# List of top-scoring protein chains for t2k-100-30-bys-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 1ex1A 605 1.55e+00 1ex1A c.1.8.7,c.23.11.1 29013,31347 1iexA 605 2.15e+00 c.1.8.7,c.23.11.1 66127,66128 1x38A 602 2.42e+00 1httA 423 2.54e+00 1adjA c.51.1.1,d.104.1.1 33178,40727 1amuA 563 2.56e+00 1amuA e.23.1.1 43351 1a2xA 159 2.70e+00 1ncx a.39.1.5 17251 1kmmA 424 3.10e+00 1adjA c.51.1.1,d.104.1.1 33174,40723 1kmnD 424 4.09e+00 1adjA c.51.1.1,d.104.1.1 33185,40734 2bjvA 265 4.62e+00 1tn4 159 5.26e+00 1ncx a.39.1.5 17248 2cu3A 64 5.70e+00 1np7A 489 5.75e+00 a.99.1.1,c.28.1.1 80677,80678 1yfm 488 6.12e+00 1furA a.127.1.1 19413 1n9lA 109 6.70e+00 d.110.3.6 85468 1xseA 295 6.90e+00 1q7rA 219 7.35e+00 c.23.16.1 96054 1w4tA 299 8.33e+00 1tv8A 340 8.75e+00 c.1.28.3 107352 1ncx 162 9.18e+00 1ncx a.39.1.5 17222 1y5mA 276 9.25e+00 1fuqA 472 9.39e+00 1furA a.127.1.1 19405 1ps9A 671 1.02e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1o50A 157 1.04e+01 d.37.1.1,d.37.1.1 92478,92479 1gpmA 525 1.04e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1fuoA 467 1.06e+01 1furA a.127.1.1 19411 1jfaA 374 1.08e+01 a.128.1.5 66622 1qmvA 197 1.09e+01 1qq2A c.47.1.10 33066 1jfgA 374 1.14e+01 a.128.1.5 66636 1sfjA 238 1.17e+01 1furA 467 1.17e+01 1furA a.127.1.1 19403 1ma3A 253 1.19e+01 c.31.1.5 78883 1yyqA 374 1.32e+01 1kiyA 374 1.33e+01 a.128.1.5 72555 2aelA 374 1.36e+01 1xu9A 286 1.40e+01 1necA 216 1.42e+01 1vfrA d.90.1.1 40249 1tfjA 219 1.64e+01 1yixA 265 1.76e+01 1qyaA 307 1.81e+01 d.21.1.2,d.21.1.2 104653,104654 1xg5A 279 1.90e+01 1yspA 181 1.93e+01 1uzbA 516 2.00e+01 c.82.1.1 100220 1sflA 238 2.01e+01 1top 162 2.02e+01 1ncx a.39.1.5 17223 1om4A 422 2.13e+01 d.174.1.1 87067 1mmvB 419 2.17e+01 d.174.1.1 91318 1v8gA 329 2.26e+01 a.46.2.1,c.27.1.1 100505,100506 2ex0A 399 2.29e+01 2fq3A 104 2.32e+01 1swxA 209 2.33e+01 a.224.1.1 106075 1fds 327 2.37e+01 1fds c.2.1.2 29838 1z57A 339 2.43e+01 2b06A 155 2.44e+01 4pfk 319 2.48e+01 3pfk c.89.1.1 35582 1wbeA 209 2.48e+01 1xvsA 126 2.60e+01 1g6aA 271 2.60e+01 1btl e.3.1.1 42704 1vls 146 2.63e+01 1vls a.24.2.1 16532 1kzhA 555 2.66e+01 c.89.1.1 73361 2aaa 484 2.67e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1zp4A 304 2.78e+01 1o6yA 299 2.82e+01 d.144.1.7 81106 1geeA 261 2.84e+01 c.2.1.2 90509 1gcoA 261 2.86e+01 1ybvA c.2.1.2 29884 2bjkA 516 2.91e+01 1sdoA 203 2.96e+01 c.52.1.21 98809 1o6uA 403 3.08e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1sdjA 310 3.16e+01 d.21.1.2,d.21.1.2 98807,98808 1pfkA 320 3.22e+01 3pfk c.89.1.1 35575 1a27 289 3.23e+01 1fds c.2.1.2 29839 1olmA 403 3.27e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1q7eA 428 3.40e+01 c.123.1.1 96035 1fj2A 232 3.42e+01 1auoA c.69.1.14 34720 2f6rA 281 3.45e+01 1ykiA 217 3.48e+01 1n3kA 130 3.50e+01 a.77.1.4 79965 1hn4A 131 3.54e+01 a.133.1.2 65893 3pfk 319 3.59e+01 3pfk c.89.1.1 35581 1fdt 327 3.61e+01 1fds c.2.1.2 29841 1hta 69 3.63e+01 1a7w a.22.1.2 16476 1s9rA 410 3.65e+01 d.126.1.4 98758 1lxyA 409 3.66e+01 d.126.1.4 91154 1i5rA 327 3.69e+01 c.2.1.2 83668 2evrA 246 3.70e+01 1lrzA 426 3.73e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1mlwA 301 3.75e+01 d.178.1.1 79289 1toh 343 3.76e+01 4pah d.178.1.1 42573 1egwA 77 3.80e+01 1mnmA d.88.1.1 40234 2d00A 109 3.81e+01 1ve6A 582 3.81e+01 2a6hD 1524 4.01e+01 1a45 173 4.10e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1icrA 217 4.13e+01 1vfrA d.90.1.1 62274 1klqA 197 4.21e+01 d.135.1.1 68689 1e8gA 560 4.22e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1qqfA 277 4.25e+01 1c3d a.102.4.4 18875 1w0mA 226 4.34e+01 c.1.1.1 109027 1jtvA 327 4.39e+01 c.2.1.2 84230 2g8lA 299 4.44e+01 1d9eA 284 4.45e+01 1d9eA c.1.10.4 29195 1prs 173 4.49e+01 1prs b.11.1.1,b.11.1.1 23625,23626 1su8A 636 4.54e+01 e.26.1.2 98999 1j8uA 325 4.57e+01 d.178.1.1 71611 1b5tA 275 4.64e+01 1b5tA c.1.23.1 29676 1prr 173 4.68e+01 1prs b.11.1.1,b.11.1.1 23623,23624 1b67A 68 4.68e+01 1a7w a.22.1.2 16474 1diwA 441 4.78e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1qk3A 233 4.85e+01 1qk3A c.61.1.1 34031 1a8d 452 4.89e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1zemA 262 4.90e+01 2ligA 164 4.92e+01 1vls a.24.2.1 16530 1zxcA 263 4.98e+01 1bm8 99 5.03e+01 1bm8 d.34.1.1 38528 2f6hX 419 5.04e+01 1bkcA 255 5.10e+01 1bkcA d.92.1.10 40331 1fc4A 401 5.24e+01 1bs0A c.67.1.4 59760 1nz0A 118 5.28e+01 d.14.1.2 86433 1qk4A 233 5.30e+01 1qk3A c.61.1.1 34037 1kveB 77 5.44e+01 1kveB 1bkcI 256 5.44e+01 1bkcA d.92.1.10 40334 1go4A 205 5.53e+01 d.135.1.1 70292 1svvA 359 5.61e+01 c.67.1.1 106054 1mb1 130 5.62e+01 1bm8 d.34.1.1 38529 1nqkA 381 5.63e+01 c.1.16.4 92050 1kn6A 90 5.63e+01 d.58.3.3 72770 4pah 308 5.71e+01 4pah d.178.1.1 42576 1im5A 180 5.75e+01 c.33.1.3 66211 2fuqA 747 5.75e+01 1m7vA 363 5.78e+01 d.174.1.1 78748 1hzmA 154 5.78e+01 c.46.1.1 65975 1vqvA 306 5.78e+01 1be3D 241 5.79e+01 1be3D a.3.1.3,f.23.11.1 15955,43666 1okrA 123 5.92e+01 a.4.5.39 93269 1ev7B 317 5.99e+01 1ev7B c.52.1.9 33316 1ur4A 399 6.00e+01 1vizA 240 6.04e+01 c.1.4.1 100784 1tzaA 134 6.08e+01 b.1.23.1 107468 1f20A 435 6.10e+01 b.43.4.1,c.25.1.4 64932,64933 1iqrA 420 6.16e+01 a.99.1.1,c.28.1.1 66275,66276 1bi5A 389 6.27e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1dmwA 307 6.29e+01 4pah d.178.1.1 42580 1jjyA 636 6.29e+01 1jjyA 1m6uA 272 6.30e+01 b.2.5.7 78706 1i86A 389 6.31e+01 c.95.1.2,c.95.1.2 66068,66069 1elpA 173 6.31e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1io2A 213 6.32e+01 1ekeA c.55.3.1 62612 4bp2 130 6.32e+01 1poa a.133.1.2 19584 1jmxB 349 6.36e+01 b.69.2.2 66906 1oyeA 1049 6.39e+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 1lmhA 184 6.48e+01 d.167.1.1 74036 1fsgA 233 6.53e+01 1qk3A c.61.1.1 34029 1zo2A 129 6.61e+01 1zxxA 319 6.69e+01 1tr7A 164 6.70e+01 1eqcA 394 6.97e+01 1cz1A c.1.8.3 28811 2fa8A 105 6.99e+01 1r13A 148 6.99e+01 d.169.1.1,h.1.1.1 96782,96783 1eblA 317 6.99e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1eblB 317 7.03e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1aa0 113 7.06e+01 1aa0 h.1.17.1 45659 1d0hA 469 7.10e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1ig3A 263 7.13e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1qltA 560 7.16e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1pah 308 7.18e+01 4pah d.178.1.1 42578 1qkrA 188 7.19e+01 1qkrA a.24.9.1 16628 1llwA 1520 7.22e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1i1qB 192 7.23e+01 1qdlB c.23.16.1 61544 1vhrA 184 7.23e+01 1vhrA c.45.1.1 32651 1qlmA 316 7.28e+01 1qlmA d.147.1.1 41765 1i88A 389 7.31e+01 c.95.1.2,c.95.1.2 66070,66071 1ofdA 1520 7.39e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1dv1A 449 7.41e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1hn9A 317 7.52e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1hnjA 317 7.53e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 2pfkA 320 7.55e+01 3pfk c.89.1.1 35577 1aj4 161 7.56e+01 1ncx a.39.1.5 17244 1dzkA 157 7.57e+01 1obpA b.60.1.1 27096 1ecl 597 7.58e+01 1ecl e.10.1.1 43238 1iruK 201 7.58e+01 d.153.1.4 71362 1h4aX 173 7.63e+01 b.11.1.1,b.11.1.1 83479,83480 1vaoA 560 7.63e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1fs1A 53 7.64e+01 1fqvA a.158.1.1 19250 1r8gA 372 7.70e+01 d.128.1.3 104845 1vdkA 466 7.70e+01 a.127.1.1 100561 2an3A 289 7.74e+01 1nksA 194 7.77e+01 1nksA c.37.1.1 31886 1jajA 174 7.77e+01 d.218.1.2 66471 1dbrA 231 7.80e+01 1qk3A c.61.1.1 34041 2c2xA 281 7.84e+01 1xc1A 309 7.88e+01 c.94.1.1 109543 1v4vA 376 7.88e+01 c.87.1.3 100313 1bn6A 294 8.04e+01 1bn6A c.69.1.8 34678 1lm4A 194 8.05e+01 d.167.1.1 84626 1cqwA 295 8.07e+01 1b6g c.69.1.8 34679 1kvdB 77 8.07e+01 1kveB 1d9tA 289 8.09e+01 1deaA 1zcjA 463 8.12e+01 1qtnA 164 8.19e+01 1pauA c.17.1.1 30999 2ddfA 257 8.22e+01 1w2yA 229 8.23e+01 a.204.1.1 109140 1jqjC 343 8.28e+01 a.80.1.1,c.37.1.20 67097,67098 2adgA 214 8.30e+01 1m41A 380 8.36e+01 c.1.16.4 78595 1dv2A 452 8.43e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1iawA 317 8.47e+01 c.52.1.9 62126 1vknA 351 8.51e+01 c.2.1.3,d.81.1.1 108676,108677 1ne7A 289 8.52e+01 c.124.1.1 91833 1zowA 313 8.61e+01 1a0eA 443 8.88e+01 1a0cA c.1.15.3 29537 1oaoC 729 8.90e+01 e.26.1.3 86746 1zzmA 259 8.94e+01