# List of top-scoring protein chains for t04-100-30-bys 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 1lqtA 456 9.78e-02 c.3.1.1 74198 c.4.1.1 74199 1o91A 178 1.28e-01 b.22.1.1 -3282 1i9gA 280 3.23e-01 c.66.1.13 62090 1ex0A 731 3.85e-01 b.1.18.9 -2754 b.1.5.1 -2778 b.1.5.1 -2779 d.3.1.4 -8889 1vhoA 346 5.53e-01 unknown_sccs -4283 c.56.5.4 -7893 1mbmA 198 6.82e-01 b.47.1.3 78916 1evuA 731 6.90e-01 1f13A b.1.18.9 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 2arcA 164 7.42e-01 2arcA b.82.4.1 28148 1thjA 214 7.75e-01 1qreA b.81.1.5 28072 1h09A 338 8.34e-01 b.109.1.1 83420 c.1.8.8 83421 1qipA 183 1.01e+00 1qipA d.32.1.1 38470 1qreA 247 1.19e+00 1qreA b.81.1.5 28066 1who 96 1.55e+00 1who b.7.3.1 23215 1lw3A 657 1.74e+00 unknown_sccs -4378 unknown_sccs -7358 1amx 180 1.77e+00 1amx b.2.3.1 22410 1hlgA 371 1.81e+00 1hlgA c.69.1.6 34656 1v4sA 455 1.81e+00 c.55.1.3 -7604 c.55.1.3 -7605 1n7vA 555 1.82e+00 b.126.1.1 85377 1p97A 114 2.10e+00 unknown_sccs -10844 1noa 113 2.42e+00 2mcm b.1.7.1 22208 2apr 325 2.76e+00 2er7E b.50.1.2 26819 5croA 66 2.88e+00 1orc a.35.1.2 17044 3aprE 325 3.06e+00 2er7E b.50.1.2 26820 1p5vA 235 3.09e+00 b.1.11.1 87812 b.7.2.1 87813 1qmvA 197 3.11e+00 1qq2A c.47.1.10 33066 1vcbC 160 3.21e+00 1vcbC b.3.3.1 22535 1gttA 429 3.92e+00 d.177.1.1 70529 d.177.1.1 70530 1lqpA 135 4.25e+00 d.32.1.2 78151 1iscA 192 4.26e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1mspA 126 4.43e+00 1mspA b.1.11.2 22333 1czaN 917 4.52e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1lm8V 160 4.53e+00 b.3.3.1 74035 1gr3A 160 4.55e+00 b.22.1.1 65476 1nkiA 135 4.56e+00 d.32.1.2 -9544 1oxdA 227 4.67e+00 d.22.1.1 -9438 1befA 181 4.76e+00 1befA b.47.1.3 26419 1tl2A 236 4.82e+00 1tl2A b.67.1.1 27541 1p3dA 475 5.18e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1d2sA 170 5.20e+00 1d2sA b.29.1.4 24221 1sjyA 159 5.36e+00 d.113.1.1 -10908 1psuA 140 5.48e+00 d.38.1.5 88285 1f6fB 210 5.59e+00 1axiB b.1.2.1 22033 b.1.2.1 22034 1ii7A 333 5.62e+00 1ii7A d.159.1.4 62415 1j5wA 298 5.77e+00 d.104.1.1 71589 1f15A 218 5.88e+00 1f15B b.121.4.5 23320 1jxpA 186 6.00e+00 1jxpA b.47.1.3 26402 1h4uA 265 6.30e+00 1h4uA d.22.1.2 60622 g.3.11.5 60623 1ema 236 6.36e+00 1ema d.22.1.1 38339 2mspA 126 6.36e+00 1mspA b.1.11.2 22335 1ehiA 377 6.42e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1hy9A 41 6.77e+00 1hy9A g.3.17.1 61398 1f5fA 205 6.85e+00 1d2sA b.29.1.4 24222 1ig8A 486 6.99e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1gl4A 285 7.67e+00 d.22.1.2 65286 g.3.11.5 65287 1f42A 306 7.81e+00 1f42A b.1.1.4 59636 b.1.2.1 59637 b.1.2.1 59638 1e3aB 560 7.82e+00 1ajqB 1obpA 159 8.10e+00 1obpA b.60.1.1 27092 1onjA 61 8.12e+00 g.7.1.1 -12530 1dy9A 187 8.36e+00 1jxpA b.47.1.3 26400 1at0 145 8.84e+00 1at0 b.86.1.1 28374 1lci 550 8.90e+00 1lci e.23.1.1 43349 2azaA 129 9.05e+00 1nwpA b.6.1.1 22901 1grj 158 9.18e+00 1grj a.2.1.1 15691 d.26.1.2 38433 2eng 210 9.27e+00 2eng b.52.1.1 26895 1h7zA 194 9.58e+00 1qhvA b.21.1.1 60733 1aun 208 9.70e+00 1thv b.25.1.1 23900 1nqjA 119 9.71e+00 b.23.2.1 86031 1crzA 403 1.03e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1fl0A 171 1.05e+01 1eujA b.40.4.4 25315 1hlrA 907 1.09e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1gk9B 557 1.10e+01 1rybA 212 1.11e+01 c.56.3.1 -7858 1urrA 102 1.12e+01 1bi5A 389 1.12e+01 1bi5A c.95.1.2 35985 c.95.1.2 35986 1pbyB 337 1.13e+01 b.69.2.2 -4611 1fs1B 141 1.14e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 2viuA 328 1.14e+01 1hgeA b.19.1.2 23797 1h3nA 878 1.16e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1vj2A 126 1.17e+01 unknown_sccs -4850 1sr4A 206 1.17e+01 1hn2A 159 1.17e+01 b.60.1.1 65890 1gv3A 248 1.21e+01 a.2.11.1 70585 d.44.1.1 70586 1gt1A 159 1.23e+01 b.60.1.1 -4436 1dzlA 505 1.24e+01 1dzlA b.121.6.1 23586 1bt3A 345 1.25e+01 1bt3A a.86.1.2 18507 1bywA 110 1.26e+01 1bywA d.110.3.6 40912 1gsmA 210 1.27e+01 b.1.1.4 65535 b.1.1.4 65536 3proC 166 1.27e+01 3proC d.52.1.1 38812 d.52.1.1 38813 1ccwA 137 1.32e+01 1be1 c.23.6.1 31238 1r9hA 135 1.32e+01 d.26.1.1 -9482 1alo 907 1.34e+01 1alo 1ijtA 128 1.38e+01 1bfg b.42.1.1 62510 1lt5D 103 1.44e+01 3chbD b.40.2.1 24875 1p5vB 147 1.44e+01 b.2.3.2 87814 1gv9A 260 1.45e+01 b.29.1.13 70596 1fvuB 125 1.45e+01 1ixxB d.169.1.1 42346 1gdoA 240 1.47e+01 1gdoA d.153.1.1 41804 1kexA 155 1.48e+01 b.18.1.2 77350 1bqsA 209 1.51e+01 1bqsA b.1.1.4 21704 b.1.1.4 21705 1ocvA 125 1.53e+01 d.17.4.3 86810 1uw4A 91 1.53e+01 unknown_sccs -10038 1or0B 528 1.54e+01 1mr7A 209 1.58e+01 b.81.1.3 -4798 1g7sA 594 1.60e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1aw7A 194 1.60e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1q87A 221 1.62e+01 unknown_sccs -12028 1bs0A 384 1.63e+01 1bs0A c.67.1.4 34490 1eybA 471 1.64e+01 1ey2A b.82.1.4 28115 1n13B 113 1.65e+01 3tss 194 1.68e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 1cr5A 189 1.71e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1ihkA 174 1.71e+01 1bfg b.42.1.1 62384 1qhoA 686 1.75e+01 1cxlA b.1.18.2 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1ff9A 450 1.75e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1eljA 381 1.75e+01 4mbp c.94.1.1 35791 1fm2B 520 1.76e+01 1fm2B 1f32A 149 1.78e+01 1f32A d.62.1.1 39539 1fp3A 402 1.79e+01 1fp3A a.102.1.3 18842 1jenA 267 1.84e+01 1jenA 1vheA 373 1.85e+01 unknown_sccs -4280 c.56.5.4 -7890 1axdA 209 1.85e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1bio 228 1.89e+01 5ptp b.47.1.2 26314 1lla 628 1.90e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1rn5A 177 1.99e+01 d.167.1.1 -11591 1ec7A 446 1.99e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1ni9A 338 2.01e+01 e.7.1.2 85739 1uxzA 131 2.04e+01 b.18.1.10 -3110 1j9lA 247 2.05e+01 c.106.1.1 62762 3chbD 104 2.06e+01 3chbD b.40.2.1 24970 1a7cA 379 2.08e+01 1sek e.1.1.1 42660 1lgpA 116 2.11e+01 b.26.1.2 73890 1n62C 288 2.11e+01 d.87.2.1 80094 d.145.1.3 80095 1jb9A 316 2.12e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1g2aA 168 2.15e+01 d.167.1.1 65109 1bu8A 452 2.15e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1et9A 204 2.22e+01 1an8 b.40.2.2 25204 d.15.6.1 37793 1n8jA 186 2.25e+01 c.47.1.10 85401 1djrD 103 2.26e+01 3chbD b.40.2.1 24865 1jl0A 334 2.28e+01 1jenA d.156.1.1 63155 1bs4A 168 2.34e+01 1bs4A d.167.1.1 42287 1dgwA 178 2.38e+01 1dgwA b.82.1.2 28090 1epwA 1290 2.39e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1k3eA 156 2.40e+01 d.198.1.1 68103 1jmxA 494 2.41e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1qwlA 505 2.42e+01 e.5.1.1 -11823 1tif 78 2.43e+01 1tif d.15.8.1 37836 1memA 215 2.43e+01 1cs8A d.3.1.1 37069 1j58A 385 2.44e+01 b.82.1.2 71531 1kypA 237 2.45e+01 d.22.1.1 73280 1qd9A 124 2.46e+01 1qu9A d.79.1.1 39758 1uf5A 303 2.46e+01 1nksA 194 2.48e+01 1nksA c.37.1.1 31886 1nngA 153 2.49e+01 d.38.1.1 -9636 1cqqA 180 2.50e+01 1cqqA b.47.1.4 26422 1p9qC 256 2.51e+01 1ocxA 182 2.52e+01 b.81.1.3 86814 1e79A 510 2.60e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 2por 301 2.60e+01 2por f.4.3.1 43759 1s1dA 331 2.61e+01 unknown_sccs -4566 1gmyA 261 2.62e+01 d.3.1.1 76236 3ullA 132 2.63e+01 3ullA b.40.4.3 25282 1wkt 88 2.63e+01 1wkt b.11.1.2 23630 1suuA 312 2.68e+01 unknown_sccs -4610 1q2wA 308 2.69e+01 b.47.1.4 88355 1e9mA 106 2.69e+01 1ayfA d.15.4.1 59397 1ixkA 315 2.70e+01 unknown_sccs -8099 1k55A 246 2.73e+01 e.3.1.1 68156 1mngA 203 2.74e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1jmcA 246 2.77e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1hbnC 248 2.78e+01 1mroC d.58.31.1 60902 1iwmA 186 2.81e+01 b.125.1.2 83758 1qfhA 212 2.82e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 3ebx 62 2.82e+01 3ebx g.7.1.1 44389 1sdwA 314 2.84e+01 b.121.1.2 -3024 b.121.1.2 -3025 1erzA 303 2.92e+01 1erzA d.160.1.2 59498 1t95A 240 2.94e+01 1kqrA 179 2.95e+01 b.29.1.14 72886 1ltoA 245 2.95e+01 b.47.1.2 84707 4pep 326 2.97e+01 1smrA b.50.1.2 26843 1j9aA 184 2.97e+01 c.55.3.5 84135 1jzgA 128 2.98e+01 b.6.1.1 67855 1e3uA 246 2.99e+01 1fofA e.3.1.1 42755 1m1cA 680 3.00e+01 e.42.1.1 78395 1kopA 223 3.01e+01 2cba b.74.1.1 27966 1ollA 188 3.02e+01 b.1.1.4 -2690 b.1.1.4 -2691 1mroC 247 3.04e+01 1mroC d.58.31.1 39437 1jv4A 162 3.09e+01 b.60.1.1 67343 1rie 129 3.10e+01 1rie b.33.1.1 24427 1phm 310 3.15e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1qpxA 218 3.15e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1is3A 135 3.16e+01 b.29.1.3 76773 1i07A 60 3.17e+01 1aojA b.34.2.1 61477 1ckaA 57 3.18e+01 1ckaA b.34.2.1 24459 1o7kA 131 3.20e+01 d.189.1.1 81144 1iznB 277 3.20e+01 e.43.1.2 83848 1ekgA 127 3.28e+01 1dlxA d.82.2.1 40021 1mup 166 3.29e+01 1mup b.60.1.1 27133 1lkkA 105 3.29e+01 1lckA d.93.1.1 40412 1pjxA 314 3.30e+01 1erxA 184 3.31e+01 1np1A b.60.1.1 27164 1gpl 432 3.31e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1oj5A 132 3.31e+01 unknown_sccs -10848 1fvrA 327 3.32e+01 d.144.1.7 60047 1o97C 264 3.33e+01 c.26.2.3 81232 1ckmA 330 3.34e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1jpc 109 3.37e+01 1b2pA b.78.1.1 27986 1i06A 180 3.39e+01 1mup b.60.1.1 27131 1kq6A 141 3.40e+01 d.189.1.1 -9926 1i05A 180 3.41e+01 1mup b.60.1.1 27130 1ddlA 188 3.44e+01 1auyA b.121.4.6 23317 1qj2C 285 3.44e+01 1qj2C 1bb8 71 3.44e+01 2bb8 d.10.1.1 37478 3ladA 476 3.57e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1pyaB 228 3.59e+01 1pyaB 1igqA 62 3.60e+01 b.34.1.3 66130 1h8eA 510 3.64e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1h6fA 193 3.69e+01 b.2.5.4 70901 1dmmA 131 3.70e+01 1opy d.17.4.3 38114 1t5yA 190 3.72e+01 1pk6A 133 3.78e+01 b.22.1.1 -3287 1koiA 184 3.78e+01 b.60.1.1 68725 3pte 349 3.83e+01 3pte e.3.1.1 42687 8tlnE 316 3.84e+01 1hyt d.92.1.2 59075 1hstA 90 3.85e+01 1hstA a.4.5.13 16140 1kllA 130 3.85e+01 d.32.1.2 72720 1o0iA 138 3.87e+01 d.38.1.5 86532 1lktA 104 3.88e+01 1lktA b.90.1.1 28398 1ofzA 312 3.88e+01 b.68.8.1 86978 3psg 370 3.89e+01 1smrA b.50.1.2 26841 1opy 131 3.92e+01 1opy d.17.4.3 38113 1f00I 282 3.94e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1bxoA 323 3.96e+01 2er7E b.50.1.2 26805 1j33A 335 3.99e+01 c.39.1.1 77069 1p6oA 161 4.00e+01 c.97.1.2 -8774