# List of top-scoring protein chains for t04-100-30-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 1na3A 91 1.31e-03 k.38.1.1 85481 2fbnA 198 1.54e-03 1elwA 118 2.63e-03 1a17 a.118.8.1 19207 2avpA 70 2.85e-03 1a17 166 7.39e-03 1a17 a.118.8.1 19206 1hz4A 373 3.69e-02 a.118.8.2 65960 1ihgA 370 5.34e-02 2cpl a.118.8.1,b.62.1.1 62380,62381 2ff4A 388 2.20e-01 1oshA 232 2.55e-01 a.123.1.1 93496 1wfdA 93 3.58e-01 1txgA 335 3.68e-01 1tujA 123 5.44e-01 1qqeA 292 7.45e-01 1qqeA a.118.8.1 19210 1x0lA 333 1.05e+00 1w36B 1180 1.06e+00 1mswD 883 1.20e+00 e.8.1.3 79427 1dc1A 323 1.50e+00 1dc1A c.52.1.11 33321 1i1iP 681 1.70e+00 1i1iP d.92.1.5 40297 1za0A 275 1.88e+00 1f6fA 199 2.02e+00 1f6fA a.26.1.1 16839 1t01A 255 2.08e+00 a.24.9.1,a.24.9.1 106188,106189 1zvzA 279 2.19e+00 1vlgA 176 2.20e+00 a.25.1.1 108816 2dg5A 366 2.26e+00 2gaiA 633 2.45e+00 1r9dA 787 2.75e+00 c.7.1.1 104865 1xnfA 275 2.99e+00 1elrA 131 3.15e+00 1a17 a.118.8.1 19209 1x46A 150 3.50e+00 1rkeA 262 3.54e+00 a.24.9.1,a.24.9.1 97608,97609 2gtrA 261 3.64e+00 1wm5A 208 3.87e+00 1jb0A 755 4.38e+00 1jb0A f.29.1.1 62820 1hh8A 213 4.41e+00 1e96B a.118.8.1 61042 1ovlA 271 4.62e+00 a.123.1.1 87455 1w79A 489 4.85e+00 1ydiA 263 4.90e+00 1paqA 189 5.27e+00 a.118.1.14 94413 1qtrA 317 5.28e+00 1qtrA c.69.1.7 34660 1n46A 258 5.37e+00 a.123.1.1 85315 1l3pA 102 5.44e+00 a.24.17.1 84520 2f3yA 148 5.50e+00 1lk9A 448 5.65e+00 c.67.1.1 78057 1upvA 257 5.75e+00 1wm1A 317 6.31e+00 c.69.1.7 109405 1lfpA 249 7.12e+00 e.39.1.1 73885 2a2mA 258 8.02e+00 1yarA 233 8.04e+00 2bl0C 142 8.23e+00 1ek9A 428 8.25e+00 1ek9A f.5.1.1 43809 1w53A 84 8.69e+00 a.186.1.2 109175 1nrgA 261 9.01e+00 b.45.1.1 80694 1fnnA 389 9.07e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 2a2oA 258 9.18e+00 2cqsA 842 9.22e+00 1wp1A 474 9.41e+00 1vkuA 100 9.46e+00 a.28.1.1 108690 1sk7A 198 9.80e+00 a.132.1.2 105671 3lynA 136 9.83e+00 1lis a.19.1.1 16413 2d2yA 145 9.86e+00 1khoA 370 9.99e+00 a.124.1.1,b.12.1.3 72489,72490 1ggzA 148 1.00e+01 a.39.1.5 70176 1v54E 109 1.02e+01 a.118.11.1 100326 1xkpC 143 1.04e+01 1p4kA 295 1.10e+01 d.153.1.5 87772 9gafA 295 1.10e+01 1apyA d.153.1.5 42008 2cx9A 387 1.11e+01 2ethA 154 1.18e+01 1lvaA 258 1.22e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1m7vA 363 1.26e+01 d.174.1.1 78748 1u14A 172 1.29e+01 c.51.4.3 107579 2crbA 97 1.31e+01 1lw1A 177 1.32e+01 a.152.1.1 74290 2awiA 317 1.35e+01 1laxA 370 1.35e+01 c.94.1.1 84576 1dqeA 137 1.37e+01 1dqeA a.39.2.1 17388 1z82A 335 1.43e+01 1ho8A 480 1.45e+01 1ho8A a.118.1.9 61107 1dz4A 414 1.50e+01 1phd a.104.1.1 18903 1dvkA 173 1.51e+01 1dvkA a.72.1.1 18319 1omp 370 1.55e+01 4mbp c.94.1.1 35778 1lis 136 1.55e+01 1lis a.19.1.1 16406 2lisA 136 1.55e+01 1lis a.19.1.1 16405 4mbp 370 1.57e+01 4mbp c.94.1.1 35777 1gu9A 177 1.58e+01 a.152.1.1 65540 2c6cA 707 1.58e+01 1tw9A 206 1.59e+01 a.45.1.1,c.47.1.5 107381,107382 1bx4A 345 1.62e+01 1bx4A c.72.1.1 34935 2etbA 256 1.62e+01 1at3A 247 1.64e+01 1at3A b.57.1.1 27021 1exrA 148 1.66e+01 1cll a.39.1.5 17299 1w5tA 412 1.67e+01 1anf 370 1.68e+01 4mbp c.94.1.1 35776 1pq9A 253 1.73e+01 a.123.1.1 95004 1aisB 200 1.75e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1guxA 218 1.76e+01 1guxA a.74.1.3 18388 1w0dA 337 1.78e+01 1i5nA 146 1.81e+01 1i5nA a.24.10.3 61805 1lxa 262 1.83e+01 1lxa b.81.1.1 28052 4crxA 322 1.87e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1tuaA 191 1.88e+01 d.51.1.1,d.51.1.1 107321,107322 2c4bA 143 1.94e+01 1sqnA 261 1.95e+01 a.123.1.1 105944 1mlwA 301 2.02e+01 d.178.1.1 79289 1a2pA 110 2.05e+01 1b20A d.1.1.2 36140 1f7uA 607 2.06e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1ow4A 129 2.09e+01 a.39.2.1 93628 1ic2A 81 2.11e+01 h.1.5.1 62247 3gcb 470 2.12e+01 3gcb d.3.1.1 37032 1wy6A 172 2.13e+01 1mtyG 162 2.14e+01 1mtyG a.23.3.1 16498 1rx0A 393 2.16e+01 a.29.3.1,e.6.1.1 98007,98008 1g4yR 148 2.16e+01 1cll a.39.1.5 60252 1gcb 454 2.19e+01 3gcb d.3.1.1 37034 1uhgA 385 2.23e+01 e.1.1.1 88491 1xo0A 324 2.27e+01 2az0A 73 2.30e+01 1nznA 126 2.30e+01 a.118.8.1 92382 1tn4 159 2.36e+01 1ncx a.39.1.5 17248 1xdzA 240 2.38e+01 1f08A 148 2.41e+01 1f08A d.89.1.2 59564 2occE 109 2.41e+01 2occE a.118.11.1 19224 1bolA 222 2.46e+01 1bolA d.124.1.1 41120 1ws9A 387 2.51e+01 1su8A 636 2.51e+01 e.26.1.2 98999 2c2aA 258 2.51e+01 1f44A 324 2.51e+01 a.60.9.1,d.163.1.1 64982,64983 1jjyA 636 2.51e+01 1jjyA 1jk0A 419 2.53e+01 a.25.1.2 63142 1gvjA 146 2.59e+01 a.4.5.21 90525 1zejA 293 2.66e+01 1f0yA 302 2.67e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1yruB 74 2.67e+01 1avoB 140 2.70e+01 1avoB 1wdcC 156 2.72e+01 1wdcC a.39.1.5 17317 2aq9A 262 2.75e+01 1or4A 178 2.75e+01 a.1.1.2 93447 1wz9A 375 2.75e+01 1nktA 922 2.79e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1th8A 145 2.80e+01 d.122.1.3 106908 1ve0A 134 2.84e+01 1cby 259 2.84e+01 1cby d.103.1.1 40705 2bvpA 276 2.86e+01 1x24A 180 2.86e+01 1pu6A 218 2.86e+01 a.96.1.5 95123 2az2A 73 2.90e+01 1re9A 414 2.90e+01 2a61A 145 2.97e+01 1z2cB 383 3.03e+01 1mvwA 840 3.04e+01 i.15.1.1 79523 1csn 298 3.07e+01 1csn d.144.1.7 41664 2fldA 165 3.07e+01 1ckiA 317 3.08e+01 1csn d.144.1.7 41660 1ytw 306 3.16e+01 1ytw c.45.1.2 32689 1nt2A 210 3.18e+01 c.66.1.3 86149 1sl8A 191 3.21e+01 1ift 263 3.30e+01 1mrj d.165.1.1 42211 1lyvA 306 3.32e+01 c.45.1.2 74348 1gtkA 313 3.34e+01 c.94.1.1,d.50.2.1 76346,76347 2d29A 387 3.36e+01 1vjoA 393 3.49e+01 c.67.1.3 100827 1vf1A 229 3.58e+01 1epxA 370 3.59e+01 1fbaA c.1.10.1 29150 2g3bA 208 3.63e+01 1i50B 1224 3.69e+01 e.29.1.1 61755 1ovaA 386 3.69e+01 1ovaA e.1.1.1 42619 1qlpA 394 3.70e+01 1ovaA e.1.1.1 42628 1zclA 180 3.71e+01 1twfB 1224 3.73e+01 1knyA 253 3.85e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1dceB 331 3.87e+01 1dceB a.102.4.3 18872 1b06A 210 3.87e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1t07A 94 3.89e+01 d.279.1.1 106196 1u2eA 289 3.90e+01 1uhkA 191 3.91e+01 1a6q 382 3.95e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1zybA 232 3.97e+01 1yrcA 414 4.09e+01 1zx4A 192 4.15e+01 1izcA 339 4.16e+01 c.1.12.5 83838 2bnxA 386 4.21e+01 1qmqA 414 4.27e+01 1phd a.104.1.1 18907 1uesA 191 4.28e+01 a.2.11.1,d.44.1.1 107798,107799 1orjA 130 4.30e+01 a.24.19.1 93456 1xteA 154 4.31e+01 1is2A 661 4.32e+01 a.29.3.2,a.29.3.2,e.6.1.2 71382,71383,71384 1evsA 187 4.32e+01 1evsA a.26.1.1 16845 1yixA 265 4.39e+01 2g7gA 213 4.44e+01 1mla 309 4.44e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1yc9A 442 4.46e+01 1wlmA 151 4.49e+01 1j1qA 261 4.61e+01 d.165.1.1 90768 1qbjA 81 4.63e+01 1qbjA a.4.5.19 16155 1ka2A 499 4.63e+01 d.92.1.5 77305 1rzsA 61 4.67e+01 a.35.1.2 105139 1qnnA 191 4.68e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1bc5A 269 4.69e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1pb6A 212 4.77e+01 a.4.1.9,a.121.1.1 88017,88018 1qb2A 109 4.78e+01 1qb2A a.36.1.1 17125 2b6cA 220 4.82e+01 1de4C 640 4.86e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1sesA 421 4.90e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 1zaiA 363 4.91e+01 1fcyA 236 5.00e+01 2lbd a.123.1.1 19282 1joyA 67 5.01e+01 1joyA a.30.2.1 16991 1ytvA 366 5.02e+01 1ux5A 411 5.03e+01 a.207.1.1 100144 1af7 274 5.03e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1my6A 199 5.04e+01 a.2.11.1,d.44.1.1 85232,85233 2fk8A 318 5.05e+01 1zsqA 528 5.06e+01 1wab 232 5.06e+01 1wab c.23.10.3 31341 1zy4A 303 5.07e+01 1e79A 510 5.11e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1p68A 102 5.16e+01 k.8.1.1 94158 1fjgT 106 5.18e+01 1fjfT a.7.6.1 16338 2abqA 306 5.21e+01 1wvvA 265 5.25e+01 1es9A 232 5.27e+01 1wab c.23.10.3 31340 1x91A 153 5.43e+01 1qo0D 196 5.46e+01 1qo0D c.23.1.3 31125 1tazA 365 5.47e+01 a.211.1.2 106734 1pa2A 306 5.52e+01 1bgp a.93.1.1 18693 2fa8A 105 5.52e+01 1k87A 669 5.54e+01 a.176.1.1,c.1.23.2 77286,77287 1xtpA 254 5.60e+01 1jqnA 883 5.60e+01 c.1.12.3 77159 1w5qA 337 5.68e+01 1b4kA 337 5.77e+01 1b4kA c.1.10.3 29184 1jb9A 316 5.82e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1kpgA 287 5.83e+01 c.66.1.18 68735 1dar 691 5.88e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 2d2sA 235 5.94e+01 1pmi 440 6.02e+01 1pmi b.82.1.3 28114 1avsA 90 6.02e+01 1cll a.39.1.5 17226 1gzgA 337 6.08e+01 c.1.10.3 70805 2b7oA 464 6.17e+01 2mhr 118 6.19e+01 2mhr a.24.4.1 16581 1sig 339 6.27e+01 1sig a.177.1.1 19068 1wy9A 147 6.27e+01 1dvoA 152 6.29e+01 1dvoA a.136.1.1 19623 1aky 221 6.29e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1xrtA 467 6.33e+01 1a28A 256 6.33e+01 1a28A a.123.1.1 19290 2abk 211 6.34e+01 2abk a.96.1.1 18743 1viuA 203 6.34e+01 d.113.1.1 100771 1p36A 164 6.37e+01 d.2.1.3 93978 1e3aB 560 6.38e+01 1ajqB 1ornA 226 6.41e+01 a.96.1.1 87342 1lk5A 229 6.42e+01 c.124.1.4,d.58.40.1 73960,73961 1fm9D 272 6.48e+01 2prgA a.123.1.1 19313 2d3dA 88 6.53e+01 2sqcA 631 6.54e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1zgyA 272 6.56e+01 1gk9B 557 6.56e+01 1h8eA 510 6.57e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1lw3A 657 6.57e+01 b.55.1.8,c.45.1.3 91152,91153 1k3yA 221 6.59e+01 a.45.1.1,c.47.1.5 77245,77246 119l 164 6.59e+01 1l92 d.2.1.3 36622 1afrA 345 6.60e+01 1afrA a.25.1.2 16805 1eemA 241 6.60e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 2afdA 88 6.64e+01 1j8yF 297 6.64e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1j8mF 297 6.64e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1iqrA 420 6.70e+01 a.99.1.1,c.28.1.1 66275,66276 1e4iA 447 6.71e+01 1e70M c.1.8.4 59225 1ppjF 110 6.72e+01 f.27.1.1 104262 1zrzA 364 6.74e+01 1t1dA 100 6.76e+01 1t1dA d.42.1.2 38637 1syyA 346 6.78e+01 a.25.1.2 106126 1io2A 213 6.83e+01 1ekeA c.55.3.1 62612 2f8kA 88 6.84e+01 1xg7A 250 6.86e+01 256bA 106 6.87e+01 256bA a.24.3.1 16539 1vkeA 133 6.88e+01 a.152.1.2 108650 2cxbA 124 6.93e+01 1ycc a.3.1.1 15891 1t5oA 351 7.06e+01 c.124.1.5 106459 1oq9A 363 7.06e+01 a.25.1.2 87257 1zckA 154 7.09e+01 1ug7A 128 7.09e+01 a.24.24.1 107824 1mxrA 375 7.10e+01 a.25.1.2 85197 1rxdA 159 7.10e+01 1clc 639 7.10e+01 1clc a.102.1.2,b.1.18.2 18835,21872 2cohA 202 7.16e+01 1nc5A 373 7.16e+01 a.102.1.6 85548 1iruK 201 7.16e+01 d.153.1.4 71362 1qgdA 662 7.18e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 2jdxA 385 7.22e+01 1jdw d.126.1.2 41139 1wdyA 285 7.22e+01 1knvA 293 7.23e+01 c.52.1.7 68707 1ca1 370 7.25e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1n1jA 93 7.28e+01 a.22.1.3 79813 2absA 383 7.29e+01 1xtnA 120 7.32e+01 1r9kA 172 7.39e+01 a.168.1.1 104869 1ga3A 113 7.43e+01 1ga3A a.26.1.2 60411 2a0iA 330 7.46e+01 1cxc 124 7.58e+01 1ycc a.3.1.1 15890 2f57A 317 7.62e+01 2acjA 66 7.62e+01 1lehA 364 7.63e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1o7kA 131 7.67e+01 d.189.1.1 81144 2ck3A 510 7.72e+01 2au3A 407 7.72e+01 1w5nA 337 7.72e+01 1om2A 95 7.75e+01 1om2A a.23.4.1 16520 2g0dA 409 7.79e+01 1cpt 412 7.85e+01 1cpt a.104.1.1 18968 1wmzA 140 7.87e+01 d.169.1.1 109422 1ojaA 520 7.93e+01 c.3.1.2,d.16.1.5 93096,93097 1y2kA 349 7.94e+01 1s3eA 520 7.98e+01 c.3.1.2,d.16.1.5 98426,98427 2ak3A 226 8.07e+01 1zin c.37.1.1,g.41.2.1 31892,45193 2b18A 164 8.08e+01 1uf2A 1019 8.09e+01 e.28.1.2 99289 1kxpD 458 8.13e+01 a.126.1.1,a.126.1.1,a.126.1.1 73160,73161,73162 1w7jB 151 8.13e+01 1umwA 237 8.13e+01 d.223.1.2,d.223.1.2 99631,99632 1wmwA 330 8.17e+01 1ra6A 461 8.22e+01 e.8.1.4 104879 1ntyA 311 8.24e+01 a.87.1.1,b.55.1.1 103873,103874 2sas 185 8.24e+01 2sas a.39.1.5 17258 1xg2B 153 8.28e+01 1xeaA 323 8.31e+01 c.2.1.3,d.81.1.5 109572,109573 1k2xB 143 8.32e+01 1tg6A 277 8.34e+01 1jdw 423 8.37e+01 1jdw d.126.1.2 41129 1y8oA 419 8.61e+01 1wvfA 520 8.61e+01 1wqwA 235 8.73e+01 1nonA 179 8.74e+01 c.61.1.1 103868 1uq5A 263 8.79e+01 d.165.1.1 99778 1f74A 293 8.81e+01 1nal3 c.1.10.1 29079 1gqaA 130 8.83e+01 a.24.3.2 76275 1wz8A 264 8.90e+01 1a68 95 8.90e+01 1t1dA d.42.1.2 38639 1bmtA 246 8.91e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1un8A 552 8.97e+01 c.119.1.2,a.208.1.1 103806,99661