# 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 1ggzA 148 1.65e-03 a.39.1.5 70176 3cln 148 2.07e-03 1cll a.39.1.5 17286 1ncx 162 2.27e-03 1ncx a.39.1.5 17222 1top 162 2.36e-03 1ncx a.39.1.5 17223 1t1dA 100 4.39e-03 1t1dA d.42.1.2 38637 1jvmA 125 4.51e-03 f.14.1.1 67351 1j95A 125 6.22e-03 1bl8A f.14.1.1 62749 1g4yR 148 7.29e-03 1cll a.39.1.5 60252 1k4cC 124 8.13e-03 f.14.1.1 68130 1r3jC 124 8.13e-03 1cll 148 9.22e-03 1cll a.39.1.5 17263 1bl8A 97 1.08e-02 1bl8A f.14.1.1 43652 1avsA 90 1.22e-02 1cll a.39.1.5 17226 1jb0A 755 1.67e-02 1jb0A f.29.1.1 62820 1a68 95 1.75e-02 1t1dA d.42.1.2 38639 2mysB 166 2.90e-02 1wdcB a.39.1.5 17308 1zac 90 3.79e-02 1ncx a.39.1.5 17236 1exrA 148 4.85e-02 1cll a.39.1.5 17299 1dsxA 87 5.05e-02 1t1dA d.42.1.2 38644 1lnh 857 9.47e-02 1yge a.119.1.1 19237 b.12.1.1 23637 1be3C 379 9.76e-02 1be3C f.32.1.1 75805 f.21.1.2 75806 1iwgA 1053 1.08e-01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1osa 148 1.18e-01 1cll a.39.1.5 17300 1j7rA 86 1.22e-01 1j7rA a.39.1.5 62701 1m46A 148 1.29e-01 a.39.1.5 78599 1byyA 53 1.34e-01 j.12.1.1 46147 1kb9C 385 1.76e-01 f.32.1.1 77315 f.21.1.2 77316 1ezvC 385 1.76e-01 1be3C f.32.1.1 75833 f.21.1.2 75834 1wdcC 156 1.97e-01 1wdcC a.39.1.5 17317 1ehkA 562 2.46e-01 1ehkA f.24.1.1 43624 1m45A 148 2.58e-01 a.39.1.5 78598 1kyoC 385 4.10e-01 f.32.1.1 75904 f.21.1.2 75905 1o1fC 147 4.39e-01 i.15.1.1 80997 1wdcB 156 4.75e-01 1wdcB a.39.1.5 17302 1nn7A 105 5.09e-01 d.42.1.2 85894 9wgaA 171 5.10e-01 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1ezfA 340 5.31e-01 1ezfA a.128.1.2 19440 1dceA 567 5.46e-01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1ho2A 20 5.52e-01 j.35.1.1 70967 1wgtA 186 6.23e-01 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 1qg9A 21 9.61e-01 j.35.1.1 46275 1dqeA 137 1.29e+00 1dqeA a.39.2.1 17388 1ggwA 140 1.55e+00 1ggwA a.39.1.5 60490 1k9uA 78 2.27e+00 a.39.1.10 84348 1orsC 132 2.30e+00 f.14.1.1 87353 1jbaA 204 2.34e+00 1rec a.39.1.5 17330 1bf2 750 2.48e+00 1bf2 b.1.18.2 21860 b.71.1.1 27787 c.1.8.1 28774 1o86A 589 2.50e+00 d.92.1.5 81177 1qlaA 656 2.63e+00 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1oyeA 1049 2.68e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1upkA 341 2.89e+00 1ulmA 82 3.33e+00 1oahA 519 3.53e+00 a.138.1.3 86736 3kvt 115 3.66e+00 1t1dA d.42.1.2 38642 1dhx 967 4.01e+00 1dhx b.121.2.2 58971 b.121.2.2 58972 2frvB 536 4.02e+00 1h2rL e.18.1.1 43291 1q9bA 43 4.14e+00 1aijL 281 4.14e+00 6prcL f.26.1.1 43461 1dceB 331 4.26e+00 1dceB a.102.4.3 18872 1hev 43 4.58e+00 1hev g.3.1.1 44060 1n9dA 199 5.07e+00 a.26.1.1 85464 1nr6A 473 5.09e+00 1g8iA 190 5.18e+00 1rec a.39.1.5 60363 1br1B 150 5.21e+00 1wdcC a.39.1.5 17309 1k94A 165 5.33e+00 a.39.1.8 68333 1o26A 232 5.70e+00 d.207.1.1 86566 1ctaA 36 5.71e+00 1ctdA a.39.1.5 17232 2scpA 174 5.76e+00 2scpA a.39.1.5 17256 1gntA 553 5.89e+00 e.26.1.1 70290 1e2uA 553 6.18e+00 1e1dA e.26.1.1 43362 1f6fA 199 6.20e+00 1f6fA a.26.1.1 16839 1jpaA 312 6.34e+00 d.144.1.7 67011 1kq4A 232 6.45e+00 d.207.1.1 68791 1irxA 523 6.55e+00 a.97.1.2 71378 c.26.1.1 71379 1mwvA 714 6.57e+00 a.93.1.3 85161 a.93.1.3 85162 1e1dA 553 6.64e+00 1e1dA e.26.1.1 43363 1q0sA 259 6.68e+00 1pal 108 7.36e+00 1a75A a.39.1.4 17209 1n6bA 473 7.43e+00 a.104.1.1 85359 1e6fA 143 7.47e+00 1e6fA b.64.1.1 59304 1dlc 584 7.82e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1c3wA 222 7.88e+00 1c3wA f.13.1.1 43405 1f4qA 165 7.99e+00 1alvA a.39.1.8 17360 1gp0A 143 8.06e+00 b.64.1.1 70300 1dt6A 473 8.06e+00 1dt6A a.104.1.1 18977 1i50A 1733 8.11e+00 e.29.1.1 61754 1h2aL 567 8.30e+00 1h2rL e.18.1.1 43299 1dcnD 436 8.31e+00 1auwA a.127.1.1 19423 1kgbA 231 8.46e+00 f.13.1.1 68581 1n93X 375 8.53e+00 1f5aA 513 8.89e+00 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1otsA 465 8.94e+00 f.20.1.1 87415 1gupA 348 9.17e+00 1guqA d.13.1.2 37534 d.13.1.2 37535 1rec 201 9.22e+00 1rec a.39.1.5 17326 5pal 109 9.78e+00 1a75A a.39.1.4 17215 1guqA 348 9.82e+00 1guqA d.13.1.2 37522 d.13.1.2 37523 1dugA 234 1.01e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 2lbp 346 1.02e+01 2liv c.93.1.1 35709 1ponA 36 1.05e+01 1ponA a.39.1.5 17239 1ulkA 126 1.06e+01 1b6a 478 1.08e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 1j7dA 145 1.09e+01 1jatB d.20.1.1 62680 1m1jA 491 1.13e+01 h.1.8.1 74369 1m48A 133 1.16e+01 a.26.1.2 74443 1c3cA 429 1.18e+01 1c3cA a.127.1.1 19425 1ctdA 36 1.22e+01 1ctdA a.39.1.5 17230 1bn5 478 1.23e+01 1bn5 a.4.5.25 16224 d.127.1.1 41161 1dxrM 323 1.27e+01 6prcM f.26.1.1 43432 2btvA 901 1.30e+01 2btvA e.28.1.1 43376 1n1cA 217 1.31e+01 a.184.1.1 85254 1omrA 201 1.33e+01 1kpkA 473 1.34e+01 f.20.1.1 68776 1mmc 30 1.35e+01 g.3.1.2 44061 1bi0 226 1.35e+01 1bi0 a.4.5.24 16202 a.76.1.1 18408 b.34.1.2 24453 1mtyD 512 1.36e+01 1mhyD a.25.1.2 16742 1nv8A 284 1.37e+01 c.66.1.30 86224 1h2rL 534 1.43e+01 1h2rL e.18.1.1 43298 1a28A 256 1.43e+01 1a28A a.123.1.1 19290 1f5sA 211 1.45e+01 1f5sA c.108.1.4 59656 6prcM 323 1.46e+01 6prcM f.26.1.1 43435 1j97A 211 1.46e+01 1f5sA c.108.1.4 62753 1keyA 235 1.48e+01 a.118.16.1 72389 2liv 344 1.52e+01 2liv c.93.1.1 35708 1m0kA 262 1.54e+01 f.13.1.1 78344 1txb 73 1.55e+01 1txb g.7.1.1 44455 6gsvA 217 1.61e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1l7mA 211 1.61e+01 c.108.1.4 73664 1e19A 314 1.62e+01 1b7bA c.73.1.1 34967 1ubkL 534 1.62e+01 e.18.1.1 88422 2pvbA 107 1.63e+01 1a75A a.39.1.4 17205 1pv5A 264 1.65e+01 1cdp 109 1.66e+01 1a75A a.39.1.4 17197 1q41A 424 1.68e+01 1phnA 162 1.74e+01 1cpcA a.1.1.3 15641 1gweA 503 1.75e+01 e.5.1.1 70667 1hcuA 503 1.80e+01 a.102.2.1 65796 1auwA 468 1.87e+01 1auwA a.127.1.1 19416 1dcnA 424 1.92e+01 1auwA a.127.1.1 19420 1h21A 247 1.95e+01 a.138.1.3 76510 1lufA 343 2.01e+01 d.144.1.7 78223 1rvgA 305 2.01e+01 1egdA 396 2.05e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1pvaA 110 2.08e+01 1a75A a.39.1.4 17207 1i1iP 681 2.14e+01 1i1iP d.92.1.5 40297 1el4A 195 2.18e+01 1ej3A a.39.1.5 59453 1fa0A 537 2.23e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1p49A 562 2.24e+01 1bolA 222 2.35e+01 1bolA d.124.1.1 41120 1hyp 80 2.36e+01 1hyp a.52.1.1 17806 1en2A 89 2.42e+01 1hev g.3.1.1 44048 g.3.1.1 44049 1dguA 183 2.45e+01 1dguA a.39.1.5 17333 1usgA 346 2.46e+01 1hbzA 498 2.50e+01 1cf9A e.5.1.1 60937 1n4qB 377 2.56e+01 1fa0B 537 2.58e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1iqbB 89 2.59e+01 g.3.1.1 66264 g.3.1.1 66265 2dtr 226 2.60e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1alvA 173 2.62e+01 1alvA a.39.1.8 17370 1wer 334 2.70e+01 1wer a.116.1.2 19108 1gx5A 536 2.74e+01 e.8.1.4 70682 1jchA 551 2.84e+01 b.101.1.1 66491 b.110.1.1 66492 h.4.9.1 66493 1jchC 551 2.84e+01 b.101.1.1 66495 b.110.1.1 66496 h.4.9.1 66497 1nw3A 416 2.88e+01 c.66.1.31 86288 1csh 435 2.88e+01 1csh a.103.1.1 18880 1j1jA 240 2.98e+01 1htjF 210 2.99e+01 1htjF a.91.1.1 61254 4cpv 109 3.12e+01 1a75A a.39.1.4 17198 1qhbA 596 3.21e+01 1qhbA a.111.1.2 19055 1jf2A 195 3.22e+01 1ej3A a.39.1.5 62930 1jf0A 195 3.24e+01 1ej3A a.39.1.5 62926 1drs 59 3.25e+01 3ebx g.7.1.2 44457 1kfuS 184 3.25e+01 a.39.1.8 68574 1k7wA 468 3.33e+01 a.127.1.1 72130 1npoC 95 3.34e+01 1npoA b.9.1.1 23271 1rxwA 336 3.34e+01 1eo9A 209 3.36e+01 3pchA b.3.6.1 22731 1o20A 427 3.40e+01 c.82.1.1 86556 1r89A 437 3.41e+01 1a4iA 301 3.42e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1allA 160 3.43e+01 1qgwC a.1.1.3 15647 1phnB 172 3.48e+01 1qgwC a.1.1.3 15642 1qcrC 378 3.61e+01 1be3C f.32.1.1 75931 f.21.1.2 75932 1hrdA 449 3.63e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1bgvA 449 3.63e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1diaA 306 3.66e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1nr3A 122 3.68e+01 d.236.1.1 86092 1cb0A 283 3.71e+01 1cb0A c.56.2.1 33790 1htxA 32 3.78e+01 1qfdA g.3.2.1 61261 1k89 449 3.80e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1mg7A 417 3.82e+01 d.14.1.6 84954 d.58.26.6 84955 1kn1A 160 3.87e+01 a.1.1.3 77455 1qqfA 277 3.89e+01 1c3d a.102.4.4 18875 1mpuA 138 3.91e+01 d.169.1.1 85040 1quvA 578 3.93e+01 1quvA e.8.1.4 43119 1mh1 186 3.97e+01 1eesA c.37.1.8 32002