# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1yr0A 175 8.05e-20 2fe7A 166 2.01e-19 1yvoA 172 3.97e-19 2bl1A 172 7.95e-19 2ge3A 170 5.18e-18 2beiA 170 2.83e-17 1vhsA 175 3.53e-16 d.108.1.1 100698 1z4eA 153 7.48e-16 1tiqA 180 1.58e-15 d.108.1.1 107010 2cy2A 174 1.92e-15 1qsoA 149 4.33e-15 1qsmA d.108.1.1 40812 1qsmA 152 5.76e-15 1qsmA d.108.1.1 40808 2ae6A 166 6.27e-15 1wwzA 159 1.79e-14 1s3zA 165 1.81e-14 d.108.1.1 105250 2b5gA 171 1.92e-14 1yx0A 159 2.25e-14 1u6mA 199 3.31e-14 1y9kA 157 3.54e-14 1mk4A 157 2.50e-13 d.108.1.1 84979 1gheA 177 5.15e-13 d.108.1.1 76222 2fl4A 149 1.18e-12 1on0A 158 1.20e-12 d.108.1.1 87095 1i1dA 161 1.51e-12 1i21A d.108.1.1 61526 1i12A 160 1.78e-12 1i21A d.108.1.1 61515 1ufhA 180 1.81e-12 d.108.1.1 88485 1i21A 159 2.58e-12 1i21A d.108.1.1 61549 1vkcA 158 2.79e-12 1yvkA 163 7.62e-12 1q2yA 140 1.31e-11 d.108.1.1 95655 1p0hA 318 1.40e-11 d.108.1.1 93866 2c27A 315 1.94e-11 2bswA 146 2.34e-11 1xebA 150 4.77e-11 1nslA 184 5.44e-11 d.108.1.1 86137 2atrA 138 8.38e-11 1y9wA 140 1.04e-10 1s7kA 182 1.11e-10 1cjwA 166 1.13e-10 1cjwA d.108.1.1 40818 1b6bA 174 1.24e-10 1cjwA d.108.1.1 40819 2a4nA 182 2.04e-10 1kuxA 207 2.21e-10 d.108.1.1 73021 1n71A 180 3.01e-10 d.108.1.1 85370 2fckA 181 3.22e-10 1b87A 181 3.32e-10 1b87A d.108.1.1 40797 2g3aA 152 3.50e-10 1yreA 197 3.82e-10 2ganA 190 6.34e-10 1bo4A 168 6.65e-10 1bo4A d.108.1.1 40798 1bo4B 168 2.57e-09 1bo4A d.108.1.1 40799 1z4rA 168 5.29e-09 1qstA 160 8.01e-09 1yghA d.108.1.1 40804 2aj6A 159 1.07e-08 1y7rA 133 2.17e-08 5gcnA 166 2.31e-08 1yghA d.108.1.1 40807 1yghA 164 1.92e-07 1yghA d.108.1.1 40802 1sqhA 312 2.15e-07 d.108.1.5 98966 1m4iA 181 4.48e-07 d.108.1.1 74457 2fsrA 195 5.49e-07 2d4pA 141 5.99e-06 1nmtA 392 8.69e-05 1nmtA d.108.1.2,d.108.1.2 40823,40824 1bob 320 6.55e-04 1bob d.108.1.1 40816 1yk3A 210 7.69e-04 1fy7A 278 1.31e-03 1fy7A d.108.1.1 40817 1yleA 342 3.51e-03 2givA 295 3.79e-03 1iicA 422 5.13e-03 1nmtA d.108.1.2,d.108.1.2 62422,62423 1xmtA 103 6.99e-03 1zy9A 564 5.66e-02 1svjA 156 8.61e-02 d.220.1.1 106049 1ne9A 335 1.33e-01 d.108.1.4,d.108.1.4 91839,91840 1ro5A 201 2.51e-01 d.108.1.3 105023 1o50A 157 3.12e-01 d.37.1.1,d.37.1.1 92478,92479 1rfmA 344 3.59e-01 c.122.1.1 97385 1zo0A 126 3.79e-01 2as9A 210 4.31e-01 1nxuA 333 8.46e-01 c.122.1.1 86389 1pvmA 184 1.18e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wrdA 103 1.18e+00 2fbyA 205 1.34e+00 1vicA 262 1.53e+00 c.68.1.13 100756 1gosA 520 1.57e+00 c.3.1.2,d.16.1.5 65425,65426 1lqpA 135 1.82e+00 d.32.1.2 78151 1iae 200 1.89e+00 1iae d.92.1.8 40311 1qysA 106 1.96e+00 k.41.1.1 96603 1nkiA 135 2.00e+00 d.32.1.2 91941 1ast 200 2.07e+00 1iae d.92.1.8 40310 1iab 200 2.12e+00 1iae d.92.1.8 40312 1pu1A 94 2.31e+00 d.266.1.1 104307 1d2tA 231 2.45e+00 1d2tA a.111.1.1 19052 1pea 385 2.61e+00 1pea c.93.1.1 35662 1oniA 137 2.86e+00 d.79.1.1 87144 1iw8A 231 3.18e+00 a.111.1.1 76866 2aboA 136 3.27e+00 1xhdA 173 3.29e+00 1ghhA 81 3.43e+00 1ghhA d.57.1.1 38940 1j2zA 270 3.48e+00 b.81.1.1 90805 1yueA 427 3.52e+00 1shdA 107 3.55e+00 1fmk d.93.1.1 40440 1ewjA 126 3.63e+00 1ecsA d.32.1.2 59526 1ml4A 308 3.91e+00 c.78.1.1,c.78.1.1 79255,79256 1kllA 130 3.91e+00 d.32.1.2 72720 2f46A 156 3.98e+00 1v2xA 194 4.02e+00 c.116.1.1 100274 1i4nA 251 4.29e+00 c.1.2.4 71114 1q3iA 214 4.62e+00 d.220.1.1 104524 1it2A 146 4.77e+00 a.1.1.2 66365 1k9vF 201 4.85e+00 c.23.16.1 68365 2bkkA 264 5.18e+00 1t5yA 190 5.18e+00 b.122.1.1,d.17.6.3 106495,106496 1t0aA 159 5.21e+00 1hv9A 456 5.67e+00 1fwyA b.81.1.4,c.68.1.5 28060,34518 1x8hA 228 5.71e+00 1dxy 333 5.81e+00 1dxy c.2.1.4,c.23.12.1 30094,31354 1l1nA 183 5.84e+00 b.47.1.4 73476 1j7lA 264 5.94e+00 d.144.1.6 62697 2fomB 185 6.20e+00 1ecsA 126 6.20e+00 1ecsA d.32.1.2 59407 1gpwB 201 6.34e+00 c.23.16.1 65461 1ojaA 520 6.50e+00 c.3.1.2,d.16.1.5 93096,93097 1dmmA 131 6.52e+00 1opy d.17.4.3 38114 1bqnB 430 6.68e+00 1rthA e.8.1.2 43065 1ebdA 455 6.71e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 2cvlA 124 6.73e+00 2b8eA 273 6.81e+00 1eiwA 111 6.81e+00 1eiwA c.23.3.1 31130 1k3fA 253 6.95e+00 c.56.2.1 68105 1ndk 155 7.29e+00 1npk d.58.6.1 39118 1iv0A 98 7.36e+00 c.55.3.8 90706 1xtlA 175 7.54e+00 1s3eA 520 7.57e+00 c.3.1.2,d.16.1.5 98426,98427 1f32A 149 7.71e+00 1f32A d.62.1.1 39539 1ybhA 590 7.73e+00 1ev7A 317 7.74e+00 1ev7B c.52.1.9 33315 1oh0A 131 7.75e+00 d.17.4.3 87004 1d2zB 153 7.78e+00 1d2zB a.77.1.2 18439 1kafA 108 7.87e+00 d.199.1.1 68372 1ea2A 131 7.92e+00 d.17.4.3 64860 1s4iA 175 8.43e+00 1s57A 153 8.87e+00 1wjxA 122 9.01e+00 1j7iA 264 9.21e+00 1j7iA d.144.1.6 62694 1g03A 134 9.25e+00 1qrjB a.73.1.1 60162 1fxjA 331 9.28e+00 1fwyA b.81.1.4,c.68.1.5 28062,34520 1bo1A 416 9.33e+00 1bo1A d.143.1.2 41591 1v9nA 360 9.45e+00 1opy 131 9.60e+00 1opy d.17.4.3 38113 1fwyA 331 9.61e+00 1fwyA b.81.1.4,c.68.1.5 28064,34522 1hniB 427 9.78e+00 1rthA e.8.1.2 43045 1kzfA 230 9.88e+00 d.108.1.3 73354 1qahA 136 1.01e+01 d.79.1.1 96338 1vlrA 350 1.01e+01 d.13.1.3,d.246.1.1 108860,108861 1swvA 267 1.02e+01 2fyxA 143 1.04e+01 1v74A 107 1.04e+01 d.243.1.1 100442 1pot 325 1.05e+01 1pot c.94.1.1 35807 1stzA 338 1.06e+01 a.4.5.51,d.110.2.3 106009,106010 2fp7B 172 1.10e+01 1xtmA 175 1.10e+01 1c1bB 440 1.10e+01 1rthA e.8.1.2 43077 1oi6A 205 1.12e+01 b.82.1.1 103940 1k4jA 230 1.13e+01 d.108.1.3 72057 1pc6A 146 1.14e+01 d.262.1.1 94430 1v4pA 157 1.17e+01 1zn6A 227 1.17e+01 1npk 154 1.18e+01 1npk d.58.6.1 39099 1pbjA 125 1.19e+01 d.37.1.1,d.37.1.1 94414,94415 1zbpA 273 1.21e+01 1y4tA 322 1.22e+01 1eetB 427 1.23e+01 1rthA e.8.1.2 43079 1ofdA 1520 1.23e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1iawA 317 1.24e+01 c.52.1.9 62126 1gl4B 98 1.24e+01 b.1.1.4 65288 1f3uB 171 1.24e+01 1f3uB b.65.1.1 27525 1kwhA 492 1.24e+01 c.94.1.1 68876 1ej2A 181 1.25e+01 1f9aA c.26.1.3 59414 1x8gA 227 1.26e+01 1ofnA 205 1.30e+01 b.82.1.1 92830 2bh7A 261 1.31e+01 1xfjA 261 1.31e+01 d.194.1.2 109585 2h0uA 217 1.33e+01 1mo7A 213 1.34e+01 d.220.1.1 85028 2cx9A 387 1.34e+01 1ztuA 341 1.35e+01 1yemA 179 1.39e+01 1xg2B 153 1.39e+01 1sqwA 188 1.39e+01 2b1xA 470 1.39e+01 1dloB 427 1.40e+01 1rthA e.8.1.2 43041 2fcjA 119 1.40e+01 1dryA 324 1.40e+01 1drtA b.82.2.2 28128 1ws9A 387 1.44e+01 1ss9A 311 1.48e+01 c.68.1.4 105978 1qs0B 338 1.50e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 1p0zA 131 1.50e+01 d.110.6.1 93882 1zmbA 290 1.53e+01 1drtA 324 1.54e+01 1drtA b.82.2.2 28130 1ipiA 123 1.54e+01 c.52.1.18 66255 1yg9A 330 1.56e+01 1befA 181 1.57e+01 1befA b.47.1.3 26419 1cx4A 305 1.59e+01 b.82.3.2,b.82.3.2 59099,59100 2d29A 387 1.60e+01 1m8jA 181 1.61e+01 c.26.1.3 84875 1itwA 741 1.62e+01 c.77.1.2 76793 2b9eA 303 1.63e+01 1rljA 139 1.65e+01 c.23.5.7 104983 1g4wR 383 1.65e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1fkoB 440 1.66e+01 1rthA e.8.1.2 43095 1ds1A 324 1.74e+01 1drtA b.82.2.2 28127 1nekA 588 1.80e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1ss4A 153 1.81e+01 d.32.1.6 105976 2fxuA 375 1.81e+01 1vrtA 560 1.83e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1har 216 1.84e+01 1rthA e.8.1.2 43025 1f1xA 322 1.86e+01 d.32.1.3,d.32.1.3 83208,83209 1nxmA 197 1.87e+01 b.82.1.1 86385 2cx1A 187 1.89e+01 1xgsA 295 1.91e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2b18A 164 1.92e+01 2essA 248 1.93e+01 1r5jA 337 1.93e+01 c.77.1.5 97097 1df9A 191 1.94e+01 1befA b.47.1.3 26420 1wuaA 375 1.98e+01 1lx7A 253 1.98e+01 c.56.2.1 74329 1rxyA 253 1.98e+01 c.56.2.1 98065 1f3fA 155 1.99e+01 1npk d.58.6.1 39101 1i3dA 146 1.99e+01 a.1.1.2 61587 1wr2A 238 2.00e+01 1o0xA 262 2.01e+01 d.127.1.1 80755 1d3yA 301 2.01e+01 1d3yA e.12.1.1 43252 1f1uA 323 2.04e+01 d.32.1.3,d.32.1.3 83200,83201 1j4aA 333 2.05e+01 c.2.1.4,c.23.12.1 71502,71503 1uae 419 2.08e+01 1uae d.68.2.2 39574 2g3kA 94 2.12e+01 1ev7B 317 2.13e+01 1ev7B c.52.1.9 33316 1yagA 375 2.15e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1rqlA 267 2.17e+01 c.108.1.3 97750 1gefA 123 2.18e+01 1gefA c.52.1.18 60465 1dloA 556 2.20e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 1hmvA 560 2.26e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1z2lA 423 2.26e+01 1a2n 419 2.27e+01 1uae d.68.2.2 39575 1zmaA 118 2.28e+01 1d4xA 375 2.30e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1v7oA 165 2.33e+01 d.67.1.2 100480 2bjrA 368 2.35e+01 2ffcA 353 2.38e+01 1qz5A 375 2.40e+01 c.55.1.1,c.55.1.1 96614,96615 1cvl 319 2.45e+01 1cvl c.69.1.18 34786 1lkdA 297 2.46e+01 d.32.1.3,d.32.1.3 78059,78060 1vmeA 410 2.47e+01 c.23.5.1,d.157.1.3 108893,108894 1wn5A 130 2.50e+01 1zs7A 190 2.51e+01 1mat 264 2.52e+01 1c24A d.127.1.1 41152 1j2jB 45 2.53e+01 a.7.8.1 84017 1lgtA 297 2.54e+01 d.32.1.3,d.32.1.3 77956,77957 1han 297 2.57e+01 1han d.32.1.3,d.32.1.3 38506,38507 1duxC 94 2.57e+01 1awcA a.4.5.21 16170 1fk9A 543 2.57e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 2bkaA 242 2.64e+01 2fi9A 128 2.65e+01 1wv9A 94 2.66e+01 1lcyA 325 2.66e+01 b.36.1.4,b.47.1.1 73834,73835 2bd0A 244 2.68e+01 1a7tA 232 2.71e+01 1a7tA d.157.1.1 42041 1rdfA 267 2.72e+01 c.108.1.3 104884 1llwA 1520 2.74e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1l3iA 192 2.79e+01 c.66.1.22 77676 2gi3A 476 2.79e+01 1hmvB 440 2.80e+01 1rthA e.8.1.2 43047 1wqaA 455 2.81e+01 2atzA 180 2.85e+01 1f8rA 498 2.87e+01 1f8rA c.3.1.2,d.16.1.5 30410,37974 1cl1A 395 2.88e+01 1cl2A c.67.1.3 34395 1mc0A 368 2.89e+01 d.110.2.1,d.110.2.1 78937,78938 1c5kA 439 2.91e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1jtdB 273 2.92e+01 b.69.5.2 67265 1rthA 560 2.93e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1st0A 337 2.93e+01 d.13.1.3,d.246.1.1 98979,98980 1y8qA 346 2.95e+01 1fkoA 543 3.06e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 1ezvE 185 3.08e+01 1rie b.33.1.1,f.23.12.1 59548,59549 1hybA 181 3.09e+01 1f9aA c.26.1.3 61399 1j6zA 376 3.09e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1mp4A 292 3.17e+01 c.68.1.6 79376 1r13A 148 3.18e+01 d.169.1.1,h.1.1.1 96782,96783 1rcwA 231 3.21e+01 a.132.1.4 97299 1ohpA 125 3.23e+01 1cl2A 395 3.23e+01 1cl2A c.67.1.3 34397 1i0vA 104 3.25e+01 9rnt d.1.1.4 36054 1eqnA 321 3.26e+01 1dd9A e.13.1.1 43256 1wmuA 141 3.30e+01 a.1.1.2 109416 1ejdA 419 3.32e+01 1uae d.68.2.2 39576 2a9gA 418 3.33e+01 1ocvA 125 3.36e+01 d.17.4.3 86810 1dd9A 338 3.36e+01 1dd9A e.13.1.1 43254 1eetA 557 3.37e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1pbgA 468 3.41e+01 1e70M c.1.8.4 28946 2hmiA 558 3.43e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 9rnt 104 3.43e+01 9rnt d.1.1.4 36055 1ib8A 164 3.45e+01 b.38.2.1,d.52.4.1 71168,71169 2tbs 222 3.47e+01 5ptp b.47.1.2 26009 1h5rA 293 3.51e+01 c.68.1.6 65623 1ift 263 3.53e+01 1mrj d.165.1.1 42211 1uq5A 263 3.56e+01 d.165.1.1 99778 8cho 125 3.56e+01 1opy d.17.4.3 38108 1n6zA 105 3.57e+01 d.263.1.1 85369 1dttA 560 3.58e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1j1nA 492 3.59e+01 c.94.1.1 83978 1zcoA 262 3.60e+01 1hj8A 222 3.65e+01 b.47.1.2 65844 1s14A 194 3.65e+01 d.122.1.2 98329 1tmxA 293 3.66e+01 1xttA 216 3.68e+01 1c0pA 363 3.71e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1m2xA 223 3.75e+01 d.157.1.1 84764 1atnA 373 3.76e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 1cqqA 180 3.78e+01 1cqqA b.47.1.4 26422 1fvgA 199 3.80e+01 1fvaA d.58.28.1 39408 1d3hA 367 3.82e+01 1d3gA c.1.4.1 28601 1fmaD 81 3.86e+01 1fmaD d.15.3.1 37643 1ht6A 405 3.87e+01 b.71.1.1,c.1.8.1 83629,83630 1qjgA 125 3.88e+01 1opy d.17.4.3 38102 1bcpB 199 3.89e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1fezA 256 3.89e+01 1fezA c.108.1.3 43343 1ejeA 192 3.91e+01 1ejeA b.45.1.2 25757 1wdyA 285 3.95e+01 1jqnA 883 3.95e+01 c.1.12.3 77159 3adk 195 3.97e+01 1zin c.37.1.1 31885 1xnzA 264 4.03e+01 1ug7A 128 4.04e+01 a.24.24.1 107824 1r8oA 96 4.13e+01 b.42.4.1 104852 1q9iA 571 4.16e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1znbA 232 4.17e+01 1a7tA d.157.1.1 42039 2bdrA 175 4.21e+01 1an7A 136 4.23e+01 1seiA d.140.1.1 41465 1fvaA 217 4.26e+01 1fvaA d.58.28.1 39409 1dxtB 147 4.29e+01 1abwA a.1.1.2 15450 1jnxX 214 4.33e+01 c.15.1.3,c.15.1.3 63201,63202 2g6tA 306 4.34e+01 1vypX 364 4.37e+01 c.1.4.1 108905 1z3eB 73 4.44e+01 1rxxA 421 4.46e+01 d.126.1.4 98061 1aop 497 4.59e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 2ax3A 502 4.61e+01 1cv2A 296 4.62e+01 1bn6A c.69.1.8 34680 2ggcA 263 4.63e+01 1zu0A 529 4.66e+01 1a01B 146 4.69e+01 1abwA a.1.1.2 15448 1t15A 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