# List of top-scoring protein chains for t2k-100-30-alpha 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 1jhdA 396 1.50e-01 b.58.1.2 66712 c.26.1.5 66713 1e15A 499 3.75e-01 1e15A b.72.2.1 27810 c.1.8.5 29006 d.26.3.1 38440 1l3kA 196 3.78e-01 1goiA 499 3.90e-01 b.72.2.1 65413 c.1.8.5 65414 d.26.3.1 65415 1e6pA 499 4.19e-01 1e15A b.72.2.1 59314 c.1.8.5 59315 d.26.3.1 59316 1ha1 184 5.59e-01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1jksA 294 6.22e-01 1c24A 263 1.16e+00 1c24A d.127.1.1 41148 1qhkA 47 1.32e+00 1qhkA d.100.1.2 40694 2matA 264 1.39e+00 1c24A d.127.1.1 41146 1in4A 334 1.83e+00 1hqcA a.4.5.11 62597 c.37.1.13 62598 1jr7A 311 1.89e+00 b.82.2.3 63255 1fj7A 101 2.09e+00 1fj7A d.58.7.1 39209 1hyuA 521 2.35e+00 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1mli 96 2.41e+00 1mli d.58.4.1 39070 1mat 264 2.51e+00 1c24A d.127.1.1 41152 1f9fA 83 2.59e+00 1f9fA d.58.8.1 39224 1evxA 162 2.84e+00 1a73A d.4.1.3 37149 1dyqA 234 2.86e+00 3seb b.40.2.2 59140 d.15.6.1 59141 1jr8A 117 3.07e+00 a.24.15.1 67115 1pls 113 3.21e+00 1pls b.55.1.1 26965 1lkzA 219 3.41e+00 1a73A 163 3.45e+00 1a73A d.4.1.3 37145 1gajA 257 4.04e+00 1gajA c.37.1.12 60416 1foeA 377 4.17e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1preA 470 4.19e+00 1preA d.169.1.2 42437 f.8.1.1 43824 1f2tB 148 4.22e+00 1f2tB 1k2yX 463 4.33e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 c.84.1.1 68066 1jraA 117 4.43e+00 a.24.15.1 67117 2bopA 85 4.73e+00 2bopA d.58.8.1 39217 1lpuA 332 4.74e+00 2cb5A 453 4.78e+00 3gcb d.3.1.1 37035 1d3hA 367 4.79e+00 1d3gA c.1.4.1 28601 1g6hA 257 4.88e+00 1gajA c.37.1.12 60318 1dbhA 354 4.99e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1g6oA 330 5.05e+00 1g6oA c.37.1.13 32430 1a4iB 301 5.37e+00 1a4iA c.2.1.7 30279 c.58.1.2 33927 1fil 139 5.44e+00 1pne d.110.1.1 40869 1qupA 222 5.57e+00 1qupA b.1.8.1 22301 d.58.17.1 39352 1plr 258 5.77e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1d3gA 367 5.87e+00 1d3gA c.1.4.1 28600 1gewA 356 6.01e+00 1gewA c.67.1.1 60470 1xyfA 436 6.29e+00 1taxA b.42.2.1 25577 c.1.8.3 28909 1i4sA 147 6.37e+00 a.149.1.1 66026 1aw0 72 6.42e+00 1aw0 d.58.17.1 39342 1g6q2 328 6.48e+00 1g6q2 1fl2A 310 6.50e+00 1hyuA c.3.1.5 59869 c.3.1.5 59870 1a4iA 301 6.65e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 1yprA 125 6.73e+00 3nul d.110.1.1 40888 1b5tA 275 6.73e+00 1b5tA c.1.23.1 29676 1js3A 486 6.74e+00 c.67.1.6 67215 1plq 258 6.77e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1bo1A 416 6.91e+00 1bo1A d.143.1.2 41591 1gc5A 467 6.93e+00 1gc5A c.72.1.3 60429 1dgsA 667 7.04e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1gegA 256 7.11e+00 1ybvA c.2.1.2 29888 1efdN 266 7.16e+00 1efdN c.92.2.1 35597 1fg7A 356 7.27e+00 1gewA c.67.1.1 59819 1pne 140 7.90e+00 1pne d.110.1.1 40866 1qb0A 211 7.94e+00 1c25 c.46.1.1 32699 1fa0B 537 8.14e+00 1fa0B d.58.16.1 39336 e.9.1.2 43230 1fzaB 328 8.29e+00 3fib d.171.1.1 42480 h.1.8.1 45621 2at2A 300 8.38e+00 3csuA c.78.1.1 35196 c.78.1.1 35197 3eugA 229 8.65e+00 3eugA c.18.1.1 31018 1preB 470 8.79e+00 1preA d.169.1.2 42438 f.8.1.1 43825 1urnA 97 9.05e+00 1urnA d.58.7.1 39153 3fruA 269 9.37e+00 1agdA b.1.1.2 20657 d.19.1.1 38150 1eayC 74 9.40e+00 1eayC d.58.24.1 39386 5cytR 104 9.49e+00 1ycc a.3.1.1 15878 2scpA 174 9.78e+00 2scpA a.39.1.5 17256 1esmA 316 9.84e+00 1esmA c.37.1.6 31953 1b7fA 168 1.00e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 4eugA 229 1.01e+01 3eugA c.18.1.1 31019 1ksiB 642 1.03e+01 1ksiB b.30.2.1 24409 d.17.2.1 38045 d.17.2.1 38046 1d09B 153 1.04e+01 8atcB d.58.2.1 39015 g.41.7.1 45267 1fgkA 310 1.05e+01 1fgkA d.144.1.2 41693 1h6zA 913 1.07e+01 1ex1A 605 1.07e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1l1sA 113 1.08e+01 1seiA 130 1.08e+01 1seiA d.140.1.1 41463 1blxA 326 1.09e+01 1hcl d.144.1.1 41596 1dcnD 436 1.11e+01 1auwA a.127.1.1 19423 2reb 352 1.11e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1evhA 112 1.12e+01 1evhA b.55.1.4 26997 1cby 259 1.12e+01 1cby d.103.1.1 40705 1ihkA 174 1.13e+01 1bfg b.42.1.1 62384 1qatB 622 1.13e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 3pbgA 468 1.15e+01 1e70M c.1.8.4 28951 1bzsA 165 1.22e+01 1hfc d.92.1.11 40348 1ksiA 642 1.24e+01 1ksiB b.30.2.1 24408 d.17.2.1 38043 d.17.2.1 38044 1liaA 164 1.25e+01 1cpcA a.1.1.3 15661 1obr 326 1.28e+01 1aye c.56.5.2 33828 1qlpA 394 1.34e+01 1ovaA e.1.1.1 42628 1esfA 233 1.36e+01 3seb b.40.2.2 25146 d.15.6.1 37735 1hruA 188 1.37e+01 1hruA d.115.1.1 40926 1c52 131 1.37e+01 1c52 a.3.1.1 15810 1avoA 60 1.38e+01 1avoA a.24.8.1 16619 1by9 81 1.41e+01 2bopA d.58.8.1 39223 1dt9A 437 1.43e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1qfxA 460 1.44e+01 1qfxA c.60.1.3 33994 1djxB 624 1.45e+01 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1bfi 112 1.46e+01 1qadA d.93.1.1 40499 1djxA 624 1.49e+01 1djxB a.39.1.7 17342 b.7.1.1 23159 c.1.18.1 29587 1iexA 605 1.50e+01 c.1.8.7 66127 c.23.11.1 66128 1jfzA 154 1.50e+01 a.149.1.1 66655 1wit 93 1.51e+01 1wit b.1.1.4 21714 1ewkA 490 1.52e+01 1ewkA c.93.1.1 35712 1thm 279 1.53e+01 1gci c.41.1.1 32544 1qd1A 325 1.55e+01 1qd1A d.58.34.1 39493 d.58.34.1 39494 1qhlA 227 1.60e+01 1qhlA c.37.1.12 32382 1mxa 383 1.60e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1fht 116 1.62e+01 1urnA d.58.7.1 39157 1ctf 74 1.63e+01 1ctf d.45.1.1 38759 1i76A 163 1.66e+01 1hfc d.92.1.11 61877 1agx 331 1.69e+01 4pgaA c.88.1.1 35564 1h8eG 272 1.72e+01 1e79G c.49.2.1 60756 1io1A 398 1.74e+01 1io1A e.32.1.1 62611 1pauA 147 1.75e+01 1pauA c.17.1.1 30994 1dkzA 219 1.78e+01 1dkzA e.20.1.1 43314 1qmuA 380 1.79e+01 1qmuA b.3.2.1 22534 c.56.5.1 33827 1h4xA 117 1.88e+01 1auz c.13.2.1 60626 1kmoA 774 1.90e+01 7at1B 154 1.91e+01 8atcB d.58.2.1 39053 g.41.7.1 45305 830cA 168 1.91e+01 1ck7A d.92.1.11 40400 1f4kA 122 1.91e+01 1bm9A a.4.5.7 59646 1mmoD 512 1.94e+01 1mhyD a.25.1.2 16770 1fc2C 58 1.97e+01 1fc2C a.8.1.1 16345 1h6kZ 98 1.98e+01 d.58.7.1 60686 1bj5 585 1.98e+01 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1fa0A 537 1.99e+01 1fa0B d.58.16.1 39335 e.9.1.2 43229 1aogA 485 1.99e+01 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 3minC 491 2.00e+01 1qguA c.92.2.3 35607 1dkxA 219 2.01e+01 1dkzA e.20.1.1 43315 8atcB 154 2.02e+01 8atcB d.58.2.1 39027 g.41.7.1 45279 1dcnA 424 2.02e+01 1auwA a.127.1.1 19420 1sqc 631 2.05e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1hloA 150 2.05e+01 1an4A a.38.1.1 17128 1pmaP 211 2.07e+01 1pmaP d.153.1.4 41863 1fjcA 96 2.11e+01 1fjcA d.58.7.1 39212 1h9oA 112 2.12e+01 1qadA d.93.1.1 60837 3timA 250 2.13e+01 1amk c.1.1.1 28483 1iqpA 327 2.14e+01 a.80.1.1 62649 c.37.1.13 62650 1lldA 319 2.14e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1j8wB 273 2.15e+01 c.68.1.2 66441 1k30A 368 2.16e+01 c.112.1.1 68067 1dqnA 230 2.17e+01 1dqnA c.61.1.1 34067 1qadA 111 2.17e+01 1qadA d.93.1.1 40498 1b3qA 379 2.17e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1g9mG 321 2.17e+01 1gc1G d.172.1.1 42492 1qgvA 142 2.18e+01 1qgvA c.47.1.8 33056 1i60A 278 2.19e+01 2minA 491 2.20e+01 1qguA c.92.2.3 35609 1aoa 275 2.22e+01 1aoa a.40.1.1 17396 a.40.1.1 17397 1dqpA 230 2.23e+01 1dqnA c.61.1.1 34069 1cp3A 277 2.24e+01 1pauA c.17.1.1 30992 1a0oD 134 2.26e+01 1eayC d.58.24.1 39391 1914 232 2.28e+01 1914 d.49.1.1 38779 1dd3A 128 2.29e+01 1dd3C a.108.1.1 19031 d.45.1.1 38760 1iicA 422 2.30e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1b8dA 164 2.30e+01 1cpcA a.1.1.3 15665 1qbeA 132 2.31e+01 1qbeA d.85.1.1 40138 1guqA 348 2.32e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 1tpfA 250 2.33e+01 1amk c.1.1.1 28467 1gupA 348 2.33e+01 1guqA d.13.1.2 37534 d.13.1.2 37535 1ql3A 99 2.34e+01 1ycc a.3.1.1 15822 9apiA 347 2.36e+01 1ovaA e.1.1.1 42630 1lghB 45 2.36e+01 1lghB f.3.1.1 43734 1efyA 350 2.39e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1c25 161 2.42e+01 1c25 c.46.1.1 32698 1idrA 136 2.42e+01 1dlyA a.1.1.1 62301 1ppt 36 2.43e+01 1ppt j.6.1.1 46089 2gcc 70 2.48e+01 2gcc d.10.1.2 37484 1ee8A 266 2.48e+01 1ee8A e.14.1.1 43261 3dapA 320 2.55e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1e79G 272 2.59e+01 1e79G c.49.2.1 33158 1mxb 383 2.61e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1ka1A 357 2.61e+01 e.7.1.1 68369 1fqvA 336 2.62e+01 1fqvA a.122.1.1 19254 c.10.1.3 30856 1auz 116 2.66e+01 1auz c.13.2.1 30883 1dapA 320 2.69e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 2pldA 105 2.70e+01 1qadA d.93.1.1 40521 1pot 325 2.70e+01 1pot c.94.1.1 35807 1btn 106 2.71e+01 1btn b.55.1.1 26952 1ihfB 94 2.74e+01 1huuA a.55.1.1 17894 1jk3A 158 2.78e+01 d.92.1.11 66790 2frvB 536 2.78e+01 1h2rL e.18.1.1 43291 1g7eA 122 2.83e+01 1g7eA c.47.1.7 33055 1f06A 320 2.84e+01 1dapA c.2.1.3 59556 d.81.1.3 59557 1j7nA 776 2.85e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1qgxA 357 2.90e+01 1qgxA e.7.1.1 42973 4xiaA 393 2.92e+01 4xis c.1.15.3 29439 1hlcA 129 2.96e+01 1c1lA b.29.1.3 24208 1pbgA 468 2.99e+01 1e70M c.1.8.4 28946 1jqsC 68 3.00e+01 i.1.1.1 63239 1ew4A 106 3.00e+01 1ew4A d.82.2.1 40023 1k3sA 113 3.04e+01 d.198.1.1 68120 1ytc 112 3.04e+01 1ycc a.3.1.1 15835 1thfD 253 3.08e+01 1thfD c.1.2.1 28535 1jnyA 435 3.08e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1d6aB 262 3.11e+01 1qi7A d.165.1.1 42198 2trcP 217 3.16e+01 1b9yC c.47.1.6 33051 1cpzA 68 3.19e+01 1aw0 d.58.17.1 39351 1b0pA 1231 3.19e+01 c.36.1.4 31831 c.36.1.4 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1qciA 262 3.21e+01 1qi7A d.165.1.1 42201 1b04A 318 3.23e+01 1b04A d.142.2.2 41579 1jyrA 96 3.25e+01 1fgxA 288 3.27e+01 1fgxA c.68.1.2 34508 2mysB 166 3.36e+01 1wdcB a.39.1.5 17308 1f5sA 211 3.37e+01 1f5sA c.108.1.4 59656 1qi9A 556 3.40e+01 1qhbA a.111.1.2 19053 1jmtA 104 3.48e+01 d.58.7.3 63180 1an7A 136 3.49e+01 1seiA d.140.1.1 41465 1i0aA 466 3.49e+01 1auwA a.127.1.1 61479 1ixmB 192 3.51e+01 1ixmA d.123.1.1 41115 1qh8A 478 3.53e+01 1qguA c.92.2.3 35633 1an2A 86 3.55e+01 1an2A a.38.1.1 17130 1tubA 440 3.58e+01 1tubA c.32.1.1 31751 d.79.2.1 39803 1ycc 108 3.58e+01 1ycc a.3.1.1 15834 1d2eA 397 3.59e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1a26 361 3.60e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1phr 157 3.62e+01 1dg9A c.44.1.1 32635 1kekA 1231 3.63e+01 c.36.1.4 68524 c.36.1.4 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 3sxlA 184 3.67e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1j97A 211 3.67e+01 1f5sA c.108.1.4 62753 1zfpE 98 3.69e+01 1griA d.93.1.1 40465 1ci6A 63 3.70e+01 1ci6A h.1.3.1 45548 1jj2O 148 3.76e+01 1ffkM a.94.1.1 63100 1l7mA 211 3.76e+01 1ixmA 192 3.78e+01 1ixmA d.123.1.1 41114 1d0qA 103 3.82e+01 1d0qA g.41.3.2 45208 1cl8A 276 3.84e+01 1ckqA c.52.1.1 33230 1b6tA 159 3.85e+01 1b6tA c.26.1.3 31600 1eonA 245 3.90e+01 1rvaA c.52.1.2 33238 4pgaA 337 3.92e+01 4pgaA c.88.1.1 35565 1j7iA 264 3.96e+01 1j7iA d.144.1.6 62694