# 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 1pft 50 3.94e-03 1pft g.41.3.1 45206 1rhoC 145 2.68e-01 1rhoA b.1.18.8 21901 1s72Z 73 3.23e-01 g.41.8.1 105345 1vqoZ 83 3.91e-01 1ww8A 439 3.96e-01 1odhA 174 4.08e-01 d.239.1.1 86850 1vk6A 269 4.29e-01 d.113.1.4,d.113.1.4 100851,100852 1kmtA 141 4.71e-01 b.1.18.8 77442 1rhoA 145 5.16e-01 1rhoA b.1.18.8 21899 1ur6B 52 7.00e-01 g.44.1.1 99812 1dgfA 497 7.39e-01 1cf9A e.5.1.1 42782 1dghB 498 8.79e-01 1cf9A e.5.1.1 42791 2ct7A 86 9.97e-01 1fsoA 139 1.29e+00 1rhoA b.1.18.8 60007 1e4uA 78 1.42e+00 1e4uA g.44.1.1 59231 2cklB 165 1.43e+00 2fqpA 97 1.53e+00 1g47A 77 1.56e+00 1g47A g.39.1.3,g.39.1.3 45147,45148 1x75A 132 1.60e+00 1wd2A 60 1.61e+00 g.44.1.1 109232 1k81A 36 1.90e+00 g.59.1.1 72136 1jm7A 112 2.02e+00 g.44.1.1 66880 1yagA 375 2.47e+00 1yagA c.55.1.1,c.55.1.1 33449,33450 2a8mA 420 2.57e+00 1jm1A 204 2.72e+00 b.33.1.1 71745 1dx8A 70 2.88e+00 1rb9 g.41.5.1 45243 1jj2Y 73 2.99e+00 1ffkW g.41.8.1 63110 1vd4A 62 3.30e+00 1vckA 115 3.42e+00 1qdlA 422 3.57e+00 1qdlA d.161.1.1 42088 1yl35 60 3.84e+00 7catA 506 3.85e+00 1cf9A e.5.1.1 42781 1d4xA 375 3.87e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 1dgaA 375 3.88e+00 1yagA 1u79A 129 4.35e+00 d.26.1.1 107714 1p9rA 418 4.40e+00 c.37.1.11 94399 2a8jA 420 4.64e+00 1theA 260 5.30e+00 1theB d.3.1.1 37056 1f62A 51 5.41e+00 1f62A g.50.1.2 45360 1zxzA 197 5.69e+00 1rlyA 60 5.79e+00 g.41.3.1 104988 2a20A 62 5.89e+00 1theB 260 6.21e+00 1theB d.3.1.1 37057 1bq9A 54 6.33e+00 1rb9 g.41.5.1 45238 1bq8A 54 6.62e+00 1rb9 g.41.5.1 45237 1brfA 53 6.65e+00 1rb9 g.41.5.1 45236 1k7cA 233 6.65e+00 c.23.10.4 68267 1ptq 50 6.71e+00 1ptq g.49.1.1 45349 1vphA 149 6.79e+00 2btfA 375 6.87e+00 1yagA c.55.1.1,c.55.1.1 33429,33430 1exkA 79 6.94e+00 1exkA g.54.1.1 45384 1pu6A 218 7.06e+00 a.96.1.5 95123 1far 52 7.20e+00 1far g.49.1.1 45351 1h38C 883 7.20e+00 e.8.1.3 76627 1h38B 883 7.26e+00 e.8.1.3 76626 1h38D 883 7.35e+00 e.8.1.3 76628 8rxnA 52 7.53e+00 1rb9 g.41.5.1 45215 1rb9 53 7.62e+00 1rb9 g.41.5.1 45214 1ee8A 266 7.66e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1g25A 65 7.84e+00 1g25A g.44.1.1 45325 2sak 121 7.92e+00 2sak d.15.5.1 37711 1rfs 139 8.13e+00 1rfs b.33.1.1 24434 1yovA 537 8.19e+00 1yk4A 52 8.26e+00 1q68B 29 8.32e+00 j.108.1.1 95963 1ile 821 8.33e+00 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1q35A 320 8.38e+00 c.94.1.1 95661 1wrvA 308 8.53e+00 2dabA 282 8.57e+00 1daaA e.17.1.1 43274 1a0gA 282 8.60e+00 1daaA e.17.1.1 43276 1ssn 136 8.62e+00 2sak d.15.5.1 37720 2c1xA 456 9.03e+00 1r6lA 239 9.07e+00 d.14.1.4,d.101.1.1 97153,97154 1ww9A 392 9.10e+00 1c76A 136 9.56e+00 2sak d.15.5.1 37718 1jm7B 117 9.58e+00 g.44.1.1 66881 1rdg 53 1.02e+01 1rb9 g.41.5.1 45221 1zy1B 197 1.03e+01 1l7bA 92 1.05e+01 c.15.1.2 91053 1ffkW 73 1.06e+01 1ffkW g.41.8.1 45315 1cokA 68 1.08e+01 1cokA a.60.1.2 17945 1daaA 282 1.08e+01 1daaA e.17.1.1 43270 1rutX 188 1.12e+01 4rxn 54 1.16e+01 1rb9 g.41.5.1 45226 2an1A 292 1.16e+01 1nv8A 284 1.18e+01 c.66.1.30 86224 1faq 52 1.19e+01 1far g.49.1.1 45352 1qxfA 66 1.22e+01 g.41.8.4 96527 2a1rA 430 1.22e+01 1dl6A 58 1.27e+01 1dl6A g.41.3.1 45207 1mr1C 99 1.29e+01 d.217.1.2 79420 2adoA 196 1.30e+01 1iml 76 1.36e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1wfeA 86 1.40e+01 1ty9A 222 1.41e+01 1nykA 165 1.41e+01 b.33.1.1 86408 1k8kA 418 1.47e+01 c.55.1.1,c.55.1.1 68305,68306 1rmd 116 1.49e+01 1rmd g.37.1.1,g.44.1.1 45025,45322 1wraA 308 1.55e+01 1weoA 93 1.55e+01 5rxn 54 1.56e+01 1rb9 g.41.5.1 45225 1tqnA 486 1.62e+01 a.104.1.1 107238 1d0qA 103 1.65e+01 1d0qA g.41.3.2 45208 1l8dA 112 1.66e+01 h.4.12.1 73687 2aq6A 147 1.70e+01 1cxxA 113 1.74e+01 1iml g.39.1.3,g.39.1.3 45139,45140 1lvoA 302 1.74e+01 b.47.1.4 74284 1deoA 233 1.75e+01 1deoA c.23.10.4 31345 1iq3A 110 1.75e+01 1iq3A a.39.1.6 62640 1atnA 373 1.77e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 1hvyA 288 1.77e+01 1bkpA d.117.1.1 41049 1chc 68 1.82e+01 1chc g.44.1.1 45323 3daaA 277 1.84e+01 1daaA e.17.1.1 43272 1mea 28 1.84e+01 g.41.1.1 45176 1wxiA 275 1.86e+01 1qqtA 551 1.91e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1s5aA 150 1.91e+01 d.17.4.10 98525 1scuA 288 1.92e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1b8tA 192 1.92e+01 1b8tA g.39.1.3,g.39.1.3,g.39.1.3,g.39.1.3 45135,45136,45137,45138 1ypvA 313 1.92e+01 2bx9A 53 1.95e+01 1f4lA 551 1.99e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1ab4 477 2.00e+01 1ab4 e.11.1.1 43251 1iro 54 2.01e+01 1rb9 g.41.5.1 45223 1o12A 376 2.04e+01 b.92.1.5,c.1.9.10 80758,80759 1twfL 70 2.06e+01 1a6yA 95 2.06e+01 2nllB g.39.1.2 45131 1q16B 512 2.09e+01 d.58.1.5 95548 1ti6B 274 2.12e+01 b.3.5.1,d.58.1.5 106976,106977 1inp 400 2.12e+01 1inp e.7.1.1 42972 1l1oC 181 2.12e+01 b.40.4.3 73480 1y5iB 512 2.13e+01 1sur 215 2.14e+01 1sur c.26.2.2 31620 1v87A 114 2.15e+01 g.44.1.1 108422 1pfvA 551 2.15e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1vq0A 302 2.15e+01 1tr9A 341 2.20e+01 1zd9A 188 2.21e+01 1lv3A 68 2.23e+01 g.39.1.9 78231 6rxn 46 2.23e+01 1rb9 g.41.5.1 45222 1q33A 292 2.24e+01 d.113.1.1 95657 2csvA 72 2.24e+01 1sp1 29 2.26e+01 g.37.1.1 45051 1b2jA 54 2.29e+01 1rb9 g.41.5.1 45231 1jmsA 381 2.30e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1ctl 85 2.30e+01 g.39.1.3,g.39.1.3 45133,45134 2bibA 547 2.32e+01 1zip 217 2.32e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1zyoA 191 2.35e+01 1ard 29 2.37e+01 g.37.1.1 45033 1iyeA 309 2.39e+01 e.17.1.1 83786 1y3nA 490 2.40e+01 1m22A 503 2.40e+01 c.117.1.1 78464 2g8yA 385 2.41e+01 2etxA 209 2.41e+01 1l1dA 152 2.41e+01 b.88.1.3 73452 1tbn 82 2.44e+01 1ptq g.49.1.1 45354 1fgs 428 2.44e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1yopA 83 2.50e+01 1uch 230 2.50e+01 1uch d.3.1.6 37129 1zin 217 2.50e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1xd3A 230 2.51e+01 1xxoA 147 2.52e+01 1qvjA 292 2.53e+01 d.113.1.1 96431 1qz5A 375 2.55e+01 c.55.1.1,c.55.1.1 96614,96615 1zkkA 167 2.55e+01 1kbeA 49 2.55e+01 g.49.1.1 68380 1z6uA 150 2.60e+01 1twfI 122 2.65e+01 4eugA 229 2.67e+01 3eugA c.18.1.1 31019 1i50I 122 2.67e+01 g.41.3.1,g.41.3.1 61762,61763 1eugA 229 2.68e+01 3eugA c.18.1.1 31021 1fl2A 310 2.69e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1qumA 285 2.72e+01 1qumA c.1.15.1 29393 1n4oA 276 2.76e+01 e.3.1.1 91621 2aaa 484 2.77e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1wjpA 107 2.80e+01 1wr8A 231 2.84e+01 2cklA 108 2.85e+01 1qqqA 264 2.86e+01 1bkpA d.117.1.1 40931 1oahA 519 2.86e+01 a.138.1.3 86736 1w9aA 147 2.90e+01 1b13A 54 2.92e+01 1rb9 g.41.5.1 45227 1jbwA 428 2.93e+01 c.59.1.2,c.72.2.2 62860,62861 1bc8C 93 3.06e+01 1awcA a.4.5.21 16168 1bgj 394 3.09e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1qyp 57 3.13e+01 1qyp g.41.3.1 45205 1cr8A 42 3.17e+01 1ajj g.12.1.1 44613 1dgsA 667 3.18e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 2cx1A 187 3.18e+01 3eugA 229 3.19e+01 3eugA c.18.1.1 31018 1ifqA 138 3.21e+01 1ifqA d.110.4.1 62350 1ldjB 90 3.22e+01 g.44.1.1 73850 1p6pA 125 3.28e+01 b.60.1.2 87839 1jzxM 60 3.28e+01 i.1.1.2 67887 1ywmA 200 3.30e+01 1dxsA 80 3.33e+01 1cokA a.60.1.2 17944 1arf 29 3.35e+01 g.37.1.1 45035 1s7jA 262 3.42e+01 d.21.1.2 98647 1zzpA 130 3.44e+01 1qtwA 285 3.51e+01 1qumA c.1.15.1 29392 1o7eA 276 3.56e+01 e.3.1.1 92622 1zs7A 190 3.62e+01 1ayfA 105 3.69e+01 1ayfA d.15.4.1 37684 1ayfB 105 3.71e+01 1ayfA d.15.4.1 37685 1plr 258 3.73e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1c3hA 137 3.74e+01 b.22.1.1 90405 1cj3A 392 3.81e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1meyC 87 3.84e+01 2gliA k.12.1.1 46430 1b2oA 54 3.87e+01 1rb9 g.41.5.1 45233 1t64A 377 3.91e+01 c.42.1.2 106543 1afp 51 3.91e+01 1afp g.26.1.1 44947 1zu1A 127 3.92e+01 1dsvA 31 3.92e+01 1dsvA g.40.1.1 45174 1lp9E 194 4.02e+01 b.1.1.1,b.1.1.2 91086,91087 1r5mA 425 4.02e+01 1a78A 134 4.08e+01 1c1lA b.29.1.3 24212 1k7hA 476 4.13e+01 c.76.1.1 72101 1dxgA 36 4.34e+01 1dxgA g.41.5.2 45247 2hrvA 142 4.39e+01 2hrvA b.47.1.4 26429 1nigA 152 4.40e+01 a.25.2.1 85740 1lm5A 214 4.44e+01 d.211.2.1 74029 1f1zA 273 4.48e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1wjvA 79 4.52e+01 1tfi 50 4.53e+01 1tfi g.41.3.1 45204 1n9dA 199 4.55e+01 a.26.1.1 85464 1e0eA 55 4.59e+01 1wjcA a.4.10.1 59147 1m1qA 91 4.61e+01 a.138.1.3 74419 1mswD 883 4.66e+01 e.8.1.3 79427 1lw7A 365 4.71e+01 c.26.1.3,c.37.1.1 74295,74296 1k3eA 156 4.71e+01 d.198.1.1 68103 2cszA 76 4.72e+01 2erxA 172 4.72e+01 2drpA 66 4.74e+01 2drpA g.37.1.1,g.37.1.1 45026,45027 1zud1 251 4.77e+01 1gp1A 198 4.78e+01 1gp1A c.47.1.10 33059 1neeA 138 4.81e+01 d.241.1.1,g.59.1.1 91841,91842 1qwlA 505 4.82e+01 e.5.1.1 96483 1woyA 500 4.86e+01 830cA 168 4.88e+01 1ck7A d.92.1.11 40400 1i50L 70 4.88e+01 g.41.9.2 61766 1jj2F 119 4.90e+01 1ffkE d.79.3.1 63091 2sicI 107 4.90e+01 3ssi d.84.1.1 40031 2fg1A 158 4.92e+01 1a7i 81 5.02e+01 1b8tA g.39.1.3,g.39.1.3 45143,45144 1e6eB 128 5.09e+01 1ayfA d.15.4.1 59300 1cxvA 164 5.11e+01 1ck7A d.92.1.11 40404 1evfA 264 5.22e+01 1bkpA d.117.1.1 40932 1cxqA 162 5.25e+01 1cxqA c.55.3.2 33621 1vfyA 73 5.29e+01 1vfyA g.50.1.1 45357 1iugA 352 5.34e+01 c.67.1.3 90699 1t0fA 276 5.36e+01 1bzsA 165 5.40e+01 1hfc d.92.1.11 40348 1p9uA 302 5.42e+01 b.47.1.4 88001 1vor2 58 5.49e+01 1qli 113 5.51e+01 1iml g.39.1.3,g.39.1.3 45141,45142 1omiA 248 5.52e+01 b.82.3.3,a.4.5.4 87079,87080 1ois 223 5.57e+01 1a36A e.15.1.1 43267 2fiyA 309 5.66e+01 1kdj 102 5.71e+01 1plc b.6.1.1 22864 1oi7A 288 5.75e+01 c.2.1.8,c.23.4.1 87049,87050 2f6eA 127 5.76e+01 1cezA 883 5.91e+01 1cezA e.8.1.3 43110 1vetA 124 5.92e+01 d.110.7.1 108553 1wgeA 83 5.93e+01 1yuiA 54 5.99e+01 1yuiA g.37.1.1 45073 2scuA 288 6.00e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1v54F 98 6.03e+01 g.41.5.3 100327 1k0mA 241 6.05e+01 a.45.1.1,c.47.1.5 67949,67950 1puc 105 6.05e+01 1puc d.97.1.1 40675 1j6zA 376 6.07e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1z94A 147 6.08e+01 1zclA 180 6.12e+01 1nrkA 328 6.13e+01 b.44.2.1,d.250.1.1 92089,92090 1sefA 274 6.27e+01 b.82.1.11 105452 1y9uA 323 6.32e+01 2ampA 304 6.37e+01 1gatA 60 6.40e+01 1gatA g.39.1.1 45106 1xmxA 385 6.49e+01 1gp4A 356 6.50e+01 b.82.2.1 65439 7taa 478 6.51e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1k0iA 394 6.54e+01 c.3.1.2,d.16.1.2 67942,67943 1are 29 6.61e+01 g.37.1.1 45034 1upiA 225 6.61e+01 b.82.1.1 99757 1uslA 170 6.64e+01 c.121.1.1 99871 1zsqA 528 6.75e+01 1am2 199 6.81e+01 1am2 b.86.1.2 28381 1k0nA 241 6.81e+01 a.45.1.1,c.47.1.5 67953,67954 2b9dA 52 6.88e+01 1gnf 46 6.89e+01 1gatA g.39.1.1 45107 1dl0A 37 6.89e+01 1dl0A g.3.6.2 44112 1ykjA 394 6.89e+01 1uw2A 61 6.93e+01 g.37.1.4 108064 2frnA 278 6.99e+01 2ccvA 101 7.01e+01 1mhlA 108 7.04e+01 1d2vA a.93.1.2 18699 2f8aA 208 7.04e+01 1gp6A 356 7.18e+01 b.82.2.1 65441 1v0jA 399 7.24e+01 1d2vA 104 7.24e+01 1d2vA a.93.1.2 18697 1etc 110 7.26e+01 1awcA a.4.5.21 16162 1cxpA 104 7.27e+01 1d2vA a.93.1.2 18695 2fqaA 27 7.37e+01 1ji1A 637 7.42e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1vhqA 232 7.45e+01 c.23.16.2 100696 1plq 258 7.46e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1lx8A 55 7.58e+01 a.6.1.7 84734 1dfoA 417 7.60e+01 1bj4A c.67.1.4 34480 1e50A 134 7.62e+01 1cmoA b.2.5.6 59244 2bt6A 108 7.77e+01 1yc5A 246 7.79e+01 1r61A 207 7.91e+01 c.8.8.1 97138 1p5tA 127 7.92e+01 b.55.1.2 94148 1ajw 145 7.94e+01 1rhoA b.1.18.8 21905 4bp2 130 8.00e+01 1poa a.133.1.2 19584 1xkwA 665 8.02e+01 1z52A 470 8.05e+01 1skoA 143 8.07e+01 d.110.7.1 105676 1yp8A 33 8.13e+01 1g0cA 364 8.13e+01 7a3hA c.1.8.3 60165 2occF 98 8.17e+01 2occF g.41.5.3 45256 1u24A 337 8.27e+01 1wimA 94 8.32e+01 1gweA 503 8.34e+01 e.5.1.1 70667 1l8cB 51 8.38e+01 j.96.1.1 73686 2fa8A 105 8.39e+01 1erd 40 8.47e+01 1erd a.10.1.1 16362 2pspA 106 8.49e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1tfuA 157 8.50e+01 c.26.1.3 106859 3sicI 107 8.51e+01 3ssi d.84.1.1 40028 2a8lA 420 8.55e+01 3gatA 66 8.70e+01 1gatA g.39.1.1 45103 1ktjA 129 8.72e+01 b.1.18.7 72974 1a3gA 308 8.73e+01 1daaA e.17.1.1 43286 1u7kA 131 8.74e+01 1qbhA 101 8.78e+01 1g3fA g.52.1.1 45374 1ew4A 106 8.80e+01 1ew4A d.82.2.1 40023 1yt5A 258 8.81e+01 1h3nA 878 8.84e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2tscA 264 8.87e+01 1bkpA d.117.1.1 40952 2g8oA 264 8.91e+01