# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1pj5A 830 1.30e-48 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1nrkA 328 3.15e-28 unknown_sccs -4071 unknown_sccs -10176 1ecxA 384 1.99e-01 1ecxA c.67.1.3 34431 1eysH 259 3.65e-01 6prcH b.41.1.1 25484 f.23.10.1 43517 1jcfA 344 3.97e-01 c.55.1.1 62878 c.55.1.1 62879 1jceA 344 4.14e-01 c.55.1.1 62876 c.55.1.1 62877 1g7tA 594 4.34e-01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1eg5A 384 4.43e-01 1ecxA c.67.1.3 34429 1g7rA 594 5.07e-01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1j6wA 175 5.33e-01 1j98A d.185.1.2 62663 1v04A 355 6.39e-01 unknown_sccs -4592 1ju2A 536 6.43e-01 c.3.1.2 77169 d.16.1.1 77170 1dbqA 289 7.98e-01 1qpzA c.93.1.1 35666 1g7sA 594 8.54e-01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1efcA 393 1.01e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1mdbA 539 1.03e+00 e.23.1.1 79008 1m98A 317 1.10e+00 a.175.1.1 78866 d.17.4.6 78867 2scuA 288 1.15e+00 2scuA c.2.1.8 30303 c.23.4.1 31131 1jepA 222 1.56e+00 d.36.1.1 66612 1eyqA 222 1.59e+00 1eypA d.36.1.1 38534 1dgsA 667 1.66e+00 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1vpwA 340 1.80e+00 1qpzA a.35.1.5 17087 c.93.1.1 35680 1ul7A 102 1.85e+00 unknown_sccs -11020 1io1A 398 1.86e+00 1io1A e.32.1.1 62611 1dkgD 383 1.88e+00 1ba1 c.55.1.1 33427 c.55.1.1 33428 1ko3A 230 1.88e+00 d.157.1.1 -11454 1fthA 122 1.93e+00 d.150.1.2 60028 1qpzA 340 1.96e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 2ebn 289 1.99e+00 2ebn c.1.8.5 28990 1eypA 222 2.07e+00 1eypA d.36.1.1 38536 1ea2A 131 2.11e+00 d.17.4.3 64860 1b1cA 181 2.21e+00 1amoA c.23.5.2 31212 1h6dA 433 2.26e+00 c.2.1.3 65656 d.81.1.5 65657 1ofgA 381 2.35e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1bob 320 2.36e+00 1bob d.108.1.1 40816 1scuA 288 2.37e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1wetA 340 2.48e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1opy 131 2.50e+00 1opy d.17.4.3 38113 1pz1A 333 2.71e+00 c.1.7.1 -5255 1a7tA 232 3.02e+00 1a7tA d.157.1.1 42041 1dmmA 131 3.14e+00 1opy d.17.4.3 38114 1eucA 311 3.21e+00 2scuA c.2.1.8 30311 c.23.4.1 31139 1eudA 311 3.26e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1dxrH 258 3.30e+00 6prcH b.41.1.1 25456 f.23.10.1 43433 6prcH 258 3.30e+00 6prcH b.41.1.1 25457 f.23.10.1 43436 1vjeA 166 3.39e+00 d.185.1.2 -10261 1dbxA 158 3.41e+00 1dbuA d.116.1.1 40928 1inp 400 3.51e+00 1inp e.7.1.1 42972 1qhqA 140 3.51e+00 1qhqA b.6.1.1 63326 1tuhA 156 3.62e+00 1jw3A 140 3.70e+00 d.208.1.1 67373 1bxsA 501 3.78e+00 1bpwA c.82.1.1 35357 1rfmA 344 3.80e+00 c.122.1.1 -8032 1fvuA 133 3.91e+00 1ixxB d.169.1.1 42345 2fcr 173 4.03e+00 1rcf c.23.5.1 31151 1rz1A 161 4.05e+00 b.45.1.2 -4088 1rlw 126 4.10e+00 1rlw b.7.1.1 23177 1bq3B 246 4.53e+00 1qhfA c.60.1.1 33979 1b93A 152 4.56e+00 1b93A c.24.1.2 31507 1g61A 228 4.66e+00 1g61A d.126.1.1 41126 1nmtA 392 4.67e+00 1nmtA d.108.1.2 40823 d.108.1.2 40824 1pv9A 348 4.71e+00 c.55.2.1 -7610 d.127.1.1 -11000 1jjtA 228 4.78e+00 1a7tA d.157.1.1 63139 1innA 166 4.92e+00 1j98A d.185.1.2 62608 1pbtA 244 4.94e+00 unknown_sccs -6866 1b5fA 239 5.01e+00 1smrA b.50.1.2 26836 1kqrA 179 5.32e+00 b.29.1.14 72886 1li4A 432 5.54e+00 c.2.1.4 84616 c.23.12.3 84617 1ybvA 283 5.54e+00 1ybvA c.2.1.2 29948 1g0oA 283 5.56e+00 1ybvA c.2.1.2 60181 1dd6A 228 5.73e+00 1a7tA d.157.1.1 42054 1id0A 152 5.89e+00 d.122.1.3 66111 1j7nA 776 5.91e+00 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1h6oA 204 5.91e+00 a.146.1.1 60689 1vjtA 483 6.30e+00 c.2.1.5 -5941 d.162.1.2 -11508 1agdA 276 6.51e+00 1agdA b.1.1.2 20741 d.19.1.1 38260 1e3mA 800 6.63e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1j7nB 776 6.67e+00 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1b93B 152 6.79e+00 1b93A c.24.1.2 31508 1ba1 386 6.83e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1k66A 149 7.08e+00 c.23.1.1 -6406 1qhdA 398 7.09e+00 1qhdA a.115.1.2 63324 b.19.1.1 63325 1ivyA 452 7.24e+00 1ivyA c.69.1.5 34654 1d2eA 397 7.25e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1kriA 186 7.32e+00 b.29.1.14 72897 1smrA 335 7.41e+00 1smrA b.50.1.2 26878 1hrhA 136 7.42e+00 1rthA c.55.3.1 33577 1nbwA 607 7.42e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1jjeA 222 7.64e+00 1a7tA d.157.1.1 63117 1fzaB 328 7.72e+00 3fib d.171.1.1 42480 h.1.8.1 45621 1qhfA 240 8.23e+00 1qhfA c.60.1.1 33960 1a7aA 432 8.32e+00 1b3rA c.2.1.4 30104 c.23.12.3 31364 1uw4A 91 8.42e+00 unknown_sccs -10038 1iq6A 134 8.83e+00 d.38.1.4 76755 1tdj 514 8.92e+00 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1krhA 338 9.28e+00 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1vjqA 79 9.70e+00 unknown_sccs -13478 1qguB 519 1.03e+01 1qguB c.92.2.3 35626 1eagA 342 1.05e+01 1eagA b.50.1.2 26826 1mdwA 328 1.05e+01 d.3.1.3 84934 1jl3A 139 1.05e+01 c.44.1.1 66826 1jdw 423 1.10e+01 1jdw d.126.1.2 41129 1ho1A 242 1.10e+01 1ho1A c.1.24.1 61097 1obbA 480 1.11e+01 c.2.1.5 86760 d.162.1.2 86761 1qltA 560 1.13e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1bupA 386 1.16e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1div 149 1.18e+01 1div d.99.1.1 40692 d.100.1.1 40693 1qhtA 775 1.18e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1ckqA 276 1.18e+01 1ckqA c.52.1.1 33229 1qftA 175 1.19e+01 1qftA b.60.1.1 27151 1cfe 135 1.23e+01 1cfe d.111.1.1 40913 1f3aA 222 1.24e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1ky9A 448 1.24e+01 b.36.1.4 73198 b.47.1.1 73199 1k07A 263 1.24e+01 d.157.1.1 77218 1jmxA 494 1.24e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1havA 217 1.25e+01 1havA b.47.1.4 26423 1e8gA 560 1.26e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1goh 639 1.33e+01 1gof b.1.18.2 21809 b.18.1.1 23711 b.69.1.1 27633 1cl8A 276 1.39e+01 1ckqA c.52.1.1 33230 1kxrA 339 1.40e+01 d.3.1.3 73175 1itwA 741 1.41e+01 c.77.1.2 76793 1df9A 191 1.43e+01 1befA b.47.1.3 26420 1n6aA 259 1.46e+01 b.76.2.1 80121 b.85.7.1 80122 1f8mA 429 1.47e+01 1dquA c.1.12.7 29315 1nd7A 374 1.47e+01 d.148.1.1 -11394 1f61A 429 1.49e+01 1dquA c.1.12.7 29319 1fgyA 127 1.51e+01 1faoA b.55.1.1 26976 1ni4B 341 1.52e+01 c.36.1.7 85729 c.48.1.2 85730 1ewqA 765 1.52e+01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1m41A 380 1.54e+01 c.1.16.4 78595 1v5sA 126 1.54e+01 1sxl 97 1.56e+01 1b7fA d.58.7.1 39180 1a4sA 503 1.56e+01 1bpwA c.82.1.1 35361 1kay 381 1.59e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1ky9B 448 1.61e+01 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1a0p 290 1.62e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1ja1A 622 1.62e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1mrzA 293 1.64e+01 b.43.5.1 -4048 c.26.1.3 -6616 1a05A 358 1.66e+01 1cnzA c.77.1.1 35059 1g5aA 628 1.68e+01 b.71.1.1 65152 c.1.8.1 65153 1cnuA 137 1.69e+01 1cof d.109.1.2 40862 1hn2A 159 1.77e+01 b.60.1.1 65890 1n2fA 142 1.77e+01 d.227.1.1 79853 1gt1A 159 1.77e+01 b.60.1.1 -4436 1jf8A 131 1.79e+01 c.44.1.1 66621 1dq3A 454 1.80e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1qovH 260 1.81e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1qa7B 217 1.84e+01 1havA b.47.1.4 26426 1vaoA 560 1.87e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1pdo 135 1.88e+01 1pdo c.54.1.1 33376 1nngA 153 1.88e+01 d.38.1.1 -9636 1gpwB 201 1.91e+01 c.23.16.1 65461 1jfvA 131 1.91e+01 c.44.1.1 66654 1miwA 404 1.97e+01 a.173.1.1 79162 d.218.1.4 79163 1mp9A 198 1.98e+01 a.74.1.2 -1127 a.74.1.2 -1128 1s72H 171 2.03e+01 1nh8A 304 2.03e+01 c.94.1.1 80507 d.58.5.3 80508 1gof 639 2.04e+01 1gof b.1.18.2 21807 b.18.1.1 23709 b.69.1.1 27631 1k68A 140 2.05e+01 c.23.1.1 -6403 1hgxA 183 2.06e+01 1tc1A c.61.1.1 34027 1hv8A 367 2.06e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1q9uA 130 2.06e+01 unknown_sccs -11025 1m5wA 243 2.09e+01 c.1.24.1 84836 1fzqA 181 2.09e+01 1hurA c.37.1.8 32060 6dfr 159 2.10e+01 1vdrA c.71.1.1 34874 1q44A 326 2.10e+01 c.37.1.5 -7037 1b4aA 149 2.12e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1sxrA 183 2.12e+01 1iy8A 267 2.12e+01 c.2.1.2 83774 1kfiA 572 2.12e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1qh8B 519 2.13e+01 1qguB c.92.2.3 35634 1php 394 2.13e+01 16pk c.86.1.1 35452 1dbuA 158 2.13e+01 1dbuA d.116.1.1 40930 1nhs 447 2.15e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1b7fA 168 2.16e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1j71A 334 2.20e+01 1eagA b.50.1.2 62669 1dih 273 2.24e+01 1drw c.2.1.3 30056 d.81.1.3 39971 1jnyA 435 2.24e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1dk4A 252 2.25e+01 1dk4A e.7.1.1 42970 1hp1A 516 2.28e+01 d.114.1.1 70976 d.159.1.2 70977 1giqA 413 2.33e+01 d.166.1.1 76224 d.166.1.1 76225 3pgm 241 2.33e+01 1qhfA c.60.1.1 33982 1befA 181 2.34e+01 1befA b.47.1.3 26419 1hvc 203 2.37e+01 1hvc b.50.1.1 26614 1mli 96 2.44e+01 1mli d.58.4.1 39070 1pauA 147 2.44e+01 1pauA c.17.1.1 30994 1ej2A 181 2.45e+01 1f9aA c.26.1.3 59414 1pbgA 468 2.45e+01 1e70M c.1.8.4 28946 1nd4A 264 2.46e+01 d.144.1.6 -11381 1g10A 102 2.46e+01 1g10A d.137.1.1 60191 1agjA 242 2.46e+01 1agjA b.47.1.1 25827 1konA 249 2.48e+01 e.39.1.1 72823 1i50C 318 2.53e+01 d.74.3.1 61756 d.181.1.1 61757 1nhp 447 2.55e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1lxdA 100 2.55e+01 1lfdA d.15.1.5 37624 1qpsA 261 2.56e+01 1ckqA c.52.1.1 33234 1chmA 401 2.58e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1sb8A 352 2.59e+01 1crzA 403 2.59e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1jytA 163 2.61e+01 b.94.1.1 67489 1hdmB 193 2.61e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1mt6A 280 2.63e+01 b.76.2.1 79446 b.85.7.1 79447 1ka9H 200 2.65e+01 c.23.16.1 77308 1devC 196 2.66e+01 1ygs b.26.1.1 23915 1g2rA 100 2.66e+01 1g2rA d.192.1.1 60231 1m32A 366 2.66e+01 c.67.1.3 78508 1ru8A 232 2.71e+01 c.26.2.1 -6635 1joa 447 2.72e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1rzhH 260 2.74e+01 b.41.1.1 -3979 f.23.10.1 -12092 1k9vF 201 2.76e+01 c.23.16.1 68365 1uch 230 2.76e+01 1uch d.3.1.6 37129 1oboA 169 2.76e+01 c.23.5.1 86776 1l8rA 101 2.77e+01 a.6.1.4 73700 1k5nA 276 2.79e+01 b.1.1.2 77266 d.19.1.1 77267 1qk3A 233 2.79e+01 1qk3A c.61.1.1 34031 1k3iA 656 2.81e+01 b.1.18.2 68113 b.18.1.1 68114 b.69.1.1 68115 1q15A 503 2.82e+01 c.26.2.1 -6625 d.153.1.1 -11400 1je5A 206 2.86e+01 1je5A b.40.4.7 62909 1p4cA 380 2.87e+01 c.1.4.1 -5201 1ra9 159 2.88e+01 1vdrA c.71.1.1 34820 1kgbA 231 2.88e+01 f.13.1.1 68581 1nz0A 118 2.89e+01 d.14.1.2 86433 1qa7A 217 2.90e+01 1havA b.47.1.4 26425 1shfA 59 2.91e+01 1bbzA b.34.2.1 24462 1b6sA 355 2.94e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1amoA 615 2.97e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1n91A 108 2.98e+01 d.206.1.1 80326 1ush 550 2.99e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1j6zA 376 3.02e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1d4fA 431 3.02e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1a44 185 3.06e+01 1a44 b.17.1.1 23704 1srrA 124 3.08e+01 1dz3A c.23.1.1 31110 1qapA 296 3.08e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1r3eA 309 3.09e+01 b.122.1.1 -5118 unknown_sccs -10146 1kk1A 410 3.09e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1mi0A 65 3.12e+01 d.15.7.1 79135 1gca 309 3.14e+01 1gca c.93.1.1 35659 1j7lA 264 3.19e+01 d.144.1.6 62697 1mqoA 227 3.20e+01 1eajA 126 3.21e+01 1f5wA b.1.1.1 59401 1f5wA 126 3.21e+01 1f5wA b.1.1.1 19705 1jjfA 268 3.21e+01 c.69.1.2 66765 1vkmA 297 3.23e+01 1squA 155 3.24e+01 unknown_sccs -10229 1m2xA 223 3.26e+01 d.157.1.1 84764 2fx2 147 3.32e+01 1rcf c.23.5.1 31158 2fsp 124 3.36e+01 1dz3A c.23.1.1 31119 1dapA 320 3.40e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 1f06A 320 3.40e+01 1dapA c.2.1.3 59556 d.81.1.3 59557 3minB 522 3.40e+01 1qguB c.92.2.3 35606 2hrvA 142 3.44e+01 2hrvA b.47.1.4 26429 1p99A 295 3.45e+01 c.94.1.1 -8697 1g3kA 174 3.47e+01 1nedA d.153.1.4 41989 8abp 306 3.49e+01 8abp c.93.1.1 35647 1bu5A 147 3.50e+01 5nul c.23.5.1 31155 1kzkA 99 3.50e+01 b.50.1.1 73371 1drw 273 3.56e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1cwvA 492 3.57e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1iq4A 179 3.61e+01 1iq4A d.77.1.1 62641 1ev7A 317 3.64e+01 1ev7B c.52.1.9 33315 2napA 723 3.64e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1j4aA 333 3.67e+01 c.2.1.4 71502 c.23.12.1 71503 3dapA 320 3.68e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1m2eA 135 3.73e+01 c.23.1.5 78478 1grj 158 3.73e+01 1grj a.2.1.1 15691 d.26.1.2 38433 5hvpA 99 3.74e+01 1fmb b.50.1.1 26605 2minB 522 3.77e+01 1qguB c.92.2.3 35610 1bpwA 503 3.78e+01 1bpwA c.82.1.1 35365 1j9eA 147 3.83e+01 c.23.5.1 62756 1difA 99 3.84e+01 1fmb b.50.1.1 26503 1h3nA 878 3.86e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1pcfA 66 3.87e+01 1pcfA d.18.1.1 38142 1taq 832 3.87e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1avwB 171 3.88e+01 1wba b.42.4.1 25599 1m2oA 768 3.94e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1klt 226 3.96e+01 5ptp b.47.1.2 26300 1bxoA 323 3.96e+01 2er7E b.50.1.2 26805 1oxkB 134 3.97e+01 c.23.1.1 -6411