# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1fjgM 126 8.99e-01 1fjfM a.156.1.1 16293 2fg9A 178 1.12e+00 1pkp 150 2.22e+00 1pkp d.14.1.1,d.50.1.2 37551,38787 1nksA 194 2.64e+00 1nksA c.37.1.1 31886 1vk1A 242 2.72e+00 d.268.1.2 108634 1e5dA 402 3.36e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1vk8A 106 3.53e+00 d.58.48.1 108636 1a9nA 176 3.54e+00 1a9nA c.10.2.4 30875 1ki9A 192 4.34e+00 c.37.1.1 84404 1lqtA 456 5.22e+00 c.3.1.1,c.4.1.1 74198,74199 1eljA 381 5.77e+00 4mbp c.94.1.1 35791 1h75A 81 6.89e+00 1h75A c.47.1.1 60716 1id1A 153 7.12e+00 1id1A c.2.1.9 62286 1pydA 556 7.13e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1khyA 148 7.51e+00 a.174.1.1 77410 2plc 274 8.04e+00 2plc c.1.18.2 29614 1u6mA 199 8.09e+00 2f1wA 158 8.55e+00 1wr2A 238 8.67e+00 1aod 289 8.90e+00 2plc c.1.18.2 29615 1l3iA 192 8.96e+00 c.66.1.22 77676 1vp8A 201 8.99e+00 1pjbA 361 9.03e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1t94A 459 9.17e+00 d.240.1.1,e.8.1.7 106701,106702 1pvdA 537 9.78e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 3pfk 319 9.92e+00 3pfk c.89.1.1 35581 2fvgA 340 9.93e+00 2fl4A 149 9.99e+00 1a0oD 134 1.01e+01 1eayC d.58.24.1 39391 1qpbA 563 1.02e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31739,31781,31782 1eueA 86 1.03e+01 1cyo d.120.1.1 59504 1vf8A 377 1.10e+01 1sayA 361 1.17e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 2fox 138 1.17e+01 5nul c.23.5.1 31197 1e9lA 377 1.19e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 2gfhA 260 1.22e+01 1t0qA 498 1.23e+01 a.25.1.2 106220 1vqzA 341 1.24e+01 2fvx 138 1.25e+01 5nul c.23.5.1 31200 2a1iA 146 1.29e+01 3nll 138 1.33e+01 5nul c.23.5.1 31206 1yz7A 188 1.34e+01 1yqhA 109 1.34e+01 1bby 69 1.36e+01 2bby a.4.5.15 16149 1bykA 255 1.36e+01 1bykA c.93.1.1 35706 1m2xA 223 1.37e+01 d.157.1.1 84764 1dusA 194 1.37e+01 1dusA c.66.1.4 34182 1m6yA 301 1.37e+01 a.60.13.1,c.66.1.23 78716,78717 1vk9A 151 1.47e+01 c.139.1.1 108640 1hs6A 611 1.49e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1sqiA 393 1.51e+01 d.32.1.3,d.32.1.3 105914,105915 1hjp 203 1.53e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 2fojA 155 1.53e+01 1ghhA 81 1.55e+01 1ghhA d.57.1.1 38940 6pfkA 319 1.61e+01 3pfk c.89.1.1 35583 1yy6A 155 1.70e+01 4pfk 319 1.70e+01 3pfk c.89.1.1 35582 1gw5S 142 1.70e+01 d.110.4.2 70633 1wozA 177 1.74e+01 5nul 138 1.79e+01 5nul c.23.5.1 31191 1awpA 92 1.80e+01 1cyo d.120.1.1 41071 1tyyA 339 1.80e+01 2c8mA 262 1.83e+01 1fr2A 86 1.84e+01 a.28.2.1 83256 1gc5A 467 1.86e+01 1gc5A c.72.1.3 60429 2nsyA 271 1.92e+01 2nsyA c.26.2.1 31612 1kqpA 271 1.97e+01 c.26.2.1 72883 1zd9A 188 1.99e+01 2bby 69 2.01e+01 2bby a.4.5.15 16148 1pjcA 361 2.02e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1yv5A 374 2.11e+01 1yq7A 374 2.12e+01 1zxxA 319 2.14e+01 1mu5A 471 2.20e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1j24A 143 2.21e+01 c.52.1.20 84008 1vc1A 110 2.26e+01 c.13.2.1 108493 1eexB 224 2.26e+01 1dioB c.51.3.1 33213 2f5xA 312 2.27e+01 1ih8A 271 2.33e+01 2nsyA c.26.2.1 62377 1du0A 57 2.33e+01 2hddA a.4.1.1 15974 1q7lA 198 2.34e+01 c.56.5.4 96044 1mqoA 227 2.37e+01 d.157.1.1 103846 1nsyA 271 2.38e+01 2nsyA c.26.2.1 31614 1jmvA 141 2.44e+01 c.26.2.4 66897 1ub3A 220 2.45e+01 c.1.10.1 88395 1npdA 288 2.45e+01 c.2.1.7,c.58.1.5 80681,80682 1q67A 231 2.46e+01 b.55.1.7 95960 1lkvX 232 2.47e+01 a.118.14.1 73980 1nv8A 284 2.49e+01 c.66.1.30 86224 1u6tA 121 2.51e+01 1rz3A 201 2.54e+01 c.37.1.6 98132 2f94F 350 2.54e+01 1v30A 124 2.59e+01 1wjgA 137 2.61e+01 1evlA 401 2.62e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1cqa 133 2.63e+01 3nul d.110.1.1 40890 1o89A 345 2.64e+01 b.35.1.2,c.2.1.1 92644,92645 1ve9A 347 2.69e+01 c.4.1.2,d.16.1.3 100571,100572 1dioB 224 2.70e+01 1dioB c.51.3.1 33219 1vi2A 300 2.73e+01 c.2.1.7,c.58.1.5 100726,100727 1go3F 107 2.77e+01 a.60.8.2 65407 1enxA 190 2.77e+01 1axkA b.29.1.11 24325 1u55A 188 2.81e+01 d.278.1.1 107677 1vehA 92 2.82e+01 1jljA 189 2.90e+01 c.57.1.1 63169 1m5q1 130 2.96e+01 1pcp 106 2.98e+01 2pspA g.16.1.1,g.16.1.1 44742,44743 1emvA 86 2.99e+01 1cei a.28.2.1 16944 2arsA 262 2.99e+01 1gp6A 356 3.02e+01 b.82.2.1 65441 1lg2A 365 3.04e+01 c.1.8.5,d.26.3.1 77950,77951 1bjaA 95 3.07e+01 1bjaA a.4.5.9 16122 1jn5B 250 3.08e+01 d.17.4.2 66922 1xypA 190 3.15e+01 1axkA b.29.1.11 24327 1mfa 247 3.16e+01 1mfa b.1.1.1,b.1.1.1 19888,19889 2cx6A 90 3.18e+01 1z5bA 469 3.18e+01 1rxxA 421 3.24e+01 d.126.1.4 98061 2blfB 81 3.28e+01 1s57A 153 3.30e+01 1nstA 325 3.31e+01 1nstA c.37.1.5 31951 1ymqA 261 3.36e+01 1ihcA 188 3.46e+01 1di6A c.57.1.1 62379 2hddA 61 3.46e+01 2hddA a.4.1.1 15971 1vrmA 325 3.61e+01 1qysA 106 3.72e+01 k.41.1.1 96603 1xtqA 177 3.73e+01 1gp4A 356 3.73e+01 b.82.2.1 65439 1kao 167 3.76e+01 1ctqA c.37.1.8 32014 2a7yA 83 3.83e+01 1lssA 140 3.84e+01 c.2.1.9 74246 1qc7A 101 3.88e+01 1qc7A a.118.14.1 18456 2bc2A 227 3.89e+01 1a7tA d.157.1.1 42031 1wu7A 434 4.02e+01 1cfr 285 4.04e+01 1cfr c.52.1.7 33312 2bc2B 227 4.09e+01 1a7tA d.157.1.1 42032 1hkkA 364 4.11e+01 c.1.8.5,d.26.3.1 90634,90635 2g0qA 173 4.12e+01 1hddC 61 4.15e+01 2hddA a.4.1.1 15978 1auz 116 4.15e+01 1auz c.13.2.1 30883 1rlmB 271 4.16e+01 2cviA 83 4.24e+01 1ffh 294 4.25e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1i1sA 96 4.29e+01 1bjaA a.4.5.9 16124 1cuk 203 4.33e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2pspA 106 4.42e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1xauA 122 4.47e+01 1raxA 115 4.50e+01 1lfdA d.15.1.5 37626 1rlmA 271 4.52e+01 1tlfA 301 4.55e+01 1tlfA c.93.1.1 35687 1asyA 490 4.56e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1enh 54 4.58e+01 2hddA a.4.1.1 15973 1bmc 221 4.58e+01 1a7tA d.157.1.1 42038 2ng1 293 4.61e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1wkbA 810 4.62e+01 1dbxA 158 4.67e+01 1dbuA d.116.1.1 40928 1z2kA 109 4.68e+01 1m9nA 613 4.70e+01 c.24.1.3,c.97.2.1 78870,78871 1m1cA 680 4.73e+01 e.42.1.1 78395 1y7pA 223 4.80e+01 2atxA 194 4.80e+01 1xppA 115 4.84e+01 1un8A 552 4.85e+01 c.119.1.2,a.208.1.1 103806,99661 1lsuA 147 4.95e+01 c.2.1.9 74250 1i1dA 161 4.97e+01 1i21A d.108.1.1 61526 1fxd 58 4.97e+01 1fxd d.58.1.4 38941 1x67A 146 4.98e+01 2d4pA 141 5.03e+01 1wb0A 445 5.12e+01 1wryA 121 5.12e+01 1xg8A 111 5.21e+01 1b7gO 340 5.21e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1nnwA 252 5.23e+01 d.159.1.5 80674 1jkgB 250 5.25e+01 d.17.4.2 66796 1z4rA 168 5.26e+01 1azsC 388 5.30e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 2dri 271 5.45e+01 2dri c.93.1.1 35637 1rfeA 162 5.54e+01 2f4nA 273 5.59e+01 1be3F 110 5.70e+01 1be3F f.27.1.1 43668 1z06A 189 5.82e+01 1fdi 715 5.87e+01 2napA b.52.2.2,c.81.1.1 26918,35326 1a1s 314 5.90e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1dbuA 158 5.98e+01 1dbuA d.116.1.1 40930 1ortA 335 6.02e+01 1othA c.78.1.1,c.78.1.1 35204,35205 2azjA 289 6.08e+01 1pguA 615 6.11e+01 b.69.4.1,b.69.4.1 88069,88070 1vjeA 166 6.16e+01 d.185.1.2 100807 1hw8A 467 6.17e+01 1dqaA d.58.20.1,d.179.1.1 61298,61299 1qlmA 316 6.18e+01 1qlmA d.147.1.1 41765 2a9gA 418 6.20e+01 1l9kA 305 6.30e+01 c.66.1.25 84569 1g8mA 593 6.30e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1ipiA 123 6.33e+01 c.52.1.18 66255 1eg3A 261 6.34e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1z5oA 242 6.39e+01 1tfe 145 6.54e+01 1tfe d.43.1.1 38680 1tazA 365 6.59e+01 a.211.1.2 106734 1fdo 715 6.62e+01 2napA b.52.2.2,c.81.1.1 26917,35325 1e8aA 91 6.63e+01 1b4cA a.39.1.2 17188 1efaA 333 6.71e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1ufkA 254 6.71e+01 c.66.1.39 99340 1zpwX 90 6.76e+01 1eayC 74 6.78e+01 1eayC d.58.24.1 39386 1jyeA 349 6.79e+01 c.93.1.1 67455 1odkA 235 6.80e+01 c.56.2.1 86863 1q2wA 308 6.81e+01 b.47.1.4 88355 1r7jA 95 6.83e+01 a.4.5.49 104836 1x9zA 188 6.85e+01 1a43 87 6.86e+01 1a8o a.28.3.1 16955 2gnoA 305 6.89e+01 1vqoX 92 6.93e+01 1u8zA 168 6.98e+01 1if1A 113 6.98e+01 2irfG a.4.5.23 16183 2ligA 164 7.01e+01 1vls a.24.2.1 16530 1innA 166 7.02e+01 1j98A d.185.1.2 62608 1akq 147 7.20e+01 5nul c.23.5.1 31159 1gefA 123 7.32e+01 1gefA c.52.1.18 60465 1uqrA 154 7.32e+01 c.23.13.1 99779 1whrA 124 7.38e+01 2ftrA 108 7.47e+01 1s72X 92 7.55e+01 d.29.1.1 105343 1azl 147 7.57e+01 5nul c.23.5.1 31154 1tidB 119 7.59e+01 c.13.2.1 107000 1jj2W 91 7.64e+01 1ffkU d.29.1.1 63108 2h1nA 567 7.69e+01 1y5eA 169 7.75e+01 1lxdA 100 7.77e+01 1lfdA d.15.1.5 37624 1kjvB 100 7.79e+01 b.1.1.2 77423 1a0k 131 7.81e+01 3nul d.110.1.1 40892 1cjxA 357 7.93e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1uumA 372 7.93e+01 c.1.4.1 100010 1xo7A 166 7.94e+01 1lk9A 448 7.97e+01 c.67.1.1 78057 1kblA 873 8.01e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1gtrA 553 8.02e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1fwp 139 8.08e+01 1eayC d.58.24.1 39396 1aa8A 347 8.10e+01 1an9A 1z5nA 242 8.11e+01 1xnb 185 8.12e+01 1axkA b.29.1.11 24308 1zejA 293 8.13e+01 1aszB 490 8.14e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1o6jA 150 8.15e+01 c.47.1.10 81089 1wzcA 249 8.20e+01 1ls1A 295 8.24e+01 a.24.13.1,c.37.1.10 78170,78171 1d1qA 161 8.24e+01 1dg9A c.44.1.1 32642 1kz7A 353 8.25e+01 a.87.1.1,b.55.1.1 73333,73334 1f4pA 147 8.28e+01 5nul c.23.5.1 59651 2dcyA 185 8.29e+01 3nul 130 8.33e+01 3nul d.110.1.1 40891 1xc3A 302 8.34e+01 1v7wA 807 8.36e+01 a.102.1.4,b.30.5.3 108411,108412 1b5m 84 8.36e+01 1cyo d.120.1.1 41073 1p99A 295 8.39e+01 c.94.1.1 94384 1ygmA 118 8.40e+01 1pch 88 8.41e+01 1ptf d.94.1.1 40564 1fyhA 258 8.45e+01 1d9cA a.26.1.3,a.26.1.3 16907,16908 1uby 367 8.47e+01 1uby a.128.1.1 19435 2iv2X 715 8.50e+01 1xt8A 292 8.52e+01 1i4yA 114 8.53e+01 2mhr a.24.4.1 61738 1np6A 174 8.61e+01 c.37.1.10 85954 1upkA 341 8.62e+01 a.118.1.15 99758 1ash 150 8.71e+01 1ash a.1.1.2 15622 1wosA 364 8.72e+01 b.44.2.1,d.250.1.1 109468,109469 1nmtA 392 8.74e+01 1nmtA d.108.1.2,d.108.1.2 40823,40824 1dqaC 467 8.78e+01 1dqaA d.58.20.1,d.179.1.1 39366,42587 1xhdA 173 8.82e+01 1m1hA 248 8.85e+01 b.114.1.1,d.58.42.1 78415,78416 1jo0A 98 8.88e+01 d.68.4.1 77140 1odoA 408 8.97e+01 a.104.1.1 92783