# List of top-scoring protein chains for T0329.t2k-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 7.38e-23 2ah5A 210 2.60e-22 1te2A 226 8.54e-22 c.108.1.6 106792 2fdrA 229 8.79e-22 1o08A 221 4.57e-21 c.108.1.6 86525 1x42A 232 6.83e-21 2go7A 207 4.74e-20 1rqlA 267 8.59e-20 c.108.1.3 97750 1jud 232 1.21e-19 1qq5A c.108.1.1 43325 1rdfA 267 1.42e-19 c.108.1.3 104884 1zrn 232 1.77e-19 1qq5A c.108.1.1 43323 1fezA 256 2.99e-19 1fezA c.108.1.3 43343 1swvA 267 3.75e-19 2fi1A 190 1.28e-17 1yv9A 264 3.99e-17 1aq6A 253 1.62e-16 1qq5A c.108.1.1 43331 1qq5A 253 1.66e-16 1qq5A c.108.1.1 43327 1qq7A 253 6.66e-16 1qq5A c.108.1.1 43329 2b0cA 206 1.87e-15 1ys9A 254 4.92e-15 1zjjA 263 6.78e-15 1ydfA 257 7.69e-15 1wviA 257 1.03e-14 1vjrA 271 4.05e-14 c.108.1.14 100832 1l7mA 211 9.94e-14 c.108.1.4 73664 1qyiA 384 1.24e-13 c.108.1.13 96595 1pw5A 253 1.38e-13 c.108.1.14 95199 2c4nA 250 1.84e-13 1j97A 211 4.32e-13 1f5sA c.108.1.4 62753 1l7pA 211 4.98e-13 c.108.1.4 73670 1zd3A 555 1.28e-12 1cr6A 554 3.82e-12 1cr6B c.69.1.11,c.108.1.2 34687,43337 1nnlA 225 2.97e-08 c.108.1.4 85906 1l8lA 225 3.60e-08 c.108.1.4 84562 1u7pA 164 8.60e-08 1ymqA 261 2.01e-06 1zs9A 261 2.53e-06 1wr8A 231 6.88e-06 2feaA 236 1.33e-05 1yj5A 383 1.43e-05 2g80A 253 1.76e-05 1k1eA 180 3.52e-05 c.108.1.5 67995 2b8eA 273 1.07e-04 1z5gA 214 1.23e-04 1z88A 214 1.34e-04 1nf2A 268 1.52e-04 c.108.1.10 91849 1nrwA 288 1.73e-04 c.108.1.10 86128 2b82A 211 8.02e-04 1rmtA 212 8.03e-04 1rlmA 271 1.01e-03 1rkqA 282 1.44e-03 c.108.1.10 97621 1rkuA 206 1.69e-03 c.108.1.11 97627 1q92A 197 3.18e-03 c.108.1.8 96250 2bdeA 470 6.36e-03 1rloA 271 7.43e-03 2b30A 301 1.02e-02 2g09A 297 1.41e-02 1ltqA 301 2.10e-02 c.108.1.9,c.37.1.1 78208,78209 2g07A 297 2.13e-02 1z4mA 197 2.48e-02 1hg3A 225 6.49e-02 1hg3A c.1.1.1 61025 1pz1A 333 8.04e-02 c.1.7.1 95390 1xviA 275 8.64e-02 1wv2A 265 1.13e-01 1l6rA 227 1.42e-01 c.108.1.10 77768 1pyfA 312 3.87e-01 c.1.7.1 95334 1ly1A 181 4.14e-01 c.37.1.1 74334 2fueA 262 4.57e-01 1o1zA 234 5.73e-01 c.1.18.3 86555 2amyA 246 5.96e-01 1w8jA 766 6.76e-01 1w7jA 795 6.85e-01 1oc2A 348 7.73e-01 c.2.1.2 92765 2dfsA 1080 8.52e-01 1t9zA 197 1.04e+00 c.108.1.16 106728 1s2oA 244 1.05e+00 1xpjA 126 1.54e+00 1pnuC 197 1.86e+00 i.1.1.1 88200 1vorF 198 1.86e+00 1nwyC 204 1.93e+00 i.1.1.2 86347 1nkwC 205 1.94e+00 i.1.1.2 80588 1y8aA 332 2.55e+00 1u02A 239 2.65e+00 c.108.1.15 107538 1uekA 275 2.95e+00 d.14.1.5,d.58.26.5 88483,88484 1uasA 362 3.09e+00 b.71.1.1,c.1.8.1 88388,88389 1ta0A 197 3.11e+00 c.108.1.16 106729 1ynpA 317 3.29e+00 1vctA 205 3.47e+00 1fehA 574 3.79e+00 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1ktbA 405 3.89e+00 b.71.1.1,c.1.8.1 72960,72961 1vbjA 281 4.18e+00 1xbtA 193 4.20e+00 1uufA 369 4.27e+00 b.35.1.2,c.2.1.1 100006,100007 1vpqA 273 4.30e+00 2cw1A 65 4.86e+00 1wpgA 994 4.88e+00 1i3kA 348 5.90e+00 1xel c.2.1.2 61595 1w4rA 195 5.95e+00 1hzjA 348 6.70e+00 1xel c.2.1.2 61450 1ek6A 348 6.73e+00 1xel c.2.1.2 29800 1we5A 772 7.09e+00 2f2hA 773 7.10e+00 1xsjA 778 7.10e+00 2g3mA 693 8.29e+00 1jzdA 220 9.57e+00 c.47.1.9,d.17.3.1 84257,84258 1jzoA 216 9.98e+00 c.47.1.9,d.17.3.1 84267,84268 1eejA 216 1.05e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1sjyA 159 1.12e+01 d.113.1.1 98900 1gs5A 258 1.28e+01 c.73.1.2 70395 1fjgH 138 1.28e+01 1seiA d.140.1.1 41468 1an7A 136 1.28e+01 1seiA d.140.1.1 41465 1sidA 383 1.31e+01 1vpsA b.121.6.1 23351 1smqA 399 1.40e+01 a.25.1.2 105766 1jk0A 419 1.43e+01 a.25.1.2 63142 1ynjC 1119 1.47e+01 1hqmC 1119 1.47e+01 i.8.1.1 45974 2fliA 220 1.49e+01 1l9uC 1118 1.55e+01 i.8.1.1 73750 1i6vC 1118 1.55e+01 e.29.1.1 61856 1xnfA 275 1.60e+01 1wxsA 90 1.63e+01 1j0gA 92 1.65e+01 d.15.1.6 90740 1j96A 323 1.70e+01 c.1.7.1 71616 1ihiA 323 1.70e+01 c.1.7.1 66142 1xjbA 325 1.70e+01 2a6hC 1119 1.88e+01 4pfk 319 1.91e+01 3pfk c.89.1.1 35582 1nbaA 264 1.92e+01 1nbaA c.33.1.3 31753 1lngA 87 1.92e+01 d.201.1.1 74045 2ctqA 112 1.96e+01 1giiA 298 2.07e+01 d.144.1.7 65218 1l9aA 87 2.11e+01 d.201.1.1 73710 1d6iA 388 2.12e+01 1bi5A c.95.1.2,c.95.1.2 36001,36002 1mrqA 323 2.21e+01 c.1.7.1 91445 1pkdA 297 2.26e+01 d.144.1.7 88141 1w98A 298 2.27e+01 1jvpP 298 2.28e+01 d.144.1.7 67371 2cchA 299 2.29e+01 1gz8A 299 2.29e+01 d.144.1.7 83405 1l7yA 94 2.30e+01 d.15.1.6 73676 1oiuA 302 2.30e+01 d.144.1.7 103958 1h1rA 303 2.31e+01 d.144.1.7 76489 1px5A 349 2.32e+01 a.160.1.2,d.218.1.6 95277,95278 1urhA 280 2.34e+01 c.46.1.2,c.46.1.2 99829,99830 1vywA 309 2.40e+01 d.144.1.7 108922 1frb 315 2.46e+01 1frb c.1.7.1 28665 1oitA 299 2.57e+01 d.144.1.7 93075 2avyB 240 2.59e+01 1tj7A 457 2.65e+01 1c9wA 315 2.78e+01 1frb c.1.7.1 28699 1iq8A 582 2.88e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1i94H 138 2.91e+01 1seiA d.140.1.1 61999 1lhpA 312 2.92e+01 c.72.1.5 77960 1gu6A 452 2.92e+01 a.138.1.3 70575 1hvd 319 2.97e+01 1avc a.65.1.1 18154 1avhA 320 3.24e+01 1avc a.65.1.1 18159 1anxA 319 3.25e+01 1avc a.65.1.1 18161 1adwA 123 3.26e+01 1bqk b.6.1.1 22893 1hvf 319 3.31e+01 1avc a.65.1.1 18155 1i86A 389 3.36e+01 c.95.1.2,c.95.1.2 66068,66069 2c7bA 311 3.40e+01 6gsvA 217 3.42e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1h6fA 193 3.44e+01 b.2.5.4 70901 1im5A 180 3.44e+01 c.33.1.3 66211 2gstA 217 3.46e+01 1b8xA a.45.1.1,c.47.1.5 17629,32923 6gsuA 217 3.49e+01 1b8xA a.45.1.1,c.47.1.5 17635,32929 6gsxA 217 3.50e+01 1b8xA a.45.1.1,c.47.1.5 17641,32935 1xyr1 232 3.52e+01 1vrbA 342 3.55e+01 1rjwA 339 3.57e+01 b.35.1.2,c.2.1.1 97582,97583 6gswA 217 3.58e+01 1b8xA a.45.1.1,c.47.1.5 17631,32927 2fgeA 995 3.59e+01 2fvzA 273 3.59e+01 1ocp 67 3.59e+01 1au7A a.4.1.1 15999 1hve 319 3.62e+01 1avc a.65.1.1 18156 2gsdA 402 3.70e+01 1mtcA 217 3.71e+01 a.45.1.1,c.47.1.5 85103,85104 1l2lA 457 3.74e+01 c.72.1.3 77656 1csjA 531 3.74e+01 1quvA e.8.1.4 43120 1jjfA 268 3.76e+01 c.69.1.2 66765 1gx6A 531 3.76e+01 e.8.1.4 70683 1gx5A 536 3.77e+01 e.8.1.4 70682 1os5A 576 3.83e+01 e.8.1.4 93475 1nhuA 578 3.86e+01 e.8.1.4 85723 2ctwA 109 3.87e+01 2ax0A 580 3.87e+01 1quvA 578 3.88e+01 1quvA e.8.1.4 43119 1z0sA 278 3.90e+01 1ar71 302 3.92e+01 1pov1 1nndA 255 3.93e+01 e.8.1.2 92002 1dgi1 288 3.94e+01 1j3nA 408 3.95e+01 c.95.1.1,c.95.1.1 84074,84075 2czrA 226 3.95e+01 2b8nA 429 3.96e+01 2ajpA 326 3.98e+01 1u0vA 393 3.99e+01 1hxs1 302 4.02e+01 1pov1 302 4.02e+01 1pov1 1c2pA 576 4.02e+01 1quvA e.8.1.4 43117 1ar61 302 4.03e+01 1pov1 1mtoA 319 4.04e+01 c.89.1.1 79458 2briA 225 4.10e+01 2bmuA 226 4.11e+01 1mkp 144 4.14e+01 1vhrA c.45.1.1 32654 1al21 302 4.14e+01 1pov1 6pfkA 319 4.14e+01 3pfk c.89.1.1 35583 1ry8A 323 4.15e+01 1jt2A 268 4.19e+01 c.69.1.2 71858 1s1pA 331 4.25e+01 c.1.7.1 98350 1dekA 241 4.27e+01 1dekA c.37.1.1 31842 1b74A 254 4.29e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1i89A 389 4.30e+01 c.95.1.2,c.95.1.2 66074,66075 1rjdA 334 4.34e+01 c.66.1.37 97558 1bq6A 388 4.38e+01 1bi5A c.95.1.2,c.95.1.2 35987,35988 1bi5A 389 4.39e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1d6hA 387 4.39e+01 1bi5A c.95.1.2,c.95.1.2 36005,36006 1i8bA 389 4.39e+01 c.95.1.2,c.95.1.2 66078,66079 1chwA 389 4.43e+01 1bi5A c.95.1.2,c.95.1.2 35997,35998 1cmlA 389 4.45e+01 1bi5A c.95.1.2,c.95.1.2 35989,35990 1hgxA 183 4.53e+01 1tc1A c.61.1.1 34027 2brxA 244 4.53e+01 1i88A 389 4.55e+01 c.95.1.2,c.95.1.2 66070,66071 1ztwA 255 4.59e+01 1i6jA 256 4.59e+01 e.8.1.2 61845 1qajA 259 4.60e+01 1mml e.8.1.2 43016 1rreA 200 4.66e+01 d.14.1.10 97791 1mml 265 4.67e+01 1mml e.8.1.2 43015 1vzwA 244 4.69e+01 1eerA 166 4.71e+01 1eerA a.26.1.2 16846 1sjpA 504 4.73e+01 1s8eA 333 4.90e+01 d.159.1.4 105368 1ro2A 216 4.93e+01 d.264.1.2 97665 1j5wA 298 4.95e+01 d.104.1.1 71589 1ii7A 333 4.96e+01 1ii7A d.159.1.4 62415 1nb4A 570 4.96e+01 e.8.1.4 85509 1gwyA 175 4.97e+01 b.97.1.1 83356 1pkm 530 4.99e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1x74A 360 5.04e+01 1m3gA 145 5.04e+01 c.45.1.1 84783 1rniA 216 5.19e+01 d.264.1.2 97663 1ve2A 235 5.20e+01 1r46A 398 5.23e+01 b.71.1.1,c.1.8.1 96973,96974 1bc3 319 5.23e+01 1avc a.65.1.1 18175 1bc1 319 5.24e+01 1avc a.65.1.1 18173 2ftsA 419 5.32e+01 1bcy 319 5.34e+01 1avc a.65.1.1 18172 1t3eA 421 5.34e+01 b.85.6.1,b.103.1.1,c.57.1.2 106348,106349,106350 1g3qA 237 5.40e+01 1hyqA c.37.1.10 60237 1yvuA 706 5.43e+01 1dp4A 435 5.50e+01 1dp4A c.93.1.1 35710 1pmy 123 5.55e+01 1bqk b.6.1.1 22888 1bc5A 269 5.68e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1af7 274 5.76e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1in8A 334 5.76e+01 1hqcA a.4.5.11,c.37.1.20 62605,62606 1wzcA 249 5.83e+01 1rw3A 455 5.84e+01 e.8.1.2 105112 1mvoA 136 5.95e+01 c.23.1.1 79513 1lwdA 413 5.98e+01 c.77.1.1 78265 1s05A 129 6.02e+01 a.24.3.2 98254 1dnv 437 6.04e+01 1dnv b.121.5.3 23332 1sznA 417 6.19e+01 b.71.1.1,c.1.8.1 106162,106163 1qpwA 141 6.20e+01 1abwA a.1.1.2 15390 1xb0A 108 6.27e+01 1yvfA 577 6.31e+01 2fiqA 420 6.37e+01 1npdA 288 6.37e+01 c.2.1.7,c.58.1.5 80681,80682 1yshC 104 6.43e+01 1wyuA 438 6.48e+01 1x0lA 333 6.59e+01 1bcw 319 6.60e+01 1avc a.65.1.1 18176 1r6bX 758 6.63e+01 a.174.1.1,c.37.1.20,c.37.1.20 104818,104819,104820 2cvjA 180 6.65e+01 2f3oA 776 6.70e+01 1z6zA 282 6.71e+01 1ix5A 151 6.77e+01 d.26.1.1 83763 1b0uA 262 6.84e+01 1b0uA c.37.1.12 32370 1b35A 260 6.85e+01 1b35A b.121.4.1 23333 1q3kA 259 6.86e+01 c.125.1.1 95693 1zjhA 548 6.93e+01 1onfA 500 6.94e+01 c.3.1.5,c.3.1.5,d.87.1.1 87141,87142,87143 1t5aA 567 7.00e+01 1vi2A 300 7.06e+01 c.2.1.7,c.58.1.5 100726,100727 1a49A 530 7.11e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1uj2A 252 7.14e+01 c.37.1.6 99452 1dgwY 93 7.15e+01 1caxB 2g50A 530 7.16e+01 1f3wA 530 7.18e+01 b.58.1.1,c.1.12.1,c.49.1.1 64934,64935,64936 1q5mA 322 7.21e+01 c.1.7.1 104539 1f3xA 530 7.23e+01 b.58.1.1,c.1.12.1,c.49.1.1 64958,64959,64960 1q13A 323 7.25e+01 1ral 308 7.25e+01 1frb c.1.7.1 28698 1xrjA 261 7.30e+01 1lwiA 322 7.45e+01 1frb c.1.7.1 28696 1r1hA 696 7.45e+01 d.92.1.4 104756 1ihp 438 7.49e+01 1ihp c.60.1.2 33993 1wekA 217 7.49e+01 1afsA 323 7.50e+01 1frb c.1.7.1 28694 1srqA 341 7.52e+01 e.55.1.1 105967 2pdzA 86 7.53e+01 1pdr b.36.1.1 24778 1zrzA 364 7.54e+01 2bszA 278 7.56e+01 1r38A 322 7.57e+01 1z86A 87 7.64e+01 1ol5A 282 7.70e+01 d.144.1.7 93310 1qavA 90 7.70e+01 1qauA b.36.1.1 24777 2gseA 501 7.73e+01 2bb3A 221 7.76e+01 1ispA 181 7.77e+01 c.69.1.18 76778 1j55A 95 7.79e+01 a.39.1.2 77078 1qrqA 325 7.82e+01 1qrqA c.1.7.1 28667 1eo1A 124 7.86e+01 1eo1A c.55.5.1 33739 1zsxA 347 7.89e+01 2b4yA 271 7.89e+01 1d5mB 192 7.92e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1d5zB 192 8.04e+01 1iakB b.1.1.2,d.19.1.1 21620,38194 1ol6A 282 8.06e+01 d.144.1.7 93311 1muoA 297 8.13e+01 d.144.1.7 85110 1vl2A 421 8.14e+01 c.26.2.1,d.210.1.1 108708,108709 1t4mA 181 8.23e+01 1v6yA 324 8.26e+01 c.1.8.3 108401 1mq4A 272 8.34e+01 d.144.1.7 91391 1n44A 319 8.38e+01 a.65.1.1 79980 1pkn 530 8.42e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1nw9A 98 8.42e+01 g.52.1.1 86293 1in4A 334 8.50e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1rkd 309 8.51e+01 1rkd c.72.1.1 34928 1ozoA 95 8.56e+01 a.39.1.2 93851 1in6A 334 8.58e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1exbA 332 8.58e+01 1qrqA c.1.7.1 28666 2a79A 333 8.60e+01 1gsoA 431 8.62e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1qriA 261 8.64e+01 1ckqA c.52.1.1 33233 1t2nA 181 8.68e+01 1v8aA 265 8.73e+01 c.72.1.2 100494 1twyA 290 8.74e+01 2c6dA 275 8.77e+01 1kfiA 572 8.78e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1l5jA 865 8.79e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 2c6eA 283 8.81e+01 1jwxA 389 8.91e+01 c.95.1.2,c.95.1.2 71920,71921