# 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 1mo9A 523 9.65e-02 c.3.1.5 79341 c.3.1.5 79342 d.87.1.1 79343 1q9uA 130 2.21e-01 unknown_sccs -11025 1gp1A 198 2.51e-01 1gp1A c.47.1.10 33059 1gv4A 528 2.53e-01 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 1ve9A 347 2.90e-01 c.4.1.2 -6056 d.16.1.3 -9214 1an9A 340 3.08e-01 1an9A c.4.1.2 30617 d.16.1.3 37904 1aa8A 347 3.34e-01 1an9A 1m6iA 493 3.81e-01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1qumA 285 4.99e-01 1qumA c.1.15.1 29393 1jflA 228 5.28e-01 c.78.2.1 71656 c.78.2.1 71657 1qtwA 285 6.96e-01 1qumA c.1.15.1 29392 1dppA 507 8.50e-01 1dpe c.94.1.1 35800 1ee9A 320 9.07e-01 1ee9A c.2.1.7 30288 c.58.1.2 33936 1ht6A 405 9.87e-01 b.71.1.1 83629 c.1.8.1 83630 1edzA 320 1.04e+00 1ee9A c.2.1.7 30287 c.58.1.2 33935 1ntvA 152 1.16e+00 b.55.1.2 86168 1jfuA 186 1.41e+00 c.47.1.10 62940 1t7pA 698 1.42e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1mdoA 393 1.42e+00 c.67.1.4 79013 1l5xA 280 1.49e+00 c.106.1.1 77718 1dpe 507 1.69e+00 1dpe c.94.1.1 35799 1uxoA 192 1.70e+00 1oi2A 366 2.02e+00 c.32.1.2 87039 d.79.2.2 87040 1t0hB 224 2.47e+00 1gseA 221 2.73e+00 1pgtA a.45.1.1 17667 c.47.1.5 32961 1gox 370 3.03e+00 1gox c.1.4.1 28607 1k3yA 221 3.15e+00 a.45.1.1 77245 c.47.1.5 77246 1q4mA 221 3.33e+00 unknown_sccs -1910 1oz9A 150 3.36e+00 unknown_sccs -10588 1i1gA 141 3.37e+00 a.4.5.32 65982 d.58.4.2 65983 1c7gA 456 3.48e+00 c.67.1.2 -8153 1pmi 440 3.50e+00 1pmi b.82.1.3 28114 1mvoA 136 3.75e+00 c.23.1.1 79513 1c0pA 363 3.79e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1ea5A 537 3.89e+00 2bce c.69.1.1 34592 1vxrA 537 3.91e+00 2bce c.69.1.1 34595 1qidA 537 4.08e+00 2bce c.69.1.1 34593 1pyfA 312 4.08e+00 c.1.7.1 -5251 1e66A 543 4.08e+00 c.69.1.1 59291 1k3lA 221 4.12e+00 a.45.1.1 77229 c.47.1.5 77230 1nnhA 294 4.15e+00 d.104.1.1 -10772 1qe3A 489 4.69e+00 2bce c.69.1.1 34630 1udxA 416 4.81e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1u4cA 349 4.91e+00 1cwyA 500 5.04e+00 1cwyA c.1.8.1 28789 1cs0C 1073 5.16e+00 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1tplA 426 5.31e+00 1ax4A c.67.1.2 34387 1jfrA 262 5.36e+00 1jfrA c.69.1.16 34724 1k8kD 300 5.93e+00 d.198.2.1 68309 d.198.2.1 68310 1f3aA 222 5.99e+00 1pgtA a.45.1.1 17701 c.47.1.5 32995 1avaA 403 6.00e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1t3lA 337 6.05e+00 1rxxA 421 6.09e+00 unknown_sccs -10982 1bxrA 1073 6.33e+00 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1mb3A 124 6.38e+00 c.23.1.1 78907 1h0cA 392 6.46e+00 c.67.1.3 83424 1d9eA 284 6.47e+00 1d9eA c.1.10.4 29195 2ae2A 260 6.48e+00 1bdb c.2.1.2 29945 1o6jA 150 6.49e+00 c.47.1.10 81089 1qf6A 642 6.52e+00 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1d7yA 408 6.99e+00 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1o60A 292 7.26e+00 c.1.10.4 -5549 1b00A 127 7.29e+00 3chy c.23.1.1 31122 8abp 306 7.35e+00 8abp c.93.1.1 35647 1a6q 382 8.17e+00 1a6q a.159.1.1 75801 d.219.1.1 75802 1m5tA 124 8.19e+00 c.23.1.1 78660 1i5gA 144 8.19e+00 1ewxA c.47.1.10 61784 1dmaA 214 8.22e+00 1aerA d.166.1.1 42251 1vdwA 254 8.35e+00 e.7.1.1 -11868 1eswA 500 8.44e+00 1cwyA c.1.8.1 59500 1j3vA 289 8.50e+00 a.100.1.1 -1303 c.2.1.6 -5947 1izcA 339 8.54e+00 c.1.12.5 83838 1gl4B 98 8.56e+00 b.1.1.4 65288 1mo2A 294 8.70e+00 c.69.1.22 79331 1xvaA 292 8.83e+00 1xvaA c.66.1.5 34183 1th8A 145 9.15e+00 1ukcA 522 9.21e+00 1aogA 485 9.44e+00 3grs c.3.1.5 30517 c.3.1.5 30518 d.87.1.1 40190 1l7vC 249 9.48e+00 c.37.1.12 73674 1e2tA 284 9.67e+00 1e2tA d.3.1.5 37121 1mjhA 162 9.84e+00 1mjhA c.26.2.4 31639 1bli 483 9.90e+00 1bli b.71.1.1 27715 c.1.8.1 28702 1qspA 165 1.01e+01 1qspA a.24.10.2 16639 1dykA 394 1.02e+01 1dykA b.29.1.4 24223 b.29.1.4 24224 1p3wA 404 1.07e+01 c.67.1.3 87752 1c0aA 585 1.10e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1g55A 343 1.15e+01 1g55A c.66.1.26 34247 1hleA 345 1.18e+01 1ovaA e.1.1.1 42618 1kafA 108 1.22e+01 d.199.1.1 68372 1cr0A 296 1.23e+01 1cr1A c.37.1.11 32287 1d2fA 390 1.24e+01 1d2fA c.67.1.3 34411 1gulA 222 1.25e+01 1pgtA a.45.1.1 17675 c.47.1.5 32969 1gumA 222 1.26e+01 1pgtA a.45.1.1 17683 c.47.1.5 32977 1chl 36 1.26e+01 1sis g.3.7.2 44157 1cr1A 296 1.27e+01 1cr1A c.37.1.11 32286 1q3kA 259 1.27e+01 unknown_sccs -6335 1n8jA 186 1.27e+01 c.47.1.10 85401 1c02A 166 1.28e+01 1qspA a.24.10.2 16633 1qhlA 227 1.29e+01 1qhlA c.37.1.12 32382 1thg 544 1.30e+01 1thg c.69.1.17 34763 1j3mA 129 1.30e+01 1ecxA 384 1.31e+01 1ecxA c.67.1.3 34431 1cs1C 386 1.32e+01 1ibjA c.67.1.3 34401 1v7zA 260 1.32e+01 unknown_sccs -6353 1lshA 1056 1.33e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1lrzA 426 1.33e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1d2gA 292 1.33e+01 1xvaA c.66.1.5 34187 1hph 37 1.34e+01 1hph j.15.1.1 46159 1eg5A 384 1.37e+01 1ecxA c.67.1.3 34429 1lroA 267 1.40e+01 c.1.10.4 78161 1hjzA 192 1.41e+01 c.50.1.2 83520 1gsa 316 1.42e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1fxpA 267 1.43e+01 1d9eA c.1.10.4 60106 1fwsA 267 1.45e+01 1d9eA c.1.10.4 60063 1jcxA 267 1.46e+01 c.1.10.4 66510 1fxqA 267 1.47e+01 1d9eA c.1.10.4 60108 1rkqA 282 1.48e+01 c.108.1.10 -6847 1vhuA 211 1.49e+01 c.50.1.2 -7934 1gal 583 1.49e+01 1gpeA c.3.1.2 30386 d.16.1.1 37950 1cs1A 386 1.50e+01 1ibjA c.67.1.3 34399 1evlA 401 1.51e+01 1qf6A c.51.1.1 33202 d.104.1.1 40751 1ohuA 175 1.54e+01 f.1.4.1 -12058 1pe1A 267 1.55e+01 c.1.10.4 -5553 5csmA 256 1.56e+01 5csmA a.130.1.2 19494 1jj2W 91 1.57e+01 1ffkU d.29.1.1 63108 1jyeA 349 1.57e+01 c.93.1.1 67455 1sv0C 82 1.60e+01 1s72X 92 1.61e+01 1nrzA 164 1.62e+01 c.38.1.1 86131 1od6A 160 1.64e+01 c.26.1.3 86836 1csmA 256 1.69e+01 5csmA a.130.1.2 19495 1p0iA 529 1.70e+01 c.69.1.1 -8291 1l2mA 118 1.72e+01 d.89.1.4 77657 1fukA 165 1.78e+01 1fukA c.37.1.19 32409 1mjhB 162 1.81e+01 1mjhA c.26.2.4 31640 1iu9A 111 1.81e+01 c.78.2.1 -8500 1b73A 254 1.81e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1nxb 62 1.87e+01 3ebx g.7.1.1 44395 1aszB 490 1.88e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1vjoA 393 1.90e+01 c.67.1.3 -8173 1c3oA 1073 1.90e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1jj2I 145 1.94e+01 1ffkG c.21.1.1 63094 1tz9A 367 1.94e+01 1l5zA 155 1.94e+01 c.23.1.1 77722 1k6wA 426 1.95e+01 b.92.1.2 68236 c.1.9.5 68237 1ux6A 350 2.03e+01 unknown_sccs -3451 unknown_sccs -12886 1vjs 483 2.03e+01 1bli b.71.1.1 27714 c.1.8.1 28701 1ax4A 467 2.03e+01 1ax4A c.67.1.2 34391 1nwbA 124 2.09e+01 b.124.1.1 86296 1aisA 182 2.10e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1keeC 1073 2.11e+01 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1r3nA 462 2.13e+01 c.56.5.4 -7872 d.58.19.1 -10096 1r26A 125 2.16e+01 c.47.1.1 -7389 1cf3A 583 2.16e+01 1gpeA c.3.1.2 30385 d.16.1.1 37949 2bce 581 2.18e+01 2bce c.69.1.1 34625 1pq1A 196 2.19e+01 f.1.4.1 -12055 1nbwA 607 2.22e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1jc4A 148 2.23e+01 1jc4A d.32.1.4 62863 1sek 378 2.24e+01 1sek e.1.1.1 42675 3ebx 62 2.24e+01 3ebx g.7.1.1 44389 1ptmA 329 2.25e+01 unknown_sccs -8456 1tlfA 301 2.27e+01 1tlfA c.93.1.1 35687 1nal1 297 2.29e+01 1nal3 1cxqA 162 2.30e+01 1cxqA c.55.3.2 33621 1k8kC 372 2.30e+01 b.69.4.1 68308 1qkkA 155 2.36e+01 1dbwA c.23.1.1 31104 2gar 212 2.37e+01 2gar c.65.1.1 34161 1jkxA 212 2.42e+01 c.65.1.1 66813 1uqrA 154 2.42e+01 c.23.13.1 -6455 1nhs 447 2.51e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1jjeA 222 2.51e+01 1a7tA d.157.1.1 63117 1dnpA 471 2.52e+01 1qnf a.99.1.1 18775 c.28.1.1 31630 1et1A 34 2.53e+01 1hpy j.15.1.1 46152 1nhp 447 2.54e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1rypK 198 2.57e+01 d.153.1.4 41879 1ejbA 168 2.58e+01 1rvv1 c.16.1.1 59417 1pzsA 208 2.59e+01 1qsgA 265 2.59e+01 1eny c.2.1.2 29935 1lqpA 135 2.61e+01 d.32.1.2 78151 1nkiA 135 2.61e+01 d.32.1.2 -9544 1f6yA 262 2.61e+01 1f6yA c.1.21.2 29673 1keeG 1073 2.64e+01 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1dhy 292 2.65e+01 1han d.32.1.3 38504 d.32.1.3 38505 1kczA 413 2.69e+01 c.1.11.2 68451 d.54.1.1 68452 1asu 162 2.69e+01 1cxqA c.55.3.2 33626 1c3oE 1073 2.71e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1ki1B 352 2.73e+01 a.87.1.1 72497 b.55.1.1 72498 1aye 401 2.73e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1kdgA 546 2.73e+01 c.3.1.2 77337 d.16.1.1 77338 1odeA 122 2.73e+01 d.79.1.2 86846 1vjqA 79 2.76e+01 unknown_sccs -13478 1bh5A 183 2.78e+01 1qipA d.32.1.1 38476 1a4mA 349 2.79e+01 1a4mA c.1.9.1 29014 1g2iA 166 2.80e+01 1g2iA c.23.16.2 31438 1glv 303 2.83e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1cz1A 394 2.83e+01 1cz1A c.1.8.3 28839 1jdbB 1073 2.84e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1keeE 1073 2.85e+01 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 9gafA 295 2.85e+01 1apyA d.153.1.5 42008 1mpyA 307 2.87e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1ex2A 189 2.88e+01 1ex2A c.51.4.2 33225 1irf 112 2.93e+01 2irfG a.4.5.23 16192 1hd2A 161 2.95e+01 c.47.1.10 60962 1edg 380 2.99e+01 1edg c.1.8.3 28807 1c3oG 1073 3.00e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1efdN 266 3.02e+01 1efdN c.92.2.1 35597 1fr9A 194 3.03e+01 1fr9A c.68.1.8 34579 1uetA 437 3.03e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1j4aA 333 3.06e+01 c.2.1.4 71502 c.23.12.1 71503 1add 349 3.07e+01 1a4mA c.1.9.1 29020 1nrwA 288 3.09e+01 c.108.1.10 86128 1v1aA 309 3.10e+01 c.72.1.1 -8400 1bhjA 292 3.10e+01 1xvaA c.66.1.5 34189 1r7aA 504 3.11e+01 b.71.1.1 -4664 c.1.8.1 -5283 1qipA 183 3.11e+01 1qipA d.32.1.1 38470 1nktA 922 3.11e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1keeA 1073 3.12e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1fkx 349 3.13e+01 1a4mA c.1.9.1 29018 1joa 447 3.13e+01 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1j0sA 157 3.21e+01 b.42.1.2 -4016 1g4fA 86 3.21e+01 1qubA g.18.1.1 44873 1b9hA 388 3.25e+01 1b9hA c.67.1.4 34488 1c3oC 1073 3.25e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1garA 212 3.26e+01 2gar c.65.1.1 34162 1ql1A 46 3.27e+01 1ql1A h.1.4.1 45564 1jg5A 83 3.27e+01 d.205.1.1 66666 1ffkG 145 3.28e+01 1ffkG c.21.1.1 31035 1jjgA 102 3.29e+01 b.40.4.5 71696 1nzjA 298 3.31e+01 c.26.1.1 -6600 1tmy 120 3.36e+01 1dbwA c.23.1.1 31083 1ss4A 153 3.37e+01 1n5nA 180 3.40e+01 d.167.1.1 85336 1uc8A 280 3.42e+01 unknown_sccs -6718 unknown_sccs -11230 1sv6A 269 3.45e+01 1qnf 484 3.46e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1hh1A 143 3.46e+01 1gefA c.52.1.18 61036 1d7kA 421 3.50e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1uayA 242 3.51e+01 c.2.1.2 88390 1m3iA 471 3.51e+01 f.9.1.1 -12374 1k4mA 213 3.52e+01 c.26.1.3 77258 1eiwA 111 3.52e+01 1eiwA c.23.3.1 31130 1taq 832 3.53e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1cleA 534 3.53e+01 1thg c.69.1.17 34771 1awcA 110 3.58e+01 1awcA a.4.5.21 16167 1vkfA 188 3.58e+01 1m3jA 471 3.63e+01 f.9.1.1 -12372 1ema 236 3.64e+01 1ema d.22.1.1 38339 1oxdA 227 3.73e+01 d.22.1.1 -9438 1k8wA 327 3.74e+01 b.122.1.1 83094 unknown_sccs -10143 1v7rA 186 3.74e+01 c.51.4.1 -7546 1fd9A 213 3.76e+01 1fd9A d.26.1.1 59771 1vin 268 3.76e+01 1vin a.74.1.1 18354 a.74.1.1 18355 1fzrA 138 3.79e+01 1fzrA c.52.1.17 33336 1odoA 408 3.82e+01 a.104.1.1 -1463 1qmzB 259 3.82e+01 1vin a.74.1.1 18338 a.74.1.1 18339 1lkdA 297 3.82e+01 d.32.1.3 78059 d.32.1.3 78060 2lfb 100 3.82e+01 1lfb a.4.1.1 15990 1uv7A 110 3.83e+01 unknown_sccs -10256 1owlA 484 3.88e+01 a.99.1.1 -1296 c.28.1.1 -6646 1kbvA 327 3.91e+01 b.6.1.3 68395 b.6.1.3 68396 1lgtA 297 3.92e+01 d.32.1.3 77956 d.32.1.3 77957 1jmoA 480 3.96e+01 e.1.1.1 77138 1gdgA 293 3.97e+01 1l0wA 580 4.00e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1k87A 669 4.00e+01 a.176.1.1 77286 c.1.23.2 77287