# 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 1c25 161 1.08e-16 1c25 c.46.1.1 32698 1qb0A 211 3.83e-16 1c25 c.46.1.1 32699 1ymkA 175 5.79e-16 1t3kA 152 1.10e-10 1gn0A 108 1.99e-07 c.46.1.3 65358 1gmxA 108 2.02e-07 c.46.1.3 65355 1yt8A 539 1.89e-06 1uarA 285 3.47e-06 1e0cA 271 3.33e-05 1e0cA c.46.1.2 32717 c.46.1.2 32718 1rhs 296 5.36e-05 1rhs c.46.1.2 32703 c.46.1.2 32704 1rhd 293 8.42e-05 1rhs c.46.1.2 32715 c.46.1.2 32716 1wv9A 94 9.59e-05 1okgA 373 5.03e-04 c.46.1.2 93250 c.46.1.2 93251 d.26.1.3 93252 1whbA 157 1.30e-03 1hzmA 154 1.47e-03 c.46.1.1 65975 1d5rA 324 3.63e-01 1d5rA b.7.1.1 23181 c.45.1.1 32697 1jl3A 139 1.10e+00 c.44.1.1 66826 1yn9A 169 1.32e+00 1g5pA 289 1.80e+00 1cp2A c.37.1.10 32253 1i9sA 210 1.84e+00 1i9sA c.45.1.1 62099 2bkaA 242 2.04e+00 1u24A 337 2.43e+00 1xriA 151 2.46e+00 1gpjA 404 2.69e+00 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1fp6A 289 4.04e+00 1cp2A c.37.1.10 32243 3adk 195 4.34e+00 1zin c.37.1.1 31885 1z83A 196 4.63e+00 1qo2A 241 4.64e+00 1qo2A c.1.2.1 28533 1vbuA 328 4.69e+00 2a0mA 316 5.00e+00 1yveJ 524 5.25e+00 1qmgA a.100.1.2 18790 c.2.1.6 30187 2fokA 579 5.33e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 2shpA 525 5.39e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1fkx 349 5.66e+00 1a4mA c.1.9.1 29018 1ur1A 378 6.23e+00 c.1.8.3 99804 1vdmA 153 6.41e+00 1ad1A 266 6.42e+00 1aj2 c.1.21.1 29668 1i88A 389 6.57e+00 c.95.1.2 66070 c.95.1.2 66071 1t9kA 347 6.57e+00 1i86A 389 6.65e+00 c.95.1.2 66068 c.95.1.2 66069 1bi5A 389 6.65e+00 1bi5A c.95.1.2 35985 c.95.1.2 35986 1d0sA 356 6.81e+00 1d0vA c.39.1.1 32477 1yveI 524 6.82e+00 1qmgA a.100.1.2 18789 c.2.1.6 30186 1qmgA 524 6.82e+00 1qmgA a.100.1.2 18785 c.2.1.6 30182 1cp2A 269 6.87e+00 1cp2A c.37.1.10 32269 1bvh 157 6.93e+00 1dg9A c.44.1.1 32640 1e5dA 402 7.22e+00 1e5dA c.23.5.1 31208 d.157.1.3 42061 1r6uA 437 7.25e+00 c.26.1.1 97163 1d0vA 356 7.82e+00 1d0vA c.39.1.1 32476 1vhrA 184 7.93e+00 1vhrA c.45.1.1 32651 1dkuA 317 7.96e+00 1dkuA c.61.1.2 34118 c.61.1.2 34119 1ad4A 266 8.20e+00 1aj2 c.1.21.1 29670 1vl6A 388 8.28e+00 1g4uS 383 8.48e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1l5oA 356 8.50e+00 c.39.1.1 77711 1phr 157 8.77e+00 1dg9A c.44.1.1 32635 1c0eA 157 8.82e+00 1dg9A c.44.1.1 32638 1dkrA 317 9.24e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1c7gA 456 9.26e+00 c.67.1.2 90415 1nijA 318 9.57e+00 c.37.1.10 85741 d.237.1.1 85742 1ecfB 504 1.00e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1vmaA 306 1.01e+01 1yptA 305 1.03e+01 1ytw c.45.1.2 32686 1add 349 1.04e+01 1a4mA c.1.9.1 29020 1ibsA 317 1.06e+01 c.61.1.2 66107 c.61.1.2 66108 1bjoA 360 1.09e+01 1bjnA c.67.1.4 34471 1jh8A 356 1.14e+01 c.39.1.1 63052 1ihnA 113 1.17e+01 1ihnA c.103.1.1 62388 1a4mA 349 1.18e+01 1a4mA c.1.9.1 29014 1t6nA 220 1.21e+01 1ecfA 504 1.21e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1mb4A 370 1.22e+01 c.2.1.3 78908 d.81.1.1 78909 1eucA 311 1.23e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 1ytw 306 1.26e+01 1ytw c.45.1.2 32689 1rpmA 278 1.27e+01 2shpA c.45.1.2 32679 1h5yA 253 1.29e+01 c.1.2.1 65638 1dg9A 157 1.29e+01 1dg9A c.44.1.1 32637 1vecA 206 1.30e+01 c.37.1.19 100575 1nsj 205 1.30e+01 1nsj c.1.2.4 28560 1jpnA 296 1.30e+01 a.24.13.1 67039 c.37.1.10 67040 1u2pA 163 1.34e+01 2ng1 293 1.40e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1ytn 306 1.42e+01 1ytw c.45.1.2 32688 1ii2A 524 1.42e+01 c.91.1.1 66146 c.109.1.1 66147 1hl2A 297 1.44e+01 c.1.10.1 83581 1m6yA 301 1.44e+01 a.60.13.1 78716 c.66.1.23 78717 1e2uA 553 1.44e+01 1e1dA e.26.1.1 43362 1brwA 433 1.45e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1gntA 553 1.45e+01 e.26.1.1 70290 1nni1 174 1.46e+01 1ewkA 490 1.46e+01 1ewkA c.93.1.1 35712 1jx4A 352 1.49e+01 d.240.1.1 90378 e.8.1.7 90379 3mag 307 1.50e+01 3mag c.66.1.25 34205 1e1dA 553 1.52e+01 1e1dA e.26.1.1 43363 1hzdA 272 1.52e+01 c.14.1.3 65969 1aky 221 1.54e+01 1zin c.37.1.1 31896 g.41.2.1 45197 1aj2 282 1.57e+01 1aj2 c.1.21.1 29665 1aj0 282 1.57e+01 1aj2 c.1.21.1 29667 1lgyA 269 1.59e+01 3tgl c.69.1.17 34758 1q0rA 298 1.59e+01 c.69.1.28 95508 1fbtA 190 1.59e+01 1bif c.60.1.4 34004 1eyeA 280 1.68e+01 1aj2 c.1.21.1 29672 1larA 575 1.69e+01 1larA c.45.1.2 32693 c.45.1.2 32694 1i9gA 280 1.70e+01 c.66.1.13 62090 1t9bA 677 1.74e+01 1e4yA 214 1.77e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1jscA 630 1.81e+01 c.31.1.3 67224 c.36.1.5 67225 c.36.1.9 67226 1ao0A 459 1.81e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 1jlnA 297 1.82e+01 1pty c.45.1.2 63172 1v37A 177 1.83e+01 2trcP 217 1.83e+01 1b9yC c.47.1.6 33051 2ptd 298 1.83e+01 2plc c.1.18.2 29605 1g6oA 330 1.84e+01 1g6oA c.37.1.11 32430 1o6dA 163 1.84e+01 c.116.1.3 92567 2scuB 388 1.84e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1vpt 348 1.86e+01 3mag c.66.1.25 34207 1g291 372 1.88e+01 1g291 1ls1A 295 1.91e+01 a.24.13.1 78170 c.37.1.10 78171 1bjnA 360 1.92e+01 1bjnA c.67.1.4 34469 1o12A 376 1.96e+01 b.92.1.5 80758 c.1.9.10 80759 1rcuA 195 1.99e+01 c.129.1.1 97295 1bgp 309 2.09e+01 1bgp a.93.1.1 18690 1yqtA 538 2.09e+01 1h1nA 305 2.11e+01 c.1.8.3 70855 2bjfA 329 2.12e+01 1v39 322 2.13e+01 3mag c.66.1.25 34206 1vp9 322 2.13e+01 3mag c.66.1.25 34210 1h8eA 510 2.15e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1eudB 396 2.16e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1zip 217 2.18e+01 1zin c.37.1.1 31916 g.41.2.1 45179 1im5A 180 2.18e+01 c.33.1.3 66211 1dtgA 334 2.20e+01 1nnt c.94.1.2 35896 1i2oA 316 2.21e+01 1onrA c.1.10.1 61574 1fokA 568 2.22e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1k87A 669 2.23e+01 a.176.1.1 77286 c.1.23.2 77287 1k66A 149 2.25e+01 c.23.1.1 90941 1iukA 140 2.27e+01 c.2.1.8 83712 1t64A 377 2.35e+01 1nipA 289 2.36e+01 1cp2A c.37.1.10 32263 1tia 279 2.42e+01 3tgl c.69.1.17 34737 1gnlA 544 2.44e+01 e.26.1.1 70287 1eudA 311 2.53e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1jqfA 334 2.56e+01 c.94.1.2 67086 1eucB 396 2.57e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1bfd 528 2.58e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1dn1A 594 2.58e+01 1dn1A e.25.1.1 43357 1svsA 353 2.60e+01 1fdyA 297 2.61e+01 1nal3 c.1.10.1 29071 1vj1A 363 2.69e+01 b.35.1.2 100794 c.2.1.1 100795 1p15A 253 2.70e+01 c.45.1.2 93894 1fg7A 356 2.72e+01 1gewA c.67.1.1 59819 1mu7A 485 2.75e+01 d.136.1.3 79475 d.136.1.3 79476 1zin 217 2.77e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1e79A 510 2.78e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1e3hA 757 2.79e+01 1e3hA a.4.9.1 16257 d.14.1.4 37572 d.14.1.4 37573 d.52.3.1 38810 d.101.1.1 40695 d.101.1.1 40696 1sfsA 240 2.81e+01 c.1.8.8 98846 1nal1 297 2.83e+01 1nal3 1rhxA 87 2.85e+01 1fsz 372 2.87e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1khdA 345 2.96e+01 a.46.2.1 77400 c.27.1.1 77401 1gewA 356 2.97e+01 1gewA c.67.1.1 60470 1auiA 521 2.99e+01 1auiA d.159.1.3 42085 1q6zA 528 3.01e+01 1xo1A 291 3.04e+01 1exnA a.60.7.1 18086 c.120.1.2 33356 1exnB 290 3.04e+01 1exnA a.60.7.1 18089 c.120.1.2 33359 1mx3A 347 3.05e+01 c.2.1.4 79638 c.23.12.1 79639 1jy1A 464 3.05e+01 d.136.1.3 67438 d.136.1.3 67439 1sqgA 429 3.08e+01 1tplA 426 3.09e+01 1ax4A c.67.1.2 34387 1rpxA 230 3.10e+01 1rpxA c.1.2.2 28536 1w30A 201 3.11e+01 1bglA 1023 3.12e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1xhbA 472 3.14e+01 1xeaA 323 3.14e+01 1j93A 353 3.16e+01 c.1.22.1 66454 1d3kA 329 3.21e+01 1nnt c.94.1.2 35889 1pgvA 197 3.22e+01 c.10.1.1 88073 1a8e 329 3.23e+01 1cb6A c.94.1.2 35888 1g57A 217 3.27e+01 1g57A d.115.1.2 60253 2bijA 305 3.29e+01 1php 394 3.31e+01 16pk c.86.1.1 35452 1vdrA 162 3.35e+01 1vdrA c.71.1.1 34893 1ngvA 534 3.37e+01 c.111.1.2 85698 1wchA 315 3.38e+01 1iezA 217 3.39e+01 d.115.1.2 66129 1t0iA 191 3.42e+01 1jilA 420 3.43e+01 c.26.1.1 66745 1uuqA 440 3.44e+01 c.1.8.3 100015 1s8nA 205 3.44e+01 1z5vA 474 3.45e+01 1ryoA 327 3.48e+01 c.94.1.2 98108 1yovA 537 3.48e+01 2hnp 321 3.49e+01 1pty c.45.1.2 32678 1eqnA 321 3.55e+01 1dd9A e.13.1.1 43256 1xcbA 211 3.56e+01 1thfD 253 3.56e+01 1thfD c.1.2.1 28535 1jfvA 131 3.60e+01 c.44.1.1 66654 1ym3A 215 3.65e+01 1tp9A 162 3.65e+01 1ra9 159 3.67e+01 1vdrA c.71.1.1 34820 1ee9A 320 3.72e+01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1mo2A 294 3.73e+01 c.69.1.22 79331 1b9yC 246 3.80e+01 1b9yC c.47.1.6 33052 1ki9A 192 3.82e+01 c.37.1.1 84404 1g7fA 298 3.86e+01 1pty c.45.1.2 60330 1yd7A 395 3.94e+01 1vmiA 355 3.95e+01 1xfoA 357 3.98e+01 1p3jA 217 3.99e+01 c.37.1.1 94022 g.41.2.1 94023