# List of top-scoring protein chains for t2k-100-30-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.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 2kruA 63 1.37e-10 2hueC 84 1.09e-01 a.22.1.1 136776 1kx5B 102 1.61e-01 a.22.1.1 77594 1aoiB 87 1.85e-01 1aoiB a.22.1.1 16470 1a7w 69 1.98e-01 1a7w 1a7wA 69 1.98e-01 a.22.1.2 16477 1tzyD 103 2.13e-01 a.22.1.1 107533 1id3B 102 2.33e-01 a.22.1.1 66113 1gp2G 71 3.31e-01 1tbgE a.137.3.1 19635 2wmmA 162 4.64e-01 1wqgA 185 7.82e-01 d.67.3.1 145821 2da4A 80 8.33e-01 3khaA 95 8.46e-01 3fozA 316 8.72e-01 1u02A 239 8.85e-01 c.108.1.15 107538 1h7mA 102 9.32e-01 d.79.3.1 83485 1b67A 68 1.05e+00 1a7w a.22.1.2 16474 2kc8A 98 1.09e+00 2grjA 192 1.48e+00 2f6mA 65 1.75e+00 a.2.17.1 133051 3ic7A 126 1.77e+00 2jvgA 72 1.77e+00 1w41A 101 1.80e+00 d.79.3.1 145812 2fu2A 102 1.85e+00 3bpqB 88 2.04e+00 2kl8A 85 2.18e+00 2p0tA 176 2.39e+00 a.290.1.1 149141 3bhpA 60 2.47e+00 3h7eA 237 3.13e+00 1q1vA 70 3.39e+00 a.159.4.1 104479 3hsiA 458 3.55e+00 1kjsA 74 3.73e+00 a.50.1.1 17792 1ru8A 232 3.82e+00 c.26.2.1 97849 2yv9A 291 3.96e+00 1y66A 52 4.20e+00 1nvpD 108 4.22e+00 a.32.1.1,b.56.1.1 92213,92214 1dd5A 185 4.38e+00 1dd5A d.67.3.1 39564 2gpiA 91 4.42e+00 d.354.1.1 147154 2hszA 243 4.44e+00 c.108.1.6 136726 1aoyA 78 4.45e+00 a.4.5.3 16087 2qhoB 53 4.46e+00 1yacA 208 4.63e+00 1yacA c.33.1.3 31757 1tafA 68 4.76e+00 1tafA a.22.1.3 16481 1guuA 52 4.84e+00 a.4.1.3 83332 3k0bA 393 4.86e+00 1wy7A 207 4.87e+00 c.66.1.32 121433 3g5oB 102 5.01e+00 1k07A 263 5.14e+00 d.157.1.1 77218 1v77A 212 5.22e+00 c.6.3.2 108402 1yt8A 539 5.31e+00 c.46.1.2,c.46.1.2,c.46.1.2,c.46.1.2 123996,123997,123998,123999 3h5tA 366 5.64e+00 2kmfA 115 5.65e+00 3bi7A 212 5.71e+00 b.122.1.12 155298 2cpgA 45 6.21e+00 2cpgA a.43.1.3 17455 2d13A 227 6.47e+00 c.26.2.1 131121 1mbe 53 6.84e+00 1mbe 3ctvA 110 7.01e+00 1ywmA 200 7.02e+00 2atxA 194 7.08e+00 c.37.1.8 127315 1sczA 233 7.18e+00 c.43.1.1 98802 1f1zA 273 7.30e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1p4cA 380 7.43e+00 c.1.4.1 94100 2otaA 76 7.72e+00 a.284.1.1 149010 1eijA 80 8.01e+00 1eijA a.5.6.1 16298 1xpxA 163 8.17e+00 a.4.1.1 122230 3gycA 393 8.27e+00 3c64A 179 8.38e+00 1jh3A 107 8.44e+00 d.66.1.4 71661 2wugA 291 8.61e+00 1h3oA 75 8.63e+00 a.22.1.3 76644 1w5tA 412 8.86e+00 a.4.5.11,c.37.1.20 114255,114256 1kmqA 184 8.99e+00 c.37.1.8 84412 2zcxA 231 9.39e+00 1f1eA 154 9.45e+00 a.22.1.2 64927 2frhA 127 9.73e+00 a.4.5.28 133988 1dbrA 231 9.92e+00 1qk3A c.61.1.1 34041 2o0i1 180 9.99e+00 1yrnA 61 1.01e+01 1akhA a.4.1.1 15981 1kyqA 274 1.04e+01 c.2.1.11,e.37.1.1 73281,73282 2o5vA 359 1.07e+01 2w83C 77 1.07e+01 3giyA 380 1.15e+01 2hd0A 128 1.15e+01 1v0jA 399 1.18e+01 2oszA 93 1.22e+01 1zt2B 212 1.24e+01 a.262.1.1 125625 1mijA 152 1.28e+01 a.4.1.1 79150 2eshA 118 1.28e+01 a.4.5.61 132325 3lxrA 185 1.30e+01 3lmoA 101 1.30e+01 2on8A 56 1.30e+01 1zkkA 167 1.32e+01 1g61A 228 1.34e+01 1g61A d.126.1.1 41126 2bo1A 101 1.39e+01 d.79.3.1 146161 3a1sA 258 1.58e+01 2fwtA 125 1.62e+01 1hqcA 324 1.63e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 2daeA 75 1.64e+01 2gcoA 201 1.65e+01 2c8eE 211 1.67e+01 1tu9A 134 1.68e+01 a.1.1.2 107320 2hzdA 82 1.68e+01 2js9A 99 1.72e+01 2qzcA 214 1.79e+01 2j67A 178 1.80e+01 1b01A 45 1.81e+01 2cpgA a.43.1.3 17458 3f9xA 166 1.85e+01 1jfiB 179 1.86e+01 1jfiB a.22.1.3 62937 2yvuA 186 1.88e+01 2gukA 120 1.91e+01 d.360.1.1 147182 3k5iA 403 1.91e+01 2a9kB 223 1.91e+01 d.166.1.1 126443 2c9oA 456 2.00e+01 2b67A 204 2.07e+01 d.90.1.1 127970 3ix7A 134 2.08e+01 2cm4A 150 2.08e+01 1p4qA 52 2.10e+01 j.96.1.1 87777 3g3sA 249 2.20e+01 1d2zA 108 2.26e+01 1d2zA a.77.1.2 18437 2ivyA 101 2.27e+01 d.58.58.1 147817 3k13A 300 2.27e+01 1mgtA 174 2.29e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 2aj6A 159 2.31e+01 d.108.1.1 126841 1a4yA 460 2.32e+01 1a4yA c.10.1.1 30852 2oq1A 254 2.33e+01 d.93.1.1,d.93.1.1 139220,139221 1gvdA 52 2.37e+01 a.4.1.3 83338 1z7xW 461 2.40e+01 c.10.1.1 124675 1vp7A 100 2.47e+01 a.7.13.1 113941 1yirA 408 2.47e+01 c.1.17.2,d.41.2.2 123330,123331 2gf4A 100 2.49e+01 a.8.10.1 135074 1ej6D 418 2.50e+01 i.7.1.1 45970 3jszA 525 2.50e+01 2hjpA 290 2.50e+01 3kyzA 125 2.51e+01 2v3uA 265 2.51e+01 1fsgA 233 2.52e+01 1qk3A c.61.1.1 34029 2e67A 264 2.55e+01 1pzlA 237 2.56e+01 a.123.1.1 104393 1jvsA 400 2.59e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 2vm5A 106 2.62e+01 2dg7A 195 2.71e+01 2hepA 85 2.72e+01 a.2.21.1 147271 3id7A 400 2.74e+01 1fjgI 128 2.74e+01 1fjfI d.14.1.1 37559 2arrA 382 2.77e+01 3gxqA 54 2.81e+01 1qynA 153 2.81e+01 d.33.1.1 96597 2zsgA 359 2.85e+01 1wmuB 146 2.87e+01 a.1.1.2 109417 2bexA 460 2.91e+01 c.10.1.1 128398 1mykA 53 2.91e+01 1bazA a.43.1.1 17425 1zuaX 317 2.91e+01 1bdtA 53 3.01e+01 1bazA a.43.1.1 17433 1h8mA 140 3.03e+01 1h8mA d.110.4.1 60782 1g8iA 190 3.12e+01 1rec a.39.1.5 60363 2ztmA 260 3.14e+01 1bazA 53 3.19e+01 1bazA a.43.1.1 17421 2gjgA 248 3.20e+01 2vqeI 128 3.22e+01 d.14.1.1 153433 3fvvA 232 3.23e+01 2iqjA 134 3.23e+01 2j9wA 102 3.25e+01 3bw8A 217 3.28e+01 2eucA 130 3.30e+01 a.249.1.1 132382 1mzbA 136 3.30e+01 a.4.5.42 91497 1ffkV 143 3.32e+01 1ffkV c.9.2.1 30849 2h8fB 146 3.43e+01 a.1.1.2 136240 3g6eY 142 3.47e+01 2g0dA 409 3.50e+01 a.102.6.1 147057 1jfbA 404 3.52e+01 a.104.1.1 66624 1qfcA 306 3.53e+01 1uteA d.159.1.1 42077 2c9wA 169 3.57e+01 a.271.1.1,d.93.1.1 145023,145024 2bayA 61 3.57e+01 g.44.1.2 128251 1tmqB 117 3.59e+01 1bea a.52.1.2 17824 3d1kB 146 3.63e+01 a.1.1.2 157209 1mylA 53 3.68e+01 1bazA a.43.1.1 17427 1tx4B 178 3.69e+01 1ctqA c.37.1.8 32045 1w36D 608 3.69e+01 c.37.1.19,c.37.1.19 114128,114129 1jrrA 382 3.70e+01 e.1.1.1 63256 1zj8A 566 3.70e+01 d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 146003,146004,146005,146006 1r45A 204 3.74e+01 d.166.1.1 111683 1nkd 65 3.79e+01 1nkd 1nkdA 65 3.79e+01 a.30.1.1 16974 1j6pA 418 3.83e+01 b.92.1.4,c.1.9.9 77089,77090 2uubI 128 3.89e+01 1v9vA 114 3.92e+01 a.29.10.1 119898 1gt6A 269 3.94e+01 c.69.1.17 76342 3i05A 395 3.96e+01 2aa1B 146 4.00e+01 a.1.1.2 144793 3d1lA 266 4.02e+01 2eq8C 40 4.03e+01 1beaA 127 4.06e+01 a.52.1.2 17826 1gudA 288 4.08e+01 c.93.1.1 83326 3ifeA 434 4.10e+01 3bjuA 521 4.12e+01 2b9hA 353 4.14e+01 1tib 269 4.14e+01 3tgl 1ny6A 267 4.16e+01 c.37.1.20 92321 1v0dA 329 4.16e+01 d.4.1.7 108204 1tibA 269 4.17e+01 c.69.1.17 34738 1ciyA 590 4.17e+01 b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1ciy 590 4.17e+01 1ciy 1eujA 166 4.20e+01 1eujA b.40.4.4 25316 3cjwA 244 4.24e+01 1cmnA 402 4.29e+01 1rom a.104.1.1 18958 3hv0A 393 4.30e+01 2opoA 86 4.31e+01 a.39.1.10 139209 1qk3A 233 4.37e+01 1qk3A c.61.1.1 34031 1c3pA 375 4.38e+01 1c3pA c.42.1.2 32606 3h2dA 155 4.39e+01 2dnxA 130 4.42e+01 1yz4A 160 4.45e+01 1uumA 372 4.45e+01 c.1.4.1 100010 3mesA 424 4.52e+01 1xkrA 206 4.53e+01 d.252.1.1 115421 1q3eA 207 4.55e+01 b.82.3.2 95669 2vofA 157 4.57e+01 2igd 61 4.62e+01 2igd 2o0jA 385 4.63e+01 2c8vA 288 4.66e+01 c.37.1.10 130128 1fx3A 169 4.69e+01 1fx3B d.33.1.1 38524 1x2iA 75 4.70e+01 a.60.2.5 121641 1akhA 61 4.71e+01 1akhA a.4.1.1 15980 2gi9A 56 4.75e+01 1wx1A 335 4.75e+01 2fk5A 200 4.75e+01 3kt0A 438 4.88e+01 1n81A 186 4.95e+01 a.185.1.1 85388 1sfsA 240 4.95e+01 c.1.8.8 98846 2fvgA 340 5.02e+01 b.49.3.1,c.56.5.4 134201,134202 1bea 127 5.04e+01 1bea 1octC 156 5.05e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 2ezhA 75 5.07e+01 a.4.1.2 16029 1q2lA 939 5.20e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 118731,118732,118733,118734 2qjcA 262 5.24e+01 3hheA 255 5.26e+01 1sjjA 863 5.37e+01 i.15.1.1 98894 1yceA 89 5.39e+01 1b9pA 34 5.41e+01 1b9pA j.49.1.1 46328 1mi0A 65 5.44e+01 d.15.7.1 79135 3jtzA 88 5.44e+01 1ufhA 180 5.46e+01 d.108.1.1 88485 1d3gA 367 5.47e+01 1d3gA c.1.4.1 28600 1hyhA 309 5.50e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 2dkoA 146 5.66e+01 2fueA 262 5.67e+01 c.108.1.10 134119 3dghA 483 5.74e+01 1o08A 221 5.77e+01 c.108.1.6 86525 1i0hA 205 5.84e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 2zw0A 57 5.86e+01 2kheA 89 5.90e+01 1wa3A 205 5.92e+01 c.1.10.1 120802 1in4A 334 5.92e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1hlvA 131 5.93e+01 a.4.1.7,a.4.1.7 65854,65855 2cbiA 594 5.95e+01 a.246.1.1,c.1.8.10,d.92.2.3 130179,130180,130181 1efdN 266 5.95e+01 1efdN c.92.2.1 35597 1a4rA 191 5.97e+01 1ctqA c.37.1.8 32063 2ccmA 191 6.03e+01 1t0fA 276 6.04e+01 a.4.5.27,c.52.1.16 112195,112196 1fl0A 171 6.06e+01 1eujA b.40.4.4 25315 1cxqA 162 6.08e+01 1cxqA c.55.3.2 33621 3ctgA 129 6.09e+01 2eh3A 179 6.10e+01 1p1mA 406 6.11e+01 b.92.1.4,c.1.9.9 87696,87697 2ozlA 365 6.11e+01 c.36.1.11 145744 1ni4A 365 6.12e+01 c.36.1.11 85728 1b3qA 379 6.14e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1n87A 56 6.29e+01 g.44.1.2 85390 3bpzA 202 6.29e+01 1h9aA 485 6.31e+01 1dpgA c.2.1.3,d.81.1.5 60816,60817 1f24A 402 6.32e+01 1rom a.104.1.1 18953 3e6mA 161 6.35e+01 2q0oC 107 6.35e+01 3hhgA 306 6.37e+01 1rom 403 6.38e+01 1rom 2vm6A 150 6.42e+01 2a1dD 329 6.43e+01 2ioyA 283 6.43e+01 2uuqA 414 6.45e+01 2zkdA 210 6.46e+01 b.122.1.12 154583 1dpgA 485 6.47e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1d5nA 205 6.47e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 1a81A 254 6.48e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 2qgoA 141 6.48e+01 2ip1A 432 6.55e+01 2v5cA 594 6.56e+01 2r80B 146 6.59e+01 2ejxA 139 6.63e+01 1xkmB 25 6.64e+01 j.4.1.6 122083 2psdA 318 6.65e+01 1n82A 331 6.67e+01 c.1.8.3 91703 3focA 451 6.68e+01 3hz7A 87 6.69e+01 2qmtA 56 6.69e+01 3ec8A 166 6.75e+01 2vjvA 159 6.77e+01 d.58.57.1 153201 2igdA 61 6.80e+01 d.15.7.1 37821 3fdeA 212 6.84e+01 1k78A 149 6.88e+01 a.4.1.5,a.4.1.5 68255,68256 2p8qB 40 6.90e+01 1z2aA 168 6.92e+01 c.37.1.8 124374 3b49A 211 6.94e+01 1in6A 334 6.95e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 3hkxA 283 6.98e+01 2whfA 413 7.00e+01 1l2lA 457 7.01e+01 c.72.1.3 77656 1j30A 144 7.02e+01 a.25.1.1 90806 2ptmA 198 7.08e+01 1rypA 243 7.22e+01 1pmaA d.153.1.4 41932 2jvwA 88 7.30e+01 3cqbA 107 7.33e+01 2wzgA 525 7.33e+01 1wkaA 147 7.35e+01 b.51.1.1 120978 2vifA 141 7.37e+01 3kztA 143 7.38e+01 2chgA 226 7.40e+01 3cp5A 124 7.41e+01 2o7gA 112 7.46e+01 1cjbA 231 7.48e+01 1qk3A c.61.1.1 34079 2dlaA 222 7.52e+01 1l8aA 886 7.53e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 3f2vA 192 7.54e+01 3iibA 444 7.55e+01 3cnrA 117 7.56e+01 2wcuA 149 7.62e+01 2ieaA 886 7.65e+01 c.36.1.6,c.36.1.10,c.48.1.1 137294,137295,137296 1b1uA 122 7.71e+01 1bea a.52.1.2 17823 2wgmA 89 7.72e+01 1nu7D 282 7.76e+01 a.8.6.1,a.8.6.1 92191,92192 3lq2A 886 7.76e+01 1aocA 175 7.79e+01 1aocA g.17.1.5 44817 1svjA 156 7.81e+01 d.220.1.1 106049 1a9nB 96 7.89e+01 1urnA d.58.7.1 39165 1g0uG 252 7.89e+01 d.153.1.4 41952 1zn8A 180 7.89e+01 c.61.1.1 125376 1vlwA 217 7.92e+01 c.1.10.1 108868 3iqtA 123 7.92e+01 1o0wA 252 7.97e+01 a.149.1.1,d.50.1.1 80751,80752 1q0qA 406 7.99e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466