# 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 1hn6A 110 5.71e-17 g.61.1.1 76721 1tocR 120 1.02e-02 1tocR g.8.1.2 44558 g.8.1.2 44559 1is1A 185 4.63e-01 d.67.3.1 83704 1m6bA 621 7.64e-01 c.10.2.5 74521 c.10.2.5 74522 g.3.9.1 74523 g.3.9.1 74524 1bhtA 176 9.57e-01 1bhtA g.10.1.1 44603 g.14.1.1 44663 1l8fA 207 1.02e+00 b.52.1.1 84537 1gmnA 183 1.15e+00 g.10.1.1 65315 g.14.1.1 65316 1bj7 156 1.24e+00 1bj7 b.60.1.1 27113 1kthA 58 1.94e+00 g.8.1.1 68863 2knt 58 1.95e+00 1bpi g.8.1.1 44537 1knt 58 2.17e+00 1bpi g.8.1.1 44538 1h3nA 878 2.56e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1iqqA 200 2.83e+00 d.124.1.1 66274 1shp 55 2.95e+00 1bpi g.8.1.1 44553 1ep3B 262 3.72e+00 1ep2B b.43.4.2 25664 c.25.1.3 31554 1f8nA 839 3.92e+00 1yge a.119.1.1 59703 b.12.1.1 59704 1lvk 762 4.25e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1ep2B 261 4.45e+00 1ep2B b.43.4.2 25666 c.25.1.3 31556 1n67A 359 4.78e+00 b.2.3.4 85354 b.2.3.4 85355 1fgqA 839 4.89e+00 1yge a.119.1.1 59826 b.12.1.1 59827 1vom 762 5.04e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 2hgf 97 5.20e+00 1bhtA g.10.1.1 44607 1k32A 1045 5.51e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 2pspA 106 6.50e+00 2pspA g.16.1.1 44730 g.16.1.1 44731 1jb7B 260 6.72e+00 1otcB b.40.4.3 62839 1avpA 204 6.82e+00 1avpA d.3.1.7 37132 1nlnA 204 6.92e+00 d.3.1.7 -8897 1mhnA 59 7.96e+00 b.34.9.1 84964 1l7jB 347 7.96e+00 b.30.5.4 73661 1a49A 530 8.30e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1p49A 562 8.37e+00 c.76.1.2 -8432 1kb0A 677 8.46e+00 a.3.1.6 68378 b.70.1.1 68379 1kgyA 181 8.52e+00 b.18.1.4 72449 1dtx 59 8.59e+00 1bpi g.8.1.1 44551 1d0yA 761 8.89e+00 1lvk b.34.3.1 24581 c.37.1.9 32178 1onwA 390 8.95e+00 b.92.1.7 87172 c.1.9.13 87173 1skyB 502 9.06e+00 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1rdzA 337 9.40e+00 1frpA e.7.1.1 42882 1j58A 385 9.71e+00 b.82.1.2 71531 1m7xA 617 9.87e+00 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1mmuA 347 1.01e+01 b.30.5.4 79303 1ifqA 138 1.03e+01 1ifqA d.110.4.1 62350 2mcm 112 1.05e+01 2mcm b.1.7.1 22207 1js8A 394 1.06e+01 a.86.1.1 67219 b.112.1.1 67220 1l7jA 347 1.06e+01 b.30.5.4 73660 2eng 210 1.13e+01 2eng b.52.1.1 26895 1c7sA 858 1.17e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1bkf 107 1.23e+01 1fkj d.26.1.1 38382 1ie7C 570 1.24e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1yge 839 1.25e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1frpA 335 1.26e+01 1frpA e.7.1.1 42875 4ubpC 570 1.30e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1fpkA 335 1.31e+01 1frpA e.7.1.1 42930 1n6eA 1071 1.33e+01 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1hd5A 213 1.35e+01 2eng b.52.1.1 26896 1s1dA 331 1.40e+01 unknown_sccs -4566 2tgpI 58 1.41e+01 1bpi g.8.1.1 44494 1pcp 106 1.43e+01 2pspA g.16.1.1 44742 g.16.1.1 44743 1ap6A 198 1.43e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1n0nA 199 1.43e+01 a.2.11.1 79750 d.44.1.1 79751 1qba 858 1.44e+01 1qba b.1.18.2 21810 b.2.2.3 22406 c.1.8.6 29009 d.92.2.1 40408 1abmA 198 1.46e+01 1avmA 1ubpC 570 1.52e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1pkn 530 1.54e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 3sxlA 184 1.64e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1fkf 107 1.66e+01 1fkj d.26.1.1 38386 1fkj 107 1.66e+01 1fkj d.26.1.1 38384 1i18A 97 1.69e+01 b.43.4.3 61520 1pl4A 198 1.71e+01 a.2.11.1 -132 d.44.1.1 -9733 1e79A 510 1.72e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1g8jB 133 1.73e+01 1g8jB b.33.1.1 24439 1bpi 58 1.73e+01 1bpi g.8.1.1 44468 5pti 58 1.74e+01 1bpi g.8.1.1 44467 1nszA 347 1.74e+01 b.30.5.4 80724 1h8eA 510 1.76e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1pguA 615 1.84e+01 b.69.4.1 88069 b.69.4.1 88070 1epfA 191 1.86e+01 2ncm b.1.1.4 21694 b.1.1.4 21695 1vjnA 220 1.87e+01 unknown_sccs -11458 1p7gA 222 1.87e+01 a.2.11.1 -108 d.44.1.1 -9742 1fmjA 351 1.89e+01 c.37.1.5 59879 7catA 506 1.92e+01 1cf9A e.5.1.1 42781 1jofA 365 1.93e+01 b.69.10.1 71775 1f1sA 814 1.93e+01 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1lv3A 68 1.95e+01 g.39.1.9 78231 1ogoX 574 1.96e+01 unknown_sccs -3237 unknown_sccs -4783 1i50B 1224 2.04e+01 e.29.1.1 61755 1uunA 184 2.04e+01 unknown_sccs -12370 1dceA 567 2.09e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1r5tA 142 2.09e+01 1g6xA 58 2.15e+01 1bpi g.8.1.1 60320 1isaA 192 2.16e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1e4uA 78 2.18e+01 1e4uA g.44.1.1 59231 1qqsA 174 2.18e+01 1nglA b.60.1.1 27143 1lnh 857 2.21e+01 1yge a.119.1.1 19237 b.12.1.1 23637 1bmfA 510 2.22e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1apj 74 2.26e+01 1apj g.23.1.1 44899 1cc1L 498 2.27e+01 1h2rL e.18.1.1 43301 1gpc 218 2.29e+01 1gpc b.40.4.7 25393 1lf7A 182 2.33e+01 b.60.1.1 73878 1cx8B 639 2.33e+01 1cx8B a.48.2.1 17783 c.8.4.1 30764 c.56.5.5 33852 1grj 158 2.34e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1g5vA 88 2.38e+01 1g5vA b.34.9.1 60292 1iscA 192 2.44e+01 1avmA a.2.11.1 15733 d.44.1.1 38726 5fbpA 335 2.45e+01 1frpA e.7.1.1 42873 1g8kB 133 2.48e+01 1g8jB b.33.1.1 24435 1oz7A 131 2.48e+01 d.169.1.1 -11622 1onxA 390 2.50e+01 b.92.1.7 87176 c.1.9.13 87177 1lpuA 332 2.50e+01 d.144.1.7 74177 1iw2A 182 2.50e+01 b.60.1.1 71468 1jffA 451 2.55e+01 c.32.1.1 62932 d.79.2.1 62933 3nodB 423 2.64e+01 1nseA d.174.1.1 42513 1b91A 118 2.68e+01 1b91A 1qubA 319 2.69e+01 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1mngA 203 2.73e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 2scuB 388 2.80e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1emsA 440 2.85e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1wad 112 2.89e+01 3cyr a.138.1.1 19658 1fwuA 134 2.95e+01 1dqgA b.42.2.2 25580 1j3bA 529 3.00e+01 c.91.1.1 77071 c.109.1.1 77072 1cx8A 639 3.02e+01 1cx8B a.48.2.1 17782 c.8.4.1 30763 c.56.5.5 33851 1m7sA 484 3.02e+01 e.5.1.1 74574 1miwA 404 3.06e+01 a.173.1.1 79162 d.218.1.4 79163 1kl9A 182 3.08e+01 b.40.4.5 72681 1idpA 172 3.19e+01 d.17.4.1 83685 1hxpA 348 3.24e+01 1guqA d.13.1.2 37530 d.13.1.2 37531 1j7rA 86 3.28e+01 1j7rA a.39.1.5 62701 1p97A 114 3.29e+01 unknown_sccs -10844 1h2bA 359 3.31e+01 b.35.1.2 -3679 c.2.1.1 -5703 1k4nA 192 3.34e+01 d.32.1.5 72059 1e32A 458 3.38e+01 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1noa 113 3.40e+01 2mcm b.1.7.1 22208 1h9oA 112 3.49e+01 1qadA d.93.1.1 60837 1mpyA 307 3.50e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1fzyA 149 3.53e+01 d.20.1.1 65072 1mspA 126 3.55e+01 1mspA b.1.11.2 22333 1ka9H 200 3.55e+01 c.23.16.1 77308 1i7oA 429 3.56e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1i1qB 192 3.59e+01 1qdlB c.23.16.1 61544 1ig8A 486 3.63e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1dqgA 135 3.70e+01 1dqgA b.42.2.2 25579 1hzoA 271 3.73e+01 e.3.1.1 71092 1slvA 142 3.74e+01 1sluA b.16.1.1 23688 1m2rA 327 3.74e+01 d.144.1.7 84760 1kz8A 337 3.77e+01 e.7.1.1 77633 1a48 306 3.79e+01 1a48 d.143.1.1 41590 1oaqH 121 3.82e+01 b.1.1.1 -2287 1i8nA 126 3.85e+01 1i8nA g.10.1.2 61976 1o5uA 101 3.87e+01 b.82.1.8 -4845 1dgfA 497 3.87e+01 1cf9A e.5.1.1 42782 1snzA 344 3.92e+01 b.30.5.4 -3496 1qqp2 218 3.93e+01 1qqp2 1gttA 429 3.94e+01 d.177.1.1 70529 d.177.1.1 70530 1dghB 498 3.96e+01 1cf9A e.5.1.1 42791