# List of top-scoring protein chains for t04-100-30-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.soe.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 2eo0A 147 5.67e-05 1hh1A 143 3.13e-04 1gefA c.52.1.18 61036 1gefA 123 5.04e-04 1gefA c.52.1.18 60465 1y88A 199 3.94e-03 a.60.4.3,c.52.1.30 116560,116561 1ob8A 135 4.45e-03 c.52.1.18 111627 1q7fA 286 2.09e-01 b.68.9.1 96036 1y0kA 209 6.10e-01 c.52.1.31 122485 1cliA 345 7.53e-01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ea5A 537 8.14e-01 2bce c.69.1.1 34592 2jesA 503 9.37e-01 2a2lA 145 1.15e+00 d.110.9.1 126035 1f9yA 158 1.31e+00 d.58.30.1 83249 1vp8A 201 1.34e+00 c.49.1.2 113947 1zjaA 557 2.00e+00 2uubD 209 2.85e+00 d.66.1.2 139935 1dxy 333 2.92e+00 1dxy 1dxyA 333 2.92e+00 c.2.1.4,c.23.12.1 30094,31354 2inbA 140 2.93e+00 2ovgA 66 3.15e+00 2gm3A 175 3.16e+00 c.26.2.4 135354 3cc6A 281 3.49e+00 1a8rA 221 3.49e+00 1a8rA d.96.1.1 40587 2bhgA 209 3.57e+00 5croA 66 3.57e+00 1orc a.35.1.2 17044 1sw5A 275 3.81e+00 c.94.1.1 106069 1eudB 396 3.97e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 2es9A 115 4.06e+00 a.247.1.1 132318 1tiiD 99 4.08e+00 1tiiD b.40.2.1 24965 1uv7A 110 4.09e+00 d.67.4.1 100040 1d7yA 408 4.15e+00 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1orc 71 4.28e+00 1orc 1orcA 71 4.28e+00 a.35.1.2 17054 1sw2A 275 4.69e+00 c.94.1.1 106064 2aexA 346 4.71e+00 1qb5D 99 4.95e+00 b.40.2.1 88357 1of5B 184 4.95e+00 d.17.4.2 86934 1xmxA 385 5.11e+00 c.52.1.26 115568 1dosA 358 5.13e+00 1dosA c.1.10.2 29175 2okfA 140 5.13e+00 2jrrA 67 5.15e+00 2e7xA 150 5.21e+00 1gvfA 286 5.25e+00 c.1.10.2 70599 1skoA 143 5.27e+00 d.110.7.1 105676 1f9zA 135 5.34e+00 1qipA d.32.1.1 38484 2r6uA 148 5.47e+00 2v79A 135 5.63e+00 2hz5A 106 5.81e+00 1e4eA 343 5.90e+00 1iow c.30.1.2,d.142.1.1 59221,59222 1lzlA 323 5.95e+00 c.69.1.2 78306 1fjgD 209 6.03e+00 1c05A d.66.1.2 39553 2imjA 166 6.03e+00 1d66A 66 6.05e+00 1d66A g.38.1.1,h.1.3.1 45076,45510 2fp4B 395 6.06e+00 c.23.4.1,d.142.1.4 133897,133898 2gqwA 408 6.12e+00 1sw5B 275 6.15e+00 c.94.1.1 106070 2vqeD 209 6.45e+00 1vetA 124 6.57e+00 d.110.7.1 108553 1kutA 230 6.71e+00 d.143.1.1 73017 2e5vA 472 6.86e+00 6rxnA 45 6.86e+00 g.41.5.1 45222 1t92A 116 6.93e+00 d.24.1.3 112326 3bv4A 341 6.94e+00 1nv8A 284 7.02e+00 c.66.1.30 86224 1jj2R 84 7.21e+00 1ffkP d.12.1.1 63103 1zh2A 121 7.22e+00 c.23.1.1 125069 1adoA 363 7.27e+00 1fbaA c.1.10.1 29124 1jf9A 408 7.38e+00 1c0nA c.67.1.3 62931 1zaiA 363 7.48e+00 c.1.10.1 124828 3cmgA 667 7.48e+00 1u8tA 129 7.64e+00 c.23.1.1 113192 1qx4A 274 7.66e+00 b.43.4.2,c.25.1.1 104624,104625 2nyiA 195 8.00e+00 1qwgA 251 8.14e+00 c.1.27.1 96473 3blnA 143 8.19e+00 1iow 306 8.30e+00 1iow 1iowA 306 8.30e+00 c.30.1.2,d.142.1.1 31713,41481 2pn6A 150 8.31e+00 1vrpA 381 8.38e+00 a.83.1.1,d.128.1.2 120473,120474 1vqoS 85 8.47e+00 d.12.1.1 120380 1n8jA 186 8.58e+00 c.47.1.10 85401 1zesA 125 8.63e+00 c.23.1.1 124994 1wdjA 187 8.65e+00 c.52.1.27 114536 1b00A 127 8.91e+00 3chy c.23.1.1 31122 1ty0A 211 8.98e+00 b.40.2.2,d.15.6.1 107440,107441 2fa8A 105 8.99e+00 c.47.1.23 133185 2bycA 137 9.26e+00 d.58.10.2 129476 2hl0A 143 9.28e+00 1yexA 186 9.34e+00 c.47.1.10 123021 2rcyA 262 9.42e+00 1to3A 304 9.48e+00 c.1.10.1 107161 3bt3A 148 9.50e+00 2i87A 364 9.52e+00 1y2qA 143 9.63e+00 2awpA 198 9.71e+00 1pv9A 348 9.81e+00 c.55.2.1,d.127.1.1 95157,95158 3bbdA 205 9.85e+00 3cryA 188 9.94e+00 1lyqA 104 1.02e+01 b.1.18.17 78302 3bhwA 209 1.03e+01 2jbaA 127 1.03e+01 2h12A 436 1.03e+01 1jbeA 128 1.08e+01 3chy c.23.1.1 62845 1guzA 310 1.10e+01 c.2.1.5,d.162.1.1 65586,65587 1we0A 187 1.10e+01 c.47.1.10 120930 1sx5A 244 1.10e+01 c.52.1.2 99023 1zmdA 474 1.12e+01 1kmkA 406 1.14e+01 c.67.1.3 68696 1e1hA 287 1.14e+01 d.92.1.7 83167 2i5tA 188 1.15e+01 2g5dA 422 1.16e+01 1zb9A 143 1.17e+01 3bixA 574 1.17e+01 1rwiA 270 1.18e+01 b.68.9.1 97987 1r42A 615 1.19e+01 d.92.1.5 96968 1j33A 335 1.21e+01 c.39.1.1 77069 2iyeA 263 1.27e+01 2oz8A 389 1.29e+01 2icgA 160 1.29e+01 2pfkA 320 1.30e+01 3pfk c.89.1.1 35577 1o12A 376 1.31e+01 b.92.1.5,c.1.9.10 80758,80759 2qdfA 335 1.33e+01 1pfkA 320 1.34e+01 3pfk c.89.1.1 35575 2q8zA 342 1.35e+01 2ostA 151 1.37e+01 1wj5A 120 1.38e+01 a.4.5.59 114692 1xvsA 126 1.38e+01 b.1.23.1 116095 2o14A 375 1.40e+01 1qmvA 197 1.41e+01 1qq2A c.47.1.10 33066 1bgvA 449 1.42e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 2bwrA 401 1.43e+01 1jwiB 125 1.43e+01 d.169.1.1 67384 1atg 231 1.44e+01 1atg 1atgA 231 1.44e+01 c.94.1.1 35834 1zotA 358 1.47e+01 1wx1A 335 1.49e+01 2ywlA 180 1.49e+01 1zgdA 312 1.50e+01 1whzA 70 1.50e+01 d.50.3.2 114656 8rucI 123 1.51e+01 1rboC d.73.1.1 39629 2cvjA 180 1.52e+01 2iruA 303 1.52e+01 1u6rA 380 1.58e+01 a.83.1.1,d.128.1.2 119600,119601 1x84A 189 1.59e+01 d.113.1.2 121795 2pvxA 54 1.65e+01 2jh1A 246 1.65e+01 3cox 507 1.68e+01 1b8sA 3coxA 507 1.68e+01 c.3.1.2,d.16.1.1 30332,37863 1qydA 313 1.70e+01 c.2.1.2 96583 3cvjA 243 1.74e+01 2hkdA 320 1.79e+01 2ajrA 331 1.80e+01 c.72.1.1 126892 1a8vA 121 1.80e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1bq9A 54 1.84e+01 1rb9 g.41.5.1 45238 1brfA 53 1.85e+01 1rb9 g.41.5.1 45236 2yzkA 178 1.86e+01 2axtB 510 1.86e+01 1onqA 283 1.86e+01 b.1.1.2,d.19.1.1 93365,93366 1w0mA 226 1.90e+01 c.1.1.1 109027 2pzhA 135 1.91e+01 1ukgA 252 1.92e+01 b.29.1.1 99489 3rubS 123 1.96e+01 1rboC d.73.1.1 39616 1eejA 216 1.97e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 2po1B 277 1.97e+01 2q7eA 291 1.98e+01 1e25A 282 1.98e+01 1e25A e.3.1.1 42731 2j5vA 367 1.99e+01 2g8cO 251 2.00e+01 1p2fA 220 2.00e+01 a.4.6.1,c.23.1.1 87720,87721 1o17A 345 2.01e+01 a.46.2.1,c.27.1.1 80765,80766 1g0cA 364 2.01e+01 7a3hA c.1.8.3 60165 1bdb 277 2.03e+01 1bdb 1bdbA 277 2.03e+01 c.2.1.2 29874 1m32A 366 2.04e+01 c.67.1.3 78508 1wwzA 159 2.07e+01 d.108.1.1 121380 2a8mA 420 2.09e+01 1fxoA 293 2.12e+01 1g0rA c.68.1.6 34524 1es6A 296 2.12e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1xfkA 336 2.18e+01 c.42.1.1 115264 2cz9A 350 2.19e+01 1qxoA 388 2.23e+01 d.258.1.1 96539 2a8jA 420 2.24e+01 2bx2L 517 2.31e+01 1gsa 316 2.31e+01 1gsa 1gsaA 316 2.31e+01 c.30.1.3,d.142.1.1 31718,41477 1xp2A 179 2.32e+01 2bmoA 447 2.36e+01 b.33.1.2,d.129.3.3 128804,128805 1mk4A 157 2.37e+01 d.108.1.1 84979 1deuA 277 2.37e+01 1theB d.3.1.1 37085 1si7A 369 2.39e+01 d.265.1.4 98883 1xjdA 345 2.40e+01 d.144.1.7 115388 3b8dA 363 2.45e+01 1yk4A 52 2.48e+01 1hw6A 278 2.50e+01 1frb c.1.7.1 61296 1xdnA 277 2.56e+01 d.142.2.4 115168 2dsxA 52 2.57e+01 g.41.5.1 131699 1hrdA 449 2.57e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 2dfuA 264 2.58e+01 1z2nX 324 2.58e+01 2anuA 255 2.60e+01 c.6.3.1 127058 1nzaA 103 2.62e+01 d.58.5.2 86444 2qhpA 296 2.62e+01 1m1lA 236 2.64e+01 d.260.1.1 91166 1iukA 140 2.65e+01 c.2.1.8 83712 1j7xA 302 2.65e+01 c.14.1.2 66425 2ajfA 597 2.66e+01 d.92.1.5 126882 2oy7A 320 2.66e+01 2jn0A 61 2.67e+01 1eg9A 449 2.67e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1utyA 187 2.68e+01 b.147.1.1 108036 2aqjA 538 2.70e+01 2zceA 291 2.70e+01 2gmnA 274 2.71e+01 2pb2A 420 2.72e+01 1cjbA 231 2.74e+01 1qk3A c.61.1.1 34079 1ro5A 201 2.74e+01 d.108.1.3 105023 1wadA 112 2.76e+01 a.138.1.1 19658 1fsuA 492 2.76e+01 c.76.1.2 35032 1qh4A 380 2.76e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1vl4A 447 2.77e+01 d.283.1.1 108718 2ae6A 166 2.80e+01 d.108.1.1 126600 1z02A 446 2.83e+01 2f57A 317 2.84e+01 1opy 131 2.86e+01 1opy 1dmmA 131 2.88e+01 1opy d.17.4.3 38114 1gouA 116 2.89e+01 d.1.1.2 65429 1o08A 221 2.90e+01 c.108.1.6 86525 1ekqA 272 2.92e+01 1c3qA c.72.1.2 34941 1iroA 54 2.92e+01 g.41.5.1 45223 1b13A 54 2.94e+01 1rb9 g.41.5.1 45227 1t0bA 252 2.94e+01 c.23.16.6 106199 2d4nA 152 2.97e+01 1p3wA 404 2.97e+01 c.67.1.3 87752 1ts9A 102 2.97e+01 b.137.1.1 112618 2nw5A 360 3.00e+01 1j3wA 163 3.03e+01 d.110.7.1 90833 1uwmA 106 3.05e+01 d.15.4.1 119763 1hztA 190 3.07e+01 1i9aA d.113.1.2 61459 2ntxA 365 3.10e+01 3bqxA 150 3.11e+01 1an8 208 3.14e+01 1an8 2ex4A 241 3.15e+01 c.66.1.42 132516 2eh6A 375 3.15e+01 1s5dA 240 3.15e+01 d.166.1.1 98541 2d1xA 66 3.15e+01 2ajgA 196 3.20e+01 1s3zA 165 3.22e+01 d.108.1.1 105250 2p14A 192 3.26e+01 1yr0A 175 3.26e+01 d.108.1.1 123905 2qulA 290 3.26e+01 2pjmA 226 3.27e+01 2gagB 405 3.28e+01 2gojA 197 3.32e+01 2yquA 455 3.32e+01 1fa8A 135 3.34e+01 1qipA d.32.1.1 38486 2j07A 420 3.35e+01 a.99.1.1,c.28.1.1 137891,137892 1umkA 275 3.38e+01 b.43.4.2,c.25.1.1 113312,113313 1g67A 225 3.39e+01 c.1.3.1 60311 1b8aA 438 3.43e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2i5vO 251 3.46e+01 1zljA 78 3.53e+01 2pveA 54 3.54e+01 1s3iA 310 3.56e+01 b.46.1.1,c.65.1.1 98435,98436 2jroA 78 3.59e+01 2rspA 124 3.61e+01 2rspB b.50.1.1 26771 2o7iA 592 3.62e+01 1eonA 245 3.63e+01 1rvaA c.52.1.2 33238 1ohvA 472 3.67e+01 c.67.1.4 93031 1jg8A 347 3.67e+01 1jg8A c.67.1.1 62946 1t9mA 214 3.67e+01 b.45.1.1 112364 2pu9A 110 3.67e+01 1m6sA 347 3.68e+01 c.67.1.1 78701 3chy 128 3.70e+01 3chy 1iirA 415 3.72e+01 1iirA c.87.1.5 62453 2o7rA 338 3.74e+01 2tpsA 227 3.74e+01 2tpsA c.1.3.1 28591 2dejA 350 3.81e+01 1iibA 106 3.81e+01 1iibA c.44.2.1 32648 2jc5A 259 3.83e+01 1ospO 257 3.83e+01 1ospO b.76.1.1 27971 1acf 125 3.85e+01 3nul 1acfA 125 3.85e+01 d.110.1.1 40882 2b3yA 888 3.88e+01 c.8.2.1,c.83.1.1 127803,127804 2vo9A 179 3.89e+01 1uf5A 303 3.94e+01 d.160.1.2 107808 1y8qA 346 3.95e+01 1o7nA 449 3.97e+01 b.33.1.2,d.129.3.3 81162,81163 2v1yA 108 4.04e+01 2fqpA 97 4.05e+01 1fp3A 402 4.08e+01 1fp3A a.102.1.3 18842 1hl9A 449 4.09e+01 b.71.1.3,c.1.8.11 90650,90651 1v76A 96 4.10e+01 b.137.1.1 113556 2fnjB 118 4.11e+01 d.15.1.1 133819 2amyA 246 4.11e+01 c.108.1.10 127026 1q7lB 88 4.12e+01 2ovlA 371 4.13e+01 2ia0A 171 4.13e+01 1tyv 542 4.14e+01 1tyv 1iz5A 249 4.15e+01 d.131.1.2,d.131.1.2 83834,83835 2hqvA 195 4.17e+01 e.62.1.2 136674 2z2nA 299 4.21e+01 2pdoA 144 4.21e+01 1k2yX 463 4.23e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1tf4A 605 4.25e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1um0A 365 4.27e+01 d.258.1.1 107942 1wwtA 88 4.29e+01 1tyvA 554 4.33e+01 b.80.1.6 28038 1erzA 303 4.34e+01 1erzA d.160.1.2 59498 1a62 130 4.34e+01 1a62 1a62A 130 4.34e+01 a.140.3.1,b.40.4.5 64708,64709 2qe8A 343 4.45e+01 2qq5A 260 4.46e+01 1wohA 305 4.47e+01 c.42.1.1 109446 1oroA 213 4.50e+01 1opr c.61.1.1 34093 1ml8A 134 4.51e+01 d.227.1.2 85013 1h05A 146 4.51e+01 c.23.13.1 76433 2a0mA 316 4.54e+01 c.42.1.1 125960 2b95A 106 4.55e+01 1wxaA 116 4.60e+01 d.15.1.5 121395 1jmxA 494 4.60e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1uwwA 191 4.60e+01 b.18.1.23 108079 1si6X 282 4.61e+01 d.151.1.2 118968 2p25A 126 4.63e+01 1s1dA 331 4.63e+01 b.67.3.1 98344 1vqoU 66 4.66e+01 g.39.1.6 120382 2ie2A 222 4.66e+01 3c5oA 157 4.67e+01 2vi7A 177 4.68e+01 2oodA 475 4.69e+01 2imqX 282 4.70e+01 2bpa2 175 4.75e+01 2bpa2 1u9jA 358 4.76e+01 c.2.1.2 113243 1jsxA 207 4.76e+01 c.66.1.20 71846 2dhqA 146 4.79e+01 2dhqA c.23.13.1 31382 2okxA 956 4.86e+01 2q43A 418 4.87e+01 c.56.5.4,d.58.19.1 139821,139822 1kxqE 120 4.88e+01 b.1.1.1 73171 1c4kA 730 4.88e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1v6tA 255 4.91e+01 c.6.2.5 113550 1h98A 78 4.92e+01 d.58.1.2 65743 1l3iA 192 4.94e+01 c.66.1.22 77676 2bw0A 329 4.97e+01 b.46.1.1,c.65.1.1 129303,129304 2yvuA 186 5.01e+01 2fjuB 799 5.10e+01 2ffcA 353 5.10e+01 c.1.2.3 133378 2h41A 95 5.15e+01 1r89A 437 5.15e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1szwA 379 5.15e+01 d.265.1.4 99047 1ro0A 216 5.15e+01 d.264.1.2 97664 1p0iA 529 5.19e+01 c.69.1.1 93867 1gqeA 365 5.19e+01 e.38.1.1 70351 1smdA 496 5.19e+01 b.71.1.1,c.1.8.1 27768,28755 1smd 496 5.19e+01 1smd 2j4xA 213 5.26e+01 1yd0A 96 5.28e+01 1nrjB 218 5.30e+01 c.37.1.8 86125 1v6zA 228 5.30e+01 b.122.1.2,c.116.1.5 113551,113552 1zq9A 285 5.30e+01 c.66.1.24 125505 1din 236 5.32e+01 1din 1i1nA 226 5.35e+01 c.66.1.7 71102 2nnuA 205 5.42e+01 b.91.1.1 138401 1b77A 228 5.44e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 3bghA 236 5.48e+01 2jsoA 88 5.54e+01 1v4vA 376 5.54e+01 c.87.1.3 100313 2eb2A 334 5.58e+01 2fg1A 158 5.59e+01 c.50.1.2 133400 1eerB 227 5.61e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1qwtA 255 5.65e+01 b.26.1.3 96501 2ol1A 147 5.66e+01 2a5yA 204 5.67e+01 f.1.4.1 126183 2cz1A 206 5.70e+01 d.149.1.1 131033 1x31B 404 5.71e+01 1s4iA 175 5.72e+01 2f62A 161 5.73e+01 c.23.14.1 133021 3cjpA 272 5.75e+01 1m0dA 138 5.75e+01 c.52.1.17 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