# List of top-scoring protein chains for t04-100-30-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 4.18e-02 2yvuA 186 8.06e-02 2axpA 173 2.83e-01 c.37.1.1 127497 2z0hA 197 3.60e-01 2pbrA 195 3.61e-01 1ukzA 203 4.10e-01 c.37.1.1 31840 1ukz 203 4.30e-01 1zin 2bwjA 199 5.52e-01 1z6gA 218 6.21e-01 2ccjA 205 6.54e-01 1nn5A 215 6.74e-01 c.37.1.1 85892 2rhmA 193 7.36e-01 2qorA 204 8.51e-01 1gtvA 214 8.70e-01 c.37.1.1 70537 1gw5S 142 8.93e-01 d.110.4.2 70633 2vglS 142 8.97e-01 1gvnB 287 9.55e-01 c.37.1.21 76354 1s4qA 228 1.21e+00 c.37.1.1 98507 1y63A 184 1.21e+00 c.37.1.1 116494 1z8fA 228 1.23e+00 1znwA 207 1.25e+00 c.37.1.1 125412 1rz3A 201 1.27e+00 c.37.1.6 98132 3tmkA 216 1.49e+00 3tmkA c.37.1.1 31920 1odfA 290 1.81e+00 c.37.1.6 92782 2j41A 207 1.84e+00 4tmkA 213 1.89e+00 5tmpA c.37.1.1 31930 2ax4A 198 1.90e+00 2ga8A 359 2.20e+00 1bif 469 2.42e+00 1bif 1bifA 469 2.42e+00 c.37.1.7,c.60.1.4 31961,34003 2f1rA 171 2.43e+00 2p5tB 253 2.49e+00 1qhxA 178 2.56e+00 1qhsA c.37.1.3 31936 2pezA 179 2.73e+00 1nksA 194 3.21e+00 1nksA c.37.1.1 31886 2f7tA 227 3.34e+00 1h65A 270 3.39e+00 c.37.1.8 65640 1np6A 174 3.99e+00 c.37.1.10 85954 1orjA 130 4.22e+00 a.24.19.1 93456 1s96A 219 4.32e+00 c.37.1.1 98740 1ye8A 178 5.05e+00 c.37.1.11 123010 1z0sA 278 5.12e+00 e.52.1.1 124328 2qxlA 658 5.14e+00 1fzqA 181 5.19e+00 1hurA c.37.1.8 32060 1u4qA 322 5.32e+00 a.7.1.1,a.7.1.1,a.7.1.1 113024,113025,113026 1kdoA 227 5.46e+00 c.37.1.1 68478 1rkbA 173 5.46e+00 c.37.1.1 111854 3c8uA 208 5.67e+00 2o8iA 165 5.88e+00 2og2A 359 6.04e+00 2pjkA 178 6.64e+00 1u5pA 216 6.99e+00 a.7.1.1,a.7.1.1 113046,113047 2c95A 196 7.13e+00 1suwA 249 7.15e+00 e.52.1.1 106027 1x6vA 630 7.38e+00 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 1gpc 218 7.59e+00 1gpc 1to3A 304 7.82e+00 c.1.10.1 107161 1xrjA 261 7.90e+00 c.37.1.6 122256 3b9qA 302 7.91e+00 1d2nA 272 7.92e+00 1d2nA c.37.1.20 32428 1txjA 171 8.93e+00 b.88.1.2 107424 2qy9A 309 9.01e+00 3bciA 186 9.25e+00 1sraA 151 9.78e+00 a.39.1.3 17190 1t7lA 766 9.84e+00 1o9gA 250 1.02e+01 c.66.1.29 86692 1sra 151 1.03e+01 1sra 2eyuA 261 1.05e+01 1vkmA 297 1.06e+01 c.138.1.1 108670 1zuhA 168 1.11e+01 2vo1A 295 1.12e+01 1izmA 184 1.12e+01 a.199.1.1 90725 2aplA 157 1.15e+01 a.258.1.1 127132 2gzaA 361 1.18e+01 1ckeA 227 1.20e+01 1ckeA c.37.1.1 31846 2an9A 207 1.21e+01 c.37.1.1 127037 2yxnA 322 1.28e+01 2bdtA 189 1.30e+01 c.37.1.25 128344 1lv7A 257 1.41e+01 c.37.1.20 78232 2chgA 226 1.43e+01 1knqA 175 1.46e+01 c.37.1.17 72786 2cdnA 201 1.50e+01 c.37.1.1 130289 1t5iA 172 1.51e+01 c.37.1.19 106450 1v6sA 390 1.52e+01 c.86.1.1 100424 1uj2A 252 1.52e+01 c.37.1.6 99452 1jjvA 206 1.52e+01 c.37.1.1 71698 1i1qB 192 1.54e+01 1qdlB c.23.16.1 61544 2i4iA 417 1.57e+01 1qu1A 155 1.60e+01 1qu1A h.3.1.1 45670 1yg2A 179 1.62e+01 a.4.5.61 116681 1wq3A 322 1.62e+01 1nzyA 269 1.64e+01 1nzyA c.14.1.3 30903 1s0uA 408 1.65e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1j8mF 297 1.68e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2a1kA 233 1.71e+01 1t1jA 125 1.74e+01 c.23.14.2 106249 1hurA 180 1.75e+01 1hurA c.37.1.8 32052 2vhjA 331 1.78e+01 2qt1A 207 1.78e+01 2h9aB 310 1.81e+01 1rw2A 152 1.81e+01 a.118.19.1 97961 1gs5A 258 1.86e+01 c.73.1.2 70395 2etsA 128 1.88e+01 a.24.26.1 132371 1ireB 228 1.92e+01 b.34.4.4 76770 1y5eA 169 1.94e+01 c.57.1.1 122632 1ugpB 226 1.98e+01 b.34.4.4 107832 2g3vA 208 2.06e+01 2oz3A 404 2.08e+01 2gaxA 135 2.11e+01 2gutA 77 2.11e+01 2quqA 562 2.12e+01 1fukA 165 2.16e+01 1fukA c.37.1.19 32409 1gky 187 2.19e+01 1gky 1i7qB 193 2.20e+01 1qdlB c.23.16.1 61902 2ts1 419 2.20e+01 2ts1 2obbA 142 2.20e+01 1w9yA 319 2.22e+01 b.82.2.1 120801 1rthA 560 2.30e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1w63Q 158 2.31e+01 i.23.1.1 109208 1gsjA 258 2.34e+01 c.73.1.2 70397 1i7qA 519 2.34e+01 1qdlA d.161.1.1 61901 1rxqA 178 2.35e+01 a.213.1.1 105118 3bioA 304 2.35e+01 2eryA 172 2.36e+01 c.37.1.8 132306 1zd8A 227 2.36e+01 1w44A 331 2.37e+01 c.37.1.11 114147 2pt5A 168 2.39e+01 1mr3F 181 2.40e+01 c.37.1.8 79422 1yrbA 262 2.41e+01 c.37.1.10 123915 2hxrA 238 2.42e+01 2obhA 143 2.42e+01 1kjvA 284 2.49e+01 b.1.1.2,d.19.1.1 77421,77422 1sviA 195 2.54e+01 c.37.1.8 106048 1ithA 141 2.57e+01 1ithA a.1.1.2 15623 1vmeA 410 2.60e+01 c.23.5.1,d.157.1.3 108893,108894 1wbeA 209 2.61e+01 1xvhA 129 2.61e+01 a.8.1.2,a.8.1.2 116084,116085 2qb7A 397 2.62e+01 1m7gA 211 2.68e+01 c.37.1.4 78724 1kjwA 295 2.75e+01 b.34.2.1,c.37.1.1 68643,68644 2ap3A 199 2.76e+01 a.24.27.1 127110 1ex7A 186 2.76e+01 1gky c.37.1.1 59537 2il5A 171 2.79e+01 1go4A 205 2.80e+01 d.135.1.1 70292 1q52A 314 2.85e+01 c.14.1.3 95846 1ucnA 152 2.86e+01 d.58.6.1 99183 1pszA 303 2.89e+01 1toaA c.92.2.2 35600 1m1zA 513 2.92e+01 c.26.2.1,d.153.1.1 78457,78458 1ak2A 233 2.95e+01 c.37.1.1,g.41.2.1 31894,45195 2r47A 157 2.98e+01 1ockA 412 2.99e+01 c.117.1.1 86802 1ki9A 192 3.05e+01 c.37.1.1 84404 2fqxA 318 3.07e+01 2j5vA 367 3.07e+01 1jilA 420 3.13e+01 c.26.1.1 66745 2pzeA 229 3.14e+01 4ts1A 319 3.15e+01 2ts1 c.26.1.1 31565 1tfjA 219 3.20e+01 1nsf 273 3.20e+01 1d2nA 3cjnA 162 3.27e+01 1sq5A 308 3.28e+01 c.37.1.6 105882 2cbzA 237 3.29e+01 1mhqA 148 3.30e+01 a.118.9.2 84973 1mj3A 260 3.32e+01 c.14.1.3 79183 2ppyA 265 3.33e+01 3bjdA 332 3.35e+01 1vqoV 71 3.36e+01 a.2.2.1 120383 1puiA 210 3.37e+01 c.37.1.8 88292 2j6vA 301 3.38e+01 1yyaA 250 3.38e+01 1viaA 175 3.41e+01 c.37.1.2 100754 2fcwA 109 3.42e+01 a.13.1.1 133288 1y42X 392 3.43e+01 1yz1A 174 3.52e+01 b.88.1.2 124264 1n81A 186 3.57e+01 a.185.1.1 85388 2joyA 96 3.58e+01 1esmA 316 3.58e+01 1esmA c.37.1.6 31953 2c1gA 431 3.67e+01 c.6.2.3,d.341.1.1 129632,129633 2aamA 309 3.73e+01 c.1.8.15 126489 1aw2A 256 3.74e+01 1amk c.1.1.1 28523 1s7iA 124 3.75e+01 d.58.4.9 105353 2qnlA 162 3.86e+01 1r8sA 164 3.91e+01 c.37.1.8 97247 2is8A 164 3.93e+01 2fswA 107 4.04e+01 a.4.5.69 134042 2gv5A 161 4.06e+01 2b6hA 192 4.09e+01 c.37.1.8 127994 2iakA 224 4.12e+01 1o7dA 298 4.12e+01 c.6.2.1 86641 2o70A 174 4.13e+01 16pkA 415 4.15e+01 c.86.1.1 35454 16pk 415 4.15e+01 16pk 2beqD 48 4.16e+01 1wwmA 190 4.22e+01 a.132.1.3 121363 2it1A 362 4.27e+01 1vqsA 116 4.29e+01 d.58.4.13 114019 2q8pA 260 4.32e+01 1nu4A 97 4.35e+01 d.58.7.1 80731 2pgnA 589 4.36e+01 2gwmA 200 4.38e+01 1xmiA 291 4.39e+01 c.37.1.12 115489 1qf9A 194 4.40e+01 1zin c.37.1.1 31848 2j5aA 110 4.45e+01 1yb3A 175 4.48e+01 d.296.1.2 122869 1vkcA 158 4.49e+01 d.108.1.1 113663 2mbrA 340 4.49e+01 d.145.1.2,d.146.1.1 41749,41762 1kgdA 180 4.58e+01 c.37.1.1 68582 2a5dA 175 4.59e+01 c.37.1.8 126172 1urnA 97 4.62e+01 1urnA d.58.7.1 39153 1z47A 355 4.64e+01 1q6zA 528 4.65e+01 c.31.1.3,c.36.1.5,c.36.1.9 111655,111656,111657 2qhpA 296 4.67e+01 2iyvA 184 4.67e+01 c.37.1.2 137812 2hvgA 482 4.68e+01 1gal 583 4.68e+01 1gpeA 1pixA 587 4.72e+01 c.14.1.4,c.14.1.4 118578,118579 1kk1A 410 4.75e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1g6hA 257 4.78e+01 1gajA c.37.1.12 60318 1vkfA 188 4.81e+01 c.1.29.1 108656 2fn9A 290 4.82e+01 1bj4A 470 4.88e+01 1bj4A c.67.1.4 34479 1j5uA 136 4.90e+01 d.208.1.1 71584 1oxxK 353 4.92e+01 b.40.6.3,c.37.1.12 93715,93716 1j7xA 302 4.93e+01 c.14.1.2 66425 1jj2U 70 4.96e+01 1ffkS a.2.2.1 63106 1kkcA 221 4.97e+01 a.2.11.1,d.44.1.1 68660,68661 2dy1A 665 4.99e+01 1sfuA 75 5.00e+01 a.4.5.19 105503 2a9iA 113 5.02e+01 1wozA 177 5.02e+01 2dc5A 231 5.15e+01 1wywA 230 5.18e+01 1pcaA 95 5.21e+01 d.58.3.1 39063 1vpqA 273 5.22e+01 c.1.32.1 113974 1zv1A 65 5.25e+01 1ds1A 324 5.28e+01 1drtA b.82.2.2 28127 1a6dB 543 5.29e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1d6jA 211 5.30e+01 1d6jA c.37.1.4 31940 1ki0A 253 5.31e+01 g.14.1.1,g.14.1.1,g.14.1.1 72493,72494,72495 3c6gA 479 5.32e+01 2yv5A 302 5.33e+01 1g73A 162 5.36e+01 1fewA a.7.4.1 16332 1g55A 343 5.36e+01 1g55A c.66.1.26 34247 1mvwB 145 5.36e+01 i.15.1.1 79524 1vsrA 136 5.36e+01 1vsrA c.52.1.15 33332 1oxsC 353 5.39e+01 b.40.6.3,c.37.1.12 87519,87520 1q0sA 259 5.40e+01 c.66.1.28 95509 2pcqA 283 5.41e+01 2g1iA 563 5.41e+01 1cf3A 583 5.49e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 1mkzA 172 5.50e+01 c.57.1.1 84998 1phpA 394 5.58e+01 c.86.1.1 35452 1v9kA 228 5.58e+01 d.265.1.3 108449 2qupA 145 5.60e+01 3cnyA 301 5.60e+01 1tk9A 188 5.60e+01 c.80.1.3 107082 3d0cA 314 5.61e+01 2dc1A 236 5.62e+01 2hf9A 226 5.64e+01 1n0zA 45 5.65e+01 g.41.11.1 85247 1exrA 148 5.66e+01 1cll a.39.1.5 17299 2fk8A 318 5.70e+01 c.66.1.18 133648 1o3yA 166 5.72e+01 c.37.1.8 86618 2fn4A 181 5.75e+01 c.37.1.8 133806 2h57A 190 5.76e+01 2qgaB 465 5.79e+01 2c1iA 431 5.79e+01 c.6.2.3,d.341.1.1 129636,129637 1a8y 367 5.82e+01 1a8y 1a8yA 367 5.82e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2ia1A 178 5.83e+01 3ccyA 203 5.84e+01 1nwwA 149 5.88e+01 d.17.4.8 86306 1zj6A 187 5.89e+01 c.37.1.8 125145 1sgwA 214 5.90e+01 c.37.1.12 105541 1ej0A 180 5.90e+01 1ej0A c.66.1.2 34179 2d4uA 176 5.97e+01 3crrA 323 5.97e+01 1f6bA 198 6.01e+01 c.37.1.8 64986 1f5mA 180 6.01e+01 1f5mB d.110.2.1 40895 1assA 159 6.11e+01 c.8.5.2 30818 1ass 159 6.11e+01 1a6dA 2fiuA 99 6.12e+01 d.58.4.16 133537 1uxyA 340 6.13e+01 d.145.1.2,d.146.1.1 41748,41761 1evyA 366 6.14e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1bfd 528 6.14e+01 1bfd 1q2zA 120 6.15e+01 a.118.19.1 95656 1uxy 340 6.15e+01 2mbr 2qgnA 322 6.23e+01 1ny6A 267 6.24e+01 c.37.1.20 92321 1ohvA 472 6.28e+01 c.67.1.4 93031 1q9uA 130 6.35e+01 d.129.7.1 96314 1lw7A 365 6.36e+01 c.26.1.3,c.37.1.1 74295,74296 1im5A 180 6.36e+01 c.33.1.3 66211 1ihuA 589 6.38e+01 c.37.1.10,c.37.1.10 62394,62395 1v5wA 343 6.45e+01 c.37.1.11 108387 1mroB 442 6.46e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1u5uA 374 6.55e+01 e.5.1.2 113052 1wy0A 342 6.58e+01 1yzgA 179 6.59e+01 c.37.1.8 124276 1hdiA 413 6.65e+01 16pk c.86.1.1 60964 2gh1A 301 6.65e+01 c.66.1.49 135170 2iutA 574 6.68e+01 1snlA 103 6.70e+01 a.39.1.7 105820 1yarO 237 6.72e+01 2oerA 214 6.73e+01 3b73A 111 6.74e+01 2oqhA 385 6.80e+01 1jdwA 423 6.81e+01 d.126.1.2 41129 1jdw 423 6.81e+01 1jdw 1y1lA 124 6.84e+01 c.44.1.1 116341 2jdxA 385 6.86e+01 1jdw d.126.1.2 41139 1avpA 204 6.87e+01 1avpA d.3.1.7 37132 2qm8A 337 6.90e+01 1y14A 187 6.91e+01 a.60.8.2 116322 2onuA 152 6.92e+01 1y80A 210 6.94e+01 2j5gA 263 7.01e+01 1gqeA 365 7.01e+01 e.38.1.1 70351 2eu8A 216 7.05e+01 1nmeB 92 7.05e+01 1vblA 416 7.06e+01 1topA 162 7.07e+01 a.39.1.5 17223 2q62A 247 7.08e+01 2j1oA 268 7.11e+01 1xhcA 367 7.12e+01 c.3.1.5,c.3.1.5,d.87.1.1 115292,115293,115294 1of1A 376 7.13e+01 c.37.1.1 103924 1pvdA 537 7.14e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1iukA 140 7.18e+01 c.2.1.8 83712 2im9A 333 7.19e+01 d.3.1.13 137508 1q3qA 548 7.24e+01 a.129.1.2,c.8.5.2,d.56.1.2 95704,95705,95706 1w9iA 770 7.24e+01 1t6aA 126 7.31e+01 d.129.8.1 106555 1s1eA 224 7.34e+01 a.39.1.5 112007 1zb1A 392 7.35e+01 1swxA 209 7.37e+01 a.224.1.1 106075 1p3jA 217 7.43e+01 c.37.1.1,g.41.2.1 94022,94023 1uptA 171 7.45e+01 c.37.1.8 99767 2qs9A 194 7.46e+01 1vlsA 146 7.48e+01 a.24.2.1 16532 1vls 146 7.50e+01 1vls 1vplA 256 7.53e+01 c.37.1.12 113966 5nulA 138 7.55e+01 c.23.5.1 31191 1wmuA 141 7.55e+01 a.1.1.2 109416 1uteA 313 7.56e+01 1uteA d.159.1.1 42078 1hbnB 442 7.59e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1jx2B 315 7.66e+01 c.37.1.8 67404 2odmA 91 7.66e+01 2hy1A 280 7.72e+01 1ugpA 203 7.73e+01 d.149.1.1 107831 1xfjA 261 7.77e+01 d.194.1.2 109585 1p1mA 406 7.78e+01 b.92.1.4,c.1.9.9 87696,87697 1iapA 211 7.83e+01 a.91.1.1 62119 2vp4A 230 7.96e+01 1a3c 181 7.97e+01 1a3c 1a3cA 181 7.97e+01 c.61.1.1 34095 1zd9A 188 7.98e+01 c.37.1.8 124938