# 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 1v7lA 163 6.73e-03 1lx7A 253 1.14e-01 c.56.2.1 74329 1rxyA 253 2.16e-01 c.56.2.1 98065 1q1gA 276 6.26e-01 c.56.2.1 95574 1dvfD 120 8.54e-01 1mfa b.1.1.1 20107 1k3fA 253 1.22e+00 c.56.2.1 68105 1vi4A 174 1.33e+00 c.8.7.1 100731 2bsxA 253 1.42e+00 1qdlB 195 1.76e+00 1qdlB c.23.16.1 31437 1k92A 455 1.90e+00 c.26.2.1,d.210.1.1 68325,68326 1vbkA 307 1.93e+00 1gz6A 319 2.03e+00 c.2.1.2 76410 1vi2A 300 2.24e+00 c.2.1.7,c.58.1.5 100726,100727 1qmeA 702 2.29e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1ufoA 238 3.08e+00 c.69.1.27 99344 1t9hA 307 3.45e+00 1coy 507 3.54e+00 1b8sA c.3.1.2,d.16.1.1 30333,37864 2stv 195 3.55e+00 2stv b.121.7.1 23287 2bukA 196 3.55e+00 1b7yB 785 3.80e+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 1gcoA 261 3.99e+00 1ybvA c.2.1.2 29884 1geeA 261 4.01e+00 c.2.1.2 90509 3cox 507 4.18e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1j0aA 325 4.36e+00 c.79.1.1 83871 2gwgA 350 4.39e+00 1ez0A 510 4.57e+00 1eyyA c.82.1.1 35385 1je0A 236 4.82e+00 c.56.2.1 66581 1npdA 288 5.08e+00 c.2.1.7,c.58.1.5 80681,80682 1eyyA 510 5.22e+00 1eyyA c.82.1.1 35389 1tksA 204 5.81e+00 d.115.1.2 107114 1xkrA 206 5.93e+00 2agyD 135 6.05e+00 1ibsA 317 6.36e+00 c.61.1.2,c.61.1.2 66107,66108 1yrvA 169 6.50e+00 2blnA 305 6.69e+00 1g57A 217 6.82e+00 1g57A d.115.1.2 60253 1ooeA 236 7.00e+00 c.2.1.2 87196 2beiA 170 7.09e+00 1lrwA 600 7.24e+00 b.70.1.1 91111 1j05B 121 7.47e+00 b.1.1.1 90736 1ve5A 311 7.63e+00 1e4eA 343 8.09e+00 1iow c.30.1.2,d.142.1.1 59221,59222 1aquA 297 8.19e+00 1aquA c.37.1.5 31942 1w2wB 191 8.22e+00 1ecpA 238 9.46e+00 1ecpA c.56.2.1 33775 1zemA 262 1.04e+01 1ln1A 214 1.04e+01 d.129.3.2 74038 1acz 108 1.06e+01 1kum b.3.1.1 22524 1eiyB 785 1.07e+01 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 16305,16306,25314,39313,40782,41458 1cjcA 460 1.11e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1g3kA 174 1.11e+01 1nedA d.153.1.4 41989 1iezA 217 1.12e+01 d.115.1.2 66129 1fjhA 257 1.22e+01 1fjhB c.2.1.2 29870 1zbqA 327 1.23e+01 1tlfA 301 1.30e+01 1tlfA c.93.1.1 35687 1ad9B 219 1.31e+01 1gc1H b.1.1.1,b.1.1.2 20215,21227 1fjhB 257 1.32e+01 1fjhB c.2.1.2 29871 2d13A 227 1.34e+01 1wraA 308 1.35e+01 1guaB 81 1.37e+01 1c1yB d.15.1.5 37619 2czlA 272 1.41e+01 2ganA 190 1.43e+01 1w99A 558 1.45e+01 1sheA 103 1.53e+01 d.274.1.1 105551 1jm1A 204 1.58e+01 b.33.1.1 71745 1efaA 333 1.60e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1nnfA 309 1.61e+01 c.94.1.1 85903 1dl2A 511 1.62e+01 1dl2A a.102.2.1 18844 1f56A 91 1.64e+01 2cbp b.6.1.1 22896 1c1yB 77 1.64e+01 1c1yB d.15.1.5 37618 2tmkA 216 1.64e+01 3tmkA c.37.1.1 31928 1dkrA 317 1.73e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1a6tB 217 1.74e+01 1igtB b.1.1.1,b.1.1.2 20249,21259 1o6aA 96 1.78e+01 b.139.1.1 92562 1pysB 785 1.78e+01 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 16299,16300,25311,39310,40779,41455 1ru8A 232 1.78e+01 c.26.2.1 97849 1e79A 510 1.81e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 3tmkA 216 1.82e+01 3tmkA c.37.1.1 31920 2a6mA 155 1.85e+01 1mrp 309 1.87e+01 1mrp c.94.1.1 35796 1duvG 333 1.87e+01 1othA c.78.1.1,c.78.1.1 35228,35229 3minB 522 1.88e+01 1qguB c.92.2.3 35606 1k7jA 206 1.96e+01 d.115.1.1 72103 1d2oA 187 1.98e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 2coeA 120 2.00e+01 1bg6 359 2.03e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1a6wH 120 2.04e+01 1mfa b.1.1.1 20253 2cayA 145 2.05e+01 1mo2A 294 2.07e+01 c.69.1.22 79331 1gp1A 198 2.11e+01 1gp1A c.47.1.10 33059 2arcB 164 2.16e+01 2arcA b.82.4.1 28149 1mnaA 298 2.17e+01 c.69.1.22 79322 2minB 522 2.20e+01 1qguB c.92.2.3 35610 1s3cA 141 2.23e+01 1zymA 258 2.25e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1uroA 367 2.31e+01 1uroA c.1.22.1 29675 2b0uC 288 2.32e+01 1vl2A 421 2.32e+01 c.26.2.1,d.210.1.1 108708,108709 1rypL 212 2.33e+01 d.153.1.4 41880 1yvrA 538 2.34e+01 1dgrW 93 2.38e+01 1caxB 1ybvA 283 2.39e+01 1ybvA c.2.1.2 29948 1r3sA 367 2.43e+01 c.1.22.1 96963 1i9sA 210 2.45e+01 1i9sA c.45.1.1 62099 1kk9A 221 2.46e+01 d.115.1.1 77432 1vcdA 126 2.47e+01 2aacA 177 2.50e+01 2arcA b.82.4.1 28150 1dgrM 93 2.51e+01 1caxB b.82.1.2 28101 2ck3A 510 2.51e+01 1xrtA 467 2.52e+01 1ja9A 274 2.53e+01 c.2.1.2 62817 1whzA 70 2.63e+01 1f2vA 219 2.63e+01 1f2vA c.23.17.1 59627 1h8eA 510 2.66e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1ik6A 369 2.67e+01 c.36.1.7,c.48.1.2 66174,66175 2arkA 188 2.67e+01 1vhwA 253 2.70e+01 c.56.2.1 100706 2b5gA 171 2.73e+01 1eza 259 2.79e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1g0oA 283 2.81e+01 1ybvA c.2.1.2 60181 1k32A 1045 2.82e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1zyiA 171 2.82e+01 1m1nB 522 2.92e+01 c.92.2.3 78418 1i1hA 219 2.94e+01 1f2vA c.23.17.1 61530 1xd3A 230 2.97e+01 1vfjA 116 3.02e+01 1kezA 300 3.03e+01 c.69.1.22 68546 1odkA 235 3.03e+01 c.56.2.1 86863 1q5xA 161 3.04e+01 c.8.7.1 95947 1fs7A 485 3.04e+01 1qdbA a.138.1.3 19691 2arcA 164 3.06e+01 2arcA b.82.4.1 28148 35c8H 217 3.08e+01 8fabA b.1.1.1,b.1.1.2 20297,21289 2cyjA 118 3.08e+01 1nhkL 144 3.16e+01 1npk d.58.6.1 39142 1jnrB 150 3.18e+01 d.58.1.5 66969 2admA 421 3.20e+01 2admA c.66.1.27 34238 2c46A 241 3.21e+01 2a74A 643 3.26e+01 1tw7A 99 3.28e+01 1s3iA 310 3.31e+01 b.46.1.1,c.65.1.1 98435,98436 1d2pA 373 3.33e+01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1qfoC 119 3.35e+01 1qfoA b.1.1.1 19710 1dgwY 93 3.42e+01 1caxB 1syxB 86 3.45e+01 2a8kA 108 3.45e+01 1q0xH 221 3.45e+01 b.1.1.1,b.1.1.2 95517,95518 1uf2A 1019 3.45e+01 e.28.1.2 99289 1iz1A 294 3.47e+01 a.4.5.37,c.94.1.1 83823,83824 1or7C 90 3.48e+01 a.180.1.1 87336 1xhlA 297 3.52e+01 c.2.1.2 109591 1twyA 290 3.54e+01 1cruA 454 3.59e+01 1c9uA b.68.2.1 27617 1a7aA 432 3.62e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1h4vB 421 3.64e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1r0wA 286 3.64e+01 c.37.1.12 96754 1uch 230 3.65e+01 1uch d.3.1.6 37129 2f23A 156 3.69e+01 1xkwA 665 3.73e+01 1qbiA 454 3.75e+01 1c9uA b.68.2.1 27619 1gl4A 285 3.80e+01 d.22.1.2,g.3.11.5 65286,65287 1xs5A 241 3.95e+01 1uwvA 433 3.99e+01 b.40.4.12,c.66.1.40 100128,100129 1wod 233 4.06e+01 1wod c.94.1.1 35832 1ac0 108 4.08e+01 1kum b.3.1.1 22526 1n6eA 1071 4.10e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1cfzA 162 4.14e+01 1cfzA c.56.1.1 33754 1sqrA 95 4.16e+01 1eg7A 557 4.19e+01 1eg7A c.37.1.10 32241 1xruA 282 4.26e+01 1li4A 432 4.28e+01 c.2.1.4,c.23.12.3 84616,84617 3ygsP 97 4.28e+01 3ygsP a.77.1.3 18435 1amf 233 4.31e+01 1wod c.94.1.1 35833 1j9bA 141 4.32e+01 c.47.1.12 66459 2d5cA 263 4.34e+01 1g65K 211 4.35e+01 d.153.1.4 41907 1ve6A 582 4.35e+01 1ijhA 504 4.37e+01 c.3.1.2,d.16.1.1 66161,66162 1nqbA 256 4.38e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 1g38A 393 4.39e+01 2admA c.66.1.27 60235 2cybA 323 4.40e+01 1w1oA 534 4.41e+01 d.58.32.4,d.145.1.1 109071,109072 1mxtA 504 4.42e+01 c.3.1.2,d.16.1.1 79671,79672 1u6dX 308 4.42e+01 1l3yA 41 4.42e+01 g.3.11.6 73558 1pk9A 237 4.43e+01 c.56.2.1 94823 1n4wA 504 4.48e+01 c.3.1.2,d.16.1.1 91676,91677 1q40B 219 4.48e+01 d.17.4.2 95771 1b8sA 504 4.55e+01 1b8sA c.3.1.2,d.16.1.1 30335,37866 1gheA 177 4.56e+01 d.108.1.1 76222 1nrfA 262 4.58e+01 e.3.1.1 92086 1mejA 223 4.59e+01 c.65.1.1 79029 1gnwA 211 4.59e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1h4uA 265 4.60e+01 1h4uA d.22.1.2,g.3.11.5 60622,60623 2evaA 307 4.62e+01 1jayA 212 4.65e+01 c.2.1.6 66478 1b4vA 504 4.67e+01 1b8sA c.3.1.2,d.16.1.1 30334,37865 2ckiA 262 4.71e+01 1ddt 535 4.74e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 1ydhA 216 4.74e+01 1jaxA 212 4.78e+01 c.2.1.6 66476 1ni5A 433 4.81e+01 c.26.2.5,d.229.1.1 80533,80534 1gyfA 62 4.83e+01 1gyfA d.76.1.1 39749 1xbiA 120 4.85e+01 1jb0A 755 4.85e+01 1jb0A f.29.1.1 62820 1i3kA 348 4.86e+01 1xel c.2.1.2 61595 1v3rA 116 4.87e+01 1vctA 205 4.88e+01 1azvA 153 4.91e+01 1mfmA b.1.8.1 22247 1i1dA 161 4.94e+01 1i21A d.108.1.1 61526 1q0rA 298 4.95e+01 c.69.1.28 95508 1gnxA 479 4.97e+01 c.1.8.4 76241 2bgkA 278 4.97e+01 1fxzA 476 4.97e+01 b.82.1.2,b.82.1.2 65059,65060 1z5vA 474 4.98e+01 1wejH 223 4.99e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1rdfA 267 5.00e+01 c.108.1.3 104884 2fi9A 128 5.03e+01 1d4fA 431 5.13e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 2f8aA 208 5.14e+01 2bw0A 329 5.14e+01 1tetH 210 5.19e+01 1igtB b.1.1.1,b.1.1.2 19903,20997 1k9sA 237 5.20e+01 c.56.2.1 68359 1fezA 256 5.21e+01 1fezA c.108.1.3 43343 1neu 124 5.29e+01 1neu b.1.1.1 19704 1k3iA 656 5.40e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1k78A 149 5.42e+01 a.4.1.5,a.4.1.5 68255,68256 1n1pA 504 5.43e+01 c.3.1.2,d.16.1.1 91546,91547 2bj7A 138 5.48e+01 1e44B 96 5.50e+01 1e44B b.101.1.1 59220 1a3rH 218 5.55e+01 1igtB b.1.1.1,b.1.1.2 19781,20891 1rqlA 267 5.57e+01 c.108.1.3 97750 1dywA 173 5.58e+01 2cpl b.62.1.1 27505 1nlbH 218 5.60e+01 b.1.1.1,b.1.1.2 80621,80622 2fe7A 166 5.61e+01 1nzjA 298 5.64e+01 c.26.1.1 92377 1b20A 110 5.69e+01 1b20A d.1.1.2 36207 1dkuA 317 5.70e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1e1aA 314 5.70e+01 1e1aA b.68.6.1 59155 1k3bB 164 5.73e+01 d.3.1.1 72015 1zghA 260 5.87e+01 1ve1A 304 5.90e+01 1pmd 675 5.93e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1zgkA 308 5.93e+01 1ub9A 100 5.94e+01 a.4.5.28 99159 1ockA 412 5.94e+01 c.117.1.1 86802 2cveA 191 5.95e+01 1cliA 345 5.96e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1x84A 189 5.96e+01 1uwkA 557 5.97e+01 e.51.1.1 108065 1vddA 228 5.98e+01 e.49.1.1 108519 1nox 205 5.99e+01 1nox d.90.1.1 40242 1euhA 475 6.00e+01 1euhA c.82.1.1 35369 1xg9A 260 6.04e+01 1gpl 432 6.08e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1g6uA 48 6.16e+01 1g6uA k.9.1.1 46425 1vk3A 615 6.22e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1bmfA 510 6.23e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1ao3A 187 6.23e+01 1atzA c.62.1.1 34134 1b35A 260 6.28e+01 1b35A b.121.4.1 23333 1t3qC 288 6.30e+01 d.87.2.1,d.145.1.3 106371,106372 1kdgA 546 6.31e+01 c.3.1.2,d.16.1.1 77337,77338 2fdrA 229 6.35e+01 1dp4A 435 6.36e+01 1dp4A c.93.1.1 35710 2fp7B 172 6.38e+01 1zbfA 142 6.43e+01 1f93E 32 6.49e+01 1f93E a.34.2.1 17013 1vlqA 337 6.50e+01 c.69.1.25 108848 1qi6A 475 6.55e+01 1euhA c.82.1.1 35373 1t0iA 191 6.58e+01 c.23.5.4 106209 1b3rA 431 6.63e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1ab3 88 6.76e+01 1a32 a.16.1.2 16395 1jbkA 195 6.77e+01 c.37.1.20 71631 1zbmA 280 6.83e+01 1nmtA 392 6.91e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1iukA 140 6.91e+01 c.2.1.8 83712 1b2wH 220 6.96e+01 1igtB b.1.1.1,b.1.1.2 20307,21299 2g64A 140 6.98e+01 1uv7A 110 7.00e+01 d.67.4.1 100040 1oi1A 221 7.02e+01 b.34.9.3,b.34.9.3 87037,87038 1swvA 267 7.13e+01 1cs1A 386 7.16e+01 1ibjA c.67.1.3 34399 1od5A 492 7.17e+01 b.82.1.2,b.82.1.2 86832,86833 1r0uA 148 7.19e+01 b.60.1.5 96741 2fvtA 135 7.19e+01 1az5 99 7.22e+01 1hvc b.50.1.1 26747 1wviA 257 7.22e+01 2gp4A 628 7.27e+01 2d0oA 610 7.31e+01 2a1kA 233 7.37e+01 1sxvA 172 7.43e+01 1rw7A 243 7.50e+01 c.23.16.2 97963 1fnsA 196 7.50e+01 1auq c.62.1.1 34136 1kum 108 7.52e+01 1kum b.3.1.1 22525 1hucA 47 7.54e+01 1hucA d.3.1.1 37049 1xvaA 292 7.56e+01 1xvaA c.66.1.5 34183 1e5mA 416 7.56e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1cs1C 386 7.61e+01 1ibjA c.67.1.3 34401 1tp6A 128 7.63e+01 d.17.4.12 107184 2g76A 335 7.63e+01 1rfa 79 7.74e+01 1c1yB d.15.1.5 37620 1f0lA 535 7.76e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 12e8H 221 7.80e+01 1igtB b.1.1.1,b.1.1.2 20269,21269 1jvwA 167 7.80e+01 d.26.1.1 71907 1iy8A 267 7.86e+01 c.2.1.2 83774 1ixcA 294 7.87e+01 a.4.5.37,c.94.1.1 83764,83765 1x0tA 120 7.95e+01 1d0dA 60 8.03e+01 1kigI g.8.1.2 44566 1y0yA 353 8.03e+01 1z96A 40 8.07e+01 2bibA 547 8.11e+01 1a8vA 121 8.15e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1atzA 189 8.17e+01 1atzA c.62.1.1 34132 1mgtA 174 8.19e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1uarA 285 8.19e+01 c.46.1.2,c.46.1.2 107762,107763 1r2mA 71 8.31e+01 b.138.1.1 96871 1wvqA 167 8.41e+01 1x8mA 288 8.42e+01 b.82.1.13 109516 1lmeA 176 8.44e+01 d.167.1.1 84629 1aj6 219 8.47e+01 1aj6 d.122.1.2 41106 1rliA 184 8.69e+01 c.23.5.6 97647 1fe8A 196 8.69e+01 1atzA c.62.1.1 59783 2cy0A 263 8.73e+01 1sco 38 8.96e+01 1sco g.3.7.2 44164 1jyeA 349 8.99e+01 c.93.1.1 67455