# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1y74B 50 9.39e-01 1vkuA 100 1.31e+00 a.28.1.1 108690 1fpzA 212 1.32e+00 1fpzA c.45.1.1 59976 2a9uA 144 1.40e+00 1d1rA 116 1.79e+00 1d1rA d.64.1.1 39548 2bkyX 89 1.96e+00 1oyzA 280 2.01e+00 a.118.1.16 93775 1u13A 455 2.08e+00 a.104.1.1 107578 1gvhA 396 2.09e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1h5zA 455 2.26e+00 a.104.1.1 90622 1uj6A 227 2.27e+00 c.124.1.4,d.58.40.1 107898,107899 1ea1A 455 2.63e+00 1ea1A a.104.1.1 18970 2ah6A 208 2.77e+00 1udvA 89 2.82e+00 d.68.6.1 99224 1x8vA 455 3.34e+00 1e9xA 455 3.52e+00 1ea1A a.104.1.1 18969 1pxwA 128 3.81e+00 d.79.3.1 95305 1lnh 857 4.68e+00 1yge a.119.1.1,b.12.1.1 19237,23637 1i4yA 114 4.70e+00 2mhr a.24.4.1 61738 1yb3A 175 4.89e+00 1hjp 203 5.01e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1lrv 244 5.14e+00 1lrv a.118.1.5 19146 1cii 602 5.34e+00 1cii f.1.1.1,h.4.3.1 43381,45787 1h9fA 57 7.43e+00 1h9fA a.140.1.1 60826 2a1iA 146 7.45e+00 1qlnA 883 7.56e+00 1cezA e.8.1.3 43111 1c1kA 217 7.76e+00 1c1kA a.120.1.1 19239 1ox3A 109 7.89e+00 h.1.17.1 93668 1akhA 61 7.89e+00 1akhA a.4.1.1 15980 1k5dB 201 8.07e+00 b.55.1.3 68169 1ialA 453 9.32e+00 1bk5A a.118.1.1 19116 1b8pA 329 9.99e+00 1bmdA c.2.1.5,d.162.1.1 30147,42114 1trrA 107 1.10e+01 1jhgA a.4.12.1 19017 1go3F 107 1.14e+01 a.60.8.2 65407 1g4yB 101 1.15e+01 1g4yB f.15.1.1 60251 1yrnA 61 1.20e+01 1akhA a.4.1.1 15981 1yn9A 169 1.22e+01 1yge 839 1.23e+01 1yge a.119.1.1,b.12.1.1 19234,23634 2ccmA 191 1.26e+01 2wrpR 107 1.28e+01 1jhgA a.4.12.1 19010 1cuk 203 1.31e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1rovA 857 1.31e+01 a.119.1.1,b.12.1.1 97674,97675 1f8nA 839 1.33e+01 1yge a.119.1.1,b.12.1.1 59703,59704 1fgqA 839 1.33e+01 1yge a.119.1.1,b.12.1.1 59826,59827 1hl2A 297 1.36e+01 c.1.10.1 83581 1lniA 96 1.36e+01 d.1.1.2 74046 1gmpA 96 1.39e+01 1rgeA d.1.1.2 36036 1h3nA 878 1.40e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1nal3 297 1.40e+01 1nal3 1h38B 883 1.44e+01 e.8.1.3 76626 1vmaA 306 1.46e+01 a.24.13.1,c.37.1.10 108887,108888 2fu4A 83 1.50e+01 1ig5A 75 1.54e+01 4icb a.39.1.1 62363 1x6vA 630 1.57e+01 1bvsB 203 1.58e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1s9rA 410 1.58e+01 d.126.1.4 98758 1fdyA 297 1.59e+01 1nal3 c.1.10.1 29071 1h38C 883 1.62e+01 e.8.1.3 76627 1ka2A 499 1.66e+01 d.92.1.5 77305 1jhgA 101 1.71e+01 1jhgA a.4.12.1 19009 1wwzA 159 1.71e+01 1cezA 883 1.72e+01 1cezA e.8.1.3 43110 1nd9A 49 1.75e+01 a.6.1.6 85575 1h38D 883 1.78e+01 e.8.1.3 76628 1nal1 297 1.88e+01 1nal3 2bemA 170 1.89e+01 1yucA 255 1.90e+01 1gxyA 226 1.92e+01 d.166.1.3 76380 1lxyA 409 1.95e+01 d.126.1.4 91154 2b59B 172 1.99e+01 1ea2A 131 2.00e+01 d.17.4.3 64860 1uekA 275 2.06e+01 d.14.1.5,d.58.26.5 88483,88484 1rxxA 421 2.20e+01 d.126.1.4 98061 1i8vA 96 2.23e+01 d.1.1.2 61985 1z91A 147 2.27e+01 1rgeA 96 2.41e+01 1rgeA d.1.1.2 36028 1mpuA 138 2.41e+01 d.169.1.1 85040 1udmA 149 2.47e+01 d.109.1.2 107780 1lea 84 2.52e+01 1lea a.4.5.2 16085 2hmzA 113 2.57e+01 2mhr a.24.4.1 16564 1jhfA 202 2.70e+01 a.4.5.2,b.87.1.1 63057,63058 2a5yB 549 2.71e+01 1t2lA 141 2.73e+01 1iq8A 582 2.76e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1x1nA 524 2.76e+01 1a5t 334 2.76e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1yemA 179 2.76e+01 1xqaA 113 2.82e+01 1gm7A 209 2.91e+01 d.153.1.2 65302 1x0tA 120 2.93e+01 1quuA 250 2.94e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1xewY 172 3.04e+01 1mp9A 198 3.08e+01 d.129.1.1,d.129.1.1 91385,91386 2hmqA 113 3.08e+01 2mhr a.24.4.1 16568 4icb 76 3.10e+01 4icb a.39.1.1 17145 1f7cA 231 3.12e+01 1f7cA a.116.1.1 19107 1sdoA 203 3.12e+01 c.52.1.21 98809 1e3aA 260 3.18e+01 1ajqA d.153.1.2 41838 1k7hA 476 3.30e+01 c.76.1.1 72101 1zs3A 182 3.33e+01 1mq4A 272 3.39e+01 d.144.1.7 91391 2cxnA 557 3.46e+01 1gjjA 168 3.47e+01 a.140.1.1,a.140.1.1 83291,83292 1u2wA 122 3.48e+01 2f6mB 109 3.59e+01 1e94F 449 3.62e+01 1do0A c.37.1.20 32443 1ofuX 119 3.63e+01 c.37.1.22 86976 1oaa 259 3.69e+01 1oaa c.2.1.2 29829 1qghA 156 3.72e+01 1qghA a.25.1.1 16728 1ewkA 490 3.72e+01 1ewkA c.93.1.1 35712 1wkbA 810 3.72e+01 1u0fA 564 3.76e+01 1xm9A 457 3.78e+01 1xqiA 195 3.80e+01 1wlyA 333 3.89e+01 1fjeB 175 3.92e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1wu7A 434 4.00e+01 1sep 261 4.07e+01 1oaa c.2.1.2 29830 2gi3A 476 4.08e+01 1q79A 514 4.11e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1qryA 80 4.12e+01 2hddA a.4.1.1 16016 1gz6A 319 4.15e+01 c.2.1.2 76410 1j3mA 129 4.26e+01 d.129.7.1 103836 6paxA 133 4.28e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 2ac3A 316 4.42e+01 1cbg 490 4.43e+01 1e70M c.1.8.4 28933 2cp8A 54 4.44e+01 1f5aA 513 4.46e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1mgrA 99 4.52e+01 d.1.1.2 79106 1wekA 217 4.53e+01 1b1gA 75 4.56e+01 1psrA a.39.1.1 17151 1ucpA 91 4.63e+01 a.77.1.5 99186 1zq4A 693 4.67e+01 1lvaA 258 4.71e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2d00A 109 4.71e+01 1ee4A 423 4.78e+01 1ee4A a.118.1.1 19128 1qnxA 209 4.82e+01 1qnxA d.111.1.1 40914 1ho8A 480 4.93e+01 1ho8A a.118.1.9 61107 1qynA 153 5.07e+01 d.33.1.1 96597 1pylA 97 5.11e+01 d.1.1.2 104391 1zl8B 54 5.13e+01 1vyiA 112 5.13e+01 1egaA 301 5.22e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1fjcA 96 5.23e+01 1fjcA d.58.7.1 39212 1gk9A 260 5.23e+01 d.153.1.2 65246 1kwfA 363 5.27e+01 a.102.1.2 73078 2ag5A 246 5.30e+01 2a50A 73 5.32e+01 1e69B 322 5.41e+01 1e69B c.37.1.12 32377 1yrbA 262 5.46e+01 1ajqA 209 5.47e+01 1ajqA d.153.1.2 41840 2ac5A 316 5.52e+01 1e8yA 966 5.54e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1w7bA 339 5.55e+01 1culA 217 5.56e+01 1azsA d.58.29.1 39417 1tw9A 206 5.62e+01 a.45.1.1,c.47.1.5 107381,107382 1ppjA 446 5.62e+01 d.185.1.1,d.185.1.1 104252,104253 1nrlA 316 5.64e+01 a.123.1.1 92091 1azsA 220 5.64e+01 1azsA d.58.29.1 39416 1jr3E 334 5.73e+01 a.80.1.1,c.37.1.20 63253,63254 1npeA 267 5.73e+01 b.68.5.1 92032 1bk6A 422 5.75e+01 1bk5A a.118.1.1 19133 1mswD 883 5.76e+01 e.8.1.3 79427 1c05A 159 5.87e+01 1c05A d.66.1.2 39559 1ai7A 209 5.88e+01 1ajqA d.153.1.2 41845 2c4nA 250 5.94e+01 1cem 363 6.02e+01 1cem a.102.1.2 18826 1eblB 317 6.11e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1brwA 433 6.11e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1ftt 68 6.16e+01 2hddA a.4.1.1 15997 1frd 98 6.26e+01 1awd d.15.4.1 37648 1acf 125 6.31e+01 3nul d.110.1.1 40882 1bxlA 181 6.32e+01 1maz f.1.4.1 43396 1avoB 140 6.35e+01 1avoB 1k6kA 143 6.41e+01 a.174.1.1 77274 2fuqA 747 6.43e+01 1ew4A 106 6.54e+01 1ew4A d.82.2.1 40023 2prf 125 6.61e+01 3nul d.110.1.1 40887 1rcsA 105 6.62e+01 1jhgA a.4.12.1 19025 1jtdB 273 6.64e+01 b.69.5.2 67265 1dmmA 131 6.67e+01 1opy d.17.4.3 38114 1gl2C 65 6.71e+01 h.1.15.1 65280 3icb 75 6.82e+01 4icb a.39.1.1 17147 2d69A 430 6.85e+01 1i1iP 681 6.87e+01 1i1iP d.92.1.5 40297 2bvaA 292 6.92e+01 1prq 125 6.93e+01 3nul d.110.1.1 40883 1aii 323 7.03e+01 1avc a.65.1.1 18150 1jkoC 52 7.04e+01 a.4.1.2 66809 1gcoA 261 7.07e+01 1ybvA c.2.1.2 29884 1i6xA 209 7.08e+01 a.4.5.4,b.82.3.2 83673,83674 1oh0A 131 7.11e+01 d.17.4.3 87004 1eca 136 7.15e+01 1flp a.1.1.2 15209 1avyC 74 7.16e+01 1avyB h.1.17.1 45658 1zbqA 327 7.18e+01 2cwxA 430 7.23e+01 1s4kA 120 7.23e+01 a.35.1.6 105254 1b3uA 588 7.30e+01 1b3uA a.118.1.2 19135 1bk5A 422 7.40e+01 1bk5A a.118.1.1 19130 1geeA 261 7.43e+01 c.2.1.2 90509 1pk5A 248 7.51e+01 a.123.1.1 88139 2dalA 62 7.55e+01 1yodA 30 7.60e+01 1cjtA 217 7.62e+01 1azsA d.58.29.1 39419 2ay1A 394 7.63e+01 1ajsA c.67.1.1 34357 1oe8A 211 7.65e+01 a.45.1.1,c.47.1.5 86905,86906 1l0lA 446 7.73e+01 d.185.1.1,d.185.1.1 84482,84483 1opy 131 7.83e+01 1opy d.17.4.3 38113 1uayA 242 7.94e+01 c.2.1.2 88390 1ecd 136 7.99e+01 1flp a.1.1.2 15211 1be3A 446 8.02e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1lpe 144 8.04e+01 1nfn a.24.1.1 16524 1e7uA 961 8.04e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2a9gA 418 8.06e+01 1pmt 203 8.09e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 1yz8P 68 8.13e+01 1i4wA 353 8.18e+01 c.66.1.24 66028 1r0vA 305 8.18e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1k07A 263 8.22e+01 d.157.1.1 77218 1hcrA 52 8.24e+01 1hcrA a.4.1.2 16020 2tpt 440 8.24e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1eco 136 8.28e+01 1flp a.1.1.2 15208 1a91 79 8.35e+01 1a91 f.17.1.1 43635 1j5yA 187 8.46e+01 a.4.5.1,d.94.2.1 71592,71593 1owcA 427 8.51e+01 a.103.1.1 104039 1odoA 408 8.53e+01 a.104.1.1 92783 1axn 323 8.57e+01 1avc a.65.1.1 18149 1h2kA 349 8.61e+01 b.82.2.6 76572 1ghtA 105 8.63e+01 2rslA c.53.1.1 60526 1tfr 305 8.76e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1wpaA 114 8.79e+01 1h6hA 143 8.84e+01 d.189.1.1 65681 1v9nA 360 8.91e+01 1zarA 282 8.92e+01 1sig 339 8.94e+01 1sig a.177.1.1 19068 1nfn 191 8.95e+01 1nfn a.24.1.1 16523