# List of top-scoring protein chains for t06-100-30-alpha-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 1o0sA 605 8.30e-01 c.2.1.7,c.58.1.3 86540,86541 1fjrA 195 1.27e+00 1fjrA b.102.1.1 59855 1ocxA 182 1.55e+00 b.81.1.3 86814 1ex7A 186 1.57e+00 1gky c.37.1.1 59537 2bmwA 304 1.65e+00 1fnd 314 1.70e+00 1fnc b.43.4.2,c.25.1.1 25626,31516 1gky 187 1.78e+00 1gky c.37.1.1 31839 1ogiA 303 1.89e+00 b.43.4.2,c.25.1.1 92914,92915 1bx1A 314 1.92e+00 1fnc b.43.4.2,c.25.1.1 25629,31519 1sxvA 172 2.01e+00 1mwwA 128 2.20e+00 d.80.1.4 91483 2a9dA 372 2.49e+00 1jltB 122 2.95e+00 a.133.1.2 66868 1tu1A 148 3.30e+00 d.107.1.3 107316 1ly1A 181 3.30e+00 c.37.1.1 74334 1dbhA 354 4.22e+00 1awe a.87.1.1,b.55.1.1 18514,26967 2f1lA 187 4.32e+00 1dy9A 187 4.81e+00 1jxpA b.47.1.3 26400 1ltqA 301 5.01e+00 c.108.1.9,c.37.1.1 78208,78209 1xd3A 230 5.26e+00 1dp4A 435 5.42e+00 1dp4A c.93.1.1 35710 1dkzA 219 5.53e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 1cjxA 357 5.54e+00 1cjxA d.32.1.3,d.32.1.3 38516,38517 2b6nA 278 6.07e+00 1aym3 238 6.33e+00 1aym3 1pyaB 228 6.71e+00 1pyaB 1bb9 115 6.99e+00 1bb9 b.34.2.1 24554 2axyA 73 7.34e+00 1gdvA 85 7.54e+00 1ctj a.3.1.1 60458 2cyeA 133 7.75e+00 1t46A 313 7.88e+00 d.144.1.7 106397 1ifrA 121 8.03e+00 b.1.16.1 71203 1x9gA 200 8.19e+00 c.33.1.3 109527 1ryoA 327 8.40e+00 c.94.1.2 98108 1zj8A 566 8.54e+00 1b65A 375 8.76e+00 1b65A d.154.1.1 42020 1y4wA 518 9.07e+00 1vj2A 126 9.20e+00 b.82.1.10 100796 1ywnA 316 9.77e+00 1g55A 343 9.85e+00 1g55A c.66.1.26 34247 1xkzA 255 9.90e+00 1vk0A 206 9.99e+00 c.55.3.5 100839 2b1xA 470 1.02e+01 2cjtA 131 1.05e+01 2gj8A 172 1.13e+01 1gcqC 70 1.14e+01 1gcpA b.34.2.1 60436 1ra0A 430 1.16e+01 2b18A 164 1.20e+01 3sil 379 1.21e+01 3sil b.68.1.1 27542 1jxcA 68 1.25e+01 g.3.7.5 77201 2cz2A 223 1.28e+01 1o4tA 133 1.28e+01 b.82.1.9 86622 1xl3C 92 1.29e+01 1j3wA 163 1.30e+01 d.110.7.1 90833 1mwmA 320 1.32e+01 c.55.1.1,c.55.1.1 79580,79581 1i19A 561 1.35e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1to2E 281 1.36e+01 1gppA 237 1.38e+01 b.86.1.2 76262 1dmhA 311 1.38e+01 1dmhA b.3.6.1 22633 2fimA 276 1.39e+01 1y43B 173 1.41e+01 1j1bA 420 1.41e+01 d.144.1.7 90758 1rlw 126 1.45e+01 1rlw b.7.1.1 23177 1tqnA 486 1.47e+01 a.104.1.1 107238 2bpsA 81 1.47e+01 1kdj 102 1.50e+01 1plc b.6.1.1 22864 1yemA 179 1.50e+01 1za7A 165 1.51e+01 1ujnA 348 1.52e+01 e.22.1.1 99460 2blkA 122 1.60e+01 1h4rA 314 1.62e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1rq2A 382 1.71e+01 c.32.1.1,d.79.2.1 105048,105049 1j1lA 290 1.71e+01 b.82.1.12 90766 1cruA 454 1.76e+01 1c9uA b.68.2.1 27617 1s4iA 175 1.81e+01 2hf9A 226 1.82e+01 2f1rA 171 1.88e+01 1rliA 184 1.91e+01 c.23.5.6 97647 1y8oB 128 1.92e+01 2eifA 136 1.93e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1nqeA 594 2.00e+01 f.4.3.3 86027 1fuiA 591 2.02e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1sbzA 197 2.10e+01 2avtA 378 2.11e+01 1g8aA 227 2.12e+01 c.66.1.3 90506 1m0wA 491 2.13e+01 c.30.1.4,d.142.1.6 78363,78364 2fmlA 273 2.16e+01 1afwA 393 2.17e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 2c0nA 203 2.19e+01 1po5A 476 2.20e+01 a.104.1.1 94963 1cl8A 276 2.25e+01 1ckqA c.52.1.1 33230 1x82A 190 2.25e+01 2cu3A 64 2.26e+01 2aegA 268 2.30e+01 1ru0A 105 2.30e+01 1s21A 206 2.31e+01 d.166.1.4 105222 1yzfA 195 2.35e+01 1xg8A 111 2.37e+01 1rjiA 31 2.43e+01 g.3.7.2 97568 1o0iA 138 2.43e+01 d.38.1.5 86532 1fxoA 293 2.50e+01 1g0rA c.68.1.6 34524 2a5jA 191 2.58e+01 1qy1A 174 2.59e+01 b.60.1.1 96568 1w85A 368 2.62e+01 1ixcA 294 2.67e+01 a.4.5.37,c.94.1.1 83764,83765 1b9wA 89 2.70e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2gpyA 233 2.70e+01 1ze3D 125 2.73e+01 1ik9A 213 2.74e+01 b.59.1.1,h.1.11.1 66176,66177 1ycdA 243 2.75e+01 1h8eH 146 2.75e+01 1e79H b.93.1.1 60757 1yn4A 99 2.82e+01 1g2nA 264 2.84e+01 1lbd a.123.1.1 60227 1cp2A 269 2.86e+01 1cp2A c.37.1.10 32269 1dm9A 133 2.88e+01 1dm9A d.66.1.3 39560 1zndA 174 2.98e+01 1sqeA 109 3.02e+01 d.58.4.5 105908 1d8hA 311 3.02e+01 1d8iA d.63.1.1 39544 1t61A 229 3.04e+01 d.169.1.6,d.169.1.6 106529,106530 1v8fA 276 3.08e+01 c.26.1.4 100503 1bs0A 384 3.10e+01 1bs0A c.67.1.4 34490 2d4rA 147 3.17e+01 1wd6A 123 3.23e+01 1ebfA 358 3.24e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1j9lA 247 3.29e+01 c.106.1.1 62762 1fjgE 162 3.29e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1x0vA 354 3.31e+01 1eljA 381 3.32e+01 4mbp c.94.1.1 35791 1kao 167 3.32e+01 1ctqA c.37.1.8 32014 1wloA 136 3.34e+01 1lst 239 3.39e+01 1lst c.94.1.1 35755 1udc 338 3.43e+01 1xel c.2.1.2 29785 1wi9A 72 3.44e+01 1nnvA 110 3.45e+01 d.17.7.1 92012 1opd 85 3.46e+01 1ptf d.94.1.1 40560 1ra9 159 3.48e+01 1vdrA c.71.1.1 34820 3proC 166 3.50e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1f5mA 180 3.51e+01 1f5mB d.110.2.1 40895 1dosA 358 3.56e+01 1dosA c.1.10.2 29175 1e19A 314 3.62e+01 1b7bA c.73.1.1 34967 1k7kA 221 3.69e+01 c.51.4.1 72104 1twuA 139 3.69e+01 d.32.1.8 107413 1r6wA 322 3.70e+01 c.1.11.2,d.54.1.1 97165,97166 2bjuA 453 3.72e+01 1kbvA 327 3.75e+01 b.6.1.3,b.6.1.3 68395,68396 2bkyA 97 3.76e+01 1ufkA 254 3.79e+01 c.66.1.39 99340 1y5eA 169 3.82e+01 2afwA 329 3.86e+01 1vl2A 421 3.89e+01 c.26.2.1,d.210.1.1 108708,108709 1fadA 99 3.90e+01 1fadA a.77.1.2 18428 2bopA 85 3.93e+01 2bopA d.58.8.1 39217 1o7dE 126 3.97e+01 2iugA 120 3.98e+01 1w2lA 99 4.03e+01 1xaoA 121 4.12e+01 2ffcA 353 4.13e+01 2gm5A 139 4.16e+01 2faoA 309 4.18e+01 2rslA 140 4.20e+01 2rslA c.53.1.1 33345 1gs5A 258 4.21e+01 c.73.1.2 70395 2gu2A 312 4.27e+01 1jp4A 308 4.29e+01 1jp4A e.7.1.1 63223 1ru4A 400 4.33e+01 b.80.1.9 97836 1pg6A 243 4.34e+01 b.82.5.2 94673 1zt2B 212 4.45e+01 2ge7A 108 4.47e+01 1rybA 212 4.54e+01 c.56.3.1 98098 1shyB 551 4.59e+01 b.69.12.1,g.16.2.1 105565,105566 1ryqA 69 4.63e+01 g.41.9.3 105126 1wgkA 114 4.66e+01 1mrzA 293 4.67e+01 b.43.5.1,c.26.1.3 91452,91453 1zgoA 223 4.70e+01 1jiwI 106 4.75e+01 1smpI b.61.2.1 63078 1k0wA 231 4.78e+01 c.74.1.1 77220 1tvdA 116 4.83e+01 1tvdA b.1.1.1 20650 1kzfA 230 4.92e+01 d.108.1.3 73354 1wqwA 235 4.94e+01 1w8oA 601 4.97e+01 1oaqL 120 5.05e+01 b.1.1.1 92708 1rwrA 301 5.06e+01 b.80.1.11 97990 2f7tA 227 5.07e+01 4dfrA 159 5.08e+01 1vdrA c.71.1.1 34822 1iwmA 186 5.18e+01 b.125.1.2 83758 1w96A 554 5.18e+01 2bh8A 101 5.24e+01 1kaeA 434 5.25e+01 c.82.1.2 72247 2f62A 161 5.27e+01 1lkkA 105 5.29e+01 1lckA d.93.1.1 40412 2cglA 489 5.31e+01 1vpqA 273 5.31e+01 1fmb 104 5.33e+01 1fmb b.50.1.1 26777 1g6hA 257 5.36e+01 1gajA c.37.1.12 60318 1ti6B 274 5.37e+01 b.3.5.1,d.58.1.5 106976,106977 1v93A 296 5.46e+01 c.1.23.1 100532 1fzqA 181 5.53e+01 1hurA c.37.1.8 32060 1o59A 355 5.56e+01 b.18.1.22,b.18.1.22 92495,92496 1wddS 128 5.56e+01 1zxuA 217 5.58e+01 1tuaA 191 5.60e+01 d.51.1.1,d.51.1.1 107321,107322 1y0zA 330 5.61e+01 1ta9A 450 5.65e+01 1ctj 89 5.69e+01 1ctj a.3.1.1 15798 1om4A 422 5.70e+01 d.174.1.1 87067 1k8kA 418 5.70e+01 c.55.1.1,c.55.1.1 68305,68306 2cviA 83 5.71e+01 1rgzA 363 5.75e+01 e.3.1.1 97457 1vlmA 219 5.76e+01 c.66.1.41 108836 1kte 105 5.78e+01 1kte c.47.1.1 32771 1y60A 169 5.78e+01 1v8yA 170 5.81e+01 1f39A 101 5.81e+01 1umuA b.87.1.1 28386 1oe1A 336 5.82e+01 b.6.1.3,b.6.1.3 86891,86892 1a4iA 301 5.83e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1yqfA 203 5.83e+01 2ai4A 119 5.84e+01 1wdvA 152 5.92e+01 1rwiA 270 5.93e+01 b.68.9.1 97987 1go3F 107 6.00e+01 a.60.8.2 65407 1zxkA 98 6.03e+01 2gxfA 142 6.08e+01 1je0A 236 6.09e+01 c.56.2.1 66581 1uj0A 62 6.14e+01 b.34.2.1 99449 1k6iA 352 6.20e+01 c.2.1.2 68223 1uj6A 227 6.20e+01 c.124.1.4,d.58.40.1 107898,107899 1k5cA 335 6.21e+01 b.80.1.3 72076 1lktA 104 6.27e+01 1lktA b.90.1.1 28398 1oxwA 373 6.29e+01 c.19.1.3 87539 2bf9A 36 6.31e+01 1yrkA 126 6.35e+01 1rwyA 109 6.36e+01 a.39.1.4 98002 1bj7 156 6.36e+01 1bj7 b.60.1.1 27113 2a2pA 129 6.38e+01 1hleA 345 6.40e+01 1ovaA e.1.1.1 42618 1i58A 189 6.40e+01 1b3qA d.122.1.3 61773 2cx1A 187 6.43e+01 1h30A 422 6.44e+01 b.29.1.4,b.29.1.4 76604,76605 1ignA 246 6.45e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 2ausB 60 6.46e+01 2gtqA 867 6.49e+01 1uteA 313 6.49e+01 1uteA d.159.1.1 42078 1jmcA 246 6.50e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1c8uA 285 6.50e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1jeyA 609 6.52e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1b8aA 438 6.56e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1xcbA 211 6.56e+01 a.4.5.38,c.2.1.12 109552,109553 1mnnA 340 6.58e+01 b.2.5.7 79324 1vd5A 377 6.62e+01 a.102.1.7 108518 1orc 71 6.63e+01 1orc a.35.1.2 17054 1eerB 227 6.66e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1f06A 320 6.67e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1r8oB 71 6.68e+01 1xtmA 175 6.68e+01 1t33A 224 6.72e+01 a.4.1.9,a.121.1.1 106295,106296 2bhvA 246 6.74e+01 2cc3A 150 6.82e+01 1m40A 263 6.84e+01 e.3.1.1 74437 2bsjA 133 6.90e+01 1ehiA 377 6.95e+01 1iow c.30.1.2,d.142.1.1 31716,41484 2b5lC 222 6.98e+01 1f7dA 136 6.98e+01 1dun b.85.4.1 28353 1bvoA 175 7.05e+01 1a3qA b.2.5.3 22457 1sr4C 166 7.05e+01 b.42.2.1 105950 2fv1A 377 7.09e+01 1utcA 363 7.09e+01 a.118.1.4,b.69.6.1 99914,99915 2a38A 194 7.12e+01 1b5pA 385 7.14e+01 c.67.1.1 90403 1jyhA 157 7.18e+01 d.60.1.3 71956 1gvp 87 7.19e+01 1gvp b.40.4.7 25369 1res 43 7.20e+01 1ret a.4.1.2 16023 1uekA 275 7.33e+01 d.14.1.5,d.58.26.5 88483,88484 2biiA 424 7.34e+01 2gs8A 317 7.37e+01 1wv9A 94 7.39e+01 1rxyA 253 7.39e+01 c.56.2.1 98065 1tp9A 162 7.41e+01 2bycA 137 7.42e+01 1ro5A 201 7.43e+01 d.108.1.3 105023 1qw1A 121 7.46e+01 2gdnA 267 7.46e+01 1uunA 184 7.48e+01 f.6.1.2 100012 1zdrA 164 7.53e+01 1ng2A 193 7.62e+01 b.34.2.1,b.34.2.1 85660,85661 1qexA 288 7.66e+01 1qexA b.32.1.1 24425 1jb9A 316 7.71e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 2a6sA 84 7.73e+01 1xgkA 352 7.78e+01 1a32 88 7.84e+01 1a32 a.16.1.2 16384 1jixA 351 7.89e+01 1c3jA c.87.1.1 63081 1b8oA 284 7.89e+01 1b8oA c.56.2.1 33762 1xneA 113 7.91e+01 2czvC 120 7.91e+01 2czdA 208 7.95e+01 2a9gA 418 7.96e+01 1x9iA 302 7.97e+01 1b34B 118 8.00e+01 1b34B b.38.1.1 24797 1deuA 277 8.00e+01 1theB d.3.1.1 37085 2g9iA 249 8.00e+01 1bw0A 416 8.11e+01 1bw0A c.67.1.1 34385 3tdt 274 8.15e+01 3tdt b.81.1.2 28053 1odkA 235 8.16e+01 c.56.2.1 86863 1vh4A 435 8.19e+01 b.80.6.1 100640 1v3vA 333 8.21e+01 b.35.1.2,c.2.1.1 108345,108346 1qg7A 67 8.21e+01 1a15A d.9.1.1 37449 1emzA 21 8.23e+01 j.35.1.1 46282 1lzjA 292 8.29e+01 c.68.1.9 74352 1g73C 121 8.30e+01 1g3fA g.52.1.1 45375 1uw4A 91 8.31e+01 d.58.7.4 100071 2c07A 285 8.32e+01 1ekeA 230 8.36e+01 1ekeA c.55.3.1 33572 1fdr 248 8.40e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1yqzA 438 8.45e+01 1r9jA 673 8.47e+01 1sddA 306 8.48e+01 b.6.1.3,b.6.1.3 105431,105432 1uxjA 309 8.57e+01 c.2.1.5,d.162.1.1 108112,108113 1dj0A 264 8.59e+01 1dj0A d.265.1.1 90337 1xr4A 509 8.61e+01 2fp7B 172 8.70e+01 2bkrA 212 8.75e+01 1svb 395 8.75e+01 1svb b.1.18.4,f.10.1.1 21814,43827 1v10A 521 8.79e+01 b.6.1.3,b.6.1.3,b.6.1.3 108224,108225,108226 1neeA 138 8.94e+01 d.241.1.1,g.59.1.1 91841,91842 2fcbA 173 8.96e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782