# 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 1bjwA 382 1.76e-02 1bjwA c.67.1.1 34349 1b5pA 385 2.83e-02 c.67.1.1 90403 1z6oM 191 5.19e-02 1v2dA 381 1.62e-01 c.67.1.1 108281 2fha 183 1.76e-01 2fha a.25.1.1 16674 1fha 183 2.77e-01 2fha a.25.1.1 16675 1o4sA 389 1.03e+00 c.67.1.1 86620 1h0cA 392 1.21e+00 c.67.1.3 83424 1bg7 176 1.24e+00 2fha a.25.1.1 16686 1bgeA 175 1.27e+00 1bgc a.26.1.1 16823 7aatA 401 1.46e+00 1ajsA c.67.1.1 34250 1h96A 182 1.50e+00 2fha a.25.1.1 60811 3xis 387 1.56e+00 4xis c.1.15.3 29423 1c1bB 440 1.64e+00 1rthA e.8.1.2 43077 1lb3A 182 1.65e+00 a.25.1.1 77873 1e4mM 501 1.92e+00 1e70M c.1.8.4 59226 1gw9A 388 1.93e+00 c.1.15.3 70658 1rthA 560 2.13e+00 1rthA c.55.3.1,e.8.1.2 33576,43028 1x9mA 698 2.14e+00 1xis 387 2.16e+00 4xis c.1.15.3 29422 4xis 387 2.30e+00 4xis c.1.15.3 29421 1t7pA 698 2.49e+00 1t7pA c.55.3.5,e.8.1.1 33712,43005 1ru0A 105 2.52e+00 1dcpA 104 2.59e+00 1dcpA d.74.1.1 39672 1e6qM 501 2.60e+00 1e70M c.1.8.4 28920 2xis 387 2.62e+00 4xis c.1.15.3 29427 2aexA 346 2.87e+00 1dcoA 104 2.96e+00 1dcpA d.74.1.1 39680 1mnzA 388 2.97e+00 c.1.15.3 79328 1rcd 173 3.01e+00 2fha a.25.1.1 16687 1akaA 401 3.28e+00 1ajsA c.67.1.1 34258 1eetA 557 3.32e+00 1rthA c.55.3.1,e.8.1.2 33608,43078 1aew 174 3.40e+00 2fha a.25.1.1 16676 1q8iA 783 3.62e+00 c.55.3.5,e.8.1.1 96208,96209 2amg 415 3.75e+00 1jdc b.71.1.1,c.1.8.1 27796,28783 1bgeB 175 3.78e+00 1bgc a.26.1.1 16824 1j31A 262 3.82e+00 d.160.1.2 90808 1jdc 429 3.90e+00 1jdc b.71.1.1,c.1.8.1 27789,28776 1fk9A 543 3.94e+00 1rthA c.55.3.1,e.8.1.2 33607,43080 1vjxA 157 4.05e+00 a.25.1.1 100837 1e70M 501 4.07e+00 1e70M c.1.8.4 28926 1f93A 104 4.23e+00 1dcpA d.74.1.1 39688 1bgc 174 4.35e+00 1bgc a.26.1.1 16822 2myr 501 4.38e+00 1s2wA 295 4.39e+00 c.1.12.7 98407 1b0aA 288 4.55e+00 1a4iA c.2.1.7,c.58.1.2 30286,33934 1dttA 560 4.66e+00 1rthA c.55.3.1,e.8.1.2 33611,43088 1uu1A 335 4.69e+00 c.67.1.1 99993 1jigA 146 4.74e+00 a.25.1.1 71685 1muwA 386 4.87e+00 c.1.15.3 79495 1zhvA 134 4.89e+00 1hniA 558 5.15e+00 1rthA c.55.3.1,e.8.1.2 33586,43044 2hmiA 558 5.17e+00 1rthA c.55.3.1,e.8.1.2 33604,43106 1vrtA 560 5.48e+00 1rthA c.55.3.1,e.8.1.2 33574,43023 1dloB 427 5.59e+00 1rthA e.8.1.2 43041 1zemA 262 5.74e+00 1hv8A 367 5.95e+00 1hv8A c.37.1.19,c.37.1.19 32405,32406 1qsdA 106 5.98e+00 1qsdA a.7.5.1 16335 1bs0A 384 6.01e+00 1bs0A c.67.1.4 34490 1dat 174 6.05e+00 2fha a.25.1.1 16677 1tjoA 182 6.09e+00 1mwqA 101 6.56e+00 d.58.4.7 91481 1p57B 255 6.81e+00 b.47.1.2 94126 1mojA 182 6.91e+00 a.25.1.1 91367 2cvzA 289 7.18e+00 1toaA 313 7.18e+00 1toaA c.92.2.2 35598 1fkoA 543 7.58e+00 1rthA c.55.3.1,e.8.1.2 33612,43094 1r03A 182 7.75e+00 a.25.1.1 104675 1vjoA 393 7.97e+00 c.67.1.3 100827 1dloA 556 8.35e+00 1rthA c.55.3.1,e.8.1.2 33584,43040 1tr1A 447 8.54e+00 1e70M c.1.8.4 28957 1jgcA 161 8.58e+00 a.25.1.1 66673 2occE 109 9.00e+00 2occE a.118.11.1 19224 2aucA 126 9.02e+00 1ug6A 431 9.03e+00 c.1.8.4 88490 1e4iA 447 9.30e+00 1e70M c.1.8.4 59225 1gnxA 479 9.43e+00 c.1.8.4 76241 1wwjA 105 9.93e+00 2bopA 85 1.01e+01 2bopA d.58.8.1 39217 1us6A 102 1.02e+01 a.2.13.1 107999 1rfyA 102 1.02e+01 1bqnA 558 1.06e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1v54E 109 1.09e+01 a.118.11.1 100326 1dchA 104 1.17e+01 1dcpA d.74.1.1 39692 2cvhA 220 1.18e+01 1kx9A 112 1.20e+01 a.118.21.1 77602 1zzgA 415 1.26e+01 1w7lA 422 1.27e+01 c.67.1.1 109226 1hmvA 560 1.35e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 2azjA 289 1.40e+01 1k0fA 277 1.41e+01 c.92.2.2 71974 2ceyA 306 1.45e+01 4lbd 267 1.46e+01 2lbd a.123.1.1 19289 2fh5A 185 1.47e+01 1bax 94 1.51e+01 1bax a.61.1.3 18133 2dchX 216 1.55e+01 1lxnA 99 1.56e+01 d.58.48.1 84737 2as9A 210 1.58e+01 2dc4A 165 1.61e+01 1cbg 490 1.62e+01 1e70M c.1.8.4 28933 1iw8A 231 1.65e+01 a.111.1.1 76866 1fmk 452 1.67e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 2lbd 267 1.67e+01 2lbd a.123.1.1 19287 1k7jA 206 1.68e+01 d.115.1.1 72103 1nxcA 478 1.69e+01 a.102.2.1 92293 1knvA 293 1.75e+01 c.52.1.7 68707 1jpmA 366 1.75e+01 c.1.11.2,d.54.1.1 67031,67032 1ypfA 336 1.78e+01 2cwkA 160 1.80e+01 1ypxA 375 1.85e+01 1vhcA 224 1.89e+01 c.1.10.1 100661 1jx4A 352 1.98e+01 d.240.1.1,e.8.1.7 90378,90379 1z41A 338 1.99e+01 1om0A 274 1.99e+01 c.1.8.5 87058 1u08A 386 2.06e+01 c.67.1.1 107543 2fkzA 155 2.09e+01 1xjjA 644 2.11e+01 1pymA 295 2.13e+01 1pymA c.1.12.7 29308 1a6dA 545 2.14e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1tzvA 142 2.15e+01 a.79.1.1 107526 1l1sA 113 2.20e+01 c.114.1.1 73484 1pszA 303 2.22e+01 1toaA c.92.2.2 35600 1ciy 590 2.23e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1kkhA 317 2.25e+01 d.14.1.5,d.58.26.3 72645,72646 1xjeA 644 2.30e+01 1eetB 427 2.32e+01 1rthA e.8.1.2 43079 1yiyA 429 2.32e+01 1wy7A 207 2.32e+01 1yqhA 109 2.33e+01 1fc4A 401 2.34e+01 1bs0A c.67.1.4 59760 1w3jA 468 2.35e+01 c.1.8.4 109156 1kk9A 221 2.35e+01 d.115.1.1 77432 1gcyA 527 2.41e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 1qqyA 130 2.41e+01 3lzt d.2.1.2 36586 1tkkA 366 2.53e+01 c.1.11.2,d.54.1.1 107089,107090 1uuzA 137 2.55e+01 d.233.1.1 100024 1xm9A 457 2.58e+01 1cnt3 187 2.64e+01 1cnt3 2bvcA 486 2.69e+01 1gd9A 389 2.75e+01 c.67.1.1 60454 1zesA 125 2.78e+01 1wvqA 167 2.78e+01 1hrhA 136 2.82e+01 1rthA c.55.3.1 33577 1rzl 91 2.89e+01 1rzl a.52.1.1 17817 1bcfA 158 2.90e+01 1bcfA a.25.1.1 16648 1f7uA 607 2.92e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 2gsfA 373 2.93e+01 1jjhA 86 2.95e+01 2bopA d.58.8.1 63119 1y2qA 143 2.97e+01 2feaA 236 2.98e+01 1wyuA 438 2.99e+01 1rxwA 336 3.07e+01 a.60.7.1,c.120.1.2 98059,98060 1yizA 429 3.07e+01 1ho8A 480 3.10e+01 1ho8A a.118.1.9 61107 1ta3A 274 3.12e+01 c.1.8.5 106731 1d2tA 231 3.13e+01 1d2tA a.111.1.1 19052 2fb1A 226 3.13e+01 1sumB 235 3.14e+01 a.7.12.1 106025 1ex2A 189 3.14e+01 1ex2A c.51.4.2 33225 1qjbA 245 3.18e+01 1qjaA a.118.7.1 19202 2cviA 83 3.21e+01 1qwlA 505 3.25e+01 e.5.1.1 96483 2awiA 317 3.31e+01 1y9uA 323 3.34e+01 1y60A 169 3.34e+01 1gkzA 388 3.35e+01 a.29.5.1,d.122.1.4 65268,65269 1g0oA 283 3.36e+01 1ybvA c.2.1.2 60181 1wwiA 148 3.38e+01 1csmA 256 3.41e+01 5csmA a.130.1.2 19495 1uz1A 468 3.43e+01 1kllA 130 3.46e+01 d.32.1.2 72720 1zq4A 693 3.50e+01 1z23A 163 3.51e+01 2cbuA 468 3.57e+01 1uok 558 3.58e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1urvA 190 3.68e+01 1ut0A 190 3.68e+01 a.1.1.2 108012 1lwdA 413 3.72e+01 c.77.1.1 78265 1rz2A 254 3.72e+01 b.100.1.1 105130 1b00A 127 3.75e+01 3chy c.23.1.1 31122 1umnA 165 3.76e+01 a.25.1.1 99607 2bl9A 238 3.93e+01 1sqgA 429 3.97e+01 a.79.1.3,c.66.1.38 105912,105913 2bfwA 200 4.02e+01 1o9rA 162 4.04e+01 a.25.1.1 86706 1e43A 483 4.06e+01 1bli b.71.1.1,c.1.8.1 59217,59218 1p4oA 322 4.07e+01 d.144.1.7 87775 1fkoB 440 4.09e+01 1rthA e.8.1.2 43095 1wbeA 209 4.13e+01 1o0wA 252 4.17e+01 a.149.1.1,d.50.1.1 80751,80752 1gdeA 389 4.18e+01 c.67.1.1 60456 1ybvA 283 4.26e+01 1ybvA c.2.1.2 29948 1quuA 250 4.34e+01 1quuA a.7.1.1,a.7.1.1 16320,16321 1d8iA 311 4.36e+01 1d8iA d.63.1.1 39541 1mgtA 174 4.40e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1bia 321 4.41e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1tk1A 260 4.43e+01 d.248.1.1 107066 1nkpA 88 4.44e+01 a.38.1.1 80573 1bhjA 292 4.49e+01 1xvaA c.66.1.5 34189 1f6yA 262 4.49e+01 1f6yA c.1.21.2 29673 1hruA 188 4.52e+01 1hruA d.115.1.1 40926 1l5jA 865 4.56e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1r5pA 108 4.65e+01 c.47.1.15 97101 1lxjA 104 4.73e+01 d.58.48.1 84736 1hx0A 496 4.73e+01 b.71.1.1,c.1.8.1 61346,61347 1i56A 130 4.74e+01 d.2.1.2 66033 1d8hA 311 4.75e+01 1d8iA d.63.1.1 39544 1fa0B 537 4.77e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 2fbkA 181 4.86e+01 1a76 326 4.95e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1bib 321 4.98e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 2fr1A 486 5.02e+01 1fa0A 537 5.05e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1evyA 366 5.17e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 2ak3A 226 5.18e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1smd 496 5.19e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1jlnA 297 5.20e+01 1pty c.45.1.2 63172 2gyqA 175 5.21e+01 1u02A 239 5.25e+01 c.108.1.15 107538 1qoxN 449 5.35e+01 1qoxN c.1.8.4 28978 1dppA 507 5.41e+01 1dpe c.94.1.1 35800 1tqjA 230 5.44e+01 c.1.2.2 107228 1r4vA 171 5.50e+01 a.197.1.1 97049 1xkqA 280 5.50e+01 1xgsA 295 5.58e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1hniB 427 5.59e+01 1rthA e.8.1.2 43045 1rpxA 230 5.60e+01 1rpxA c.1.2.2 28536 1kqqA 139 5.67e+01 a.4.3.1 72885 1pi1A 185 5.68e+01 a.29.7.1 94699 1nrgA 261 5.73e+01 b.45.1.1 80694 1dmwA 307 5.76e+01 4pah d.178.1.1 42580 1egzA 291 5.78e+01 7a3hA c.1.8.3 28828 1mlwA 301 5.79e+01 d.178.1.1 79289 1hmvB 440 5.80e+01 1rthA e.8.1.2 43047 1mtpA 323 5.87e+01 e.1.1.1 85107 1qjaA 245 5.87e+01 1qjaA a.118.7.1 19204 1pah 308 5.92e+01 4pah d.178.1.1 42578 1qrjB 199 5.93e+01 1qrjB a.28.3.1 16952 2a7oA 112 5.94e+01 1qysA 106 5.98e+01 k.41.1.1 96603 1jpaA 312 6.05e+01 d.144.1.7 67011 1jfxA 217 6.06e+01 c.1.8.8 62943 2iugA 120 6.12e+01 4xiaA 393 6.12e+01 4xis c.1.15.3 29439 1kpsB 171 6.13e+01 a.118.12.1 68787 1bli 483 6.19e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1heiA 451 6.20e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 2c3nA 247 6.20e+01 2b7uA 257 6.25e+01 1sur 215 6.26e+01 1sur c.26.2.2 31620 2blcA 238 6.27e+01 1aorA 605 6.32e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1i7qA 519 6.34e+01 1qdlA d.161.1.1 61901 2ccyA 128 6.34e+01 2ccyA a.24.3.2 16544 2rslA 140 6.37e+01 2rslA c.53.1.1 33345 2bwnA 401 6.39e+01 1dbhA 354 6.42e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1tfjA 219 6.43e+01 1ir21 140 6.44e+01 2fztA 79 6.47e+01 1wr2A 238 6.49e+01 1jqhA 308 6.51e+01 d.144.1.7 71793 1s4nA 348 6.54e+01 c.68.1.16 98501 1fk5A 93 6.54e+01 1rzl a.52.1.1 59866 2f1kA 279 6.58e+01 2f62A 161 6.64e+01 1r13A 148 6.74e+01 d.169.1.1,h.1.1.1 96782,96783 1a27 289 6.74e+01 1fds c.2.1.2 29839 1gkxA 388 6.76e+01 a.29.5.1,d.122.1.4 65266,65267 1r5rA 119 6.79e+01 a.39.2.1 97104 1xqaA 113 6.79e+01 1mzm 93 6.84e+01 1rzl a.52.1.1 17814 1afh 93 6.86e+01 1rzl a.52.1.1 17816 1v02A 565 6.93e+01 c.1.8.4 108194 1wfdA 93 6.97e+01 1htqA 477 6.99e+01 d.15.9.1,d.128.1.1 71035,71036 1n6zA 105 6.99e+01 d.263.1.1 85369 1prtA 234 7.05e+01 1bcpA d.166.1.1 42253 2hnp 321 7.06e+01 1pty c.45.1.2 32678 1knqA 175 7.07e+01 c.37.1.17 72786 1gmlA 178 7.14e+01 c.8.5.2 70273 1dpe 507 7.25e+01 1dpe c.94.1.1 35799 2ezh 75 7.25e+01 2ezh a.4.1.2 16029 1pdz 434 7.26e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1v25A 541 7.29e+01 e.23.1.1 108275 1xg5A 279 7.31e+01 2bd0A 244 7.36e+01 1d2gA 292 7.39e+01 1xvaA c.66.1.5 34187 1gk8I 140 7.41e+01 d.73.1.1 65242 1ru3A 732 7.57e+01 e.26.1.3 97835 1h5vA 304 7.57e+01 c.1.8.3 70898 1cd9C 175 7.62e+01 1bgc a.26.1.1 16816 1f37A 110 7.62e+01 1f37A c.47.1.11 33088 1k04A 162 7.62e+01 a.24.14.1 67904 1a5y 330 7.66e+01 1pty c.45.1.2 32673 1iicA 422 7.70e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1ndbA 596 7.87e+01 c.43.1.3,c.43.1.3 80411,80412 1w19A 160 7.90e+01 1y2mA 716 7.91e+01 1g4uS 383 7.92e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1ktbA 405 7.92e+01 b.71.1.1,c.1.8.1 72960,72961 1k0dA 260 7.94e+01 a.45.1.1,c.47.1.5 67930,67931 1jt6A 188 7.97e+01 a.4.1.9,a.121.1.1 67247,67248 2fymA 431 7.98e+01 1n69A 81 7.99e+01 a.64.1.3 80118 1n8vA 112 8.02e+01 a.118.21.1 85457 1j8uA 325 8.09e+01 d.178.1.1 71611 1de5A 426 8.15e+01 1de5A c.1.15.2 29402 1fdt 327 8.15e+01 1fds c.2.1.2 29841 4pah 308 8.16e+01 4pah d.178.1.1 42576 2grrB 170 8.16e+01 1unnC 115 8.16e+01 d.240.1.1 99680 1huw 166 8.17e+01 1huw a.26.1.1 16831 2a0b 125 8.27e+01 2a0b a.24.10.1 16630 1q0sA 259 8.40e+01 c.66.1.28 95509 1d2mA 665 8.41e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 2b05A 246 8.47e+01 1zkjA 359 8.48e+01 1rktA 205 8.48e+01 a.4.1.9,a.121.1.1 97623,97624 1swxA 209 8.48e+01 a.224.1.1 106075 1q3kA 259 8.56e+01 c.125.1.1 95693 1et0A 269 8.56e+01 1et0A e.17.1.1 43289 1h1yA 228 8.61e+01 c.1.2.2 76506 1htoA 477 8.66e+01 d.15.9.1,d.128.1.1 70987,70988 2f6lA 166 8.73e+01 2f2tA 161 8.74e+01 2hmqA 113 8.82e+01 2mhr a.24.4.1 16568 1ql3A 99 8.84e+01 1ycc a.3.1.1 15822 1jzxK 205 8.92e+01 i.1.1.2 67885