# List of top-scoring protein chains for t04-100-30-alpha-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 1na3A 91 8.98e-04 k.38.1.1 85481 2fbnA 198 1.12e-03 2avpA 70 1.60e-03 1elwA 118 1.83e-03 1a17 a.118.8.1 19207 1a17 166 1.62e-02 1a17 a.118.8.1 19206 1hz4A 373 1.97e-02 a.118.8.2 65960 1ihgA 370 7.27e-02 2cpl a.118.8.1,b.62.1.1 62380,62381 2ff4A 388 8.95e-02 1wfdA 93 1.89e-01 1qqeA 292 6.13e-01 1qqeA a.118.8.1 19210 1x0lA 333 6.39e-01 1vlgA 176 1.09e+00 a.25.1.1 108816 1za0A 275 1.29e+00 1elrA 131 1.52e+00 1a17 a.118.8.1 19209 1x46A 150 1.58e+00 1xnfA 275 1.91e+00 1oshA 232 2.25e+00 a.123.1.1 93496 1fjgT 106 2.47e+00 1fjfT a.7.6.1 16338 1dc1A 323 2.71e+00 1dc1A c.52.1.11 33321 1uzbA 516 2.91e+00 c.82.1.1 100220 2bjkA 516 2.91e+00 2dg5A 366 3.31e+00 2g7gA 213 3.37e+00 1txgA 335 3.45e+00 3lynA 136 3.48e+00 1lis a.19.1.1 16413 2azjA 289 3.51e+00 1vf1A 229 3.56e+00 1mswD 883 4.27e+00 e.8.1.3 79427 2d2yA 145 4.51e+00 1orjA 130 4.62e+00 a.24.19.1 93456 1zvzA 279 4.64e+00 1ek9A 428 5.00e+00 1ek9A f.5.1.1 43809 1sl8A 191 5.49e+00 1rkeA 262 5.96e+00 a.24.9.1,a.24.9.1 97608,97609 1gpjA 404 5.98e+00 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1w36B 1180 5.98e+00 1lis 136 6.12e+00 1lis a.19.1.1 16406 1khoA 370 6.22e+00 a.124.1.1,b.12.1.3 72489,72490 1t01A 255 6.23e+00 a.24.9.1,a.24.9.1 106188,106189 1paqA 189 6.35e+00 a.118.1.14 94413 2gtrA 261 6.41e+00 1ppjF 110 6.67e+00 f.27.1.1 104262 1knqA 175 6.85e+00 c.37.1.17 72786 1re9A 414 7.23e+00 2lisA 136 7.26e+00 1lis a.19.1.1 16405 1w79A 489 7.41e+00 1i1iP 681 7.57e+00 1i1iP d.92.1.5 40297 1zejA 293 7.73e+00 1qmqA 414 7.81e+00 1phd a.104.1.1 18907 1lfpA 249 7.96e+00 e.39.1.1 73885 2gboA 104 8.08e+00 1r0dA 206 8.40e+00 a.216.1.1 104715 1de4C 640 8.58e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1n46A 258 8.61e+00 a.123.1.1 85315 1riqA 465 8.81e+00 a.203.1.1,d.104.1.1 97516,97517 1mlwA 301 9.15e+00 d.178.1.1 79289 1yfsA 465 9.74e+00 1pq9A 253 9.96e+00 a.123.1.1 95004 2bl2A 156 1.03e+01 1ic2A 81 1.09e+01 h.1.5.1 62247 2c2aA 258 1.09e+01 1uhkA 191 1.10e+01 1wp1A 474 1.10e+01 1hh8A 213 1.12e+01 1e96B a.118.8.1 61042 1sig 339 1.19e+01 1sig a.177.1.1 19068 1pb6A 212 1.21e+01 a.4.1.9,a.121.1.1 88017,88018 1ug7A 128 1.27e+01 a.24.24.1 107824 1wm5A 208 1.30e+01 1f6fA 199 1.34e+01 1f6fA a.26.1.1 16839 1bx4A 345 1.37e+01 1bx4A c.72.1.1 34935 1ydiA 263 1.38e+01 1j8uA 325 1.39e+01 d.178.1.1 71611 2bnxA 386 1.39e+01 1xo0A 324 1.40e+01 3gcb 470 1.44e+01 3gcb d.3.1.1 37032 1pyoB 105 1.53e+01 4pah 308 1.56e+01 4pah d.178.1.1 42576 2ghjA 118 1.58e+01 2d29A 387 1.58e+01 1upvA 257 1.62e+01 1dz4A 414 1.63e+01 1phd a.104.1.1 18903 1ng6A 148 1.63e+01 a.182.1.1 85670 1lk9A 448 1.67e+01 c.67.1.1 78057 1ve5A 311 1.70e+01 1ka2A 499 1.70e+01 d.92.1.5 77305 1k3yA 221 1.75e+01 a.45.1.1,c.47.1.5 77245,77246 1r2fA 319 1.77e+01 1r2fA a.25.1.2 16800 2crbA 97 1.78e+01 1yrcA 414 1.81e+01 1gcb 454 1.85e+01 3gcb d.3.1.1 37034 2g7sA 194 1.89e+01 4crxA 322 1.92e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1l3pA 102 1.92e+01 a.24.17.1 84520 1x3kA 152 1.95e+01 1ggzA 148 1.98e+01 a.39.1.5 70176 2f3yA 148 2.00e+01 1ux5A 411 2.03e+01 a.207.1.1 100144 1t8sA 484 2.05e+01 c.56.2.1 106679 1izcA 339 2.06e+01 c.1.12.5 83838 1ws9A 387 2.08e+01 1w5tA 412 2.10e+01 1jjyA 636 2.10e+01 1jjyA 1m7vA 363 2.10e+01 d.174.1.1 78748 2awiA 317 2.12e+01 2gaiA 633 2.15e+01 1knyA 253 2.16e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1t2bA 397 2.18e+01 1in6A 334 2.19e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1uliA 460 2.21e+01 b.33.1.2,d.129.3.3 107921,107922 1in4A 334 2.22e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1ovlA 271 2.27e+01 a.123.1.1 87455 1z2cB 383 2.28e+01 1avsA 90 2.31e+01 1cll a.39.1.5 17226 2f57A 317 2.34e+01 1af7 274 2.34e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1f44A 324 2.36e+01 a.60.9.1,d.163.1.1 64982,64983 1zrn 232 2.38e+01 1qq5A c.108.1.1 43323 1w0dA 337 2.41e+01 1abrA 251 2.41e+01 1mrj d.165.1.1 42196 1i5nA 146 2.44e+01 1i5nA a.24.10.3 61805 1orsC 132 2.57e+01 f.14.1.1 87353 1su8A 636 2.59e+01 e.26.1.2 98999 1rss 151 2.65e+01 1rss a.75.1.1 18392 1wm1A 317 2.67e+01 c.69.1.7 109405 1pl5A 142 2.69e+01 h.1.23.1 104186 1csn 298 2.81e+01 1csn d.144.1.7 41664 1twfB 1224 2.84e+01 1qtrA 317 2.93e+01 1qtrA c.69.1.7 34660 1ca1 370 3.03e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 2bikB 313 3.06e+01 1bc5A 269 3.13e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1x91A 153 3.19e+01 1n83A 270 3.27e+01 a.123.1.1 80276 1evsA 187 3.29e+01 1evsA a.26.1.1 16845 2fztA 79 3.35e+01 1io2A 213 3.37e+01 1ekeA c.55.3.1 62612 1xwsA 313 3.44e+01 1zrzA 364 3.45e+01 1fnnA 389 3.46e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1at3A 247 3.48e+01 1at3A b.57.1.1 27021 2sqcA 631 3.50e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1exrA 148 3.53e+01 1cll a.39.1.5 17299 1rrmA 386 3.55e+01 e.22.1.2 105081 1di1A 300 3.57e+01 1di1A a.128.1.4 19446 1wy6A 172 3.62e+01 1kxpD 458 3.65e+01 a.126.1.1,a.126.1.1,a.126.1.1 73160,73161,73162 1ouvA 273 3.65e+01 a.118.18.1 93570 1ic8A 194 3.68e+01 a.4.1.1,a.35.1.1 76740,76741 2bl0C 142 3.72e+01 1a6i 217 3.79e+01 2tct a.4.1.9,a.121.1.1 16066,19243 2h1nA 567 3.80e+01 2c5kT 95 3.81e+01 1go3F 107 3.81e+01 a.60.8.2 65407 1urvA 190 3.85e+01 1ut0A 190 3.85e+01 a.1.1.2 108012 1p3jA 217 3.90e+01 c.37.1.1,g.41.2.1 94022,94023 1ustA 93 3.90e+01 a.4.5.13 99884 1wdgA 94 3.93e+01 h.3.3.1 109248 2az0A 73 3.94e+01 2cx9A 387 4.00e+01 1od8A 313 4.07e+01 c.1.8.3 86838 1ra6A 461 4.11e+01 e.8.1.4 104879 1kcfA 258 4.16e+01 a.140.2.1,c.55.3.7 68434,68435 2abk 211 4.18e+01 2abk a.96.1.1 18743 1xdzA 240 4.27e+01 2btdA 210 4.27e+01 1qnf 484 4.29e+01 1qnf a.99.1.1,c.28.1.1 18777,31632 1dvkA 173 4.41e+01 1dvkA a.72.1.1 18319 1tw9A 206 4.46e+01 a.45.1.1,c.47.1.5 107381,107382 2aq9A 262 4.50e+01 1m7xA 617 4.68e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1owlA 484 4.69e+01 a.99.1.1,c.28.1.1 93647,93648 1sesA 421 4.71e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1jb0A 755 4.72e+01 1jb0A f.29.1.1 62820 1e0wA 313 4.74e+01 1taxA c.1.8.3 59150 1tujA 123 4.78e+01 2bo4A 397 4.78e+01 2g42A 79 4.83e+01 2d2mA 140 4.87e+01 1mvwA 840 4.89e+01 i.15.1.1 79523 1qb2A 109 4.91e+01 1qb2A a.36.1.1 17125 1u2eA 289 4.91e+01 1v0lA 313 4.96e+01 c.1.8.3 108207 1g4yR 148 4.97e+01 1cll a.39.1.5 60252 1nc5A 373 4.99e+01 a.102.1.6 85548 1m0kA 262 5.02e+01 f.13.1.1 78344 1zy4A 303 5.02e+01 1nu5A 370 5.03e+01 c.1.11.2,d.54.1.1 92183,92184 1p4kA 295 5.05e+01 d.153.1.5 87772 1wxcA 281 5.09e+01 1joyA 67 5.17e+01 1joyA a.30.2.1 16991 1z6oM 191 5.21e+01 1t1dA 100 5.22e+01 1t1dA d.42.1.2 38637 1xg7A 250 5.30e+01 1rx0A 393 5.30e+01 a.29.3.1,e.6.1.1 98007,98008 1dar 691 5.32e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1v1rA 400 5.35e+01 c.36.1.11 108272 1yc9A 442 5.38e+01 2ak3A 226 5.40e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1hhsA 664 5.41e+01 1hi0P e.8.1.6 61045 1bdmA 327 5.41e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 9gafA 295 5.43e+01 1apyA d.153.1.5 42008 1uvjA 664 5.46e+01 e.8.1.6 100045 1umwA 237 5.48e+01 d.223.1.2,d.223.1.2 99631,99632 1nyhA 166 5.51e+01 h.1.23.1 86403 1uddA 226 5.53e+01 a.132.1.3 107776 2az2A 73 5.58e+01 1ykhA 108 5.63e+01 1nrgA 261 5.64e+01 b.45.1.1 80694 1vz6A 393 5.65e+01 d.154.1.2 108949 1zd8A 227 5.66e+01 1w5nA 337 5.72e+01 1y7tA 327 5.85e+01 1n5uA 585 5.99e+01 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1bmdA 327 6.00e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1rxdA 159 6.07e+01 1i50B 1224 6.10e+01 e.29.1.1 61755 1kn1B 161 6.13e+01 a.1.1.3 77456 1jalA 363 6.17e+01 c.37.1.8,d.15.10.2 84138,84139 2abqA 306 6.28e+01 2cchB 260 6.32e+01 2tct 207 6.34e+01 2tct a.4.1.9,a.121.1.1 16063,19240 2bg1A 494 6.35e+01 1g9gA 629 6.40e+01 a.102.1.2 83279 2f4lA 297 6.42e+01 1kb9I 55 6.44e+01 f.23.14.1 77324 1jb9A 316 6.47e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 2a65A 519 6.52e+01 1iq8A 582 6.54e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1lq7A 67 6.56e+01 k.9.1.1 74183 1u9lA 70 6.56e+01 a.60.4.2 107751 1xtpA 254 6.57e+01 1yarA 233 6.59e+01 1hqsA 423 6.67e+01 1iso c.77.1.1 61154 1xm9A 457 6.75e+01 1u14A 172 6.78e+01 c.51.4.3 107579 1lxa 262 6.78e+01 1lxa b.81.1.1 28052 1c4oA 664 6.83e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1e8yA 966 6.83e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1ojaA 520 6.87e+01 c.3.1.2,d.16.1.5 93096,93097 1qgdA 662 6.90e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1ornA 226 6.90e+01 a.96.1.1 87342 1wg8A 285 6.95e+01 1omp 370 6.96e+01 4mbp c.94.1.1 35778 1dbhA 354 6.97e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1b06A 210 7.09e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1t7lA 766 7.19e+01 2f71A 298 7.25e+01 1pmi 440 7.26e+01 1pmi b.82.1.3 28114 2c30A 321 7.27e+01 2d2sA 235 7.31e+01 1nznA 126 7.34e+01 a.118.8.1 92382 1mtyG 162 7.34e+01 1mtyG a.23.3.1 16498 1d2mA 665 7.36e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1jxhA 288 7.38e+01 c.72.1.2 67415 1s3eA 520 7.44e+01 c.3.1.2,d.16.1.5 98426,98427 1gu9A 177 7.47e+01 a.152.1.1 65540 1p68A 102 7.53e+01 k.8.1.1 94158 1aky 221 7.67e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1ofuA 320 7.69e+01 c.32.1.1,d.79.2.1 86972,86973 1i36A 264 7.72e+01 a.100.1.8,c.2.1.6 71108,71109 1ezvI 55 7.73e+01 1be3J f.23.14.1 59553 1xeaA 323 7.77e+01 c.2.1.3,d.81.1.5 109572,109573 1zckA 154 7.78e+01 2erbA 125 7.78e+01 1el4A 195 7.79e+01 1ej3A a.39.1.5 59453 1lw1A 177 7.88e+01 a.152.1.1 74290 2cw9A 194 7.88e+01 2ct8A 497 7.96e+01 1ylmA 144 8.00e+01 1unlD 208 8.01e+01 1bco 327 8.05e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1puzA 82 8.07e+01 a.218.1.1 104320 1g6uA 48 8.08e+01 1g6uA k.9.1.1 46425 2g38B 198 8.11e+01 1qnnA 191 8.13e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1cby 259 8.14e+01 1cby d.103.1.1 40705 1dfoA 417 8.18e+01 1bj4A c.67.1.4 34480 1bt3A 345 8.25e+01 1bt3A a.86.1.2 18507 1ufaA 520 8.29e+01 a.8.3.3,c.6.2.4 99329,99330 1ne9A 335 8.31e+01 d.108.1.4,d.108.1.4 91839,91840 1alu 186 8.33e+01 1alu a.26.1.1 16826 1nktA 922 8.35e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1a3c 181 8.37e+01 1a3c c.61.1.1 34095 1o20A 427 8.44e+01 c.82.1.1 86556 1ow4A 129 8.46e+01 a.39.2.1 93628 1avoB 140 8.49e+01 1avoB 1ayaA 101 8.50e+01 1qadA d.93.1.1 40460 1yixA 265 8.57e+01 1lucB 324 8.69e+01 1lucA c.1.16.1 29548 2bg5A 324 8.76e+01 1u2zA 433 8.76e+01 c.66.1.31 107626 2g0dA 409 8.78e+01 1yiiA 320 8.81e+01 1v54E 109 8.95e+01 a.118.11.1 100326 1wchA 315 8.96e+01 2gmyA 153 8.96e+01 2sas 185 8.97e+01 2sas a.39.1.5 17258