# 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.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 1h1iB 350 1.60e-03 b.82.1.5 76470 1h1iC 350 2.60e-03 b.82.1.5 76471 1juhA 350 3.26e-03 b.82.1.5 71884 1h1iD 350 5.76e-03 b.82.1.5 76472 1plzA 189 1.06e-02 b.82.1.7 88160 1qxrA 189 1.31e-02 1od5A 492 2.99e-02 b.82.1.2 86832 b.82.1.2 86833 1cawB 184 5.29e-02 1caxB b.82.1.2 28113 1j58A 385 5.50e-02 b.82.1.2 71531 2phlA 397 7.06e-02 1dgwA b.82.1.2 28082 b.82.1.2 28083 1dlc 584 1.46e-01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1j1tA 233 1.59e-01 8acn 754 2.74e-01 1amj c.8.2.1 30724 c.83.1.1 35400 1cauB 184 2.84e-01 1caxB b.82.1.2 28103 1amj 754 2.89e-01 1amj c.8.2.1 30725 c.83.1.1 35401 1fxzA 476 3.20e-01 b.82.1.2 65059 b.82.1.2 65060 7acn 754 3.43e-01 1amj c.8.2.1 30717 c.83.1.1 35393 1c96A 753 3.68e-01 1amj c.8.2.1 30727 c.83.1.1 35403 6acn 754 6.09e-01 1amj c.8.2.1 30721 c.83.1.1 35397 2cgpA 210 6.42e-01 2cgpA a.4.5.4 16102 b.82.3.2 28141 1b0jA 754 6.54e-01 1amj c.8.2.1 30719 c.83.1.1 35395 1bix 287 6.58e-01 1bix d.151.1.1 41781 1iscA 192 7.23e-01 1avmA a.2.11.1 15733 d.44.1.1 38726 1isaA 192 7.42e-01 1avmA a.2.11.1 15731 d.44.1.1 38724 1aerA 205 8.00e-01 1aerA d.166.1.1 42249 1hd7A 318 9.20e-01 1bix d.151.1.1 41780 1caxB 184 9.40e-01 1caxB b.82.1.2 28105 1elpA 173 1.10e+00 1amm b.11.1.1 23596 b.11.1.1 23597 1dc1A 323 1.33e+00 1dc1A c.52.1.11 33321 4aahA 571 1.38e+00 4aahA b.70.1.1 27678 1eybA 471 1.44e+00 1ey2A b.82.1.4 28115 1c8zA 265 1.47e+00 1c8zA d.23.1.1 38375 1dmaA 214 1.55e+00 1aerA d.166.1.1 42251 1m8uA 173 1.62e+00 1c5kA 439 1.62e+00 1crzA b.68.4.1 27630 c.51.2.1 33212 1dcuA 357 1.68e+00 1frpA e.7.1.1 42943 1a6q 382 1.68e+00 1a6q a.159.1.1 75801 d.219.1.1 75802 1g72A 573 1.77e+00 4aahA b.70.1.1 27680 1ca1 370 1.94e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1crzA 403 2.03e+00 1crzA b.68.4.1 27629 c.51.2.1 33211 2dnjA 260 2.27e+00 3dni d.151.1.1 41790 1khbA 625 2.57e+00 c.91.1.1 68606 c.109.1.1 68607 1ih7A 903 3.10e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1fw9A 164 3.18e+00 1fw9A d.190.1.1 60059 1oo2A 119 3.23e+00 1hw5A 210 3.26e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1uvqA 197 3.49e+00 1m4jA 142 3.75e+00 d.109.1.2 78602 1d2eA 397 3.79e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1e79H 146 3.95e+00 1e79H a.2.10.1 15721 b.93.1.1 28438 1i4uA 181 4.00e+00 b.60.1.1 61732 1evhA 112 4.15e+00 1evhA b.55.1.4 26997 1orvA 728 4.65e+00 b.70.3.1 87354 c.69.1.24 87355 3dni 260 4.92e+00 3dni d.151.1.1 41791 1g1sA 162 4.94e+00 d.169.1.1 65100 g.3.11.1 65101 1ey2A 471 4.96e+00 1ey2A b.82.1.4 28116 1clqA 903 5.04e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1q1fA 151 5.15e+00 1ofuA 320 5.20e+00 c.32.1.1 86972 d.79.2.1 86973 1ciy 590 5.26e+00 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1nkr 201 5.31e+00 1nkr b.1.1.4 21799 b.1.1.4 21800 1ttbA 127 5.37e+00 1etb1 b.3.4.1 22543 1n6eA 1071 5.58e+00 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1hkvA 453 5.59e+00 b.49.2.3 83559 c.1.6.1 83560 1aqt 138 5.69e+00 1aqt a.2.10.1 15718 b.93.1.1 28435 1ri6A 343 5.70e+00 2bb2 181 5.90e+00 2bb2 b.11.1.1 23604 b.11.1.1 23605 1n1mA 728 5.91e+00 b.70.3.1 79815 c.69.1.24 79816 1n0uA 842 5.94e+00 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1gv3A 248 5.95e+00 a.2.11.1 70585 d.44.1.1 70586 1eta1 127 6.03e+00 1etb1 1pmmA 466 6.38e+00 1liiA 363 6.38e+00 c.72.1.1 73921 4gcr 174 6.44e+00 1amm b.11.1.1 23589 b.11.1.1 23590 8prkA 287 6.45e+00 1wgjA b.40.5.1 25395 1rypE 242 6.60e+00 1rypE d.153.1.4 41936 1a16 440 6.66e+00 1az9 c.55.2.1 33548 d.127.1.1 41165 1mkeA 152 6.83e+00 b.55.1.4 79231 1qbiA 454 7.00e+00 1c9uA b.68.2.1 27619 1soxA 466 7.14e+00 1soxA b.1.18.6 21947 d.120.1.1 41090 d.176.1.1 42563 1hx0A 496 7.46e+00 b.71.1.1 61346 c.1.8.1 61347 1mu5A 471 7.47e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1kbvA 327 7.48e+00 b.6.1.3 68395 b.6.1.3 68396 1az9 457 7.70e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 2prd 174 7.70e+00 2prd b.40.5.1 25435 1k5dB 201 7.84e+00 b.55.1.3 68169 1fzdA 201 7.89e+00 3fib d.171.1.1 42484 1mt6A 280 8.05e+00 b.76.2.1 79446 b.85.7.1 79447 1ng4A 390 8.06e+00 c.3.1.2 85666 d.16.1.3 85667 1mngA 203 8.31e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1i2hA 168 8.34e+00 b.55.1.4 71103 1oj6A 151 8.34e+00 1sdwA 314 8.37e+00 1dgmA 363 8.90e+00 1bx4A c.72.1.1 34936 1jhsA 188 9.11e+00 d.107.1.1 84172 1frpA 335 9.24e+00 1frpA e.7.1.1 42875 1svq 114 9.27e+00 1svy d.109.1.1 40832 1fnmA 691 9.30e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1uesA 191 9.67e+00 1h91A 180 9.71e+00 b.60.1.1 60805 1b65A 375 9.75e+00 1b65A d.154.1.1 42020 1smd 496 9.78e+00 1smd b.71.1.1 27768 c.1.8.1 28755 1o7nA 449 9.87e+00 b.33.1.2 81162 d.129.3.3 81163 1eg9A 449 1.04e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1mrzA 293 1.04e+01 1kk1A 410 1.06e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1v5mA 136 1.06e+01 1f86A 115 1.06e+01 1etb1 b.3.4.1 59689 1wgjA 286 1.07e+01 1wgjA b.40.5.1 25397 1e9gA 286 1.07e+01 1wgjA b.40.5.1 59393 1e1hA 287 1.07e+01 d.92.1.7 83167 1hdhA 536 1.10e+01 c.76.1.2 65805 1tfpA 130 1.11e+01 1etb1 b.3.4.1 22623 1su4A 994 1.14e+01 1bag 425 1.16e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1kczA 413 1.16e+01 c.1.11.2 68451 d.54.1.1 68452 1m55A 197 1.17e+01 d.89.1.3 74469 1b3jA 274 1.17e+01 1agdA b.1.1.2 20855 d.19.1.1 38319 1aqjA 421 1.19e+01 2admA c.66.1.27 34242 1uxzA 131 1.19e+01 2cavA 445 1.20e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1svr 114 1.21e+01 1svy d.109.1.1 40833 1jmcA 246 1.25e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1c9uA 454 1.25e+01 1c9uA b.68.2.1 27623 1ve9A 347 1.29e+01 1who 96 1.30e+01 1who b.7.3.1 23215 1e5pA 151 1.33e+01 1bj7 b.60.1.1 59272 1sviA 195 1.33e+01 1i5pA 633 1.33e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1ur5A 309 1.36e+01 1bu8A 452 1.39e+01 1gpl b.12.1.2 23647 c.69.1.19 34795 1dgrM 93 1.41e+01 1caxB b.82.1.2 28101 1qnnA 191 1.43e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1ndoA 449 1.44e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1r4pA 297 1.45e+01 1eq6A 189 1.48e+01 1eq6A d.107.1.1 40796 1hqz1 141 1.48e+01 1amm 174 1.48e+01 1amm b.11.1.1 23587 b.11.1.1 23588 1e9gB 286 1.48e+01 1wgjA b.40.5.1 59394 1fs0E 138 1.50e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1kid 203 1.53e+01 1derA c.8.5.1 30771 1dgrW 93 1.58e+01 1caxB 1lox 662 1.61e+01 1lox a.119.1.2 19238 b.12.1.1 23638 1an8 208 1.62e+01 1an8 b.40.2.2 25202 d.15.6.1 37791 1h2xA 710 1.62e+01 b.69.7.1 76598 c.69.1.4 76599 1g38A 393 1.69e+01 2admA c.66.1.27 60235 1svy 114 1.70e+01 1svy d.109.1.1 40831 1ut0A 190 1.71e+01 1pt1A 143 1.72e+01 1f41A 127 1.74e+01 1etb1 b.3.4.1 22539 1h2wA 710 1.75e+01 b.69.7.1 76596 c.69.1.4 76597 1iakA 199 1.77e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1etb1 127 1.78e+01 1etb1 1mo9A 523 1.78e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1j3mA 129 1.86e+01 1umhA 184 1.86e+01 1q7fA 286 1.87e+01 1c8uA 285 1.90e+01 1c8uA d.38.1.3 38547 d.38.1.3 38548 1aj6 219 1.90e+01 1aj6 d.122.1.2 41106 1jgtA 513 1.92e+01 c.26.2.1 66684 d.153.1.1 66685 1ckmA 330 1.92e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1p9vA 310 1.93e+01 d.21.1.2 88007 d.21.1.2 88008 1sdjA 310 1.93e+01 1p5tA 127 1.95e+01 1fpzA 212 1.99e+01 1fpzA c.45.1.1 59976 1dqnA 230 2.01e+01 1dqnA c.61.1.1 34067 1noyA 388 2.02e+01 1clqA c.55.3.5 33713 1h3iA 293 2.02e+01 b.76.2.1 76635 b.85.7.1 76636 1fpkA 335 2.03e+01 1frpA e.7.1.1 42930 1jvwA 167 2.05e+01 d.26.1.1 71907 8prkB 287 2.07e+01 1wgjA b.40.5.1 25396 1m4vA 204 2.07e+01 b.40.2.2 74459 d.15.6.1 74460 2admA 421 2.10e+01 2admA c.66.1.27 34238 1bp1 456 2.10e+01 1bp1 d.83.1.1 40026 d.83.1.1 40027 1phm 310 2.12e+01 1phm b.121.1.2 59015 b.121.1.2 59016 1gppA 237 2.17e+01 b.86.1.2 76262 1v3eA 431 2.21e+01 1ollA 188 2.23e+01 1qqp2 218 2.24e+01 1qqp2 1cruA 454 2.25e+01 1c9uA b.68.2.1 27617 1qvjA 292 2.27e+01 1pqhA 143 2.28e+01 1k32A 1045 2.28e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1qfmA 710 2.32e+01 1qfmA b.69.7.1 27673 c.69.1.4 34641 1bcpC 199 2.32e+01 1bcpB b.40.2.1 25121 d.169.1.2 42430 1ewfA 456 2.33e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1o59A 355 2.36e+01 1prxA 224 2.38e+01 1prxA c.47.1.10 33076 1f2tA 149 2.38e+01 1f2tA c.37.1.12 32373 1jjuB 337 2.40e+01 b.69.2.2 66779 1q3eA 207 2.43e+01 1qa7A 217 2.43e+01 1havA b.47.1.4 26425 1kcw 1046 2.43e+01 1kcw b.6.1.3 23151 b.6.1.3 23152 b.6.1.3 23153 b.6.1.3 23154 b.6.1.3 23155 b.6.1.3 23156 1babB 146 2.44e+01 1abwA a.1.1.2 15414 1kz8A 337 2.45e+01 e.7.1.1 77633 1ff9A 450 2.46e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1kk9A 221 2.47e+01 d.115.1.1 77432 1rdzA 337 2.49e+01 1frpA e.7.1.1 42882 1ntvA 152 2.51e+01 b.55.1.2 86168 1pguA 615 2.53e+01 b.69.4.1 88069 b.69.4.1 88070 1h2kA 349 2.56e+01 b.82.2.6 76572 1fi2A 201 2.58e+01 1fi2A b.82.1.2 59845 1pbyB 337 2.63e+01 1dm0A 287 2.67e+01 1dm0A d.165.1.2 42227 1i3dA 146 2.69e+01 a.1.1.2 61587 2pabA 127 2.70e+01 1etb1 b.3.4.1 22597 2pil 159 2.70e+01 2pil d.24.1.1 38376 1pbe 394 2.72e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1mwsA 646 2.72e+01 d.17.4.5 79592 d.175.1.1 79593 e.3.1.1 79594 1lktA 104 2.77e+01 1lktA b.90.1.1 28398 3chbD 104 2.81e+01 3chbD b.40.2.1 24970 1qklA 127 2.81e+01 1qklA d.78.1.2 39754 5fbpA 335 2.82e+01 1frpA e.7.1.1 42873 1p32C 209 2.83e+01 1p32A d.25.1.1 38381 2pvaA 345 2.83e+01 3pvaA d.153.1.3 41850 1nstA 325 2.86e+01 1nstA c.37.1.5 31951 1f5fA 205 2.86e+01 1d2sA b.29.1.4 24222 1jofA 365 2.88e+01 b.69.10.1 71775 1efcA 393 2.91e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1ako 268 2.93e+01 1ako d.151.1.1 41779 1lr5A 163 3.02e+01 b.82.1.2 74215 1dqpA 230 3.08e+01 1dqnA c.61.1.1 34069 1jae 471 3.08e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1d7kA 421 3.13e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1khdA 345 3.14e+01 a.46.2.1 77400 c.27.1.1 77401 1e8nA 710 3.14e+01 1qfmA b.69.7.1 27675 c.69.1.4 34643 1lrwA 600 3.15e+01 3psg 370 3.17e+01 1smrA b.50.1.2 26841 1hn0A 1021 3.18e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1irdB 146 3.21e+01 a.1.1.2 66287 1kngA 156 3.24e+01 c.47.1.10 72777 1viwB 198 3.24e+01 1led b.29.1.1 24170 1ki1B 352 3.26e+01 a.87.1.1 72497 b.55.1.1 72498 1a2vA 655 3.26e+01 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1nuyA 337 3.27e+01 e.7.1.1 86213 1prxB 224 3.27e+01 1prxA c.47.1.10 33077 1qu5A 182 3.29e+01 1qu5A b.26.1.2 23922 1dxtB 147 3.30e+01 1abwA a.1.1.2 15450 1kgyA 181 3.30e+01 b.18.1.4 72449 2prf 125 3.33e+01 3nul d.110.1.1 40887 2fbjL 213 3.35e+01 8fabA b.1.1.1 19850 b.1.1.2 20954 1nb8A 353 3.35e+01 d.3.1.9 80385 1m1zA 513 3.37e+01 c.26.2.1 78457 d.153.1.1 78458 1irsA 112 3.37e+01 1qqgA b.55.1.2 26991 1m6kA 251 3.37e+01 e.3.1.1 78695 1vdeA 454 3.40e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1ltsD 103 3.41e+01 3chbD b.40.2.1 24900 1djrD 103 3.43e+01 3chbD b.40.2.1 24865 1lay 256 3.43e+01 1lay b.57.1.1 27014 2eifA 136 3.45e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1iwhB 146 3.47e+01 a.1.1.2 76883 1d2sA 170 3.54e+01 1d2sA b.29.1.4 24221 1jb0D 138 3.55e+01 1jb0D d.187.1.1 62823 1kcvL 214 3.60e+01 b.1.1.1 72317 b.1.1.2 72318 1iwmA 186 3.61e+01 b.125.1.2 83758 1ibvB 229 3.62e+01 1efiD 103 3.63e+01 3chbD b.40.2.1 24870 1pjxA 314 3.65e+01 1qstA 160 3.65e+01 1yghA d.108.1.1 40804 1avmA 201 3.65e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1npsA 88 3.69e+01 1prs b.11.1.1 23622 1k8kC 372 3.72e+01 b.69.4.1 68308 1s1dA 331 3.77e+01 1o7fA 469 3.86e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 2i1b 153 3.90e+01 2i1b b.42.1.2 25538 1q33A 292 3.92e+01 3fib 249 3.93e+01 3fib d.171.1.1 42455 1f60A 458 3.93e+01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 2fhi 147 3.94e+01 1fit d.13.1.1 37505 1bv4A 118 3.96e+01 1rtm1 d.169.1.1 42380 1i7fA 292 3.97e+01 1i7fA d.193.1.1 61888 1ft9A 222 4.00e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131