# 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 1wjxA 122 7.21e-01 2cblA 305 8.60e-01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1yvhA 329 1.06e+00 1vetA 124 1.09e+00 d.110.7.1 108553 2sak 121 1.14e+00 2sak d.15.5.1 37711 1q5hA 147 1.16e+00 b.85.4.1 95893 2ch8A 201 1.26e+00 1mzbA 136 1.28e+00 a.4.5.42 91497 1skoA 143 1.42e+00 d.110.7.1 105676 1fu1A 203 1.57e+00 1fu1B b.59.1.1,h.1.11.1 27076,45630 1u7bA 261 1.73e+00 2djkA 133 1.83e+00 1jj2T 66 2.14e+00 1ffkR g.39.1.6 63105 1s72U 66 2.14e+00 g.39.1.6 105340 1hleB 31 2.19e+00 1hleB 1syxB 86 2.29e+00 1rpyA 114 2.63e+00 d.93.1.1 97718 1aoeA 192 2.79e+00 1aoeA c.71.1.1 34923 1vqoU 66 2.90e+00 2aj6A 159 2.99e+00 1v52A 133 3.04e+00 1wi0A 113 3.05e+00 1yzbA 182 3.39e+00 1xs1A 193 3.42e+00 2b5iC 199 3.47e+00 1knwA 425 4.01e+00 b.49.2.3,c.1.6.1 90969,90970 1ig5A 75 4.25e+00 4icb a.39.1.1 62363 1mw7A 240 4.30e+00 e.39.1.1 79557 1mtpB 43 4.32e+00 1g5bA 221 5.18e+00 1g5bA d.159.1.3 60261 1shbA 104 5.35e+00 1fmk d.93.1.1 40425 1gyfA 62 5.89e+00 1gyfA d.76.1.1 39749 1uheA 97 5.94e+00 1cojA 212 6.00e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1k0wA 231 6.11e+00 c.74.1.1 77220 1qqrA 138 6.58e+00 1bmlC d.15.5.1 37721 1mg4A 113 6.60e+00 d.15.11.1 84953 1ermA 263 6.65e+00 1btl e.3.1.1 42690 1iz5A 249 6.67e+00 d.131.1.2,d.131.1.2 83834,83835 1at0 145 6.80e+00 1at0 b.86.1.1 28374 1ygs 234 6.90e+00 1ygs b.26.1.1 23907 1ze3C 205 7.24e+00 2f1kA 279 7.33e+00 1m40A 263 7.47e+00 e.3.1.1 74437 1o4rA 108 7.49e+00 d.93.1.1 92469 2a1rA 430 7.55e+00 1tufA 434 7.70e+00 b.49.2.3,c.1.6.1 107335,107336 2bsjA 133 7.86e+00 1tzpA 255 8.29e+00 d.65.1.3 107520 1khxA 227 8.42e+00 b.26.1.1 68631 1go4A 205 8.45e+00 d.135.1.1 70292 2fflA 756 8.71e+00 1tp9A 162 8.98e+00 1plq 258 9.29e+00 1plq d.131.1.2,d.131.1.2 41388,41389 1gxuA 91 9.78e+00 d.58.10.1 76378 1gpr 162 9.80e+00 1gpr b.84.3.1 28267 1fr3A 67 1.01e+01 1fr3A b.40.6.1 25436 1f7dA 136 1.03e+01 1dun b.85.4.1 28353 1twiA 434 1.03e+01 b.49.2.3,c.1.6.1 107399,107400 2fkiA 126 1.04e+01 1bfg 146 1.06e+01 1bfg b.42.1.1 25485 1wmhA 89 1.07e+01 1gutA 68 1.11e+01 b.40.6.1 65576 2axwA 134 1.15e+01 2bayA 61 1.16e+01 1bueA 265 1.23e+01 1btl e.3.1.1 42727 2f1lA 187 1.26e+01 1p65A 73 1.27e+01 d.254.1.1 94156 4icb 76 1.27e+01 4icb a.39.1.1 17145 1n9bA 265 1.27e+01 e.3.1.1 85463 1btl 263 1.28e+01 1btl e.3.1.1 42691 1lq8B 31 1.29e+01 2tgi 112 1.29e+01 2tgi g.17.1.2 44777 1pz1A 333 1.34e+01 c.1.7.1 95390 1kmdA 117 1.41e+01 d.189.1.1 72744 4fgf 146 1.43e+01 1bfg b.42.1.1 25486 1z1nX 560 1.43e+01 2aobA 99 1.45e+01 2fz4A 237 1.50e+01 2agyA 361 1.50e+01 1y71A 130 1.55e+01 1whzA 70 1.56e+01 1n3gA 113 1.63e+01 d.204.1.1 79962 1w24A 182 1.64e+01 2ey4C 82 1.65e+01 1h6fA 193 1.68e+01 b.2.5.4 70901 1xu6A 80 1.69e+01 1nvpD 108 1.75e+01 a.32.1.1,b.56.1.1 92213,92214 1x93A 55 1.75e+01 2bkyA 97 1.77e+01 1ef1A 294 1.85e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1lfc 25 1.85e+01 j.3.1.5 46074 1zdrA 164 1.92e+01 1nciA 110 1.93e+01 1edhA b.1.6.1 22191 1gg6B 131 1.98e+01 5ptp 1rwzA 245 1.98e+01 d.131.1.2,d.131.1.2 98005,98006 1mml 265 2.00e+01 1mml e.8.1.2 43015 1v05A 96 2.08e+01 1quqB 121 2.09e+01 1quqB b.40.4.3 25305 1i3zA 103 2.12e+01 d.93.1.1 83667 1ecrA 309 2.14e+01 1ecrA e.2.1.1 42678 1jsdB 176 2.16e+01 h.3.1.1 63259 1unnC 115 2.16e+01 d.240.1.1 99680 2trxA 108 2.19e+01 1thx c.47.1.1 32719 1vq0A 302 2.28e+01 1h0xA 100 2.30e+01 d.68.6.1 76451 1m93C 41 2.31e+01 1cmcA 104 2.32e+01 1cmbA a.43.1.5 17462 1vc3B 97 2.35e+01 1a48 306 2.36e+01 1a48 d.143.1.1 41590 1j55A 95 2.37e+01 a.39.1.2 77078 1oo0A 147 2.37e+01 d.232.1.1 87182 1gjwA 637 2.38e+01 b.71.1.1,c.1.8.1 60582,60583 2gqrA 237 2.39e+01 2arcA 164 2.41e+01 2arcA b.82.4.1 28148 1wi5A 119 2.43e+01 2gnrA 145 2.44e+01 1si2A 149 2.50e+01 b.34.14.1 105569 1auuA 55 2.51e+01 1auuA b.35.2.1 24769 1pbuA 162 2.53e+01 d.58.46.1 88030 2agaA 190 2.56e+01 1zowA 313 2.60e+01 1yphC 131 2.61e+01 1o54A 277 2.67e+01 c.66.1.13 92482 1f35A 162 2.73e+01 1f35A b.94.1.1 59628 2bh8A 101 2.76e+01 1tidB 119 2.80e+01 c.13.2.1 107000 1n5nA 180 2.81e+01 d.167.1.1 85336 1v3wA 173 2.86e+01 b.81.1.5 100291 1n0uA 842 2.94e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1ok7A 366 2.96e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 2gfaA 119 3.06e+01 1ghpA 258 3.11e+01 1btl e.3.1.1 60520 1x8vA 455 3.14e+01 1r7aA 504 3.16e+01 b.71.1.1,c.1.8.1 97192,97193 1ve6A 582 3.21e+01 1obdA 306 3.24e+01 d.143.1.1 86767 1owxA 121 3.29e+01 d.58.7.1 87494 1o17A 345 3.34e+01 a.46.2.1,c.27.1.1 80765,80766 1dmtA 696 3.38e+01 1dmtA d.92.1.4 40296 1f3z 161 3.39e+01 1gpr b.84.3.1 28273 1a8y 367 3.40e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1wi6A 88 3.43e+01 1krs 120 3.50e+01 1krs b.40.4.1 25256 1yewB 247 3.52e+01 1ik9A 213 3.53e+01 b.59.1.1,h.1.11.1 66176,66177 1deoA 233 3.57e+01 1deoA c.23.10.4 31345 1k7cA 233 3.60e+01 c.23.10.4 68267 1k2xB 143 3.61e+01 2g0qA 173 3.63e+01 2g2kA 170 3.64e+01 1lkkA 105 3.64e+01 1lckA d.93.1.1 40412 1mmiA 366 3.68e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1r1qA 100 3.68e+01 d.93.1.1 104763 2evbA 74 3.72e+01 1bdo 80 3.73e+01 1bdo b.84.1.1 28214 1o7fA 469 3.77e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1k8mA 93 3.77e+01 b.84.1.1 68314 1pqzA 238 3.81e+01 b.1.1.2,d.19.1.1 104297,104298 2cqeA 98 3.83e+01 1vd3A 217 3.93e+01 1o51A 114 4.00e+01 d.58.5.4 92480 2polA 366 4.07e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1tc6A 236 4.10e+01 d.122.1.1 106756 1vpkA 378 4.10e+01 1p0zA 131 4.12e+01 d.110.6.1 93882 1s72I 162 4.15e+01 a.4.7.1 105328 1r1hA 696 4.21e+01 d.92.1.4 104756 1g60A 260 4.27e+01 c.66.1.11 70151 1lhpA 312 4.34e+01 c.72.1.5 77960 1y6hA 177 4.40e+01 1yukA 103 4.40e+01 1v4pA 157 4.45e+01 1jb0D 138 4.48e+01 1jb0D d.187.1.1 62823 1th8A 145 4.49e+01 d.122.1.3 106908 1azo 232 4.53e+01 1azo c.52.1.14 33329 1rypJ 204 4.63e+01 d.153.1.4 41878 5croA 66 4.66e+01 1orc a.35.1.2 17044 1yopA 83 4.71e+01 2c1iA 431 4.73e+01 1jsuC 84 4.76e+01 1jsuC j.55.1.1 46339 1g38A 393 4.82e+01 2admA c.66.1.27 60235 1hl9A 449 4.90e+01 b.71.1.3,c.1.8.11 90650,90651 1cmbA 104 4.95e+01 1cmbA a.43.1.5 17460 1hqsA 423 5.00e+01 1iso c.77.1.1 61154 1jiwI 106 5.03e+01 1smpI b.61.2.1 63078 1aw8B 91 5.04e+01 1aw8B 1rypD 241 5.09e+01 1rypD d.153.1.4 41935 1idpA 172 5.16e+01 d.17.4.1 83685 1f39A 101 5.20e+01 1umuA b.87.1.1 28386 1vqoY 241 5.23e+01 1ct9A 553 5.24e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1e0fI 57 5.33e+01 1e0fI g.3.15.2 44377 8acn 754 5.35e+01 1amj c.8.2.1,c.83.1.1 30724,35400 2cfaA 217 5.36e+01 1apyB 141 5.43e+01 1apyB 1jj2H 167 5.43e+01 1ffkF d.41.4.1 63093 1flcB 175 5.45e+01 1flcB h.3.1.1 45716 1vqoI 162 5.49e+01 2b20A 403 5.49e+01 1shdA 107 5.50e+01 1fmk d.93.1.1 40440 1e79I 50 5.52e+01 1e79I a.137.8.1 19647 1u07A 90 5.54e+01 1thx 115 5.57e+01 1thx c.47.1.1 32732 1vi6A 208 5.62e+01 c.23.15.1 100736 1hdmB 193 5.71e+01 1hdmB b.1.1.2,d.19.1.1 21584,38158 2cb2A 318 5.75e+01 1ucsA 64 5.82e+01 b.85.1.1 88466 1mq7A 154 5.89e+01 b.85.4.1 79404 1xewX 182 5.90e+01 1q0xH 221 5.91e+01 b.1.1.1,b.1.1.2 95517,95518 1jj2X 240 5.93e+01 1ffkV c.9.2.1 63109 1vkiA 181 5.95e+01 d.116.1.1 108664 1a79A 171 5.96e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1div 149 6.00e+01 1div d.99.1.1,d.100.1.1 40692,40693 1byqA 228 6.05e+01 1yer d.122.1.1 41100 1nixA 34 6.20e+01 g.3.6.2 80541 1us5A 314 6.21e+01 c.94.1.1 99856 1y1uA 585 6.22e+01 1u13A 455 6.23e+01 a.104.1.1 107578 1r8eA 278 6.26e+01 a.6.1.3,d.60.1.1 104843,104844 2azeB 106 6.33e+01 1bylA 125 6.35e+01 1bylA d.32.1.2 38495 2f96A 224 6.41e+01 1p7gA 222 6.47e+01 a.2.11.1,d.44.1.1 94223,94224 1kgcE 242 6.54e+01 b.1.1.1,b.1.1.2 77386,77387 1h5zA 455 6.57e+01 a.104.1.1 90622 1pkhA 204 6.58e+01 b.85.4.1 94832 1whtB 153 6.60e+01 1whtB 1zwpA 121 6.63e+01 1qy5A 269 6.66e+01 d.122.1.1 96573 1u58A 253 6.72e+01 1uurA 473 6.73e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1jx2B 315 6.74e+01 c.37.1.8 67404 1c96A 753 6.75e+01 1amj c.8.2.1,c.83.1.1 30727,35403 3fruA 269 6.80e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 2c1gA 431 6.92e+01 1s72Y 241 6.95e+01 c.9.2.1 105344 2breA 219 6.96e+01 1t8hA 277 7.06e+01 d.194.1.2 106664 1mixA 206 7.12e+01 a.11.2.1,b.55.1.5 79166,79167 1xxnA 185 7.15e+01 1uocA 289 7.19e+01 c.55.3.9 99686 2b0rA 202 7.19e+01 1o22A 170 7.23e+01 d.238.1.1 86557 1ojqA 212 7.23e+01 d.166.1.1 93146 1pcfA 66 7.30e+01 1pcfA d.18.1.1 38142 1jhdA 396 7.32e+01 b.122.1.3,c.26.1.5 66712,66713 1y9wA 140 7.33e+01 3eipA 84 7.34e+01 3eipA d.26.2.1 38434 1wzvA 155 7.34e+01 1v76A 96 7.37e+01 1lmmA 40 7.47e+01 g.3.6.2 91080 1itcA 516 7.53e+01 b.3.1.1,c.1.8.1 83705,83706 1ap6A 198 7.59e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 2fe7A 166 7.68e+01 1adjA 421 7.70e+01 1adjA c.51.1.1,d.104.1.1 33188,40737 1ue1A 164 7.75e+01 b.40.4.3 99243 1avqA 228 7.77e+01 1avqA c.52.1.13 33326 1puc 105 7.80e+01 1puc d.97.1.1 40675 1l5pA 93 7.80e+01 d.15.4.1 73598 1vemA 516 7.81e+01 1tv8A 340 7.86e+01 c.1.28.3 107352 2dbsA 90 7.88e+01 1bdfA 235 7.92e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1ifrA 121 7.95e+01 b.1.16.1 71203 1yspA 181 7.95e+01 2ch4A 320 7.97e+01 1j1hA 144 8.00e+01 b.111.1.1 77056 1h09A 338 8.08e+01 b.109.1.1,c.1.8.8 83420,83421 1w2fA 276 8.10e+01 d.143.1.3 109125 1ppjI 78 8.13e+01 d.184.1.3 104265 1hcd 118 8.15e+01 1hce b.42.5.2 25624 1hq3A 129 8.17e+01 1aoiC a.22.1.1 16434 1pl4A 198 8.18e+01 a.2.11.1,d.44.1.1 94854,94855 1osdA 72 8.19e+01 d.58.17.1 104022 1lq9A 112 8.19e+01 d.58.4.3 78129 3dfr 162 8.20e+01 3dfr c.71.1.1 34880 1whsB 153 8.21e+01 1whtB 2bvfA 459 8.25e+01 1ud9A 245 8.33e+01 d.131.1.2,d.131.1.2 107768,107769 1xeaA 323 8.35e+01 c.2.1.3,d.81.1.5 109572,109573 1irsA 112 8.39e+01 1qqgA b.55.1.2 26991 1wtaA 275 8.43e+01 2gnqA 336 8.49e+01 2bngA 149 8.52e+01 2cx5A 158 8.54e+01 1h8eI 50 8.56e+01 1e79I a.137.8.1 60758 2gpiA 91 8.59e+01 1e3mA 800 8.68e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1n0nA 199 8.71e+01 a.2.11.1,d.44.1.1 79750,79751 2cs2A 134 8.77e+01 1v7lA 163 8.78e+01 1floA 422 8.79e+01 1floA a.60.9.1,d.163.1.1 18106,42166 2gatA 66 8.80e+01 1gatA g.39.1.1 45102 2fc7A 82 8.81e+01 2fsrA 195 8.84e+01 1xrkA 124 8.85e+01 1vqoC 246 8.87e+01 1qx2A 76 8.95e+01 a.39.1.1 104622 1vd2A 89 8.96e+01 d.15.2.2 108517