# List of top-scoring protein chains for t04-100-30-n_sep-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 1mugA 168 3.43e-02 1mugA c.18.1.2 31030 1qynA 153 4.77e-02 d.33.1.1 96597 1z54A 132 3.09e-01 1oshA 232 4.47e-01 a.123.1.1 93496 1fcyA 236 4.63e-01 2lbd a.123.1.1 19282 1ijbA 202 5.13e-01 c.62.1.1 71229 1qysA 106 5.47e-01 k.41.1.1 96603 1yvoA 172 6.28e-01 1fnsA 196 7.53e-01 1auq c.62.1.1 34136 1u6zA 513 7.92e-01 1g7dA 106 8.03e-01 1g7dA a.71.1.1 18318 1rz1A 161 8.49e-01 b.45.1.2 98124 2ggcA 263 8.80e-01 1yqtA 538 9.40e-01 1ttuA 477 9.41e-01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 2bl1A 172 1.04e+00 1oxxK 353 1.07e+00 b.40.6.3,c.37.1.12 93715,93716 1c24A 263 1.09e+00 1c24A d.127.1.1 41148 7odcA 424 1.16e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1zsoA 164 1.18e+00 1xnzA 264 1.37e+00 1oqjA 97 1.70e+00 d.217.1.1 93417 1y9wA 140 1.76e+00 1oxsC 353 1.91e+00 b.40.6.3,c.37.1.12 87519,87520 1cyj 90 1.91e+00 1ctj a.3.1.1 15805 1dqiA 124 1.93e+00 1do6A b.1.13.1 22357 1gtmA 419 1.98e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1o0xA 262 2.02e+00 d.127.1.1 80755 2kfnA 605 2.08e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1wywA 230 2.16e+00 1zcbA 362 2.18e+00 1k3xA 262 2.26e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1koiA 184 2.61e+00 b.60.1.1 68725 1tf1A 198 2.65e+00 d.110.2.2 106826 1fl1A 230 2.76e+00 1at3A b.57.1.1 27023 1z4rA 168 3.05e+00 1jp4A 308 3.08e+00 1jp4A e.7.1.1 63223 1oj4A 283 3.10e+00 d.14.1.5,d.58.26.5 93083,93084 1o69A 394 3.18e+00 c.67.1.4 92560 1ryp2 233 3.22e+00 1ryp2 2c43A 323 3.27e+00 1jk7A 323 3.29e+00 1auiA d.159.1.3 63144 1aszB 490 3.30e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 1jhdA 396 3.44e+00 b.122.1.3,c.26.1.5 66712,66713 1x8qA 184 3.51e+00 2gx9A 129 3.60e+00 1sy3A 184 3.83e+00 b.60.1.1 106110 2fvvA 194 3.88e+00 1pv5A 264 3.90e+00 d.251.1.1 95150 1bmdA 327 3.99e+00 1bmdA c.2.1.5,d.162.1.1 30139,42106 1uyjA 296 4.04e+00 f.8.1.2 108143 1do6A 124 4.07e+00 1do6A b.1.13.1 22361 1kopA 223 4.14e+00 2cba b.74.1.1 27966 1lssA 140 4.16e+00 c.2.1.9 74246 2d9rA 104 4.21e+00 1y7tA 327 4.22e+00 1ex2A 189 4.23e+00 1ex2A c.51.4.2 33225 1mm4A 170 4.25e+00 f.4.1.2 79294 1vkhA 273 4.27e+00 c.69.1.32 108662 1sr9A 644 4.30e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1m4iA 181 4.37e+00 d.108.1.1 74457 2g6yA 217 4.53e+00 1erxA 184 4.60e+00 1np1A b.60.1.1 27164 2bydA 323 4.68e+00 1mkyA 439 4.77e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1bh9A 45 4.77e+00 1bh9A a.22.1.3 16483 1jjtA 228 4.92e+00 1a7tA d.157.1.1 63139 2fxqA 264 4.93e+00 1etxA 98 4.97e+00 1fipA a.4.1.12 18978 2gf6A 135 5.14e+00 1q77A 138 5.23e+00 c.26.2.4 96023 2giyA 191 5.24e+00 1f2tA 149 5.37e+00 1f2tA c.37.1.12 32373 1vjlA 164 5.56e+00 d.257.1.1 100822 1u32A 293 5.62e+00 d.159.1.3 107631 1h75A 81 5.83e+00 1h75A c.47.1.1 60716 1mc0A 368 6.58e+00 d.110.2.1,d.110.2.1 78937,78938 1jjeA 222 6.80e+00 1a7tA d.157.1.1 63117 1vcoA 550 6.82e+00 c.23.16.1,c.37.1.10 108508,108509 1mkmA 249 6.85e+00 a.4.5.33,d.110.2.2 79242,79243 1rypL 212 6.85e+00 d.153.1.4 41880 1t1jA 125 7.00e+00 c.137.1.1 106249 1vhmA 195 7.01e+00 d.110.2.1 100691 2mcm 112 7.04e+00 2mcm b.1.7.1 22207 1y8qB 640 7.10e+00 2dkb 433 7.30e+00 2dkb c.67.1.4 34438 2c4nA 250 7.34e+00 1h7sA 365 7.96e+00 d.14.1.3,d.122.1.2 65705,65706 1g6hA 257 7.97e+00 1gajA c.37.1.12 60318 1vjnA 220 8.03e+00 d.157.1.4 100825 1fvrA 327 8.21e+00 d.144.1.7 60047 2fvgA 340 8.30e+00 1ctj 89 8.43e+00 1ctj a.3.1.1 15798 2b8eA 273 8.83e+00 1i39A 225 8.98e+00 1ekeA c.55.3.1 61585 2gpiA 91 9.15e+00 1zpyA 95 9.16e+00 1fs7A 485 9.17e+00 1qdbA a.138.1.3 19691 1hkkA 364 9.37e+00 c.1.8.5,d.26.3.1 90634,90635 1w07A 659 9.53e+00 1hf2A 210 9.62e+00 1hf2A b.80.3.1,c.102.1.1 60992,60993 1zgoA 223 9.63e+00 1ukfA 188 9.64e+00 d.3.1.10 99488 1uujA 88 9.66e+00 a.221.1.1 108046 1sjqA 105 1.01e+01 d.58.7.1 105660 1us8A 147 1.01e+01 c.37.1.12 99859 2d37A 176 1.02e+01 1wzcA 249 1.02e+01 1e9gA 286 1.05e+01 1wgjA b.40.5.1 59393 1dqnA 230 1.05e+01 1dqnA c.61.1.1 34067 1uq5A 263 1.08e+01 d.165.1.1 99778 1ylxA 103 1.09e+01 1dqpA 230 1.09e+01 1dqnA c.61.1.1 34069 1tuhA 156 1.11e+01 d.17.4.11 107345 2bmoB 194 1.11e+01 2h4uA 145 1.12e+01 1ggxA 223 1.14e+01 1ggxA d.22.1.1 38367 1qmeA 702 1.15e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1itxA 419 1.20e+01 c.1.8.5,d.26.3.1 71425,71426 1thqA 170 1.21e+01 f.4.1.2 106920 1fit 147 1.21e+01 1fit d.13.1.1 37499 1s1eA 224 1.21e+01 1jj2E 177 1.22e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1fjmA 330 1.22e+01 1auiA d.159.1.3 42082 2d7vA 162 1.22e+01 1s72E 178 1.24e+01 d.141.1.1,d.141.1.1 105323,105324 1uliB 187 1.25e+01 d.17.4.4 107923 1s3zA 165 1.25e+01 d.108.1.1 105250 1qxyA 252 1.27e+01 d.127.1.1 96565 1eceA 358 1.28e+01 1eceA c.1.8.3 28813 1a68 95 1.28e+01 1t1dA d.42.1.2 38639 1imjA 210 1.30e+01 c.69.1.23 71246 1led 243 1.32e+01 1led b.29.1.1 24039 1i9bA 217 1.32e+01 1i9bA b.96.1.1 62084 1hskA 326 1.32e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1vp4A 425 1.33e+01 1yckA 175 1.33e+01 1rypJ 204 1.34e+01 d.153.1.4 41878 1vhcA 224 1.35e+01 c.1.10.1 100661 1m4zA 238 1.36e+01 b.34.12.1 78630 1c52 131 1.38e+01 1c52 a.3.1.1 15810 1khdA 345 1.38e+01 a.46.2.1,c.27.1.1 77400,77401 2bj0A 203 1.39e+01 2d8aA 348 1.39e+01 1de4C 640 1.40e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1mnnA 340 1.43e+01 b.2.5.7 79324 1gyxA 76 1.45e+01 d.80.1.1 76387 1s7kA 182 1.46e+01 1p7tA 731 1.47e+01 c.1.13.1 94319 1wgeA 83 1.48e+01 1v61A 132 1.48e+01 b.55.1.1 108389 1vr5A 547 1.50e+01 1dzkA 157 1.50e+01 1obpA b.60.1.1 27096 1snzA 344 1.51e+01 b.30.5.4 98930 2c6cA 707 1.51e+01 1zupA 315 1.56e+01 1vqzA 341 1.62e+01 1uv6A 210 1.63e+01 b.96.1.1 100030 1xauA 122 1.63e+01 1ytw 306 1.66e+01 1ytw c.45.1.2 32689 1faaA 124 1.66e+01 1erv c.47.1.1 32738 2d5cA 263 1.66e+01 1s0yA 76 1.69e+01 d.80.1.1 98314 1wpoA 256 1.69e+01 1lay b.57.1.1 27012 1ji8A 111 1.70e+01 d.203.1.1 66733 2dddA 225 1.72e+01 1pg4A 652 1.75e+01 e.23.1.1 88067 1lyvA 306 1.75e+01 c.45.1.2 74348 1svsA 353 1.77e+01 c.37.1.8 106051 1forL 210 1.77e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 1b7yA 350 1.77e+01 1pysA d.104.1.1 40776 1cqqA 180 1.78e+01 1cqqA b.47.1.4 26422 1iz0A 302 1.79e+01 b.35.1.2,c.2.1.1 83821,83822 2fhi 147 1.80e+01 1fit d.13.1.1 37505 1fepA 724 1.80e+01 1fepA f.4.3.3 43808 1g5aA 628 1.81e+01 b.71.1.1,c.1.8.1 65152,65153 1kypA 237 1.81e+01 d.22.1.1 73280 1d8cA 723 1.83e+01 1d8cA c.1.13.1 29325 1vkyA 347 1.83e+01 e.53.1.1 108696 1zy9A 564 1.84e+01 1edg 380 1.88e+01 1edg c.1.8.3 28807 1seqL 213 1.88e+01 1mml 265 1.90e+01 1mml e.8.1.2 43015 1gpqA 135 1.90e+01 d.233.1.1 83295 1sviA 195 1.90e+01 c.37.1.8 106048 1j1bA 420 1.93e+01 d.144.1.7 90758 1vqoE 178 1.94e+01 1wxdA 263 1.96e+01 2etjA 250 1.96e+01 1xodA 118 1.96e+01 1q0bA 367 1.98e+01 c.37.1.9 95502 2fkbA 180 1.99e+01 1fiwA 290 2.00e+01 5ptp 1xoyA 161 2.01e+01 2b4lA 268 2.01e+01 1d7uA 433 2.01e+01 2dkb c.67.1.4 34439 2f51A 118 2.04e+01 1pguA 615 2.05e+01 b.69.4.1,b.69.4.1 88069,88070 1kbjA 412 2.07e+01 c.1.4.1 72280 1t1dA 100 2.07e+01 1t1dA d.42.1.2 38637 1vq0A 302 2.08e+01 1j5yA 187 2.09e+01 a.4.5.1,d.94.2.1 71592,71593 1tetL 216 2.11e+01 32c2A b.1.1.1,b.1.1.2 19902,20996 1ijgA 309 2.11e+01 1fouA e.27.1.1 62493 1phk 298 2.12e+01 1cdkA d.144.1.7 41635 2trcP 217 2.15e+01 1b9yC c.47.1.6 33051 1e5pA 151 2.15e+01 1bj7 b.60.1.1 59272 1m98A 317 2.16e+01 a.175.1.1,d.17.4.6 78866,78867 2bjrA 368 2.21e+01 1ekrA 161 2.22e+01 1ekrA d.58.21.1 39380 1mlbA 214 2.26e+01 8fabA b.1.1.1,b.1.1.2 20050,21092 1fm4A 159 2.26e+01 1bv1 d.129.3.1 76186 1x13A 401 2.27e+01 2ajuL 216 2.27e+01 1di2A 69 2.30e+01 1di2A d.50.1.1 38780 2ad9A 119 2.30e+01 1r2zA 274 2.31e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1bdmA 327 2.31e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1j27A 102 2.32e+01 d.58.50.1 90778 1u9iA 519 2.32e+01 1r3dA 264 2.33e+01 2dd8S 202 2.35e+01 3pmgA 561 2.36e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1z5yE 149 2.36e+01 1uekA 275 2.40e+01 d.14.1.5,d.58.26.5 88483,88484 1vrpA 381 2.40e+01 2c2xA 281 2.40e+01 1c4kA 730 2.40e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 2aneA 125 2.41e+01 1zuxA 224 2.41e+01 1q9rA 219 2.42e+01 b.1.1.1,b.1.1.2 96305,96306 1rurL 217 2.44e+01 b.1.1.1,b.1.1.2 97881,97882 1ox6A 555 2.45e+01 c.1.2.1,c.23.16.1 87505,87506 1sauA 115 2.47e+01 1ym5A 300 2.48e+01 1tbfA 347 2.48e+01 a.211.1.2 106743 1xvsA 126 2.50e+01 1ew0A 130 2.50e+01 1drmA d.110.3.2 40905 1ospO 257 2.51e+01 1ospO b.76.1.1 27971 2aabL 218 2.51e+01 1o5iA 249 2.52e+01 c.2.1.2 92499 1xgyL 216 2.53e+01 1ift 263 2.54e+01 1mrj d.165.1.1 42211 1uw6A 211 2.57e+01 b.96.1.1 100079 2d83A 363 2.57e+01 1yb2A 275 2.58e+01 2anpA 291 2.60e+01 1q98A 165 2.61e+01 c.47.1.10 96253 2cy0A 263 2.61e+01 1e6bA 221 2.62e+01 1e6bA a.45.1.1,c.47.1.5 59294,59295 1qcwA 410 2.64e+01 1gox c.1.4.1 28622 1i1qA 520 2.65e+01 1qdlA d.161.1.1 61543 1y8cA 246 2.65e+01 1mjuL 219 2.66e+01 b.1.1.1,b.1.1.2 91304,91305 1xssA 225 2.67e+01 1n1jA 93 2.67e+01 a.22.1.3 79813 1iqcA 308 2.68e+01 a.3.1.5,a.3.1.5 66266,66267 2g38B 198 2.68e+01 2bvpA 276 2.68e+01 1pysA 350 2.69e+01 1pysA d.104.1.1 40775 1gcvB 136 2.69e+01 1cg5B a.1.1.2 15589 1x88A 359 2.69e+01 1brwA 433 2.71e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1gy7A 125 2.72e+01 d.17.4.2 70738 1jfmA 174 2.72e+01 d.19.1.1 66640 1f9mA 112 2.75e+01 1erv c.47.1.1 32736 5rubA 490 2.75e+01 1burA c.1.14.1,d.58.9.1 29382,39288 1a04A 215 2.75e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1msk 331 2.75e+01 1msk d.173.1.1 42495 1ema 236 2.76e+01 1ema d.22.1.1 38339 1sqgA 429 2.76e+01 a.79.1.3,c.66.1.38 105912,105913 1pz4A 116 2.77e+01 d.106.1.1 95400 1l0wA 580 2.77e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1l1zA 274 2.79e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 3daaA 277 2.79e+01 1daaA e.17.1.1 43272 1rtqA 299 2.80e+01 c.56.5.4 97819 1ospL 214 2.80e+01 32c2A b.1.1.1,b.1.1.2 20116,21146 1wb0A 445 2.81e+01 1yqvL 211 2.82e+01 1jenB 67 2.82e+01 1jenB d.156.1.1 42029 1ll7A 392 2.83e+01 c.1.8.5,d.26.3.1 78085,78086 1t64A 377 2.85e+01 c.42.1.2 106543 1zwxA 301 2.85e+01 1am9A 82 2.85e+01 1am9A a.38.1.1 17140 1xkyA 301 2.86e+01 1w44A 331 2.86e+01 1ux2A 212 2.86e+01 b.96.1.1 100132 2fbjL 213 2.87e+01 8fabA b.1.1.1,b.1.1.2 19850,20954 1ax4A 467 2.87e+01 1ax4A c.67.1.2 34391 2breA 219 2.89e+01 1whsA 255 2.90e+01 1ivyA c.69.1.5 34649 1bo1A 416 2.92e+01 1bo1A d.143.1.2 41591 1ztxL 212 2.92e+01 1amp 291 2.93e+01 1amp c.56.5.4 33837 1xklA 273 2.94e+01 1iu4A 331 2.95e+01 d.3.1.8 71430 1a58 177 2.97e+01 2cpl b.62.1.1 27495 1vr4A 103 2.98e+01 1wubA 178 2.98e+01 1wzlA 585 2.98e+01 2ethA 154 3.00e+01 1a5t 334 3.02e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1njkA 156 3.06e+01 d.38.1.1 85818 1ysqA 193 3.06e+01 2acvA 463 3.07e+01 1vl4A 447 3.08e+01 d.283.1.1 108718 1sgwA 214 3.08e+01 c.37.1.12 105541 2bfdA 400 3.09e+01 1j5wA 298 3.10e+01 d.104.1.1 71589 1uluA 261 3.12e+01 1nmoA 247 3.12e+01 c.135.1.1 91980 1i8aA 189 3.14e+01 1i82A b.1.9.2 61951 1qwiA 143 3.14e+01 d.227.1.1 96474 1fx3A 169 3.16e+01 1fx3B d.33.1.1 38524 2gnqA 336 3.17e+01 1winA 143 3.19e+01 1onxA 390 3.19e+01 b.92.1.7,c.1.9.13 87176,87177 1p32A 209 3.21e+01 1p32A d.25.1.1 38379 1exmA 405 3.21e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1whtA 256 3.22e+01 1ivyA c.69.1.5 34646 1bdb 277 3.24e+01 1bdb c.2.1.2 29874 1y01A 102 3.24e+01 1sk4A 163 3.29e+01 d.118.1.1 105664 2aqlA 173 3.30e+01 1lk2B 99 3.32e+01 b.1.1.2 91058 1fzkB 99 3.32e+01 1agdB b.1.1.2 60151 1yzbA 182 3.33e+01 1onwA 390 3.37e+01 b.92.1.7,c.1.9.13 87172,87173 1xkzA 255 3.41e+01 2czrA 226 3.45e+01 1f1xA 322 3.46e+01 d.32.1.3,d.32.1.3 83208,83209 1kjvB 100 3.46e+01 b.1.1.2 77423 1gl4A 285 3.47e+01 d.22.1.2,g.3.11.5 65286,65287 1f3aA 222 3.47e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1ta0A 197 3.47e+01 c.108.1.16 106729 2bhoA 130 3.48e+01 1o5kA 306 3.49e+01 c.1.10.1 92504 1io2A 213 3.50e+01 1ekeA c.55.3.1 62612 2bolA 314 3.50e+01 1tkiA 321 3.51e+01 1tkiA d.144.1.7 41638 2c78A 405 3.53e+01 1fzoB 99 3.55e+01 1agdB b.1.1.2 60157 1mexL 213 3.56e+01 b.1.1.1,b.1.1.2 91259,91260 1w9pA 433 3.56e+01 1lsuA 147 3.56e+01 c.2.1.9 74250 1rvaA 244 3.61e+01 1rvaA c.52.1.2 33240 1xgsA 295 3.61e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 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