# 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 1rfeA 162 1.37e-20 2asfA 137 7.92e-18 2fg9A 178 1.03e-15 1xxoA 147 4.28e-15 2aq6A 147 5.68e-15 1w9aA 147 7.92e-15 2fhqA 141 8.85e-14 2furA 209 2.69e-12 1dnlA 199 1.33e-11 1ci0A b.45.1.1 25753 1g79A 218 4.49e-11 1ci0A b.45.1.1 25752 1t9mA 214 6.05e-09 2arzA 247 6.98e-09 1vl7A 157 7.60e-09 b.45.1.1 108732 1nrgA 261 9.96e-09 b.45.1.1 80694 1w3oA 216 1.89e-08 1ty9A 222 2.11e-07 1flmA 122 1.49e-06 1axj b.45.1.1 25747 1ejeA 192 3.15e-06 1ejeA b.45.1.2 25757 1axj 122 1.24e-05 1axj b.45.1.1 25749 1ci0A 228 2.25e-04 1ci0A b.45.1.1 25750 1ko3A 230 6.62e-03 d.157.1.1 90974 1xhnA 184 1.03e-02 1pvtA 238 7.29e-02 c.74.1.1 95189 1qyaA 307 8.85e-02 d.21.1.2,d.21.1.2 104653,104654 1sdjA 310 1.09e-01 d.21.1.2,d.21.1.2 98807,98808 1tuaA 191 2.28e-01 d.51.1.1,d.51.1.1 107321,107322 1tr8A 102 2.53e-01 1m40A 263 2.84e-01 e.3.1.1 74437 1fqgA 263 2.88e-01 1btl e.3.1.1 42699 1obpA 159 2.88e-01 1obpA b.60.1.1 27092 1btl 263 3.13e-01 1btl e.3.1.1 42691 1ermA 263 3.58e-01 1btl e.3.1.1 42690 1snzA 344 4.52e-01 b.30.5.4 98930 1xrhA 351 7.40e-01 1hc7A 477 1.05e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1xt8A 292 1.10e+00 1xv2A 237 1.28e+00 1f6fB 210 1.43e+00 1axiB b.1.2.1,b.1.2.1 22033,22034 1ob8A 135 1.68e+00 1zarA 282 2.13e+00 1eu3A 210 2.49e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1b00A 127 2.77e+00 3chy c.23.1.1 31122 2ak4E 245 2.82e+00 1p9yA 121 2.92e+00 d.241.2.1 94402 1zesA 125 3.31e+00 1qmyA 167 3.40e+00 1qmyA d.3.1.2 37094 1dgwX 79 3.58e+00 1caxB b.82.1.2 28091 1zx8A 136 3.99e+00 2bnuB 241 4.04e+00 7pcy 98 4.05e+00 1plc b.6.1.1 22863 1e8bA 160 4.43e+00 1e8bA g.14.1.2,g.14.1.2,g.27.1.1 44671,44672,44951 2fsqA 243 4.55e+00 2fo3A 125 5.05e+00 1yo8A 634 5.55e+00 1gmlA 178 5.67e+00 c.8.5.2 70273 1i4uA 181 5.79e+00 b.60.1.1 61732 1r5mA 425 5.94e+00 1vpmA 169 6.51e+00 1gph1 465 6.93e+00 1ecfB 1vqoE 178 7.03e+00 1v9fA 325 7.07e+00 d.265.1.3 108448 2pcy 99 7.13e+00 1plc b.6.1.1 22849 1tqmA 282 7.14e+00 a.4.5.56,d.144.1.9 107236,107237 1h91A 180 7.19e+00 b.60.1.1 60805 1x3lA 440 7.42e+00 1kgcE 242 7.45e+00 b.1.1.1,b.1.1.2 77386,77387 1k8kD 300 7.52e+00 d.198.2.1,d.198.2.1 68309,68310 1eo6A 117 7.53e+00 1eo6A d.15.1.3 37609 1e88A 160 7.61e+00 g.14.1.2,g.14.1.2,g.27.1.1 44669,44670,44950 1dgrN 79 7.89e+00 1caxB 2gibA 103 7.93e+00 1nr4A 71 7.96e+00 d.9.1.1 92077 1mg4A 113 7.97e+00 d.15.11.1 84953 1vyfA 135 8.19e+00 b.60.1.2 108902 1n13B 113 8.37e+00 2d93A 134 8.43e+00 1k4iA 233 8.44e+00 d.115.1.2 72056 1ogaE 252 8.89e+00 b.1.1.1,b.1.1.2 86992,86993 1d7pM 159 9.50e+00 1cztA b.18.1.2 23718 1j5kA 89 1.03e+01 d.51.1.1 71565 1widA 130 1.09e+01 1dgrV 79 1.15e+01 1caxB b.82.1.2 28099 1z0mA 96 1.16e+01 1n9lA 109 1.21e+01 d.110.3.6 85468 1yjmA 110 1.21e+01 1cxwA 60 1.22e+01 g.14.1.2 44677 1t71A 281 1.28e+01 1npdA 288 1.29e+01 c.2.1.7,c.58.1.5 80681,80682 2axhA 242 1.30e+01 1vs0A 310 1.35e+01 1plc 99 1.38e+01 1plc b.6.1.1 22846 1xreA 217 1.41e+01 1qusA 322 1.44e+01 1ltm d.2.1.6 36991 1bolA 222 1.47e+01 1bolA d.124.1.1 41120 1aquA 297 1.51e+01 1aquA c.37.1.5 31942 1zzkA 82 1.53e+01 1a9r 282 1.54e+01 1b8oA c.56.2.1 33767 1ji8A 111 1.56e+01 d.203.1.1 66733 2bjrA 368 1.57e+01 1k3eA 156 1.57e+01 d.198.1.1 68103 1fezA 256 1.59e+01 1fezA c.108.1.3 43343 2axjA 242 1.59e+01 2culA 232 1.60e+01 1wn5A 130 1.61e+01 2bgiA 272 1.62e+01 2f9dP 43 1.66e+01 1b8oA 284 1.70e+01 1b8oA c.56.2.1 33762 1aoqA 567 1.71e+01 1qksA a.3.1.2,b.70.2.1 15934,27692 1s2wA 295 1.73e+01 c.1.12.7 98407 1ak4C 145 1.77e+01 1ak4C a.73.1.1 18321 1dgwA 178 1.80e+01 1dgwA b.82.1.2 28090 1iqrA 420 1.80e+01 a.99.1.1,c.28.1.1 66275,66276 3pnp 289 1.81e+01 1b8oA c.56.2.1 33763 1ae3 86 1.85e+01 1gvp b.40.4.7 25381 1k92A 455 1.90e+01 c.26.2.1,d.210.1.1 68325,68326 1pysA 350 1.91e+01 1pysA d.104.1.1 40775 1a9t 284 1.98e+01 1b8oA c.56.2.1 33765 2basA 431 2.02e+01 1vkkA 154 2.06e+01 d.109.1.2 108669 1vm6A 228 2.07e+01 c.2.1.3,d.81.1.3 108876,108877 1q74A 303 2.08e+01 c.134.1.1 96019 1qksA 567 2.09e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1z2uA 150 2.09e+01 1zboA 210 2.09e+01 1gof 639 2.10e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 2bw2A 140 2.11e+01 1xcrA 316 2.11e+01 1c0aA 585 2.11e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1a9s 289 2.15e+01 1b8oA c.56.2.1 33768 1pbn 289 2.15e+01 1b8oA c.56.2.1 33771 2f46A 156 2.19e+01 1z4rA 168 2.40e+01 1azpA 66 2.46e+01 1azpA b.34.13.1 37467 2agyA 361 2.48e+01 1fzyA 149 2.52e+01 d.20.1.1 65072 1wd5A 208 2.55e+01 1azqA 66 2.55e+01 1azpA b.34.13.1 37469 1aqb 183 2.56e+01 1aqb b.60.1.1 27084 1jo8A 58 2.57e+01 b.34.2.1 71774 1ou8A 111 2.65e+01 b.136.1.1 93543 1irk 306 2.68e+01 1fmk d.144.1.7 41703 1cvrA 435 2.73e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1zo0A 126 2.73e+01 1tl2A 236 2.74e+01 1tl2A b.67.1.1 27541 2ccjA 205 2.75e+01 1vqb 87 2.75e+01 1gvp b.40.4.7 25370 2c5uA 375 2.75e+01 1itvA 195 2.77e+01 b.66.1.1 76791 1xmaA 145 2.79e+01 1z0nA 96 2.81e+01 1uurA 473 2.81e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1goh 639 2.81e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1x23A 155 2.82e+01 1vpbA 451 2.85e+01 1qpxA 218 2.88e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1do6A 124 2.93e+01 1do6A b.1.13.1 22361 1w5fA 353 2.96e+01 1ao7E 245 2.96e+01 1bec b.1.1.1,b.1.1.2 20646,21575 1a8p 258 3.01e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1a8h 500 3.16e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1whmA 92 3.17e+01 1gvp 87 3.24e+01 1gvp b.40.4.7 25369 1c2pA 576 3.25e+01 1quvA e.8.1.4 43117 1m9xC 146 3.26e+01 a.73.1.1 84907 1rdfA 267 3.26e+01 c.108.1.3 104884 1dhy 292 3.30e+01 1han d.32.1.3,d.32.1.3 38504,38505 1qtnA 164 3.30e+01 1pauA c.17.1.1 30999 1g1kA 143 3.31e+01 1aohA b.2.2.2 22404 1qs1A 462 3.32e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1o98A 511 3.33e+01 c.105.1.1,c.76.1.3 86684,86685 1fil 139 3.37e+01 1pne d.110.1.1 40869 2bmfA 451 3.38e+01 1atr 386 3.42e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1qr4A 186 3.42e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 1fivA 113 3.43e+01 1fmb b.50.1.1 26764 1nrzA 164 3.50e+01 c.38.1.1 86131 1w98B 283 3.55e+01 1j6uA 469 3.59e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1njhA 119 3.60e+01 b.128.1.1 85787 1wj9A 211 3.66e+01 1smrA 335 3.69e+01 1smrA b.50.1.2 26878 1vp4A 425 3.71e+01 1k8hA 133 3.73e+01 b.111.1.1 72176 1k3iA 656 3.79e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1ofdA 1520 3.81e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1vi2A 300 3.82e+01 c.2.1.7,c.58.1.5 100726,100727 1xsoA 150 3.83e+01 1mfmA b.1.8.1 22273 1pauA 147 3.87e+01 1pauA c.17.1.1 30994 1gd0A 122 3.87e+01 1dptA d.80.1.3 39834 1przA 252 3.88e+01 d.265.1.3 95064 1bo4A 168 3.90e+01 1bo4A d.108.1.1 40798 2b9sB 62 3.96e+01 2b5oA 402 3.98e+01 2fblA 153 4.00e+01 2axoA 270 4.04e+01 1h1wA 289 4.05e+01 d.144.1.7 83460 1pne 140 4.06e+01 1pne d.110.1.1 40866 1gifA 115 4.07e+01 1dptA d.80.1.3 39837 2bneA 241 4.08e+01 1qryA 80 4.15e+01 2hddA a.4.1.1 16016 1b9hA 388 4.19e+01 1b9hA c.67.1.4 34488 1hr0W 71 4.22e+01 1ah9 b.40.4.5 25329 1qs2A 401 4.28e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1wxaA 116 4.28e+01 1jb0F 164 4.39e+01 1jb0F f.23.16.1 62825 1qayA 428 4.42e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 2gukA 120 4.50e+01 1dmhA 311 4.50e+01 1dmhA b.3.6.1 22633 1ae2 87 4.53e+01 1gvp b.40.4.7 25382 1gx5A 536 4.59e+01 e.8.1.4 70682 1bo4B 168 4.61e+01 1bo4A d.108.1.1 40799 1erjA 393 4.62e+01 1erjA b.69.4.1 27660 1nmeA 146 4.63e+01 c.17.1.1 85874 1vk6A 269 4.67e+01 d.113.1.4,d.113.1.4 100851,100852 1v7rA 186 4.67e+01 c.51.4.1 100482 1g0uE 234 4.68e+01 d.153.1.4 41950 1fr1A 361 4.69e+01 1gceA e.3.1.1 42734 2f9fA 177 4.70e+01 1es6A 296 4.94e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1fnmA 691 4.97e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 1ecl 597 4.98e+01 1ecl e.10.1.1 43238 1ihnA 113 5.04e+01 1ihnA c.103.1.1 62388 1wv3A 238 5.10e+01 1ofuA 320 5.11e+01 c.32.1.1,d.79.2.1 86972,86973 1ck7A 631 5.14e+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 1pbyA 489 5.16e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1gtxA 472 5.18e+01 1gtxA 1aomA 567 5.19e+01 1qksA b.70.2.1 27694 1afvA 151 5.20e+01 1ak4C a.73.1.1 18324 1yagA 375 5.27e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1q9jA 422 5.30e+01 c.43.1.2,c.43.1.2 104590,104591 1vmeA 410 5.32e+01 c.23.5.1,d.157.1.3 108893,108894 1augA 215 5.33e+01 1a2zA c.56.4.1 33798 1a8rA 221 5.36e+01 1a8rA d.96.1.1 40587 1vkwA 218 5.38e+01 d.90.1.2 108695 1gw0A 559 5.42e+01 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1jkmA 358 5.44e+01 1jkmA c.69.1.2 34633 2ewrA 170 5.48e+01 1adqL 213 5.54e+01 8fabA b.1.1.1,b.1.1.2 20272,21272 1r77A 103 5.58e+01 1gyxA 76 5.64e+01 d.80.1.1 76387 1n0lA 224 5.72e+01 b.1.11.1,b.7.2.1 79744,79745 1hbp 183 5.76e+01 1aqb b.60.1.1 27079 2b4wA 315 5.77e+01 2bnfB 241 5.79e+01 2gimA 106 5.79e+01 1w5rA 278 5.79e+01 2cxaA 256 5.81e+01 1cy9A 264 5.88e+01 1ecl e.10.1.1 43236 1cq4B 24 5.99e+01 1gr0A 367 6.12e+01 c.2.1.3,d.81.1.3 70379,70380 1g9mG 321 6.17e+01 1gc1G d.172.1.1 42492 2avtA 378 6.18e+01 1dutA 133 6.21e+01 1dun b.85.4.1 28355 1r31A 428 6.28e+01 d.58.20.1,d.179.1.1 96897,96898 1a9cA 221 6.32e+01 1a8rA d.96.1.1 40602 1rzjG 321 6.35e+01 d.172.1.1 98200 1rqlA 267 6.40e+01 c.108.1.3 97750 2fywA 267 6.42e+01 1tc6A 236 6.43e+01 d.122.1.1 106756 1i7kA 179 6.45e+01 1u9aA d.20.1.1 61889 1ivg 388 6.45e+01 2qwc b.68.1.1 27578 1hpm 386 6.50e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1jkmB 361 6.50e+01 1jkmA c.69.1.2 34634 1kveB 77 6.53e+01 1kveB 1ltm 320 6.53e+01 1ltm d.2.1.6 36992 1xyiA 66 6.63e+01 1o5oA 221 6.68e+01 c.61.1.1 92509 1ejjA 511 6.74e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1iuz 98 6.77e+01 1plc b.6.1.1 22861 1vybA 238 6.78e+01 d.151.1.1 108897 1jdbB 1073 6.78e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1eqjA 511 6.78e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1ag6 99 6.81e+01 1plc b.6.1.1 22857 1n0wA 243 6.81e+01 c.37.1.11 79772 1kbvA 327 6.83e+01 b.6.1.3,b.6.1.3 68395,68396 1swvA 267 6.86e+01 1bupA 386 7.02e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2afbA 351 7.04e+01 2blsA 358 7.10e+01 1gceA e.3.1.1 42747 1qy5A 269 7.14e+01 d.122.1.1 96573 1eajA 126 7.22e+01 1f5wA b.1.1.1 59401 1theA 260 7.22e+01 1theB d.3.1.1 37056 1fecA 490 7.24e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1y8cA 246 7.31e+01 1jj2E 177 7.40e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1qaxA 428 7.49e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1hskA 326 7.53e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1jfmA 174 7.55e+01 d.19.1.1 66640 1psuA 140 7.64e+01 d.38.1.5 88285 1b7bA 310 7.66e+01 1b7bA c.73.1.1 34963 2pia 321 7.74e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1woyA 500 7.78e+01 1xhfA 123 7.81e+01 1fw9A 164 7.83e+01 1fw9A d.190.1.1 60059 1mc0A 368 7.87e+01 d.110.2.1,d.110.2.1 78937,78938 2d81A 318 7.88e+01 1m4iA 181 7.89e+01 d.108.1.1 74457 1tt8A 164 7.89e+01 1ju3A 583 7.95e+01 b.18.1.13,c.69.1.21 67300,67301 2fvgA 340 7.99e+01 1qhqA 140 8.01e+01 1qhqA b.6.1.1 63326 1wnyA 186 8.04e+01 1ssfA 156 8.05e+01 b.34.9.1,b.34.9.1 105982,105983 1b7yA 350 8.08e+01 1pysA d.104.1.1 40776 1j5vA 351 8.10e+01 c.72.1.1 71585 1uv7A 110 8.12e+01 d.67.4.1 100040 1s72E 178 8.30e+01 d.141.1.1,d.141.1.1 105323,105324 1yt3A 375 8.30e+01 1sceA 112 8.33e+01 1puc d.97.1.1 40676 2dg5B 190 8.38e+01 1lfdA 87 8.38e+01 1lfdA d.15.1.5 37622 2fs2A 151 8.40e+01 1cp3A 277 8.47e+01 1pauA c.17.1.1 30992 1fp5A 222 8.47e+01 1f6aB b.1.1.2,b.1.1.2 21530,21531 1a1vA 476 8.58e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1pz7A 204 8.58e+01 b.29.1.4 95405 1wk8A 194 8.59e+01 1xj4A 119 8.66e+01 1m2xA 223 8.68e+01 d.157.1.1 84764 1pymA 295 8.71e+01 1pymA c.1.12.7 29308 1auvA 311 8.71e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1mw9X 592 8.79e+01 e.10.1.1 91480 1kt6A 183 8.79e+01 b.60.1.1 84466 2gdnA 267 8.80e+01 2cavA 445 8.82e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 8ohm 435 8.83e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1dc7A 124 8.90e+01 1dbwA c.23.1.1 31093