# List of top-scoring protein chains for t04-100-30-dssp-ehl2-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 1ri7A 171 1.63e-21 a.4.5.32,d.58.4.2 97504,97505 2cg4A 152 7.54e-20 2cfxA 144 5.76e-18 1sfxA 109 1.68e-05 a.4.5.50 105505 2a61A 145 7.11e-05 1s3jA 155 1.89e-04 a.4.5.28 98437 1ulyA 192 7.16e-04 2fbiA 142 1.28e-03 1xnpA 202 1.55e-03 1ub9A 100 1.61e-03 a.4.5.28 99159 2csbA 519 2.44e-03 2fbhA 146 3.43e-03 1je8A 82 3.74e-03 a.4.6.2 77108 2g7uA 257 4.35e-03 1j5yA 187 4.51e-03 a.4.5.1,d.94.2.1 71592,71593 1q1hA 110 5.30e-03 a.4.5.41 95580 1lj9A 144 5.75e-03 a.4.5.28 78035 1z91A 147 6.03e-03 2b0lA 102 7.10e-03 1p4xA 250 9.55e-03 a.4.5.28,a.4.5.28 87784,87785 1mkmA 249 1.11e-02 a.4.5.33,d.110.2.2 79242,79243 1u2wA 122 1.18e-02 1lnwA 147 1.25e-02 a.4.5.28 78104 1r1tA 122 1.29e-02 a.4.5.5 104769 1zljA 78 1.62e-02 1smtA 122 1.80e-02 1smtA a.4.5.5 16109 1lvaA 258 2.27e-02 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2fxaA 207 3.11e-02 1i6xA 209 3.21e-02 a.4.5.4,b.82.3.2 83673,83674 1bia 321 3.27e-02 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1jhfA 202 3.48e-02 a.4.5.2,b.87.1.1 63057,63058 1jgsA 138 3.49e-02 a.4.5.28 66683 1xd7A 145 3.82e-02 a.4.5.55 109566 1on2A 142 4.19e-02 a.4.5.24,a.76.1.1 87103,87104 1hw5A 210 4.27e-02 2cgpA a.4.5.4,b.82.3.2 16098,28137 1in6A 334 4.91e-02 1hqcA a.4.5.11,c.37.1.20 62601,62602 6paxA 133 6.79e-02 6paxA a.4.1.5,a.4.1.5 64758,64759 1in4A 334 7.36e-02 1hqcA a.4.5.11,c.37.1.20 62597,62598 2dtr 226 8.04e-02 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1y0uA 96 8.38e-02 2ethA 154 8.88e-02 1k78A 149 1.19e-01 a.4.1.5,a.4.1.5 68255,68256 1sd4A 126 1.32e-01 a.4.5.39 105428 1qbjA 81 2.06e-01 1qbjA a.4.5.19 16155 1j75A 67 2.08e-01 a.4.5.19 62673 1zybA 232 2.23e-01 1s7oA 113 2.44e-01 a.4.13.3 105354 1hw1A 239 2.56e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1fseA 74 3.10e-01 1fseA a.4.6.2 60000 1yyvA 131 3.51e-01 1a04A 215 3.57e-01 1a04A a.4.6.2,c.23.1.1 16234,31089 1aisB 200 3.64e-01 1aisB a.74.1.2,a.74.1.2 18384,18385 2fswA 107 3.65e-01 2cohA 202 4.38e-01 1hlvA 131 5.17e-01 a.4.1.7,a.4.1.7 65854,65855 1ufmA 84 5.22e-01 a.4.5.47 107816 1wi9A 72 5.25e-01 1xmaA 145 5.53e-01 1r1uA 106 5.98e-01 a.4.5.5 104771 1r7jA 95 7.03e-01 a.4.5.49 104836 1uxtA 501 7.15e-01 c.82.1.1 108125 1j3mA 129 7.23e-01 d.129.7.1 103836 1g2hA 61 8.15e-01 1g2hA a.4.1.12 60224 1xmkA 79 8.31e-01 1okrA 123 8.40e-01 a.4.5.39 93269 2acjA 66 1.05e+00 1q2lA 939 1.45e+00 1ofuA 320 1.61e+00 c.32.1.1,d.79.2.1 86972,86973 1xsvA 113 1.74e+00 1xviA 275 1.82e+00 1stzA 338 2.12e+00 a.4.5.51,d.110.2.3 106009,106010 1bm9A 122 2.26e+00 1bm9A a.4.5.7 16116 1ixcA 294 2.33e+00 a.4.5.37,c.94.1.1 83764,83765 2ab5A 269 2.46e+00 2f2eA 146 2.62e+00 1jhgA 101 2.63e+00 1jhgA a.4.12.1 19009 2fu4A 83 2.65e+00 1pbgA 468 2.72e+00 1e70M c.1.8.4 28946 1rr7A 129 2.72e+00 a.4.1.14 105075 1qzzA 374 2.88e+00 a.4.5.29,c.66.1.12 96719,96720 1s6lA 212 2.89e+00 1fsz 372 2.92e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1t56A 216 2.93e+00 a.4.1.9,a.121.1.1 106428,106429 2bj7A 138 3.36e+00 2a6cA 83 3.85e+00 1rkqA 282 4.23e+00 c.108.1.10 97621 1mai 131 4.28e+00 1mai b.55.1.1 26951 1uj6A 227 4.44e+00 c.124.1.4,d.58.40.1 107898,107899 1mgtA 174 4.95e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1qipA 183 4.96e+00 1qipA d.32.1.1 38470 1umqA 81 4.96e+00 a.4.1.12 99625 1ne2A 200 4.96e+00 c.66.1.32 85586 1or7A 194 5.01e+00 a.4.13.2,a.177.1.1 87332,87333 1p4wA 99 5.23e+00 a.4.6.2 87783 1bbpA 173 5.58e+00 1bbpA b.60.1.1 27147 1pufB 73 5.78e+00 a.4.1.1 95132 1z7uA 112 6.01e+00 1b72B 87 6.21e+00 1akhA a.4.1.1 16001 1tbxA 99 6.35e+00 a.4.5.48 106748 1o54A 277 6.40e+00 c.66.1.13 92482 2cujA 108 6.62e+00 1jayA 212 6.67e+00 c.2.1.6 66478 1utxA 66 6.80e+00 a.35.1.3 108034 1wpkA 146 7.13e+00 1u8bA 133 7.49e+00 1gvdA 52 7.58e+00 a.4.1.3 83338 1xn7A 78 7.85e+00 1pwmA 316 8.40e+00 c.1.7.1 95231 2c5uA 375 9.06e+00 1etxA 98 9.10e+00 1fipA a.4.1.12 18978 2afwA 329 9.20e+00 2fokA 579 9.27e+00 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1p0hA 318 9.27e+00 d.108.1.1 93866 1z1dA 103 9.33e+00 1dpuA 99 9.37e+00 1dpuA a.4.5.16 16150 1m32A 366 9.88e+00 c.67.1.3 78508 1tx4B 178 1.06e+01 1ctqA c.37.1.8 32045 2agtA 319 1.07e+01 1ads 315 1.08e+01 1frb c.1.7.1 28671 1zgwA 139 1.11e+01 1zx4A 192 1.11e+01 2b9eA 303 1.11e+01 2g7gA 213 1.13e+01 1us0A 316 1.14e+01 c.1.7.1 99850 1bl0A 129 1.15e+01 1d5yA a.4.1.8,a.4.1.8 16053,16054 1i7dA 659 1.16e+01 1d6mA e.10.1.1 61886 2esnA 310 1.17e+01 1fipA 98 1.21e+01 1fipA a.4.1.12 18980 1shyB 551 1.23e+01 b.69.12.1,g.16.2.1 105565,105566 2bgcA 238 1.24e+01 1xuuA 349 1.25e+01 2ao9A 155 1.28e+01 2ad9A 119 1.28e+01 1jh6A 189 1.33e+01 d.61.1.1 66707 1tc3C 51 1.35e+01 1tc3C a.4.1.2 16025 2adbA 148 1.36e+01 1u04A 771 1.36e+01 b.34.14.1,c.55.3.10 107539,107540 2axoA 270 1.44e+01 1kxoA 184 1.45e+01 b.60.1.1 84475 1vk1A 242 1.46e+01 d.268.1.2 108634 1fnnA 389 1.47e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 2ae6A 166 1.51e+01 2ax3A 502 1.52e+01 1cjgA 62 1.53e+01 1pru a.35.1.5 17112 1wa3A 205 1.56e+01 1r69 69 1.57e+01 1r69 a.35.1.2 17028 1fa0A 537 1.59e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1yb2A 275 1.59e+01 1jc4A 148 1.65e+01 1jc4A d.32.1.4 62863 1r71A 178 1.69e+01 a.4.14.1 104823 1jggA 60 1.71e+01 2hddA a.4.1.1 62950 1mhdA 132 1.72e+01 1mhdA d.164.1.1 42175 2bjcA 62 1.74e+01 2d27A 149 1.75e+01 2gmqA 118 1.84e+01 1b0nA 111 1.86e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1dwkA 156 1.88e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 2fq4A 192 1.89e+01 1pru 56 1.93e+01 1pru a.35.1.5 17104 1hr6A 475 2.00e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1neq 74 2.02e+01 1neq a.35.1.2 17063 1q79A 514 2.04e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1zh5A 195 2.07e+01 1hqz1 141 2.07e+01 1yrlA 491 2.10e+01 1jd1A 129 2.12e+01 1qu9A d.79.1.1 62890 1bjaA 95 2.14e+01 1bjaA a.4.5.9 16122 2b5aA 77 2.16e+01 2abqA 306 2.24e+01 1zarA 282 2.24e+01 1tqmA 282 2.26e+01 a.4.5.56,d.144.1.9 107236,107237 2cro 71 2.27e+01 1r69 a.35.1.2 17038 1xgsA 295 2.29e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1adr 76 2.29e+01 1r69 a.35.1.2 17042 1t0fA 276 2.37e+01 1p9qC 256 2.42e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1mi3A 322 2.52e+01 c.1.7.1 91274 1r5jA 337 2.60e+01 c.77.1.5 97097 1res 43 2.63e+01 1ret a.4.1.2 16023 1cy9A 264 2.65e+01 1ecl e.10.1.1 43236 2bnmA 198 2.78e+01 1u0mA 382 2.81e+01 c.95.1.2,c.95.1.2 107557,107558 1tk9A 188 2.82e+01 c.80.1.3 107082 2c27A 315 2.83e+01 1e2uA 553 2.85e+01 1e1dA e.26.1.1 43362 1gntA 553 2.85e+01 e.26.1.1 70290 1sjqA 105 2.92e+01 d.58.7.1 105660 1p8kZ 254 2.92e+01 d.95.2.1,d.95.2.1 94361,94362 1vhiA 142 2.99e+01 1b3tA d.58.8.1 39230 1ckiA 317 3.00e+01 1csn d.144.1.7 41660 1f5aA 513 3.01e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1kfwA 435 3.01e+01 c.1.8.5,d.26.3.1 77376,77377 2aj0A 71 3.05e+01 1t95A 240 3.07e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1k4nA 192 3.10e+01 d.32.1.5 72059 1zzcA 198 3.11e+01 1qgoA 264 3.16e+01 1qgoA c.92.1.2 35596 1gnlA 544 3.25e+01 e.26.1.1 70287 3pmgA 561 3.27e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1b3tA 147 3.27e+01 1b3tA d.58.8.1 39228 1kqpA 271 3.33e+01 c.26.2.1 72883 1gtdA 85 3.38e+01 d.284.1.1 76344 1abv 134 3.41e+01 1abv a.70.1.1 18317 2f06A 144 3.41e+01 1y1pA 342 3.41e+01 2c5rA 67 3.51e+01 1vqsA 116 3.52e+01 1pxwA 128 3.54e+01 d.79.3.1 95305 1rzsA 61 3.61e+01 a.35.1.2 105139 1f1zA 273 3.62e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1kmqA 184 3.66e+01 c.37.1.8 84412 1ypfA 336 3.73e+01 1kqfB 294 3.73e+01 d.58.1.5,f.23.22.1 75900,75901 1qc7A 101 3.74e+01 1qc7A a.118.14.1 18456 1mtpA 323 3.74e+01 e.1.1.1 85107 1neeA 138 3.78e+01 d.241.1.1,g.59.1.1 91841,91842 2sga 181 3.80e+01 1qq4A b.47.1.1 25808 1chuA 540 3.82e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ozjA 144 3.83e+01 d.164.1.1 93846 1mzbA 136 4.04e+01 a.4.5.42 91497 1ku3A 73 4.09e+01 a.4.13.2 73000 2gcfA 73 4.11e+01 1zkcA 197 4.13e+01 1vmaA 306 4.20e+01 a.24.13.1,c.37.1.10 108887,108888 1sqeA 109 4.20e+01 d.58.4.5 105908 1oz9A 150 4.25e+01 d.92.1.15 93808 1azo 232 4.26e+01 1azo c.52.1.14 33329 1ta0A 197 4.26e+01 c.108.1.16 106729 1q1aA 289 4.29e+01 c.31.1.5 95561 1f0xA 571 4.29e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 2gefA 217 4.29e+01 1gxqA 106 4.30e+01 a.4.6.1 70721 1fxlA 167 4.31e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1x89A 178 4.39e+01 1x71A 178 4.39e+01 1rec 201 4.41e+01 1rec a.39.1.5 17326 1wu7A 434 4.42e+01 1ym5A 300 4.44e+01 2be4A 272 4.50e+01 1sdoA 203 4.63e+01 c.52.1.21 98809 2b71A 196 4.68e+01 1uarA 285 4.69e+01 c.46.1.2,c.46.1.2 107762,107763 1akhA 61 4.71e+01 1akhA a.4.1.1 15980 1qfjA 232 4.75e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1js3A 486 4.76e+01 c.67.1.6 67215 1fjlA 81 4.80e+01 2hddA a.4.1.1 16017 1h5uA 842 4.83e+01 1a8i c.87.1.4 60655 1omiA 248 4.86e+01 b.82.3.3,a.4.5.4 87079,87080 1ftrA 296 4.86e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1h1dA 221 4.87e+01 c.66.1.1 83452 1t9iA 163 4.98e+01 1omrA 201 5.01e+01 a.39.1.5 93349 1sqsA 242 5.05e+01 c.23.5.5 98968 1o8bA 219 5.10e+01 c.124.1.4,d.58.40.1 81180,81181 1j8fA 323 5.17e+01 1j8fA c.31.1.5 62738 3rubS 123 5.17e+01 1rboC d.73.1.1 39616 1g9zA 152 5.20e+01 1bp7A d.95.2.1 60408 1mwqA 101 5.24e+01 d.58.4.7 91481 1v95A 130 5.30e+01 c.51.1.1 108435 5nul 138 5.30e+01 5nul c.23.5.1 31191 1xubA 298 5.31e+01 1yc5A 246 5.34e+01 1gkpA 458 5.37e+01 b.92.1.3,c.1.9.6 70231,70232 1rloA 271 5.39e+01 1onrA 316 5.42e+01 1onrA c.1.10.1 29169 2c9wA 169 5.44e+01 1zthA 258 5.47e+01 2fk8A 318 5.50e+01 1seiA 130 5.50e+01 1seiA d.140.1.1 41463 2guhA 214 5.51e+01 1u1wA 298 5.64e+01 1p7tA 731 5.65e+01 c.1.13.1 94319 1fexA 59 5.75e+01 a.4.1.3 59803 1ih8A 271 5.77e+01 2nsyA c.26.2.1 62377 2bnjA 303 5.87e+01 2arzA 247 5.90e+01 2etxA 209 6.00e+01 1hcrA 52 6.00e+01 1hcrA a.4.1.2 16020 1y5mA 276 6.01e+01 1eyvA 156 6.08e+01 1eyvA a.79.1.1 18446 2gauA 232 6.12e+01 2bgkA 278 6.12e+01 1u02A 239 6.16e+01 c.108.1.15 107538 1r8hA 87 6.18e+01 d.58.8.1 97233 2adoA 196 6.20e+01 1ujmA 342 6.21e+01 1u8sA 192 6.39e+01 d.58.18.5,d.58.18.5 107737,107738 1of8A 370 6.39e+01 c.1.10.4 92819 2pgd 482 6.39e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1zoiA 276 6.41e+01 1rlmA 271 6.41e+01 1xseA 295 6.41e+01 1uekA 275 6.44e+01 d.14.1.5,d.58.26.5 88483,88484 1fsiA 189 6.52e+01 1fsiA d.61.1.1 39536 1lk5A 229 6.55e+01 c.124.1.4,d.58.40.1 73960,73961 2tct 207 6.59e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1un8A 552 6.60e+01 c.119.1.2,a.208.1.1 103806,99661 2givA 295 6.67e+01 1csn 298 6.68e+01 1csn d.144.1.7 41664 1fy7A 278 6.69e+01 1fy7A d.108.1.1 40817 1i2oA 316 6.69e+01 1onrA c.1.10.1 61574 1y74A 57 6.79e+01 1k3eA 156 6.79e+01 d.198.1.1 68103 1kpgA 287 6.81e+01 c.66.1.18 68735 1v9dA 340 6.81e+01 a.207.1.1 100535 2f8mA 244 6.90e+01 1nxiA 132 6.91e+01 d.58.47.1 86381 1uz3A 102 6.91e+01 1fc3A 120 6.97e+01 1fc3A a.4.6.3 16237 1sfuA 75 7.06e+01 a.4.5.19 105503 1oaoC 729 7.10e+01 e.26.1.3 86746 1naqA 112 7.11e+01 d.58.5.2 91761 1xyzA 347 7.20e+01 1taxA c.1.8.3 28804 1ppjA 446 7.20e+01 d.185.1.1,d.185.1.1 104252,104253 1wtyA 119 7.25e+01 1vlwA 217 7.26e+01 c.1.10.1 108868 1wa8B 95 7.37e+01 1zq9A 285 7.42e+01 2b33A 140 7.48e+01 1cpcB 172 7.49e+01 1qgwC a.1.1.3 15644 1lopA 164 7.49e+01 2cpl b.62.1.1 27510 2d0oA 610 7.50e+01 1ns5A 155 7.54e+01 c.116.1.3 80705 1pmzA 86 7.57e+01 a.39.1.10 104195 1xy7A 166 7.57e+01 1hy7A 173 7.61e+01 d.92.1.11 65957 1heiA 451 7.68e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1jkoC 52 7.71e+01 a.4.1.2 66809 1ej1A 190 7.73e+01 1ejhA d.86.1.1 40144 1wrjA 156 7.73e+01 1t0tV 248 7.86e+01 d.58.4.10 106229 1fxxA 482 7.90e+01 1fxxA c.55.3.5 33726 1tz0A 114 8.01e+01 d.58.4.5 107463 1a32 88 8.02e+01 1a32 a.16.1.2 16384 2bjiA 277 8.06e+01 1r9wA 145 8.06e+01 d.89.1.2 97264 1a6jA 163 8.11e+01 1a6jA d.112.1.1 40915 1ecrA 309 8.12e+01 1ecrA e.2.1.1 42678 1cf2O 337 8.13e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1tkiA 321 8.20e+01 1tkiA d.144.1.7 41638 1a8i 842 8.33e+01 1a8i c.87.1.4 35490 1np6A 174 8.34e+01 c.37.1.10 85954 1j97A 211 8.34e+01 1f5sA c.108.1.4 62753 1oxkB 134 8.35e+01 c.23.1.1 93691 2cw8A 537 8.38e+01 1d2kA 392 8.41e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1fp2A 352 8.52e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 2bkaA 242 8.52e+01 1q16B 512 8.56e+01 d.58.1.5 95548 1zhhB 242 8.57e+01 1e7uA 961 8.60e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1xi1A 575 8.72e+01 1y5iB 512 8.76e+01 2g3bA 208 8.77e+01 1d5yA 292 8.77e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 1w9pA 433 8.82e+01 1d8cA 723 8.86e+01 1d8cA c.1.13.1 29325 1t6kA 278 8.89e+01 1oyiA 82 8.89e+01 a.4.5.19 93729 1lmb3 92 8.94e+01 1lmb3 1i1wA 303 8.95e+01 c.1.8.3 76732 1xzoA 174 8.99e+01