# List of top-scoring protein chains for t04-100-40-40-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 1tiqA 180 7.76e-20 1vhsA 175 2.80e-18 d.108.1.1 -10794 1nslA 184 5.42e-17 d.108.1.1 86137 1gheA 177 3.06e-15 d.108.1.1 76222 1qsmA 152 1.33e-14 1qsmA d.108.1.1 40808 1s3zA 165 2.24e-14 1qsoA 149 1.30e-13 1qsmA d.108.1.1 40812 1n71A 180 4.11e-13 d.108.1.1 85370 1i1dA 161 5.71e-13 1i21A d.108.1.1 61526 1i12A 160 6.85e-13 1i21A d.108.1.1 61515 1cjwA 166 1.08e-12 1cjwA d.108.1.1 40818 1p0hA 318 4.24e-12 d.108.1.1 -10802 1qstA 160 4.28e-12 1yghA d.108.1.1 40804 1on0A 158 4.97e-12 d.108.1.1 87095 1mk4A 157 6.13e-12 d.108.1.1 84979 1q2yA 140 2.33e-11 d.108.1.1 -10791 1yghA 164 3.47e-10 1yghA d.108.1.1 40802 1bo4A 168 9.43e-10 1bo4A d.108.1.1 40798 1sqhA 312 1.96e-08 unknown_sccs -10812 1m4iA 181 4.55e-08 d.108.1.1 74457 1bob 320 2.15e-06 1bob d.108.1.1 40816 1iicA 422 4.61e-05 1nmtA d.108.1.2 62422 d.108.1.2 62423 1lrzA 426 4.68e-04 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1ne9A 335 1.52e-03 d.108.1.4 -10805 d.108.1.4 -10806 1kzfA 230 4.15e-03 d.108.1.3 73354 1fy7A 278 4.24e-03 1fy7A d.108.1.1 40817 1uyrA 737 1.41e-01 c.14.1.4 -6258 c.14.1.4 -6259 1fjgK 129 2.91e-01 1fjfK c.55.4.1 33733 1lkdA 297 4.10e-01 d.32.1.3 78059 d.32.1.3 78060 1han 297 5.87e-01 1han d.32.1.3 38506 d.32.1.3 38507 1kw3B 292 5.88e-01 d.32.1.3 77549 d.32.1.3 77550 1qipA 183 8.54e-01 1qipA d.32.1.1 38470 1dar 691 9.34e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1i1iP 681 9.66e-01 1i1iP d.92.1.5 40297 1fa8A 135 1.43e+00 1qipA d.32.1.1 38486 1mngA 203 1.44e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1udvA 89 1.46e+00 d.68.6.1 -10280 1vicA 262 1.53e+00 c.68.1.13 -8252 1f1xA 322 1.56e+00 d.32.1.3 83208 d.32.1.3 83209 1eulA 994 1.56e+00 1eulA 1oheA 348 1.57e+00 c.45.1.1 87013 c.45.1.1 87014 1pvmA 184 1.60e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1su4A 994 1.65e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1cqxA 403 1.68e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1f9zA 135 1.71e+00 1qipA d.32.1.1 38484 1v6fA 151 1.73e+00 1f1uA 323 1.73e+00 d.32.1.3 83200 d.32.1.3 83201 1an9A 340 1.83e+00 1an9A c.4.1.2 30617 d.16.1.3 37904 1nkiA 135 2.01e+00 d.32.1.2 -9544 1dd9A 338 2.18e+00 1dd9A e.13.1.1 43254 1ls1A 295 2.20e+00 a.24.13.1 78170 c.37.1.10 78171 1jykA 254 2.46e+00 c.68.1.13 67458 1lqpA 135 2.53e+00 d.32.1.2 78151 1w1kA 560 2.56e+00 1vk9A 151 2.57e+00 1gv3A 248 2.61e+00 a.2.11.1 70585 d.44.1.1 70586 1amp 291 2.72e+00 1amp c.56.5.4 33837 1j3kA 280 2.79e+00 c.71.1.1 84070 1udmA 149 2.79e+00 1aop 497 2.80e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1ahxA 396 3.01e+00 1ajsA c.67.1.1 34293 1i0rA 169 3.05e+00 1i0rA b.45.1.2 61489 5rubA 490 3.07e+00 1burA c.1.14.1 29382 d.58.9.1 39288 1pbjA 125 3.09e+00 d.37.1.1 -9608 d.37.1.1 -9609 1ds1A 324 3.21e+00 1drtA b.82.2.2 28127 1iscA 192 3.28e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1i0sA 169 3.54e+00 1i0rA b.45.1.2 61491 1pmhX 185 3.59e+00 1nrfA 262 3.78e+00 e.3.1.1 -11780 1p0zA 131 3.88e+00 unknown_sccs -10853 1lokA 291 3.90e+00 c.56.5.4 78122 1iznB 277 4.02e+00 e.43.1.2 83848 1f8gA 384 4.15e+00 1sayA c.2.1.4 59695 c.23.12.2 59696 1ve9A 347 4.32e+00 c.4.1.2 -6056 d.16.1.3 -9214 1tiyA 164 4.40e+00 1l7dA 384 4.44e+00 c.2.1.4 77774 c.23.12.2 77775 1omp 370 4.59e+00 4mbp c.94.1.1 35778 1o50A 157 4.76e+00 d.37.1.1 -9604 d.37.1.1 -9605 1uesA 191 4.77e+00 1riqA 465 4.85e+00 unknown_sccs -1295 d.104.1.1 -10769 1hh1A 143 4.94e+00 1gefA c.52.1.18 61036 1kkcA 221 4.94e+00 a.2.11.1 68660 d.44.1.1 68661 1hdoA 206 5.10e+00 1he2A c.2.1.2 60965 1rtqA 299 5.15e+00 c.56.5.4 -7864 1qnnA 191 5.23e+00 1avmA a.2.11.1 15792 d.44.1.1 38755 1uehA 253 5.47e+00 c.101.1.1 -6879 1g2qA 187 5.50e+00 c.61.1.1 65117 1p7gA 222 5.53e+00 a.2.11.1 -108 d.44.1.1 -9742 1hqsA 423 5.69e+00 1iso c.77.1.1 61154 1mkmA 249 5.88e+00 a.4.5.33 79242 d.110.2.2 79243 1qh4A 380 5.90e+00 1qh4A a.83.1.1 18462 d.128.1.2 41197 1ars 396 6.23e+00 1ajsA c.67.1.1 34287 1jl0A 334 6.82e+00 1jenA d.156.1.1 63155 1aa8A 347 7.16e+00 1an9A 1l3iA 192 7.37e+00 c.66.1.22 77676 1pb1A 416 7.41e+00 c.77.1.1 88014 1p4kA 295 7.61e+00 d.153.1.5 87772 1ka1A 357 8.06e+00 e.7.1.1 68369 4mbp 370 8.11e+00 4mbp c.94.1.1 35777 1gk8A 475 8.18e+00 c.1.14.1 65234 d.58.9.1 65235 1vi7A 217 8.26e+00 unknown_sccs -9115 unknown_sccs -10052 1jndA 420 8.26e+00 c.1.8.5 71757 d.26.3.1 71758 1hi9A 274 8.36e+00 1hi9A c.99.1.1 61063 1louA 101 8.46e+00 1ris d.58.14.1 39323 1i0vA 104 8.51e+00 9rnt d.1.1.4 36054 1ecsA 126 8.54e+00 1ecsA d.32.1.2 59407 1dzfA 215 8.56e+00 1dzfA c.52.3.1 33344 d.78.1.1 39753 3dni 260 8.64e+00 3dni d.151.1.1 41791 1v8fA 276 8.67e+00 c.26.1.4 -6618 1gx1A 160 9.08e+00 d.79.5.1 70675 1puiA 210 9.71e+00 c.37.1.8 88292 1s14A 194 9.90e+00 d.122.1.2 -10973 1itwA 741 1.00e+01 c.77.1.2 76793 2dnjA 260 1.03e+01 3dni d.151.1.1 41790 1qgxA 357 1.03e+01 1qgxA e.7.1.1 42973 1o13A 136 1.05e+01 c.55.5.1 80762 1sn4A 64 1.08e+01 1aho g.3.7.1 44136 1q35A 320 1.10e+01 c.94.1.1 -8658 2ng1 293 1.11e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1fpzA 212 1.13e+01 1fpzA c.45.1.1 59976 1dugA 234 1.15e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1npk 154 1.18e+01 1npk d.58.6.1 39099 1eexB 224 1.21e+01 1dioB c.51.3.1 33213 1d1gA 168 1.22e+01 1d1gA c.71.1.1 34889 3cms 323 1.22e+01 1smrA b.50.1.2 26865 1uhvA 500 1.24e+01 b.71.1.2 -4683 c.1.8.3 -5354 1f75A 249 1.25e+01 1f75A c.101.1.1 59662 1k8kA 418 1.29e+01 c.55.1.1 68305 c.55.1.1 68306 1qtqA 553 1.31e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1hv9A 456 1.31e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1g97A 459 1.36e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1r89A 437 1.36e+01 unknown_sccs -1147 unknown_sccs -9801 unknown_sccs -10061 1idsA 207 1.38e+01 1avmA a.2.11.1 15722 d.44.1.1 38730 1tluA 130 1.38e+01 1h1aA 191 1.39e+01 b.29.1.11 83450 1vhwA 253 1.39e+01 c.56.2.1 -7765 1e19A 314 1.40e+01 1b7bA c.73.1.1 34967 1q7lA 198 1.41e+01 c.56.5.4 -7886 1cvl 319 1.42e+01 1cvl c.69.1.18 34786 1s4bP 674 1.43e+01 1iso 416 1.44e+01 1iso c.77.1.1 35065 1v1aA 309 1.45e+01 c.72.1.1 -8400 1n40A 396 1.51e+01 a.104.1.1 79977 1rztA 331 1.52e+01 a.60.6.1 -1023 a.60.12.1 -1030 d.218.1.2 -9807 6mhtA 327 1.53e+01 6mhtA c.66.1.26 34226 1gox 370 1.55e+01 1gox c.1.4.1 28607 1mc0A 368 1.56e+01 d.110.2.1 78937 d.110.2.1 78938 1uurA 473 1.61e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1v93A 296 1.62e+01 c.1.23.1 -5654 1r6xA 395 1.62e+01 b.122.1.3 -5125 c.26.1.5 -6620 1fecA 490 1.63e+01 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1rypF 233 1.63e+01 1rypF d.153.1.4 41937 1c24A 263 1.67e+01 1c24A d.127.1.1 41148 1gd0A 122 1.69e+01 1dptA d.80.1.3 39834 1ukfA 188 1.73e+01 unknown_sccs -8886 1et0A 269 1.74e+01 1et0A e.17.1.1 43289 1h7eA 245 1.74e+01 c.68.1.13 60717 1jhfA 202 1.74e+01 a.4.5.2 63057 b.87.1.1 63058 1xjo 284 1.74e+01 1xjo c.56.5.4 33843 1vjrA 271 1.75e+01 unknown_sccs -6853 1fn8A 224 1.76e+01 5ptp b.47.1.2 26012 1gsa 316 1.77e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1cqmA 101 1.78e+01 1ris d.58.14.1 39321 1lx7A 253 1.80e+01 c.56.2.1 74329 1lsuA 147 1.81e+01 c.2.1.9 74250 1j8yF 297 1.82e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1ipaA 274 1.82e+01 c.116.1.1 71254 d.79.3.3 71255 1j7nA 776 1.86e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1fxjA 331 1.86e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1my6A 199 1.89e+01 a.2.11.1 85232 d.44.1.1 85233 1lmeA 176 1.90e+01 d.167.1.1 84629 1qisA 396 1.94e+01 1ajsA c.67.1.1 34284 1jyeA 349 1.95e+01 c.93.1.1 67455 1kcfA 258 1.96e+01 a.140.2.1 68434 c.55.3.7 68435 1gof 639 1.98e+01 1gof b.1.18.2 21807 b.18.1.1 23709 b.69.1.1 27631 1fc6A 388 1.99e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1oejA 193 1.99e+01 unknown_sccs -4461 1jxhA 288 2.01e+01 c.72.1.2 67415 1bpyA 335 2.02e+01 1bpyA a.60.6.1 17980 a.60.12.1 75819 d.218.1.2 75820 1ea7A 310 2.02e+01 c.41.1.1 70086 1fmtA 314 2.08e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1oltA 457 2.09e+01 unknown_sccs -5688 1thtA 305 2.09e+01 1thtA c.69.1.13 34711 1rz3A 201 2.10e+01 c.37.1.6 -7048 1i0hA 205 2.10e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1dkuA 317 2.13e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1txlA 215 2.16e+01 1rxxA 421 2.17e+01 unknown_sccs -10982 1reqB 637 2.17e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1bsmA 201 2.18e+01 1avmA a.2.11.1 15780 d.44.1.1 38743 1anf 370 2.18e+01 4mbp c.94.1.1 35776 1g55A 343 2.19e+01 1g55A c.66.1.26 34247 1flcA 432 2.22e+01 1flcA b.19.1.3 23837 c.23.10.2 31337 1avmA 201 2.24e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1j6zA 376 2.26e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1mla 309 2.28e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1xypA 190 2.30e+01 1axkA b.29.1.11 24327 1adjA 421 2.31e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1qq9A 284 2.31e+01 1xjo c.56.5.4 33841 1h4vB 421 2.31e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1hfoA 113 2.32e+01 d.80.1.3 61006 1ouwA 152 2.32e+01 b.77.3.1 -4759 1o5oA 221 2.33e+01 c.61.1.1 -7954 8abp 306 2.33e+01 8abp c.93.1.1 35647 1ooeA 236 2.33e+01 c.2.1.2 87196 1qtsA 247 2.37e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1s72N 187 2.37e+01 1r62A 160 2.37e+01 1tljA 213 2.40e+01 1pixA 587 2.41e+01 c.14.1.4 -6282 1qz5A 375 2.41e+01 c.55.1.1 -7590 c.55.1.1 -7591 1um0A 365 2.43e+01 1ew4A 106 2.43e+01 1ew4A d.82.2.1 40023 1tfr 305 2.46e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1eqjA 511 2.47e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ufkA 254 2.47e+01 unknown_sccs -8103 1jflA 228 2.47e+01 c.78.2.1 71656 c.78.2.1 71657 1befA 181 2.48e+01 1befA b.47.1.3 26419 1k8wA 327 2.51e+01 b.122.1.1 83094 unknown_sccs -10143 1j7lA 264 2.53e+01 d.144.1.6 62697 1qopB 396 2.54e+01 2tysB c.79.1.1 35270 1f7uA 607 2.56e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1jc4A 148 2.57e+01 1jc4A d.32.1.4 62863 1gmmA 133 2.59e+01 b.18.1.10 65314 1iw7C 1119 2.59e+01 e.29.1.1 71474 1jj2M 186 2.64e+01 1ffkK c.55.4.1 63098 1nmoA 247 2.64e+01 unknown_sccs -8746 1i2aA 219 2.65e+01 e.24.1.1 -12012 1a8d 452 2.67e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1jenA 267 2.67e+01 1jenA 1bywA 110 2.69e+01 1bywA d.110.3.6 40912 1npyA 271 2.70e+01 c.2.1.7 85995 c.58.1.5 85996 1shdA 107 2.70e+01 1fmk d.93.1.1 40440 1go4A 205 2.73e+01 d.135.1.1 70292 1d4xA 375 2.74e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1i5gA 144 2.74e+01 1ewxA c.47.1.10 61784 1gsoA 431 2.78e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1g4wR 383 2.80e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1hm9A 468 2.81e+01 b.81.1.4 65866 c.68.1.5 65867 1eziA 228 2.82e+01 1eyrA c.68.1.13 34512 1eexA 554 2.84e+01 1dioA c.1.19.3 29650 1a53 247 2.90e+01 1a53 c.1.2.4 28564 1h1nA 305 2.91e+01 c.1.8.3 70855 1evlA 401 2.96e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1shbA 104 2.99e+01 1fmk d.93.1.1 40425 1b77A 228 3.01e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1zfjA 491 3.06e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1k2xB 143 3.09e+01 1sgvA 316 3.09e+01 b.122.1.1 -5120 unknown_sccs -10148 1o97C 264 3.10e+01 c.26.2.3 81232 1oroA 213 3.10e+01 1opr c.61.1.1 34093 1d2eA 397 3.11e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1qysA 106 3.13e+01 unknown_sccs -13432 1erzA 303 3.14e+01 1erzA d.160.1.2 59498 1fus 106 3.16e+01 9rnt d.1.1.4 36050 1od3A 168 3.17e+01 b.18.1.10 86825 1khiA 176 3.17e+01 b.34.5.2 77408 b.40.4.5 77409 1try 224 3.25e+01 5ptp b.47.1.2 26017 1m4jA 142 3.26e+01 d.109.1.2 78602 1uy4A 145 3.28e+01 1kyfA 247 3.32e+01 b.1.10.1 73220 d.105.1.1 73221 1djtA 64 3.34e+01 1aho g.3.7.1 44132 1ecfA 504 3.37e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1gefA 123 3.39e+01 1gefA c.52.1.18 60465 1opr 213 3.41e+01 1opr c.61.1.1 34091 1wkqA 164 3.41e+01 1em8A 147 3.44e+01 unknown_sccs -7272 9gafA 295 3.44e+01 1apyA d.153.1.5 42008 1nzyA 269 3.45e+01 1nzyA c.14.1.3 30903 1v8dA 235 3.46e+01 1pea 385 3.51e+01 1pea c.93.1.1 35662 1k9sA 237 3.54e+01 c.56.2.1 68359 1pq7A 224 3.56e+01 b.47.1.2 -4190 1j3wA 163 3.61e+01 unknown_sccs -10870 1gpjA 404 3.62e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1rxyA 253 3.63e+01 c.56.2.1 -7834 1e8gA 560 3.70e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1l2tA 235 3.70e+01 c.37.1.12 73514 1kssA 571 3.73e+01 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1mvoA 136 3.73e+01 c.23.1.1 79513 1st9A 143 3.75e+01 c.47.1.10 -7503 1igs 248 3.83e+01 1a53 c.1.2.4 28565 1c7qA 445 3.84e+01 2pgi c.80.1.2 35307 1bj4A 470 3.88e+01 1bj4A c.67.1.4 34479 1ix9A 205 3.93e+01 a.2.11.1 76899 d.44.1.1 76900 1jm6A 407 3.94e+01 a.29.5.1 66876 d.122.1.4 66877 1cg2A 393 3.95e+01 1cg2A c.56.5.4 33844 d.58.19.1 39360 1rkuA 206 3.96e+01 unknown_sccs -6823 1whsB 153 3.99e+01 1whtB