# List of top-scoring protein chains for t2k-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 1vjkA 98 4.59e-03 d.15.3.1 108631 1frrA 95 6.26e-02 1awd d.15.4.1 37674 1xlqA 106 6.51e-02 1oqqA 106 7.07e-02 d.15.4.1 93422 1ryjA 70 1.55e-01 d.15.3.2 98104 2bb6A 414 1.96e-01 1rwsA 77 4.01e-01 d.15.3.2 97991 1uwmA 106 4.48e-01 1e9mA 106 4.67e-01 1ayfA d.15.4.1 59397 2aj2A 208 5.12e-01 1vybA 238 5.76e-01 d.151.1.1 108897 1put 106 6.62e-01 1ayfA d.15.4.1 37680 1fmaD 81 6.68e-01 1fmaD d.15.3.1 37643 1awd 94 7.07e-01 1awd d.15.4.1 37673 1qorA 327 7.90e-01 1qorA b.35.1.2,c.2.1.1 24766,29782 1frd 98 8.06e-01 1awd d.15.4.1 37648 1zud2 66 8.32e-01 2bwfA 77 1.14e+00 1offA 97 1.31e+00 d.15.4.1 86947 1a70 97 1.54e+00 1awd d.15.4.1 37678 1fm0D 81 1.60e+00 1fmaD d.15.3.1 37642 2cu3A 64 2.07e+00 1guaB 81 2.38e+00 1c1yB d.15.1.5 37619 1dmhA 311 2.42e+00 1dmhA b.3.6.1 22633 1c1yB 77 2.53e+00 1c1yB d.15.1.5 37618 1czpA 98 2.78e+00 1awd d.15.4.1 37645 1qt9A 98 2.78e+00 1awd d.15.4.1 37647 1kf6B 243 2.92e+00 a.1.2.1,d.15.4.2 72397,72398 2g1lA 104 3.20e+00 1n2eA 300 3.42e+00 c.26.1.4 85268 1mopA 300 3.42e+00 c.26.1.4 85035 1qysA 106 3.53e+00 k.41.1.1 96603 1yqbA 100 3.64e+00 1l5pA 93 3.98e+00 d.15.4.1 73598 1doi 128 4.08e+00 1awd d.15.4.1 37676 1dih 273 4.34e+00 1drw c.2.1.3,d.81.1.3 30056,39971 1d4vB 163 4.45e+00 1d4vB b.22.1.1 23884 1drw 273 4.50e+00 1drw c.2.1.3,d.81.1.3 30057,39972 1yj1A 76 4.67e+00 2bpsA 81 4.76e+00 1k07A 263 4.76e+00 d.157.1.1 77218 1wjnA 97 4.85e+00 1rfkA 98 4.90e+00 1xc3A 302 4.98e+00 1wgrA 100 5.03e+00 1fxiA 96 5.06e+00 1awd d.15.4.1 37664 1nbfD 76 5.09e+00 d.15.1.1 80390 1lfdA 87 5.10e+00 1lfdA d.15.1.5 37622 1ryaA 160 5.78e+00 d.113.1.5 105122 1xgsA 295 5.96e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 2rgf 97 6.12e+00 1lfdA d.15.1.5 37627 1ogwA 76 6.53e+00 d.15.1.1 87001 1i7hA 111 6.61e+00 d.15.4.1 71122 1ubq 76 6.65e+00 1ubi d.15.1.1 37585 1ubi 76 6.70e+00 1ubi d.15.1.1 37584 1d3zA 76 6.78e+00 1ubi d.15.1.1 37592 1s0uA 408 7.35e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1zq7A 207 8.42e+00 2dafA 118 8.82e+00 1qlaB 239 8.84e+00 1qlaB a.1.2.1,d.15.4.2 15679,37707 1e0zA 128 9.09e+00 1awd d.15.4.1 59153 2gupA 292 9.14e+00 1dg6A 191 9.19e+00 1d4vB b.22.1.1 23883 1f0zA 66 9.32e+00 1f0zA d.15.3.2 37644 1atiB 505 9.42e+00 1atiA c.51.1.1,d.104.1.1 33197,40746 1jqhA 308 9.55e+00 d.144.1.7 71793 1atiA 505 9.95e+00 1atiA c.51.1.1,d.104.1.1 33196,40745 1gg4A 452 1.04e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1ihgA 370 1.07e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1yqzA 438 1.07e+01 1agnA 373 1.11e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 2al3A 90 1.12e+01 2gk3A 256 1.15e+01 8adh 374 1.15e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1l7yA 94 1.19e+01 d.15.1.6 73676 1lxdA 100 1.20e+01 1lfdA d.15.1.5 37624 1yb5A 351 1.21e+01 1se4 239 1.23e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1vqb 87 1.27e+01 1gvp b.40.4.7 25370 1gvp 87 1.27e+01 1gvp b.40.4.7 25369 1b76A 442 1.29e+01 1atiA c.51.1.1,d.104.1.1 33198,40747 1wwtA 88 1.29e+01 2pia 321 1.31e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1ra6A 461 1.31e+01 e.8.1.4 104879 1a71A 374 1.32e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1euvB 86 1.38e+01 1a5r d.15.1.1 37598 2a84A 300 1.42e+01 2a4hA 126 1.42e+01 1u3wA 374 1.44e+01 2f96A 224 1.47e+01 2ohxA 374 1.49e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1ae3 86 1.59e+01 1gvp b.40.4.7 25381 1gaxA 862 1.63e+01 1gaxA b.51.1.1,c.26.1.1,a.2.7.3,a.27.1.1 26893,31595,75842,75843 1y1nA 291 1.72e+01 1mhxA 65 1.76e+01 d.15.7.1 79134 2bt6A 108 1.76e+01 1wriA 93 1.78e+01 1axeA 374 1.82e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 2c5lC 117 1.84e+01 1raxA 115 1.90e+01 1lfdA d.15.1.5 37626 1o0xA 262 1.96e+01 d.127.1.1 80755 1heuA 374 1.97e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1hetA 374 1.98e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1n8kA 374 1.98e+01 b.35.1.2,c.2.1.1 80298,80299 1ayfA 105 2.09e+01 1ayfA d.15.4.1 37684 1gehA 444 2.15e+01 c.1.14.1,d.58.9.1 65181,65182 1ynmA 247 2.19e+01 1p4oA 322 2.22e+01 d.144.1.7 87775 1dqtA 117 2.22e+01 1ah1 b.1.1.1 20653 1rdr 461 2.24e+01 1rdr e.8.1.4 43116 1z2mA 155 2.28e+01 1v86A 95 2.33e+01 d.15.1.1 108421 1se9A 126 2.41e+01 d.15.1.1 98821 1wmhB 86 2.41e+01 1iow 306 2.41e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1ayfB 105 2.50e+01 1ayfA d.15.4.1 37685 1d5mC 239 2.60e+01 3seb b.40.2.2,d.15.6.1 25185,37774 1lm8B 118 2.63e+01 d.15.1.1 74033 1b9rA 105 2.66e+01 1ayfA d.15.4.1 37683 1cbf 285 2.69e+01 1cbf c.90.1.1 35587 1umuA 116 2.72e+01 1umuA b.87.1.1 28382 1j5yA 187 2.75e+01 a.4.5.1,d.94.2.1 71592,71593 2dln 306 2.75e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1gcpA 70 2.76e+01 1gcpA b.34.2.1 60430 1umuB 116 2.76e+01 1umuA b.87.1.1 28383 1tjxA 159 2.78e+01 1v2yA 105 2.78e+01 d.15.1.1 100275 1ee2A 373 2.78e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1v8fA 276 2.82e+01 c.26.1.4 100503 1iueA 98 2.83e+01 d.15.4.1 90697 1ib8A 164 2.84e+01 b.38.2.1,d.52.4.1 71168,71169 1epfA 191 2.88e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1wi0A 113 2.91e+01 1e6eB 128 2.91e+01 1ayfA d.15.4.1 59300 1ay9A 108 2.93e+01 1umuA b.87.1.1 28384 1vcbA 118 2.96e+01 1vcbA d.15.1.1 37603 1t0qC 86 2.97e+01 d.15.12.1 106222 1u94A 356 3.00e+01 c.37.1.11,d.48.1.1 107743,107744 1aqzB 149 3.01e+01 1aqzA d.1.1.3 36239 2cbf 234 3.04e+01 1cbf c.90.1.1 35588 1b4rA 80 3.10e+01 1b4rA b.1.3.1 22072 1pl8A 356 3.11e+01 b.35.1.2,c.2.1.1 94878,94879 1e69B 322 3.18e+01 1e69B c.37.1.12 32377 1arzC 273 3.18e+01 1drw c.2.1.3,d.81.1.3 30061,39976 2azwA 148 3.19e+01 1ygs 234 3.20e+01 1ygs b.26.1.1 23907 1g19A 350 3.22e+01 2reb c.37.1.11,d.48.1.1 32284,38770 2bw3A 534 3.27e+01 1p5tA 127 3.34e+01 b.55.1.2 94148 1woqA 267 3.36e+01 c.55.1.10,c.55.1.10 109462,109463 3seb 238 3.43e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2bkfA 87 3.44e+01 1pkp 150 3.53e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1j5eE 161 3.57e+01 d.14.1.1,d.50.1.2 71547,71548 1rfa 79 3.62e+01 1c1yB d.15.1.5 37620 1o54A 277 3.63e+01 c.66.1.13 92482 2gpr 154 3.63e+01 1gpr b.84.3.1 28269 1wm3A 72 3.64e+01 1wzlA 585 3.65e+01 1ji2A 585 3.69e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1avbA 226 3.69e+01 1led b.29.1.1 24158 1mgpA 313 3.72e+01 c.119.1.1 79098 3prn 289 3.72e+01 3prn f.4.3.1 43761 1ukmB 128 3.74e+01 d.169.1.1 99500 2reb 352 3.75e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1sfe 180 3.76e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1d2qA 173 3.76e+01 1d4vB b.22.1.1 23894 1ae2 87 3.76e+01 1gvp b.40.4.7 25382 1tmxA 293 3.77e+01 1eb7A 323 3.83e+01 1eb7A a.3.1.5,a.3.1.5 59404,59405 1k1zA 78 3.85e+01 b.34.2.1 68026 1hc7A 477 3.89e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1g6oA 330 3.90e+01 1g6oA c.37.1.11 32430 1cnzA 363 3.90e+01 1cnzA c.77.1.1 35061 1rq2A 382 3.93e+01 c.32.1.1,d.79.2.1 105048,105049 1bmg 98 3.99e+01 1agdB b.1.1.2 20667 2fnjB 118 4.03e+01 1meoA 209 4.04e+01 c.65.1.1 79035 1jenA 267 4.05e+01 1jenA 1axgA 374 4.10e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1xdpA 687 4.15e+01 1xuvA 178 4.16e+01 2mjpA 193 4.17e+01 1b78A c.51.4.1 33223 1adqA 206 4.18e+01 1igtB b.1.1.2,b.1.1.2 21518,21519 1rypI 222 4.18e+01 d.153.1.4 41877 1g5hA 454 4.19e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1c24A 263 4.21e+01 1c24A d.127.1.1 41148 4matA 278 4.22e+01 1c24A d.127.1.1 41150 1wkaA 147 4.26e+01 2aefA 234 4.38e+01 1knlA 130 4.42e+01 b.42.2.1 72780 2fcr 173 4.42e+01 1rcf c.23.5.1 31151 1vc3B 97 4.45e+01 1kevA 351 4.49e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1pvmA 184 4.52e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zavA 180 4.56e+01 2gptA 523 4.58e+01 1pedA 351 4.58e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 2ap1A 327 4.59e+01 1knmA 130 4.59e+01 b.42.2.1 72781 1fjgE 162 4.67e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1v7pB 128 4.74e+01 d.169.1.1 108407 1azdA 237 4.79e+01 1nls b.29.1.1 24020 1b78A 193 4.87e+01 1b78A c.51.4.1 33221 1dljA 402 4.89e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1ihoA 283 4.90e+01 1ihoA c.26.1.4 62390 1t3qA 168 4.96e+01 a.56.1.1,d.15.4.2 106367,106368 1mat 264 4.97e+01 1c24A d.127.1.1 41152 1a5r 103 5.01e+01 1a5r d.15.1.1 37597 1p0fA 373 5.03e+01 b.35.1.2,c.2.1.1 87642,87643 2cyjA 118 5.13e+01 1h0hA 977 5.15e+01 b.52.2.2,c.81.1.1 76435,76436 1vm6A 228 5.20e+01 c.2.1.3,d.81.1.3 108876,108877 1snzA 344 5.24e+01 b.30.5.4 98930 1uh6A 100 5.27e+01 d.15.1.1 99394 1aqzA 149 5.28e+01 1aqzA d.1.1.3 36238 1c4zA 358 5.28e+01 1c4zA d.148.1.1 41766 1jqbA 351 5.29e+01 b.35.1.2,c.2.1.1 77151,77152 2b3hA 329 5.30e+01 1r3eA 309 5.31e+01 b.122.1.1,d.265.1.2 96907,96908 1p7gA 222 5.45e+01 a.2.11.1,d.44.1.1 94223,94224 1mtpA 323 5.47e+01 e.1.1.1 85107 1jx4A 352 5.49e+01 d.240.1.1,e.8.1.7 90378,90379 1uowA 159 5.62e+01 b.7.1.2 107975 2matA 264 5.67e+01 1c24A d.127.1.1 41146 1bvzA 585 5.71e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 2bw0A 329 5.76e+01 1cf2O 337 5.77e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1gcqC 70 5.80e+01 1gcpA b.34.2.1 60436 1uuqA 440 5.80e+01 c.1.8.3 100015 1wloA 136 5.85e+01 1xnzA 264 5.86e+01 2cwpA 112 5.88e+01 1yoxA 250 5.96e+01 1t6aA 126 6.16e+01 d.129.8.1 106555 2avxA 171 6.16e+01 1k5wA 152 6.16e+01 b.7.1.2 68212 1rm6C 161 6.17e+01 1p4uA 153 6.30e+01 b.1.10.2 87780 1pgs 314 6.30e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1ofdA 1520 6.30e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1wwaX 109 6.31e+01 1wwcA b.1.1.4 21775 1mi0A 65 6.35e+01 d.15.7.1 79135 2fh1A 344 6.48e+01 1vr6A 350 6.48e+01 1llwA 1520 6.48e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 2bbvC 363 6.55e+01 2bbvA b.121.4.4 23325 1pmd 675 6.58e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1k8kC 372 6.59e+01 b.69.4.1 68308 1sv6A 269 6.61e+01 d.177.1.1 106043 1q1oA 98 6.61e+01 d.15.2.2 95596 1whxA 111 6.76e+01 1omzA 293 6.85e+01 c.68.1.15 87093 1b59A 370 6.86e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1mejA 223 6.89e+01 c.65.1.1 79029 1v5mA 136 6.91e+01 b.55.1.1 108379 1n62A 166 7.01e+01 a.56.1.1,d.15.4.2 80090,80091 1z2wA 192 7.01e+01 1f1xA 322 7.04e+01 d.32.1.3,d.32.1.3 83208,83209 1mhcB 99 7.05e+01 1agdB b.1.1.2 20832 2b0vA 153 7.09e+01 2gl5A 410 7.09e+01 1he7A 126 7.15e+01 1wwcA b.1.1.4 60970 1s3iA 310 7.16e+01 b.46.1.1,c.65.1.1 98435,98436 3ait 74 7.17e+01 1hoe b.5.1.1 22835 1f1uA 323 7.22e+01 d.32.1.3,d.32.1.3 83200,83201 1te0A 318 7.31e+01 1e01A 48 7.33e+01 1e01A 1xzoA 174 7.33e+01 1xmbA 418 7.34e+01 1fc1A 224 7.37e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1bbhA 131 7.38e+01 1bbhA a.24.3.2 16546 1qfxA 460 7.40e+01 1qfxA c.60.1.2 33994 2fcfA 103 7.43e+01 1h9sA 140 7.46e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1w78A 422 7.46e+01 1qmhA 347 7.48e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1vdeA 454 7.49e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 1wvqA 167 7.58e+01 1vbiA 344 7.62e+01 1dlc 584 7.62e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 2fkcA 247 7.67e+01 2f4pA 147 7.75e+01 1w24A 182 7.76e+01 1prn 289 7.83e+01 3prn f.4.3.1 43762 1k0eA 453 7.89e+01 d.161.1.1 67938 1ku0A 388 7.90e+01 c.69.1.18 72994 1agjA 242 7.90e+01 1agjA b.47.1.1 25827 1eokA 290 7.95e+01 1eokA c.1.8.5 28991 1uxxX 133 7.99e+01 b.18.1.10 100169 1acx 108 7.99e+01 2mcm b.1.7.1 22211 1dn1A 594 8.05e+01 1dn1A e.25.1.1 43357 1s9jA 341 8.09e+01 2c1vA 338 8.10e+01 1qj2A 166 8.14e+01 1qj2A 2g5cA 281 8.19e+01 1jq4A 98 8.26e+01 d.15.4.2 67083 2bbvA 363 8.28e+01 2bbvA b.121.4.4 23323 1e8gA 560 8.30e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1pvc3 238 8.34e+01 1aym3 1gmmA 133 8.34e+01 b.18.1.10 65314 1jroA 462 8.35e+01 a.56.1.1,d.15.4.2,d.87.2.1,d.145.1.3 67137,67138,67139,67140 1gsmA 210 8.40e+01 b.1.1.4,b.1.1.4 65535,65536 1uhgA 385 8.42e+01 e.1.1.1 88491 2ncm 99 8.45e+01 2ncm b.1.1.4 21703 2cfeA 162 8.46e+01 1z3qA 200 8.49e+01 1ykfA 352 8.62e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1j6uA 469 8.62e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1shcA 195 8.78e+01 1shcA b.55.1.2 26992 2fm8A 135 8.83e+01 1q8rA 120 8.93e+01 d.79.6.1 96225 1gttA 429 8.95e+01 d.177.1.1,d.177.1.1 70529,70530 1ovaA 386 8.98e+01 1ovaA e.1.1.1 42619 1ew4A 106 8.98e+01 1ew4A d.82.2.1 40023