# 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 2b06A 155 8.00e-01 1np7A 489 2.50e+00 a.99.1.1,c.28.1.1 80677,80678 1pfkA 320 3.30e+00 3pfk c.89.1.1 35575 2pfkA 320 4.02e+00 3pfk c.89.1.1 35577 1necA 216 4.50e+00 1vfrA d.90.1.1 40249 1httA 423 4.69e+00 1adjA c.51.1.1,d.104.1.1 33178,40727 1khtA 192 4.96e+00 c.37.1.1 84401 1f6fB 210 5.63e+00 1axiB b.1.2.1,b.1.2.1 22033,22034 4pfk 319 6.41e+00 3pfk c.89.1.1 35582 2f6rA 281 6.48e+00 1yspA 181 6.48e+00 1dv1A 449 7.24e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1kmmA 424 7.37e+00 1adjA c.51.1.1,d.104.1.1 33174,40723 3pfk 319 7.52e+00 3pfk c.89.1.1 35581 1zxxA 319 7.73e+00 1mmvB 419 7.99e+00 d.174.1.1 91318 1om4A 422 8.27e+00 d.174.1.1 87067 1q7rA 219 9.46e+00 c.23.16.1 96054 1ofdA 1520 1.04e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1iexA 605 1.07e+01 c.1.8.7,c.23.11.1 66127,66128 1x38A 602 1.08e+01 2bjvA 265 1.09e+01 1ykiA 217 1.09e+01 1icrA 217 1.09e+01 1vfrA d.90.1.1 62274 1pbyB 337 1.11e+01 b.69.2.2 94422 1jjuB 337 1.13e+01 b.69.2.2 66779 1ex1A 605 1.21e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 2aelA 374 1.26e+01 6pfkA 319 1.30e+01 3pfk c.89.1.1 35583 1bncA 449 1.32e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1w2yA 229 1.35e+01 a.204.1.1 109140 1dv2A 452 1.37e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1ps9A 671 1.37e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1o50A 157 1.48e+01 d.37.1.1,d.37.1.1 92478,92479 1fuqA 472 1.50e+01 1furA a.127.1.1 19405 1furA 467 1.50e+01 1furA a.127.1.1 19403 2b0lA 102 1.52e+01 1yfm 488 1.61e+01 1furA a.127.1.1 19413 1m7vA 363 1.62e+01 d.174.1.1 78748 1a0eA 443 1.63e+01 1a0cA c.1.15.3 29537 1bp3B 211 1.64e+01 1axiB b.1.2.1,b.1.2.1 22031,22032 1fuoA 467 1.65e+01 1furA a.127.1.1 19411 1kvdB 77 1.72e+01 1kveB 1kveB 77 1.72e+01 1kveB 1jfaA 374 1.81e+01 a.128.1.5 66622 1amuA 563 1.86e+01 1amuA e.23.1.1 43351 1k7yA 577 1.86e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1tfjA 219 1.95e+01 1stzA 338 2.10e+01 a.4.5.51,d.110.2.3 106009,106010 1j27A 102 2.10e+01 d.58.50.1 90778 1a32 88 2.13e+01 1a32 a.16.1.2 16384 1msk 331 2.20e+01 1msk d.173.1.1 42495 1kmnD 424 2.27e+01 1adjA c.51.1.1,d.104.1.1 33185,40734 1zzmA 259 2.46e+01 2g8lA 299 2.48e+01 2dorA 311 2.52e+01 2dorA c.1.4.1 28593 1iwgA 1053 2.55e+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 2dkaA 544 2.60e+01 1dorA 311 2.60e+01 2dorA c.1.4.1 28595 1i1nA 226 2.62e+01 c.66.1.7 71102 1kr5A 226 2.76e+01 c.66.1.7 68847 1hdr 244 2.87e+01 1dhr c.2.1.2 29837 1fqvD 149 2.90e+01 1fqvD a.157.1.1,d.42.1.1 19263,38667 1ma3A 253 2.93e+01 c.31.1.5 78883 1t9mA 214 3.00e+01 2fq3A 104 3.22e+01 1cz1A 394 3.26e+01 1cz1A c.1.8.3 28839 1xr4A 509 3.35e+01 1eqcA 394 3.36e+01 1cz1A c.1.8.3 28811 1mrg 263 3.53e+01 1mrj d.165.1.1 42183 1u9iA 519 3.57e+01 1ooeA 236 3.69e+01 c.2.1.2 87196 2a6hD 1524 3.76e+01 1fqvJ 149 3.89e+01 1fqvD a.157.1.1,d.42.1.1 19266,38670 1zxmA 400 3.93e+01 1hcz 252 3.96e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1fdt 327 4.05e+01 1fds c.2.1.2 29841 1elpA 173 4.05e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1iqrA 420 4.10e+01 a.99.1.1,c.28.1.1 66275,66276 1i5rA 327 4.12e+01 c.2.1.2 83668 1jtvA 327 4.14e+01 c.2.1.2 84230 1fds 327 4.15e+01 1fds c.2.1.2 29838 1ahc 246 4.17e+01 1mrj d.165.1.1 42184 1tr7A 164 4.19e+01 1r13A 148 4.20e+01 d.169.1.1,h.1.1.1 96782,96783 1jmxB 349 4.25e+01 b.69.2.2 66906 2fhzA 109 4.28e+01 2gsq 202 4.29e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 2pcfB 250 4.54e+01 1hcz i.4.1.1 45911 1nksA 194 4.54e+01 1nksA c.37.1.1 31886 1zhxA 438 4.66e+01 1hstA 90 4.67e+01 1hstA a.4.5.13 16140 1fkmA 396 4.72e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1vjoA 393 4.76e+01 c.67.1.3 100827 2cu3A 64 4.77e+01 3sxlA 184 4.78e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1sflA 238 4.81e+01 1llwA 1520 4.92e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1jg1A 235 5.05e+01 c.66.1.7 66661 1g8jA 825 5.07e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1dd9A 338 5.11e+01 1dd9A e.13.1.1 43254 1zo2A 129 5.12e+01 1sfjA 238 5.14e+01 1t9xA 1049 5.17e+01 1dkfA 233 5.18e+01 3erdA a.123.1.1 19280 1rkbA 173 5.24e+01 1a27 289 5.27e+01 1fds c.2.1.2 29839 2fkzA 155 5.30e+01 1olmA 403 5.37e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1ibsA 317 5.47e+01 c.61.1.2,c.61.1.2 66107,66108 1wz3A 96 5.49e+01 1vhrA 184 5.74e+01 1vhrA c.45.1.1 32651 1n3kA 130 5.81e+01 a.77.1.4 79965 1lrzA 426 5.83e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1swxA 209 5.90e+01 a.224.1.1 106075 1xseA 295 6.00e+01 1uwfA 158 6.01e+01 2g03A 194 6.03e+01 1g8kA 825 6.09e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 2a9gA 418 6.12e+01 1jfmA 174 6.14e+01 d.19.1.1 66640 1l3kA 196 6.14e+01 d.58.7.1,d.58.7.1 73539,73540 1dkrA 317 6.15e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1gpc 218 6.24e+01 1gpc b.40.4.7 25393 1ws6A 171 6.27e+01 1m8uA 173 6.28e+01 b.11.1.1,b.11.1.1 91233,91234 1lmhA 184 6.28e+01 d.167.1.1 74036 1coy 507 6.30e+01 1b8sA c.3.1.2,d.16.1.1 30333,37864 1bkcE 256 6.31e+01 1bkcA d.92.1.10 40333 1bkcA 255 6.36e+01 1bkcA d.92.1.10 40331 1dkuA 317 6.38e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1dgsA 667 6.43e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1ydhA 216 6.43e+01 1zxcA 263 6.46e+01 1a0dA 440 6.55e+01 1a0cA c.1.15.3 29533 3cox 507 6.58e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1vqoE 178 6.61e+01 1z90A 469 6.65e+01 1kmiZ 214 6.67e+01 h.4.11.1 72752 2g1lA 104 6.67e+01 1bkcI 256 6.67e+01 1bkcA d.92.1.10 40334 1r6lA 239 6.72e+01 d.14.1.4,d.101.1.1 97153,97154 1luzA 88 6.73e+01 b.40.4.5 74271 1ddeA 338 6.74e+01 1dd9A e.13.1.1 43255 1go4A 205 6.82e+01 d.135.1.1 70292 1qk3A 233 6.85e+01 1qk3A c.61.1.1 34031 1wbeA 209 6.86e+01 1lm4A 194 6.92e+01 d.167.1.1 84626 1f8yA 157 6.96e+01 1f8xA c.23.14.1 31395 2aucA 126 7.00e+01 1y5mA 276 7.04e+01 1rfeA 162 7.06e+01 1kgcE 242 7.07e+01 b.1.1.1,b.1.1.2 77386,77387 2ddfA 257 7.11e+01 1eqnA 321 7.17e+01 1dd9A e.13.1.1 43256 2a33A 215 7.20e+01 1hta 69 7.28e+01 1a7w a.22.1.2 16476 1go3E 187 7.31e+01 b.40.4.5,d.230.1.1 83054,83055 1dhr 241 7.36e+01 1dhr c.2.1.2 29832 1yyqA 374 7.42e+01 1molA 94 7.45e+01 1molA d.17.1.1 37988 1a45 173 7.46e+01 1amm b.11.1.1,b.11.1.1 23602,23603 2afwA 329 7.55e+01 1odeA 122 7.57e+01 d.79.1.2 86846 1s72E 178 7.62e+01 d.141.1.1,d.141.1.1 105323,105324 1jfgA 374 7.63e+01 a.128.1.5 66636 1hzxA 349 7.69e+01 1f88A f.13.1.2 61466 1jubA 311 7.71e+01 c.1.4.1 90908 1sdoA 203 7.74e+01 c.52.1.21 98809 1iz6A 138 7.77e+01 b.34.5.2,b.40.4.5 76976,76977 1treA 255 7.77e+01 1amk c.1.1.1 28505 1p4wA 99 7.88e+01 a.4.6.2 87783 1f8xA 157 7.89e+01 1f8xA c.23.14.1 31397 1l4dB 122 7.99e+01 d.15.5.1 77684 2fq4A 192 8.03e+01 1jmsA 381 8.03e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1ae7 119 8.09e+01 1poa a.133.1.2 19553 1u19A 349 8.13e+01 2a1kA 233 8.15e+01 1pqsA 77 8.18e+01 d.15.2.2 88277 1z83A 196 8.19e+01 1r9dA 787 8.21e+01 c.7.1.1 104865 1zemA 262 8.22e+01 1qkrA 188 8.29e+01 1qkrA a.24.9.1 16628 1vig 71 8.30e+01 1vih d.51.1.1 38806 1xg5A 279 8.30e+01 1xu9A 286 8.32e+01 1nq6A 302 8.33e+01 c.1.8.3 92046 1vls 146 8.38e+01 1vls a.24.2.1 16532 1l9hA 349 8.39e+01 f.13.1.2 73720 2awpA 198 8.50e+01 1h4aX 173 8.51e+01 b.11.1.1,b.11.1.1 83479,83480 1kzhA 555 8.54e+01 c.89.1.1 73361 1tv8A 340 8.54e+01 c.1.28.3 107352 1o6uA 403 8.56e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1ng6A 148 8.57e+01 a.182.1.1 85670 1gdoA 240 8.65e+01 1gdoA 1xffA 240 8.71e+01 d.153.1.1 109580 1rybA 212 8.81e+01 c.56.3.1 98098 1b67A 68 8.83e+01 1a7w a.22.1.2 16474 1iawA 317 8.90e+01 c.52.1.9 62126 2f6sA 201 8.98e+01 1wguA 136 9.00e+01