# 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 1bpv 112 1.01e-01 1bpv b.1.2.1 22071 1mjgM 729 4.64e-01 e.26.1.3 79204 1k42A 168 9.17e-01 b.18.1.14 72032 1hdkA 141 9.21e-01 b.29.1.3 65807 1qtsA 247 1.10e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1kyfA 247 1.16e+00 b.1.10.1 73220 d.105.1.1 73221 1b9kA 238 1.24e+00 1qtsA b.1.10.1 22315 d.105.1.1 40791 1hfuA 503 1.31e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1a65A 504 1.40e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1gd5A 130 1.57e+00 1gd5A d.189.1.1 60439 3cd4 182 1.58e+00 1cdy b.1.1.1 19720 b.1.1.3 21659 1kq6A 141 1.66e+00 d.189.1.1 -9926 1o7kA 131 1.80e+00 d.189.1.1 81144 1oaoC 729 1.95e+00 e.26.1.3 86746 1cdi 179 2.02e+00 1cdy b.1.1.1 19727 b.1.1.3 21666 1g86A 142 2.09e+00 b.29.1.3 70161 1e7uA 961 2.16e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1lcl 142 2.16e+00 1lcl b.29.1.3 24216 1cdy 178 2.39e+00 1cdy b.1.1.1 19719 b.1.1.3 21658 1r8oA 96 2.57e+00 1o4rA 108 2.77e+00 d.93.1.1 -10624 1danU 121 2.84e+00 1boy b.1.2.1 21954 1ekfA 365 3.15e+00 1ekfA e.17.1.1 59445 1shbA 104 3.48e+00 1fmk d.93.1.1 40425 1avaC 181 3.57e+00 1avaC b.42.4.1 25604 1vavA 222 3.67e+00 1g9mC 185 3.68e+00 1cdy b.1.1.1 19721 b.1.1.3 21660 1m1cA 680 3.73e+00 e.42.1.1 78395 1boy 219 3.98e+00 1boy b.1.2.1 21955 b.1.2.1 21956 1jlnA 297 4.00e+00 1pty c.45.1.2 63172 1vhoA 346 4.11e+00 unknown_sccs -4283 c.56.5.4 -7893 1a3k 137 4.18e+00 1a3k b.29.1.3 24218 1a8p 258 4.75e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1rie 129 4.82e+00 1rie b.33.1.1 24427 1kyaA 499 5.03e+00 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1shaA 104 5.12e+00 1fmk d.93.1.1 40424 1ru3A 732 5.18e+00 e.26.1.3 -12021 1f2fA 104 5.32e+00 1fmk d.93.1.1 40455 1fna 93 5.69e+00 1fnf b.1.2.1 21971 1e8yA 966 5.76e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1nkqA 259 5.90e+00 1mjc 69 6.12e+00 1mjc b.40.4.5 25319 1kt8A 365 6.16e+00 e.17.1.1 77531 1cc3A 130 6.43e+00 1nwpA b.6.1.1 23008 1c1lA 136 6.60e+00 1c1lA b.29.1.3 24219 2hft 218 7.05e+00 1boy b.1.2.1 21951 b.1.2.1 21952 1aipE 405 7.05e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1jsdA 319 7.25e+00 b.19.1.2 63258 1pmi 440 7.32e+00 1pmi b.82.1.3 28114 1ktaA 365 7.64e+00 e.17.1.1 77533 1f15A 218 7.69e+00 1f15B b.121.4.5 23320 1on0A 158 7.78e+00 d.108.1.1 87095 1ha3A 405 7.93e+00 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1fc4A 401 8.12e+00 1bs0A c.67.1.4 59760 1krhA 338 8.26e+00 b.43.4.2 72891 c.25.1.2 72892 d.15.4.2 72893 1vddA 228 8.29e+00 1f3rB 257 8.41e+00 1f3rB b.1.1.1 20417 b.1.1.1 20416 1iarB 207 9.03e+00 1iarB b.1.2.1 22037 b.1.2.1 22038 1je5A 206 9.15e+00 1je5A b.40.4.7 62909 1pmy 123 9.53e+00 1bqk b.6.1.1 22888 1m4jA 142 9.93e+00 d.109.1.2 78602 1c9oA 66 1.03e+01 1mjc b.40.4.5 25325 1i7oA 429 1.03e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1k0wA 231 1.05e+01 c.74.1.1 77220 1n0uA 842 1.06e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1tqyB 415 1.07e+01 1kr5A 226 1.11e+01 c.66.1.7 68847 1jdiA 231 1.11e+01 c.74.1.1 66551 1qr4A 186 1.11e+01 1qr4B b.1.2.1 21986 b.1.2.1 21987 1bp3B 211 1.14e+01 1axiB b.1.2.1 22031 b.1.2.1 22032 1je0A 236 1.19e+01 c.56.2.1 66581 1g0dA 695 1.20e+01 1f13A b.1.18.9 60166 b.1.5.1 60167 b.1.5.1 60168 d.3.1.4 60169 1iz6A 138 1.21e+01 b.34.5.2 76976 b.40.4.5 76977 1h9sA 140 1.23e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1csp 67 1.23e+01 1mjc b.40.4.5 25321 1exmA 405 1.29e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1pxvA 183 1.31e+01 d.3.1.1 -8881 1ncg 110 1.34e+01 1edhA b.1.6.1 22193 1i1nA 226 1.36e+01 c.66.1.7 71102 1gttA 429 1.39e+01 d.177.1.1 70529 d.177.1.1 70530 1ocxA 182 1.40e+01 b.81.1.3 86814 1efcA 393 1.42e+01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1ikoP 178 1.43e+01 b.6.1.5 71243 1c8pA 102 1.44e+01 1c8pA b.1.2.1 22040 1cyx 205 1.45e+01 1cyx b.6.1.2 23023 1b2sD 90 1.47e+01 1ay7B c.9.1.1 30837 1shdA 107 1.47e+01 1fmk d.93.1.1 40440 1i50C 318 1.48e+01 d.74.3.1 61756 d.181.1.1 61757 1e8xA 961 1.48e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1przA 252 1.49e+01 unknown_sccs -10158 1jzgA 128 1.50e+01 b.6.1.1 67855 1ts3A 194 1.51e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1rhfA 182 1.53e+01 b.1.1.1 -2335 b.1.1.4 -2684 1dv1A 449 1.62e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1p7hL 286 1.66e+01 b.1.18.1 -2700 b.2.5.3 -2894 1fftB 315 1.69e+01 1cyx b.6.1.2 23025 f.17.2.1 43628 1i82A 189 1.70e+01 1i82A b.1.9.2 61937 2eifA 136 1.70e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1e0tA 470 1.70e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1cw0A 155 1.71e+01 1vsrA c.52.1.15 33333 1i8aA 189 1.71e+01 1i82A b.1.9.2 61951 1bkzA 135 1.74e+01 1a3k b.29.1.3 24202 1mjfA 281 1.78e+01 c.66.1.17 79198 1rcd 173 1.79e+01 2fha a.25.1.1 16687 1gkgA 136 1.85e+01 g.18.1.1 70219 g.18.1.1 70220 1nct 106 1.88e+01 1wit b.1.1.4 21708 1qwtA 255 1.91e+01 unknown_sccs -3329 1gu7A 364 1.93e+01 b.35.1.2 83321 c.2.1.1 83322 1jsmA 325 1.93e+01 b.19.1.2 63264 1qrkA 731 1.98e+01 1f13A b.1.18.9 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1qr4B 186 2.00e+01 1qr4B b.1.2.1 21988 b.1.2.1 21989 1ntyA 311 2.03e+01 1q0uA 219 2.06e+01 c.37.1.19 -7205 1f13A 731 2.07e+01 1f13A b.1.18.9 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1ggtB 731 2.07e+01 1f13A b.1.18.9 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1plc 99 2.11e+01 1plc b.6.1.1 22846 1dg6A 191 2.14e+01 1d4vB b.22.1.1 23883 3ebx 62 2.16e+01 3ebx g.7.1.1 44389 3bamA 213 2.18e+01 1bam c.52.1.3 33288 1f6fB 210 2.20e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 2dabA 282 2.20e+01 1daaA e.17.1.1 43274 1cxzB 86 2.24e+01 1cxzB a.2.6.1 15705 1onjA 61 2.27e+01 g.7.1.1 -12530 1itvA 195 2.28e+01 b.66.1.1 76791 1na3A 91 2.30e+01 k.38.1.1 85481 1k7kA 221 2.33e+01 c.51.4.1 72104 1a49A 530 2.33e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1ab7 89 2.36e+01 1ay7B c.9.1.1 30835 1ysc 421 2.37e+01 1ivyA c.69.1.5 34652 1iq9A 61 2.39e+01 g.7.1.1 -12528 1ebaA 215 2.40e+01 1eerB b.1.2.1 22015 b.1.2.1 22016 1s68A 249 2.42e+01 unknown_sccs -11253 1d4vB 163 2.44e+01 1d4vB b.22.1.1 23884 1pba 81 2.45e+01 1pytA d.58.3.1 39067 1h6yA 170 2.46e+01 b.18.1.7 70904 1qh0A 295 2.55e+01 b.43.4.2 68891 c.25.1.1 68892 1vsrA 136 2.56e+01 1vsrA c.52.1.15 33332 1aonO 97 2.57e+01 b.35.1.1 24642 1m7xA 617 2.58e+01 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1kdj 102 2.58e+01 1plc b.6.1.1 22864 1kzhA 555 2.61e+01 c.89.1.1 73361 1kbvA 327 2.66e+01 b.6.1.3 68395 b.6.1.3 68396 1q7hA 153 2.75e+01 b.122.1.1 -5124 unknown_sccs -9313 1aw7A 194 2.76e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1hwwA 1015 2.81e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1sddA 306 2.81e+01 1ufhA 180 2.82e+01 d.108.1.1 88485 1hyeA 313 2.83e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1fjjA 159 2.83e+01 1fjjA b.17.1.2 59852 1daaA 282 2.88e+01 1daaA e.17.1.1 43270 1iw7C 1119 2.89e+01 e.29.1.1 71474 1brsD 89 2.91e+01 1ay7B c.9.1.1 30825 1r94A 118 2.93e+01 b.124.1.1 -4402 1kkhA 317 2.94e+01 d.14.1.5 72645 d.58.26.3 72646 1o5uA 101 2.99e+01 b.82.1.8 -4845 1theA 260 3.01e+01 1theB d.3.1.1 37056 1pl8A 356 3.02e+01 b.35.1.2 -3716 c.2.1.1 -5740 1lj9A 144 3.06e+01 a.4.5.28 78035 1repC 251 3.10e+01 1repC a.4.5.10 16125 a.4.5.10 16126 2pcfB 250 3.10e+01 1hcz i.4.1.1 45911 2fnbA 95 3.15e+01 2fnbA b.1.2.1 21979 1od5A 492 3.16e+01 b.82.1.2 86832 b.82.1.2 86833 3daaA 277 3.18e+01 1daaA e.17.1.1 43272 1eqkA 102 3.18e+01 1eqkA d.17.1.2 37998 1q15A 503 3.20e+01 c.26.2.1 -6625 d.153.1.1 -11400 1i3zA 103 3.22e+01 d.93.1.1 83667 1lr0A 129 3.27e+01 d.212.1.1 74213 1odkA 235 3.31e+01 c.56.2.1 86863 1htyA 1015 3.33e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1fa4A 105 3.33e+01 1plc b.6.1.1 22867 2plt 98 3.39e+01 1plc b.6.1.1 22862 1h3fA 432 3.39e+01 c.26.1.1 76631 d.66.1.4 76632 1jl0A 334 3.43e+01 1jenA d.156.1.1 63155 3bamB 213 3.43e+01 1bam c.52.1.3 33289 1mli 96 3.47e+01 1mli d.58.4.1 39070 1j6rA 214 3.48e+01 d.173.1.2 71598 1dyoA 160 3.49e+01 1dyoA b.18.1.7 23771 1e42A 258 3.54e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1mfgA 95 3.55e+01 b.36.1.1 79043 2hgsA 474 3.55e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1kb5B 117 3.56e+01 1kb5B b.1.1.1 20632 1cjtA 217 3.57e+01 1azsA d.58.29.1 39419 1dk0A 188 3.59e+01 1b2vA d.35.1.1 38530 1bj8 109 3.59e+01 1bquA b.1.2.1 22070 1ebpA 211 3.62e+01 1eerB b.1.2.1 22023 b.1.2.1 22024 1oghA 204 3.64e+01 b.85.4.1 86994 1b2vA 188 3.65e+01 1b2vA d.35.1.1 38532 1mexH 215 3.66e+01 b.1.1.1 -2237 b.1.1.2 -2487 1b2rA 304 3.72e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1fdr 248 3.72e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1azu 128 3.72e+01 1nwpA b.6.1.1 23007 1cyw 205 3.73e+01 1cyx b.6.1.2 23024 1n9lA 109 3.80e+01 d.110.3.6 85468 1g8qA 90 3.81e+01 1g8qA a.135.1.1 19621 1ll1 590 3.84e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.18.3 21864 1ex0A 731 3.88e+01 b.1.18.9 -2754 b.1.5.1 -2778 b.1.5.1 -2779 d.3.1.4 -8889 1sk7A 198 3.91e+01 1db3A 372 3.93e+01 1db3A c.2.1.2 29813 1hn2A 159 3.95e+01 b.60.1.1 65890