# 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 1zynA 202 4.20e-02 1hyuA 521 1.62e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1esfA 233 2.16e-01 3seb b.40.2.2,d.15.6.1 25146,37735 2rslA 140 6.17e-01 2rslA c.53.1.1 33345 1dyqA 234 7.26e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2fclA 169 9.39e-01 1juk 248 9.78e-01 1a53 c.1.2.4 28567 1a53 247 1.00e-00 1a53 c.1.2.4 28564 1igs 248 1.03e+00 1a53 c.1.2.4 28565 2ewrA 170 1.14e+00 1ghtA 105 1.85e+00 2rslA c.53.1.1 60526 1gdtA 183 2.41e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1m93A 55 2.99e+00 e.1.1.1 91235 1agnA 373 3.43e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 2fvtA 135 4.20e+00 1a0rP 245 4.46e+00 1b9yC c.47.1.6 33054 2flsA 132 4.58e+00 2bg5A 324 4.80e+00 1zp4A 304 5.93e+00 1regX 122 6.08e+00 1regX d.58.27.1 39406 2aioA 269 6.11e+00 2c3zA 222 6.29e+00 1qzgA 187 6.63e+00 b.40.4.3 96643 1pbgA 468 6.87e+00 1e70M c.1.8.4 28946 3pbgA 468 7.14e+00 1e70M c.1.8.4 28951 1smlA 269 7.67e+00 1smlA d.157.1.1 42053 1j5vA 351 7.81e+00 c.72.1.1 71585 1focA 132 7.98e+00 1c52 a.3.1.1 15812 1qhlA 227 8.62e+00 1qhlA c.37.1.12 32382 2axwA 134 8.66e+00 2g9iA 249 8.73e+00 1xkiA 162 8.95e+00 1fl2A 310 1.03e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1repC 251 1.07e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1xwvA 129 1.10e+01 1ih8A 271 1.13e+01 2nsyA c.26.2.1 62377 1iz5A 249 1.14e+01 d.131.1.2,d.131.1.2 83834,83835 1thg 544 1.22e+01 1thg c.69.1.17 34763 1ma3A 253 1.29e+01 c.31.1.5 78883 1grvB 182 1.30e+01 c.61.1.1 76322 1kqpA 271 1.33e+01 c.26.2.1 72883 2pil 159 1.33e+01 2pil d.24.1.1 38376 1qdlB 195 1.39e+01 1qdlB c.23.16.1 31437 1dg3A 592 1.41e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1t64A 377 1.41e+01 c.42.1.2 106543 1c52 131 1.42e+01 1c52 a.3.1.1 15810 2d1uA 104 1.44e+01 1h8vA 218 1.46e+01 2nlrA b.29.1.11 60795 1s55A 156 1.47e+01 5gcnA 166 1.48e+01 1yghA d.108.1.1 40807 2b33A 140 1.52e+01 1nsyA 271 1.55e+01 2nsyA c.26.2.1 31614 1tiqA 180 1.56e+01 d.108.1.1 107010 1d2oA 187 1.58e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1oa2A 218 1.59e+01 b.29.1.11 86721 2nsyA 271 1.59e+01 2nsyA c.26.2.1 31612 1cjbA 231 1.62e+01 1qk3A c.61.1.1 34079 2afbA 351 1.63e+01 1pnsC 206 1.64e+01 i.1.1.1 88170 1v30A 124 1.69e+01 1gm6A 175 1.76e+01 b.60.1.1 70272 1he2A 206 1.79e+01 1he2A c.2.1.2 60966 1h72C 296 1.80e+01 d.14.1.5,d.58.26.1 60712,60713 1zpvA 91 1.81e+01 1gyxA 76 1.82e+01 d.80.1.1 76387 1lufA 343 1.96e+01 d.144.1.7 78223 2gfgA 193 2.00e+01 1larA 575 2.02e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1iqaA 160 2.04e+01 b.22.1.1 71274 1a99A 344 2.09e+01 1pot c.94.1.1 35812 1hdoA 206 2.10e+01 1he2A c.2.1.2 60965 1vr0A 247 2.12e+01 1o58A 303 2.13e+01 c.79.1.1 92491 2gw6A 123 2.19e+01 1k38A 254 2.20e+01 e.3.1.1 84303 2fh7A 595 2.24e+01 1sqsA 242 2.26e+01 c.23.5.5 98968 1d2rA 326 2.27e+01 1d2rB c.26.1.1 31572 1xedA 117 2.28e+01 1fwkA 296 2.29e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1tzaA 134 2.33e+01 b.1.23.1 107468 1o0pA 104 2.40e+01 d.58.7.1 86535 1aogA 485 2.42e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1yr2A 741 2.47e+01 1f8nA 839 2.47e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1sek 378 2.47e+01 1sek e.1.1.1 42675 1vr7A 142 2.55e+01 1ap0 73 2.55e+01 1ap0 b.34.13.2 37475 2gmqA 118 2.63e+01 1b25A 619 2.64e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1ay2 159 2.75e+01 2pil d.24.1.1 38377 1i8fA 81 2.79e+01 1i8fA b.38.1.1 61959 1tf1A 198 2.81e+01 d.110.2.2 106826 2cxcA 144 2.88e+01 2asbA 251 2.90e+01 1my6A 199 2.93e+01 a.2.11.1,d.44.1.1 85232,85233 1m07A 111 2.95e+01 d.5.1.1 78328 1ycyA 71 2.95e+01 1wmqA 147 3.05e+01 1yb2A 275 3.12e+01 1ge8A 249 3.17e+01 1plq d.131.1.2,d.131.1.2 41398,41399 1ej0A 180 3.23e+01 1ej0A c.66.1.2 34179 1juvA 193 3.29e+01 c.71.1.1 90912 1y96B 85 3.31e+01 1qlmA 316 3.38e+01 1qlmA d.147.1.1 41765 1ockA 412 3.42e+01 c.117.1.1 86802 1qavA 90 3.46e+01 1qauA b.36.1.1 24777 1bib 321 3.49e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1o6dA 163 3.59e+01 c.116.1.3 92567 1u00A 227 3.61e+01 1g8lA 411 3.74e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 2b7eA 59 3.76e+01 1tygB 87 3.79e+01 d.15.3.2 107455 1wpuA 147 3.85e+01 1v5tA 90 3.86e+01 d.15.1.1 108385 1bc4 111 4.00e+01 1onc d.5.1.1 37279 1b56 135 4.03e+01 1hmt b.60.1.2 27183 1lwjA 441 4.14e+01 b.71.1.1,c.1.8.1 74303,74304 1qi9A 556 4.19e+01 1qhbA a.111.1.2 19053 4uagA 437 4.22e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1adl 131 4.23e+01 1hmt b.60.1.2 27186 1u2xA 474 4.23e+01 c.72.1.3 107622 1uag 437 4.25e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1vddA 228 4.27e+01 e.49.1.1 108519 1ggwA 140 4.30e+01 1ggwA a.39.1.5 60490 2ohxA 374 4.37e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1ft5A 211 4.47e+01 1bvb a.138.1.3 19681 1es6A 296 4.49e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1fc2D 224 4.49e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1t0aA 159 4.51e+01 3nll 138 4.53e+01 5nul c.23.5.1 31206 1b5tA 275 4.54e+01 1b5tA c.1.23.1 29676 1rwiA 270 4.54e+01 b.68.9.1 97987 2g0uA 92 4.60e+01 1x74A 360 4.62e+01 2gi3A 476 4.66e+01 1epwA 1290 4.67e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1p35A 299 4.68e+01 1p35A b.28.1.1 23925 1q48A 134 4.76e+01 d.224.1.2 95783 1lid 131 4.85e+01 1hmt b.60.1.2 27184 1a9v 129 4.91e+01 1a9v b.1.18.7 21946 1ll2A 333 4.95e+01 c.68.1.14 74005 1axgA 374 4.98e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1i6kA 328 4.99e+01 c.26.1.1 66040 1ydmA 187 5.01e+01 2aefA 234 5.02e+01 1ktjA 129 5.12e+01 b.1.18.7 72974 1uc7A 125 5.14e+01 c.47.1.1 99163 1ee2A 373 5.16e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1p5vA 235 5.18e+01 b.1.11.1,b.7.2.1 87812,87813 1xdpA 687 5.23e+01 1ri7A 171 5.27e+01 a.4.5.32,d.58.4.2 97504,97505 2bby 69 5.28e+01 2bby a.4.5.15 16148 1ta8A 332 5.31e+01 1j5eC 239 5.49e+01 d.52.3.1,d.53.1.1 71544,71545 1ns5A 155 5.53e+01 c.116.1.3 80705 1duvG 333 5.54e+01 1othA c.78.1.1,c.78.1.1 35228,35229 3kar 346 5.55e+01 1bg2 c.37.1.9 32198 1q59A 172 5.57e+01 f.1.4.1 95881 1wjbA 55 5.57e+01 1wjcA a.4.10.1 16265 1vicA 262 5.68e+01 c.68.1.13 100756 1se4 239 5.69e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1mmiA 366 5.75e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 2fox 138 5.78e+01 5nul c.23.5.1 31197 1souA 194 5.78e+01 c.124.1.6 105858 1fgqA 839 5.82e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1v0lA 313 5.85e+01 c.1.8.3 108207 1bg6 359 5.85e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1nijA 318 5.87e+01 c.37.1.10,d.237.1.1 85741,85742 1zhvA 134 5.88e+01 1a71A 374 5.89e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1g7nA 131 5.91e+01 b.60.1.2 83274 1jhfA 202 5.98e+01 a.4.5.2,b.87.1.1 63057,63058 3uagA 437 6.01e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1zthA 258 6.11e+01 1qk3A 233 6.16e+01 1qk3A c.61.1.1 34031 1shsA 147 6.17e+01 1shsA b.15.1.1 23675 1tueA 212 6.17e+01 c.37.1.20 107323 1ble 163 6.21e+01 1ble c.38.1.1 32475 1v93A 296 6.21e+01 c.1.23.1 100532 1kfiA 572 6.23e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 2bo4A 397 6.27e+01 1smrA 335 6.29e+01 1smrA b.50.1.2 26878 2bwfA 77 6.30e+01 1wmhA 89 6.31e+01 1exg 110 6.39e+01 1exg b.2.2.1 22387 1ab0 131 6.39e+01 1hmt b.60.1.2 27190 1vr4A 103 6.41e+01 2a2pA 129 6.42e+01 1hfbA 370 6.42e+01 c.1.10.4 76706 1pk9A 237 6.51e+01 c.56.2.1 94823 1njhA 119 6.56e+01 b.128.1.1 85787 1cbg 490 6.58e+01 1e70M c.1.8.4 28933 3seb 238 6.59e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1t9bA 677 6.69e+01 3pfk 319 6.69e+01 3pfk c.89.1.1 35581 1pnsB 234 6.79e+01 i.1.1.1 88169 1fc1A 224 6.80e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1bvb 211 6.83e+01 1bvb a.138.1.3 19683 1d2rB 326 6.88e+01 1d2rB c.26.1.1 31573 1f3hA 142 6.91e+01 1f3hA g.52.1.1 45381 2f4mA 295 6.93e+01 1ll0A 339 6.95e+01 c.68.1.14 73995 5nul 138 7.01e+01 5nul c.23.5.1 31191 1bby 69 7.04e+01 2bby a.4.5.15 16149 1u6tA 121 7.06e+01 2a3mA 130 7.08e+01 1of8A 370 7.10e+01 c.1.10.4 92819 1k0rA 366 7.11e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1axeA 374 7.12e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1b9xC 246 7.15e+01 1b9yC c.47.1.6 33053 1wlyA 333 7.21e+01 1irxA 523 7.27e+01 a.97.1.2,c.26.1.1 71378,71379 1rypI 222 7.30e+01 d.153.1.4 41877 1fg7A 356 7.30e+01 1gewA c.67.1.1 59819 1vcvA 226 7.32e+01 1ve6A 582 7.44e+01 2cygA 312 7.44e+01 1wlzA 105 7.57e+01 1j5eB 256 7.64e+01 c.23.15.1 71543 1vfsA 386 7.66e+01 b.49.2.2,c.1.6.1 108584,108585 2trcP 217 7.68e+01 1b9yC c.47.1.6 33051 1quqB 121 7.72e+01 1quqB b.40.4.3 25305 1s9rA 410 7.74e+01 d.126.1.4 98758 1kal 29 7.92e+01 g.3.3.1 44077 2b3wA 168 7.92e+01 1bxlA 181 7.99e+01 1maz f.1.4.1 43396 2axpA 173 8.00e+01 1mm4A 170 8.11e+01 f.4.1.2 79294 1fsgA 233 8.12e+01 1qk3A c.61.1.1 34029 1t8qA 336 8.15e+01 c.1.18.3 106669 1j1lA 290 8.15e+01 b.82.1.12 90766 2amyA 246 8.20e+01 1wjcA 47 8.23e+01 1wjcA a.4.10.1 16261 2bce 581 8.27e+01 2bce c.69.1.1 34625 1lxyA 409 8.27e+01 d.126.1.4 91154 1qrkA 731 8.34e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1p6pA 125 8.34e+01 b.60.1.2 87839 8adh 374 8.39e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1wu3I 161 8.41e+01 2a41C 32 8.43e+01 1yqzA 438 8.44e+01 1y96A 86 8.66e+01 1ck2A 104 8.69e+01 1ck9A d.79.3.1 39809 1bc9 200 8.71e+01 1pbv a.118.3.1 19180 1ok7A 366 8.72e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1b0zA 445 8.81e+01 2pgi c.80.1.2 35309 2pgi 445 8.81e+01 2pgi c.80.1.2 35308 2gnxA 365 8.83e+01 1i6lA 328 8.83e+01 c.26.1.1 66041 1pyfA 312 8.89e+01 c.1.7.1 95334 1v04A 355 8.96e+01 b.68.6.2 100240 2fcjA 119 8.99e+01