# List of top-scoring protein chains for t2k-100-30-bys-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 2a9uA 144 9.69e-02 1ea1A 455 4.18e-01 1ea1A a.104.1.1 18970 1h5zA 455 4.67e-01 a.104.1.1 90622 1e9xA 455 5.16e-01 1ea1A a.104.1.1 18969 1u13A 455 5.63e-01 a.104.1.1 107578 1x8vA 455 6.28e-01 1gvhA 396 6.93e-01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1w68A 390 1.37e+00 a.25.1.2 109216 1mswD 883 1.91e+00 e.8.1.3 79427 1h3nA 878 1.93e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1ka2A 499 1.95e+00 d.92.1.5 77305 1n6bA 473 2.40e+00 a.104.1.1 85359 1qlnA 883 2.59e+00 1cezA e.8.1.3 43111 1dt6A 473 2.61e+00 1dt6A a.104.1.1 18977 1sqgA 429 3.29e+00 a.79.1.3,c.66.1.38 105912,105913 1lfkA 398 3.46e+00 a.104.1.1 77926 1wu7A 434 3.80e+00 1iq8A 582 3.87e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1cezA 883 4.42e+00 1cezA e.8.1.3 43110 1i7kA 179 4.51e+00 1u9aA d.20.1.1 61889 1y6zA 263 4.64e+00 1q5dA 419 4.67e+00 a.104.1.1 95891 1nr6A 473 4.90e+00 a.104.1.1 92085 1h9fA 57 5.08e+00 1h9fA a.140.1.1 60826 1deeG 54 5.12e+00 1fc2C a.8.1.1 16343 1odoA 408 5.60e+00 a.104.1.1 92783 1h38B 883 5.77e+00 e.8.1.3 76626 1h38D 883 5.81e+00 e.8.1.3 76628 1h38C 883 6.23e+00 e.8.1.3 76627 1kkhA 317 6.39e+00 d.14.1.5,d.58.26.3 72645,72646 1gmpA 96 6.78e+00 1rgeA d.1.1.2 36036 1rgeA 96 6.80e+00 1rgeA d.1.1.2 36028 1i8vA 96 6.81e+00 d.1.1.2 61985 2fd5A 180 6.90e+00 1ho8A 480 6.96e+00 1ho8A a.118.1.9 61107 1udvA 89 7.46e+00 d.68.6.1 99224 1gl2C 65 8.01e+00 h.1.15.1 65280 1xsm 390 8.40e+00 1xsm a.25.1.2 16804 1w5tA 412 8.72e+00 1lniA 96 8.93e+00 d.1.1.2 74046 1h0oA 390 9.23e+00 a.25.1.2 70845 1i4yA 114 9.87e+00 2mhr a.24.4.1 61738 1e94F 449 9.99e+00 1do0A c.37.1.20 32443 1j7nB 776 1.03e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 2bkyX 89 1.12e+01 1pszA 303 1.16e+01 1toaA c.92.2.2 35600 1trrA 107 1.18e+01 1jhgA a.4.12.1 19017 1d1rA 116 1.27e+01 1d1rA d.64.1.1 39548 1up7A 417 1.31e+01 1up6A 416 1.36e+01 c.2.1.5,d.162.1.2 107976,107977 2wrpR 107 1.37e+01 1jhgA a.4.12.1 19010 1mgrA 99 1.43e+01 d.1.1.2 79106 1go3F 107 1.44e+01 a.60.8.2 65407 1f5aA 513 1.46e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1a5t 334 1.52e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1yf9A 171 1.52e+01 2fq4A 192 1.60e+01 1jr3E 334 1.67e+01 a.80.1.1,c.37.1.20 63253,63254 1q79A 514 1.75e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1rcsA 105 1.76e+01 1jhgA a.4.12.1 19025 1uj6A 227 1.77e+01 c.124.1.4,d.58.40.1 107898,107899 1j7nA 776 1.78e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1w99A 558 1.78e+01 1hjp 203 1.84e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1ir6A 424 1.90e+01 c.107.1.2 71342 1jhgA 101 1.90e+01 1jhgA a.4.12.1 19009 2a9iA 113 1.91e+01 1yn9A 169 1.91e+01 1yh6A 179 1.97e+01 1pylA 97 1.98e+01 d.1.1.2 104391 1b8pA 329 1.99e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1oyzA 280 2.04e+01 a.118.1.16 93775 1ox3A 109 2.07e+01 h.1.17.1 93668 1yb3A 175 2.13e+01 2bcqA 335 2.14e+01 2h1nA 567 2.15e+01 1gjjA 168 2.18e+01 a.140.1.1,a.140.1.1 83291,83292 1envA 123 2.21e+01 1envA h.3.2.1 45726 1w7bA 339 2.23e+01 1kwfA 363 2.25e+01 a.102.1.2 73078 1zl8B 54 2.26e+01 1ibjA 464 2.26e+01 1ibjA c.67.1.3 62162 1gseA 221 2.28e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1cem 363 2.29e+01 1cem a.102.1.2 18826 1wa8A 99 2.29e+01 1wj7A 104 2.29e+01 1bvsB 203 2.30e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1vl7A 157 2.35e+01 b.45.1.1 108732 1jbgA 109 2.36e+01 a.6.1.3 66480 1jk0A 419 2.45e+01 a.25.1.2 63142 1avoB 140 2.46e+01 1avoB 1cqxA 403 2.50e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2bwbA 46 2.55e+01 1lrv 244 2.69e+01 1lrv a.118.1.5 19146 1ovaA 386 2.89e+01 1ovaA e.1.1.1 42619 1vddA 228 2.93e+01 e.49.1.1 108519 1rzrA 332 2.96e+01 1p5sA 203 3.00e+01 a.40.1.1 94147 1i52A 236 3.01e+01 1i52A c.68.1.13 61767 1t2bA 397 3.02e+01 1y74B 50 3.06e+01 1wgzA 510 3.09e+01 1k3lA 221 3.12e+01 a.45.1.1,c.47.1.5 77229,77230 1q5zA 177 3.15e+01 a.196.1.1 95954 1hm6A 346 3.20e+01 1avc a.65.1.1 18147 1rovA 857 3.25e+01 a.119.1.1,b.12.1.1 97674,97675 1jchC 551 3.27e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1jchA 551 3.27e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1vqoW 154 3.34e+01 1nal1 297 3.34e+01 1nal3 1khdA 345 3.45e+01 a.46.2.1,c.27.1.1 77400,77401 1fdyA 297 3.45e+01 1nal3 c.1.10.1 29071 1k3yA 221 3.46e+01 a.45.1.1,c.47.1.5 77245,77246 1yucA 255 3.48e+01 2ah6A 208 3.49e+01 1lxyA 409 3.50e+01 d.126.1.4 91154 1s72W 154 3.52e+01 d.59.1.1 105342 1s9rA 410 3.53e+01 d.126.1.4 98758 1c8kA 842 3.56e+01 1a8i c.87.1.4 35491 1hz6A 72 3.57e+01 2ptl d.15.7.1 61429 1wh5A 80 3.63e+01 1jj2V 154 3.65e+01 1ffkT d.59.1.1 63107 1i4mA 108 3.78e+01 d.6.1.1 66025 1g8pA 350 3.78e+01 1g8pA c.37.1.20 60376 1do0A 442 3.80e+01 1do0A c.37.1.20 32432 1g5aA 628 3.99e+01 b.71.1.1,c.1.8.1 65152,65153 1ee4A 423 4.03e+01 1ee4A a.118.1.1 19128 1gpb 842 4.08e+01 1a8i c.87.1.4 35478 2f05A 105 4.09e+01 2cwyA 94 4.10e+01 1zhxA 438 4.10e+01 1wr1B 58 4.11e+01 1edi 56 4.16e+01 1fc2C a.8.1.1 16349 1a8i 842 4.18e+01 1a8i c.87.1.4 35490 1hdmA 201 4.22e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1uruA 244 4.28e+01 h.4.14.1 99835 1ujwB 135 4.32e+01 h.4.9.1 99472 1wloA 136 4.35e+01 1b3uA 588 4.38e+01 1b3uA a.118.1.2 19135 1l0lA 446 4.40e+01 d.185.1.1,d.185.1.1 84482,84483 1fx7A 230 4.41e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2hmzA 113 4.49e+01 2mhr a.24.4.1 16564 1kmiZ 214 4.53e+01 h.4.11.1 72752 1axn 323 4.54e+01 1avc a.65.1.1 18149 2hmqA 113 4.56e+01 2mhr a.24.4.1 16568 1h5uA 842 4.59e+01 1a8i c.87.1.4 60655 1aii 323 4.61e+01 1avc a.65.1.1 18150 2fuqA 747 4.68e+01 1rm6C 161 4.73e+01 6gsvA 217 4.78e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1vkuA 100 4.79e+01 a.28.1.1 108690 1x1nA 524 4.83e+01 1nd9A 49 4.86e+01 a.6.1.6 85575 1pmzA 86 5.00e+01 a.39.1.10 104195 1wljA 189 5.01e+01 1jk0B 345 5.03e+01 a.25.1.2 63143 1otkA 249 5.03e+01 a.25.1.2 93521 1yiiA 320 5.05e+01 2bzgA 232 5.08e+01 2fiyA 309 5.13e+01 1s8nA 205 5.15e+01 c.23.1.1 105374 1ala 321 5.19e+01 1avc a.65.1.1 18153 1tiiC 53 5.25e+01 1tiiC 2gh1A 301 5.27e+01 2cvxA 888 5.27e+01 1ouvA 273 5.28e+01 a.118.18.1 93570 1hl2A 297 5.32e+01 c.1.10.1 83581 1nal3 297 5.33e+01 1nal3 1k52A 72 5.33e+01 d.15.7.1 68148 1pm6A 72 5.33e+01 a.6.1.7 94894 1x0tA 120 5.34e+01 2cp8A 54 5.37e+01 1kr7A 110 5.38e+01 a.1.1.4 72890 2h58A 330 5.43e+01 1jubA 311 5.44e+01 c.1.4.1 90908 2bbhA 269 5.45e+01 1qynA 153 5.46e+01 d.33.1.1 96597 1oj4A 283 5.52e+01 d.14.1.5,d.58.26.5 93083,93084 1g5cA 170 5.60e+01 1g5cA c.53.2.1 60264 1ztuA 341 5.64e+01 1dorA 311 5.65e+01 2dorA c.1.4.1 28595 1tjoA 182 5.65e+01 2dorA 311 5.66e+01 2dorA c.1.4.1 28593 1rztA 331 5.69e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1xsnA 335 5.74e+01 1mfgA 95 5.75e+01 b.36.1.1 79043 1dc1A 323 5.88e+01 1dc1A c.52.1.11 33321 1wwzA 159 5.89e+01 2bemA 170 5.90e+01 2e2c 156 6.00e+01 1u9aA d.20.1.1 38336 2cohA 202 6.01e+01 1y9bA 90 6.02e+01 1b1bA 140 6.11e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 1hkcA 917 6.13e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1ofhA 310 6.15e+01 c.37.1.20 86948 1p2xA 159 6.19e+01 a.40.1.1 104062 1qm1A 143 6.21e+01 1b10A d.6.1.1 37312 1dk5A 322 6.24e+01 1dk5A a.65.1.1 18192 2cqsA 842 6.27e+01 1vejA 74 6.36e+01 1zarA 282 6.38e+01 1j9bA 141 6.38e+01 c.47.1.12 66459 1pk5A 248 6.39e+01 a.123.1.1 88139 1s3cA 141 6.45e+01 1quuA 250 6.46e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1eza 259 6.66e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1bdc 60 6.74e+01 1fc2C a.8.1.1 16350 1wpaA 114 6.78e+01 1um8A 376 6.84e+01 c.37.1.20 99580 2ccmA 191 6.86e+01 1abbA 828 7.02e+01 1a8i c.87.1.4 35536 1vrmA 325 7.02e+01 1rh6A 55 7.07e+01 a.6.1.7 104935 1k51A 72 7.09e+01 d.15.7.1 68147 1hleA 345 7.12e+01 1ovaA e.1.1.1 42618 1x6zA 123 7.13e+01 1aroP 883 7.17e+01 1cezA e.8.1.3 43112 1tqmA 282 7.17e+01 a.4.5.56,d.144.1.9 107236,107237 1qhaA 917 7.19e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1ixkA 315 7.20e+01 c.66.1.38 90716 1rw2A 152 7.28e+01 a.118.19.1 97961 1jiwI 106 7.28e+01 1smpI b.61.2.1 63078 2aamA 309 7.31e+01 1i17A 107 7.33e+01 1i17A d.6.1.1 61519 2f4mA 295 7.45e+01 1yodA 30 7.45e+01 1qm3A 112 7.48e+01 1b10A d.6.1.1 37313 1yarA 233 7.54e+01 1qexA 288 7.56e+01 1qexA b.32.1.1 24425 1tx4A 198 7.67e+01 1tx4A a.116.1.1 19098 1ifyA 49 7.71e+01 a.5.2.1 71207 2h3lA 103 7.78e+01 1vd3A 217 7.87e+01 1yrbA 262 7.87e+01 1rhs 296 7.91e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1wzcA 249 7.93e+01 1lnh 857 7.98e+01 1yge a.119.1.1,b.12.1.1 19237,23637 1po5A 476 8.06e+01 a.104.1.1 94963 1iygA 133 8.12e+01 a.118.8.1 76947 1avyB 74 8.14e+01 1avyB h.1.17.1 45657 1usuA 260 8.21e+01 d.14.1.8 99885 1kwsA 261 8.25e+01 c.68.1.7 73083 1eblB 317 8.25e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1le4 144 8.31e+01 1nfn a.24.1.1 16528 1ntcA 91 8.33e+01 1ntcA a.4.1.12 19004 1wurA 220 8.36e+01 2bptA 861 8.37e+01 1qayA 428 8.39e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1xw5A 217 8.40e+01 1fbnA 230 8.40e+01 1fbnA c.66.1.3 34181 2b4jC 98 8.46e+01 1b10A 142 8.52e+01 1b10A d.6.1.1 37306 1i1iP 681 8.54e+01 1i1iP d.92.1.5 40297 1eblA 317 8.56e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1lx8A 55 8.59e+01 a.6.1.7 84734 1bz4A 144 8.60e+01 1nfn a.24.1.1 16521 1uhgA 385 8.60e+01 e.1.1.1 88491 1zuhA 168 8.61e+01 1colA 204 8.68e+01 1a87 f.1.1.1 43378 1qmgA 524 8.73e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 2a6qA 86 8.76e+01 2c4nA 250 8.85e+01 1ujcA 161 8.91e+01 1g4yB 101 8.91e+01 1g4yB f.15.1.1 60251 1dzoA 123 8.94e+01 1dzoA d.24.1.1 38378