# List of top-scoring protein chains for T0329.t04-w0.5 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 2gfhA 260 4.49e-23 2ah5A 210 1.39e-22 1jud 232 3.23e-22 1qq5A c.108.1.1 43325 1zrn 232 3.65e-22 1qq5A c.108.1.1 43323 2fdrA 229 1.55e-21 1te2A 226 2.54e-21 c.108.1.6 106792 1x42A 232 3.47e-21 1o08A 221 1.03e-20 c.108.1.6 86525 1rqlA 267 6.00e-20 c.108.1.3 97750 1fezA 256 1.75e-19 1fezA c.108.1.3 43343 1rdfA 267 1.83e-19 c.108.1.3 104884 1swvA 267 2.20e-19 1qq5A 253 1.07e-18 1qq5A c.108.1.1 43327 1aq6A 253 1.35e-18 1qq5A c.108.1.1 43331 1qq7A 253 3.96e-18 1qq5A c.108.1.1 43329 2go7A 207 6.23e-18 2fi1A 190 9.91e-16 2b0cA 206 9.58e-15 1zd3A 555 8.60e-14 1cr6A 554 1.33e-13 1cr6B c.69.1.11,c.108.1.2 34687,43337 1qyiA 384 2.16e-12 c.108.1.13 96595 1l7mA 211 6.36e-12 c.108.1.4 73664 1j97A 211 2.61e-11 1f5sA c.108.1.4 62753 1l7pA 211 2.80e-11 c.108.1.4 73670 1vjrA 271 1.37e-10 c.108.1.14 100832 1pw5A 253 3.86e-10 c.108.1.14 95199 1yv9A 264 3.25e-09 1zjjA 263 3.90e-09 1wviA 257 5.02e-09 1ys9A 254 5.75e-09 2c4nA 250 7.02e-09 1ydfA 257 1.03e-08 1nnlA 225 4.32e-07 c.108.1.4 85906 1l8lA 225 5.33e-07 c.108.1.4 84562 1u7pA 164 8.88e-07 1zs9A 261 1.37e-05 2g80A 253 2.51e-05 1wr8A 231 4.45e-05 2feaA 236 9.30e-05 2b8eA 273 3.08e-04 1yj5A 383 3.17e-04 2bdeA 470 1.18e-03 1z88A 214 1.31e-03 1z5gA 214 1.33e-03 1nf2A 268 2.44e-03 c.108.1.10 91849 1rkuA 206 4.66e-03 c.108.1.11 97627 2b82A 211 6.06e-03 1rmtA 212 6.08e-03 1ymqA 261 6.10e-03 1q92A 197 1.20e-02 c.108.1.8 96250 2b30A 301 1.83e-02 1nrwA 288 4.56e-02 c.108.1.10 86128 1hg3A 225 4.65e-02 1hg3A c.1.1.1 61025 1rkqA 282 4.75e-02 c.108.1.10 97621 2g09A 297 5.16e-02 1z4mA 197 6.62e-02 2g07A 297 6.87e-02 1rlmA 271 7.18e-02 1k1eA 180 8.84e-02 c.108.1.5 67995 1pz1A 333 9.58e-02 c.1.7.1 95390 1ltqA 301 1.00e-01 c.108.1.9,c.37.1.1 78208,78209 2amyA 246 1.70e-01 1vctA 205 4.21e-01 1rloA 271 4.86e-01 1pyfA 312 6.43e-01 c.1.7.1 95334 1wv2A 265 7.69e-01 1s2oA 244 9.50e-01 1l6rA 227 1.05e+00 c.108.1.10 77768 1gs5A 258 1.24e+00 c.73.1.2 70395 1oc2A 348 1.41e+00 c.2.1.2 92765 1rjdA 334 1.62e+00 c.66.1.37 97558 1ynpA 317 1.72e+00 1vbjA 281 2.30e+00 1u02A 239 3.26e+00 c.108.1.15 107538 1rjwA 339 3.67e+00 b.35.1.2,c.2.1.1 97582,97583 2cyjA 118 3.89e+00 1xviA 275 4.67e+00 1ly1A 181 5.07e+00 c.37.1.1 74334 1ta0A 197 5.35e+00 c.108.1.16 106729 2fueA 262 5.74e+00 1uasA 362 6.09e+00 b.71.1.1,c.1.8.1 88388,88389 1rtrA 301 6.29e+00 a.128.1.1 97820 1wzcA 249 1.00e+01 1mrqA 323 1.07e+01 c.1.7.1 91445 1xpjA 126 1.08e+01 1tj7A 457 1.13e+01 1wyuA 438 1.13e+01 1bcw 319 1.19e+01 1avc a.65.1.1 18176 1bc3 319 1.24e+01 1avc a.65.1.1 18175 1j96A 323 1.28e+01 c.1.7.1 71616 1bc1 319 1.28e+01 1avc a.65.1.1 18173 1ihiA 323 1.28e+01 c.1.7.1 66142 1xjbA 325 1.28e+01 1n44A 319 1.31e+01 a.65.1.1 79980 1n42A 319 1.40e+01 a.65.1.1 79979 1bcz 319 1.46e+01 1avc a.65.1.1 18177 1qpwA 141 1.46e+01 1abwA a.1.1.2 15390 2ran 316 1.48e+01 1avc a.65.1.1 18170 1a8b 318 1.50e+01 1avc a.65.1.1 18171 1bcy 319 1.56e+01 1avc a.65.1.1 18172 1n41A 319 1.62e+01 a.65.1.1 79978 2g8lA 299 1.70e+01 1bc0 319 1.71e+01 1avc a.65.1.1 18174 1wpgA 994 1.76e+01 1rreA 200 1.79e+01 d.14.1.10 97791 1pnuC 197 1.99e+01 i.1.1.1 88200 1vorF 198 1.99e+01 1u5fA 148 2.03e+01 1nwyC 204 2.04e+01 i.1.1.2 86347 1nkwC 205 2.05e+01 i.1.1.2 80588 1j5wA 298 2.06e+01 d.104.1.1 71589 1dms 781 2.07e+01 1dmr b.52.2.2,c.81.1.1 26906,35314 1uufA 369 2.28e+01 b.35.1.2,c.2.1.1 100006,100007 1w8jA 766 2.29e+01 1w7jA 795 2.30e+01 1x0lA 333 2.44e+01 1x13A 401 2.45e+01 1e08A 371 2.48e+01 i.4.1.1 45914 1zcaA 359 2.51e+01 1t9zA 197 2.54e+01 c.108.1.16 106728 1sxeA 97 2.58e+01 a.60.1.1 106080 1e61A 823 2.58e+01 1dmr b.52.2.2,c.81.1.1 26908,35316 1dmr 823 2.59e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 4dmr 823 2.60e+01 1dmr b.52.2.2,c.81.1.1 26905,35313 1e18A 823 2.65e+01 1dmr b.52.2.2,c.81.1.1 26907,35315 1hfeL 421 2.66e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1y8aA 332 2.68e+01 1z0sA 278 2.72e+01 1rymA 212 2.77e+01 c.56.3.1 98106 1wndA 495 2.78e+01 1rynA 202 2.85e+01 c.56.3.1 98107 1rifA 282 2.92e+01 c.37.1.23 97507 1fehA 574 2.92e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2dfsA 1080 2.94e+01 2cw1A 65 2.96e+01 1bw0A 416 2.99e+01 1bw0A c.67.1.1 34385 1avhA 320 3.13e+01 1avc a.65.1.1 18159 2bfqA 192 3.14e+01 1im5A 180 3.15e+01 c.33.1.3 66211 1anxA 319 3.18e+01 1avc a.65.1.1 18161 1dekA 241 3.20e+01 1dekA c.37.1.1 31842 2g3mA 693 3.21e+01 1vhuA 211 3.24e+01 c.50.1.2 100703 1e3oC 160 3.29e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1qrqA 325 3.34e+01 1qrqA c.1.7.1 28667 1fjgH 138 3.40e+01 1seiA d.140.1.1 41468 1an7A 136 3.40e+01 1seiA d.140.1.1 41465 1hvd 319 3.42e+01 1avc a.65.1.1 18154 2fliA 220 3.44e+01 1ab4 493 3.51e+01 1ab4 e.11.1.1 43251 1o1zA 234 3.52e+01 c.1.18.3 86555 1ihgA 370 3.53e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1dgsA 667 3.54e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1ihp 438 3.56e+01 1ihp c.60.1.2 33993 2fb2A 340 3.58e+01 1wxsA 90 3.72e+01 1j0gA 92 3.73e+01 d.15.1.6 90740 1xzuA 141 3.73e+01 1gsoA 431 3.74e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1exbA 332 3.77e+01 1qrqA c.1.7.1 28666 1v6aA 332 3.78e+01 2a79A 333 3.78e+01 1smqA 399 3.79e+01 a.25.1.2 105766 1hve 319 3.79e+01 1avc a.65.1.1 18156 1fg7A 356 3.81e+01 1gewA c.67.1.1 59819 1jk0A 419 3.82e+01 a.25.1.2 63142 2bbrA 195 3.87e+01 1l7yA 94 3.91e+01 d.15.1.6 73676 1tv8A 340 3.92e+01 c.1.28.3 107352 1klzA 247 3.92e+01 c.1.2.3 72731 1yvuA 706 3.97e+01 2bjfA 329 3.98e+01 1hvf 319 4.08e+01 1avc a.65.1.1 18155 1v9dA 340 4.09e+01 a.207.1.1 100535 1we5A 772 4.09e+01 2f2hA 773 4.09e+01 1xsjA 778 4.10e+01 1klyA 247 4.14e+01 c.1.2.3 72730 1o9gA 250 4.15e+01 c.66.1.29 86692 1e3jA 352 4.30e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1t33A 224 4.37e+01 a.4.1.9,a.121.1.1 106295,106296 1vp8A 201 4.37e+01 1o9hA 250 4.40e+01 c.66.1.29 86693 1losA 224 4.46e+01 c.1.2.3 74157 1i10A 331 4.58e+01 3ldh c.2.1.5,d.162.1.1 61499,61500 1r1yA 141 4.60e+01 a.1.1.2 96836 1lf1A 308 4.65e+01 c.1.8.3 73877 1ww1A 280 4.68e+01 1r30A 369 4.73e+01 c.1.28.1 96895 1jt9A 266 4.74e+01 c.124.1.1 67259 1fs5A 266 4.81e+01 c.124.1.1 65044 1oqyA 368 4.83e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 1wmuA 141 4.86e+01 a.1.1.2 109416 1ry8A 323 4.94e+01 1s1pA 331 4.96e+01 c.1.7.1 98350 1ezfA 340 5.00e+01 1ezfA a.128.1.2 19440 1xwfA 431 5.03e+01 1t31A 226 5.18e+01 2avyB 240 5.18e+01 1b3rA 431 5.19e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1km5A 247 5.22e+01 c.1.2.3 72741 1bjt 793 5.31e+01 1bjt e.11.1.1 43249 1d2fA 390 5.32e+01 1d2fA c.67.1.3 34411 1tjnA 156 5.33e+01 c.92.1.3 107048 1fhjA 141 5.36e+01 a.1.1.2 59837 1cp3A 277 5.37e+01 1pauA c.17.1.1 30992 1dgwY 93 5.37e+01 1caxB 1yacA 208 5.38e+01 1yacA c.33.1.3 31757 1zsxA 347 5.48e+01 1lzlA 323 5.48e+01 c.69.1.2 78306 1x94A 191 5.54e+01 c.80.1.3 109522 2d5xA 141 5.66e+01 1q6uA 245 5.67e+01 d.26.1.1 95998 1oxy 628 5.68e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18486,18497,21862 1rz3A 201 5.71e+01 c.37.1.6 98132 1dv7A 227 5.76e+01 1dvjA c.1.2.3 28550 1d4fA 431 5.77e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1ll1 628 5.80e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 2ctwA 109 5.80e+01 1loqA 228 5.80e+01 c.1.2.3 74155 1oheA 348 5.81e+01 c.45.1.1,c.45.1.1 87013,87014 1hgxA 183 5.81e+01 1tc1A c.61.1.1 34027 2ctqA 112 5.83e+01 1q3kA 259 5.85e+01 c.125.1.1 95693 1li4A 432 5.87e+01 c.2.1.4,c.23.12.3 84616,84617 1d3yA 301 5.88e+01 1d3yA e.12.1.1 43252 1lla 628 5.92e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1ral 308 5.95e+01 1frb c.1.7.1 28698 1km0A 247 5.99e+01 c.1.2.3 72732 1a7aA 432 6.00e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1ur4A 399 6.13e+01 1dvjA 246 6.17e+01 1dvjA c.1.2.3 28546 1uekA 275 6.21e+01 d.14.1.5,d.58.26.5 88483,88484 1tqjA 230 6.28e+01 c.1.2.2 107228 1km3A 247 6.29e+01 c.1.2.3 72739 1suwA 249 6.37e+01 e.52.1.1 106027 1yhvA 297 6.40e+01 1te5A 257 6.40e+01 d.153.1.1 106795 1x1zA 252 6.41e+01 2f1sA 186 6.42e+01 1r5vB 185 6.46e+01 b.1.1.2,d.19.1.1 97118,97119 1q5mA 322 6.49e+01 c.1.7.1 104539 1q13A 323 6.50e+01 1q77A 138 6.57e+01 c.26.2.4 96023 2avyK 128 6.58e+01 1ipaA 274 6.66e+01 c.116.1.1,d.79.3.3 71254,71255 1fhb 108 6.68e+01 1ycc a.3.1.1 15862 1lwiA 322 6.70e+01 1frb c.1.7.1 28696 1dv2A 452 6.70e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1qmrA 159 6.71e+01 1bv1 d.129.3.1 41314 1afsA 323 6.73e+01 1frb c.1.7.1 28694 1qwkA 317 6.73e+01 c.1.7.1 96482 1km2A 247 6.75e+01 c.1.2.3 72738 4pfk 319 6.77e+01 3pfk c.89.1.1 35582 1s20A 340 6.77e+01 c.122.1.1 98356 1c9wA 315 6.79e+01 1frb c.1.7.1 28699 1dd9A 338 6.81e+01 1dd9A e.13.1.1 43254 2bbzA 249 6.83e+01 1qwgA 251 6.84e+01 c.1.27.1 96473 1s05A 129 6.94e+01 a.24.3.2 98254 1h1dA 221 6.99e+01 c.66.1.1 83452 1lp6A 229 7.01e+01 c.1.2.3 74171 5cytR 104 7.03e+01 1ycc a.3.1.1 15878 1v2xA 194 7.03e+01 c.116.1.1 100274 1lfmA 103 7.08e+01 a.3.1.1 73883 1op0A 234 7.09e+01 b.47.1.2 104019 2ldxA 331 7.11e+01 1os5A 576 7.17e+01 e.8.1.4 93475 1tiiA 190 7.18e+01 1lt3A d.166.1.1 42238 1bdfA 235 7.24e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1xq6A 253 7.28e+01 1km6A 247 7.30e+01 c.1.2.3 72742 2b8nA 429 7.38e+01 1b35A 260 7.41e+01 1b35A b.121.4.1 23333 1km4A 247 7.45e+01 c.1.2.3 72740 1dv1A 449 7.46e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1u7xA 312 7.47e+01 1a9nA 176 7.49e+01 1a9nA c.10.2.4 30875 1n8kA 374 7.49e+01 b.35.1.2,c.2.1.1 80298,80299 1nmsA 249 7.50e+01 c.17.1.1 85879 1cs0A 1073 7.53e+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 1m6vA 1073 7.57e+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 74536,74537,74538,74539,74540,74541 2ajpA 326 7.60e+01 1kd6A 179 7.60e+01 b.97.1.1 68459 1qx3A 257 7.62e+01 c.17.1.1 96515 1iazA 179 7.63e+01 1iazA b.97.1.1 62131 1vjuA 309 7.64e+01 d.248.1.1 100835 1gwyA 175 7.64e+01 b.97.1.1 83356 2cvhA 220 7.65e+01 1ktdB 215 7.73e+01 b.1.1.2,d.19.1.1 72966,72967 1tv5A 443 7.79e+01 1rp3A 239 7.87e+01 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 1op2A 234 7.89e+01 b.47.1.2 104020 1drw 273 7.90e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1kt2B 213 8.00e+01 b.1.1.2,d.19.1.1 72953,72954 1fneB 224 8.02e+01 1iakB b.1.1.2,d.19.1.1 59898,59899 2briA 225 8.02e+01 1w0mA 226 8.05e+01 c.1.1.1 109027 2gp4A 628 8.06e+01 1gliA 141 8.08e+01 1abwA a.1.1.2 15353 1fngB 224 8.08e+01 1iakB b.1.1.2,d.19.1.1 59906,59907 2bmuA 226 8.12e+01 1nndA 255 8.13e+01 e.8.1.2 92002 1s0uA 408 8.15e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1cliA 345 8.16e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1h5vA 304 8.20e+01 c.1.8.3 70898 2abbA 364 8.27e+01 2gf2A 296 8.33e+01 7a3hA 303 8.36e+01 7a3hA c.1.8.3 28817 1uz5A 402 8.36e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1qi2A 305 8.37e+01 7a3hA c.1.8.3 28824 1i3kA 348 8.46e+01 1xel c.2.1.2 61595 1f25A 402 8.48e+01 1rom a.104.1.1 18952 2bszA 278 8.55e+01 1njgA 250 8.56e+01 c.37.1.20 85785 1ieaB 228 8.63e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1eqnA 321 8.65e+01 1dd9A e.13.1.1 43256 1vggA 161 8.66e+01 1vypX 364 8.68e+01 c.1.4.1 108905 1vyrA 364 8.69e+01 c.1.4.1 108906 1hzjA 348 8.73e+01 1xel c.2.1.2 61450 1ek6A 348 8.80e+01 1xel c.2.1.2 29800 1vysX 364 8.83e+01 c.1.4.1 108907 1i3oA 175 8.89e+01 1pauA c.17.1.1 61603 1uc2A 481 8.92e+01 d.261.1.1 99161 1ocp 67 9.00e+01 1au7A a.4.1.1 15999