# 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 1mk4A 157 6.56e-03 d.108.1.1 84979 1y0zA 330 1.04e-01 1q44A 326 1.60e-01 c.37.1.5 95779 3pfk 319 2.71e-01 3pfk c.89.1.1 35581 1kuxA 207 2.85e-01 d.108.1.1 73021 6pfkA 319 3.63e-01 3pfk c.89.1.1 35583 4pfk 319 4.17e-01 3pfk c.89.1.1 35582 1ugmA 125 4.25e-01 d.15.1.3 107827 1hs6A 611 5.85e-01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1cjwA 166 6.88e-01 1cjwA d.108.1.1 40818 1twyA 290 1.44e+00 1yozA 116 1.50e+00 1b04A 318 1.55e+00 1b04A d.142.2.2 41579 1vqzA 341 1.67e+00 1wwzA 159 1.84e+00 3crxA 343 1.97e+00 4crxA a.60.9.1,d.163.1.1 18101,42161 1vpqA 273 2.01e+00 1iu9A 111 2.16e+00 c.78.2.1 90694 1tgoA 773 2.33e+00 1tgoA c.55.3.5,e.8.1.1 33721,43010 2aqlA 173 2.69e+00 2arhA 203 2.72e+00 2fueA 262 2.76e+00 1ujkA 147 2.96e+00 a.118.9.2 99457 1cqqA 180 3.11e+00 1cqqA b.47.1.4 26422 1qumA 285 3.15e+00 1qumA c.1.15.1 29393 1wq6A 72 3.36e+00 2f5tX 233 3.36e+00 1zuhA 168 3.68e+00 1nu5A 370 3.97e+00 c.1.11.2,d.54.1.1 92183,92184 1xt8A 292 4.20e+00 4crxA 322 4.22e+00 4crxA a.60.9.1,d.163.1.1 18095,42155 1ln1A 214 4.28e+00 d.129.3.2 74038 1avoA 60 4.33e+00 1avoA a.24.8.1 16619 1nksA 194 4.41e+00 1nksA c.37.1.1 31886 1dc1A 323 4.89e+00 1dc1A c.52.1.11 33321 1d3uB 201 5.10e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 2faoA 309 5.30e+00 1uliB 187 5.31e+00 d.17.4.4 107923 2ge3A 170 5.33e+00 2d4pA 141 5.72e+00 2h3bA 494 5.93e+00 1qqcA 773 6.16e+00 1tgoA c.55.3.5,e.8.1.1 33724,43013 1xo0A 324 6.24e+00 1ccwA 137 6.29e+00 1be1 c.23.6.1 31238 1jkmB 361 6.39e+00 1jkmA c.69.1.2 34634 1np6A 174 6.66e+00 c.37.1.10 85954 1jwgA 147 7.46e+00 a.118.9.2 71911 1y8aA 332 7.77e+00 1qtwA 285 7.84e+00 1qumA c.1.15.1 29392 1e5dA 402 7.85e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1jkmA 358 8.37e+00 1jkmA c.69.1.2 34633 1d7cA 190 8.92e+00 1d7bA b.1.9.1 22309 1yvhA 329 9.22e+00 1sziA 247 9.23e+00 a.24.23.1 106159 1qwgA 251 9.43e+00 c.1.27.1 96473 1n81A 186 9.57e+00 a.185.1.1 85388 2fe7A 166 9.60e+00 1qpbA 563 9.66e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1crxA 322 9.72e+00 4crxA a.60.9.1,d.163.1.1 18097,42157 1d7bA 186 9.73e+00 1d7bA b.1.9.1 22307 1pydA 556 9.84e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1pvdA 537 9.93e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 2aq9A 262 1.02e+01 1ngkA 128 1.03e+01 a.1.1.1 85673 1d9eA 284 1.05e+01 1d9eA c.1.10.4 29195 1wolA 122 1.10e+01 1b6bA 174 1.13e+01 1cjwA d.108.1.1 40819 1mu5A 471 1.16e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1gkuB 1054 1.21e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1lxa 262 1.23e+01 1lxa b.81.1.1 28052 1g61A 228 1.24e+01 1g61A d.126.1.1 41126 1pfxC 235 1.24e+01 5ptp b.47.1.2 26353 1q2wA 308 1.25e+01 b.47.1.4 88355 2dpmA 284 1.28e+01 2dpmA c.66.1.28 34246 1po5A 476 1.30e+01 a.104.1.1 94963 1gg3A 279 1.31e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1jflA 228 1.32e+01 c.78.2.1,c.78.2.1 71656,71657 1s6cA 183 1.33e+01 a.39.1.5 98594 1ujcA 161 1.35e+01 2ctoA 93 1.36e+01 1s21A 206 1.38e+01 d.166.1.4 105222 1si2A 149 1.40e+01 b.34.14.1 105569 1gcoA 261 1.40e+01 1ybvA c.2.1.2 29884 1kbuA 349 1.41e+01 a.60.9.1,d.163.1.1 72284,72285 2fg9A 178 1.41e+01 1m0wA 491 1.44e+01 c.30.1.4,d.142.1.6 78363,78364 2amyA 246 1.50e+01 2c5kT 95 1.51e+01 1zkrA 153 1.53e+01 1ge9A 184 1.53e+01 1dd5A d.67.3.1 60463 1rpjA 288 1.53e+01 2dri c.93.1.1 35656 1geeA 261 1.57e+01 c.2.1.2 90509 1pkp 150 1.59e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1z5bA 469 1.61e+01 1ipwA 175 1.63e+01 2prd b.40.5.1 25427 1gegA 256 1.63e+01 1ybvA c.2.1.2 29888 2a1iA 146 1.65e+01 1o5uA 101 1.65e+01 b.82.1.8 92518 1gudA 288 1.67e+01 c.93.1.1 83326 2g7jA 124 1.67e+01 2cobA 70 1.68e+01 1aoiB 87 1.73e+01 1aoiB a.22.1.1 16470 1xahA 354 1.73e+01 2hvm 273 1.73e+01 1cnv c.1.8.5 28985 1kqzA 273 1.85e+01 c.1.8.5 68844 1qhdA 398 1.87e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1l3iA 192 1.91e+01 c.66.1.22 77676 1oxkB 134 1.91e+01 c.23.1.1 93691 2gwhA 298 1.96e+01 2bbhA 269 1.96e+01 1rdr 461 1.97e+01 1rdr e.8.1.4 43116 2ex5A 207 1.97e+01 1q8dA 108 1.98e+01 a.228.1.1 104554 1l1nA 183 2.05e+01 b.47.1.4 73476 1zxxA 319 2.07e+01 1no5A 114 2.13e+01 d.218.1.5 92014 1t6gC 184 2.16e+01 b.29.1.11 106569 1ton 235 2.19e+01 5ptp b.47.1.2 26307 3minB 522 2.20e+01 1qguB c.92.2.3 35606 1ro5A 201 2.22e+01 d.108.1.3 105023 1ghhA 81 2.24e+01 1ghhA d.57.1.1 38940 1u20A 212 2.29e+01 1syyA 346 2.32e+01 a.25.1.2 106126 1x1gA 129 2.33e+01 1q7lA 198 2.34e+01 c.56.5.4 96044 2aotA 292 2.36e+01 1p3qQ 54 2.37e+01 a.5.2.4 87748 1kfiA 572 2.40e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 1w99A 558 2.40e+01 2fox 138 2.44e+01 5nul c.23.5.1 31197 1w9gA 104 2.45e+01 1bk1 184 2.51e+01 1axkA b.29.1.11 24340 1aoiF 87 2.52e+01 1aoiB a.22.1.1 16471 2fp8A 322 2.52e+01 1odeA 122 2.54e+01 d.79.1.2 86846 2amdA 311 2.54e+01 1kqyA 273 2.61e+01 c.1.8.5 68843 1kx5B 102 2.61e+01 a.22.1.1 77594 1tzyD 103 2.64e+01 a.22.1.1 107533 1ufyA 122 2.65e+01 d.79.1.2 88489 2gnoA 305 2.77e+01 1kkhA 317 2.78e+01 d.14.1.5,d.58.26.3 72645,72646 1r4kA 169 2.79e+01 b.34.14.1 96997 1gvzA 237 2.80e+01 b.47.1.2 76360 1wz7A 111 2.84e+01 1wzcA 249 2.85e+01 1m1nB 522 2.89e+01 c.92.2.3 78418 1nycA 111 2.89e+01 b.61.2.2 92336 1id3B 102 2.91e+01 a.22.1.1 66113 1ki9A 192 2.92e+01 c.37.1.1 84404 2a5kA 307 2.95e+01 1qhtA 775 2.98e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1xauA 122 3.03e+01 1x59A 73 3.07e+01 1wmiB 67 3.11e+01 1g7vA 284 3.13e+01 1d9eA c.1.10.4 60335 2fvx 138 3.18e+01 5nul c.23.5.1 31200 1cnv 299 3.18e+01 1cnv c.1.8.5 28989 1aol 228 3.20e+01 1aol b.20.1.1 23840 1lgtA 297 3.22e+01 d.32.1.3,d.32.1.3 77956,77957 2bw3A 534 3.22e+01 1mkmA 249 3.25e+01 a.4.5.33,d.110.2.2 79242,79243 2cblA 305 3.26e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1ehiA 377 3.31e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1zckA 154 3.31e+01 1z8sA 146 3.38e+01 3nll 138 3.41e+01 5nul c.23.5.1 31206 1c9bA 207 3.41e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 5nul 138 3.42e+01 5nul c.23.5.1 31191 1han 297 3.43e+01 1han d.32.1.3,d.32.1.3 38506,38507 1wj7A 104 3.45e+01 1idy 54 3.55e+01 1a5j a.4.1.3 16034 1kw3B 292 3.57e+01 d.32.1.3,d.32.1.3 77549,77550 1olrA 224 3.62e+01 b.29.1.11 93330 1s0pA 176 3.72e+01 a.192.1.1 98300 1j0hA 588 3.75e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1pcp 106 3.79e+01 2pspA g.16.1.1,g.16.1.1 44742,44743 2minB 522 3.82e+01 1qguB c.92.2.3 35610 1kn1A 160 3.83e+01 a.1.1.3 77455 6rlxB 28 3.84e+01 g.1.1.1 43988 1hssA 124 3.89e+01 1bea a.52.1.2 17819 1hq3D 103 3.89e+01 1aoiB a.22.1.1 16464 1a12A 413 3.93e+01 1a12A b.69.5.1 27663 1qrjB 199 3.97e+01 1qrjB a.28.3.1 16952 1g1eB 89 3.97e+01 1g1eB a.59.1.1 17931 1y9zA 441 3.97e+01 1qckA 89 3.98e+01 1qckA a.60.5.1 17976 1rxdA 159 4.13e+01 1vk1A 242 4.20e+01 d.268.1.2 108634 1uuyA 167 4.21e+01 c.57.1.1 108059 1lkdA 297 4.24e+01 d.32.1.3,d.32.1.3 78059,78060 1v6cA 441 4.30e+01 2sfa 191 4.32e+01 1qq4A b.47.1.1 25815 1jqeA 292 4.35e+01 c.66.1.19 71789 1g03A 134 4.35e+01 1qrjB a.73.1.1 60162 1ji2A 585 4.35e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 2f1wA 158 4.36e+01 1b1a 137 4.36e+01 1be1 c.23.6.1 31242 1fmjA 351 4.36e+01 c.37.1.5 59879 1yz4A 160 4.43e+01 1x2iA 75 4.44e+01 1tiyA 164 4.47e+01 c.97.1.2 107012 1l8wA 348 4.52e+01 a.154.1.1 73704 1s3zA 165 4.59e+01 d.108.1.1 105250 1volA 204 4.63e+01 1tfb a.74.1.2,a.74.1.2 18370,18371 1t6cA 315 4.74e+01 c.55.1.8,c.55.1.8 106558,106559 1anb 223 4.77e+01 5ptp b.47.1.2 25998 1bf2 750 4.82e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1f7zA 233 4.83e+01 5ptp b.47.1.2 59681 1gw5S 142 4.85e+01 d.110.4.2 70633 1lucA 355 4.93e+01 1lucA c.1.16.1 29547 1egaA 301 4.94e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1vrmA 325 4.97e+01 1biqA 375 4.99e+01 1xikA a.25.1.2 16786 1enxA 190 5.00e+01 1axkA b.29.1.11 24325 2fbiA 142 5.02e+01 1pfkA 320 5.02e+01 3pfk c.89.1.1 35575 1amhA 223 5.03e+01 5ptp b.47.1.2 25994 1b47A 304 5.08e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 2db2A 119 5.10e+01 1q53A 112 5.14e+01 d.58.4.4 95858 1y13A 181 5.17e+01 1anc 223 5.20e+01 5ptp b.47.1.2 25982 1dhy 292 5.22e+01 1han d.32.1.3,d.32.1.3 38504,38505 1y7pA 223 5.24e+01 2b9eA 303 5.26e+01 1mn3A 54 5.35e+01 a.5.2.4 85024 1gp6A 356 5.35e+01 b.82.2.1 65441 1ocsA 162 5.36e+01 d.189.1.1 92776 1puoA 170 5.36e+01 a.101.1.1,a.101.1.1 95134,95135 2fswA 107 5.40e+01 1bh9B 89 5.43e+01 1bh9B a.22.1.3 16485 2fvgA 340 5.43e+01 1ru8A 232 5.46e+01 c.26.2.1 97849 1xat 212 5.47e+01 2xat b.81.1.3 28059 1mqoA 227 5.50e+01 d.157.1.1 103846 2irfG 113 5.52e+01 2irfG a.4.5.23 16185 1wxdA 263 5.57e+01 2hbg 147 5.60e+01 2hbg a.1.1.2 15014 1lu4A 136 5.64e+01 c.47.1.10 91124 1i40A 175 5.64e+01 b.40.5.1 66024 1xx0A 127 5.72e+01 1nox 205 5.74e+01 1nox d.90.1.1 40242 1yspA 181 5.75e+01 1sa3A 262 5.75e+01 c.52.1.23 105400 1ra6A 461 5.85e+01 e.8.1.4 104879 1ynuA 473 5.88e+01 1bqg 451 5.91e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 2occI 73 5.92e+01 2occI f.23.3.1 43523 1ppfE 218 5.97e+01 1a7s b.47.1.2 26234 1yprA 125 5.98e+01 3nul d.110.1.1 40888 1xypA 190 5.99e+01 1axkA b.29.1.11 24327 1okiA 210 6.02e+01 b.11.1.1,b.11.1.1 93255,93256 1and 223 6.04e+01 5ptp b.47.1.2 25985 1itkA 731 6.14e+01 a.93.1.3,a.93.1.3 71417,71418 2plc 274 6.16e+01 2plc c.1.18.2 29614 1vig 71 6.19e+01 1vih d.51.1.1 38806 1sgpE 185 6.19e+01 1qq4A b.47.1.1 25816 1paqA 189 6.24e+01 a.118.1.14 94413 1gp4A 356 6.27e+01 b.82.2.1 65439 1alvA 173 6.39e+01 1alvA a.39.1.8 17370 2bl0C 142 6.40e+01 1dt6A 473 6.43e+01 1dt6A a.104.1.1 18977 1xszA 356 6.43e+01 7odcA 424 6.43e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1b8gA 429 6.56e+01 1b8gA c.67.1.4 34499 1xyn 178 6.58e+01 1axkA b.29.1.11 24322 1zatA 250 6.60e+01 1vehA 92 6.61e+01 1f44A 324 6.62e+01 a.60.9.1,d.163.1.1 64982,64983 1eetA 557 6.63e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1ci4A 89 6.67e+01 1qckA a.60.5.1 17970 1pu1A 94 6.77e+01 d.266.1.1 104307 2xat 212 6.79e+01 2xat b.81.1.3 28058 1ukxA 137 6.81e+01 d.20.1.3 107919 1uehA 253 6.81e+01 c.101.1.1 99259 1fsd 28 6.83e+01 k.14.1.1 46439 2b82A 211 6.85e+01 1rmwA 212 6.86e+01 1in0A 163 6.88e+01 d.58.49.1,d.58.49.1 83694,83695 1wekA 217 6.88e+01 1zm0A 114 6.89e+01 1bvzA 585 6.99e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 1v3vA 333 7.02e+01 b.35.1.2,c.2.1.1 108345,108346 2sgpE 185 7.05e+01 1qq4A b.47.1.1 25825 1hjzA 192 7.06e+01 c.50.1.2 83520 1yarH 217 7.10e+01 1v7oA 165 7.16e+01 d.67.1.2 100480 1opjA 293 7.18e+01 d.144.1.7 87230 2bc2A 227 7.19e+01 1a7tA d.157.1.1 42031 1b0fA 218 7.21e+01 1a7s b.47.1.2 26237 1wlfA 179 7.23e+01 b.52.2.3,d.31.1.1 109396,109397 1v54I 73 7.24e+01 f.23.3.1 100330 1ym5A 300 7.24e+01 1sf9A 128 7.30e+01 b.34.15.1 98831 1nzaA 103 7.33e+01 d.58.5.2 86444 1otvA 259 7.35e+01 a.132.1.4 93526 1zfpE 98 7.41e+01 1griA d.93.1.1 40465 1fqtA 112 7.47e+01 1fqtA b.33.1.1 24441 1szwA 379 7.47e+01 d.265.1.4 99047 1k07A 263 7.47e+01 d.157.1.1 77218 2pf1 156 7.48e+01 5hpgA g.14.1.1,g.32.1.1 44652,44968 2aa1A 144 7.49e+01 1n8nA 212 7.54e+01 c.108.1.12 91706 1zchA 255 7.55e+01 1js8A 394 7.57e+01 a.86.1.1,b.112.1.1 67219,67220 1m2xA 223 7.63e+01 d.157.1.1 84764 1aod 289 7.66e+01 2plc c.1.18.2 29615 2b67A 204 7.69e+01 2cx1A 187 7.71e+01 2cy0A 263 7.72e+01 1ggvA 232 7.75e+01 1din c.69.1.9 34683 1vih 71 7.81e+01 1vih d.51.1.1 38807 2ah5A 210 7.85e+01 1nsyA 271 7.87e+01 2nsyA c.26.2.1 31614 2d5cA 263 7.92e+01 1wkqA 164 7.93e+01 c.97.1.2 109393 1glv 303 7.95e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1x24A 180 7.96e+01 1dpo 223 7.99e+01 5ptp b.47.1.2 25975 2f5xA 312 8.04e+01 1q4rA 112 8.07e+01 d.58.4.4 95823 1z3eB 73 8.11e+01 1ryaA 160 8.12e+01 d.113.1.5 105122 1jyrA 96 8.15e+01 d.93.1.1 71969 3nul 130 8.21e+01 3nul d.110.1.1 40891 1zmtA 254 8.24e+01 2abqA 306 8.26e+01 1jrjA 39 8.27e+01 j.6.1.1 67135 1a0k 131 8.29e+01 3nul d.110.1.1 40892 1pwxA 254 8.30e+01 c.2.1.2 95262 1e8uA 454 8.31e+01 1e8tA b.68.1.1 59389 1pmaP 211 8.32e+01 1pmaP d.153.1.4 41863 1jihA 531 8.35e+01 d.240.1.1,e.8.1.7 90374,90375 1m6yA 301 8.39e+01 a.60.13.1,c.66.1.23 78716,78717 1nq7A 244 8.43e+01 a.123.1.1 92047 1zvdA 380 8.43e+01 1if1A 113 8.44e+01 2irfG a.4.5.23 16183 1eztA 166 8.47e+01 1agrE a.91.1.1 18541 1tfb 208 8.50e+01 1tfb a.74.1.2,a.74.1.2 18382,18383 1ald 363 8.58e+01 1fbaA c.1.10.1 29100 2blfB 81 8.59e+01 2b1xA 470 8.62e+01 1z9hA 290 8.64e+01 1afrA 345 8.65e+01 1afrA a.25.1.2 16805 1ffkJ 164 8.72e+01 1ffkJ c.12.1.1 30880 2be4A 272 8.76e+01 2cciF 30 8.81e+01 1tqhA 247 8.85e+01 c.69.1.29 107225 1fgkA 310 8.91e+01 1fgkA d.144.1.7 41693 1ewxA 146 8.99e+01 1ewxA c.47.1.10 33062 1r0pA 312 9.00e+01 d.144.1.7 96734