# 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 1zpwX 90 5.99e-15 1uw1A 80 9.38e-03 k.42.1.1 100069 1gyxA 76 1.36e-01 d.80.1.1 76387 1vdxA 184 1.98e-01 1oz9A 150 2.57e-01 d.92.1.15 93808 1vgjA 184 2.87e-01 1z08A 170 3.26e-01 1m7bA 184 3.42e-01 c.37.1.8 74572 1huqA 164 3.93e-01 1byuA c.37.1.8 32020 1ydyA 356 4.48e-01 1r2qA 170 4.98e-01 c.37.1.8 96874 1n6hA 170 5.04e-01 c.37.1.8 80197 2bcgY 206 5.57e-01 1ukvY 206 6.26e-01 c.37.1.8 107918 1t8qA 336 7.38e-01 c.1.18.3 106669 1wzcA 249 7.43e-01 1d3uA 181 7.90e-01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1ta9A 450 1.10e+00 1aisA 182 1.16e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1fmcA 255 1.17e+00 1cydA c.2.1.2 29856 1han 297 1.19e+00 1han d.32.1.3,d.32.1.3 38506,38507 1pczA 191 1.33e+00 1ytbA d.129.1.1,d.129.1.1 41292,41293 1mo2A 294 1.41e+00 c.69.1.22 79331 1lgtA 297 1.43e+00 d.32.1.3,d.32.1.3 77956,77957 1lkdA 297 1.44e+00 d.32.1.3,d.32.1.3 78059,78060 1z0jA 170 1.48e+00 1mfiA 114 1.62e+00 1dptA d.80.1.3 39856 1gd0A 122 1.69e+00 1dptA d.80.1.3 39834 1cx4A 305 1.73e+00 b.82.3.2,b.82.3.2 59099,59100 1sr9A 644 1.95e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1hv8A 367 2.00e+00 1hv8A c.37.1.19,c.37.1.19 32405,32406 2gdqA 382 2.18e+00 1sqgA 429 2.81e+00 a.79.1.3,c.66.1.38 105912,105913 1v72A 356 2.89e+00 2bmeA 186 3.16e+00 3rabA 169 3.21e+00 1ctqA c.37.1.8 32018 1gifA 115 3.29e+00 1dptA d.80.1.3 39837 1txuA 273 3.64e+00 a.222.1.1 107439 1z3eA 132 3.75e+00 5ukdA 194 3.83e+00 1zin c.37.1.1 31851 1d5cA 162 3.90e+00 1ctqA c.37.1.8 32021 1hfoA 113 4.19e+00 d.80.1.3 61006 1b4qA 105 4.22e+00 1kte c.47.1.1 32773 1ycrA 109 4.45e+00 1ycqA a.42.1.1 17420 2a5jA 191 4.62e+00 1qf9A 194 4.71e+00 1zin c.37.1.1 31848 1ek0A 170 4.94e+00 1ctqA c.37.1.8 32076 1jflA 228 5.28e+00 c.78.2.1,c.78.2.1 71656,71657 1nbwB 117 5.49e+00 c.51.3.2 80396 1vl4A 447 6.15e+00 d.283.1.1 108718 1iruK 201 6.55e+00 d.153.1.4 71362 1nhkL 144 6.79e+00 1npk d.58.6.1 39142 1m5wA 243 6.98e+00 c.1.24.1 84836 1ho1A 242 7.33e+00 1ho1A c.1.24.1 61097 1dptA 117 7.56e+00 1dptA d.80.1.3 39862 1p9qC 256 8.21e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1eypA 222 8.34e+00 1eypA d.36.1.1 38536 2fafA 608 8.73e+00 1vllA 334 8.74e+00 c.2.1.13 108834 1eyqA 222 9.19e+00 1eypA d.36.1.1 38534 1jepA 222 9.26e+00 d.36.1.1 66612 1omoA 322 9.30e+00 c.2.1.13 104017 2axiA 115 9.93e+00 1regX 122 1.02e+01 1regX d.58.27.1 39406 1i19A 561 1.05e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1amoA 615 1.06e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 1y1xA 191 1.07e+01 1gpc 218 1.08e+01 1gpc b.40.4.7 25393 1ae1A 273 1.09e+01 1bdb c.2.1.2 29943 1t4fM 110 1.11e+01 1td5A 202 1.15e+01 d.110.2.2 106767 1x3sA 195 1.18e+01 2ae2A 260 1.18e+01 1bdb c.2.1.2 29945 1cxqA 162 1.18e+01 1cxqA c.55.3.2 33621 1ve4A 206 1.21e+01 1bvsB 203 1.21e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1ughI 82 1.24e+01 1ugiA d.17.5.1 38133 1tllA 688 1.25e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1asu 162 1.27e+01 1cxqA c.55.3.2 33626 2fu4A 83 1.27e+01 1otfA 62 1.28e+01 1otfA d.80.1.1 39820 1uu1A 335 1.28e+01 c.67.1.1 99993 1e0cA 271 1.29e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1v4pA 157 1.30e+01 1ja1A 622 1.30e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1adjA 421 1.34e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1seiA 130 1.35e+01 1seiA d.140.1.1 41463 1a5v 162 1.36e+01 1cxqA c.55.3.2 33629 1q9uA 130 1.37e+01 d.129.7.1 96314 1ohvA 472 1.40e+01 c.67.1.4 93031 1w2xA 758 1.41e+01 c.14.1.4,c.14.1.4 109134,109135 1h4vB 421 1.42e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1aua 296 1.43e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1f20A 435 1.44e+01 b.43.4.1,c.25.1.4 64932,64933 2gf9A 189 1.45e+01 1v7oA 165 1.47e+01 d.67.1.2 100480 1hgeB 175 1.49e+01 1hgeB h.3.1.1 45680 1t95A 240 1.50e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1rypJ 204 1.52e+01 d.153.1.4 41878 1od2A 805 1.59e+01 c.14.1.4,c.14.1.4 86821,86822 1oixA 191 1.60e+01 1dgsA 667 1.67e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1jsxA 207 1.69e+01 c.66.1.20 71846 1qysA 106 1.70e+01 k.41.1.1 96603 1mxiA 160 1.77e+01 c.116.1.1 79646 1vl5A 260 1.81e+01 c.66.1.41 108720 1gtxA 472 1.83e+01 1gtxA 1ba1 386 1.85e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 2be4A 272 1.85e+01 1cfpA 92 1.90e+01 1b4cA a.39.1.2 17172 1kay 381 1.93e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1fseA 74 1.93e+01 1fseA a.4.6.2 60000 1uyrA 737 1.99e+01 c.14.1.4,c.14.1.4 100188,100189 1ats 386 2.02e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1cczA 171 2.05e+01 1cczA b.1.1.1,b.1.1.3 19758,21683 1s5jA 847 2.09e+01 1hpm 386 2.10e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1s0yB 71 2.11e+01 d.80.1.1 98315 1g0uI 205 2.12e+01 d.153.1.4 41891 1ju5A 109 2.15e+01 d.93.1.1 77173 1vsd 152 2.17e+01 1cxqA c.55.3.2 33625 1vm8A 534 2.18e+01 2cq2A 114 2.19e+01 1kw3B 292 2.23e+01 d.32.1.3,d.32.1.3 77549,77550 1itpA 77 2.23e+01 d.58.3.2 66371 1hqsA 423 2.23e+01 1iso c.77.1.1 61154 1y8cA 246 2.23e+01 1gtdA 85 2.24e+01 d.284.1.1 76344 1iyxA 432 2.25e+01 c.1.11.1,d.54.1.1 83815,83816 1zlmA 58 2.27e+01 1a2zA 220 2.29e+01 1a2zA c.56.4.1 33794 1oe0A 230 2.31e+01 c.37.1.1 92788 1uslA 170 2.33e+01 c.121.1.1 99871 2a1kA 233 2.37e+01 1ukz 203 2.38e+01 1zin c.37.1.1 31840 1zckA 154 2.41e+01 2fueA 262 2.41e+01 1lfpA 249 2.41e+01 e.39.1.1 73885 1a9xB 379 2.44e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1n81A 186 2.44e+01 a.185.1.1 85388 1oivA 191 2.45e+01 c.37.1.8 93076 2f15A 96 2.46e+01 2cw8A 537 2.48e+01 1cs0B 382 2.49e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1ufmA 84 2.50e+01 a.4.5.47 107816 2viuB 175 2.56e+01 1hgeB h.3.1.1 45676 2bgkA 278 2.57e+01 1c3oB 382 2.57e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 3hmgB 175 2.58e+01 1hgeB h.3.1.1 45704 1us5A 314 2.58e+01 c.94.1.1 99856 1m7vA 363 2.58e+01 d.174.1.1 78748 1dhy 292 2.66e+01 1han d.32.1.3,d.32.1.3 38504,38505 1jq5A 370 2.67e+01 e.22.1.2 67084 1xqiA 195 2.69e+01 1wznA 252 2.71e+01 1edoA 244 2.74e+01 1ybvA c.2.1.2 29896 1gz2A 142 2.75e+01 d.169.1.1 83392 2fq3A 104 2.82e+01 1c30B 382 2.86e+01 c.8.3.1,c.23.16.1 30736,31413 1uujA 88 2.88e+01 a.221.1.1 108046 1dcoA 104 2.90e+01 1dcpA d.74.1.1 39680 1jqaA 370 2.96e+01 e.22.1.2 67085 1b04A 318 2.97e+01 1b04A d.142.2.2 41579 1jsdB 176 3.04e+01 h.3.1.1 63259 1t6t1 118 3.09e+01 2f9lA 199 3.09e+01 1tvlA 454 3.10e+01 c.1.16.4 107366 1pq1A 196 3.10e+01 f.1.4.1 94986 1e6mA 128 3.12e+01 3chy c.23.1.1 31039 1kkhA 317 3.13e+01 d.14.1.5,d.58.26.3 72645,72646 1e5uI 187 3.14e+01 1f00I b.1.14.1,d.169.1.3 22372,42441 1vgwA 231 3.18e+01 c.68.1.13 100612 1dcpA 104 3.25e+01 1dcpA d.74.1.1 39672 1wfxA 186 3.32e+01 1jbeA 128 3.35e+01 3chy c.23.1.1 62845 3chy 128 3.39e+01 3chy c.23.1.1 31038 1v5iB 76 3.41e+01 1kafA 108 3.42e+01 d.199.1.1 68372 1mwwA 128 3.42e+01 d.80.1.4 91483 1vb3A 428 3.44e+01 1cye 129 3.59e+01 3chy c.23.1.1 31077 1eayC 74 3.60e+01 1eayC d.58.24.1 39386 2ftxB 64 3.61e+01 2c1gA 431 3.63e+01 1kte 105 3.64e+01 1kte c.47.1.1 32771 2aexA 346 3.64e+01 1fs1B 141 3.66e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 2d1eA 248 3.66e+01 1914 232 3.67e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1eqnA 321 3.71e+01 1dd9A e.13.1.1 43256 1vp4A 425 3.72e+01 1e8aA 91 3.76e+01 1b4cA a.39.1.2 17188 1jhb 106 3.78e+01 1kte c.47.1.1 32772 1lyp 32 3.80e+01 1lyp j.17.1.1 46169 1fukA 165 3.81e+01 1fukA c.37.1.19 32409 1o63A 219 3.81e+01 c.94.1.1 92540 1dd9A 338 3.82e+01 1dd9A e.13.1.1 43254 1jkeA 145 3.83e+01 c.110.1.1 66791 1w1oA 534 3.85e+01 d.58.32.4,d.145.1.1 109071,109072 2arkA 188 3.89e+01 1kfuL 699 3.91e+01 a.39.1.8,b.14.1.1,d.3.1.3 68571,68572,68573 4tmkA 213 3.91e+01 5tmpA c.37.1.1 31930 1b7nA 130 3.97e+01 3lzt d.2.1.2 36468 1konA 249 3.98e+01 e.39.1.1 72823 1fo1A 271 4.00e+01 1fo1A c.10.2.3,d.58.7.2 30869,39213 2fiuA 99 4.04e+01 1pzgA 331 4.04e+01 c.2.1.5,d.162.1.1 95425,95426 1rboC 123 4.09e+01 1rboC d.73.1.1 39634 2c1iA 431 4.10e+01 5tmpA 213 4.10e+01 5tmpA c.37.1.1 31931 2ahjA 206 4.10e+01 2ahjA d.149.1.1 41772 1d1rA 116 4.11e+01 1d1rA d.64.1.1 39548 1htmB 138 4.14e+01 1htmB h.3.1.1 45677 8rucI 123 4.14e+01 1rboC d.73.1.1 39629 1uc2A 481 4.15e+01 d.261.1.1 99161 1ab6A 125 4.18e+01 3chy c.23.1.1 31054 1bo1A 416 4.21e+01 1bo1A d.143.1.2 41591 1wwhA 119 4.32e+01 1x24A 180 4.33e+01 2ahjC 206 4.36e+01 2ahjA d.149.1.1 41773 5csmA 256 4.36e+01 5csmA a.130.1.2 19494 1rypF 233 4.38e+01 1rypF d.153.1.4 41937 1eps 427 4.46e+01 1eps d.68.2.2 39586 2bh7A 261 4.48e+01 1nxiA 132 4.58e+01 d.58.47.1 86381 1yb2A 275 4.61e+01 1gdeA 389 4.75e+01 c.67.1.1 60456 2cz1A 206 4.76e+01 1jbiA 100 4.80e+01 d.209.1.1 66481 1dt9A 437 4.80e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1q8bA 105 4.83e+01 d.58.4.6 96201 1hi9A 274 4.86e+01 1hi9A c.99.1.1 61063 1bb9 115 4.90e+01 1bb9 b.34.2.1 24554 1u55A 188 4.94e+01 d.278.1.1 107677 1vljA 407 5.00e+01 e.22.1.2 108832 1ug8A 87 5.03e+01 d.68.7.1 107825 1mp9A 198 5.03e+01 d.129.1.1,d.129.1.1 91385,91386 1dchA 104 5.04e+01 1dcpA d.74.1.1 39692 1dw0A 112 5.06e+01 1dw0A a.3.1.1 15911 1bfmA 69 5.20e+01 1a7w a.22.1.2 16479 1a4yB 123 5.24e+01 7rsa d.5.1.1 37296 1atr 386 5.28e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1zm7A 230 5.29e+01 1uarA 285 5.30e+01 c.46.1.2,c.46.1.2 107762,107763 1bupA 386 5.33e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1w6tA 444 5.36e+01 1l9vA 317 5.39e+01 d.13.2.1,d.216.1.1 73760,73761 2a1iA 146 5.40e+01 1hxhA 253 5.41e+01 c.2.1.2 76725 1knmA 130 5.44e+01 b.42.2.1 72781 1gd9A 389 5.44e+01 c.67.1.1 60454 1f93A 104 5.48e+01 1dcpA d.74.1.1 39688 1iqsA 88 5.49e+01 d.214.1.1 71278 1l0qA 391 5.51e+01 b.1.3.1,b.69.2.3 77644,77645 1a2n 419 5.52e+01 1uae d.68.2.2 39575 1vjpA 394 5.61e+01 c.2.1.3,d.81.1.3 100828,100829 1zj8A 566 5.70e+01 1dkvA 699 5.73e+01 1dkvA 1a0oD 134 5.74e+01 1eayC d.58.24.1 39391 2c9wA 169 5.76e+01 1zhsA 113 5.83e+01 2g6bA 180 5.84e+01 1zroA 602 5.85e+01 1g6sA 427 5.86e+01 1eps d.68.2.2 39584 2breA 219 5.88e+01 1ycqA 107 5.92e+01 1ycqA a.42.1.1 17419 1o5xA 248 5.93e+01 c.1.1.1 92528 1xviA 275 5.93e+01 1lkxA 697 5.96e+01 c.37.1.9 73981 1ceqA 316 5.98e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 1uae 419 6.04e+01 1uae d.68.2.2 39574 1vmeA 410 6.05e+01 c.23.5.1,d.157.1.3 108893,108894 1zud2 66 6.05e+01 1ru0A 105 6.12e+01 1nox 205 6.13e+01 1nox d.90.1.1 40242 1v7rA 186 6.17e+01 c.51.4.1 100482 1j90A 230 6.19e+01 c.37.1.1 66448 1y0vH 146 6.23e+01 2c71A 216 6.23e+01 1ejdA 419 6.27e+01 1uae d.68.2.2 39576 2b9eA 303 6.29e+01 1yucA 255 6.32e+01 2bgcA 238 6.35e+01 1hta 69 6.35e+01 1a7w a.22.1.2 16476 1qs2A 401 6.36e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1r5qA 102 6.39e+01 a.186.1.1 97103 1qu9A 128 6.42e+01 1qu9A d.79.1.1 39755 1qu9C 128 6.42e+01 1qu9A d.79.1.1 39757 1rxdA 159 6.43e+01 1nz0A 118 6.44e+01 d.14.1.2 86433 1go3F 107 6.45e+01 a.60.8.2 65407 1jnyA 435 6.46e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1e5rA 290 6.48e+01 1e5rA b.82.2.4 59276 1vi0A 206 6.49e+01 a.4.1.9,a.121.1.1 100720,100721 1x2kA 68 6.52e+01 1ugjA 141 6.53e+01 b.41.1.3 107826 1b67A 68 6.56e+01 1a7w a.22.1.2 16474 2cx1A 187 6.67e+01 1pk5A 248 6.68e+01 a.123.1.1 88139 2co5A 99 6.73e+01 2fl4A 149 6.82e+01 1a3qA 285 6.88e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1ipaA 274 6.88e+01 c.116.1.1,d.79.3.3 71254,71255 1ekeA 230 6.94e+01 1ekeA c.55.3.1 33572 1vcvA 226 6.94e+01 1v71A 323 6.94e+01 1nra 63 6.95e+01 1aho g.3.7.1 44126 1t2dA 322 7.12e+01 c.2.1.5,d.162.1.1 99084,99085 1y44A 320 7.15e+01 1agnA 373 7.20e+01 2ohxA b.35.1.2,c.2.1.1 24737,29753 2ex4A 241 7.20e+01 1x46A 150 7.22e+01 1rypI 222 7.27e+01 d.153.1.4 41877 1v7zA 260 7.35e+01 c.125.1.1 100488 1rw1A 114 7.36e+01 1r4wA 226 7.46e+01 c.47.1.13 97050 2gu3A 136 7.47e+01 2bb2 181 7.48e+01 2bb2 b.11.1.1,b.11.1.1 23604,23605 1tz0A 114 7.49e+01 d.58.4.5 107463 1s6yA 450 7.51e+01 c.2.1.5,d.162.1.2 105314,105315 1ldg 316 7.53e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1mw7A 240 7.54e+01 e.39.1.1 79557 1ffkM 148 7.55e+01 1ffkM a.94.1.1 18740 1dqnA 230 7.58e+01 1dqnA c.61.1.1 34067 1lyxA 248 7.62e+01 c.1.1.1 78304 1ytfB 53 7.62e+01 1ytfB a.32.1.1 16997 1yzqA 170 7.64e+01 1dqpA 230 7.64e+01 1dqnA c.61.1.1 34069 2g19A 244 7.66e+01 1ytqA 204 7.67e+01 1g0uE 234 7.72e+01 d.153.1.4 41950 1jh6A 189 7.77e+01 d.61.1.1 66707 1hr6B 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