# List of top-scoring protein chains for t04-100-30-bys-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 2.47e-03 k.38.1.1 85481 2fbnA 198 2.59e-03 2avpA 70 4.02e-03 1elwA 118 5.96e-03 1a17 a.118.8.1 19207 1a17 166 1.40e-02 1a17 a.118.8.1 19206 1ihgA 370 4.38e-02 2cpl a.118.8.1,b.62.1.1 62380,62381 1hz4A 373 1.07e-01 a.118.8.2 65960 1oshA 232 3.27e-01 a.123.1.1 93496 1wfdA 93 3.39e-01 1qqeA 292 4.87e-01 1qqeA a.118.8.1 19210 2ff4A 388 6.38e-01 1xnfA 275 1.24e+00 1x0lA 333 1.28e+00 1elrA 131 1.37e+00 1a17 a.118.8.1 19209 2f3yA 148 1.73e+00 1sl8A 191 2.16e+00 1uhkA 191 2.67e+00 1ovlA 271 3.09e+00 a.123.1.1 87455 1txgA 335 3.49e+00 1pq9A 253 3.58e+00 a.123.1.1 95004 1nktA 922 4.10e+00 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1yrcA 414 4.11e+00 1el4A 195 4.22e+00 1ej3A a.39.1.5 59453 1dz4A 414 4.24e+00 1phd a.104.1.1 18903 1re9A 414 4.32e+00 1ggzA 148 4.32e+00 a.39.1.5 70176 1x46A 150 4.32e+00 1paqA 189 4.51e+00 a.118.1.14 94413 1tujA 123 4.72e+00 1mlwA 301 4.74e+00 d.178.1.1 79289 1qmqA 414 4.80e+00 1phd a.104.1.1 18907 1hh8A 213 4.89e+00 1e96B a.118.8.1 61042 1jf2A 195 5.04e+00 1ej3A a.39.1.5 62930 1ydiA 263 5.43e+00 1wm5A 208 5.45e+00 1ux5A 411 6.36e+00 a.207.1.1 100144 1ek9A 428 6.37e+00 1ek9A f.5.1.1 43809 3lynA 136 6.74e+00 1lis a.19.1.1 16413 1n46A 258 7.03e+00 a.123.1.1 85315 1qv1A 195 7.23e+00 a.39.1.5 96347 1w36B 1180 7.25e+00 1w79A 489 7.36e+00 1vlgA 176 7.46e+00 a.25.1.1 108816 1fjgT 106 7.64e+00 1fjfT a.7.6.1 16338 1upvA 257 7.76e+00 1khoA 370 7.84e+00 a.124.1.1,b.12.1.3 72489,72490 1rkeA 262 8.09e+00 a.24.9.1,a.24.9.1 97608,97609 1avsA 90 8.60e+00 1cll a.39.1.5 17226 1vf1A 229 8.77e+00 1i1iP 681 8.81e+00 1i1iP d.92.1.5 40297 1uzbA 516 8.89e+00 c.82.1.1 100220 2bjkA 516 8.91e+00 2a2oA 258 9.22e+00 1g4yR 148 9.24e+00 1cll a.39.1.5 60252 2g7gA 213 9.74e+00 1riqA 465 1.01e+01 a.203.1.1,d.104.1.1 97516,97517 1exrA 148 1.02e+01 1cll a.39.1.5 17299 1lfpA 249 1.05e+01 e.39.1.1 73885 1t2bA 397 1.06e+01 2a2mA 258 1.08e+01 2crbA 97 1.22e+01 1lis 136 1.35e+01 1lis a.19.1.1 16406 2lisA 136 1.35e+01 1lis a.19.1.1 16405 1t01A 255 1.35e+01 a.24.9.1,a.24.9.1 106188,106189 1pb6A 212 1.36e+01 a.4.1.9,a.121.1.1 88017,88018 1zvzA 279 1.37e+01 1uliA 460 1.42e+01 b.33.1.2,d.129.3.3 107921,107922 1i36A 264 1.43e+01 a.100.1.8,c.2.1.6 71108,71109 1ouvA 273 1.44e+01 a.118.18.1 93570 1mswD 883 1.49e+01 e.8.1.3 79427 1yfsA 465 1.50e+01 2awiA 317 1.51e+01 1r0dA 206 1.61e+01 a.216.1.1 104715 1knqA 175 1.68e+01 c.37.1.17 72786 1m7vA 363 1.78e+01 d.174.1.1 78748 1qtrA 317 1.83e+01 1qtrA c.69.1.7 34660 1urvA 190 1.84e+01 1ut0A 190 1.84e+01 a.1.1.2 108012 2az0A 73 1.84e+01 2bikB 313 1.91e+01 1orjA 130 1.93e+01 a.24.19.1 93456 1xwsA 313 1.96e+01 1xg7A 250 1.98e+01 2dg5A 366 1.98e+01 1lk9A 448 1.99e+01 c.67.1.1 78057 1p68A 102 1.99e+01 k.8.1.1 94158 4crxA 322 2.07e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1dc1A 323 2.14e+01 1dc1A c.52.1.11 33321 2bl0C 142 2.18e+01 1i5nA 146 2.23e+01 1i5nA a.24.10.3 61805 1r2fA 319 2.25e+01 1r2fA a.25.1.2 16800 1sig 339 2.30e+01 1sig a.177.1.1 19068 1ve0A 134 2.31e+01 2ghjA 118 2.33e+01 1f44A 324 2.33e+01 a.60.9.1,d.163.1.1 64982,64983 2gtrA 261 2.38e+01 1ca1 370 2.40e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1wm1A 317 2.43e+01 c.69.1.7 109405 1wp1A 474 2.44e+01 1zejA 293 2.46e+01 1ic2A 81 2.54e+01 h.1.5.1 62247 1xdzA 240 2.60e+01 1pyoB 105 2.63e+01 2btdA 210 2.64e+01 2bl2A 156 2.64e+01 2c2aA 258 2.67e+01 1at3A 247 2.71e+01 1at3A b.57.1.1 27021 1u14A 172 2.75e+01 c.51.4.3 107579 2d29A 387 2.76e+01 1xo0A 324 2.78e+01 1pl5A 142 2.81e+01 h.1.23.1 104186 2gmyA 153 2.88e+01 1axdA 209 2.93e+01 1gnwA a.45.1.1,c.47.1.5 17730,33024 1sazA 381 3.01e+01 1wy6A 172 3.06e+01 1ve5A 311 3.10e+01 1n83A 270 3.11e+01 a.123.1.1 80276 1j8uA 325 3.13e+01 d.178.1.1 71611 1go3F 107 3.21e+01 a.60.8.2 65407 1ws9A 387 3.29e+01 1csn 298 3.31e+01 1csn d.144.1.7 41664 1xo5A 183 3.34e+01 1ezvI 55 3.40e+01 1be3J f.23.14.1 59553 1evsA 187 3.45e+01 1evsA a.26.1.1 16845 1kb9I 55 3.47e+01 f.23.14.1 77324 1af7 274 3.48e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1d8dA 377 3.50e+01 1ft1A a.118.6.1 19185 1bx4A 345 3.53e+01 1bx4A c.72.1.1 34935 1nigA 152 3.58e+01 a.25.2.1 85740 1w0dA 337 3.58e+01 1ppjF 110 3.65e+01 f.27.1.1 104262 1k3xA 262 3.68e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1ustA 93 3.75e+01 a.4.5.13 99884 2cw9A 194 3.78e+01 2aaoA 166 3.79e+01 2gboA 104 3.86e+01 1l5wA 796 3.88e+01 c.87.1.4 73605 1kkhA 317 3.91e+01 d.14.1.5,d.58.26.3 72645,72646 2d2yA 145 3.96e+01 1bc5A 269 4.01e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1x3kA 152 4.06e+01 1rss 151 4.07e+01 1rss a.75.1.1 18392 1i4jA 110 4.09e+01 d.55.1.1 76734 2cvzA 289 4.10e+01 1np3A 338 4.13e+01 a.100.1.2,c.2.1.6 85946,85947 1za0A 275 4.13e+01 1ka2A 499 4.17e+01 d.92.1.5 77305 1w5tA 412 4.18e+01 1tn4 159 4.19e+01 1ncx a.39.1.5 17248 1d2mA 665 4.22e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1y1xA 191 4.29e+01 2az2A 73 4.40e+01 2cx9A 387 4.51e+01 2cqsA 842 4.54e+01 1qnf 484 4.55e+01 1qnf a.99.1.1,c.28.1.1 18777,31632 1izcA 339 4.58e+01 c.1.12.5 83838 1xteA 154 4.65e+01 4pah 308 4.72e+01 4pah d.178.1.1 42576 1avoB 140 4.79e+01 1avoB 2bk9A 153 4.80e+01 2g0dA 409 4.85e+01 1orsC 132 4.86e+01 f.14.1.1 87353 2abk 211 4.88e+01 2abk a.96.1.1 18743 2bvlA 543 4.91e+01 1yurA 98 4.95e+01 1e4iA 447 5.05e+01 1e70M c.1.8.4 59225 1jb0A 755 5.14e+01 1jb0A f.29.1.1 62820 1q5nA 454 5.15e+01 a.127.1.1 95901 1n5uA 585 5.15e+01 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1qgwB 67 5.22e+01 1qgwA d.184.1.1 42617 1ib2A 349 5.29e+01 1ib2A a.118.1.8 62141 1f0yA 302 5.35e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1gu9A 177 5.38e+01 a.152.1.1 65540 1m9xC 146 5.39e+01 a.73.1.1 84907 1t1dA 100 5.40e+01 1t1dA d.42.1.2 38637 1e7uA 961 5.40e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1lq7A 67 5.41e+01 k.9.1.1 74183 1in6A 334 5.41e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 2sas 185 5.42e+01 2sas a.39.1.5 17258 1in4A 334 5.46e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1vimA 200 5.56e+01 c.80.1.3 100758 2btzA 394 5.57e+01 1zrn 232 5.57e+01 1qq5A c.108.1.1 43323 1ow4A 129 5.57e+01 a.39.2.1 93628 1wz9A 375 5.58e+01 1zwwA 256 5.67e+01 1mvwB 145 5.68e+01 i.15.1.1 79524 1nznA 126 5.75e+01 a.118.8.1 92382 1poiA 317 5.85e+01 1poiA c.124.1.2 34153 1fnnA 389 5.91e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1rdr 461 5.94e+01 1rdr e.8.1.4 43116 3sdhA 146 5.94e+01 3sdhA a.1.1.2 14984 2sqcA 631 5.96e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 2mgg 154 5.98e+01 1a6m a.1.1.2 15069 1joyA 67 5.99e+01 1joyA a.30.2.1 16991 1rx0A 393 6.03e+01 a.29.3.1,e.6.1.1 98007,98008 2afaA 425 6.05e+01 1g6uA 48 6.11e+01 1g6uA k.9.1.1 46425 1lf6A 684 6.18e+01 a.102.1.5,b.30.5.5 77918,77919 1w99A 558 6.25e+01 1g8iA 190 6.25e+01 1rec a.39.1.5 60363 1x91A 153 6.26e+01 1y0vH 146 6.28e+01 1musA 477 6.31e+01 c.55.3.4 79494 1k9uA 78 6.38e+01 a.39.1.10 84348 1xeaA 323 6.43e+01 c.2.1.3,d.81.1.5 109572,109573 1xiuA 230 6.48e+01 2d8dA 90 6.50e+01 1v0lA 313 6.51e+01 c.1.8.3 108207 1c4oA 664 6.60e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1l3pA 102 6.61e+01 a.24.17.1 84520 2bo4A 397 6.61e+01 1a6m 151 6.62e+01 1a6m a.1.1.2 15018 1e0wA 313 6.65e+01 1taxA c.1.8.3 59150 2dc3A 193 6.65e+01 2spl 154 6.67e+01 1a6m a.1.1.2 15047 1od8A 313 6.67e+01 c.1.8.3 86838 1y82A 157 6.67e+01 1io7A 368 6.72e+01 1f4tA a.104.1.1 18971 1w53A 84 6.79e+01 a.186.1.2 109175 1wxcA 281 6.82e+01 1g8eA 116 6.85e+01 1g8eA a.145.1.1 60346 1oxjA 173 6.92e+01 a.60.1.2,a.118.1.13 87517,87518 1xfxO 149 6.94e+01 1nyhA 166 7.00e+01 h.1.23.1 86403 1r9kA 172 7.02e+01 a.168.1.1 104869 1ykhA 108 7.04e+01 1qtnB 95 7.07e+01 1pauB 1y97A 238 7.08e+01 2h1rA 299 7.10e+01 1xmeA 568 7.11e+01 1zx1A 231 7.13e+01 1ehyA 294 7.17e+01 1ehyA c.69.1.11 34693 1bzpA 153 7.19e+01 1a6m a.1.1.2 15020 2ahrA 259 7.26e+01 1rhcA 330 7.28e+01 c.1.16.3 97468 1cipA 353 7.33e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1zx4A 192 7.34e+01 1yc9A 442 7.34e+01 1aky 221 7.37e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1jalA 363 7.39e+01 c.37.1.8,d.15.10.2 84138,84139 2g19A 244 7.40e+01 1n08A 163 7.40e+01 b.43.5.1 79730 1wt4A 73 7.45e+01 1f6fA 199 7.52e+01 1f6fA a.26.1.1 16839 1ofuA 320 7.52e+01 c.32.1.1,d.79.2.1 86972,86973 1dj8A 89 7.53e+01 1bg8A a.57.1.1 17919 2f57A 317 7.56e+01 2d2sA 235 7.57e+01 1nc5A 373 7.58e+01 a.102.1.6 85548 1owlA 484 7.62e+01 a.99.1.1,c.28.1.1 93647,93648 2hbtA 247 7.65e+01 2aq9A 262 7.68e+01 1w7jB 151 7.69e+01 2cxbA 124 7.72e+01 1ycc a.3.1.1 15891 1k3yA 221 7.73e+01 a.45.1.1,c.47.1.5 77245,77246 1or4A 178 7.76e+01 a.1.1.2 93447 1om2A 95 7.77e+01 1om2A a.23.4.1 16520 1di1A 300 7.88e+01 1di1A a.128.1.4 19446 2g7sA 194 7.91e+01 1xtnA 120 7.94e+01 2azjA 289 7.94e+01 1xtpA 254 7.96e+01 1ng6A 148 8.03e+01 a.182.1.1 85670 1ireB 228 8.09e+01 b.34.4.4 76770 1lw1A 177 8.14e+01 a.152.1.1 74290 2aclB 244 8.14e+01 1a6i 217 8.19e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1t8sA 484 8.21e+01 c.56.2.1 106679 1ornA 226 8.25e+01 a.96.1.1 87342 1usgA 346 8.27e+01 c.93.1.1 99864 2erbA 125 8.30e+01 1ltlA 279 8.34e+01 b.40.4.11 84701 2bxkA 585 8.34e+01 1qusA 322 8.37e+01 1ltm d.2.1.6 36991 1ugpB 226 8.44e+01 b.34.4.4 107832 1uhnA 189 8.53e+01 a.39.1.5 99399 1pgtA 210 8.55e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1mod 154 8.63e+01 1a6m a.1.1.2 15107 1s1eA 224 8.71e+01 1tbmA 326 8.79e+01 a.211.1.2 106744 1hw1A 239 8.80e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1p3jA 217 8.81e+01 c.37.1.1,g.41.2.1 94022,94023 1o2dA 371 8.85e+01 e.22.1.2 86591 1mym 154 8.85e+01 1a6m a.1.1.2 15054 1i7wB 151 8.85e+01 1i7wB j.71.1.1 61910 1ckiA 317 8.86e+01 1csn d.144.1.7 41660 1laxA 370 8.87e+01 c.94.1.1 84576 1rxqA 178 8.91e+01 a.213.1.1 105118 1ra6A 461 8.99e+01 e.8.1.4 104879 2d3dA 88 9.00e+01