# 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.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 1yrlA 491 7.66e-02 1u2zA 433 1.97e-01 c.66.1.31 107626 1xdwA 331 3.85e-01 1snyA 267 6.65e-01 c.2.1.2 105833 1j0hA 588 7.75e-01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 2ffeA 311 1.03e+00 1meoA 209 1.46e+00 c.65.1.1 79035 1mldA 314 1.49e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1w6sA 599 1.80e+00 1n71A 180 2.00e+00 d.108.1.1 85370 1mejA 223 2.23e+00 c.65.1.1 79029 1rcuA 195 2.34e+00 c.129.1.1 97295 1b87A 181 2.39e+00 1b87A d.108.1.1 40797 1tqjA 230 2.63e+00 c.1.2.2 107228 1su4A 994 2.93e+00 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1np3A 338 3.14e+00 a.100.1.2,c.2.1.6 85946,85947 1vizA 240 3.15e+00 c.1.4.1 100784 1hyeA 313 3.66e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1eulA 994 3.75e+00 1eulA 1gsoA 431 3.77e+00 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1wy6A 172 3.84e+00 1wpgA 994 3.86e+00 2bjxA 110 3.96e+00 1bjx c.47.1.2 32776 1bjx 110 3.96e+00 1bjx c.47.1.2 32774 1quqB 121 4.40e+00 1quqB b.40.4.3 25305 1lrwA 600 4.44e+00 b.70.1.1 91111 1jb3A 131 4.49e+00 1jc7A b.40.3.2 62833 1jc7A 131 4.53e+00 1jc7A b.40.3.2 62873 1wwkA 307 4.85e+00 1a12A 413 4.92e+00 1a12A b.69.5.1 27663 1sc6A 404 5.07e+00 2bfwA 200 5.16e+00 1u8vA 490 5.25e+00 3nll 138 5.32e+00 5nul c.23.5.1 31206 1qopA 268 5.37e+00 2tysA c.1.2.4 28570 1yxyA 234 5.47e+00 2a4nA 182 5.72e+00 1jysA 242 5.76e+00 c.56.2.1 77216 1lldA 319 6.18e+00 3ldh c.2.1.5,d.162.1.1 30177,42144 1d4oA 184 6.52e+00 1d4oA c.31.1.4 31748 1g8aA 227 6.80e+00 c.66.1.3 90506 1fl2A 310 6.97e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1vjnA 220 7.06e+00 d.157.1.4 100825 1pyfA 312 7.12e+00 c.1.7.1 95334 2fvx 138 7.33e+00 5nul c.23.5.1 31200 1qr0A 228 7.36e+00 1qr0A d.150.1.1,d.150.1.1 59038,59039 1y81A 138 7.83e+00 1ihoA 283 7.94e+00 1ihoA c.26.1.4 62390 1ykwA 435 8.01e+00 5nul 138 8.72e+00 5nul c.23.5.1 31191 2fox 138 8.74e+00 5nul c.23.5.1 31197 1rq2A 382 9.13e+00 c.32.1.1,d.79.2.1 105048,105049 1vpdA 299 9.26e+00 2fywA 267 9.66e+00 1cuk 203 9.85e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1z5nA 242 9.86e+00 2aeuA 374 9.96e+00 1rpxA 230 1.03e+01 1rpxA c.1.2.2 28536 2avnA 260 1.03e+01 1y08A 323 1.08e+01 2f51A 118 1.10e+01 1txgA 335 1.15e+01 1uz1A 468 1.18e+01 1rifA 282 1.23e+01 c.37.1.23 97507 1pjqA 457 1.23e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1lnh 857 1.25e+01 1yge a.119.1.1,b.12.1.1 19237,23637 1nqeA 594 1.26e+01 f.4.3.3 86027 1g9gA 629 1.30e+01 a.102.1.2 83279 1jkiA 533 1.32e+01 c.2.1.3,d.81.1.3 71704,71705 1fce 629 1.33e+01 1fce a.102.1.2 18836 1p0hA 318 1.36e+01 d.108.1.1 93866 1j4aA 333 1.37e+01 c.2.1.4,c.23.12.1 71502,71503 2b4wA 315 1.40e+01 1m7bA 184 1.41e+01 c.37.1.8 74572 1wuiS 267 1.43e+01 1faeA 629 1.45e+01 1fce a.102.1.2 18837 1ubkS 267 1.46e+01 e.19.1.1 88423 1rovA 857 1.53e+01 a.119.1.1,b.12.1.1 97674,97675 1aba 87 1.55e+01 1aba c.47.1.1 32760 1t6kA 278 1.57e+01 1nnsA 326 1.58e+01 c.88.1.1 85910 1psdA 409 1.58e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1hyuA 521 1.58e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1kgdA 180 1.63e+01 c.37.1.1 68582 1gg4A 452 1.64e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1lmeA 176 1.72e+01 d.167.1.1 84629 2cbuA 468 1.72e+01 1zyeA 220 1.72e+01 1bxeA 113 1.75e+01 1bxeA d.55.1.1 38898 1i4jA 110 1.79e+01 d.55.1.1 76734 1oi2A 366 1.81e+01 c.119.1.2 103802 1vm6A 228 1.83e+01 c.2.1.3,d.81.1.3 108876,108877 1u1wA 298 1.84e+01 1z5oA 242 1.86e+01 2bb3A 221 1.89e+01 1php 394 2.04e+01 16pk c.86.1.1 35452 1aazA 87 2.06e+01 1aba c.47.1.1 32761 1aj6 219 2.07e+01 1aj6 d.122.1.2 41106 2cmd 312 2.10e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1l3iA 192 2.13e+01 c.66.1.22 77676 1g66A 207 2.15e+01 1bs9 c.69.1.30 31329 2c27A 315 2.16e+01 1jkfA 533 2.18e+01 c.2.1.3,d.81.1.3 71700,71701 1ekxA 311 2.19e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 2dfkA 402 2.20e+01 1hjp 203 2.21e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1n25A 368 2.22e+01 c.37.1.20 85264 1f89A 291 2.25e+01 d.160.1.1 64988 1t3lA 337 2.26e+01 b.34.2.1,c.37.1.1 106358,106359 1p1jA 533 2.28e+01 c.2.1.3,d.81.1.3 87687,87688 1h2rS 267 2.30e+01 2frvA e.19.1.1 43310 1svmA 377 2.35e+01 1n57A 291 2.45e+01 c.23.16.2 85328 2bz8A 58 2.53e+01 2gar 212 2.58e+01 2gar c.65.1.1 34161 1a3h 300 2.63e+01 7a3hA c.1.8.3 28819 1ofuA 320 2.63e+01 c.32.1.1,d.79.2.1 86972,86973 1bs9 207 2.67e+01 1bs9 c.69.1.30 31330 1xubA 298 2.68e+01 1w4xA 542 2.71e+01 c.3.1.5,c.3.1.5 109171,109172 1cz3A 168 2.72e+01 1d1gA c.71.1.1 34891 1m2kA 249 2.75e+01 c.31.1.5 84754 1tlfA 301 2.76e+01 1tlfA c.93.1.1 35687 1sjdA 368 2.86e+01 c.1.11.2,d.54.1.1 105632,105633 1acmA 310 2.87e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1pea 385 2.90e+01 1pea c.93.1.1 35662 1d1gA 168 2.92e+01 1d1gA c.71.1.1 34889 1uch 230 2.97e+01 1uch d.3.1.6 37129 1oi7A 288 2.97e+01 c.2.1.8,c.23.4.1 87049,87050 2a0fA 310 2.99e+01 1paqA 189 3.02e+01 a.118.1.14 94413 1h2aS 317 3.08e+01 2frvA e.19.1.1 43311 1azl 147 3.10e+01 5nul c.23.5.1 31154 2eshA 118 3.12e+01 1ybhA 590 3.25e+01 1y0eA 223 3.26e+01 2ashA 381 3.26e+01 1iciA 256 3.28e+01 1iciA c.31.1.5 62266 1w3jA 468 3.30e+01 c.1.8.4 109156 7a3hA 303 3.32e+01 7a3hA c.1.8.3 28817 1gxrA 337 3.45e+01 b.69.4.1 70722 1lybB 241 3.47e+01 1smrA 1y8aA 332 3.50e+01 3dapA 320 3.57e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 3csuA 310 3.62e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1b43A 340 3.68e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 8atcA 310 3.70e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1ecd 136 3.79e+01 1flp a.1.1.2 15211 1xv2A 237 3.79e+01 1xiuA 230 3.87e+01 1mioB 458 3.97e+01 1qguB c.92.2.3 35602 1h5vA 304 4.01e+01 c.1.8.3 70898 1tltA 319 4.01e+01 c.2.1.3,d.81.1.5 107135,107136 2fz0A 149 4.14e+01 16pk 415 4.15e+01 16pk c.86.1.1 35454 1cjsA 219 4.16e+01 1cjsA e.24.1.1 43354 1at1A 310 4.17e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1ituA 369 4.23e+01 c.1.9.7 71423 1pkp 150 4.24e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 2dldA 337 4.24e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1dvjC 246 4.29e+01 1dvjA c.1.2.3 28548 1ku1A 230 4.32e+01 a.118.3.1 72996 1xq6A 253 4.33e+01 1zkiA 133 4.38e+01 1dusA 194 4.38e+01 1dusA c.66.1.4 34182 1xhkA 187 4.39e+01 1vmaA 306 4.42e+01 a.24.13.1,c.37.1.10 108887,108888 1eco 136 4.42e+01 1flp a.1.1.2 15208 1csn 298 4.44e+01 1csn d.144.1.7 41664 1repC 251 4.50e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1ibsA 317 4.53e+01 c.61.1.2,c.61.1.2 66107,66108 1kl7A 514 4.55e+01 c.79.1.1 72678 1y80A 210 4.61e+01 1ve3A 227 4.62e+01 1ea9C 583 4.64e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1dd5A 185 4.64e+01 1dd5A d.67.3.1 39564 1vkmA 297 4.78e+01 c.138.1.1 108670 1smrA 335 4.88e+01 1smrA b.50.1.2 26878 1eca 136 4.94e+01 1flp a.1.1.2 15209 1mroB 442 4.95e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1griA 217 4.97e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1dvjA 246 5.16e+01 1dvjA c.1.2.3 28546 1tx4B 178 5.16e+01 1ctqA c.37.1.8 32045 1qtfA 246 5.17e+01 1agjA b.47.1.1 25830 1dosA 358 5.20e+01 1dosA c.1.10.2 29175 1t0hB 224 5.26e+01 c.37.1.1 106208 1sr9A 644 5.37e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2awdA 323 5.40e+01 1x6vA 630 5.44e+01 1dapA 320 5.52e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1g4wR 383 5.52e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1nb9A 147 5.52e+01 b.43.5.1 85515 1hbnB 442 5.54e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1uf3A 228 5.55e+01 d.159.1.6 99317 1uufA 369 5.58e+01 b.35.1.2,c.2.1.1 100006,100007 1nrwA 288 5.61e+01 c.108.1.10 86128 1ua7A 422 5.66e+01 b.71.1.1,c.1.8.1 107759,107760 1b57A 358 5.69e+01 1dosA c.1.10.2 29177 1h0pA 182 5.81e+01 b.62.1.1 76450 1budA 197 5.87e+01 1atlA d.92.1.9 40328 1jg1A 235 5.90e+01 c.66.1.7 66661 1oe4A 247 5.92e+01 c.18.1.3 86895 1fsz 372 5.92e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1cz1A 394 5.94e+01 1cz1A c.1.8.3 28839 2f02A 323 5.98e+01 1cjbA 231 6.05e+01 1qk3A c.61.1.1 34079 1dkrA 317 6.13e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1yy5B 513 6.23e+01 1gdvA 85 6.23e+01 1ctj a.3.1.1 60458 1rsgA 516 6.27e+01 4pgaA 337 6.43e+01 4pgaA c.88.1.1 35565 1b74A 254 6.45e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1yqdA 366 6.47e+01 2tysA 268 6.52e+01 2tysA c.1.2.4 28572 1q0bA 367 6.56e+01 c.37.1.9 95502 1ponA 36 6.66e+01 1ponA a.39.1.5 17239 2gasA 307 6.66e+01 1ei1A 391 6.70e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1g4uS 383 6.73e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1pv1A 299 6.83e+01 1frvA 264 6.83e+01 2frvA e.19.1.1 43308 2tpt 440 6.86e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1f06A 320 6.90e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 2cw5A 255 6.93e+01 1idk 359 7.01e+01 1qcxA b.80.1.2 28025 1fmaE 150 7.12e+01 1fmaE d.41.5.1 38630 1dkuA 317 7.12e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1aoeA 192 7.20e+01 1aoeA c.71.1.1 34923 1yrbA 262 7.26e+01 1hbxG 157 7.26e+01 1awcA a.4.5.21 60934 1uz5A 402 7.28e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1x88A 359 7.29e+01 1kmqA 184 7.35e+01 c.37.1.8 84412 1bag 425 7.38e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1o12A 376 7.39e+01 b.92.1.5,c.1.9.10 80758,80759 1jeoA 180 7.40e+01 c.80.1.3 66611 1ufkA 254 7.45e+01 c.66.1.39 99340 2lbp 346 7.57e+01 2liv c.93.1.1 35709 2frvA 264 7.59e+01 2frvA e.19.1.1 43303 1usgA 346 7.59e+01 c.93.1.1 99864 1tidB 119 7.64e+01 c.13.2.1 107000 1pydA 556 7.67e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1tffA 234 7.71e+01 d.3.1.11 106854 1stzA 338 7.72e+01 a.4.5.51,d.110.2.3 106009,106010 1ndh 272 7.76e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 2liv 344 7.81e+01 2liv c.93.1.1 35708 1rykA 69 7.92e+01 a.60.11.1 98105 1x1zA 252 7.94e+01 1n6bA 473 7.96e+01 a.104.1.1 85359 1cmxA 236 7.97e+01 1uch d.3.1.6 37130 1eqcA 394 8.02e+01 1cz1A c.1.8.3 28811 3dni 260 8.06e+01 3dni d.151.1.1 41791 1gd1O 334 8.07e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1ctaA 36 8.08e+01 1ctdA a.39.1.5 17232 1mdl 359 8.10e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1f75A 249 8.15e+01 1f75A c.101.1.1 59662 2b4aA 138 8.17e+01 1vraB 215 8.18e+01 1mgtA 174 8.19e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1j6oA 268 8.23e+01 c.1.9.12 77088 1pvdA 537 8.24e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1cyj 90 8.30e+01 1ctj a.3.1.1 15805 1tpt 440 8.36e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17763,31627,38625 1fm0E 150 8.47e+01 1fmaE d.41.5.1 38629 1xfkA 336 8.51e+01 1cv8 174 8.52e+01 1cv8 d.3.1.1 37089 1ypxA 375 8.67e+01 1nr6A 473 8.68e+01 a.104.1.1 92085 1r0kA 388 8.73e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1ws0A 156 8.80e+01 1o94A 729 8.80e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1qp8A 303 8.81e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1ml4A 308 8.82e+01 c.78.1.1,c.78.1.1 79255,79256 1dt6A 473 8.83e+01 1dt6A a.104.1.1 18977 1i2aA 219 8.89e+01 e.24.1.1 90660 1aj5A 173 8.90e+01 1alvA a.39.1.8 17367 2gnpA 266 8.90e+01 1g5cA 170 8.91e+01 1g5cA c.53.2.1 60264 1q3iA 214 8.93e+01 d.220.1.1 104524 2fkiA 126 8.96e+01