# List of top-scoring protein chains for t2k-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.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 1ufhA 180 3.11e-02 d.108.1.1 88485 1on0A 158 3.72e-02 d.108.1.1 87095 3d3yA 425 2.34e-01 2q4vA 170 2.37e-01 d.108.1.1 139878 3bn8A 128 2.42e-01 2q0yA 153 2.97e-01 1fx3A 169 3.92e-01 1fx3B d.33.1.1 38524 3e4wA 320 4.22e-01 1xccA 220 4.31e-01 c.47.1.10 115113 1qynA 153 4.45e-01 d.33.1.1 96597 3go9A 492 4.84e-01 3mgdA 157 5.08e-01 2fe7A 166 5.28e-01 d.108.1.1 133325 1prxA 224 5.44e-01 1prxA c.47.1.10 33076 2ozhA 142 5.87e-01 1ispA 181 6.55e-01 c.69.1.18 76778 3cnuA 116 7.03e-01 2r7hA 177 8.90e-01 2r6oA 294 9.36e-01 2atrA 138 1.03e+00 d.108.1.1 127305 1i6wA 181 1.03e+00 1i6wA c.69.1.18 61859 3hv8A 268 1.27e+00 3bdqA 110 1.33e+00 2cy2A 174 1.37e+00 d.108.1.1 131016 3k6oA 224 1.39e+00 3fynA 176 1.41e+00 3khkA 544 1.43e+00 3exnA 160 1.84e+00 3gkuA 225 1.90e+00 2qztA 111 1.90e+00 2ox7A 155 1.97e+00 b.172.1.1 149054 2i9wA 184 2.00e+00 d.17.4.30,g.74.1.1,g.74.1.1 147576,147577,147578 1clqA 903 2.19e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 1z9lA 128 2.35e+00 2i8dA 123 2.38e+00 d.198.4.1 147561 1ywmA 200 2.45e+00 1hniB 427 2.49e+00 1rthA e.8.1.2 43045 2ae6A 166 2.57e+00 d.108.1.1 126600 2irfG 113 2.67e+00 2irfG a.4.5.23 16185 2pdoA 144 2.93e+00 2dfkA 402 2.93e+00 a.87.1.1,b.55.1.1 145077,145078 2v2gA 233 3.06e+00 1a66A 178 3.14e+00 1a02N b.2.5.3 22441 3eg7A 176 3.45e+00 2o0i1 180 3.53e+00 3dni 260 3.60e+00 3dni 2z6cA 129 3.83e+00 1qamA 244 3.98e+00 2ercA c.66.1.24 34220 1hv2A 99 4.11e+00 d.42.1.1 61287 2dvyA 226 4.21e+00 1nycA 111 4.41e+00 b.61.2.2 92336 1f46A 140 4.87e+00 1f46A d.129.4.1 59643 2dnjA 260 4.92e+00 3dni d.151.1.1 41790 3iwgA 276 4.95e+00 1vkcA 158 4.95e+00 d.108.1.1 113663 3isnC 560 4.96e+00 3h5lA 419 5.23e+00 1rsy 152 5.25e+00 1rsy 1rsyA 152 5.25e+00 b.7.1.2 23192 2h1rA 299 5.31e+00 1lyvA 306 5.57e+00 c.45.1.2 74348 3ds8A 254 5.61e+00 1w63Q 158 5.74e+00 i.23.1.1 109208 1wyuB 474 6.01e+00 c.67.1.7 121453 2eyqA 1151 6.47e+00 b.34.18.1,c.37.1.19,c.37.1.19,c.37.1.19,c.37.1.19,d.315.1.1 132590,132591,132592,132593,132594,132595 3l8bA 906 6.95e+00 2w2gA 264 7.20e+00 1qmvA 197 7.29e+00 1qq2A c.47.1.10 33066 3ehdA 162 7.44e+00 1xxpA 306 7.51e+00 c.45.1.2 122423 1jnuA 104 7.55e+00 d.110.3.6 71762 2r1iA 172 7.58e+00 2fsrA 195 7.74e+00 d.108.1.1 134036 2nqrA 411 7.79e+00 b.85.6.1,b.103.1.1,c.57.1.2 138490,138491,138492 1ih7A 903 7.90e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1fkoB 440 7.96e+00 1rthA e.8.1.2 43095 3bluA 305 7.99e+00 c.45.1.2 155402 1atnD 260 8.06e+00 3dni d.151.1.1 41793 2h1tA 188 8.12e+00 b.178.1.1 147215 2ppqA 322 8.17e+00 d.144.1.6 149782 1nrjA 158 8.28e+00 d.110.4.4 86124 2wkrA 332 8.42e+00 2z2mA 168 8.43e+00 3dsbA 157 8.45e+00 1hniA 558 8.84e+00 1rthA c.55.3.1,e.8.1.2 33586,43044 2c2pA 199 8.85e+00 1mb4A 370 8.94e+00 c.2.1.3,d.81.1.1 78908,78909 3fycA 265 8.94e+00 1tiqA 180 8.96e+00 d.108.1.1 107010 3dy0A 336 9.02e+00 2c2qA 199 9.21e+00 1g8lA 411 9.24e+00 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1q1oA 98 9.30e+00 d.15.2.2 95596 1usmA 80 9.34e+00 d.74.1.1 99876 2vi7A 177 9.45e+00 3medB 440 9.64e+00 1ywsA 82 9.75e+00 g.41.17.1 124163 3k26A 366 1.00e+01 1kaeA 434 1.03e+01 c.82.1.2 72247 2yxmA 100 1.03e+01 3b50A 310 1.03e+01 1txnA 328 1.03e+01 d.248.1.1 112779 3g9kF 177 1.03e+01 2jleA 566 1.03e+01 1ignA 246 1.04e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1bqnA 558 1.04e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 2d9zA 129 1.04e+01 1xebA 150 1.05e+01 d.108.1.1 115219 3f14A 112 1.05e+01 1obpA 159 1.08e+01 1obpA b.60.1.1 27092 2v4cA 309 1.09e+01 1vfvA 366 1.11e+01 c.37.1.9 108592 1bob 320 1.12e+01 1bob 1bobA 320 1.12e+01 d.108.1.1 40816 3htrA 120 1.13e+01 2jxnA 127 1.13e+01 1ytw 306 1.13e+01 1ytw 1g60A 260 1.17e+01 c.66.1.11 70151 2zjtA 247 1.19e+01 2wkpA 332 1.19e+01 1gt1A 159 1.19e+01 b.60.1.1 90515 3kk1B 452 1.20e+01 2j3tD 219 1.20e+01 2zc3A 168 1.21e+01 2k14A 84 1.22e+01 1y10A 407 1.22e+01 1js8A 394 1.22e+01 a.86.1.1,b.112.1.1 67219,67220 3enbA 222 1.23e+01 c.55.3.14 158189 2p14A 192 1.23e+01 1f47B 144 1.23e+01 1f46A d.129.4.1 59645 2v0uA 146 1.24e+01 3f7xA 151 1.27e+01 2jzdA 129 1.29e+01 3b9fI 395 1.29e+01 2rliA 171 1.30e+01 1gheA 177 1.31e+01 d.108.1.1 76222 1v6fA 151 1.31e+01 d.109.1.2 108395 2d4pA 141 1.37e+01 d.108.1.1 146459 3k6qA 139 1.37e+01 3f04A 143 1.41e+01 1nslA 184 1.41e+01 d.108.1.1 86137 3bkrA 126 1.44e+01 2ol2A 395 1.46e+01 2whnA 116 1.47e+01 2ox6A 166 1.51e+01 a.35.1.6 149053 2es9A 115 1.51e+01 a.247.1.1 132318 2p5qA 170 1.52e+01 1ew4A 106 1.55e+01 1ew4A d.82.2.1 40023 2qxvA 361 1.57e+01 3lzjA 903 1.60e+01 2euiA 153 1.61e+01 d.108.1.1 132387 1vqrA 297 1.61e+01 a.211.1.3 114015 2a2aA 321 1.62e+01 3l1wA 257 1.63e+01 1qsmA 152 1.63e+01 1qsmA d.108.1.1 40808 2ceyA 306 1.66e+01 2fl4A 149 1.66e+01 d.108.1.1 133706 1m1sA 116 1.69e+01 b.1.11.2 84747 3d6rA 158 1.69e+01 3dlkA 556 1.70e+01 3cygA 222 1.72e+01 2uytA 489 1.74e+01 1wzvA 155 1.75e+01 d.20.1.1 121529 1wryA 121 1.76e+01 1f7wA 144 1.77e+01 1f46A d.129.4.1 59679 1l4sA 112 1.77e+01 d.204.1.1 77693 3l0wA 169 1.78e+01 2b5gA 171 1.79e+01 d.108.1.1 127892 1jr5A 90 1.80e+01 a.150.1.1 67113 2pr8A 196 1.81e+01 2wkqA 332 1.85e+01 2nykA 285 1.87e+01 2rdeA 251 1.88e+01 b.45.2.1,b.45.2.2 151924,151925 3iiwA 365 1.88e+01 1yptA 305 1.89e+01 1ytw c.45.1.2 32686 1yewA 382 1.90e+01 1vrtA 560 1.92e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1iknA 286 1.93e+01 1a3qA b.1.18.1,b.2.5.3 21936,22449 3b8mA 280 1.96e+01 d.58.60.1 154961 2a6mA 155 1.96e+01 d.58.57.1 126287 1uocA 289 1.98e+01 c.55.3.9 99686 2j8gA 339 1.98e+01 b.109.1.1,c.1.8.8 147915,147916 3e0kA 150 1.99e+01 3fleA 249 2.00e+01 2eknA 159 2.00e+01 2o0yA 260 2.03e+01 1bdtA 53 2.03e+01 1bazA a.43.1.1 17433 2j3wA 142 2.04e+01 d.110.4.3 137981 1iznB 277 2.06e+01 e.43.1.2 83848 3hvbA 437 2.06e+01 1n9lA 109 2.06e+01 d.110.3.6 85468 3hv9A 265 2.09e+01 2jzfA 143 2.12e+01 1rthA 560 2.13e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 3gwiA 170 2.15e+01 1wu3I 161 2.15e+01 a.26.1.3 114890 3lhnA 126 2.20e+01 2fxtA 192 2.21e+01 d.17.4.13 147051 1c1bB 440 2.21e+01 1rthA e.8.1.2 43077 3b96A 587 2.21e+01 2a40B 260 2.22e+01 d.151.1.1 126139 1yo5C 97 2.24e+01 a.4.5.21 123768 2pn8A 211 2.26e+01 1yoyA 175 2.27e+01 a.211.1.1 123795 1ia0K 394 2.27e+01 i.10.1.1 71167 2z10A 194 2.30e+01 3muqA 237 2.31e+01 1i6iA 366 2.31e+01 1bg2 c.37.1.9 61844 1tk1A 260 2.36e+01 d.248.1.1 107066 1vlrA 350 2.39e+01 d.13.1.3,d.246.1.1 108860,108861 2pr1A 163 2.41e+01 3e70C 328 2.41e+01 3g8wA 169 2.42e+01 3f9sA 146 2.42e+01 1vqoJ 145 2.42e+01 c.21.1.1 120371 2uubK 129 2.43e+01 c.55.4.1 139942 3co8A 380 2.43e+01 2bkrA 212 2.44e+01 d.3.1.7 128710 2a7lA 136 2.44e+01 d.20.1.1 126350 2nxpA 156 2.48e+01 d.379.1.1 148504 6mhtA 327 2.50e+01 6mhtA c.66.1.26 34226 3hg7A 324 2.51e+01 3idqA 369 2.51e+01 2vqeK 129 2.51e+01 c.55.4.1 153435 3f5bA 182 2.54e+01 3f9xA 166 2.55e+01 3f43A 125 2.56e+01 3fbuA 168 2.57e+01 1e32A 458 2.57e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1jksA 294 2.57e+01 d.144.1.7 71710 2uxwA 607 2.59e+01 3fouA 156 2.59e+01 2bryA 497 2.59e+01 1z4rA 168 2.59e+01 d.108.1.1 124444 1pf5A 131 2.59e+01 d.79.1.1 94604 1t4bA 367 2.59e+01 c.2.1.3,d.81.1.1 106406,106407 1m4jA 142 2.60e+01 d.109.1.2 78602 3is9A 558 2.64e+01 1dloB 427 2.65e+01 1rthA e.8.1.2 43041 1zupA 315 2.67e+01 c.55.3.11 125681 3bt3A 148 2.72e+01 1bd0A 388 2.74e+01 1bd0A b.49.2.2,c.1.6.1 26480,28642 1xjaA 178 2.74e+01 b.82.4.1 115382 1rtwA 220 2.79e+01 a.132.1.3 97823 1a02N 301 2.79e+01 1a02N b.1.18.1,b.2.5.3 21923,22440 2o4tA 100 2.81e+01 a.69.4.1 148590 1vkkA 154 2.84e+01 d.109.1.2 108669 3biyA 380 2.85e+01 3cuoA 99 2.85e+01 1qmyA 167 2.88e+01 1qmyA d.3.1.2 37094 3hs3A 277 2.89e+01 1nqnA 122 2.90e+01 b.61.1.1 86042 3in6A 148 2.92e+01 2vjvA 159 2.94e+01 d.58.57.1 153201 2i79A 172 2.97e+01 1gmeA 151 2.98e+01 b.15.1.1 65305 1fk9A 543 2.99e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 2z8zA 617 3.02e+01 2vezA 190 3.02e+01 2aacA 177 3.04e+01 2arcA b.82.4.1 28150 1jmsA 381 3.05e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2vk3A 142 3.06e+01 2rr3A 130 3.06e+01 3iuzA 340 3.08e+01 3kk1A 560 3.09e+01 3krwA 688 3.15e+01 1xn5A 146 3.15e+01 d.129.3.5 115574 2arcA 164 3.15e+01 2arcA b.82.4.1 28148 2i1sA 188 3.18e+01 d.343.1.1 147488 3kq0A 192 3.18e+01 1k75A 434 3.19e+01 c.82.1.2 68253 1fkoA 543 3.20e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 2camA 127 3.22e+01 1swuA b.61.1.1 27407 1xmtA 103 3.25e+01 d.108.1.1 115561 2jzbB 74 3.25e+01 2dxqA 150 3.26e+01 1dloA 556 3.28e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 2k06A 123 3.29e+01 2w0iA 135 3.33e+01 2jr7A 89 3.35e+01 3a75B 185 3.36e+01 1mspA 126 3.39e+01 1mspA b.1.11.2 22333 1t9hA 307 3.40e+01 b.40.4.5,c.37.1.8 112358,112359 1bynA 128 3.42e+01 1rsy b.7.1.2 23193 1vgjA 184 3.46e+01 3gwaA 365 3.52e+01 2hngA 127 3.53e+01 d.33.1.2 147311 3ezyA 344 3.55e+01 3cjkB 75 3.57e+01 1mylA 53 3.62e+01 1bazA a.43.1.1 17427 2zd1A 557 3.66e+01 1lkoA 191 3.66e+01 a.25.1.1,g.41.5.1 78063,78064 2zmvA 227 3.71e+01 1fjgK 129 3.74e+01 1fjfK c.55.4.1 33733 2yu4A 94 3.74e+01 2uubP 88 3.76e+01 d.27.1.1 139947 1qwtA 255 3.78e+01 b.26.1.3 96501 1x25A 128 3.78e+01 d.79.1.1 121619 3kphA 217 3.78e+01 2wqlA 154 3.78e+01 2p8iA 117 3.80e+01 d.58.55.1 139522 2qq4A 138 3.81e+01 1s6lA 212 3.83e+01 a.4.5.79,d.357.1.2 145773,145774 2v6uA 104 3.83e+01 3c1qA 123 3.83e+01 1s98A 107 3.85e+01 b.124.1.1 105377 2oaaA 249 3.86e+01 1zq9A 285 3.86e+01 c.66.1.24 125505 2w4jA 277 3.87e+01 2ivyA 101 3.87e+01 d.58.58.1 147817 1lshB 319 3.88e+01 f.7.1.1 74245 2qnuA 226 3.90e+01 1jc4A 148 3.90e+01 1jc4A d.32.1.4 62863 2uubI 128 3.94e+01 3c7bA 417 3.94e+01 d.58.1.5,d.58.36.2,d.134.1.1 156001,156002,156003 3gu4A 299 3.96e+01 2eabA 899 3.97e+01 2bjoA 136 3.97e+01 3kboA 315 3.99e+01 1mu5A 471 3.99e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1a7tA 232 4.00e+01 1a7tA d.157.1.1 42041 3mmcA 418 4.02e+01 1b71A 191 4.03e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1ij8A 128 4.04e+01 b.61.1.1 62480 2zd1B 428 4.05e+01 e.8.1.2 154388 2w7vA 95 4.05e+01 2a4nA 182 4.06e+01 d.108.1.1 126159 1r9cA 139 4.09e+01 d.32.1.2 97255 1y7wA 291 4.09e+01 3fg7A 398 4.10e+01 1y88A 199 4.13e+01 a.60.4.3,c.52.1.30 116560,116561 1eetA 557 4.18e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1uylA 236 4.18e+01 d.122.1.1 108147 1znbA 232 4.22e+01 1a7tA d.157.1.1 42039 2pd8A 149 4.22e+01 3bwlA 126 4.27e+01 1grwA 126 4.28e+01 b.1.11.2 70391 1r71A 178 4.31e+01 a.4.14.1 104823 1h5rA 293 4.34e+01 c.68.1.6 65623 2mspA 126 4.36e+01 1mspA b.1.11.2 22335 3blnA 143 4.36e+01 1e8yA 966 4.40e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 3eb8A 358 4.41e+01 2ifsA 169 4.50e+01 3jv1A 182 4.51e+01 3csvA 333 4.53e+01 1v5vA 401 4.55e+01 b.44.2.1,d.250.1.1 113539,113540 3i4kA 383 4.56e+01 2bbhA 269 4.57e+01 d.328.1.1 128266 1aijH 260 4.58e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 1oniA 137 4.58e+01 d.79.1.1 87144 2wwxA 175 4.61e+01 3h9wA 115 4.61e+01 1u2cA 246 4.66e+01 b.1.6.2,d.272.1.1 107610,107611 1w2wA 211 4.67e+01 c.124.1.5 109130 3l1zA 157 4.68e+01 1ravA 127 4.72e+01 1swuA b.61.1.1 27409 2fnoA 248 4.73e+01 a.45.1.1,c.47.1.5 133821,133822 1jr1A 514 4.73e+01 d.37.1.1,c.1.5.1 144358,63241 2f5gA 133 4.74e+01 d.58.57.1 132991 1fjgI 128 4.76e+01 1fjfI d.14.1.1 37559 2gagA 965 4.76e+01 2q6fA 309 4.78e+01 1yghA 164 4.82e+01 1yghA d.108.1.1 40802 2gj3A 120 4.88e+01 3hn0A 283 4.92e+01 2ve7C 250 4.93e+01 3medA 560 4.93e+01 1qczA 169 4.94e+01 1qczA c.23.8.1 31276 1ei1A 391 5.05e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 2pavP 139 5.10e+01 d.110.1.1 149350 3hluA 96 5.12e+01 2wp8A 305 5.13e+01 2pbdP 139 5.13e+01 d.110.1.1 149354 1sf8A 126 5.18e+01 d.271.1.1 105472 1nkiA 135 5.18e+01 d.32.1.2 91941 3hx9A 124 5.19e+01 1yer 228 5.21e+01 1yer 2j3tC 145 5.22e+01 1y5oA 115 5.22e+01 b.55.1.9 122650 2g2qA 124 5.26e+01 1ifqA 138 5.28e+01 1ifqA d.110.4.1 62350 2hvqA 335 5.32e+01 2vjgA 154 5.33e+01 3h43A 85 5.35e+01 1ryt 190 5.39e+01 1ryt 3fydA 263 5.41e+01 1ko3A 230 5.43e+01 d.157.1.1 90974 1ohuA 175 5.48e+01 f.1.4.1 93029 2a1vA 144 5.51e+01 d.198.3.1 126019 2vx8A 169 5.57e+01 1vfsA 386 5.57e+01 b.49.2.2,c.1.6.1 108584,108585 3kuuA 174 5.60e+01 1wywA 230 5.61e+01 c.18.1.2 144566 3bwnA 391 5.61e+01 1zncA 266 5.62e+01 2cba b.74.1.1 27955 2fccA 137 5.63e+01 a.18.1.1 133264 2wo1A 185 5.64e+01 3fq3A 197 5.66e+01 1su0B 159 5.70e+01 d.224.1.2 106015 3hurA 395 5.73e+01 3i0yA 140 5.73e+01 3doaA 288 5.76e+01 1l4dB 122 5.80e+01 d.15.5.1 77684 2dchX 216 5.82e+01 1ig9A 903 5.84e+01 1clqA c.55.3.5,e.8.1.1 62367,62368 2h58A 330 5.85e+01 1pbaA 81 5.91e+01 d.58.3.1 39067 1eyvA 156 5.91e+01 1eyvA a.79.1.1 18446 1h09A 338 5.91e+01 b.109.1.1,c.1.8.8 83420,83421 1q7rA 219 5.93e+01 c.23.16.1 96054 1i5sA 367 5.95e+01 1bg2 c.37.1.9 61822 2c9wA 169 5.96e+01 a.271.1.1,d.93.1.1 145023,145024 1awiA 138 5.96e+01 1pne d.110.1.1 40871 2vacA 134 5.99e+01 1mqoA 227 6.01e+01 d.157.1.1 103846 3d72A 149 6.09e+01 2nyhA 117 6.12e+01 d.58.55.1 138813 3ebyA 163 6.16e+01 d.17.4.4 158087 1g79A 218 6.24e+01 1ci0A b.45.1.1 25752 1vyoA 128 6.26e+01 1yopA 83 6.27e+01 g.41.17.1 123782 2gu3A 136 6.28e+01 d.17.1.6,d.17.1.6 147178,147179 3cniA 156 6.31e+01 1q52A 314 6.31e+01 c.14.1.3 95846 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