# List of top-scoring protein chains for t2k-100-30-str2 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 1gdgA 293 1.63e-04 1kw3B 292 2.04e-04 d.32.1.3 77549 d.32.1.3 77550 1dhy 292 3.96e-04 1han d.32.1.3 38504 d.32.1.3 38505 1han 297 1.25e-03 1han d.32.1.3 38506 d.32.1.3 38507 1lkdA 297 1.28e-03 d.32.1.3 78059 d.32.1.3 78060 1lgtA 297 1.96e-03 d.32.1.3 77956 d.32.1.3 77957 1fa8A 135 2.37e-02 1qipA d.32.1.1 38486 1f9zA 135 2.44e-02 1qipA d.32.1.1 38484 1jc4A 148 1.68e-01 1jc4A d.32.1.4 62863 1q1gA 276 2.30e-01 c.56.2.1 -7846 1kllA 130 6.17e-01 d.32.1.2 72720 1lqpA 135 7.94e-01 d.32.1.2 78151 1nkiA 135 7.94e-01 d.32.1.2 -9544 7aatA 401 8.23e-01 1ajsA c.67.1.1 34250 1jtkA 136 9.86e-01 c.97.1.1 71862 1o0wA 252 1.07e+00 a.149.1.1 80751 d.50.1.1 80752 1uwzA 136 1.21e+00 1sr9A 644 1.25e+00 1ddgA 374 1.41e+00 1amoA b.43.4.1 25671 c.25.1.4 31559 1ogiA 303 1.56e+00 b.43.4.2 -4042 c.25.1.1 -6587 1b2rA 304 1.58e+00 1fnc b.43.4.2 25648 c.25.1.1 31538 1que 303 1.58e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1ewjA 126 1.61e+00 1ecsA d.32.1.2 59526 1f1uA 323 1.62e+00 d.32.1.3 83200 d.32.1.3 83201 1go2A 304 1.77e+00 b.43.4.2 76243 c.25.1.1 76244 1amoA 615 1.80e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1ecsA 126 1.83e+00 1ecsA d.32.1.2 59407 1qh0A 295 2.11e+00 b.43.4.2 68891 c.25.1.1 68892 1dc1A 323 2.26e+00 1dc1A c.52.1.11 33321 1ftrA 296 2.44e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1r9cA 139 2.50e+00 d.32.1.2 -9557 1g9zA 152 2.61e+00 1bp7A d.95.2.1 60408 1eazA 125 2.64e+00 b.55.1.1 70113 1pbn 289 2.69e+00 1b8oA c.56.2.1 33771 1jn5A 140 2.80e+00 d.17.4.2 66921 1gcuA 295 2.96e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 2dynA 122 3.00e+00 1dynA b.55.1.1 26957 1fxlA 167 3.11e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1nijA 318 3.22e+00 c.37.1.10 85741 d.237.1.1 85742 1af5 126 3.22e+00 1bp7A d.95.2.1 40572 3pnp 289 3.44e+00 1b8oA c.56.2.1 33763 1lc0A 294 3.44e+00 c.2.1.3 73823 d.81.1.4 73824 1i9yA 347 3.48e+00 1i9yA d.151.1.2 62101 1sty 150 3.50e+00 1snc b.40.1.1 24812 1i9zA 347 3.51e+00 1i9yA d.151.1.2 62102 1mpyA 307 3.52e+00 1mpyA d.32.1.3 38508 d.32.1.3 38509 1dynA 125 3.55e+00 1dynA b.55.1.1 26955 1lrzA 426 3.71e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1hrhA 136 3.72e+00 1rthA c.55.3.1 33577 1qtsA 247 3.74e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1ja1A 622 3.78e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1kyfA 247 3.84e+00 b.1.10.1 73220 d.105.1.1 73221 1q8iA 783 3.96e+00 c.55.3.5 -7635 e.8.1.1 -11885 1nzoA 363 4.14e+00 b.105.1.1 -2933 e.3.1.1 -11784 1jkgA 140 4.20e+00 d.17.4.2 66795 1b7fA 168 4.29e+00 1b7fA d.58.7.1 39169 d.58.7.1 39170 1f1xA 322 4.34e+00 d.32.1.3 83208 d.32.1.3 83209 1b9kA 238 4.86e+00 1qtsA b.1.10.1 22315 d.105.1.1 40791 1qqgA 264 5.04e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1cwoA 165 5.41e+00 2cpl b.62.1.1 27445 1bp7A 152 5.78e+00 1bp7A d.95.2.1 40568 2cpl 165 5.84e+00 2cpl b.62.1.1 27420 1b8oA 284 5.95e+00 1b8oA c.56.2.1 33762 1lshA 1056 5.95e+00 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1t82A 155 6.14e+00 1bh5A 183 6.35e+00 1qipA d.32.1.1 38476 1ey4A 149 6.49e+00 1snc b.40.1.1 24815 1j5yA 187 6.58e+00 a.4.5.1 71592 d.94.2.1 71593 1hd8A 363 6.87e+00 b.105.1.1 65803 e.3.1.1 65804 1k0gA 453 6.94e+00 d.161.1.1 67940 1snc 149 7.16e+00 1snc b.40.1.1 24813 1nj4A 363 7.28e+00 b.105.1.1 80545 e.3.1.1 80546 1k0eA 453 7.43e+00 d.161.1.1 67938 1jotA 133 7.44e+00 1jotA 1mopA 300 7.44e+00 c.26.1.4 85035 1n2eA 300 7.44e+00 c.26.1.4 85268 1obpA 159 8.18e+00 1obpA b.60.1.1 27092 1nu5A 370 8.34e+00 c.1.11.2 -5565 d.54.1.1 -9823 1i9gA 280 8.49e+00 c.66.1.13 62090 1nkqA 259 8.61e+00 1uw4A 91 8.68e+00 unknown_sccs -10038 1hn2A 159 8.83e+00 b.60.1.1 65890 1gt1A 159 8.83e+00 b.60.1.1 -4436 1havA 217 8.87e+00 1havA b.47.1.4 26423 1awqA 164 8.92e+00 2cpl b.62.1.1 27461 1jacC 133 9.54e+00 1jotA 1v61A 132 1.01e+01 1m26A 133 1.03e+01 1d2pA 373 1.03e+01 1d2oA b.3.5.1 22629 b.3.5.1 22630 b.3.5.1 22631 b.3.5.1 22632 1g2iA 166 1.04e+01 1g2iA c.23.16.2 31438 1ku8A 133 1.09e+01 1on3A 523 1.12e+01 c.14.1.4 87107 c.14.1.4 87108 1jacA 133 1.15e+01 1jotA 1f0iA 504 1.18e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1v0wA 506 1.19e+01 1btn 106 1.23e+01 1btn b.55.1.1 26952 1faoA 126 1.26e+01 1faoA b.55.1.1 26974 1b4aA 149 1.33e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1nf2A 268 1.38e+01 c.108.1.10 -6842 1p1lA 102 1.41e+01 d.58.5.2 87695 1vk3A 615 1.42e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1mu5A 471 1.43e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1jb1A 205 1.44e+01 1jb1A c.91.1.2 62832 1tmcA 175 1.44e+01 1agdA d.19.1.1 38258 1q16B 512 1.44e+01 d.58.1.5 -9938 1d2oA 187 1.45e+01 1d2oA b.3.5.1 22625 b.3.5.1 22626 1ptf 88 1.46e+01 1ptf d.94.1.1 40549 1qfrA 89 1.49e+01 1ptf d.94.1.1 40552 1b4bA 71 1.53e+01 1b4aA d.74.2.1 39718 1lvaA 258 1.53e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1dfx 125 1.53e+01 1dfx b.1.13.1 22367 g.41.5.2 45255 1l6rA 227 1.54e+01 c.108.1.10 77768 1fa0A 537 1.54e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1fw9A 164 1.56e+01 1fw9A d.190.1.1 60059 1itpA 77 1.57e+01 d.58.3.2 66371 3fruA 269 1.60e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1jpdX 324 1.62e+01 c.1.11.2 67014 d.54.1.1 67015 1q9uA 130 1.63e+01 unknown_sccs -11025 1hkeA 137 1.68e+01 1hsbA 270 1.68e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1op0A 234 1.72e+01 1f20A 435 1.73e+01 b.43.4.1 64932 c.25.1.4 64933 3sxlA 184 1.75e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1pixA 587 1.81e+01 c.14.1.4 -6282 2oneA 436 1.92e+01 4enl c.1.11.1 29203 d.54.1.1 38847 2gsaA 432 1.92e+01 2gsaA c.67.1.4 34446 2ran 316 1.95e+01 1avc a.65.1.1 18170 1a8a 318 1.95e+01 1avc a.65.1.1 18169 1oneA 436 1.95e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1khdA 345 1.99e+01 a.46.2.1 77400 c.27.1.1 77401 2ltnA 181 2.00e+01 1led b.29.1.1 24024 1qisA 396 2.02e+01 1ajsA c.67.1.1 34284 1uxy 340 2.02e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1a8b 318 2.03e+01 1avc a.65.1.1 18171 1ihgA 370 2.03e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1uuzA 137 2.05e+01 d.233.1.1 -9478 1cjxA 357 2.06e+01 1cjxA d.32.1.3 38516 d.32.1.3 38517 2mbr 340 2.06e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1udvA 89 2.06e+01 d.68.6.1 -10280 1e42A 258 2.07e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1vmoA 163 2.13e+01 1vmoA b.77.1.1 27974 1ugxA 133 2.14e+01 1i39A 225 2.17e+01 1ekeA c.55.3.1 61585 1qipA 183 2.23e+01 1qipA d.32.1.1 38470 1uptB 60 2.25e+01 unknown_sccs -1163 1fe0A 68 2.25e+01 1cc8A d.58.17.1 39345 1cqqA 180 2.27e+01 1cqqA b.47.1.4 26422 1lenA 181 2.30e+01 1led b.29.1.1 24032 1e8yA 966 2.30e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1dw9A 156 2.31e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 1m5sA 297 2.33e+01 d.58.33.1 74511 d.58.33.1 74512 1e8xA 961 2.35e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1crwG 333 2.50e+01 1dssG c.2.1.3 30026 d.81.1.1 39941 1awsA 164 2.54e+01 2cpl b.62.1.1 27431 1dkgA 197 2.59e+01 1dkgA b.73.1.1 27812 h.1.9.1 45626 1l4sA 112 2.60e+01 d.204.1.1 77693 1draA 159 2.60e+01 1vdrA c.71.1.1 34831 1p27B 106 2.62e+01 d.58.7.1 -10020 1pz7A 204 2.63e+01 b.29.1.4 -3439 1mrg 263 2.65e+01 1mrj d.165.1.1 42183 1mo1A 87 2.65e+01 d.94.1.1 -10640 1ckv 141 2.65e+01 1ckv d.137.1.1 41452 1spa 396 2.66e+01 1ajsA c.67.1.1 34291 1umzA 278 2.67e+01 b.29.1.2 -3398 1h0xA 100 2.67e+01 d.68.6.1 76451 1lx7A 253 2.71e+01 c.56.2.1 74329 1rxyA 253 2.73e+01 c.56.2.1 -7834 1h10A 125 2.73e+01 b.55.1.1 83446 1fa0B 537 2.73e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1qa7B 217 2.74e+01 1havA b.47.1.4 26426 1anxA 319 2.75e+01 1avc a.65.1.1 18161 1n3gA 113 2.77e+01 d.204.1.1 79962 1j7gA 144 2.80e+01 c.110.1.1 84130 1lrrA 131 2.85e+01 d.228.1.1 78165 1io7A 368 2.87e+01 1f4tA a.104.1.1 18971 1osyA 115 2.88e+01 unknown_sccs -2857 1art 396 2.92e+01 1ajsA c.67.1.1 34285 1j0hA 588 3.07e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1q5yA 85 3.07e+01 unknown_sccs -10081 2hmiA 558 3.08e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1j5wA 298 3.09e+01 d.104.1.1 71589 1g3kA 174 3.11e+01 1nedA d.153.1.4 41989 1dwkA 156 3.14e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1dssG 333 3.15e+01 1dssG c.2.1.3 30022 d.81.1.1 39937 1kjvA 284 3.17e+01 b.1.1.2 77421 d.19.1.1 77422 1hl6A 165 3.21e+01 d.58.7.1 83609 1pdz 434 3.23e+01 4enl c.1.11.1 29215 d.54.1.1 38859 1jp4A 308 3.28e+01 1jp4A e.7.1.1 63223 1h6dA 433 3.34e+01 c.2.1.3 65656 d.81.1.5 65657 1kr4A 125 3.37e+01 d.58.5.2 72889 1mogA 67 3.40e+01 d.230.2.1 85034 1wdcB 156 3.40e+01 1wdcB a.39.1.5 17302 1qvjA 292 3.41e+01 d.113.1.1 -10902 1fxoA 293 3.41e+01 1g0rA c.68.1.6 34524 1a78A 134 3.44e+01 1c1lA b.29.1.3 24212 1sphA 88 3.44e+01 1ptf d.94.1.1 40544 1fg7A 356 3.44e+01 1gewA c.67.1.1 59819 1e7uA 961 3.49e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1qfhA 212 3.52e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1gwyA 175 3.53e+01 b.97.1.1 83356 1ofgA 381 3.54e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 2aat 396 3.60e+01 1ajsA c.67.1.1 34348 1iakA 199 3.63e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 2fcbA 173 3.64e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 1korA 400 3.65e+01 c.26.2.1 72824 d.210.1.1 72825 1kkeA 210 3.65e+01 b.21.1.2 68669 b.83.1.2 68670 1jajA 174 3.66e+01 d.218.1.2 66471 1jr3A 373 3.68e+01 a.80.1.1 63245 c.37.1.20 63246 1zxq 192 3.69e+01 1zxq b.1.1.3 21657 b.1.1.4 21693 1fjgL 135 3.73e+01 1fjfL b.40.4.5 25346 1v9kA 228 3.74e+01 1ub0A 258 3.77e+01 c.72.1.2 88394 6dfr 159 3.82e+01 1vdrA c.71.1.1 34874 1g38A 393 3.82e+01 2admA c.66.1.27 60235 1k0sA 151 3.87e+01 b.40.7.1 67969 1sdoA 203 3.88e+01 unknown_sccs -7558 1qg0A 308 3.91e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1agdA 276 3.92e+01 1agdA b.1.1.2 20741 d.19.1.1 38260