# List of top-scoring protein chains for t2k-100-30-alpha 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 1kfuS 184 2.84e-03 a.39.1.8 68574 1alvA 173 3.27e-02 1alvA a.39.1.8 17370 1bupA 386 3.32e-02 1ba1 c.55.1.1 33377 c.55.1.1 33378 1ba1 386 4.00e-02 1ba1 c.55.1.1 33387 c.55.1.1 33388 3fruA 269 4.74e-02 1agdA b.1.1.2 20657 d.19.1.1 38150 1kay 381 4.78e-02 1ba1 c.55.1.1 33385 c.55.1.1 33386 1q7lA 198 4.28e-01 1d7kA 421 5.39e-01 7odcA b.49.2.3 26486 c.1.6.1 28648 1bueA 265 9.46e-01 1btl e.3.1.1 42727 1auz 116 1.32e+00 1auz c.13.2.1 30883 1q4uA 151 1.61e+00 7odcA 424 1.71e+00 7odcA b.49.2.3 26488 c.1.6.1 28650 1j3mA 129 2.76e+00 1un8A 552 3.08e+00 1bouB 302 3.09e+00 1bouB c.56.6.1 33859 1edzA 320 3.15e+00 1ee9A c.2.1.7 30287 c.58.1.2 33935 1kjvB 100 3.35e+00 b.1.1.2 77423 1jdfA 447 3.60e+00 c.1.11.2 62897 d.54.1.1 62898 1dgsA 667 3.71e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1fo5A 85 3.92e+00 1fo5A c.47.1.1 59922 1ki1B 352 4.09e+00 a.87.1.1 72497 b.55.1.1 72498 1krhA 338 4.34e+00 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1v7rA 186 4.63e+00 1xgsA 295 4.73e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1b4uB 302 4.78e+00 1bouB c.56.6.1 33861 1ee9A 320 4.89e+00 1ee9A c.2.1.7 30288 c.58.1.2 33936 1b54 257 4.96e+00 1ct5A c.1.6.2 28664 1q7zA 566 5.25e+00 1v4vA 376 5.30e+00 1ln1A 214 5.46e+00 d.129.3.2 74038 1mogA 67 5.65e+00 d.230.2.1 85034 1h6kA 757 5.83e+00 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 1hsbB 99 6.05e+00 1agdB b.1.1.2 20737 1k5nB 100 6.11e+00 b.1.1.2 77268 1i4fB 100 6.18e+00 1agdB b.1.1.2 61689 1duzB 100 6.20e+00 1agdB b.1.1.2 20671 1lddA 74 6.23e+00 a.4.5.34 73841 1jnjA 100 6.28e+00 b.1.1.2 66955 1o6jA 150 6.35e+00 c.47.1.10 81089 1agdB 99 6.41e+00 1agdB b.1.1.2 20742 1p4xA 250 6.47e+00 a.4.5.28 87784 a.4.5.28 87785 1n9lA 109 6.57e+00 d.110.3.6 85468 1go2A 304 6.62e+00 b.43.4.2 76243 c.25.1.1 76244 1cfzA 162 6.71e+00 1cfzA c.56.1.1 33754 1f0yA 302 6.93e+00 2hdhA a.100.1.3 18793 c.2.1.6 30197 1nw1A 429 7.03e+00 d.144.1.8 86286 1qnrA 344 7.46e+00 1qnoA c.1.8.3 28834 1thtA 305 7.95e+00 1thtA c.69.1.13 34711 1qnoA 344 8.27e+00 1qnoA c.1.8.3 28838 1bbn 133 8.54e+00 1rcb a.26.1.2 16861 1ogiA 303 8.81e+00 1mwmA 320 9.75e+00 c.55.1.1 79580 c.55.1.1 79581 153l 185 1.01e+01 153l d.2.1.5 36984 1h7wD 1025 1.06e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1gthA 1025 1.11e+01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1gthD 1025 1.11e+01 a.1.2.2 70498 c.1.4.1 70499 c.3.1.1 70500 c.4.1.1 70501 d.58.1.5 70502 1qh0A 295 1.13e+01 b.43.4.2 68891 c.25.1.1 68892 2hdhA 293 1.14e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1g291 372 1.14e+01 1g291 1rcb 129 1.15e+01 1rcb a.26.1.2 16854 1gteD 1025 1.15e+01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1h7xA 1025 1.16e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1h7xC 1025 1.16e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1oivA 191 1.16e+01 1h7wA 1025 1.16e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1jvr 137 1.18e+01 1jvr a.61.1.2 18132 1que 303 1.19e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1ltqA 301 1.20e+01 c.108.1.9 78208 c.37.1.1 78209 1h7xD 1025 1.23e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1ncx 162 1.23e+01 1ncx a.39.1.5 17222 1b2rA 304 1.25e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1i5gA 144 1.28e+01 1ewxA c.47.1.10 61784 1i2sA 282 1.28e+01 e.3.1.1 71104 2cmd 312 1.28e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1trb 320 1.30e+01 1trb c.3.1.5 30529 c.3.1.5 30530 1ayaA 101 1.32e+01 1qadA d.93.1.1 40460 1h7xB 1025 1.32e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1gt8A 1025 1.33e+01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1ako 268 1.34e+01 1ako d.151.1.1 41779 1top 162 1.39e+01 1ncx a.39.1.5 17223 1h7wB 1025 1.40e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1q40B 219 1.48e+01 1nffA 260 1.50e+01 c.2.1.2 80457 1gthC 1025 1.50e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1f5nA 592 1.53e+01 1dg3A a.114.1.1 19077 c.37.1.8 32152 1gthB 1025 1.55e+01 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 1e3yA 104 1.59e+01 1fadA a.77.1.2 18426 1mml 265 1.67e+01 1mml e.8.1.2 43015 1db3A 372 1.68e+01 1db3A c.2.1.2 29813 1p8kZ 254 1.70e+01 1ezvF 125 1.73e+01 1be3F f.27.1.1 59550 1kb9G 125 1.73e+01 f.27.1.1 77322 1o12A 376 1.76e+01 b.92.1.5 80758 c.1.9.10 80759 1f1mA 164 1.77e+01 1ggqA a.24.12.1 59598 1gteA 1025 1.78e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1ewjA 126 1.79e+01 1ecsA d.32.1.2 59526 3adk 195 1.79e+01 1zin c.37.1.1 31885 1q2wA 308 1.80e+01 b.47.1.4 88355 1edhA 226 1.86e+01 1edhA b.1.6.1 22198 b.1.6.1 22199 1suh 146 1.86e+01 1edhA b.1.6.1 22206 1lhpA 312 1.88e+01 c.72.1.5 77960 1mlwA 301 2.00e+01 d.178.1.1 79289 1dcqA 278 2.03e+01 1dcqA d.211.1.1 19178 g.45.1.1 45326 1j99A 293 2.04e+01 c.37.1.5 71618 1nlwA 80 2.09e+01 a.38.1.1 80633 1gt8B 1025 2.11e+01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1sjdA 368 2.11e+01 1p5jA 372 2.11e+01 1pd21 199 2.13e+01 1pd21 1kyoG 126 2.19e+01 f.27.1.1 73259 1gt8D 1025 2.20e+01 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1nh1A 330 2.23e+01 1gt8C 1025 2.23e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1rypD 241 2.24e+01 1rypD d.153.1.4 41935 1n8nA 212 2.25e+01 1ct5A 256 2.25e+01 1ct5A c.1.6.2 28663 1rypK 198 2.30e+01 d.153.1.4 41879 1ufoA 238 2.30e+01 1bea 127 2.35e+01 1bea a.52.1.2 17826 2shpA 525 2.36e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1dzfA 215 2.37e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 2pta 35 2.38e+01 2pta g.3.7.2 44168 1m6jA 261 2.38e+01 c.1.1.1 78693 1ois 223 2.39e+01 1a36A e.15.1.1 43267 1fqvJ 149 2.41e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1aho 64 2.47e+01 1aho g.3.7.1 44127 1gbs 185 2.47e+01 153l d.2.1.5 36986 1alq 266 2.50e+01 1btl e.3.1.1 42707 1kebA 108 2.56e+01 c.47.1.1 77341 1fj2A 232 2.56e+01 1auoA c.69.1.14 34720 1owfB 94 2.58e+01 a.55.1.1 87488 1ohvA 472 2.65e+01 2trxA 108 2.73e+01 1thx c.47.1.1 32719 1bkdS 439 2.77e+01 1bkdS a.117.1.1 19111 1c49A 35 2.77e+01 2pta g.3.7.2 44169 1ecsA 126 2.81e+01 1ecsA d.32.1.2 59407 1eudB 396 2.82e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1ihfB 94 2.84e+01 1huuA a.55.1.1 17894 1im8A 244 2.89e+01 c.66.1.14 66212 1b9dA 163 2.90e+01 1b9dA c.55.3.2 33649 1nkpA 88 2.92e+01 a.38.1.1 80573 1dg3A 592 2.94e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1ffkG 145 3.02e+01 1ffkG c.21.1.1 31035 1vk8A 106 3.08e+01 1dd3C 32 3.09e+01 1dd3C a.108.1.1 19033 1j96A 323 3.10e+01 c.1.7.1 71616 1i0rA 169 3.10e+01 1i0rA b.45.1.2 61489 1bfa 134 3.11e+01 1bea a.52.1.2 17827 1sfsA 240 3.13e+01 1jsdB 176 3.13e+01 h.3.1.1 63259 1ah7 245 3.14e+01 1ah7 a.124.1.1 19339 1op0A 234 3.14e+01 1bix 287 3.22e+01 1bix d.151.1.1 41781 1n7vA 555 3.22e+01 b.126.1.1 85377 1exqA 154 3.25e+01 1b9dA c.55.3.2 33646 1rwzA 245 3.26e+01 2rslA 140 3.39e+01 2rslA c.53.1.1 33345 1jr1A 514 3.41e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1jykA 254 3.41e+01 c.68.1.13 67458 1jj2I 145 3.45e+01 1ffkG c.21.1.1 63094 1hziA 129 3.45e+01 1rcb a.26.1.2 61449 1m2eA 135 3.46e+01 c.23.1.5 78478 1b3jA 274 3.47e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1r1dA 247 3.50e+01 1e4cP 215 3.50e+01 2fua c.74.1.1 34969 1eucB 396 3.51e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1i40A 175 3.51e+01 b.40.5.1 66024 1gtxA 472 3.51e+01 1gtxA c.67.1.4 34464 1culA 217 3.51e+01 1azsA d.58.29.1 39417 1a7vA 125 3.55e+01 1cpq a.24.3.2 16562 1mqvA 125 3.56e+01 a.24.3.2 79415 1ek6A 348 3.56e+01 1xel c.2.1.2 29800 1jcfA 344 3.62e+01 c.55.1.1 62878 c.55.1.1 62879 1a7tA 232 3.66e+01 1a7tA d.157.1.1 42041 1pioA 257 3.68e+01 1btl e.3.1.1 42719 1af3 196 3.70e+01 1maz f.1.4.1 43397 1hd7A 318 3.70e+01 1bix d.151.1.1 41780 1auoA 218 3.73e+01 1auoA c.69.1.14 34716 1bowA 159 3.75e+01 1bowA d.60.1.1 39528 1aj6 219 3.77e+01 1aj6 d.122.1.2 41106 1ipwA 175 3.78e+01 2prd b.40.5.1 25427 1azsA 220 3.82e+01 1azsA d.58.29.1 39416 1et0A 269 3.95e+01 1et0A e.17.1.1 43289 1esmA 316 3.95e+01 1esmA c.37.1.6 31953 1i2kA 269 3.96e+01 1fua 215 3.97e+01 2fua c.74.1.1 34973