# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1n99A 166 3.77e-03 b.36.1.1 85459 b.36.1.1 85460 1pcfA 66 2.48e-01 1pcfA d.18.1.1 38142 1s72Q 96 2.78e-01 1jj2P 95 3.47e-01 1ffkN b.34.5.1 63101 1nm1G 125 4.37e-01 d.109.1.1 80653 1yagG 125 4.55e-01 1d0nA d.109.1.1 40846 1umgA 362 4.90e-01 1d4xG 126 5.55e-01 1d0nA d.109.1.1 59109 1gmyA 261 9.57e-01 d.3.1.1 76236 1h9oA 112 1.03e+00 1qadA d.93.1.1 60837 1fy2A 229 1.14e+00 1fyeA c.23.16.4 31478 1ffkN 95 1.33e+00 1ffkN b.34.5.1 24606 1theB 260 1.34e+00 1theB d.3.1.1 37057 1bdo 80 1.42e+00 1bdo b.84.1.1 28214 1o12A 376 1.45e+00 b.92.1.5 80758 c.1.9.10 80759 1theA 260 1.47e+00 1theB d.3.1.1 37056 1delA 241 1.51e+00 1dekA c.37.1.1 31844 1e19A 314 1.51e+00 1b7bA c.73.1.1 34967 1m4tA 392 1.63e+00 c.95.1.1 78617 c.95.1.1 78618 1inp 400 1.80e+00 1inp e.7.1.1 42972 1dekA 241 1.81e+00 1dekA c.37.1.1 31842 1qadA 111 1.83e+00 1qadA d.93.1.1 40498 1d7yA 408 1.89e+00 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1m3kA 392 1.94e+00 c.95.1.1 78565 c.95.1.1 78566 1csbB 205 2.01e+00 1theB 1h2aL 567 2.11e+00 1h2rL e.18.1.1 43299 1qflA 389 2.17e+00 1afwA c.95.1.1 35908 c.95.1.1 35909 1aisA 182 2.37e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1q7zA 566 2.44e+00 c.1.21.2 -5638 c.1.26.1 -5666 1v5sA 126 2.63e+00 1fyeA 229 2.70e+00 1fyeA c.23.16.4 31477 1bfi 112 2.74e+00 1qadA d.93.1.1 40499 1g9oA 91 2.74e+00 1pdr b.36.1.1 60400 1ot5A 477 2.79e+00 b.18.1.20 87409 c.41.1.1 87410 1d8hA 311 2.84e+00 1d8iA d.63.1.1 39544 1bzyA 217 3.16e+00 1qk3A c.61.1.1 34071 1r9hA 135 3.22e+00 d.26.1.1 -9482 1a65A 504 3.36e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1deuA 277 3.42e+00 1theB d.3.1.1 37085 1dpo 223 3.44e+00 5ptp b.47.1.2 25975 1h2rL 534 3.47e+00 1h2rL e.18.1.1 43298 1un3A 123 3.61e+00 d.5.1.1 -8933 1h0fA 123 3.62e+00 1hbyA 123 3.67e+00 7rsa d.5.1.1 60936 1ton 235 3.68e+00 5ptp b.47.1.2 26307 1ubkL 534 3.73e+00 e.18.1.1 88422 1ju3A 583 3.74e+00 b.18.1.13 67300 c.69.1.21 67301 1k6wA 426 3.74e+00 b.92.1.2 68236 c.1.9.5 68237 2cro 71 3.80e+00 1r69 a.35.1.2 17038 1ush 550 3.83e+00 1ush d.114.1.1 40923 d.159.1.2 42079 1zug 71 3.85e+00 1r69 a.35.1.2 17041 1onxA 390 4.16e+00 b.92.1.7 87176 c.1.9.13 87177 1r6jA 82 4.17e+00 b.36.1.1 -3732 1i92A 91 4.18e+00 1pdr b.36.1.1 61990 1qq2A 199 4.22e+00 1qq2A c.47.1.10 33064 1ehiA 377 4.40e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1a4yB 123 4.47e+00 7rsa d.5.1.1 37296 1nteA 82 4.54e+00 b.36.1.1 86163 1dypA 271 4.68e+00 1dypA b.29.1.2 24185 1k3fA 253 4.76e+00 c.56.2.1 68105 1eo9B 241 4.82e+00 3pchM b.3.6.1 22826 1k59A 123 4.93e+00 d.5.1.1 72073 1g1cA 99 5.01e+00 b.1.1.4 65078 1e3pA 757 5.16e+00 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 1fr2B 134 5.18e+00 d.4.1.1 83257 1s83A 223 5.22e+00 b.47.1.2 -4178 1umhA 184 5.27e+00 unknown_sccs -3127 1lrzA 426 5.34e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1p1lA 102 5.37e+00 d.58.5.2 87695 1df9A 191 5.42e+00 1befA b.47.1.3 26420 1nh1A 330 5.48e+00 unknown_sccs -11798 1i81A 83 5.49e+00 1d3bB b.38.1.1 61930 1q3eA 207 5.76e+00 b.82.3.2 -4922 1mp9A 198 5.80e+00 a.74.1.2 -1127 a.74.1.2 -1128 1o5uA 101 5.95e+00 b.82.1.8 -4845 1emvB 134 5.96e+00 1bxiB d.4.1.1 37135 1l7mA 211 6.09e+00 c.108.1.4 73664 1r64A 481 6.15e+00 b.18.1.20 -3151 c.41.1.1 -7297 1bxiB 134 6.29e+00 1bxiB d.4.1.1 37136 1befA 181 6.39e+00 1befA b.47.1.3 26419 1mgqA 83 6.81e+00 b.38.1.1 79099 1buuA 168 7.09e+00 1rtm1 d.169.1.1 42366 h.1.1.1 45388 1f60B 94 7.22e+00 1b64 d.58.12.1 39307 1f7zA 233 7.76e+00 5ptp b.47.1.2 59681 1hrnA 337 7.84e+00 1smrA b.50.1.2 26869 1kwhA 492 8.00e+00 c.94.1.1 68876 1rhfA 182 8.22e+00 b.1.1.1 -2335 b.1.1.4 -2684 1erjA 393 8.27e+00 1erjA b.69.4.1 27660 1hfuA 503 8.35e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1uag 437 8.54e+00 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1qd6C 240 8.61e+00 1qd5A 1mctA 223 8.73e+00 5ptp b.47.1.2 25961 4uagA 437 8.74e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1ca1 370 8.99e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1j6pA 418 9.01e+00 b.92.1.4 77089 c.1.9.9 77090 2aacA 177 9.01e+00 2arcA b.82.4.1 28150 1f5sA 211 9.06e+00 1f5sA c.108.1.4 59656 1e8pA 46 9.11e+00 g.55.1.1 59385 1gt1A 159 9.21e+00 b.60.1.1 -4436 1hn2A 159 9.21e+00 b.60.1.1 65890 1hp1A 516 9.32e+00 d.114.1.1 70976 d.159.1.2 70977 3uagA 437 9.54e+00 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 1ayyA 151 9.94e+00 1apyA d.153.1.5 42016 1kjkA 64 9.96e+00 d.10.1.4 72613 1sv6A 269 1.02e+01 1a0jA 223 1.02e+01 5ptp b.47.1.2 26002 1j1nA 492 1.03e+01 c.94.1.1 83978 2arcA 164 1.06e+01 2arcA b.82.4.1 28148 1g7cB 94 1.06e+01 1b64 d.58.12.1 39308 2arcB 164 1.08e+01 2arcA b.82.4.1 28149 1dr9A 201 1.08e+01 1dr9A b.1.1.1 19762 b.1.1.3 21684 1qa1A 554 1.10e+01 1tyv b.80.1.6 28047 1kebA 108 1.12e+01 c.47.1.1 77341 1q5xA 161 1.15e+01 c.8.7.1 -6068 1lktA 104 1.16e+01 1lktA b.90.1.1 28398 3ncmA 92 1.16e+01 3ncmA b.1.1.4 21702 1obpA 159 1.16e+01 1obpA b.60.1.1 27092 1tyu 543 1.18e+01 1tyv b.80.1.6 28037 1iyeA 309 1.18e+01 e.17.1.1 83786 1s72H 171 1.19e+01 1tyv 542 1.22e+01 1tyv b.80.1.6 28038 1pjqA 457 1.24e+01 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1vk6A 269 1.25e+01 unknown_sccs -10923 unknown_sccs -10924 1j97A 211 1.25e+01 1f5sA c.108.1.4 62753 1fniA 223 1.27e+01 5ptp b.47.1.2 25962 1p1mA 406 1.32e+01 b.92.1.4 87696 c.1.9.9 87697 1lpuA 332 1.35e+01 d.144.1.7 74177 1m2rA 327 1.35e+01 d.144.1.7 84760 1qd5A 275 1.37e+01 1qd5A f.4.2.1 43748 1fehA 574 1.39e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1a7aA 432 1.40e+01 1b3rA c.2.1.4 30104 c.23.12.3 31364 1rxyA 253 1.41e+01 c.56.2.1 -7834 1d0nA 729 1.42e+01 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1r9lA 309 1.46e+01 c.94.1.1 -8700 1pzxA 289 1.47e+01 c.119.1.1 -8623 1jobA 162 1.48e+01 1f35A b.94.1.1 63207 1yal 218 1.49e+01 1cs8A d.3.1.1 37025 1v6fA 151 1.51e+01 1ionA 243 1.54e+01 c.37.1.10 62633 1hxmA 229 1.55e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1iyu 79 1.56e+01 1iyu b.84.1.1 28227 1hyuA 521 1.63e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 830cA 168 1.63e+01 1ck7A d.92.1.11 40400 1qpbA 563 1.64e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1a05A 358 1.66e+01 1cnzA c.77.1.1 35059 1lx7A 253 1.74e+01 c.56.2.1 74329 1hj8A 222 1.74e+01 b.47.1.2 65844 1cjbA 231 1.75e+01 1qk3A c.61.1.1 34079 1bag 425 1.78e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1eqnA 321 1.79e+01 1dd9A e.13.1.1 43256 1o6uA 403 1.82e+01 a.5.3.1 -366 unknown_sccs -3048 c.13.1.1 -6221 1cv8 174 1.85e+01 1cv8 d.3.1.1 37089 1tsp 559 1.85e+01 1tyv b.80.1.6 28044 1pcs 98 1.86e+01 1plc b.6.1.1 22871 1ukuA 102 1.87e+01 d.58.5.2 -9992 1th8A 145 1.88e+01 2tbs 222 1.88e+01 5ptp b.47.1.2 26009 1sgzA 389 1.91e+01 b.50.1.2 -4301 1fknA 391 1.92e+01 1fknA b.50.1.2 26879 1ii7A 333 2.01e+01 1ii7A d.159.1.4 62415 1hkxA 147 2.08e+01 d.17.4.7 83567 1v58A 241 2.08e+01 1i82A 189 2.09e+01 1i82A b.1.9.2 61937 1fa0B 537 2.11e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1ifqA 138 2.12e+01 1ifqA d.110.4.1 62350 1lurA 339 2.12e+01 b.30.5.4 84717 1c8zA 265 2.14e+01 1c8zA d.23.1.1 38375 1bqyA 234 2.15e+01 5ptp b.47.1.2 26332 1t82A 155 2.16e+01 1fc6A 388 2.18e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1ivg 388 2.21e+01 2qwc b.68.1.1 27578 1g3qA 237 2.22e+01 1hyqA c.37.1.10 60237 1fct 32 2.25e+01 1fct j.36.1.1 46283 1qg3A 195 2.26e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1li4A 432 2.26e+01 c.2.1.4 84616 c.23.12.3 84617 1h09A 338 2.29e+01 b.109.1.1 83420 c.1.8.8 83421 1naqA 112 2.29e+01 d.58.5.2 -9984 1lmhA 184 2.30e+01 d.167.1.1 74036 9gafA 295 2.31e+01 1apyA d.153.1.5 42008 1nrzA 164 2.31e+01 c.38.1.1 86131 1qftA 175 2.33e+01 1qftA b.60.1.1 27151 1fh0A 221 2.38e+01 1cs8A d.3.1.1 59832 1fvaA 217 2.39e+01 1fvaA d.58.28.1 39409 1b3rA 431 2.42e+01 1b3rA c.2.1.4 30106 c.23.12.3 31366 1ry6A 360 2.42e+01 c.37.1.9 -7111 1bkf 107 2.43e+01 1fkj d.26.1.1 38382 1on3A 523 2.44e+01 c.14.1.4 87107 c.14.1.4 87108 1memA 215 2.46e+01 1cs8A d.3.1.1 37069 1ib8A 164 2.46e+01 b.38.2.1 71168 d.52.4.1 71169 1ei6A 406 2.47e+01 unknown_sccs -8436 1d8iA 311 2.48e+01 1d8iA d.63.1.1 39541 1glm 470 2.48e+01 1ayx a.102.1.1 18821 1xtcA 194 2.51e+01 1lt3A d.166.1.1 42259 1uy4A 145 2.51e+01 1gai 472 2.57e+01 1ayx a.102.1.1 18819 1fvgA 199 2.58e+01 1fvaA d.58.28.1 39408 1b3qA 379 2.59e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 2trxA 108 2.59e+01 1thx c.47.1.1 32719 1kn0A 212 2.60e+01 d.50.1.3 77444 1o1yA 239 2.61e+01 c.23.16.1 86554 1iz0A 302 2.63e+01 b.35.1.2 83821 c.2.1.1 83822 1gio 125 2.63e+01 7rsa d.5.1.1 37304 1nv8A 284 2.63e+01 c.66.1.30 86224 1i8aA 189 2.63e+01 1i82A b.1.9.2 61951 1f97A 212 2.68e+01 1f97A b.1.1.1 19763 b.1.1.4 21764 1hurA 180 2.69e+01 1hurA c.37.1.8 32052 1qlgA 355 2.72e+01 1qlgA b.68.3.1 27627 1riqA 465 2.73e+01 unknown_sccs -1295 d.104.1.1 -10769 1p4kA 295 2.73e+01 d.153.1.5 87772 1l6oA 95 2.74e+01 b.36.1.1 84534 1fnuA 221 2.87e+01 3seb b.40.2.2 25212 d.15.6.1 37801 1r9gA 216 2.89e+01 c.23.16.1 -6504 1lqwA 183 2.90e+01 d.167.1.1 74210 1agi 125 2.93e+01 7rsa d.5.1.1 37303 3sil 379 2.94e+01 3sil b.68.1.1 27542 1fa0A 537 2.95e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 2sil 381 2.96e+01 3sil b.68.1.1 27543 1i1kA 309 2.98e+01 1daaA e.17.1.1 61533 1dim 381 2.98e+01 3sil b.68.1.1 27544 1pv5A 264 3.01e+01 unknown_sccs -10182 1bmv2 374 3.03e+01 1bmv2 1k9dA 679 3.03e+01 c.1.8.10 77292 d.92.2.2 77293 1crzA 403 3.09e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1aop 497 3.11e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1lm4A 194 3.11e+01 d.167.1.1 84626 2aop 497 3.13e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1onwA 390 3.14e+01 b.92.1.7 87172 c.1.9.13 87173 1jj2H 167 3.15e+01 1ffkF d.41.4.1 63093 1ivd 388 3.17e+01 2qwc b.68.1.1 27568 1i50C 318 3.23e+01 d.74.3.1 61756 d.181.1.1 61757 1nar 290 3.26e+01 1nar c.1.8.5 28988 1ris 101 3.30e+01 1ris d.58.14.1 39314 1kr4A 125 3.31e+01 d.58.5.2 72889 1rot 149 3.37e+01 1fkj d.26.1.1 38429 1jqhA 308 3.40e+01 d.144.1.7 71793 1s4nA 348 3.42e+01 unknown_sccs -8262 1hgxA 183 3.42e+01 1tc1A c.61.1.1 34027 2plt 98 3.47e+01 1plc b.6.1.1 22862 1h4wA 224 3.47e+01 b.47.1.2 65622 1fnf 368 3.64e+01 1fnf b.1.2.1 21972 b.1.2.1 21973 b.1.2.1 21974 b.1.2.1 21975 1cknA 330 3.71e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 1e3dB 542 3.72e+01 1h2rL e.18.1.1 59189 2msbA 115 3.72e+01 1rtm1 d.169.1.1 42355 1qmvA 197 3.75e+01 1qq2A c.47.1.10 33066 1fkd 107 3.77e+01 1fkj d.26.1.1 38383 1ub1A 133 3.77e+01 d.10.1.3 -8969 1o4yA 288 3.82e+01 b.29.1.2 -3404 1np1A 184 3.87e+01 1np1A b.60.1.1 27155 1et9A 204 3.90e+01 1an8 b.40.2.2 25204 d.15.6.1 37793 1i1hA 219 3.92e+01 1f2vA c.23.17.1 61530 1bolA 222 3.93e+01 1bolA d.124.1.1 41120 1mrzA 293 3.93e+01 b.43.5.1 -4048 c.26.1.3 -6616 1r7lA 110 3.97e+01 1ny72 369 3.97e+01