# 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.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 1mk4A 157 1.17e-04 d.108.1.1 84979 2aj6A 159 3.02e-02 1yvkA 163 1.28e-01 2fe7A 166 1.35e-01 1ne9A 335 1.40e-01 d.108.1.4,d.108.1.4 91839,91840 1cnv 299 2.13e-01 1cnv c.1.8.5 28989 1hc7A 477 2.23e-01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2ge3A 170 2.59e-01 1vhsA 175 2.98e-01 d.108.1.1 100698 1z4eA 153 4.19e-01 1y9kA 157 4.67e-01 1s3zA 165 6.08e-01 d.108.1.1 105250 1yx0A 159 6.10e-01 1cjwA 166 6.15e-01 1cjwA d.108.1.1 40818 1twyA 290 6.67e-01 1tiqA 180 7.73e-01 d.108.1.1 107010 2fliA 220 8.62e-01 2d4pA 141 1.01e+00 1a53 247 1.49e+00 1a53 c.1.2.4 28564 1z9hA 290 1.52e+00 1okrA 123 1.60e+00 a.4.5.39 93269 1puiA 210 1.69e+00 c.37.1.8 88292 1tidB 119 1.70e+00 c.13.2.1 107000 1wz7A 111 1.82e+00 1kkhA 317 1.83e+00 d.14.1.5,d.58.26.3 72645,72646 1igs 248 1.84e+00 1a53 c.1.2.4 28565 2cy2A 174 1.91e+00 2c3zA 222 2.60e+00 1w9gA 104 2.70e+00 1vqzA 341 2.96e+00 1wdcC 156 2.96e+00 1wdcC a.39.1.5 17317 1u9lA 70 3.05e+00 a.60.4.2 107751 1tqjA 230 3.16e+00 c.1.2.2 107228 1qfmA 710 3.33e+00 1qfmA b.69.7.1,c.69.1.4 27673,34641 1sqhA 312 3.77e+00 d.108.1.5 98966 1tvjA 166 3.95e+00 2bl1A 172 4.19e+00 1b04A 318 4.35e+00 1b04A d.142.2.2 41579 2rslA 140 4.44e+00 2rslA c.53.1.1 33345 1ea5A 537 4.86e+00 2bce c.69.1.1 34592 1h09A 338 4.96e+00 b.109.1.1,c.1.8.8 83420,83421 2f1rA 171 5.04e+00 1jmvA 141 5.11e+00 c.26.2.4 66897 2agkA 260 5.27e+00 1vrtA 560 5.56e+00 1rthA c.55.3.1,e.8.1.2 33574,43023 1h2wA 710 5.59e+00 b.69.7.1,c.69.1.4 76596,76597 2cxaA 256 5.74e+00 1mho 88 6.03e+00 1b4cA a.39.1.2 17171 1gpmA 525 6.26e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ho1A 242 6.26e+00 1ho1A c.1.24.1 61097 1dxeA 256 6.82e+00 1dxeA c.1.12.5 29310 1mu5A 471 6.84e+00 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1e3oC 160 7.06e+00 1au7A a.4.1.1,a.35.1.1 59197,59198 1izcA 339 7.33e+00 c.1.12.5 83838 1pkp 150 7.47e+00 1pkp d.14.1.1,d.50.1.2 37551,38787 1s99A 200 7.57e+00 1maz 221 7.85e+00 1maz f.1.4.1 43393 1s4iA 175 7.93e+00 1zczA 464 8.06e+00 2ccmA 191 8.20e+00 1r5jA 337 8.47e+00 c.77.1.5 97097 1n4kA 381 8.62e+00 a.118.22.1,b.42.6.1 79992,79993 1sqwA 188 8.73e+00 1t5yA 190 9.06e+00 b.122.1.1,d.17.6.3 106495,106496 1v74A 107 9.21e+00 d.243.1.1 100442 1lj8A 493 9.39e+00 a.100.1.9,c.2.1.6 90392,90393 1af3 196 9.61e+00 1maz f.1.4.1 43397 1pgvA 197 1.00e+01 c.10.1.1 88073 1kg0C 136 1.01e+01 d.169.1.1 72445 1wy9A 147 1.01e+01 1xtlA 175 1.01e+01 1xtmA 175 1.10e+01 1yr0A 175 1.11e+01 1lcyA 325 1.11e+01 b.36.1.4,b.47.1.1 73834,73835 1dusA 194 1.15e+01 1dusA c.66.1.4 34182 1xmxA 385 1.18e+01 1iicA 422 1.19e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1yvoA 172 1.19e+01 1rthA 560 1.22e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1gp6A 356 1.23e+01 b.82.2.1 65441 1o20A 427 1.24e+01 c.82.1.1 86556 1wo8A 126 1.26e+01 1mf7A 194 1.26e+01 c.62.1.1 84937 1s7hA 200 1.27e+01 d.58.48.2 105349 1t0tV 248 1.28e+01 d.58.4.10 106229 1w8iA 156 1.30e+01 1e5kA 201 1.31e+01 1fr9A c.68.1.8 34578 1m0wA 491 1.33e+01 c.30.1.4,d.142.1.6 78363,78364 1r77A 103 1.38e+01 2beiA 170 1.42e+01 2fl4A 149 1.42e+01 1ru8A 232 1.48e+01 c.26.2.1 97849 1hs6A 611 1.48e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1j0hA 588 1.50e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 2amyA 246 1.52e+01 1z5bA 469 1.54e+01 2c71A 216 1.56e+01 1rz3A 201 1.56e+01 c.37.1.6 98132 1uf3A 228 1.64e+01 d.159.1.6 99317 2f5tX 233 1.67e+01 2c1gA 431 1.69e+01 1tqgA 105 1.70e+01 a.24.10.3 107224 1o5uA 101 1.70e+01 b.82.1.8 92518 1a0jA 223 1.73e+01 5ptp b.47.1.2 26002 1cqqA 180 1.74e+01 1cqqA b.47.1.4 26422 4crxA 322 1.76e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1z7aA 308 1.76e+01 1vmeA 410 1.78e+01 c.23.5.1,d.157.1.3 108893,108894 1f5nA 592 1.85e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1qoyA 318 1.89e+01 1qoyA h.4.4.1 45788 1z4rA 168 1.90e+01 1d4xA 375 1.93e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1x7oA 287 1.93e+01 1sgjA 284 1.94e+01 c.1.12.5 105535 1ihcA 188 1.95e+01 1di6A c.57.1.1 62379 1ton 235 1.98e+01 5ptp b.47.1.2 26307 1uch 230 2.07e+01 1uch d.3.1.6 37129 1m5wA 243 2.08e+01 c.1.24.1 84836 1lc5A 364 2.10e+01 c.67.1.1 73827 1nd7A 374 2.11e+01 d.148.1.1 91817 1y7qA 98 2.17e+01 1i40A 175 2.20e+01 b.40.5.1 66024 1lw7A 365 2.23e+01 c.26.1.3,c.37.1.1 74295,74296 1hj8A 222 2.26e+01 b.47.1.2 65844 1i1dA 161 2.27e+01 1i21A d.108.1.1 61526 1z85A 234 2.28e+01 1wkbA 810 2.30e+01 1jljA 189 2.32e+01 c.57.1.1 63169 1h4xA 117 2.33e+01 1auz c.13.2.1 60626 2bkxA 242 2.38e+01 1ujkA 147 2.40e+01 a.118.9.2 99457 1u8vA 490 2.43e+01 2ah5A 210 2.45e+01 1obwA 175 2.46e+01 2prd b.40.5.1 25416 1muwA 386 2.50e+01 c.1.15.3 79495 1vhzA 198 2.51e+01 d.113.1.1 100718 1wehA 171 2.51e+01 1ro5A 201 2.53e+01 d.108.1.3 105023 1np6A 174 2.54e+01 c.37.1.10 85954 1ehiA 377 2.57e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1dpo 223 2.57e+01 5ptp b.47.1.2 25975 1a3aA 148 2.62e+01 1a3aA d.112.1.1 40917 2b5gA 171 2.64e+01 2faoA 309 2.70e+01 1pg5A 299 2.75e+01 c.78.1.1,c.78.1.1 104146,104147 1gw5S 142 2.75e+01 d.110.4.2 70633 2fjbA 643 2.78e+01 2a1iA 146 2.82e+01 1wpgA 994 2.85e+01 1q44A 326 2.88e+01 c.37.1.5 95779 2tpsA 227 2.92e+01 2tpsA c.1.3.1 28591 2ga9D 469 2.92e+01 1em9A 154 2.93e+01 1d1dA a.73.1.1 18333 2tbs 222 2.93e+01 5ptp b.47.1.2 26009 1nksA 194 2.94e+01 1nksA c.37.1.1 31886 1f9vA 347 2.95e+01 1bg2 c.37.1.9 59745 2ex5A 207 2.98e+01 1ad2 228 3.00e+01 1ad2 e.24.1.1 43353 1u46A 291 3.02e+01 d.144.1.7 107656 1octC 156 3.04e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1lrzA 426 3.06e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1dlyA 164 3.06e+01 1dlyA a.1.1.1 14983 1j6zA 376 3.08e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1eulA 994 3.09e+01 1eulA 1k6xA 352 3.19e+01 c.2.1.2 68238 2fmpA 335 3.19e+01 1su4A 994 3.20e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1e29A 135 3.20e+01 1e29A a.3.1.1 59161 1p0hA 318 3.23e+01 d.108.1.1 93866 2ahrA 259 3.28e+01 1wd5A 208 3.29e+01 2gb7A 305 3.29e+01 1f7zA 233 3.31e+01 5ptp b.47.1.2 59681 1dy9A 187 3.35e+01 1jxpA b.47.1.3 26400 1colA 204 3.35e+01 1a87 f.1.1.1 43378 1vk0A 206 3.35e+01 c.55.3.5 100839 1nzjA 298 3.35e+01 c.26.1.1 92377 1kafA 108 3.37e+01 d.199.1.1 68372 1l8wA 348 3.37e+01 a.154.1.1 73704 1xfjA 261 3.38e+01 d.194.1.2 109585 1zchA 255 3.41e+01 1bpyA 335 3.46e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1ci4A 89 3.51e+01 1qckA a.60.5.1 17970 1qz5A 375 3.55e+01 c.55.1.1,c.55.1.1 96614,96615 2cvbA 188 3.58e+01 2av4A 162 3.62e+01 2fxuA 375 3.66e+01 1v7wA 807 3.69e+01 a.102.1.4,b.30.5.3 108411,108412 1iyxA 432 3.70e+01 c.1.11.1,d.54.1.1 83815,83816 1vzyA 291 3.71e+01 1jnrA 643 3.71e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 2fp8A 322 3.72e+01 2ts1 419 3.72e+01 2ts1 c.26.1.1 31564 1frb 315 3.72e+01 1frb c.1.7.1 28665 1yrnB 83 3.74e+01 1akhB a.4.1.1 15986 2fcr 173 3.76e+01 1rcf c.23.5.1 31151 1y8aA 332 3.81e+01 1f0nA 285 3.85e+01 1dqyA c.69.1.3 34636 1fmcA 255 3.87e+01 1cydA c.2.1.2 29856 1har 216 3.88e+01 1rthA e.8.1.2 43025 2cwkA 160 3.91e+01 1f8gA 384 3.94e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 2f7tA 227 3.97e+01 1pou 71 3.98e+01 1au7A a.35.1.1 17020 1vkmA 297 3.99e+01 c.138.1.1 108670 2fomB 185 4.02e+01 1yz7A 188 4.02e+01 1f44A 324 4.05e+01 a.60.9.1,d.163.1.1 64982,64983 1xo0A 324 4.05e+01 1k3yA 221 4.08e+01 a.45.1.1,c.47.1.5 77245,77246 5nul 138 4.11e+01 5nul c.23.5.1 31191 1pzxA 289 4.11e+01 c.119.1.1 95484 1dc1A 323 4.12e+01 1dc1A c.52.1.11 33321 1eiwA 111 4.21e+01 1eiwA c.23.3.1 31130 1rpxA 230 4.23e+01 1rpxA c.1.2.2 28536 1xqiA 195 4.25e+01 2cvjA 180 4.26e+01 1st0A 337 4.32e+01 d.13.1.3,d.246.1.1 98979,98980 1k61A 60 4.33e+01 a.4.1.1 77270 1xw5A 217 4.37e+01 1nu5A 370 4.38e+01 c.1.11.2,d.54.1.1 92183,92184 1wnaA 131 4.38e+01 1k94A 165 4.42e+01 a.39.1.8 68333 1es9A 232 4.43e+01 1wab c.23.10.3 31340 1vliA 385 4.45e+01 b.85.1.1,c.1.10.6 108830,108831 2f8lA 344 4.48e+01 1z8sA 146 4.48e+01 2iu4A 336 4.60e+01 1h9hE 223 4.63e+01 b.47.1.2 103810 1sz9A 144 4.68e+01 a.118.9.4 106139 1l8dA 112 4.70e+01 h.4.12.1 73687 2c1iA 431 4.78e+01 1ghhA 81 4.83e+01 1ghhA d.57.1.1 38940 1xjcA 169 4.83e+01 1ep0A 185 4.83e+01 1dzrA b.82.1.1 28080 1ounA 127 4.84e+01 1ounA d.17.4.2 38090 2btfA 375 4.84e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 3nul 130 4.84e+01 3nul d.110.1.1 40891 1eexB 224 4.86e+01 1dioB c.51.3.1 33213 1lox 662 4.86e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1ir3A 306 4.89e+01 1fmk d.144.1.7 41702 2bg1A 494 4.89e+01 1tzyD 103 4.95e+01 a.22.1.1 107533 1dzkA 157 4.98e+01 1obpA b.60.1.1 27096 2bgsA 344 4.98e+01 1tv9A 335 4.99e+01 1p5dX 463 5.01e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1spjA 238 5.03e+01 1wab 232 5.12e+01 1wab c.23.10.3 31341 2gsaA 432 5.15e+01 2gsaA c.67.1.4 34446 1zo0A 126 5.15e+01 1nf3A 195 5.20e+01 c.37.1.8 85594 2g40A 224 5.23e+01 2b7oA 464 5.27e+01 2bhuA 602 5.34e+01 1obbA 480 5.45e+01 c.2.1.5,d.162.1.2 86760,86761 1wmiB 67 5.54e+01 1n71A 180 5.55e+01 d.108.1.1 85370 2bswA 146 5.58e+01 1o5kA 306 5.58e+01 c.1.10.1 92504 1rlkA 117 5.60e+01 c.131.1.1 97651 1vc1A 110 5.62e+01 c.13.2.1 108493 1h4wA 224 5.66e+01 b.47.1.2 65622 2fp7B 172 5.67e+01 1ri5A 298 5.79e+01 c.66.1.34 97502 1k2yX 463 5.82e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1i1iP 681 5.84e+01 1i1iP d.92.1.5 40297 1eo6A 117 5.88e+01 1eo6A d.15.1.3 37609 2d13A 227 5.93e+01 1ulyA 192 5.93e+01 1pjcA 361 5.97e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1o0yA 260 6.04e+01 c.1.10.1 80756 1vk8A 106 6.08e+01 d.58.48.1 108636 1kx5B 102 6.09e+01 a.22.1.1 77594 1i12A 160 6.10e+01 1i21A d.108.1.1 61515 2ctoA 93 6.26e+01 1lxjA 104 6.35e+01 d.58.48.1 84736 1x59A 73 6.37e+01 1pq1A 196 6.43e+01 f.1.4.1 94986 1l7dA 384 6.44e+01 c.2.1.4,c.23.12.2 77774,77775 1ktaA 365 6.50e+01 e.17.1.1 77533 2plc 274 6.50e+01 2plc c.1.18.2 29614 1vsrA 136 6.53e+01 1vsrA c.52.1.15 33332 1v8aA 265 6.56e+01 c.72.1.2 100494 2fcwA 109 6.60e+01 2a10A 125 6.60e+01 1gtzA 156 6.62e+01 c.23.13.1 70539 1n3yA 198 6.64e+01 c.62.1.1 79976 1elkA 157 6.65e+01 1dvpA a.118.9.2 19217 1xiuA 230 6.68e+01 1gy6A 127 6.76e+01 d.17.4.2 70736 1nslA 184 6.79e+01 d.108.1.1 86137 1s83A 223 6.80e+01 b.47.1.2 98718 4xis 387 6.80e+01 4xis c.1.15.3 29421 1dt9A 437 6.80e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1xk4C 113 6.89e+01 1xgkA 352 6.89e+01 2c2nA 339 6.94e+01 1xmaA 145 6.94e+01 1d0iA 156 6.97e+01 2dhqA c.23.13.1 31383 1wxdA 263 7.02e+01 1ki9A 192 7.06e+01 c.37.1.1 84404 2gviA 204 7.08e+01 1nh2B 53 7.10e+01 a.32.1.1 91874 2as9A 210 7.16e+01 1ne8A 117 7.19e+01 b.34.6.2 80424 1ybhA 590 7.21e+01 3xis 387 7.27e+01 4xis c.1.15.3 29423 2h1rA 299 7.27e+01 1k8kA 418 7.28e+01 c.55.1.1,c.55.1.1 68305,68306 1u6mA 199 7.29e+01 1pii 452 7.30e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1hf8A 289 7.35e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1j5vA 351 7.36e+01 c.72.1.1 71585 1q2wA 308 7.37e+01 b.47.1.4 88355 1ogsA 497 7.57e+01 b.71.1.2,c.1.8.3 86997,86998 1oshA 232 7.57e+01 a.123.1.1 93496 1m7bA 184 7.57e+01 c.37.1.8 74572 1o8xA 146 7.59e+01 c.47.1.10 86681 1xfuA 747 7.63e+01 1tjyA 316 7.64e+01 c.93.1.1 107062 4ptp 223 7.66e+01 2bp1A 360 7.67e+01 2aboA 136 7.71e+01 1ppfE 218 7.73e+01 1a7s b.47.1.2 26234 1fw1A 216 7.78e+01 a.45.1.1,c.47.1.5 60051,60052 1l1jA 239 7.79e+01 b.47.1.1 84516 2arsA 262 7.79e+01 1xfxA 777 7.85e+01 1j6pA 418 7.90e+01 b.92.1.4,c.1.9.9 77089,77090 1llfA 534 7.90e+01 c.69.1.17 78094 1tuzA 118 7.91e+01 2coiA 386 7.98e+01 1lucA 355 7.99e+01 1lucA c.1.16.1 29547 1p1mA 406 8.04e+01 b.92.1.4,c.1.9.9 87696,87697 2c27A 315 8.08e+01 1wwzA 159 8.12e+01 2a4nA 182 8.12e+01 1wuaA 375 8.14e+01 1o98A 511 8.17e+01 c.105.1.1,c.76.1.3 86684,86685 1sffA 426 8.19e+01 c.67.1.4 105482 1m22A 503 8.20e+01 c.117.1.1 78464 1s1hM 132 8.22e+01 i.1.1.1 105165 2hrvA 142 8.25e+01 2hrvA b.47.1.4 26429 1dgaA 375 8.27e+01 1yagA 1f0xA 571 8.33e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1z47A 355 8.38e+01 1b25A 619 8.54e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1jwgA 147 8.65e+01 a.118.9.2 71911 1s0pA 176 8.67e+01 a.192.1.1 98300 1wj5A 120 8.79e+01 1uliB 187 8.81e+01 d.17.4.4 107923 1e5mA 416 8.81e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 5pal 109 8.83e+01 1a75A a.39.1.4 17215 1ne2A 200 8.83e+01 c.66.1.32 85586 1o4wA 147 8.85e+01 c.120.1.1 86629 1cx4A 305 8.85e+01 b.82.3.2,b.82.3.2 59099,59100 1wyuA 438 8.86e+01 1n81A 186 8.93e+01 a.185.1.1 85388 1zupA 315 8.96e+01 1uby 367 8.97e+01 1uby a.128.1.1 19435 1trb 320 8.97e+01 1trb c.3.1.5,c.3.1.5 30529,30530