# List of top-scoring protein chains for t2k-100-30-n_sep-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 2c46A 241 2.47e-01 2sas 185 2.54e-01 2sas a.39.1.5 17258 1ow4A 129 2.56e-01 a.39.2.1 93628 1d3gA 367 2.76e-01 1d3gA c.1.4.1 28600 1d3hA 367 2.76e-01 1d3gA c.1.4.1 28601 1i9sA 210 3.41e-01 1i9sA c.45.1.1 62099 2b0mA 393 3.57e-01 1uumA 372 3.80e-01 c.1.4.1 100010 1db1A 259 9.05e-01 1db1A a.123.1.1 19329 1tx4B 178 1.19e+00 1ctqA c.37.1.8 32045 1y60A 169 1.56e+00 1jlwA 219 1.97e+00 a.45.1.1,c.47.1.5 71741,71742 2abk 211 2.08e+00 2abk a.96.1.1 18743 1efcA 393 2.52e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1uvzA 119 2.55e+00 1ie9A 259 2.59e+00 1db1A a.123.1.1 62318 1huqA 164 2.61e+00 1byuA c.37.1.8 32020 1w4vA 119 2.68e+00 1w9gA 104 2.87e+00 1g8jB 133 3.12e+00 1g8jB b.33.1.1 24439 1g8kB 133 3.56e+00 1g8jB b.33.1.1 24435 1s1eA 224 3.89e+00 1efuA 385 4.62e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1kmqA 184 4.68e+00 c.37.1.8 84412 1n6hA 170 4.71e+00 c.37.1.8 80197 1v4pA 157 5.78e+00 1n6bA 473 5.79e+00 a.104.1.1 85359 1sqhA 312 6.52e+00 d.108.1.5 98966 1g72A 573 6.68e+00 4aahA b.70.1.1 27680 4aahA 571 6.77e+00 4aahA b.70.1.1 27678 1z08A 170 6.84e+00 2dhqA 146 7.73e+00 2dhqA c.23.13.1 31382 1vfgA 390 7.78e+00 a.173.1.1,d.218.1.4 108570,108571 1kbqA 273 7.86e+00 c.23.5.3 68391 1f93A 104 8.39e+00 1dcpA d.74.1.1 39688 2iu4A 336 8.43e+00 1tf0B 53 8.43e+00 a.8.1.2 106825 1dioA 554 8.53e+00 1dioA c.1.19.3 29656 1ypqA 135 9.27e+00 1r5zA 323 9.56e+00 f.40.1.1 97135 1gw5S 142 1.02e+01 d.110.4.2 70633 2au3A 407 1.05e+01 1nt2A 210 1.06e+01 c.66.1.3 86149 3rp2A 224 1.11e+01 1a7s b.47.1.2 26298 1w6sA 599 1.12e+01 1f4tA 368 1.14e+01 1f4tA a.104.1.1 18973 1zcjA 463 1.15e+01 2c78A 405 1.17e+01 1zbsA 291 1.17e+01 1kebA 108 1.18e+01 c.47.1.1 77341 1jrkA 156 1.18e+01 d.113.1.1 71827 2ffqA 171 1.22e+01 1oivA 191 1.25e+01 c.37.1.8 93076 2ad6A 571 1.27e+01 1oixA 191 1.28e+01 1sceA 112 1.28e+01 1puc d.97.1.1 40676 2trxA 108 1.29e+01 1thx c.47.1.1 32719 1ukvY 206 1.34e+01 c.37.1.8 107918 1v93A 296 1.35e+01 c.1.23.1 100532 2reb 352 1.37e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1wz7A 111 1.41e+01 2clbA 188 1.46e+01 1wv2A 265 1.52e+01 1puc 105 1.59e+01 1puc d.97.1.1 40675 2bl0B 145 1.60e+01 1zzgA 415 1.63e+01 1d4aA 273 1.65e+01 1d4aA c.23.5.3 31219 1htoA 477 1.65e+01 d.15.9.1,d.128.1.1 70987,70988 1v7oA 165 1.70e+01 d.67.1.2 100480 1jr7A 311 1.70e+01 b.82.2.3 63255 1eljA 381 1.72e+01 4mbp c.94.1.1 35791 1htqA 477 1.73e+01 d.15.9.1,d.128.1.1 71035,71036 1pvyA 227 1.75e+01 d.115.1.2 95195 1nd7A 374 1.75e+01 d.148.1.1 91817 1bgvA 449 1.81e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1uh4A 637 1.82e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1snnA 227 1.86e+01 d.115.1.2 105821 2bwvA 440 1.90e+01 2a1xA 308 1.90e+01 1aii 323 1.93e+01 1avc a.65.1.1 18150 1hrdA 449 1.95e+01 1k89 c.2.1.7,c.58.1.1 30219,33867 1fzqA 181 2.01e+01 1hurA c.37.1.8 32060 1ji1A 637 2.02e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1ijtA 128 2.03e+01 1bfg b.42.1.1 62510 2d83A 363 2.03e+01 1ie5A 107 2.05e+01 b.1.1.4 62312 1bm8 99 2.06e+01 1bm8 d.34.1.1 38528 2drwA 363 2.11e+01 1wl9A 440 2.13e+01 1mc2A 122 2.14e+01 a.133.1.2 74622 2fcr 173 2.14e+01 1rcf c.23.5.1 31151 1s8fA 177 2.15e+01 c.37.1.8 105370 1r2qA 170 2.16e+01 c.37.1.8 96874 1xpxA 163 2.16e+01 1eexA 554 2.18e+01 1dioA c.1.19.3 29650 1f7zA 233 2.19e+01 5ptp b.47.1.2 59681 1v9mA 323 2.24e+01 f.40.1.1 100543 2lgsA 468 2.25e+01 1lgr d.15.9.1,d.128.1.1 37838,41168 1lgr 468 2.25e+01 1lgr d.15.9.1,d.128.1.1 37837,41167 2c5qA 240 2.27e+01 1axn 323 2.30e+01 1avc a.65.1.1 18149 2fbqA 235 2.32e+01 1nr6A 473 2.36e+01 a.104.1.1 92085 1eyuA 157 2.41e+01 3pviA c.52.1.6 33304 1b37B 472 2.44e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 1fuqA 472 2.45e+01 1furA a.127.1.1 19405 1e5eA 404 2.46e+01 1ibjA c.67.1.3 59265 1exmA 405 2.51e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1lxnA 99 2.51e+01 d.58.48.1 84737 1t1vA 93 2.51e+01 c.47.1.14 106278 1k89 449 2.62e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 1b37A 472 2.64e+01 1b37B c.3.1.2,d.16.1.5 30389,37953 1c14A 262 2.65e+01 1eny c.2.1.2 29927 1rtxA 123 2.67e+01 a.1.1.1 97827 1rxdA 159 2.69e+01 1tp6A 128 2.71e+01 d.17.4.12 107184 1xg7A 250 2.78e+01 1f76A 336 2.78e+01 c.1.4.1 76160 1qbgA 272 2.79e+01 1d4aA c.23.5.3 31227 1ecsA 126 2.81e+01 1ecsA d.32.1.2 59407 1vj0A 380 2.87e+01 b.35.1.2,c.2.1.1 100786,100787 1dcoA 104 2.89e+01 1dcpA d.74.1.1 39680 2bcgY 206 2.89e+01 1avc 673 2.90e+01 1avc a.65.1.1,a.65.1.1 18178,18179 1h05A 146 2.91e+01 c.23.13.1 76433 2d9bA 109 2.92e+01 1az9 457 2.94e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1je5A 206 2.96e+01 1je5A b.40.4.7 62909 1qg6A 261 2.97e+01 1eny c.2.1.2 29919 2fgoA 82 2.99e+01 1wmsA 177 3.00e+01 c.37.1.8 109414 1s6cA 183 3.02e+01 a.39.1.5 98594 2c5uA 375 3.04e+01 1xzoA 174 3.04e+01 1pvuA 154 3.06e+01 3pviA c.52.1.6 33306 1ifqA 138 3.07e+01 1ifqA d.110.4.1 62350 1qsgA 265 3.09e+01 1eny c.2.1.2 29935 1zkiA 133 3.12e+01 1rh9A 373 3.17e+01 1dcpA 104 3.18e+01 1dcpA d.74.1.1 39672 2cviA 83 3.20e+01 1aqcA 172 3.23e+01 1x11A b.55.1.2 26983 1n46A 258 3.24e+01 a.123.1.1 85315 1fuoA 467 3.24e+01 1furA a.127.1.1 19411 1ef1C 90 3.30e+01 1ef1C a.137.5.1 19642 1x3xA 82 3.31e+01 1k26A 156 3.32e+01 d.113.1.1 72003 1t00A 112 3.32e+01 1nekA 588 3.33e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1vdkA 466 3.39e+01 a.127.1.1 100561 1aipA 405 3.40e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1jr1A 514 3.41e+01 c.1.5.1,d.37.1.1,d.37.1.1 63241,63242,63243 1iapA 211 3.44e+01 a.91.1.1 62119 2gmyA 153 3.49e+01 2cs7A 55 3.50e+01 1y4lA 121 3.52e+01 1va6A 518 3.55e+01 1zckA 154 3.58e+01 2gasA 307 3.58e+01 1aipE 405 3.61e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1hpt 56 3.70e+01 1tgsI g.68.1.1 44703 1etu 394 3.73e+01 1efcA c.37.1.8 64737 1sx5A 244 3.74e+01 c.52.1.2 99023 1eft 405 3.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1jnrB 150 3.76e+01 d.58.1.5 66969 1ha3A 405 3.77e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1fa0A 537 3.78e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1iarB 207 3.82e+01 1iarB b.1.2.1,b.1.2.1 22037,22038 2cw9A 194 3.83e+01 2cmwA 310 3.92e+01 1hm6A 346 3.98e+01 1avc a.65.1.1 18147 2napA 723 4.02e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1xw5A 217 4.06e+01 1dt6A 473 4.11e+01 1dt6A a.104.1.1 18977 1yt3A 375 4.15e+01 1aj4 161 4.17e+01 1ncx a.39.1.5 17244 1up8A 598 4.18e+01 a.111.1.2 99710 1b04A 318 4.27e+01 1b04A d.142.2.2 41579 1uok 558 4.29e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1ewjA 126 4.33e+01 1ecsA d.32.1.2 59526 1i9aA 182 4.33e+01 1i9aA d.113.1.2 62082 2atxA 194 4.33e+01 1k2eA 156 4.34e+01 d.113.1.1 72010 1nffA 260 4.36e+01 c.2.1.2 80457 1yqfA 203 4.38e+01 1w7bA 339 4.42e+01 2bbeA 108 4.46e+01 1sf8A 126 4.47e+01 d.271.1.1 105472 2pviA 157 4.47e+01 3pviA c.52.1.6 33302 2coeA 120 4.50e+01 2bvcA 486 4.51e+01 1djtA 64 4.53e+01 1aho g.3.7.1 44132 1lap 488 4.58e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1oi2A 366 4.59e+01 c.119.1.2 103802 1b13A 54 4.62e+01 1rb9 g.41.5.1 45227 1v58A 241 4.62e+01 c.47.1.9,d.17.3.1 108371,108372 1bf2 750 4.66e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1h3gA 601 4.68e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1xszA 356 4.70e+01 1b2sD 90 4.72e+01 1ay7B c.9.1.1 30837 1b27D 90 4.74e+01 1ay7B c.9.1.1 30840 1dik 874 4.79e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1b5qA 472 4.80e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 3pviA 157 4.82e+01 3pviA c.52.1.6 33300 1hztA 190 4.89e+01 1i9aA d.113.1.2 61459 1ay7B 89 4.90e+01 1ay7B c.9.1.1 30836 1ky3A 182 4.94e+01 c.37.1.8 73193 1g19A 350 4.95e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1vhoA 346 4.96e+01 b.49.3.1,c.56.5.4 100694,100695 1cnt2 187 4.97e+01 1cnt3 1aszB 490 4.97e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1u94A 356 4.98e+01 c.37.1.11,d.48.1.1 107743,107744 1dchA 104 4.99e+01 1dcpA d.74.1.1 39692 1x84A 189 5.01e+01 2d2yA 145 5.02e+01 1taq 832 5.04e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1or4A 178 5.12e+01 a.1.1.2 93447 1hi9A 274 5.13e+01 1hi9A c.99.1.1 61063 1mt6A 280 5.21e+01 b.76.2.1,b.85.7.1 79446,79447 2gk9A 426 5.21e+01 1x24A 180 5.24e+01 1h3iA 293 5.27e+01 b.76.2.1,b.85.7.1 76635,76636 1b2uD 90 5.33e+01 1ay7B c.9.1.1 30843 2ganA 190 5.36e+01 1xrtA 467 5.36e+01 1hv9A 456 5.39e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1ann 318 5.40e+01 1avc a.65.1.1 18151 1ovnA 248 5.51e+01 a.71.1.1,c.47.1.7 93602,93603 1fxjA 331 5.52e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1q4uA 151 5.54e+01 d.38.1.5 95828 2bwbA 46 5.57e+01 1f52A 468 5.57e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1y6lA 149 5.68e+01 1ywzA 175 5.69e+01 1fwyA 331 5.69e+01 1fwyA b.81.1.4,c.68.1.5 28064,34522 1jgjA 217 5.69e+01 1c3wA f.13.1.1 62952 3rabA 169 5.71e+01 1ctqA c.37.1.8 32018 1thx 115 5.73e+01 1thx c.47.1.1 32732 1efuB 282 5.84e+01 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 2b18A 164 5.87e+01 1fchA 368 5.89e+01 1fchA a.118.8.1 19212 1jtgB 165 5.93e+01 d.98.1.1 67267 1ym3A 215 5.93e+01 1ubeA 349 5.95e+01 c.37.1.11,d.48.1.1 88412,88413 3proD 166 6.06e+01 3proC d.52.1.1,d.52.1.1 38814,38815 1qp6A 35 6.13e+01 1qp6A k.16.1.1 46443 2b5rC 165 6.17e+01 1z0jA 170 6.21e+01 1vq3A 94 6.33e+01 1a6g 151 6.36e+01 1a6m a.1.1.2 15021 1h4xA 117 6.39e+01 1auz c.13.2.1 60626 1q42A 201 6.40e+01 d.17.4.2 95776 1n1mA 728 6.42e+01 b.70.3.1,c.69.1.24 79815,79816 1dxsA 80 6.48e+01 1cokA a.60.1.2 17944 1itbB 315 6.55e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1h2sA 225 6.58e+01 f.13.1.1 76578 2g2uB 165 6.60e+01 1xxsA 122 6.66e+01 2gaeA 346 6.68e+01 1ncx 162 6.71e+01 1ncx a.39.1.5 17222 2sqcA 631 6.71e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1jj2O 148 6.72e+01 1ffkM a.94.1.1 63100 1xm3A 264 6.73e+01 2mtaC 147 6.73e+01 2mtaC a.3.1.1 15908 1jltA 122 6.74e+01 a.133.1.2 66867 2fb1A 226 6.76e+01 3lck 271 6.76e+01 1fmk d.144.1.7 41686 1iro 54 6.77e+01 1rb9 g.41.5.1 45223 1e1dA 553 6.78e+01 1e1dA e.26.1.1 43363 2f4lA 297 6.81e+01 1t9iA 163 6.83e+01 2erbA 125 6.84e+01 1anb 223 6.90e+01 5ptp b.47.1.2 25998 1b96A 244 7.01e+01 1rvaA c.52.1.2 33268 2a5vA 213 7.07e+01 1g24A 211 7.10e+01 1g24A d.166.1.1 42270 1b2jA 54 7.13e+01 1rb9 g.41.5.1 45231 1amuA 563 7.13e+01 1amuA e.23.1.1 43351 1upvA 257 7.15e+01 1zclA 180 7.20e+01 1s72P 149 7.21e+01 a.94.1.1 105335 2f69A 261 7.28e+01 2bl2A 156 7.28e+01 1jb1A 205 7.30e+01 1jb1A c.91.1.2 62832 1b97A 244 7.34e+01 1rvaA c.52.1.2 33252 3proC 166 7.38e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1dwkA 156 7.42e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1brsD 89 7.43e+01 1ay7B c.9.1.1 30825 1zoyC 140 7.46e+01 1gmlA 178 7.46e+01 c.8.5.2 70273 1fa0B 537 7.50e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1kvnA 104 7.52e+01 d.201.1.1 73066 1zthA 258 7.52e+01 1mp4A 292 7.54e+01 c.68.1.6 79376 1a4rA 191 7.55e+01 1ctqA c.37.1.8 32063 1a4uA 254 7.55e+01 1b16A c.2.1.2 29878 1gzwA 134 7.56e+01 b.29.1.3 90535 1x8hA 228 7.57e+01 1k20A 310 7.60e+01 c.107.1.1 68027 1top 162 7.62e+01 1ncx a.39.1.5 17223 1ua4A 455 7.63e+01 c.72.1.3 99128 1b3sD 90 7.67e+01 1ay7B c.9.1.1 30846 1ddjA 247 7.68e+01 5ptp b.47.1.2 26362 1h7cA 108 7.72e+01 a.7.5.1 70914 1q7bA 244 7.73e+01 c.2.1.2 96026 1nf3A 195 7.77e+01 c.37.1.8 85594 1kvkA 395 7.77e+01 d.14.1.5,d.58.26.3 73060,73061 1y0yA 353 7.80e+01 1i7hA 111 7.83e+01 d.15.4.1 71122 1w6nA 134 7.86e+01 1qpcA 279 7.86e+01 1fgkA d.144.1.7 41685 1gmwA 143 7.92e+01 b.107.1.1,d.58.38.1 65347,65348 1jbuH 254 7.93e+01 5ptp b.47.1.2 62856 1gmuA 143 7.93e+01 b.107.1.1,d.58.38.1 65335,65336 1g9zA 152 7.95e+01 1bp7A d.95.2.1 60408 1danH 254 7.96e+01 5ptp b.47.1.2 26292 5ptp 223 7.96e+01 5ptp b.47.1.2 25831 1nkxA 348 7.98e+01 c.94.1.2 91943 1go4E 100 7.99e+01 h.1.22.1 70296 1n6aA 259 8.04e+01 b.76.2.1,b.85.7.1 80121,80122 2c4jA 218 8.05e+01 1is2A 661 8.08e+01 a.29.3.2,a.29.3.2,e.6.1.2 71382,71383,71384 1and 223 8.09e+01 5ptp b.47.1.2 25985 1acj 537 8.09e+01 2bce c.69.1.1 34588 1uohA 226 8.11e+01 d.211.1.1 99690 1b16A 254 8.15e+01 1b16A c.2.1.2 29875 1k9uA 78 8.15e+01 a.39.1.10 84348 4ptp 223 8.21e+01 1hj9A 226 8.24e+01 b.47.1.2 65845 1m2dA 110 8.28e+01 c.47.1.11 78476 1a16 440 8.33e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 2g2dA 193 8.36e+01 1rkd 309 8.36e+01 1rkd c.72.1.1 34928 1tzaA 134 8.38e+01 b.1.23.1 107468 2gkpA 167 8.44e+01 1pveA 72 8.47e+01 a.189.1.1 104322 1e9eA 215 8.50e+01 c.37.1.1 64810 1wh8A 111 8.50e+01 2fi1A 190 8.57e+01 2bz6H 254 8.73e+01 1p0hA 318 8.81e+01 d.108.1.1 93866 1o8vA 134 8.81e+01 b.60.1.2 86680 2ixiA 184 8.86e+01 2ae0X 345 8.87e+01 1amhA 223 8.90e+01 5ptp b.47.1.2 25994 1orvA 728 8.95e+01 b.70.3.1,c.69.1.24 87354,87355