# List of top-scoring protein chains for t04-100-30-n_notor2-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 2fikA 287 1.57e-01 b.1.1.2,d.19.1.1 133524,133525 1a48 306 2.95e-01 1a48 1d8cA 723 3.83e-01 1d8cA c.1.13.1 29325 1vb3A 428 4.23e-01 c.79.1.1 119942 1jchA 551 4.39e-01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1lwjA 441 4.70e-01 b.71.1.1,c.1.8.1 74303,74304 1lycA 343 6.36e-01 a.93.1.1 74344 2ck3A 510 7.25e-01 1yuwA 554 8.06e-01 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 1zk7A 467 8.17e-01 2gu3A 136 9.62e-01 1h8eA 510 1.10e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1ihuA 589 1.10e+00 c.37.1.10,c.37.1.10 62394,62395 1a9xA 1058 1.30e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1jclA 260 1.30e+00 c.1.10.1 66501 2ajfA 597 1.35e+00 d.92.1.5 126882 1sat 471 1.44e+00 1sat 1pxzA 346 1.52e+00 b.80.1.1 111643 1a9xB 379 1.67e+00 1c3oB c.8.3.1,c.23.16.1 30732,31409 1de4C 640 1.71e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1k0wA 231 1.84e+00 c.74.1.1 77220 1xqoA 256 1.85e+00 a.96.1.6 115853 1xahA 354 2.23e+00 1wpgA 994 2.40e+00 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 114806,114807,114808,114809 1m65A 245 2.46e+00 c.6.3.1 84847 3proC 166 2.84e+00 3proC d.52.1.1,d.52.1.1 38812,38813 2cxaA 256 3.00e+00 d.108.1.6 130993 1xh9A 350 3.30e+00 1nrlA 316 3.33e+00 a.123.1.1 92091 2gx9A 129 3.36e+00 d.299.1.1 135828 1ia8A 289 3.41e+00 1ia8A d.144.1.7 62112 1ym5A 300 3.42e+00 1vemA 516 3.44e+00 b.3.1.1,c.1.8.1 120021,120022 1xsjA 778 3.51e+00 b.150.1.1,b.30.5.11,b.71.1.4,c.1.8.13 115951,115952,115953,115954 1wmxA 205 3.51e+00 b.18.1.24 109418 1wlsA 328 3.59e+00 1ohtA 215 3.63e+00 d.118.1.1 87036 2ftwA 521 3.69e+00 b.92.1.3,c.1.9.6 134083,134084 1kutA 230 3.83e+00 d.143.1.1 73017 2bp1A 360 3.97e+00 1jsdB 176 4.08e+00 h.3.1.1 63259 1cs0A 1073 4.09e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1lci 550 4.10e+00 1lci 1itcA 516 4.11e+00 b.3.1.1,c.1.8.1 83705,83706 1bn8A 420 4.18e+00 1pcl b.80.1.1 28022 1qwzA 235 4.21e+00 b.100.1.1 96510 1rg9A 383 4.22e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1pprM 312 4.32e+00 1pprM a.131.1.1,a.131.1.1 19502,19503 1hr6B 443 4.57e+00 1be3A d.185.1.1,d.185.1.1 61166,61167 1vp4A 425 4.62e+00 c.67.1.1 113935 1uanA 227 4.80e+00 c.134.1.1 99135 2f2hA 773 5.00e+00 b.150.1.1,b.30.5.11,b.71.1.4,c.1.8.13 132818,132819,132820,132821 1a0cA 438 5.48e+00 1a0cA c.1.15.3 29529 2c46A 241 5.53e+00 1zbfA 142 5.69e+00 c.55.3.1 124850 1b4vA 504 5.70e+00 1b8sA c.3.1.2,d.16.1.1 30334,37865 1t6sA 162 5.71e+00 a.4.5.60,a.4.5.60 112271,112272 1aoa 275 5.96e+00 1aoa 1yspA 181 6.20e+00 1p1xA 260 6.23e+00 c.1.10.1 104060 1sflA 238 6.25e+00 c.1.10.1 112077 1vm7A 311 6.33e+00 c.72.1.1 108884 1jvsA 400 6.45e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1xfkA 336 6.72e+00 c.42.1.1 115264 1kwgA 645 7.02e+00 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1eu8A 409 7.07e+00 1eu8A c.94.1.1 59502 1e79A 510 7.08e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1auiB 169 7.20e+00 1auiB a.39.1.5 17325 2fuvA 549 7.20e+00 2iu5A 195 7.40e+00 1v4vA 376 7.59e+00 c.87.1.3 100313 1wyuB 474 8.03e+00 c.67.1.7 121453 1ps9A 671 8.03e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1gr0A 367 8.05e+00 c.2.1.3,d.81.1.3 70379,70380 1xd8A 289 8.06e+00 1hlrA 907 8.18e+00 1azo 232 8.18e+00 1azo 2boqA 331 8.36e+00 2aamA 309 8.38e+00 c.1.8.15 126489 2bhuA 602 8.55e+00 b.1.18.2,b.71.1.1,c.1.8.1 128554,128555,128556 1vlbA 907 8.58e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 2reb 352 8.64e+00 2reb 1v0eA 666 8.64e+00 b.68.1.2,b.108.1.3 113466,113467 1xl7A 612 8.75e+00 c.43.1.3,c.43.1.3 115438,115439 1a88A 275 9.05e+00 1brt c.69.1.12 34707 1dkiA 371 9.36e+00 1dkiA d.3.1.1 37090 1b0pA 1231 9.41e+00 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1eexA 554 9.53e+00 1dioA c.1.19.3 29650 1eexG 173 9.63e+00 1dioG a.23.2.1 16490 1k28A 584 9.66e+00 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 2gnqA 336 9.74e+00 1gjjA 168 9.88e+00 a.140.1.1,a.140.1.1 83291,83292 1vkmA 297 1.02e+01 c.138.1.1 108670 1ea7A 310 1.05e+01 c.41.1.1 70086 2c07A 285 1.05e+01 c.2.1.2 129577 1gt91 357 1.05e+01 1ohvA 472 1.06e+01 c.67.1.4 93031 1gt1A 159 1.09e+01 b.60.1.1 90515 1k0fA 277 1.09e+01 c.92.2.2 71974 1hw7A 255 1.10e+01 1i7fA d.193.1.1 61297 1zvkA 358 1.11e+01 2az4A 429 1.11e+01 d.157.1.10 127597 1e0tA 470 1.12e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1is1A 185 1.16e+01 d.67.3.1 83704 1vyoA 128 1.17e+01 1xwfA 431 1.17e+01 c.2.1.4,c.23.12.3 122392,122393 2cn3A 737 1.18e+01 1pl8A 356 1.18e+01 b.35.1.2,c.2.1.1 94878,94879 1ir3A 306 1.19e+01 1fmk d.144.1.7 41702 1avaA 403 1.20e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 1q0sA 259 1.20e+01 c.66.1.28 95509 1e2wA 251 1.21e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1hnnA 282 1.22e+01 c.66.1.15 65895 1blxA 326 1.23e+01 1hcl d.144.1.7 41596 1xovA 326 1.23e+01 b.34.11.4,c.56.5.6 122206,122207 1hn2A 159 1.23e+01 b.60.1.1 65890 1ad2 228 1.25e+01 1ad2 1ffyA 917 1.26e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 2b4gA 317 1.27e+01 c.1.4.1 127829 1n35A 1267 1.30e+01 e.8.1.4 79935 1914 232 1.30e+01 1914 1bbpA 173 1.37e+01 1bbpA b.60.1.1 27147 1xeoA 168 1.39e+01 d.167.1.1 121913 1d0yA 761 1.39e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1cauB 184 1.40e+01 1caxB b.82.1.2 28103 1o7jA 327 1.40e+01 c.88.1.1 81140 1puiA 210 1.42e+01 c.37.1.8 88292 1m2kA 249 1.43e+01 c.31.1.5 84754 2liv 344 1.44e+01 2liv 1qtrA 317 1.47e+01 1qtrA c.69.1.7 34660 1l0qA 391 1.49e+01 b.1.3.1,b.69.2.3 77644,77645 1ayx 492 1.50e+01 1ayx 2fbaA 492 1.53e+01 a.102.1.1 133239 1aisA 182 1.53e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1g5aA 628 1.55e+01 b.71.1.1,c.1.8.1 65152,65153 2bvfA 459 1.56e+01 1odzA 386 1.58e+01 c.1.8.3 86889 1a99A 344 1.61e+01 1pot c.94.1.1 35812 1bhe 376 1.61e+01 1bhe 1zxzA 197 1.62e+01 1qr6A 584 1.63e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 2eu9A 355 1.63e+01 1qf5A 431 1.64e+01 1adeA c.37.1.10 32212 1n7hA 381 1.64e+01 c.2.1.2 80250 1bg6 359 1.64e+01 1bg6 1zk4A 251 1.66e+01 c.2.1.2 125176 1ll7A 392 1.66e+01 c.1.8.5,d.26.3.1 78085,78086 1pv6A 417 1.68e+01 f.38.1.2 95151 1j96A 323 1.74e+01 c.1.7.1 71616 1e4yA 214 1.75e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1wruA 379 1.77e+01 1n8fA 350 1.79e+01 c.1.10.4 85397 1itwA 741 1.79e+01 c.77.1.2 76793 1j9yA 385 1.80e+01 1j9yA c.1.8.3 62791 1phk 298 1.81e+01 1cdkA 1c4zA 358 1.81e+01 1c4zA d.148.1.1 41766 1fobA 334 1.81e+01 c.1.8.3 83255 1hyoA 421 1.83e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1g2aA 168 1.85e+01 d.167.1.1 65109 1tx4A 198 1.87e+01 1tx4A a.116.1.1 19098 1gzcA 239 1.89e+01 b.29.1.1 70803 1ry9A 145 1.89e+01 d.198.1.1 98094 1bcpD 110 1.90e+01 1bcpD b.40.2.1 25132 1nbwB 117 1.91e+01 c.51.3.2 80396 1vcvA 226 1.91e+01 c.1.10.1 119988 2g5cA 281 1.92e+01 a.100.1.12,c.2.1.6 134646,134647 1vlaA 150 1.93e+01 d.227.1.2 108735 1qcsA 211 1.94e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1d2kA 392 1.96e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1hxs1 302 1.97e+01 1bf6A 291 1.97e+01 1pscA c.1.9.3 29065 1xgsA 295 2.00e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1g5hA 454 2.03e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1fcdA 401 2.05e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 2c1vA 338 2.05e+01 1m5wA 243 2.06e+01 c.1.24.1 84836 1dkzA 219 2.07e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1ex0A 731 2.07e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ecfA 504 2.07e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2bjbA 462 2.08e+01 1ztpA 251 2.13e+01 d.86.1.2 125649 1vclA 432 2.15e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 2fw2A 260 2.16e+01 c.14.1.3 134231 1a65A 504 2.16e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2cvzA 289 2.17e+01 a.100.1.1,c.2.1.6 130890,130891 1s6cA 183 2.19e+01 a.39.1.5 98594 1qmvA 197 2.19e+01 1qq2A c.47.1.10 33066 1ax0 239 2.20e+01 1led 2f9lA 199 2.23e+01 c.37.1.8 133166 1z5vA 474 2.23e+01 1k2xB 143 2.23e+01 1eg7A 557 2.25e+01 1eg7A c.37.1.10 32241 1vybA 238 2.27e+01 d.151.1.1 108897 1kqfB 294 2.28e+01 d.58.1.5,f.23.22.1 75900,75901 1yydA 357 2.29e+01 a.93.1.1 124212 1n4wA 504 2.30e+01 c.3.1.2,d.16.1.1 91676,91677 2ajrA 331 2.30e+01 c.72.1.1 126892 1tr0A 108 2.33e+01 d.58.4.4 107261 1zq1C 633 2.35e+01 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 1l8nA 679 2.37e+01 c.1.8.10,d.92.2.2 84564,84565 1f4qA 165 2.37e+01 1alvA a.39.1.8 17360 1l5oA 356 2.41e+01 c.39.1.1 77711 1fy7A 278 2.42e+01 1fy7A d.108.1.1 40817 1v33A 366 2.44e+01 d.264.1.1 100278 1wcqA 601 2.47e+01 b.1.18.2,b.18.1.1,b.68.1.1 120894,120895,120896 1mzjA 339 2.49e+01 c.95.1.2,c.95.1.2 79700,79701 1wd7A 261 2.50e+01 c.113.1.1 114526 2g0wA 296 2.50e+01 c.1.15.4 134503 1x42A 232 2.51e+01 c.108.1.1 121677 1ohlA 342 2.52e+01 c.1.10.3 87035 1efyA 350 2.54e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1bs4A 168 2.55e+01 1bs4A d.167.1.1 42287 2b81A 323 2.55e+01 1zcjA 463 2.56e+01 1p57B 255 2.56e+01 b.47.1.2 94126 1hh1A 143 2.57e+01 1gefA c.52.1.18 61036 1uasA 362 2.58e+01 b.71.1.1,c.1.8.1 88388,88389 1usyA 275 2.59e+01 d.104.1.1 113422 2ezvA 269 2.59e+01 1hkkA 364 2.67e+01 c.1.8.5,d.26.3.1 90634,90635 1gox 370 2.68e+01 1gox 1hjxA 362 2.70e+01 c.1.8.5,d.26.3.1 83512,83513 1icpA 376 2.70e+01 1oyc c.1.4.1 62270 1wb0A 445 2.71e+01 c.1.8.5,d.26.3.1 120825,120826 1v93A 296 2.72e+01 c.1.23.1 100532 1hyuA 521 2.72e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1wpoA 256 2.74e+01 1lay b.57.1.1 27012 1mroB 442 2.76e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1sh7A 284 2.79e+01 1sh8A 154 2.80e+01 d.38.1.5 105549 1sqjA 789 2.81e+01 b.69.13.1,b.69.13.1 105918,105919 1ox0A 430 2.81e+01 c.95.1.1,c.95.1.1 87495,87496 1q7lA 198 2.83e+01 c.56.5.4 96044 1gof 639 2.86e+01 1gof 1cnzA 363 2.87e+01 1cnzA c.77.1.1 35061 1xwl 580 2.87e+01 1xwl 1xviA 275 2.87e+01 c.108.1.10 116088 1r8gA 372 2.88e+01 d.128.1.3 104845 1musA 477 2.91e+01 c.55.3.4 79494 1c1lA 136 2.91e+01 1c1lA b.29.1.3 24219 1hm9A 468 2.91e+01 b.81.1.4,c.68.1.5 65866,65867 1djxB 624 2.92e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1fm0E 150 2.94e+01 1fmaE d.41.5.1 38629 1ct9A 553 2.94e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1ty0A 211 2.96e+01 b.40.2.2,d.15.6.1 107440,107441 1id1A 153 2.98e+01 1id1A c.2.1.9 62286 2sas 185 2.98e+01 2sas 1cb0A 283 2.98e+01 1cb0A c.56.2.1 33790 1y6hA 177 3.00e+01 d.167.1.1 116505 1div 149 3.01e+01 1div 1cid 177 3.02e+01 1cid 1n91A 108 3.04e+01 d.206.1.1 80326 1g9gA 629 3.04e+01 a.102.1.2 83279 1sqgA 429 3.07e+01 a.79.1.3,c.66.1.38 105912,105913 1fohA 664 3.10e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1u1wA 298 3.10e+01 d.21.1.2,d.21.1.2 112957,112958 1sjiA 350 3.12e+01 1ux6A 350 3.12e+01 b.29.1.16,g.75.1.1 100145,100146 1ftrA 296 3.12e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1ykhB 132 3.16e+01 a.252.1.1 123519 3tmkA 216 3.18e+01 3tmkA c.37.1.1 31920 1sc3A 178 3.19e+01 c.17.1.1 105416 1zcoA 262 3.20e+01 1fit 147 3.22e+01 1fit 2gnoA 305 3.24e+01 a.80.1.1,c.37.1.20 135414,135415 1p1mA 406 3.25e+01 b.92.1.4,c.1.9.9 87696,87697 1zh5A 195 3.25e+01 a.4.5.46,d.58.7.1 125073,125074 1rqbA 539 3.28e+01 a.5.7.2,c.1.10.5 105057,105058 1q0qA 406 3.29e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1edzA 320 3.30e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 2a6hD 1524 3.30e+01 e.29.1.2 126265 1n67A 359 3.33e+01 b.2.3.4,b.2.3.4 85354,85355 1vl2A 421 3.33e+01 c.26.2.1,d.210.1.1 108708,108709 1ndh 272 3.34e+01 1ndh 2cw6A 298 3.34e+01 1xv2A 237 3.34e+01 d.290.1.1 116076 1oi7A 288 3.35e+01 c.2.1.8,c.23.4.1 87049,87050 1hzdA 272 3.40e+01 c.14.1.3 65969 1l9kA 305 3.41e+01 c.66.1.25 84569 2nr1 27 3.42e+01 1gxjA 186 3.43e+01 d.215.1.1 70707 1w78A 422 3.43e+01 1kwaA 88 3.44e+01 1kwaA b.36.1.1 24772 1q7fA 286 3.45e+01 b.68.9.1 96036 1apyB 141 3.46e+01 1apyB 1p3jA 217 3.49e+01 c.37.1.1,g.41.2.1 94022,94023 1rq2A 382 3.50e+01 c.32.1.1,d.79.2.1 105048,105049 1xkpC 143 3.51e+01 d.198.1.1 122088 1gq6A 313 3.52e+01 c.42.1.1 70341 1w53A 84 3.53e+01 a.186.1.2 109175 1g71A 347 3.57e+01 1g71A d.264.1.1 43268 2biqA 219 3.58e+01 1wbiA 129 3.59e+01 1p1jA 533 3.59e+01 c.2.1.3,d.81.1.3 87687,87688 1z3eB 73 3.62e+01 a.60.3.1 124401 1q4rA 112 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