# List of top-scoring protein chains for t04-100-30-stride-ebghtl 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 1eemA 241 6.82e-28 1eemA a.45.1.1 17717 c.47.1.5 33011 1e6bA 221 1.71e-27 1e6bA a.45.1.1 59294 c.47.1.5 59295 1jlvA 209 2.31e-27 a.45.1.1 71729 c.47.1.5 71730 1fw1A 216 5.01e-27 a.45.1.1 60051 c.47.1.5 60052 1axdA 209 8.77e-27 1gnwA a.45.1.1 17730 c.47.1.5 33024 6gsvA 217 2.24e-26 1b8xA a.45.1.1 17633 c.47.1.5 32925 1n2aA 201 3.69e-26 a.45.1.1 -938 c.47.1.5 -7463 1gnwA 211 4.44e-26 1gnwA a.45.1.1 17727 c.47.1.5 33021 1b4pA 217 4.47e-26 a.45.1.1 83158 c.47.1.5 83159 1a0fA 201 4.85e-26 1a0fA a.45.1.1 17737 c.47.1.5 33031 1oyjA 231 2.46e-25 a.45.1.1 87597 c.47.1.5 87598 1k0dA 260 9.21e-25 a.45.1.1 67930 c.47.1.5 67931 1f2eA 201 1.51e-24 1a0fA a.45.1.1 17745 c.47.1.5 33039 1pgtA 210 1.66e-24 1pgtA a.45.1.1 17515 c.47.1.5 32809 1f3aA 222 2.59e-24 1pgtA a.45.1.1 17701 c.47.1.5 32995 1dugA 234 3.46e-24 1b8xA a.45.1.1 17718 c.47.1.5 33012 2gsq 202 8.73e-24 1pd21 a.45.1.1 17715 c.47.1.5 33009 1pd21 199 2.03e-23 1pd21 1k3yA 221 2.81e-23 a.45.1.1 77245 c.47.1.5 77246 1iyhA 198 3.45e-23 a.45.1.1 83790 c.47.1.5 83791 1m0uA 249 4.88e-22 a.45.1.1 78359 c.47.1.5 78360 1oktA 211 5.88e-22 a.45.1.1 -942 c.47.1.5 -7467 1oe8A 211 4.05e-20 a.45.1.1 86905 c.47.1.5 86906 1k0mA 241 2.67e-18 a.45.1.1 67949 c.47.1.5 67950 1nhyA 219 2.56e-15 a.45.1.1 80520 c.47.1.5 80521 1g7oA 215 9.85e-15 1g7oA a.45.1.1 60332 c.47.1.5 60333 1h75A 81 2.35e-03 1h75A c.47.1.1 60716 1kewA 361 4.83e-02 c.2.1.2 68544 1aj8A 371 9.07e-02 1aj8A a.103.1.1 18900 1kte 105 1.05e-01 1kte c.47.1.1 32771 1aba 87 1.06e-01 1aba c.47.1.1 32760 1f20A 435 1.35e-01 b.43.4.1 64932 c.25.1.4 64933 1gpmA 525 1.51e-01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1lc5A 364 1.70e-01 c.67.1.1 73827 1iy8A 267 2.45e-01 c.2.1.2 83774 1riqA 465 3.16e-01 unknown_sccs -1295 d.104.1.1 -10769 1eq2A 310 3.73e-01 1eq2A c.2.1.2 29814 1mzjA 339 3.92e-01 c.95.1.1 79700 c.95.1.1 79701 1lldA 319 4.68e-01 3ldh c.2.1.5 30177 d.162.1.1 42144 1q0sA 259 5.45e-01 c.66.1.28 -8110 1p7tA 731 5.83e-01 c.1.13.1 -5600 1ako 268 6.01e-01 1ako d.151.1.1 41779 1vhnA 318 6.08e-01 c.1.4.1 -5209 1j0fA 100 6.15e-01 unknown_sccs -7483 1guzA 310 6.59e-01 c.2.1.5 65586 d.162.1.1 65587 1d8cA 723 7.50e-01 1d8cA c.1.13.1 29325 1pjqA 457 8.22e-01 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1exmA 405 9.20e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1n35A 1267 9.93e-01 e.8.1.4 79935 1k0eA 453 1.01e+00 d.161.1.1 67938 1gggA 226 1.06e+00 1lst c.94.1.1 35817 1ha3A 405 1.07e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1grx 85 1.33e+00 1kte c.47.1.1 32766 1b16A 254 1.41e+00 1b16A c.2.1.2 29875 1iqrA 420 1.45e+00 a.99.1.1 66275 c.28.1.1 66276 1t1vA 93 1.50e+00 2sqcA 631 1.64e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1q7bA 244 1.71e+00 c.2.1.2 -5826 1o4vA 183 1.71e+00 c.23.8.1 86628 1nu0A 138 1.71e+00 unknown_sccs -7658 1avqA 228 1.92e+00 1avqA c.52.1.13 33326 1mkmA 249 1.96e+00 a.4.5.33 79242 d.110.2.2 79243 1g8pA 350 2.04e+00 1g8pA c.37.1.20 60376 1iloA 77 2.23e+00 c.47.1.1 66205 1kdgA 546 2.42e+00 c.3.1.2 77337 d.16.1.1 77338 1uch 230 2.53e+00 1uch d.3.1.6 37129 1c9kA 180 2.62e+00 1c9kB c.37.1.11 32363 1nw2A 105 2.87e+00 c.47.1.1 -7380 1c0pA 363 2.93e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1ro2A 216 2.98e+00 unknown_sccs -11391 3cox 507 2.99e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1gveA 327 3.02e+00 c.1.7.1 70597 3tmkA 216 3.29e+00 3tmkA c.37.1.1 31920 1kz7A 353 3.30e+00 a.87.1.1 73333 b.55.1.1 73334 1db3A 372 3.41e+00 1db3A c.2.1.2 29813 1qmhA 347 3.80e+00 1qmhA c.47.2.1 33082 d.68.2.1 39568 1ro0A 216 4.84e+00 unknown_sccs -11390 1js1X 324 4.95e+00 c.78.1.1 71834 c.78.1.1 71835 1oe4A 247 4.96e+00 c.18.1.3 86895 1iugA 352 5.06e+00 c.67.1.3 -8176 1t2aA 375 5.15e+00 c.2.1.2 -5764 1bpoA 494 5.29e+00 1bpoA a.118.1.4 19143 b.69.6.1 27670 1e2kA 331 6.04e+00 1qhiA c.37.1.1 31854 1ej6D 418 6.16e+00 i.7.1.1 45970 1kyqA 274 6.23e+00 c.2.1.11 73281 e.37.1.1 73282 1jfuA 186 6.32e+00 c.47.1.10 62940 1nytA 271 6.37e+00 c.2.1.7 86417 c.58.1.5 86418 1rliA 184 6.42e+00 unknown_sccs -6438 2gsaA 432 6.60e+00 2gsaA c.67.1.4 34446 1us5A 314 6.61e+00 c.94.1.1 -8686 1l5xA 280 6.66e+00 c.106.1.1 77718 1jb9A 316 6.72e+00 1fnc b.43.4.2 62840 c.25.1.1 62841 1bif 469 7.11e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1vjzA 341 7.16e+00 c.1.8.3 -5318 1wdnA 226 7.48e+00 1lst c.94.1.1 35816 1kutA 230 7.51e+00 d.143.1.1 73017 1npyA 271 7.74e+00 c.2.1.7 85995 c.58.1.5 85996 1sur 215 7.83e+00 1sur c.26.2.2 31620 1qh5A 260 8.15e+00 1qh5A d.157.1.2 42057 1j08A 226 8.16e+00 c.47.1.2 83855 c.47.1.2 83856 1j9lA 247 8.38e+00 c.106.1.1 62762 1uyrA 737 8.57e+00 c.14.1.4 -6258 c.14.1.4 -6259 1qhiA 366 8.73e+00 1qhiA c.37.1.1 31860 1m0dA 138 8.78e+00 c.52.1.17 74354 1d7oA 297 8.88e+00 1enp c.2.1.2 29907 1vjrA 271 9.16e+00 unknown_sccs -6853 1kqfC 217 9.29e+00 f.21.1.1 72874 1ofgA 381 9.43e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1fzrA 138 9.47e+00 1fzrA c.52.1.17 33336 2fha 183 9.69e+00 2fha a.25.1.1 16674 1qydA 313 9.75e+00 c.2.1.2 -5786 1ldg 316 1.00e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 1muwA 386 1.04e+01 c.1.15.3 79495 2reb 352 1.04e+01 2reb c.37.1.11 32282 d.48.1.1 38767 1f7uA 607 1.10e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1josA 128 1.10e+01 d.52.7.1 84191 1eg5A 384 1.12e+01 1ecxA c.67.1.3 34429 1d0yA 761 1.12e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1ab4 477 1.12e+01 1ab4 e.11.1.1 43251 1qh8A 478 1.12e+01 1qguA c.92.2.3 35633 1sxjE 354 1.14e+01 1rypE 242 1.14e+01 1rypE d.153.1.4 41936 1gox 370 1.15e+01 1gox c.1.4.1 28607 1uv7A 110 1.16e+01 unknown_sccs -10256 1bo1A 416 1.17e+01 1bo1A d.143.1.2 41591 1thx 115 1.19e+01 1thx c.47.1.1 32732 1fjhA 257 1.20e+01 1fjhB c.2.1.2 29870 1a8l 226 1.20e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 2ak3A 226 1.20e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1qlaA 656 1.22e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1kepA 348 1.24e+01 c.2.1.2 68536 1c7sA 858 1.26e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1brt 277 1.26e+01 1brt c.69.1.12 34699 1mldA 314 1.27e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1qvbA 481 1.30e+01 1qvbA c.1.8.4 28983 1enp 312 1.33e+01 1enp c.2.1.2 29906 1ngvA 534 1.34e+01 c.111.1.2 85698 1oc2A 348 1.34e+01 c.2.1.2 -5753 1v4vA 376 1.36e+01 c.87.1.3 -8583 1j1lA 290 1.36e+01 unknown_sccs -4877 1s48A 609 1.36e+01 e.8.1.4 -11955 1m1nA 491 1.41e+01 c.92.2.3 78417 1kinA 366 1.41e+01 3xis 387 1.43e+01 4xis c.1.15.3 29423 1jvnA 555 1.43e+01 c.1.2.1 67355 c.23.16.1 67356 1kngA 156 1.45e+01 c.47.1.10 72777 1a6q 382 1.47e+01 1a6q a.159.1.1 75801 d.219.1.1 75802 1qmvA 197 1.48e+01 1qq2A c.47.1.10 33066 1pq4A 291 1.48e+01 c.92.2.2 -8633 1mwmA 320 1.48e+01 c.55.1.1 79580 c.55.1.1 79581 1h6dA 433 1.49e+01 c.2.1.3 65656 d.81.1.5 65657 1ry9A 145 1.53e+01 d.198.1.1 -9020 1oneA 436 1.54e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1a99A 344 1.56e+01 1pot c.94.1.1 35812 1dbqA 289 1.56e+01 1qpzA c.93.1.1 35666 1lf6A 684 1.58e+01 a.102.1.5 77918 b.30.5.5 77919 1t2dA 322 1.58e+01 c.2.1.5 -5920 d.162.1.1 -11487 1lzlA 323 1.58e+01 c.69.1.2 78306 1nzeA 149 1.62e+01 unknown_sccs -599 1o2dA 371 1.62e+01 e.22.1.2 86591 1jbeA 128 1.63e+01 3chy c.23.1.1 62845 4xis 387 1.64e+01 4xis c.1.15.3 29421 1fiqC 763 1.66e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1mi1A 414 1.67e+01 a.169.1.1 79137 b.55.1.6 79138 1vjqA 79 1.69e+01 unknown_sccs -13478 1poiA 317 1.69e+01 1poiA unknown_sccs 34153 1e4iA 447 1.75e+01 1e70M c.1.8.4 59225 1kb0A 677 1.80e+01 a.3.1.6 68378 b.70.1.1 68379 1gy8A 397 1.80e+01 c.2.1.2 83376 1na6A 404 1.83e+01 unknown_sccs -4715 unknown_sccs -7564 3ladA 476 1.84e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1eyvA 156 1.85e+01 1eyvA a.79.1.1 18446 1i3cA 149 1.88e+01 c.23.1.1 71112 1h4pA 408 1.88e+01 c.1.8.3 -5314 1h1yA 228 1.89e+01 c.1.2.2 76506 1fnnA 389 1.89e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1eqcA 394 1.90e+01 1cz1A c.1.8.3 28811 1nbwB 117 1.91e+01 c.51.3.2 80396 1uayA 242 1.91e+01 c.2.1.2 88390 1mu5A 471 2.06e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1b8gA 429 2.06e+01 1b8gA c.67.1.4 34499 1ff9A 450 2.09e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1qh3A 260 2.09e+01 1qh5A d.157.1.2 42059 1n2zA 245 2.10e+01 c.92.2.2 79865 1dv1A 449 2.10e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bs0A 384 2.10e+01 1bs0A c.67.1.4 34490 1fzoA 274 2.12e+01 1agdA b.1.1.2 60155 d.19.1.1 60156 1p0iA 529 2.12e+01 c.69.1.1 -8291 1lk2A 274 2.13e+01 b.1.1.2 -2610 d.19.1.1 -9365 1ituA 369 2.13e+01 c.1.9.7 71423 1g8aA 227 2.19e+01 c.66.1.3 -8049 1mdoA 393 2.19e+01 c.67.1.4 79013 1e79D 482 2.19e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1rovA 857 2.21e+01 a.119.1.1 -1656 b.12.1.1 -3034 1broA 277 2.21e+01 1brt c.69.1.12 34700 1nzoA 363 2.23e+01 b.105.1.1 -2933 e.3.1.1 -11784 1lvk 762 2.27e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1j6pA 418 2.34e+01 b.92.1.4 77089 c.1.9.9 77090 1m3uA 264 2.39e+01 c.1.12.8 84784 1q35A 320 2.40e+01 c.94.1.1 -8658 1zin 217 2.42e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1kid 203 2.42e+01 1derA c.8.5.1 30771 1yge 839 2.42e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1f52A 468 2.43e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1bed 181 2.44e+01 1fvkA unknown_sccs -7444 1fzqA 181 2.46e+01 1hurA c.37.1.8 32060 1orrA 347 2.47e+01 c.2.1.2 -5776 1n25A 368 2.47e+01 c.37.1.20 85264 1j9bA 141 2.47e+01 c.47.1.12 66459 1qv9A 283 2.49e+01 unknown_sccs -6888 1eny 268 2.51e+01 1eny c.2.1.2 29910 1b0pA 1231 2.53e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1m7yA 435 2.54e+01 c.67.1.4 78761 2dri 271 2.54e+01 2dri c.93.1.1 35637 6ldh 330 2.55e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1d4oA 184 2.56e+01 1d4oA c.31.1.4 31748 1lktA 104 2.58e+01 1lktA b.90.1.1 28398 1l3sA 580 2.60e+01 c.55.3.5 84521 e.8.1.1 84522 1hf2A 210 2.63e+01 1hf2A b.80.3.1 60992 c.102.1.1 60993 1p1mA 406 2.64e+01 b.92.1.4 87696 c.1.9.9 87697 1pytA 94 2.66e+01 1pytA d.58.3.1 39064 1l2uA 245 2.66e+01 c.1.2.3 73516 1yaiA 151 2.66e+01 1yaiA b.1.8.1 22289 4blmA 265 2.78e+01 1btl e.3.1.1 42721 1dosA 358 2.85e+01 1dosA c.1.10.2 29175 1o5hA 214 2.85e+01 unknown_sccs -1078 1k20A 310 2.85e+01 c.107.1.1 68027 1nthA 458 2.86e+01 c.1.25.1 80730 1qfeA 252 2.87e+01 1qfeA c.1.10.1 29167 1q7zA 566 2.90e+01 c.1.21.2 -5638 c.1.26.1 -5666 1fmjA 351 2.90e+01 c.37.1.5 59879 4enl 436 2.90e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1ryjA 70 2.92e+01 d.15.3.2 -9179 1o58A 303 2.97e+01 c.79.1.1 -8503 1fi4A 416 2.98e+01 1fi4A d.14.1.5 59847 d.58.26.2 59848 1omwA 689 2.98e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1hzxA 349 2.99e+01 1f88A f.13.1.2 61466 1uby 367 3.01e+01 1uby a.128.1.1 19435 1oalA 151 3.01e+01 b.1.8.1 86739 1dxeA 256 3.17e+01 1dxeA c.1.12.5 29310 1oxwA 373 3.17e+01 c.19.1.3 87539 1i2sA 282 3.18e+01 e.3.1.1 71104 1r6dA 337 3.21e+01 c.2.1.2 -5757 1fs1B 141 3.22e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1aisA 182 3.25e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1p49A 562 3.27e+01 c.76.1.2 -8432 1kekA 1231 3.28e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1o6yA 299 3.29e+01 d.144.1.7 81106 1lox 662 3.31e+01 1lox a.119.1.2 19238 b.12.1.1 23638 1rybA 212 3.33e+01 c.56.3.1 -7858 1itwA 741 3.34e+01 c.77.1.2 76793 1p4oA 322 3.37e+01 d.144.1.7 87775 1j30A 144 3.40e+01 a.25.1.1 -650 1p0kA 349 3.40e+01 c.1.4.1 87648 1viaA 175 3.41e+01 c.37.1.2 -7021 1ei9A 279 3.42e+01 1ei9A c.69.1.13 34713 2trxA 108 3.45e+01 1thx c.47.1.1 32719 3chy 128 3.45e+01 3chy c.23.1.1 31038 1h8lA 380 3.47e+01 b.3.2.1 65737 c.56.5.1 65738 1vk4A 298 3.50e+01 c.72.1.1 -8414 1howA 373 3.53e+01 1hcl d.144.1.7 41679 1bupA 386 3.53e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1kay 381 3.53e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1vicA 262 3.54e+01 c.68.1.13 -8252 1upaA 573 3.55e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1d7uA 433 3.57e+01 2dkb c.67.1.4 34439 1ehkA 562 3.59e+01 1ehkA f.24.1.1 43624 1s0uA 408 3.67e+01 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1q1rA 431 3.71e+01 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1sly 618 3.74e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 1m2eA 135 3.74e+01 c.23.1.5 78478 1uhvA 500 3.75e+01 b.71.1.2 -4683 c.1.8.3 -5354 1m32A 366 3.75e+01 c.67.1.3 78508 1f7lA 121 3.77e+01 1f7lA d.150.1.2 59666 1a8i 842 3.81e+01 1a8i c.87.1.4 35490 1g3qA 237 3.83e+01 1hyqA c.37.1.10 60237 1iqcA 308 3.87e+01 a.3.1.5 66266 a.3.1.5 66267 1kbjA 412 3.88e+01 c.1.4.1 72280 1bv1 159 3.88e+01 1bv1 d.129.3.1 41313 1e5eA 404 3.90e+01 1ibjA c.67.1.3 59265 1kwgA 645 3.91e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1wab 232 3.94e+01 1wab c.23.10.3 31341 1pcxA 810 3.99e+01 a.71.2.1 -1098 b.2.8.1 -2910 c.62.1.2 -7984 d.109.2.1 -10823 g.41.10.1 -12792