# 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.soe.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 3lmmA 583 1.09e-05 1yzgA 179 2.31e-01 c.37.1.8 124276 1wcuA 153 2.65e-01 2gu3A 136 3.69e-01 d.17.1.6,d.17.1.6 147178,147179 2oezA 247 3.87e-01 e.68.1.1 148758 3hmiA 292 9.51e-01 1mfaH 120 1.03e+00 b.1.1.1 19889 1vs0A 310 1.07e+00 2h17A 181 1.65e+00 2a6tA 271 1.79e+00 a.242.1.1,d.113.1.7 126309,126310 3glaA 100 1.86e+00 3d7rA 326 2.61e+00 1gmeA 151 2.66e+00 b.15.1.1 65305 1y10A 407 2.91e+00 3dkuA 153 3.18e+00 3k6kA 322 3.19e+00 3lmlA 460 3.38e+00 2c9jA 223 3.43e+00 1ieaB 228 3.47e+00 1iakB b.1.1.2,d.19.1.1 21632,38206 1kobA 387 3.77e+00 1tkiA d.144.1.7 41640 1o3yA 166 3.78e+00 c.37.1.8 86618 2pqvA 154 3.96e+00 1ln1A 214 4.23e+00 d.129.3.2 74038 1a6uL 108 4.41e+00 1mfa b.1.1.1 20254 2retA 103 4.42e+00 d.24.1.7 151983 2hziA 277 4.56e+00 2kc8A 98 4.92e+00 1a6wL 109 5.23e+00 1mfa b.1.1.1 20252 1fngA 192 5.42e+00 1iakA b.1.1.2,d.19.1.1 59904,59905 1pqzA 238 5.49e+00 b.1.1.2,d.19.1.1 104297,104298 1opjA 293 5.59e+00 d.144.1.7 87230 1bvoA 175 5.69e+00 1a3qA b.2.5.3 22457 1g8sA 230 5.90e+00 c.66.1.3 90507 1onqA 283 6.03e+00 b.1.1.2,d.19.1.1 93365,93366 1sjyA 159 6.28e+00 d.113.1.1 98900 1ieaA 192 6.53e+00 1iakA b.1.1.2,d.19.1.1 21631,38205 1u58A 253 6.67e+00 b.1.1.2,d.19.1.1 144387,144388 3c5jA 181 6.72e+00 1waaA 93 6.74e+00 1mqkL 120 6.84e+00 b.1.1.1 85054 3kfaA 288 6.99e+00 3fspA 369 7.05e+00 2a8eA 220 7.10e+00 d.296.1.1 126397 1m2rA 327 7.11e+00 d.144.1.7 84760 3kk8A 284 7.11e+00 3citA 160 7.51e+00 2d7tH 139 8.02e+00 2qggA 182 8.13e+00 1m2oB 190 8.13e+00 c.37.1.8 78485 2ppqA 322 8.17e+00 d.144.1.6 149782 3hmmA 303 8.18e+00 3cwvA 369 8.39e+00 1r8nA 185 8.58e+00 b.42.4.1 104851 3dnmA 336 8.68e+00 1zj6A 187 8.90e+00 c.37.1.8 125145 2k54A 123 8.90e+00 d.17.4.29 148271 3c0iA 351 8.92e+00 1vjyA 303 9.25e+00 d.144.1.7 108633 1y44A 320 9.26e+00 d.157.1.7 122608 2vqeE 162 9.37e+00 i.1.1.3 153429 1qpcA 279 9.87e+00 1fgkA d.144.1.7 41685 2zjrG 174 9.96e+00 c.21.1.1 154560 2qsrA 173 1.01e+01 3g8yA 391 1.01e+01 2bdwA 362 1.05e+01 1kxvC 121 1.07e+01 b.1.1.1 73190 2fx7H 228 1.07e+01 b.1.1.1,b.1.1.2 134276,134277 2jbwA 386 1.08e+01 c.69.1.41 147962 1fv1B 190 1.16e+01 1iakB b.1.1.2,d.19.1.1 21606,38180 1cojA 212 1.16e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1aqdA 192 1.16e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 2wgoA 98 1.16e+01 2uubE 162 1.16e+01 d.14.1.1,d.50.1.2 139936,139937 3eesA 153 1.19e+01 3e23A 211 1.19e+01 3khaA 95 1.19e+01 1qb5D 99 1.19e+01 b.40.2.1 88357 1f6bA 198 1.20e+01 c.37.1.8 64986 2dvyA 226 1.22e+01 2ij0C 118 1.26e+01 b.1.1.1 145525 1ab8A 220 1.27e+01 1azsA d.58.29.1 39414 2w83A 165 1.28e+01 1smoA 119 1.29e+01 b.1.1.1 105764 1u5xA 140 1.30e+01 b.22.1.1 113055 3k86A 185 1.31e+01 3dc6A 198 1.31e+01 1cfyA 143 1.32e+01 1cof d.109.1.2 40858 1d2gA 292 1.35e+01 1xvaA c.66.1.5 34187 1wh0A 134 1.38e+01 b.15.1.3 114628 1oaqL 120 1.39e+01 b.1.1.1 92708 2afcA 168 1.40e+01 c.50.1.2 126676 2dnrA 91 1.41e+01 1e8oB 106 1.42e+01 1914 d.49.1.1 38775 1zunB 434 1.42e+01 b.43.3.1,b.44.1.1,c.37.1.8 125677,125678,125679 1bccE 196 1.43e+01 1rie b.33.1.1,f.23.12.1 24431,43699 2qm4A 235 1.43e+01 2welA 327 1.46e+01 3a6sA 129 1.49e+01 2fkbA 180 1.50e+01 d.113.1.2 133650 1sgoA 139 1.50e+01 d.82.3.1 98857 1vcdA 126 1.52e+01 d.113.1.1 119970 1ry9A 145 1.54e+01 d.198.1.1 98094 1bx2B 191 1.55e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 2avdA 219 1.56e+01 c.66.1.1 127377 2ahoB 266 1.57e+01 a.60.14.1,b.40.4.5,d.58.51.1 126770,126771,126772 3f3zA 277 1.60e+01 2q83A 346 1.61e+01 1fjgE 162 1.62e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1n0nA 199 1.64e+01 a.2.11.1,d.44.1.1 79750,79751 2o6pA 161 1.65e+01 b.1.28.1 148635 3ff0A 163 1.66e+01 1jk8B 190 1.71e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1a6aA 176 1.71e+01 1iakA b.1.1.2,d.19.1.1 21615,38189 2vgpA 284 1.71e+01 1r8sA 164 1.78e+01 c.37.1.8 97247 1j5yA 187 1.79e+01 a.4.5.1,d.94.2.1 71592,71593 3bevA 274 1.82e+01 1om1A 332 1.82e+01 d.144.1.7 93347 2kksA 146 1.82e+01 3lw6A 287 1.86e+01 1htwA 158 1.87e+01 c.37.1.18 71083 1d5mB 192 1.90e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1ryaA 160 1.91e+01 d.113.1.5 105122 3fnbA 405 1.91e+01 3lmjH 231 1.95e+01 1ro5A 201 1.96e+01 d.108.1.3 105023 1ic7H 114 1.96e+01 1f3rB b.1.1.1 62258 2ebbA 101 1.97e+01 1yemA 179 1.97e+01 d.63.1.2 116646 3c5jB 190 1.99e+01 1fzqA 181 2.00e+01 1hurA c.37.1.8 32060 1ooyA 481 2.01e+01 c.124.1.3,c.124.1.2 93388,93389 1s98A 107 2.01e+01 b.124.1.1 105377 2fk6A 320 2.02e+01 d.157.1.7 133646 2wotA 306 2.07e+01 3fpqA 290 2.10e+01 1wpgA 994 2.12e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 114806,114807,114808,114809 3eqcA 360 2.14e+01 1vfgA 390 2.15e+01 a.173.1.1,d.218.1.4 108570,108571 1u4nA 310 2.16e+01 c.69.1.2 113021 1roaA 122 2.17e+01 d.17.1.2 105024 1gyhA 318 2.18e+01 b.67.2.1 70757 3gd7A 390 2.21e+01 3ke7A 134 2.23e+01 2fg1A 158 2.23e+01 c.50.1.2 133400 2g9hD 218 2.25e+01 b.40.2.2,d.15.6.1 145188,145189 2hm7A 310 2.25e+01 1ap2A 113 2.25e+01 8fabA b.1.1.1 20182 1x19A 359 2.28e+01 2rqkA 141 2.29e+01 1zc1A 208 2.29e+01 1r7mA 235 2.30e+01 d.95.2.1,d.95.2.1 111713,111714 1exuA 267 2.33e+01 1agdA b.1.1.2,d.19.1.1 20864,38324 2iteA 127 2.37e+01 b.1.28.1 147795 1x9nA 688 2.37e+01 a.235.1.1,b.40.4.6,d.142.2.1 115002,115003,115004 3efyA 195 2.37e+01 2fikA 287 2.39e+01 b.1.1.2,d.19.1.1 133524,133525 3grnA 153 2.39e+01 1tigA 94 2.41e+01 d.68.1.1 39566 2gcoA 201 2.42e+01 1eeuA 114 2.46e+01 32c2A b.1.1.1 20546 1hw7A 255 2.48e+01 1i7fA d.193.1.1 61297 1pl4A 198 2.49e+01 a.2.11.1,d.44.1.1 94854,94855 1g7jA 107 2.52e+01 32c2A b.1.1.1 19932 2w87A 139 2.53e+01 2r4iA 123 2.55e+01 d.17.4.15 151576 1aqdB 198 2.63e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 3ew1A 135 2.64e+01 3cgxA 242 2.67e+01 3kb5A 193 2.68e+01 1uptA 171 2.68e+01 c.37.1.8 99767 3eysH 223 2.69e+01 1a7qL 106 2.69e+01 8fabA b.1.1.1 19954 3d79A 179 2.70e+01 2i8tA 167 2.71e+01 2omlA 189 2.71e+01 2a5dA 175 2.72e+01 c.37.1.8 126172 3c0dA 119 2.72e+01 b.33.1.3 155819 1idsA 207 2.73e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 2omdA 154 2.76e+01 3jumA 185 2.76e+01 1p4oA 322 2.77e+01 d.144.1.7 87775 3kymB 227 2.82e+01 3f62A 109 2.85e+01 2r0hA 164 2.92e+01 1eeqA 114 2.93e+01 32c2A b.1.1.1 20544 1wloA 136 2.96e+01 2cfmA 561 2.97e+01 2vxtH 216 2.99e+01 2eu9A 355 3.01e+01 1gydB 315 3.01e+01 b.67.2.1 70751 2gq0A 303 3.04e+01 3eqeA 171 3.06e+01 2vjxA 846 3.07e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153203,153204,153205,153206,153207 1jqhA 308 3.10e+01 d.144.1.7 71793 1uv4A 293 3.11e+01 b.67.2.1 119705 1v2bA 177 3.12e+01 d.107.1.2 108279 3d36A 244 3.12e+01 1xu1A 138 3.14e+01 b.22.1.1 116033 3fruA 269 3.15e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 2b0rA 202 3.15e+01 1ppjE 196 3.19e+01 b.33.1.1,f.23.12.1 104260,104261 2x77A 189 3.22e+01 1z57A 339 3.26e+01 3dmgA 381 3.31e+01 2gysA 419 3.32e+01 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 1j1xH 114 3.37e+01 b.1.1.1 77063 2akrA 285 3.40e+01 b.1.1.2,d.19.1.1 126931,126932 1i8aA 189 3.41e+01 1i82A b.1.9.2 61951 1a2yA 107 3.41e+01 8fabA b.1.1.1 19926 1gtdA 85 3.41e+01 d.284.1.1 76344 3a1pB 93 3.43e+01 3ga2A 246 3.43e+01 1bh5A 183 3.44e+01 1qipA d.32.1.1 38476 3gneA 252 3.44e+01 2q20A 109 3.49e+01 3greA 437 3.49e+01 1u55A 188 3.54e+01 d.278.1.1 107677 2adgB 222 3.57e+01 b.1.1.2 126588 2fgeA 995 3.58e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 2yxmA 100 3.59e+01 2qpzA 103 3.59e+01 2fm8A 135 3.60e+01 d.198.1.1 133767 2vxtL 214 3.60e+01 1ymmA 191 3.63e+01 b.1.1.2,d.19.1.1 123701,123702 1un3A 123 3.64e+01 d.5.1.1 99646 3cnmA 185 3.65e+01 2q4mA 217 3.68e+01 d.23.1.2 139870 1jj2E 177 3.69e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 2ra1A 412 3.70e+01 1vloA 381 3.71e+01 b.44.2.1,d.250.1.1 108838,108839 2vr4A 846 3.71e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153495,153496,153497,153498,153499 2hp4A 114 3.73e+01 1t4hA 290 3.75e+01 d.144.1.7 106420 1p57A 114 3.77e+01 d.170.1.2 94125 1a7qH 116 3.87e+01 1gc1H b.1.1.1 19955 3gpgA 168 3.89e+01 1hkfA 122 3.93e+01 b.1.1.1 83553 1nqbA 256 3.94e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 2qr7A 342 3.99e+01 1a6vL 110 4.07e+01 1mfa b.1.1.1 20256 3ejcA 169 4.07e+01 3baeH 228 4.09e+01 b.1.1.2 155029 3bikB 134 4.11e+01 b.1.1.1 155309 2dyiA 162 4.16e+01 1u9kA 114 4.16e+01 b.1.1.1 113244 2qkmB 266 4.17e+01 1b0wA 108 4.24e+01 8fabA b.1.1.1 20532 2bk8A 97 4.27e+01 1xneA 113 4.28e+01 b.122.1.6 115579 2h57A 190 4.30e+01 3aazA 229 4.32e+01 2je8A 848 4.36e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 147998,147999,148000,148001,148002 3bd3A 112 4.38e+01 3i23A 349 4.40e+01 1uacH 114 4.41e+01 b.1.1.1 99132 1qw2A 102 4.42e+01 d.249.1.1 96456 1vkiA 181 4.43e+01 d.116.1.1 108664 1mvuA 114 4.48e+01 b.1.1.1 91474 1xtmA 175 4.48e+01 1a7nL 107 4.49e+01 8fabA b.1.1.1 19940 2aw2A 120 4.49e+01 b.1.1.1 144863 2qg3A 208 4.51e+01 3lh5A 251 4.52e+01 1a14L 104 4.55e+01 8fabA b.1.1.1 20060 1xmzA 241 4.57e+01 2dylA 318 4.61e+01 1vk6A 269 4.61e+01 d.113.1.4,d.113.1.4,g.41.14.1 100852,111609,111610 1ol0A 121 4.66e+01 b.1.1.1 93296 3fo5A 258 4.67e+01 1nqcA 217 4.68e+01 d.3.1.1 86024 1k2dB 189 4.72e+01 b.1.1.2,d.19.1.1 84293,84294 1uliB 187 4.74e+01 d.17.4.4 107923 1ib8A 164 4.75e+01 b.38.2.1,d.52.4.1 71168,71169 3bp6A 117 4.79e+01 3cfzA 292 4.79e+01 2oc6A 124 4.79e+01 d.198.4.1 148721 1zhsA 113 4.84e+01 3g9xA 299 4.84e+01 1a6aB 187 4.86e+01 1iakB b.1.1.2,d.19.1.1 21616,38190 1a7oL 106 4.89e+01 8fabA b.1.1.1 19942 3lzfL 217 4.89e+01 2f2hA 773 4.89e+01 b.150.1.1,b.30.5.11,b.71.1.4,c.1.8.13 132818,132819,132820,132821 3hblA 1150 4.90e+01 3hr6A 436 4.97e+01 3lxrA 185 4.99e+01 1f2hA 169 5.02e+01 1f3vA d.58.22.1 59612 1o22A 170 5.06e+01 d.238.1.1 86557 3fwhA 299 5.07e+01 3fvtA 320 5.14e+01 3ckwA 304 5.19e+01 2a6vA 226 5.20e+01 b.29.1.13 126312 1um5L 219 5.21e+01 b.1.1.1,b.1.1.2 113304,113305 2cxcA 144 5.21e+01 1uvqB 198 5.22e+01 b.1.1.2,d.19.1.1 100064,100065 1imuA 107 5.23e+01 d.204.1.1 66218 1oaqH 121 5.24e+01 b.1.1.1 92707 2frqA 225 5.29e+01 d.3.1.1 133999 1su0B 159 5.32e+01 d.224.1.2 106015 1rieA 129 5.35e+01 b.33.1.1 24427 1w2fA 276 5.38e+01 d.143.1.3 109125 1xzwA 426 5.45e+01 b.1.12.1,d.159.1.1 116270,116271 2asfA 137 5.46e+01 b.45.1.1 127253 3hnpA 353 5.46e+01 2a9mH 126 5.47e+01 2v33A 91 5.49e+01 b.1.18.4 152439 1b1iA 123 5.49e+01 7rsa d.5.1.1 37295 1ekgA 127 5.54e+01 1dlxA d.82.2.1 40021 3c0wA 235 5.54e+01 3a35A 190 5.55e+01 3cx5B 352 5.58e+01 d.185.1.1,d.185.1.1 157078,157079 2b0vA 153 5.59e+01 d.113.1.1 127650 1ospH 218 5.61e+01 1igtB b.1.1.1,b.1.1.2 20117,21147 2i79A 172 5.67e+01 1a7pL 107 5.67e+01 8fabA b.1.1.1 19950 2gr8A 99 5.72e+01 d.24.1.4 135522 1t7vA 278 5.76e+01 b.1.1.2,d.19.1.1 112302,112303 1xedA 117 5.82e+01 b.1.1.1 115229 1a7oH 116 5.85e+01 1gc1H b.1.1.1 19943 2sliA 679 5.90e+01 b.29.1.9,b.68.1.1 24274,27611 1k59A 123 5.91e+01 d.5.1.1 72073 2iabA 155 5.91e+01 1r62A 160 5.94e+01 d.122.1.3 104816 1z90A 469 5.99e+01 b.81.1.4,c.68.1.5 124732,124733 3kspA 129 6.05e+01 2gumA 628 6.12e+01 e.76.1.1 147184 2p13A 90 6.13e+01 d.145.1.4 149152 1r8eA 278 6.15e+01 a.6.1.3,d.60.1.1 104843,104844 2h26A 291 6.15e+01 b.1.1.2,d.19.1.1 135990,135991 2covD 104 6.16e+01 2z06A 252 6.17e+01 d.159.1.10 153906 2o2iA 300 6.21e+01 2gwmA 200 6.21e+01 2f57A 317 6.22e+01 1phkA 298 6.23e+01 d.144.1.7 41635 2bfxA 284 6.25e+01 3bp5A 117 6.26e+01 b.1.1.1 155462 3hnrA 220 6.26e+01 3fbwA 299 6.29e+01 1yezA 68 6.38e+01 b.40.4.12 123026 1vqoE 178 6.39e+01 d.141.1.1,d.141.1.1 120366,120367 2hzmA 212 6.41e+01 2r41A 110 6.41e+01 3h0dA 155 6.42e+01 3dbxA 289 6.42e+01 3f7sA 142 6.42e+01 1r89A 437 6.47e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1zkkA 167 6.49e+01 2za0A 184 6.49e+01 1xezA 721 6.51e+01 3gwrA 144 6.58e+01 2d37A 176 6.63e+01 1nb5I 98 6.67e+01 d.17.1.2 80381 1szoA 257 6.70e+01 c.14.1.3 106164 2yqzA 263 6.74e+01 1q9rB 222 6.82e+01 b.1.1.1,b.1.1.2 96307,96308 2qnkA 286 6.90e+01 2gxfA 142 6.92e+01 d.17.4.22 147191 1i1nA 226 6.93e+01 c.66.1.7 71102 1wi1A 126 6.96e+01 b.55.1.1 114658 2bw8A 227 6.98e+01 b.29.1.11 129324 2pvrA 334 6.99e+01 d.144.1.7 149893 1h0bA 256 7.08e+01 b.29.1.11 83422 3bu3A 306 7.12e+01 d.144.1.7 155590 3lurA 158 7.12e+01 1q7hA 153 7.13e+01 b.122.1.1,d.17.6.2 96042,96043 3e0lA 455 7.13e+01 2a8sA 212 7.14e+01 d.113.1.1 126416 1azsB 212 7.17e+01 1azsA d.58.29.1 39423 3a0oA 776 7.17e+01 2quoA 126 7.20e+01 2vv6A 119 7.21e+01 2ek0A 90 7.25e+01 2a2nA 176 7.26e+01 b.62.1.1 126041 3hb9A 1150 7.26e+01 3devA 320 7.27e+01 1rypH 205 7.27e+01 d.153.1.4 41876 1q7lA 198 7.30e+01 c.56.5.4 96044 2h7jA 220 7.33e+01 d.3.1.1 136216 2d7tL 116 7.33e+01 3fmeA 290 7.38e+01 2f4eA 180 7.49e+01 1r4aA 165 7.54e+01 c.37.1.8 96986 3dr5A 221 7.58e+01 2kqnA 110 7.62e+01 2gqcA 70 7.64e+01 1znpA 154 7.65e+01 b.82.1.16 125394 2nqcA 138 7.67e+01 b.1.18.10 148344 1vlmA 219 7.67e+01 c.66.1.41 108836 3fjsA 114 7.68e+01 2icyA 469 7.70e+01 b.81.1.4,c.68.1.5 137257,137258 2p0kA 212 7.73e+01 1r94A 118 7.75e+01 b.124.1.1 97251 1nnvA 110 7.79e+01 d.17.7.1 92012 3besR 250 7.82e+01 2apxA 112 7.82e+01 3a0yA 152 7.83e+01 2dj5A 133 7.88e+01 c.92.1.3 131536 1t9xA 1049 7.93e+01 3fcdA 134 7.95e+01 3g9aB 139 7.97e+01