e.26.1.1 70290 1khcA 147 2.35e+01 b.34.9.2 68608 1j5vA 351 2.38e+01 c.72.1.1 71585 2liv 344 2.40e+01 2liv c.93.1.1 35708 1f75A 249 2.45e+01 1f75A c.101.1.1 59662 1e2uA 553 2.52e+01 1e1dA e.26.1.1 43362 1eg5A 384 2.54e+01 1ecxA c.67.1.3 34429 1qf9A 194 2.63e+01 1zin c.37.1.1 31848 1h0pA 182 2.64e+01 b.62.1.1 76450 1qq8A 214 2.72e+01 1qq8A 2dri 271 2.75e+01 2dri c.93.1.1 35637 1qyaA 307 2.76e+01 1go4E 100 2.77e+01 h.1.22.1 70296 1di2A 69 2.79e+01 1di2A d.50.1.1 38780 1ni4B 341 2.80e+01 c.36.1.7 85729 c.48.1.2 85730 1juvA 193 2.80e+01 c.71.1.1 -8363 1fmtA 314 2.80e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1mml 265 2.82e+01 1mml e.8.1.2 43015 1aw7A 194 2.83e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 2shpA 525 2.87e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1rkqA 282 2.87e+01 c.108.1.10 -6847 1v7oA 165 2.88e+01 unknown_sccs -10249 1e42A 258 2.88e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1oi2A 366 2.89e+01 c.32.1.2 87039 d.79.2.2 87040 1r1dA 247 2.91e+01 unknown_sccs -8335 1pq1A 196 2.92e+01 f.1.4.1 -12055 1p2fA 220 3.03e+01 a.4.6.1 87720 c.23.1.1 87721 1wdcA 64 3.09e+01 1wdcA 1dceA 567 3.10e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1c3pA 375 3.19e+01 1c3pA c.42.1.2 32606 1dyr 206 3.23e+01 1aoeA c.71.1.1 34916 1n7kA 234 3.30e+01 c.1.10.1 85374 1h1nA 305 3.30e+01 c.1.8.3 70855 1s4qA 228 3.37e+01 c.37.1.1 -6975 1gxjA 186 3.42e+01 d.215.1.1 70707 1umgA 362 3.43e+01 1d0cA 444 3.44e+01 d.174.1.1 64769 1g57A 217 3.44e+01 1g57A d.115.1.2 60253 1l3lA 234 3.55e+01 a.4.6.2 73541 d.110.5.1 73542 1d7uA 433 3.55e+01 2dkb c.67.1.4 34439 1nowA 507 3.59e+01 c.1.8.6 85936 d.92.2.1 85937 1ka1A 357 3.60e+01 e.7.1.1 68369 1tcrA 202 3.62e+01 1tcrA b.1.1.1 20605 b.1.1.2 21549 2eifA 136 3.64e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1gkpA 458 3.74e+01 b.92.1.3 70231 c.1.9.6 70232 1fyhB 229 3.80e+01 1jrhI b.1.2.1 22055 b.1.2.1 22056 1vddA 228 3.81e+01 1uurA 473 3.82e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1lhpA 312 3.83e+01 c.72.1.5 77960 1lc0A 294 3.84e+01 c.2.1.3 73823 d.81.1.4 73824 1b4pA 217 3.85e+01 a.45.1.1 83158 c.47.1.5 83159 1ik9A 213 3.89e+01 b.59.1.1 66176 h.1.11.1 66177 1iz0A 302 3.89e+01 b.35.1.2 83821 c.2.1.1 83822 1hdoA 206 3.93e+01 1he2A c.2.1.2 60965 1dxeA 256 3.94e+01 1dxeA c.1.12.5 29310