# List of top-scoring protein chains for t2k-100-30-str2 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 1tzbA 302 9.08e-09 1moq 368 5.57e-02 1moq c.80.1.1 35302 1g0hA 252 2.51e-01 1dk4A e.7.1.1 60171 1dk4A 252 3.41e-01 1dk4A e.7.1.1 42970 1fezA 256 4.01e-01 1fezA c.108.1.3 43343 1rqlA 267 5.42e-01 c.108.1.3 -6814 1j5xA 342 7.40e-01 c.80.1.1 71591 1su8A 636 1.04e+00 e.26.1.2 -12015 1aa6 715 1.52e+00 2napA b.52.2.2 26916 c.81.1.1 35324 1fdo 715 2.11e+00 2napA b.52.2.2 26917 c.81.1.1 35325 1b1cA 181 2.17e+00 1amoA c.23.5.2 31212 1umwA 237 2.75e+00 unknown_sccs -9455 unknown_sccs -9456 1duvG 333 2.85e+00 1othA c.78.1.1 35228 c.78.1.1 35229 1b0zA 445 2.88e+00 2pgi c.80.1.2 35309 2pgi 445 2.88e+00 2pgi c.80.1.2 35308 1h2sA 225 2.88e+00 f.13.1.1 76578 1oqvA 192 3.07e+00 d.24.1.2 87320 1fdi 715 3.21e+00 2napA b.52.2.2 26918 c.81.1.1 35326 1qnf 484 3.31e+00 1qnf a.99.1.1 18777 c.28.1.1 31632 1i2aA 219 3.73e+00 e.24.1.1 -12012 1e1oA 504 3.81e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1owlA 484 4.08e+00 a.99.1.1 -1296 c.28.1.1 -6646 1jaxA 212 4.09e+00 c.2.1.6 66476 1vi6A 208 4.27e+00 c.23.15.1 -6489 3csuA 310 4.36e+00 3csuA c.78.1.1 35094 c.78.1.1 35095 1ja1A 622 4.66e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1jayA 212 4.81e+00 c.2.1.6 66478 1jztA 246 4.95e+00 c.104.1.1 63319 1poxA 585 5.68e+00 1poxA c.31.1.3 31731 c.36.1.5 31793 c.36.1.9 31794 1orvA 728 5.73e+00 b.70.3.1 87354 c.69.1.24 87355 1l3iA 192 5.82e+00 c.66.1.22 77676 1cjsA 219 5.94e+00 1cjsA e.24.1.1 43354 1jgjA 217 5.95e+00 1c3wA f.13.1.1 62952 1m3sA 186 6.02e+00 c.80.1.3 78573 1cwyA 500 6.02e+00 1cwyA c.1.8.1 28789 1c7qA 445 6.10e+00 2pgi c.80.1.2 35307 1kid 203 7.11e+00 1derA c.8.5.1 30771 1at1A 310 7.24e+00 3csuA c.78.1.1 35168 c.78.1.1 35169 1eswA 500 7.39e+00 1cwyA c.1.8.1 59500 1ohuA 175 7.55e+00 f.1.4.1 -12058 1rwyA 109 8.13e+00 a.39.1.4 -825 1t35A 191 8.16e+00 unknown_sccs -7285 1ukuA 102 9.11e+00 d.58.5.2 -9992 1jjyA 636 9.21e+00 1jjyA 1szqA 483 9.33e+00 unknown_sccs -11791 1j4nA 271 9.67e+00 f.19.1.1 71510 1tqyB 415 1.01e+01 1kb9B 352 1.03e+01 d.185.1.1 77313 d.185.1.1 77314 1n57A 291 1.03e+01 c.23.16.2 85328 1d3uB 201 1.04e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1teaA 299 1.04e+01 1prxA 224 1.05e+01 1prxA c.47.1.10 33076 1lucB 324 1.07e+01 1lucA c.1.16.1 29548 1apyA 162 1.11e+01 1apyA d.153.1.5 42004 1kzyC 259 1.11e+01 c.15.1.4 73383 c.15.1.4 73384 1ezvB 352 1.18e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1mqvA 125 1.25e+01 a.24.3.2 79415 1f0kA 364 1.28e+01 1f0kA c.87.1.2 35465 1lylA 504 1.32e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1mjgM 729 1.36e+01 e.26.1.3 79204 1nijA 318 1.39e+01 c.37.1.10 85741 d.237.1.1 85742 1i1gA 141 1.39e+01 a.4.5.32 65982 d.58.4.2 65983 1h68A 239 1.41e+01 f.13.1.1 60664 1brlB 324 1.42e+01 1lucA c.1.16.1 29554 5pal 109 1.44e+01 1a75A a.39.1.4 17215 1ko7A 314 1.46e+01 c.98.2.1 72797 c.91.1.2 72798 1vimA 200 1.52e+01 c.80.1.3 -8532 1nxzA 246 1.54e+01 b.122.1.2 86391 c.116.1.5 86392 1oaoC 729 1.54e+01 e.26.1.3 86746 1vhyA 257 1.61e+01 b.122.1.2 -5129 c.116.1.5 -6705 1hl8A 449 1.67e+01 unknown_sccs -4690 unknown_sccs -5361 1efcA 393 1.71e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1amoA 615 1.82e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1r8sE 203 1.84e+01 a.118.3.1 -1579 1pkp 150 1.86e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1az9 457 1.90e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1c24A 263 1.93e+01 1c24A d.127.1.1 41148 1eudA 311 1.97e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1g99A 408 1.99e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1uxoA 192 1.99e+01 2sxl 88 2.00e+01 1b7fA d.58.7.1 39179 1buuA 168 2.04e+01 1rtm1 d.169.1.1 42366 h.1.1.1 45388 1o5zA 442 2.04e+01 c.59.1.2 -7939 c.72.2.2 -8418 1ekxA 311 2.04e+01 3csuA c.78.1.1 35088 c.78.1.1 35089 4matA 278 2.06e+01 1c24A d.127.1.1 41150 1aisB 200 2.12e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1no1A 126 2.18e+01 a.179.1.1 85913 1sjdA 368 2.19e+01 2matA 264 2.20e+01 1c24A d.127.1.1 41146 1m7vA 363 2.27e+01 d.174.1.1 78748 1mat 264 2.33e+01 1c24A d.127.1.1 41152 1a7vA 125 2.34e+01 1cpq a.24.3.2 16562 1m6jA 261 2.34e+01 c.1.1.1 78693 1m1nB 522 2.35e+01 c.92.2.3 78418 1ohtA 215 2.35e+01 d.118.1.1 87036 1fukA 165 2.38e+01 1fukA c.37.1.19 32409 1a16 440 2.41e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1o04A 500 2.42e+01 c.82.1.1 86508 1bncA 449 2.47e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1eucA 311 2.50e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 3minB 522 2.57e+01 1qguB c.92.2.3 35606 1zin 217 2.57e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1g5hA 454 2.58e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1yer 228 2.63e+01 1yer d.122.1.1 41101 1prxB 224 2.68e+01 1prxA c.47.1.10 33077 1a26 361 2.71e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1volA 204 2.72e+01 1tfb a.74.1.2 18370 a.74.1.2 18371 1uw4A 91 2.73e+01 unknown_sccs -10038 1l9vA 317 2.80e+01 d.13.2.1 73760 d.216.1.1 73761 1iq4A 179 2.83e+01 1iq4A d.77.1.1 62641 1nfp 228 2.85e+01 1nfp c.1.16.2 29555 1ml4A 308 2.86e+01 c.78.1.1 79255 c.78.1.1 79256 1f4tA 368 2.87e+01 1f4tA a.104.1.1 18973 1nytA 271 2.88e+01 c.2.1.7 86417 c.58.1.5 86418 1dv1A 449 2.89e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1p1lA 102 2.90e+01 d.58.5.2 87695 1vjxA 157 2.91e+01 a.25.1.1 -654 1jlnA 297 2.93e+01 1pty c.45.1.2 63172 1n1cA 217 2.97e+01 a.184.1.1 85254 1kkhA 317 2.99e+01 d.14.1.5 72645 d.58.26.3 72646 1efyA 350 3.00e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1ftrA 296 3.03e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1ufoA 238 3.11e+01 unknown_sccs -8303 1otgA 125 3.15e+01 1otgA d.80.1.2 39831 1in0A 163 3.18e+01 d.58.49.1 83694 d.58.49.1 83695 1ckv 141 3.19e+01 1ckv d.137.1.1 41452 1mbxC 106 3.20e+01 d.45.1.2 78929 1m22A 503 3.27e+01 c.117.1.1 78464 1uylA 236 3.30e+01 1colA 204 3.31e+01 1a87 f.1.1.1 43378 1srvA 145 3.33e+01 1derA c.8.5.1 30817 1grj 158 3.36e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1brwA 433 3.36e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1bbhA 131 3.40e+01 1bbhA a.24.3.2 16546 1ejhA 190 3.43e+01 1ejhA d.86.1.1 40147 2minB 522 3.43e+01 1qguB c.92.2.3 35610 1e19A 314 3.45e+01 1b7bA c.73.1.1 34967 1n1mA 728 3.47e+01 b.70.3.1 79815 c.69.1.24 79816 1omzA 293 3.47e+01 c.68.1.15 87093 1bq0 103 3.48e+01 1bqz a.2.3.1 15698 1jkfA 533 3.50e+01 c.2.1.3 71700 d.81.1.3 71701 1npyA 271 3.51e+01 c.2.1.7 85995 c.58.1.5 85996 1qe3A 489 3.53e+01 2bce c.69.1.1 34630 1ky3A 182 3.54e+01 c.37.1.8 73193 1lwdA 413 3.56e+01 c.77.1.1 78265 1np7A 489 3.59e+01 a.99.1.1 80677 c.28.1.1 80678 1j0aA 325 3.60e+01 c.79.1.1 83871 1xbl 107 3.64e+01 1bqz a.2.3.1 15697 1iyhA 198 3.72e+01 a.45.1.1 83790 c.47.1.5 83791 1jr1A 514 3.73e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1dq3A 454 3.75e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1at3A 247 3.75e+01 1at3A b.57.1.1 27021 1ixkA 315 3.79e+01 unknown_sccs -8099 1lucA 355 3.81e+01 1lucA c.1.16.1 29547 1byqA 228 3.83e+01 1yer d.122.1.1 41100 1mkaA 171 3.85e+01 1mkaA d.38.1.2 38543 1aw9 216 3.88e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1pu6A 218 3.94e+01 unknown_sccs -1282 2msbA 115 3.94e+01 1rtm1 d.169.1.1 42355 1o4wA 147 3.98e+01 c.120.1.1 86629