# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1t95A 240 1.20e-01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1a8h 500 3.33e-01 1a8h a.27.1.1,c.26.1.1 16922,31589 2b1eA 564 7.36e-01 2aexA 346 8.50e-01 1p9qC 256 8.91e-01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1f7wA 144 9.34e-01 1f46A d.129.4.1 59679 1woyA 500 9.52e-01 1oyb 400 1.11e+00 1oyc c.1.4.1 28602 1oya 400 1.12e+00 1oyc c.1.4.1 28604 1oyc 400 1.13e+00 1oyc c.1.4.1 28603 1f46A 140 1.13e+00 1f46A d.129.4.1 59643 1f47B 144 1.16e+00 1f46A d.129.4.1 59645 1o6dA 163 1.41e+00 c.116.1.3 92567 1tn4 159 1.42e+00 1ncx a.39.1.5 17248 1wdpA 495 1.72e+00 1byb 495 1.75e+00 1byb c.1.8.1 28790 1q6cA 495 1.75e+00 c.1.8.1 95970 1v3hA 495 1.80e+00 c.1.8.1 108303 1avsA 90 1.88e+00 1cll a.39.1.5 17226 1b1yA 500 2.11e+00 1byb c.1.8.1 28796 1id3B 102 2.38e+00 a.22.1.1 66113 2tpsA 227 2.43e+00 2tpsA c.1.3.1 28591 1y96B 85 2.62e+00 1g5pA 289 2.64e+00 1cp2A c.37.1.10 32253 2adoA 196 2.72e+00 2etxA 209 2.85e+00 1p5jA 372 3.08e+00 c.79.1.1 104067 2c5kT 95 3.36e+00 1gzqA 300 3.40e+00 b.1.1.2,d.19.1.1 70818,70819 1cvrA 435 3.57e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1aj4 161 3.63e+00 1ncx a.39.1.5 17244 1tzzA 392 3.70e+00 1eca 136 3.82e+00 1flp a.1.1.2 15209 1eco 136 4.00e+00 1flp a.1.1.2 15208 1xd8A 289 4.01e+00 1ecd 136 4.20e+00 1flp a.1.1.2 15211 2aukA 190 4.49e+00 1y1xA 191 4.73e+00 2cvhA 220 4.88e+00 1vgoA 253 5.00e+00 1b5sA 242 5.49e+00 1eaf c.43.1.1 32626 1zac 90 5.59e+00 1ncx a.39.1.5 17236 1e5pA 151 5.71e+00 1bj7 b.60.1.1 59272 1ym3A 215 6.05e+00 1cmcA 104 6.66e+00 1cmbA a.43.1.5 17462 2a5vA 213 6.83e+00 2tmkA 216 6.89e+00 3tmkA c.37.1.1 31928 1lj9A 144 6.95e+00 a.4.5.28 78035 1q6aA 107 7.22e+00 a.186.1.1 95966 2fbhA 146 7.30e+00 2ay1A 394 7.60e+00 1ajsA c.67.1.1 34357 1pkhA 204 7.87e+00 b.85.4.1 94832 1cmaA 104 7.97e+00 1cmbA a.43.1.5 17486 1ekqA 272 8.01e+00 1c3qA c.72.1.2 34941 1oghA 204 8.18e+00 b.85.4.1 86994 1bj7 156 8.29e+00 1bj7 b.60.1.1 27113 1ydmA 187 8.29e+00 1c3qA 272 8.55e+00 1c3qA c.72.1.2 34948 1omrA 201 8.88e+00 a.39.1.5 93349 1xfxO 149 8.92e+00 1tw9A 206 8.99e+00 a.45.1.1,c.47.1.5 107381,107382 1grj 158 9.14e+00 1grj a.2.1.1,d.26.1.2 15691,38433 1fp6A 289 9.47e+00 1cp2A c.37.1.10 32243 2amyA 246 9.90e+00 1xhdA 173 9.97e+00 1uw4A 91 1.00e+01 d.58.7.4 100071 2au5A 139 1.02e+01 1cmbA 104 1.03e+01 1cmbA a.43.1.5 17460 1bbhA 131 1.05e+01 1bbhA a.24.3.2 16546 1txnA 328 1.07e+01 1m1eB 81 1.09e+01 a.161.1.1 78400 1jixA 351 1.10e+01 1c3jA c.87.1.1 63081 1jg7A 351 1.10e+01 1c3jA c.87.1.1 62945 1v2zA 111 1.10e+01 a.186.1.1 108300 1q0sA 259 1.11e+01 c.66.1.28 95509 1eijA 80 1.11e+01 1eijA a.5.6.1 16298 1ockA 412 1.12e+01 c.117.1.1 86802 1c3jA 351 1.12e+01 1c3jA c.87.1.1 35459 2bgu 351 1.13e+01 1c3jA c.87.1.1 35460 1ap4 89 1.17e+01 1ncx a.39.1.5 17253 2bkaA 242 1.18e+01 1h6pA 203 1.21e+01 a.146.1.1 60690 1j93A 353 1.21e+01 c.1.22.1 66454 2amdA 311 1.24e+01 1hwtC 81 1.36e+01 1hwtC g.38.1.1,h.1.3.1 45085,45518 1vd2A 89 1.39e+01 d.15.2.2 108517 1e3pA 757 1.43e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1o5zA 442 1.50e+01 c.59.1.2,c.72.2.2 92530,92531 3tmkA 216 1.50e+01 3tmkA c.37.1.1 31920 1jsxA 207 1.58e+01 c.66.1.20 71846 1ut8A 291 1.58e+01 a.60.7.1,c.120.1.2 99908,99909 1e3hA 757 1.59e+01 1e3hA a.4.9.1,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16257,37572,37573,38810,40695,40696 1tqhA 247 1.59e+01 c.69.1.29 107225 1k2xB 143 1.59e+01 1g0cA 364 1.61e+01 7a3hA c.1.8.3 60165 1exnA 290 1.64e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1y9qA 192 1.64e+01 1g01A 364 1.65e+01 7a3hA c.1.8.3 60161 1pgvA 197 1.66e+01 c.10.1.1 88073 1mjoA 104 1.66e+01 1cmbA a.43.1.5 17466 2fu2A 102 1.73e+01 1kx5B 102 1.73e+01 a.22.1.1 77594 1f37A 110 1.75e+01 1f37A c.47.1.11 33088 1aj8A 371 1.76e+01 1aj8A a.103.1.1 18900 2b18A 164 1.76e+01 2a6sA 84 1.78e+01 1pvmA 184 1.79e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2af4C 333 1.82e+01 1aoiB 87 1.84e+01 1aoiB a.22.1.1 16470 1pmzA 86 1.89e+01 a.39.1.10 104195 2cq2A 114 1.92e+01 1qh3A 260 1.94e+01 1qh5A d.157.1.2 42059 2bnh 457 1.95e+01 1a4yA c.10.1.1 30850 1snnA 227 1.95e+01 d.115.1.2 105821 1pvyA 227 1.97e+01 d.115.1.2 95195 1y791 680 2.02e+01 1aoiF 87 2.07e+01 1aoiB a.22.1.1 16471 1p5zB 263 2.10e+01 c.37.1.1 87815 1dekA 241 2.13e+01 1dekA c.37.1.1 31842 1a6q 382 2.13e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 2fueA 262 2.17e+01 1qh5A 260 2.19e+01 1qh5A d.157.1.2 42057 1r13A 148 2.19e+01 d.169.1.1,h.1.1.1 96782,96783 1ajsA 412 2.23e+01 1ajsA c.67.1.1 34276 2erbA 125 2.23e+01 1hq3D 103 2.24e+01 1aoiB a.22.1.1 16464 1tzyD 103 2.24e+01 a.22.1.1 107533 1foeA 377 2.32e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 2a5kA 307 2.33e+01 1vflA 356 2.35e+01 1t3wA 148 2.40e+01 1h97A 147 2.41e+01 1h97A a.1.1.2 60812 1zbsA 291 2.41e+01 2cqsA 842 2.41e+01 1fkx 349 2.49e+01 1a4mA c.1.9.1 29018 1sczA 233 2.50e+01 c.43.1.1 98802 1add 349 2.52e+01 1a4mA c.1.9.1 29020 1g4yR 148 2.60e+01 1cll a.39.1.5 60252 1tfjA 219 2.67e+01 1kkuA 279 2.72e+01 c.26.1.3 72661 1wbeA 209 2.73e+01 1vjeA 166 2.75e+01 d.185.1.2 100807 1innA 166 2.75e+01 1j98A d.185.1.2 62608 1wdtA 665 2.79e+01 1n4kA 381 2.83e+01 a.118.22.1,b.42.6.1 79992,79993 1j79A 347 2.86e+01 1j79A c.1.9.4 62675 2f6mA 65 2.92e+01 1z0xA 220 2.97e+01 1qgxA 357 3.00e+01 1qgxA e.7.1.1 42973 1ka1A 357 3.00e+01 e.7.1.1 68369 1zckA 154 3.01e+01 1r0mA 375 3.02e+01 c.1.11.2,d.54.1.1 104747,104748 1z7xW 461 3.03e+01 2ao9A 155 3.04e+01 1fosF 57 3.07e+01 h.1.3.1 45538 1jo0A 98 3.07e+01 d.68.4.1 77140 2fefA 294 3.10e+01 1ofcX 304 3.14e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1ap6A 198 3.14e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 2c4jA 218 3.14e+01 1b0nA 111 3.15e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1u53A 196 3.18e+01 1w1iE 357 3.19e+01 c.1.9.1 109051 1a52A 258 3.20e+01 3erdA a.123.1.1 19296 1rhd 293 3.26e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1fw1A 216 3.32e+01 a.45.1.1,c.47.1.5 60051,60052 1iw0A 215 3.35e+01 a.132.1.1 83720 2fcwA 109 3.36e+01 1wzdA 215 3.38e+01 1r1dA 247 3.39e+01 c.69.1.29 96813 1dp3A 55 3.42e+01 1dp3A a.55.1.2 59128 1kqnA 279 3.48e+01 c.26.1.3 77492 2gl5A 410 3.49e+01 2f3yA 148 3.54e+01 1t0iA 191 3.57e+01 c.23.5.4 106209 1bfmA 69 3.60e+01 1a7w a.22.1.2 16479 2fbmA 291 3.64e+01 1t5bA 201 3.70e+01 c.23.5.3 106433 2bexA 460 3.71e+01 1delA 241 3.71e+01 1dekA c.37.1.1 31844 1a4yA 460 3.73e+01 1a4yA c.10.1.1 30852 1ncx 162 3.75e+01 1ncx a.39.1.5 17222 1top 162 3.76e+01 1ncx a.39.1.5 17223 2beqD 48 3.84e+01 1y0vH 146 3.88e+01 1s48A 609 3.89e+01 e.8.1.4 98475 1q74A 303 3.94e+01 c.134.1.1 96019 1kq8A 100 4.00e+01 a.4.5.14 68797 1x54A 434 4.00e+01 1mfqC 129 4.04e+01 a.36.1.1 79046 1qhtA 775 4.07e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1kn1B 161 4.14e+01 a.1.1.3 77456 1nvmA 345 4.19e+01 a.5.7.1,c.1.10.5 86249,86250 1y97A 238 4.20e+01 1keaA 221 4.22e+01 a.96.1.2 68491 1sauA 115 4.24e+01 1srqA 341 4.26e+01 e.55.1.1 105967 1a4mA 349 4.33e+01 1a4mA c.1.9.1 29014 1imoA 88 4.39e+01 1imoA c.15.1.2 62590 1a7w 69 4.50e+01 1a7w a.22.1.2 16477 1a32 88 4.55e+01 1a32 a.16.1.2 16384 2a4vA 159 4.56e+01 1xeuA 263 4.57e+01 1q2wA 308 4.60e+01 b.47.1.4 88355 1rhs 296 4.62e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1v3wA 173 4.63e+01 b.81.1.5 100291 1n0wA 243 4.64e+01 c.37.1.11 79772 1otjA 283 4.67e+01 b.82.2.5 93517 1pyfA 312 4.69e+01 c.1.7.1 95334 1pq9A 253 4.73e+01 a.123.1.1 95004 1jbaA 204 4.80e+01 1rec a.39.1.5 17330 1ltaC 49 4.87e+01 1ltaC 1dqsA 393 4.89e+01 1dqsA e.22.1.1 43347 1vlpA 441 4.92e+01 d.41.2.2,d.41.2.3 108840,108841 1wpgA 994 5.01e+01 1t3qB 788 5.04e+01 d.41.1.1,d.133.1.1 106369,106370 2c3nA 247 5.05e+01 1exnB 290 5.07e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1n9dA 199 5.14e+01 a.26.1.1 85464 1flp 142 5.19e+01 1flp a.1.1.2 15011 1moh 142 5.21e+01 1flp a.1.1.2 15012 1cll 148 5.26e+01 1cll a.39.1.5 17263 1xfxA 777 5.30e+01 1fr2A 86 5.31e+01 a.28.2.1 83256 1v6tA 255 5.31e+01 1vqoN 187 5.34e+01 1b33B 161 5.36e+01 1qgwC a.1.1.3 15650 1xw5A 217 5.42e+01 1rt8A 513 5.42e+01 a.40.1.1 105095 1ug6A 431 5.42e+01 c.1.8.4 88490 2b43A 526 5.47e+01 1b67A 68 5.50e+01 1a7w a.22.1.2 16474 1hta 69 5.56e+01 1a7w a.22.1.2 16476 1emvA 86 5.59e+01 1cei a.28.2.1 16944 1bmfA 510 5.61e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1ggzA 148 5.63e+01 a.39.1.5 70176 1m2aA 110 5.77e+01 c.47.1.11 78472 1r9lA 309 5.79e+01 c.94.1.1 97262 1b0b 142 5.87e+01 2fal a.1.1.2 15010 1m2bA 110 5.90e+01 c.47.1.11 78474 1yf3A 259 5.94e+01 1uvqB 198 5.97e+01 b.1.1.2,d.19.1.1 100064,100065 2itg 163 6.00e+01 1b9dA c.55.3.2 33669 1qbgA 272 6.06e+01 1d4aA c.23.5.3 31227 2b3yA 888 6.10e+01 1miwA 404 6.11e+01 a.173.1.1,d.218.1.4 79162,79163 1zzcA 198 6.11e+01 1yzyA 413 6.13e+01 1icpA 376 6.14e+01 1oyc c.1.4.1 62270 2b5aA 77 6.16e+01 1sbp 310 6.16e+01 1sbp c.94.1.1 35760 1xgwA 176 6.17e+01 1prq 125 6.20e+01 3nul d.110.1.1 40883 1wa3A 205 6.21e+01 1ztpA 251 6.21e+01 2fliA 220 6.34e+01 1mj3A 260 6.34e+01 c.14.1.3 79183 2aclB 244 6.35e+01 1ywfA 296 6.38e+01 1upvA 257 6.43e+01 1yruB 74 6.44e+01 1hnr 47 6.47e+01 1hnr a.155.1.1 17896 1nkpA 88 6.48e+01 a.38.1.1 80573 1pl4A 198 6.54e+01 a.2.11.1,d.44.1.1 94854,94855 1onxA 390 6.54e+01 b.92.1.7,c.1.9.13 87176,87177 1abmA 198 6.54e+01 1avmA 1y7yA 74 6.56e+01 1idrA 136 6.61e+01 1dlyA a.1.1.1 62301 1v1dA 31 6.62e+01 1v77A 212 6.63e+01 c.6.3.2 108402 2f6uA 234 6.66e+01 1ezvB 352 6.69e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1r5jA 337 6.72e+01 c.77.1.5 97097 2abbA 364 6.73e+01 1allA 160 6.73e+01 1qgwC a.1.1.3 15647 1m2dA 110 6.74e+01 c.47.1.11 78476 1vypX 364 6.74e+01 c.1.4.1 108905 1onwA 390 6.74e+01 b.92.1.7,c.1.9.13 87172,87173 1z0kB 69 6.75e+01 3ertA 261 6.76e+01 3erdA a.123.1.1 19292 1cpq 129 6.83e+01 1cpq a.24.3.2 16556 2mysB 166 6.83e+01 1wdcB a.39.1.5 17308 1qrdA 273 6.84e+01 1d4aA c.23.5.3 31217 1vjvA 415 6.86e+01 d.3.1.9 108632 1ijgA 309 6.87e+01 1fouA e.27.1.1 62493 1wy1A 172 6.88e+01 1i37A 260 6.90e+01 1a28A a.123.1.1 61583 1mp4A 292 6.92e+01 c.68.1.6 79376 1yirA 408 6.95e+01 2dubE 261 6.95e+01 1nzyA c.14.1.3 30916 1gln 468 6.97e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1ox0A 430 7.00e+01 c.95.1.1,c.95.1.1 87495,87496 1xpcA 248 7.04e+01 1dpsA 167 7.07e+01 1dpsA a.25.1.1 16716 1q1hA 110 7.15e+01 a.4.5.41 95580 1r9kA 172 7.17e+01 a.168.1.1 104869 1dpsD 167 7.21e+01 1dpsA a.25.1.1 16719 2es9A 115 7.23e+01 2aaoA 166 7.26e+01 1y74A 57 7.28e+01 1dugA 234 7.30e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 2gokA 429 7.33e+01 1ck7A 631 7.40e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1t7rA 269 7.42e+01 a.123.1.1 106635 2ct8A 497 7.48e+01 1ku2A 241 7.49e+01 a.4.13.1,a.177.1.1 83096,83097 1woqA 267 7.49e+01 c.55.1.10,c.55.1.10 109462,109463 1qznA 173 7.50e+01 b.2.2.2 104669 2ax8A 256 7.53e+01 1pdz 434 7.53e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1h4pA 408 7.54e+01 c.1.8.3 90617 1h0aA 158 7.59e+01 a.118.9.1 76434 1sh0A 510 7.67e+01 e.8.1.4 98876 1ywsA 82 7.70e+01 1jthD 77 7.72e+01 h.1.15.1 67273 1ia8A 289 7.72e+01 1ia8A d.144.1.7 62112 2bm5A 186 7.83e+01 1xk5A 204 7.86e+01 1gnxA 479 7.87e+01 c.1.8.4 76241 1ih8A 271 7.97e+01 2nsyA c.26.2.1 62377 1lt4A 247 7.98e+01 1lt3A d.166.1.1 42231 3erdA 261 7.98e+01 3erdA a.123.1.1 19293 1aow 309 7.98e+01 1avc a.65.1.1 18152 2nsyA 271 8.05e+01 2nsyA c.26.2.1 31612 1nsyA 271 8.05e+01 2nsyA c.26.2.1 31614 1n83A 270 8.08e+01 a.123.1.1 80276 1u8bA 133 8.08e+01 1wmhA 89 8.09e+01 1useA 45 8.10e+01 1rw1A 114 8.12e+01 1whzA 70 8.13e+01 1paqA 189 8.16e+01 a.118.1.14 94413 1izmA 184 8.17e+01 a.199.1.1 90725 1m12A 84 8.18e+01 a.64.1.1 84745 1yfbA 59 8.19e+01 1regX 122 8.19e+01 1regX d.58.27.1 39406 1h5rA 293 8.20e+01 c.68.1.6 65623 1c52 131 8.20e+01 1c52 a.3.1.1 15810 1n1jA 93 8.35e+01 a.22.1.3 79813 1g24A 211 8.38e+01 1g24A d.166.1.1 42270 1or4A 178 8.38e+01 a.1.1.2 93447 3cln 148 8.39e+01 1cll a.39.1.5 17286 1oq9A 363 8.40e+01 a.25.1.2 87257 1iq4A 179 8.40e+01 1iq4A d.77.1.1 62641 2cfxA 144 8.42e+01 1o50A 157 8.44e+01 d.37.1.1,d.37.1.1 92478,92479 1eyhA 144 8.47e+01 1eduA a.118.9.1 19214 1g59A 468 8.50e+01 a.97.1.1,c.26.1.1 60257,60258 2ar0A 541 8.50e+01 1afrA 345 8.50e+01 1afrA a.25.1.2 16805 1yzmA 51 8.52e+01 1vjuA 309 8.55e+01 d.248.1.1 100835 1cqa 133 8.56e+01 3nul d.110.1.1 40890 1ds9A 198 8.58e+01 1ds9A c.10.3.1 30879 1kqpA 271 8.59e+01 c.26.2.1 72883 1ypyA 184 8.59e+01 3nodB 423 8.63e+01 1nseA d.174.1.1 42513 1q8cA 151 8.65e+01 a.79.1.2 96202 1xfuA 747 8.81e+01 1p3wA 404 8.83e+01 c.67.1.3 87752 1eduA 149 8.84e+01 1eduA a.118.9.1 19215 1oe8A 211 8.87e+01 a.45.1.1,c.47.1.5 86905,86906 1cpcL 172 8.91e+01 1qgwC a.1.1.3 15646 1tr0A 108 8.93e+01 d.58.4.4 107261 1czqA 46 8.94e+01 1czqA h.3.2.1 45720 1jfiB 179 8.97e+01 1jfiB a.22.1.3 62937 1k8tA 510 8.97e+01 e.41.1.1 68316 1kbqA 273 8.98e+01 c.23.5.3 68391 1xubA 298 8.99e+01