# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1qk8A 146 5.54e-05 1ewxA c.47.1.10 33061 1o8xA 146 2.23e-04 c.47.1.10 86681 1i5gA 144 5.92e-04 1ewxA c.47.1.10 61784 1v58A 241 1.79e-03 1josA 128 4.91e-03 d.52.7.1 84191 1v6fA 151 6.96e-03 1lu4A 136 2.96e-02 c.47.1.10 -7509 1bed 181 6.46e-02 1fvkA unknown_sccs -7444 1jfuA 186 7.56e-02 c.47.1.10 62940 1pa4A 116 9.77e-02 d.52.7.1 -9780 1osdA 72 2.01e-01 1nw2A 105 2.35e-01 c.47.1.1 -7380 1kmqA 184 2.64e-01 c.37.1.8 84412 1tx4B 178 3.11e-01 1ctqA c.37.1.8 32045 1eejA 216 3.67e-01 1eejA c.47.1.9 33057 d.17.3.1 38071 1rpjA 288 4.54e-01 2dri c.93.1.1 35656 1cc8A 73 4.59e-01 1cc8A d.58.17.1 39343 1fvkA 189 4.83e-01 1fvkA unknown_sccs -7419 1egaA 301 5.73e-01 1egaA c.37.1.8 32150 d.52.3.1 38836 1h6kZ 98 6.24e-01 d.58.7.1 60686 1gudA 288 6.38e-01 c.93.1.1 83326 2dri 271 8.07e-01 2dri c.93.1.1 35637 1acvA 189 8.79e-01 1fvkA unknown_sccs -7428 1hcl 298 9.50e-01 1hcl d.144.1.7 41593 1uc2A 481 1.02e+00 unknown_sccs -11725 1mw7A 240 1.32e+00 e.39.1.1 79557 2acy 98 1.32e+00 2acy d.58.10.1 39298 1uwvA 433 1.34e+00 unknown_sccs -3950 unknown_sccs -8107 1r31A 428 1.41e+00 d.58.20.1 -10108 d.179.1.1 -11716 1ako 268 1.53e+00 1ako d.151.1.1 41779 1r26A 125 1.54e+00 c.47.1.1 -7389 1fb6A 105 1.62e+00 1thx c.47.1.1 32739 1st9A 143 1.67e+00 c.47.1.10 -7503 1drw 273 1.69e+00 1drw c.2.1.3 30057 d.81.1.3 39972 1rro 108 1.70e+00 1a75A a.39.1.4 17195 1i9bA 217 1.75e+00 1i9bA b.96.1.1 62084 1dmgA 225 1.75e+00 1dmgA c.22.1.1 31036 1dhn 121 2.02e+00 1dhn d.96.1.3 40663 1cl8A 276 2.10e+00 1ckqA c.52.1.1 33230 1k3sA 113 2.17e+00 d.198.1.1 68120 1iyrA 111 2.43e+00 a.164.1.1 76973 1jysA 242 2.43e+00 c.56.2.1 77216 1fxlA 167 2.44e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1t95A 240 2.60e+00 1ecpA 238 2.61e+00 1ecpA c.56.2.1 33775 1ln1A 214 2.64e+00 d.129.3.2 74038 3rabA 169 2.75e+00 1ctqA c.37.1.8 32018 1gz8A 299 2.78e+00 d.144.1.7 83405 1q7bA 244 2.86e+00 c.2.1.2 -5826 1sqlA 146 3.13e+00 1dqaA 467 3.25e+00 1dqaA d.58.20.1 39364 d.179.1.1 42585 1a8l 226 3.27e+00 1a8l c.47.1.2 32777 c.47.1.2 32778 1uw6A 211 3.39e+00 b.96.1.1 -3077 1grx 85 3.42e+00 1kte c.47.1.1 32766 1p9qC 256 3.58e+00 1urnA 97 3.77e+00 1urnA d.58.7.1 39153 1dmhA 311 3.84e+00 1dmhA b.3.6.1 22633 1is1A 185 3.89e+00 d.67.3.1 83704 1urrA 102 3.91e+00 1ek0A 170 3.95e+00 1ctqA c.37.1.8 32076 1aqb 183 3.99e+00 1aqb b.60.1.1 27084 1oapA 109 4.08e+00 unknown_sccs -10428 1d4aA 273 4.11e+00 1d4aA c.23.5.3 31219 1n71A 180 4.39e+00 d.108.1.1 85370 1thx 115 4.55e+00 1thx c.47.1.1 32732 1k9sA 237 4.68e+00 c.56.2.1 68359 1dg9A 157 4.71e+00 1dg9A c.44.1.1 32637 1qzgA 187 4.89e+00 b.40.4.3 -3920 1c0eA 157 5.00e+00 1dg9A c.44.1.1 32638 1d4oA 184 5.04e+00 1d4oA c.31.1.4 31748 1j98A 157 5.09e+00 1j98A d.185.1.2 62755 1pda 315 5.17e+00 1pda c.94.1.1 35751 d.50.2.1 38794 1mk4A 157 5.29e+00 d.108.1.1 84979 1hd2A 161 5.30e+00 c.47.1.10 60962 1b9mA 265 5.50e+00 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 1d4xG 126 5.59e+00 1d0nA d.109.1.1 59109 1gx1A 160 5.64e+00 d.79.5.1 70675 1nm1G 125 5.78e+00 d.109.1.1 80653 1cjxA 357 5.84e+00 1cjxA d.32.1.3 38516 d.32.1.3 38517 1e7wA 291 6.31e+00 c.2.1.2 59373 1huqA 164 6.70e+00 1byuA c.37.1.8 32020 1aiu 105 6.84e+00 1erv c.47.1.1 32746 1o4vA 183 7.01e+00 c.23.8.1 86628 1i12A 160 7.02e+00 1i21A d.108.1.1 61515 1erv 105 7.02e+00 1erv c.47.1.1 32743 1ctqA 166 7.12e+00 1ctqA c.37.1.8 31965 1blxA 326 7.23e+00 1hcl d.144.1.7 41596 1uc7A 125 7.24e+00 c.47.1.1 -7414 1tfe 145 7.39e+00 1tfe d.43.1.1 38680 1e8gA 560 7.50e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1mzbA 136 7.56e+00 unknown_sccs -266 1f9mA 112 7.57e+00 1erv c.47.1.1 32736 1j08A 226 7.74e+00 c.47.1.2 83855 c.47.1.2 83856 1o0pA 104 8.12e+00 d.58.7.1 86535 1knb 196 8.34e+00 1qhvA b.21.1.1 23841 1v84A 253 9.26e+00 1oiaA 95 9.30e+00 d.58.7.1 87051 1vhwA 253 9.48e+00 c.56.2.1 -7765 1eemA 241 9.50e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1f3mC 297 9.61e+00 1hcl d.144.1.7 41677 1gtkA 313 9.63e+00 c.94.1.1 76346 d.50.2.1 76347 1euvA 221 9.67e+00 1euvA d.3.1.7 37133 1rk8A 165 9.69e+00 d.58.7.1 -10018 1a8y 367 9.72e+00 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1f7sA 139 9.75e+00 1cof d.109.1.2 40857 1i1dA 161 1.03e+01 1i21A d.108.1.1 61526 1o5iA 249 1.05e+01 c.2.1.2 -5833 1gca 309 1.07e+01 1gca c.93.1.1 35659 1ib8A 164 1.08e+01 b.38.2.1 71168 d.52.4.1 71169 1v9jA 113 1.10e+01 d.52.6.1 -9781 1d1qA 161 1.13e+01 1dg9A c.44.1.1 32642 1dvoA 152 1.14e+01 1dvoA a.136.1.1 19623 1szwA 379 1.14e+01 unknown_sccs -10164 1kao 167 1.17e+01 1ctqA c.37.1.8 32014 1s2dA 167 1.18e+01 c.23.14.1 -6469 1fp2A 352 1.18e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1b3tA 147 1.23e+01 1b3tA d.58.8.1 39228 1mwpA 96 1.24e+01 1mwpA d.170.2.1 42453 1nbuA 119 1.24e+01 d.96.1.3 -10699 1lxiA 139 1.25e+01 g.17.1.2 84735 1gp1A 198 1.27e+01 1gp1A c.47.1.10 33059 1gt6A 269 1.27e+01 c.69.1.17 76342 1kzlA 208 1.30e+01 b.43.4.3 77635 b.43.4.3 77636 1faaA 124 1.30e+01 1erv c.47.1.1 32738 1je0A 236 1.30e+01 c.56.2.1 66581 1r2qA 170 1.33e+01 c.37.1.8 -7071 1dpe 507 1.34e+01 1dpe c.94.1.1 35799 3bamA 213 1.34e+01 1bam c.52.1.3 33288 1i2mA 216 1.35e+01 1byuA c.37.1.8 61568 1jksA 294 1.36e+01 d.144.1.7 71710 1jmtA 104 1.40e+01 d.58.7.3 63180 1dozA 309 1.41e+01 1ak1 c.92.1.1 35592 1lfpA 249 1.41e+01 e.39.1.1 73885 1f46A 140 1.41e+01 1f46A d.129.4.1 59643 1kt6A 183 1.42e+01 b.60.1.1 84466 1qpcA 279 1.49e+01 1fgkA d.144.1.7 41685 1hbq 183 1.50e+01 1aqb b.60.1.1 27078 1nffA 260 1.52e+01 c.2.1.2 80457 1a8vA 121 1.53e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1l3iA 192 1.54e+01 c.66.1.22 77676 1oo0B 110 1.57e+01 d.58.7.1 87183 1omzA 293 1.59e+01 c.68.1.15 87093 1s14A 194 1.59e+01 d.122.1.2 -10973 1vioA 243 1.63e+01 unknown_sccs -10154 d.66.1.5 -10240 1tib 269 1.63e+01 3tgl c.69.1.17 34738 1a48 306 1.66e+01 1a48 d.143.1.1 41590 1jqeA 292 1.66e+01 c.66.1.19 71789 1v4vA 376 1.67e+01 c.87.1.3 -8583 1otgA 125 1.67e+01 1otgA d.80.1.2 39831 1tq8A 163 1.68e+01 1oz9A 150 1.69e+01 unknown_sccs -10588 2bc2A 227 1.70e+01 1a7tA d.157.1.1 42031 1jatA 155 1.74e+01 1u9aA d.20.1.1 62818 1hrkA 359 1.74e+01 1hrkA c.92.1.1 61228 2trxA 108 1.78e+01 1thx c.47.1.1 32719 1ush 550 1.79e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1ej8A 140 1.86e+01 1qupA b.1.8.1 22300 1k38A 254 1.86e+01 e.3.1.1 84303 1r1mA 164 1.86e+01 unknown_sccs -10431 1cwvA 492 1.86e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1j1hA 144 1.87e+01 b.111.1.1 77056 1ef1A 294 1.87e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1rcy 151 1.88e+01 1rcy b.6.1.1 23018 1qh4A 380 1.88e+01 1qh4A a.83.1.1 18462 d.128.1.2 41197 1f08A 148 1.92e+01 1f08A d.89.1.2 59564 1q7lA 198 1.94e+01 c.56.5.4 -7886 1sur 215 1.94e+01 1sur c.26.2.2 31620 1esgA 213 1.96e+01 1bam c.52.1.3 33286 1s3zA 165 1.97e+01 1oivA 191 2.00e+01 c.37.1.8 -7074 1h0bA 256 2.02e+01 b.29.1.11 83422 1dp4A 435 2.02e+01 1dp4A c.93.1.1 35710 1qauA 112 2.13e+01 1qauA b.36.1.1 24779 1k8kD 300 2.15e+01 d.198.2.1 68309 d.198.2.1 68310 1vhiA 142 2.18e+01 1b3tA d.58.8.1 39230 1vgyA 393 2.20e+01 c.56.5.4 -7882 d.58.19.1 -10106 1e6uA 321 2.21e+01 1bsvA c.2.1.2 29805 1ky3A 182 2.22e+01 c.37.1.8 73193 1jyeA 349 2.23e+01 c.93.1.1 67455 1bob 320 2.23e+01 1bob d.108.1.1 40816 1e79H 146 2.23e+01 1e79H a.2.10.1 15721 b.93.1.1 28438 1dcoA 104 2.26e+01 1dcpA d.74.1.1 39680 1e30A 155 2.27e+01 1rcy b.6.1.1 23016 1tkiA 321 2.31e+01 1tkiA d.144.1.7 41638 1a7tA 232 2.33e+01 1a7tA d.157.1.1 42041 1f7uA 607 2.35e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1qnf 484 2.37e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1qsmA 152 2.40e+01 1qsmA d.108.1.1 40808 1ekeA 230 2.44e+01 1ekeA c.55.3.1 33572 1h6kA 757 2.45e+01 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1g5tA 196 2.45e+01 1g5rA c.37.1.11 32366 1qsgA 265 2.46e+01 1eny c.2.1.2 29935 1vhh 162 2.47e+01 1vhh d.65.1.2 39550 1kte 105 2.57e+01 1kte c.47.1.1 32771 1m15A 357 2.61e+01 a.83.1.1 78368 d.128.1.2 78369 1kgyA 181 2.63e+01 b.18.1.4 72449 1ko3A 230 2.68e+01 d.157.1.1 -11454 3pmgA 561 2.69e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1bg0 356 2.76e+01 1qh4A a.83.1.1 18476 d.128.1.2 41211 1no5A 114 2.77e+01 unknown_sccs -9785 1nukA 183 2.79e+01 1nukA b.18.1.4 23721 1ci3M 249 2.80e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1m7bA 184 2.80e+01 c.37.1.8 74572 1cydA 244 2.83e+01 1cydA c.2.1.2 29825 1gheA 177 2.85e+01 d.108.1.1 76222 1lw9A 164 2.86e+01 d.2.1.3 84727 1btl 263 2.91e+01 1btl e.3.1.1 42691 1usuA 260 2.96e+01 unknown_sccs -9045 1vddA 228 3.01e+01 1quqA 129 3.02e+01 1quqA b.40.4.3 25303 1n2fA 142 3.03e+01 d.227.1.1 79853 1udxA 416 3.05e+01 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1odkA 235 3.08e+01 c.56.2.1 86863 1mwyA 73 3.08e+01 d.58.17.1 79616 1i8dA 213 3.15e+01 b.43.4.3 61953 b.43.4.3 61954 1iv3A 152 3.20e+01 d.79.5.1 76828 1p36A 164 3.22e+01 d.2.1.3 -8840 1tlk 154 3.23e+01 1tlk b.1.1.4 21707 1opjA 293 3.24e+01 d.144.1.7 87230 1sgt 223 3.25e+01 5ptp b.47.1.1 25814 1nbwA 607 3.26e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1r3eA 309 3.31e+01 b.122.1.1 -5118 unknown_sccs -10146 1os8A 223 3.33e+01 b.47.1.1 -4113 1ne9A 335 3.36e+01 d.108.1.4 -10805 d.108.1.4 -10806 1evfA 264 3.36e+01 1bkpA d.117.1.1 40932 1t8hA 277 3.40e+01 1lxnA 99 3.41e+01 d.58.48.1 84737 1ukkA 142 3.43e+01 d.227.1.1 -11206 1v0wA 506 3.45e+01 1fsz 372 3.48e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1b5tA 275 3.51e+01 1b5tA c.1.23.1 29676 1qniA 581 3.51e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1h9sA 140 3.55e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1mgtA 174 3.56e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 2fmr 65 3.57e+01 2fmr d.51.1.1 38808 1jyaA 130 3.60e+01 d.198.1.1 67453 1nf9A 207 3.61e+01 unknown_sccs 85631 1bykA 255 3.62e+01 1bykA c.93.1.1 35706 1i88A 389 3.64e+01 c.95.1.2 66070 c.95.1.2 66071 1mq4A 272 3.70e+01 d.144.1.7 -11349 119l 164 3.71e+01 1l92 d.2.1.3 36622 1q48A 134 3.72e+01 unknown_sccs -9776 1v7zA 260 3.82e+01 unknown_sccs -6353 1nktA 922 3.87e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1vhsA 175 3.97e+01 d.108.1.1 -10794 1p9yA 121 3.97e+01 unknown_sccs -8996