# List of top-scoring protein chains for t04-100-40-40-str2+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 1f9zA 135 1.14e-08 1qipA d.32.1.1 38484 1kllA 130 2.43e-08 d.32.1.2 72720 1fa8A 135 3.29e-08 1qipA d.32.1.1 38486 1ecsA 126 6.33e-08 1ecsA d.32.1.2 59407 1kw3B 292 2.24e-07 d.32.1.3 77549 d.32.1.3 77550 1lkdA 297 2.61e-07 d.32.1.3 78059 d.32.1.3 78060 1han 297 5.04e-07 1han d.32.1.3 38506 d.32.1.3 38507 1nkiA 135 2.95e-06 d.32.1.2 -9544 1f1uA 323 5.58e-06 d.32.1.3 83200 d.32.1.3 83201 1lqpA 135 6.59e-06 d.32.1.2 78151 1qipA 183 1.40e-05 1qipA d.32.1.1 38470 1f1xA 322 4.03e-05 d.32.1.3 83208 d.32.1.3 83209 1jc4A 148 2.12e-04 1jc4A d.32.1.4 62863 1qtoA 122 4.15e-04 1bylA d.32.1.2 38494 1bylA 125 4.81e-04 1bylA d.32.1.2 38495 1r9cA 139 1.86e-03 d.32.1.2 -9557 1cjxA 357 6.31e-03 1cjxA d.32.1.3 38516 d.32.1.3 38517 1i9gA 280 3.81e-02 c.66.1.13 62090 1mp9A 198 5.44e-02 a.74.1.2 -1127 a.74.1.2 -1128 1r72A 211 1.03e-01 unknown_sccs -215 unknown_sccs -5981 1hskA 326 1.05e-01 2mbr d.145.1.2 61241 d.146.1.1 61242 3proC 166 1.21e-01 3proC d.52.1.1 38812 d.52.1.1 38813 1o54A 277 1.55e-01 c.66.1.13 -8095 1p1lA 102 1.88e-01 d.58.5.2 87695 1v61A 132 2.82e-01 1jfuA 186 2.83e-01 c.47.1.10 62940 1ftrA 296 5.40e-01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1m2eA 135 5.85e-01 c.23.1.5 78478 1j5pA 253 6.84e-01 c.2.1.3 83092 d.81.1.3 71577 1sr9A 644 6.86e-01 1rrpB 134 7.14e-01 1rrpB b.55.1.3 26995 1eazA 125 7.96e-01 b.55.1.1 70113 1kafA 108 8.07e-01 d.199.1.1 68372 1jyaA 130 8.82e-01 d.198.1.1 67453 1ja1A 622 8.99e-01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1psdA 409 9.72e-01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1nw1A 429 1.08e+00 d.144.1.8 86286 1o0wA 252 1.11e+00 a.149.1.1 80751 d.50.1.1 80752 1g9zA 152 1.21e+00 1bp7A d.95.2.1 60408 1aisA 182 1.24e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1pqnA 127 1.27e+00 c.47.1.8 -7479 1fxlA 167 1.40e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1r2rA 248 1.48e+00 c.1.1.1 -5147 1atiA 505 1.64e+00 1atiA c.51.1.1 33196 d.104.1.1 40745 1p8xA 344 1.85e+00 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1hr6A 475 2.11e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1owxA 121 2.20e+00 d.58.7.1 87494 1kr4A 125 2.20e+00 d.58.5.2 72889 1lfpA 249 2.20e+00 e.39.1.1 73885 1j7gA 144 2.31e+00 c.110.1.1 84130 1f6bA 198 2.49e+00 c.37.1.8 64986 1fc6A 388 2.50e+00 1fc6A b.36.1.3 64738 c.14.1.2 64739 1qmhA 347 2.56e+00 1qmhA c.47.2.1 33082 d.68.2.1 39568 1ihgA 370 2.60e+00 2cpl a.118.8.1 62380 b.62.1.1 62381 1st9A 143 2.78e+00 c.47.1.10 -7503 1kc6A 257 2.86e+00 c.52.1.19 68419 1kyqA 274 3.17e+00 c.2.1.11 73281 e.37.1.1 73282 1mkeA 152 3.29e+00 b.55.1.4 79231 1t0hB 224 3.40e+00 1g4wR 383 3.60e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 1qksA 567 3.62e+00 1qksA a.3.1.2 15951 b.70.2.1 27710 1szwA 379 3.69e+00 unknown_sccs -10164 1d2oA 187 3.73e+00 1d2oA b.3.5.1 22625 b.3.5.1 22626 1qgvA 142 3.85e+00 1qgvA c.47.1.8 33056 1by2 119 3.97e+00 1by2 d.170.1.1 42452 1scuA 288 4.09e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1kxlA 199 4.10e+00 b.40.4.3 73155 1b5qA 472 4.11e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1btn 106 4.29e+00 1btn b.55.1.1 26952 1s72H 171 4.31e+00 1ukuA 102 4.34e+00 d.58.5.2 -9992 1fg7A 356 4.38e+00 1gewA c.67.1.1 59819 1oo0B 110 4.39e+00 d.58.7.1 87183 1ej1A 190 4.43e+00 1ejhA d.86.1.1 40144 1jsxA 207 4.49e+00 c.66.1.20 71846 1jtkA 136 4.61e+00 c.97.1.1 71862 1spxA 278 4.89e+00 c.2.1.2 -5870 1kid 203 5.02e+00 1derA c.8.5.1 30771 1q1gA 276 5.06e+00 c.56.2.1 -7846 1ddgA 374 5.15e+00 1amoA b.43.4.1 25671 c.25.1.4 31559 1ddwA 120 5.34e+00 1evhA b.55.1.4 27001 1lc0A 294 5.36e+00 c.2.1.3 73823 d.81.1.4 73824 1ek8A 185 5.41e+00 1ek8A d.67.3.1 59444 1kao 167 5.55e+00 1ctqA c.37.1.8 32014 1l5aA 436 5.59e+00 c.43.1.2 75923 c.43.1.2 75924 1fsz 372 5.83e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1gcuA 295 6.06e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 1lylA 504 6.15e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1go2A 304 6.22e+00 b.43.4.2 76243 c.25.1.1 76244 1eokA 290 6.29e+00 1eokA c.1.8.5 28991 1vicA 262 6.29e+00 c.68.1.13 -8252 1ckv 141 6.59e+00 1ckv d.137.1.1 41452 1qqgA 264 6.64e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1que 303 6.77e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1h7sA 365 7.07e+00 d.14.1.3 65705 d.122.1.2 65706 1lvaA 258 7.13e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1f20A 435 7.41e+00 b.43.4.1 64932 c.25.1.4 64933 1j5yA 187 7.49e+00 a.4.5.1 71592 d.94.2.1 71593 1jenA 267 7.79e+00 1jenA 1tph1 247 7.88e+00 1amk 1e42A 258 7.94e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1ogiA 303 7.99e+00 b.43.4.2 -4042 c.25.1.1 -6587 1bxoA 323 8.12e+00 2er7E b.50.1.2 26805 2fcr 173 8.15e+00 1rcf c.23.5.1 31151 1rk8A 165 8.15e+00 d.58.7.1 -10018 1n8jA 186 8.17e+00 c.47.1.10 85401 1r8sA 164 8.33e+00 c.37.1.8 -7082 1ptf 88 8.35e+00 1ptf d.94.1.1 40549 1mkiA 330 8.41e+00 e.3.1.2 84994 1n13B 113 8.48e+00 1npk 154 8.49e+00 1npk d.58.6.1 39099 1mai 131 8.58e+00 1mai b.55.1.1 26951 1jjtA 228 8.59e+00 1a7tA d.157.1.1 63139 1a48 306 8.72e+00 1a48 d.143.1.1 41590 1jj2Q 154 8.72e+00 1ffkO d.55.1.1 63102 1uc8A 280 8.92e+00 unknown_sccs -6718 unknown_sccs -11230 1ttzA 87 9.18e+00 1mo0A 275 9.33e+00 c.1.1.1 79329 1b4bA 71 9.34e+00 1b4aA d.74.2.1 39718 1h3nA 878 9.34e+00 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1r5pA 108 9.38e+00 unknown_sccs -7487 1jjeA 222 9.41e+00 1a7tA d.157.1.1 63117 1mwqA 101 9.55e+00 unknown_sccs -9962 1q7bA 244 9.62e+00 c.2.1.2 -5826 1jl0A 334 9.74e+00 1jenA d.156.1.1 63155 1ble 163 9.76e+00 1ble c.38.1.1 32475 1tl2A 236 9.81e+00 1tl2A b.67.1.1 27541 1k20A 310 1.01e+01 c.107.1.1 68027 1jkeA 145 1.02e+01 c.110.1.1 66791 1j98A 157 1.02e+01 1j98A d.185.1.2 62755 1ko7A 314 1.02e+01 c.98.2.1 72797 c.91.1.2 72798 1qtsA 247 1.03e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1ll2A 333 1.05e+01 c.68.1.14 74005 1v33A 366 1.06e+01 unknown_sccs -11384 1jj2B 337 1.08e+01 1ffkB b.43.3.2 63086 1s72B 338 1.08e+01 1l8bA 190 1.08e+01 d.86.1.1 73683 1pd21 199 1.13e+01 1pd21 1fhuA 320 1.16e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1gewA 356 1.16e+01 1gewA c.67.1.1 60470 1rvkA 382 1.18e+01 c.1.11.2 -5568 d.54.1.1 -9826 1gsoA 431 1.18e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1riqA 465 1.20e+01 unknown_sccs -1295 d.104.1.1 -10769 1l3kA 196 1.22e+01 d.58.7.1 73539 d.58.7.1 73540 1is1A 185 1.24e+01 d.67.3.1 83704 1r31A 428 1.24e+01 d.58.20.1 -10108 d.179.1.1 -11716 1qamA 244 1.25e+01 2ercA c.66.1.24 34220 1qoiA 177 1.26e+01 2cpl b.62.1.1 27490 1qmvA 197 1.27e+01 1qq2A c.47.1.10 33066 1k3tA 359 1.29e+01 c.2.1.3 72022 d.81.1.1 72023 1nb8A 353 1.32e+01 d.3.1.9 80385 1rypI 222 1.33e+01 d.153.1.4 41877 1ivzA 132 1.34e+01 d.58.41.1 76863 1h4wA 224 1.35e+01 b.47.1.2 65622 1nzaA 103 1.35e+01 d.58.5.2 86444 1s3eA 520 1.35e+01 c.3.1.2 -6022 d.16.1.5 -9242 1n08A 163 1.37e+01 b.43.5.1 79730 1i50K 120 1.38e+01 d.74.3.2 61765 1in0A 163 1.39e+01 d.58.49.1 83694 d.58.49.1 83695 1kyfA 247 1.39e+01 b.1.10.1 73220 d.105.1.1 73221 1jkxA 212 1.42e+01 c.65.1.1 66813 1r6wA 322 1.43e+01 c.1.11.2 -5563 d.54.1.1 -9821 1di2A 69 1.44e+01 1di2A d.50.1.1 38780 1bm9A 122 1.44e+01 1bm9A a.4.5.7 16116 1f46A 140 1.45e+01 1f46A d.129.4.1 59643 1s72R 155 1.45e+01 2cpl 165 1.46e+01 2cpl b.62.1.1 27420 1ojaA 520 1.46e+01 c.3.1.2 -6000 d.16.1.5 -9220 1c8zA 265 1.49e+01 1c8zA d.23.1.1 38375 1e7uA 961 1.50e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1obdA 306 1.51e+01 d.143.1.1 86767 1h4rA 314 1.52e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1q8iA 783 1.54e+01 c.55.3.5 -7635 e.8.1.1 -11885 1gypA 358 1.55e+01 1dssG c.2.1.3 30004 d.81.1.1 39919 1uxy 340 1.56e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1r5tA 142 1.56e+01 1am2 199 1.57e+01 1am2 b.86.1.2 28381 1a44 185 1.57e+01 1a44 b.17.1.1 23704 1h70A 255 1.60e+01 1h70A d.126.1.3 60711 1jl3A 139 1.62e+01 c.44.1.1 66826 1eq6A 189 1.66e+01 1eq6A d.107.1.1 40796 1k2yX 463 1.67e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1ha1 184 1.67e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1udvA 89 1.68e+01 d.68.6.1 -10280 1eudA 311 1.68e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1c4kA 730 1.69e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1k8kF 168 1.70e+01 d.198.2.1 68312 1qniA 581 1.72e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1je6A 275 1.74e+01 b.1.1.2 71638 d.19.1.1 71639 1me8A 503 1.77e+01 c.1.5.1 79028 1uwzA 136 1.79e+01 1gvjA 146 1.80e+01 a.4.5.21 -293 1nd4A 264 1.81e+01 d.144.1.6 -11381 1nijA 318 1.83e+01 c.37.1.10 85741 d.237.1.1 85742 1s96A 219 1.84e+01 c.37.1.1 -6972 1go3F 107 1.85e+01 a.60.8.2 65407 1jv1A 505 1.87e+01 c.68.1.5 71892 1naqA 112 1.88e+01 d.58.5.2 -9984 1f08A 148 1.94e+01 1f08A d.89.1.2 59564 1btkA 169 1.94e+01 1btkA b.55.1.1 26959 1awqA 164 1.97e+01 2cpl b.62.1.1 27461 1oi7A 288 1.98e+01 c.2.1.8 87049 c.23.4.1 87050 1heiA 451 2.00e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 3fruA 269 2.02e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1d9tA 289 2.02e+01 1deaA 1dynA 125 2.05e+01 1dynA b.55.1.1 26955 1ne7A 289 2.12e+01 unknown_sccs -6858 1fgyA 127 2.14e+01 1faoA b.55.1.1 26976 1j3wA 163 2.14e+01 unknown_sccs -10870 1k8kD 300 2.14e+01 d.198.2.1 68309 d.198.2.1 68310 1ak5 503 2.16e+01 1ak5 c.1.5.1 28639 1np6A 174 2.16e+01 c.37.1.10 85954 1hv9A 456 2.17e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1omzA 293 2.18e+01 c.68.1.15 87093 1kopA 223 2.20e+01 2cba b.74.1.1 27966 1g5hA 454 2.22e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1j6wA 175 2.29e+01 1j98A d.185.1.2 62663 1dywA 173 2.30e+01 2cpl b.62.1.1 27505 1tvlA 454 2.31e+01 1p5dX 463 2.35e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1dqnA 230 2.36e+01 1dqnA c.61.1.1 34067 1sviA 195 2.37e+01 1dqpA 230 2.38e+01 1dqnA c.61.1.1 34069 1bhtA 176 2.39e+01 1bhtA g.10.1.1 44603 g.14.1.1 44663 1phk 298 2.40e+01 1cdkA d.144.1.7 41635 1ne9A 335 2.41e+01 d.108.1.4 -10805 d.108.1.4 -10806 1k4nA 192 2.42e+01 d.32.1.5 72059 1bfd 528 2.44e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1uw4A 91 2.44e+01 unknown_sccs -10038 1th8A 145 2.47e+01 1g71A 347 2.53e+01 1g71A unknown_sccs 43268 1nnwA 252 2.54e+01 d.159.1.5 80674 1r4pB 70 2.61e+01 b.40.2.1 -3887 1dyr 206 2.62e+01 1aoeA c.71.1.1 34916 1q8yA 373 2.62e+01 d.144.1.7 -11319 1b9mA 265 2.63e+01 1b9mA a.4.5.8 16118 b.40.6.2 58938 b.40.6.2 58939 2arcA 164 2.67e+01 2arcA b.82.4.1 28148 1i9zA 347 2.67e+01 1i9yA d.151.1.2 62102 1kb9B 352 2.72e+01 d.185.1.1 77313 d.185.1.1 77314 1prxA 224 2.74e+01 1prxA c.47.1.10 33076 1lenA 181 2.75e+01 1led b.29.1.1 24032 1r9fA 136 2.77e+01 unknown_sccs -10736 1lwjA 441 2.79e+01 b.71.1.1 74303 c.1.8.1 74304 1e8gA 560 2.79e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1jhsA 188 2.80e+01 d.107.1.1 84172 1ms9A 648 2.81e+01 b.29.1.15 85088 b.68.1.1 85089 1nb9A 147 2.83e+01 b.43.5.1 85515 1e8yA 966 2.86e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1b5tA 275 2.87e+01 1b5tA c.1.23.1 29676 1gadO 330 2.88e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 3psg 370 2.95e+01 1smrA b.50.1.2 26841 1f3vA 179 3.03e+01 1f3vA d.58.22.1 39382 1q3eA 207 3.03e+01 b.82.3.2 -4922 1bd0A 388 3.04e+01 1bd0A b.49.2.2 26480 c.1.6.1 28642 1isiA 265 3.12e+01 e.4.1.1 71394 1lrzA 426 3.16e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1pinA 163 3.21e+01 1pinA b.72.1.1 27802 d.26.1.1 38431 1f8yA 157 3.24e+01 1f8xA c.23.14.1 31395 1ezvB 352 3.26e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1vk3A 615 3.27e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1pvmA 184 3.28e+01 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 7aatA 401 3.31e+01 1ajsA c.67.1.1 34250 1tiiD 99 3.31e+01 1tiiD b.40.2.1 24965 1w1kA 560 3.33e+01 1i4wA 353 3.33e+01 c.66.1.24 66028 1uq5A 263 3.34e+01 d.165.1.1 -11555 1b12A 248 3.35e+01 1b12A b.87.1.2 28388 1oejA 193 3.36e+01 unknown_sccs -4461 1fxjA 331 3.38e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1iqvA 218 3.39e+01 1rss a.75.1.1 62661 1n6zA 105 3.41e+01 unknown_sccs 85369 1mrj 247 3.43e+01 1mrj d.165.1.1 42177 1m3iA 471 3.45e+01 f.9.1.1 -12374 1kjwA 295 3.46e+01 b.34.2.1 68643 c.37.1.1 68644 1v7rA 186 3.47e+01 c.51.4.1 -7546 1awsA 164 3.48e+01 2cpl b.62.1.1 27431 1pz1A 333 3.51e+01 c.1.7.1 -5255 1nz6A 101 3.55e+01 a.2.3.1 86441 1tc5A 194 3.56e+01 1fnd 314 3.58e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1eudB 396 3.59e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1o7fA 469 3.64e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1lxnA 99 3.68e+01 d.58.48.1 84737 1fukA 165 3.71e+01 1fukA c.37.1.19 32409 1o0uA 429 3.72e+01 c.118.1.1 80743 1eur 365 3.72e+01 1eut b.68.1.1 27607 1o04A 500 3.73e+01 c.82.1.1 86508 1sftA 388 3.73e+01 1bd0A b.49.2.2 26482 c.1.6.1 28644 1vhwA 253 3.77e+01 c.56.2.1 -7765 1mgtA 174 3.84e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1itwA 741 3.84e+01 c.77.1.2 76793 1lq9A 112 3.84e+01 d.58.4.3 78129 1pjr 724 3.85e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1n0uA 842 3.86e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1otjA 283 3.88e+01 b.82.2.5 -4893 1sr4C 166 3.90e+01 1pg4A 652 3.91e+01 e.23.1.1 88067 1g0oA 283 3.91e+01 1ybvA c.2.1.2 60181 1pyaB 228 3.98e+01 1pyaB