# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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.soe.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 2plrA 213 3.29e-02 2yvuA 186 4.31e-02 2axpA 173 1.11e-01 c.37.1.1 127497 2z0hA 197 2.19e-01 2pbrA 195 2.21e-01 1nn5A 215 3.80e-01 c.37.1.1 85892 2ccjA 205 4.51e-01 1ukzA 203 4.52e-01 c.37.1.1 31840 1ukz 203 4.63e-01 1zin 1e9eA 215 4.84e-01 c.37.1.1 64810 2bwjA 199 5.38e-01 1gvnB 287 5.63e-01 c.37.1.21 76354 1gtvA 214 6.14e-01 c.37.1.1 70537 2ax4A 198 6.82e-01 2rhmA 193 6.92e-01 3tmkA 216 8.10e-01 3tmkA c.37.1.1 31920 1rz3A 201 9.31e-01 c.37.1.6 98132 1odfA 290 9.53e-01 c.37.1.6 92782 1y63A 184 9.85e-01 c.37.1.1 116494 2pezA 179 9.87e-01 2ga8A 359 1.07e+00 2p5tB 253 1.08e+00 4tmkA 213 1.13e+00 5tmpA c.37.1.1 31930 2qorA 204 1.18e+00 2j41A 207 1.27e+00 1z8fA 228 1.32e+00 1s4qA 228 1.33e+00 c.37.1.1 98507 1z6gA 218 1.38e+00 5tmpA 213 1.51e+00 5tmpA c.37.1.1 31931 1qhxA 178 1.64e+00 1qhsA c.37.1.3 31936 1znwA 207 1.72e+00 c.37.1.1 125412 1qhsA 178 1.84e+00 1qhsA c.37.1.3 31938 2bifA 469 1.85e+00 1bif c.37.1.7,c.60.1.4 31963,34009 3bifA 468 1.89e+00 1bif c.37.1.7,c.60.1.4 31962,34008 1gw5S 142 2.02e+00 d.110.4.2 70633 2vglS 142 2.05e+00 1bif 469 2.13e+00 1bif 1bifA 469 2.13e+00 c.37.1.7,c.60.1.4 31961,34003 1x6vA 630 2.20e+00 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 2f1rA 171 2.20e+00 1h65A 270 2.55e+00 c.37.1.8 65640 1np6A 174 2.77e+00 c.37.1.10 85954 1nksA 194 2.87e+00 1nksA c.37.1.1 31886 1nzyA 269 2.89e+00 1nzyA c.14.1.3 30903 3c8uA 208 3.18e+00 1kdoA 227 3.49e+00 c.37.1.1 68478 1ye8A 178 3.68e+00 c.37.1.11 123010 1rkbA 173 4.10e+00 c.37.1.1 111854 2f7tA 227 4.57e+00 1zuhA 168 4.62e+00 1xrjA 261 4.74e+00 c.37.1.6 122256 1z0sA 278 4.81e+00 e.52.1.1 124328 1ckeA 227 5.15e+00 1ckeA c.37.1.1 31846 1yg2A 179 6.01e+00 a.4.5.61 116681 2eyuA 261 6.26e+00 1suwA 249 6.31e+00 e.52.1.1 106027 2j1oA 268 6.78e+00 1d2nA 272 6.92e+00 1d2nA c.37.1.20 32428 1sq5A 308 7.46e+00 c.37.1.6 105882 2pt5A 168 7.52e+00 1s96A 219 7.60e+00 c.37.1.1 98740 2gzaA 361 7.61e+00 2qxlA 658 7.75e+00 3b9qA 302 7.90e+00 2qy9A 309 8.04e+00 1fzqA 181 8.45e+00 1hurA c.37.1.8 32060 2og2A 359 8.49e+00 1lv7A 257 8.79e+00 c.37.1.20 78232 2o8iA 165 9.39e+00 1r1dA 247 9.50e+00 c.69.1.29 96813 1uj2A 252 9.68e+00 c.37.1.6 99452 1m7gA 211 1.00e+01 c.37.1.4 78724 1t1jA 125 1.02e+01 c.23.14.2 106249 2vo1A 295 1.03e+01 2bdtA 189 1.07e+01 c.37.1.25 128344 2etsA 128 1.09e+01 a.24.26.1 132371 1esmA 316 1.12e+01 1esmA c.37.1.6 31953 1txjA 171 1.12e+01 b.88.1.2 107424 2yxnA 322 1.13e+01 1j8mF 297 1.14e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1knqA 175 1.17e+01 c.37.1.17 72786 2cdnA 201 1.18e+01 c.37.1.1 130289 2il5A 171 1.18e+01 2pjkA 178 1.19e+01 1viaA 175 1.20e+01 c.37.1.2 100754 1sraA 151 1.22e+01 a.39.1.3 17190 1hurA 180 1.22e+01 1hurA c.37.1.8 32052 1ireB 228 1.27e+01 b.34.4.4 76770 1t7lA 766 1.28e+01 1ugpB 226 1.29e+01 b.34.4.4 107832 2vhjA 331 1.30e+01 1sra 151 1.30e+01 1sra 2oz3A 404 1.31e+01 1u4qA 322 1.33e+01 a.7.1.1,a.7.1.1,a.7.1.1 113024,113025,113026 2an9A 207 1.35e+01 c.37.1.1 127037 1um8A 376 1.36e+01 c.37.1.20 99580 1s0uA 408 1.36e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2qt1A 207 1.46e+01 1v6sA 390 1.48e+01 c.86.1.1 100424 1orjA 130 1.50e+01 a.24.19.1 93456 1mj3A 260 1.51e+01 c.14.1.3 79183 1u5pA 216 1.53e+01 a.7.1.1,a.7.1.1 113046,113047 1tqhA 247 1.58e+01 c.69.1.29 107225 2obbA 142 1.62e+01 1wq3A 322 1.63e+01 1o9gA 250 1.63e+01 c.66.1.29 86692 2i4iA 417 1.64e+01 1i1qB 192 1.67e+01 1qdlB c.23.16.1 61544 3bciA 186 1.68e+01 2qb7A 397 1.69e+01 1w44A 331 1.69e+01 c.37.1.11 114147 1guaA 167 1.69e+01 1ctqA c.37.1.8 32013 2hxrA 238 1.76e+01 1t5iA 172 1.84e+01 c.37.1.19 106450 1to3A 304 1.91e+01 c.1.10.1 107161 2pzeA 229 1.91e+01 1qf9A 194 1.91e+01 1zin c.37.1.1 31848 1gs5A 258 1.96e+01 c.73.1.2 70395 2q8pA 260 1.97e+01 1izmA 184 1.97e+01 a.199.1.1 90725 1vmeA 410 1.97e+01 c.23.5.1,d.157.1.3 108893,108894 1jjvA 206 1.98e+01 c.37.1.1 71698 2eryA 172 2.01e+01 c.37.1.8 132306 1y5eA 169 2.02e+01 c.57.1.1 122632 2g3vA 208 2.02e+01 1gky 187 2.04e+01 1gky 3cjnA 162 2.05e+01 1lkvX 232 2.05e+01 a.118.14.1 73980 1m1zA 513 2.06e+01 c.26.2.1,d.153.1.1 78457,78458 1yrbA 262 2.07e+01 c.37.1.10 123915 1kjvA 284 2.18e+01 b.1.1.2,d.19.1.1 77421,77422 1zd8A 227 2.18e+01 1ucnA 152 2.20e+01 d.58.6.1 99183 1vqsA 116 2.22e+01 d.58.4.13 114019 1nsf 273 2.22e+01 1d2nA 1jxmA 301 2.25e+01 b.34.2.1,c.37.1.1 67420,67421 2rajA 392 2.26e+01 1d6jA 211 2.26e+01 1d6jA c.37.1.4 31940 1mr3F 181 2.28e+01 c.37.1.8 79422 1ak2A 233 2.30e+01 c.37.1.1,g.41.2.1 31894,45195 2ts1 419 2.31e+01 2ts1 1j5uA 136 2.32e+01 d.208.1.1 71584 1ockA 412 2.32e+01 c.117.1.1 86802 1q52A 314 2.37e+01 c.14.1.3 95846 1wwmA 190 2.37e+01 a.132.1.3 121363 1sviA 195 2.39e+01 c.37.1.8 106048 3bioA 304 2.42e+01 1cw0A 155 2.47e+01 1vsrA c.52.1.15 33333 1w8iA 156 2.49e+01 c.120.1.1 114368 1vqoV 71 2.50e+01 a.2.2.1 120383 2c95A 196 2.51e+01 2cbzA 237 2.51e+01 1r8sA 164 2.54e+01 c.37.1.8 97247 1mhqA 148 2.56e+01 a.118.9.2 84973 1i7qB 193 2.56e+01 1qdlB c.23.16.1 61902 2iyvA 184 2.57e+01 c.37.1.2 137812 1vkmA 297 2.58e+01 c.138.1.1 108670 2hf9A 226 2.67e+01 1audA 101 2.67e+01 1urnA d.58.7.1 39156 2a61A 145 2.72e+01 a.4.5.28 126187 2qhpA 296 2.73e+01 2gaxA 135 2.74e+01 2b6hA 192 2.74e+01 c.37.1.8 127994 1kjwA 295 2.85e+01 b.34.2.1,c.37.1.1 68643,68644 1ex7A 186 2.87e+01 1gky c.37.1.1 59537 1ki9A 192 2.90e+01 c.37.1.1 84404 1vsrA 136 2.91e+01 1vsrA c.52.1.15 33332 1gsjA 258 2.95e+01 c.73.1.2 70397 16pkA 415 2.96e+01 c.86.1.1 35454 3pfk 319 2.96e+01 3pfk 16pk 415 2.96e+01 16pk 4ts1A 319 2.99e+01 2ts1 c.26.1.1 31565 1vkfA 188 3.17e+01 c.1.29.1 108656 1quuA 250 3.17e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 2j5aA 110 3.18e+01 1i7qA 519 3.28e+01 1qdlA d.161.1.1 61901 1rw6A 210 3.29e+01 a.47.4.1 105113 1xmiA 291 3.45e+01 c.37.1.12 115489 2pgnA 589 3.45e+01 2h57A 190 3.49e+01 1pixA 587 3.51e+01 c.14.1.4,c.14.1.4 118578,118579 1gajA 257 3.53e+01 1gajA c.37.1.12 60416 1v9kA 228 3.55e+01 d.265.1.3 108449 1puiA 210 3.55e+01 c.37.1.8 88292 3cnyA 301 3.56e+01 1jj2U 70 3.60e+01 1ffkS a.2.2.1 63106 1n81A 186 3.60e+01 a.185.1.1 85388 2gutA 77 3.61e+01 1vmaA 306 3.63e+01 a.24.13.1,c.37.1.10 108887,108888 2a5dA 175 3.68e+01 c.37.1.8 126172 2g1kA 176 3.68e+01 c.37.1.2 134519 3bjdA 332 3.76e+01 2quqA 562 3.77e+01 2d4uA 176 3.80e+01 1qcrF 103 3.81e+01 1be3F f.27.1.1 43676 1zx4A 192 3.85e+01 2avwA 311 3.88e+01 1kk1A 410 3.88e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2j1pA 293 3.90e+01 1g6hA 257 3.91e+01 1gajA c.37.1.12 60318 1yzgA 179 3.95e+01 c.37.1.8 124276 2gtrA 261 3.96e+01 1lkxA 697 3.98e+01 c.37.1.9 73981 2g5gX 268 4.07e+01 2obhA 143 4.11e+01 2a9iA 113 4.13e+01 1evyA 366 4.18e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 2chgA 226 4.18e+01 1q6zA 528 4.19e+01 c.31.1.3,c.36.1.5,c.36.1.9 111655,111656,111657 1cqwA 295 4.20e+01 1b6g c.69.1.8 34679 1of1A 376 4.28e+01 c.37.1.1 103924 3bddA 142 4.34e+01 1c9kB 180 4.35e+01 1c9kB c.37.1.11 32364 2is8A 164 4.35e+01 1bn6A 294 4.43e+01 1bn6A c.69.1.8 34678 1vpvA 300 4.46e+01 c.119.1.1 113975 2qm8A 337 4.48e+01 1o3yA 166 4.49e+01 c.37.1.8 86618 1s7iA 124 4.49e+01 d.58.4.9 105353 2zfyA 234 4.50e+01 2iakA 224 4.51e+01 1zj6A 187 4.53e+01 c.37.1.8 125145 2dc1A 236 4.61e+01 2fiuA 99 4.66e+01 d.58.4.16 133537 1gpc 218 4.67e+01 1gpc 1aw2A 256 4.72e+01 1amk c.1.1.1 28523 2fk8A 318 4.73e+01 c.66.1.18 133648 1pszA 303 4.81e+01 1toaA c.92.2.2 35600 2fqxA 318 4.83e+01 1uptA 171 4.84e+01 c.37.1.8 99767 1w9iA 770 4.85e+01 1h6zA 913 4.94e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2jdxA 385 4.94e+01 1jdw d.126.1.2 41139 3crrA 323 4.98e+01 1nu4A 97 5.02e+01 d.58.7.1 80731 1n0zA 45 5.04e+01 g.41.11.1 85247 1oxxK 353 5.05e+01 b.40.6.3,c.37.1.12 93715,93716 1f5mA 180 5.06e+01 1f5mB d.110.2.1 40895 1vi0A 206 5.10e+01 a.4.1.9,a.121.1.1 100720,100721 1wbeA 209 5.10e+01 1bn7A 294 5.14e+01 1bn6A c.69.1.8 34677 1w63Q 158 5.15e+01 i.23.1.1 109208 2fn9A 290 5.18e+01 1f6bA 198 5.18e+01 c.37.1.8 64986 1e3sA 261 5.22e+01 1e6wA c.2.1.2 59201 2yv9A 291 5.31e+01 1kgdA 180 5.32e+01 c.37.1.1 68582 1e1hB 174 5.32e+01 3b73A 111 5.38e+01 2nnwA 376 5.38e+01 1kkcA 221 5.45e+01 a.2.11.1,d.44.1.1 68660,68661 1t6aA 126 5.45e+01 d.129.8.1 106555 1z47A 355 5.47e+01 1oxsC 353 5.48e+01 b.40.6.3,c.37.1.12 87519,87520 2j6vA 301 5.50e+01 2fswA 107 5.51e+01 a.4.5.69 134042 1urnA 97 5.51e+01 1urnA d.58.7.1 39153 2p3zA 415 5.53e+01 1bfd 528 5.54e+01 1bfd 1jdwA 423 5.54e+01 d.126.1.2 41129 1jdw 423 5.55e+01 1jdw 1qhiA 366 5.56e+01 1qhiA c.37.1.1 31860 2heuA 401 5.57e+01 2fn4A 181 5.58e+01 c.37.1.8 133806 1lnwA 147 5.59e+01 a.4.5.28 78104 1mw9X 592 5.60e+01 e.10.1.1 91480 1y14A 187 5.62e+01 a.60.8.2 116322 1xfjA 261 5.63e+01 d.194.1.2 109585 2joyA 96 5.64e+01 1shkA 173 5.67e+01 1shkA c.37.1.2 31932 2i5qA 415 5.67e+01 2ywuA 181 5.69e+01 1ny6A 267 5.74e+01 c.37.1.20 92321 1tfjA 219 5.74e+01 1lvk 762 5.75e+01 1lvk 1yyaA 250 5.77e+01 1f76A 336 5.84e+01 c.1.4.1 76160 1ihuA 589 5.87e+01 c.37.1.10,c.37.1.10 62394,62395 1y42X 392 5.89e+01 1lnsA 763 5.91e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1gal 583 5.91e+01 1gpeA 1vkcA 158 5.92e+01 d.108.1.1 113663 2o70A 174 5.99e+01 1mkzA 172 5.99e+01 c.57.1.1 84998 1r4aA 165 6.02e+01 c.37.1.8 96986 1mvwA 840 6.04e+01 i.15.1.1 79523 1tkeA 224 6.04e+01 d.15.10.1,d.67.1.1 112470,112471 1w77A 228 6.04e+01 c.68.1.13 120679 1iukA 140 6.05e+01 c.2.1.8 83712 2yv5A 302 6.07e+01 2akaA 776 6.10e+01 1rss 151 6.15e+01 1rss 2rdmA 132 6.15e+01 1uteA 313 6.16e+01 1uteA d.159.1.1 42078 1sgwA 214 6.17e+01 c.37.1.12 105541 1n3bA 216 6.17e+01 c.37.1.1 79959 1ki1B 352 6.18e+01 a.87.1.1,b.55.1.1 72497,72498 1rxqA 178 6.24e+01 a.213.1.1 105118 1rthA 560 6.25e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1rssA 151 6.25e+01 a.75.1.1 18392 2bkhA 814 6.28e+01 2dykA 161 6.31e+01 1p5zB 263 6.35e+01 c.37.1.1 87815 1v5wA 343 6.36e+01 c.37.1.11 108387 1zv1A 65 6.37e+01 3boxA 415 6.44e+01 1pq4A 291 6.46e+01 c.92.2.2 94995 1u5uA 374 6.50e+01 e.5.1.2 113052 3cg6A 146 6.51e+01 1wywA 230 6.51e+01 1vls 146 6.51e+01 1vls 1vlsA 146 6.53e+01 a.24.2.1 16532 2qgnA 322 6.56e+01 3ccyA 203 6.57e+01 2uz0A 263 6.58e+01 1cunA 213 6.60e+01 1cunA a.7.1.1,a.7.1.1 16313,16314 6pfkA 319 6.62e+01 3pfk c.89.1.1 35583 1p9rA 418 6.63e+01 c.37.1.11 94399 2ap3A 199 6.66e+01 a.24.27.1 127110 2gwmA 200 6.70e+01 1g55A 343 6.70e+01 1g55A c.66.1.26 34247 1vhtA 218 6.72e+01 c.37.1.1 100700 1sfuA 75 6.74e+01 a.4.5.19 105503 2c1gA 431 6.75e+01 c.6.2.3,d.341.1.1 129632,129633 1ithA 141 6.76e+01 1ithA a.1.1.2 15623 1qqiA 104 6.76e+01 1opc a.4.6.1 16233 2oqyA 391 6.84e+01 2j9wA 102 6.88e+01 1e2kA 331 6.91e+01 1qhiA c.37.1.1 31854 1qu1A 155 6.94e+01 1qu1A h.3.1.1 45670 1fc2C 58 6.95e+01 1fc2C a.8.1.1 16345 1ohvA 472 6.95e+01 c.67.1.4 93031 1cf3A 583 6.96e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 1owfA 99 6.97e+01 a.55.1.1 87487 2eu8A 216 6.98e+01 1tr0A 108 7.03e+01 d.58.4.4 107261 2f6rA 281 7.05e+01 2a6mA 155 7.07e+01 d.58.57.1 126287 1u7pA 164 7.12e+01 c.108.1.17 113095 1vplA 256 7.13e+01 c.37.1.12 113966 1mgpA 313 7.13e+01 c.119.1.1 79098 1iapA 211 7.13e+01 a.91.1.1 62119 3ctaA 230 7.25e+01 1htwA 158 7.27e+01 c.37.1.18 71083 2h9aB 310 7.29e+01 1cx0A 95 7.34e+01 1urnA d.58.7.1 39158 1jilA 420 7.38e+01 c.26.1.1 66745 1xhcA 367 7.39e+01 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 1c1gB 284 7.45e+01 1c1gB h.1.5.1 45574 2c0hA 353 7.46e+01 c.1.8.3 129594 3d0cA 314 7.51e+01 2phcB 225 7.52e+01 1wzdA 215 7.56e+01 a.132.1.1 121493 2pcqA 283 7.60e+01 1xnfA 275 7.64e+01 a.118.8.1 115580 1bouA 139 7.66e+01 1bouA a.88.1.1 18521 1hdiA 413 7.66e+01 16pk c.86.1.1 60964 2ab0A 205 7.70e+01 c.23.16.2 126501 2p32A 120 7.74e+01 2hy1A 280 7.74e+01 1k77A 260 7.74e+01 c.1.15.5 72096 2de0X 526 7.75e+01 2iutA 574 7.79e+01 1u6bA 98 7.81e+01 d.58.7.1 107703 2gpfA 72 7.84e+01 3byiA 214 7.84e+01 1g6oA 330 7.85e+01 1g6oA c.37.1.11 32430 1fukA 165 7.88e+01 1fukA c.37.1.19 32409 1rj9A 304 7.91e+01 a.24.13.1,c.37.1.10 97553,97554 1ji0A 240 7.91e+01 c.37.1.12 71665 1i1gA 141 7.93e+01 a.4.5.32,d.58.4.2 65982,65983 2au3A 407 7.94e+01 2i9dA 217 7.96e+01