# 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 1lkxA 697 2.53e-01 c.37.1.9 73981 1nnfA 309 2.74e-01 c.94.1.1 85903 1xc1A 309 3.66e-01 c.94.1.1 109543 1iyxA 432 3.70e-01 c.1.11.1,d.54.1.1 83815,83816 1o7tA 309 3.70e-01 c.94.1.1 86645 1w6tA 444 3.84e-01 1ak9 275 1.22e+00 1gci c.41.1.1 32517 1s01 283 1.44e+00 1gci c.41.1.1 32511 1l6sA 323 2.34e+00 c.1.10.3 73627 1aqn 275 2.44e+00 1gci c.41.1.1 32514 2av4A 162 2.89e+00 1gowA 489 2.95e+00 1qvbA c.1.8.4 28981 2ab5A 269 4.51e+00 1xpxA 163 4.76e+00 1kbqA 273 4.92e+00 c.23.5.3 68391 1fdd 106 5.05e+00 1a6l d.58.1.2 38960 1gefA 123 5.13e+00 1gefA c.52.1.18 60465 3minB 522 5.14e+00 1qguB c.92.2.3 35606 1qhbA 596 5.18e+00 1qhbA a.111.1.2 19055 1klnA 605 5.84e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1gycA 499 6.07e+00 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1uumA 372 6.21e+00 c.1.4.1 100010 1hzdA 272 6.54e+00 c.14.1.3 65969 2a67A 167 6.65e+00 1g0u1 266 6.69e+00 2vsgA 358 6.77e+00 2vsgA h.4.1.1 45780 1hqsA 423 6.96e+00 1iso c.77.1.1 61154 1liuA 528 7.16e+00 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 1cxlA 686 7.23e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1d4aA 273 7.38e+00 1d4aA c.23.5.3 31219 175lA 164 7.45e+00 1l92 d.2.1.3 36924 1w7jA 795 7.53e+00 1ats 386 7.75e+00 1ba1 c.55.1.1,c.55.1.1 33423,33424 1ox0A 430 7.77e+00 c.95.1.1,c.95.1.1 87495,87496 1nrfA 262 8.48e+00 e.3.1.1 92086 2dkaA 544 8.53e+00 1cdwA 179 8.64e+00 1ytbA d.129.1.1,d.129.1.1 41212,41213 1ow4A 129 8.87e+00 a.39.2.1 93628 1w1oA 534 9.65e+00 d.58.32.4,d.145.1.1 109071,109072 1f82A 424 1.05e+01 1f82A d.92.1.7 40307 1fo1A 271 1.09e+01 1fo1A c.10.2.3,d.58.7.2 30869,39213 1b5m 84 1.10e+01 1cyo d.120.1.1 41073 1mxgA 435 1.11e+01 b.71.1.1,c.1.8.1 85193,85194 1vfgA 390 1.12e+01 a.173.1.1,d.218.1.4 108570,108571 1bncB 449 1.14e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1kz8A 337 1.16e+01 e.7.1.1 77633 1sat 471 1.16e+01 1sat b.80.7.1,d.92.1.6 28014,40300 1v9mA 323 1.16e+01 f.40.1.1 100543 1z9tA 255 1.17e+01 1oe9A 795 1.19e+01 b.34.3.1,c.37.1.9 92792,92793 1mijA 152 1.23e+01 a.4.1.1 79150 2sas 185 1.30e+01 2sas a.39.1.5 17258 1ba1 386 1.30e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1hkkA 364 1.30e+01 c.1.8.5,d.26.3.1 90634,90635 6tmnE 316 1.32e+01 1hyt d.92.1.2 59071 1jmuB 666 1.36e+01 1d8wA 426 1.36e+01 1de5A c.1.15.2 29394 1rz2A 254 1.48e+01 b.100.1.1 105130 1hj9A 226 1.52e+01 b.47.1.2 65845 1vlyA 338 1.52e+01 b.44.2.1,d.250.1.1 108871,108872 1ypyA 184 1.53e+01 1fmk 452 1.53e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1yqfA 203 1.55e+01 1zbsA 291 1.56e+01 1d3gA 367 1.58e+01 1d3gA c.1.4.1 28600 1j79A 347 1.59e+01 1j79A c.1.9.4 62675 1wb0A 445 1.83e+01 1jchC 551 1.86e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1jchA 551 1.86e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1dzlA 505 1.87e+01 1dzlA b.121.6.1 23586 2gk9A 426 1.90e+01 1vpwA 340 1.91e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1c0pA 363 2.06e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2furA 209 2.06e+01 1arv 344 2.09e+01 1arv a.93.1.1 18590 1jftA 340 2.12e+01 a.35.1.5,c.93.1.1 66652,66653 1a16 440 2.13e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1lycA 343 2.17e+01 a.93.1.1 74344 1e4mM 501 2.24e+01 1e70M c.1.8.4 59226 1tluA 130 2.28e+01 d.156.1.2 107139 1hjxA 362 2.31e+01 c.1.8.5,d.26.3.1 83512,83513 2fymA 431 2.35e+01 1i19A 561 2.37e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1fnuA 221 2.39e+01 3seb b.40.2.2,d.15.6.1 25212,37801 1g0uG 252 2.39e+01 d.153.1.4 41952 1quvA 578 2.48e+01 1quvA e.8.1.4 43119 1tf4A 605 2.52e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 2a1kA 233 2.53e+01 2btfA 375 2.54e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1vkhA 273 2.56e+01 c.69.1.32 108662 1pl8A 356 2.58e+01 b.35.1.2,c.2.1.1 94878,94879 1e5uI 187 2.60e+01 1f00I b.1.14.1,d.169.1.3 22372,42441 1jilA 420 2.62e+01 c.26.1.1 66745 1zgmA 248 2.63e+01 1keeE 1073 2.63e+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 68508,68509,68510,68511,68512,68513 1ido 192 2.64e+01 1ido c.62.1.1 34139 1pvyA 227 2.74e+01 d.115.1.2 95195 1k28A 584 2.81e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1go8P 462 2.82e+01 b.80.7.1,d.92.1.6 76247,76248 1a0rP 245 2.84e+01 1b9yC c.47.1.6 33054 1y8qA 346 2.85e+01 1pe9A 361 2.85e+01 b.80.1.1 94595 1aru 344 2.86e+01 1arv a.93.1.1 18589 1e6qM 501 2.88e+01 1e70M c.1.8.4 28920 1rqbA 539 2.94e+01 a.5.7.2,c.1.10.5 105057,105058 1a1vA 476 2.98e+01 1heiA c.37.1.14,c.37.1.14 32467,32468 1d3hA 367 3.06e+01 1d3gA c.1.4.1 28601 1py5A 326 3.07e+01 d.144.1.7 104389 1br2A 791 3.15e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 2b59B 172 3.16e+01 1kqfB 294 3.18e+01 d.58.1.5,f.23.22.1 75900,75901 1l1qA 186 3.21e+01 c.61.1.1 77653 1b8pA 329 3.23e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1c3oE 1073 3.24e+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 18564,31493,31685,31686,41530,41531 3pgk 416 3.26e+01 16pk c.86.1.1 35451 1j8wB 273 3.26e+01 1nbwB 117 3.30e+01 c.51.3.2 80396 1wrvA 308 3.32e+01 1an9A 340 3.33e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1t3bA 211 3.34e+01 c.47.1.9,d.17.3.1 106341,106342 1zkpA 268 3.44e+01 1lam 484 3.45e+01 1lam c.50.1.1,c.56.5.3 33166,33829 2sak 121 3.46e+01 2sak d.15.5.1 37711 1tqnA 486 3.47e+01 a.104.1.1 107238 2bhuA 602 3.54e+01 1prcC 336 3.55e+01 6prcC a.138.1.2 19674 1eexB 224 3.56e+01 1dioB c.51.3.1 33213 1yc5A 246 3.58e+01 2gakA 391 3.59e+01 1ry9A 145 3.59e+01 d.198.1.1 98094 1dar 691 3.61e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1mrg 263 3.61e+01 1mrj d.165.1.1 42183 1x84A 189 3.62e+01 1gt7A 274 3.63e+01 c.74.1.1 70398 2cduA 452 3.63e+01 1vgvA 384 3.75e+01 c.87.1.3 100608 2fbwB 252 3.76e+01 3chbD 104 3.77e+01 3chbD b.40.2.1 24970 2wsyB 396 3.82e+01 2tysB c.79.1.1 35288 3rp2A 224 3.83e+01 1a7s b.47.1.2 26298 1yyqA 374 3.84e+01 1k2xB 143 3.84e+01 1djxB 624 3.84e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1vjs 483 3.86e+01 1bli b.71.1.1,c.1.8.1 27714,28701 1icfA 175 3.87e+01 1cs8A d.3.1.1 37067 1j6wA 175 3.89e+01 1j98A d.185.1.2 62663 1xvxA 312 3.89e+01 4bcl 366 3.90e+01 4bcl b.75.1.1 27968 1rwzA 245 3.90e+01 d.131.1.2,d.131.1.2 98005,98006 1gctA 245 3.92e+01 5ptp b.47.1.2 26021 1cjaA 342 4.06e+01 1cjaA d.144.1.3 41708 1drqA 131 4.08e+01 1drmA 1bvoA 175 4.12e+01 1a3qA b.2.5.3 22457 1d4xG 126 4.18e+01 1d0nA d.109.1.1 59109 1b0uA 262 4.24e+01 1b0uA c.37.1.12 32370 1yozA 116 4.28e+01 1cur 155 4.29e+01 1rcy b.6.1.1 23021 1jsqA 582 4.30e+01 i.13.1.1 63270 1vr7A 142 4.32e+01 1d3cA 686 4.33e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1xrtA 467 4.37e+01 1rh9A 373 4.42e+01 1ni4A 365 4.44e+01 c.36.1.11 85728 2ceyA 306 4.44e+01 1ncx 162 4.44e+01 1ncx a.39.1.5 17222 1xfdA 723 4.51e+01 1ayzA 169 4.60e+01 1u9aA d.20.1.1 38326 1b54 257 4.60e+01 1ct5A c.1.6.2 28664 2cfuA 658 4.63e+01 1kl7A 514 4.65e+01 c.79.1.1 72678 2ffqA 171 4.70e+01 2f6kA 307 4.73e+01 1hyoA 421 4.84e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1eudA 311 4.93e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 2bmaA 470 4.95e+01 1top 162 5.06e+01 1ncx a.39.1.5 17223 1nq7A 244 5.07e+01 a.123.1.1 92047 1k4wA 252 5.07e+01 a.123.1.1 72068 1vf8A 377 5.13e+01 1a36A 592 5.20e+01 1a36A a.2.8.1,d.163.1.2,e.15.1.1 15715,42173,43266 1vs0A 310 5.21e+01 1fukA 165 5.25e+01 1fukA c.37.1.19 32409 1e8uA 454 5.33e+01 1e8tA b.68.1.1 59389 1u04A 771 5.34e+01 b.34.14.1,c.55.3.10 107539,107540 1mqeA 207 5.34e+01 d.113.1.1 91394 2cyp 294 5.37e+01 1ryc a.93.1.1 18600 1gmuA 143 5.38e+01 b.107.1.1,d.58.38.1 65335,65336 1xkqA 280 5.46e+01 1z63A 500 5.50e+01 1zk7A 467 5.60e+01 1igwA 434 5.65e+01 c.1.12.7 62370 1eucA 311 5.67e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 1jrkA 156 5.76e+01 d.113.1.1 71827 2eu9A 355 5.77e+01 1duzA 275 5.80e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 1mrp 309 5.81e+01 1mrp c.94.1.1 35796 1j3kA 280 5.84e+01 c.71.1.1 84070 1d2tA 231 5.85e+01 1d2tA a.111.1.1 19052 1wz7A 111 5.87e+01 1a8e 329 5.87e+01 1cb6A c.94.1.2 35888 1aipA 405 5.93e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 2azeA 155 5.94e+01 1zd7A 159 5.95e+01 1pioA 257 5.98e+01 1btl e.3.1.1 42719 1p1jA 533 6.02e+01 c.2.1.3,d.81.1.3 87687,87688 1k4vA 289 6.05e+01 c.68.1.9 72066 1jc4A 148 6.05e+01 1jc4A d.32.1.4 62863 1on3A 523 6.06e+01 c.14.1.4,c.14.1.4 87107,87108 1s9rA 410 6.14e+01 d.126.1.4 98758 1jm4B 118 6.19e+01 a.29.2.1 71746 1f13A 731 6.19e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1fl0A 171 6.32e+01 1eujA b.40.4.4 25315 2dhqA 146 6.35e+01 2dhqA c.23.13.1 31382 1kssA 571 6.37e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1mnp 357 6.46e+01 1arv a.93.1.1 18668 1rlr 761 6.47e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 1u07A 90 6.48e+01 1w4vA 119 6.48e+01 1imdA 277 6.49e+01 1imbA e.7.1.1 42968 1i9sA 210 6.59e+01 1i9sA c.45.1.1 62099 1vr0A 247 6.67e+01 2apxA 112 6.70e+01 1xxsA 122 6.70e+01 1uvzA 119 6.72e+01 1pv1A 299 6.73e+01 1ot1A 686 6.77e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1tl0D 103 6.83e+01 1jdw 423 6.85e+01 1jdw d.126.1.2 41129 1y07A 128 6.87e+01 1qjdA 571 6.88e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1ru3A 732 6.91e+01 e.26.1.3 97835 1keeC 1073 6.94e+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 68500,68501,68502,68503,68504,68505 1mb4A 370 6.97e+01 c.2.1.3,d.81.1.1 78908,78909 1jsmB 176 7.04e+01 h.3.1.1 63265 1w9gA 104 7.06e+01 1delA 241 7.07e+01 1dekA c.37.1.1 31844 1oe1A 336 7.23e+01 b.6.1.3,b.6.1.3 86891,86892 1gifA 115 7.25e+01 1dptA d.80.1.3 39837 1b0pA 1231 7.31e+01 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 1ms9A 648 7.35e+01 b.29.1.15,b.68.1.1 85088,85089 1xl7A 612 7.41e+01 1ji2A 585 7.43e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1n8jA 186 7.53e+01 c.47.1.10 85401 1cl8A 276 7.55e+01 1ckqA c.52.1.1 33230 2ganA 190 7.61e+01 2hj2A 396 7.62e+01 1tys 265 7.62e+01 1bkpA d.117.1.1 40937 1j5eK 129 7.74e+01 c.55.4.1 71554 3kar 346 7.77e+01 1bg2 c.37.1.9 32198 1j09A 468 7.87e+01 a.97.1.1,c.26.1.1 77025,77026 1xruA 282 7.91e+01 1hkcA 917 7.96e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1cs1C 386 7.97e+01 1ibjA c.67.1.3 34401 1vemA 516 7.98e+01 1p32A 209 8.00e+01 1p32A d.25.1.1 38379 1vqoE 178 8.03e+01 1vb3A 428 8.06e+01 1e3hA 757 8.15e+01 1e3hA a.4.9.1,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16257,37572,37573,38810,40695,40696 1mg2D 155 8.20e+01 a.3.1.1 79062 1gppA 237 8.22e+01 b.86.1.2 76262 1g9mG 321 8.27e+01 1gc1G d.172.1.1 42492 8ohm 435 8.29e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1g8aA 227 8.39e+01 c.66.1.3 90506 1e39A 571 8.43e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1q9iA 571 8.50e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1dioB 224 8.51e+01 1dioB c.51.3.1 33219 2fpqA 444 8.59e+01 1m7vA 363 8.65e+01 d.174.1.1 78748 1yf2A 425 8.65e+01 1ps9A 671 8.66e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1aqlA 532 8.74e+01 2bce c.69.1.1 34627 1zkiA 133 8.75e+01 1bu8A 452 8.78e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1fzqA 181 8.81e+01 1hurA c.37.1.8 32060 1vkmA 297 8.82e+01 c.138.1.1 108670 2ajrA 331 8.84e+01 1gtrA 553 8.86e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1tn4 159 9.00e+01 1ncx a.39.1.5 17248