# List of top-scoring protein chains for t2k-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 1itwA 741 9.79e-01 c.77.1.2 76793 1mmvB 419 1.67e+00 d.174.1.1 91318 1om4A 422 1.87e+00 d.174.1.1 87067 1pfkA 320 2.03e+00 3pfk c.89.1.1 35575 1necA 216 2.06e+00 1vfrA d.90.1.1 40249 1uw4B 248 2.18e+00 a.118.1.14 100072 4pfk 319 2.35e+00 3pfk c.89.1.1 35582 2pfkA 320 2.38e+00 3pfk c.89.1.1 35577 3pfk 319 2.46e+00 3pfk c.89.1.1 35581 1np7A 489 2.57e+00 a.99.1.1,c.28.1.1 80677,80678 1httA 423 2.71e+00 1adjA c.51.1.1,d.104.1.1 33178,40727 1a0eA 443 4.76e+00 1a0cA c.1.15.3 29537 1ykiA 217 4.95e+00 1icrA 217 5.59e+00 1vfrA d.90.1.1 62274 1kmmA 424 5.72e+00 1adjA c.51.1.1,d.104.1.1 33174,40723 1a45 173 5.86e+00 1amm b.11.1.1,b.11.1.1 23602,23603 1zxxA 319 6.62e+00 2bjvA 265 6.99e+00 1w2yA 229 7.16e+00 a.204.1.1 109140 2sxl 88 7.86e+00 1b7fA d.58.7.1 39179 1t9xA 1049 7.86e+00 1amuA 563 8.75e+00 1amuA e.23.1.1 43351 1tfjA 219 9.02e+00 1m7vA 363 9.50e+00 d.174.1.1 78748 1o5hA 214 9.75e+00 a.191.1.1 92497 1kvdB 77 1.01e+01 1kveB 1kveB 77 1.01e+01 1kveB 1mrg 263 1.03e+01 1mrj d.165.1.1 42183 1gudA 288 1.07e+01 c.93.1.1 83326 2a6hD 1524 1.07e+01 1r13A 148 1.12e+01 d.169.1.1,h.1.1.1 96782,96783 6pfkA 319 1.12e+01 3pfk c.89.1.1 35583 1dv2A 452 1.16e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1sfjA 238 1.16e+01 1qkrA 188 1.32e+01 1qkrA a.24.9.1 16628 1d6jA 211 1.34e+01 1d6jA c.37.1.4 31940 2f6rA 281 1.34e+01 1s72E 178 1.36e+01 d.141.1.1,d.141.1.1 105323,105324 1jmsA 381 1.37e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1q7rA 219 1.39e+01 c.23.16.1 96054 1dv1A 449 1.40e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1n9lA 109 1.45e+01 d.110.3.6 85468 2aelA 374 1.56e+01 1j27A 102 1.60e+01 d.58.50.1 90778 1gnlA 544 1.60e+01 e.26.1.1 70287 1iwgA 1053 1.63e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1sflA 238 1.64e+01 1ahc 246 1.70e+01 1mrj d.165.1.1 42184 2b0tA 738 1.73e+01 1rpjA 288 1.85e+01 2dri c.93.1.1 35656 1jj2E 177 1.86e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1elpA 173 1.88e+01 1amm b.11.1.1,b.11.1.1 23596,23597 2b06A 155 1.88e+01 1ex1A 605 1.91e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1t9mA 214 1.91e+01 1dvpA 220 1.91e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 5fbpA 335 1.96e+01 1frpA e.7.1.1 42873 1h4aX 173 2.04e+01 b.11.1.1,b.11.1.1 83479,83480 1cz1A 394 2.06e+01 1cz1A c.1.8.3 28839 1eulA 994 2.18e+01 1eulA 1iexA 605 2.19e+01 c.1.8.7,c.23.11.1 66127,66128 1x38A 602 2.20e+01 1a5dA 173 2.20e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1eqcA 394 2.21e+01 1cz1A c.1.8.3 28811 1gntA 553 2.24e+01 e.26.1.1 70290 1e1dA 553 2.27e+01 1e1dA e.26.1.1 43363 1m5yA 408 2.29e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1e2uA 553 2.29e+01 1e1dA e.26.1.1 43362 2dorA 311 2.38e+01 2dorA c.1.4.1 28593 1swxA 209 2.39e+01 a.224.1.1 106075 1li5A 461 2.40e+01 a.27.1.1,c.26.1.1 73912,73913 1jfaA 374 2.43e+01 a.128.1.5 66622 1gpuA 680 2.47e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1kz8A 337 2.54e+01 e.7.1.1 77633 1f82A 424 2.57e+01 1f82A d.92.1.7 40307 1kxu 333 2.58e+01 1jkw a.74.1.1,a.74.1.1 18358,18359 1vqoE 178 2.60e+01 1oyeA 1049 2.64e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1wbeA 209 2.64e+01 1tv8A 340 2.68e+01 c.1.28.3 107352 1fpkA 335 2.70e+01 1frpA e.7.1.1 42930 1nf1A 333 2.74e+01 1nf1A a.116.1.2 19110 1kmnD 424 2.84e+01 1adjA c.51.1.1,d.104.1.1 33185,40734 1khtA 192 2.87e+01 c.37.1.1 84401 1jubA 311 2.89e+01 c.1.4.1 90908 1e4eA 343 2.91e+01 1iow c.30.1.2,d.142.1.1 59221,59222 104lA 166 2.93e+01 1l92 d.2.1.3 36969 1ofdA 1520 2.99e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1vls 146 3.01e+01 1vls a.24.2.1 16532 1a0dA 440 3.02e+01 1a0cA c.1.15.3 29533 1hta 69 3.04e+01 1a7w a.22.1.2 16476 2ligA 164 3.05e+01 1vls a.24.2.1 16530 1jkw 323 3.09e+01 1jkw a.74.1.1,a.74.1.1 18356,18357 1gzgA 337 3.14e+01 c.1.10.3 70805 2g03A 194 3.14e+01 1zu4A 320 3.16e+01 1aa0 113 3.17e+01 1aa0 h.1.17.1 45659 3sxlA 184 3.22e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1w6kA 732 3.23e+01 1b4kA 337 3.31e+01 1b4kA c.1.10.3 29184 1sdoA 203 3.34e+01 c.52.1.21 98809 1iab 200 3.45e+01 1iae d.92.1.8 40312 1iae 200 3.47e+01 1iae d.92.1.8 40311 1ast 200 3.47e+01 1iae d.92.1.8 40310 1n2sA 299 3.58e+01 c.2.1.2 79857 1frpA 335 3.59e+01 1frpA e.7.1.1 42875 1dorA 311 3.61e+01 2dorA c.1.4.1 28595 1r9dA 787 3.63e+01 c.7.1.1 104865 1b67A 68 3.72e+01 1a7w a.22.1.2 16474 1mli 96 3.75e+01 1mli d.58.4.1 39070 1bkcE 256 3.76e+01 1bkcA d.92.1.10 40333 1bkcA 255 3.77e+01 1bkcA d.92.1.10 40331 1zxcA 263 3.80e+01 1lucA 355 3.81e+01 1lucA c.1.16.1 29547 1furA 467 3.91e+01 1furA a.127.1.1 19403 1zirA 173 3.91e+01 2dh4A 340 3.95e+01 1bkcI 256 3.96e+01 1bkcA d.92.1.10 40334 1dbtA 239 3.98e+01 1dbtA c.1.2.3 28539 1top 162 4.03e+01 1ncx a.39.1.5 17223 2ddfA 257 4.11e+01 1tr7A 164 4.11e+01 1fqvD 149 4.14e+01 1fqvD a.157.1.1,d.42.1.1 19263,38667 1o7xC 377 4.15e+01 a.103.1.1 81173 2gq1A 332 4.15e+01 1bxsA 501 4.16e+01 1bpwA c.82.1.1 35357 1a32 88 4.22e+01 1a32 a.16.1.2 16384 1tn4 159 4.24e+01 1ncx a.39.1.5 17248 1oj6A 151 4.24e+01 a.1.1.2 93088 1ng6A 148 4.27e+01 a.182.1.1 85670 1ncx 162 4.30e+01 1ncx a.39.1.5 17222 1o50A 157 4.31e+01 d.37.1.1,d.37.1.1 92478,92479 1tg6A 277 4.32e+01 1sesA 421 4.42e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 2awpA 198 4.49e+01 1li5B 461 4.51e+01 a.27.1.1,c.26.1.1 73914,73915 2gsq 202 4.62e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1yfm 488 4.63e+01 1furA a.127.1.1 19413 1eyvA 156 4.64e+01 1eyvA a.79.1.1 18446 1k87A 669 4.71e+01 a.176.1.1,c.1.23.2 77286,77287 1tkaA 678 4.72e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31815,31816,33096 1hg4A 279 4.73e+01 1lbd a.123.1.1 19333 1vqoB 338 4.84e+01 1bncA 449 4.86e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1jj2B 337 4.90e+01 1ffkB b.43.3.2 63086 1gpmA 525 4.91e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1vhrA 184 4.92e+01 1vhrA c.45.1.1 32651 1p4wA 99 4.92e+01 a.4.6.2 87783 1s72B 338 4.93e+01 b.43.3.2 105320 1z83A 196 4.94e+01 1ve6A 582 4.98e+01 1uwfA 158 4.98e+01 1jr3D 343 5.22e+01 a.80.1.1,c.37.1.20 63251,63252 2cu3A 64 5.38e+01 1g8oA 310 5.43e+01 1g8oA c.68.1.9 60375 1bt4A 362 5.44e+01 1bjnA c.67.1.4 34468 1fuqA 472 5.44e+01 1furA a.127.1.1 19405 1iow 306 5.68e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1jajA 174 5.68e+01 d.218.1.2 66471 1o7xD 377 5.76e+01 a.103.1.1 81174 1f83A 425 5.80e+01 1f82A d.92.1.7 40306 1oe8A 211 5.82e+01 a.45.1.1,c.47.1.5 86905,86906 1n3kA 130 5.83e+01 a.77.1.4 79965 1ra6A 461 5.90e+01 e.8.1.4 104879 1sg6A 393 5.95e+01 e.22.1.1 105522 1hn4A 131 5.96e+01 a.133.1.2 65893 1egwA 77 5.98e+01 1mnmA d.88.1.1 40234 1u19A 349 6.02e+01 1nvpD 108 6.08e+01 a.32.1.1,b.56.1.1 92213,92214 1xl7A 612 6.13e+01 1fuoA 467 6.17e+01 1furA a.127.1.1 19411 1toh 343 6.20e+01 4pah d.178.1.1 42573 1f6fB 210 6.21e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1hqz1 141 6.21e+01 1nseA 444 6.23e+01 1nseA d.174.1.1 42534 1w5nA 337 6.26e+01 2ax4A 198 6.30e+01 2c0rA 362 6.35e+01 1pqsA 77 6.39e+01 d.15.2.2 88277 1hzxA 349 6.53e+01 1f88A f.13.1.2 61466 1j6oA 268 6.59e+01 c.1.9.12 77088 2fxaA 207 6.61e+01 1b3rA 431 6.61e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 2bvyA 475 6.62e+01 1trkA 680 6.71e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1w3uA 362 6.73e+01 3mdeA 385 6.85e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 1m8uA 173 6.95e+01 b.11.1.1,b.11.1.1 91233,91234 1a0cA 438 6.97e+01 1a0cA c.1.15.3 29529 1klfB 279 7.04e+01 b.2.3.2,b.2.3.2 72684,72685 1kiuB 279 7.07e+01 b.2.3.2,b.2.3.2 72525,72526 1yarH 217 7.24e+01 1rypF 233 7.30e+01 1rypF d.153.1.4 41937 1m7gA 211 7.31e+01 c.37.1.4 78724 1li4A 432 7.33e+01 c.2.1.4,c.23.12.3 84616,84617 1wpgA 994 7.33e+01 1pah 308 7.33e+01 4pah d.178.1.1 42578 1lssA 140 7.35e+01 c.2.1.9 74246 1tzvA 142 7.41e+01 a.79.1.1 107526 1nz0A 118 7.41e+01 d.14.1.2 86433 1yspA 181 7.42e+01 1ag2 103 7.43e+01 1b10A d.6.1.1 37305 1w5qA 337 7.46e+01 2fpqA 444 7.48e+01 1xeqA 103 7.55e+01 1q1fA 151 7.58e+01 a.1.1.2 104476 1ev7A 317 7.61e+01 1ev7B c.52.1.9 33315 1vjoA 393 7.64e+01 c.67.1.3 100827 1bf5A 545 7.73e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1gr5A 547 7.73e+01 i.16.1.1 65478 1jk0B 345 7.84e+01 a.25.1.2 63143 1ba1 386 7.87e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1dkuA 317 7.87e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1fqvJ 149 7.87e+01 1fqvD a.157.1.1,d.42.1.1 19266,38670 1q7sA 117 7.93e+01 c.131.1.1 96055 1gw5B 591 7.93e+01 a.118.1.10 70630 1ni3A 392 7.96e+01 c.37.1.8,d.15.10.2 80531,80532 1wj5A 120 8.00e+01 1rwhA 757 8.05e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1j8uA 325 8.05e+01 d.178.1.1 71611 1a6s 87 8.07e+01 1a6s a.61.1.4 18134 1zlbA 122 8.08e+01 1z8sA 146 8.08e+01 1dqsA 393 8.20e+01 1dqsA e.22.1.1 43347 1wu7A 434 8.23e+01 1izcA 339 8.36e+01 c.1.12.5 83838 1jfgA 374 8.43e+01 a.128.1.5 66636 1dmwA 307 8.46e+01 4pah d.178.1.1 42580 1a4iA 301 8.46e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1rdzA 337 8.48e+01 1frpA e.7.1.1 42882 2gjlA 328 8.48e+01 1g6aA 271 8.52e+01 1btl e.3.1.1 42704 1wfdA 93 8.54e+01 4pah 308 8.56e+01 4pah d.178.1.1 42576 1diaA 306 8.57e+01 1a4iA c.2.1.7,c.58.1.2 30280,33928 1e3yA 104 8.57e+01 1fadA a.77.1.2 18426 1rfeA 162 8.63e+01 1uurA 473 8.63e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1gx4A 289 8.72e+01 c.68.1.9 83362 1k4vA 289 8.74e+01 c.68.1.9 72066 1o7qA 289 8.76e+01 c.68.1.9 92626 1ibsA 317 8.81e+01 c.61.1.2,c.61.1.2 66107,66108 1fzaB 328 8.81e+01 3fib d.171.1.1,h.1.8.1 42480,45621 1d0cA 444 8.82e+01 d.174.1.1 64769 1dbrA 231 8.87e+01 1qk3A c.61.1.1 34041 1qk3A 233 8.88e+01 1qk3A c.61.1.1 34031 1ay0A 680 8.89e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31823,31824,33100 1l9hA 349 8.96e+01 f.13.1.2 73720 1nxqA 251 8.97e+01 c.2.1.2 86388