# 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 1ejeA 192 7.50e-02 1ejeA b.45.1.2 25757 1ko3A 230 1.53e+00 d.157.1.1 90974 1hrhA 136 1.58e+00 1rthA c.55.3.1 33577 1kgsA 225 2.35e+00 a.4.6.1,c.23.1.1 68596,68597 1m2xA 223 2.59e+00 d.157.1.1 84764 1ejbA 168 2.85e+00 1rvv1 c.16.1.1 59417 1v0wA 506 3.18e+00 d.136.1.2,d.136.1.2 108220,108221 1f0iA 504 3.68e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 2tbd 134 3.70e+00 2tbd d.89.1.1 40241 1o22A 170 4.02e+00 d.238.1.1 86557 1nmuB 104 4.39e+00 d.79.3.1 80666 1nt4A 391 4.48e+00 c.60.1.2 92102 1rz1A 161 4.53e+00 b.45.1.2 98124 1obdA 306 4.82e+00 d.143.1.1 86767 1xfsA 178 4.82e+00 d.129.3.5 109589 1a48 306 4.89e+00 1a48 d.143.1.1 41590 2cnqA 306 5.47e+00 1k4mA 213 5.72e+00 c.26.1.3 77258 1ykfA 352 6.39e+00 1pedA b.35.1.2,c.2.1.1 24757,29773 1przA 252 6.90e+00 d.265.1.3 95064 2fiqA 420 6.93e+00 1tbd 134 7.39e+00 2tbd d.89.1.1 40240 1dt9A 437 7.79e+00 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1qlpA 394 7.97e+00 1ovaA e.1.1.1 42628 1kzhA 555 8.45e+00 c.89.1.1 73361 2hmiA 558 8.88e+00 1rthA c.55.3.1,e.8.1.2 33604,43106 9apiA 347 9.29e+00 1ovaA e.1.1.1 42630 1hniA 558 9.60e+00 1rthA c.55.3.1,e.8.1.2 33586,43044 2fliA 220 9.65e+00 1mkyA 439 1.04e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1bj7 156 1.18e+01 1bj7 b.60.1.1 27113 1ptmA 329 1.18e+01 c.77.1.3 95104 1y9aA 360 1.20e+01 1i0rA 169 1.30e+01 1i0rA b.45.1.2 61489 1i0sA 169 1.30e+01 1i0rA b.45.1.2 61491 1hn2A 159 1.31e+01 b.60.1.1 65890 1gt1A 159 1.31e+01 b.60.1.1 90515 1obpA 159 1.39e+01 1obpA b.60.1.1 27092 1o66A 275 1.42e+01 c.1.12.8 92547 1e5pA 151 1.46e+01 1bj7 b.60.1.1 59272 1ctqA 166 1.56e+01 1ctqA c.37.1.8 31965 1lr0A 129 1.56e+01 d.212.1.1 74213 1eetA 557 1.56e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1v9fA 325 1.57e+01 d.265.1.3 108448 1kfwA 435 1.60e+01 c.1.8.5,d.26.3.1 77376,77377 1y7pA 223 1.63e+01 1pedA 351 1.63e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1vzyA 291 1.67e+01 1o2dA 371 1.67e+01 e.22.1.2 86591 2bgzA 299 1.72e+01 1xppA 115 1.74e+01 1ujpA 271 1.74e+01 c.1.2.4 99462 1p8xA 344 1.76e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1pxwA 128 1.77e+01 d.79.3.1 95305 1hqkA 154 1.77e+01 c.16.1.1 65902 1jjtA 228 1.78e+01 1a7tA d.157.1.1 63139 2bodX 286 1.85e+01 1uirA 314 1.89e+01 c.66.1.17 99429 1xgsA 295 1.89e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1w78A 422 1.90e+01 1jjeA 222 1.91e+01 1a7tA d.157.1.1 63117 1cvrA 435 1.99e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1ck2A 104 1.99e+01 1ck9A d.79.3.1 39809 2agkA 260 2.00e+01 1ws6A 171 2.02e+01 1jqlB 140 2.05e+01 c.37.1.20 63234 1ukuA 102 2.09e+01 d.58.5.2 99533 1xzoA 174 2.10e+01 1oxxK 353 2.10e+01 b.40.6.3,c.37.1.12 93715,93716 1nh1A 330 2.11e+01 e.45.1.1 91871 1aky 221 2.12e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1dd6A 228 2.16e+01 1a7tA d.157.1.1 42054 1x1gA 129 2.16e+01 1ak2 233 2.18e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1wxcA 281 2.23e+01 1kevA 351 2.26e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1uvjA 664 2.33e+01 e.8.1.6 100045 2evwX 166 2.34e+01 1yal 218 2.35e+01 1cs8A d.3.1.1 37025 1ve2A 235 2.42e+01 1oe4A 247 2.44e+01 c.18.1.3 86895 1dciA 275 2.46e+01 1dciA c.14.1.3 30918 1zd9A 188 2.49e+01 821p 166 2.50e+01 1ctqA c.37.1.8 31969 1f20A 435 2.64e+01 b.43.4.1,c.25.1.4 64932,64933 1wlgA 299 2.68e+01 1thfD 253 2.78e+01 1thfD c.1.2.1 28535 1hhsA 664 2.82e+01 1hi0P e.8.1.6 61045 1vpt 348 2.83e+01 3mag c.66.1.25 34207 1s1iG 119 2.86e+01 i.1.1.1 105181 1l9xA 315 2.86e+01 c.23.16.1 73762 1om0A 274 2.88e+01 c.1.8.5 87058 1dr9A 201 2.91e+01 1dr9A b.1.1.1,b.1.1.3 19762,21684 1mldA 314 2.92e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 2fhxA 246 2.93e+01 1pueE 89 2.97e+01 1awcA a.4.5.21 16165 1r5jA 337 2.99e+01 c.77.1.5 97097 1a1aA 107 3.02e+01 1fmk d.93.1.1 40449 1krhA 338 3.16e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 2bogX 286 3.17e+01 5p21 166 3.19e+01 1ctqA c.37.1.8 31966 1szoA 257 3.20e+01 c.14.1.3 106164 2ga9A 297 3.21e+01 1o8uA 257 3.21e+01 c.14.1.3 81194 1jqbA 351 3.23e+01 b.35.1.2,c.2.1.1 77151,77152 1b57A 358 3.28e+01 1dosA c.1.10.2 29177 1oxsC 353 3.30e+01 b.40.6.3,c.37.1.12 87519,87520 1mjfA 281 3.37e+01 c.66.1.17 79198 1ihjA 98 3.37e+01 1pdr b.36.1.1 62382 1v7oA 165 3.38e+01 d.67.1.2 100480 1zesA 125 3.41e+01 2a9kA 187 3.44e+01 1bqnA 558 3.45e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1oj7A 408 3.49e+01 e.22.1.2 103971 1u8zA 168 3.52e+01 1xt5A 135 3.54e+01 1td4A 115 3.57e+01 1cleA 534 3.58e+01 1thg c.69.1.17 34771 1f2fA 104 3.59e+01 1fmk d.93.1.1 40455 1k1gA 131 3.59e+01 d.51.1.1 68015 3mag 307 3.68e+01 3mag c.66.1.25 34205 1bjt 793 3.72e+01 1bjt e.11.1.1 43249 1xviA 275 3.73e+01 1v39 322 3.74e+01 3mag c.66.1.25 34206 1vp9 322 3.74e+01 3mag c.66.1.25 34210 1ta3A 274 3.75e+01 c.1.8.5 106731 1fjgP 88 3.77e+01 1emwA d.27.1.1 38444 1llfA 534 3.79e+01 c.69.1.17 78094 1odfA 290 3.81e+01 c.37.1.6 92782 1uekA 275 3.90e+01 d.14.1.5,d.58.26.5 88483,88484 1hfeL 421 3.93e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1f3aA 222 3.96e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1ur1A 378 3.98e+01 c.1.8.3 99804 1ej8A 140 3.99e+01 1qupA b.1.8.1 22300 1tp9A 162 4.02e+01 1rybA 212 4.07e+01 c.56.3.1 98098 1m6pA 152 4.12e+01 1m6pA b.64.1.1 27519 1sxgA 280 4.13e+01 1eazA 125 4.19e+01 b.55.1.1 70113 1o4rA 108 4.21e+01 d.93.1.1 92469 1d3vA 323 4.24e+01 1d3vA c.42.1.1 32559 1f76A 336 4.25e+01 c.1.4.1 76160 1v5eA 590 4.29e+01 1xkyA 301 4.33e+01 1evxA 162 4.33e+01 1a73A d.4.1.3 37149 1shbA 104 4.40e+01 1fmk d.93.1.1 40425 1gnhA 206 4.41e+01 1sacA b.29.1.5 24252 1gseA 221 4.41e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1vm7A 311 4.43e+01 c.72.1.1 108884 1q0uA 219 4.43e+01 c.37.1.19 95512 1x8qA 184 4.47e+01 1ww9A 392 4.50e+01 1ovaA 386 4.50e+01 1ovaA e.1.1.1 42619 1y89A 238 4.55e+01 1inlA 296 4.59e+01 c.66.1.17 66220 1agp 166 4.62e+01 1ctqA c.37.1.8 31985 1a7tA 232 4.63e+01 1a7tA d.157.1.1 42041 2cxcA 144 4.66e+01 1tml 286 4.68e+01 1tml c.6.1.1 30656 1oj4A 283 4.71e+01 d.14.1.5,d.58.26.5 93083,93084 1jq3A 296 4.71e+01 c.66.1.17 67079 1hkfA 122 4.72e+01 b.1.1.1 83553 1hi0P 664 4.73e+01 1hi0P e.8.1.6 61051 1sjwA 144 4.79e+01 d.17.4.9 98899 1t95A 240 4.79e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1w0mA 226 4.79e+01 c.1.1.1 109027 1shaA 104 4.82e+01 1fmk d.93.1.1 40424 1rlaA 323 4.87e+01 1d3vA c.42.1.1 32561 1dqtA 117 4.88e+01 1ah1 b.1.1.1 20653 1a8s 273 4.88e+01 1brt c.69.1.12 34710 2aqjA 538 4.91e+01 2eveA 157 4.93e+01 1zgzA 122 4.97e+01 1nhs 447 5.12e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1v4pA 157 5.13e+01 1dosA 358 5.15e+01 1dosA c.1.10.2 29175 1o0yA 260 5.15e+01 c.1.10.1 80756 1k1eA 180 5.16e+01 c.108.1.5 67995 1ck9A 104 5.19e+01 1ck9A d.79.3.1 39806 1d3uB 201 5.20e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1qrrA 394 5.21e+01 1qrrA c.2.1.2 29824 1h1yA 228 5.28e+01 c.1.2.2 76506 1u8sA 192 5.29e+01 d.58.18.5,d.58.18.5 107737,107738 1t61A 229 5.29e+01 d.169.1.6,d.169.1.6 106529,106530 1xvwA 160 5.30e+01 1u9cA 224 5.31e+01 2bzlA 325 5.34e+01 1zd7A 159 5.34e+01 1aisB 200 5.34e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1d3yA 301 5.35e+01 1d3yA e.12.1.1 43252 2amlA 373 5.39e+01 1wapA 75 5.43e+01 1wapA b.82.5.1 28153 1hyeA 313 5.44e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1i24A 404 5.46e+01 c.2.1.2 83663 1ou0A 207 5.51e+01 c.23.17.1 93536 1s62A 106 5.52e+01 1f3vA 179 5.53e+01 1f3vA d.58.22.1 39382 1a76 326 5.54e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1g2oA 268 5.55e+01 1b8oA c.56.2.1 60228 1t17A 148 5.56e+01 1w6uA 302 5.60e+01 1yukB 120 5.60e+01 1rzrA 332 5.61e+01 1vq2A 193 5.62e+01 1np1A 184 5.63e+01 1np1A b.60.1.1 27155 2pia 321 5.72e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1ez0A 510 5.78e+01 1eyyA c.82.1.1 35385 1kq3A 376 5.79e+01 e.22.1.2 68790 1eyyA 510 5.80e+01 1eyyA c.82.1.1 35389 2pth 193 5.91e+01 2pth c.56.3.1 33793 4ts1A 319 5.93e+01 2ts1 c.26.1.1 31565 1p3jA 217 5.96e+01 c.37.1.1,g.41.2.1 94022,94023 1np4A 184 5.99e+01 1np1A b.60.1.1 27166 2fm8A 135 6.00e+01 2eu8A 216 6.01e+01 1a8q 274 6.04e+01 1brt c.69.1.12 34702 3ullA 132 6.05e+01 3ullA b.40.4.3 25282 1j0aA 325 6.06e+01 c.79.1.1 83871 1x05A 129 6.12e+01 1rxyA 253 6.12e+01 c.56.2.1 98065 1kb9B 352 6.14e+01 d.185.1.1,d.185.1.1 77313,77314 1pfkA 320 6.14e+01 3pfk c.89.1.1 35575 1i8dA 213 6.18e+01 b.43.4.3,b.43.4.3 61953,61954 2h3jA 75 6.19e+01 4uagA 437 6.20e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1kl9A 182 6.24e+01 b.40.4.5 72681 1zoiA 276 6.27e+01 1irxA 523 6.29e+01 a.97.1.2,c.26.1.1 71378,71379 1nhp 447 6.35e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1yfqA 342 6.40e+01 1o5zA 442 6.43e+01 c.59.1.2,c.72.2.2 92530,92531 1mjhA 162 6.50e+01 1mjhA c.26.2.4 31639 1ezvB 352 6.50e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1uhgA 385 6.54e+01 e.1.1.1 88491 1h7mA 102 6.56e+01 d.79.3.1 83485 1p9qC 256 6.60e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1nwwA 149 6.64e+01 d.17.4.8 86306 2fh1A 344 6.64e+01 1g61A 228 6.68e+01 1g61A d.126.1.1 41126 1b59A 370 6.69e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1rvv1 154 6.73e+01 1rvv1 1rvvA 154 6.73e+01 1rvv1 c.16.1.1 30927 1b6rA 355 6.76e+01 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1qgvA 142 6.78e+01 1qgvA c.47.1.8 33056 1w85A 368 6.80e+01 1hmvA 560 6.81e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1ddzA 496 6.84e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1sayA 361 6.85e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 3bamA 213 6.86e+01 1bam c.52.1.3 33288 3bamB 213 6.89e+01 1bam c.52.1.3 33289 2madH 373 6.90e+01 2bbkH b.69.2.1 27639 1iqsA 88 6.94e+01 d.214.1.1 71278 1q7sA 117 6.94e+01 c.131.1.1 96055 1uag 437 6.95e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1gs5A 258 6.97e+01 c.73.1.2 70395 2apoA 357 6.98e+01 3uagA 437 7.14e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1fmk 452 7.15e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1vliA 385 7.15e+01 b.85.1.1,c.1.10.6 108830,108831 1pfvA 551 7.28e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1k3lA 221 7.30e+01 a.45.1.1,c.47.1.5 77229,77230 1wq3A 322 7.32e+01 1jzuA 157 7.33e+01 b.60.1.1 84271 1qqtA 551 7.33e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1o6aA 96 7.34e+01 b.139.1.1 92562 1wyuA 438 7.34e+01 1y4jA 284 7.35e+01 1xgkA 352 7.38e+01 1av6A 289 7.40e+01 3mag c.66.1.25 34218 1wohA 305 7.43e+01 c.42.1.1 109446 1f4lA 551 7.43e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1vl1A 232 7.46e+01 c.124.1.1 108707 1jftA 340 7.49e+01 a.35.1.5,c.93.1.1 66652,66653 2g1uA 155 7.50e+01 1wetA 340 7.50e+01 1qpzA a.35.1.5,c.93.1.1 17093,35670 2d3jA 157 7.56e+01 1qfxA 460 7.57e+01 1qfxA c.60.1.2 33994 1tyyA 339 7.59e+01 1q77A 138 7.62e+01 c.26.2.4 96023 1xm8A 254 7.65e+01 1l5zA 155 7.67e+01 c.23.1.1 77722 1f2vA 219 7.71e+01 1f2vA c.23.17.1 59627 1pbtA 244 7.75e+01 c.124.1.1 94416 1qpzA 340 7.78e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1bxkA 355 7.80e+01 1bxkA c.2.1.2 29803 1vpwA 340 7.81e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1qkkA 155 7.84e+01 1dbwA c.23.1.1 31104 3stdA 165 7.88e+01 3stdA d.17.4.1 38073 2dcnA 311 7.98e+01 1rthA 560 8.05e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1pu5A 164 8.09e+01 b.95.1.1 104310 1n2zA 245 8.12e+01 c.92.2.2 79865 1kewA 361 8.14e+01 c.2.1.2 68544 1derA 547 8.15e+01 1derA 1tllA 688 8.16e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1tluA 130 8.19e+01 d.156.1.2 107139 1i1hA 219 8.22e+01 1f2vA c.23.17.1 61530 1ro7A 259 8.26e+01 c.130.1.1 97667 1e8yA 966 8.27e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2std 172 8.28e+01 3stdA d.17.4.1 38085 2achA 360 8.33e+01 1c8oA e.1.1.1 42626 1em2A 229 8.45e+01 1em2A d.129.3.2 41321 2d00A 109 8.50e+01 1nbwB 117 8.54e+01 c.51.3.2 80396 1kid 203 8.56e+01 1derA c.8.5.1 30771 1fzqA 181 8.62e+01 1hurA c.37.1.8 32060 1wcuA 153 8.70e+01 1vb5A 276 8.72e+01 1o8xA 146 8.72e+01 c.47.1.10 86681 3pfk 319 8.77e+01 3pfk c.89.1.1 35581 1wtjA 343 8.80e+01 1nnwA 252 8.82e+01 d.159.1.5 80674 1pe0A 197 8.88e+01 c.23.16.2 88045 1mat 264 8.88e+01 1c24A d.127.1.1 41152 1m8jA 181 8.89e+01 c.26.1.3 84875 1xodA 118 8.97e+01