# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 1yndA 165 7.07e-13 1dywA 173 7.72e-13 2cpl b.62.1.1 27505 1ihgA 370 8.60e-13 2cpl a.118.8.1,b.62.1.1 62380,62381 1h0pA 182 3.43e-12 b.62.1.1 76450 1lopA 164 1.40e-09 2cpl b.62.1.1 27510 1juvA 193 7.67e-01 c.71.1.1 90912 1i8dA 213 9.10e-01 b.43.4.3,b.43.4.3 61953,61954 1jyaA 130 1.16e+00 d.198.1.1 67453 1em2A 229 1.77e+00 1em2A d.129.3.2 41321 1ja1A 622 2.06e+00 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1mh1 186 2.43e+00 1eesA c.37.1.8 32002 1h9mA 145 2.97e+00 1h9jA b.40.6.2,b.40.6.2 60833,60834 2gf9A 189 3.22e+00 1fvuB 125 3.22e+00 1ixxB d.169.1.1 42346 1jssA 224 3.55e+00 d.129.3.2 71844 1vr8A 142 3.62e+00 1fl1A 230 3.73e+00 1at3A b.57.1.1 27023 1dg9A 157 3.74e+00 1dg9A c.44.1.1 32637 1gpc 218 3.81e+00 1gpc b.40.4.7 25393 1rhs 296 4.64e+00 1rhs c.46.1.2,c.46.1.2 32703,32704 1fjgQ 105 4.73e+00 1fjfQ b.40.4.5 25352 1g0sA 209 5.07e+00 1g0sA d.113.1.1 60187 1vknA 351 5.72e+00 c.2.1.3,d.81.1.1 108676,108677 1tjxA 159 5.82e+00 1pbyA 489 5.84e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1htwA 158 6.63e+00 c.37.1.18 71083 1ve2A 235 6.68e+00 1in0A 163 6.84e+00 d.58.49.1,d.58.49.1 83694,83695 1s0aA 429 7.00e+00 c.67.1.4 98263 1cbf 285 7.14e+00 1cbf c.90.1.1 35587 1h6tA 291 7.24e+00 b.1.18.15,c.10.2.1 65686,65687 1lugA 259 7.31e+00 b.74.1.1 91127 1bqk 124 7.60e+00 1bqk b.6.1.1 22889 1k07A 263 7.82e+00 d.157.1.1 77218 1o8bA 219 8.17e+00 c.124.1.4,d.58.40.1 81180,81181 1aisA 182 8.17e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1rkiA 102 8.48e+00 2sli 679 8.48e+00 2sli b.29.1.9,b.68.1.1 24274,27611 1lfpA 249 8.82e+00 e.39.1.1 73885 1mixA 206 9.23e+00 a.11.2.1,b.55.1.5 79166,79167 1lq9A 112 9.35e+00 d.58.4.3 78129 1jh6A 189 9.54e+00 d.61.1.1 66707 1jc4A 148 9.70e+00 1jc4A d.32.1.4 62863 1x8qA 184 9.81e+00 1vfjA 116 9.81e+00 1fsgA 233 9.89e+00 1qk3A c.61.1.1 34029 2bkxA 242 9.96e+00 1nkiA 135 1.03e+01 d.32.1.2 91941 1faaA 124 1.03e+01 1erv c.47.1.1 32738 1vlyA 338 1.04e+01 b.44.2.1,d.250.1.1 108871,108872 1ej8A 140 1.08e+01 1qupA b.1.8.1 22300 1uylA 236 1.09e+01 d.122.1.1 108147 1brwA 433 1.10e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1h4vB 421 1.11e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 3cla 213 1.12e+01 3cla c.43.1.1 32610 1qh5A 260 1.12e+01 1qh5A d.157.1.2 42057 1kaeA 434 1.13e+01 c.82.1.2 72247 1v5vA 401 1.15e+01 1xocA 520 1.16e+01 1fxxA 482 1.17e+01 1fxxA c.55.3.5 33726 1jndA 420 1.17e+01 c.1.8.5,d.26.3.1 71757,71758 1iq4A 179 1.17e+01 1iq4A d.77.1.1 62641 1lzlA 323 1.19e+01 c.69.1.2 78306 1f1xA 322 1.25e+01 d.32.1.3,d.32.1.3 83208,83209 1dc1A 323 1.27e+01 1dc1A c.52.1.11 33321 1dytA 133 1.31e+01 7rsa d.5.1.1 37288 1ikoP 178 1.31e+01 b.6.1.5 71243 1tyjA 170 1.31e+01 1g8sA 230 1.32e+01 c.66.1.3 90507 1gmiA 136 1.33e+01 b.7.1.1 65309 1txlA 215 1.33e+01 b.60.1.4 107429 1mqoA 227 1.34e+01 d.157.1.1 103846 1v5iB 76 1.36e+01 1agjA 242 1.36e+01 1agjA b.47.1.1 25827 1xjvA 294 1.36e+01 1h70A 255 1.38e+01 1h70A d.126.1.3 60711 1v0wA 506 1.39e+01 d.136.1.2,d.136.1.2 108220,108221 3proC 166 1.48e+01 3proC d.52.1.1,d.52.1.1 38812,38813 1b5eA 246 1.49e+01 1b5eA d.117.1.1 41056 1cjaA 342 1.52e+01 1cjaA d.144.1.3 41708 1qw9A 502 1.54e+01 b.71.1.2,c.1.8.3 96466,96467 1jdw 423 1.54e+01 1jdw d.126.1.2 41129 1vjvA 415 1.55e+01 d.3.1.9 108632 1e9gA 286 1.56e+01 1wgjA b.40.5.1 59393 1f6bA 198 1.57e+01 c.37.1.8 64986 1dkuA 317 1.58e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1btn 106 1.58e+01 1btn b.55.1.1 26952 1gt1A 159 1.58e+01 b.60.1.1 90515 1bco 327 1.59e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1bebA 162 1.59e+01 1bebA b.60.1.1 27115 16pk 415 1.60e+01 16pk c.86.1.1 35454 1u7lA 392 1.61e+01 1h6uA 308 1.64e+01 b.1.18.15,c.10.2.1 65688,65689 1iseA 185 1.66e+01 d.67.3.1 90691 1dzkA 157 1.68e+01 1obpA b.60.1.1 27096 1yb3A 175 1.68e+01 1f8fA 371 1.69e+01 b.35.1.2,c.2.1.1 83246,83247 1je0A 236 1.69e+01 c.56.2.1 66581 1bdfA 235 1.71e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1rk6A 496 1.71e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 1qy1A 174 1.72e+01 b.60.1.1 96568 1p3dA 475 1.73e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1hq8A 123 1.76e+01 1b6e d.169.1.1 61127 1o6vA 466 1.76e+01 b.1.18.15,c.10.2.1 81099,81100 1cjxA 357 1.77e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1gnkA 112 1.77e+01 2pii d.58.5.1 39073 3nul 130 1.79e+01 3nul d.110.1.1 40891 1rc9A 221 1.82e+01 1f0xA 571 1.85e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1vjpA 394 1.87e+01 c.2.1.3,d.81.1.3 100828,100829 1f1uA 323 1.88e+01 d.32.1.3,d.32.1.3 83200,83201 1bli 483 1.88e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1o7iA 119 1.89e+01 b.40.4.3 86642 1im5A 180 1.92e+01 c.33.1.3 66211 1l3lA 234 1.92e+01 a.4.6.2,d.110.5.1 73541,73542 1c4oA 664 1.94e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1uscA 178 1.95e+01 b.45.1.2 99860 1y8oB 128 1.96e+01 1e5pA 151 1.97e+01 1bj7 b.60.1.1 59272 1u7iA 136 2.02e+01 d.32.1.7 107724 1lniA 96 2.03e+01 d.1.1.2 74046 1gpmA 525 2.03e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1n8kA 374 2.04e+01 b.35.1.2,c.2.1.1 80298,80299 1h5rA 293 2.05e+01 c.68.1.6 65623 1xy7A 166 2.08e+01 1h8eD 482 2.09e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1i40A 175 2.10e+01 b.40.5.1 66024 1d2fA 390 2.11e+01 1d2fA c.67.1.3 34411 1l3kA 196 2.13e+01 d.58.7.1,d.58.7.1 73539,73540 1o54A 277 2.13e+01 c.66.1.13 92482 1pa1A 310 2.19e+01 c.45.1.2 94404 1v30A 124 2.20e+01 1fljA 260 2.20e+01 2cba b.74.1.1 27954 1ekrA 161 2.20e+01 1ekrA d.58.21.1 39380 1i7dA 659 2.27e+01 1d6mA e.10.1.1 61886 1dkmA 410 2.30e+01 1dklA c.60.1.2 34000 1pj5A 830 2.31e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1cyx 205 2.34e+01 1cyx b.6.1.2 23023 1h80A 464 2.37e+01 b.80.1.8 65714 1ej0A 180 2.38e+01 1ej0A c.66.1.2 34179 1byrA 155 2.38e+01 1byrA d.136.1.1 41450 1jykA 254 2.39e+01 c.68.1.13 67458 1f60B 94 2.40e+01 1b64 d.58.12.1 39307 1idpA 172 2.42e+01 d.17.4.1 83685 1gqvA 135 2.42e+01 d.5.1.1 70376 1xppA 115 2.44e+01 1nrjA 158 2.44e+01 d.110.4.4 86124 1h4gA 207 2.45e+01 b.29.1.11 70863 1y0kA 209 2.47e+01 1vr5A 547 2.49e+01 1xk7A 408 2.50e+01 1ckmA 330 2.50e+01 1ckmA b.40.4.6,d.142.2.3 25358,41585 1o9wA 177 2.51e+01 b.2.3.5 86713 1h3qA 140 2.52e+01 d.110.4.3 76652 1x8gA 227 2.52e+01 1kicA 339 2.55e+01 c.70.1.1 72510 1h5bA 113 2.60e+01 1tvdA b.1.1.1 60638 1e8gA 560 2.61e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1gadO 330 2.61e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1fiqC 763 2.62e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1wddA 477 2.64e+01 1evyA 366 2.65e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1si6X 282 2.65e+01 1jhsA 188 2.67e+01 d.107.1.1 84172 1hr6A 475 2.69e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1uzbA 516 2.72e+01 c.82.1.1 100220 1d4oA 184 2.73e+01 1d4oA c.31.1.4 31748 1ks9A 291 2.74e+01 a.100.1.7,c.2.1.6 68857,68858 1dfmA 223 2.74e+01 1d2iA c.52.1.5 33295 1vioA 243 2.78e+01 d.265.1.3,d.66.1.5 100762,100763 1ec7A 446 2.80e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1nnhA 294 2.81e+01 d.104.1.1 92005 1ii7A 333 2.81e+01 1ii7A d.159.1.4 62415 1cqmA 101 2.82e+01 1ris d.58.14.1 39321 1h2bA 359 2.82e+01 b.35.1.2,c.2.1.1 90543,90544 1a53 247 2.83e+01 1a53 c.1.2.4 28564 1g5bA 221 2.86e+01 1g5bA d.159.1.3 60261 1vns 609 2.87e+01 1vns a.111.1.3 19061 1fxoA 293 2.87e+01 1g0rA c.68.1.6 34524 1lfwA 470 2.89e+01 c.56.5.4,d.58.19.1 77942,77943 1d1qA 161 2.90e+01 1dg9A c.44.1.1 32642 1dcs 311 2.90e+01 1dcs b.82.2.1 28124 1xzoA 174 2.91e+01 1g7sA 594 2.92e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1r8sA 164 2.92e+01 c.37.1.8 97247 1dz3A 130 2.95e+01 1dz3A c.23.1.1 31105 2bikB 313 2.95e+01 1jetA 517 2.96e+01 1jevA c.94.1.1 35718 1fzqA 181 2.96e+01 1hurA c.37.1.8 32060 1rcqA 357 2.99e+01 b.49.2.2,c.1.6.1 104882,104883 1gk9B 557 3.02e+01 1jer 138 3.03e+01 2cbp b.6.1.1 23022 1djxA 624 3.06e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1z57A 339 3.06e+01 1edg 380 3.07e+01 1edg c.1.8.3 28807 2arcA 164 3.07e+01 2arcA b.82.4.1 28148 1cuk 203 3.11e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1g87A 614 3.16e+01 a.102.1.2,b.2.2.2 83275,83276 1pfvA 551 3.17e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1rreA 200 3.23e+01 d.14.1.10 97791 1bj7 156 3.24e+01 1bj7 b.60.1.1 27113 1dnlA 199 3.26e+01 1ci0A b.45.1.1 25753 1ej2A 181 3.26e+01 1f9aA c.26.1.3 59414 1gk8A 475 3.32e+01 c.1.14.1,d.58.9.1 65234,65235 1n4wA 504 3.37e+01 c.3.1.2,d.16.1.1 91676,91677 1gsoA 431 3.38e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1h8dH 260 3.39e+01 5ptp 1m22A 503 3.39e+01 c.117.1.1 78464 1w50A 411 3.42e+01 b.50.1.2 109173 1c0pA 363 3.42e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1gd1O 334 3.43e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1fuiA 591 3.43e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1g6aA 271 3.44e+01 1btl e.3.1.1 42704 1ctqA 166 3.45e+01 1ctqA c.37.1.8 31965 1jmxA 494 3.45e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1ikpA 613 3.46e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1fxlA 167 3.47e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1ut1A 148 3.48e+01 b.2.3.6 108014 1byi 224 3.48e+01 1byi c.37.1.10 32199 1dbqA 289 3.52e+01 1qpzA c.93.1.1 35666 1x7dA 350 3.63e+01 1gqzA 274 3.63e+01 d.21.1.1,d.21.1.1 83311,83312 1ymkA 175 3.64e+01 1u0fA 564 3.66e+01 1s99A 200 3.68e+01 1jhfA 202 3.69e+01 a.4.5.2,b.87.1.1 63057,63058 1mgtA 174 3.70e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1afwA 393 3.70e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1g1tA 157 3.71e+01 d.169.1.1,g.3.11.1 65104,65105 1hbnC 248 3.72e+01 1mroC d.58.31.1 60902 1uufA 369 3.73e+01 b.35.1.2,c.2.1.1 100006,100007 1fh9A 312 3.73e+01 1taxA c.1.8.3 28913 1r2qA 170 3.74e+01 c.37.1.8 96874 1hyeA 313 3.74e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1jyeA 349 3.77e+01 c.93.1.1 67455 1ftrA 296 3.84e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1io2A 213 3.88e+01 1ekeA c.55.3.1 62612 1i4uA 181 3.94e+01 b.60.1.1 61732 1vpbA 451 3.96e+01 1jb3A 131 3.98e+01 1jc7A b.40.3.2 62833 1ihkA 174 4.00e+01 1bfg b.42.1.1 62384 1fthA 122 4.00e+01 d.150.1.2 60028 2por 301 4.01e+01 2por f.4.3.1 43759 1pvgA 418 4.08e+01 d.14.1.3,d.122.1.2 95161,95162 1fjrA 195 4.09e+01 1fjrA b.102.1.1 59855 1kw3B 292 4.09e+01 d.32.1.3,d.32.1.3 77549,77550 1m40A 263 4.12e+01 e.3.1.1 74437 1g291 372 4.12e+01 1g291 1ijbA 202 4.13e+01 c.62.1.1 71229 1eyeA 280 4.15e+01 1aj2 c.1.21.1 29672 1j6wA 175 4.17e+01 1j98A d.185.1.2 62663 1ehyA 294 4.18e+01 1ehyA c.69.1.11 34693 1g8kA 825 4.23e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1azsA 220 4.31e+01 1azsA d.58.29.1 39416 1vbiA 344 4.33e+01 1nrzA 164 4.35e+01 c.38.1.1 86131 1o4vA 183 4.38e+01 c.23.8.1 86628 1knmA 130 4.39e+01 b.42.2.1 72781 1pg4A 652 4.41e+01 e.23.1.1 88067 1vziA 126 4.42e+01 b.1.13.1,g.41.5.2 108967,108968 1kjwA 295 4.50e+01 b.34.2.1,c.37.1.1 68643,68644 1dkqA 410 4.52e+01 1dklA c.60.1.2 33998 1gqiA 708 4.54e+01 c.1.8.10,d.92.2.2 76279,76280 1a6jA 163 4.54e+01 1a6jA d.112.1.1 40915 1fonA 240 4.55e+01 5ptp b.47.1.2 26231 1jd0A 263 4.57e+01 2cba b.74.1.1 62888 1q8fA 313 4.61e+01 c.70.1.1 96203 1i2mA 216 4.62e+01 1byuA c.37.1.8 61568 1jovA 270 4.65e+01 b.30.5.7 84192 1yfqA 342 4.67e+01 1h4xA 117 4.70e+01 1auz c.13.2.1 60626 1l8rA 101 4.70e+01 a.6.1.4 73700 1gpqA 135 4.73e+01 d.233.1.1 83295 1x74A 360 4.74e+01 1vhnA 318 4.76e+01 c.1.4.1 100693 1gp0A 143 4.77e+01 b.64.1.1 70300 1xffA 240 4.78e+01 d.153.1.1 109580 1b35A 260 4.80e+01 1b35A b.121.4.1 23333 1fmb 104 4.80e+01 1fmb b.50.1.1 26777 1jfuA 186 4.86e+01 c.47.1.10 62940 1zjjA 263 4.86e+01 2trxA 108 4.88e+01 1thx c.47.1.1 32719 1cznA 169 4.88e+01 1rcf c.23.5.1 31181 1vmeA 410 4.92e+01 c.23.5.1,d.157.1.3 108893,108894 1evlA 401 4.92e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1jr2A 286 4.92e+01 c.113.1.1 67111 1sqeA 109 4.95e+01 d.58.4.5 105908 1g8lA 411 4.95e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1yxyA 234 4.96e+01 1ewnA 219 4.97e+01 1bnkA b.46.1.2 25762 1gttA 429 4.97e+01 d.177.1.1,d.177.1.1 70529,70530 1gu7A 364 4.98e+01 b.35.1.2,c.2.1.1 83321,83322 2ci9A 102 4.98e+01 1bkpA 278 5.13e+01 1bkpA d.117.1.1 41029 1p90A 145 5.15e+01 c.55.5.2 94377 1suuA 312 5.15e+01 b.68.10.1 99006 1gxyA 226 5.20e+01 d.166.1.3 76380 1jb7B 260 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