# 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 1lkxA 697 9.98e-02 c.37.1.9 73981 1x3xA 82 1.21e-01 1i9sA 210 3.69e-01 1i9sA c.45.1.1 62099 2c46A 241 8.16e-01 1lvk 762 1.78e+00 1lvk b.34.3.1,c.37.1.9 24576,32173 1i7hA 111 2.17e+00 d.15.4.1 71122 1q4uA 151 2.44e+00 d.38.1.5 95828 1ypqA 135 2.67e+00 1d4aA 273 2.75e+00 1d4aA c.23.5.3 31219 1qbgA 272 2.76e+00 1d4aA c.23.5.3 31227 1kbqA 273 2.79e+00 c.23.5.3 68391 1nr6A 473 2.84e+00 a.104.1.1 92085 2akaA 776 3.18e+00 1gmuA 143 3.71e+00 b.107.1.1,d.58.38.1 65335,65336 1uvzA 119 3.93e+00 1w4vA 119 3.96e+00 1zkiA 133 4.38e+00 1gc5A 467 5.26e+00 1gc5A c.72.1.3 60429 1yqfA 203 5.36e+00 2sas 185 5.73e+00 2sas a.39.1.5 17258 1s6cA 183 5.86e+00 a.39.1.5 98594 1s1eA 224 5.94e+00 2fcr 173 5.94e+00 1rcf c.23.5.1 31151 1vom 762 6.27e+00 1lvk b.34.3.1,c.37.1.9 24577,32174 1lj0A 92 6.36e+00 d.120.1.1 78019 1db1A 259 6.60e+00 1db1A a.123.1.1 19329 2gf6A 135 6.60e+00 1jr7A 311 6.74e+00 b.82.2.3 63255 1w9iA 770 6.79e+00 1g8jB 133 6.84e+00 1g8jB b.33.1.1 24439 1ow4A 129 7.45e+00 a.39.2.1 93628 1d0yA 761 7.61e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 1gmwA 143 7.70e+00 b.107.1.1,d.58.38.1 65347,65348 1nd7A 374 8.14e+00 d.148.1.1 91817 1eljA 381 8.80e+00 4mbp c.94.1.1 35791 1mc2A 122 8.90e+00 a.133.1.2 74622 1vj0A 380 9.56e+00 b.35.1.2,c.2.1.1 100786,100787 2c5qA 240 1.06e+01 1vfgA 390 1.11e+01 a.173.1.1,d.218.1.4 108570,108571 1mnd 762 1.12e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 1g8kB 133 1.13e+01 1g8jB b.33.1.1 24435 1f7zA 233 1.20e+01 5ptp b.47.1.2 59681 3rp2A 224 1.28e+01 1a7s b.47.1.2 26298 2b2nA 344 1.31e+01 1anb 223 1.34e+01 5ptp b.47.1.2 25998 1dwkA 156 1.37e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1ie9A 259 1.39e+01 1db1A a.123.1.1 62318 2gk9A 426 1.52e+01 1dw9A 156 1.53e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 1je5A 206 1.54e+01 1je5A b.40.4.7 62909 1hj9A 226 1.60e+01 b.47.1.2 65845 1rtxA 123 1.67e+01 a.1.1.1 97827 4ptp 223 1.70e+01 1n6bA 473 1.71e+01 a.104.1.1 85359 1d3hA 367 1.72e+01 1d3gA c.1.4.1 28601 1dpo 223 1.73e+01 5ptp b.47.1.2 25975 1eueA 86 1.74e+01 1cyo d.120.1.1 59504 1zzgA 415 1.75e+01 2b0mA 393 1.75e+01 2abk 211 1.80e+01 2abk a.96.1.1 18743 1d3gA 367 1.81e+01 1d3gA c.1.4.1 28600 1ll2A 333 1.82e+01 c.68.1.14 74005 1anc 223 1.89e+01 5ptp b.47.1.2 25982 5ptp 223 2.03e+01 5ptp b.47.1.2 25831 1v7oA 165 2.03e+01 d.67.1.2 100480 1sceA 112 2.17e+01 1puc d.97.1.1 40676 1uumA 372 2.25e+01 c.1.4.1 100010 1y4lA 121 2.26e+01 1oqyA 368 2.29e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1wz7A 111 2.31e+01 1ar72 272 2.33e+01 1aym2 1hxs2 272 2.37e+01 1v4pA 157 2.37e+01 1and 223 2.39e+01 5ptp b.47.1.2 25985 1amhA 223 2.56e+01 5ptp b.47.1.2 25994 1aksA 125 2.65e+01 5ptp b.47.1.2 25969 1jw2A 72 2.70e+01 a.23.5.1 67372 1poiA 317 2.73e+01 1poiA c.124.1.2 34153 2bwvA 440 2.74e+01 1knt 58 2.75e+01 1bpi g.8.1.1 44538 1mctA 223 2.75e+01 5ptp b.47.1.2 25961 1a16 440 2.77e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1az9 457 2.77e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1wl9A 440 2.79e+01 1e55A 512 2.80e+01 1e70M c.1.8.4 28934 1h49A 512 2.82e+01 c.1.8.4 83477 1w9gA 104 2.83e+01 2knt 58 2.87e+01 1bpi g.8.1.1 44537 1r5zA 323 2.94e+01 f.40.1.1 97135 1awpA 92 3.04e+01 1cyo d.120.1.1 41071 2fujA 137 3.07e+01 1kthA 58 3.09e+01 g.8.1.1 68863 1s83A 223 3.10e+01 b.47.1.2 98718 1e9cA 215 3.14e+01 c.37.1.1 64808 1b5m 84 3.17e+01 1cyo d.120.1.1 41073 1s9rA 410 3.19e+01 d.126.1.4 98758 2a31A 223 3.20e+01 1e9eA 215 3.20e+01 c.37.1.1 64810 1tx4B 178 3.21e+01 1ctqA c.37.1.8 32045 1lxyA 409 3.29e+01 d.126.1.4 91154 1up8A 598 3.31e+01 a.111.1.2 99710 1ucpA 91 3.44e+01 a.77.1.5 99186 1lvfA 110 3.45e+01 a.47.2.1 74280 1efcA 393 3.46e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1atg 231 3.55e+01 1atg c.94.1.1 35834 1oejA 193 3.56e+01 b.60.1.4 92798 1an1E 223 3.61e+01 5ptp b.47.1.2 25970 1xxsA 122 3.73e+01 1y0yA 353 3.81e+01 1h9hE 223 3.82e+01 b.47.1.2 103810 1j90A 230 3.83e+01 c.37.1.1 66448 1zm7A 230 3.83e+01 1cb6A 691 3.84e+01 1cb6A c.94.1.2,c.94.1.2 35840,35841 1nekA 588 3.85e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1oe0A 230 3.90e+01 c.37.1.1 92788 1kmqA 184 3.94e+01 c.37.1.8 84412 1iapA 211 4.01e+01 a.91.1.1 62119 1xfoA 357 4.10e+01 1t00A 112 4.15e+01 1t1vA 93 4.16e+01 c.47.1.14 106278 4aahA 571 4.26e+01 4aahA b.70.1.1 27678 1b0lA 691 4.27e+01 1cb6A c.94.1.2,c.94.1.2 35847,35848 1rh9A 373 4.31e+01 1ovnA 248 4.35e+01 a.71.1.1,c.47.1.7 93602,93603 1cwxA 44 4.39e+01 1cwxA j.54.1.1 46338 1qhbA 596 4.39e+01 1qhbA a.111.1.2 19055 2g0qA 173 4.41e+01 1aqcA 172 4.48e+01 1x11A b.55.1.2 26983 1qlaB 239 4.51e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1xrtA 467 4.54e+01 1pvuA 154 4.64e+01 3pviA c.52.1.6 33306 1kqfC 217 4.65e+01 f.21.1.1 72874 1aszB 490 4.66e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1vhoA 346 4.66e+01 b.49.3.1,c.56.5.4 100694,100695 1p9cA 45 4.70e+01 j.105.1.1 94386 1fouA 309 4.73e+01 1fouA e.27.1.1 43364 1sqhA 312 4.74e+01 d.108.1.5 98966 1lcf 691 4.75e+01 1cb6A c.94.1.2,c.94.1.2 35838,35839 1rxdA 159 4.78e+01 1zckA 154 4.79e+01 1jltA 122 4.91e+01 a.133.1.2 66867 1gxyA 226 4.92e+01 d.166.1.3 76380 1cnt2 187 4.95e+01 1cnt3 1ddjA 247 4.95e+01 5ptp b.47.1.2 26362 2ad6A 571 4.97e+01 1acj 537 4.99e+01 2bce c.69.1.1 34588 1yz7A 188 5.04e+01 1e66A 543 5.05e+01 c.69.1.1 59291 1vpi 122 5.12e+01 1poa a.133.1.2 19559 1e58A 249 5.16e+01 1qhfA c.60.1.1 59262 1cyo 93 5.31e+01 1cyo d.120.1.1 41065 1avwA 223 5.33e+01 5ptp b.47.1.2 25965 2trxA 108 5.34e+01 1thx c.47.1.1 32719 1vxrA 537 5.38e+01 2bce c.69.1.1 34595 1htoA 477 5.38e+01 d.15.9.1,d.128.1.1 70987,70988 1xw5A 217 5.39e+01 1k1vA 41 5.45e+01 a.37.1.1 71999 1ea5A 537 5.47e+01 2bce c.69.1.1 34592 1g72A 573 5.50e+01 4aahA b.70.1.1 27680 1nn5A 215 5.70e+01 c.37.1.1 85892 1fniA 223 5.74e+01 5ptp b.47.1.2 25962 1rsgA 516 5.77e+01 1j0fA 100 5.79e+01 c.47.1.14 90739 1qrzA 246 5.90e+01 5ptp b.47.1.2 26366 3pviA 157 5.98e+01 3pviA c.52.1.6 33300 1ponB 36 6.05e+01 1ponB 1lam 484 6.08e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1ltdA 506 6.09e+01 1gox c.1.4.1,d.120.1.1 28618,41086 2anxA 146 6.14e+01 2pviA 157 6.17e+01 3pviA c.52.1.6 33302 1eyuA 157 6.23e+01 3pviA c.52.1.6 33304 2fgoA 82 6.40e+01 2c4jA 218 6.40e+01 1n46A 258 6.46e+01 a.123.1.1 85315 1yr1A 119 6.66e+01 1f47B 144 6.72e+01 1f46A d.129.4.1 59645 1jr3A 373 6.79e+01 a.80.1.1,c.37.1.20 63245,63246 1kvnA 104 6.85e+01 d.201.1.1 73066 1ua4A 455 6.90e+01 c.72.1.3 99128 1wv2A 265 6.93e+01 1mb4A 370 6.95e+01 c.2.1.3,d.81.1.1 78908,78909 1j1yA 136 6.98e+01 d.38.1.5 90776 1z2nX 324 7.00e+01 1bllE 488 7.20e+01 1lam c.50.1.1,c.56.5.3 33170,33833 2hekA 371 7.26e+01 1i3zA 103 7.29e+01 d.93.1.1 83667 1zd7A 159 7.29e+01 1fuoA 467 7.29e+01 1furA a.127.1.1 19411 1kebA 108 7.32e+01 c.47.1.1 77341 1txlA 215 7.37e+01 b.60.1.4 107429 1ji2A 585 7.38e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1ijtA 128 7.51e+01 1bfg b.42.1.1 62510 2aukA 190 7.56e+01 2cyeA 133 7.58e+01 1fuqA 472 7.61e+01 1furA a.127.1.1 19405 1puc 105 7.63e+01 1puc d.97.1.1 40675 1wluA 136 7.69e+01 2bvcA 486 7.70e+01 1jvr 137 7.72e+01 1jvr a.61.1.2 18132 1bgvA 449 7.72e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1ppa 121 7.76e+01 1poa a.133.1.2 19550 1s8iA 121 7.88e+01 a.133.1.2 98735 1ef1C 90 7.91e+01 1ef1C a.137.5.1 19642 1zt2B 212 7.92e+01 1vp6A 138 7.92e+01 2drwA 363 8.06e+01 1j96A 323 8.07e+01 c.1.7.1 71616 2d83A 363 8.10e+01 1g24A 211 8.16e+01 1g24A d.166.1.1 42270 2a3nA 355 8.18e+01 1f4tA 368 8.26e+01 1f4tA a.104.1.1 18973 1b1xA 689 8.30e+01 1cb6A c.94.1.2,c.94.1.2 35865,35866 1furA 467 8.34e+01 1furA a.127.1.1 19403 1suuA 312 8.43e+01 b.68.10.1 99006 2clbA 188 8.50e+01 1khqA 212 8.53e+01 d.3.1.1 90964 1mb1 130 8.56e+01 1bm8 d.34.1.1 38529 2dhqA 146 8.59e+01 2dhqA c.23.13.1 31382 2gmyA 153 8.60e+01 2a9kB 223 8.63e+01 1k89 449 8.77e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 1w6sA 599 8.81e+01 1fafA 79 8.84e+01 1fafA a.2.3.1 15700 1ctaA 36 8.89e+01 1ctdA a.39.1.5 17232