# List of top-scoring protein chains for t2k-80-60-80-str2+near-backbone-11-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 1a58 177 6.67e-20 2cpl b.62.1.1 27495 1dywA 173 2.16e-19 2cpl b.62.1.1 27505 2cpl 165 2.40e-19 2cpl b.62.1.1 27420 2rmcA 182 2.58e-19 2cpl b.62.1.1 27491 2bitX 165 3.08e-19 1cwoA 165 3.13e-19 2cpl b.62.1.1 27445 1yndA 165 4.92e-19 1qoiA 177 5.00e-19 2cpl b.62.1.1 27490 1xo7A 166 6.77e-19 1awsA 164 6.96e-19 2cpl b.62.1.1 27431 1zcxA 178 8.96e-19 1awqA 164 9.68e-19 2cpl b.62.1.1 27461 1ihgA 370 1.14e-18 2cpl a.118.8.1,b.62.1.1 62380,62381 2cfeA 162 1.85e-18 1h0pA 182 2.57e-18 b.62.1.1 76450 1vdnA 162 3.29e-18 1zkcA 197 1.99e-16 2a2nA 176 3.47e-16 2fu0A 160 3.47e-16 2b71A 196 7.24e-16 1xwnA 174 4.61e-15 1v9tA 166 3.25e-14 b.62.1.1 108451 1j2aA 166 6.57e-14 b.62.1.1 90779 1lopA 164 2.79e-13 2cpl b.62.1.1 27510 1clh 166 1.03e-11 2cpl b.62.1.1 27512 1zx8A 136 7.33e-02 1rkiA 102 6.45e-01 1m1hA 248 7.35e-01 b.114.1.1,d.58.42.1 78415,78416 2apoA 357 1.74e+00 1mua 256 2.53e+00 2cba b.74.1.1 27831 1fr7A 260 2.93e+00 2cba b.74.1.1 27828 1h3iA 293 3.35e+00 b.76.2.1,b.85.7.1 76635,76636 1lugA 259 3.48e+00 b.74.1.1 91127 12ca 260 4.65e+00 2cba b.74.1.1 27942 2b25A 336 4.66e+00 2a1rA 430 4.80e+00 1pczA 191 4.85e+00 1ytbA d.129.1.1,d.129.1.1 41292,41293 1a4sA 503 4.90e+00 1bpwA c.82.1.1 35361 1yo1A 260 5.10e+00 1d3uA 181 5.41e+00 1ytbA d.129.1.1,d.129.1.1 41290,41291 1jj2E 177 5.55e+00 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1qcsA 211 6.23e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1v5iB 76 6.33e+00 1sxvA 172 6.35e+00 2fxqA 264 6.44e+00 1f6oA 219 7.65e+00 1bnkA b.46.1.2 25763 2cba 260 8.33e+00 2cba b.74.1.1 27821 1vqvA 306 8.38e+00 1caj 260 8.43e+00 2cba b.74.1.1 27841 1ja1A 622 8.45e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 2gvkA 317 8.57e+00 1lniA 96 8.60e+00 d.1.1.2 74046 1cqa 133 8.70e+00 3nul d.110.1.1 40890 1mooA 260 8.86e+00 b.74.1.1 79359 1s72E 178 9.73e+00 d.141.1.1,d.141.1.1 105323,105324 1vqoE 178 1.03e+01 1i8dA 213 1.07e+01 b.43.4.3,b.43.4.3 61953,61954 1mgrA 99 1.08e+01 d.1.1.2 79106 1t5yA 190 1.11e+01 b.122.1.1,d.17.6.3 106495,106496 1k8kD 300 1.12e+01 d.198.2.1,d.198.2.1 68309,68310 1fljA 260 1.16e+01 2cba b.74.1.1 27954 1gnkA 112 1.17e+01 2pii d.58.5.1 39073 1rgeA 96 1.17e+01 1rgeA d.1.1.2 36028 3nul 130 1.18e+01 3nul d.110.1.1 40891 1y7pA 223 1.18e+01 1ab8A 220 1.18e+01 1azsA d.58.29.1 39414 2fr1A 486 1.19e+01 2pii 112 1.25e+01 2pii d.58.5.1 39071 1i8vA 96 1.26e+01 d.1.1.2 61985 1louA 101 1.28e+01 1ris d.58.14.1 39323 1px5A 349 1.29e+01 a.160.1.2,d.218.1.6 95277,95278 2eu9A 355 1.31e+01 1uscA 178 1.36e+01 b.45.1.2 99860 3grs 478 1.36e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 3gcb 470 1.39e+01 3gcb d.3.1.1 37032 2bf6A 449 1.40e+01 1a0k 131 1.46e+01 3nul d.110.1.1 40892 1itpA 77 1.49e+01 d.58.3.2 66371 1vioA 243 1.52e+01 d.265.1.3,d.66.1.5 100762,100763 1gcb 454 1.52e+01 3gcb d.3.1.1 37034 2cwaA 263 1.53e+01 1rc9A 221 1.57e+01 1cqmA 101 1.58e+01 1ris d.58.14.1 39321 1ris 101 1.59e+01 1ris d.58.14.1 39314 1gmpA 96 1.67e+01 1rgeA d.1.1.2 36036 1a6r 471 1.69e+01 3gcb d.3.1.1 37033 4gr1 478 1.71e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30461,30462,40162 1xppA 115 1.77e+01 1rzjG 321 1.79e+01 d.172.1.1 98200 1xipA 388 1.82e+01 1bnkA 216 1.85e+01 1bnkA b.46.1.2 25765 1n7vA 555 1.95e+01 b.126.1.1 85377 1g7vA 284 1.95e+01 1d9eA c.1.10.4 60335 1bpwA 503 1.96e+01 1bpwA c.82.1.1 35365 1gm5A 780 1.99e+01 a.24.21.1,b.40.4.9,c.37.1.19,c.37.1.19 65298,65299,65300,65301 1ckmA 330 2.06e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1xtaA 221 2.07e+01 1ej8A 140 2.08e+01 1qupA b.1.8.1 22300 1pylA 97 2.13e+01 d.1.1.2 104391 1nd4A 264 2.16e+01 d.144.1.6 91815 1konA 249 2.17e+01 e.39.1.1 72823 1xgsA 295 2.19e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1byuA 216 2.21e+01 1byuA c.37.1.8 32032 1g9mG 321 2.26e+01 1gc1G d.172.1.1 42492 2b8eA 273 2.27e+01 1j6qA 136 2.27e+01 b.40.9.1 77091 1f60B 94 2.27e+01 1b64 d.58.12.1 39307 1yymG 313 2.27e+01 1v3rA 116 2.35e+01 2napA 723 2.39e+01 2napA b.52.2.2,c.81.1.1 26926,35334 2pth 193 2.43e+01 2pth c.56.3.1 33793 1kzlA 208 2.43e+01 b.43.4.3,b.43.4.3 77635,77636 1azsB 212 2.49e+01 1azsA d.58.29.1 39423 1brwA 433 2.51e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1qk3A 233 2.56e+01 1qk3A c.61.1.1 34031 1vfjA 116 2.58e+01 1sb2A 133 2.58e+01 1o8bA 219 2.59e+01 c.124.1.4,d.58.40.1 81180,81181 1zoxA 113 2.64e+01 1im5A 180 2.71e+01 c.33.1.3 66211 1uj6A 227 2.73e+01 c.124.1.4,d.58.40.1 107898,107899 1wocA 103 2.73e+01 1cz7A 406 2.74e+01 1bg2 c.37.1.9 32194 2ae0X 345 2.74e+01 1shcA 195 2.80e+01 1shcA b.55.1.2 26992 1nbfA 353 2.84e+01 d.3.1.9 80387 2gfoA 396 2.84e+01 1o51A 114 2.87e+01 d.58.5.4 92480 1f0xA 571 2.93e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1b7fA 168 2.98e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1wlsA 328 3.00e+01 1xsnA 335 3.01e+01 1ffk1 177 3.06e+01 1ffk1 1k8wA 327 3.07e+01 b.122.1.1,d.265.1.2 83094,90388 2b4wA 315 3.10e+01 3pmgA 561 3.11e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1gctA 245 3.11e+01 5ptp b.47.1.2 26021 1g99A 408 3.14e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1h9mA 145 3.14e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1yoaA 159 3.14e+01 1iujA 106 3.15e+01 d.58.4.5 90701 1gsoA 431 3.16e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1ltlA 279 3.21e+01 b.40.4.11 84701 1umuB 116 3.23e+01 1umuA b.87.1.1 28383 1u0sA 86 3.24e+01 d.58.24.1 107565 1ewnA 219 3.27e+01 1bnkA b.46.1.2 25762 1cjxA 357 3.27e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1vgyA 393 3.34e+01 c.56.5.4,d.58.19.1 100620,100621 2cx7A 130 3.40e+01 1ysjA 404 3.41e+01 1m6iA 493 3.41e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1nnsA 326 3.43e+01 c.88.1.1 85910 2bw2A 140 3.43e+01 2cb2A 318 3.45e+01 1wmqA 147 3.51e+01 1xe7A 203 3.52e+01 1t4hA 290 3.58e+01 d.144.1.7 106420 1juvA 193 3.66e+01 c.71.1.1 90912 1mz5A 638 3.67e+01 b.29.1.15,b.68.1.1 79679,79680 1pbyA 489 3.69e+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 1fl1A 230 3.69e+01 1at3A b.57.1.1 27023 2gaxA 135 3.70e+01 1vpjA 192 3.70e+01 1a2vA 655 3.70e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1zjkA 403 3.71e+01 1iatA 557 3.74e+01 1dqrA c.80.1.2 62123 1aisA 182 3.77e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1ri7A 171 3.78e+01 a.4.5.32,d.58.4.2 97504,97505 1pmy 123 3.82e+01 1bqk b.6.1.1 22888 1g65K 211 3.84e+01 d.153.1.4 41907 1wpuA 147 3.84e+01 1pil 112 3.86e+01 2pii d.58.5.1 39072 1rypL 212 3.87e+01 d.153.1.4 41880 1i4uA 181 3.90e+01 b.60.1.1 61732 1hh1A 143 4.00e+01 1gefA c.52.1.18 61036 1o60A 292 4.04e+01 c.1.10.4 92532 1umgA 362 4.06e+01 d.280.1.1 107956 1qczA 169 4.06e+01 1qczA c.23.8.1 31276 1h9jA 145 4.14e+01 1h9jA b.40.6.2,b.40.6.2 60829,60830 1fxzA 476 4.14e+01 b.82.1.2,b.82.1.2 65059,65060 1g7cB 94 4.14e+01 1b64 d.58.12.1 39308 1gc1G 321 4.14e+01 1gc1G d.172.1.1 42493 1nb8A 353 4.17e+01 d.3.1.9 80385 1zd7A 159 4.19e+01 1np1A 184 4.24e+01 1np1A b.60.1.1 27155 1in0A 163 4.26e+01 d.58.49.1,d.58.49.1 83694,83695 1ei6A 406 4.29e+01 c.76.1.4 90443 1dtyA 429 4.32e+01 1dtyA c.67.1.4 34495 1tjxA 159 4.38e+01 1t77A 414 4.39e+01 2fp4B 395 4.40e+01 1yemA 179 4.41e+01 1fa0B 537 4.44e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 2bcqA 335 4.46e+01 1b6cB 342 4.50e+01 1b6cB d.144.1.7 41673 1iseA 185 4.57e+01 d.67.3.1 90691 1vp4A 425 4.58e+01 1ntyA 311 4.58e+01 a.87.1.1,b.55.1.1 103873,103874 1np4A 184 4.62e+01 1np1A b.60.1.1 27166 1mp9A 198 4.63e+01 d.129.1.1,d.129.1.1 91385,91386 1wgbA 159 4.65e+01 1s99A 200 4.72e+01 1dqrA 557 4.80e+01 1dqrA c.80.1.2 35305 1uptA 171 4.82e+01 c.37.1.8 99767 1si6X 282 4.83e+01 1r64A 481 4.85e+01 b.18.1.20,c.41.1.1 97140,97141 1amoA 615 4.85e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 25669,31210,31557 2cw8A 537 4.87e+01 1mdbA 539 4.87e+01 e.23.1.1 79008 1vjvA 415 4.89e+01 d.3.1.9 108632 1grj 158 4.94e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1at0 145 4.94e+01 1at0 b.86.1.1 28374 1qg3A 195 4.94e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1u8sA 192 5.00e+01 d.58.18.5,d.58.18.5 107737,107738 1cknA 330 5.02e+01 1ckmA b.40.4.6,d.142.2.3 25360,41587 1s72R 155 5.02e+01 d.55.1.1 105337 1jhsA 188 5.02e+01 d.107.1.1 84172 1ay9A 108 5.04e+01 1umuA b.87.1.1 28384 2gd1O 334 5.08e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1j4wA 174 5.15e+01 d.51.1.1,d.51.1.1 71529,71530 1qmeA 702 5.17e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1smlA 269 5.19e+01 1smlA d.157.1.1 42053 1p32A 209 5.21e+01 1p32A d.25.1.1 38379 1h8dH 260 5.25e+01 5ptp 1coy 507 5.26e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1tuwA 109 5.30e+01 d.58.4.8 107346 1xhcA 367 5.30e+01 2c78A 405 5.32e+01 1scjB 71 5.34e+01 1scjB d.58.3.2 39069 1v1qA 134 5.34e+01 1ot5A 477 5.35e+01 b.18.1.20,c.41.1.1 87409,87410 1i2mA 216 5.35e+01 1byuA c.37.1.8 61568 1h91A 180 5.38e+01 b.60.1.1 60805 1dnlA 199 5.40e+01 1ci0A b.45.1.1 25753 2ddfA 257 5.50e+01 2cg4A 152 5.52e+01 1r9cA 139 5.54e+01 d.32.1.2 97255 1ovaA 386 5.57e+01 1ovaA e.1.1.1 42619 1r45A 204 5.58e+01 1p9yA 121 5.58e+01 d.241.2.1 94402 1s0aA 429 5.60e+01 c.67.1.4 98263 1ea0A 1479 5.61e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 2a7mA 250 5.62e+01 2exrA 524 5.63e+01 1m2oB 190 5.64e+01 c.37.1.8 78485 1iuhA 198 5.65e+01 d.61.1.2 83711 1b9mA 265 5.65e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1jhfA 202 5.65e+01 a.4.5.2,b.87.1.1 63057,63058 1b5eA 246 5.66e+01 1b5eA d.117.1.1 41056 1mmuA 347 5.71e+01 b.30.5.4 79303 2cbf 234 5.72e+01 1cbf c.90.1.1 35588 1f3uA 118 5.75e+01 1f3uA b.65.1.1 27521 1y21A 282 5.78e+01 1bkcE 256 5.81e+01 1bkcA d.92.1.10 40333 1kskA 234 5.83e+01 d.66.1.5,d.265.1.3 72920,90389 1xyfA 436 5.85e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1zkoA 136 5.89e+01 1w15A 153 5.90e+01 b.7.1.2 109041 2glzA 153 5.95e+01 1kuuA 202 5.97e+01 d.153.2.1 73019 1p9rA 418 5.99e+01 c.37.1.11 94399 1f9zA 135 5.99e+01 1qipA d.32.1.1 38484 1knmA 130 5.99e+01 b.42.2.1 72781 1fvuB 125 6.05e+01 1ixxB d.169.1.1 42346 1yphC 131 6.10e+01 1klt 226 6.16e+01 5ptp b.47.1.2 26300 1knlA 130 6.19e+01 b.42.2.1 72780 1k2i1 245 6.21e+01 1os8A 223 6.23e+01 b.47.1.1 93481 1umuA 116 6.25e+01 1umuA b.87.1.1 28382 1qnjA 240 6.27e+01 5ptp b.47.1.2 26238 1bjwA 382 6.30e+01 1bjwA c.67.1.1 34349 1b5pA 385 6.33e+01 c.67.1.1 90403 1danH 254 6.34e+01 5ptp b.47.1.2 26292 1f1uA 323 6.34e+01 d.32.1.3,d.32.1.3 83200,83201 1yr2A 741 6.39e+01 1f0iA 504 6.44e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1zglM 209 6.44e+01 1fonA 240 6.48e+01 5ptp b.47.1.2 26231 1sqwA 188 6.50e+01 1wvfA 520 6.51e+01 2d2eA 250 6.54e+01 3tss 194 6.54e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1rr9A 200 6.56e+01 d.14.1.10 97783 1c0pA 363 6.62e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2cab 261 6.67e+01 2cba b.74.1.1 27906 1tljA 213 6.68e+01 d.282.1.1 107126 1v0wA 506 6.76e+01 d.136.1.2,d.136.1.2 108220,108221 1d9eA 284 6.78e+01 1d9eA c.1.10.4 29195 1uowA 159 6.80e+01 b.7.1.2 107975 2aynA 404 6.80e+01 1wguA 136 6.82e+01 1jjuA 489 6.90e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1k0iA 394 6.93e+01 c.3.1.2,d.16.1.2 67942,67943 1bli 483 7.02e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1gpmA 525 7.03e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1n1tA 641 7.03e+01 b.29.1.15,b.68.1.1 79821,79822 1nzaA 103 7.04e+01 d.58.5.2 86444 1cr5A 189 7.05e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1aps 98 7.05e+01 2acy d.58.10.1 39299 1kexA 155 7.05e+01 b.18.1.2 77350 1kr4A 125 7.07e+01 d.58.5.2 72889 1xwyA 264 7.11e+01 1mu7A 485 7.13e+01 d.136.1.3,d.136.1.3 79475,79476 1t4wA 196 7.13e+01 b.2.5.2 106427 2g5dA 422 7.16e+01 1dbrA 231 7.18e+01 1qk3A c.61.1.1 34041 1g8sA 230 7.22e+01 c.66.1.3 90507 1n2fA 142 7.24e+01 d.227.1.1 79853 1h4vB 421 7.29e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1q5fA 156 7.33e+01 d.24.1.1 104536 2akaA 776 7.33e+01 2phh 394 7.33e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1sgt 223 7.34e+01 5ptp b.47.1.1 25814 2cy5A 140 7.35e+01 2bz6H 254 7.35e+01 1gesA 450 7.38e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1qj5A 429 7.40e+01 1dtyA c.67.1.4 34493 3sxlA 184 7.41e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1fx2A 235 7.42e+01 1fx2A d.58.29.1 39430 3cla 213 7.43e+01 3cla c.43.1.1 32610 1tyjA 170 7.44e+01 1hqz1 141 7.47e+01 1qwtA 255 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8.56e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1uhgA 385 8.56e+01 e.1.1.1 88491 1qwyA 291 8.56e+01 b.84.3.2 96509 1h70A 255 8.58e+01 1h70A d.126.1.3 60711 1bmv2 374 8.59e+01 1bmv2 1x8qA 184 8.64e+01 1o91A 178 8.64e+01 b.22.1.1 92656 1btu 240 8.65e+01 5ptp b.47.1.2 26241 1hskA 326 8.66e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 3bamA 213 8.67e+01 1bam c.52.1.3 33288 1mxiA 160 8.69e+01 c.116.1.1 79646 1pch 88 8.69e+01 1ptf d.94.1.1 40564 1lk5A 229 8.75e+01 c.124.1.4,d.58.40.1 73960,73961 1bw0A 416 8.78e+01 1bw0A c.67.1.1 34385 1wexA 104 8.79e+01 1hqz9 141 8.81e+01 1elt 236 8.85e+01 5ptp b.47.1.2 26281 1p1lA 102 8.85e+01 d.58.5.2 87695 1j1lA 290 8.90e+01 b.82.1.12 90766 1wstA 417 8.91e+01