# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1jdw 423 5.12e-03 1jdw d.126.1.2 41129 1rxxA 421 1.34e-02 1b6tA 159 5.94e-02 1b6tA c.26.1.3 31600 1qjcA 158 6.46e-02 1b6tA c.26.1.3 63328 3pgk 416 2.33e-01 16pk c.86.1.1 35451 1hqcA 324 3.04e-01 1hqcA a.4.5.11 16127 c.37.1.20 32424 1h70A 255 5.64e-01 1h70A d.126.1.3 60711 1fwyA 331 6.39e-01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1hv9A 456 6.59e-01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1tdj 514 6.99e-01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1ej6A 1289 1.10e+00 i.7.1.1 45967 1egzA 291 1.11e+00 7a3hA c.1.8.3 28828 1hlrA 907 1.15e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1fztA 211 1.18e+00 1qhfA c.60.1.1 60158 1fxjA 331 1.27e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1gdeA 389 1.34e+00 c.67.1.1 60456 1gd9A 389 1.37e+00 c.67.1.1 60454 1ji8A 111 1.62e+00 d.203.1.1 66733 1d3hA 367 1.82e+00 1d3gA c.1.4.1 28601 1mzhA 225 1.89e+00 c.1.10.1 79698 1d3gA 367 1.98e+00 1d3gA c.1.4.1 28600 1bzyA 217 2.15e+00 1qk3A c.61.1.1 34071 1q7zA 566 2.30e+00 1lxyA 409 2.34e+00 1riqA 465 2.43e+00 1s9rA 410 2.47e+00 1o6zA 303 2.78e+00 c.2.1.5 81107 d.162.1.1 81108 1hkcA 917 2.79e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1hrnA 337 3.13e+00 1smrA b.50.1.2 26869 1hd2A 161 3.38e+00 c.47.1.10 60962 1e58A 249 3.54e+00 1qhfA c.60.1.1 59262 1dgjA 907 3.55e+00 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1v93A 296 3.79e+00 1he2A 206 3.97e+00 1he2A c.2.1.2 60966 1fc4A 401 4.24e+00 1bs0A c.67.1.4 59760 1v4sA 455 4.35e+00 1czaN 917 4.38e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1fbtA 190 4.56e+00 1bif c.60.1.4 34004 1hkbA 917 4.78e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1dgkN 917 4.84e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1gehA 444 5.01e+00 c.1.14.1 65181 d.58.9.1 65182 1bcpC 199 5.10e+00 1bcpB b.40.2.1 25121 d.169.1.2 42430 8ohm 435 5.15e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 1hdoA 206 5.31e+00 1he2A c.2.1.2 60965 7at1B 154 5.49e+00 8atcB d.58.2.1 39053 g.41.7.1 45305 8atcB 154 5.68e+00 8atcB d.58.2.1 39027 g.41.7.1 45279 1qhaA 917 6.02e+00 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1qr7A 350 6.08e+00 1qr7A c.1.10.4 29191 1heiA 451 6.41e+00 1heiA c.37.1.14 32463 c.37.1.14 32464 1hdiA 413 6.46e+00 16pk c.86.1.1 60964 1e19A 314 6.49e+00 1b7bA c.73.1.1 34967 1ak1 310 6.81e+00 1ak1 c.92.1.1 35594 1ctt 294 7.17e+00 1ctt c.97.1.1 36022 c.97.1.1 36023 1ujpA 271 7.23e+00 1eqnA 321 7.73e+00 1dd9A e.13.1.1 43256 3bifA 468 7.86e+00 1bif c.37.1.7 31962 c.60.1.4 34008 1a3h 300 8.14e+00 7a3hA c.1.8.3 28819 1lyvA 306 8.51e+00 c.45.1.2 74348 1nngA 153 8.55e+00 1dpgA 485 8.82e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1qvjA 292 8.83e+00 1a5t 334 8.84e+00 1a5t a.80.1.1 18450 c.37.1.20 32423 1h5vA 304 8.90e+00 c.1.8.3 70898 1k8cA 322 9.05e+00 c.1.7.1 72172 1bq3B 246 9.32e+00 1qhfA c.60.1.1 33979 1bif 469 9.39e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1kwhA 492 9.62e+00 c.94.1.1 68876 1bg6 359 9.74e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 1qhfA 240 9.74e+00 1qhfA c.60.1.1 33960 1nipA 289 1.00e+01 1cp2A c.37.1.10 32263 1rybA 212 1.01e+01 1o8bA 219 1.02e+01 c.35.1.2 81180 d.58.40.1 81181 1fzrA 138 1.06e+01 1fzrA c.52.1.17 33336 1ks2A 219 1.07e+01 c.35.1.2 72908 d.58.40.1 72909 1ispA 181 1.08e+01 c.69.1.18 76778 1f2dA 341 1.10e+01 1f2dA c.79.1.1 35298 1qrqA 325 1.14e+01 1qrqA c.1.7.1 28667 1exbA 332 1.14e+01 1qrqA c.1.7.1 28666 1msc 129 1.16e+01 1msc d.85.1.1 40039 1m0dA 138 1.20e+01 c.52.1.17 74354 2bifA 469 1.22e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1lkzA 219 1.24e+01 c.35.1.2 73991 d.58.40.1 73992 1id0A 152 1.24e+01 d.122.1.3 66111 1onwA 390 1.25e+01 b.92.1.7 87172 c.1.9.13 87173 1iw5A 113 1.27e+01 d.52.6.1 76864 1v9jA 113 1.27e+01 1gg1A 350 1.28e+01 1qr7A c.1.10.4 29187 1hmpA 217 1.29e+01 1qk3A c.61.1.1 34075 1e0tA 470 1.31e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 7a3hA 303 1.32e+01 7a3hA c.1.8.3 28817 1uumA 372 1.41e+01 1n2eA 300 1.42e+01 c.26.1.4 85268 1ytn 306 1.43e+01 1ytw c.45.1.2 32688 1tfr 305 1.44e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1qo0D 196 1.44e+01 1qo0D c.23.1.3 31125 1nnmA 652 1.45e+01 1pg4A 652 1.45e+01 e.23.1.1 88067 1mopA 300 1.46e+01 c.26.1.4 85035 2ms2A 129 1.46e+01 1msc d.85.1.1 40049 1jr3E 334 1.50e+01 a.80.1.1 63253 c.37.1.20 63254 1bs0A 384 1.54e+01 1bs0A c.67.1.4 34490 1ytw 306 1.56e+01 1ytw c.45.1.2 32689 1r2rA 248 1.57e+01 1fqvA 336 1.57e+01 1fqvA a.158.1.1 19254 c.10.1.3 30856 1r3sA 367 1.59e+01 2ebn 289 1.60e+01 2ebn c.1.8.5 28990 1g2iA 166 1.62e+01 1g2iA c.23.16.2 31438 1uu1A 335 1.63e+01 1od6A 160 1.63e+01 c.26.1.3 86836 1i6wA 181 1.65e+01 1i6wA c.69.1.18 61859 1uanA 227 1.65e+01 1q77A 138 1.65e+01 1p32C 209 1.66e+01 1p32A d.25.1.1 38381 4bcl 366 1.68e+01 4bcl b.75.1.1 27968 1o57A 291 1.69e+01 1p41A 291 1.69e+01 1e9iA 431 1.77e+01 c.1.11.1 64818 d.54.1.1 64819 1ogdA 131 1.79e+01 1j9eA 147 1.82e+01 c.23.5.1 62756 2u1a 88 1.84e+01 2u1a d.58.7.1 39164 1knqA 175 1.84e+01 c.37.1.17 72786 1ny1A 240 1.85e+01 c.6.2.3 86395 1ufhA 180 1.86e+01 d.108.1.1 88485 1i9aA 182 1.88e+01 1i9aA d.113.1.2 62082 1qk4A 233 1.93e+01 1qk3A c.61.1.1 34037 1n8fA 350 1.94e+01 c.1.10.4 85397 1g6oA 330 1.95e+01 1g6oA c.37.1.11 32430 1b6sA 355 2.00e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1f4pA 147 2.02e+01 5nul c.23.5.1 59651 1id1A 153 2.03e+01 1id1A c.2.1.9 62286 1o0yA 260 2.03e+01 c.1.10.1 80756 1iv8A 720 2.03e+01 b.71.1.1 76842 c.1.8.1 76843 1hztA 190 2.04e+01 1i9aA d.113.1.2 61459 1b7fA 168 2.08e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1zymA 258 2.10e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1jhb 106 2.11e+01 1kte c.47.1.1 32772 1vhxA 150 2.13e+01 1uroA 367 2.14e+01 1uroA c.1.22.1 29675 1ocnA 362 2.18e+01 c.6.1.1 86808 1kk9A 221 2.19e+01 d.115.1.1 77432 1tph1 247 2.21e+01 1amk 1otcB 260 2.21e+01 1otcB b.40.4.3 25310 1i2kA 269 2.27e+01 16pk 415 2.28e+01 16pk c.86.1.1 35454 1p3dA 475 2.33e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1q33A 292 2.33e+01 1f74A 293 2.38e+01 1nal3 c.1.10.1 29079 7odcA 424 2.40e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1hfbA 370 2.41e+01 c.1.10.4 76706 1dozA 309 2.42e+01 1ak1 c.92.1.1 35592 1ddeA 338 2.43e+01 1dd9A e.13.1.1 43255 1nu0A 138 2.50e+01 1dkuA 317 2.51e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1on0A 158 2.51e+01 d.108.1.1 87095 1g6sA 427 2.51e+01 1eps d.68.2.2 39584 1b6rA 355 2.53e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1xyfA 436 2.56e+01 1taxA b.42.2.1 25577 c.1.8.3 28909 1h5rA 293 2.60e+01 c.68.1.6 65623 1o1yA 239 2.63e+01 c.23.16.1 86554 1dqaC 467 2.64e+01 1dqaA d.58.20.1 39366 d.179.1.1 42587 1cydA 244 2.69e+01 1cydA c.2.1.2 29825 1mdoA 393 2.69e+01 c.67.1.4 79013 1vi1A 345 2.70e+01 1dqaA 467 2.74e+01 1dqaA d.58.20.1 39364 d.179.1.1 42585 1qgvA 142 2.78e+01 1qgvA c.47.1.8 33056 1hw8A 467 2.78e+01 1dqaA d.58.20.1 61298 d.179.1.1 61299 3mag 307 2.79e+01 3mag c.66.1.25 34205 1d09B 153 2.80e+01 8atcB d.58.2.1 39015 g.41.7.1 45267 1l9mA 692 2.90e+01 b.1.18.9 73732 b.1.5.1 73733 b.1.5.1 73734 d.3.1.4 73735 1hqz9 141 2.92e+01 3ladA 476 2.93e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1pz1A 333 2.95e+01 1a8y 367 2.95e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1bix 287 2.97e+01 1bix d.151.1.1 41781 1nofA 383 2.99e+01 1dljA 402 3.02e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1bvwA 360 3.03e+01 1bvwA c.6.1.1 30668 1vp9 322 3.04e+01 3mag c.66.1.25 34210 1g61A 228 3.04e+01 1g61A d.126.1.1 41126 1a53 247 3.09e+01 1a53 c.1.2.4 28564 1fkx 349 3.10e+01 1a4mA c.1.9.1 29018 1add 349 3.13e+01 1a4mA c.1.9.1 29020 1eza 259 3.21e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1igs 248 3.21e+01 1a53 c.1.2.4 28565 1dctA 324 3.23e+01 6mhtA c.66.1.26 34244 1aoxA 203 3.24e+01 1aoxA c.62.1.1 34151 1v4vA 376 3.27e+01 1jeyA 609 3.30e+01 1jeqA e.31.1.1 62924 1f6kA 293 3.31e+01 1nal3 c.1.10.1 29081 1psqA 163 3.32e+01 c.47.1.10 88283 1aogA 485 3.41e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1juk 248 3.43e+01 1a53 c.1.2.4 28567 1ky9A 448 3.44e+01 b.36.1.4 73198 b.47.1.1 73199 1l9vA 317 3.45e+01 d.13.2.1 73760 d.216.1.1 73761 1qmvA 197 3.46e+01 1qq2A c.47.1.10 33066 2fox 138 3.47e+01 5nul c.23.5.1 31197 1dtwB 342 3.55e+01 1qs0B c.36.1.7 31828 c.48.1.2 33102 1vjzA 341 3.58e+01 1oc7A 364 3.58e+01 c.6.1.1 86794 1ao0A 459 3.60e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 4xiaA 393 3.61e+01 4xis c.1.15.3 29439 1f5aA 513 3.63e+01 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1dzlA 505 3.65e+01 1dzlA b.121.6.1 23586 1d4aA 273 3.67e+01 1d4aA c.23.5.3 31219 1bdg 451 3.68e+01 1qhaA c.55.1.3 33461 c.55.1.3 33462 1qp2A 70 3.71e+01 1pse b.34.4.2 24596 1dd9A 338 3.72e+01 1dd9A e.13.1.1 43254 1rf6A 427 3.76e+01 3xis 387 3.80e+01 4xis c.1.15.3 29423 1xis 387 3.80e+01 4xis c.1.15.3 29422 2xis 387 3.80e+01 4xis c.1.15.3 29427 1nepA 130 3.81e+01 b.1.18.7 80440 1mnzA 388 3.81e+01 c.1.15.3 79328 1gw9A 388 3.81e+01 c.1.15.3 70658 1jb7B 260 3.82e+01 1otcB b.40.4.3 62839 1kte 105 3.82e+01 1kte c.47.1.1 32771 2bvwA 362 3.84e+01 1bvwA c.6.1.1 30666 2fx2 147 3.86e+01 1rcf c.23.5.1 31158 1v1rB 342 3.87e+01 1mi3A 322 3.89e+01 1nxjA 183 3.97e+01 c.8.7.1 86382 1uspA 139 3.98e+01 1asx 159 3.99e+01 1a6dA c.8.5.2 30821 1ksfX 758 3.99e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1qp8A 303 4.00e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352