# List of top-scoring protein chains for t2k-100-30-CB_burial_14_7 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 1fwsA 267 1.15e-19 1d9eA c.1.10.4 60063 1jcxA 267 1.17e-19 c.1.10.4 66510 1pe1A 267 1.37e-19 1fxpA 267 1.48e-19 1d9eA c.1.10.4 60106 1fxqA 267 1.52e-19 1d9eA c.1.10.4 60108 1lroA 267 3.16e-18 c.1.10.4 78161 1o60A 292 7.88e-18 1d9eA 284 2.15e-15 1d9eA c.1.10.4 29195 1g7vA 284 3.48e-15 1d9eA c.1.10.4 60335 1juk 248 6.66e-07 1a53 c.1.2.4 28567 1a53 247 8.47e-07 1a53 c.1.2.4 28564 1igs 248 1.05e-06 1a53 c.1.2.4 28565 1i4nA 251 3.84e-04 c.1.2.4 71114 1ak5 503 6.76e-04 1ak5 c.1.5.1 28639 1ucsA 64 8.36e-04 b.85.1.1 88466 1erzA 303 8.50e-04 1erzA d.160.1.2 59498 1p4cA 380 1.80e-03 1uf5A 303 2.18e-03 1me8A 503 2.20e-03 c.1.5.1 79028 1j6oA 268 2.41e-03 c.1.9.12 77088 1msi 70 2.99e-03 1msi b.85.1.1 28281 2tpsA 227 3.56e-03 2tpsA c.1.3.1 28591 1c89A 134 5.08e-03 1msi b.85.1.1 28314 b.85.1.1 28315 1thfD 253 5.28e-03 1thfD c.1.2.1 28535 1p0kA 349 6.08e-03 c.1.4.1 87648 1vc4A 254 6.90e-03 1huvA 380 7.36e-03 c.1.4.1 61277 1pymA 295 8.45e-03 1pymA c.1.12.7 29308 1hg7A 66 9.57e-03 1msi b.85.1.1 28280 1ub3A 220 1.16e-02 c.1.10.1 88395 1h5yA 253 1.74e-02 c.1.2.1 65638 1vh7A 265 2.02e-02 1uasA 362 2.07e-02 b.71.1.1 88388 c.1.8.1 88389 1pii 452 2.45e-02 1pii c.1.2.4 28559 c.1.2.4 28563 1o5kA 306 2.53e-02 1qwgA 251 2.59e-02 1m3uA 264 2.66e-02 c.1.12.8 84784 1cec 343 2.70e-02 1ceo c.1.8.3 28809 1tr1A 447 2.71e-02 1e70M c.1.8.4 28957 1bqcA 302 2.94e-02 1bqcA c.1.8.3 28831 2wsyA 268 3.28e-02 2tysA c.1.2.4 28588 1vjrA 271 4.30e-02 1v02A 565 4.52e-02 1rvgA 305 4.59e-02 1fwrA 213 4.61e-02 1fwrA c.1.10.1 29164 1nvmA 345 4.69e-02 a.5.7.1 86249 c.1.10.5 86250 1e4iA 447 4.92e-02 1e70M c.1.8.4 59225 1euaA 213 5.08e-02 1fwrA c.1.10.1 29155 1aj0 282 6.42e-02 1aj2 c.1.21.1 29667 1mzhA 225 6.81e-02 c.1.10.1 79698 1fq0A 213 7.41e-02 1fwrA c.1.10.1 29161 1ceo 343 7.51e-02 1ceo c.1.8.3 28808 1rvkA 382 8.24e-02 1h49A 512 8.60e-02 c.1.8.4 83477 1ad1A 266 9.77e-02 1aj2 c.1.21.1 29668 1gt8A 1025 1.05e-01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1s2wA 295 1.07e-01 2tysA 268 1.13e-01 2tysA c.1.2.4 28572 1f6kA 293 1.20e-01 1nal3 c.1.10.1 29081 1vhcA 224 1.20e-01 1uwsA 489 1.29e-01 1gt8D 1025 1.31e-01 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1qopA 268 1.32e-01 2tysA c.1.2.4 28570 1e55A 512 1.45e-01 1e70M c.1.8.4 28934 1aj2 282 1.46e-01 1aj2 c.1.21.1 29665 1eyeA 280 1.55e-01 1aj2 c.1.21.1 29672 1gox 370 1.63e-01 1gox c.1.4.1 28607 1h1yA 228 1.64e-01 c.1.2.2 76506 1qoxN 449 1.70e-01 1qoxN c.1.8.4 28978 1fc4A 401 1.73e-01 1bs0A c.67.1.4 59760 1bksA 268 1.75e-01 2tysA c.1.2.4 28585 1ojxA 263 1.94e-01 1gt8B 1025 1.98e-01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1zfjA 491 2.00e-01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1ltdA 506 2.64e-01 1gox c.1.4.1 28618 d.120.1.1 41086 1din 236 2.66e-01 1din c.69.1.9 34682 1fobA 334 2.80e-01 c.1.8.3 83255 1f74A 293 2.80e-01 1nal3 c.1.10.1 29079 1h7wB 1025 2.94e-01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1jclA 260 2.96e-01 c.1.10.1 66501 1jcjA 260 3.10e-01 c.1.10.1 66499 1h7wA 1025 3.21e-01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1o66A 275 3.36e-01 1e6qM 501 3.41e-01 1e70M c.1.8.4 28920 1tahA 318 3.63e-01 1cvl c.69.1.18 34775 1tahB 318 3.68e-01 1cvl c.69.1.18 34774 1hg3A 225 3.70e-01 1hg3A c.1.1.1 61025 1gylA 369 3.83e-01 1gox c.1.4.1 28610 1gt8C 1025 4.02e-01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1e70M 501 4.10e-01 1e70M c.1.8.4 28926 1h7xB 1025 4.37e-01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1p1xA 260 4.58e-01 1gnxA 479 4.58e-01 c.1.8.4 76241 1of8A 370 4.60e-01 1pbgA 468 4.61e-01 1e70M c.1.8.4 28946 1ho1A 242 4.77e-01 1ho1A c.1.24.1 61097 1ggvA 232 4.81e-01 1din c.69.1.9 34683 1nal1 297 4.94e-01 1nal3 1h7xA 1025 4.94e-01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1hl2A 297 5.19e-01 c.1.10.1 83581 1edg 380 5.21e-01 1edg c.1.8.3 28807 1h7xC 1025 5.39e-01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1upaA 573 5.39e-01 1brt 277 5.40e-01 1brt c.69.1.12 34699 1e4mM 501 5.52e-01 1e70M c.1.8.4 59226 3pbgA 468 5.81e-01 1e70M c.1.8.4 28951 3tgl 269 6.23e-01 3tgl c.69.1.17 34733 1jndA 420 6.42e-01 c.1.8.5 71757 d.26.3.1 71758 1h7wD 1025 6.82e-01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1n7kA 234 6.87e-01 c.1.10.1 85374 1fdyA 297 6.99e-01 1nal3 c.1.10.1 29071 1eceA 358 7.54e-01 1eceA c.1.8.3 28813 1cvl 319 7.70e-01 1cvl c.69.1.18 34786 1hfbA 370 7.93e-01 c.1.10.4 76706 1a88A 275 7.99e-01 1brt c.69.1.12 34707 1tib 269 8.75e-01 3tgl c.69.1.17 34738 1gteA 1025 8.80e-01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1jbaA 204 9.05e-01 1rec a.39.1.5 17330 1o1zA 234 9.71e-01 c.1.18.3 86555 1sqsA 242 1.01e+00 1m5wA 243 1.01e+00 c.1.24.1 84836 1uf3A 228 1.03e+00 1nal3 297 1.04e+00 1nal3 1iirA 415 1.05e+00 1iirA c.87.1.5 62453 1c0dA 358 1.08e+00 1eceA c.1.8.3 28815 1vjzA 341 1.10e+00 1j31A 262 1.14e+00 1k6dA 220 1.18e+00 c.63.1.2 72082 1khdA 345 1.25e+00 a.46.2.1 77400 c.27.1.1 77401 1h0hA 977 1.32e+00 b.52.2.2 76435 c.81.1.1 76436 1sviA 195 1.33e+00 1pdz 434 1.38e+00 4enl c.1.11.1 29215 d.54.1.1 38859 1j5uA 136 1.40e+00 d.208.1.1 71584 1kagA 173 1.44e+00 c.37.1.2 72249 1dhpA 292 1.45e+00 1dhpA c.1.10.1 29097 1broA 277 1.46e+00 1brt c.69.1.12 34700 1ecl 597 1.51e+00 1ecl e.10.1.1 43238 1fcbA 511 1.55e+00 1gox c.1.4.1 28620 d.120.1.1 41087 1uuqA 440 1.69e+00 1gteD 1025 1.76e+00 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1ktbA 405 1.77e+00 b.71.1.1 72960 c.1.8.1 72961 1cqxA 403 1.86e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1jr2A 286 1.86e+00 c.113.1.1 67111 1pvdA 537 1.87e+00 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1h7xD 1025 1.92e+00 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1gt6A 269 1.96e+00 c.69.1.17 76342 1vhnA 318 1.97e+00 1dliA 402 2.06e+00 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 4cpv 109 2.15e+00 1a75A a.39.1.4 17198 2sas 185 2.18e+00 2sas a.39.1.5 17258 1n0wA 243 2.22e+00 c.37.1.11 79772 1nnwA 252 2.23e+00 d.159.1.5 80674 1dik 874 2.23e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1vi9A 299 2.33e+00 1pydA 556 2.35e+00 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1dljA 402 2.40e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1vj7A 393 2.41e+00 1nu5A 370 2.49e+00 1qpbA 563 2.49e+00 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1mw9X 592 2.51e+00 1q0rA 298 2.60e+00 1pfkA 320 2.61e+00 3pfk c.89.1.1 35575 1mumA 295 2.64e+00 c.1.12.7 85108 1cbg 490 2.71e+00 1e70M c.1.8.4 28933 1pvvA 315 2.71e+00 1uufA 369 2.78e+00 1v1rA 400 2.80e+00 6pfkA 319 2.87e+00 3pfk c.89.1.1 35583 1cdp 109 2.87e+00 1a75A a.39.1.4 17197 1jvnA 555 2.89e+00 c.1.2.1 67355 c.23.16.1 67356 1n2eA 300 3.00e+00 c.26.1.4 85268 1mdl 359 3.06e+00 2mnr c.1.11.2 29247 d.54.1.1 38891 1emvB 134 3.09e+00 1bxiB d.4.1.1 37135 1emsA 440 3.25e+00 1emsA d.13.1.1 37520 d.160.1.1 42086 1bxiB 134 3.26e+00 1bxiB d.4.1.1 37136 1j0hA 588 3.42e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1kqnA 279 3.43e+00 c.26.1.3 77492 1nxqA 251 3.45e+00 c.2.1.2 86388 1mopA 300 3.47e+00 c.26.1.4 85035 2mnr 357 3.47e+00 2mnr c.1.11.2 29245 d.54.1.1 38889 1nni1 174 3.50e+00 1a1s 314 3.59e+00 1othA c.78.1.1 35258 c.78.1.1 35259 1qcwA 410 3.60e+00 1gox c.1.4.1 28622 1l4uA 176 3.61e+00 c.37.1.2 73568 1bag 425 3.62e+00 1bag b.71.1.1 27720 c.1.8.1 28707 1tia 279 3.75e+00 3tgl c.69.1.17 34737 1wetA 340 3.80e+00 1qpzA a.35.1.5 17093 c.93.1.1 35670 1bo4B 168 3.83e+00 1bo4A d.108.1.1 40799 1m6jA 261 4.02e+00 c.1.1.1 78693 1bo4A 168 4.06e+00 1bo4A d.108.1.1 40798 1oi2A 366 4.15e+00 c.32.1.2 87039 d.79.2.2 87040 1kwfA 363 4.28e+00 a.102.1.2 73078 1cem 363 4.29e+00 1cem a.102.1.2 18826 1i60A 278 4.36e+00 c.1.15.4 71118 3ullA 132 4.37e+00 3ullA b.40.4.3 25282 1gpr 162 4.41e+00 1gpr b.84.3.1 28267 1vpwA 340 4.47e+00 1qpzA a.35.1.5 17087 c.93.1.1 35680 1b54 257 4.49e+00 1ct5A c.1.6.2 28664 1a48 306 4.56e+00 1a48 d.143.1.1 41590 1pta 318 4.61e+00 1pscA c.1.9.3 29064 1fjcA 96 4.66e+00 1fjcA d.58.7.1 39212 1eywA 331 4.77e+00 1pscA c.1.9.3 29057 1dbs 224 4.89e+00 1byi c.37.1.10 32209 1rcuA 195 5.00e+00 2hsdA 253 5.05e+00 1e6wA c.2.1.2 29866 1kyhA 276 5.05e+00 c.72.1.4 73222 3csuA 310 5.09e+00 3csuA c.78.1.1 35094 c.78.1.1 35095 7odcA 424 5.12e+00 7odcA b.49.2.3 26488 c.1.6.1 28650 1bf6A 291 5.16e+00 1pscA c.1.9.3 29065 1km4A 247 5.18e+00 c.1.2.3 72740 1kblA 873 5.21e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1mnaA 298 5.23e+00 c.69.1.22 79322 1pal 108 5.33e+00 1a75A a.39.1.4 17209 1hdcA 253 5.39e+00 1e6wA c.2.1.2 29862 1q3oA 109 5.47e+00 1ehaA 558 5.50e+00 1ehaA b.1.18.2 21859 b.71.1.1 27786 c.1.8.1 28773 1v2xA 194 5.58e+00 4pgaA 337 5.74e+00 4pgaA c.88.1.1 35565 3pfk 319 5.79e+00 3pfk c.89.1.1 35581 1jscA 630 5.95e+00 c.31.1.3 67224 c.36.1.5 67225 c.36.1.9 67226 1jpdX 324 6.11e+00 c.1.11.2 67014 d.54.1.1 67015 1g66A 207 6.20e+00 1bs9 c.23.9.1 31329 1eh9A 558 6.42e+00 1ehaA b.1.18.2 21858 b.71.1.1 27785 c.1.8.1 28772 3pga1 337 6.56e+00 4pgaA 1o22A 170 6.59e+00 d.238.1.1 86557 1ml9A 302 6.65e+00 b.85.7.1 79282 1obdA 306 6.66e+00 d.143.1.1 86767 1gsa 316 6.69e+00 1gsa c.30.1.3 31718 d.142.1.1 41477 1j8mF 297 6.76e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1l5zA 155 6.77e+00 c.23.1.1 77722 1byi 224 6.79e+00 1byi c.37.1.10 32199 1fr2B 134 6.82e+00 d.4.1.1 83257 1idpA 172 6.96e+00 d.17.4.1 83685 1jj2F 119 7.22e+00 1ffkE d.79.3.1 63091 1gs5A 258 7.25e+00 c.73.1.2 70395 1plr 258 7.26e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1gthB 1025 7.52e+00 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 2pfkA 320 7.60e+00 3pfk c.89.1.1 35577 1qo2A 241 7.61e+00 1qo2A c.1.2.1 28533 1rjdA 334 7.67e+00 1dts 221 7.70e+00 1byi c.37.1.10 32200 1g0oA 283 7.90e+00 1ybvA c.2.1.2 60181 1c0pA 363 7.97e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1fkx 349 8.13e+00 1a4mA c.1.9.1 29018 1dvjA 246 8.39e+00 1dvjA c.1.2.3 28546 1lgyA 269 8.42e+00 3tgl c.69.1.17 34758 1ekxA 311 8.48e+00 3csuA c.78.1.1 35088 c.78.1.1 35089 1dvjC 246 8.53e+00 1dvjA c.1.2.3 28548 1c3yA 108 8.54e+00 1c3yA a.39.2.1 17387 1fjeB 175 8.69e+00 1fj7A d.58.7.1 39210 d.58.7.1 39211 1gkpA 458 8.79e+00 b.92.1.3 70231 c.1.9.6 70232 2pvbA 107 8.83e+00 1a75A a.39.1.4 17205 1dad 224 8.84e+00 1byi c.37.1.10 32204 1g2oA 268 8.91e+00 1b8oA c.56.2.1 60228 1mp9A 198 8.92e+00 1h6wA 312 9.14e+00 b.108.1.1 83060 d.231.1.1 83059 1h1nA 305 9.14e+00 c.1.8.3 70855 1d2fA 390 9.40e+00 1d2fA c.67.1.3 34411 1qpzA 340 9.83e+00 1qpzA a.35.1.5 17097 c.93.1.1 35673 1bs9 207 9.92e+00 1bs9 c.23.9.1 31330 1exbA 332 1.00e+01 1qrqA c.1.7.1 28666 1viaA 175 1.02e+01 1pscA 365 1.02e+01 1pscA c.1.9.3 29058 4pfk 319 1.02e+01 3pfk c.89.1.1 35582 1jr1A 514 1.03e+01 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1b74A 254 1.03e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1d4aA 273 1.05e+01 1d4aA c.23.5.3 31219 1lwjA 441 1.06e+01 b.71.1.1 74303 c.1.8.1 74304 1b73A 254 1.07e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1plq 258 1.07e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1p5dX 463 1.08e+01 1s35A 214 1.08e+01 1a8s 273 1.09e+01 1brt c.69.1.12 34710 1itcA 516 1.10e+01 b.3.1.1 83705 c.1.8.1 83706 1lfaA 187 1.11e+01 1ido c.62.1.1 34122 4enl 436 1.13e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1a7vA 125 1.14e+01 1cpq a.24.3.2 16562 1aep 161 1.16e+01 1aep a.63.1.1 18139 1kbqA 273 1.16e+01 c.23.5.3 68391 1rj9A 304 1.18e+01 1nsj 205 1.18e+01 1nsj c.1.2.4 28560 1a4mA 349 1.18e+01 1a4mA c.1.9.1 29014 1at1A 310 1.19e+01 3csuA c.78.1.1 35168 c.78.1.1 35169 1jflA 228 1.20e+01 c.78.2.1 71656 c.78.2.1 71657 1q9jA 422 1.20e+01 1aohA 147 1.20e+01 1aohA b.2.2.2 22401 1ffkE 119 1.21e+01 1ffkE d.79.3.1 39812 1byb 495 1.21e+01 1byb c.1.8.1 28790 1gthC 1025 1.22e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1ct5A 256 1.22e+01 1ct5A c.1.6.2 28663 1qghA 156 1.23e+01 1qghA a.25.1.1 16728 1qfeA 252 1.24e+01 1qfeA c.1.10.1 29167 1g291 372 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