# 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.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 2ap1A 327 5.19e-02 1rqlA 267 3.17e-01 c.108.1.3 97750 1ofgA 381 3.55e-01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1swvA 267 3.59e-01 1h6dA 433 4.54e-01 c.2.1.3,d.81.1.5 65656,65657 1xqaA 113 7.54e-01 1yrvA 169 8.01e-01 1jy2O 56 9.77e-01 h.1.8.1 67441 1fezA 256 1.05e+00 1fezA c.108.1.3 43343 1yirA 408 1.13e+00 1pysA 350 1.38e+00 1pysA d.104.1.1 40775 1zd9A 188 1.67e+00 1zoyC 140 1.71e+00 1s1qA 145 1.74e+00 d.20.1.2 98351 1u9aA 160 1.77e+00 1u9aA d.20.1.1 38333 1ufiA 64 2.13e+00 a.30.4.1 99336 1nepA 130 2.33e+00 b.1.18.7 80440 1h2kA 349 2.71e+00 b.82.2.6 76572 1kshA 186 2.77e+00 c.37.1.8 72914 1b7yA 350 3.36e+00 1pysA d.104.1.1 40776 2grrA 161 3.47e+00 2h88C 140 3.63e+00 1ug0A 88 3.82e+00 a.217.1.1 107822 1u08A 386 4.22e+00 c.67.1.1 107543 1r0pA 312 4.36e+00 d.144.1.7 96734 1xawA 140 5.10e+00 1ujwB 135 5.14e+00 h.4.9.1 99472 1sziA 247 5.16e+00 a.24.23.1 106159 1u2eA 289 5.20e+00 1kr4A 125 5.41e+00 d.58.5.2 72889 1nvvS 481 5.52e+00 a.117.1.1 86279 1twuA 139 5.69e+00 d.32.1.8 107413 1hzxA 349 5.78e+00 1f88A f.13.1.2 61466 1l9hA 349 5.92e+00 f.13.1.2 73720 1gd8A 118 5.95e+00 d.188.1.1 60445 1u19A 349 5.95e+00 1sxjE 354 5.96e+00 a.80.1.1,c.37.1.20 106089,106090 2fbwC 141 6.15e+00 1xttA 216 6.36e+00 2d81A 318 6.47e+00 1kvkA 395 6.54e+00 d.14.1.5,d.58.26.3 73060,73061 1yrcA 414 6.70e+00 2fi9A 128 6.72e+00 1re9A 414 6.85e+00 1hcd 118 6.90e+00 1hce b.42.5.2 25624 1wzvA 155 7.05e+00 1a8y 367 7.07e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2ahqA 76 7.18e+00 1otsA 465 7.24e+00 f.20.1.1 87415 1dz4A 414 7.26e+00 1phd a.104.1.1 18903 1r85A 379 7.32e+00 c.1.8.3 104839 1nrjA 158 7.35e+00 d.110.4.4 86124 1yg2A 179 7.59e+00 1exrA 148 7.73e+00 1cll a.39.1.5 17299 1yf2A 425 7.77e+00 1yf9A 171 8.23e+00 1akz 223 8.27e+00 3eugA c.18.1.1 31007 1uzbA 516 9.15e+00 c.82.1.1 100220 1z8uA 102 9.25e+00 1ov2A 99 9.60e+00 a.13.1.1 93580 1z6uA 150 1.00e+01 2bjkA 516 1.02e+01 2b20A 403 1.04e+01 1eyzA 392 1.05e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 1ggzA 148 1.05e+01 a.39.1.5 70176 1yh6A 179 1.08e+01 1qmqA 414 1.11e+01 1phd a.104.1.1 18907 1jsdA 319 1.15e+01 b.19.1.2 63258 1eqfA 280 1.18e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 2a5lA 200 1.21e+01 1y01A 102 1.27e+01 1z08A 170 1.43e+01 1gu7A 364 1.44e+01 b.35.1.2,c.2.1.1 83321,83322 1eg3A 261 1.49e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1o3yA 166 1.50e+01 c.37.1.8 86618 1lvfA 110 1.53e+01 a.47.2.1 74280 1jchA 551 1.58e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1fzqA 181 1.69e+01 1hurA c.37.1.8 32060 2bjqA 345 1.72e+01 1ois 223 1.78e+01 1a36A e.15.1.1 43267 1w9yA 319 1.80e+01 1z5bA 469 1.83e+01 2fjlA 150 1.83e+01 1a17 166 1.84e+01 1a17 a.118.8.1 19206 1a92A 50 1.92e+01 1a92A h.4.6.1 45791 1sk4A 163 1.96e+01 d.118.1.1 105664 1w2xA 758 2.02e+01 c.14.1.4,c.14.1.4 109134,109135 1w0bA 102 2.04e+01 a.7.11.1 108985 1gqeA 365 2.07e+01 e.38.1.1 70351 1wpaA 114 2.11e+01 1jl5A 454 2.12e+01 c.10.2.6 66830 1v9mA 323 2.12e+01 f.40.1.1 100543 1go4E 100 2.16e+01 h.1.22.1 70296 1p1mA 406 2.16e+01 b.92.1.4,c.1.9.9 87696,87697 1z21A 112 2.19e+01 1lre 81 2.20e+01 1lre a.13.1.1 16376 2a3qA 170 2.26e+01 2f3yA 148 2.45e+01 1td6A 306 2.47e+01 1r4aA 165 2.61e+01 c.37.1.8 96986 1o5iA 249 2.62e+01 c.2.1.2 92499 1wp5A 323 2.69e+01 2b7kA 200 2.69e+01 1mzjA 339 2.77e+01 c.95.1.2,c.95.1.2 79700,79701 1l6kA 77 2.80e+01 h.6.1.1 77724 1bjwA 382 2.82e+01 1bjwA c.67.1.1 34349 1wgxA 73 2.83e+01 1wxcB 134 2.84e+01 1ni5A 433 2.97e+01 c.26.2.5,d.229.1.1 80533,80534 1wg8A 285 3.01e+01 1zb1A 392 3.03e+01 1m12A 84 3.08e+01 a.64.1.1 84745 1hynP 379 3.09e+01 1hynP d.112.1.2 61408 1bs0A 384 3.11e+01 1bs0A c.67.1.4 34490 2acvA 463 3.15e+01 1u69A 163 3.16e+01 d.32.1.7 107699 2fa8A 105 3.19e+01 2feaA 236 3.19e+01 1opjA 293 3.21e+01 d.144.1.7 87230 1r8sA 164 3.22e+01 c.37.1.8 97247 1wmhA 89 3.26e+01 2a0iA 330 3.26e+01 1w6sB 74 3.27e+01 2cblA 305 3.27e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1cnt1 187 3.28e+01 1cnt3 1z6oM 191 3.29e+01 1naqA 112 3.30e+01 d.58.5.2 91761 1r5zA 323 3.33e+01 f.40.1.1 97135 1qqgA 264 3.36e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1w77A 228 3.37e+01 1xn9A 101 3.46e+01 1gg3A 279 3.52e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1uptA 171 3.56e+01 c.37.1.8 99767 1h0hA 977 3.60e+01 b.52.2.2,c.81.1.1 76435,76436 2occE 109 3.66e+01 2occE a.118.11.1 19224 1top 162 3.66e+01 1ncx a.39.1.5 17223 1k8rB 110 3.68e+01 d.15.1.5 72180 1yoeA 322 3.71e+01 1p5fA 189 3.71e+01 c.23.16.2 94142 1kveB 77 3.74e+01 1kveB 1g8iA 190 3.75e+01 1rec a.39.1.5 60363 1wqgA 185 3.75e+01 1yruB 74 3.78e+01 1yz4A 160 3.80e+01 1s0yB 71 3.82e+01 d.80.1.1 98315 1rr7A 129 3.92e+01 a.4.1.14 105075 1b5pA 385 3.95e+01 c.67.1.1 90403 2bydA 323 4.02e+01 1tn4 159 4.08e+01 1ncx a.39.1.5 17248 2bwvA 440 4.13e+01 1k24A 253 4.14e+01 f.4.4.2 72002 1n13B 113 4.14e+01 1cpcA 162 4.16e+01 1cpcA a.1.1.3 15643 1t6cA 315 4.22e+01 c.55.1.8,c.55.1.8 106558,106559 1zclA 180 4.22e+01 1neyA 247 4.22e+01 c.1.1.1 80449 2cglA 489 4.23e+01 1avsA 90 4.27e+01 1cll a.39.1.5 17226 1ax8 146 4.31e+01 1ax8 a.26.1.1 16844 1nmeB 92 4.36e+01 1i7nA 309 4.37e+01 c.30.1.5,d.142.1.3 83681,83682 1rxdA 159 4.40e+01 2c43A 323 4.40e+01 1rypA 243 4.45e+01 1pmaA d.153.1.4 41932 2tmnE 316 4.46e+01 1hyt d.92.1.2 59055 1az9 457 4.48e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1zckA 154 4.48e+01 8rucI 123 4.49e+01 1rboC d.73.1.1 39629 1j6pA 418 4.51e+01 b.92.1.4,c.1.9.9 77089,77090 1iapA 211 4.52e+01 a.91.1.1 62119 1mlwA 301 4.57e+01 d.178.1.1 79289 1kllA 130 4.57e+01 d.32.1.2 72720 1zyeA 220 4.64e+01 1p4oA 322 4.70e+01 d.144.1.7 87775 1fseA 74 4.72e+01 1fseA a.4.6.2 60000 1wl9A 440 4.75e+01 1yvhA 329 4.79e+01 1k1fA 72 4.87e+01 a.147.1.1 68007 1wrmA 165 4.90e+01 1yt3A 375 4.95e+01 1k4nA 192 4.98e+01 d.32.1.5 72059 1p5zB 263 5.08e+01 c.37.1.1 87815 1a02F 56 5.18e+01 1a02F h.1.3.1 45534 1xsjA 778 5.21e+01 1qksA 567 5.22e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1vmiA 355 5.22e+01 2aegA 268 5.25e+01 1jflA 228 5.25e+01 c.78.2.1,c.78.2.1 71656,71657 1xd7A 145 5.25e+01 a.4.5.55 109566 1ail 73 5.28e+01 1ail a.16.1.1 16381 1q2hA 69 5.28e+01 a.34.4.1 104498 2f2hA 773 5.28e+01 2bwfA 77 5.29e+01 2ffsA 157 5.35e+01 1g4yR 148 5.36e+01 1cll a.39.1.5 60252 1i45A 248 5.41e+01 1amk c.1.1.1 61665 1fthA 122 5.41e+01 d.150.1.2 60028 1eyvA 156 5.43e+01 1eyvA a.79.1.1 18446 2akrA 285 5.45e+01 1s9kD 53 5.46e+01 2db9A 149 5.47e+01 1lyvA 306 5.49e+01 c.45.1.2 74348 1p8xA 344 5.52e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1mu5A 471 5.53e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 2dfkA 402 5.63e+01 2fupA 168 5.63e+01 1qlwA 328 5.64e+01 1qlwA c.69.1.15 34722 1t7lA 766 5.66e+01 1u8xX 472 5.84e+01 c.2.1.5,d.162.1.2 107741,107742 1zy9A 564 5.92e+01 1rdfA 267 5.92e+01 c.108.1.3 104884 1uj8A 77 5.92e+01 1v54E 109 5.98e+01 a.118.11.1 100326 1ytw 306 6.01e+01 1ytw c.45.1.2 32689 1yx1A 264 6.03e+01 8tlnE 316 6.06e+01 1hyt d.92.1.2 59075 1ajsA 412 6.07e+01 1ajsA c.67.1.1 34276 1vgmA 378 6.18e+01 2bpsA 81 6.25e+01 1rgxA 114 6.25e+01 g.77.1.1 104932 1uzcA 71 6.38e+01 a.159.2.1 100222 1s72M 194 6.43e+01 d.12.1.2 105332 1tzpA 255 6.46e+01 d.65.1.3 107520 1pl5A 142 6.53e+01 h.1.23.1 104186 1b3uA 588 6.53e+01 1b3uA a.118.1.2 19135 1ymmA 191 6.60e+01 1wocA 103 6.63e+01 1rp0A 284 6.74e+01 1qsdA 106 6.79e+01 1qsdA a.7.5.1 16335 1q18A 332 6.86e+01 c.55.1.7,c.55.1.7 104470,104471 1g0uG 252 6.87e+01 d.153.1.4 41952 1t3jA 96 7.00e+01 h.4.16.1 106356 1zwwA 256 7.03e+01 1stzA 338 7.04e+01 a.4.5.51,d.110.2.3 106009,106010 1hfoA 113 7.05e+01 d.80.1.3 61006 1vjeA 166 7.20e+01 d.185.1.2 100807 1f24A 402 7.31e+01 1rom a.104.1.1 18953 1tzbA 302 7.35e+01 c.80.1.1 107470 1onwA 390 7.38e+01 b.92.1.7,c.1.9.13 87172,87173 2d2sA 235 7.40e+01 2b6hA 192 7.43e+01 2carA 196 7.43e+01 1uv7A 110 7.47e+01 d.67.4.1 100040 1hn0A 1021 7.48e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1q1vA 70 7.49e+01 a.159.4.1 104479 1jnmA 62 7.54e+01 h.1.3.1 84181 1auvA 311 7.54e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 1mjc 69 7.60e+01 1mjc b.40.4.5 25319 1qp6A 35 7.73e+01 1qp6A k.16.1.1 46443 2f6uA 234 7.74e+01 1jfbA 404 7.78e+01 a.104.1.1 66624 1ktjA 129 7.81e+01 b.1.18.7 72974 1ww8A 439 7.82e+01 1gkzA 388 7.89e+01 a.29.5.1,d.122.1.4 65268,65269 1lrzA 426 7.93e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 2fh1A 344 7.94e+01 1r59O 505 7.99e+01 1wf9A 107 8.01e+01 1r4wA 226 8.03e+01 c.47.1.13 97050 1x9iA 302 8.15e+01 1g94A 448 8.17e+01 b.71.1.1,c.1.8.1 65169,65170 1x91A 153 8.23e+01 1wovA 250 8.24e+01 1jggA 60 8.36e+01 2hddA a.4.1.1 62950 1fcdA 401 8.36e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1lmeA 176 8.38e+01 d.167.1.1 84629 2g0uA 92 8.40e+01 1nd4A 264 8.51e+01 d.144.1.6 91815 1lngA 87 8.57e+01 d.201.1.1 74045 1jfmA 174 8.57e+01 d.19.1.1 66640 1vd2A 89 8.60e+01 d.15.2.2 108517 1o5kA 306 8.60e+01 c.1.10.1 92504 2covD 104 8.62e+01 1jj2L 194 8.64e+01 1ffkI d.12.1.2 63097 1lyxA 248 8.65e+01 c.1.1.1 78304 1r62A 160 8.65e+01 d.122.1.3 104816 1ydmA 187 8.66e+01 1slqA 278 8.68e+01 f.47.1.1 105719 1tueA 212 8.70e+01 c.37.1.20 107323 1ko6A 187 8.73e+01 b.119.1.1 77471 1wekA 217 8.74e+01 1cznA 169 8.81e+01 1rcf c.23.5.1 31181 2b8iA 77 8.82e+01 1aqm 453 8.86e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1s4kA 120 8.86e+01 a.35.1.6 105254 1mijA 152 8.95e+01 a.4.1.1 79150 2h1nA 567 8.98e+01