# List of top-scoring protein chains for t04-100-30-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.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 2jz5A 91 7.91e-15 2qx2A 344 5.12e-01 2yxyA 115 5.19e-01 1u55A 188 5.41e-01 d.278.1.1 107677 2ux9A 69 5.59e-01 2cz8A 69 8.89e-01 2obdA 476 9.66e-01 1k2yX 463 1.02e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1p5dX 463 1.10e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1icxA 155 1.21e+00 d.129.3.1 71191 1skoB 130 1.53e+00 d.110.7.1 105677 2cy7A 396 1.63e+00 1vetB 125 2.00e+00 d.110.7.1 108554 2g6yA 217 2.17e+00 1a6zA 275 2.23e+00 1agdA b.1.1.2,d.19.1.1 20781,38280 2fjlA 150 2.70e+00 b.55.1.1 133611 1th7A 81 2.72e+00 b.38.1.1 119264 1kcgC 178 3.04e+00 d.19.1.1 68440 1u58A 253 3.22e+00 2rb9A 334 3.22e+00 2cstA 411 3.33e+00 1ajsA c.67.1.1 34273 2ah6A 208 3.53e+00 2iykA 162 3.55e+00 1y23A 145 3.86e+00 d.13.1.1 116394 1r7lA 110 3.88e+00 d.277.1.1 104837 2o5aA 125 4.04e+00 2e5vA 472 4.39e+00 1wsrA 375 4.44e+00 1xkzA 255 4.97e+00 e.3.1.1 115426 2g30A 258 5.55e+00 b.1.10.1,d.105.1.1 134546,134547 1yycA 174 5.73e+00 3b8mA 280 5.85e+00 2z1eA 342 5.97e+00 2zfzA 79 6.03e+00 2pvpA 367 6.23e+00 1ttwA 138 6.29e+00 d.198.1.1 107308 2q22A 139 6.34e+00 2hqkA 219 6.36e+00 2r2zA 93 6.46e+00 1y4oA 104 6.65e+00 1eaf 243 6.72e+00 1eaf 1vq2A 193 6.81e+00 c.97.1.2 114004 2rn2 155 7.03e+00 2rn2 1n3yA 198 7.32e+00 c.62.1.1 79976 1dpbA 243 7.33e+00 c.43.1.1 32618 2z1uA 343 7.48e+00 1gyhA 318 7.50e+00 b.67.2.1 70757 1e42A 258 7.70e+00 1e42A b.1.10.1,d.105.1.1 22316,40792 2pptA 155 7.86e+00 1ss9A 311 8.16e+00 c.68.1.4 105978 2fipA 115 8.22e+00 1mkmA 249 8.24e+00 a.4.5.33,d.110.2.2 79242,79243 1gydB 315 8.25e+00 b.67.2.1 70751 1irsA 112 8.50e+00 1qqgA b.55.1.2 26991 1jl2A 156 9.07e+00 c.55.3.1 66822 2fokA 579 9.13e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1mai 131 9.34e+00 1mai 1maiA 131 9.34e+00 b.55.1.1 26951 1uhvA 500 9.36e+00 b.71.1.2,c.1.8.3 99402,99403 1fnoA 417 9.52e+00 d.58.19.1,c.56.5.4 70145,75841 1tkeA 224 9.60e+00 d.15.10.1,d.67.1.1 112470,112471 1pjqA 457 9.61e+00 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1ylxA 103 9.64e+00 d.82.5.1 123677 1zb9A 143 9.67e+00 2iruA 303 9.79e+00 1sf9A 128 9.83e+00 b.34.15.1 98831 1qgvA 142 1.01e+01 1qgvA c.47.1.8 33056 3bueA 79 1.03e+01 1wr2A 238 1.10e+01 1we0A 187 1.11e+01 c.47.1.10 120930 1k5nA 276 1.12e+01 b.1.1.2,d.19.1.1 77266,77267 1yixA 265 1.13e+01 c.1.9.12 123371 1f45B 197 1.13e+01 1f45B a.26.1.1 59642 1rlhA 173 1.15e+01 d.256.1.1 97646 2gagA 965 1.17e+01 2dkhA 639 1.21e+01 1uouA 474 1.22e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1p3dA 475 1.25e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 3bv0A 437 1.28e+01 2h6bA 250 1.28e+01 1vk8A 106 1.33e+01 d.58.48.1 108636 1g3p 217 1.33e+01 1g3p 1g3pA 217 1.33e+01 b.37.1.1,b.37.1.1 24788,24789 2ftrA 108 1.34e+01 d.58.4.15 134077 3blcA 330 1.37e+01 2i39A 137 1.39e+01 1cy9A 264 1.39e+01 1ecl e.10.1.1 43236 1vixA 420 1.41e+01 c.56.5.4,d.58.19.1 100777,100778 2b1pA 355 1.44e+01 d.144.1.7 127672 2hytA 197 1.46e+01 2pspA 106 1.46e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1pqzA 238 1.47e+01 b.1.1.2,d.19.1.1 104297,104298 1evhA 112 1.50e+01 1evhA b.55.1.4 26997 2aehA 369 1.51e+01 a.11.2.1,b.55.1.5,d.15.1.4 126625,126626,126627 1xwyA 264 1.52e+01 c.1.9.12 122411 1c7nA 399 1.54e+01 1d2fA c.67.1.3 34413 2i5uA 83 1.54e+01 1ko3A 230 1.57e+01 d.157.1.1 90974 1ay7B 89 1.58e+01 1ay7B c.9.1.1 30836 2azwA 148 1.60e+01 d.113.1.1 127615 3bevA 274 1.61e+01 1jfmA 174 1.62e+01 d.19.1.1 66640 3bs6A 280 1.64e+01 2o0uA 364 1.66e+01 d.144.1.7 138868 3cj8A 236 1.67e+01 2cqeA 98 1.70e+01 g.66.1.1,g.66.1.1 130720,130721 2je8A 848 1.70e+01 1yspA 181 1.75e+01 2dtcA 126 1.76e+01 3bwaA 276 1.80e+01 1mw9X 592 1.87e+01 e.10.1.1 91480 1t7vA 278 1.89e+01 b.1.1.2,d.19.1.1 112302,112303 1xh3A 276 1.90e+01 b.1.1.2,d.19.1.1 115287,115288 2imjA 166 1.90e+01 1ga8A 311 1.90e+01 1ga8A c.68.1.4 34516 2hd5A 359 1.91e+01 1f9mA 112 1.92e+01 1erv c.47.1.1 32736 2dy0A 190 1.94e+01 1uzmA 247 1.94e+01 c.2.1.2 119811 2uvjA 408 1.95e+01 1id0A 152 2.00e+01 d.122.1.3 66111 1ib8A 164 2.01e+01 b.38.2.1,d.52.4.1 71168,71169 2op5A 117 2.04e+01 1vbkA 307 2.12e+01 c.26.2.6,d.308.1.1 119957,119958 1e25A 282 2.13e+01 1e25A e.3.1.1 42731 1y93A 159 2.13e+01 d.92.1.11 122772 2b25A 336 2.15e+01 c.66.1.13 127699 2vr4A 846 2.18e+01 1tdtA 259 2.30e+01 3tdt b.81.1.2 28055 1ijbA 202 2.31e+01 c.62.1.1 71229 2ie2A 222 2.33e+01 1wl7A 312 2.34e+01 b.67.2.1 120996 1umgA 362 2.35e+01 d.280.1.1 107956 2fe3A 145 2.37e+01 1s9aA 257 2.38e+01 b.3.6.1 105379 2calA 154 2.46e+01 1qysA 106 2.47e+01 k.41.1.1 96603 1iq8A 582 2.52e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2av4A 162 2.54e+01 1in0A 163 2.55e+01 d.58.49.1,d.58.49.1 83694,83695 1pmnA 364 2.57e+01 d.144.1.7 94907 1ktbA 405 2.57e+01 b.71.1.1,c.1.8.1 72960,72961 1u04A 771 2.58e+01 b.34.14.1,c.55.3.10 107539,107540 1rcy 151 2.60e+01 1rcy 1xkgA 312 2.68e+01 d.3.1.1 122081 1zpwX 90 2.74e+01 d.58.58.1 125478 2a15A 139 2.81e+01 d.17.4.3 125973 2vjxA 846 2.85e+01 1xfdA 723 2.85e+01 b.70.3.1,c.69.1.24 115251,115252 1pyaB 228 2.87e+01 1pyaB 1t7sA 137 2.88e+01 a.7.7.1 106636 1e30A 155 2.91e+01 1rcy b.6.1.1 23016 1w4vA 119 2.92e+01 1iujA 106 2.95e+01 d.58.4.5 90701 2gpyA 233 2.95e+01 2cunA 410 3.00e+01 2ia7A 134 3.03e+01 1zq1C 633 3.09e+01 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 1ng4A 390 3.10e+01 c.3.1.2,d.16.1.3 85666,85667 1lucB 324 3.12e+01 1lucA c.1.16.1 29548 1dssG 333 3.15e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 1u14A 172 3.16e+01 c.51.4.3 107579 1th8A 145 3.20e+01 d.122.1.3 106908 2bvpA 276 3.20e+01 b.1.1.2,d.19.1.1 129291,129292 1qf6A 642 3.23e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1fnsA 196 3.27e+01 1auq c.62.1.1 34136 1wbiA 129 3.28e+01 1upqA 123 3.30e+01 b.55.1.1 113392 2za4B 90 3.32e+01 2j0fA 482 3.41e+01 2oojA 141 3.42e+01 1v5vA 401 3.44e+01 b.44.2.1,d.250.1.1 113539,113540 1a1oA 276 3.49e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 2olnA 397 3.49e+01 1tr0A 108 3.51e+01 d.58.4.4 107261 3biqA 467 3.53e+01 2db9A 149 3.54e+01 2rghA 571 3.55e+01 1rz2A 254 3.57e+01 b.100.1.1 105130 1a1nA 276 3.59e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 2jyaA 106 3.68e+01 1ryiA 382 3.75e+01 c.3.1.2,d.16.1.3 118813,118814 1v0aA 178 3.77e+01 b.18.1.30 119815 1r89A 437 3.89e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1exg 110 4.01e+01 1exg 2al6A 375 4.05e+01 a.11.2.1,b.55.1.5,d.15.1.4 126966,126967,126968 1xo8A 151 4.06e+01 b.1.25.1 115698 3tdt 274 4.09e+01 3tdt 3tdtA 274 4.09e+01 b.81.1.2 28053 2vadA 223 4.09e+01 2gw4B 162 4.09e+01 2bfgA 503 4.10e+01 b.71.1.2,c.1.8.3 128423,128424 1faaA 124 4.14e+01 1erv c.47.1.1 32738 2uubJ 105 4.14e+01 d.58.15.1 139941 1n13B 113 4.19e+01 2b5eA 504 4.19e+01 c.47.1.2,c.47.1.2,c.47.1.2,c.47.1.2 127888,127889,127890,127891 2q24A 194 4.21e+01 2o18A 340 4.22e+01 1f08A 148 4.30e+01 1f08A d.89.1.2 59564 1xhdA 173 4.38e+01 b.81.1.5 115295 2z0dA 357 4.38e+01 1lfoA 127 4.39e+01 b.60.1.2 27223 2iv2X 715 4.41e+01 b.52.2.2,c.81.1.1 137714,137715 2olgA 278 4.45e+01 1h70A 255 4.50e+01 1h70A d.126.1.3 60711 2v5iA 559 4.54e+01 2jsxA 95 4.58e+01 2d1hA 109 4.67e+01 a.4.5.50 131125 2ekdA 207 4.67e+01 1u8fO 335 4.69e+01 c.2.1.3,d.81.1.1 119626,119627 1nswA 105 4.75e+01 c.47.1.1 92097 1t0hA 132 4.76e+01 b.34.2.1 106207 2rcyA 262 4.79e+01 2csuA 457 4.80e+01 c.2.1.8,c.23.4.1,c.23.4.1 130781,130782,130783 2cjjA 93 4.82e+01 a.4.1.3 130540 1jk3A 158 4.82e+01 d.92.1.11 66790 1nuyA 337 4.82e+01 e.7.1.1 86213 2joeA 139 4.85e+01 1r9wA 145 4.86e+01 d.89.1.2 97264 2nlyA 245 4.86e+01 c.6.2.7 138364 2pfrA 294 4.87e+01 2pqpA 421 4.89e+01 2ikkA 173 4.89e+01 1qqgA 264 4.92e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 2bdtA 189 4.99e+01 c.37.1.25 128344 1q0pA 223 5.01e+01 c.62.1.1 95507 2dgbA 84 5.01e+01 1wdjA 187 5.08e+01 c.52.1.27 114536 1h98A 78 5.09e+01 d.58.1.2 65743 1j7gA 144 5.09e+01 c.110.1.1 84130 1jjeA 222 5.10e+01 1a7tA d.157.1.1 63117 1r55A 214 5.11e+01 d.92.1.9 111694 2uuzA 99 5.11e+01 3buuA 229 5.11e+01 1gsoA 431 5.14e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1avwB 171 5.15e+01 1wba b.42.4.1 25599 2nvrA 423 5.17e+01 2afbA 351 5.18e+01 c.72.1.1 126674 2amhA 207 5.19e+01 c.51.4.2 127019 2od6A 110 5.20e+01 1y7pA 223 5.30e+01 c.23.1.7,d.58.18.12 122708,122709 1kq6A 141 5.32e+01 d.189.1.1 91020 1a3wA 500 5.33e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1vqoU 66 5.38e+01 g.39.1.6 120382 2p0oA 372 5.38e+01 2qt3A 403 5.41e+01 3c10A 423 5.42e+01 1ww7A 160 5.43e+01 2vg0A 227 5.48e+01 2fb2A 340 5.52e+01 2hs8A 402 5.52e+01 2hdiA 639 5.52e+01 1jkeA 145 5.53e+01 c.110.1.1 66791 1zuxA 224 5.54e+01 3ciwA 348 5.54e+01 1mqvA 125 5.56e+01 a.24.3.2 79415 1pv9A 348 5.61e+01 c.55.2.1,d.127.1.1 95157,95158 1drw 273 5.66e+01 1drw 1drwA 273 5.66e+01 c.2.1.3,d.81.1.3 30057,39972 2g3bA 208 5.67e+01 a.4.1.9,a.121.1.1 134558,134559 1kkeA 210 5.70e+01 b.83.1.2,b.21.1.2 68669,68670 1qxyA 252 5.71e+01 d.127.1.1 96565 1iznB 277 5.73e+01 e.43.1.2 83848 1cydA 244 5.74e+01 1cydA c.2.1.2 29825 2fp4B 395 5.74e+01 c.23.4.1,d.142.1.4 133897,133898 1i58A 189 5.76e+01 1b3qA d.122.1.3 61773 2bs9A 503 5.80e+01 b.71.1.2,c.1.8.3 129062,129063 2ywlA 180 5.82e+01 2avdA 219 5.83e+01 c.66.1.1 127377 2asfA 137 5.86e+01 b.45.1.1 127253 1txjA 171 5.91e+01 b.88.1.2 107424 2vsmA 416 5.94e+01 1bywA 110 5.96e+01 1bywA d.110.3.6 40912 2ys1A 113 6.02e+01 1nb9A 147 6.03e+01 b.43.5.1 85515 1zl0A 311 6.03e+01 c.8.10.1,c.23.16.7 125231,125232 2gw3A 225 6.05e+01 1shwB 181 6.05e+01 b.18.1.4 105563 1j5kA 89 6.14e+01 d.51.1.1 71565 1b7gO 340 6.16e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1yx1A 264 6.18e+01 c.1.15.7 124169 1u5fA 148 6.19e+01 b.55.1.1 119542 2j13A 247 6.21e+01 c.6.2.3 137934 2if1A 126 6.30e+01 d.64.1.1 39547 1vkwA 218 6.33e+01 d.90.1.2 108695 2bvyA 475 6.37e+01 b.1.18.2,c.1.8.3 129301,129302 1pfsA 78 6.39e+01 1pfsA b.40.4.7 25391 2ptfA 233 6.45e+01 1y4iA 398 6.48e+01 c.67.1.3 122619 1wstA 417 6.56e+01 c.67.1.1 121244 1oyc 400 6.57e+01 1oyc 1oycA 400 6.57e+01 c.1.4.1 28603 1q7lA 198 6.62e+01 c.56.5.4 96044 1qb2A 109 6.66e+01 1qb2A a.36.1.1 17125 1go4A 205 6.67e+01 d.135.1.1 70292 1f9vA 347 6.70e+01 1bg2 c.37.1.9 59745 2aydA 76 6.72e+01 1l2mA 118 6.75e+01 d.89.1.4 77657 2bj0A 203 6.77e+01 2dsjA 423 6.80e+01 1cfb 205 6.81e+01 1cfb 1cfbA 205 6.81e+01 b.1.2.1,b.1.2.1 21991,21992 1fo3A 460 6.90e+01 1dl2A a.102.2.1 18845 3cgvA 397 6.91e+01 2nm0A 253 6.93e+01 2ftsA 419 6.94e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 2nxfA 322 6.96e+01 2aunA 317 6.99e+01 c.8.10.1,c.23.16.7 127334,127335 1tv8A 340 7.00e+01 c.1.28.3 107352 2fltA 149 7.05e+01 1cs0A 1073 7.07e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 2vn6A 151 7.11e+01 3bgyA 237 7.14e+01 2pu9C 111 7.15e+01 2ch4A 320 7.16e+01 b.40.7.1,d.122.1.3 130447,130448 2hsaA 402 7.16e+01 1nw2A 105 7.19e+01 c.47.1.1 92215 2camA 127 7.23e+01 1swuA b.61.1.1 27407 2cvjA 180 7.31e+01 2dvzA 314 7.35e+01 2nrqA 159 7.35e+01 2prvA 153 7.36e+01 1j9yA 385 7.38e+01 1j9yA c.1.8.3 62791 2aumA 317 7.39e+01 c.8.10.1,c.23.16.7 127330,127331 1zrsA 317 7.40e+01 c.8.10.1,c.23.16.7 125556,125557 1wteA 272 7.47e+01 c.52.1.29 114876 1u2zA 433 7.50e+01 c.66.1.31 107626 1tz0A 114 7.51e+01 d.58.4.5 107463 1a9xA 1058 7.53e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 2av7A 275 7.54e+01 b.1.1.2,d.19.1.1 127359,127360 1tw0A 157 7.71e+01 d.129.3.1 119364 1zo2A 129 7.72e+01 2f02A 323 7.72e+01 c.72.1.1 132649 2jigA 224 7.76e+01 1jjtA 228 7.77e+01 1a7tA d.157.1.1 63139 2b9wA 424 7.77e+01 1rvv1 154 7.81e+01 1rvv1 1q8iA 783 7.86e+01 c.55.3.5,e.8.1.1 96208,96209 2bsxA 253 7.93e+01 c.56.2.1 129128 1zzkA 82 7.94e+01 d.51.1.1 125909 2c81A 418 7.95e+01 1yx2A 365 7.96e+01 2fggA 101 7.97e+01 d.50.5.1 133438 1kveB 77 7.97e+01 1kveB