# List of top-scoring protein chains for t2k-100-30-str2-scores 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 1bu8A 452 6.97e-01 1gpl b.12.1.2 23647 c.69.1.19 34795 2madH 373 9.52e-01 2bbkH b.69.2.1 27639 1gpl 432 1.07e+00 1gpl b.12.1.2 23645 c.69.1.19 34793 1a78A 134 1.37e+00 1c1lA b.29.1.3 24212 1rhoA 145 1.43e+00 1rhoA b.1.18.8 21899 1c5kA 439 1.54e+00 1crzA b.68.4.1 27630 c.51.2.1 33212 1otcA 495 1.60e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1crzA 403 1.65e+00 1crzA b.68.4.1 27629 c.51.2.1 33211 1rerA 391 1.70e+00 b.1.18.4 -2740 f.10.1.1 -12385 1rhoC 145 1.82e+00 1rhoA b.1.18.8 21901 1o91A 178 1.84e+00 b.22.1.1 -3282 1kmtA 141 2.05e+00 b.1.18.8 77442 1qrkA 731 2.24e+00 1f13A b.1.18.9 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1a12A 413 2.59e+00 1a12A b.69.5.1 27663 1v3eA 431 2.64e+00 b.68.1.1 -4584 1s1dA 331 2.71e+00 unknown_sccs -4566 1who 96 2.87e+00 1who b.7.3.1 23215 1gqyA 475 2.98e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1h6hA 143 2.99e+00 d.189.1.1 65681 1ds6B 180 3.07e+00 1rhoA b.1.18.8 21898 1f13A 731 3.07e+00 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1p3dA 475 3.08e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1of4A 179 3.18e+00 b.18.1.18 86932 1ex0A 731 3.87e+00 b.1.18.9 -2754 b.1.5.1 -2778 b.1.5.1 -2779 d.3.1.4 -8889 1oh4A 179 3.90e+00 b.18.1.18 -3123 1vcbC 160 4.02e+00 1vcbC b.3.3.1 22535 1oxdA 227 4.18e+00 d.22.1.1 -9438 1gvmA 136 4.19e+00 b.109.1.1 70612 1noa 113 4.35e+00 2mcm b.1.7.1 22208 1qksA 567 4.53e+00 1qksA a.3.1.2 15951 b.70.2.1 27710 1hcxA 127 4.56e+00 b.109.1.1 65800 1lqbC 162 4.63e+00 b.3.3.1 74186 1lm8V 160 4.73e+00 b.3.3.1 74035 1qwrA 319 4.77e+00 b.82.1.3 -4880 2bbkH 355 4.78e+00 2bbkH b.69.2.1 27634 1ikpA 613 4.80e+00 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1sltA 134 4.82e+00 1c1lA b.29.1.3 24186 1aoqA 567 5.00e+00 1qksA a.3.1.2 15934 b.70.2.1 27692 1g86A 142 5.02e+00 b.29.1.3 70161 1lcl 142 5.02e+00 1lcl b.29.1.3 24216 1hdkA 141 5.11e+00 b.29.1.3 65807 1fsoA 139 5.12e+00 1rhoA b.1.18.8 60007 1kypA 237 5.17e+00 d.22.1.1 73280 1r6wA 322 5.20e+00 c.1.11.2 -5563 d.54.1.1 -9821 1j5eK 129 5.54e+00 c.55.4.1 71554 1aomA 567 5.63e+00 1qksA b.70.2.1 27694 1fhuA 320 5.92e+00 1fhuA c.1.11.2 29234 d.54.1.1 38878 1psuA 140 5.96e+00 d.38.1.5 88285 1nepA 130 6.27e+00 b.1.18.7 80440 8fabA 212 6.32e+00 8fabA b.1.1.1 19772 b.1.1.2 20882 1jb7A 495 6.38e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1hq0A 295 6.77e+00 1hzgA d.194.1.1 61122 1ggtB 731 6.80e+00 1f13A b.1.18.9 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1hzgA 295 6.89e+00 1hzgA d.194.1.1 61436 1gr3A 160 6.90e+00 b.22.1.1 65476 1ema 236 6.99e+00 1ema d.22.1.1 38339 1evuA 731 7.25e+00 1f13A b.1.18.9 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1lj5A 379 7.55e+00 e.1.1.1 73928 1sltB 134 8.13e+00 1c1lA b.29.1.3 24187 1befA 181 8.41e+00 1befA b.47.1.3 26419 1umhA 184 8.65e+00 unknown_sccs -3127 1acx 108 8.79e+00 2mcm b.1.7.1 22211 1wwbX 103 8.90e+00 1wwcA b.1.1.4 21777 1g2aA 168 9.00e+00 d.167.1.1 65109 1qftA 175 9.08e+00 1qftA b.60.1.1 27151 1fjgK 129 9.54e+00 1fjfK c.55.4.1 33733 1ii7A 333 9.63e+00 1ii7A d.159.1.4 62415 1epwA 1290 9.84e+00 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1lw3A 657 1.00e+01 unknown_sccs -4378 unknown_sccs -7358 1j48A 110 1.00e+01 b.1.7.1 84112 2emo 237 1.01e+01 1ema d.22.1.1 38366 1jv4A 162 1.02e+01 b.60.1.1 67343 1df9A 191 1.03e+01 1befA b.47.1.3 26420 1wwaX 109 1.11e+01 1wwcA b.1.1.4 21775 1mdaH 368 1.12e+01 2bbkH b.69.2.1 27637 1mqkL 120 1.13e+01 b.1.1.1 85054 1j0hA 588 1.14e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1e2wA 251 1.19e+01 1hcz b.2.6.1 22466 b.84.2.2 28252 1qjgA 125 1.19e+01 1opy d.17.4.3 38102 1o0iA 138 1.19e+01 d.38.1.5 86532 1ocvA 125 1.23e+01 d.17.4.3 86810 1rypF 233 1.25e+01 1rypF d.153.1.4 41937 1ckaA 57 1.26e+01 1ckaA b.34.2.1 24459 1i9gA 280 1.29e+01 c.66.1.13 62090 1bjmA 216 1.30e+01 8fabA b.1.1.1 20524 b.1.1.2 21460 1j5wA 298 1.31e+01 d.104.1.1 71589 1fc1A 224 1.32e+01 1igtB b.1.1.2 21520 b.1.1.2 21521 1eylA 186 1.34e+01 1wba b.42.4.1 25593 1ktjA 129 1.35e+01 b.1.18.7 72974 1an8 208 1.36e+01 1an8 b.40.2.2 25202 d.15.6.1 37791 1g0uE 234 1.37e+01 d.153.1.4 41950 1slaA 134 1.45e+01 1c1lA b.29.1.3 24196 8cho 125 1.47e+01 1opy d.17.4.3 38108 1pgs 314 1.49e+01 1pgs b.121.1.1 23653 b.121.1.1 23654 1rovA 857 1.49e+01 a.119.1.1 -1656 b.12.1.1 -3034 1iwmA 186 1.53e+01 b.125.1.2 83758 1bp3B 211 1.57e+01 1axiB b.1.2.1 22031 b.1.2.1 22032 1c3hA 137 1.57e+01 b.22.1.1 -3255 1abmA 198 1.57e+01 1avmA 1f6fB 210 1.59e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1j05B 121 1.60e+01 b.1.1.1 -2251 1hw7A 255 1.62e+01 1i7fA d.193.1.1 61297 2mspA 126 1.64e+01 1mspA b.1.11.2 22335 1jnyA 435 1.70e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1eybA 471 1.70e+01 1ey2A b.82.1.4 28115 1fgqA 839 1.72e+01 1yge a.119.1.1 59826 b.12.1.1 59827 1mup 166 1.74e+01 1mup b.60.1.1 27133 1h8gA 95 1.76e+01 b.109.1.1 65735 1cqkA 101 1.76e+01 1cqkA b.1.1.2 21547 1aun 208 1.77e+01 1thv b.25.1.1 23900 1i05A 180 1.79e+01 1mup b.60.1.1 27130 1wkt 88 1.80e+01 1wkt b.11.1.2 23630 1ea2A 131 1.82e+01 d.17.4.3 64860 1dmmA 131 1.82e+01 1opy d.17.4.3 38114 1i0cA 60 1.82e+01 1aojA b.34.2.1 61485 1j9aA 184 1.83e+01 c.55.3.5 84135 1gguA 731 1.85e+01 1f13A b.1.18.9 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1lo7A 141 1.88e+01 d.38.1.1 74144 1qh0A 295 1.91e+01 b.43.4.2 68891 c.25.1.1 68892 1rl2A 137 1.91e+01 1rl2A b.34.5.3 24610 b.40.4.5 25342 1opy 131 1.94e+01 1opy d.17.4.3 38113 1suuA 312 1.95e+01 unknown_sccs -4610 1aw7A 194 1.96e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1ftrA 296 1.97e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1gc1H 229 1.99e+01 1gc1H b.1.1.1 20265 b.1.1.2 21265 1gzwA 134 2.00e+01 b.29.1.3 -3412 1ca1 370 2.00e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 2tnfA 156 2.01e+01 2tnfA b.22.1.1 23880 1ap6A 198 2.02e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1n0nA 199 2.03e+01 a.2.11.1 79750 d.44.1.1 79751 1n8jA 186 2.05e+01 c.47.1.10 85401 1icjA 168 2.06e+01 1bs4A d.167.1.1 42284 1bsjA 168 2.07e+01 1bs4A d.167.1.1 42302 1lktA 104 2.10e+01 1lktA b.90.1.1 28398 1h6rA 236 2.11e+01 d.22.1.1 65683 1o75A 415 2.16e+01 b.1.20.1 81117 b.1.20.1 81118 b.120.1.1 81119 1aizA 129 2.16e+01 1nwpA b.6.1.1 22903 3tss 194 2.16e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 1bhgA 613 2.19e+01 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1qg0A 308 2.23e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1rqwA 207 2.23e+01 b.25.1.1 -3313 1l6xA 207 2.23e+01 b.1.1.2 73642 b.1.1.2 73643 1thw 207 2.23e+01 1thv b.25.1.1 23903 1jdfA 447 2.25e+01 c.1.11.2 62897 d.54.1.1 62898 1pl4A 198 2.25e+01 a.2.11.1 -132 d.44.1.1 -9733 1oh0A 131 2.26e+01 d.17.4.3 87004 1fc2D 224 2.26e+01 1igtB b.1.1.2 21516 b.1.1.2 21517 1bs4A 168 2.29e+01 1bs4A d.167.1.1 42287 1bvqA 141 2.29e+01 1bvqA d.38.1.1 38542 1qy1A 174 2.33e+01 b.60.1.1 -4445 1drs 59 2.38e+01 3ebx g.7.1.2 44457 1g9mC 185 2.42e+01 1cdy b.1.1.1 19721 b.1.1.3 21660 1kjvB 100 2.44e+01 b.1.1.2 77423 1ii6A 368 2.44e+01 1bg2 c.37.1.9 62413 1n4xH 120 2.45e+01 b.1.1.1 85324 1ts3A 194 2.46e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1dyoA 160 2.46e+01 1dyoA b.18.1.7 23771 1memA 215 2.46e+01 1cs8A d.3.1.1 37069 1h1iB 350 2.47e+01 b.82.1.5 76470 1gv3A 248 2.48e+01 a.2.11.1 70585 d.44.1.1 70586 1h1iD 350 2.50e+01 b.82.1.5 76472 1yge 839 2.51e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1c5cH 215 2.51e+01 1igtB b.1.1.1 20475 b.1.1.2 21439 1h1iC 350 2.56e+01 b.82.1.5 76471 1pysA 350 2.57e+01 1pysA d.104.1.1 40775 1ecfA 504 2.61e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1f8nA 839 2.61e+01 1yge a.119.1.1 59703 b.12.1.1 59704 1vh5A 148 2.61e+01 d.38.1.5 -9677 1h09A 338 2.63e+01 b.109.1.1 83420 c.1.8.8 83421 1fs1B 141 2.63e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1is3A 135 2.64e+01 b.29.1.3 76773 1ngzB 220 2.64e+01 b.1.1.1 80502 b.1.1.2 80503 2eifA 136 2.66e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1iscA 192 2.66e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1elpA 173 2.67e+01 1amm b.11.1.1 23596 b.11.1.1 23597 1ec7A 446 2.68e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1go2A 304 2.68e+01 b.43.4.2 76243 c.25.1.1 76244 1qg7A 67 2.69e+01 1a15A d.9.1.1 37449 1h9sA 140 2.69e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1qynA 153 2.70e+01 d.33.1.1 -9585 1juhA 350 2.70e+01 b.82.1.5 71884 1o7kA 131 2.71e+01 d.189.1.1 81144 1isaA 192 2.72e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1kxgA 152 2.74e+01 b.22.1.1 73145 1qmvA 197 2.74e+01 1qq2A c.47.1.10 33066 1thv 207 2.77e+01 1thv b.25.1.1 23904 1kwnA 207 2.77e+01 b.25.1.1 77568 1c28A 135 2.84e+01 1c28A b.22.1.1 23857 1uyrA 737 2.88e+01 c.14.1.4 -6258 c.14.1.4 -6259 1b9mA 265 2.89e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1ecfB 504 2.90e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1ms9A 648 2.96e+01 b.29.1.15 85088 b.68.1.1 85089 1fhvA 323 2.96e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1g0dA 695 2.96e+01 1f13A b.1.18.9 60166 b.1.5.1 60167 b.1.5.1 60168 d.3.1.4 60169 1h6yA 170 2.99e+01 b.18.1.7 70904 1qxrA 189 2.99e+01 b.82.1.7 -4834 1fyhB 229 3.00e+01 1jrhI b.1.2.1 22055 b.1.2.1 22056 2fnbA 95 3.01e+01 2fnbA b.1.2.1 21979 1ey2A 471 3.02e+01 1ey2A b.82.1.4 28116 1jjuB 337 3.02e+01 b.69.2.2 66779 1tcrA 202 3.03e+01 1tcrA b.1.1.1 20605 b.1.1.2 21549 1b7yA 350 3.03e+01 1pysA d.104.1.1 40776 1ll1 590 3.04e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.18.3 21864 1c1lA 136 3.04e+01 1c1lA b.29.1.3 24219 1i7fA 292 3.04e+01 1i7fA d.193.1.1 61888 2azaA 129 3.05e+01 1nwpA b.6.1.1 22901 1plzA 189 3.07e+01 b.82.1.7 88160 1uxzA 131 3.08e+01 b.18.1.10 -3110 1qfhA 212 3.12e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1bncB 449 3.13e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1j1tA 233 3.14e+01 unknown_sccs -3462 1gu3A 149 3.15e+01 b.18.1.14 76350 1gcqC 70 3.17e+01 1gcpA b.34.2.1 60436 1jb9A 316 3.22e+01 1fnc b.43.4.2 62840 c.25.1.1 62841 1lla 628 3.22e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1vavA 222 3.24e+01 1g99A 408 3.26e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1o5uA 101 3.28e+01 b.82.1.8 -4845 1iz6A 138 3.28e+01 b.34.5.2 76976 b.40.4.5 76977 1qq2A 199 3.32e+01 1qq2A c.47.1.10 33064 1gd5A 130 3.33e+01 1gd5A d.189.1.1 60439 1fqvD 149 3.34e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1que 303 3.37e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1b2rA 304 3.41e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1pbyB 337 3.42e+01 b.69.2.2 -4611 1hlrA 907 3.46e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1gnhA 206 3.47e+01 1sacA b.29.1.5 24252 1psqA 163 3.49e+01 c.47.1.10 88283 1ift 263 3.53e+01 1mrj d.165.1.1 42211 1bkb 136 3.55e+01 1bkb b.34.5.2 24609 b.40.4.5 25341 1qfcA 306 3.57e+01 1uteA d.159.1.1 42077 3mspA 126 3.59e+01 1mspA b.1.11.2 22343 1a15A 67 3.61e+01 1a15A d.9.1.1 37451 1at0 145 3.61e+01 1at0 b.86.1.1 28374 1bqg 451 3.63e+01 1bqg c.1.11.2 29217 d.54.1.1 38861 1hxmD 242 3.64e+01 b.1.1.1 61373 b.1.1.2 61374 1liuA 528 3.66e+01 b.58.1.1 77970 c.1.12.1 77971 c.49.1.1 77972 1iam 185 3.74e+01 1zxq b.1.1.3 21653 b.1.1.4 21689 1mspA 126 3.74e+01 1mspA b.1.11.2 22333 1fonA 240 3.76e+01 5ptp b.47.1.2 26231 3chbD 104 3.77e+01 3chbD b.40.2.1 24970 1o5nA 126 3.79e+01 1vj2A 126 3.79e+01 unknown_sccs -4850 1e5pA 151 3.79e+01 1bj7 b.60.1.1 59272 1rvkA 382 3.80e+01 c.1.11.2 -5568 d.54.1.1 -9826 1fqvJ 149 3.80e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 3aprE 325 3.85e+01 2er7E b.50.1.2 26820 1sva1 361 3.88e+01 1vpsA 1pjxA 314 3.92e+01 1fna 93 3.94e+01 1fnf b.1.2.1 21971 1p5vA 235 3.94e+01 b.1.11.1 87812 b.7.2.1 87813 1jdpA 441 3.95e+01 c.93.1.1 62906 1i07A 60 3.98e+01 1aojA b.34.2.1 61477