# 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 1ccwA 137 2.61e-01 1be1 c.23.6.1 31238 2g8lA 299 3.92e-01 1qycA 308 1.38e+00 c.2.1.2 96581 1nz0A 118 1.50e+00 d.14.1.2 86433 1oz9A 150 2.26e+00 d.92.1.15 93808 1ei7A 158 2.94e+00 1rmvA a.24.5.1 16584 1qapA 296 3.15e+00 1qpoA c.1.17.1,d.41.2.1 29559,38595 1ap8 213 3.27e+00 1ap8 d.86.1.1 40151 1b7yB 785 4.12e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1vyiA 112 4.82e+00 2g42A 79 4.88e+00 1khyA 148 5.09e+00 a.174.1.1 77410 1bjaA 95 5.16e+00 1bjaA a.4.5.9 16122 1tzvA 142 5.20e+00 a.79.1.1 107526 1xhfA 123 5.22e+00 1zrjA 50 6.25e+00 1aa7A 158 6.37e+00 1aa7A a.95.1.1 18741 1v4pA 157 6.50e+00 1ix9A 205 6.58e+00 a.2.11.1,d.44.1.1 76899,76900 1ei7B 158 6.62e+00 1rmvA a.24.5.1 16585 1dekA 241 6.69e+00 1dekA c.37.1.1 31842 1pysB 785 6.74e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1z5nA 242 7.21e+00 1fjeB 175 7.32e+00 1fj7A d.58.7.1,d.58.7.1 39210,39211 1d5nA 205 7.36e+00 1avmA a.2.11.1,d.44.1.1 15762,38687 1d3gA 367 7.84e+00 1d3gA c.1.4.1 28600 2b0mA 393 8.05e+00 2fztA 79 8.14e+00 1delA 241 8.48e+00 1dekA c.37.1.1 31844 1v7oA 165 8.50e+00 d.67.1.2 100480 1aw0 72 8.62e+00 1aw0 d.58.17.1 39342 1l2lA 457 8.62e+00 c.72.1.3 77656 1d3hA 367 8.67e+00 1d3gA c.1.4.1 28601 1ugiA 84 8.70e+00 1ugiA d.17.5.1 38125 2abk 211 8.71e+00 2abk a.96.1.1 18743 1qm4A 396 8.75e+00 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1jysA 242 8.78e+00 c.56.2.1 77216 1aua 296 8.81e+00 1aua a.5.3.1,c.13.1.1 16290,30882 1ykhB 132 9.35e+00 1cqwA 295 9.89e+00 1b6g c.69.1.8 34679 1d2eA 397 1.00e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1xreA 217 1.02e+01 1wdjA 187 1.02e+01 2a4nA 182 1.06e+01 1udiI 83 1.07e+01 1ugiA d.17.5.1 38124 1hh1A 143 1.07e+01 1gefA c.52.1.18 61036 1ea3A 164 1.07e+01 1aa7A a.95.1.1 59398 1z5oA 242 1.08e+01 1v4eA 299 1.17e+01 a.128.1.1 100296 1zsyA 357 1.21e+01 1vgyA 393 1.22e+01 c.56.5.4,d.58.19.1 100620,100621 1b1a 137 1.22e+01 1be1 c.23.6.1 31242 1bn6A 294 1.22e+01 1bn6A c.69.1.8 34678 1fj7A 101 1.29e+01 1fj7A d.58.7.1 39209 1or4A 178 1.31e+01 a.1.1.2 93447 1tlk 154 1.31e+01 1tlk b.1.1.4 21707 1ywfA 296 1.36e+01 1eiyB 785 1.39e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1ornA 226 1.41e+01 a.96.1.1 87342 1u5tB 169 1.43e+01 a.4.5.54,a.4.5.54 107686,107687 1bn7A 294 1.45e+01 1bn6A c.69.1.8 34677 1gnkA 112 1.49e+01 2pii d.58.5.1 39073 1gt6A 269 1.49e+01 c.69.1.17 76342 1i0hA 205 1.58e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1pd21 199 1.62e+01 1pd21 1n71A 180 1.64e+01 d.108.1.1 85370 1gzgA 337 1.64e+01 c.1.10.3 70805 1yw3A 208 1.68e+01 3dapA 320 1.69e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 1gxyA 226 1.70e+01 d.166.1.3 76380 1w36D 608 1.71e+01 1pfkA 320 1.78e+01 3pfk c.89.1.1 35575 1sdoA 203 1.82e+01 c.52.1.21 98809 1qmpA 130 1.83e+01 1dz3A c.23.1.1 31106 1wekA 217 1.84e+01 1z6oA 212 1.85e+01 1zgzA 122 1.86e+01 1w5nA 337 1.86e+01 1xzoA 174 1.88e+01 1s7zA 117 1.91e+01 a.159.3.1 98715 1m5tA 124 1.92e+01 c.23.1.1 78660 1w5qA 337 1.96e+01 1i8fA 81 1.97e+01 1i8fA b.38.1.1 61959 1wiwA 290 1.97e+01 1whuA 104 2.00e+01 1y4jA 284 2.04e+01 1i6wA 181 2.08e+01 1i6wA c.69.1.18 61859 1b4kA 337 2.08e+01 1b4kA c.1.10.3 29184 1ireA 204 2.08e+01 d.149.1.1 76769 1jpmA 366 2.10e+01 c.1.11.2,d.54.1.1 67031,67032 2a2fX 325 2.11e+01 1ddt 535 2.13e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 2c60A 111 2.16e+01 1i1sA 96 2.16e+01 1bjaA a.4.5.9 16124 1zn6A 227 2.17e+01 1tib 269 2.17e+01 3tgl c.69.1.17 34738 1sgg 75 2.19e+01 1b4fA a.60.1.2 17943 1konA 249 2.24e+01 e.39.1.1 72823 1ugpA 203 2.25e+01 d.149.1.1 107831 1yn3A 98 2.29e+01 2c4wA 176 2.30e+01 1d6tA 117 2.31e+01 1a6f d.14.1.2 37565 1jbeA 128 2.35e+01 3chy c.23.1.1 62845 1dlwA 116 2.35e+01 1dlyA a.1.1.1 14982 1mb3A 124 2.37e+01 c.23.1.1 78907 1wkcA 184 2.47e+01 1lfpA 249 2.49e+01 e.39.1.1 73885 1e6mA 128 2.49e+01 3chy c.23.1.1 31039 2pfkA 320 2.52e+01 3pfk c.89.1.1 35577 1oxkB 134 2.55e+01 c.23.1.1 93691 1h05A 146 2.55e+01 c.23.13.1 76433 1uumA 372 2.59e+01 c.1.4.1 100010 1x6mA 196 2.64e+01 1cye 129 2.69e+01 3chy c.23.1.1 31077 1vr4A 103 2.71e+01 2ap3A 199 2.72e+01 3chy 128 2.74e+01 3chy c.23.1.1 31038 2aalA 131 2.76e+01 1ctf 74 2.78e+01 1ctf d.45.1.1 38759 1ab6A 125 2.78e+01 3chy c.23.1.1 31054 1u2xA 474 2.84e+01 c.72.1.3 107622 1tkeA 224 2.86e+01 2kfnA 605 2.87e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1vqoX 92 2.88e+01 1pil 112 2.91e+01 2pii d.58.5.1 39072 2dhqA 146 2.92e+01 2dhqA c.23.13.1 31382 1fhgA 154 2.93e+01 1tlk b.1.1.4 21706 1a26 361 2.94e+01 1a26 a.41.1.1,d.166.1.2 17412,42274 1t56A 216 2.96e+01 a.4.1.9,a.121.1.1 106428,106429 1gc5A 467 2.96e+01 1gc5A c.72.1.3 60429 2c78A 405 2.97e+01 1vlmA 219 2.97e+01 c.66.1.41 108836 1jwwA 80 2.98e+01 d.58.17.1 71919 1wy9A 147 3.00e+01 1qlmA 316 3.00e+01 1qlmA d.147.1.1 41765 1f0lA 535 3.01e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1k20A 310 3.09e+01 c.107.1.1 68027 1my6A 199 3.12e+01 a.2.11.1,d.44.1.1 85232,85233 1yioA 208 3.12e+01 2tmvP 158 3.12e+01 1rmvA a.24.5.1 16586 2bmeA 186 3.15e+01 1ughI 82 3.17e+01 1ugiA d.17.5.1 38133 1b3bA 415 3.18e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1ek0A 170 3.18e+01 1ctqA c.37.1.8 32076 1dapA 320 3.19e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1a7vA 125 3.24e+01 1cpq a.24.3.2 16562 1c7gA 456 3.28e+01 c.67.1.2 90415 1innA 166 3.30e+01 1j98A d.185.1.2 62608 1q3kA 259 3.37e+01 c.125.1.1 95693 1j1tA 233 3.38e+01 b.29.1.18 90771 2aplA 157 3.39e+01 1b68A 191 3.40e+01 1nfn a.24.1.1 59076 1cunA 213 3.50e+01 1cunA a.7.1.1,a.7.1.1 16313,16314 1efyA 350 3.52e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1bob 320 3.52e+01 1bob d.108.1.1 40816 2b1eA 564 3.52e+01 1rypJ 204 3.52e+01 d.153.1.4 41878 2pii 112 3.54e+01 2pii d.58.5.1 39071 1i2tA 61 3.54e+01 1i2tA a.144.1.1 61582 1q1lA 401 3.55e+01 d.258.1.1 95591 2cvdA 198 3.69e+01 1jj2W 91 3.74e+01 1ffkU d.29.1.1 63108 1s72X 92 3.74e+01 d.29.1.1 105343 1rwyA 109 3.74e+01 a.39.1.4 98002 1sheA 103 3.74e+01 d.274.1.1 105551 1yr2A 741 3.76e+01 1ispA 181 3.76e+01 c.69.1.18 76778 1sfjA 238 3.80e+01 1uhkA 191 3.83e+01 1kk8B 139 3.84e+01 a.39.1.5 77430 1vppV 102 3.84e+01 1vpfA g.17.1.1 44753 1gtzA 156 3.89e+01 c.23.13.1 70539 1nijA 318 3.91e+01 c.37.1.10,d.237.1.1 85741,85742 1wdcC 156 3.94e+01 1wdcC a.39.1.5 17317 1a04A 215 3.94e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1i1iP 681 3.99e+01 1i1iP d.92.1.5 40297 1r13A 148 4.00e+01 d.169.1.1,h.1.1.1 96782,96783 1v32A 101 4.03e+01 a.42.1.1 100277 1d8yA 605 4.04e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1m46A 148 4.06e+01 a.39.1.5 78599 1aipE 405 4.07e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1fp6A 289 4.17e+01 1cp2A c.37.1.10 32243 1pieA 419 4.19e+01 d.14.1.5,d.58.26.7 94706,94707 1k68A 140 4.25e+01 c.23.1.1 90943 1vjeA 166 4.25e+01 d.185.1.2 100807 1xvjA 109 4.27e+01 1b87A 181 4.36e+01 1b87A d.108.1.1 40797 2g6tA 306 4.37e+01 1wu4A 396 4.37e+01 7reqA 727 4.41e+01 1reqA c.1.19.1,c.23.6.1 29616,31243 1aoiG 116 4.42e+01 1aoiC a.22.1.1 16441 2f4iA 197 4.44e+01 1x42A 232 4.47e+01 1srrA 124 4.58e+01 1dz3A c.23.1.1 31110 1v66A 65 4.66e+01 1mkkA 96 4.70e+01 g.17.1.1 79240 1bed 181 4.73e+01 1fvkA c.47.1.13 90330 1ztcA 221 4.74e+01 1xcrA 316 4.74e+01 1uarA 285 4.77e+01 c.46.1.2,c.46.1.2 107762,107763 1s8nA 205 4.80e+01 c.23.1.1 105374 3lriA 83 4.80e+01 1zeiA g.1.1.1 43995 1a8vA 121 4.81e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1z9hA 290 4.88e+01 1oxjA 173 4.92e+01 a.60.1.2,a.118.1.13 87517,87518 1rcuA 195 4.94e+01 c.129.1.1 97295 2gjlA 328 4.98e+01 1iwmA 186 5.00e+01 b.125.1.2 83758 1uf5A 303 5.01e+01 d.160.1.2 107808 2fokA 579 5.01e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1omrA 201 5.04e+01 a.39.1.5 93349 1yqhA 109 5.05e+01 1xklA 273 5.08e+01 1mgpA 313 5.10e+01 c.119.1.1 79098 1xu9A 286 5.11e+01 1hjzA 192 5.19e+01 c.50.1.2 83520 1iyhA 198 5.29e+01 a.45.1.1,c.47.1.5 83790,83791 1zxxA 319 5.29e+01 1yliA 153 5.36e+01 1k6kA 143 5.42e+01 a.174.1.1 77274 1puoA 170 5.42e+01 a.101.1.1,a.101.1.1 95134,95135 1ru8A 232 5.44e+01 c.26.2.1 97849 1izmA 184 5.46e+01 a.199.1.1 90725 1eijA 80 5.51e+01 1eijA a.5.6.1 16298 1n93X 375 5.52e+01 a.206.1.1 91707 1wviA 257 5.55e+01 1ua4A 455 5.56e+01 c.72.1.3 99128 1jrmA 104 5.59e+01 d.206.1.1 67136 1sffA 426 5.63e+01 c.67.1.4 105482 1kvkA 395 5.69e+01 d.14.1.5,d.58.26.3 73060,73061 1g0uI 205 5.69e+01 d.153.1.4 41891 1urvA 190 5.73e+01 1ut0A 190 5.73e+01 a.1.1.2 108012 1d0iA 156 5.73e+01 2dhqA c.23.13.1 31383 1eft 405 5.73e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1aipA 405 5.73e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1mvoA 136 5.74e+01 c.23.1.1 79513 1pueE 89 5.74e+01 1awcA a.4.5.21 16165 1dz3A 130 5.74e+01 1dz3A c.23.1.1 31105 1zgmA 248 5.78e+01 1j31A 262 5.78e+01 d.160.1.2 90808 1qpaA 345 5.79e+01 1arv a.93.1.1 18585 1yvvA 336 5.84e+01 1jk0A 419 5.85e+01 a.25.1.2 63142 1di6A 195 5.85e+01 1di6A c.57.1.1 33863 1vhuA 211 5.89e+01 c.50.1.2 100703 1eiwA 111 5.91e+01 1eiwA c.23.3.1 31130 1jfkA 134 5.91e+01 a.39.1.5 66639 1njrA 284 5.96e+01 c.50.1.2 103858 1ucaA 190 6.04e+01 d.124.1.1 88462 5pal 109 6.07e+01 1a75A a.39.1.4 17215 1vtmP 158 6.14e+01 1rmvA a.24.5.1 16587 1kc6A 257 6.14e+01 c.52.1.19 68419 1dmgA 225 6.19e+01 1dmgA c.22.1.1 31036 1b0xA 94 6.19e+01 1b4fA a.60.1.2 17933 2fnoA 248 6.20e+01 1aoiC 116 6.24e+01 1aoiC a.22.1.1 16440 1eucA 311 6.24e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 2fa8A 105 6.25e+01 2d0oA 610 6.29e+01 1w36B 1180 6.34e+01 1o0yA 260 6.35e+01 c.1.10.1 80756 1o7nA 449 6.43e+01 b.33.1.2,d.129.3.3 81162,81163 1mqvA 125 6.46e+01 a.24.3.2 79415 1kcfA 258 6.48e+01 a.140.2.1,c.55.3.7 68434,68435 1m45A 148 6.50e+01 a.39.1.5 78598 1winA 143 6.53e+01 1fjcA 96 6.59e+01 1fjcA d.58.7.1 39212 1ejjA 511 6.62e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1mdbA 539 6.67e+01 e.23.1.1 79008 1geqA 248 6.69e+01 2tysA c.1.2.4 28589 2gf1 70 6.71e+01 2gf1 g.1.1.1 43990 1d2mA 665 6.71e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1p0kA 349 6.72e+01 c.1.4.1 87648 2b18A 164 6.79e+01 1g59A 468 6.79e+01 a.97.1.1,c.26.1.1 60257,60258 2audA 257 6.80e+01 1y8cA 246 6.81e+01 1zk7A 467 6.81e+01 1vzyA 291 6.82e+01 1fokA 568 6.82e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1xg9A 260 6.88e+01 1erzA 303 6.88e+01 1erzA d.160.1.2 59498 1isiA 265 6.89e+01 e.4.1.1 71394 1xqiA 195 6.90e+01 1qrqA 325 6.99e+01 1qrqA c.1.7.1 28667 1gtrA 553 7.04e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1a62 130 7.09e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 2f9sA 151 7.09e+01 1a63 130 7.10e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1myt 146 7.10e+01 1a6m a.1.1.2 15207 1b4fG 82 7.16e+01 1b4fA a.60.1.2 17940 1cqmA 101 7.17e+01 1ris d.58.14.1 39321 1jclA 260 7.17e+01 c.1.10.1 66501 1yruB 74 7.21e+01 1g5pA 289 7.24e+01 1cp2A c.37.1.10 32253 1wcwA 261 7.32e+01 2a67A 167 7.33e+01 1klnA 605 7.35e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1bk7A 190 7.37e+01 1bk7A d.124.1.1 41121 2awpA 198 7.40e+01 1mjhB 162 7.41e+01 1mjhA c.26.2.4 31640 1ndoA 449 7.42e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1uz5A 402 7.47e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1ad3A 452 7.47e+01 1ad3A c.82.1.1 35335 1eudA 311 7.53e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1i5rA 327 7.54e+01 c.2.1.2 83668 1ft1B 437 7.54e+01 1ft1B a.102.4.3 18867 1a9nB 96 7.57e+01 1urnA d.58.7.1 39165 1xhvA 257 7.60e+01 c.52.1.19 109597 1r77A 103 7.60e+01 1f06A 320 7.66e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1tzyA 129 7.68e+01 a.22.1.1 107530 1xezA 721 7.69e+01 1eqjA 511 7.69e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1s4bP 674 7.73e+01 d.92.1.5 105252 1eg9A 449 7.77e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1exqA 154 7.84e+01 1b9dA c.55.3.2 33646 1fvaA 217 7.84e+01 1fvaA d.58.28.1 39409 1ao8 162 7.85e+01 3dfr c.71.1.1 34883 1us5A 314 7.92e+01 c.94.1.1 99856 1st9A 143 7.92e+01 c.47.1.10 98987 1ghsA 306 7.93e+01 1aq0A c.1.8.3 28840 1x3sA 195 8.01e+01 2g7jA 124 8.09e+01 1jjvA 206 8.09e+01 c.37.1.1 71698 1c4oA 664 8.10e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1ld8B 437 8.11e+01 a.102.4.3 73839 1ce9A 34 8.12e+01 1ce9C h.1.3.1 45483 1ag9A 175 8.13e+01 1rcf c.23.5.1 31178 1ucdA 190 8.22e+01 d.124.1.1 107767 1f60B 94 8.29e+01 1b64 d.58.12.1 39307 1rvvA 154 8.32e+01 1rvv1 c.16.1.1 30927 1rvv1 154 8.32e+01 1rvv1 1j8fA 323 8.32e+01 1j8fA c.31.1.5 62738 1i1dA 161 8.33e+01 1i21A d.108.1.1 61526 1p1xA 260 8.38e+01 c.1.10.1 104060 1cx4A 305 8.42e+01 b.82.3.2,b.82.3.2 59099,59100 2cxxA 190 8.53e+01 1atg 231 8.57e+01 1atg c.94.1.1 35834 3cln 148 8.57e+01 1cll a.39.1.5 17286 2as9A 210 8.57e+01 2azjA 289 8.60e+01 1qwgA 251 8.63e+01 c.1.27.1 96473 2fazA 78 8.65e+01 1aj4 161 8.72e+01 1ncx a.39.1.5 17244 1hl2A 297 8.72e+01 c.1.10.1 83581 2cqnA 77 8.78e+01 1p9oA 313 8.78e+01 c.72.3.1 94397 1g7cB 94 8.81e+01 1b64 d.58.12.1 39308 2d9rA 104 8.84e+01 1vbkA 307 8.86e+01 1s4nA 348 8.88e+01 c.68.1.16 98501 1d3yA 301 8.91e+01 1d3yA e.12.1.1 43252 1tn6B 437 8.98e+01