# 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 1ap6A 198 1.06e-02 1avmA a.2.11.1 15746 d.44.1.1 38705 1pl4A 198 1.32e-02 a.2.11.1 -132 d.44.1.1 -9733 1n0nA 199 1.34e-02 a.2.11.1 79750 d.44.1.1 79751 1abmA 198 1.36e-02 1avmA 1tocR 120 1.98e-02 1tocR g.8.1.2 44558 g.8.1.2 44559 1kkcA 221 5.33e-01 a.2.11.1 68660 d.44.1.1 68661 1idsA 207 6.34e-01 1avmA a.2.11.1 15722 d.44.1.1 38730 1p7gA 222 9.18e-01 a.2.11.1 -108 d.44.1.1 -9742 1c3oE 1073 1.34e+00 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 1c3oC 1073 1.38e+00 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 1keeE 1073 1.48e+00 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 1vmoA 163 1.69e+00 1vmoA b.77.1.1 27974 1c3oG 1073 1.81e+00 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 1keeG 1073 1.82e+00 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 1psdA 409 1.90e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1p97A 114 1.95e+00 unknown_sccs -10844 1ly7A 121 2.07e+00 d.82.2.1 74339 1bxrA 1073 2.17e+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 1mngA 203 2.32e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 1aboA 62 2.63e+00 1bbzA b.34.2.1 24474 1bbzE 58 2.65e+00 1bbzA b.34.2.1 24479 1bbzA 58 2.76e+00 1bbzA b.34.2.1 24477 1keeC 1073 2.97e+00 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 1b06A 210 2.99e+00 1avmA a.2.11.1 15740 d.44.1.1 38737 1jdbB 1073 3.05e+00 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 1omwA 689 3.15e+00 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1a9xA 1058 3.16e+00 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1rypC 244 3.20e+00 1rypC d.153.1.4 41934 1cs0C 1073 3.20e+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 1keeA 1073 3.42e+00 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 1f5mB 180 3.53e+00 1f5mB d.110.2.1 40896 1j0hA 588 3.55e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1c3oA 1073 3.85e+00 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 1mspA 126 4.04e+00 1mspA b.1.11.2 22333 1avpA 204 4.24e+00 1avpA d.3.1.7 37132 1igqA 62 4.35e+00 b.34.1.3 66130 1ji2A 585 4.47e+00 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 1f5mA 180 4.54e+00 1f5mB d.110.2.1 40895 1rypK 198 5.03e+00 d.153.1.4 41879 3mspA 126 5.31e+00 1mspA b.1.11.2 22343 1m6pA 152 5.32e+00 1m6pA b.64.1.1 27519 1kf6D 119 5.83e+00 f.21.2.2 72400 1bvzA 585 5.95e+00 1bvzA b.1.18.2 21856 b.71.1.1 27783 c.1.8.1 28770 1q87A 221 5.95e+00 unknown_sccs -12028 1dgqA 188 5.96e+00 1ido c.62.1.1 34131 2hgf 97 6.09e+00 1bhtA g.10.1.1 44607 1lfaA 187 6.26e+00 1ido c.62.1.1 34122 1nlnA 204 6.47e+00 d.3.1.7 -8897 1v33A 366 6.54e+00 unknown_sccs -11384 1awo 62 6.61e+00 1bbzA b.34.2.1 24482 1g0uI 205 6.68e+00 d.153.1.4 41891 1uasA 362 6.69e+00 b.71.1.1 88388 c.1.8.1 88389 1mjnA 179 7.01e+00 c.62.1.1 79210 1nm8A 616 7.95e+00 c.43.1.3 85872 c.43.1.3 85873 1iscA 192 8.11e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1isaA 192 8.21e+00 1avmA a.2.11.1 15731 d.44.1.1 38724 1elpA 173 8.62e+00 1amm b.11.1.1 23596 b.11.1.1 23597 1gps 47 8.69e+00 1gpt g.3.7.5 44176 1v25A 541 9.38e+00 1f0cA 305 1.02e+01 1c8oA e.1.1.1 42676 1ndbA 596 1.03e+01 c.43.1.3 80411 c.43.1.3 80412 1jb7B 260 1.04e+01 1otcB b.40.4.3 62839 1gv3A 248 1.10e+01 a.2.11.1 70585 d.44.1.1 70586 1td5A 202 1.11e+01 1ekgA 127 1.13e+01 1dlxA d.82.2.1 40021 1jjiA 311 1.13e+01 c.69.1.2 66766 1dkuA 317 1.13e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1rypJ 204 1.15e+01 d.153.1.4 41878 1grj 158 1.17e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1c8oA 300 1.20e+01 1c8oA e.1.1.1 42677 1pysA 350 1.23e+01 1pysA d.104.1.1 40775 1g0uE 234 1.24e+01 d.153.1.4 41950 1rypF 233 1.27e+01 1rypF d.153.1.4 41937 1aohA 147 1.27e+01 1aohA b.2.2.2 22401 1keoA 154 1.29e+01 b.64.1.1 68534 1ud0A 113 1.29e+01 unknown_sccs -450 1dkrA 317 1.33e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1a6wH 120 1.34e+01 1mfa b.1.1.1 20253 1m48A 133 1.39e+01 a.26.1.2 74443 1dgfA 497 1.39e+01 1cf9A e.5.1.1 42782 1mk0A 97 1.42e+01 d.226.1.1 79216 1idpA 172 1.43e+01 d.17.4.1 83685 1b7yA 350 1.44e+01 1pysA d.104.1.1 40776 1n9bA 265 1.44e+01 e.3.1.1 85463 1kczA 413 1.45e+01 c.1.11.2 68451 d.54.1.1 68452 1a0tP 413 1.51e+01 1a0tP f.4.3.2 43794 1dghB 498 1.51e+01 1cf9A e.5.1.1 42791 1qwlA 505 1.54e+01 e.5.1.1 -11823 1c3mA 147 1.56e+01 1jotA b.77.3.1 27983 1snzA 344 1.58e+01 b.30.5.4 -3496 1g7sA 594 1.60e+01 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1m93B 245 1.60e+01 1ibsA 317 1.65e+01 c.61.1.2 66107 c.61.1.2 66108 1a0sP 413 1.66e+01 1a0tP f.4.3.2 43797 1i85A 110 1.66e+01 1i85A b.1.1.1 61946 1em2A 229 1.67e+01 1em2A d.129.3.2 41321 1aohB 147 1.67e+01 1aohA b.2.2.2 22402 1qz8A 113 1.69e+01 unknown_sccs -4264 1hk9A 74 1.69e+01 b.38.1.2 83541 1pmaA 233 1.71e+01 1pmaA d.153.1.4 41918 1oxwA 373 1.71e+01 c.19.1.3 87539 1g6aA 271 1.83e+01 1btl e.3.1.1 42704 1llwA 1520 1.88e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 2prd 174 1.90e+01 2prd b.40.5.1 25435 1gmnA 183 2.07e+01 g.10.1.1 65315 g.14.1.1 65316 1kvkA 395 2.16e+01 d.14.1.5 73060 d.58.26.3 73061 1oafA 261 2.18e+01 a.93.1.1 86734 1noa 113 2.23e+01 2mcm b.1.7.1 22208 1shp 55 2.30e+01 1bpi g.8.1.1 44553 2nllB 103 2.31e+01 2nllB g.39.1.2 45115 1nmtA 392 2.34e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1otcB 260 2.37e+01 1otcB b.40.4.3 25310 1icxA 155 2.42e+01 d.129.3.1 71191 1ep2B 261 2.44e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1qw2A 102 2.45e+01 unknown_sccs -9601 1lm8B 118 2.45e+01 d.15.1.1 74033 1txjA 171 2.46e+01 1gpt 47 2.46e+01 1gpt g.3.7.5 44175 1m8uA 173 2.54e+01 b.11.1.1 -3027 b.11.1.1 -3028 3gcb 470 2.55e+01 3gcb d.3.1.1 37032 1cvjB 190 2.56e+01 1cvjB d.58.7.1 39193 d.58.7.1 39194 1gcb 454 2.58e+01 3gcb d.3.1.1 37034 1bhtA 176 2.64e+01 1bhtA g.10.1.1 44603 g.14.1.1 44663 1qr7A 350 2.69e+01 1qr7A c.1.10.4 29191 1k8wA 327 2.70e+01 b.122.1.1 83094 unknown_sccs -10143 1nb5I 98 2.73e+01 d.17.1.2 80381 2mllB 255 2.73e+01 1abrB b.42.2.1 25567 b.42.2.1 25568 1gg1A 350 2.82e+01 1qr7A c.1.10.4 29187 1a6r 471 2.85e+01 3gcb d.3.1.1 37033 1ne6A 283 2.90e+01 b.82.3.2 -4918 b.82.3.2 -4919 1eal 127 2.93e+01 1hmt b.60.1.2 27227 1c4kA 730 2.95e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1mm4A 170 2.99e+01 f.4.1.2 79294 1dvfD 120 3.04e+01 1mfa b.1.1.1 20107 1g7rA 594 3.06e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1sly 618 3.09e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 1ct9A 553 3.09e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1ej0A 180 3.09e+01 1ej0A c.66.1.2 34179 1r8sA 164 3.16e+01 c.37.1.8 -7082 1pmnA 364 3.17e+01 d.144.1.7 -11297 1olrA 224 3.18e+01 b.29.1.11 -3489 1ordA 730 3.18e+01 1ordA c.23.1.4 31274 c.67.1.5 34503 d.125.1.1 41124 1g71A 347 3.19e+01 1g71A unknown_sccs 43268 1qe3A 489 3.24e+01 2bce c.69.1.1 34630 1nb8A 353 3.26e+01 d.3.1.9 80385 1qr0A 228 3.30e+01 1qr0A d.150.1.1 59038 d.150.1.1 59039 1r3cA 366 3.32e+01 d.144.1.7 -11296 1szqA 483 3.33e+01 unknown_sccs -11791 1j2iA 166 3.35e+01 1o3yA 166 3.35e+01 c.37.1.8 86618 1a9xB 379 3.36e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409 1lxtA 561 3.38e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1oaqH 121 3.39e+01 b.1.1.1 -2287 1aoqA 567 3.40e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 1o5uA 101 3.41e+01 b.82.1.8 -4845 1f6bA 198 3.52e+01 c.37.1.8 64986 1vcbA 118 3.63e+01 1vcbA d.15.1.1 37603 1h6oA 204 3.64e+01 a.146.1.1 60689 2sil 381 3.66e+01 3sil b.68.1.1 27543 1m7sA 484 3.69e+01 e.5.1.1 74574 1ng4A 390 3.74e+01 c.3.1.2 85666 d.16.1.3 85667 1cmiA 85 3.75e+01 1cmiA d.39.1.1 38551 9rnt 104 3.76e+01 9rnt d.1.1.4 36055 1gxqA 106 3.82e+01 a.4.6.1 70721 1g7tA 594 3.86e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 153l 185 3.87e+01 153l d.2.1.5 36984 1qksA 567 3.88e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1qsaA 618 3.92e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988