# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 2es4D 332 2.48e-03 1jeqB 565 3.51e-01 1jeqB b.131.1.2 90368 c.62.1.4 90369 1jeyB 565 4.96e-01 1jeqB b.131.1.2 90372 c.62.1.4 90373 1ntyA 311 7.85e-01 a.87.1.1 103873 b.55.1.1 103874 1ecrA 309 8.42e-01 1ecrA e.2.1.1 42678 1ek9A 428 9.27e-01 1ek9A f.5.1.1 43809 1h4rA 314 1.03e+00 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1rhi1 288 1.70e+00 1pov1 2aaxA 275 1.78e+00 1vjvA 415 1.94e+00 d.3.1.9 108632 1aoa 275 2.06e+00 1aoa a.40.1.1 17396 a.40.1.1 17397 1cjcA 460 2.42e+00 1cjcA c.3.1.1 30319 c.4.1.1 30604 1mp1A 111 2.58e+00 a.188.1.1 91382 1v9dA 340 2.59e+00 a.207.1.1 100535 1xpcA 248 2.71e+00 1zkiA 133 2.78e+00 1dbhA 354 2.80e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1l2iA 261 2.89e+00 a.123.1.1 73503 1dg3A 592 2.90e+00 1dg3A a.114.1.1 19078 c.37.1.8 32153 2cq2A 114 3.18e+00 1us7B 265 3.41e+00 a.205.1.1 99858 2at9 247 3.80e+00 1c3wA f.13.1.1 43427 1q87A 221 3.81e+00 e.47.1.1 96192 1a6zA 275 3.92e+00 1agdA b.1.1.2 20781 d.19.1.1 38280 1m0kA 262 4.16e+00 f.13.1.1 78344 1ffkQ 119 4.43e+00 1ffkQ b.34.5.1 24605 1uruA 244 4.56e+00 h.4.14.1 99835 1kgbA 231 4.69e+00 f.13.1.1 68581 1kcmA 270 4.92e+00 d.129.3.4 72300 2cw9A 194 5.10e+00 1f5nA 592 5.25e+00 1dg3A a.114.1.1 19077 c.37.1.8 32152 1vkcA 158 5.30e+00 1jj2O 148 5.47e+00 1ffkM a.94.1.1 63100 1qu7A 227 5.55e+00 1qu7A h.4.5.1 45789 2al6A 375 5.84e+00 1kfuS 184 6.21e+00 a.39.1.8 68574 1f6dA 376 6.37e+00 1f6dA c.87.1.3 35467 3ertA 261 6.42e+00 3erdA a.123.1.1 19292 1wa5C 960 6.44e+00 1m16A 146 6.55e+00 b.42.1.1 91164 1vgvA 384 6.61e+00 c.87.1.3 100608 4rhv1 289 6.95e+00 1pov1 1dloB 427 6.99e+00 1rthA e.8.1.2 43041 1ab4 477 7.54e+00 1ab4 e.11.1.1 43251 1rg8A 146 7.64e+00 1hg4A 279 7.95e+00 1lbd a.123.1.1 19333 1vqoP 149 8.00e+00 1s72P 149 8.16e+00 a.94.1.1 105335 1ef1A 294 8.38e+00 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1il6 185 8.57e+00 1alu a.26.1.1 16827 1nrlA 316 8.71e+00 a.123.1.1 92091 1p32A 209 8.76e+00 1p32A d.25.1.1 38379 1mc0A 368 8.83e+00 d.110.2.1 78937 d.110.2.1 78938 1s6cA 183 9.12e+00 a.39.1.5 98594 1z5bA 469 9.18e+00 1fzrA 138 9.41e+00 1fzrA c.52.1.17 33336 1bjt 793 9.61e+00 1bjt e.11.1.1 43249 1f75A 249 1.01e+01 1f75A c.101.1.1 59662 2d1eA 248 1.04e+01 1y88A 199 1.05e+01 3erdA 261 1.05e+01 3erdA a.123.1.1 19293 1jsqA 582 1.05e+01 i.13.1.1 63270 1np6A 174 1.06e+01 c.37.1.10 85954 1jqzA 146 1.06e+01 b.42.1.1 67109 1qgvA 142 1.07e+01 1qgvA c.47.1.8 33056 1ahjB 212 1.08e+01 2ahjB b.34.4.4 24601 1b3qA 379 1.10e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1fpoA 171 1.14e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1sa3A 262 1.15e+01 c.52.1.23 105400 1a5j 110 1.16e+01 1a5j a.4.1.3 16043 a.4.1.3 16044 1o7iA 119 1.17e+01 b.40.4.3 86642 1mw5A 187 1.18e+01 d.259.1.1 91477 2aehA 369 1.18e+01 2d2sA 235 1.23e+01 1jt7A 146 1.24e+01 b.42.1.1 67255 2be4A 272 1.24e+01 2f1fA 164 1.24e+01 2bhmA 164 1.26e+01 1ujrA 110 1.29e+01 1v58A 241 1.31e+01 c.47.1.9 108371 d.17.3.1 108372 1pvc1 301 1.32e+01 1pov1 1ffkM 148 1.33e+01 1ffkM a.94.1.1 18740 2a3qA 170 1.43e+01 1r8iA 213 1.47e+01 a.8.7.1 97239 1ozjA 144 1.51e+01 d.164.1.1 93846 1m0dA 138 1.52e+01 c.52.1.17 74354 1a52A 258 1.52e+01 3erdA a.123.1.1 19296 1hw1A 239 1.54e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1h99A 224 1.58e+01 a.142.1.1 60814 a.142.1.1 60815 1pf4A 582 1.58e+01 c.37.1.12 88052 f.37.1.1 88053 1bc9 200 1.62e+01 1pbv a.118.3.1 19180 1sxjE 354 1.67e+01 a.80.1.1 106089 c.37.1.20 106090 1rkeA 262 1.67e+01 a.24.9.1 97608 a.24.9.1 97609 1l3lA 234 1.69e+01 a.4.6.2 73541 d.110.5.1 73542 1c1bB 440 1.70e+01 1rthA e.8.1.2 43077 1p63A 144 1.72e+01 b.42.1.1 94153 1hxs1 302 1.72e+01 2fg9A 178 1.73e+01 2cujA 108 1.75e+01 2bvlA 543 1.84e+01 1vpbA 451 1.84e+01 2b5eA 504 1.85e+01 1t01A 255 1.87e+01 a.24.9.1 106188 a.24.9.1 106189 1yt3A 375 1.87e+01 2aq4A 434 1.89e+01 1flmA 122 1.91e+01 1axj b.45.1.1 25747 1v88A 130 1.91e+01 b.55.1.1 108423 1zh5A 195 1.93e+01 1pl3A 186 1.96e+01 b.1.9.1 88158 2ao9A 155 1.97e+01 1zavA 180 1.99e+01 1hbzA 498 1.99e+01 1cf9A e.5.1.1 60937 1r85A 379 2.02e+01 c.1.8.3 104839 1bccE 196 2.04e+01 1rie b.33.1.1 24431 f.23.12.1 43699 1h6hA 143 2.05e+01 d.189.1.1 65681 1eta1 127 2.07e+01 1etb1 2ahmA 88 2.12e+01 1zyiA 171 2.13e+01 1p2fA 220 2.14e+01 a.4.6.1 87720 c.23.1.1 87721 1qasA 622 2.15e+01 1djxB a.39.1.7 17340 b.7.1.1 23157 c.1.18.1 29585 1y0gA 191 2.16e+01 1alu 186 2.16e+01 1alu a.26.1.1 16826 1d7cA 190 2.20e+01 1d7bA b.1.9.1 22309 1k94A 165 2.20e+01 a.39.1.8 68333 2irfG 113 2.20e+01 2irfG a.4.5.23 16185 1h2vC 771 2.24e+01 a.118.1.14 76592 a.118.1.14 76593 a.118.1.14 76594 1ekeA 230 2.26e+01 1ekeA c.55.3.1 33572 1gm5A 780 2.27e+01 a.24.21.1 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1xngA 268 2.29e+01 1m7sA 484 2.29e+01 e.5.1.1 74574 1mixA 206 2.30e+01 a.11.2.1 79166 b.55.1.5 79167 1msc 129 2.31e+01 1msc d.85.1.1 40039 1yq2A 1024 2.33e+01 1o7kA 131 2.37e+01 d.189.1.1 81144 1tovA 98 2.38e+01 b.34.10.1 107179 1w36B 1180 2.39e+01 1d7bA 186 2.41e+01 1d7bA b.1.9.1 22307 1qatB 622 2.42e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1c3wA 222 2.51e+01 1c3wA f.13.1.1 43405 1ttbA 127 2.53e+01 1etb1 b.3.4.1 22543 1sr7A 259 2.54e+01 a.123.1.1 105957 2ew2A 316 2.56e+01 1m13A 316 2.57e+01 a.123.1.1 84746 2afgA 140 2.59e+01 1bfg b.42.1.1 25514 1gweA 503 2.60e+01 e.5.1.1 70667 1fouA 309 2.63e+01 1fouA e.27.1.1 43364 1qgbA 93 2.64e+01 1qgbA g.27.1.1 44952 g.27.1.1 44953 1axj 122 2.65e+01 1axj b.45.1.1 25749 1mlvA 444 2.67e+01 a.166.1.1 79283 b.85.7.3 79284 1w3oA 216 2.77e+01 1h5wA 309 2.77e+01 e.27.1.1 65635 1c4oA 664 2.80e+01 1d2mA c.37.1.19 32415 c.37.1.19 32416 1dn1A 594 2.82e+01 1dn1A e.25.1.1 43357 1zt2B 212 2.83e+01 2fh5A 185 2.85e+01 1uurA 473 2.85e+01 a.47.1.1 100016 b.2.5.5 100017 d.93.1.1 100018 1pbk 116 2.85e+01 1fkj d.26.1.1 38428 1sskA 158 2.86e+01 b.148.1.1 105986 1psuA 140 2.89e+01 d.38.1.5 88285 1fewA 184 2.89e+01 1fewA a.7.4.1 16334 1u4qA 322 2.91e+01 1j27A 102 2.91e+01 d.58.50.1 90778 2pabA 127 2.93e+01 1etb1 b.3.4.1 22597 2ahjB 212 2.95e+01 2ahjB b.34.4.4 24599 1q8iA 783 2.96e+01 c.55.3.5 96208 e.8.1.1 96209 1lrv 244 3.01e+01 1lrv a.118.1.5 19146 1pbwA 216 3.04e+01 1pbwA a.116.1.1 19103 2glsA 470 3.05e+01 1lgr d.15.9.1 37851 d.128.1.1 41181 1jmuB 666 3.05e+01 2cz1B 212 3.10e+01 1hizA 379 3.11e+01 c.1.8.3 65841 1ydiA 263 3.15e+01 1vqzA 341 3.17e+01 1a28A 256 3.17e+01 1a28A a.123.1.1 19290 1zvzA 279 3.20e+01 1w5tA 412 3.24e+01 1ykdA 398 3.25e+01 1etb1 127 3.31e+01 1etb1 1xk7A 408 3.31e+01 1wer 334 3.31e+01 1wer a.116.1.2 19108 2bcmA 165 3.34e+01 1s3zA 165 3.37e+01 d.108.1.1 105250 1al21 302 3.42e+01 1pov1 1wovA 250 3.45e+01 1nox 205 3.46e+01 1nox d.90.1.1 40242 2c43A 323 3.48e+01 1fyeA 229 3.50e+01 1fyeA c.23.16.4 31477 1lnqA 336 3.54e+01 c.2.1.9 74049 f.14.1.1 74050 1lqvA 193 3.58e+01 d.19.1.1 74206 1h9sA 140 3.59e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 2feaA 236 3.62e+01 2fnaA 357 3.63e+01 1oj5A 132 3.63e+01 d.110.3.8 93087 1qipA 183 3.64e+01 1qipA d.32.1.1 38470 1ss4A 153 3.67e+01 d.32.1.6 105976 1ymtA 246 3.69e+01 1p0yA 444 3.72e+01 a.166.1.1 87654 b.85.7.3 87655 1qjtA 99 3.78e+01 1eh2 a.39.1.6 17335 2b5gA 171 3.88e+01 1jl0A 334 3.89e+01 1jenA d.156.1.1 63155 2fs2A 151 3.89e+01 1ofcX 304 3.92e+01 a.4.1.3 92826 a.4.1.13 92827 a.187.1.1 92828 1u7lA 392 3.93e+01 1sqsA 242 3.95e+01 c.23.5.5 98968 1u9aA 160 3.96e+01 1u9aA d.20.1.1 38333 2b9hA 353 3.96e+01 1yw3A 208 4.00e+01