# List of top-scoring protein chains for t2k-100-30-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 1mkmA 249 1.04e-27 a.4.5.33,d.110.2.2 79242,79243 2g7uA 257 1.01e-26 1yspA 181 1.55e-21 1td5A 202 3.60e-21 d.110.2.2 106767 1tf1A 198 5.07e-21 d.110.2.2 106826 1ysqA 193 2.47e-20 1q1hA 110 2.51e-03 a.4.5.41 95580 2fbhA 146 5.57e-03 2a61A 145 8.52e-03 1ulyA 192 8.69e-03 1ft9A 222 9.65e-03 1ft9A a.4.5.4,b.82.3.1 16107,28131 1j5yA 187 1.31e-02 a.4.5.1,d.94.2.1 71592,71593 2b0lA 102 3.19e-02 1smtB 122 4.25e-02 1smtA a.4.5.5 16110 1r1tA 122 4.60e-02 a.4.5.5 104769 1sfxA 109 4.68e-02 a.4.5.50 105505 1on2A 142 8.08e-02 a.4.5.24,a.76.1.1 87103,87104 1smtA 122 9.60e-02 1smtA a.4.5.5 16109 1qgpA 77 1.20e-01 1qbjA a.4.5.19 16158 2fnaA 357 1.20e-01 1u2wA 122 1.28e-01 1s3jA 155 1.99e-01 a.4.5.28 98437 2ethA 154 2.20e-01 2fxaA 207 3.00e-01 1qbjA 81 3.21e-01 1qbjA a.4.5.19 16155 1vd5A 377 3.51e-01 a.102.1.7 108518 1fpxA 352 3.64e-01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1lnwA 147 3.71e-01 a.4.5.28 78104 1fp2A 352 3.87e-01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1j75A 67 4.10e-01 a.4.5.19 62673 1lj9A 144 5.41e-01 a.4.5.28 78035 1r1uA 106 6.70e-01 a.4.5.5 104771 1qzzA 374 7.02e-01 a.4.5.29,c.66.1.12 96719,96720 1jgsA 138 7.11e-01 a.4.5.28 66683 2fv1A 377 7.32e-01 1bib 321 7.63e-01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1lvaA 258 8.39e-01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1mzbA 136 9.12e-01 a.4.5.42 91497 2fu4A 83 1.04e+00 2fbiA 142 1.48e+00 1b1bA 140 1.63e+00 1bi0 a.4.5.24,a.76.1.1 16215,18421 2gauA 232 1.70e+00 2fx0A 201 2.47e+00 1bia 321 2.49e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1h1yA 228 2.61e+00 c.1.2.2 76506 1r7jA 95 2.80e+00 a.4.5.49 104836 2acjA 66 2.85e+00 2cgpA 210 3.00e+00 2cgpA a.4.5.4,b.82.3.2 16102,28141 1td2A 287 3.07e+00 c.72.1.5 106765 2a2cA 478 3.15e+00 2a2dA 478 3.61e+00 1orjA 130 3.72e+00 a.24.19.1 93456 1f5mB 180 3.81e+00 1f5mB d.110.2.1 40896 1hw5A 210 4.06e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 1jc4A 148 4.15e+00 1jc4A d.32.1.4 62863 1xnpA 202 4.16e+00 1e2xA 243 4.28e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 1r5jA 337 4.49e+00 c.77.1.5 97097 2cglA 489 4.55e+00 1y0uA 96 4.62e+00 1vi9A 299 4.80e+00 c.72.1.5 100750 1qdlA 422 4.82e+00 1qdlA d.161.1.1 42088 1z91A 147 4.89e+00 1f5tA 121 5.22e+00 1bi0 a.4.5.24,a.76.1.1 16203,18409 1gkuB 1054 5.22e+00 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1hw1A 239 6.19e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1p4kA 295 6.30e+00 d.153.1.5 87772 1ub9A 100 6.47e+00 a.4.5.28 99159 1i6xA 209 6.47e+00 a.4.5.4,b.82.3.2 83673,83674 1mtyD 512 6.52e+00 1mhyD a.25.1.2 16742 1t5bA 201 6.54e+00 c.23.5.3 106433 1g6nA 210 6.69e+00 2cgpA a.4.5.4,b.82.3.2 16100,28139 1f5mA 180 7.31e+00 1f5mB d.110.2.1 40895 1mmoD 512 7.43e+00 1mhyD a.25.1.2 16770 1try 224 7.44e+00 5ptp b.47.1.2 26017 2af4C 333 7.53e+00 1pq7A 224 8.07e+00 b.47.1.2 95002 1ddnA 226 8.16e+00 1bi0 a.4.5.24,a.76.1.1 16207,18413 1qtqA 553 8.70e+00 1gtrA b.53.1.2,c.26.1.1 26940,31579 2f9zC 159 8.85e+00 1dceB 331 9.08e+00 1dceB a.102.4.3 18872 1j6wA 175 9.18e+00 1j98A d.185.1.2 62663 1gtrA 553 9.36e+00 1gtrA b.53.1.2,c.26.1.1 26939,31578 1ri7A 171 9.72e+00 a.4.5.32,d.58.4.2 97504,97505 1mqeA 207 1.00e+01 d.113.1.1 91394 1tikA 213 1.01e+01 c.23.5.3 107003 1a04A 215 1.04e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1sfuA 75 1.05e+01 a.4.5.19 105503 1fwkA 296 1.07e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1izcA 339 1.08e+01 c.1.12.5 83838 1h72C 296 1.08e+01 d.14.1.5,d.58.26.1 60712,60713 1fn8A 224 1.10e+01 5ptp b.47.1.2 26012 1bueA 265 1.11e+01 1btl e.3.1.1 42727 1k8kF 168 1.13e+01 d.198.2.1 68312 1c0wA 225 1.13e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2cfxA 144 1.21e+01 2cujA 108 1.23e+01 1z47A 355 1.30e+01 1oxxK 353 1.31e+01 b.40.6.3,c.37.1.12 93715,93716 2aieP 203 1.32e+01 9gafA 295 1.33e+01 1apyA d.153.1.5 42008 1yljA 263 1.35e+01 1mc0A 368 1.36e+01 d.110.2.1,d.110.2.1 78937,78938 1hqcA 324 1.36e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 1bi0 226 1.36e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1xd7A 145 1.43e+01 a.4.5.55 109566 1dcuA 357 1.43e+01 1frpA e.7.1.1 42943 1yyvA 131 1.43e+01 1fx7A 230 1.44e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1u55A 188 1.45e+01 d.278.1.1 107677 1i1gA 141 1.49e+01 a.4.5.32,d.58.4.2 65982,65983 1fy7A 278 1.52e+01 1fy7A d.108.1.1 40817 1ymiA 334 1.56e+01 2bjcA 62 1.62e+01 1oyzA 280 1.66e+01 a.118.1.16 93775 1inzA 148 1.75e+01 1eduA a.118.9.1 62610 1v38A 78 1.83e+01 a.60.1.2 100280 2f2eA 146 1.88e+01 1oxsC 353 1.90e+01 b.40.6.3,c.37.1.12 87519,87520 2napA 723 1.92e+01 2napA b.52.2.2,c.81.1.1 26926,35334 1xn7A 78 1.96e+01 1in4A 334 2.00e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1fmjA 351 2.07e+01 c.37.1.5 59879 1bg2 325 2.07e+01 1bg2 c.37.1.9 32189 1cg2A 393 2.08e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2bmaA 470 2.14e+01 2as9A 210 2.21e+01 1p4xA 250 2.22e+01 a.4.5.28,a.4.5.28 87784,87785 1vfsA 386 2.29e+01 b.49.2.2,c.1.6.1 108584,108585 1aj0 282 2.32e+01 1aj2 c.1.21.1 29667 2a8lA 420 2.38e+01 1wojA 214 2.39e+01 1v7nV 163 2.45e+01 a.26.1.2 100476 1zarA 282 2.53e+01 1ufmA 84 2.53e+01 a.4.5.47 107816 1ecl 597 2.54e+01 1ecl e.10.1.1 43238 1jwhA 337 2.58e+01 d.144.1.7 71913 1y0yA 353 2.59e+01 1bgvA 449 2.62e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1wdvA 152 2.64e+01 1z21A 112 2.83e+01 1zbsA 291 2.83e+01 1tqmA 282 3.01e+01 a.4.5.56,d.144.1.9 107236,107237 1k9vF 201 3.03e+01 c.23.16.1 68365 2cxbA 124 3.04e+01 1ycc a.3.1.1 15891 1i1sA 96 3.04e+01 1bjaA a.4.5.9 16124 1lm6A 215 3.08e+01 d.167.1.1 84628 1aozA 552 3.09e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 1ovnA 248 3.12e+01 a.71.1.1,c.47.1.7 93602,93603 1wu7A 434 3.18e+01 1mb1 130 3.22e+01 1bm8 d.34.1.1 38529 1hlvA 131 3.23e+01 a.4.1.7,a.4.1.7 65854,65855 1svdM 110 3.26e+01 1xfoA 357 3.28e+01 1tbxA 99 3.34e+01 a.4.5.48 106748 1b0nA 111 3.36e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 2dtr 226 3.37e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1cxc 124 3.37e+01 1ycc a.3.1.1 15890 1je8A 82 3.38e+01 a.4.6.2 77108 1r59O 505 3.39e+01 1k89 449 3.41e+01 1k89 c.2.1.7,c.58.1.1 30218,33866 1in6A 334 3.42e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1mw9X 592 3.53e+01 e.10.1.1 91480 1o5iA 249 3.53e+01 c.2.1.2 92499 1e32A 458 3.59e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1wd3A 482 3.62e+01 b.29.1.21,b.42.8.1 109233,109234 1jhfA 202 3.69e+01 a.4.5.2,b.87.1.1 63057,63058 1cjgA 62 3.70e+01 1pru a.35.1.5 17112 2bh7A 261 3.74e+01 1gpwB 201 3.75e+01 c.23.16.1 65461 2cw8A 537 3.80e+01 1lcdA 51 3.85e+01 1pru a.35.1.5 17111 2b5dX 528 4.00e+01 1b0uA 262 4.01e+01 1b0uA c.37.1.12 32370 1aurA 218 4.07e+01 1auoA c.69.1.14 34718 1jy8A 159 4.15e+01 d.79.5.1 67452 1bjaA 95 4.20e+01 1bjaA a.4.5.9 16122 1auoA 218 4.21e+01 1auoA c.69.1.14 34716 1hq0A 295 4.26e+01 1hzgA d.194.1.1 61122 1p0zA 131 4.29e+01 d.110.6.1 93882 1lmhA 184 4.33e+01 d.167.1.1 74036 2cmxA 118 4.33e+01 1lm4A 194 4.45e+01 d.167.1.1 84626 1lccA 51 4.53e+01 1pru a.35.1.5 17110 1yroB 286 4.54e+01 2cohA 202 4.62e+01 1a8p 258 4.62e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1hm5A 558 4.66e+01 c.80.1.2 76717 1ro2A 216 4.68e+01 d.264.1.2 97665 2a8jA 420 4.71e+01 1wj5A 120 4.72e+01 2d13A 227 4.72e+01 1zljA 78 4.73e+01 1lea 84 4.79e+01 1lea a.4.5.2 16085 2eshA 118 4.81e+01 1sqsA 242 4.81e+01 c.23.5.5 98968 2cygA 312 4.83e+01 1rypB 250 4.85e+01 1rypB d.153.1.4 41933 1lqc 56 4.86e+01 1pru a.35.1.5 17109 1o6eA 235 4.87e+01 b.57.1.1 81083 2tct 207 4.91e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1fa8A 135 4.95e+01 1qipA d.32.1.1 38486 1yveI 524 4.96e+01 1qmgA a.100.1.2,c.2.1.6 18789,30186 2h3bA 494 5.03e+01 1f3yA 165 5.05e+01 d.113.1.1 59635 1io0A 185 5.05e+01 c.10.1.1 76753 1dqrA 557 5.06e+01 1dqrA c.80.1.2 35305 1hzgA 295 5.11e+01 1hzgA d.194.1.1 61436 2cw5A 255 5.13e+01 1nf5B 286 5.17e+01 c.68.1.2 80454 1j8wB 273 5.29e+01 1txvA 452 5.40e+01 1u0fA 564 5.41e+01 1g7dA 106 5.48e+01 1g7dA a.71.1.1 18318 1g6aA 271 5.52e+01 1btl e.3.1.1 42704 1yw5A 177 5.60e+01 2c78A 405 5.61e+01 1nmmB 286 5.64e+01 c.68.1.2 80662 1f4kA 122 5.64e+01 1bm9A a.4.5.7 59646 1z67A 135 5.75e+01 1aup 449 5.81e+01 1k89 c.2.1.7,c.58.1.1 30222,33870 1gx1A 160 5.89e+01 d.79.5.1 70675 1ct9A 553 5.98e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1dw9A 156 5.98e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 1w7lA 422 6.07e+01 c.67.1.1 109226 1kdgA 546 6.12e+01 c.3.1.2,d.16.1.1 77337,77338 1mhyD 521 6.17e+01 1mhyD a.25.1.2 16780 1jkxA 212 6.21e+01 c.65.1.1 66813 1ro0A 216 6.33e+01 d.264.1.2 97664 1t6kA 278 6.35e+01 1eft 405 6.43e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1qmgA 524 6.53e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1ii6A 368 6.71e+01 1bg2 c.37.1.9 62413 1ug3A 339 6.74e+01 1f9zA 135 6.81e+01 1qipA d.32.1.1 38484 1id0A 152 6.89e+01 d.122.1.3 66111 1bjz 207 6.91e+01 2tct a.4.1.9,a.121.1.1 16065,19242 2cxnA 557 6.93e+01 1tns 76 6.96e+01 1qpmA a.6.1.7 16228 1sdjA 310 7.01e+01 d.21.1.2,d.21.1.2 98807,98808 2b0vA 153 7.03e+01 1dwkA 156 7.13e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1n8vA 112 7.16e+01 a.118.21.1 85457 1r0kA 388 7.26e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1rhcA 330 7.27e+01 c.1.16.3 97468 1kx9A 112 7.34e+01 a.118.21.1 77602 1xubA 298 7.36e+01 1zx4A 192 7.46e+01 2mysB 166 7.56e+01 1wdcB a.39.1.5 17308 1t33A 224 7.57e+01 a.4.1.9,a.121.1.1 106295,106296 1o4uA 285 7.71e+01 c.1.17.1,d.41.2.1 86624,86625 1a6i 217 7.71e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1uocA 289 7.74e+01 c.55.3.9 99686 1a4pA 96 7.79e+01 1b4cA a.39.1.2 17176 1dqeA 137 7.81e+01 1dqeA a.39.2.1 17388 1meoA 209 7.81e+01 c.65.1.1 79035 2givA 295 7.91e+01 1dpuA 99 7.94e+01 1dpuA a.4.5.16 16150 1zc6A 305 7.95e+01 1lqwA 183 7.95e+01 d.167.1.1 74210 1aj2 282 7.98e+01 1aj2 c.1.21.1 29665 1sffA 426 7.98e+01 c.67.1.4 105482 2dpg 485 8.03e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1dpgA 485 8.18e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 2a2lA 145 8.20e+01 1yveJ 524 8.27e+01 1qmgA a.100.1.2,c.2.1.6 18790,30187 1rd5A 262 8.27e+01 1iatA 557 8.31e+01 1dqrA c.80.1.2 62123 1omiA 248 8.39e+01 b.82.3.3,a.4.5.4 87079,87080 1k0gA 453 8.41e+01 d.161.1.1 67940 1z1dA 103 8.47e+01 1twdA 256 8.52e+01 c.1.30.1 107397 1ha3A 405 8.59e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1kwhA 492 8.59e+01 c.94.1.1 68876 1qz9A 416 8.62e+01 c.67.1.3 96621 1izmA 184 8.63e+01 a.199.1.1 90725 2czvC 120 8.71e+01 1qj5A 429 8.76e+01 1dtyA c.67.1.4 34493 1sbyA 254 8.79e+01 1ykwA 435 8.87e+01 1u1wA 298 8.98e+01 1m4jA 142 8.99e+01 d.109.1.2 78602