# 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 1esfA 233 1.39e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1zynA 202 2.76e-01 1dyqA 234 3.49e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 5.56e-01 2rslA c.53.1.1 33345 2fclA 169 1.08e+00 2ewrA 170 1.14e+00 1hyuA 521 1.14e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ghtA 105 1.39e+00 2rslA c.53.1.1 60526 1gdtA 183 1.62e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1m93A 55 1.98e+00 e.1.1.1 91235 1pbgA 468 2.45e+00 1e70M c.1.8.4 28946 3pbgA 468 2.55e+00 1e70M c.1.8.4 28951 2afbA 351 2.56e+00 1agnA 373 2.59e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 2bg5A 324 2.90e+00 1d2oA 187 3.17e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1a0rP 245 3.63e+00 1b9yC c.47.1.6 33054 1regX 122 4.75e+00 1regX d.58.27.1 39406 1xkiA 162 5.41e+00 1focA 132 5.49e+00 1c52 a.3.1.1 15812 1ih8A 271 5.64e+00 2nsyA c.26.2.1 62377 2flsA 132 6.00e+00 1zp4A 304 6.26e+00 1j5vA 351 6.36e+00 c.72.1.1 71585 1kqpA 271 6.59e+00 c.26.2.1 72883 1xwvA 129 7.15e+00 1qhlA 227 7.61e+00 1qhlA c.37.1.12 32382 2g9iA 249 7.76e+00 1vr7A 142 7.84e+00 1repC 251 7.93e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1nsyA 271 9.40e+00 2nsyA c.26.2.1 31614 2nsyA 271 9.50e+00 2nsyA c.26.2.1 31612 1gyxA 76 9.72e+00 d.80.1.1 76387 2asbA 251 9.97e+00 1tiqA 180 1.06e+01 d.108.1.1 107010 5gcnA 166 1.07e+01 1yghA d.108.1.1 40807 1h8vA 218 1.11e+01 2nlrA b.29.1.11 60795 1s55A 156 1.17e+01 1iz5A 249 1.20e+01 d.131.1.2,d.131.1.2 83834,83835 2b33A 140 1.24e+01 1oa2A 218 1.26e+01 b.29.1.11 86721 2pil 159 1.42e+01 2pil d.24.1.1 38376 1o0pA 104 1.43e+01 d.58.7.1 86535 1iqaA 160 1.44e+01 b.22.1.1 71274 1qdlB 195 1.54e+01 1qdlB c.23.16.1 31437 2gmqA 118 1.54e+01 1d2rA 326 1.57e+01 1d2rB c.26.1.1 31572 1ycyA 71 1.58e+01 1a99A 344 1.62e+01 1pot c.94.1.1 35812 1d2pA 373 1.63e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1h72C 296 1.64e+01 d.14.1.5,d.58.26.1 60712,60713 1pnsC 206 1.68e+01 i.1.1.1 88170 1he2A 206 1.70e+01 1he2A c.2.1.2 60966 2gw6A 123 1.70e+01 1aogA 485 1.71e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1c52 131 1.72e+01 1c52 a.3.1.1 15810 1larA 575 1.73e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1f8nA 839 1.78e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1juvA 193 1.79e+01 c.71.1.1 90912 1sqsA 242 1.82e+01 c.23.5.5 98968 4uagA 437 1.83e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1b25A 619 1.89e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1uag 437 1.90e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1gm6A 175 1.92e+01 b.60.1.1 70272 1grvB 182 1.95e+01 c.61.1.1 76322 1yb2A 275 1.95e+01 1i8fA 81 1.96e+01 1i8fA b.38.1.1 61959 1fl2A 310 2.00e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1y96B 85 2.02e+01 1lwjA 441 2.03e+01 b.71.1.1,c.1.8.1 74303,74304 1k38A 254 2.05e+01 e.3.1.1 84303 2gfgA 193 2.06e+01 2fh7A 595 2.10e+01 1wmqA 147 2.14e+01 1m07A 111 2.15e+01 d.5.1.1 78328 1fwkA 296 2.17e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1hdoA 206 2.20e+01 1he2A c.2.1.2 60965 1bc4 111 2.29e+01 1onc d.5.1.1 37279 1b56 135 2.30e+01 1hmt b.60.1.2 27183 1ap0 73 2.31e+01 1ap0 b.34.13.2 37475 1u00A 227 2.32e+01 1bib 321 2.36e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 3uagA 437 2.38e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1cjbA 231 2.40e+01 1qk3A c.61.1.1 34079 1tf1A 198 2.43e+01 d.110.2.2 106826 1ge8A 249 2.44e+01 1plq d.131.1.2,d.131.1.2 41398,41399 2myr 501 2.46e+01 1wpuA 147 2.54e+01 1wjcA 47 2.58e+01 1wjcA a.4.10.1 16261 2b7eA 59 2.61e+01 1ll2A 333 2.70e+01 c.68.1.14 74005 1k0rA 366 2.71e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1x74A 360 2.71e+01 2cxcA 144 2.77e+01 1p35A 299 2.78e+01 1p35A b.28.1.1 23925 1fc2D 224 2.78e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1i6kA 328 2.80e+01 c.26.1.1 66040 1qavA 90 2.82e+01 1qauA b.36.1.1 24777 1quqB 121 2.86e+01 1quqB b.40.4.3 25305 1shsA 147 2.86e+01 1shsA b.15.1.1 23675 1sek 378 2.87e+01 1sek e.1.1.1 42675 1a9v 129 2.87e+01 1a9v b.1.18.7 21946 1o58A 303 2.94e+01 c.79.1.1 92491 1tygB 87 3.01e+01 d.15.3.2 107455 2adoA 196 3.01e+01 1tluA 130 3.04e+01 d.156.1.2 107139 1qi9A 556 3.06e+01 1qhbA a.111.1.2 19053 1qrkA 731 3.07e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1njhA 119 3.18e+01 b.128.1.1 85787 1zpvA 91 3.21e+01 1adl 131 3.23e+01 1hmt b.60.1.2 27186 1ll0A 339 3.25e+01 c.68.1.14 73995 1qoxN 449 3.26e+01 1qoxN c.1.8.4 28978 1juk 248 3.28e+01 1a53 c.1.2.4 28567 1qlmA 316 3.29e+01 1qlmA d.147.1.1 41765 1ma3A 253 3.30e+01 c.31.1.5 78883 3kar 346 3.36e+01 1bg2 c.37.1.9 32198 1s9rA 410 3.39e+01 d.126.1.4 98758 1wjbA 55 3.44e+01 1wjcA a.4.10.1 16265 2ohxA 374 3.47e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1a53 247 3.56e+01 1a53 c.1.2.4 28564 1exg 110 3.57e+01 1exg b.2.2.1 22387 1lxyA 409 3.57e+01 d.126.1.4 91154 1ay2 159 3.60e+01 2pil d.24.1.1 38377 1ktjA 129 3.63e+01 b.1.18.7 72974 1ydmA 187 3.63e+01 1igs 248 3.66e+01 1a53 c.1.2.4 28565 2aefA 234 3.70e+01 1t0aA 159 3.72e+01 1fgqA 839 3.74e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1axgA 374 3.75e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1fc1A 224 3.77e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1lid 131 3.78e+01 1hmt b.60.1.2 27184 1al0F 426 3.87e+01 2bpa1 b.121.5.1 23274 1ex0A 731 3.90e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1h4gA 207 3.93e+01 b.29.1.11 70863 2bby 69 3.95e+01 2bby a.4.5.15 16148 1wlzA 105 3.95e+01 1cbg 490 4.02e+01 1e70M c.1.8.4 28933 1evuA 731 4.04e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ur1A 378 4.08e+01 c.1.8.3 99804 1ns5A 155 4.09e+01 c.116.1.3 80705 1dg3A 592 4.10e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1ft5A 211 4.18e+01 1bvb a.138.1.3 19681 1ve6A 582 4.19e+01 1kal 29 4.23e+01 g.3.3.1 44077 1ab0 131 4.23e+01 1hmt b.60.1.2 27190 1pnsB 234 4.24e+01 i.1.1.1 88169 3nll 138 4.24e+01 5nul c.23.5.1 31206 1bg6 359 4.26e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1xdpA 687 4.30e+01 1nijA 318 4.32e+01 c.37.1.10,d.237.1.1 85741,85742 1qh7A 207 4.40e+01 1axkA b.29.1.11 24317 1wlyA 333 4.41e+01 1v04A 355 4.47e+01 b.68.6.2 100240 1kfiA 572 4.48e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1ee2A 373 4.50e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1e4mM 501 4.56e+01 1e70M c.1.8.4 59226 2bspA 420 4.56e+01 1pcl b.80.1.1 28023 1g7nA 131 4.58e+01 b.60.1.2 83274 1ibsA 317 4.58e+01 c.61.1.2,c.61.1.2 66107,66108 1e6qM 501 4.64e+01 1e70M c.1.8.4 28920 1ri7A 171 4.65e+01 a.4.5.32,d.58.4.2 97504,97505 2etxA 209 4.66e+01 1b5tA 275 4.71e+01 1b5tA c.1.23.1 29676 1epwA 1290 4.73e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1o6dA 163 4.74e+01 c.116.1.3 92567 1d2rB 326 4.78e+01 1d2rB c.26.1.1 31573 1uc7A 125 4.78e+01 c.47.1.1 99163 1xyiA 66 4.81e+01 1j5eB 256 4.81e+01 c.23.15.1 71543 1hqz1 141 4.83e+01 1duvG 333 4.84e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1bn8A 420 4.93e+01 1pcl b.80.1.1 28022 1adqA 206 4.94e+01 1igtB b.1.1.2,b.1.1.2 21518,21519 1i6lA 328 4.95e+01 c.26.1.1 66041 1a71A 374 4.98e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1zthA 258 4.98e+01 1bby 69 5.00e+01 2bby a.4.5.15 16149 1wr1B 58 5.03e+01 1xtoA 311 5.05e+01 1e70M 501 5.08e+01 1e70M c.1.8.4 28926 1o0yA 260 5.08e+01 c.1.10.1 80756 2amyA 246 5.13e+01 2cxaA 256 5.16e+01 1dkuA 317 5.17e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1o1zA 234 5.18e+01 c.1.18.3 86555 2bwbA 46 5.23e+01 2ffeA 311 5.29e+01 1fg7A 356 5.32e+01 1gewA c.67.1.1 59819 2bo4A 397 5.33e+01 1ej0A 180 5.35e+01 1ej0A c.66.1.2 34179 1hfbA 370 5.56e+01 c.1.10.4 76706 1se4 239 5.57e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1of8A 370 5.61e+01 c.1.10.4 92819 1j1vA 94 5.66e+01 a.4.12.2 83981 1vcvA 226 5.68e+01 1mmiA 366 5.69e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1n8jA 186 5.76e+01 c.47.1.10 85401 1ghr 306 5.77e+01 1aq0A c.1.8.3 28844 1j5eC 239 5.78e+01 d.52.3.1,d.53.1.1 71544,71545 2fox 138 5.82e+01 5nul c.23.5.1 31197 2bce 581 5.82e+01 2bce c.69.1.1 34625 2dfkA 402 5.83e+01 1t8qA 336 5.84e+01 c.1.18.3 106669 1tueA 212 5.85e+01 c.37.1.20 107323 1p8xA 344 5.85e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1bvb 211 5.89e+01 1bvb a.138.1.3 19683 1v0lA 313 5.98e+01 c.1.8.3 108207 8adh 374 6.01e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1oj4A 283 6.01e+01 d.14.1.5,d.58.26.5 93083,93084 3seb 238 6.20e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1qzgA 187 6.22e+01 b.40.4.3 96643 1ti6B 274 6.23e+01 b.3.5.1,d.58.1.5 106976,106977 1v93A 296 6.24e+01 c.1.23.1 100532 1bf4A 63 6.25e+01 1azpA b.34.13.1 37461 1axeA 374 6.25e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 3pfk 319 6.30e+01 3pfk c.89.1.1 35581 1ta8A 332 6.30e+01 1vicA 262 6.36e+01 c.68.1.13 100756 2bw0A 329 6.36e+01 2a41C 32 6.38e+01 1wrjA 156 6.41e+01 1wu3I 161 6.42e+01 1ck2A 104 6.44e+01 1ck9A d.79.3.1 39809 1pk9A 237 6.47e+01 c.56.2.1 94823 1azpA 66 6.52e+01 1azpA b.34.13.1 37467 1smrA 335 6.52e+01 1smrA b.50.1.2 26878 1f6dA 376 6.55e+01 1f6dA c.87.1.3 35467 1fhgA 154 6.56e+01 1tlk b.1.1.4 21706 1ydyA 356 6.58e+01 1p6pA 125 6.59e+01 b.60.1.2 87839 1vr4A 103 6.66e+01 2gi3A 476 6.70e+01 1tyjA 170 6.73e+01 1vpzA 73 6.76e+01 1wcdJ 441 6.81e+01 1f76A 336 6.88e+01 c.1.4.1 76160 1vjpA 394 6.91e+01 c.2.1.3,d.81.1.3 100828,100829 1qk3A 233 6.92e+01 1qk3A c.61.1.1 34031 2fcjA 119 6.96e+01 1dkrA 317 7.00e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1cvmA 353 7.00e+01 1qlgA b.68.3.1 27628 2bwfA 77 7.04e+01 1f9vA 347 7.15e+01 1bg2 c.37.1.9 59745 1z2uA 150 7.16e+01 1gh6A 114 7.22e+01 a.2.3.1 65191 1xkqA 280 7.29e+01 1hetA 374 7.49e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 5nul 138 7.54e+01 5nul c.23.5.1 31191 1irxA 523 7.54e+01 a.97.1.2,c.26.1.1 71378,71379 1n8kA 374 7.68e+01 b.35.1.2,c.2.1.1 80298,80299 1vm6A 228 7.73e+01 c.2.1.3,d.81.1.3 108876,108877 1yr2A 741 7.73e+01 1r64A 481 7.77e+01 b.18.1.20,c.41.1.1 97140,97141 1ponB 36 7.84e+01 1ponB 1vddA 228 7.85e+01 e.49.1.1 108519 1u3wA 374 7.88e+01 1f2tB 148 7.89e+01 1f2tB 1r5jA 337 7.93e+01 c.77.1.5 97097 1hqz9 141 7.95e+01 1xrjA 261 7.96e+01 1heuA 374 8.03e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1mixA 206 8.10e+01 a.11.2.1,b.55.1.5 79166,79167 1b0zA 445 8.14e+01 2pgi c.80.1.2 35309 2pgi 445 8.14e+01 2pgi c.80.1.2 35308 1fieA 731 8.19e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 1ok7A 366 8.19e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1cfr 285 8.21e+01 1cfr c.52.1.7 33312 1a8q 274 8.24e+01 1brt c.69.1.12 34702 1gewA 356 8.30e+01 1gewA c.67.1.1 60470 1iwmA 186 8.32e+01 b.125.1.2 83758 2trcP 217 8.32e+01 1b9yC c.47.1.6 33051 1vgvA 384 8.34e+01 c.87.1.3 100608 1jy5A 212 8.34e+01 d.124.1.1 71940 1azqA 66 8.35e+01 1azpA b.34.13.1 37469 1mjc 69 8.40e+01 1mjc b.40.4.5 25319 1b9xC 246 8.41e+01 1b9yC c.47.1.6 33053 1f5jA 199 8.41e+01 1axkA b.29.1.11 24342 1tlk 154 8.41e+01 1tlk b.1.1.4 21707 1pmt 203 8.47e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 1f0cA 305 8.51e+01 1c8oA e.1.1.1 42676 1m4jA 142 8.54e+01 d.109.1.2 78602 2b4rO 345 8.56e+01 1vqoL 165 8.56e+01 1squA 155 8.61e+01 d.252.1.1 98971 1kpuA 274 8.64e+01 b.1.1.2,d.19.1.1 84456,84457 1xn9A 101 8.69e+01 1rr7A 129 8.70e+01 a.4.1.14 105075 1dbrA 231 8.73e+01 1qk3A c.61.1.1 34041 1uj2A 252 8.75e+01 c.37.1.6 99452 1lk2A 274 8.76e+01 b.1.1.2,d.19.1.1 91056,91057 1s0pA 176 8.79e+01 a.192.1.1 98300 2f42A 179 8.82e+01 2as9A 210 8.85e+01 1gs5A 258 8.91e+01 c.73.1.2 70395