# List of top-scoring protein chains for T0379.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 2fdrA 229 2.77e-22 2b0cA 206 8.35e-22 1x42A 232 3.88e-21 1jud 232 1.01e-20 1qq5A c.108.1.1 43325 1o08A 221 1.20e-20 c.108.1.6 86525 1zrn 232 1.38e-20 1qq5A c.108.1.1 43323 1aq6A 253 7.40e-20 1qq5A c.108.1.1 43331 2gfhA 260 7.65e-20 1qq5A 253 9.85e-20 1qq5A c.108.1.1 43327 1te2A 226 1.54e-19 c.108.1.6 106792 1qq7A 253 3.82e-19 1qq5A c.108.1.1 43329 1zd3A 555 6.76e-19 1cr6A 554 7.47e-19 1cr6B c.69.1.11,c.108.1.2 34687,43337 2ah5A 210 2.34e-17 2go7A 207 4.31e-15 2fi1A 190 2.22e-14 1fezA 256 8.73e-12 1fezA c.108.1.3 43343 1rqlA 267 8.76e-12 c.108.1.3 97750 1rdfA 267 1.59e-11 c.108.1.3 104884 1l7mA 211 6.62e-11 c.108.1.4 73664 1swvA 267 6.93e-11 1j97A 211 3.24e-10 1f5sA c.108.1.4 62753 1l7pA 211 3.71e-10 c.108.1.4 73670 1vjrA 271 5.40e-10 c.108.1.14 100832 1pw5A 253 7.09e-10 c.108.1.14 95199 2c4nA 250 1.86e-09 1zjjA 263 5.48e-09 2g80A 253 1.45e-08 1u7pA 164 1.58e-08 1yv9A 264 2.80e-08 1qyiA 384 4.66e-08 c.108.1.13 96595 1ydfA 257 1.08e-07 1wviA 257 2.02e-07 1ys9A 254 4.58e-07 1zs9A 261 8.23e-07 1nnlA 225 3.87e-05 c.108.1.4 85906 1l8lA 225 4.16e-05 c.108.1.4 84562 1wr8A 231 5.47e-05 1yj5A 383 9.79e-05 2bdeA 470 1.89e-04 1nf2A 268 3.31e-04 c.108.1.10 91849 1ymqA 261 1.06e-03 1rkuA 206 3.30e-03 c.108.1.11 97627 2feaA 236 3.65e-03 1q92A 197 5.63e-03 c.108.1.8 96250 1k1eA 180 1.28e-02 c.108.1.5 67995 2b82A 211 1.40e-02 1rmtA 212 1.41e-02 1z5gA 214 1.90e-02 1z88A 214 2.17e-02 1z4mA 197 3.43e-02 1rkqA 282 5.66e-02 c.108.1.10 97621 2b8eA 273 7.68e-02 1pz1A 333 8.42e-02 c.1.7.1 95390 1ltqA 301 1.31e-01 c.108.1.9,c.37.1.1 78208,78209 1pyfA 312 1.46e-01 c.1.7.1 95334 1nrwA 288 2.51e-01 c.108.1.10 86128 2b30A 301 2.54e-01 1xviA 275 5.73e-01 1vrbA 342 7.30e-01 1t9zA 197 7.62e-01 c.108.1.16 106728 1s2oA 244 8.46e-01 1l6rA 227 1.11e+00 c.108.1.10 77768 1rlmA 271 1.24e+00 2g09A 297 1.41e+00 2g07A 297 1.76e+00 2cn1A 292 1.94e+00 2fueA 262 2.04e+00 1frb 315 2.23e+00 1frb c.1.7.1 28665 1ly1A 181 2.23e+00 c.37.1.1 74334 1ta0A 197 2.45e+00 c.108.1.16 106729 1ynpA 317 2.48e+00 1vqvA 306 2.95e+00 1gs5A 258 3.03e+00 c.73.1.2 70395 1vbjA 281 3.23e+00 1px5A 349 3.27e+00 a.160.1.2,d.218.1.6 95277,95278 2amyA 246 3.53e+00 1wpgA 994 3.81e+00 2bwkA 121 4.02e+00 1glqA 209 5.06e+00 1pgtA a.45.1.1,c.47.1.5 17588,32882 1s58A 554 5.40e+00 b.121.5.2 105262 1rloA 271 6.13e+00 2bszA 278 6.26e+00 1wzcA 249 6.74e+00 1m3gA 145 7.67e+00 c.45.1.1 84783 1k30A 368 8.04e+00 c.112.1.1 68067 1fntF 234 8.08e+00 1rypF 233 8.14e+00 1rypF d.153.1.4 41937 1iuqA 367 8.19e+00 c.112.1.1 90703 1g0uE 234 8.54e+00 d.153.1.4 41950 1og6A 298 8.89e+00 c.1.7.1 86984 1zh2A 121 9.47e+00 1b35A 260 9.82e+00 1b35A b.121.4.1 23333 1ur3M 319 1.05e+01 c.1.7.1 99806 1u02A 239 1.06e+01 c.108.1.15 107538 1ev5A 264 1.16e+01 1bkpA d.117.1.1 40935 1c9wA 315 1.17e+01 1frb c.1.7.1 28699 2g40A 224 1.18e+01 1ys4A 354 1.25e+01 1q6uA 245 1.28e+01 d.26.1.1 95998 1xiqA 157 1.28e+01 2cyjA 118 1.33e+01 1ev8A 264 1.39e+01 1bkpA d.117.1.1 40989 1l9vA 317 1.39e+01 d.13.2.1,d.216.1.1 73760,73761 1iq8A 582 1.40e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1j5wA 298 1.41e+01 d.104.1.1 71589 1tiiA 190 1.43e+01 1lt3A d.166.1.1 42238 2c35A 152 1.43e+01 1nsqA 153 1.45e+01 1npk d.58.6.1 39135 1uz5A 402 1.50e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 2gd9A 189 1.51e+01 1hg3A 225 1.52e+01 1hg3A c.1.1.1 61025 1uasA 362 1.57e+01 b.71.1.1,c.1.8.1 88388,88389 1csjA 531 1.64e+01 1quvA e.8.1.4 43120 1os5A 576 1.64e+01 e.8.1.4 93475 1gx6A 531 1.64e+01 e.8.1.4 70683 1gx5A 536 1.65e+01 e.8.1.4 70682 1mkp 144 1.66e+01 1vhrA c.45.1.1 32654 1nhuA 578 1.67e+01 e.8.1.4 85723 2gc8A 578 1.69e+01 2ax0A 580 1.70e+01 1xpjA 126 1.70e+01 1yshC 104 1.76e+01 1c2pA 576 1.81e+01 1quvA e.8.1.4 43117 1regX 122 1.82e+01 1regX d.58.27.1 39406 1jqlA 366 1.83e+01 d.131.1.1,d.131.1.1,d.131.1.1 63231,63232,63233 2cv4A 250 1.84e+01 1fzrA 138 1.85e+01 1fzrA c.52.1.17 33336 1eepA 404 1.86e+01 1ak5 c.1.5.1 28636 1x0rA 249 1.87e+01 1lngA 87 1.89e+01 d.201.1.1 74045 1evfA 264 1.91e+01 1bkpA d.117.1.1 40932 1l9aA 87 1.93e+01 d.201.1.1 73710 1bq2 264 2.03e+01 1bkpA d.117.1.1 40971 1ok7A 366 2.10e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1wv2A 265 2.10e+01 1nceA 264 2.12e+01 d.117.1.1 80401 1m0dA 138 2.14e+01 c.52.1.17 74354 1fwmA 264 2.14e+01 d.117.1.1 90500 2tscA 264 2.22e+01 1bkpA d.117.1.1 40952 2g8oA 264 2.25e+01 1axwA 265 2.27e+01 1bkpA d.117.1.1 40938 1qqqA 264 2.28e+01 1bkpA d.117.1.1 40931 2g8mA 264 2.29e+01 1h8tC 238 2.29e+01 b.121.4.1 70922 2ftnA 264 2.30e+01 1s8aA 152 2.32e+01 c.24.1.2 98727 1b93A 152 2.33e+01 1b93A c.24.1.2 31507 1wxsA 90 2.44e+01 2h2yA 136 2.48e+01 1zprA 264 2.48e+01 1bkpA d.117.1.1 40978 1tys 265 2.49e+01 1bkpA d.117.1.1 40937 1nb4A 570 2.53e+01 e.8.1.4 85509 1j0gA 92 2.54e+01 d.15.1.6 90740 1f4dA 264 2.58e+01 1bkpA d.117.1.1 40972 1ml5S 91 2.58e+01 i.1.1.1 79274 1kzjA 264 2.62e+01 d.117.1.1 73365 1ocp 67 2.64e+01 1au7A a.4.1.1 15999 1o1zA 234 2.65e+01 c.1.18.3 86555 2cw1A 65 2.84e+01 2c7bA 311 2.85e+01 1mtcA 217 2.86e+01 a.45.1.1,c.47.1.5 85103,85104 6gsvA 217 2.98e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 6gsuA 217 3.02e+01 1b8xA a.45.1.1,c.47.1.5 17635,32929 2gstA 217 3.02e+01 1b8xA a.45.1.1,c.47.1.5 17629,32923 1z63A 500 3.04e+01 1q6hA 224 3.05e+01 d.26.1.1 95975 1s89A 152 3.05e+01 c.24.1.2 98721 6gsxA 217 3.07e+01 1b8xA a.45.1.1,c.47.1.5 17641,32935 1l7yA 94 3.18e+01 d.15.1.6 73676 1xr4A 509 3.22e+01 1m9lA 199 3.26e+01 c.10.3.1 84903 6gswA 217 3.27e+01 1b8xA a.45.1.1,c.47.1.5 17631,32927 1nwwA 149 3.28e+01 d.17.4.8 86306 1nu3A 149 3.28e+01 d.17.4.8 86170 1z6zA 282 3.30e+01 1ds9A 198 3.32e+01 1ds9A c.10.3.1 30879 1adwA 123 3.37e+01 1bqk b.6.1.1 22893 1i31A 314 3.42e+01 1bw8A b.2.7.1 22481 1bw8A 321 3.43e+01 1bw8A b.2.7.1 22482 1mfrA 176 3.61e+01 2fha a.25.1.1 16692 1ezfA 340 3.65e+01 1ezfA a.128.1.2 19440 1ymuA 130 3.70e+01 3chy c.23.1.1 31066 1ogqA 313 3.80e+01 c.10.2.8 86996 2avyK 128 3.85e+01 2foyA 260 3.92e+01 1qrhA 261 3.93e+01 1ckqA c.52.1.1 33232 1an7A 136 3.94e+01 1seiA d.140.1.1 41465 1jv0A 260 3.95e+01 b.74.1.1 63303 1q0uA 219 3.96e+01 c.37.1.19 95512 1crm 260 3.98e+01 2cba b.74.1.1 27816 1mrqA 323 3.99e+01 c.1.7.1 91445 2cab 261 4.00e+01 2cba b.74.1.1 27906 2f2hA 773 4.02e+01 1we5A 772 4.02e+01 1xsjA 778 4.04e+01 1tj7A 457 4.04e+01 1im5A 180 4.21e+01 c.33.1.3 66211 1pvmA 184 4.24e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1qwkA 317 4.29e+01 c.1.7.1 96482 1bxxA 285 4.33e+01 1bw8A b.2.7.1 22483 1pnsP 83 4.36e+01 i.1.1.1 88183 1fjgH 138 4.37e+01 1seiA d.140.1.1 41468 6chyA 128 4.40e+01 3chy c.23.1.1 31062 1lhpA 312 4.45e+01 c.72.1.5 77960 1cye 129 4.45e+01 3chy c.23.1.1 31077 1qriA 261 4.48e+01 1ckqA c.52.1.1 33233 1u8tA 128 4.49e+01 1nat 124 4.50e+01 1dz3A c.23.1.1 31113 1mk7B 192 4.54e+01 a.11.2.1,b.55.1.5 79219,79220 1kmiY 129 4.54e+01 c.23.1.1 72751 1vlzA 128 4.56e+01 3chy c.23.1.1 31048 1ehc 128 4.62e+01 3chy c.23.1.1 31053 2f6qA 280 4.64e+01 5chy 128 4.64e+01 3chy c.23.1.1 31050 2fo3A 125 4.65e+01 2ctqA 112 4.70e+01 1y71A 130 4.70e+01 1knb 196 4.71e+01 1qhvA b.21.1.1 23841 1e6lA 127 4.72e+01 3chy c.23.1.1 59307 1dnaA 264 4.73e+01 1bkpA d.117.1.1 40956 1rkd 309 4.75e+01 1rkd c.72.1.1 34928 1jbeA 128 4.78e+01 3chy c.23.1.1 62845 1fjgP 88 4.80e+01 1emwA d.27.1.1 38444 1mizB 201 4.80e+01 a.11.2.1,b.55.1.5 79172,79173 1njgA 250 4.81e+01 c.37.1.20 85785 1e6kA 130 4.83e+01 3chy c.23.1.1 59306 1ymv 129 4.84e+01 3chy c.23.1.1 31045 1yf2A 425 4.84e+01 1udrA 129 4.86e+01 3chy c.23.1.1 31041 1d4zA 128 4.87e+01 3chy c.23.1.1 31047 1mixA 206 4.92e+01 a.11.2.1,b.55.1.5 79166,79167 1gtvA 214 4.97e+01 c.37.1.1 70537 1ah4 315 4.99e+01 1frb c.1.7.1 28684 1dlaA 314 4.99e+01 1frb c.1.7.1 28690 1ah0 316 4.99e+01 1frb c.1.7.1 28685 1oc2A 348 5.01e+01 c.2.1.2 92765 1qpsA 261 5.08e+01 1ckqA c.52.1.1 33234 2fmkA 129 5.11e+01 1cl8A 276 5.17e+01 1ckqA c.52.1.1 33230 1y8aA 332 5.17e+01 1yy3A 346 5.17e+01 1z0sA 278 5.27e+01 1y4oA 104 5.28e+01 1ab5A 125 5.29e+01 3chy c.23.1.1 31056 1rniA 216 5.30e+01 d.264.1.2 97663 2cvzA 289 5.30e+01 2chf 128 5.36e+01 3chy c.23.1.1 31079 1kit 757 5.41e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1jg0A 264 5.43e+01 d.117.1.1 66659 1zdmA 129 5.44e+01 1w0pA 781 5.45e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1r46A 398 5.47e+01 b.71.1.1,c.1.8.1 96973,96974 1y19B 202 5.59e+01 1ro2A 216 5.64e+01 d.264.1.2 97665 4gssA 209 5.66e+01 1pgtA a.45.1.1,c.47.1.5 17570,32864 1c4wA 128 5.73e+01 3chy c.23.1.1 31046 2d5cA 263 5.80e+01 1d8vA 263 5.81e+01 1mrj d.165.1.1 42193 1ral 308 5.83e+01 1frb c.1.7.1 28698 1ab6A 125 5.89e+01 3chy c.23.1.1 31054 2b61A 377 5.96e+01 1smqA 399 5.96e+01 a.25.1.2 105766 2ldxA 331 5.98e+01 2gfqA 298 6.00e+01 1jk0A 419 6.01e+01 a.25.1.2 63142 1lwiA 322 6.01e+01 1frb c.1.7.1 28696 1afsA 323 6.03e+01 1frb c.1.7.1 28694 1x74A 360 6.09e+01 1zldA 118 6.11e+01 1srrA 124 6.15e+01 1dz3A c.23.1.1 31110 1f51E 119 6.25e+01 1dz3A c.23.1.1 31114 1gzkA 315 6.27e+01 d.144.1.7 83406 1gw5M 435 6.29e+01 b.2.7.1,d.110.4.2 70631,70632 1x94A 191 6.33e+01 c.80.1.3 109522 1iokA 545 6.38e+01 a.129.1.1,c.8.5.1,d.56.1.1 66224,66225,66226 1wj4A 124 6.41e+01 2ajpA 326 6.45e+01 2f7kA 327 6.50e+01 1h6eA 288 6.56e+01 b.2.7.1 65680 1j96A 323 6.61e+01 c.1.7.1 71616 1ihiA 323 6.61e+01 c.1.7.1 66142 1vybA 238 6.63e+01 d.151.1.1 108897 1xjbA 325 6.63e+01 1sjpA 504 6.65e+01 1vctA 205 6.68e+01 1hgxA 183 6.76e+01 1tc1A c.61.1.1 34027 1l1sA 113 6.77e+01 c.114.1.1 73484 1w0hA 204 6.82e+01 2bp5M 435 6.82e+01 1knwA 425 6.90e+01 b.49.2.3,c.1.6.1 90969,90970 1aiqA 264 6.92e+01 1bkpA d.117.1.1 40967 1dp4A 435 6.96e+01 1dp4A c.93.1.1 35710 1az1 315 6.99e+01 1frb c.1.7.1 28677 2esvE 240 7.06e+01 1xgdA 315 7.10e+01 1el3A 316 7.12e+01 1frb c.1.7.1 28672 1ads 315 7.12e+01 1frb c.1.7.1 28671 1us0A 316 7.12e+01 c.1.7.1 99850 2agtA 319 7.13e+01 1abn 315 7.13e+01 1frb c.1.7.1 28683 1z3nA 319 7.15e+01 1npdA 288 7.15e+01 c.2.1.7,c.58.1.5 80681,80682 1q5mA 322 7.16e+01 c.1.7.1 104539 1gznA 335 7.17e+01 d.144.1.7 83407 2ctwA 109 7.20e+01 1mryA 339 7.21e+01 d.144.1.7 91451 2gsfA 373 7.26e+01 1q13A 323 7.28e+01 1a6aA 176 7.31e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 2acu 315 7.32e+01 1frb c.1.7.1 28676 1klgA 177 7.35e+01 b.1.1.2,d.19.1.1 72714,72715 2b95A 106 7.43e+01 1vi2A 300 7.44e+01 c.2.1.7,c.58.1.5 100726,100727 1o6kA 336 7.45e+01 d.144.1.7 81091 1b74A 254 7.52e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1toaA 313 7.55e+01 1toaA c.92.2.2 35598 1dms 781 7.59e+01 1dmr b.52.2.2,c.81.1.1 26906,35314 1i94H 138 7.66e+01 1seiA d.140.1.1 61999 1hbrB 146 7.68e+01 1cg5B a.1.1.2 15571 1gvzA 237 7.69e+01 b.47.1.2 76360 1v2aA 210 7.73e+01 a.45.1.1,c.47.1.5 100263,100264 1t5wA 180 7.74e+01 b.1.1.2,d.19.1.1 106481,106482 1kluA 179 7.75e+01 b.1.1.2,d.19.1.1 72724,72725 1a4fB 146 7.76e+01 1abwA a.1.1.2 15573 1v3eA 431 7.79e+01 b.68.1.1 100287 1fv1A 181 7.82e+01 1iakA b.1.1.2,d.19.1.1 21605,38179 1sjhA 180 7.82e+01 b.1.1.2,d.19.1.1 105648,105649 1j4zA 547 7.84e+01 a.129.1.1,c.8.5.1,d.56.1.1 90838,90839,90840 2hvm 273 7.84e+01 1cnv c.1.8.5 28985 1p4xA 250 7.84e+01 a.4.5.28,a.4.5.28 87784,87785 1svtA 524 7.86e+01 1fawB 146 7.88e+01 a.1.1.2 65003 1sx3A 525 7.88e+01 1ss8A 524 7.88e+01 1e61A 823 7.92e+01 1dmr b.52.2.2,c.81.1.1 26908,35316 1t5xA 181 7.92e+01 b.1.1.2,d.19.1.1 106489,106490 1op0A 234 7.93e+01 b.47.1.2 104019 1kp8A 547 7.96e+01 a.129.1.1,c.8.5.1,d.56.1.1 84414,84415,84416 1xckA 547 7.99e+01 1gr5A 547 8.01e+01 i.16.1.1 65478 1pywA 182 8.01e+01 b.1.1.2,d.19.1.1 95377,95378 1nt2A 210 8.03e+01 c.66.1.3 86149 1e18A 823 8.05e+01 1dmr b.52.2.2,c.81.1.1 26907,35315 1rqfA 184 8.09e+01 1mi5E 241 8.12e+01 b.1.1.1,b.1.1.2 79147,79148 1oelA 547 8.12e+01 1derA a.129.1.1,c.8.5.1,d.56.1.1 19452,30781,38900 2a72A 146 8.13e+01 1dmr 823 8.15e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 1grlA 548 8.15e+01 1kgcE 242 8.22e+01 b.1.1.1,b.1.1.2 77386,77387 1uc2A 481 8.29e+01 d.261.1.1 99161 1tfr 305 8.31e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1xzpA 482 8.39e+01 1bi9A 499 8.58e+01 1bpwA c.82.1.1 35337 2c5lC 117 8.60e+01 1cf5A 249 8.61e+01 1mrj d.165.1.1 42191 4dmr 823 8.71e+01 1dmr b.52.2.2,c.81.1.1 26905,35313 1kr0A 273 8.91e+01 c.1.8.5 68845 1op2A 234 8.93e+01 b.47.1.2 104020 1r38A 322 8.98e+01 1k0fA 277 8.98e+01 c.92.2.2 71974