# List of top-scoring protein chains for t2k-100-30-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 2yvuA 186 3.10e-04 2plrA 213 7.13e-04 1y63A 184 1.68e-02 c.37.1.1 116494 1ukz 203 3.45e-02 1zin 1ukzA 203 3.45e-02 c.37.1.1 31840 2rhmA 193 5.18e-02 2ax4A 198 6.68e-02 2ccjA 205 7.17e-02 2qorA 204 9.08e-02 1h65A 270 9.85e-02 c.37.1.8 65640 1z6gA 218 1.03e-01 2bwjA 199 1.03e-01 2pbrA 195 1.11e-01 1nn5A 215 1.47e-01 c.37.1.1 85892 2axpA 173 1.57e-01 c.37.1.1 127497 1e9eA 215 2.02e-01 c.37.1.1 64810 1bif 469 2.11e-01 1bif 1bifA 469 2.11e-01 c.37.1.7,c.60.1.4 31961,34003 2pt5A 168 2.32e-01 1gvnB 287 2.62e-01 c.37.1.21 76354 1odfA 290 2.66e-01 c.37.1.6 92782 2c95A 196 2.97e-01 2ga8A 359 3.29e-01 2z0hA 197 3.64e-01 1x6vA 630 4.07e-01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 2p90A 319 4.34e-01 2p5tB 253 4.78e-01 2bifA 469 4.95e-01 1bif c.37.1.7,c.60.1.4 31963,34009 2g5gX 268 5.01e-01 2pezA 179 5.10e-01 3tmkA 216 5.19e-01 3tmkA c.37.1.1 31920 2rgxA 206 5.67e-01 3bifA 468 6.01e-01 1bif c.37.1.7,c.60.1.4 31962,34008 1gtvA 214 7.67e-01 c.37.1.1 70537 2jesA 503 7.71e-01 1gky 187 7.91e-01 1gky 1r1dA 247 9.01e-01 c.69.1.29 96813 1tqhA 247 9.58e-01 c.69.1.29 107225 1esmA 316 9.75e-01 1esmA c.37.1.6 31953 1znwA 207 9.87e-01 c.37.1.1 125412 1ak2A 233 1.01e+00 c.37.1.1,g.41.2.1 31894,45195 1vmaA 306 1.11e+00 a.24.13.1,c.37.1.10 108887,108888 1qhsA 178 1.14e+00 1qhsA c.37.1.3 31938 1ex7A 186 1.16e+00 1gky c.37.1.1 59537 1z8fA 228 1.35e+00 1xrjA 261 1.36e+00 c.37.1.6 122256 1rkbA 173 1.39e+00 c.37.1.1 111854 2h58A 330 1.48e+00 1v6sA 390 1.49e+00 c.86.1.1 100424 2ak3A 226 1.50e+00 1zin c.37.1.1,g.41.2.1 31892,45193 2fk8A 318 1.61e+00 c.66.1.18 133648 1nsf 273 1.63e+00 1d2nA 1p5zB 263 1.67e+00 c.37.1.1 87815 1s4qA 228 1.74e+00 c.37.1.1 98507 1yrbA 262 1.83e+00 c.37.1.10 123915 1viaA 175 1.85e+00 c.37.1.2 100754 5tmpA 213 1.92e+00 5tmpA c.37.1.1 31931 4tmkA 213 1.97e+00 5tmpA c.37.1.1 31930 1m7gA 211 2.05e+00 c.37.1.4 78724 1knqA 175 2.37e+00 c.37.1.17 72786 3ldh 330 2.48e+00 3ldh i.12.1.1 46015 1jjvA 206 2.49e+00 c.37.1.1 71698 3c8uA 208 2.61e+00 1uj2A 252 2.61e+00 c.37.1.6 99452 1qf9A 194 2.61e+00 1zin c.37.1.1 31848 2v40A 459 2.64e+00 1nksA 194 2.67e+00 1nksA c.37.1.1 31886 1qhxA 178 2.72e+00 1qhsA c.37.1.3 31936 1ockA 412 2.84e+00 c.117.1.1 86802 1zuhA 168 2.93e+00 3b9qA 302 2.93e+00 2cdnA 201 3.16e+00 c.37.1.1 130289 1d6jA 211 3.23e+00 1d6jA c.37.1.4 31940 1kmdA 117 3.29e+00 d.189.1.1 72744 2a6mA 155 3.58e+00 d.58.57.1 126287 2vjvA 159 3.60e+00 1c9kB 180 3.77e+00 1c9kB c.37.1.11 32364 1im5A 180 3.78e+00 c.33.1.3 66211 1zd8A 227 3.79e+00 2og2A 359 3.81e+00 1kdoA 227 3.98e+00 c.37.1.1 68478 1sra 151 4.01e+00 1sra 1sraA 151 4.01e+00 a.39.1.3 17190 2qt1A 207 4.25e+00 2hxrA 238 4.28e+00 1vp8A 201 4.45e+00 c.49.1.2 113947 2qy9A 309 4.48e+00 1d2nA 272 4.73e+00 1d2nA c.37.1.20 32428 1ye8A 178 4.84e+00 c.37.1.11 123010 1t3lA 337 4.87e+00 b.34.2.1,c.37.1.1 106358,106359 1um8A 376 5.31e+00 c.37.1.20 99580 1h6zA 913 5.50e+00 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1pixA 587 6.11e+00 c.14.1.4,c.14.1.4 118578,118579 1kn0A 212 6.53e+00 d.50.1.3 77444 2vglS 142 6.61e+00 2vgnA 386 6.73e+00 2il5A 171 6.96e+00 1wd5A 208 7.33e+00 c.61.1.1 114524 2de0X 526 7.57e+00 2ozbB 260 7.81e+00 1gw5S 142 8.00e+00 d.110.4.2 70633 2b8wA 328 8.40e+00 1gs5A 258 8.53e+00 c.73.1.2 70395 2podA 410 8.93e+00 1vfvA 366 9.14e+00 c.37.1.9 108592 1e9gA 286 9.15e+00 1wgjA b.40.5.1 59393 2bbsA 290 9.18e+00 1m1zA 513 9.19e+00 c.26.2.1,d.153.1.1 78457,78458 1azwA 313 9.32e+00 1qtrA c.69.1.7 34658 2olrA 540 9.63e+00 c.91.1.1,c.109.1.1 139140,139141 1h2iA 209 9.70e+00 d.50.1.3 76550 1rxqA 178 9.99e+00 a.213.1.1 105118 1gsjA 258 1.02e+01 c.73.1.2 70397 1z47A 355 1.06e+01 1rz3A 201 1.07e+01 c.37.1.6 98132 2eu8A 216 1.11e+01 1xx6A 191 1.11e+01 c.37.1.24,g.39.1.14 116139,116140 1lw7A 365 1.13e+01 c.26.1.3,c.37.1.1 74295,74296 1g41A 444 1.13e+01 1do0A c.37.1.20 32450 2pgnA 589 1.14e+01 1ayl 541 1.15e+01 1ayl 6ldhA 329 1.17e+01 c.2.1.5,d.162.1.1 30161,42128 1p2xA 159 1.19e+01 a.40.1.1 104062 1yppA 286 1.19e+01 1wgjA b.40.5.1 25407 8prkA 287 1.23e+01 1wgjA b.40.5.1 25395 1p5sA 203 1.27e+01 a.40.1.1 94147 1qpbA 563 1.28e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 2j41A 207 1.29e+01 1lv7A 257 1.31e+01 c.37.1.20 78232 1sq5A 308 1.39e+01 c.37.1.6 105882 1jx2B 315 1.44e+01 c.37.1.8 67404 1evyA 366 1.48e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1pgjA 478 1.48e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 2eyuA 261 1.51e+01 2gzaA 361 1.52e+01 1shkA 173 1.54e+01 1shkA c.37.1.2 31932 2hf9A 226 1.55e+01 1byuA 216 1.55e+01 1byuA c.37.1.8 32032 1i6iA 366 1.57e+01 1bg2 c.37.1.9 61844 1n3bA 216 1.58e+01 c.37.1.1 79959 1oafA 261 1.59e+01 a.93.1.1 86734 2qmcB 188 1.62e+01 1qg4A 216 1.63e+01 1byuA c.37.1.8 32035 2nqoB 188 1.68e+01 2j1oA 268 1.69e+01 1zin 217 1.70e+01 1zin 1zinA 217 1.70e+01 c.37.1.1,g.41.2.1 31915,45178 2c1gA 431 1.72e+01 c.6.2.3,d.341.1.1 129632,129633 2j23A 121 1.78e+01 1cz7A 406 1.82e+01 1bg2 c.37.1.9 32194 2g1iA 563 1.83e+01 2ao9A 155 1.85e+01 a.4.1.17 127069 2bdtA 189 1.88e+01 c.37.1.25 128344 2ihtA 573 1.90e+01 1ugpB 226 1.93e+01 b.34.4.4 107832 1xd7A 145 1.94e+01 a.4.5.55 109566 1y5eA 169 1.94e+01 c.57.1.1 122632 2e0tA 151 1.96e+01 16pk 415 2.00e+01 16pk 16pkA 415 2.00e+01 c.86.1.1 35454 2ab0A 205 2.08e+01 c.23.16.2 126501 2h7oA 303 2.11e+01 2uubB 256 2.15e+01 c.23.15.1 139932 2cvhA 220 2.15e+01 2gsqA 202 2.20e+01 a.45.1.1,c.47.1.5 17715,33009 1akyA 220 2.22e+01 c.37.1.1,g.41.2.1 31896,45197 1ireB 228 2.25e+01 b.34.4.4 76770 2pi0A 116 2.27e+01 2vqeB 256 2.27e+01 1q6zA 528 2.27e+01 c.31.1.3,c.36.1.5,c.36.1.9 111655,111656,111657 2cxxA 190 2.29e+01 c.37.1.8 131013 2f6rA 281 2.30e+01 1sviA 195 2.36e+01 c.37.1.8 106048 1aozA 552 2.39e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1s96A 219 2.40e+01 c.37.1.1 98740 2iyvA 184 2.41e+01 c.37.1.2 137812 2g3vA 208 2.41e+01 1j8mF 297 2.42e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1w77A 228 2.43e+01 c.68.1.13 120679 1bfd 528 2.44e+01 1bfd 1lkxA 697 2.46e+01 c.37.1.9 73981 2f07A 197 2.52e+01 2c1iA 431 2.52e+01 c.6.2.3,d.341.1.1 129636,129637 1j1iA 296 2.53e+01 c.69.1.10 83977 1htwA 158 2.54e+01 c.37.1.18 71083 2yv5A 302 2.64e+01 1pnsB 234 2.69e+01 i.1.1.1 88169 1fds 327 2.71e+01 1fds 1r3dA 264 2.73e+01 c.69.1.35 111680 1apxA 249 2.73e+01 1ryc a.93.1.1 18669 2pjkA 178 2.79e+01 2ki5A 366 2.79e+01 1qhiA c.37.1.1 31862 1tk9A 188 2.81e+01 c.80.1.3 107082 1kyqA 274 2.81e+01 c.2.1.11,e.37.1.1 73281,73282 1wq3A 322 2.83e+01 1lbkA 208 2.84e+01 a.45.1.1,c.47.1.5 73809,73810 1of1A 376 2.85e+01 c.37.1.1 103924 2nq2C 253 2.89e+01 1p3jA 217 2.90e+01 c.37.1.1,g.41.2.1 94022,94023 1fj2A 232 2.91e+01 1auoA c.69.1.14 34720 1puiA 210 2.94e+01 c.37.1.8 88292 1yqtA 538 2.97e+01 1bjt 793 2.99e+01 1bjt 1bjtA 793 2.99e+01 e.11.1.1 43249 1m4rA 151 3.03e+01 a.26.1.3 84799 1nnlA 225 3.04e+01 c.108.1.4 85906 1i5sA 367 3.07e+01 1bg2 c.37.1.9 61822 1o1yA 239 3.15e+01 c.23.16.1 86554 2cygA 312 3.16e+01 c.1.8.3 131025 2c31A 568 3.21e+01 c.31.1.3,c.36.1.5,c.36.1.9 129704,129705,129706 1i7qB 193 3.22e+01 1qdlB c.23.16.1 61902 2it1A 362 3.22e+01 2gwgA 350 3.31e+01 c.1.9.15 135805 2qm8A 337 3.31e+01 2a2rA 210 3.35e+01 a.45.1.1,c.47.1.5 126058,126059 2q1zA 184 3.39e+01 2j5iA 276 3.40e+01 1p9bA 442 3.42e+01 c.37.1.10 94385 2iakA 224 3.43e+01 1w44A 331 3.49e+01 c.37.1.11 114147 2yxnA 322 3.51e+01 1vmeA 410 3.54e+01 c.23.5.1,d.157.1.3 108893,108894 1yhtA 367 3.56e+01 c.1.8.6 123213 1c9kA 180 3.59e+01 1c9kB c.37.1.11 32363 1toaA 313 3.61e+01 1toaA c.92.2.2 35598 2culA 232 3.62e+01 c.3.1.7 130813 1phpA 394 3.62e+01 c.86.1.1 35452 1iq3A 110 3.65e+01 1iq3A a.39.1.6 62640 2djiA 590 3.66e+01 c.31.1.3,c.36.1.5,c.36.1.9 131544,131545,131546 1mkzA 172 3.71e+01 c.57.1.1 84998 1sgoA 139 3.74e+01 d.82.3.1 98857 1cf3A 583 3.78e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 2v0pA 234 3.79e+01 1t8tA 271 3.85e+01 c.37.1.5 106685 2i7vA 459 3.85e+01 1b4pA 217 3.87e+01 a.45.1.1,c.47.1.5 83158,83159 2j1pA 293 3.88e+01 2eq5A 228 3.93e+01 1f9vA 347 3.95e+01 1bg2 c.37.1.9 59745 1t7lA 766 3.99e+01 3bq5A 766 4.00e+01 1y8cA 246 4.02e+01 c.66.1.43 116563 1ckeA 227 4.03e+01 1ckeA c.37.1.1 31846 3ckdA 312 4.07e+01 1fkoA 543 4.11e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 2dqwA 294 4.11e+01 1qhiA 366 4.12e+01 1qhiA c.37.1.1 31860 1i69A 219 4.14e+01 c.94.1.1 61825 2vcnA 261 4.16e+01 1rthA 560 4.19e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1pgtA 210 4.23e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 2qv5A 261 4.23e+01 2gh1A 301 4.29e+01 c.66.1.49 135170 1hdiA 413 4.31e+01 16pk c.86.1.1 60964 9ldtA 332 4.33e+01 3ldh c.2.1.5,d.162.1.1 30154,42121 1wbeA 209 4.34e+01 1w63Q 158 4.34e+01 i.23.1.1 109208 1jtvA 327 4.37e+01 c.2.1.2 84230 1gal 583 4.38e+01 1gpeA 2pw6A 271 4.50e+01 1ylhA 560 4.51e+01 2qm0A 275 4.55e+01 1w8iA 156 4.57e+01 c.120.1.1 114368 1kagA 173 4.61e+01 c.37.1.2 72249 2feaA 236 4.64e+01 c.108.1.20 133327 17gsA 210 4.69e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 3crrA 323 4.80e+01 1o6jA 150 4.81e+01 c.47.1.10 81089 1na3A 91 4.86e+01 k.38.1.1 85481 2bkhA 814 4.86e+01 1e69B 322 4.91e+01 1e69B c.37.1.12 32377 1v7pA 134 4.92e+01 d.169.1.1 108406 1vf8A 377 4.96e+01 c.1.8.5,d.26.3.1 120029,120030 3bioA 304 4.98e+01 2j5vA 367 5.00e+01 1wmjA 130 5.05e+01 6gsvA 217 5.09e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2aplA 157 5.09e+01 a.258.1.1 127132 2f5gA 133 5.12e+01 d.58.57.1 132991 1rd5A 262 5.21e+01 c.1.2.4 111772 2ghcX 261 5.21e+01 1fjgB 256 5.23e+01 1fjfB c.23.15.1 31400 1nzyA 269 5.25e+01 1nzyA c.14.1.3 30903 1rkuA 206 5.27e+01 c.108.1.11 97627 3b2yA 275 5.31e+01 2a5hA 416 5.35e+01 3c24A 286 5.43e+01 1ki9A 192 5.61e+01 c.37.1.1 84404 1jljA 189 5.62e+01 c.57.1.1 63169 1qr7A 350 5.66e+01 1qr7A c.1.10.4 29191 2akaA 776 5.75e+01 2an9A 207 5.76e+01 c.37.1.1 127037 2yv9A 291 5.78e+01 1lrrA 131 5.86e+01 d.228.1.1 78165 1pydA 556 5.88e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 2o7oA 207 5.89e+01 a.4.1.9,a.121.1.1 138930,138931 1ofhA 310 5.90e+01 c.37.1.20 86948 1u5pA 216 5.91e+01 a.7.1.1,a.7.1.1 113046,113047 2uz0A 263 5.94e+01 1xw5A 217 6.02e+01 a.45.1.1,c.47.1.5 116099,116100 2cdqA 510 6.11e+01 c.73.1.3,d.58.18.10,d.58.18.10 130290,130291,130292 1zx5A 300 6.12e+01 b.82.1.3 125763 1ujqA 305 6.12e+01 c.1.12.7 99463 1d3yA 301 6.17e+01 1d3yA e.12.1.1 43252 2v5iA 559 6.19e+01 1otjA 283 6.21e+01 b.82.2.5 93517 2c4jA 218 6.30e+01 a.45.1.1,c.47.1.5 129816,129817 2oqhA 385 6.31e+01 2oggA 152 6.34e+01 2pzeA 229 6.38e+01 1twdA 256 6.53e+01 c.1.30.1 107397 2g1kA 176 6.53e+01 c.37.1.2 134519 1i1qB 192 6.57e+01 1qdlB c.23.16.1 61544 1snyA 267 6.62e+01 c.2.1.2 105833 1orjA 130 6.68e+01 a.24.19.1 93456 1dhr 241 6.70e+01 1dhr 2dwuA 276 6.72e+01 2grjA 192 6.72e+01 1xel 338 6.73e+01 1xel 1aqwA 209 6.77e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1ejjA 511 6.81e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1t0hB 224 6.82e+01 c.37.1.1 106208 1dqwA 267 6.83e+01 1dqwA c.1.2.3 28551 2h57A 190 6.86e+01 1zi8A 236 6.88e+01 1j3eA 115 6.92e+01 d.228.1.1 103834 1v37A 177 6.93e+01 c.60.1.1 113497 1o7dA 298 6.96e+01 c.6.2.1 86641 2qptA 550 7.00e+01 1dn1A 594 7.02e+01 1dn1A e.25.1.1 43357 1kpgA 287 7.03e+01 c.66.1.18 68735 2rc5A 314 7.15e+01 2is8A 164 7.20e+01 2nxwA 565 7.22e+01 1o9gA 250 7.22e+01 c.66.1.29 86692 1hkvA 453 7.26e+01 b.49.2.3,c.1.6.1 83559,83560 2i5eA 211 7.35e+01 2dc5A 231 7.42e+01 1izmA 184 7.43e+01 a.199.1.1 90725 1ohvA 472 7.43e+01 c.67.1.4 93031 1gg1A 350 7.47e+01 1qr7A c.1.10.4 29187 2f48A 555 7.51e+01 c.89.1.1 132915 2p4qA 497 7.56e+01 2hy1A 280 7.59e+01 1zunA 325 7.61e+01 c.26.2.2 125676 2fn9A 290 7.64e+01 2yzqA 282 7.75e+01 1xeaA 323 7.86e+01 c.2.1.3,d.81.1.5 109572,109573 1ufoA 238 7.88e+01 c.69.1.27 99344 1fzqA 181 7.89e+01 1hurA c.37.1.8 32060 1rrvA 416 7.94e+01 c.87.1.5 105083 1adeA 431 7.96e+01 1adeA c.37.1.10 32213