# List of top-scoring protein chains for t04-100-30-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 1tiqA 180 4.15e-16 1vhsA 175 7.81e-15 d.108.1.1 -10794 1nslA 184 2.39e-13 d.108.1.1 86137 1s3zA 165 2.96e-12 1gheA 177 4.53e-12 d.108.1.1 76222 1qsmA 152 5.81e-12 1qsmA d.108.1.1 40808 1qsoA 149 1.43e-11 1qsmA d.108.1.1 40812 1i12A 160 4.87e-11 1i21A d.108.1.1 61515 1i1dA 161 7.41e-11 1i21A d.108.1.1 61526 1cjwA 166 9.55e-11 1cjwA d.108.1.1 40818 1n71A 180 2.12e-10 d.108.1.1 85370 1on0A 158 2.47e-10 d.108.1.1 87095 1mk4A 157 3.13e-10 d.108.1.1 84979 1bo4A 168 1.67e-09 1bo4A d.108.1.1 40798 1p0hA 318 1.79e-09 d.108.1.1 -10802 1qstA 160 1.94e-09 1yghA d.108.1.1 40804 1q2yA 140 2.85e-09 d.108.1.1 -10791 1yghA 164 6.81e-08 1yghA d.108.1.1 40802 1sqhA 312 7.05e-07 unknown_sccs -10812 1m4iA 181 3.82e-06 d.108.1.1 74457 1iicA 422 6.64e-05 1nmtA d.108.1.2 62422 d.108.1.2 62423 1bob 320 8.41e-05 1bob d.108.1.1 40816 1fy7A 278 6.14e-03 1fy7A d.108.1.1 40817 1lrzA 426 4.43e-02 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1ne9A 335 4.87e-02 d.108.1.4 -10805 d.108.1.4 -10806 1kzfA 230 8.17e-02 d.108.1.3 73354 1uyrA 737 1.56e-01 c.14.1.4 -6258 c.14.1.4 -6259 1to6A 371 5.25e-01 1lkdA 297 5.45e-01 d.32.1.3 78059 d.32.1.3 78060 1han 297 6.48e-01 1han d.32.1.3 38506 d.32.1.3 38507 1vicA 262 7.10e-01 c.68.1.13 -8252 1kw3B 292 9.22e-01 d.32.1.3 77549 d.32.1.3 77550 1ofdA 1520 1.65e+00 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1hqsA 423 1.90e+00 1iso c.77.1.1 61154 1su4A 994 2.16e+00 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1o50A 157 2.22e+00 d.37.1.1 -9604 d.37.1.1 -9605 1p5dX 463 2.25e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1flcA 432 2.32e+00 1flcA b.19.1.3 23837 c.23.10.2 31337 1eulA 994 2.38e+00 1eulA 1f1uA 323 2.59e+00 d.32.1.3 83200 d.32.1.3 83201 1dar 691 2.73e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1dik 874 3.13e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1pvmA 184 3.71e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1edzA 320 3.92e+00 1ee9A c.2.1.7 30287 c.58.1.2 33935 1gd0A 122 3.96e+00 1dptA d.80.1.3 39834 1pbjA 125 4.06e+00 d.37.1.1 -9608 d.37.1.1 -9609 1o9yA 84 4.11e+00 unknown_sccs -4105 1cg2A 393 4.43e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1ofuA 320 4.94e+00 c.32.1.1 86972 d.79.2.1 86973 1f1xA 322 5.16e+00 d.32.1.3 83208 d.32.1.3 83209 1rfmA 344 5.18e+00 c.122.1.1 -8032 1lqpA 135 5.29e+00 d.32.1.2 78151 1nkiA 135 5.29e+00 d.32.1.2 -9544 1oalA 151 5.64e+00 b.1.8.1 86739 1f9mA 112 5.65e+00 1erv c.47.1.1 32736 1qysA 106 5.68e+00 unknown_sccs -13432 1seiA 130 5.69e+00 1seiA d.140.1.1 41463 1hi9A 274 5.86e+00 1hi9A c.99.1.1 61063 1kblA 873 5.87e+00 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1s4bP 674 5.88e+00 1k2yX 463 5.89e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1i1iP 681 5.98e+00 1i1iP d.92.1.5 40297 1fjgK 129 6.09e+00 1fjfK c.55.4.1 33733 1faaA 124 6.12e+00 1erv c.47.1.1 32738 1gv3A 248 7.11e+00 a.2.11.1 70585 d.44.1.1 70586 1aop 497 7.17e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1s48A 609 7.24e+00 e.8.1.4 -11955 1vhmA 195 7.60e+00 d.110.2.1 -10828 1ecsA 126 7.77e+00 1ecsA d.32.1.2 59407 1jflA 228 8.14e+00 c.78.2.1 71656 c.78.2.1 71657 1jc4A 148 8.18e+00 1jc4A d.32.1.4 62863 1awqA 164 8.29e+00 2cpl b.62.1.1 27461 1gpeA 587 8.39e+00 1gpeA c.3.1.2 30387 d.16.1.1 37951 2cpl 165 8.78e+00 2cpl b.62.1.1 27420 1tuhA 156 9.19e+00 1ojrA 274 9.30e+00 c.74.1.1 -8441 1mxgA 435 9.50e+00 b.71.1.1 85193 c.1.8.1 85194 1v93A 296 9.56e+00 c.1.23.1 -5654 1clc 639 9.63e+00 1clc a.102.1.2 18835 b.1.18.2 21872 1cvl 319 9.91e+00 1cvl c.69.1.18 34786 1oltA 457 9.95e+00 unknown_sccs -5688 1pb1A 416 1.01e+01 c.77.1.1 88014 1jykA 254 1.02e+01 c.68.1.13 67458 1npk 154 1.06e+01 1npk d.58.6.1 39099 1o6aA 96 1.06e+01 unknown_sccs -4101 1iso 416 1.08e+01 1iso c.77.1.1 35065 1rkqA 282 1.10e+01 c.108.1.10 -6847 1fa8A 135 1.12e+01 1qipA d.32.1.1 38486 1yaiA 151 1.15e+01 1yaiA b.1.8.1 22289 1uf5A 303 1.15e+01 1o5oA 221 1.17e+01 c.61.1.1 -7954 1f9zA 135 1.19e+01 1qipA d.32.1.1 38484 1uehA 253 1.20e+01 c.101.1.1 -6879 1awsA 164 1.22e+01 2cpl b.62.1.1 27431 1o0wA 252 1.22e+01 a.149.1.1 80751 d.50.1.1 80752 1i0vA 104 1.23e+01 9rnt d.1.1.4 36054 1mngA 203 1.23e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1p0zA 131 1.33e+01 unknown_sccs -10853 1iznB 277 1.40e+01 e.43.1.2 83848 1qipA 183 1.41e+01 1qipA d.32.1.1 38470 1j2rA 199 1.42e+01 unknown_sccs -6799 1pe1A 267 1.44e+01 c.1.10.4 -5553 1ukkA 142 1.45e+01 d.227.1.1 -11206 1h75A 81 1.47e+01 1h75A c.47.1.1 60716 4pfk 319 1.48e+01 3pfk c.89.1.1 35582 1hfoA 113 1.51e+01 d.80.1.3 61006 1udmA 149 1.52e+01 1fwsA 267 1.52e+01 1d9eA c.1.10.4 60063 1hh1A 143 1.54e+01 1gefA c.52.1.18 61036 1j5yA 187 1.56e+01 a.4.5.1 71592 d.94.2.1 71593 1pixA 587 1.57e+01 c.14.1.4 -6282 1iscA 192 1.60e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 1mc0A 368 1.61e+01 d.110.2.1 78937 d.110.2.1 78938 1l7dA 384 1.64e+01 c.2.1.4 77774 c.23.12.2 77775 1fxqA 267 1.66e+01 1d9eA c.1.10.4 60108 1vjqA 79 1.66e+01 unknown_sccs -13478 1cqxA 403 1.70e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1jcxA 267 1.70e+01 c.1.10.4 66510 1puiA 210 1.72e+01 c.37.1.8 88292 1fc6A 388 1.74e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1ds1A 324 1.74e+01 1drtA b.82.2.2 28127 1ne6A 283 1.79e+01 b.82.3.2 -4918 b.82.3.2 -4919 1sn4A 64 1.83e+01 1aho g.3.7.1 44136 1shdA 107 1.85e+01 1fmk d.93.1.1 40440 1gox 370 1.86e+01 1gox c.1.4.1 28607 1erzA 303 1.86e+01 1erzA d.160.1.2 59498 1stfI 98 1.89e+01 1stfI d.17.1.2 38006 1r0rE 274 1.93e+01 c.41.1.1 -7293 1jy5A 212 1.96e+01 d.124.1.1 71940 1q2wA 308 1.97e+01 b.47.1.4 88355 1nvmA 345 1.97e+01 a.5.7.1 86249 c.1.10.5 86250 1nlfA 279 2.00e+01 c.37.1.11 85850 1o13A 136 2.03e+01 c.55.5.1 80762 1sczA 233 2.03e+01 c.43.1.1 -7326 1ahxA 396 2.06e+01 1ajsA c.67.1.1 34293 1g2qA 187 2.07e+01 c.61.1.1 65117 1g6oA 330 2.09e+01 1g6oA c.37.1.11 32430 1go4A 205 2.12e+01 d.135.1.1 70292 1ve9A 347 2.12e+01 c.4.1.2 -6056 d.16.1.3 -9214 1kllA 130 2.12e+01 d.32.1.2 72720 1h7wA 1025 2.14e+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 1hv9A 456 2.16e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1tiyA 164 2.17e+01 1v2xA 194 2.20e+01 c.116.1.1 -6704 1p4kA 295 2.21e+01 d.153.1.5 87772 1mo9A 523 2.21e+01 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1g4wR 383 2.23e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1q9iA 571 2.24e+01 a.138.1.3 -2051 c.3.1.4 -6041 d.168.1.1 -11607 2polA 366 2.26e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1gpl 432 2.27e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1nw2A 105 2.29e+01 c.47.1.1 -7380 1gteA 1025 2.34e+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 1nrgA 261 2.36e+01 b.45.1.1 80694 1i5gA 144 2.36e+01 1ewxA c.47.1.10 61784 1rypH 205 2.37e+01 d.153.1.4 41876 5croA 66 2.37e+01 1orc a.35.1.2 17044 1fxlA 167 2.37e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1fmtA 314 2.38e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1p5vB 147 2.43e+01 b.2.3.2 87814 1fxjA 331 2.46e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1dd9A 338 2.46e+01 1dd9A e.13.1.1 43254 1htrB 329 2.47e+01 1smrA 1r31A 428 2.53e+01 d.58.20.1 -10108 d.179.1.1 -11716 1jvbA 347 2.58e+01 b.35.1.2 77181 c.2.1.1 77182 1ssxA 198 2.58e+01 b.47.1.1 -4112 1nxuA 333 2.60e+01 c.122.1.1 86389 1pea 385 2.60e+01 1pea c.93.1.1 35662 1vheA 373 2.63e+01 unknown_sccs -4280 c.56.5.4 -7890 1qq4A 198 2.64e+01 1qq4A b.47.1.1 25768 1an9A 340 2.65e+01 1an9A c.4.1.2 30617 d.16.1.3 37904 1vjrA 271 2.67e+01 unknown_sccs -6853 1g55A 343 2.67e+01 1g55A c.66.1.26 34247 1j4aA 333 2.72e+01 c.2.1.4 71502 c.23.12.1 71503 1n0uA 842 2.76e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1l1oC 181 2.77e+01 b.40.4.3 73480 9gafA 295 2.80e+01 1apyA d.153.1.5 42008 1g8yA 279 2.81e+01 1g8yA c.37.1.11 32302 1gsa 316 2.83e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1l3kA 196 2.85e+01 d.58.7.1 73539 d.58.7.1 73540 1qisA 396 2.86e+01 1ajsA c.67.1.1 34284 1mmiA 366 2.86e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1hrdA 449 2.87e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1svy 114 2.89e+01 1svy d.109.1.1 40831 1s1dA 331 2.92e+01 unknown_sccs -4566 1cseE 274 2.93e+01 1gci c.41.1.1 32481 1befA 181 2.98e+01 1befA b.47.1.3 26419 1qgxA 357 2.98e+01 1qgxA e.7.1.1 42973 1eexA 554 3.04e+01 1dioA c.1.19.3 29650 1k4nA 192 3.05e+01 d.32.1.5 72059 1im5A 180 3.10e+01 unknown_sccs 66211 1w1kA 560 3.11e+01 1e19A 314 3.11e+01 1b7bA c.73.1.1 34967 1uesA 191 3.13e+01 1oj5A 132 3.18e+01 unknown_sccs -10848 1ars 396 3.19e+01 1ajsA c.67.1.1 34287 1try 224 3.21e+01 5ptp b.47.1.2 26017 1fn8A 224 3.26e+01 5ptp b.47.1.2 26012 1f8gA 384 3.29e+01 1sayA c.2.1.4 59695 c.23.12.2 59696 1qnnA 191 3.31e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1ok7A 366 3.31e+01 1bmtA 246 3.31e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1ka1A 357 3.34e+01 e.7.1.1 68369 1thm 279 3.34e+01 1gci c.41.1.1 32544 1q16A 1247 3.36e+01 b.52.2.2 -4337 c.81.1.1 -8547 1qhxA 178 3.36e+01 1qhsA c.37.1.3 31936 3ladA 476 3.37e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1q7lA 198 3.37e+01 c.56.5.4 -7886 1dbqA 289 3.40e+01 1qpzA c.93.1.1 35666 1rds 105 3.40e+01 9rnt d.1.1.4 36236 1v4vA 376 3.41e+01 c.87.1.3 -8583 1fknA 391 3.52e+01 1fknA b.50.1.2 26879 1udvA 89 3.52e+01 d.68.6.1 -10280 1d3vA 323 3.55e+01 1d3vA c.42.1.1 32559 1afwA 393 3.56e+01 1afwA c.95.1.1 35900 c.95.1.1 35901 1iugA 352 3.56e+01 c.67.1.3 -8176 1hdoA 206 3.57e+01 1he2A c.2.1.2 60965 1lam 484 3.65e+01 1lam c.56.5.3 33829 c.50.1.1 33166 2bbkH 355 3.70e+01 2bbkH b.69.2.1 27634 1a58 177 3.70e+01 2cpl b.62.1.1 27495 1jyeA 349 3.72e+01 c.93.1.1 67455 1ri6A 343 3.73e+01 unknown_sccs -4621 1e39A 571 3.73e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1fp3A 402 3.75e+01 1fp3A a.102.1.3 18842 1ugpB 226 3.75e+01 1d7yA 408 3.82e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1uurA 473 3.85e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1r7aA 504 3.88e+01 b.71.1.1 -4664 c.1.8.1 -5283 1st9A 143 3.91e+01 c.47.1.10 -7503 1eceA 358 3.92e+01 1eceA c.1.8.3 28813 1eexB 224 3.94e+01 1dioB c.51.3.1 33213 1pq4A 291 3.96e+01 c.92.2.2 -8633 1h05A 146 3.97e+01 c.23.13.1 76433