# List of top-scoring protein chains for t04-100-30-dssp-ebghstl-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 5.42e-05 d.15.3.1 108631 1xlqA 106 1.03e-03 1oqqA 106 1.07e-03 d.15.4.1 93422 1frrA 95 1.05e-02 1awd d.15.4.1 37674 1qorA 327 1.39e-02 1qorA b.35.1.2,c.2.1.1 24766,29782 1ryjA 70 1.49e-02 d.15.3.2 98104 1e9mA 106 2.42e-02 1ayfA d.15.4.1 59397 1uwmA 106 2.45e-02 2bb6A 414 2.59e-02 1zud2 66 5.58e-02 2bwfA 77 7.17e-02 1yb5A 351 8.78e-02 2bpsA 81 9.14e-02 1rwsA 77 9.65e-02 d.15.3.2 97991 1fm0D 81 1.31e-01 1fmaD d.15.3.1 37642 1dmhA 311 1.61e-01 1dmhA b.3.6.1 22633 2cu3A 64 1.94e-01 1lfdA 87 2.58e-01 1lfdA d.15.1.5 37622 1wjnA 97 3.14e-01 1frd 98 3.32e-01 1awd d.15.4.1 37648 1awd 94 3.56e-01 1awd d.15.4.1 37673 1c1yB 77 4.71e-01 1c1yB d.15.1.5 37618 1nbfD 76 6.38e-01 d.15.1.1 80390 1yj1A 76 7.54e-01 1ryaA 160 7.56e-01 d.113.1.5 105122 1ib8A 164 8.42e-01 b.38.2.1,d.52.4.1 71168,71169 1eb7A 323 8.54e-01 1eb7A a.3.1.5,a.3.1.5 59404,59405 1r3eA 309 8.75e-01 b.122.1.1,d.265.1.2 96907,96908 1ubi 76 9.30e-01 1ubi d.15.1.1 37584 1uh6A 100 9.88e-01 d.15.1.1 99394 1offA 97 1.04e+00 d.15.4.1 86947 1o5oA 221 1.16e+00 c.61.1.1 92509 1wgrA 100 1.19e+00 1vcbA 118 1.25e+00 1vcbA d.15.1.1 37603 1i7hA 111 1.30e+00 d.15.4.1 71122 1ogwA 76 1.38e+00 d.15.1.1 87001 1a70 97 1.39e+00 1awd d.15.4.1 37678 1czpA 98 1.40e+00 1awd d.15.4.1 37645 1lm8B 118 1.41e+00 d.15.1.1 74033 1se9A 126 1.47e+00 d.15.1.1 98821 1l5pA 93 1.51e+00 d.15.4.1 73598 2al3A 90 1.69e+00 2fnjB 118 1.71e+00 1doi 128 1.78e+00 1awd d.15.4.1 37676 1s0uA 408 1.82e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1rfkA 98 1.83e+00 1ra6A 461 1.92e+00 e.8.1.4 104879 2c5lC 117 2.05e+00 1jenA 267 2.06e+00 1jenA 2aj2A 208 2.10e+00 1ayfA 105 2.11e+00 1ayfA d.15.4.1 37684 2bt6A 108 2.20e+00 1dg6A 191 2.25e+00 1d4vB b.22.1.1 23883 1t6aA 126 2.47e+00 d.129.8.1 106555 1k07A 263 2.88e+00 d.157.1.1 77218 1e6eB 128 2.90e+00 1ayfA d.15.4.1 59300 1jj2H 167 2.94e+00 1ffkF d.41.4.1 63093 1yqbA 100 3.22e+00 2fcfA 103 3.22e+00 1u3wA 374 3.25e+00 1wwtA 88 3.31e+00 2ohxA 374 3.36e+00 2ohxA b.35.1.2,c.2.1.1 24669,29685 1zu0A 529 3.94e+00 1t0qC 86 3.98e+00 d.15.12.1 106222 2a4hA 126 4.44e+00 1pvmA 184 4.61e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1b9rA 105 4.68e+00 1ayfA d.15.4.1 37683 2fcr 173 4.73e+00 1rcf c.23.5.1 31151 1ws8A 109 4.78e+00 1euvB 86 5.02e+00 1a5r d.15.1.1 37598 1l2hA 153 5.04e+00 b.42.1.2 77655 2apoA 357 5.17e+00 1l7yA 94 5.54e+00 d.15.1.6 73676 1f1xA 322 5.70e+00 d.32.1.3,d.32.1.3 83208,83209 1tmxA 293 5.86e+00 1p99A 295 5.87e+00 c.94.1.1 94384 1vybA 238 6.05e+00 d.151.1.1 108897 1n8kA 374 6.16e+00 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 6.18e+00 2ohxA b.35.1.2,c.2.1.1 60975,60976 1ooyA 481 7.15e+00 c.124.1.3,c.124.1.2 93388,93389 1rdr 461 7.18e+00 1rdr e.8.1.4 43116 2b5wA 357 7.21e+00 1f1uA 323 8.12e+00 d.32.1.3,d.32.1.3 83200,83201 1knmA 130 8.16e+00 b.42.2.1 72781 1k8wA 327 8.33e+00 b.122.1.1,d.265.1.2 83094,90388 1fsz 372 8.78e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1siqA 392 9.07e+00 a.29.3.1,e.6.1.1 105585,105586 2fazA 78 9.28e+00 2g1lA 104 9.46e+00 1k7hA 476 9.76e+00 c.76.1.1 72101 1v2yA 105 9.78e+00 d.15.1.1 100275 2azwA 148 1.04e+01 2pia 321 1.07e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1mh1 186 1.10e+01 1eesA c.37.1.8 32002 1z06A 189 1.11e+01 2c1vA 338 1.17e+01 1xc3A 302 1.21e+01 1z2mA 155 1.24e+01 1shsA 147 1.25e+01 1shsA b.15.1.1 23675 1wm3A 72 1.31e+01 1sg1X 161 1.33e+01 g.24.1.1,g.24.1.1,g.24.1.1,g.24.1.1 105515,105516,105517,105518 1snzA 344 1.33e+01 b.30.5.4 98930 1so9A 164 1.35e+01 b.146.1.1 105842 1omzA 293 1.37e+01 c.68.1.15 87093 2fm8A 135 1.39e+01 1pt6A 213 1.43e+01 c.62.1.1 95091 1x8bA 289 1.46e+01 1d2eA 397 1.47e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1jl0A 334 1.47e+01 1jenA d.156.1.1 63155 1cnzA 363 1.48e+01 1cnzA c.77.1.1 35061 1pl8A 356 1.52e+01 b.35.1.2,c.2.1.1 94878,94879 1yqzA 438 1.54e+01 2b0vA 153 1.55e+01 1v86A 95 1.58e+01 d.15.1.1 108421 1ku0A 388 1.59e+01 c.69.1.18 72994 1t3qA 168 1.62e+01 a.56.1.1,d.15.4.2 106367,106368 1p0fA 373 1.67e+01 b.35.1.2,c.2.1.1 87642,87643 1cf2O 337 1.67e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2i1b 153 1.69e+01 2i1b b.42.1.2 25538 2gaxA 135 1.81e+01 1xi1A 575 1.81e+01 2h3lA 103 1.83e+01 1nytA 271 1.87e+01 c.2.1.7,c.58.1.5 86417,86418 1vmiA 355 1.91e+01 2f4pA 147 2.01e+01 2f69A 261 2.02e+01 1uuqA 440 2.03e+01 c.1.8.3 100015 1q8rA 120 2.03e+01 d.79.6.1 96225 1y0bA 197 2.04e+01 1zx8A 136 2.08e+01 1pvc3 238 2.10e+01 1aym3 1twuA 139 2.10e+01 d.32.1.8 107413 1h0hA 977 2.14e+01 b.52.2.2,c.81.1.1 76435,76436 2fug1 438 2.19e+01 2bzoB 79 2.22e+01 1iyjB 817 2.26e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 1ihjA 98 2.26e+01 1pdr b.36.1.1 62382 1woqA 267 2.27e+01 c.55.1.10,c.55.1.10 109462,109463 1w3iA 293 2.30e+01 c.1.10.1 109152 1tjxA 159 2.35e+01 1b9mA 265 2.35e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1bbhA 131 2.37e+01 1bbhA a.24.3.2 16546 1r5lA 262 2.38e+01 a.5.3.1,c.13.1.1 97099,97100 1vc3B 97 2.47e+01 1vhzA 198 2.47e+01 d.113.1.1 100718 1agjA 242 2.50e+01 1agjA b.47.1.1 25827 1e0gA 48 2.53e+01 1e01A d.7.1.1 37325 2fqmA 75 2.53e+01 1b4rA 80 2.57e+01 1b4rA b.1.3.1 22072 1q1oA 98 2.59e+01 d.15.2.2 95596 1z6bA 154 2.59e+01 1qlaB 239 2.69e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1p4oA 322 2.71e+01 d.144.1.7 87775 1f06A 320 2.74e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1iueA 98 2.77e+01 d.15.4.1 90697 2fsqA 243 2.84e+01 1oqyA 368 2.86e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1zy4A 303 2.86e+01 1yqgA 263 2.90e+01 1fvrA 327 2.90e+01 d.144.1.7 60047 1ni3A 392 2.93e+01 c.37.1.8,d.15.10.2 80531,80532 1ygs 234 2.97e+01 1ygs b.26.1.1 23907 1whvA 100 2.98e+01 1mgpA 313 3.03e+01 c.119.1.1 79098 2cfeA 162 3.07e+01 1v5mA 136 3.08e+01 b.55.1.1 108379 1bt0A 76 3.08e+01 1ubi d.15.1.1 37607 2gupA 292 3.15e+01 2bolA 314 3.16e+01 1mfgA 95 3.17e+01 b.36.1.1 79043 2gptA 523 3.18e+01 1s9jA 341 3.18e+01 1nw1A 429 3.18e+01 d.144.1.8 86286 1uowA 159 3.19e+01 b.7.1.2 107975 1j5yA 187 3.22e+01 a.4.5.1,d.94.2.1 71592,71593 1pcxA 810 3.23e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1n6aA 259 3.27e+01 b.76.2.1,b.85.7.1 80121,80122 1xe1A 116 3.27e+01 b.43.3.1 109571 1vr6A 350 3.30e+01 1sacA 204 3.31e+01 1sacA b.29.1.5 24237 2c27A 315 3.34e+01 1h9sA 140 3.39e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2btzA 394 3.44e+01 1wb4A 297 3.50e+01 1eudB 396 3.61e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1ofuA 320 3.62e+01 c.32.1.1,d.79.2.1 86972,86973 1vioA 243 3.65e+01 d.265.1.3,d.66.1.5 100762,100763 1zvtA 256 3.78e+01 1gklA 297 3.79e+01 c.69.1.2 65250 1zpuA 534 3.81e+01 1bf6A 291 3.85e+01 1pscA c.1.9.3 29065 1tygB 87 3.88e+01 d.15.3.2 107455 1ypyA 184 3.88e+01 1befA 181 3.88e+01 1befA b.47.1.3 26419 2fp4B 395 3.95e+01 1vr9A 213 3.97e+01 1sfe 180 3.98e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1wruA 379 3.99e+01 1n62A 166 4.01e+01 a.56.1.1,d.15.4.2 80090,80091 1uovA 159 4.06e+01 b.7.1.2 107974 1ty0A 211 4.07e+01 b.40.2.2,d.15.6.1 107440,107441 1wriA 93 4.09e+01 1g5cA 170 4.09e+01 1g5cA c.53.2.1 60264 1dljA 402 4.11e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1t71A 281 4.11e+01 1krhA 338 4.12e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1msk 331 4.21e+01 1msk d.173.1.1 42495 1ad2 228 4.22e+01 1ad2 e.24.1.1 43353 1j3mA 129 4.24e+01 d.129.7.1 103836 1inlA 296 4.25e+01 c.66.1.17 66220 2ghpA 292 4.26e+01 1jb3A 131 4.27e+01 1jc7A b.40.3.2 62833 1rm6C 161 4.33e+01 3pcgA 200 4.34e+01 3pchA b.3.6.1 22647 1kqfC 217 4.38e+01 f.21.1.1 72874 1k0eA 453 4.39e+01 d.161.1.1 67938 2bkrB 77 4.45e+01 1qc5A 192 4.46e+01 1aoxA c.62.1.1 34147 1e6pA 499 4.56e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1ey4A 149 4.57e+01 1snc b.40.1.1 24815 1uxy 340 4.60e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 2h2bA 107 4.62e+01 1c4zA 358 4.67e+01 1c4zA d.148.1.1 41766 1i2aA 219 4.68e+01 e.24.1.1 90660 1uqtA 482 4.70e+01 c.87.1.6 99794 1u94A 356 4.73e+01 c.37.1.11,d.48.1.1 107743,107744 1oruA 195 4.74e+01 b.58.1.2 93464 1aqzA 149 4.76e+01 1aqzA d.1.1.3 36238 1b1cA 181 4.79e+01 1amoA c.23.5.2 31212 2bh1A 250 4.82e+01 1owfB 94 4.93e+01 a.55.1.1 87488 1q4rA 112 4.94e+01 d.58.4.4 95823 1cxyA 90 4.98e+01 1cyo d.120.1.1 41085 1lxiA 139 5.04e+01 g.17.1.2 84735 1avbA 226 5.07e+01 1led b.29.1.1 24158 1x8qA 184 5.07e+01 1yopA 83 5.15e+01 1eokA 290 5.19e+01 1eokA c.1.8.5 28991 2act 220 5.21e+01 1cs8A d.3.1.1 37002 1ktgA 138 5.21e+01 d.113.1.1 72972 2fr1A 486 5.23e+01 1goiA 499 5.27e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1kepA 348 5.28e+01 c.2.1.2 68536 1rkuA 206 5.28e+01 c.108.1.11 97627 1k94A 165 5.30e+01 a.39.1.8 68333 2a5kA 307 5.31e+01 2reb 352 5.32e+01 2reb c.37.1.11,d.48.1.1 32282,38767 2b7aA 293 5.34e+01 1meoA 209 5.35e+01 c.65.1.1 79035 1t9fA 187 5.42e+01 b.42.6.1 106710 1j4nA 271 5.51e+01 f.19.1.1 71510 1j7gA 144 5.51e+01 c.110.1.1 84130 1zq7A 207 5.55e+01 1wmzA 140 5.56e+01 d.169.1.1 109422 1f4qA 165 5.57e+01 1alvA a.39.1.8 17360 1udkA 51 5.58e+01 g.3.14.1 99211 1gvp 87 5.65e+01 1gvp b.40.4.7 25369 1vqb 87 5.65e+01 1gvp b.40.4.7 25370 1fiqB 350 5.67e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1ng2A 193 5.73e+01 b.34.2.1,b.34.2.1 85660,85661 1kk1A 410 5.73e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1yqtA 538 5.77e+01 1w5fA 353 5.82e+01 1zbtA 371 5.82e+01 1zavA 180 5.94e+01 1o50A 157 5.95e+01 d.37.1.1,d.37.1.1 92478,92479 1i0rA 169 5.96e+01 1i0rA b.45.1.2 61489 1i0sA 169 5.96e+01 1i0rA b.45.1.2 61491 2bmaA 470 6.11e+01 1g0sA 209 6.12e+01 1g0sA d.113.1.1 60187 2c8mA 262 6.15e+01 1svvA 359 6.19e+01 c.67.1.1 106054 1p0hA 318 6.21e+01 d.108.1.1 93866 1x1mA 107 6.21e+01 1jer 138 6.27e+01 2cbp b.6.1.1 23022 2as0A 396 6.34e+01 1oc2A 348 6.37e+01 c.2.1.2 92765 1rwxA 178 6.41e+01 1qmyA 167 6.43e+01 1qmyA d.3.1.2 37094 2fd4A 122 6.45e+01 1dxy 333 6.45e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1sc3A 178 6.49e+01 c.17.1.1 105416 2a6mA 155 6.49e+01 1yf5L 254 6.59e+01 2c2hA 192 6.62e+01 2asuB 234 6.65e+01 1mr3F 181 6.68e+01 c.37.1.8 79422 1o54A 277 6.71e+01 c.66.1.13 92482 1ubeA 349 6.76e+01 c.37.1.11,d.48.1.1 88412,88413 1nddA 76 6.90e+01 1ubi d.15.1.1 37599 1jx4A 352 6.91e+01 d.240.1.1,e.8.1.7 90378,90379 1qlaC 256 6.92e+01 1qlaC f.21.2.1 43722 1a4sA 503 6.98e+01 1bpwA c.82.1.1 35361 1xqwA 293 7.06e+01 1hc7A 477 7.09e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2fn4A 181 7.13e+01 2ervA 150 7.14e+01 2d7nA 93 7.20e+01 1auiA 521 7.21e+01 1auiA d.159.1.3 42085 1zn8A 180 7.25e+01 1xgsA 295 7.26e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2fyxA 143 7.29e+01 2cyjA 118 7.42e+01 2ex2A 458 7.48e+01 2aefA 234 7.56e+01 2h0eA 121 7.57e+01 1yzgA 179 7.60e+01 1tksA 204 7.61e+01 d.115.1.2 107114 1rq2A 382 7.65e+01 c.32.1.1,d.79.2.1 105048,105049 1e3jA 352 7.67e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1ghhA 81 7.72e+01 1ghhA d.57.1.1 38940 1koiA 184 7.82e+01 b.60.1.1 68725 1bmqA 167 7.85e+01 1pauA c.17.1.1 30998 2amdA 311 7.88e+01 1q2wA 308 7.88e+01 b.47.1.4 88355 1yarA 233 7.90e+01 2cwzA 141 7.93e+01 1jnyA 435 7.95e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1wl9A 440 7.97e+01 1az9 457 8.01e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1kevA 351 8.04e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1dqaA 467 8.07e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1el6A 219 8.09e+01 1el6B d.182.1.1 42606 1wkaA 147 8.11e+01 1imbA 277 8.21e+01 1imbA e.7.1.1 42957 2cr5A 109 8.23e+01 2hhmA 276 8.26e+01 1imbA e.7.1.1 42955 1erxA 184 8.35e+01 1np1A b.60.1.1 27164 1r31A 428 8.37e+01 d.58.20.1,d.179.1.1 96897,96898 1jqbA 351 8.41e+01 b.35.1.2,c.2.1.1 77151,77152 1xuvA 178 8.45e+01 1k47A 337 8.46e+01 d.14.1.5,d.58.26.4 72040,72041 1prxA 224 8.51e+01 1prxA c.47.1.10 33076 1uptC 170 8.61e+01 c.37.1.8 99769 1n2eA 300 8.64e+01 c.26.1.4 85268 1eejA 216 8.69e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1zldA 120 8.69e+01 1wdkC 390 8.72e+01 c.95.1.1,c.95.1.1 109258,109259 1m93B 245 8.79e+01 2sns 149 8.81e+01 1snc b.40.1.1 24860 1ra9 159 8.87e+01 1vdrA c.71.1.1 34820 2bwvA 440 8.96e+01