# List of top-scoring protein chains for t06-80-60-80-str2+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 2c78A 405 4.85e-03 1kk1A 410 3.67e-02 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2c5qA 240 1.08e-01 1hd7A 318 1.89e-01 1bix d.151.1.1 41780 2as9A 210 2.21e-01 2fhxA 246 3.33e-01 1uebA 184 4.22e-01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1m2xA 223 5.19e-01 d.157.1.1 84764 1cid 177 5.38e-01 1cid b.1.1.1,b.1.1.3 19740,21679 2g1lA 104 9.24e-01 1yloA 348 1.10e+00 1ftrA 296 1.18e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 1p80A 753 1.35e+00 c.23.16.3,e.5.1.1 94337,94338 2sfa 191 1.48e+00 1qq4A b.47.1.1 25815 2eifA 136 1.81e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1z6bA 154 2.21e+00 1am2 199 2.32e+00 1am2 b.86.1.2 28381 1g38A 393 2.59e+00 2admA c.66.1.27 60235 1wqsA 173 2.88e+00 1i1qB 192 3.07e+00 1qdlB c.23.16.1 61544 1vqoA 240 3.10e+00 1dgfA 497 3.23e+00 1cf9A e.5.1.1 42782 1sr9A 644 3.48e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1neu 124 3.53e+00 1neu b.1.1.1 19704 2a7yA 83 3.84e+00 1earA 147 4.25e+00 b.107.1.1,d.58.38.1 64875,64876 2cvhA 220 4.27e+00 1x8hA 228 4.57e+00 2fytA 340 4.72e+00 1fvuB 125 4.83e+00 1ixxB d.169.1.1 42346 2an1A 292 4.97e+00 1s1dA 331 5.30e+00 b.67.3.1 98344 1hfuA 503 6.10e+00 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1aozA 552 6.27e+00 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1utiA 58 6.84e+00 b.34.2.1 99962 2a7mA 250 6.88e+00 2alaA 391 6.94e+00 2d1eA 248 7.02e+00 1jjtA 228 7.17e+00 1a7tA d.157.1.1 63139 1zo0A 126 7.77e+00 1q1rA 431 7.82e+00 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1v0eA 666 7.89e+00 1nxmA 197 8.23e+00 b.82.1.1 86385 1nb8A 353 8.24e+00 d.3.1.9 80385 1zvyA 136 8.42e+00 1whi 122 8.63e+00 1whi b.39.1.1 24810 1w61A 414 8.71e+00 1b8kA 119 8.89e+00 1bndA g.17.1.3 44795 1uypA 432 8.99e+00 b.29.1.19,b.67.2.3 100176,100177 1v05A 96 9.32e+00 1xauA 122 9.35e+00 1ylnA 252 9.48e+00 1ypqA 135 9.50e+00 1oalA 151 9.65e+00 b.1.8.1 86739 1vhyA 257 9.68e+00 b.122.1.2,c.116.1.5 100714,100715 2gaiA 633 9.92e+00 2azeA 155 1.03e+01 2cw8A 537 1.09e+01 1w2tA 432 1.16e+01 2cxkA 95 1.20e+01 1drw 273 1.21e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1xkpC 143 1.24e+01 1xe7A 203 1.27e+01 1bbzA 58 1.27e+01 1bbzA b.34.2.1 24477 1yukB 120 1.29e+01 1wraA 308 1.31e+01 1mqoA 227 1.33e+01 d.157.1.1 103846 1at0 145 1.35e+01 1at0 b.86.1.1 28374 1quqB 121 1.37e+01 1quqB b.40.4.3 25305 2d83A 363 1.37e+01 1gxuA 91 1.40e+01 d.58.10.1 76378 1ux6A 350 1.41e+01 b.29.1.16,g.75.1.1 100145,100146 2bhuA 602 1.44e+01 1twfH 146 1.44e+01 1hn0A 1021 1.46e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1iakA 199 1.47e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1fhgA 154 1.49e+01 1tlk b.1.1.4 21706 1kjvB 100 1.51e+01 b.1.1.2 77423 1lm8V 160 1.55e+01 b.3.3.1 74035 1z9lA 128 1.55e+01 1wkrA 340 1.58e+01 b.50.1.2 109395 1hrhA 136 1.61e+01 1rthA c.55.3.1 33577 1z8gA 372 1.62e+01 1pm1X 180 1.64e+01 b.60.1.1 104189 1uq5A 263 1.65e+01 d.165.1.1 99778 2d29A 387 1.66e+01 1jmxA 494 1.68e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1w99A 558 1.68e+01 1a7tA 232 1.72e+01 1a7tA d.157.1.1 42041 1sgpE 185 1.76e+01 1qq4A b.47.1.1 25816 1gweA 503 1.77e+01 e.5.1.1 70667 1gycA 499 1.79e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 2a6sA 84 1.82e+01 1u2hA 99 1.85e+01 1a12A 413 1.85e+01 1a12A b.69.5.1 27663 1k5nB 100 1.85e+01 b.1.1.2 77268 1xp8A 366 1.86e+01 1x8gA 227 1.86e+01 2bibA 547 1.87e+01 2d4qA 257 1.89e+01 1f60A 458 1.90e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1bxvA 91 1.92e+01 1aac b.6.1.1 22875 1pmy 123 1.92e+01 1bqk b.6.1.1 22888 2abwA 227 1.93e+01 1lk2B 99 2.03e+01 b.1.1.2 91058 1yl3V 253 2.04e+01 1zczA 464 2.09e+01 1v76A 96 2.13e+01 1cr1A 296 2.13e+01 1cr1A c.37.1.11 32286 1m07A 111 2.16e+01 d.5.1.1 78328 1h8eA 510 2.16e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1lqvA 193 2.17e+01 d.19.1.1 74206 1ukfA 188 2.22e+01 d.3.1.10 99488 1j48A 110 2.25e+01 b.1.7.1 84112 1vzqH 250 2.27e+01 1r0mA 375 2.28e+01 c.1.11.2,d.54.1.1 104747,104748 1nepA 130 2.38e+01 b.1.18.7 80440 1u3wA 374 2.38e+01 1n0lA 224 2.39e+01 b.1.11.1,b.7.2.1 79744,79745 1x89A 178 2.39e+01 1ppfE 218 2.42e+01 1a7s b.47.1.2 26234 1kcqA 104 2.44e+01 d.109.1.1 68449 1yn8A 59 2.48e+01 1mw9X 592 2.53e+01 e.10.1.1 91480 1gg4A 452 2.53e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1ym5A 300 2.57e+01 2ck3A 510 2.60e+01 1e7uA 961 2.62e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1gsoA 431 2.64e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2az4A 429 2.65e+01 2sga 181 2.69e+01 1qq4A b.47.1.1 25808 1cqxA 403 2.72e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1x99A 145 2.73e+01 2brqA 97 2.74e+01 1zkpA 268 2.76e+01 1siqA 392 2.77e+01 a.29.3.1,e.6.1.1 105585,105586 1dj7B 75 2.77e+01 1dj7B b.34.4.3 24598 1ok8A 394 2.79e+01 b.1.18.4,f.10.1.1 93236,93237 1uvqA 197 2.83e+01 b.1.1.2,d.19.1.1 100062,100063 1qwlA 505 2.84e+01 e.5.1.1 96483 1umzA 278 2.88e+01 b.29.1.2 99639 1olzA 663 2.89e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1ep0A 185 2.91e+01 1dzrA b.82.1.1 28080 2b5eA 504 2.93e+01 1vqoE 178 2.95e+01 1qwdA 177 3.01e+01 b.60.1.1 96471 1g1cA 99 3.03e+01 b.1.1.4 65078 1n8kA 374 3.04e+01 b.35.1.2,c.2.1.1 80298,80299 1khbA 625 3.05e+01 c.91.1.1,c.109.1.1 68606,68607 2fimA 276 3.07e+01 2ciaA 102 3.08e+01 1w0nA 131 3.08e+01 1j1tA 233 3.13e+01 b.29.1.18 90771 2bwkA 121 3.13e+01 1t77A 414 3.14e+01 1mkaA 171 3.17e+01 1mkaA d.38.1.2 38543 1qy6A 274 3.19e+01 b.47.1.1 96574 1q32A 544 3.22e+01 d.136.1.3,d.136.1.3 104507,104508 1vjnA 220 3.23e+01 d.157.1.4 100825 1t0pB 86 3.24e+01 1oh0A 131 3.27e+01 d.17.4.3 87004 1v04A 355 3.28e+01 b.68.6.2 100240 1wexA 104 3.31e+01 2bz6H 254 3.31e+01 2fhzB 108 3.31e+01 1jg1A 235 3.32e+01 c.66.1.7 66661 1r9fA 136 3.34e+01 d.255.1.1 97257 1qx4A 274 3.37e+01 b.43.4.2,c.25.1.1 104624,104625 1wucA 250 3.39e+01 7odcA 424 3.39e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1i8dA 213 3.45e+01 b.43.4.3,b.43.4.3 61953,61954 1bkb 136 3.52e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1y1oA 203 3.52e+01 1tbuA 118 3.53e+01 1xwvA 129 3.53e+01 2carA 196 3.54e+01 1ifrA 121 3.60e+01 b.1.16.1 71203 1gvhA 396 3.60e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1sr4B 261 3.62e+01 d.151.1.1 105949 1ckaA 57 3.66e+01 1ckaA b.34.2.1 24459 1ts9A 102 3.74e+01 1cs6A 382 3.75e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1dkuA 317 3.79e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1vzyA 291 3.79e+01 1r6vA 671 3.82e+01 1yhfA 115 3.85e+01 1zh5A 195 3.85e+01 2b4wA 315 3.87e+01 1bqsA 209 3.98e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1iz6A 138 3.98e+01 b.34.5.2,b.40.4.5 76976,76977 1upqA 123 4.04e+01 2fcbA 173 4.06e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1pg6A 243 4.06e+01 b.82.5.2 94673 1r6wA 322 4.08e+01 c.1.11.2,d.54.1.1 97165,97166 2sli 679 4.16e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1arb 268 4.16e+01 1arb b.47.1.1 25766 1v7lA 163 4.16e+01 1dgwX 79 4.22e+01 1caxB b.82.1.2 28091 1yhpA 212 4.24e+01 1j34B 123 4.25e+01 d.169.1.1 84049 1nycA 111 4.27e+01 b.61.2.2 92336 2biwA 490 4.27e+01 1wc3A 219 4.27e+01 1jfmA 174 4.28e+01 d.19.1.1 66640 1p2zA 968 4.34e+01 b.121.2.2,b.121.2.2 93962,93963 1tw7A 99 4.35e+01 2f9nA 245 4.35e+01 1l7yA 94 4.38e+01 d.15.1.6 73676 1yv4A 104 4.40e+01 1mrg 263 4.42e+01 1mrj d.165.1.1 42183 1h8dH 260 4.42e+01 5ptp 1gsmA 210 4.43e+01 b.1.1.4,b.1.1.4 65535,65536 1v10A 521 4.46e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 2b3nA 159 4.48e+01 1g8mA 593 4.51e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1u9aA 160 4.54e+01 1u9aA d.20.1.1 38333 2cyjA 118 4.55e+01 1dzkA 157 4.55e+01 1obpA b.60.1.1 27096 1u7zA 226 4.61e+01 2apr 325 4.66e+01 2er7E b.50.1.2 26819 2fvgA 340 4.67e+01 1p4uA 153 4.67e+01 b.1.10.2 87780 1fnlA 175 4.68e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1e8yA 966 4.69e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1ukgA 252 4.71e+01 b.29.1.1 99489 2frgP 106 4.71e+01 2fblA 153 4.77e+01 1a7j 290 4.78e+01 1a7j c.37.1.6 31952 2crvA 120 4.82e+01 1vioA 243 4.85e+01 d.265.1.3,d.66.1.5 100762,100763 2f4lA 297 4.87e+01 1fjjA 159 4.95e+01 1fjjA b.17.1.2 59852 1btkA 169 4.98e+01 1btkA b.55.1.1 26959 2fs2A 151 5.03e+01 2ci9A 102 5.03e+01 1elvA 333 5.04e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1cdcA 99 5.07e+01 1cdcA b.1.1.1 19746 1zxq 192 5.10e+01 1zxq b.1.1.3,b.1.1.4 21657,21693 1q7fA 286 5.13e+01 b.68.9.1 96036 1uufA 369 5.14e+01 b.35.1.2,c.2.1.1 100006,100007 1e5dA 402 5.14e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1rg8A 146 5.22e+01 1un3A 123 5.23e+01 d.5.1.1 99646 1owxA 121 5.28e+01 d.58.7.1 87494 1o6aA 96 5.32e+01 b.139.1.1 92562 1p3cA 215 5.40e+01 b.47.1.1 93996 2aioA 269 5.41e+01 1ka9H 200 5.41e+01 c.23.16.1 77308 1n7oA 721 5.42e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1gpc 218 5.44e+01 1gpc b.40.4.7 25393 1w2iA 91 5.45e+01 d.58.10.1 109127 1iq6A 134 5.47e+01 d.38.1.4 76755 1qzgA 187 5.48e+01 b.40.4.3 96643 1mrj 247 5.52e+01 1mrj d.165.1.1 42177 1nkgA 508 5.53e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1gl4B 98 5.53e+01 b.1.1.4 65288 2bjdA 101 5.54e+01 1qlpA 394 5.54e+01 1ovaA e.1.1.1 42628 1mla 309 5.58e+01 1mla c.19.1.1,d.58.23.1 31031,39383 2grrA 161 5.63e+01 1ztcA 221 5.69e+01 1jyoA 130 5.84e+01 d.198.1.1 67483 1uirA 314 5.85e+01 c.66.1.17 99429 1xe1A 116 5.89e+01 b.43.3.1 109571 1ootA 60 5.93e+01 b.34.2.1 93386 1pwaA 162 5.93e+01 b.42.1.1 95211 1svy 114 5.95e+01 1svy d.109.1.1 40831 1puiA 210 5.95e+01 c.37.1.8 88292 2bb6A 414 6.08e+01 1jmtA 104 6.13e+01 d.58.7.3 63180 2cr4A 126 6.18e+01 1o9yA 84 6.20e+01 b.139.1.1 92692 1hpgA 187 6.30e+01 1qq4A b.47.1.1 25813 2a1kA 233 6.45e+01 1zkkA 167 6.46e+01 1dc1A 323 6.51e+01 1dc1A c.52.1.11 33321 1ryoA 327 6.52e+01 c.94.1.2 98108 1fviA 297 6.57e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1ulrA 88 6.61e+01 1ep3B 262 6.62e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 2cohA 202 6.64e+01 1tvxA 75 6.64e+01 1tvxA d.9.1.1 37441 1mhnA 59 6.65e+01 b.34.9.1 84964 1vr8A 142 6.69e+01 1ko3A 230 6.71e+01 d.157.1.1 90974 2bsfA 176 6.72e+01 1jmuB 666 6.75e+01 1w0pA 781 6.84e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1m7sA 484 6.89e+01 e.5.1.1 74574 1ifqA 138 6.90e+01 1ifqA d.110.4.1 62350 1r6jA 82 7.05e+01 b.36.1.1 97151 1v9tA 166 7.07e+01 b.62.1.1 108451 2c7hA 86 7.09e+01 1rhfA 182 7.13e+01 b.1.1.1,b.1.1.4 97469,97470 1jsdA 319 7.14e+01 b.19.1.2 63258 2bf6A 449 7.22e+01 1wj9A 211 7.28e+01 1uacH 114 7.28e+01 b.1.1.1 99132 1mveA 243 7.39e+01 b.29.1.2 85140 1ycsB 239 7.41e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1lfwA 470 7.45e+01 c.56.5.4,d.58.19.1 77942,77943 2fpqA 444 7.46e+01 1zkiA 133 7.50e+01 1u4bA 580 7.55e+01 c.55.3.5,e.8.1.1 107664,107665 1qavA 90 7.56e+01 1qauA b.36.1.1 24777 1gx1A 160 7.64e+01 d.79.5.1 70675 1whvA 100 7.64e+01 1sqwA 188 7.71e+01 1jnyA 435 7.75e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1cs0A 1073 7.79e+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 18558,31487,31673,31674,41518,41519 1bkzA 135 7.80e+01 1a3k b.29.1.3 24202 1e8cA 498 7.96e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1tjxA 159 7.96e+01 2f1lA 187 8.00e+01 1wyxA 69 8.01e+01 2f7tA 227 8.07e+01 1ey4A 149 8.07e+01 1snc b.40.1.1 24815 2g50A 530 8.08e+01 1u20A 212 8.12e+01 1kkeA 210 8.15e+01 b.21.1.2,b.83.1.2 68669,68670 1f3lA 321 8.19e+01 1g6q2 c.66.1.6 59630 1m2tA 254 8.20e+01 d.165.1.1 84761 1kmtA 141 8.21e+01 b.1.18.8 77442 1o9gA 250 8.21e+01 c.66.1.29 86692 1zc6A 305 8.25e+01 1zupA 315 8.29e+01 1tg7A 971 8.35e+01 1xzpB 150 8.35e+01 1noa 113 8.35e+01 2mcm b.1.7.1 22208 1j0sA 157 8.46e+01 b.42.1.2 90747 2f9dA 125 8.47e+01 1t6cA 315 8.47e+01 c.55.1.8,c.55.1.8 106558,106559 1of5A 221 8.47e+01 d.17.4.2 86933 2fdiA 211 8.48e+01 1vjqA 79 8.49e+01 k.43.1.1 100830 1r2jA 366 8.49e+01 a.29.3.1,e.6.1.1 96869,96870 1yz1A 174 8.50e+01 1k2xA 177 8.58e+01 d.153.1.5 90929 1h8uA 117 8.60e+01 1h8uA d.169.1.1 60793 1a7s 221 8.62e+01 1a7s b.47.1.2 26284 1zn8A 180 8.63e+01 1dmhA 311 8.64e+01 1dmhA b.3.6.1 22633 1ytaA 180 8.73e+01 1f00I 282 8.74e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2byoA 207 8.74e+01 1qreA 247 8.83e+01 1qreA b.81.1.5 28066 1ji6A 589 8.86e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1wrvA 308 8.89e+01 1i4uA 181 8.89e+01 b.60.1.1 61732 2fcfA 103 8.93e+01 1vb0A 61 8.95e+01