# 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 1v7lA 163 1.14e-03 1q1gA 276 3.25e-01 c.56.2.1 95574 1lx7A 253 3.56e-01 c.56.2.1 74329 1vbkA 307 6.83e-01 1rxyA 253 7.16e-01 c.56.2.1 98065 2bsxA 253 9.11e-01 1vi4A 174 1.53e+00 c.8.7.1 100731 1vi2A 300 1.64e+00 c.2.1.7,c.58.1.5 100726,100727 1yrvA 169 1.77e+00 1gz6A 319 1.92e+00 c.2.1.2 76410 2d13A 227 1.95e+00 2blnA 305 2.05e+00 1ecpA 238 2.07e+00 1ecpA c.56.2.1 33775 2gwgA 350 2.14e+00 1qmeA 702 2.36e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1wraA 308 2.39e+00 2beiA 170 2.97e+00 1ufoA 238 3.18e+00 c.69.1.27 99344 1q0xH 221 3.20e+00 b.1.1.1,b.1.1.2 95517,95518 1ez0A 510 3.26e+00 1eyyA c.82.1.1 35385 1l7dA 384 3.35e+00 c.2.1.4,c.23.12.2 77774,77775 1odkA 235 3.37e+00 c.56.2.1 86863 2gupA 292 3.48e+00 1b7yB 785 3.49e+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 1f8gA 384 4.51e+00 1sayA c.2.1.4,c.23.12.2 59695,59696 1xkwA 665 4.73e+00 2gp4A 628 4.85e+00 2gfaA 119 4.89e+00 1aquA 297 5.13e+00 1aquA c.37.1.5 31942 1gcoA 261 5.14e+00 1ybvA c.2.1.2 29884 1geeA 261 5.14e+00 c.2.1.2 90509 1w99A 558 5.33e+00 1k92A 455 5.47e+00 c.26.2.1,d.210.1.1 68325,68326 1je0A 236 5.71e+00 c.56.2.1 66581 3cox 507 5.88e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 2bibA 547 5.96e+00 1ru8A 232 6.38e+00 c.26.2.1 97849 1ln1A 214 6.61e+00 d.129.3.2 74038 2alaA 391 7.06e+00 1zbqA 327 7.17e+00 1g57A 217 7.39e+00 1g57A d.115.1.2 60253 1zemA 262 7.55e+00 1t0iA 191 7.87e+00 c.23.5.4 106209 2ganA 190 7.98e+00 1t9hA 307 8.12e+00 1j05B 121 8.48e+00 b.1.1.1 90736 1k7jA 206 8.56e+00 d.115.1.1 72103 2b5gA 171 8.62e+00 1vjlA 164 8.74e+00 d.257.1.1 100822 1g8fA 511 8.78e+00 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1nbwA 607 8.95e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 2stv 195 9.21e+00 2stv b.121.7.1 23287 2bukA 196 9.22e+00 2f1rA 171 9.43e+00 1cjcA 460 9.81e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1sheA 103 9.91e+00 d.274.1.1 105551 1bg6 359 1.03e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1ve5A 311 1.04e+01 1ydhA 216 1.05e+01 1tlfA 301 1.07e+01 1tlfA c.93.1.1 35687 1tksA 204 1.12e+01 d.115.1.2 107114 1r6xA 395 1.15e+01 b.122.1.3,c.26.1.5 97167,97168 1dl2A 511 1.18e+01 1dl2A a.102.2.1 18844 1x13A 401 1.22e+01 1lrwA 600 1.24e+01 b.70.1.1 91111 1duvG 333 1.28e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1a6wH 120 1.28e+01 1mfa b.1.1.1 20253 1vl2A 421 1.29e+01 c.26.2.1,d.210.1.1 108708,108709 1whzA 70 1.30e+01 1mlcB 218 1.31e+01 1igtB b.1.1.1,b.1.1.2 20053,21095 1g0oA 283 1.31e+01 1ybvA c.2.1.2 60181 1k9sA 237 1.31e+01 c.56.2.1 68359 2czlA 272 1.33e+01 1f2vA 219 1.36e+01 1f2vA c.23.17.1 59627 1nlbH 218 1.36e+01 b.1.1.1,b.1.1.2 80621,80622 1yjsA 419 1.38e+01 2agyD 135 1.38e+01 1kl1A 419 1.39e+01 c.67.1.4 72663 1knwA 425 1.40e+01 b.49.2.3,c.1.6.1 90969,90970 1sxvA 172 1.46e+01 1ja9A 274 1.47e+01 c.2.1.2 62817 1gp1A 198 1.48e+01 1gp1A c.47.1.10 33059 2a4dA 160 1.51e+01 1am2 199 1.51e+01 1am2 b.86.1.2 28381 1uroA 367 1.57e+01 1uroA c.1.22.1 29675 1r3sA 367 1.58e+01 c.1.22.1 96963 1ne9A 335 1.62e+01 d.108.1.4,d.108.1.4 91839,91840 2a8kA 108 1.64e+01 1nnfA 309 1.65e+01 c.94.1.1 85903 1xruA 282 1.68e+01 1vhwA 253 1.73e+01 c.56.2.1 100706 1b4bA 71 1.76e+01 1b4aA d.74.2.1 39718 1fs7A 485 1.83e+01 1qdbA a.138.1.3 19691 1s3cA 141 1.86e+01 1xhlA 297 1.91e+01 c.2.1.2 109591 1cliA 345 1.91e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1kjkA 64 1.94e+01 d.10.1.4 72613 1fjhA 257 1.95e+01 1fjhB c.2.1.2 29870 1zbfA 142 1.96e+01 1rliA 184 2.01e+01 c.23.5.6 97647 1k78A 149 2.02e+01 a.4.1.5,a.4.1.5 68255,68256 1rerA 391 2.04e+01 b.1.18.4,f.10.1.1 97327,97328 1o6aA 96 2.05e+01 b.139.1.1 92562 2g8lA 299 2.05e+01 1mrp 309 2.05e+01 1mrp c.94.1.1 35796 1c1yB 77 2.07e+01 1c1yB d.15.1.5 37618 1e79A 510 2.09e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1cfzA 162 2.11e+01 1cfzA c.56.1.1 33754 1t46A 313 2.12e+01 d.144.1.7 106397 1f56A 91 2.18e+01 2cbp b.6.1.1 22896 1or7C 90 2.24e+01 a.180.1.1 87336 1pxwA 128 2.24e+01 d.79.3.1 95305 1x8mA 288 2.26e+01 b.82.1.13 109516 1zanH 224 2.33e+01 1uu1A 335 2.36e+01 c.67.1.1 99993 2fdiA 211 2.36e+01 2f23A 156 2.43e+01 2fe7A 166 2.44e+01 2b0uC 288 2.50e+01 1d2oA 187 2.50e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1gnxA 479 2.52e+01 c.1.8.4 76241 1k3iA 656 2.52e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 2f8aA 208 2.52e+01 2ck3A 510 2.54e+01 1gheA 177 2.55e+01 d.108.1.1 76222 1zosA 230 2.57e+01 2coeA 120 2.59e+01 1jb0A 755 2.59e+01 1jb0A f.29.1.1 62820 1nhkL 144 2.61e+01 1npk d.58.6.1 39142 1wejH 223 2.63e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1ooeA 236 2.64e+01 c.2.1.2 87196 1rhs 296 2.68e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 2fp7B 172 2.71e+01 1t4wA 196 2.73e+01 b.2.5.2 106427 1rurH 218 2.74e+01 b.1.1.1,b.1.1.2 97879,97880 1syxB 86 2.74e+01 1df7A 159 2.78e+01 3dfr c.71.1.1 34885 2cayA 145 2.79e+01 1jnrB 150 2.82e+01 d.58.1.5 66969 1zyiA 171 2.88e+01 1dusA 194 2.93e+01 1dusA c.66.1.4 34182 1r0wA 286 2.93e+01 c.37.1.12 96754 2fhzB 108 3.01e+01 2arkA 188 3.04e+01 1owfA 99 3.06e+01 a.55.1.1 87487 1go2A 304 3.06e+01 b.43.4.2,c.25.1.1 76243,76244 1mjuH 227 3.06e+01 b.1.1.1,b.1.1.2 91302,91303 2cyjA 118 3.07e+01 1i9sA 210 3.08e+01 1i9sA c.45.1.1 62099 1dp4A 435 3.08e+01 1dp4A c.93.1.1 35710 1h2kA 349 3.15e+01 b.82.2.6 76572 1ouoA 210 3.16e+01 d.4.1.6 93554 1rdfA 267 3.18e+01 c.108.1.3 104884 1h8eA 510 3.23e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1ywnA 316 3.23e+01 2bsaA 303 3.25e+01 1rqlA 267 3.25e+01 c.108.1.3 97750 1w2wB 191 3.25e+01 1dgwY 93 3.27e+01 1caxB 1k4iA 233 3.29e+01 d.115.1.2 72056 1l3yA 41 3.30e+01 g.3.11.6 73558 1k3bB 164 3.31e+01 d.3.1.1 72015 1z85A 234 3.32e+01 1xd3A 230 3.34e+01 2b59B 172 3.34e+01 1t8hA 277 3.34e+01 d.194.1.2 106664 1mnaA 298 3.38e+01 c.69.1.22 79322 1b7yA 350 3.39e+01 1pysA d.104.1.1 40776 1dl5A 317 3.42e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1xgyH 219 3.44e+01 1gl4A 285 3.45e+01 d.22.1.2,g.3.11.5 65286,65287 1z02A 446 3.47e+01 2adgB 222 3.47e+01 1wod 233 3.49e+01 1wod c.94.1.1 35832 2a77H 222 3.50e+01 1xvaA 292 3.53e+01 1xvaA c.66.1.5 34183 1fezA 256 3.55e+01 1fezA c.108.1.3 43343 1rv3A 483 3.55e+01 c.67.1.4 105101 2bgkA 278 3.57e+01 1yvrA 538 3.63e+01 1ko3A 230 3.65e+01 d.157.1.1 90974 1uch 230 3.65e+01 1uch d.3.1.6 37129 1yllA 200 3.71e+01 2g64A 140 3.72e+01 1xebA 150 3.74e+01 2a84A 300 3.74e+01 2c46A 241 3.76e+01 1zesA 125 3.77e+01 1wi6A 88 3.78e+01 1h4uA 265 3.79e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 1mxtA 504 3.79e+01 c.3.1.2,d.16.1.1 79671,79672 1w34A 304 3.80e+01 1kblA 873 3.82e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1swvA 267 3.83e+01 1zbmA 280 3.84e+01 1xovA 326 3.85e+01 1s3iA 310 3.85e+01 b.46.1.1,c.65.1.1 98435,98436 1n4wA 504 3.86e+01 c.3.1.2,d.16.1.1 91676,91677 2cb4A 291 3.89e+01 1vddA 228 3.91e+01 e.49.1.1 108519 1amf 233 3.92e+01 1wod c.94.1.1 35833 1z5vA 474 3.94e+01 1sqrA 95 3.94e+01 1xkrA 206 3.95e+01 2c2hA 192 3.96e+01 1in4A 334 3.97e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1ixcA 294 3.98e+01 a.4.5.37,c.94.1.1 83764,83765 1vrbA 342 3.98e+01 1q9rB 222 4.00e+01 b.1.1.1,b.1.1.2 96307,96308 1jayA 212 4.02e+01 c.2.1.6 66478 2bmwA 304 4.03e+01 1iy8A 267 4.05e+01 c.2.1.2 83774 1b4vA 504 4.10e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 1e44B 96 4.11e+01 1e44B b.101.1.1 59220 1ogiA 303 4.11e+01 b.43.4.2,c.25.1.1 92914,92915 1cs1A 386 4.15e+01 1ibjA c.67.1.3 34399 1vf8A 377 4.19e+01 1vc3B 97 4.22e+01 1kdgA 546 4.22e+01 c.3.1.2,d.16.1.1 77337,77338 1tqnA 486 4.25e+01 a.104.1.1 107238 1q67A 231 4.26e+01 b.55.1.7 95960 1ww8A 439 4.27e+01 1gyfA 62 4.30e+01 1gyfA d.76.1.1 39749 1eg7A 557 4.31e+01 1eg7A c.37.1.10 32241 1j9bA 141 4.32e+01 c.47.1.12 66459 4ubpC 570 4.33e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1li4A 432 4.33e+01 c.2.1.4,c.23.12.3 84616,84617 2a1kA 233 4.33e+01 1rw7A 243 4.34e+01 c.23.16.2 97963 1xbiA 120 4.35e+01 1iugA 352 4.35e+01 c.67.1.3 90699 2d5cA 263 4.36e+01 1g38A 393 4.39e+01 2admA c.66.1.27 60235 2c2xA 281 4.48e+01 1vctA 205 4.49e+01 1meoA 209 4.49e+01 c.65.1.1 79035 1hilB 220 4.52e+01 1igtB b.1.1.1,b.1.1.2 19787,20897 1p42A 270 4.53e+01 d.14.1.7,d.14.1.7 87754,87755 1g3kA 174 4.63e+01 1nedA d.153.1.4 41989 1mroC 247 4.70e+01 1mroC d.58.31.1 39437 1y0yA 353 4.73e+01 2pth 193 4.74e+01 2pth c.56.3.1 33793 2ahmE 203 4.76e+01 1e4fT 419 4.78e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1so9A 164 4.78e+01 b.146.1.1 105842 1hyxH 224 4.81e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1ve6A 582 4.84e+01 1xs5A 241 4.84e+01 1d4fA 431 4.88e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 2aq5A 402 4.88e+01 1xf1A 926 4.96e+01 6paxA 133 4.99e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 2ckiA 262 5.00e+01 1q0rA 298 5.05e+01 c.69.1.28 95508 1w1oA 534 5.05e+01 d.58.32.4,d.145.1.1 109071,109072 1euhA 475 5.09e+01 1euhA c.82.1.1 35369 2g76A 335 5.09e+01 1bs0A 384 5.10e+01 1bs0A c.67.1.4 34490 1zymA 258 5.10e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1x82A 190 5.17e+01 1zgkA 308 5.18e+01 1ukuA 102 5.18e+01 d.58.5.2 99533 1vlqA 337 5.19e+01 c.69.1.25 108848 1pmd 675 5.20e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1que 303 5.21e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 2furA 209 5.27e+01 2aabH 243 5.27e+01 2arcA 164 5.28e+01 2arcA b.82.4.1 28148 2f5uA 447 5.28e+01 2mspA 126 5.29e+01 1mspA b.1.11.2 22335 1i1dA 161 5.32e+01 1i21A d.108.1.1 61526 1jguH 217 5.33e+01 b.1.1.1,b.1.1.2 66688,66689 1qvzA 237 5.33e+01 c.23.16.2 96453 2bu3A 254 5.34e+01 1ntvA 152 5.37e+01 b.55.1.2 86168 1vfjA 116 5.41e+01 1xrtA 467 5.43e+01 1xdwA 331 5.44e+01 1e4yA 214 5.46e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1fmb 104 5.48e+01 1fmb b.50.1.1 26777 1oroA 213 5.53e+01 1opr c.61.1.1 34093 1dqqB 210 5.54e+01 1igtB b.1.1.1,b.1.1.2 20421,21391 1u6dX 308 5.55e+01 1xfoA 357 5.55e+01 1vmeA 410 5.56e+01 c.23.5.1,d.157.1.3 108893,108894 3ygsP 97 5.57e+01 3ygsP a.77.1.3 18435 1r53A 382 5.58e+01 d.258.1.1 97063 1qxrA 189 5.61e+01 b.82.1.7 96552 1t3qC 288 5.64e+01 d.87.2.1,d.145.1.3 106371,106372 3thiA 371 5.66e+01 2thiA c.94.1.1 35792 2ccjA 205 5.75e+01 1ngzB 220 5.76e+01 b.1.1.1,b.1.1.2 80502,80503 2bh8A 101 5.77e+01 1dc1A 323 5.77e+01 1dc1A c.52.1.11 33321 1ivyA 452 5.86e+01 1ivyA c.69.1.5 34654 1vcdA 126 5.96e+01 1zbpA 273 5.96e+01 1vl8A 267 5.98e+01 c.2.1.2 108733 1d0dA 60 6.00e+01 1kigI g.8.1.2 44566 1j0aA 325 6.01e+01 c.79.1.1 83871 1z2aA 168 6.02e+01 2evaA 307 6.06e+01 1uf2A 1019 6.07e+01 e.28.1.2 99289 1c3cA 429 6.08e+01 1c3cA a.127.1.1 19425 1g6uA 48 6.08e+01 1g6uA k.9.1.1 46425 1g72A 573 6.15e+01 4aahA b.70.1.1 27680 1pv9A 348 6.27e+01 c.55.2.1,d.127.1.1 95157,95158 1nrfA 262 6.27e+01 e.3.1.1 92086 1ni5A 433 6.32e+01 c.26.2.5,d.229.1.1 80533,80534 1yr2A 741 6.34e+01 2bw0A 329 6.35e+01 1fc6A 388 6.38e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 2choA 716 6.39e+01 2fsjA 346 6.44e+01 1mp8A 281 6.45e+01 d.144.1.7 91384 1r2mA 71 6.51e+01 b.138.1.1 96871 1uxtA 501 6.53e+01 c.82.1.1 108125 1ii2A 524 6.57e+01 c.91.1.1,c.109.1.1 66146,66147 1woqA 267 6.58e+01 c.55.1.10,c.55.1.10 109462,109463 1ig5A 75 6.59e+01 4icb a.39.1.1 62363 1gpc 218 6.62e+01 1gpc b.40.4.7 25393 1e4mM 501 6.63e+01 1e70M c.1.8.4 59226 1gs5A 258 6.66e+01 c.73.1.2 70395 1qu9A 128 6.68e+01 1qu9A d.79.1.1 39755 1o54A 277 6.69e+01 c.66.1.13 92482 1v5eA 590 6.70e+01 1hf2A 210 6.70e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 2a0jA 149 6.71e+01 1mexH 215 6.72e+01 b.1.1.1,b.1.1.2 91257,91258 2cbiA 594 6.73e+01 1wmhB 86 6.74e+01 2f2eA 146 6.76e+01 2fldA 165 6.81e+01 2f06A 144 6.83e+01 1twyA 290 6.85e+01 1in6A 334 6.87e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1oo0A 147 6.87e+01 d.232.1.1 87182 2aorA 223 6.93e+01 1k0hA 117 6.98e+01 b.106.1.2 71975 2cveA 191 6.99e+01 1ub9A 100 7.01e+01 a.4.5.28 99159 1pamA 686 7.04e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1v5tA 90 7.05e+01 d.15.1.1 108385 1vkfA 188 7.07e+01 c.1.29.1 108656 2fdrA 229 7.08e+01 2arpA 116 7.12e+01 2bgiA 272 7.13e+01 1m4iA 181 7.14e+01 d.108.1.1 74457 1x84A 189 7.15e+01 1lzlA 323 7.26e+01 c.69.1.2 78306 1rpnA 335 7.27e+01 c.2.1.2 97708 1cjbA 231 7.29e+01 1qk3A c.61.1.1 34079 2bnfB 241 7.42e+01 1mvfD 82 7.43e+01 b.129.1.1 85143 1z96A 40 7.46e+01 1imjA 210 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1iz5A 249 8.39e+01 d.131.1.2,d.131.1.2 83834,83835 1c5cH 215 8.41e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1yavA 159 8.44e+01 1xtaA 221 8.51e+01 1yezA 68 8.54e+01 1gpl 432 8.54e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1ju3A 583 8.65e+01 b.18.1.13,c.69.1.21 67300,67301 2a74A 643 8.66e+01 1ncwH 222 8.71e+01 b.1.1.1,b.1.1.2 85555,85556 1j7dA 145 8.78e+01 1jatB d.20.1.1 62680 1up6A 416 8.82e+01 c.2.1.5,d.162.1.2 107976,107977 1qlmA 316 8.90e+01 1qlmA d.147.1.1 41765 1b00A 127 8.94e+01 3chy c.23.1.1 31122 1oaoC 729 8.95e+01 e.26.1.3 86746 1kcvH 217 8.96e+01 b.1.1.1,b.1.1.2 72315,72316 1um5H 217 8.96e+01 2cybA 323 8.99e+01