# List of top-scoring protein chains for t06-100-30-alpha-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 1xubA 298 1.17e-03 2b3nA 159 1.30e-02 1w61A 414 2.44e-02 1ym5A 300 2.55e-02 2gkeA 274 2.87e-02 1gqzA 274 4.71e-02 d.21.1.1,d.21.1.1 83311,83312 1p3dA 475 1.80e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1ixlA 131 1.94e-01 d.38.1.5 90717 1dp4A 435 2.70e-01 1dp4A c.93.1.1 35710 2azpA 318 3.82e-01 1dkqA 410 5.26e-01 1dklA c.60.1.2 33998 1sr8A 298 6.15e-01 e.54.1.1 105959 1dkmA 410 6.46e-01 1dklA c.60.1.2 34000 1wznA 252 6.98e-01 1yqfA 203 7.56e-01 1ycoA 279 9.10e-01 1nnxA 109 1.13e+00 b.40.10.1 92013 1vdkA 466 1.24e+00 a.127.1.1 100561 1o17A 345 1.35e+00 a.46.2.1,c.27.1.1 80765,80766 1qx4A 274 1.36e+00 b.43.4.2,c.25.1.1 104624,104625 1mxmA 254 1.46e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 2fr2A 172 1.60e+00 1jf9A 408 1.79e+00 1c0nA c.67.1.3 62931 1rzhL 281 1.91e+00 f.26.1.1 98164 2cxcA 144 2.16e+00 1j5pA 253 2.33e+00 d.81.1.3,c.2.1.3 71577,83092 1xtqA 177 2.36e+00 1umkA 275 2.46e+00 1gtzA 156 2.51e+00 c.23.13.1 70539 1tzfA 259 2.89e+00 c.68.1.13 107476 1jc9A 269 3.06e+00 d.171.1.1 66490 2aliA 158 3.35e+00 1t6aA 126 3.38e+00 d.129.8.1 106555 1nscA 390 3.49e+00 2qwc b.68.1.1 27591 1bupA 386 3.50e+00 1ba1 c.55.1.1,c.55.1.1 33377,33378 1sziA 247 3.58e+00 a.24.23.1 106159 1josA 128 3.81e+00 d.52.7.1 84191 2d93A 134 4.01e+00 1nrjB 218 4.02e+00 c.37.1.8 86125 2fs2A 151 4.04e+00 1f3uA 118 4.07e+00 1f3uA b.65.1.1 27521 1oe4A 247 4.18e+00 c.18.1.3 86895 1iznB 277 4.90e+00 e.43.1.2 83848 1b56 135 4.93e+00 1hmt b.60.1.2 27183 1u3wA 374 5.07e+00 1wtaA 275 5.10e+00 1wosA 364 5.43e+00 b.44.2.1,d.250.1.1 109468,109469 4uagA 437 5.45e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1z94A 147 5.51e+00 1g5cA 170 5.66e+00 1g5cA c.53.2.1 60264 1uwkA 557 6.30e+00 e.51.1.1 108065 1ecfA 504 6.47e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1vljA 407 6.55e+00 e.22.1.2 108832 1uebA 184 6.61e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1qipA 183 7.02e+00 1qipA d.32.1.1 38470 1q2yA 140 7.12e+00 d.108.1.1 95655 1f06A 320 7.13e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 1y791 680 7.14e+00 1pjxA 314 7.24e+00 b.68.6.1 104167 1nnsA 326 7.67e+00 c.88.1.1 85910 1pfsA 78 7.69e+00 1pfsA b.40.4.7 25391 1q15A 503 7.78e+00 c.26.2.1,d.153.1.1 95538,95539 1snzA 344 7.84e+00 b.30.5.4 98930 2h0bA 184 7.95e+00 1xttA 216 7.98e+00 2bm3A 166 8.07e+00 1bebA 162 8.13e+00 1bebA b.60.1.1 27115 1hp1A 516 8.15e+00 d.114.1.1,d.159.1.2 70976,70977 1evhA 112 8.83e+00 1evhA b.55.1.4 26997 1ogsA 497 8.84e+00 b.71.1.2,c.1.8.3 86997,86998 1tafB 70 8.96e+00 1tafB a.22.1.3 16482 1r5eA 115 9.38e+00 4ubpC 570 9.49e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 2a1kA 233 9.53e+00 1i1nA 226 9.63e+00 c.66.1.7 71102 2a8yA 270 1.03e+01 1ogdA 131 1.03e+01 c.133.1.1 92893 1jhjA 171 1.04e+01 b.18.1.9 66714 1wycA 392 1.05e+01 2aneA 125 1.09e+01 1vh5A 148 1.09e+01 d.38.1.5 100642 2d4qA 257 1.11e+01 1wuiL 534 1.12e+01 1alu 186 1.14e+01 1alu a.26.1.1 16826 1wudA 89 1.16e+01 1rsy 152 1.16e+01 1rsy b.7.1.2 23192 2f4nA 273 1.20e+01 1sk4A 163 1.22e+01 d.118.1.1 105664 1gt1A 159 1.26e+01 b.60.1.1 90515 1z54A 132 1.28e+01 1e1oA 504 1.29e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1vpjA 192 1.29e+01 1ubkL 534 1.30e+01 e.18.1.1 88422 2etvA 346 1.33e+01 2bywA 418 1.33e+01 1q87A 221 1.34e+01 e.47.1.1 96192 2aioA 269 1.39e+01 1ukkA 142 1.40e+01 d.227.1.1 99491 2dbbA 151 1.40e+01 1lj5A 379 1.46e+01 e.1.1.1 73928 1ym0A 238 1.47e+01 1z5hA 780 1.50e+01 1qwnA 1045 1.52e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1a8rA 221 1.57e+01 1a8rA d.96.1.1 40587 2fkbA 180 1.61e+01 1rl0A 255 1.62e+01 2cw8A 537 1.62e+01 1kk1A 410 1.62e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1ab8A 220 1.63e+01 1azsA d.58.29.1 39414 1v4pA 157 1.67e+01 1xjvA 294 1.74e+01 1y1nA 291 1.76e+01 1nbwA 607 1.78e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1e30A 155 1.81e+01 1rcy b.6.1.1 23016 2g1lA 104 1.82e+01 2calA 154 1.87e+01 1h9dB 134 1.91e+01 2jhbA b.54.1.1 60822 2h4uA 145 1.94e+01 1dykA 394 1.96e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1izmA 184 1.96e+01 a.199.1.1 90725 1jb7A 495 1.96e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 2a74A 643 1.97e+01 2yhx 457 2.06e+01 2yhx i.12.1.1 46024 1ygaA 342 2.11e+01 1rreA 200 2.14e+01 d.14.1.10 97791 1vi6A 208 2.20e+01 c.23.15.1 100736 1qfgA 725 2.25e+01 1by5A f.4.3.3 43803 1c96A 753 2.31e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1vl2A 421 2.32e+01 c.26.2.1,d.210.1.1 108708,108709 1xizA 159 2.34e+01 3proC 166 2.35e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1f08A 148 2.51e+01 1f08A d.89.1.2 59564 1fm4A 159 2.51e+01 1bv1 d.129.3.1 76186 1kv7A 488 2.53e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 2d0oA 610 2.56e+01 1tt8A 164 2.56e+01 1gkmA 509 2.59e+01 a.127.1.2 70228 1twuA 139 2.64e+01 d.32.1.8 107413 1ig8A 486 2.68e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1pzsA 208 2.69e+01 b.1.8.1 104397 1ebfA 358 2.71e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1xjcA 169 2.72e+01 1k24A 253 2.82e+01 f.4.4.2 72002 1ztdA 133 2.84e+01 1r44A 202 2.86e+01 d.65.1.4 104787 1wxxA 382 2.86e+01 1ash 150 2.88e+01 1ash a.1.1.2 15622 2gjgA 248 2.91e+01 1q1rA 431 2.95e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2a19A 175 2.96e+01 1on3A 523 2.97e+01 c.14.1.4,c.14.1.4 87107,87108 1v8yA 170 2.99e+01 1kpf 126 3.00e+01 1kpf d.13.1.1 37507 1q1fA 151 3.01e+01 a.1.1.2 104476 1jcfA 344 3.01e+01 c.55.1.1,c.55.1.1 62878,62879 1ejxC 567 3.03e+01 b.92.1.1,c.1.9.2 83184,83185 1spf 35 3.04e+01 1spf j.35.1.1 46254 1srqA 341 3.06e+01 e.55.1.1 105967 2a35A 215 3.07e+01 1hf8A 289 3.08e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1ylnA 252 3.16e+01 1t0qC 86 3.19e+01 d.15.12.1 106222 1zvpA 133 3.20e+01 1mvfD 82 3.29e+01 b.129.1.1 85143 2bx6A 350 3.31e+01 1tkeA 224 3.33e+01 1rmg 422 3.33e+01 1rmg b.80.1.3 28029 1bdo 80 3.36e+01 1bdo b.84.1.1 28214 1yc9A 442 3.41e+01 1kdgA 546 3.42e+01 c.3.1.2,d.16.1.1 77337,77338 1gmiA 136 3.43e+01 b.7.1.1 65309 1xe1A 116 3.47e+01 b.43.3.1 109571 1pyoA 167 3.49e+01 c.17.1.1 95370 2fn0A 437 3.49e+01 2fsrA 195 3.55e+01 1zm0A 114 3.66e+01 1rzuA 485 3.66e+01 c.87.1.8 105140 1w8oA 601 3.69e+01 1by2 119 3.69e+01 1by2 d.170.1.1 42452 1brwA 433 3.70e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2lhb 149 3.73e+01 2fal a.1.1.2 15597 1o20A 427 3.75e+01 c.82.1.1 86556 1ecmA 109 3.78e+01 1ecmA a.130.1.1 19492 1mkiA 330 3.79e+01 e.3.1.2 84994 1cjcA 460 3.82e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1vqoW 154 3.85e+01 1mngA 203 3.86e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1j1iA 296 3.92e+01 c.69.1.10 83977 1avyA 74 3.96e+01 1avyB h.1.17.1 45656 1tueB 218 4.02e+01 b.91.1.1 107324 1k82A 268 4.03e+01 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1wq3A 322 4.04e+01 1y9wA 140 4.05e+01 1y8tA 324 4.06e+01 1e3dB 542 4.06e+01 1h2rL e.18.1.1 59189 1szoA 257 4.06e+01 c.14.1.3 106164 1g1kA 143 4.12e+01 1aohA b.2.2.2 22404 1yphC 131 4.13e+01 1oohA 126 4.15e+01 a.39.2.1 93383 1rq2A 382 4.17e+01 c.32.1.1,d.79.2.1 105048,105049 1jogA 146 4.23e+01 a.24.16.2 77142 1q5dA 419 4.24e+01 a.104.1.1 95891 1ua4A 455 4.25e+01 c.72.1.3 99128 1od3A 168 4.25e+01 b.18.1.10 86825 1qfhA 212 4.30e+01 1qfhA b.1.18.10,b.1.18.10 21893,21894 1fjgK 129 4.34e+01 1fjfK c.55.4.1 33733 1g8pA 350 4.36e+01 1g8pA c.37.1.20 60376 1zb9A 143 4.37e+01 1et9A 204 4.37e+01 1an8 b.40.2.2,d.15.6.1 25204,37793 1t6cA 315 4.39e+01 c.55.1.8,c.55.1.8 106558,106559 1o8bA 219 4.42e+01 c.124.1.4,d.58.40.1 81180,81181 1lo7A 141 4.42e+01 d.38.1.1 74144 1awd 94 4.42e+01 1awd d.15.4.1 37673 1ykdA 398 4.46e+01 1ryiA 382 4.46e+01 1g5aA 628 4.47e+01 b.71.1.1,c.1.8.1 65152,65153 1go4A 205 4.53e+01 d.135.1.1 70292 1k66A 149 4.54e+01 c.23.1.1 90941 1jp4A 308 4.57e+01 1jp4A e.7.1.1 63223 1gttA 429 4.62e+01 d.177.1.1,d.177.1.1 70529,70530 1s4bP 674 4.63e+01 d.92.1.5 105252 1ukfA 188 4.66e+01 d.3.1.10 99488 1fuxA 166 4.76e+01 1fjjA b.17.1.2 60034 1uf3A 228 4.78e+01 d.159.1.6 99317 1kgdA 180 4.82e+01 c.37.1.1 68582 1rybA 212 4.88e+01 c.56.3.1 98098 1prxA 224 4.99e+01 1prxA c.47.1.10 33076 1fcdA 401 5.02e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1vhyA 257 5.03e+01 b.122.1.2,c.116.1.5 100714,100715 2bw0A 329 5.06e+01 1txvA 452 5.07e+01 2b5lC 222 5.11e+01 1h4xA 117 5.12e+01 1auz c.13.2.1 60626 1gz2A 142 5.13e+01 d.169.1.1 83392 1w77A 228 5.20e+01 1k8kE 178 5.25e+01 a.148.1.1 68311 1i4uA 181 5.26e+01 b.60.1.1 61732 1zy7A 403 5.31e+01 1bec 238 5.39e+01 1bec b.1.1.1,b.1.1.2 20627,21561 2ga9D 469 5.42e+01 2bvbA 137 5.43e+01 1x8vA 455 5.47e+01 1lurA 339 5.49e+01 b.30.5.4 84717 1rm6A 769 5.52e+01 1ckmA 330 5.52e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1te5A 257 5.55e+01 d.153.1.1 106795 1uliA 460 5.58e+01 b.33.1.2,d.129.3.3 107921,107922 1vqzA 341 5.58e+01 2afwA 329 5.60e+01 2f2hA 773 5.61e+01 1g55A 343 5.63e+01 1g55A c.66.1.26 34247 1q5zA 177 5.65e+01 a.196.1.1 95954 2af4C 333 5.65e+01 1n13B 113 5.66e+01 2fymA 431 5.67e+01 1ftrA 296 5.71e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2cpgA 45 5.73e+01 2cpgA a.43.1.3 17455 1uy4A 145 5.74e+01 b.18.1.10 108131 1wmhB 86 5.74e+01 2fbqA 235 5.75e+01 1yb3A 175 5.76e+01 1sdjA 310 5.79e+01 d.21.1.2,d.21.1.2 98807,98808 2f1kA 279 5.85e+01 2ajtA 500 5.86e+01 1x8hA 228 5.88e+01 1bolA 222 5.91e+01 1bolA d.124.1.1 41120 1dmhA 311 5.92e+01 1dmhA b.3.6.1 22633 1jae 471 5.93e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1tw7A 99 5.96e+01 1rjoA 646 5.98e+01 1lyqA 104 6.01e+01 b.1.18.17 78302 2bjbA 462 6.01e+01 1p7tA 731 6.02e+01 c.1.13.1 94319 1mzyA 333 6.02e+01 b.6.1.3,b.6.1.3 103848,103849 1xypA 190 6.07e+01 1axkA b.29.1.11 24327 1pea 385 6.08e+01 1pea c.93.1.1 35662 2g09A 297 6.10e+01 2iu4A 336 6.10e+01 2gfgA 193 6.13e+01 1y12A 165 6.14e+01 1h2bA 359 6.22e+01 b.35.1.2,c.2.1.1 90543,90544 1j3aA 142 6.24e+01 c.21.1.1 77070 1tuhA 156 6.26e+01 d.17.4.11 107345 2eutA 294 6.26e+01 1x8gA 227 6.28e+01 2fvhA 120 6.28e+01 1sz7A 200 6.28e+01 1xipA 388 6.36e+01 2bw8A 227 6.41e+01 1zkiA 133 6.42e+01 1zhhB 242 6.45e+01 1fmtA 314 6.52e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1o5zA 442 6.52e+01 c.59.1.2,c.72.2.2 92530,92531 1zh5A 195 6.54e+01 1wekA 217 6.54e+01 1gskA 513 6.57e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1kqqA 139 6.60e+01 a.4.3.1 72885 1es9A 232 6.60e+01 1wab c.23.10.3 31340 1r59O 505 6.70e+01 1m6eX 359 6.70e+01 c.66.1.35 91188 1io1A 398 6.71e+01 1io1A e.32.1.1 62611 1swvA 267 6.72e+01 1s12A 94 6.79e+01 1vyfA 135 6.81e+01 b.60.1.2 108902 1rds 105 6.87e+01 9rnt d.1.1.4 36236 1bu6O 501 6.90e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1f1uA 323 6.95e+01 d.32.1.3,d.32.1.3 83200,83201 2fm8A 135 6.98e+01 2ao9A 155 6.98e+01 1odfA 290 7.00e+01 c.37.1.6 92782 1fcyA 236 7.04e+01 2lbd a.123.1.1 19282 1w6gA 646 7.06e+01 1oxdA 227 7.08e+01 d.22.1.1 93687 1cl8A 276 7.09e+01 1ckqA c.52.1.1 33230 1ka2A 499 7.11e+01 d.92.1.5 77305 1tfe 145 7.13e+01 1tfe d.43.1.1 38680 2dbgA 103 7.14e+01 3tdt 274 7.17e+01 3tdt b.81.1.2 28053 1h9oA 112 7.26e+01 1qadA d.93.1.1 60837 1oo0A 147 7.27e+01 d.232.1.1 87182 1p5zB 263 7.29e+01 c.37.1.1 87815 1p5dX 463 7.32e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1o97D 320 7.36e+01 c.26.2.3,c.31.1.2 81233,81234 1ouwA 152 7.40e+01 b.77.3.1 93571 2f23A 156 7.40e+01 1rypD 241 7.42e+01 1rypD d.153.1.4 41935 2a13A 166 7.44e+01 1b65A 375 7.46e+01 1b65A d.154.1.1 42020 1otfA 62 7.48e+01 1otfA d.80.1.1 39820 1u7iA 136 7.55e+01 d.32.1.7 107724 1q4gA 553 7.57e+01 a.93.1.2,g.3.11.1 95789,95790 1seiA 130 7.60e+01 1seiA d.140.1.1 41463 1pj5A 830 7.68e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1kveA 63 7.70e+01 1kveA d.70.1.2 39590 1vpbA 451 7.71e+01 2h1tA 188 7.71e+01 1w6nA 134 7.73e+01 1c7qA 445 7.73e+01 2pgi c.80.1.2 35307 1ycdA 243 7.78e+01 1i5pA 633 7.86e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1lshA 1056 7.87e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1x88A 359 7.91e+01 2aefA 234 7.92e+01 1w9aA 147 7.92e+01 2gwnA 452 8.07e+01 1n67A 359 8.08e+01 b.2.3.4,b.2.3.4 85354,85355 1jovA 270 8.12e+01 b.30.5.7 84192 1mqvA 125 8.12e+01 a.24.3.2 79415 1vlyA 338 8.15e+01 b.44.2.1,d.250.1.1 108871,108872 2sns 149 8.19e+01 1snc b.40.1.1 24860 1v10A 521 8.19e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2av4A 162 8.21e+01 1nmoA 247 8.22e+01 c.135.1.1 91980 1ofdA 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