# 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 7.24e-03 1pft g.41.3.1 45206 1s72Z 73 2.15e-01 g.41.8.1 105345 1vqoZ 83 2.48e-01 1ww8A 439 4.99e-01 1rhoC 145 5.09e-01 1rhoA b.1.18.8 21901 1vk6A 269 5.21e-01 d.113.1.4,d.113.1.4 100851,100852 1odhA 174 8.10e-01 d.239.1.1 86850 1kmtA 141 8.98e-01 b.1.18.8 77442 1rhoA 145 1.02e+00 1rhoA b.1.18.8 21899 2ct7A 86 1.36e+00 1ur6B 52 1.43e+00 g.44.1.1 99812 1dgfA 497 1.89e+00 1cf9A e.5.1.1 42782 1x75A 132 1.90e+00 1wd2A 60 2.12e+00 g.44.1.1 109232 1jj2Y 73 2.22e+00 1ffkW g.41.8.1 63110 1dghB 498 2.37e+00 1cf9A e.5.1.1 42791 2fqpA 97 2.42e+00 1fsoA 139 2.44e+00 1rhoA b.1.18.8 60007 1k81A 36 2.62e+00 g.59.1.1 72136 2cklB 165 2.63e+00 1e4uA 78 2.85e+00 1e4uA g.44.1.1 59231 1vckA 115 2.87e+00 1jm7A 112 2.89e+00 g.44.1.1 66880 2a8mA 420 3.11e+00 1h38C 883 3.74e+00 e.8.1.3 76627 1h38B 883 3.75e+00 e.8.1.3 76626 1h38D 883 3.79e+00 e.8.1.3 76628 1jm1A 204 3.94e+00 b.33.1.1 71745 1zxzA 197 4.07e+00 1g47A 77 4.11e+00 1g47A g.39.1.3,g.39.1.3 45147,45148 1dx8A 70 4.28e+00 1rb9 g.41.5.1 45243 1k7cA 233 4.54e+00 c.23.10.4 68267 2g2kA 170 4.58e+00 1yl35 60 4.59e+00 1yagA 375 4.86e+00 1yagA c.55.1.1,c.55.1.1 33449,33450 1vd4A 62 5.13e+00 1qdlA 422 5.17e+00 1qdlA d.161.1.1 42088 1p9rA 418 5.37e+00 c.37.1.11 94399 2a8jA 420 5.65e+00 1rlyA 60 5.88e+00 g.41.3.1 104988 1dgaA 375 6.17e+00 1yagA 1d4xA 375 6.57e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 1u79A 129 7.06e+00 d.26.1.1 107714 1r6lA 239 7.50e+00 d.14.1.4,d.101.1.1 97153,97154 1wrvA 308 7.54e+00 1zy1B 197 7.70e+00 1a0gA 282 7.94e+00 1daaA e.17.1.1 43276 2dabA 282 7.97e+00 1daaA e.17.1.1 43274 2cjsC 62 8.51e+00 1ptq 50 8.60e+00 1ptq g.49.1.1 45349 1rfs 139 8.63e+00 1rfs b.33.1.1 24434 1theA 260 8.75e+00 1theB d.3.1.1 37056 2c1xA 456 8.94e+00 1exkA 79 8.97e+00 1exkA g.54.1.1 45384 1vphA 149 9.08e+00 1f62A 51 9.11e+00 1f62A g.50.1.2 45360 1far 52 9.13e+00 1far g.49.1.1 45351 1theB 260 9.67e+00 1theB d.3.1.1 37057 1bq9A 54 9.86e+00 1rb9 g.41.5.1 45238 2a20A 62 1.01e+01 1bq8A 54 1.02e+01 1rb9 g.41.5.1 45237 7catA 506 1.03e+01 1cf9A e.5.1.1 42781 1ee8A 266 1.04e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1ffkW 73 1.04e+01 1ffkW g.41.8.1 45315 1brfA 53 1.05e+01 1rb9 g.41.5.1 45236 2btfA 375 1.09e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1ssn 136 1.10e+01 2sak d.15.5.1 37720 2sak 121 1.10e+01 2sak d.15.5.1 37711 1q35A 320 1.11e+01 c.94.1.1 95661 8rxnA 52 1.12e+01 1rb9 g.41.5.1 45215 1deoA 233 1.13e+01 1deoA c.23.10.4 31345 1rb9 53 1.13e+01 1rb9 g.41.5.1 45214 1pu6A 218 1.19e+01 a.96.1.5 95123 2an1A 292 1.20e+01 1c76A 136 1.22e+01 2sak d.15.5.1 37718 1ww9A 392 1.23e+01 1dl6A 58 1.25e+01 1dl6A g.41.3.1 45207 1g25A 65 1.26e+01 1g25A g.44.1.1 45325 1q68B 29 1.31e+01 j.108.1.1 95963 1yovA 537 1.31e+01 1cokA 68 1.32e+01 1cokA a.60.1.2 17945 1yk4A 52 1.34e+01 1ile 821 1.34e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1daaA 282 1.40e+01 1daaA e.17.1.1 43270 1l1oC 181 1.41e+01 b.40.4.3 73480 1jm7B 117 1.42e+01 g.44.1.1 66881 1zu0A 529 1.43e+01 1rdg 53 1.47e+01 1rb9 g.41.5.1 45221 1qxfA 66 1.48e+01 g.41.8.4 96527 1faq 52 1.51e+01 1far g.49.1.1 45352 1iq3A 110 1.61e+01 1iq3A a.39.1.6 62640 1q33A 292 1.63e+01 d.113.1.1 95657 1qqtA 551 1.64e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 4rxn 54 1.65e+01 1rb9 g.41.5.1 45226 1wfeA 86 1.67e+01 1f4lA 551 1.68e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1wraA 308 1.69e+01 1ypvA 313 1.69e+01 1rmd 116 1.73e+01 1rmd g.37.1.1,g.44.1.1 45025,45322 1hvyA 288 1.74e+01 1bkpA d.117.1.1 41049 1pfvA 551 1.81e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2d8vA 67 1.85e+01 1ty9A 222 1.86e+01 1nykA 165 1.88e+01 b.33.1.1 86408 1tbn 82 1.89e+01 1ptq g.49.1.1 45354 2adoA 196 1.89e+01 1qvjA 292 1.90e+01 d.113.1.1 96431 1k8kA 418 1.90e+01 c.55.1.1,c.55.1.1 68305,68306 1weoA 93 1.90e+01 2a1rA 430 1.91e+01 1mr1C 99 1.96e+01 d.217.1.2 79420 3daaA 277 1.98e+01 1daaA e.17.1.1 43272 1d0qA 103 1.99e+01 1d0qA g.41.3.2 45208 2aq6A 147 2.05e+01 1mea 28 2.10e+01 g.41.1.1 45176 1ldjB 90 2.12e+01 g.44.1.1 73850 1mswD 883 2.15e+01 e.8.1.3 79427 1lvoA 302 2.16e+01 b.47.1.4 74284 1zd9A 188 2.24e+01 1rutX 188 2.25e+01 1m22A 503 2.25e+01 c.117.1.1 78464 1nv8A 284 2.30e+01 c.66.1.30 86224 1sur 215 2.30e+01 1sur c.26.2.2 31620 5rxn 54 2.30e+01 1rb9 g.41.5.1 45225 1l7bA 92 2.31e+01 c.15.1.2 91053 1zkkA 167 2.33e+01 1ab4 477 2.33e+01 1ab4 e.11.1.1 43251 2aaa 484 2.35e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1wxiA 275 2.36e+01 1bc8C 93 2.36e+01 1awcA a.4.5.21 16168 1y3nA 490 2.37e+01 1s5aA 150 2.39e+01 d.17.4.10 98525 1qqqA 264 2.40e+01 1bkpA d.117.1.1 40931 2bx9A 53 2.41e+01 1n4oA 276 2.41e+01 e.3.1.1 91621 2bibA 547 2.47e+01 1l8dA 112 2.52e+01 h.4.12.1 73687 1f1zA 273 2.55e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1ard 29 2.66e+01 g.37.1.1 45033 1sp1 29 2.72e+01 g.37.1.1 45051 1v87A 114 2.74e+01 g.44.1.1 108422 1vq0A 302 2.81e+01 1kbeA 49 2.81e+01 g.49.1.1 68380 1ywmA 200 2.86e+01 1chc 68 2.87e+01 1chc g.44.1.1 45323 1o12A 376 2.89e+01 b.92.1.5,c.1.9.10 80758,80759 1atnA 373 2.90e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 2dasA 62 2.93e+01 1zzpA 130 2.96e+01 1iro 54 2.97e+01 1rb9 g.41.5.1 45223 1iml 76 2.99e+01 1iml g.39.1.3,g.39.1.3 45145,45146 6rxn 46 3.03e+01 1rb9 g.41.5.1 45222 1qyp 57 3.06e+01 1qyp g.41.3.1 45205 1qumA 285 3.08e+01 1qumA c.1.15.1 29393 1t0fA 276 3.12e+01 1ti6B 274 3.12e+01 b.3.5.1,d.58.1.5 106976,106977 1iyeA 309 3.12e+01 e.17.1.1 83786 1zip 217 3.13e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1b2jA 54 3.20e+01 1rb9 g.41.5.1 45231 2csvA 72 3.21e+01 1c3hA 137 3.21e+01 b.22.1.1 90405 1oahA 519 3.24e+01 a.138.1.3 86736 1o7eA 276 3.25e+01 e.3.1.1 92622 1cezA 883 3.26e+01 1cezA e.8.1.3 43110 4eugA 229 3.27e+01 3eugA c.18.1.1 31019 1xxoA 147 3.28e+01 1zin 217 3.28e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1bgj 394 3.29e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1eugA 229 3.29e+01 3eugA c.18.1.1 31021 1cr8A 42 3.31e+01 1ajj g.12.1.1 44613 1a6yA 95 3.31e+01 2nllB g.39.1.2 45131 2cx1A 187 3.36e+01 1n9dA 199 3.42e+01 a.26.1.1 85464 1lv3A 68 3.45e+01 g.39.1.9 78231 1inp 400 3.46e+01 1inp e.7.1.1 42972 1tr9A 341 3.49e+01 1b8tA 192 3.49e+01 1b8tA g.39.1.3,g.39.1.3,g.39.1.3,g.39.1.3 45135,45136,45137,45138 1wjpA 107 3.49e+01 1qz5A 375 3.52e+01 c.55.1.1,c.55.1.1 96614,96615 1z6uA 150 3.55e+01 2etxA 209 3.58e+01 1w9aA 147 3.64e+01 1twfL 70 3.64e+01 1dxsA 80 3.67e+01 1cokA a.60.1.2 17944 1scuA 288 3.73e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1afp 51 3.74e+01 1afp g.26.1.1 44947 1i50I 122 3.74e+01 g.41.3.1,g.41.3.1 61762,61763 1arf 29 3.77e+01 g.37.1.1 45035 3eugA 229 3.80e+01 3eugA c.18.1.1 31018 1twfI 122 3.81e+01 1zs7A 190 3.86e+01 1jzxM 60 3.88e+01 i.1.1.2 67887 1qtwA 285 4.00e+01 1qumA c.1.15.1 29392 2cklA 108 4.04e+01 1jmsA 381 4.05e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1q16B 512 4.07e+01 d.58.1.5 95548 1y5iB 512 4.14e+01 1cj3A 392 4.16e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1neeA 138 4.16e+01 d.241.1.1,g.59.1.1 91841,91842 1l1dA 152 4.19e+01 b.88.1.3 73452 1a78A 134 4.19e+01 1c1lA b.29.1.3 24212 1t64A 377 4.23e+01 c.42.1.2 106543 1b13A 54 4.27e+01 1rb9 g.41.5.1 45227 1r61A 207 4.27e+01 c.8.8.1 97138 1meyC 87 4.29e+01 2gliA k.12.1.1 46430 1ifqA 138 4.36e+01 1ifqA d.110.4.1 62350 1wr8A 231 4.41e+01 1uch 230 4.44e+01 1uch d.3.1.6 37129 1dsvA 31 4.46e+01 1dsvA g.40.1.1 45174 1p6pA 125 4.54e+01 b.60.1.2 87839 1fl2A 310 4.55e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1evfA 264 4.58e+01 1bkpA d.117.1.1 40932 1zyoA 191 4.62e+01 2g8yA 385 4.65e+01 1yopA 83 4.84e+01 1xd3A 230 4.92e+01 1ctl 85 4.93e+01 g.39.1.3,g.39.1.3 45133,45134 1r5mA 425 4.94e+01 1tqnA 486 5.01e+01 a.104.1.1 107238 1lx8A 55 5.09e+01 a.6.1.7 84734 1woyA 500 5.11e+01 1uslA 170 5.12e+01 c.121.1.1 99871 7taa 478 5.16e+01 7taa b.71.1.1,c.1.8.1 27778,28765 2f6eA 127 5.16e+01 1ayfA 105 5.20e+01 1ayfA d.15.4.1 37684 1zu1A 127 5.25e+01 2hrvA 142 5.25e+01 2hrvA b.47.1.4 26429 1k7hA 476 5.26e+01 c.76.1.1 72101 1nigA 152 5.29e+01 a.25.2.1 85740 1lp9E 194 5.32e+01 b.1.1.1,b.1.1.2 91086,91087 1ayfB 105 5.34e+01 1ayfA d.15.4.1 37685 1wjvA 79 5.34e+01 1fgs 428 5.34e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1jj2F 119 5.39e+01 1ffkE d.79.3.1 63091 1cxxA 113 5.46e+01 1iml g.39.1.3,g.39.1.3 45139,45140 1b2oA 54 5.52e+01 1rb9 g.41.5.1 45233 1tfi 50 5.52e+01 1tfi g.41.3.1 45204 1ois 223 5.58e+01 1a36A e.15.1.1 43267 1k0mA 241 5.63e+01 a.45.1.1,c.47.1.5 67949,67950 1lm5A 214 5.69e+01 d.211.2.1 74029 1gp1A 198 5.87e+01 1gp1A c.47.1.10 33059 1zclA 180 5.88e+01 1etc 110 5.91e+01 1awcA a.4.5.21 16162 1dl0A 37 6.04e+01 1dl0A g.3.6.2 44112 1s7jA 262 6.13e+01 d.21.1.2 98647 1plr 258 6.17e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1m1qA 91 6.22e+01 a.138.1.3 74419 2erxA 172 6.22e+01 1mg2D 155 6.28e+01 a.3.1.1 79062 1upiA 225 6.29e+01 b.82.1.1 99757 1iugA 352 6.31e+01 c.67.1.3 90699 1k3eA 156 6.34e+01 d.198.1.1 68103 2drpA 66 6.38e+01 2drpA g.37.1.1,g.37.1.1 45026,45027 1yp8A 33 6.40e+01 1dgsA 667 6.40e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1k0nA 241 6.41e+01 a.45.1.1,c.47.1.5 67953,67954 1kdj 102 6.45e+01 1plc b.6.1.1 22864 2tscA 264 6.47e+01 1bkpA d.117.1.1 40952 1p9uA 302 6.53e+01 b.47.1.4 88001 1e6eB 128 6.60e+01 1ayfA d.15.4.1 59300 2cszA 76 6.61e+01 2cyeA 133 6.62e+01 4bp2 130 6.63e+01 1poa a.133.1.2 19584 1fn9A 365 6.63e+01 1fn9A d.196.1.1 59894 1aiqA 264 6.65e+01 1bkpA d.117.1.1 40967 1qwlA 505 6.76e+01 e.5.1.1 96483 2g8oA 264 6.80e+01 2fqaA 27 6.88e+01 1k0iA 394 6.91e+01 c.3.1.2,d.16.1.2 67942,67943 1tys 265 6.92e+01 1bkpA d.117.1.1 40937 1jbwA 428 6.93e+01 c.59.1.2,c.72.2.2 62860,62861 1gatA 60 7.04e+01 1gatA g.39.1.1 45106 1g0cA 364 7.05e+01 7a3hA c.1.8.3 60165 1z52A 470 7.06e+01 1zsqA 528 7.08e+01 1u24A 337 7.16e+01 1y9uA 323 7.21e+01 2fiyA 309 7.29e+01 2fo3A 125 7.30e+01 1vor2 58 7.31e+01 1uw2A 61 7.33e+01 g.37.1.4 108064 1vfyA 73 7.40e+01 1vfyA g.50.1.1 45357 1nrkA 328 7.41e+01 b.44.2.1,d.250.1.1 92089,92090 2ampA 304 7.44e+01 1xakA 83 7.45e+01 1guiA 155 7.48e+01 b.18.1.14 76351 1ykjA 394 7.50e+01 2sicI 107 7.54e+01 3ssi d.84.1.1 40031 1a7cA 379 7.59e+01 1sek e.1.1.1 42660 1ezvE 185 7.59e+01 1rie b.33.1.1,f.23.12.1 59548,59549 1are 29 7.61e+01 g.37.1.1 45034 2g8mA 264 7.64e+01 2fg1A 158 7.66e+01 1omiA 248 7.69e+01 b.82.3.3,a.4.5.4 87079,87080 1p5tA 127 7.78e+01 b.55.1.2 94148 1lw7A 365 7.79e+01 c.26.1.3,c.37.1.1 74295,74296 1j6zA 376 7.80e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1am2 199 7.81e+01 1am2 b.86.1.2 28381 1yt5A 258 7.83e+01 1v54F 98 7.84e+01 g.41.5.3 100327 1vetA 124 7.90e+01 d.110.7.1 108553 2frnA 278 7.92e+01 1zud1 251 8.07e+01 2f8aA 208 8.22e+01 1xkwA 665 8.23e+01 1i50L 70 8.23e+01 g.41.9.2 61766 1gnf 46 8.26e+01 1gatA g.39.1.1 45107 1eggA 147 8.34e+01 1eggA d.169.1.1 42333 1qlnA 883 8.36e+01 1cezA e.8.1.3 43111 2aifA 135 8.38e+01 1z02A 446 8.46e+01 1ywzA 175 8.47e+01 1ew4A 106 8.49e+01 1ew4A d.82.2.1 40023 1axwA 265 8.49e+01 1bkpA d.117.1.1 40938 1wgeA 83 8.69e+01 2mev1 277 8.69e+01 2mev1 1ktjA 129 8.70e+01 b.1.18.7 72974 1dtoA 221 8.81e+01 1dtoA b.91.1.1 28405 1ji1A 637 8.86e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 2a8lA 420 8.89e+01 1d4oA 184 8.92e+01 1d4oA c.31.1.4 31748 1puc 105 8.92e+01 1puc d.97.1.1 40675 1yuiA 54 8.96e+01 1yuiA g.37.1.1 45073