# List of top-scoring protein chains for t2k-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 1mhyB 395 2.02e-03 1mtyB a.25.1.2 16781 1o86A 589 8.39e-03 d.92.1.5 81177 1ku2A 241 1.46e-01 a.4.13.1 83096 a.177.1.1 83097 1jalA 363 1.47e-01 c.37.1.8 84138 d.15.10.2 84139 1ut0A 190 1.87e-01 1pfvA 551 4.05e-01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1ncx 162 4.38e-01 1ncx a.39.1.5 17222 1paqA 189 5.18e-01 unknown_sccs -1557 1f4lA 551 5.52e-01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1bolA 222 7.98e-01 1bolA d.124.1.1 41120 1top 162 8.26e-01 1ncx a.39.1.5 17223 1oo0A 147 9.08e-01 d.232.1.1 87182 1ezvF 125 9.70e-01 1be3F f.27.1.1 59550 1kx9A 112 9.86e-01 unknown_sccs 77602 1kb9G 125 9.92e-01 f.27.1.1 77322 1cqxA 403 1.04e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1m6yA 301 1.05e+00 a.60.13.1 78716 c.66.1.23 78717 1lfkA 398 1.19e+00 a.104.1.1 77926 1rypJ 204 1.21e+00 d.153.1.4 41878 1orsC 132 1.33e+00 f.14.1.1 87353 1dvkA 173 1.42e+00 1dvkA a.72.1.1 18319 1na3A 91 1.46e+00 k.38.1.1 85481 1j54A 186 1.58e+00 c.55.3.5 77077 1kyoG 126 1.64e+00 f.27.1.1 73259 1om2A 95 1.84e+00 1om2A a.23.4.1 16520 1l6nA 289 1.94e+00 a.61.1.1 73624 a.73.1.1 73625 1n8vA 112 2.07e+00 unknown_sccs 85457 1elrA 131 2.21e+00 1a17 a.118.8.1 19209 1hiwA 133 2.29e+00 1hiwA a.61.1.1 18122 1sur 215 2.79e+00 1sur c.26.2.2 31620 1fioA 196 2.85e+00 1fioA a.47.2.1 17773 1g8qA 90 2.91e+00 1g8qA a.135.1.1 19621 1hzdA 272 3.00e+00 c.14.1.3 65969 1hme 77 3.01e+00 1cktA a.21.1.1 16418 1guxA 218 3.06e+00 1guxA a.74.1.3 18388 1n5uA 585 3.07e+00 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1qqtA 551 3.28e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1j6rA 214 3.35e+00 d.173.1.2 71598 1p7gA 222 3.46e+00 a.2.11.1 -108 d.44.1.1 -9742 1g0uI 205 3.91e+00 d.153.1.4 41891 1bj5 585 4.01e+00 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1b06A 210 4.05e+00 1avmA a.2.11.1 15740 d.44.1.1 38737 1irqA 71 4.15e+00 unknown_sccs 66297 1mvcA 240 4.19e+00 a.123.1.1 79499 1mmoD 512 4.28e+00 1mhyD a.25.1.2 16770 1k8tA 510 4.38e+00 e.41.1.1 68316 1h6oA 204 4.45e+00 a.146.1.1 60689 1pi1A 185 4.52e+00 unknown_sccs -762 1pbwA 216 4.61e+00 1pbwA a.116.1.1 19103 1n46A 258 5.17e+00 a.123.1.1 85315 1sedA 117 5.19e+00 1ha2A 585 5.21e+00 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1pauB 102 5.42e+00 1pauB 1hkvA 453 5.48e+00 b.49.2.3 83559 c.1.6.1 83560 1or7C 90 5.48e+00 a.180.1.1 87336 1dxtB 147 5.57e+00 1abwA a.1.1.2 15450 1rxxA 421 5.81e+00 unknown_sccs -10982 1vkiA 181 5.90e+00 1nt2B 258 6.08e+00 a.183.1.1 86150 1nmeB 92 6.16e+00 1cp3A 277 6.18e+00 1pauA c.17.1.1 30992 1gewA 356 6.27e+00 1gewA c.67.1.1 60470 1tam 132 6.34e+00 1hiwA a.61.1.1 18128 1e7aA 585 6.57e+00 1bj5 a.126.1.1 19360 a.126.1.1 19361 a.126.1.1 19362 2hmx 133 6.67e+00 1hiwA a.61.1.1 18129 1m12A 84 6.74e+00 a.64.1.1 84745 1ad3A 452 6.81e+00 1ad3A c.82.1.1 35335 1pxgA 382 7.00e+00 c.1.20.1 -5616 1k4gA 386 7.08e+00 c.1.20.1 72054 1pud 386 7.12e+00 1pud c.1.20.1 29658 1f3eA 386 7.13e+00 1pud c.1.20.1 29661 1vns 609 7.36e+00 1vns a.111.1.3 19061 1vnc 609 7.41e+00 1vns a.111.1.3 19065 1tbmA 326 7.74e+00 1lvfA 110 7.98e+00 a.47.2.1 74280 1qr0A 228 8.07e+00 1qr0A d.150.1.1 59038 d.150.1.1 59039 1babB 146 8.17e+00 1abwA a.1.1.2 15414 1ub9A 100 8.18e+00 a.4.5.28 -231 1ngmB 72 8.79e+00 j.104.1.1 85687 1q9jA 422 8.87e+00 1kqfC 217 8.88e+00 f.21.1.1 72874 1j7yB 146 8.91e+00 a.1.1.2 66427 1it2A 146 9.03e+00 a.1.1.2 66365 1r5yA 386 9.10e+00 c.1.20.1 -5626 1oq9A 363 9.16e+00 a.25.1.2 87257 1h3nA 878 9.26e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1in6A 334 9.36e+00 1hqcA a.4.5.11 62601 c.37.1.20 62602 1n97A 389 9.45e+00 a.104.1.1 80335 1iuqA 367 9.60e+00 c.112.1.1 -8440 1k6xA 352 9.65e+00 c.2.1.2 68238 1k30A 368 1.00e+01 c.112.1.1 68067 1afrA 345 1.03e+01 1afrA a.25.1.2 16805 1kkhA 317 1.04e+01 d.14.1.5 72645 d.58.26.3 72646 1m2oA 768 1.04e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1odoA 408 1.05e+01 a.104.1.1 -1463 1ciy 590 1.05e+01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1p2fA 220 1.09e+01 a.4.6.1 87720 c.23.1.1 87721 1ixmA 192 1.09e+01 1ixmA d.123.1.1 41114 1qk4A 233 1.09e+01 1qk3A c.61.1.1 34037 1i37A 260 1.11e+01 1a28A a.123.1.1 61583 1o0wA 252 1.16e+01 a.149.1.1 80751 d.50.1.1 80752 1nrjA 158 1.17e+01 d.110.4.4 86124 1fsgA 233 1.19e+01 1qk3A c.61.1.1 34029 1gh8A 89 1.20e+01 1gh8A d.58.12.1 39309 1k6iA 352 1.23e+01 c.2.1.2 68223 1sk7A 198 1.27e+01 1dbqA 289 1.32e+01 1qpzA c.93.1.1 35666 1fg7A 356 1.34e+01 1gewA c.67.1.1 59819 1lshA 1056 1.34e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1lk5A 229 1.35e+01 unknown_sccs 73960 d.58.40.1 73961 1hbkA 94 1.35e+01 1aca a.11.1.1 60887 1vkeA 133 1.36e+01 1cjbA 231 1.40e+01 1qk3A c.61.1.1 34079 1irdB 146 1.41e+01 a.1.1.2 66287 1mgn 154 1.42e+01 1a6m a.1.1.2 15097 1h6pA 203 1.42e+01 a.146.1.1 60690 1d2zA 108 1.42e+01 1d2zA a.77.1.2 18437 1sig 339 1.44e+01 1sig a.177.1.1 19068 1av1A 201 1.44e+01 1av1A h.5.1.1 45796 1ki1B 352 1.44e+01 a.87.1.1 72497 b.55.1.1 72498 1in4A 334 1.45e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1eza 259 1.47e+01 1zymA a.60.10.1 18113 c.8.1.2 30708 1e3pA 757 1.55e+01 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698 1k89 449 1.56e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1a32 88 1.56e+01 1a32 a.16.1.2 16384 1eqfA 280 1.57e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1os8A 223 1.57e+01 b.47.1.1 -4113 1m4vA 204 1.58e+01 b.40.2.2 74459 d.15.6.1 74460 1sgt 223 1.59e+01 5ptp b.47.1.1 25814 1gnwA 211 1.64e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1j8yF 297 1.65e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1o9rA 162 1.68e+01 a.25.1.1 86706 1a87 321 1.74e+01 1a87 f.1.1.1 43380 1qtnB 95 1.76e+01 1pauB 1hsm 79 1.76e+01 1cktA a.21.1.1 16421 1rypD 241 1.81e+01 1rypD d.153.1.4 41935 1ash 150 1.84e+01 1ash a.1.1.2 15622 1bgvA 449 1.86e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1qpzA 340 1.90e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1vk3A 615 1.92e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1oxjA 173 1.95e+01 a.60.1.2 87517 a.118.1.13 87518 1ao6A 585 1.95e+01 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1lvaA 258 1.95e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1oyzA 280 1.95e+01 unknown_sccs -1573 1kkcA 221 1.97e+01 a.2.11.1 68660 d.44.1.1 68661 1dj8A 89 1.97e+01 1bg8A a.57.1.1 17919 1r9dA 787 1.97e+01 1dceA 567 2.03e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 2hrvA 142 2.09e+01 2hrvA b.47.1.4 26429 1a8h 500 2.09e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1wetA 340 2.16e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1dkxA 219 2.20e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1k1vA 41 2.23e+01 a.37.1.1 71999 1zymA 258 2.23e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1onwA 390 2.25e+01 b.92.1.7 87172 c.1.9.13 87173 1bg8A 89 2.27e+01 1bg8A a.57.1.1 17925 1eco 136 2.27e+01 1flp a.1.1.2 15208 1d9cA 121 2.29e+01 1d9cA a.26.1.3 16901 1vpwA 340 2.30e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1f07A 321 2.39e+01 1ezwA c.1.16.3 59560 1gvnA 90 2.39e+01 a.8.2.1 76353 1m2tA 254 2.40e+01 d.165.1.1 84761 1be3C 379 2.41e+01 1be3C f.32.1.1 75805 f.21.1.2 75806 1oruA 195 2.41e+01 unknown_sccs -4390 1eca 136 2.50e+01 1flp a.1.1.2 15209 1ecd 136 2.50e+01 1flp a.1.1.2 15211 1ixmB 192 2.51e+01 1ixmA d.123.1.1 41115 1i3dA 146 2.51e+01 a.1.1.2 61587 1qgrA 876 2.53e+01 1qgrA a.118.1.1 19119 1e2xA 243 2.56e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1gu9A 177 2.56e+01 a.152.1.1 65540 1bzyA 217 2.58e+01 1qk3A c.61.1.1 34071 1mtyD 512 2.59e+01 1mhyD a.25.1.2 16742 1qoyA 318 2.61e+01 1qoyA h.4.4.1 45788 1b47A 304 2.63e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1adt 356 2.65e+01 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1guxB 152 2.69e+01 1guxB a.74.1.3 18389 1lnwA 147 2.69e+01 a.4.5.28 78104 1uedA 406 2.72e+01 a.104.1.1 -1459 1hrdA 449 2.73e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1q0gA 117 2.94e+01 1j8mF 297 2.96e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1wer 334 2.96e+01 1wer a.116.1.2 19108 1hh8A 213 2.97e+01 1e96B a.118.8.1 61042 1zac 90 2.98e+01 1ncx a.39.1.5 17236 1khyA 148 2.98e+01 a.174.1.1 77410 1en7A 157 3.02e+01 1en7A a.140.4.1 64733 d.4.1.5 64734 1kncA 177 3.02e+01 a.152.1.1 68703 1b0nB 57 3.08e+01 1b0nB a.34.1.1 17002 1dmuA 299 3.11e+01 1dmuA c.52.1.4 33294 1a4iA 301 3.12e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1onxA 390 3.16e+01 b.92.1.7 87176 c.1.9.13 87177 1fkmA 396 3.16e+01 1fkmA a.69.2.1 18315 a.69.2.1 18316 1s35A 214 3.18e+01 a.7.1.1 -391 a.7.1.1 -392 1h6kA 757 3.30e+01 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1k04A 162 3.31e+01 a.24.14.1 67904 1ax8 146 3.33e+01 1ax8 a.26.1.1 16844 1pd3A 58 3.35e+01 unknown_sccs -767 1m33A 258 3.37e+01 c.69.1.26 78514 1ohuA 175 3.37e+01 f.1.4.1 -12058 1f16A 192 3.38e+01 1f16A f.1.4.1 43400 1qgtA 149 3.39e+01 1qgtA a.62.1.1 18135 1f7lA 121 3.42e+01 1f7lA d.150.1.2 59666 1h0aA 158 3.49e+01 a.118.9.1 76434 1v61A 132 3.49e+01 1kjwA 295 3.53e+01 b.34.2.1 68643 c.37.1.1 68644 1d5nA 205 3.53e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 1peqA 714 3.56e+01 1fdi 715 3.61e+01 2napA b.52.2.2 26918 c.81.1.1 35326 1anv 356 3.62e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1sek 378 3.72e+01 1sek e.1.1.1 42675 1eumA 165 3.72e+01 1eumA a.25.1.1 59507 1d1dA 262 3.76e+01 1d1dA a.28.3.1 16958 a.73.1.1 18335 1diaA 306 3.78e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1a4iB 301 3.83e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1em9A 154 3.84e+01 1d1dA a.73.1.1 18333 1j7nB 776 3.85e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1reoA 486 3.86e+01 c.3.1.2 -5997 d.16.1.5 -9217 1colA 204 3.89e+01 1a87 f.1.1.1 43378 2btvA 901 3.91e+01 2btvA e.28.1.1 43376 1v9dA 340 3.91e+01 unknown_sccs -1762