# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1h5rA 293 7.17e-29 c.68.1.6 65623 1mp4A 292 3.20e-28 c.68.1.6 79376 1fxoA 293 4.24e-28 1g0rA c.68.1.6 34524 1g0rA 293 7.86e-28 1g0rA c.68.1.6 34532 1lvwA 295 8.67e-28 c.68.1.6 84723 1mc3A 296 5.47e-27 c.68.1.6 78943 1hm9A 468 6.10e-21 b.81.1.4 65866 c.68.1.5 65867 1g97A 459 1.10e-20 1fwyA b.81.1.4 60394 c.68.1.5 60395 1fxjA 331 1.33e-20 1fwyA b.81.1.4 28062 c.68.1.5 34520 1hv9A 456 1.54e-20 1fwyA b.81.1.4 28060 c.68.1.5 34518 1fwyA 331 1.60e-20 1fwyA b.81.1.4 28064 c.68.1.5 34522 1jykA 254 1.91e-16 c.68.1.13 67458 1h7eA 245 6.73e-12 c.68.1.13 60717 1vicA 262 1.54e-11 c.68.1.13 -8252 1i52A 236 2.88e-10 1i52A c.68.1.13 61767 1e5kA 201 1.30e-06 1fr9A c.68.1.8 34578 1vgwA 231 3.02e-06 c.68.1.13 -8237 1fr9A 194 7.98e-06 1fr9A c.68.1.8 34579 1eyrA 228 4.76e-05 1eyrA c.68.1.13 34514 1jv1A 505 1.14e-04 c.68.1.5 71892 1eziA 228 1.73e-04 1eyrA c.68.1.13 34512 1dqwA 267 3.88e-01 1dqwA c.1.2.3 28551 1i1wA 303 5.17e-01 c.1.8.3 76732 1eu8A 409 5.91e-01 1eu8A c.94.1.1 59502 1omzA 293 6.11e-01 c.68.1.15 87093 1k6aA 303 6.74e-01 c.1.8.3 72081 1gokA 303 6.80e-01 c.1.8.3 65420 1fxmA 302 6.82e-01 1taxA 1o4sA 389 8.69e-01 c.67.1.1 86620 1eluB 390 9.21e-01 1elqA c.67.1.3 34435 1fc4A 401 9.36e-01 1bs0A c.67.1.4 59760 1cs1A 386 1.05e+00 1ibjA c.67.1.3 34399 1cs1C 386 1.17e+00 1ibjA c.67.1.3 34401 1lkcA 364 1.18e+00 c.67.1.1 73978 1gewA 356 1.22e+00 1gewA c.67.1.1 60470 1kamA 194 1.32e+00 c.26.1.3 72254 1c7nA 399 1.63e+00 1d2fA c.67.1.3 34413 1elqA 390 1.69e+00 1elqA c.67.1.3 34436 1ie7C 570 1.71e+00 1ubpC b.92.1.1 62315 c.1.9.2 62316 1eluA 390 1.91e+00 1elqA c.67.1.3 34434 1fg7A 356 2.07e+00 1gewA c.67.1.1 59819 1ubpC 570 2.12e+00 1ubpC b.92.1.1 28432 c.1.9.2 29054 4ubpC 570 2.19e+00 1ubpC b.92.1.1 28431 c.1.9.2 29053 1jscA 630 2.73e+00 c.31.1.3 67224 c.36.1.5 67225 c.36.1.9 67226 1ir6A 424 2.79e+00 c.107.1.2 71342 1o69A 394 3.13e+00 c.67.1.4 -8209 1i60A 278 3.14e+00 c.1.15.4 71118 1ozhA 566 3.24e+00 c.31.1.3 -6737 c.36.1.5 -6895 c.36.1.9 -6935 1qh3A 260 4.02e+00 1qh5A d.157.1.2 42059 1poxA 585 4.09e+00 1poxA c.31.1.3 31731 c.36.1.5 31793 c.36.1.9 31794 1lc5A 364 4.54e+00 c.67.1.1 73827 3tgl 269 4.58e+00 3tgl c.69.1.17 34733 1tux 301 4.83e+00 1taxA c.1.8.3 28907 1o2dA 371 4.93e+00 e.22.1.2 86591 1j5rA 371 5.03e+00 1yasA 257 5.22e+00 1qj4A c.69.1.20 34801 1e9lA 377 5.34e+00 1e9lA c.1.8.5 59395 d.26.3.1 59396 1iugA 352 5.53e+00 c.67.1.3 -8176 1cf9A 753 5.69e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1bg4 302 5.95e+00 1taxA c.1.8.3 28806 1h70A 255 5.97e+00 1h70A d.126.1.3 60711 4xiaA 393 5.98e+00 4xis c.1.15.3 29439 1ee9A 320 6.13e+00 1ee9A c.2.1.7 30288 c.58.1.2 33936 1tfr 305 6.18e+00 1tfr a.60.7.1 18081 c.120.1.2 33351 1v84A 253 6.23e+00 1cl1A 395 6.35e+00 1cl2A c.67.1.3 34395 1lqtA 456 6.36e+00 c.3.1.1 74198 c.4.1.1 74199 1bli 483 6.45e+00 1bli b.71.1.1 27715 c.1.8.1 28702 1b31A 302 6.55e+00 1taxA c.1.8.3 28892 1b0pA 1231 6.64e+00 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1ayaA 101 7.22e+00 1qadA d.93.1.1 40460 1gsa 316 7.23e+00 1gsa c.30.1.3 31718 d.142.1.1 41477 1lgyA 269 7.29e+00 3tgl c.69.1.17 34758 1odfA 290 7.34e+00 c.37.1.6 -7045 1fs0G 230 7.38e+00 1fs0G c.49.2.1 59999 1ep3A 311 7.46e+00 2dorA c.1.4.1 28597 1ecxA 384 7.84e+00 1ecxA c.67.1.3 34431 1bi5A 389 7.90e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1v1rA 400 8.06e+00 1k77A 260 8.36e+00 c.1.15.5 72096 1gt6A 269 8.48e+00 c.69.1.17 76342 1h5yA 253 8.55e+00 c.1.2.1 65638 1qv9A 283 8.57e+00 unknown_sccs -6888 1gdeA 389 8.79e+00 c.67.1.1 60456 1s1pA 331 8.89e+00 c.1.7.1 -5240 1i86A 389 8.89e+00 c.95.1.2 66068 c.95.1.2 66069 1e5eA 404 8.96e+00 1ibjA c.67.1.3 59265 5fbpA 335 9.18e+00 1frpA e.7.1.1 42873 1jx7A 117 9.26e+00 c.114.1.1 77195 1tib 269 9.46e+00 3tgl c.69.1.17 34738 1qj4A 257 9.78e+00 1qj4A c.69.1.20 34796 1nvmA 345 9.85e+00 a.5.7.1 86249 c.1.10.5 86250 1i6pA 220 9.96e+00 1ddzA c.53.2.1 61848 1jp3A 253 9.96e+00 1f75A c.101.1.1 63221 1he2A 206 1.00e+01 1he2A c.2.1.2 60966 1nhkL 144 1.01e+01 1npk d.58.6.1 39142 1rdzA 337 1.01e+01 1frpA e.7.1.1 42882 1ezwA 349 1.03e+01 1ezwA c.1.16.3 29558 1pfkA 320 1.04e+01 3pfk c.89.1.1 35575 1hdoA 206 1.05e+01 1he2A c.2.1.2 60965 1gd9A 389 1.05e+01 c.67.1.1 60454 1khdA 345 1.08e+01 a.46.2.1 77400 c.27.1.1 77401 2pfkA 320 1.08e+01 3pfk c.89.1.1 35577 1p80A 753 1.09e+01 c.23.16.3 -6547 e.5.1.1 -11840 1cl2A 395 1.10e+01 1cl2A c.67.1.3 34397 1i88A 389 1.11e+01 c.95.1.2 66070 c.95.1.2 66071 1g3qA 237 1.14e+01 1hyqA c.37.1.10 60237 1kz8A 337 1.19e+01 e.7.1.1 77633 1fpkA 335 1.21e+01 1frpA e.7.1.1 42930 1eg5A 384 1.22e+01 1ecxA c.67.1.3 34429 1bjwA 382 1.24e+01 1bjwA c.67.1.1 34349 1eyqA 222 1.29e+01 1eypA d.36.1.1 38534 1efvA 315 1.29e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1bdfA 235 1.30e+01 1bdfA d.74.3.1 39727 d.181.1.1 42602 1cnv 299 1.31e+01 1cnv c.1.8.5 28989 1jepA 222 1.32e+01 d.36.1.1 66612 1b5pA 385 1.33e+01 c.67.1.1 -8133 1mxgA 435 1.35e+01 b.71.1.1 85193 c.1.8.1 85194 1olsA 400 1.39e+01 c.36.1.11 -6959 1q3kA 259 1.42e+01 unknown_sccs -6335 1fwcC 567 1.44e+01 1ubpC b.92.1.1 28410 c.1.9.2 29032 1qh5A 260 1.44e+01 1qh5A d.157.1.2 42057 1i4nA 251 1.45e+01 c.1.2.4 71114 1ejxC 567 1.46e+01 b.92.1.1 83184 c.1.9.2 83185 1thm 279 1.46e+01 1gci c.41.1.1 32544 2pia 321 1.48e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1og6A 298 1.48e+01 c.1.7.1 86984 1agx 331 1.50e+01 4pgaA c.88.1.1 35564 1m65A 245 1.53e+01 c.6.3.1 84847 1kekA 1231 1.58e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1yacA 208 1.61e+01 1yacA unknown_sccs 31757 1uehA 253 1.61e+01 c.101.1.1 -6879 1cb7B 483 1.62e+01 1cb7B c.1.19.2 29648 1tluA 130 1.62e+01 1ionA 243 1.62e+01 c.37.1.10 62633 1dvjC 246 1.65e+01 1dvjA c.1.2.3 28548 1rxxA 421 1.66e+01 unknown_sccs -10982 1b8gA 429 1.67e+01 1b8gA c.67.1.4 34499 1nni1 174 1.69e+01 1luaA 287 1.70e+01 c.2.1.7 78216 c.58.1.4 78217 1ccwB 483 1.70e+01 1cb7B c.1.19.2 29646 1dvjA 246 1.80e+01 1dvjA c.1.2.3 28546 1cp2A 269 1.80e+01 1cp2A c.37.1.10 32269 1k8cA 322 1.80e+01 c.1.7.1 72172 1iy8A 267 1.83e+01 c.2.1.2 83774 1m7yA 435 1.84e+01 c.67.1.4 78761 1ci8A 392 1.85e+01 e.3.1.1 64765 1bmbA 123 1.86e+01 1griA d.93.1.1 40466 1jr3A 373 1.86e+01 a.80.1.1 63245 c.37.1.20 63246 1frpA 335 1.87e+01 1frpA e.7.1.1 42875 1uroA 367 1.88e+01 1uroA c.1.22.1 29675 1jpnA 296 1.89e+01 a.24.13.1 67039 c.37.1.10 67040 1rpxA 230 1.91e+01 1rpxA c.1.2.2 28536 1jx6A 342 1.92e+01 c.93.1.1 67406 1ejrC 567 1.96e+01 1ubpC b.92.1.1 28420 c.1.9.2 29042 1dkgD 383 1.97e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1gefA 123 1.98e+01 1gefA c.52.1.18 60465 1un7A 400 2.00e+01 b.92.1.5 -5077 c.1.9.10 -5429 2pldA 105 2.00e+01 1qadA d.93.1.1 40521 1s4nA 348 2.06e+01 unknown_sccs -8262 1vc4A 254 2.06e+01 c.1.2.4 -5172 1j7dA 145 2.07e+01 1jatB d.20.1.1 62680 1icpA 376 2.08e+01 1oyc c.1.4.1 62270 1fggA 261 2.10e+01 1fggA c.68.1.7 34576 1kwsA 261 2.10e+01 c.68.1.7 73083 1griA 217 2.14e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1d7uA 433 2.16e+01 2dkb c.67.1.4 34439 1b16A 254 2.19e+01 1b16A c.2.1.2 29875 1r3sA 367 2.21e+01 c.1.22.1 -5648 1ma3A 253 2.24e+01 c.31.1.5 78883 1gwcA 230 2.24e+01 a.45.1.1 70660 c.47.1.5 70661 1eypA 222 2.27e+01 1eypA d.36.1.1 38536 1nuyA 337 2.31e+01 e.7.1.1 86213 1cr6B 554 2.36e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1v7zA 260 2.37e+01 unknown_sccs -6353 1a4uA 254 2.38e+01 1b16A c.2.1.2 29878 1cb0A 283 2.40e+01 1cb0A c.56.2.1 33790 1nnwA 252 2.42e+01 d.159.1.5 80674 1mi3A 322 2.43e+01 c.1.7.1 -5257 1m0qA 433 2.48e+01 c.67.1.4 78350 1hf2A 210 2.50e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1zfpE 98 2.53e+01 1griA d.93.1.1 40465 1umdA 367 2.54e+01 c.36.1.11 -6969 1dhpA 292 2.58e+01 1dhpA c.1.10.1 29097 1rvgA 305 2.60e+01 c.1.10.2 -5500 2bpa2 175 2.61e+01 2bpa2 1usgA 346 2.62e+01 c.93.1.1 -8635 1f2fA 104 2.62e+01 1fmk d.93.1.1 40455 1uuqA 440 2.63e+01 c.1.8.3 -5321 1jyrA 96 2.63e+01 d.93.1.1 71969 1ci9A 392 2.63e+01 e.3.1.1 64767 1dq3A 454 2.65e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1cydA 244 2.66e+01 1cydA c.2.1.2 29825 1nrzA 164 2.70e+01 c.38.1.1 86131 1yrgA 385 2.70e+01 1yrgA c.10.1.2 30854 1oxsC 353 2.71e+01 b.40.6.3 87519 c.37.1.12 87520 1edzA 320 2.73e+01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1km4A 247 2.75e+01 c.1.2.3 72740 2vhbA 146 2.75e+01 2vhbA a.1.1.2 15629 1evlA 401 2.77e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 2glsA 470 2.81e+01 1lgr d.15.9.1 37851 d.128.1.1 41181 2dkb 433 2.88e+01 2dkb c.67.1.4 34438 1mroB 442 2.90e+01 1mroB a.89.1.1 18531 d.58.31.2 39449 1uayA 242 2.93e+01 c.2.1.2 88390 1bf6A 291 2.94e+01 1pscA c.1.9.3 29065 1ngvA 534 2.94e+01 c.111.1.2 85698 1ipiA 123 2.95e+01 c.52.1.18 66255 1jf9A 408 2.98e+01 1c0nA c.67.1.3 62931 1n7kA 234 3.05e+01 c.1.10.1 85374 1hbnB 442 3.07e+01 1mroB a.89.1.1 60900 d.58.31.2 60901 1ii7A 333 3.13e+01 1ii7A d.159.1.4 62415 1b5tA 275 3.18e+01 1b5tA c.1.23.1 29676 2cevA 299 3.21e+01 1d3vA c.42.1.1 32576 1nd4A 264 3.24e+01 d.144.1.6 -11381 1vjrA 271 3.24e+01 unknown_sccs -6853 1t0iA 191 3.25e+01 1ls1A 295 3.27e+01 a.24.13.1 78170 c.37.1.10 78171 1vjpA 394 3.31e+01 c.2.1.3 -5897 d.81.1.3 -10480 1h05A 146 3.35e+01 c.23.13.1 76433 1j31A 262 3.39e+01 d.160.1.2 -11473 1vhcA 224 3.41e+01 c.1.10.1 -5488 1rlaA 323 3.42e+01 1d3vA c.42.1.1 32561 1o5kA 306 3.56e+01 c.1.10.1 -5482 1ni4A 365 3.58e+01 c.36.1.7 85728 1cec 343 3.60e+01 1ceo c.1.8.3 28809 1yrgB 385 3.68e+01 1yrgA c.10.1.2 30855 1nkxA 348 3.72e+01 c.94.1.2 -8704 1rxwA 336 3.74e+01 a.60.7.1 -1041 c.120.1.2 -6680 1liiA 363 3.75e+01 c.72.1.1 73921 1exnA 290 3.76e+01 1exnA a.60.7.1 18088 c.120.1.2 33358 1dxy 333 3.78e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1bqcA 302 3.82e+01 1bqcA c.1.8.3 28831 1fxtA 149 3.84e+01 d.20.1.1 65055 1uu1A 335 3.87e+01 c.67.1.1 -8146 1pvvA 315 3.89e+01 c.78.1.1 -8495 c.78.1.1 -8496 1dg3A 592 3.93e+01 1dg3A a.114.1.1 19078 c.37.1.8 32153 1c0nA 406 3.94e+01 1c0nA c.67.1.3 34433 1hvbA 349 3.96e+01 3pte e.3.1.1 42686 1fpzA 212 3.97e+01 1fpzA c.45.1.1 59976 1oltA 457 3.99e+01 unknown_sccs -5688 1gkzA 388 4.00e+01 a.29.5.1 65268 d.122.1.4 65269