# 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 1s5uA 138 3.37e-18 d.38.1.1 98573 1z54A 132 1.01e-17 2gf6A 135 8.96e-16 1lo7A 141 9.91e-16 d.38.1.1 74144 1bvqA 141 1.16e-15 1bvqA d.38.1.1 38542 2cyeA 133 1.51e-15 1njkA 156 6.47e-15 d.38.1.1 85818 2av9A 147 2.25e-13 2aliA 158 1.65e-12 1yliA 153 5.21e-08 1vpmA 169 2.38e-07 2h4uA 145 3.14e-06 2b3nA 159 8.55e-06 2gvhA 288 1.40e-05 1u1zA 168 2.88e-05 d.38.1.6 107602 1ixlA 131 4.37e-05 d.38.1.5 90717 1zkiA 133 1.74e-04 2essA 248 2.22e-04 1j1yA 136 2.74e-04 d.38.1.5 90776 1wluA 136 3.89e-04 2fs2A 151 4.13e-04 1psuA 140 5.64e-04 d.38.1.5 88285 2cwzA 141 7.90e-04 2b6eA 146 1.30e-03 1c8uA 285 1.38e-03 1c8uA d.38.1.3,d.38.1.3 38547,38548 1o0iA 138 2.28e-03 d.38.1.5 86532 1iq6A 134 3.30e-03 d.38.1.4 76755 1q4uA 151 1.17e-02 d.38.1.5 95828 1t82A 155 1.64e-02 d.38.1.5 106639 1vh5A 148 1.89e-02 d.38.1.5 100642 1z6bA 154 4.88e-02 2bi0A 337 1.98e-01 2arsA 262 6.84e-01 1f8rA 498 1.10e+00 1f8rA c.3.1.2,d.16.1.5 30410,37974 1zxkA 98 1.16e+00 1f3mA 80 1.61e+00 1f3mA j.66.1.1 46358 2c8mA 262 1.75e+00 1ieaA 192 1.96e+00 1iakA b.1.1.2,d.19.1.1 21631,38205 1ah9 71 1.99e+00 1ah9 b.40.4.5 25330 1adqL 213 2.00e+00 8fabA b.1.1.1,b.1.1.2 20272,21272 1neu 124 2.21e+00 1neu b.1.1.1 19704 1u8fO 335 2.40e+00 1fngA 192 3.31e+00 1iakA b.1.1.2,d.19.1.1 59904,59905 1pn2A 280 3.90e+00 d.38.1.4,d.38.1.4 94930,94931 1fneA 192 4.13e+00 1iakA b.1.1.2,d.19.1.1 59896,59897 1u7kA 131 4.40e+00 4xiaA 393 4.49e+00 4xis c.1.15.3 29439 2bnkA 67 4.92e+00 1owqA 361 5.45e+00 c.1.8.5,d.26.3.1 104041,104042 1cye 129 5.93e+00 3chy c.23.1.1 31077 1widA 130 6.05e+00 1hr0W 71 6.08e+00 1ah9 b.40.4.5 25329 1e8yA 966 6.54e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1xj4A 119 6.55e+00 1rbp 182 6.84e+00 1aqb b.60.1.1 27085 1fmaD 81 6.92e+00 1fmaD d.15.3.1 37643 1fm0D 81 7.22e+00 1fmaD d.15.3.1 37642 1gkxA 388 7.44e+00 a.29.5.1,d.122.1.4 65266,65267 1xn8A 131 7.66e+00 1ztsA 139 7.69e+00 1gkzA 388 7.80e+00 a.29.5.1,d.122.1.4 65268,65269 1lswA 131 8.16e+00 d.110.3.2 78181 1mxmA 254 8.24e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 2c5rA 67 8.77e+00 1k2xB 143 9.16e+00 1drqA 131 9.35e+00 1drmA 1jbeA 128 9.58e+00 3chy c.23.1.1 62845 1g79A 218 1.02e+01 1ci0A b.45.1.1 25752 1drmA 131 1.02e+01 1drmA d.110.3.2 40908 3chy 128 1.05e+01 3chy c.23.1.1 31038 2fi9A 128 1.06e+01 1w66A 232 1.14e+01 1v6tA 255 1.15e+01 1hjxA 362 1.18e+01 c.1.8.5,d.26.3.1 83512,83513 1cj3A 392 1.27e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1v8yA 170 1.41e+01 1bgj 394 1.44e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1gm7A 209 1.44e+01 d.153.1.2 65302 2b7uA 257 1.45e+01 1aj8A 371 1.49e+01 1aj8A a.103.1.1 18900 2azpA 318 1.54e+01 1uok 558 1.66e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1pbe 394 1.74e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1te5A 257 1.74e+01 d.153.1.1 106795 1tyjA 170 1.81e+01 1vm7A 311 1.82e+01 c.72.1.1 108884 1tbuA 118 1.83e+01 1e6mA 128 1.90e+01 3chy c.23.1.1 31039 1dnlA 199 1.92e+01 1ci0A b.45.1.1 25753 1v93A 296 1.93e+01 c.1.23.1 100532 2crvA 120 1.96e+01 2fhi 147 2.01e+01 1fit d.13.1.1 37505 1ab5A 125 2.04e+01 3chy c.23.1.1 31056 1ajqA 209 2.06e+01 1ajqA d.153.1.2 41840 1ks2A 219 2.08e+01 c.124.1.4,d.58.40.1 72908,72909 1ai7A 209 2.09e+01 1ajqA d.153.1.2 41845 1kg0C 136 2.16e+01 d.169.1.1 72445 1r8gA 372 2.18e+01 d.128.1.3 104845 1p3dA 475 2.20e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1k0iA 394 2.22e+01 c.3.1.2,d.16.1.2 67942,67943 1csyA 112 2.24e+01 1lckA d.93.1.1 40519 1lkzA 219 2.24e+01 c.124.1.4,d.58.40.1 73991,73992 2aw4P 114 2.30e+01 1pnkA 209 2.31e+01 1ajqA d.153.1.2 41839 2bhoA 130 2.39e+01 1wgeA 83 2.50e+01 1hbq 183 2.57e+01 1aqb b.60.1.1 27078 1aqb 183 2.58e+01 1aqb b.60.1.1 27084 1pkp 150 2.60e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1e3aA 260 2.64e+01 1ajqA d.153.1.2 41838 1ab6A 125 2.65e+01 3chy c.23.1.1 31054 1gk9A 260 2.72e+01 d.153.1.2 65246 1ww7A 160 2.74e+01 1uj6A 227 2.74e+01 c.124.1.4,d.58.40.1 107898,107899 1pp7U 131 2.91e+01 a.4.5.44 94973 2phh 394 2.92e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1cpq 129 2.93e+01 1cpq a.24.3.2 16556 2cu3A 64 3.02e+01 1avmA 201 3.04e+01 1avmA a.2.11.1,d.44.1.1 15782,38745 1n9lA 109 3.04e+01 d.110.3.6 85468 1bsmA 201 3.12e+01 1avmA a.2.11.1,d.44.1.1 15780,38743 1ug3A 339 3.15e+01 1fuiA 591 3.26e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1yveJ 524 3.26e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1gqyA 475 3.26e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1pmd 675 3.29e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1aohA 147 3.33e+01 1aohA b.2.2.2 22401 1a9v 129 3.38e+01 1a9v b.1.18.7 21946 1ftpA 133 3.43e+01 1hmt b.60.1.2 27199 1yveI 524 3.47e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 2btzA 394 3.55e+01 1spgB 147 3.56e+01 1cg5B a.1.1.2 15588 1hbp 183 3.62e+01 1aqb b.60.1.1 27079 1d06A 130 3.67e+01 1drmA d.110.3.2 40906 1ioaA 240 3.68e+01 1led b.29.1.1 24168 2ffjA 300 3.68e+01 1o8vA 134 3.72e+01 b.60.1.2 86680 1b4eA 323 3.72e+01 1b4kA c.1.10.3 29186 1rot 149 3.73e+01 1fkj d.26.1.1 38429 1ew0A 130 3.73e+01 1drmA d.110.3.2 40905 1m3sA 186 3.75e+01 c.80.1.3 78573 1b2wL 214 3.85e+01 8fabA b.1.1.1,b.1.1.2 20306,21298 1a8uA 277 3.87e+01 1brt c.69.1.12 34703 1bcpC 199 3.90e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1vcaA 202 3.91e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1aqdA 192 3.92e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1ka8A 100 3.92e+01 a.4.5.20 72241 1broA 277 4.02e+01 1brt c.69.1.12 34700 1ew3A 159 4.04e+01 1mup b.60.1.1 27114 1yopA 83 4.04e+01 1f56A 91 4.06e+01 2cbp b.6.1.1 22896 1qp2A 70 4.08e+01 1pse b.34.4.2 24596 2eu8A 216 4.11e+01 1oe4A 247 4.14e+01 c.18.1.3 86895 1hjsA 332 4.15e+01 c.1.8.3 83492 1xodA 118 4.16e+01 1aijL 281 4.26e+01 6prcL f.26.1.1 43461 1iuhA 198 4.28e+01 d.61.1.2 83711 2fd5A 180 4.32e+01 1gai 472 4.33e+01 1ayx a.102.1.1 18819 1v4sA 455 4.41e+01 c.55.1.3,c.55.1.3 100309,100310 1blr 137 4.42e+01 1hmt b.60.1.2 27208 1cmbA 104 4.45e+01 1cmbA a.43.1.5 17460 1ktjA 129 4.45e+01 b.1.18.7 72974 1wwuA 99 4.53e+01 2cevA 299 4.60e+01 1d3vA c.42.1.1 32576 1ykjA 394 4.61e+01 1bv1 159 4.66e+01 1bv1 d.129.3.1 41313 2bz8A 58 4.69e+01 1ywsA 82 4.72e+01 1cmcA 104 4.72e+01 1cmbA a.43.1.5 17462 1pnj 86 4.84e+01 1ckaA b.34.2.1 24487 1myn 44 4.87e+01 1gpt g.3.7.4 44172 1jf0A 195 4.88e+01 1ej3A a.39.1.5 62926 1gm6A 175 5.01e+01 b.60.1.1 70272 1pht 85 5.03e+01 1ckaA b.34.2.1 24483 1cmaA 104 5.10e+01 1cmbA a.43.1.5 17486 1ckaA 57 5.17e+01 1ckaA b.34.2.1 24459 1s9rA 410 5.19e+01 d.126.1.4 98758 1reoA 486 5.21e+01 c.3.1.2,d.16.1.5 97325,97326 1wisA 124 5.25e+01 1q6hA 224 5.26e+01 d.26.1.1 95975 1p3jA 217 5.28e+01 c.37.1.1,g.41.2.1 94022,94023 1lxyA 409 5.29e+01 d.126.1.4 91154 2b59A 187 5.29e+01 1xyiA 66 5.33e+01 1kt6A 183 5.34e+01 b.60.1.1 84466 1hvyA 288 5.35e+01 1bkpA d.117.1.1 41049 1oahA 519 5.42e+01 a.138.1.3 86736 1octC 156 5.42e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1glm 470 5.44e+01 1ayx a.102.1.1 18821 1l6sA 323 5.47e+01 c.1.10.3 73627 1qmgA 524 5.64e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 2ax4A 198 5.65e+01 1n3jA 119 5.66e+01 b.85.7.2 79963 1cdi 179 5.67e+01 1cdy b.1.1.1,b.1.1.3 19727,21666 1smoA 119 5.72e+01 b.1.1.1 105764 1kmnD 424 5.83e+01 1adjA c.51.1.1,d.104.1.1 33185,40734 2booA 247 5.84e+01 2bsjA 133 5.84e+01 1sh8A 154 5.85e+01 d.38.1.5 105549 1rreA 200 5.88e+01 d.14.1.10 97791 2bm3A 166 5.89e+01 2ftbA 125 5.91e+01 2cwpA 112 5.92e+01 1qidA 537 5.92e+01 2bce c.69.1.1 34593 1brt 277 5.93e+01 1brt c.69.1.12 34699 1y8aA 332 6.03e+01 1txqA 93 6.05e+01 3cd4 182 6.10e+01 1cdy b.1.1.1,b.1.1.3 19720,21659 2ewrA 170 6.19e+01 1y8oA 419 6.20e+01 1v32A 101 6.21e+01 a.42.1.1 100277 1sc6A 404 6.22e+01 1u2xA 474 6.24e+01 c.72.1.3 107622 1mpgA 282 6.28e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1x6vA 630 6.32e+01 1otvA 259 6.38e+01 a.132.1.4 93526 1jm6A 407 6.40e+01 a.29.5.1,d.122.1.4 66876,66877 1k77A 260 6.52e+01 c.1.15.5 72096 1azqA 66 6.55e+01 1azpA b.34.13.1 37469 2a74A 643 6.59e+01 1j5uA 136 6.62e+01 d.208.1.1 71584 1pytA 94 6.62e+01 1pytA d.58.3.1 39064 1p6pA 125 6.66e+01 b.60.1.2 87839 1rypC 244 6.72e+01 1rypC d.153.1.4 41934 1vxrA 537 6.76e+01 2bce c.69.1.1 34595 2a8jA 420 6.78e+01 1rzjG 321 6.79e+01 d.172.1.1 98200 1e66A 543 6.89e+01 c.69.1.1 59291 1vjqA 79 6.91e+01 k.43.1.1 100830 1j6oA 268 6.95e+01 c.1.9.12 77088 1u0tA 307 6.96e+01 e.52.1.1 107567 1azpA 66 6.97e+01 1azpA b.34.13.1 37467 1b07A 59 7.00e+01 1ckaA b.34.2.1 24461 1s2oA 244 7.12e+01 1ea5A 537 7.14e+01 2bce c.69.1.1 34592 1to6A 371 7.29e+01 c.141.1.1 107170 1ekyA 129 7.31e+01 1cpq i.11.1.1 46012 1v7lA 163 7.35e+01 1i8jA 323 7.35e+01 1b4kA c.1.10.3 61968 1luzA 88 7.40e+01 b.40.4.5 74271 1oxsC 353 7.40e+01 b.40.6.3,c.37.1.12 87519,87520 1dgwA 178 7.41e+01 1dgwA b.82.1.2 28090 1mjoA 104 7.41e+01 1cmbA a.43.1.5 17466 1jfuA 186 7.48e+01 c.47.1.10 62940 1aohB 147 7.50e+01 1aohA b.2.2.2 22402 1krs 120 7.52e+01 1krs b.40.4.1 25256 1rr9A 200 7.53e+01 d.14.1.10 97783 1adwA 123 7.55e+01 1bqk b.6.1.1 22893 1js8A 394 7.57e+01 a.86.1.1,b.112.1.1 67219,67220 1mqkH 127 7.64e+01 b.1.1.1 85053 1aihA 170 7.68e+01 1aihA d.163.1.1 42149 2fa8A 105 7.76e+01 1grj 158 7.77e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1nnjA 271 7.79e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1a62 130 7.88e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1oxxK 353 7.88e+01 b.40.6.3,c.37.1.12 93715,93716 1dbiA 280 7.93e+01 1gci c.41.1.1 32543 2db9A 149 7.93e+01 1jeoA 180 7.94e+01 c.80.1.3 66611 1g9mG 321 7.99e+01 1gc1G d.172.1.1 42492 1y2tA 142 8.01e+01 2cwcA 303 8.06e+01 1ywmA 200 8.06e+01 1jb0E 75 8.12e+01 1pse b.34.4.2 62824 1paz 123 8.16e+01 1bqk b.6.1.1 22878 1i3zA 103 8.26e+01 d.93.1.1 83667 1ymmA 191 8.27e+01 1ab2 109 8.27e+01 1lckA d.93.1.1 40506 1g9mC 185 8.31e+01 1cdy b.1.1.1,b.1.1.3 19721,21660 1b2vA 188 8.31e+01 1b2vA d.35.1.1 38532 1ymqA 261 8.45e+01 1mak 113 8.45e+01 8fabA b.1.1.1 19825 1pxfA 111 8.46e+01 b.40.4.4 88341 2bh1A 250 8.52e+01 1cauA 181 8.54e+01 1dgwA b.82.1.2 28102 1ospL 214 8.56e+01 32c2A b.1.1.1,b.1.1.2 20116,21146 1jftA 340 8.57e+01 a.35.1.5,c.93.1.1 66652,66653 2a72A 146 8.61e+01 1rzhL 281 8.62e+01 f.26.1.1 98164 1z5yE 149 8.66e+01 1gc1G 321 8.70e+01 1gc1G d.172.1.1 42493 1nf9A 207 8.72e+01 c.33.1.3 85631 1fd9A 213 8.74e+01 1fd9A d.26.1.1 59771 2cbp 96 8.81e+01 2cbp b.6.1.1 22895 1v05A 96 8.82e+01 1pse 69 8.84e+01 1pse b.34.4.2 24595 1dgrC 178 8.86e+01 1dgwA b.82.1.2 28100 1psdA 409 8.91e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1t5jA 313 8.92e+01 a.209.1.1 99125 1jjtA 228 8.92e+01 1a7tA d.157.1.1 63139 2bm8A 236 8.94e+01