# List of top-scoring protein chains for t2k-100-30-alpha 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 1ncx 162 1.97e-04 1ncx a.39.1.5 17222 1top 162 2.52e-04 1ncx a.39.1.5 17223 1t1dA 100 4.32e-04 1t1dA d.42.1.2 38637 1jvmA 125 6.21e-04 f.14.1.1 67351 1r3jC 124 9.09e-04 1k4cC 124 1.00e-03 f.14.1.1 68130 1j95A 125 1.67e-03 1bl8A f.14.1.1 62749 1g4yR 148 1.80e-03 1cll a.39.1.5 60252 1a68 95 2.20e-03 1t1dA d.42.1.2 38639 1bl8A 97 2.86e-03 1bl8A f.14.1.1 43652 1zac 90 2.99e-03 1ncx a.39.1.5 17236 1kyoC 385 3.23e-03 f.32.1.1 75904 f.21.1.2 75905 3cln 148 3.34e-03 1cll a.39.1.5 17286 1ggzA 148 3.98e-03 a.39.1.5 70176 1dsxA 87 4.01e-03 1t1dA d.42.1.2 38644 1avsA 90 4.23e-03 1cll a.39.1.5 17226 1kb9C 385 4.31e-03 f.32.1.1 77315 f.21.1.2 77316 1cll 148 4.37e-03 1cll a.39.1.5 17263 1ezvC 385 8.17e-03 1be3C f.32.1.1 75833 f.21.1.2 75834 1exrA 148 1.65e-02 1cll a.39.1.5 17299 1osa 148 1.68e-02 1cll a.39.1.5 17300 1ho2A 20 2.75e-02 j.35.1.1 70967 1qg9A 21 5.03e-02 j.35.1.1 46275 1nn7A 105 6.40e-02 d.42.1.2 85894 1j7rA 86 9.81e-02 1j7rA a.39.1.5 62701 1byyA 53 1.13e-01 j.12.1.1 46147 2mysB 166 1.20e-01 1wdcB a.39.1.5 17308 1wdcC 156 1.94e-01 1wdcC a.39.1.5 17317 1oyeA 1049 2.16e-01 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 1iwgA 1053 3.03e-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 1wdcB 156 4.26e-01 1wdcB a.39.1.5 17302 1m46A 148 4.93e-01 a.39.1.5 78599 9wgaA 171 5.46e-01 9wgaA g.3.1.1 44000 g.3.1.1 44001 g.3.1.1 44002 g.3.1.1 44003 1o1fC 147 5.94e-01 i.15.1.1 80997 1ggwA 140 6.06e-01 1ggwA a.39.1.5 60490 1wgtA 186 7.57e-01 9wgaA g.3.1.1 44008 g.3.1.1 44009 g.3.1.1 44010 g.3.1.1 44011 1nr6A 473 7.60e-01 1br1B 150 9.29e-01 1wdcC a.39.1.5 17309 1m45A 148 9.36e-01 a.39.1.5 78598 1ezfA 340 9.60e-01 1ezfA a.128.1.2 19440 3kvt 115 1.08e+00 1t1dA d.42.1.2 38642 1ehkA 562 1.22e+00 1ehkA f.24.1.1 43624 1orsC 132 1.29e+00 f.14.1.1 87353 1alvA 173 1.35e+00 1alvA a.39.1.8 17370 1n6bA 473 1.42e+00 a.104.1.1 85359 1k94A 165 1.45e+00 a.39.1.8 68333 1dt6A 473 1.60e+00 1dt6A a.104.1.1 18977 1scmB 145 1.66e+00 1wdcB a.39.1.5 17304 1be3C 379 1.75e+00 1be3C f.32.1.1 75805 f.21.1.2 75806 1gtxA 472 1.81e+00 1gtxA c.67.1.4 34464 1f4qA 165 1.88e+00 1alvA a.39.1.8 17360 1ohvA 472 1.91e+00 1ctdA 36 2.34e+00 1ctdA a.39.1.5 17230 1kfuS 184 2.46e+00 a.39.1.8 68574 1nr3A 122 2.49e+00 d.236.1.1 86092 1mmoD 512 2.59e+00 1mhyD a.25.1.2 16770 1j97A 211 2.59e+00 1f5sA c.108.1.4 62753 1brd 248 2.70e+00 1c3wA f.13.1.1 43404 1k9uA 78 2.77e+00 a.39.1.10 84348 1o86A 589 3.15e+00 d.92.1.5 81177 1f5sA 211 3.33e+00 1f5sA c.108.1.4 59656 1upkA 341 3.39e+00 1fp3A 402 3.65e+00 1fp3A a.102.1.3 18842 1q9bA 43 3.69e+00 1otsA 465 3.97e+00 f.20.1.1 87415 1lufA 343 3.97e+00 d.144.1.7 78223 1ldfA 281 4.01e+00 f.19.1.1 73845 1l7mA 211 4.14e+00 c.108.1.4 73664 1aijL 281 4.23e+00 6prcL f.26.1.1 43461 1c3wA 222 4.28e+00 1c3wA f.13.1.1 43405 1o20A 427 4.35e+00 c.82.1.1 86556 1e6fA 143 4.42e+00 1e6fA b.64.1.1 59304 2liv 344 4.44e+00 2liv c.93.1.1 35708 1gp0A 143 4.51e+00 b.64.1.1 70300 1hqvA 191 4.73e+00 1hqvA a.39.1.8 61160 1b6a 478 4.75e+00 1bn5 a.4.5.25 16223 d.127.1.1 41160 1e12A 253 4.81e+00 1c3wA f.13.1.1 43428 1dguA 183 5.07e+00 1dguA a.39.1.5 17333 1fx8A 281 5.44e+00 f.19.1.1 43651 1e2uA 553 5.93e+00 1e1dA e.26.1.1 43362 1e1dA 553 5.98e+00 1e1dA e.26.1.1 43363 1mtyD 512 6.20e+00 1mhyD a.25.1.2 16742 1gntA 553 6.25e+00 e.26.1.1 70290 1dceA 567 6.43e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1kcxA 518 6.47e+00 1bn5 478 7.25e+00 1bn5 a.4.5.25 16224 d.127.1.1 41161 1kktA 511 7.32e+00 a.102.2.1 68687 1hev 43 7.41e+00 1hev g.3.1.1 44060 6prcM 323 7.41e+00 6prcM f.26.1.1 43435 1o9gA 250 7.85e+00 c.66.1.29 86692 1h38C 883 8.18e+00 e.8.1.3 76627 1em2A 229 8.40e+00 1em2A d.129.3.2 41321 1a87 321 8.55e+00 1a87 f.1.1.1 43380 1e19A 314 8.56e+00 1b7bA c.73.1.1 34967 1jb0A 755 8.65e+00 1jb0A f.29.1.1 62820 1ulmA 82 8.67e+00 1ctaA 36 8.84e+00 1ctdA a.39.1.5 17232 1m0kA 262 8.92e+00 f.13.1.1 78344 1jbaA 204 8.96e+00 1rec a.39.1.5 17330 1g8iA 190 9.52e+00 1rec a.39.1.5 60363 1jk0A 419 9.62e+00 a.25.1.2 63142 1btkA 169 9.62e+00 1btkA b.55.1.1 26959 1h38B 883 9.76e+00 e.8.1.3 76626 1keyA 235 9.80e+00 a.118.16.1 72389 1dxrM 323 1.01e+01 6prcM f.26.1.1 43432 1kgbA 231 1.04e+01 f.13.1.1 68581 2lbp 346 1.05e+01 2liv c.93.1.1 35709 2scpA 174 1.06e+01 2scpA a.39.1.5 17256 1phnA 162 1.10e+01 1cpcA a.1.1.3 15641 1giqA 413 1.13e+01 d.166.1.1 76224 d.166.1.1 76225 1od5A 492 1.13e+01 b.82.1.2 86832 b.82.1.2 86833 1j1jA 240 1.16e+01 1kf6C 130 1.21e+01 f.21.2.2 72399 1dmuA 299 1.23e+01 1dmuA c.52.1.4 33294 1mswD 883 1.24e+01 e.8.1.3 79427 1jpzA 473 1.28e+01 a.104.1.1 67069 1m1jA 491 1.28e+01 h.1.8.1 74369 1dqeA 137 1.31e+01 1dqeA a.39.2.1 17388 1ulkA 126 1.35e+01 1ponA 36 1.38e+01 1ponA a.39.1.5 17239 1qcrC 378 1.38e+01 1be3C f.32.1.1 75931 f.21.1.2 75932 1btkB 169 1.38e+01 1btkA b.55.1.1 26960 1ivhA 394 1.46e+01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1pal 108 1.46e+01 1a75A a.39.1.4 17209 1fa0B 537 1.47e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1p49A 562 1.50e+01 1h38D 883 1.53e+01 e.8.1.3 76628 1jpaA 312 1.53e+01 d.144.1.7 67011 1a28A 256 1.59e+01 1a28A a.123.1.1 19290 1uhnA 189 1.61e+01 1mmc 30 1.62e+01 g.3.1.2 44061 1lnqA 336 1.63e+01 c.2.1.9 74049 f.14.1.1 74050 1omrA 201 1.65e+01 1ca1 370 1.67e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1mxgA 435 1.73e+01 b.71.1.1 85193 c.1.8.1 85194 1sesA 421 1.73e+01 1sesA a.2.7.1 15710 d.104.1.1 40710 1dlc 584 1.86e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1a4iA 301 1.92e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1colA 204 1.94e+01 1a87 f.1.1.1 43378 2bn2A 95 1.95e+01 1npoA b.9.1.1 23266 2pvbA 107 1.97e+01 1a75A a.39.1.4 17205 1rec 201 2.00e+01 1rec a.39.1.5 17326 1a4iB 301 2.01e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1k8kG 151 2.01e+01 a.118.13.1 68313 1npoC 95 2.01e+01 1npoA b.9.1.1 23271 1fa0A 537 2.06e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1as4A 341 2.07e+01 1sek e.1.1.1 42623 1cii 602 2.09e+01 1cii f.1.1.1 43381 h.4.3.1 45787 1diaA 306 2.09e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1pvaA 110 2.15e+01 1a75A a.39.1.4 17207 1ng5A 215 2.15e+01 1phnB 172 2.15e+01 1qgwC a.1.1.3 15642 1ffkB 338 2.16e+01 1ffkB b.43.3.2 25719 1cdp 109 2.20e+01 1a75A a.39.1.4 17197 1pixA 587 2.27e+01 4cpv 109 2.27e+01 1a75A a.39.1.4 17198 1oshA 232 2.37e+01 1usgA 346 2.37e+01 1clvI 32 2.38e+01 1qfdA g.3.2.1 44075 1q0sA 259 2.46e+01 1bd3A 243 2.47e+01 1bd3A c.61.1.1 34098 1o0xA 262 2.48e+01 d.127.1.1 80755 1gm9B 557 2.49e+01 1gk9B 557 2.50e+01 1hyp 80 2.58e+01 1hyp a.52.1.1 17806 1jk4A 89 2.59e+01 b.9.1.1 77130 1dro 122 2.81e+01 1btn b.55.1.1 26954 1prxA 224 2.83e+01 1prxA c.47.1.10 33076 1n83A 270 2.88e+01 a.123.1.1 80276 2bmhA 455 2.91e+01 1bu7A a.104.1.1 18941 1bbn 133 2.93e+01 1rcb a.26.1.2 16861 1lngA 87 2.95e+01 d.201.1.1 74045 1iqbB 89 3.05e+01 g.3.1.1 66264 g.3.1.1 66265 1i37A 260 3.09e+01 1a28A a.123.1.1 61583 2aaiB 262 3.09e+01 1abrB b.42.2.1 25561 b.42.2.1 25562 1jogA 146 3.10e+01 a.24.16.2 77142 1uaaA 673 3.12e+01 1pjr c.37.1.19 32401 c.37.1.19 32402 1en2A 89 3.25e+01 1hev g.3.1.1 44048 g.3.1.1 44049 1ki1B 352 3.27e+01 a.87.1.1 72497 b.55.1.1 72498 1dx5I 118 3.34e+01 1dx5I g.3.11.1 44302 g.3.11.1 44303 g.3.11.1 44304 1eulA 994 3.38e+01 1eulA b.82.7.1 75829 c.108.1.7 75830 d.220.1.1 75831 f.33.1.1 75832 1oohA 126 3.38e+01 1epwA 1290 3.39e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1sva1 361 3.40e+01 1vpsA 1tf4A 605 3.40e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1r9cA 139 3.43e+01 1nijA 318 3.44e+01 c.37.1.10 85741 d.237.1.1 85742 1n9dA 199 3.48e+01 a.26.1.1 85464 1e3aB 560 3.51e+01 1ajqB 1abv 134 3.53e+01 1abv a.70.1.1 18317 1gotG 73 3.55e+01 1tbgE a.137.3.1 19629 1ad3A 452 3.62e+01 1ad3A c.82.1.1 35335 1q33A 292 3.81e+01 1ii7A 333 3.83e+01 1ii7A d.159.1.4 62415 1htxA 32 3.85e+01 1qfdA g.3.2.1 61261 1nd7A 374 3.85e+01 1gm7B 557 3.90e+01 2bpa1 426 3.94e+01 2bpa1 1npoA 95 3.99e+01 1npoA b.9.1.1 23270