# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1efcA 393 3.09e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1d2eA 397 2.05e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1jenA 267 3.27e-01 1jenA 1b7fA 168 3.86e-01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1theA 260 7.08e-01 1theB d.3.1.1 37056 1efuA 385 7.31e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1hn0A 1021 8.01e-01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1theB 260 8.26e-01 1theB d.3.1.1 37057 1eylA 186 1.13e+00 1wba b.42.4.1 25593 1dq3A 454 1.17e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1kk1A 410 1.27e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1fxlA 167 1.64e+00 1b7fA d.58.7.1,d.58.7.1 39183,39184 2c78A 405 1.69e+00 1bndB 119 1.90e+00 1bndA g.17.1.3 44794 1vr8A 142 1.90e+00 2ghpA 292 1.91e+00 1b8mA 119 2.02e+00 1bndA g.17.1.3 44797 1nkgA 508 2.03e+00 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 1un3A 123 2.22e+00 d.5.1.1 99646 1csbB 205 2.23e+00 1theB 1gmyA 261 2.26e+00 d.3.1.1 76236 1ha3A 405 2.65e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1exmA 405 2.93e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1xfsA 178 3.21e+00 d.129.3.5 109589 1kskA 234 3.42e+00 d.66.1.5,d.265.1.3 72920,90389 1eft 405 3.57e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1x8hA 228 3.63e+00 1ivg 388 3.65e+00 2qwc b.68.1.1 27578 1j9bA 141 4.33e+00 c.47.1.12 66459 2cokA 113 4.58e+00 1ux2A 212 4.62e+00 b.96.1.1 100132 1mgtA 174 4.66e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1s3cA 141 4.85e+00 1go3E 187 4.92e+00 b.40.4.5,d.230.1.1 83054,83055 3sxlA 184 5.70e+00 1b7fA d.58.7.1,d.58.7.1 39173,39174 1v8hA 107 6.04e+00 1uv6A 210 6.17e+00 b.96.1.1 100030 2fhxA 246 6.24e+00 1bndA 119 6.34e+00 1bndA g.17.1.3 44793 1s6lA 212 6.39e+00 1jj2E 177 6.39e+00 1ffk1 d.141.1.1,d.141.1.1 63089,63090 2bibA 547 6.39e+00 2cxhA 217 6.43e+00 2d4qA 257 6.60e+00 1h2vZ 156 6.64e+00 d.58.7.1 76595 2cayA 145 6.73e+00 1uw6A 211 6.97e+00 b.96.1.1 100079 1rwhA 757 7.18e+00 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1avbA 226 7.57e+00 1led b.29.1.1 24158 2breA 219 7.73e+00 1u8sA 192 7.78e+00 d.58.18.5,d.58.18.5 107737,107738 1jhfA 202 7.94e+00 a.4.5.2,b.87.1.1 63057,63058 1jjeA 222 8.10e+00 1a7tA d.157.1.1 63117 1jjtA 228 8.62e+00 1a7tA d.157.1.1 63139 1wh0A 134 8.93e+00 1q79A 514 9.04e+00 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 2ewcA 126 9.14e+00 1ah6 220 9.18e+00 1yer d.122.1.1 41094 1amw 214 9.19e+00 1yer d.122.1.1 41093 2cwsA 237 9.32e+00 1vqoE 178 9.32e+00 1b8kA 119 9.35e+00 1bndA g.17.1.3 44795 1jl0A 334 9.70e+00 1jenA d.156.1.1 63155 1r6vA 671 9.83e+00 1wdcC 156 9.83e+00 1wdcC a.39.1.5 17317 1lylA 504 9.88e+00 1lylA b.40.4.1,d.104.1.1 25261,40717 1aoiB 87 1.04e+01 1aoiB a.22.1.1 16470 2aneA 125 1.06e+01 1v1pA 211 1.10e+01 b.40.2.2,d.15.6.1 108268,108269 1k59A 123 1.10e+01 d.5.1.1 72073 1rthA 560 1.13e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1x8gA 227 1.13e+01 1pmzA 86 1.14e+01 a.39.1.10 104195 2fcbA 173 1.14e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1iloA 77 1.15e+01 c.47.1.1 66205 1hnf 182 1.17e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1m2xA 223 1.18e+01 d.157.1.1 84764 1z8gA 372 1.18e+01 1louA 101 1.19e+01 1ris d.58.14.1 39323 1qlpA 394 1.20e+01 1ovaA e.1.1.1 42628 1dd6A 228 1.21e+01 1a7tA d.157.1.1 42054 1aoiF 87 1.22e+01 1aoiB a.22.1.1 16471 1bmc 221 1.22e+01 1a7tA d.157.1.1 42038 1h9dA 134 1.24e+01 1cmoA b.2.5.6 60821 1ov3A 138 1.27e+01 b.34.2.1,b.34.2.1 87451,87452 1b1iA 123 1.28e+01 7rsa d.5.1.1 37295 1hq3D 103 1.29e+01 1aoiB a.22.1.1 16464 1id3B 102 1.32e+01 a.22.1.1 66113 1v7oA 165 1.34e+01 d.67.1.2 100480 1r8nA 185 1.35e+01 b.42.4.1 104851 1aipE 405 1.38e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1a4h 230 1.38e+01 1yer d.122.1.1 41099 1hbyA 123 1.39e+01 7rsa d.5.1.1 60936 1tif 78 1.42e+01 1tif d.15.8.1 37836 1v4pA 157 1.43e+01 1ux6A 350 1.45e+01 b.29.1.16,g.75.1.1 100145,100146 1hvc 203 1.48e+01 1hvc b.50.1.1 26614 1i9bA 217 1.49e+01 1i9bA b.96.1.1 62084 1konA 249 1.51e+01 e.39.1.1 72823 1vioA 243 1.52e+01 d.265.1.3,d.66.1.5 100762,100763 1tzyD 103 1.53e+01 a.22.1.1 107533 1xuvA 178 1.54e+01 1jmoA 480 1.54e+01 e.1.1.1 77138 1io1A 398 1.55e+01 1io1A e.32.1.1 62611 1ru8A 232 1.56e+01 c.26.2.1 97849 1btgA 110 1.59e+01 1bndA g.17.1.3 44802 1h6kX 97 1.61e+01 d.58.7.1 60684 1s72E 178 1.63e+01 d.141.1.1,d.141.1.1 105323,105324 1kx5B 102 1.65e+01 a.22.1.1 77594 1gbg 214 1.66e+01 1axkA b.29.1.2 24171 1zljA 78 1.66e+01 1ris 101 1.69e+01 1ris d.58.14.1 39314 1am1 213 1.70e+01 1yer d.122.1.1 41095 2bynA 227 1.70e+01 1hup 141 1.74e+01 1rtm1 d.169.1.1,h.1.1.1 42354,45422 1wu7A 434 1.76e+01 1l0qA 391 1.84e+01 b.1.3.1,b.69.2.3 77644,77645 2bypA 214 1.88e+01 2fomB 185 1.89e+01 1yqfA 203 1.90e+01 1z6bA 154 1.95e+01 1zvnA 99 1.95e+01 1fxzA 476 1.96e+01 b.82.1.2,b.82.1.2 65059,65060 1qmyA 167 2.00e+01 1qmyA d.3.1.2 37094 1agi 125 2.02e+01 7rsa d.5.1.1 37303 2bc2B 227 2.03e+01 1a7tA d.157.1.1 42032 2gfaA 119 2.07e+01 1b77A 228 2.10e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1rk8A 165 2.10e+01 d.58.7.1 97603 1tjxA 159 2.18e+01 1opoA 348 2.20e+01 b.121.4.7 87240 1e8yA 966 2.22e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1xovA 326 2.23e+01 1b1jA 123 2.27e+01 7rsa d.5.1.1 37298 2ca6A 386 2.31e+01 1cmoA 127 2.32e+01 1cmoA b.2.5.6 22462 1f5aA 513 2.32e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1yhpA 212 2.32e+01 1dzaA 129 2.35e+01 7rsa d.5.1.1 37275 2scuB 388 2.37e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1j58A 385 2.37e+01 b.82.1.2 71531 2g7jA 124 2.41e+01 1s0uA 408 2.43e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1xfxO 149 2.46e+01 1b1eA 123 2.46e+01 7rsa d.5.1.1 37300 1a4pA 96 2.46e+01 1b4cA a.39.1.2 17176 1l7bA 92 2.50e+01 c.15.1.2 91053 1cll 148 2.50e+01 1cll a.39.1.5 17263 1gxuA 91 2.52e+01 d.58.10.1 76378 1zzcA 198 2.59e+01 2brcA 214 2.63e+01 2g76A 335 2.67e+01 1u69A 163 2.67e+01 d.32.1.7 107699 1in0A 163 2.68e+01 d.58.49.1,d.58.49.1 83694,83695 1osa 148 2.71e+01 1cll a.39.1.5 17300 1vr5A 547 2.73e+01 1bet 107 2.74e+01 1bndA g.17.1.3 44801 1vfgA 390 2.76e+01 a.173.1.1,d.218.1.4 108570,108571 1g4yR 148 2.76e+01 1cll a.39.1.5 60252 1pg6A 243 2.76e+01 b.82.5.2 94673 3cln 148 2.82e+01 1cll a.39.1.5 17286 1qa9A 102 2.84e+01 1qa9A b.1.1.1 19742 1xjvA 294 2.84e+01 1sznA 417 2.85e+01 b.71.1.1,c.1.8.1 106162,106163 1xngA 268 2.85e+01 1yrgA 385 2.89e+01 1yrgA c.10.1.2 30854 1xjcA 169 2.90e+01 1avwB 171 2.90e+01 1wba b.42.4.1 25599 1wdcB 156 2.91e+01 1wdcB a.39.1.5 17302 1eonA 245 2.96e+01 1rvaA c.52.1.2 33238 1b4aA 149 3.00e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1od5A 492 3.01e+01 b.82.1.2,b.82.1.2 86832,86833 1rz4A 226 3.04e+01 a.4.5.53,a.118.1.18 105131,105132 2bnmA 198 3.04e+01 1uowA 159 3.04e+01 b.7.1.2 107975 1exrA 148 3.04e+01 1cll a.39.1.5 17299 1yruB 74 3.07e+01 1aipA 405 3.10e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1b6fA 159 3.11e+01 1bv1 d.129.3.1 41316 1nciA 110 3.11e+01 1edhA b.1.6.1 22191 1lktA 104 3.15e+01 1lktA b.90.1.1 28398 1l9mA 692 3.22e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 73732,73733,73734,73735 1fl9A 161 3.22e+01 c.37.1.18 70137 2bvyA 475 3.24e+01 1a12A 413 3.27e+01 1a12A b.69.5.1 27663 1ffkQ 119 3.32e+01 1ffkQ b.34.5.1 24605 1oo0B 110 3.33e+01 d.58.7.1 87183 1j7nA 776 3.35e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2fauA 341 3.36e+01 1rhfA 182 3.39e+01 b.1.1.1,b.1.1.4 97469,97470 1ylnA 252 3.39e+01 1cqmA 101 3.42e+01 1ris d.58.14.1 39321 1suh 146 3.42e+01 1edhA b.1.6.1 22206 1hh2P 344 3.44e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1h09A 338 3.45e+01 b.109.1.1,c.1.8.8 83420,83421 3nn9 388 3.45e+01 2qwc b.68.1.1 27566 1l8nA 679 3.46e+01 c.1.8.10,d.92.2.2 84564,84565 1b97A 244 3.48e+01 1rvaA c.52.1.2 33252 1kk8B 139 3.50e+01 a.39.1.5 77430 1e50A 134 3.50e+01 1cmoA b.2.5.6 59244 1scmB 145 3.52e+01 1wdcB a.39.1.5 17304 1e69B 322 3.53e+01 1e69B c.37.1.12 32377 1k9dA 679 3.53e+01 c.1.8.10,d.92.2.2 77292,77293 1nxiA 132 3.55e+01 d.58.47.1 86381 2ch4A 320 3.55e+01 1a78A 134 3.57e+01 1c1lA b.29.1.3 24212 1vjjA 692 3.59e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 2bwkA 121 3.64e+01 1sx5A 244 3.69e+01 c.52.1.2 99023 1yb3A 175 3.70e+01 1jopA 155 3.71e+01 b.82.2.7 84187 1xsjA 778 3.71e+01 1lb2B 84 3.73e+01 a.60.3.1 77871 1l3kA 196 3.74e+01 d.58.7.1,d.58.7.1 73539,73540 1lfpA 249 3.74e+01 e.39.1.1 73885 2f2hA 773 3.75e+01 1m5sA 297 3.78e+01 d.58.33.1,d.58.33.1 74511,74512 1l3aA 228 3.79e+01 d.18.1.2 73531 1cid 177 3.80e+01 1cid b.1.1.1,b.1.1.3 19740,21679 1fwp 139 3.82e+01 1eayC d.58.24.1 39396 2bl0C 142 3.86e+01 1wluA 136 3.88e+01 1rzfL 213 3.92e+01 b.1.1.1,b.1.1.2 98152,98153 1rifA 282 3.93e+01 c.37.1.23 97507 1f3rB 257 3.93e+01 1f3rB b.1.1.1,b.1.1.1 20416,20417 1nb8A 353 3.93e+01 d.3.1.9 80385 1wy5A 317 3.95e+01 2gu3A 136 3.95e+01 1yu4A 381 3.97e+01 1hpgA 187 3.98e+01 1qq4A b.47.1.1 25813 1zxfA 155 4.02e+01 1xk7A 408 4.14e+01 1gg4A 452 4.18e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1e7uA 961 4.20e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2cq2A 114 4.22e+01 2ffuA 501 4.22e+01 1i1qB 192 4.25e+01 1qdlB c.23.16.1 61544 1ax0 239 4.27e+01 1led b.29.1.1 24042 1zdyA 307 4.27e+01 1mp9A 198 4.29e+01 d.129.1.1,d.129.1.1 91385,91386 2bc2A 227 4.31e+01 1a7tA d.157.1.1 42031 1mqoA 227 4.38e+01 d.157.1.1 103846 1n99A 166 4.39e+01 b.36.1.1,b.36.1.1 85459,85460 1h6kZ 98 4.42e+01 d.58.7.1 60686 1rl2A 137 4.48e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 2c9wA 169 4.49e+01 2a6cA 83 4.50e+01 1r13A 148 4.51e+01 d.169.1.1,h.1.1.1 96782,96783 1o6sB 105 4.55e+01 b.1.6.1 81096 1obpA 159 4.55e+01 1obpA b.60.1.1 27092 1gya 105 4.58e+01 1qa9A b.1.1.1 19745 1vavA 222 4.61e+01 b.29.1.18 108472 1avsA 90 4.64e+01 1cll a.39.1.5 17226 1o6uA 403 4.66e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1gt1A 159 4.69e+01 b.60.1.1 90515 1tgrA 52 4.70e+01 1of5A 221 4.74e+01 d.17.4.2 86933 1zxkA 98 4.76e+01 1tu1A 148 4.76e+01 d.107.1.3 107316 5nn9 388 4.85e+01 2qwc b.68.1.1 27563 1bj7 156 4.86e+01 1bj7 b.60.1.1 27113 1k42A 168 4.86e+01 b.18.1.14 72032 1qsgA 265 4.87e+01 1eny c.2.1.2 29935 1wfxA 186 4.88e+01 1amuA 563 4.89e+01 1amuA e.23.1.1 43351 1i7qB 193 4.89e+01 1qdlB c.23.16.1 61902 2adcA 229 4.90e+01 1j1yA 136 4.91e+01 d.38.1.5 90776 1ut1A 148 4.91e+01 b.2.3.6 108014 1pvyA 227 4.93e+01 d.115.1.2 95195 1mc3A 296 4.96e+01 c.68.1.6 78943 1rzmA 338 5.02e+01 c.1.10.4 105137 1eagA 342 5.06e+01 1eagA b.50.1.2 26826 1hn2A 159 5.06e+01 b.60.1.1 65890 1snnA 227 5.06e+01 d.115.1.2 105821 2f3yA 148 5.07e+01 2a6sA 84 5.11e+01 1z2wA 192 5.15e+01 1t17A 148 5.15e+01 1yioA 208 5.16e+01 1x99A 145 5.18e+01 1ftrA 296 5.19e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1f3lA 321 5.22e+01 1g6q2 c.66.1.6 59630 1j6uA 469 5.24e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1qo3C 137 5.26e+01 1qo3C d.169.1.1 42350 1dqeA 137 5.29e+01 1dqeA a.39.2.1 17388 1hjrA 158 5.38e+01 1hjrA c.55.3.6 33727 1u1zA 168 5.43e+01 d.38.1.6 107602 2c4bA 143 5.46e+01 1p5hA 428 5.50e+01 c.123.1.1 87802 1uptB 60 5.55e+01 a.193.1.1 99768 2f1lA 187 5.55e+01 1h6lA 353 5.59e+01 b.68.3.1 60687 1bssA 244 5.59e+01 1rvaA c.52.1.2 33256 2bgcA 238 5.61e+01 1k12A 158 5.63e+01 b.18.1.15 71978 2d13A 227 5.64e+01 2a8kA 108 5.66e+01 1nnxA 109 5.71e+01 b.40.10.1 92013 1m6yA 301 5.72e+01 a.60.13.1,c.66.1.23 78716,78717 1xa3A 437 5.73e+01 1mr4A 47 5.80e+01 g.3.7.5 91429 1zt2B 212 5.82e+01 1e5pA 151 5.82e+01 1bj7 b.60.1.1 59272 1h05A 146 5.82e+01 c.23.13.1 76433 1ycsB 239 5.84e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1nxzA 246 5.91e+01 b.122.1.2,c.116.1.5 86391,86392 1gpb 842 5.92e+01 1a8i c.87.1.4 35478 1cv8 174 5.93e+01 1cv8 d.3.1.1 37089 1ukgA 252 5.96e+01 b.29.1.1 99489 2d1uA 104 5.97e+01 1p27B 106 6.00e+01 d.58.7.1 93908 1faoA 126 6.01e+01 1faoA b.55.1.1 26974 1mdaH 368 6.02e+01 2bbkH b.69.2.1 27637 1axkA 394 6.04e+01 1axkA b.29.1.2,b.29.1.11 24181,24315 2d27A 149 6.15e+01 1a4yB 123 6.16e+01 7rsa d.5.1.1 37296 1s4cA 155 6.20e+01 1rvaA 244 6.20e+01 1rvaA c.52.1.2 33240 1dih 273 6.27e+01 1drw c.2.1.3,d.81.1.3 30056,39971 1xfrA 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