# List of top-scoring protein chains for t2k-100-30-bys 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 1s1dA 331 3.33e-03 unknown_sccs -4566 1bncB 449 7.92e-01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1meoA 209 8.02e-01 c.65.1.1 79035 1b4aA 149 8.18e-01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1qmyA 167 8.35e-01 1qmyA d.3.1.2 37094 1amuA 563 8.54e-01 1amuA e.23.1.1 43351 1bncA 449 8.61e-01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1mejA 223 9.30e-01 c.65.1.1 79029 1dv2A 452 1.18e+00 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1us8A 147 1.35e+00 c.37.1.12 -7194 1ii7A 333 1.46e+00 1ii7A d.159.1.4 62415 1r4wA 226 1.58e+00 unknown_sccs -7447 1dv1A 449 1.59e+00 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1b4bA 71 1.61e+00 1b4aA d.74.2.1 39718 5hvpA 99 1.66e+00 1fmb b.50.1.1 26605 1difA 99 1.81e+00 1fmb b.50.1.1 26503 1o12A 376 1.92e+00 b.92.1.5 80758 c.1.9.10 80759 1dl5A 317 2.64e+00 1dl5A c.66.1.7 64720 d.197.1.1 64721 1uxxX 133 2.73e+00 b.18.1.10 -3107 1hvc 203 2.77e+00 1hvc b.50.1.1 26614 1fua 215 2.78e+00 2fua c.74.1.1 34973 2fua 215 2.93e+00 2fua c.74.1.1 34977 1smlA 269 3.32e+00 1smlA d.157.1.1 42053 1e4cP 215 3.69e+00 2fua c.74.1.1 34969 1dpjA 329 3.90e+00 1smrA b.50.1.2 26828 1k3sA 113 4.10e+00 d.198.1.1 68120 1trrA 107 4.37e+00 1jhgA a.4.12.1 19017 1f8rA 498 5.18e+00 1f8rA c.3.1.2 30410 d.16.1.5 37974 1jpc 109 5.32e+00 1b2pA b.78.1.1 27986 1obpA 159 5.43e+00 1obpA b.60.1.1 27092 1glv 303 5.56e+00 1gsa c.30.1.3 31721 d.142.1.1 41480 1r0vA 305 5.67e+00 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1eljA 381 5.70e+00 4mbp c.94.1.1 35791 1ukmB 128 6.05e+00 d.169.1.1 -11625 1msaA 109 6.57e+00 1b2pA b.78.1.1 27987 3psg 370 6.59e+00 1smrA b.50.1.2 26841 1kzkA 99 6.64e+00 b.50.1.1 73371 2tmdA 729 6.71e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1jkxA 212 6.76e+00 c.65.1.1 66813 1bveA 99 6.83e+00 1hvc b.50.1.1 26713 1l4zB 136 6.88e+00 d.15.5.1 77704 1gt1A 159 6.92e+00 b.60.1.1 -4436 1hn2A 159 7.02e+00 b.60.1.1 65890 1r8oA 96 7.34e+00 1djnA 729 7.94e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2wrpR 107 8.04e+00 1jhgA a.4.12.1 19010 1jhgA 101 8.27e+00 1jhgA a.4.12.1 19009 1fnnA 389 8.34e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1rcsA 105 8.55e+00 1jhgA a.4.12.1 19025 4pep 326 9.07e+00 1smrA b.50.1.2 26843 1nzhA 282 9.12e+00 d.151.1.2 -11398 1qp8A 303 9.17e+00 1qp8A c.2.1.4 30092 c.23.12.1 31352 1ctj 89 9.40e+00 1ctj a.3.1.1 15798 1n1tA 641 9.42e+00 b.29.1.15 79821 b.68.1.1 79822 1nh0A 99 9.50e+00 b.50.1.1 -4299 1csgA 127 9.80e+00 2gmfA a.26.1.2 16851 1d3bA 75 9.93e+00 1d3bA b.38.1.1 24798 1l4dB 122 1.07e+01 d.15.5.1 77684 1ugpB 226 1.08e+01 1ireB 228 1.09e+01 b.34.4.4 76770 1iknA 286 1.12e+01 1a3qA b.1.18.1 21936 b.2.5.3 22449 1f2tA 149 1.16e+01 1f2tA c.37.1.12 32373 8prkA 287 1.27e+01 1wgjA b.40.5.1 25395 2gmfA 127 1.31e+01 2gmfA a.26.1.2 16849 1reoA 486 1.31e+01 c.3.1.2 -5997 d.16.1.5 -9217 1pvxA 194 1.33e+01 1axkA b.29.1.11 24341 1htqA 477 1.34e+01 d.15.9.1 71035 d.128.1.1 71036 1cklB 126 1.36e+01 1cklB g.18.1.1 44853 g.18.1.1 44854 1jqpA 438 1.40e+01 b.61.5.1 77162 d.3.1.1 77163 1rypB 250 1.40e+01 1rypB d.153.1.4 41933 1d5tA 433 1.40e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1dazC 99 1.42e+01 1hvc b.50.1.1 26501 1o94A 729 1.45e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1wgjA 286 1.45e+01 1wgjA b.40.5.1 25397 1d2qA 173 1.46e+01 1d4vB b.22.1.1 23894 2gar 212 1.46e+01 2gar c.65.1.1 34161 1qx2A 76 1.47e+01 1i5pA 633 1.50e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1e9gA 286 1.51e+01 1wgjA b.40.5.1 59393 1e6wA 260 1.56e+01 1e6wA c.2.1.2 59326 1viaA 175 1.57e+01 c.37.1.2 -7021 1jj2S 119 1.64e+01 1ffkQ b.34.5.1 63104 1s72T 120 1.65e+01 1oj5A 132 1.67e+01 unknown_sccs -10848 1rljA 139 1.69e+01 1k2fA 190 1.70e+01 b.8.1.2 68054 1vhsA 175 1.70e+01 d.108.1.1 -10794 1h4rA 314 1.75e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1hce 118 1.75e+01 1hce b.42.5.2 25625 1ton 235 1.78e+01 5ptp b.47.1.2 26307 1ip9A 85 1.78e+01 1ip9A d.15.2.2 62638 1gmmA 133 1.79e+01 b.18.1.10 65314 2aacA 177 1.84e+01 2arcA b.82.4.1 28150 1thjA 214 1.94e+01 1qreA b.81.1.5 28072 1ufkA 254 1.95e+01 unknown_sccs -8103 1gz2A 142 1.96e+01 d.169.1.1 83392 1orc 71 1.98e+01 1orc a.35.1.2 17054 1ntfA 282 2.00e+01 d.151.1.2 -11397 1i50K 120 2.04e+01 d.74.3.2 61765 1f07A 321 2.08e+01 1ezwA c.1.16.3 59560 1o0pA 104 2.09e+01 d.58.7.1 86535 1rypG 244 2.10e+01 d.153.1.4 41938 1olrA 224 2.10e+01 b.29.1.11 -3489 1in6A 334 2.11e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1cklA 126 2.12e+01 1cklB g.18.1.1 44851 g.18.1.1 44852 1k2yX 463 2.13e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1p5dX 463 2.13e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1bmlC 362 2.15e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1hcxA 127 2.16e+01 b.109.1.1 65800 4pgaA 337 2.16e+01 4pgaA c.88.1.1 35565 1vkxA 273 2.17e+01 1a3qA b.1.18.1 21941 b.2.5.3 22454 1k1tA 99 2.19e+01 b.50.1.1 71995 1oghA 204 2.20e+01 b.85.4.1 86994 1j3wA 163 2.23e+01 unknown_sccs -10870 1q15A 503 2.23e+01 c.26.2.1 -6625 d.153.1.1 -11400 6ldh 330 2.24e+01 3ldh c.2.1.5 30161 d.162.1.1 42128 1iow 306 2.26e+01 1iow c.30.1.2 31713 d.142.1.1 41481 1yna 194 2.28e+01 1axkA b.29.1.11 24335 1htoA 477 2.37e+01 d.15.9.1 70987 d.128.1.1 70988 1d3bB 91 2.43e+01 1d3bB b.38.1.1 24804 1e9gB 286 2.44e+01 1wgjA b.40.5.1 59394 3dapA 320 2.47e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1r62A 160 2.50e+01 1q4rA 112 2.51e+01 d.58.4.4 -9943 1in4A 334 2.52e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1cjdA 394 2.52e+01 1cjdA b.121.2.1 58963 b.121.2.1 58964 2e2c 156 2.54e+01 1u9aA d.20.1.1 38336 1b8tA 192 2.56e+01 1b8tA g.39.1.3 45135 g.39.1.3 45136 g.39.1.3 45137 g.39.1.3 45138 2dln 306 2.59e+01 1iow c.30.1.2 31715 d.142.1.1 41483 1pjxA 314 2.62e+01 1f8yA 157 2.65e+01 1f8xA c.23.14.1 31395 1ugmA 125 2.66e+01 2arcB 164 2.71e+01 2arcA b.82.4.1 28149 1vheA 373 2.71e+01 unknown_sccs -4280 c.56.5.4 -7890 1r53A 382 2.74e+01 unknown_sccs -11177 1kb0A 677 2.80e+01 a.3.1.6 68378 b.70.1.1 68379 3pcnA 200 2.80e+01 3pchA b.3.6.1 22725 1h09A 338 2.81e+01 b.109.1.1 83420 c.1.8.8 83421 1fc4A 401 2.85e+01 1bs0A c.67.1.4 59760 1evsA 187 2.89e+01 1evsA a.26.1.1 16845 1k8kF 168 2.91e+01 d.198.2.1 68312 1jenA 267 2.93e+01 1jenA 1q53A 112 2.95e+01 d.58.4.4 -9944 1pkhA 204 2.97e+01 b.85.4.1 -5053 1ed7A 45 2.98e+01 1ed7A b.72.2.1 27809 1k6dA 220 2.98e+01 unknown_sccs 72082 1sk7A 198 3.02e+01 1ud9A 245 3.05e+01 1oeyA 83 3.05e+01 d.15.2.2 -9162 1qg3A 195 3.07e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1e3sA 261 3.07e+01 1e6wA c.2.1.2 59201 1sv6A 269 3.09e+01 7a3hA 303 3.13e+01 7a3hA c.1.8.3 28817 1gefA 123 3.14e+01 1gefA c.52.1.18 60465 1uurA 473 3.14e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 3pcgA 200 3.15e+01 3pchA b.3.6.1 22647 1ctaA 36 3.16e+01 1ctdA a.39.1.5 17232 1vif 62 3.17e+01 1vie b.34.4.1 24593 1bhjA 292 3.17e+01 1xvaA c.66.1.5 34189 3pchA 200 3.20e+01 3pchA b.3.6.1 22653 3adk 195 3.21e+01 1zin c.37.1.1 31885 4pfk 319 3.22e+01 3pfk c.89.1.1 35582 1h5vA 304 3.22e+01 c.1.8.3 70898 1ughI 82 3.26e+01 1ugiA d.17.5.1 38133 1hcd 118 3.32e+01 1hce b.42.5.2 25624 1vj0A 380 3.37e+01 b.35.1.2 -3697 c.2.1.1 -5721 1td5A 202 3.39e+01 1viuA 203 3.42e+01 d.113.1.1 -10889 1i81A 83 3.48e+01 1d3bB b.38.1.1 61930 1cr5A 189 3.51e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1s14A 194 3.51e+01 d.122.1.2 -10973 1kv9A 668 3.59e+01 a.3.1.6 73056 b.70.1.1 73057 1ffkW 73 3.60e+01 1ffkW g.41.8.1 45315 1garA 212 3.62e+01 2gar c.65.1.1 34162 1xvaA 292 3.63e+01 1xvaA c.66.1.5 34183 1qwyA 291 3.65e+01 unknown_sccs -5023 1gvmA 136 3.71e+01 b.109.1.1 70612 1uch 230 3.74e+01 1uch d.3.1.6 37129 1ghj 79 3.75e+01 1ghj b.84.1.1 28232 1o5zA 442 3.77e+01 c.59.1.2 -7939 c.72.2.2 -8418 1mgqA 83 3.78e+01 b.38.1.1 79099 1qreA 247 3.79e+01 1qreA b.81.1.5 28066 1hb5A 394 3.85e+01 i.6.1.1 65752 1hx6A 394 3.85e+01 1cjdA b.121.2.1 58995 b.121.2.1 58996 1o6aA 96 3.86e+01 unknown_sccs -4101 2pcdA 200 3.88e+01 3pchA b.3.6.1 22665 1ponA 36 3.92e+01 1ponA a.39.1.5 17239 1suuA 312 3.94e+01 unknown_sccs -4610