# List of top-scoring protein chains for t04-100-40-40-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 2fhqA 141 1.12e-06 1rfeA 162 2.18e-06 1t9mA 214 5.87e-06 1nrgA 261 6.08e-06 b.45.1.1 80694 1dnlA 199 7.49e-06 1ci0A b.45.1.1 25753 1g79A 218 1.46e-05 1ci0A b.45.1.1 25752 1vl7A 157 1.77e-05 b.45.1.1 108732 1ty9A 222 1.89e-05 2aq6A 147 1.74e-04 1xxoA 147 7.05e-04 1w9aA 147 8.63e-04 2furA 209 1.63e-03 2asfA 137 5.65e-03 2fg9A 178 6.14e-03 2arzA 247 1.18e-02 1flmA 122 2.21e-02 1axj b.45.1.1 25747 1xhnA 184 4.24e-02 1r6xA 395 1.25e-01 b.122.1.3,c.26.1.5 97167,97168 1g8fA 511 1.79e-01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1kdj 102 7.53e-01 1plc b.6.1.1 22864 1kcvH 217 1.45e+00 b.1.1.1,b.1.1.2 72315,72316 1ru8A 232 1.64e+00 c.26.2.1 97849 1r75A 141 2.00e+00 b.134.1.1 97189 1j58A 385 2.58e+00 b.82.1.2 71531 2czrA 226 2.62e+00 2fywA 267 2.99e+00 1bxvA 91 4.02e+00 1aac b.6.1.1 22875 2a6hA 315 4.94e+00 1ve6A 582 5.49e+00 1xphA 150 5.82e+00 1lci 550 5.85e+00 1lci e.23.1.1 43349 1ag6 99 5.92e+00 1plc b.6.1.1 22857 1l7mA 211 5.97e+00 c.108.1.4 73664 1ejeA 192 6.02e+00 1ejeA b.45.1.2 25757 3sil 379 6.33e+00 3sil b.68.1.1 27542 1svpA 161 6.44e+00 1svpA b.47.1.3 26384 1v5rA 97 6.45e+00 1j97A 211 6.47e+00 1f5sA c.108.1.4 62753 1d1gA 168 7.00e+00 1d1gA c.71.1.1 34889 1ofuA 320 7.39e+00 c.32.1.1,d.79.2.1 86972,86973 1gcvB 136 7.45e+00 1cg5B a.1.1.2 15589 2axwA 134 7.61e+00 2gc9A 179 7.78e+00 1vhsA 175 7.90e+00 d.108.1.1 100698 2fibA 269 8.51e+00 3fib d.171.1.1 42457 1v30A 124 9.22e+00 1eulA 994 9.29e+00 1eulA 2trcP 217 9.94e+00 1b9yC c.47.1.6 33051 1yn3A 98 1.00e+01 3fib 249 1.06e+01 3fib d.171.1.1 42455 1uf2C 421 1.06e+01 a.115.1.3,b.19.1.1 99291,99292 1bypA 99 1.07e+01 1plc b.6.1.1 22858 1w24A 182 1.09e+01 1a1x 108 1.13e+01 1a1x b.63.1.1 27514 1yhuB 144 1.23e+01 1uxaA 194 1.29e+01 b.21.1.1 108091 1k9jA 139 1.30e+01 d.169.1.1 68353 1w1hA 151 1.32e+01 1su4A 994 1.32e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1plc 99 1.34e+01 1plc b.6.1.1 22846 1vs0A 310 1.36e+01 1kjlA 146 1.44e+01 2lhb 149 1.48e+01 2fal a.1.1.2 15597 1xdnA 277 1.50e+01 1cg5B 141 1.50e+01 1cg5B a.1.1.2 15585 7pcy 98 1.51e+01 1plc b.6.1.1 22863 1ri6A 343 1.56e+01 b.69.11.1 97503 1n8jA 186 1.56e+01 c.47.1.10 85401 7ahlA 293 1.57e+01 7ahlA f.6.1.1 43812 1fjgQ 105 1.62e+01 1fjfQ b.40.4.5 25352 1jyhA 157 1.65e+01 d.60.1.3 71956 1iuz 98 1.73e+01 1plc b.6.1.1 22861 1xb3A 128 1.74e+01 1twfK 120 1.76e+01 2cu5A 129 1.77e+01 2acaA 189 1.79e+01 1a78A 134 1.82e+01 1c1lA b.29.1.3 24212 1zdrA 164 1.83e+01 1pk6B 132 1.83e+01 b.22.1.1 94802 1umuA 116 1.84e+01 1umuA b.87.1.1 28382 1kr7A 110 1.85e+01 a.1.1.4 72890 1wpgA 994 1.91e+01 1z2wA 192 1.94e+01 1jzgA 128 1.96e+01 b.6.1.1 67855 1w3fA 315 1.97e+01 1pl3A 186 2.02e+01 b.1.9.1 88158 2f96A 224 2.05e+01 1ckmA 330 2.06e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 2d2mB 142 2.11e+01 1oxdA 227 2.16e+01 d.22.1.1 93687 2ai4A 119 2.16e+01 1i52A 236 2.18e+01 1i52A c.68.1.13 61767 1myt 146 2.20e+01 1a6m a.1.1.2 15207 1q1aA 289 2.22e+01 c.31.1.5 95561 1w07A 659 2.24e+01 1dbhA 354 2.28e+01 1awe a.87.1.1,b.55.1.1 18514,26967 2bduA 297 2.36e+01 1vmfA 145 2.37e+01 1xneA 113 2.38e+01 1kxgA 152 2.42e+01 b.22.1.1 73145 1y0gA 191 2.42e+01 1vheA 373 2.48e+01 b.49.3.1,c.56.5.4 100669,100670 1u4bA 580 2.48e+01 c.55.3.5,e.8.1.1 107664,107665 1xv2A 237 2.62e+01 1pkp 150 2.62e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1fsz 372 2.64e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 2fy6A 143 2.67e+01 1h7zA 194 2.70e+01 1qhvA b.21.1.1 60733 2awkA 228 2.71e+01 1v4pA 157 2.73e+01 1sl4A 155 2.74e+01 d.169.1.1 105710 1p4uA 153 2.87e+01 b.1.10.2 87780 1cv8 174 2.87e+01 1cv8 d.3.1.1 37089 1pk6A 133 2.89e+01 b.22.1.1 94801 1gcuA 295 2.98e+01 1gcuA c.2.1.3,d.81.1.4 30063,39978 2bb2 181 3.02e+01 2bb2 b.11.1.1,b.11.1.1 23604,23605 2a74A 643 3.07e+01 1tvjA 166 3.07e+01 1q0sA 259 3.13e+01 c.66.1.28 95509 1i50K 120 3.14e+01 d.74.3.2 61765 1dkgA 197 3.16e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1a0rP 245 3.26e+01 1b9yC c.47.1.6 33054 1cg5A 141 3.34e+01 1abwA a.1.1.2 15406 1d7cA 190 3.35e+01 1d7bA b.1.9.1 22309 1zgoA 223 3.41e+01 1u0kA 288 3.46e+01 d.21.1.2,d.21.1.2 107547,107548 1pgl1 185 3.47e+01 1n9pA 207 3.51e+01 b.1.18.16 80343 1q6uA 245 3.52e+01 d.26.1.1 95998 1nk4A 580 3.55e+01 c.55.3.5,e.8.1.1 91923,91924 1xfjA 261 3.56e+01 d.194.1.2 109585 1wznA 252 3.62e+01 1ggxA 223 3.63e+01 1ggxA d.22.1.1 38367 1vajA 214 3.63e+01 1ry6A 360 3.63e+01 c.37.1.9 98090 2d5xA 141 3.65e+01 2d37A 176 3.72e+01 1a3k 137 3.75e+01 1a3k b.29.1.3 24218 1lc0A 294 3.76e+01 c.2.1.3,d.81.1.4 73823,73824 1y7bA 542 3.78e+01 1ri7A 171 3.82e+01 a.4.5.32,d.58.4.2 97504,97505 1vjvA 415 3.86e+01 d.3.1.9 108632 2d13A 227 3.87e+01 2fcbA 173 3.94e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1j98A 157 3.95e+01 1j98A d.185.1.2 62755 1g6oA 330 4.00e+01 1g6oA c.37.1.11 32430 1yycA 174 4.02e+01 2gdm 153 4.04e+01 2gdm a.1.1.2 15212 1udxA 416 4.08e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1s12A 94 4.08e+01 1irdA 141 4.08e+01 a.1.1.2 66286 1iwhA 141 4.08e+01 a.1.1.2 76882 1oapA 109 4.15e+01 d.79.7.1 92706 2cyeA 133 4.19e+01 1cdzA 96 4.20e+01 1cdzA c.15.1.1 30925 1l3sA 580 4.26e+01 c.55.3.5,e.8.1.1 84521,84522 1jmsA 381 4.28e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1mba 147 4.33e+01 2fal a.1.1.2 15149 1r6lA 239 4.37e+01 d.14.1.4,d.101.1.1 97153,97154 1fw1A 216 4.41e+01 a.45.1.1,c.47.1.5 60051,60052 2g0wA 296 4.48e+01 1di2A 69 4.49e+01 1di2A d.50.1.1 38780 1vjkA 98 4.60e+01 d.15.3.1 108631 1is3A 135 4.62e+01 b.29.1.3 76773 1mai 131 4.63e+01 1mai b.55.1.1 26951 1kypA 237 4.65e+01 d.22.1.1 73280 1yf3A 259 4.72e+01 1r4kA 169 4.72e+01 b.34.14.1 96997 1f2eA 201 4.73e+01 1a0fA a.45.1.1,c.47.1.5 17745,33039 1okiA 210 4.79e+01 b.11.1.1,b.11.1.1 93255,93256 2bzvA 181 4.79e+01 1dhr 241 4.79e+01 1dhr c.2.1.2 29832 1v9yA 167 4.81e+01 d.110.3.2 108454 1ttwA 138 4.84e+01 d.198.1.1 107308 1regX 122 4.86e+01 1regX d.58.27.1 39406 1mi8A 158 4.88e+01 b.86.1.2 91279 1cwvA 492 4.88e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 2vhbA 146 4.91e+01 2vhbA a.1.1.2 15629 1s4cA 155 4.93e+01 2atrA 138 5.00e+01 1i58A 189 5.01e+01 1b3qA d.122.1.3 61773 1ojrA 274 5.07e+01 c.74.1.1 93147 1nt2A 210 5.13e+01 c.66.1.3 86149 1xwl 580 5.18e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 3daaA 277 5.24e+01 1daaA e.17.1.1 43272 1c8zA 265 5.24e+01 1c8zA d.23.1.1 38375 1vjlA 164 5.26e+01 d.257.1.1 100822 2g09A 297 5.32e+01 1wjvA 79 5.38e+01 2bxxA 134 5.39e+01 1babA 143 5.42e+01 1abwA a.1.1.2 15235 1zq7A 207 5.42e+01 2chnA 716 5.43e+01 1ovnA 248 5.47e+01 a.71.1.1,c.47.1.7 93602,93603 1bmv1 198 5.51e+01 1bmv1 1i2aA 219 5.54e+01 e.24.1.1 90660 1mkfA 382 5.54e+01 b.116.1.1 79232 2audA 257 5.56e+01 1wmuA 141 5.56e+01 a.1.1.2 109416 1t2wA 145 5.57e+01 b.100.1.1 106289 1q6hA 224 5.58e+01 d.26.1.1 95975 1ux8A 132 5.60e+01 1v7lA 163 5.66e+01 1uisA 231 5.72e+01 d.22.1.1 99431 1j5sA 463 5.73e+01 c.1.9.8 71580 1jwqA 179 5.75e+01 c.56.5.6 90921 2cw9A 194 5.76e+01 2gfoA 396 5.77e+01 1bkzA 135 5.78e+01 1a3k b.29.1.3 24202 1vc1A 110 5.79e+01 c.13.2.1 108493 2giyA 191 5.80e+01 1vsd 152 5.84e+01 1cxqA c.55.3.2 33625 1cxqA 162 5.85e+01 1cxqA c.55.3.2 33621 1nwpA 128 5.86e+01 1nwpA b.6.1.1 23011 1guiA 155 5.89e+01 b.18.1.14 76351 1e8yA 966 5.95e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1u0sA 86 6.05e+01 d.58.24.1 107565 1q5qA 259 6.15e+01 d.153.1.4 95904 1xfoA 357 6.18e+01 2g7zA 282 6.18e+01 1kt6A 183 6.21e+01 b.60.1.1 84466 1y0yA 353 6.24e+01 2bzuA 181 6.28e+01 2por 301 6.32e+01 2por f.4.3.1 43759 1uwdA 103 6.35e+01 1vraB 215 6.42e+01 1b7gO 340 6.43e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 2cwsA 237 6.49e+01 1s3aA 102 6.50e+01 1wi5A 119 6.53e+01 2bolA 314 6.57e+01 2aa1A 144 6.60e+01 1xdfA 157 6.61e+01 1xcrA 316 6.62e+01 1mxmA 254 6.64e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1tzzA 392 6.67e+01 2atzA 180 6.70e+01 1wqgA 185 6.72e+01 1azo 232 6.79e+01 1azo c.52.1.14 33329 1zyoA 191 6.80e+01 1s1dA 331 6.81e+01 b.67.3.1 98344 1fjgI 128 6.85e+01 1fjfI d.14.1.1 37559 1v7oA 165 6.85e+01 d.67.1.2 100480 2gmqA 118 6.87e+01 2ap1A 327 6.87e+01 1hdhA 536 6.95e+01 c.76.1.2 65805 1o7dE 126 7.03e+01 2bdvA 231 7.04e+01 2f7tA 227 7.08e+01 1ilr1 152 7.12e+01 1irp 1bbt1 213 7.13e+01 1qqp1 2amhA 207 7.13e+01 1q92A 197 7.16e+01 c.108.1.8 96250 1gmeA 151 7.19e+01 b.15.1.1 65305 2bexA 460 7.20e+01 1c0pA 363 7.25e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1is1A 185 7.27e+01 d.67.3.1 83704 2eveA 157 7.33e+01 1ysrA 150 7.45e+01 1pvmA 184 7.47e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1aym3 238 7.49e+01 1aym3 1uh5A 329 7.49e+01 c.2.1.2 107840 1l4dB 122 7.50e+01 d.15.5.1 77684 1lwjA 441 7.50e+01 b.71.1.1,c.1.8.1 74303,74304 1zboA 210 7.52e+01 2a6hD 1524 7.53e+01 1ej1A 190 7.56e+01 1ejhA d.86.1.1 40144 2auwA 170 7.66e+01 2ayh 214 7.69e+01 1axkA b.29.1.2 24172 1mh9A 197 7.76e+01 c.108.1.8 79118 2bkrA 212 7.79e+01 1n71A 180 7.85e+01 d.108.1.1 85370 2cz2A 223 7.86e+01 1tn3 137 7.89e+01 1htn d.169.1.1 42423 1gs5A 258 7.98e+01 c.73.1.2 70395 1fthA 122 8.02e+01 d.150.1.2 60028 1rxxA 421 8.08e+01 d.126.1.4 98061 1gr3A 160 8.11e+01 b.22.1.1 65476 1nfp 228 8.30e+01 1nfp c.1.16.2 29555 1fjgS 93 8.30e+01 1qkfA d.28.1.1 38451 2f9hA 129 8.31e+01 2bltA 361 8.37e+01 1gceA e.3.1.1 42739 2aibA 98 8.41e+01 1binB 143 8.45e+01 2gdm a.1.1.2 15232 1qddA 144 8.48e+01 1qddA d.169.1.1 42324 1zwxA 301 8.49e+01 2an9A 207 8.50e+01 1f2tB 148 8.51e+01 1f2tB 1ytqA 204 8.58e+01 1zghA 260 8.59e+01 1xg9A 260 8.62e+01 1irdB 146 8.64e+01 a.1.1.2 66287 1mhyD 521 8.69e+01 1mhyD a.25.1.2 16780 1mspA 126 8.70e+01 1mspA b.1.11.2 22333 2biwA 490 8.70e+01 1mpuA 138 8.74e+01 d.169.1.1 85040 1fxkC 133 8.75e+01 1fxkC a.2.5.1 15702 1amx 180 8.77e+01 1amx b.2.3.1 22410 1jyoA 130 8.81e+01 d.198.1.1 67483 1j0hA 588 8.83e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1gcvA 140 8.86e+01 1cg5B a.1.1.2 15410 1qtnA 164 8.86e+01 1pauA c.17.1.1 30999 1m2dA 110 8.88e+01 c.47.1.11 78476 1srqA 341 8.95e+01 e.55.1.1 105967 1ro5A 201 8.96e+01 d.108.1.3 105023