# List of top-scoring protein chains for t2k-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 1vgvA 384 1.96e-01 c.87.1.3 100608 1sffA 426 2.85e-01 c.67.1.4 105482 1mrg 263 5.75e-01 1mrj d.165.1.1 42183 1ceo 343 1.59e+00 1ceo c.1.8.3 28808 1r1hA 696 1.97e+00 d.92.1.4 104756 1riqA 465 2.09e+00 a.203.1.1,d.104.1.1 97516,97517 1o70A 324 2.36e+00 b.118.1.1,b.118.1.1 81115,81116 1d7uA 433 2.39e+00 2dkb c.67.1.4 34439 1musA 477 3.08e+00 c.55.3.4 79494 1arzC 273 3.17e+00 1drw c.2.1.3,d.81.1.3 30061,39976 1a2xA 159 3.26e+00 1ncx a.39.1.5 17251 1eulA 994 3.39e+00 1eulA 1e3aB 560 3.44e+00 1ajqB 1d9tA 289 3.58e+00 1deaA 2cw6A 298 3.58e+00 1ne7A 289 3.59e+00 c.124.1.1 91833 1wiwA 290 3.59e+00 1cviA 342 3.67e+00 1cviA c.60.1.2 33989 1hbnB 442 4.07e+00 1mroB a.89.1.1,d.58.31.2 60900,60901 1mroB 442 4.77e+00 1mroB a.89.1.1,d.58.31.2 18531,39449 1gt91 357 4.92e+00 1e2uA 553 4.93e+00 1e1dA e.26.1.1 43362 1wmbA 260 4.99e+00 1i1hA 219 5.15e+00 1f2vA c.23.17.1 61530 1vjpA 394 5.49e+00 c.2.1.3,d.81.1.3 100828,100829 1lf6A 684 5.77e+00 a.102.1.5,b.30.5.5 77918,77919 2bjfA 329 5.97e+00 1mqeA 207 6.07e+00 d.113.1.1 91394 1tp9A 162 6.08e+00 1t1gA 364 6.45e+00 c.41.1.2 106246 1ex1A 605 6.64e+00 1ex1A c.1.8.7,c.23.11.1 29013,31347 1j4aA 333 7.03e+00 c.2.1.4,c.23.12.1 71502,71503 1ofhA 310 7.17e+00 c.37.1.20 86948 1fwcC 567 7.25e+00 1ubpC b.92.1.1,c.1.9.2 28410,29032 1cfyA 143 7.32e+00 1cof d.109.1.2 40858 1fe8A 196 7.33e+00 1atzA c.62.1.1 59783 1b1yA 500 7.88e+00 1byb c.1.8.1 28796 1elyA 449 7.91e+00 1b8jA c.76.1.1 35028 1fcjA 322 8.01e+00 1oasA c.79.1.1 35289 1gwcA 230 8.40e+00 a.45.1.1,c.47.1.5 70660,70661 1yy7A 213 8.54e+00 2b6nA 278 8.69e+00 1eexB 224 8.78e+00 1dioB c.51.3.1 33213 1j7nA 776 9.01e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1ncx 162 9.16e+00 1ncx a.39.1.5 17222 1xfdA 723 9.18e+00 1d8cA 723 9.28e+00 1d8cA c.1.13.1 29325 2dkb 433 9.31e+00 2dkb c.67.1.4 34438 1h1nA 305 9.54e+00 c.1.8.3 70855 1q59A 172 9.74e+00 f.1.4.1 95881 1bf2 750 9.77e+00 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1nksA 194 9.79e+00 1nksA c.37.1.1 31886 1d2kA 392 1.00e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1whsA 255 1.01e+01 1ivyA c.69.1.5 34649 2c1vA 338 1.04e+01 1e4mM 501 1.10e+01 1e70M c.1.8.4 59226 2fymA 431 1.12e+01 1wpgA 994 1.14e+01 1a0eA 443 1.15e+01 1a0cA c.1.15.3 29537 1eetA 557 1.15e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1gr0A 367 1.15e+01 c.2.1.3,d.81.1.3 70379,70380 1y1xA 191 1.16e+01 1eejA 216 1.17e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1akaA 401 1.18e+01 1ajsA c.67.1.1 34258 2az4A 429 1.18e+01 1xdwA 331 1.20e+01 7aatA 401 1.26e+01 1ajsA c.67.1.1 34250 1v58A 241 1.26e+01 c.47.1.9,d.17.3.1 108371,108372 2gnoA 305 1.26e+01 1d0yA 761 1.28e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1r6uA 437 1.32e+01 c.26.1.1 97163 1m0qA 433 1.35e+01 c.67.1.4 78350 1wd7A 261 1.36e+01 1osa 148 1.38e+01 1cll a.39.1.5 17300 2d2jA 329 1.38e+01 1w98B 283 1.39e+01 1fnb 314 1.40e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1ihuA 589 1.42e+01 c.37.1.10,c.37.1.10 62394,62395 1dioA 554 1.43e+01 1dioA c.1.19.3 29656 1wlgA 299 1.45e+01 1hyoA 421 1.47e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1g0uG 252 1.47e+01 d.153.1.4 41952 1jvnA 555 1.48e+01 c.1.2.1,c.23.16.1 67355,67356 1lehA 364 1.48e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1eu8A 409 1.53e+01 1eu8A c.94.1.1 59502 1yrgB 385 1.55e+01 1yrgA c.10.1.2 30855 1a9xB 379 1.61e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1xx1A 285 1.66e+01 1dmtA 696 1.66e+01 1dmtA d.92.1.4 40296 1a5mC 566 1.66e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 2bgzA 299 1.67e+01 2ftwA 521 1.74e+01 2b4gA 317 1.74e+01 1a05A 358 1.75e+01 1cnzA c.77.1.1 35059 1d8dB 437 1.76e+01 1ft1B a.102.4.3 18866 1g0dA 695 1.76e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1tml 286 1.78e+01 1tml c.6.1.1 30656 1ea7A 310 1.79e+01 c.41.1.1 70086 1csc 433 1.80e+01 1csh a.103.1.1 18886 1wl4A 397 1.82e+01 2gnpA 266 1.83e+01 1t94A 459 1.85e+01 d.240.1.1,e.8.1.7 106701,106702 1cjaA 342 1.86e+01 1cjaA d.144.1.3 41708 1w6tA 444 1.90e+01 1quvA 578 1.92e+01 1quvA e.8.1.4 43119 1gk9B 557 1.96e+01 1ajqB 557 1.97e+01 1ajqB 1jnrA 643 1.98e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1kqfA 1015 1.99e+01 b.52.2.2,c.81.1.1 72871,72872 1exrA 148 2.01e+01 1cll a.39.1.5 17299 1l5aA 436 2.01e+01 c.43.1.2,c.43.1.2 75923,75924 1fdi 715 2.04e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1glqA 209 2.07e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 1dnlA 199 2.07e+01 1ci0A b.45.1.1 25753 1g8oA 310 2.08e+01 1g8oA c.68.1.9 60375 1e6qM 501 2.08e+01 1e70M c.1.8.4 28920 2gupA 292 2.13e+01 2avnA 260 2.13e+01 1twuA 139 2.15e+01 d.32.1.8 107413 1ct9A 553 2.16e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1gm7B 557 2.16e+01 1spa 396 2.19e+01 1ajsA c.67.1.1 34291 1ll7A 392 2.19e+01 c.1.8.5,d.26.3.1 78085,78086 1pg4A 652 2.21e+01 e.23.1.1 88067 1vkhA 273 2.21e+01 c.69.1.32 108662 1p80A 753 2.26e+01 c.23.16.3,e.5.1.1 94337,94338 1de4C 640 2.29e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1yc5A 246 2.35e+01 1c14A 262 2.38e+01 1eny c.2.1.2 29927 1aisA 182 2.39e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1nouA 507 2.46e+01 c.1.8.6,d.92.2.1 85932,85933 1zvkA 358 2.51e+01 1auiB 169 2.53e+01 1auiB a.39.1.5 17325 1p30A 952 2.58e+01 b.121.2.2,b.121.2.2 93964,93965 1dgsA 667 2.61e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1m5eA 263 2.61e+01 c.94.1.1 78642 1yu3A 381 2.65e+01 2acvA 463 2.67e+01 1e7wA 291 2.69e+01 c.2.1.2 59373 1preB 470 2.71e+01 1preA d.169.1.2,f.8.1.1 42438,43825 1o0uA 429 2.74e+01 c.118.1.1 80743 1wdkC 390 2.74e+01 c.95.1.1,c.95.1.1 109258,109259 1vixA 420 2.76e+01 c.56.5.4,d.58.19.1 100777,100778 1ta8A 332 2.79e+01 1bgp 309 2.87e+01 1bgp a.93.1.1 18690 1st9A 143 2.89e+01 c.47.1.10 98987 2ff4A 388 2.91e+01 1lrzA 426 2.92e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1a36A 592 2.93e+01 1a36A a.2.8.1,d.163.1.2,e.15.1.1 15715,42173,43266 1kssA 571 2.99e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1l9kA 305 3.00e+01 c.66.1.25 84569 1zk7A 467 3.02e+01 1is1A 185 3.02e+01 d.67.3.1 83704 1otsA 465 3.03e+01 f.20.1.1 87415 1hjxA 362 3.06e+01 c.1.8.5,d.26.3.1 83512,83513 1h3qA 140 3.07e+01 d.110.4.3 76652 1jzuA 157 3.07e+01 b.60.1.1 84271 1zy9A 564 3.09e+01 2a74A 643 3.09e+01 1o7tA 309 3.10e+01 c.94.1.1 86645 2bodX 286 3.14e+01 1gm9B 557 3.16e+01 1hmvA 560 3.17e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1rypL 212 3.21e+01 d.153.1.4 41880 1uiuA 502 3.25e+01 c.94.1.1 99434 2ak3A 226 3.26e+01 1zin c.37.1.1,g.41.2.1 31892,45193 2gz4A 207 3.30e+01 2fjbA 643 3.38e+01 1j7dA 145 3.41e+01 1jatB d.20.1.1 62680 1lopA 164 3.44e+01 2cpl b.62.1.1 27510 1bunA 120 3.47e+01 1poa a.133.1.2 19614 1iyxA 432 3.49e+01 c.1.11.1,d.54.1.1 83815,83816 1ju2A 536 3.53e+01 c.3.1.2,d.16.1.1 77169,77170 1f0kA 364 3.55e+01 1f0kA c.87.1.2 35465 1qysA 106 3.59e+01 k.41.1.1 96603 1wb0A 445 3.60e+01 1w79A 489 3.62e+01 1ak0 270 3.62e+01 1ak0 a.124.1.2 19345 1xv5A 401 3.64e+01 2b30A 301 3.64e+01 1olsA 400 3.68e+01 c.36.1.11 93331 1w9pA 433 3.68e+01 1x0rA 249 3.69e+01 2b0tA 738 3.71e+01 1orvA 728 3.73e+01 b.70.3.1,c.69.1.24 87354,87355 1k4vA 289 3.73e+01 c.68.1.9 72066 1gpeA 587 3.90e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1ta9A 450 3.98e+01 1ht6A 405 4.00e+01 b.71.1.1,c.1.8.1 83629,83630 1b8jA 449 4.01e+01 1b8jA c.76.1.1 34992 1m2kA 249 4.02e+01 c.31.1.5 84754 1c3oG 1073 4.02e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1gdoB 240 4.04e+01 1gdoA 1ebdA 455 4.07e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 2bg9A 370 4.08e+01 1zp4A 304 4.09e+01 1g5aA 628 4.11e+01 b.71.1.1,c.1.8.1 65152,65153 1rz2A 254 4.12e+01 b.100.1.1 105130 1e9lA 377 4.12e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1n93X 375 4.12e+01 a.206.1.1 91707 1o7jA 327 4.12e+01 c.88.1.1 81140 1jq5A 370 4.13e+01 e.22.1.2 67084 1oyeA 1049 4.21e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1gkfB 557 4.23e+01 1hqsA 423 4.24e+01 1iso c.77.1.1 61154 1eexA 554 4.29e+01 1dioA c.1.19.3 29650 1o7xB 377 4.30e+01 a.103.1.1 81172 1fobA 334 4.30e+01 c.1.8.3 83255 1j09A 468 4.33e+01 a.97.1.1,c.26.1.1 77025,77026 1zxiF 288 4.34e+01 1e39A 571 4.34e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1zcdA 388 4.36e+01 2aamA 309 4.39e+01 1lg2A 365 4.41e+01 c.1.8.5,d.26.3.1 77950,77951 1t3bA 211 4.44e+01 c.47.1.9,d.17.3.1 106341,106342 1kz8A 337 4.47e+01 e.7.1.1 77633 1o7fA 469 4.48e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1i1kA 309 4.48e+01 1daaA e.17.1.1 61533 1yuwA 554 4.50e+01 1imdA 277 4.54e+01 1imbA e.7.1.1 42968 1c0dA 358 4.61e+01 1eceA c.1.8.3 28815 1vlmA 219 4.64e+01 c.66.1.41 108836 6cts 433 4.66e+01 1csh a.103.1.1 18891 1c3oC 1073 4.70e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1qhsA 178 4.73e+01 1qhsA c.37.1.3 31938 1qj2C 285 4.73e+01 1qj2C 2af6A 258 4.76e+01 1eg3A 261 4.80e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 2es7A 142 4.83e+01 1n62C 288 4.84e+01 d.87.2.1,d.145.1.3 80094,80095 1kqfB 294 4.87e+01 d.58.1.5,f.23.22.1 75900,75901 1k2xB 143 4.95e+01 1xrsA 516 4.99e+01 1cs1C 386 5.00e+01 1ibjA c.67.1.3 34401 1fgxA 288 5.02e+01 1fgxA c.68.1.2 34508 1f1sA 814 5.03e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1gjuA 637 5.04e+01 b.71.1.1,c.1.8.1 60580,60581 1xd8A 289 5.07e+01 2fh5A 185 5.09e+01 1dqyA 283 5.09e+01 1dqyA c.69.1.3 34640 1d8vA 263 5.14e+01 1mrj d.165.1.1 42193 1qapA 296 5.24e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1l5oA 356 5.26e+01 c.39.1.1 77711 1g0u1 266 5.30e+01 1ohvA 472 5.31e+01 c.67.1.4 93031 1qcrC 378 5.36e+01 1be3C f.32.1.1,f.21.1.2 75931,75932 1ri6A 343 5.38e+01 b.69.11.1 97503 1mqoA 227 5.40e+01 d.157.1.1 103846 3pbgA 468 5.42e+01 1e70M c.1.8.4 28951 2dbqA 334 5.42e+01 1ozhA 566 5.47e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1qjdA 571 5.47e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1g3kA 174 5.51e+01 1nedA d.153.1.4 41989 2d5cA 263 5.51e+01 1a3yA 149 5.54e+01 1obpA b.60.1.1 27110 1nrjA 158 5.57e+01 d.110.4.4 86124 1dqzA 280 5.59e+01 1dqyA c.69.1.3 34638 1nf2A 268 5.59e+01 c.108.1.10 91849 1jqbA 351 5.59e+01 b.35.1.2,c.2.1.1 77151,77152 1d5rA 324 5.61e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1sauA 115 5.62e+01 1kijA 390 5.64e+01 d.14.1.3,d.122.1.2 72514,72515 1oz2A 331 5.68e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1iyeA 309 5.69e+01 e.17.1.1 83786 1rqwA 207 5.72e+01 b.25.1.1 97781 1jf0A 195 5.77e+01 1ej3A a.39.1.5 62926 1apyB 141 5.77e+01 1apyB 1u0mA 382 5.79e+01 c.95.1.2,c.95.1.2 107557,107558 1mixA 206 5.79e+01 a.11.2.1,b.55.1.5 79166,79167 1qg6A 261 5.80e+01 1eny c.2.1.2 29919 1sxgA 280 5.83e+01 1ve4A 206 5.88e+01 2cvzA 289 5.92e+01 1dioB 224 6.00e+01 1dioB c.51.3.1 33219 1f3iA 481 6.00e+01 1b7eA 1tn4 159 6.02e+01 1ncx a.39.1.5 17248 1igwA 434 6.03e+01 c.1.12.7 62370 1vioA 243 6.12e+01 d.265.1.3,d.66.1.5 100762,100763 1skoA 143 6.13e+01 d.110.7.1 105676 2bogX 286 6.22e+01 1xhcA 367 6.27e+01 1jqiA 388 6.28e+01 a.29.3.1,e.6.1.1 67087,67088 1wyuA 438 6.30e+01 1dctA 324 6.30e+01 6mhtA c.66.1.26 34244 2aop 497 6.32e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1gox 370 6.32e+01 1gox c.1.4.1 28607 1ejxC 567 6.33e+01 b.92.1.1,c.1.9.2 83184,83185 1vjfA 180 6.34e+01 d.116.1.1 100809 1xfkA 336 6.34e+01 1iejA 332 6.36e+01 1nnt c.94.1.2 62328 2bcqA 335 6.36e+01 1xaa 345 6.38e+01 1cnzA c.77.1.1 35033 1ay0A 680 6.41e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31823,31824,33100 1gwuA 309 6.41e+01 a.93.1.1 83351 1aop 497 6.46e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 2fbqA 235 6.53e+01 1k4iA 233 6.58e+01 d.115.1.2 72056 1htqA 477 6.59e+01 d.15.9.1,d.128.1.1 71035,71036 1csjA 531 6.66e+01 1quvA e.8.1.4 43120 1el3A 316 6.73e+01 1frb c.1.7.1 28672 1a88A 275 6.75e+01 1brt c.69.1.12 34707 1y3nA 490 6.78e+01 1pn0A 665 6.83e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1n8kA 374 6.84e+01 b.35.1.2,c.2.1.1 80298,80299 1wxdA 263 6.88e+01 1a8d 452 6.88e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1rthA 560 6.91e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1a8e 329 6.91e+01 1cb6A 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