# List of top-scoring protein chains for t04-100-30-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 1c24A 263 2.35e-01 1c24A d.127.1.1 41148 2ggcA 263 2.55e-01 1xnzA 264 2.59e-01 1vjpA 394 2.76e-01 c.2.1.3,d.81.1.3 100828,100829 1u6zA 513 4.60e-01 2kfnA 605 4.85e-01 1xwl c.55.3.5,e.8.1.1 33682,42975 2bl1A 172 8.79e-01 1yvoA 172 1.00e-00 1k3xA 262 1.00e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1azpA 66 1.38e+00 1azpA b.34.13.1 37467 1j93A 353 1.42e+00 c.1.22.1 66454 1qynA 153 1.56e+00 d.33.1.1 96597 1vhmA 195 1.72e+00 d.110.2.1 100691 1mugA 168 2.38e+00 1mugA c.18.1.2 31030 1o0xA 262 2.42e+00 d.127.1.1 80755 1erjA 393 2.57e+00 1erjA b.69.4.1 27660 2ltnA 181 2.65e+00 1led b.29.1.1 24024 1oshA 232 2.95e+00 a.123.1.1 93496 1fl1A 230 2.97e+00 1at3A b.57.1.1 27023 2bmoB 194 3.15e+00 1ttuA 477 3.25e+00 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1fit 147 3.27e+00 1fit d.13.1.1 37499 2fhi 147 3.45e+00 1fit d.13.1.1 37505 1mkmA 249 3.46e+00 a.4.5.33,d.110.2.2 79242,79243 1m9sA 605 3.54e+00 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1xyiA 66 3.66e+00 1sjqA 105 3.67e+00 d.58.7.1 105660 1qxyA 252 3.72e+00 d.127.1.1 96565 1sr9A 644 3.97e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1phk 298 4.56e+00 1cdkA d.144.1.7 41635 1wywA 230 4.71e+00 1bh9A 45 4.71e+00 1bh9A a.22.1.3 16483 1njkA 156 4.75e+00 d.38.1.1 85818 3pmgA 561 5.12e+00 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1f2tA 149 5.41e+00 1f2tA c.37.1.12 32373 1z54A 132 5.60e+00 1h6tA 291 5.70e+00 b.1.18.15,c.10.2.1 65686,65687 1zwxA 301 5.82e+00 1i0rA 169 7.07e+00 1i0rA b.45.1.2 61489 1i0sA 169 7.07e+00 1i0rA b.45.1.2 61491 1fnsA 196 7.20e+00 1auq c.62.1.1 34136 1us8A 147 7.29e+00 c.37.1.12 99859 1lenA 181 7.36e+00 1led b.29.1.1 24032 1xoyA 161 7.41e+00 1ovaA 386 7.71e+00 1ovaA e.1.1.1 42619 1ijbA 202 7.89e+00 c.62.1.1 71229 1ukfA 188 8.15e+00 d.3.1.10 99488 1hwxA 501 8.21e+00 1hwyA c.2.1.7,c.58.1.1 30250,33898 2b3hA 329 8.23e+00 1qmeA 702 8.45e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1mkyA 439 8.48e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1atiA 505 8.67e+00 1atiA c.51.1.1,d.104.1.1 33196,40745 2pooA 355 8.73e+00 1qlgA b.68.3.1 27626 1w6uA 302 8.83e+00 1dowA 205 8.98e+00 1dovA a.24.9.1 16626 1zpyA 95 9.17e+00 1avbA 226 9.74e+00 1led b.29.1.1 24158 2b1xB 172 9.89e+00 2h58A 330 9.95e+00 2b7yA 182 1.01e+01 1mup 166 1.08e+01 1mup b.60.1.1 27133 1mc0A 368 1.09e+01 d.110.2.1,d.110.2.1 78937,78938 1j1qA 261 1.09e+01 d.165.1.1 90768 1ji8A 111 1.10e+01 d.203.1.1 66733 1w1kA 560 1.10e+01 d.58.32.1,d.145.1.1 109059,109060 1dm0A 287 1.13e+01 1dm0A d.165.1.2 42227 1qciA 262 1.13e+01 1qi7A d.165.1.1 42201 1cs0A 1073 1.17e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1dqiA 124 1.20e+01 1do6A b.1.13.1 22357 2gf6A 135 1.22e+01 2aneA 125 1.23e+01 1uyjA 296 1.29e+01 f.8.1.2 108143 1vrpA 381 1.34e+01 1hyeA 313 1.35e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1vl2A 421 1.35e+01 c.26.2.1,d.210.1.1 108708,108709 1uhgA 385 1.37e+01 e.1.1.1 88491 1jenB 67 1.39e+01 1jenB d.156.1.1 42029 1xauA 122 1.40e+01 1w36C 1122 1.41e+01 1jv4A 162 1.42e+01 b.60.1.1 67343 1uekA 275 1.42e+01 d.14.1.5,d.58.26.5 88483,88484 1e8gA 560 1.43e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 2bskB 90 1.44e+01 1pqzA 238 1.45e+01 b.1.1.2,d.19.1.1 104297,104298 1ftrA 296 1.46e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1zndA 174 1.49e+01 1qwiA 143 1.55e+01 d.227.1.1 96474 1vq0A 302 1.60e+01 1ze3C 205 1.60e+01 1i05A 180 1.63e+01 1mup b.60.1.1 27130 1fcyA 236 1.64e+01 2lbd a.123.1.1 19282 1led 243 1.64e+01 1led b.29.1.1 24039 1cqqA 180 1.71e+01 1cqqA b.47.1.4 26422 1sdjA 310 1.72e+01 d.21.1.2,d.21.1.2 98807,98808 1qy1A 174 1.73e+01 b.60.1.1 96568 1u58A 253 1.77e+01 1fvrA 327 1.79e+01 d.144.1.7 60047 1h6lA 353 1.82e+01 b.68.3.1 60687 1qyaA 307 1.86e+01 d.21.1.2,d.21.1.2 104653,104654 1nfjA 89 1.89e+01 d.68.6.1 91866 1wl9A 440 1.90e+01 2bwvA 440 1.91e+01 2ag4A 164 1.92e+01 2h4uA 145 1.92e+01 1sauA 115 1.94e+01 2bhvA 246 2.00e+01 1wucA 250 2.09e+01 1u1iA 392 2.10e+01 c.2.1.3,d.81.1.3 107582,107583 1i06A 180 2.12e+01 1mup b.60.1.1 27131 1yzbA 182 2.15e+01 4icb 76 2.19e+01 4icb a.39.1.1 17145 1lshA 1056 2.22e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1bdmA 327 2.24e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1bmdA 327 2.24e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 2ag9A 164 2.27e+01 1y7tA 327 2.27e+01 1pv5A 264 2.27e+01 d.251.1.1 95150 1no7A 604 2.28e+01 e.48.1.1 92016 1gpqA 135 2.28e+01 d.233.1.1 83295 2d9rA 104 2.34e+01 1amuA 563 2.40e+01 1amuA e.23.1.1 43351 1d4fA 431 2.45e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 2a1dD 329 2.64e+01 1ts9A 102 2.66e+01 1uujA 88 2.68e+01 a.221.1.1 108046 1uliB 187 2.71e+01 d.17.4.4 107923 1o6vA 466 2.73e+01 b.1.18.15,c.10.2.1 81099,81100 2b8eA 273 2.75e+01 1dykA 394 2.84e+01 1dykA b.29.1.4,b.29.1.4 24223,24224 1hp1A 516 2.86e+01 d.114.1.1,d.159.1.2 70976,70977 1az9 457 2.91e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1dwnA 127 2.91e+01 1dwnA d.85.1.1 40141 1pjhA 280 2.99e+01 c.14.1.3 94761 1v6cA 441 3.00e+01 1l3aA 228 3.01e+01 d.18.1.2 73531 1t01B 24 3.01e+01 2agcA 162 3.06e+01 1gz6A 319 3.07e+01 c.2.1.2 76410 1vs0A 310 3.14e+01 1vl4A 447 3.17e+01 d.283.1.1 108718 1vclA 432 3.19e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1cx4A 305 3.24e+01 b.82.3.2,b.82.3.2 59099,59100 2bvpA 276 3.26e+01 1pk5A 248 3.32e+01 a.123.1.1 88139 1e5pA 151 3.34e+01 1bj7 b.60.1.1 59272 1r6wA 322 3.41e+01 c.1.11.2,d.54.1.1 97165,97166 1snzA 344 3.42e+01 b.30.5.4 98930 1k2eA 156 3.45e+01 d.113.1.1 72010 1mkaA 171 3.47e+01 1mkaA d.38.1.2 38543 1hnuA 280 3.48e+01 1hnoA c.14.1.3 61096 1h10A 125 3.56e+01 b.55.1.1 83446 1unqA 125 3.56e+01 b.55.1.1 107968 1do6A 124 3.56e+01 1do6A b.1.13.1 22361 1stzA 338 3.60e+01 a.4.5.51,d.110.2.3 106009,106010 1z94A 147 3.62e+01 1c8cA 64 3.66e+01 1azpA b.34.13.1 59084 1guqA 348 3.67e+01 1guqA d.13.1.2,d.13.1.2 37522,37523 1jp4A 308 3.67e+01 1jp4A e.7.1.1 63223 2g38B 198 3.68e+01 1mgtA 174 3.69e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1z5yE 149 3.71e+01 2bkfA 87 3.73e+01 1x7yA 400 3.74e+01 1zq9A 285 3.76e+01 1uspA 139 3.80e+01 d.227.1.1 99879 1vp4A 425 3.84e+01 2d37A 176 3.85e+01 1y9zA 441 3.87e+01 1vrmA 325 3.87e+01 1t3qC 288 3.91e+01 d.87.2.1,d.145.1.3 106371,106372 2b33A 140 3.91e+01 2bfdA 400 3.99e+01 1r31A 428 3.99e+01 d.58.20.1,d.179.1.1 96897,96898 1i39A 225 4.01e+01 1ekeA c.55.3.1 61585 1dpjA 329 4.02e+01 1smrA b.50.1.2 26828 1jjeA 222 4.04e+01 1a7tA d.157.1.1 63117 1j7gA 144 4.09e+01 c.110.1.1 84130 1mw7A 240 4.10e+01 e.39.1.1 79557 1y10A 407 4.11e+01 2a3qA 170 4.14e+01 1wd3A 482 4.22e+01 b.29.1.21,b.42.8.1 109233,109234 1bv1 159 4.26e+01 1bv1 d.129.3.1 41313 2b1xA 470 4.36e+01 1v1rA 400 4.40e+01 c.36.1.11 108272 2a15A 139 4.42e+01 1mnnA 340 4.44e+01 b.2.5.7 79324 1x31D 99 4.45e+01 1svb 395 4.49e+01 1svb b.1.18.4,f.10.1.1 21814,43827 2bzpA 226 4.55e+01 1s1eA 224 4.58e+01 2gz4A 207 4.61e+01 1souA 194 4.63e+01 c.124.1.6 105858 1oygA 447 4.69e+01 b.67.2.2 93726 1xs0A 136 4.71e+01 1pmd 675 4.72e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1f3iA 481 4.74e+01 1b7eA 1pg4A 652 4.80e+01 e.23.1.1 88067 1p1jA 533 4.80e+01 c.2.1.3,d.81.1.3 87687,87688 1umgA 362 4.89e+01 d.280.1.1 107956 1s0yA 76 4.90e+01 d.80.1.1 98314 1kshB 152 4.92e+01 b.1.18.8 72915 1l4iA 206 4.93e+01 b.1.11.1,b.7.2.1 73564,73565 3dni 260 5.01e+01 3dni d.151.1.1 41791 1ejeA 192 5.03e+01 1ejeA b.45.1.2 25757 1sviA 195 5.03e+01 c.37.1.8 106048 1ysqA 193 5.04e+01 2cwzA 141 5.06e+01 1s28A 132 5.08e+01 d.198.1.1 105223 1olsA 400 5.09e+01 c.36.1.11 93331 1xkyA 301 5.13e+01 1ypvA 313 5.18e+01 1q8iA 783 5.23e+01 c.55.3.5,e.8.1.1 96208,96209 1xgsA 295 5.28e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1s7kA 182 5.34e+01 1wtaA 275 5.43e+01 2comA 124 5.49e+01 1x13A 401 5.55e+01 1o0wA 252 5.60e+01 a.149.1.1,d.50.1.1 80751,80752 1hvyA 288 5.63e+01 1bkpA d.117.1.1 41049 2fp4B 395 5.66e+01 2fg1A 158 5.67e+01 1y96A 86 5.68e+01 1oj4A 283 5.68e+01 d.14.1.5,d.58.26.5 93083,93084 1v7rA 186 5.68e+01 c.51.4.1 100482 1ewfA 456 5.74e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 2agaA 190 5.88e+01 1v97A 1332 5.96e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1w2xA 758 5.97e+01 c.14.1.4,c.14.1.4 109134,109135 1q5hA 147 5.98e+01 b.85.4.1 95893 1xfsA 178 6.06e+01 d.129.3.5 109589 1ympA 135 6.08e+01 1pu5A 164 6.14e+01 b.95.1.1 104310 2afcA 168 6.21e+01 1y14B 171 6.25e+01 1yucA 255 6.31e+01 1rtxA 123 6.53e+01 a.1.1.1 97827 1dqpA 230 6.53e+01 1dqnA c.61.1.1 34069 1dqnA 230 6.54e+01 1dqnA c.61.1.1 34067 1q6zA 528 6.60e+01 1n3gA 113 6.61e+01 d.204.1.1 79962 1v9yA 167 6.65e+01 d.110.3.2 108454 1e6oL 212 6.69e+01 32c2A b.1.1.1,b.1.1.2 20494,21452 1qfgA 725 6.76e+01 1by5A f.4.3.3 43803 1g7nA 131 6.77e+01 b.60.1.2 83274 1s69A 124 6.83e+01 a.1.1.1 105305 1hq3B 126 6.85e+01 1aoiD a.22.1.1 16444 1tzyB 126 6.85e+01 a.22.1.1 107531 2f6rA 281 6.85e+01 1j1yA 136 6.86e+01 d.38.1.5 90776 1ml4A 308 6.87e+01 c.78.1.1,c.78.1.1 79255,79256 1xl7A 612 6.90e+01 1xh3A 276 6.91e+01 1ta0A 197 6.91e+01 c.108.1.16 106729 2ccyA 128 6.95e+01 2ccyA a.24.3.2 16544 1upvA 257 7.00e+01 1bfd 528 7.01e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1l1jA 239 7.04e+01 b.47.1.1 84516 1whtB 153 7.06e+01 1whtB 1gtmA 419 7.07e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1xfkA 336 7.10e+01 1pda 315 7.13e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1whsB 153 7.15e+01 1whtB 1wpoA 256 7.18e+01 1lay b.57.1.1 27012 2fug7 129 7.19e+01 1f5mA 180 7.20e+01 1f5mB d.110.2.1 40895 1mvcA 240 7.21e+01 a.123.1.1 79499 1innA 166 7.28e+01 1j98A d.185.1.2 62608 1g13A 162 7.30e+01 1g13A b.95.1.1 60194 2bdvA 231 7.30e+01 1yr0A 175 7.38e+01 1m98A 317 7.43e+01 a.175.1.1,d.17.4.6 78866,78867 1u35D 126 7.48e+01 1icxA 155 7.51e+01 d.129.3.1 71191 1ud0A 113 7.59e+01 a.8.4.1 99198 2giyA 191 7.62e+01 1t5hX 504 7.65e+01 e.23.1.1 106449 1c5yB 253 7.66e+01 5ptp 1at3A 247 7.69e+01 1at3A b.57.1.1 27021 2givA 295 7.73e+01 1eudB 396 7.73e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1wudA 89 7.75e+01 1zkiA 133 7.78e+01 1ud9A 245 7.79e+01 d.131.1.2,d.131.1.2 107768,107769 1lswA 131 7.79e+01 d.110.3.2 78181 2gpiA 91 7.81e+01 1msk 331 7.83e+01 1msk d.173.1.1 42495 1dkzA 219 7.88e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 3mddA 385 7.91e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1w07A 659 7.92e+01 1esmA 316 7.93e+01 1esmA c.37.1.6 31953 1xuvA 178 7.94e+01 1a8d 452 7.96e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1ohzB 60 7.97e+01 a.139.1.1 93044 1u69A 163 7.98e+01 d.32.1.7 107699 1ne9A 335 8.00e+01 d.108.1.4,d.108.1.4 91839,91840 1l5wA 796 8.01e+01 c.87.1.4 73605 2be3A 226 8.04e+01 1o5kA 306 8.07e+01 c.1.10.1 92504 1xvsA 126 8.09e+01 1x1iA 752 8.09e+01 1gyxA 76 8.09e+01 d.80.1.1 76387 1pq9A 253 8.10e+01 a.123.1.1 95004 1r2zA 274 8.13e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1j5wA 298 8.17e+01 d.104.1.1 71589 2gviA 204 8.18e+01 1u8vA 490 8.20e+01 1li4A 432 8.23e+01 c.2.1.4,c.23.12.3 84616,84617 1h6fA 193 8.23e+01 b.2.5.4 70901 1xk4C 113 8.29e+01 1l1zA 274 8.30e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1vjeA 166 8.36e+01 d.185.1.2 100807 1jyhA 157 8.37e+01 d.60.1.3 71956 1m15A 357 8.37e+01 a.83.1.1,d.128.1.2 78368,78369 1vf6A 83 8.43e+01 a.194.1.1 100600 1t0qB 330 8.43e+01 a.25.1.2 106221 2gi3A 476 8.51e+01 1ei1A 391 8.52e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1ek9A 428 8.62e+01 1ek9A f.5.1.1 43809 2b5gA 171 8.65e+01 1qf5A 431 8.67e+01 1adeA c.37.1.10 32212 1r8mE 203 8.69e+01 a.118.3.1 97242 1i58A 189 8.69e+01 1b3qA d.122.1.3 61773 1ijtA 128 8.69e+01 1bfg b.42.1.1 62510 1lf7A 182 8.72e+01 b.60.1.1 73878 1wb9A 800 8.74e+01 1mrg 263 8.75e+01 1mrj d.165.1.1 42183 1phnB 172 8.80e+01 1qgwC a.1.1.3 15642 1ig5A 75 8.80e+01 4icb a.39.1.1 62363 1tm0A 350 8.83e+01 d.21.1.3 107147 1iicA 422 8.92e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1wluA 136 8.96e+01