# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-scores 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 1qzzA 374 3.66e-01 a.4.5.29,c.66.1.12 96719,96720 1bob 320 9.21e-01 1bob d.108.1.1 40816 1dx8A 70 1.13e+00 1rb9 g.41.5.1 45243 1v87A 114 1.82e+00 g.44.1.1 108422 1neeA 138 1.85e+00 d.241.1.1,g.59.1.1 91841,91842 1af8 86 2.27e+00 2af8 a.28.1.1 16932 1taq 832 3.69e+00 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1u5kA 244 3.99e+00 1rlyA 60 4.01e+00 g.41.3.1 104988 1kzfA 230 4.07e+00 d.108.1.3 73354 2af8 86 4.38e+00 2af8 a.28.1.1 16933 1dl6A 58 4.46e+00 1dl6A g.41.3.1 45207 1gpmA 525 4.89e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2f4mA 295 5.50e+00 1qpbA 563 5.59e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1k4jA 230 5.60e+00 d.108.1.3 72057 1a8q 274 5.75e+00 1brt c.69.1.12 34702 1yk4A 52 5.81e+00 2b5eA 504 6.01e+00 1j7xA 302 6.30e+00 c.14.1.2 66425 1wdjA 187 6.77e+00 1oyzA 280 6.78e+00 a.118.1.16 93775 2a8eA 220 7.04e+00 1qs2A 401 8.17e+00 1qs1A d.166.1.1,d.166.1.1 42268,42269 1ykhA 108 8.60e+00 1jjrA 151 8.62e+00 a.140.2.1 66772 1ub4A 110 9.46e+00 b.34.6.2 88399 1a6aB 187 9.63e+00 1iakB b.1.1.2,d.19.1.1 21616,38190 1pft 50 9.66e+00 1pft g.41.3.1 45206 1u7eB 154 1.02e+01 1bx2B 191 1.05e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1agdB 99 1.10e+01 1agdB b.1.1.2 20742 1hsbB 99 1.10e+01 1agdB b.1.1.2 20737 1duzB 100 1.13e+01 1agdB b.1.1.2 20671 1i4fB 100 1.13e+01 1agdB b.1.1.2 61689 1k5nB 100 1.13e+01 b.1.1.2 77268 2axwA 134 1.13e+01 1uz3A 102 1.17e+01 2fokA 579 1.18e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 3pvaA 335 1.19e+01 3pvaA d.153.1.3 41854 1vp6A 138 1.21e+01 1vq0A 302 1.22e+01 2pvaA 345 1.24e+01 3pvaA d.153.1.3 41850 1ezjA 115 1.28e+01 1ezjA h.1.14.1 45638 1dlhB 188 1.31e+01 1iakB b.1.1.2,d.19.1.1 21598,38172 1wgxA 73 1.38e+01 2fztA 79 1.40e+01 1d5mB 192 1.42e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1xreA 217 1.42e+01 1aqdB 198 1.44e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 1yua 122 1.48e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1aa6 715 1.49e+01 2napA b.52.2.2,c.81.1.1 26916,35324 1meyC 87 1.50e+01 2gliA k.12.1.1 46430 1ao7B 100 1.50e+01 1agdB b.1.1.2 20697 1jqlB 140 1.51e+01 c.37.1.20 63234 2ng1 293 1.52e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1weoA 93 1.66e+01 1ii2A 524 1.76e+01 c.91.1.1,c.109.1.1 66146,66147 1ieaB 228 1.79e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1glv 303 1.80e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1n9dA 199 1.82e+01 a.26.1.1 85464 1utuA 108 1.83e+01 1zdzA 302 1.86e+01 1sqc 631 1.87e+01 2sqcA a.102.4.2,a.102.4.2 18858,18859 1adoA 363 1.89e+01 1fbaA c.1.10.1 29124 1d8bA 81 1.91e+01 1d8bA a.60.8.1 18094 1fdi 715 1.94e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1zaiA 363 1.94e+01 1b2jA 54 1.94e+01 1rb9 g.41.5.1 45231 1m4zA 238 1.96e+01 b.34.12.1 78630 1fpqA 372 1.98e+01 1fpqA a.4.5.29,c.66.1.12 59947,59948 1iro 54 1.98e+01 1rb9 g.41.5.1 45223 1umgA 362 2.06e+01 d.280.1.1 107956 1rh2F 165 2.08e+01 1rh2F a.26.1.3 16898 1cojA 212 2.15e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1woyA 500 2.15e+01 1ald 363 2.16e+01 1fbaA c.1.10.1 29100 1fp1D 372 2.17e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1ffh 294 2.18e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1yz4A 160 2.28e+01 1aosA 464 2.30e+01 1auwA a.127.1.1 19414 2sqcA 631 2.46e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1c3qA 272 2.47e+01 1c3qA c.72.1.2 34948 1kfiA 572 2.47e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68555,68556,68557,68558 4rxn 54 2.51e+01 1rb9 g.41.5.1 45226 5rxn 54 2.51e+01 1rb9 g.41.5.1 45225 1nthA 458 2.53e+01 c.1.25.1 80730 1l2qA 458 2.53e+01 c.1.25.1 73510 8rxnA 52 2.55e+01 1rb9 g.41.5.1 45215 1rb9 53 2.59e+01 1rb9 g.41.5.1 45214 1qs1A 462 2.60e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1nh1A 330 2.61e+01 e.45.1.1 91871 1a8h 500 2.61e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1gx1A 160 2.65e+01 d.79.5.1 70675 1oqcA 125 2.69e+01 a.24.15.1 87264 1brfA 53 2.70e+01 1rb9 g.41.5.1 45236 1bq8A 54 2.71e+01 1rb9 g.41.5.1 45237 1bq9A 54 2.71e+01 1rb9 g.41.5.1 45238 1jdlA 121 2.71e+01 a.3.1.1 66557 1iyxA 432 2.72e+01 c.1.11.1,d.54.1.1 83815,83816 1yhvA 297 2.74e+01 1mb4A 370 2.76e+01 c.2.1.3,d.81.1.1 78908,78909 2czcA 334 2.87e+01 1yxmA 303 2.88e+01 1jnjA 100 2.94e+01 b.1.1.2 66955 1zin 217 2.97e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1mp1A 111 2.97e+01 a.188.1.1 91382 1lnsA 763 2.99e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1zip 217 2.99e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1rdg 53 3.01e+01 1rb9 g.41.5.1 45221 1t3qB 788 3.02e+01 d.41.1.1,d.133.1.1 106369,106370 1lrv 244 3.08e+01 1lrv a.118.1.5 19146 2aa1B 146 3.08e+01 1l7vC 249 3.09e+01 c.37.1.12 73674 1fbaA 361 3.17e+01 1fbaA c.1.10.1 29120 2basA 431 3.26e+01 1zbyA 294 3.28e+01 1z53A 294 3.28e+01 2cc0A 195 3.29e+01 1kjvB 100 3.34e+01 b.1.1.2 77423 2cyp 294 3.36e+01 1ryc a.93.1.1 18600 1x1fA 149 3.36e+01 1wphA 201 3.44e+01 1cx4A 305 3.46e+01 b.82.3.2,b.82.3.2 59099,59100 2eutA 294 3.53e+01 1yf3A 259 3.58e+01 1q0sA 259 3.67e+01 c.66.1.28 95509 2g42A 79 3.69e+01 1y8qA 346 3.70e+01 1jr8A 117 3.72e+01 a.24.15.1 67115 1jy8A 159 3.72e+01 d.79.5.1 67452 1i1gA 141 3.78e+01 a.4.5.32,d.58.4.2 65982,65983 1ls1A 295 3.81e+01 a.24.13.1,c.37.1.10 78170,78171 1jraA 117 3.82e+01 a.24.15.1 67117 1jpnA 296 3.82e+01 a.24.13.1,c.37.1.10 67039,67040 1vmfA 145 3.93e+01 1cxzB 86 4.06e+01 1cxzB a.2.6.1 15705 1uu1A 335 4.08e+01 c.67.1.1 99993 1lv7A 257 4.09e+01 c.37.1.20 78232 1ed1A 135 4.11e+01 1hiwA a.61.1.1 18130 1uvqB 198 4.19e+01 b.1.1.2,d.19.1.1 100064,100065 1zkeA 83 4.24e+01 1vckA 115 4.25e+01 2aw4Q 117 4.25e+01 1jk8B 190 4.28e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1cznA 169 4.31e+01 1rcf c.23.5.1 31181 1ofv 169 4.31e+01 1rcf c.23.5.1 31184 1dpe 507 4.34e+01 1dpe c.94.1.1 35799 1v6zA 228 4.35e+01 1ng1 294 4.36e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 2gsaA 432 4.37e+01 2gsaA c.67.1.4 34446 1cvjB 190 4.48e+01 1cvjB d.58.7.1,d.58.7.1 39193,39194 1dklA 410 4.81e+01 1dklA c.60.1.2 33996 1v2bA 177 4.83e+01 d.107.1.2 108279 1f6rA 123 4.88e+01 3lzt d.2.1.2 36606 1nm2A 317 4.88e+01 c.19.1.1,d.58.23.1 80654,80655 2bkkA 264 4.93e+01 1v4eA 299 4.94e+01 a.128.1.1 100296 1mkrA 294 4.94e+01 a.93.1.1 84997 1n40A 396 5.11e+01 a.104.1.1 79977 1jdrA 294 5.14e+01 1ryc a.93.1.1 62908 1vmjA 151 5.14e+01 2b0jA 358 5.19e+01 1fdo 715 5.30e+01 2napA b.52.2.2,c.81.1.1 26917,35325 1fp0A 88 5.33e+01 1fp0A g.50.1.2 45361 1cwyA 500 5.40e+01 1cwyA c.1.8.1 28789 1b9zA 516 5.42e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1dkqA 410 5.42e+01 1dklA c.60.1.2 33998 1vemA 516 5.44e+01 1f62A 51 5.51e+01 1f62A g.50.1.2 45360 1j3mA 129 5.54e+01 d.129.7.1 103836 2avnA 260 5.54e+01 1p3jA 217 5.59e+01 c.37.1.1,g.41.2.1 94022,94023 1eswA 500 5.63e+01 1cwyA c.1.8.1 59500 1bncA 449 5.75e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1v54F 98 5.77e+01 g.41.5.3 100327 1z5sD 83 5.86e+01 1xg2B 153 5.97e+01 7reqA 727 5.99e+01 1reqA c.1.19.1,c.23.6.1 29616,31243 2occF 98 6.09e+01 2occF g.41.5.3 45256 1sv0C 82 6.15e+01 a.60.1.1 106037 5reqA 727 6.15e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1z41A 338 6.17e+01 1ds4A 292 6.22e+01 1ryc a.93.1.1 59129 1lvaA 258 6.23e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1pls 113 6.24e+01 1pls b.55.1.1 26965 1kvnA 104 6.27e+01 d.201.1.1 73066 1itcA 516 6.32e+01 b.3.1.1,c.1.8.1 83705,83706 1yukB 120 6.37e+01 1rkbA 173 6.43e+01 1reqA 727 6.49e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1j1uA 306 6.49e+01 c.26.1.1 83980 1vphA 149 6.59e+01 1dk5A 322 6.61e+01 1dk5A a.65.1.1 18192 1fqyA 269 6.62e+01 1fqyA f.19.1.1 43649 1wwiA 148 6.71e+01 5bcaA 516 6.71e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1dv1A 449 6.93e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1miuA 738 7.03e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 79153,79154,79155,79156,79157 1b0pA 1231 7.05e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1d5nA 205 7.07e+01 1avmA a.2.11.1,d.44.1.1 15762,38687 1ee8A 266 7.21e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1pydA 556 7.22e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1x13A 401 7.26e+01 1ytlA 174 7.33e+01 1k7yA 577 7.42e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1ix9A 205 7.44e+01 a.2.11.1,d.44.1.1 76899,76900 1fuqA 472 7.47e+01 1furA a.127.1.1 19405 2bidA 197 7.48e+01 2bidA f.1.4.1 43398 1cpcA 162 7.60e+01 1cpcA a.1.1.3 15643 1wer 334 7.62e+01 1wer a.116.1.2 19108 1ni3A 392 7.63e+01 c.37.1.8,d.15.10.2 80531,80532 1furA 467 7.64e+01 1furA a.127.1.1 19403 1ltlA 279 7.67e+01 b.40.4.11 84701 1mk4A 157 7.68e+01 d.108.1.1 84979 1j4nA 271 7.68e+01 f.19.1.1 71510 1dv2A 452 7.70e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1i0hA 205 7.72e+01 1avmA a.2.11.1,d.44.1.1 15760,38685 1xkmB 25 7.74e+01 2ahyA 110 7.77e+01 1ufbA 127 7.81e+01 a.24.16.3 99331 1wgwA 99 7.82e+01 1dkmA 410 7.83e+01 1dklA c.60.1.2 34000 1oltA 457 7.89e+01 c.1.28.2 93334 1f3mC 297 7.92e+01 1hcl d.144.1.7 41677 1zbmA 280 7.95e+01 2a14A 263 7.98e+01 1jyoE 105 8.10e+01 d.184.1.2 67487 1m56D 51 8.12e+01 f.23.8.1 74475 1bncB 449 8.21e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28237,31644,41489 1fuoA 467 8.22e+01 1furA a.127.1.1 19411 1xd7A 145 8.32e+01 a.4.5.55 109566 1mwsA 646 8.34e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1zglB 192 8.40e+01 1iyjB 817 8.55e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 76948,76949,76950,76951,76952 2fdrA 229 8.55e+01 1v52A 133 8.55e+01 1g2fC 90 8.56e+01 k.12.1.1 60222 1sr2A 116 8.57e+01 1ykhB 132 8.58e+01 1nal1 297 8.63e+01 1nal3 1vqqA 646 8.66e+01 1jigA 146 8.78e+01 a.25.1.1 71685 1ebuA 358 8.78e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1kbhA 47 8.79e+01 a.153.1.1 68382 1k8tA 510 8.80e+01 e.41.1.1 68316 1alu 186 8.93e+01 1alu a.26.1.1 16826 1xh9A 350 8.99e+01