# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1g9gA 629 3.34e-01 a.102.1.2 83279 1ohvA 472 3.35e-01 c.67.1.4 -8181 1ogiA 303 4.95e-01 b.43.4.2 -4042 c.25.1.1 -6587 1faeA 629 5.17e-01 1fce a.102.1.2 18837 1k3sA 113 7.33e-01 d.198.1.1 68120 1h16A 759 7.73e-01 c.7.1.1 76462 1v7oA 165 7.77e-01 unknown_sccs -10249 1lxnA 99 7.80e-01 d.58.48.1 84737 1go2A 304 8.12e-01 b.43.4.2 76243 c.25.1.1 76244 1que 303 9.06e-01 1fnc b.43.4.2 25647 c.25.1.1 31537 1osdA 72 9.85e-01 1cm5A 759 1.15e+00 1cm5A c.7.1.1 30671 1fe0A 68 1.16e+00 1cc8A d.58.17.1 39345 1is1A 185 1.75e+00 d.67.3.1 83704 1mc2A 122 1.93e+00 a.133.1.2 74622 1gmeA 151 1.96e+00 b.15.1.1 65305 1iwlA 182 2.49e+00 b.125.1.1 83757 1ek8A 185 2.50e+00 1ek8A d.67.3.1 59444 1j5uA 136 2.58e+00 d.208.1.1 71584 1htqA 477 2.79e+00 d.15.9.1 71035 d.128.1.1 71036 1esgA 213 2.95e+00 1bam c.52.1.3 33286 1me4A 215 3.01e+00 d.3.1.1 79023 1s72E 178 3.13e+00 1ef1A 294 3.18e+00 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1kl9A 182 3.19e+00 b.40.4.5 72681 1jj2E 177 3.20e+00 1ffk1 d.141.1.1 63089 d.141.1.1 63090 1jyoA 130 3.22e+00 d.198.1.1 67483 1uv7A 110 3.35e+00 unknown_sccs -10256 1gqzA 274 3.37e+00 d.21.1.1 83311 d.21.1.1 83312 1lvaA 258 3.43e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1r6lA 239 3.58e+00 d.14.1.4 -9057 d.101.1.1 -10747 1f2aA 215 3.71e+00 1cs8A d.3.1.1 37040 1vjeA 166 3.78e+00 d.185.1.2 -10261 1obr 326 3.81e+00 1aye c.56.5.2 33828 1s8iA 121 3.94e+00 a.133.1.2 -1968 1n2fA 142 3.94e+00 d.227.1.1 79853 1hqsA 423 4.17e+00 1iso c.77.1.1 61154 1iba 101 4.18e+00 1iba d.95.1.1 40567 1ppo 216 4.92e+00 1cs8A d.3.1.1 37020 1vpi 122 4.98e+00 1poa a.133.1.2 19559 1dq3A 454 4.98e+00 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1ga3A 113 5.00e+00 1ga3A a.26.1.2 60411 1aokB 122 5.08e+00 1poa a.133.1.2 19561 1vapA 123 5.12e+00 1poa a.133.1.2 19548 1mwyA 73 5.13e+00 d.58.17.1 79616 1rl6A 177 5.71e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1i2aA 219 5.77e+00 e.24.1.1 -12012 1ufwA 95 5.78e+00 d.58.7.1 -10034 1furA 467 5.94e+00 1furA a.127.1.1 19403 1bwzA 274 6.01e+00 1bwzA d.21.1.1 38337 d.21.1.1 38338 1vi7A 217 6.06e+00 unknown_sccs -9115 unknown_sccs -10052 1n2zA 245 6.42e+00 c.92.2.2 79865 1m6dA 214 6.48e+00 d.3.1.1 84849 1v7cA 351 6.64e+00 c.79.1.1 -8512 1mwwA 128 6.66e+00 unknown_sccs -10451 1q67A 231 6.71e+00 unknown_sccs -4373 1jj2M 186 6.99e+00 1ffkK c.55.4.1 63098 1f46A 140 7.08e+00 1f46A d.129.4.1 59643 1innA 166 7.08e+00 1j98A d.185.1.2 62608 1h4rA 314 7.14e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1gk9B 557 7.24e+00 1qnaA 200 7.26e+00 1ytbA d.129.1.1 41226 d.129.1.1 41227 1kutA 230 7.37e+00 d.143.1.1 73017 1nqcA 217 7.57e+00 d.3.1.1 86024 1s72N 187 7.69e+00 1k3eA 156 7.90e+00 d.198.1.1 68103 1j27A 102 8.28e+00 unknown_sccs -10116 1bowA 159 8.41e+00 1bowA d.60.1.1 39528 1vk8A 106 8.42e+00 1iv3A 152 8.84e+00 d.79.5.1 76828 1h12A 405 8.88e+00 a.102.1.2 83447 1f52A 468 8.89e+00 1lgr d.15.9.1 37839 d.128.1.1 41169 1jqgA 433 8.96e+00 c.56.5.1 71791 d.58.3.1 71792 1mai 131 9.16e+00 1mai b.55.1.1 26951 1ijgA 309 9.19e+00 1fouA e.27.1.1 62493 1jltA 122 9.27e+00 a.133.1.2 66867 1l7mA 211 9.28e+00 c.108.1.4 73664 1i7qA 519 9.34e+00 1qdlA d.161.1.1 61901 1moq 368 9.38e+00 1moq c.80.1.1 35302 1ekeA 230 9.41e+00 1ekeA c.55.3.1 33572 1khqA 212 9.48e+00 d.3.1.1 -8868 1smd 496 9.52e+00 1smd b.71.1.1 27768 c.1.8.1 28755 1avpA 204 9.68e+00 1avpA d.3.1.7 37132 1hi9A 274 1.00e+01 1hi9A c.99.1.1 61063 1oo0B 110 1.01e+01 d.58.7.1 87183 1cs8A 316 1.02e+01 1cs8A d.3.1.1 37065 1ppn 212 1.04e+01 1cs8A d.3.1.1 37004 1in0A 163 1.04e+01 d.58.49.1 83694 d.58.49.1 83695 1k32A 1045 1.06e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1g87A 614 1.07e+01 a.102.1.2 83275 b.2.2.2 83276 1pd21 199 1.08e+01 1pd21 1umvX 122 1.09e+01 a.133.1.2 -1994 1fh0A 221 1.10e+01 1cs8A d.3.1.1 59832 1bylA 125 1.10e+01 1bylA d.32.1.2 38495 1ak5 503 1.12e+01 1ak5 c.1.5.1 28639 3tss 194 1.12e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 2irfG 113 1.12e+01 2irfG a.4.5.23 16185 1kwfA 363 1.13e+01 a.102.1.2 73078 1p7tA 731 1.14e+01 c.1.13.1 -5600 1lngA 87 1.15e+01 d.201.1.1 74045 1bueA 265 1.15e+01 1btl e.3.1.1 42727 1qlaB 239 1.16e+01 1qlaB a.1.2.1 15679 d.15.4.2 37707 1rybA 212 1.17e+01 c.56.3.1 -7858 1uw4A 91 1.17e+01 unknown_sccs -10038 1vdkA 466 1.17e+01 a.127.1.1 -1752 1hx0A 496 1.18e+01 b.71.1.1 61346 c.1.8.1 61347 1j97A 211 1.20e+01 1f5sA c.108.1.4 62753 1cem 363 1.21e+01 1cem a.102.1.2 18826 1j1yA 136 1.23e+01 d.38.1.5 -9671 1oiaA 95 1.24e+01 d.58.7.1 87051 1zin 217 1.27e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1bdmA 327 1.31e+01 1bmdA c.2.1.5 30137 d.162.1.1 42104 1if1A 113 1.31e+01 2irfG a.4.5.23 16183 1h8lA 380 1.31e+01 b.3.2.1 65737 c.56.5.1 65738 1ln1A 214 1.32e+01 d.129.3.2 74038 1eu8A 409 1.32e+01 1eu8A c.94.1.1 59502 1jae 471 1.32e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1qm4A 396 1.35e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1e3aB 560 1.37e+01 1ajqB 1ry9A 145 1.37e+01 d.198.1.1 -9020 1hc7A 477 1.39e+01 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1jyaA 130 1.40e+01 d.198.1.1 67453 1jltB 122 1.43e+01 a.133.1.2 66868 1fxlA 167 1.43e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1tidB 119 1.44e+01 1kafA 108 1.46e+01 d.199.1.1 68372 1h5wA 309 1.49e+01 e.27.1.1 65635 1io2A 213 1.57e+01 1ekeA c.55.3.1 62612 1ouoA 210 1.57e+01 unknown_sccs -8903 2plc 274 1.64e+01 2plc c.1.18.2 29614 1khbA 625 1.65e+01 c.91.1.1 68606 c.109.1.1 68607 1cc8A 73 1.67e+01 1cc8A d.58.17.1 39343 1ppa 121 1.69e+01 1poa a.133.1.2 19550 1gtmA 419 1.72e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1shsA 147 1.72e+01 1shsA b.15.1.1 23675 1jj2R 84 1.72e+01 1ffkP d.12.1.1 63103 1koqA 253 1.73e+01 2cba b.74.1.1 27964 1kwmA 402 1.74e+01 c.56.5.1 73079 d.58.3.1 73080 1q4uA 151 1.74e+01 d.38.1.5 -9701 1nxiA 132 1.75e+01 d.58.47.1 86381 1lba 146 1.76e+01 1lba d.118.1.1 41062 1s72S 85 1.77e+01 1nc5A 373 1.77e+01 a.102.1.6 85548 1omwA 689 1.85e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1m6iA 493 1.86e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1c7gA 456 1.87e+01 c.67.1.2 -8153 1bo1A 416 1.89e+01 1bo1A d.143.1.2 41591 1dtdA 303 1.89e+01 1aye c.56.5.1 33823 1yal 218 1.90e+01 1cs8A d.3.1.1 37025 1urnA 97 1.90e+01 1urnA d.58.7.1 39153 1t7pA 698 1.90e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1r1uA 106 1.91e+01 1j5pA 253 1.92e+01 c.2.1.3 83092 d.81.1.3 71577 1a2yA 107 1.93e+01 8fabA b.1.1.1 19926 1ca1 370 1.97e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1qgiA 259 2.00e+01 1qgiA d.2.1.7 37001 1e6yC 247 2.00e+01 1mroC d.58.31.1 39441 1cqmA 101 2.01e+01 1ris d.58.14.1 39321 1iso 416 2.08e+01 1iso c.77.1.1 35065 1ecsA 126 2.10e+01 1ecsA d.32.1.2 59407 1nkiA 135 2.13e+01 d.32.1.2 -9544 2bpa2 175 2.15e+01 2bpa2 1u2fA 90 2.16e+01 1u2fA d.58.7.1 39168 1pf5A 131 2.16e+01 d.79.1.1 -10368 1repC 251 2.17e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1i7pA 274 2.19e+01 b.43.4.2 66048 c.25.1.1 66049 1g8lA 411 2.22e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1me8A 503 2.23e+01 c.1.5.1 79028 1vjqA 79 2.25e+01 unknown_sccs -13478 1nu4A 97 2.26e+01 d.58.7.1 80731 1nrjA 158 2.28e+01 d.110.4.4 86124 1hkfA 122 2.30e+01 b.1.1.1 83553 1e6bA 221 2.31e+01 1e6bA a.45.1.1 59294 c.47.1.5 59295 2rhe 114 2.33e+01 8fabA b.1.1.1 20523 256bA 106 2.33e+01 256bA a.24.3.1 16539 1aw7A 194 2.34e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1ex7A 186 2.36e+01 1gky c.37.1.1 59537 1v5sA 126 2.38e+01 1m4lA 307 2.39e+01 c.56.5.1 78604 1qqgA 264 2.39e+01 1qqgA b.55.1.2 26987 b.55.1.2 26988 2bopA 85 2.40e+01 2bopA d.58.8.1 39217 2if1 126 2.41e+01 2if1 d.64.1.1 39547 1sqzA 121 2.43e+01 a.133.1.2 -1971 1rk8A 165 2.43e+01 d.58.7.1 -10018 1l6pA 125 2.47e+01 b.1.17.1 73626 1g7jA 107 2.48e+01 32c2A b.1.1.1 19932 1nlnA 204 2.48e+01 d.3.1.7 -8897 1b4bA 71 2.48e+01 1b4aA d.74.2.1 39718 1ew4A 106 2.51e+01 1ew4A d.82.2.1 40023 1nd4A 264 2.52e+01 d.144.1.6 -11381 1c5cL 214 2.56e+01 32c2A b.1.1.1 20474 b.1.1.2 21438 1d8cA 723 2.58e+01 1d8cA c.1.13.1 29325 1mzjA 339 2.60e+01 c.95.1.1 79700 c.95.1.1 79701 1guiA 155 2.64e+01 b.18.1.14 76351 1a6q 382 2.66e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 1o7eA 276 2.69e+01 e.3.1.1 -11766 1lqpA 135 2.70e+01 d.32.1.2 78151 1gcoA 261 2.70e+01 1ybvA c.2.1.2 29884 1rf6A 427 2.71e+01 d.68.2.2 -10314 1bv1 159 2.72e+01 1bv1 d.129.3.1 41313 1tj9A 121 2.72e+01 2act 220 2.72e+01 1cs8A d.3.1.1 37002 1hd7A 318 2.74e+01 1bix d.151.1.1 41780 1gky 187 2.82e+01 1gky c.37.1.1 31839 1tk4A 121 2.86e+01 1louA 101 2.90e+01 1ris d.58.14.1 39323 1s3jA 155 2.93e+01 a.4.5.28 -227 1ekqA 272 2.93e+01 1c3qA c.72.1.2 34941 1s7zA 117 2.96e+01 unknown_sccs -344 1xel 338 2.97e+01 1xel c.2.1.2 29786 1pguA 615 3.02e+01 b.69.4.1 88069 b.69.4.1 88070 1i88A 389 3.03e+01 c.95.1.2 66070 c.95.1.2 66071 2ctc 307 3.04e+01 1aye c.56.5.1 33802 1bza 262 3.04e+01 1btl e.3.1.1 42701 3proC 166 3.05e+01 3proC d.52.1.1 38812 d.52.1.1 38813 1ckv 141 3.07e+01 1ckv d.137.1.1 41452 1q4rA 112 3.14e+01 d.58.4.4 -9943 1vkhA 273 3.14e+01 1ejdA 419 3.19e+01 1uae d.68.2.2 39576 1qtoA 122 3.20e+01 1bylA d.32.1.2 38494 1o8uA 257 3.22e+01 c.14.1.3 81194 1ivyA 452 3.24e+01 1ivyA c.69.1.5 34654 1jb9A 316 3.26e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1memA 215 3.26e+01 1cs8A d.3.1.1 37069 1iyhA 198 3.26e+01 a.45.1.1 83790 c.47.1.5 83791 1lxjA 104 3.29e+01 d.58.48.1 84736 1d8hA 311 3.29e+01 1d8iA d.63.1.1 39544 1hzpA 335 3.32e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1cv8 174 3.35e+01 1cv8 d.3.1.1 37089 1kmdA 117 3.39e+01 d.189.1.1 72744 1l8bA 190 3.43e+01 d.86.1.1 73683 1ng4A 390 3.46e+01 c.3.1.2 85666 d.16.1.3 85667 1gwmA 153 3.50e+01 b.18.1.19 83348 1nm2A 317 3.57e+01 c.19.1.1 80654 d.58.23.1 80655 1ghpA 258 3.58e+01 1btl e.3.1.1 60520 2baa 243 3.59e+01 1cnsA d.2.1.1 36243 1psuA 140 3.62e+01 d.38.1.5 88285 1ml8A 134 3.63e+01 d.227.1.2 85013 1fe7A 121 3.64e+01 1poa 1qfjA 232 3.67e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1geeA 261 3.68e+01 c.2.1.2 -5814 1c8cA 64 3.72e+01 1azpA b.34.13.1 59084 1p8kZ 254 3.72e+01 d.95.2.1 -10648 d.95.2.1 -10649 1mb4A 370 3.76e+01 c.2.1.3 78908 d.81.1.1 78909 1fnc 314 3.77e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 1gnwA 211 3.86e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1or0A 160 3.89e+01 d.153.1.2 -11415 1clc 639 3.90e+01 1clc a.102.1.2 18835 b.1.18.2 21872 1i50K 120 3.91e+01 d.74.3.2 61765 1hf2A 210 3.92e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1iwdA 215 3.95e+01 d.3.1.1 83756 1e5mA 416 3.97e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1tml 286 3.97e+01 1tml c.6.1.1 30656 1ekrA 161 3.99e+01 1ekrA d.58.21.1 39380 1lfjA 119 4.00e+01 1o22A 170 4.00e+01 d.238.1.1 86557