# List of top-scoring protein chains for t2k-w0.5 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 1f07A 321 6.40e-01 1ezwA c.1.16.3 59560 1qm5A 796 1.87e+00 1a8i c.87.1.4 35542 1l5wA 796 1.93e+00 1ezwA 349 3.30e+00 1ezwA c.1.16.3 29558 1eswA 500 4.30e+00 1cwyA c.1.8.1 59500 1cwyA 500 4.30e+00 1cwyA c.1.8.1 28789 1qk1A 379 4.48e+00 1qh4A a.83.1.1 18466 d.128.1.2 41201 1c9wA 315 4.51e+00 1frb c.1.7.1 28699 2hlcA 230 4.75e+00 5ptp b.47.1.2 26074 1hylA 230 4.75e+00 5ptp b.47.1.2 26076 1dlaB 314 4.76e+00 1frb c.1.7.1 28691 1ah4 315 4.78e+00 1frb c.1.7.1 28684 1ah0 316 4.79e+00 1frb c.1.7.1 28685 1g6cB 227 5.56e+00 c.1.3.1 60316 1g67A 225 5.57e+00 c.1.3.1 60311 1g69B 228 5.57e+00 c.1.3.1 60314 1g4sA 226 5.61e+00 c.1.3.1 60247 2tpsA 227 5.77e+00 2tpsA c.1.3.1 28591 1kz7A 353 6.22e+00 1ehiA 377 6.79e+00 1iow c.30.1.2 31716 d.142.1.1 41484 2crkA 381 6.80e+00 1qh4A a.83.1.1 18474 d.128.1.2 41209 1uio 349 7.45e+00 1a4mA c.1.9.1 29021 1uip 349 7.57e+00 1a4mA c.1.9.1 29022 1fkw 349 7.77e+00 1a4mA c.1.9.1 29019 1fkx 349 7.78e+00 1a4mA c.1.9.1 29018 1gveB 327 7.80e+00 1a4mA 349 7.84e+00 1a4mA c.1.9.1 29014 1add 349 7.84e+00 1a4mA c.1.9.1 29020 1gveA 327 7.92e+00 2ada 352 8.03e+00 1a4mA c.1.9.1 29027 1kzgA 353 8.04e+00 1lb1A 353 8.06e+00 1bymA 97 8.16e+00 1bi0 b.34.1.2 24458 1ag9A 175 8.55e+00 1rcf c.23.5.1 31178 1cjsA 219 8.76e+00 1cjsA e.24.1.1 43354 1j4pA 151 9.08e+00 b.26.1.2 66387 1g3gA 164 9.20e+00 1g6gA b.26.1.2 23918 1g6gA 127 1.04e+01 1g6gA b.26.1.2 23916 1cliA 345 1.13e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1crkA 380 1.13e+01 1qh4A a.83.1.1 18458 d.128.1.2 41193 1j5eJ 104 1.25e+01 1fjgJ 105 1.26e+01 1fjfJ d.58.15.1 39330 1al7 359 1.27e+01 1gox c.1.4.1 28609 1gox 369 1.32e+01 1gox c.1.4.1 28607 1qqwB 527 1.35e+01 1cf9A e.5.1.1 42803 1gylA 369 1.35e+01 1gox c.1.4.1 28610 1dghB 498 1.38e+01 1cf9A e.5.1.1 42791 1de4A 275 1.43e+01 1agdA b.1.1.2 20775 d.19.1.1 38277 1sig 339 1.44e+01 1sig a.112.1.1 19068 1a9xA 1058 1.55e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1vng 609 1.56e+01 1vns a.111.1.3 19066 1l9vA 317 1.58e+01 1dgfA 497 1.64e+01 1cf9A e.5.1.1 42782 1bnlA 178 1.64e+01 1koe d.169.1.5 42444 1dghC 498 1.64e+01 1cf9A e.5.1.1 42792 1d2fA 390 1.64e+01 1d2fA c.67.1.3 34411 1tkiA 321 1.66e+01 1tkiA d.144.1.1 41638 1vnf 609 1.74e+01 1vns a.111.1.3 19067 1ce8A 1073 1.75e+01 a.92.1.1 18566 c.24.1.1 31495 c.30.1.1 31689 c.30.1.1 31690 d.142.1.2 41534 d.142.1.2 41535 1g3yA 226 1.78e+01 a.4.5.24 65136 a.76.1.1 65137 b.34.1.2 65138 1vnh 609 1.78e+01 1vns a.111.1.3 19062 1bxrA 1073 1.79e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1cs0C 1073 1.79e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1c3oA 1073 1.79e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1c3oC 1073 1.79e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1c3oE 1073 1.79e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1c3oG 1073 1.79e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1jdbB 1073 1.79e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1c0wB 225 1.79e+01 1bi0 a.4.5.24 16212 a.76.1.1 18418 b.34.1.2 24454 2dtr 226 1.80e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1fwzA 226 1.83e+01 a.4.5.24 60077 a.76.1.1 60078 b.34.1.2 60079 1bi0 226 1.84e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1iduA 609 1.85e+01 1vns a.111.1.3 62303 1bwnA 169 1.85e+01 1btkA b.55.1.1 26961 1b55A 169 1.86e+01 1btkA b.55.1.1 26963 1vns 609 1.88e+01 1vns a.111.1.3 19061 1vnc 609 1.88e+01 1vns a.111.1.3 19065 1koe 172 1.89e+01 1koe d.169.1.5 42448 1cglA 169 1.90e+01 1hfc d.92.1.11 40341 1g3tA 226 1.91e+01 a.4.5.24 65127 a.76.1.1 65128 b.34.1.2 65129 1dkrA 317 1.91e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1dkuA 317 1.91e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1dv2A 452 1.96e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 205l 167 1.99e+01 1l92 d.2.1.3 36910 1frb 315 2.01e+01 1frb c.1.7.1 28665 1ddnA 226 2.02e+01 1bi0 a.4.5.24 16207 a.76.1.1 18413 1dy1A 188 2.03e+01 1koe d.169.1.5 42450 1btkA 169 2.03e+01 1btkA b.55.1.1 26959 1btkB 169 2.03e+01 1btkA b.55.1.1 26960 1l9mA 692 2.04e+01 1eepB 404 2.06e+01 1ak5 c.1.5.1 28637 1qo2A 241 2.17e+01 1qo2A c.1.2.1 28533 1bncA 449 2.18e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1dv1A 449 2.18e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bncB 449 2.18e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1dot 686 2.24e+01 1nnt c.94.1.2 35876 c.94.1.2 35877 1avaA 403 2.24e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 2aacB 177 2.41e+01 2arcA b.82.4.1 28151 1im5A 180 2.48e+01 c.33.1.2 66211 1qgjA 300 2.55e+01 1bgp a.93.1.1 18691 7at1B 146 2.55e+01 8atcB d.58.2.1 39053 g.41.7.1 45305 8atcB 153 2.56e+01 8atcB d.58.2.1 39027 g.41.7.1 45279 1lf1A 308 2.57e+01 9atcB 146 2.59e+01 8atcB d.58.2.1 39057 g.41.7.1 45309 1qlgA 355 2.71e+01 1qlgA b.68.3.1 27627 1h6lA 353 2.72e+01 b.68.3.1 60687 1cvmA 353 2.72e+01 1qlgA b.68.3.1 27628 1vne 609 2.76e+01 1vns a.111.1.3 19063 1cgfA 162 2.79e+01 1hfc d.92.1.11 40339 1e58A 249 2.80e+01 1qhfA c.60.1.1 59262 966c 157 2.83e+01 1hfc d.92.1.11 40338 1jiwP 470 2.87e+01 1sat b.79.1.1 63079 d.92.1.6 63080 2arcB 164 2.94e+01 2arcA b.82.4.1 28149 2arcA 164 2.94e+01 2arcA b.82.4.1 28148 1d09B 153 2.98e+01 8atcB d.58.2.1 39015 g.41.7.1 45267 1kapP 479 2.99e+01 1sat b.79.1.1 28012 d.92.1.6 40298 1cge 168 2.99e+01 1hfc d.92.1.11 40336 1hfc 169 3.01e+01 1hfc d.92.1.11 40335 4pfk 319 3.04e+01 3pfk c.89.1.1 35582 3pfk 319 3.04e+01 3pfk c.89.1.1 35581 1ignA 246 3.06e+01 1ignA a.4.1.6 16048 a.4.1.6 16049 1qh4A 380 3.07e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1k23C 309 3.10e+01 c.107.1.1 68031 6pfkA 319 3.14e+01 3pfk c.89.1.1 35583 1bdb 277 3.20e+01 1bdb c.2.1.2 29874 1iq7A 345 3.27e+01 c.94.1.2 66261 1tpwA 247 3.49e+01 1amk c.1.1.1 28449 2tmgA 415 3.54e+01 1hwyA c.2.1.7 30238 c.58.1.1 33886 1nbeB 153 3.54e+01 8atcB d.58.2.1 39041 g.41.7.1 45293 1gnkB 112 3.59e+01 2pii d.58.5.1 39074 1pbwA 216 3.63e+01 1pbwA a.116.1.1 19103 1dmzA 158 3.64e+01 1qu5A b.26.1.2 23921 1bwvA 493 3.66e+01 1burA c.1.14.1 29372 d.58.9.1 39278 1i5eA 209 3.67e+01 1qknA 255 3.67e+01 3erdA a.123.1.1 19310 1f0kA 364 3.67e+01 1f0kA c.87.1.2 35465 1tpc1 247 3.68e+01 1amk 1pa2A 306 3.76e+01 1bgp a.93.1.1 18693 1lwhA 441 3.77e+01 2pooA 355 3.80e+01 1qlgA b.68.3.1 27626 2atcB 152 3.83e+01 8atcB d.58.2.1 39062 g.41.7.1 45314 1ea9C 583 3.85e+01 2gnkA 112 3.85e+01 2pii d.58.5.1 39075 1vpe 398 3.93e+01 16pk c.86.1.1 35453 1c0dA 358 3.95e+01 1eceA c.1.8.3 28815 1eceA 358 3.99e+01 1eceA c.1.8.3 28813