# 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 2fneA 117 1.46e-16 2fe5A 94 3.85e-15 1bfeA 119 4.55e-15 1pdr b.36.1.1 24775 2fcfA 103 6.22e-15 1tp5A 119 6.56e-15 1be9A 119 9.47e-15 1pdr b.36.1.1 24774 1pdr 99 1.37e-14 1pdr b.36.1.1 24771 1i92A 91 1.65e-14 1pdr b.36.1.1 61990 1qavA 90 2.64e-14 1qauA b.36.1.1 24777 1g9oA 91 2.69e-14 1pdr b.36.1.1 60400 1ihjA 98 1.07e-13 1pdr b.36.1.1 62382 1n7eA 97 1.69e-13 b.36.1.1 91691 1q3oA 109 1.95e-13 b.36.1.1 95700 2h2bA 107 2.22e-13 1n7fA 97 2.24e-13 b.36.1.1 91692 2f0aA 98 6.90e-13 1l6oA 95 7.23e-13 b.36.1.1 84534 1wf7A 103 9.25e-13 1mfgA 95 1.31e-12 b.36.1.1 79043 1qauA 112 1.45e-12 1qauA b.36.1.1 24779 1qavB 115 1.52e-12 1qauA b.36.1.1 24780 2h3lA 103 1.61e-12 1v5lA 103 1.64e-12 b.36.1.1 108378 1b8qA 127 7.20e-12 1qauA b.36.1.1 24781 1kwaB 88 7.56e-12 1kwaA b.36.1.1 24773 1nf3C 128 8.16e-12 b.36.1.1 85596 1kwaA 88 8.18e-12 1kwaA b.36.1.1 24772 1i16 130 1.11e-11 1i16 b.36.1.2 24787 1n99A 166 3.85e-11 b.36.1.1,b.36.1.1 85459,85460 2f5yA 91 5.56e-11 1m5zA 91 7.03e-11 b.36.1.1 78676 1r6jA 82 2.99e-09 b.36.1.1 97151 1nteA 82 5.24e-09 b.36.1.1 86163 1fc6A 388 1.30e-07 1fc6A b.36.1.3,c.14.1.2 64738,64739 1lcyA 325 2.79e-06 b.36.1.4,b.47.1.1 73834,73835 1te0A 318 1.34e-05 1ky9B 448 3.43e-05 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1sotA 320 8.11e-05 b.36.1.4,b.47.1.1 105852,105853 1ky9A 448 1.24e-04 b.36.1.4,b.47.1.1 73198,73199 1y8tA 324 1.31e-03 1db3A 372 2.47e-01 1db3A c.2.1.2 29813 2a6tA 271 4.51e-01 1a6f 119 9.61e-01 1a6f d.14.1.2 37564 1lw6I 64 1.02e+00 d.40.1.1 74294 1cis 66 1.14e+00 2sniI k.1.1.1 46375 1t6t1 118 1.44e+00 1coaI 64 1.54e+00 2sniI d.40.1.1 38574 1d6tA 117 1.61e+00 1a6f d.14.1.2 37565 1to2I 64 1.67e+00 1fmaE 150 1.80e+00 1fmaE d.41.5.1 38630 1fm0E 150 1.80e+00 1fmaE d.41.5.1 38629 2sniI 83 2.11e+00 2sniI d.40.1.1 38573 1reqD 637 2.11e+00 1reqB c.1.19.1,c.23.6.1 29623,31250 7reqB 637 2.17e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 1reqB 637 2.47e+00 1reqB c.1.19.1,c.23.6.1 29621,31248 1vpqA 273 2.67e+00 1d4vB 163 3.18e+00 1d4vB b.22.1.1 23884 2d4pA 141 3.73e+00 1l1dA 152 4.42e+00 b.88.1.3 73452 2bh4X 134 4.70e+00 1dg6A 191 5.47e+00 1d4vB b.22.1.1 23883 1bx4A 345 5.59e+00 1bx4A c.72.1.1 34935 1koe 172 5.72e+00 1koe d.169.1.5 42448 2f51A 118 6.06e+00 3tmkA 216 6.21e+00 3tmkA c.37.1.1 31920 2c9wA 169 6.40e+00 1cv8 174 6.59e+00 1cv8 d.3.1.1 37089 2cc0A 195 6.89e+00 1rypH 205 7.07e+00 d.153.1.4 41876 1h6kA 757 7.45e+00 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1zckA 154 7.83e+00 1x24A 180 8.02e+00 2bshA 125 8.14e+00 1kw4A 89 8.86e+00 a.60.1.2 73077 1ypcI 64 8.93e+00 2sniI d.40.1.1 38570 1h05A 146 8.98e+00 c.23.13.1 76433 1gph1 465 9.20e+00 1ecfB 1axiA 191 9.31e+00 1huw a.26.1.1 16832 1ujqA 305 9.51e+00 c.1.12.7 99463 2bhoA 130 9.64e+00 1nmeA 146 9.64e+00 c.17.1.1 85874 2bsjA 133 1.01e+01 3sxlA 184 1.07e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1yjmA 110 1.07e+01 1a22A 180 1.11e+01 1huw a.26.1.1 16833 1rxdA 159 1.11e+01 1fxlA 167 1.15e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1t9iA 163 1.15e+01 1uzcA 71 1.18e+01 a.159.2.1 100222 1ujxA 119 1.29e+01 b.26.1.2 99473 1py5A 326 1.29e+01 d.144.1.7 104389 1uc2A 481 1.30e+01 d.261.1.1 99161 1bxeA 113 1.33e+01 1bxeA d.55.1.1 38898 1ju5A 109 1.37e+01 d.93.1.1 77173 1evlA 401 1.38e+01 1qf6A c.51.1.1,d.104.1.1 33202,40751 1pauA 147 1.39e+01 1pauA c.17.1.1 30994 1xewY 172 1.41e+01 1ciqA 40 1.42e+01 2sniI d.40.1.1 38576 1ojhA 65 1.42e+01 a.214.1.1 103976 1cot 129 1.43e+01 1ycc a.3.1.1 15899 1uh5A 329 1.46e+01 c.2.1.2 107840 1r6xA 395 1.46e+01 b.122.1.3,c.26.1.5 97167,97168 1pueE 89 1.49e+01 1awcA a.4.5.21 16165 1l3iA 192 1.51e+01 c.66.1.22 77676 1k4mA 213 1.52e+01 c.26.1.3 77258 1jjtA 228 1.52e+01 1a7tA d.157.1.1 63139 1sfjA 238 1.53e+01 1b6cB 342 1.54e+01 1b6cB d.144.1.7 41673 1b7fA 168 1.56e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1h2vC 771 1.58e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1n0qA 93 1.59e+01 k.37.1.1 79754 1sflA 238 1.61e+01 1rypL 212 1.62e+01 d.153.1.4 41880 1unkA 87 1.62e+01 1cei a.28.2.1 16935 1ifyA 49 1.62e+01 a.5.2.1 71207 1mwrA 646 1.65e+01 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1fdr 248 1.67e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2bw3A 534 1.67e+01 2brfA 110 1.67e+01 1zq9A 285 1.68e+01 1gjjA 168 1.68e+01 a.140.1.1,a.140.1.1 83291,83292 1qw2A 102 1.69e+01 d.249.1.1 96456 1yy6A 155 1.71e+01 1z8gA 372 1.72e+01 1vqqA 646 1.72e+01 1vj0A 380 1.74e+01 b.35.1.2,c.2.1.1 100786,100787 2fojA 155 1.74e+01 1r13A 148 1.81e+01 d.169.1.1,h.1.1.1 96782,96783 1g7sA 594 1.81e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1mwsA 646 1.85e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 2axcA 264 1.85e+01 1zhvA 134 1.86e+01 2tmkA 216 1.86e+01 3tmkA c.37.1.1 31928 1yf3A 259 1.86e+01 2dhqA 146 1.89e+01 2dhqA c.23.13.1 31382 2f5tX 233 1.90e+01 1zn8A 180 1.98e+01 1q0sA 259 1.98e+01 c.66.1.28 95509 1z3eA 132 2.03e+01 1iyu 79 2.03e+01 1iyu b.84.1.1 28227 155c 135 2.04e+01 1ycc a.3.1.1 15900 2sxl 88 2.08e+01 1b7fA d.58.7.1 39179 1pk1B 89 2.10e+01 1al6 437 2.12e+01 1csh a.103.1.1 18885 1vjyA 303 2.13e+01 d.144.1.7 108633 1txvA 452 2.25e+01 1amz 435 2.26e+01 1csh a.103.1.1 18884 1vekA 84 2.27e+01 1g2hA 61 2.31e+01 1g2hA a.4.1.12 60224 1zclA 180 2.34e+01 1cp3A 277 2.36e+01 1pauA c.17.1.1 30992 1js8A 394 2.38e+01 a.86.1.1,b.112.1.1 67219,67220 1p99A 295 2.40e+01 c.94.1.1 94384 1fxkC 133 2.44e+01 1fxkC a.2.5.1 15702 1yi9A 309 2.50e+01 1csh 435 2.53e+01 1csh a.103.1.1 18880 1g7tA 594 2.53e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 2ffuA 501 2.54e+01 1iruK 201 2.57e+01 d.153.1.4 71362 1rrmA 386 2.59e+01 e.22.1.2 105081 1q7hA 153 2.62e+01 b.122.1.1,d.17.6.2 96042,96043 1h9fA 57 2.69e+01 1h9fA a.140.1.1 60826 1xtmA 175 2.79e+01 2ahqA 76 2.80e+01 1yeyA 444 2.81e+01 1g65K 211 2.83e+01 d.153.1.4 41907 1z1dA 103 2.89e+01 1nkqA 259 2.92e+01 d.177.1.1 103862 2b4aA 138 2.95e+01 1s4iA 175 2.95e+01 1prcH 259 2.99e+01 6prcH b.41.1.1,f.23.10.1 25460,43445 1viuA 203 3.00e+01 d.113.1.1 100771 1cei 94 3.03e+01 1cei a.28.2.1 16939 1kk1A 410 3.13e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1wqsA 173 3.18e+01 1rutX 188 3.23e+01 1fxrA 64 3.29e+01 1fxd d.58.1.4 38993 1fvrA 327 3.36e+01 d.144.1.7 60047 1d1nA 99 3.36e+01 1d1nA b.43.3.1 25718 1b4aA 149 3.36e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1ao0A 459 3.38e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1dxrH 258 3.38e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1xtlA 175 3.43e+01 1mzbA 136 3.47e+01 a.4.5.42 91497 1g7rA 594 3.49e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 1jvwA 167 3.53e+01 d.26.1.1 71907 1xv5A 401 3.56e+01 1zuoA 186 3.65e+01 1ti6A 875 3.69e+01 b.52.2.2,c.81.1.1 106974,106975 1dvoA 152 3.71e+01 1dvoA a.136.1.1 19623 6prcH 258 3.71e+01 6prcH b.41.1.1,f.23.10.1 25457,43436 1diiC 80 3.72e+01 1diiC a.3.1.1 15925 1q67A 231 3.89e+01 b.55.1.7 95960 1aod 289 3.97e+01 2plc c.1.18.2 29615 1liuA 528 4.02e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 1pgvA 197 4.03e+01 c.10.1.1 88073 1jnyA 435 4.06e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1t3qB 788 4.10e+01 d.41.1.1,d.133.1.1 106369,106370 1wwkA 307 4.11e+01 1or7A 194 4.11e+01 a.4.13.2,a.177.1.1 87332,87333 1rxwA 336 4.13e+01 a.60.7.1,c.120.1.2 98059,98060 1a79A 171 4.18e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1phm 310 4.20e+01 1phm b.121.1.2,b.121.1.2 59015,59016 1rz2A 254 4.29e+01 b.100.1.1 105130 1p57B 255 4.35e+01 b.47.1.2 94126 1dpuA 99 4.40e+01 1dpuA a.4.5.16 16150 2dvh 79 4.45e+01 1c53 a.3.1.1 15803 1dvh 79 4.48e+01 1c53 a.3.1.1 15802 1fpkA 335 4.48e+01 1frpA e.7.1.1 42930 1sw5A 275 4.50e+01 c.94.1.1 106069 1o54A 277 4.54e+01 c.66.1.13 92482 1aaj 105 4.58e+01 1aac b.6.1.1 22841 1fr3A 67 4.71e+01 1fr3A b.40.6.1 25436 1aac 105 4.72e+01 1aac b.6.1.1 22838 1oroA 213 4.74e+01 1opr c.61.1.1 34093 1g5tA 196 4.77e+01 1g5rA c.37.1.11 32366 1cq3A 233 4.79e+01 1cq3A b.27.1.1 23923 2gm5A 139 4.80e+01 1mq7A 154 4.87e+01 b.85.4.1 79404 1h3fA 432 4.88e+01 c.26.1.1,d.66.1.4 76631,76632 1j5eK 129 4.89e+01 c.55.4.1 71554 1dulA 69 4.90e+01 1dulA a.36.1.1 17121 1i4jA 110 4.90e+01 d.55.1.1 76734 1sw5B 275 4.91e+01 c.94.1.1 106070 1m5dA 263 4.91e+01 c.94.1.1 78641 1bxaA 105 4.99e+01 1aac b.6.1.1 22839 1ialA 453 5.03e+01 1bk5A a.118.1.1 19116 1hssA 124 5.04e+01 1bea a.52.1.2 17819 1vzyA 291 5.06e+01 1qhlA 227 5.09e+01 1qhlA c.37.1.12 32382 1qadA 111 5.09e+01 1qadA d.93.1.1 40498 5fbpA 335 5.10e+01 1frpA e.7.1.1 42873 1nwbA 124 5.12e+01 b.124.1.1 86296 1uwdA 103 5.13e+01 2fp4B 395 5.20e+01 1mqdA 261 5.37e+01 c.94.1.1 85049 1wveC 80 5.39e+01 2as0A 396 5.45e+01 2b0vA 153 5.46e+01 1earA 147 5.46e+01 b.107.1.1,d.58.38.1 64875,64876 2crvA 120 5.50e+01 1sfdA 105 5.59e+01 b.6.1.1 105480 1h9oA 112 5.61e+01 1qadA d.93.1.1 60837 1d4oA 184 5.71e+01 1d4oA c.31.1.4 31748 1avaC 181 5.80e+01 1avaC b.42.4.1 25604 1aipC 196 5.86e+01 1tfe a.5.2.2,d.43.1.1 58930,58931 2btvA 901 5.91e+01 2btvA e.28.1.1 43376 1nykA 165 5.96e+01 b.33.1.1 86408 1fpzA 212 6.00e+01 1fpzA c.45.1.1 59976 1iscA 192 6.01e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1r61A 207 6.06e+01 c.8.8.1 97138 1a62 130 6.09e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1cliA 345 6.11e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1d2qA 173 6.13e+01 1d4vB b.22.1.1 23894 1eudB 396 6.16e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1hra 81 6.21e+01 2nllB g.39.1.2 45130 1k8wA 327 6.24e+01 b.122.1.1,d.265.1.2 83094,90388 1sdwA 314 6.35e+01 b.121.1.2,b.121.1.2 98810,98811 1wi9A 72 6.39e+01 1uc8A 280 6.46e+01 c.30.1.6,d.142.1.7 99165,99166 1m5eA 263 6.48e+01 c.94.1.1 78642 1x3mA 415 6.49e+01 1yg2A 179 6.51e+01 1gky 187 6.57e+01 1gky c.37.1.1 31839 1um0A 365 6.59e+01 d.258.1.1 107942 1xsvA 113 6.63e+01 1wmiA 90 6.67e+01 2fsxA 148 6.70e+01 1mkmA 249 6.77e+01 a.4.5.33,d.110.2.2 79242,79243 2bsyA 278 6.82e+01 1sknP 92 6.85e+01 1sknP a.37.1.1 17127 1l7bA 92 6.88e+01 c.15.1.2 91053 1r62A 160 6.88e+01 d.122.1.3 104816 1foaA 348 6.90e+01 1foaA c.68.1.10 59929 1cseI 71 6.93e+01 1egpA d.40.1.1 38559 1xo5A 183 6.93e+01 3chy 128 6.97e+01 3chy c.23.1.1 31038 2d9iA 96 6.99e+01 2gu3A 136 7.09e+01 1ufkA 254 7.12e+01 c.66.1.39 99340 1at0 145 7.15e+01 1at0 b.86.1.1 28374 1isaA 192 7.27e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1qexA 288 7.29e+01 1qexA b.32.1.1 24425 1mqiA 263 7.30e+01 c.94.1.1 91398 1k4iA 233 7.35e+01 d.115.1.2 72056 1semA 58 7.38e+01 1ckaA b.34.2.1 24544 1z5yE 149 7.43e+01 1avv 151 7.44e+01 1efnB d.102.1.1 40703 1mkp 144 7.47e+01 1vhrA c.45.1.1 32654 1sixA 174 7.50e+01 b.85.4.1 98892 1ztdA 133 7.56e+01 1jpaA 312 7.57e+01 d.144.1.7 67011 1f3z 161 7.60e+01 1gpr b.84.3.1 28273 1ebuA 358 7.61e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1yloA 348 7.66e+01 2iu4A 336 7.67e+01 2db1A 118 7.67e+01 2f9fA 177 7.70e+01 1xv2A 237 7.72e+01 1qbiA 454 7.78e+01 1c9uA b.68.2.1 27619 1id2A 106 7.78e+01 1aac b.6.1.1 62288 1qj2C 285 7.78e+01 1qj2C 1ci9A 392 7.90e+01 e.3.1.1 64767 1qo0D 196 7.90e+01 1qo0D c.23.1.3 31125 2affA 120 7.93e+01 2csbA 519 7.97e+01 1duxC 94 8.06e+01 1awcA a.4.5.21 16170 1v5iB 76 8.16e+01 1ldtL 46 8.20e+01 1tgsI g.68.1.1 44722 1n3jA 119 8.22e+01 b.85.7.2 79963 2c5qA 240 8.23e+01 1pswA 348 8.24e+01 c.87.1.7 88287 1b43A 340 8.24e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2bnfB 241 8.27e+01 1cye 129 8.38e+01 3chy c.23.1.1 31077 1epwA 1290 8.41e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1kz8A 337 8.46e+01 e.7.1.1 77633 1ueoA 63 8.46e+01 j.107.1.1 99269 1id3B 102 8.55e+01 a.22.1.1 66113 1ql3A 99 8.55e+01 1ycc a.3.1.1 15822 1fo8A 343 8.61e+01 1foaA c.68.1.10 59927 1qapA 296 8.65e+01 1qpoA c.1.17.1,d.41.2.1 29559,38595 1glaF 168 8.66e+01 1gpr b.84.3.1 28274 2matA 264 8.66e+01 1c24A d.127.1.1 41146 1e0tA 470 8.70e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1he1A 135 8.71e+01 1he1A a.24.11.1 16641 1yb2A 275 8.72e+01 2ggcA 263 8.72e+01 1kjyB 36 8.77e+01 1yg9A 330 8.78e+01 1ggrA 168 8.82e+01 1gpr b.84.3.1 28279 1ex7A 186 8.83e+01 1gky c.37.1.1 59537 2napA 723 8.88e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1lcjA 109 8.90e+01 1qadA d.93.1.1 40414 1cb7B 483 8.90e+01 1cb7B c.1.19.2 29648 2pleA 105 8.94e+01 1qadA d.93.1.1 40522 1sv6A 269 8.99e+01 d.177.1.1 106043