# 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 1s5jA 847 3.15e-02 c.55.3.5,e.8.1.1 112040,112041 1ylxA 103 7.23e-02 d.82.5.1 123677 2gu3A 136 9.93e-02 2cnqA 306 1.15e-01 d.143.1.1 130646 1a48 306 1.85e-01 1a48 1aqcA 172 2.13e-01 1x11A b.55.1.2 26983 1obdA 306 2.58e-01 d.143.1.1 86767 1klqA 197 2.59e-01 d.135.1.1 68689 1t6sA 162 2.66e-01 a.4.5.60,a.4.5.60 112271,112272 1dujA 187 2.68e-01 1dujA d.135.1.1 41449 1rypK 198 3.31e-01 d.153.1.4 41879 1pguA 615 3.94e-01 b.69.4.1,b.69.4.1 88069,88070 1i1iP 681 4.07e-01 1i1iP d.92.1.5 40297 2gnqA 336 4.72e-01 1jrmA 104 5.84e-01 d.206.1.1 67136 1zbfA 142 6.05e-01 c.55.3.1 124850 1gxrA 337 6.69e-01 b.69.4.1 70722 1ilyA 90 9.94e-01 c.55.4.1 71245 1mixA 206 9.99e-01 a.11.2.1,b.55.1.5 79166,79167 2agyA 361 1.07e+00 1ec7A 446 1.14e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 1p5dX 463 1.16e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1phk 298 1.16e+00 1cdkA 2gk9A 426 1.18e+00 1ospO 257 1.18e+00 1ospO b.76.1.1 27971 1yqtA 538 1.25e+00 1j4wA 174 1.33e+00 d.51.1.1,d.51.1.1 71529,71530 3aig 202 1.43e+00 1atlA 1e2wA 251 1.44e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 1vpkA 378 1.53e+00 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1z5bA 469 1.53e+00 a.156.1.3,d.14.1.3,d.122.1.2 124464,124465,124466 1n91A 108 1.58e+00 d.206.1.1 80326 1go4A 205 1.59e+00 d.135.1.1 70292 1jdfA 447 1.72e+00 c.1.11.2,d.54.1.1 62897,62898 1in0A 163 1.72e+00 d.58.49.1,d.58.49.1 83694,83695 1txvA 452 1.80e+00 b.69.8.1 112783 2aeuA 374 1.80e+00 c.67.1.8 126646 1weyA 104 1.81e+00 d.58.7.1 114569 1fuxA 166 1.94e+00 1fjjA b.17.1.2 60034 1p9qC 256 1.96e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1k2yX 463 1.96e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2essA 248 1.96e+00 d.38.1.8,d.38.1.8 132346,132347 1l0qA 391 1.96e+00 b.1.3.1,b.69.2.3 77644,77645 1a3qA 285 2.06e+00 1a3qA b.1.18.1,b.2.5.3 21932,22447 1u96A 69 2.17e+00 a.17.1.2 113232 2bbkH 355 2.17e+00 2bbkH b.69.2.1 27634 2c2aA 258 2.18e+00 a.30.2.1,d.122.1.3 129662,129663 2a3qA 170 2.27e+00 a.204.1.2 126092 1f1sA 814 2.34e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 2gi9A 56 2.71e+00 1f1xA 322 2.74e+00 d.32.1.3,d.32.1.3 83208,83209 1s6cA 183 2.86e+00 a.39.1.5 98594 1o7eA 276 2.90e+00 e.3.1.1 92622 1n4oA 276 2.91e+00 e.3.1.1 91621 1ci3M 249 2.91e+00 1hcz b.2.6.1,b.84.2.2 22480,28266 1pgx 83 3.04e+00 2igd 1jnyA 435 3.16e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2amyA 246 3.21e+00 c.108.1.10 127026 1zceA 155 3.31e+00 b.122.1.8 124907 1qa9A 102 3.35e+00 1qa9A b.1.1.1 19742 1f1uA 323 3.36e+00 d.32.1.3,d.32.1.3 83200,83201 1w4xA 542 3.42e+00 c.3.1.5,c.3.1.5 109171,109172 1ctn 540 3.52e+00 1ctn 2nr1 27 3.53e+00 1ysc 421 3.55e+00 1ivyA 1g6aA 271 3.59e+00 1btl e.3.1.1 42704 1mu5A 471 3.64e+00 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1x3mA 415 3.66e+00 c.55.1.2,c.55.1.2 121664,121665 1usyA 275 3.73e+00 d.104.1.1 113422 1cpy 421 3.83e+00 1ivyA 1e8oA 85 3.89e+00 1914 d.49.1.1 38773 2c6cA 707 3.89e+00 a.48.2.1,c.8.4.1,c.56.5.5 129989,129990,129991 1igd 61 3.97e+00 2igd 2igd 61 3.97e+00 2igd 2fo3A 125 4.39e+00 d.20.1.1 133868 1k9tA 540 4.41e+00 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1edqA 540 4.44e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1r7aA 504 4.64e+00 b.71.1.1,c.1.8.1 97192,97193 3proC 166 4.64e+00 3proC d.52.1.1,d.52.1.1 38812,38813 1h5wA 309 4.78e+00 e.27.1.1 65635 1mkeA 152 4.87e+00 b.55.1.4 79231 1bxdA 161 5.14e+00 1bxdA d.122.1.3 41111 1a6pA 94 5.18e+00 1cdcA b.1.1.1 19748 1tr0A 108 5.23e+00 d.58.4.4 107261 1ud0A 113 5.38e+00 a.8.4.1 99198 1kutA 230 5.58e+00 d.143.1.1 73017 1914 232 5.60e+00 1914 1udxA 416 5.68e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2g84A 197 5.78e+00 c.97.1.2 134766 1kx5A 135 5.88e+00 a.22.1.1 77593 1shp 55 6.12e+00 1bpi 2h4uA 145 6.13e+00 d.38.1.5 136082 1c44A 123 6.23e+00 1qndA d.106.1.1 40795 1d4oA 184 6.31e+00 1d4oA c.31.1.4 31748 1x11A 172 6.38e+00 1x11A b.55.1.2 26985 2fueA 262 6.44e+00 c.108.1.10 134119 1kshB 152 6.44e+00 b.1.18.8 72915 1kufA 203 6.46e+00 d.92.1.9 73007 1kugA 203 6.46e+00 d.92.1.9 73008 1qwyA 291 6.55e+00 b.84.3.2 96509 1lfb 99 6.79e+00 1lfb 1svvA 359 6.84e+00 c.67.1.1 106054 1aoiA 116 7.26e+00 1aoiA a.22.1.1 16462 1atlA 202 7.35e+00 1atlA d.92.1.9 40322 1rwiA 270 7.42e+00 b.68.9.1 97987 1c5kA 439 7.51e+00 1crzA b.68.4.1,c.51.2.1 27630,33212 1a64A 97 7.53e+00 1cdcA b.1.1.1 19750 1ksgB 152 7.55e+00 b.1.18.8 72913 1cdcA 99 7.56e+00 1cdcA b.1.1.1 19746 1f66A 136 7.64e+00 1aoiA a.22.1.1 16460 3proD 166 7.67e+00 3proC d.52.1.1,d.52.1.1 38814,38815 1em2A 229 7.80e+00 1em2A d.129.3.2 41321 1vkcA 158 7.91e+00 d.108.1.1 113663 1jm1A 204 8.06e+00 b.33.1.1 71745 1iybA 208 8.10e+00 d.124.1.1 90720 1dq3A 454 8.10e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2bosA 68 8.12e+00 2bosA b.40.2.1 25025 1i1gA 141 8.17e+00 a.4.5.32,d.58.4.2 65982,65983 1r8gA 372 8.19e+00 d.128.1.3 104845 1hcz 252 8.33e+00 1hcz 2lfb 100 8.34e+00 1lfb 2pcfB 250 8.35e+00 1hcz i.4.1.1 45911 1fjgK 129 8.46e+00 1fjfK c.55.4.1 33733 1lqwA 183 8.54e+00 d.167.1.1 74210 1cnuA 137 8.82e+00 1cof d.109.1.2 40862 2pooA 355 9.05e+00 1qlgA b.68.3.1 27626 1qlgA 355 9.07e+00 1qlgA b.68.3.1 27627 2jdxA 385 9.23e+00 1jdw d.126.1.2 41139 2a2lA 145 9.27e+00 d.110.9.1 126035 1pvgA 418 9.27e+00 d.14.1.3,d.122.1.2 95161,95162 1jdw 423 9.29e+00 1jdw 2b9hA 353 9.46e+00 1e1xA 299 9.55e+00 1hcl d.144.1.7 59157 1cvmA 353 9.62e+00 1qlgA b.68.3.1 27628 1ogoX 574 9.73e+00 b.133.1.1,b.80.1.10 92925,92926 1zgmA 248 9.99e+00 2fnoA 248 9.99e+00 a.45.1.1,c.47.1.5 133821,133822 1vjlA 164 1.00e+01 d.257.1.1 100822 1dzkA 157 1.01e+01 1obpA b.60.1.1 27096 1hnf 182 1.02e+01 1qa9A 1dthA 203 1.06e+01 1atlA d.92.1.9 40324 1o70A 324 1.08e+01 b.118.1.1,b.118.1.1 81115,81116 2c7hA 86 1.08e+01 1cdcB 99 1.08e+01 1cdcA b.1.1.1 19747 1rypB 250 1.09e+01 1rypB d.153.1.4 41933 1lkkA 105 1.11e+01 1lckA d.93.1.1 40412 4pah 308 1.12e+01 4pah 1b43A 340 1.13e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1s1eA 224 1.15e+01 a.39.1.5 112007 1fxzA 476 1.16e+01 b.82.1.2,b.82.1.2 65059,65060 1e6pA 499 1.16e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1yarH 217 1.18e+01 d.153.1.4 122844 1rypD 241 1.18e+01 1rypD d.153.1.4 41935 1bpoA 494 1.20e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1d3yA 301 1.20e+01 1d3yA e.12.1.1 43252 1j8uA 325 1.21e+01 d.178.1.1 71611 1ovqA 138 1.22e+01 c.55.3.8 93607 1i58A 189 1.27e+01 1b3qA d.122.1.3 61773 1utcA 363 1.29e+01 a.118.1.4,b.69.6.1 99914,99915 1tiqA 180 1.30e+01 d.108.1.1 107010 1qmvA 197 1.31e+01 1qq2A c.47.1.10 33066 1e4eA 343 1.31e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1jbaA 204 1.34e+01 1rec a.39.1.5 17330 1x6oA 174 1.34e+01 b.34.5.2,b.40.4.5 109493,109494 1oxxK 353 1.34e+01 b.40.6.3,c.37.1.12 93715,93716 1oxsC 353 1.35e+01 b.40.6.3,c.37.1.12 87519,87520 1crzA 403 1.35e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1dqtA 117 1.39e+01 1ah1 b.1.1.1 20653 1mhxA 65 1.43e+01 d.15.7.1 79134 1fjjA 159 1.43e+01 1fjjA b.17.1.2 59852 1s5aA 150 1.43e+01 d.17.4.10 98525 1ohtA 215 1.44e+01 d.118.1.1 87036 1keeE 1073 1.45e+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 68508,68509,68510,68511,68512,68513 1qh3A 260 1.45e+01 1qh5A d.157.1.2 42059 1uyjA 296 1.45e+01 f.8.1.2 108143 1c3oE 1073 1.45e+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 18564,31493,31685,31686,41530,41531 1b63A 333 1.45e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1u0sA 86 1.45e+01 d.58.24.1 107565 1t95A 240 1.47e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1lcjA 109 1.49e+01 1qadA d.93.1.1 40414 1v74A 107 1.49e+01 d.243.1.1 100442 1c3oC 1073 1.49e+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 18563,31492,31683,31684,41528,41529 1gqoS 143 1.52e+01 c.23.13.1 76313 1gqoF 143 1.53e+01 c.23.13.1 76300 1w53A 84 1.53e+01 a.186.1.2 109175 1jjuB 337 1.53e+01 b.69.2.2 66779 1pbyB 337 1.54e+01 b.69.2.2 94422 1w79A 489 1.54e+01 e.3.1.3 120680 2gqrA 237 1.55e+01 1yzsA 121 1.56e+01 1qh5A 260 1.57e+01 1qh5A d.157.1.2 42057 1ykdA 398 1.57e+01 1enp 312 1.60e+01 1enp 1e15A 499 1.60e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 1goiA 499 1.62e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1keeG 1073 1.63e+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 68516,68517,68518,68519,68520,68521 1gqoE 143 1.66e+01 c.23.13.1 76299 1gqoB 143 1.66e+01 c.23.13.1 76296 1jdiA 231 1.68e+01 c.74.1.1 66551 1k0wA 231 1.68e+01 c.74.1.1 77220 1ii2A 524 1.71e+01 c.91.1.1,c.109.1.1 66146,66147 2bkfA 87 1.72e+01 d.15.2.2 128699 1gzcA 239 1.72e+01 b.29.1.1 70803 1j5eK 129 1.72e+01 c.55.4.1 71554 1wq3A 322 1.77e+01 1gqoK 143 1.79e+01 c.23.13.1 76305 1c3oG 1073 1.79e+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 18565,31494,31687,31688,41532,41533 1gqoP 143 1.79e+01 c.23.13.1 76310 1bxrA 1073 1.81e+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 18570,31499,31697,31698,41542,41543 1dixA 208 1.81e+01 1bk7A d.124.1.1 41122 1erjA 393 1.81e+01 1erjA b.69.4.1 27660 1cdzA 96 1.82e+01 1cdzA c.15.1.1 30925 1gqoY 143 1.83e+01 c.23.13.1 76318 1jmxB 349 1.83e+01 b.69.2.2 66906 1gqoH 143 1.85e+01 c.23.13.1 76302 2bwqA 129 1.86e+01 b.7.1.2 129380 1qfmA 710 1.88e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1e8nA 710 1.88e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1fxxA 482 1.88e+01 1fxxA c.55.3.5 33726 1bg2 325 1.89e+01 1bg2 1pysA 350 1.91e+01 1pysA d.104.1.1 40775 1ebuA 358 1.92e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1h2xA 710 1.92e+01 b.69.7.1,c.69.1.4 76598,76599 1h2wA 710 1.92e+01 b.69.7.1,c.69.1.4 76596,76597 1jvpP 298 1.93e+01 d.144.1.7 67371 1ako 268 1.93e+01 1ako 1qq2A 199 1.93e+01 1qq2A c.47.1.10 33064 1vd3A 217 1.94e+01 1vr6A 350 1.95e+01 c.1.10.4 120439 1b62A 349 1.95e+01 1b63A d.14.1.3,d.122.1.2 37567,41108 1qd1A 325 1.95e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1lrwA 600 1.96e+01 b.70.1.1 91111 1gqoC 143 1.97e+01 c.23.13.1 76297 1y2mA 716 1.97e+01 1gqoJ 143 1.98e+01 c.23.13.1 76304 1gqoO 143 1.98e+01 c.23.13.1 76309 1gqoG 143 1.98e+01 c.23.13.1 76301 1flp 142 2.00e+01 1flp 1moh 142 2.00e+01 1flp 1osdA 72 2.00e+01 d.58.17.1 104022 1fxrA 64 2.01e+01 1fxd d.58.1.4 38993 1z47A 355 2.03e+01 1lm4A 194 2.04e+01 d.167.1.1 84626 1ykuA 136 2.05e+01 9gafA 295 2.05e+01 1apyA d.153.1.5 42008 1gqoI 143 2.05e+01 c.23.13.1 76303 1gqoL 143 2.05e+01 c.23.13.1 76306 1ll8A 114 2.06e+01 d.110.3.5 78089 1lvhA 221 2.07e+01 c.108.1.6 74282 2fsrA 195 2.08e+01 d.108.1.1 134036 1gqoR 143 2.09e+01 c.23.13.1 76312 2fhzB 108 2.09e+01 d.243.1.2 133506 1o8xA 146 2.10e+01 c.47.1.10 86681 1p4kA 295 2.13e+01 d.153.1.5 87772 2bifA 469 2.15e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1wr2A 238 2.15e+01 1ijgA 309 2.17e+01 1fouA e.27.1.1 62493 2cunA 410 2.17e+01 1gqoT 143 2.19e+01 c.23.13.1 76314 1mwsA 646 2.20e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1pz4A 116 2.23e+01 d.106.1.1 95400 1hq3C 136 2.24e+01 1aoiA a.22.1.1 16454 1gqoX 143 2.29e+01 c.23.13.1 76317 1gqoQ 143 2.30e+01 c.23.13.1 76311 1iyxA 432 2.32e+01 c.1.11.1,d.54.1.1 83815,83816 1tn6B 437 2.32e+01 a.102.4.3 112528 1rjcA 137 2.33e+01 1uheA 97 2.34e+01 1ash 150 2.37e+01 1ash 1bo1A 416 2.38e+01 1bo1A d.143.1.2 41591 1pmaP 211 2.38e+01 1pmaP d.153.1.4 41863 1ewxA 146 2.39e+01 1ewxA c.47.1.10 33062 2ch4A 320 2.40e+01 b.40.7.1,d.122.1.3 130447,130448 2biwA 490 2.41e+01 1gqoM 143 2.42e+01 c.23.13.1 76307 2cvdA 198 2.42e+01 a.45.1.1,c.47.1.5 130861,130862 5csmA 256 2.43e+01 5csmA a.130.1.2 19494 1i40A 175 2.44e+01 b.40.5.1 66024 1u0jA 267 2.46e+01 c.37.1.20 107546 1qk8A 146 2.50e+01 1ewxA c.47.1.10 33061 1rzmA 338 2.50e+01 c.1.10.4 105137 1muwA 386 2.51e+01 c.1.15.3 79495 1kvdB 77 2.53e+01 1kveB 1kveB 77 2.53e+01 1kveB 1y96B 85 2.53e+01 1wvnA 82 2.54e+01 d.51.1.1 121345 1vg0A 650 2.54e+01 c.3.1.3,d.16.1.6 108596,108597 1zejA 293 2.54e+01 3bifA 468 2.58e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1snzA 344 2.59e+01 b.30.5.4 98930 1g65K 211 2.59e+01 d.153.1.4 41907 1obwA 175 2.62e+01 2prd b.40.5.1 25416 1obbA 480 2.63e+01 c.2.1.5,d.162.1.2 86760,86761 1gqoV 143 2.66e+01 c.23.13.1 76316 9apiA 347 2.69e+01 1ovaA e.1.1.1 42630 1b9mA 265 2.72e+01 1b9mA 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1hbkA 94 8.81e+01 1aca a.11.1.1 60887 1rpl 251 8.81e+01 1bpyA 1uebA 184 8.82e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1hizA 379 8.82e+01 c.1.8.3 65841 2aq4A 434 8.85e+01 1skhA 30 8.85e+01 1fnb 314 8.89e+01 1fnc 1sa0E 143 8.93e+01 a.137.10.1 98777 2frgP 106 8.99e+01