# List of top-scoring protein chains for t04-100-30-str2 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 1kllA 130 1.62e-10 d.32.1.2 72720 1f9zA 135 3.47e-09 1qipA d.32.1.1 38484 1fa8A 135 6.36e-09 1qipA d.32.1.1 38486 1ecsA 126 1.20e-08 1ecsA d.32.1.2 59407 1lqpA 135 1.78e-08 d.32.1.2 78151 1nkiA 135 1.78e-08 d.32.1.2 -9544 1kw3B 292 1.24e-06 d.32.1.3 77549 d.32.1.3 77550 1han 297 5.00e-06 1han d.32.1.3 38506 d.32.1.3 38507 1lkdA 297 6.93e-06 d.32.1.3 78059 d.32.1.3 78060 1qipA 183 2.16e-05 1qipA d.32.1.1 38470 1f1uA 323 3.75e-05 d.32.1.3 83200 d.32.1.3 83201 1r9cA 139 1.57e-04 d.32.1.2 -9557 1f1xA 322 2.59e-04 d.32.1.3 83208 d.32.1.3 83209 1jc4A 148 7.08e-04 1jc4A d.32.1.4 62863 1bylA 125 8.08e-04 1bylA d.32.1.2 38495 1qtoA 122 2.10e-03 1bylA d.32.1.2 38494 1cjxA 357 1.92e-02 1cjxA d.32.1.3 38516 d.32.1.3 38517 1g9zA 152 1.33e-01 1bp7A d.95.2.1 60408 1ftrA 296 1.42e-01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1o54A 277 4.26e-01 c.66.1.13 -8095 1pg4A 652 6.67e-01 e.23.1.1 88067 1uc8A 280 6.86e-01 unknown_sccs -6718 unknown_sccs -11230 1j5yA 187 7.15e-01 a.4.5.1 71592 d.94.2.1 71593 1hskA 326 7.33e-01 2mbr d.145.1.2 61241 d.146.1.1 61242 1i9gA 280 7.42e-01 c.66.1.13 62090 1r72A 211 7.86e-01 unknown_sccs -215 unknown_sccs -5981 1jfuA 186 8.80e-01 c.47.1.10 62940 1p1lA 102 9.15e-01 d.58.5.2 87695 1mkiA 330 1.03e+00 e.3.1.2 84994 1j7gA 144 1.09e+00 c.110.1.1 84130 1o04A 500 1.11e+00 c.82.1.1 86508 1eazA 125 1.13e+00 b.55.1.1 70113 1sr9A 644 1.20e+00 1q1gA 276 1.40e+00 c.56.2.1 -7846 1n8jA 186 1.50e+00 c.47.1.10 85401 1lvaA 258 1.54e+00 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1pvmA 184 1.62e+00 d.37.1.1 -9612 d.37.1.1 -9613 unknown_sccs -12799 1o0wA 252 1.69e+00 a.149.1.1 80751 d.50.1.1 80752 3proC 166 1.98e+00 3proC d.52.1.1 38812 d.52.1.1 38813 1khdA 345 2.05e+00 a.46.2.1 77400 c.27.1.1 77401 1ja1A 622 2.06e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1ckv 141 2.17e+00 1ckv d.137.1.1 41452 1vicA 262 2.25e+00 c.68.1.13 -8252 1mp9A 198 2.33e+00 a.74.1.2 -1127 a.74.1.2 -1128 1mkeA 152 2.37e+00 b.55.1.4 79231 1v61A 132 2.86e+00 1tl2A 236 2.89e+00 1tl2A b.67.1.1 27541 1kr4A 125 2.93e+00 d.58.5.2 72889 7aatA 401 2.98e+00 1ajsA c.67.1.1 34250 2ran 316 3.04e+00 1avc a.65.1.1 18170 1a8b 318 3.07e+00 1avc a.65.1.1 18171 1mngA 203 3.17e+00 1avmA a.2.11.1 15776 d.44.1.1 38701 2cpl 165 3.34e+00 2cpl b.62.1.1 27420 1dynA 125 3.53e+00 1dynA b.55.1.1 26955 1l6rA 227 3.67e+00 c.108.1.10 77768 1jy1A 464 3.68e+00 d.136.1.3 67438 d.136.1.3 67439 1nkqA 259 3.80e+00 1hkeA 137 3.87e+00 1jyaA 130 4.32e+00 d.198.1.1 67453 1d9tA 289 4.35e+00 1deaA 1ne7A 289 4.54e+00 unknown_sccs -6858 1k20A 310 4.62e+00 c.107.1.1 68027 1ht6A 405 4.63e+00 b.71.1.1 83629 c.1.8.1 83630 1psdA 409 4.74e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1d2oA 187 4.78e+00 1d2oA b.3.5.1 22625 b.3.5.1 22626 1awqA 164 5.01e+00 2cpl b.62.1.1 27461 1ecfA 504 5.20e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1apyA 162 5.26e+00 1apyA d.153.1.5 42004 1ptf 88 5.64e+00 1ptf d.94.1.1 40549 1nw1A 429 5.87e+00 d.144.1.8 86286 1uxy 340 5.87e+00 2mbr d.145.1.2 41748 d.146.1.1 41761 1lshA 1056 5.96e+00 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1on3A 523 5.98e+00 c.14.1.4 87107 c.14.1.4 87108 1uz5A 402 6.10e+00 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1qqgA 264 6.32e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1by2 119 6.55e+00 1by2 d.170.1.1 42452 1fg7A 356 6.58e+00 1gewA c.67.1.1 59819 1aisA 182 6.60e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1k0eA 453 6.90e+00 d.161.1.1 67938 1f2tA 149 7.05e+00 1f2tA c.37.1.12 32373 1ihgA 370 7.18e+00 2cpl a.118.8.1 62380 b.62.1.1 62381 1jkeA 145 7.30e+00 c.110.1.1 66791 1gcuA 295 7.35e+00 1gcuA c.2.1.3 30063 d.81.1.4 39978 1ci9A 392 7.40e+00 e.3.1.1 64767 1lc0A 294 7.43e+00 c.2.1.3 73823 d.81.1.4 73824 9gafA 295 7.76e+00 1apyA d.153.1.5 42008 1qtsA 247 7.79e+00 1qtsA b.1.10.1 22313 d.105.1.1 40789 1b4bA 71 7.99e+00 1b4aA d.74.2.1 39718 1nxzA 246 8.21e+00 b.122.1.2 86391 c.116.1.5 86392 1kyqA 274 8.69e+00 c.2.1.11 73281 e.37.1.1 73282 1kyfA 247 9.59e+00 b.1.10.1 73220 d.105.1.1 73221 1uwzA 136 9.60e+00 1ej1A 190 9.75e+00 1ejhA d.86.1.1 40144 1l8bA 190 9.92e+00 d.86.1.1 73683 1mo1A 87 1.00e+01 d.94.1.1 -10640 1n6zA 105 1.03e+01 unknown_sccs 85369 3fruA 269 1.03e+01 1agdA b.1.1.2 20657 d.19.1.1 38150 1uuzA 137 1.04e+01 d.233.1.1 -9478 1pba 81 1.08e+01 1pytA d.58.3.1 39067 1gk9A 260 1.11e+01 d.153.1.2 65246 1b8oA 284 1.14e+01 1b8oA c.56.2.1 33762 1lfwA 470 1.15e+01 c.56.5.4 77942 d.58.19.1 77943 1th8A 145 1.15e+01 1rrpB 134 1.16e+01 1rrpB b.55.1.3 26995 1j5pA 253 1.20e+01 c.2.1.3 83092 d.81.1.3 71577 1nzaA 103 1.21e+01 d.58.5.2 86444 2gcc 70 1.23e+01 2gcc d.10.1.2 37484 1heiA 451 1.24e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1jtkA 136 1.24e+01 c.97.1.1 71862 1gsoA 431 1.27e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1e3aA 260 1.30e+01 1ajqA d.153.1.2 41838 1oo0B 110 1.31e+01 d.58.7.1 87183 1p8xA 344 1.32e+01 d.109.1.1 -10813 d.109.1.1 -10814 d.109.1.1 -10815 1fxoA 293 1.34e+01 1g0rA c.68.1.6 34524 1q8iA 783 1.38e+01 c.55.3.5 -7635 e.8.1.1 -11885 1fxlA 167 1.39e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1r5tA 142 1.42e+01 1iujA 106 1.45e+01 unknown_sccs -9953 1nijA 318 1.47e+01 c.37.1.10 85741 d.237.1.1 85742 1fviA 297 1.48e+01 1fviA b.40.4.6 25364 d.142.2.1 41578 1qmvA 197 1.51e+01 1qq2A c.47.1.10 33066 1nzoA 363 1.51e+01 b.105.1.1 -2933 e.3.1.1 -11784 1gewA 356 1.54e+01 1gewA c.67.1.1 60470 1uw4A 91 1.56e+01 unknown_sccs -10038 1awsA 164 1.57e+01 2cpl b.62.1.1 27431 1kao 167 1.59e+01 1ctqA c.37.1.8 32014 1vk3A 615 1.59e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1ll2A 333 1.60e+01 c.68.1.14 74005 1ia8A 289 1.65e+01 1ia8A d.144.1.7 62112 1j5wA 298 1.70e+01 d.104.1.1 71589 1q0bA 367 1.71e+01 c.37.1.9 -7105 1oe8A 211 1.73e+01 a.45.1.1 86905 c.47.1.5 86906 1btn 106 1.75e+01 1btn b.55.1.1 26952 1nnwA 252 1.81e+01 d.159.1.5 80674 1rk8A 165 1.82e+01 d.58.7.1 -10018 1i9zA 347 1.82e+01 1i9yA d.151.1.2 62102 1ko7A 314 1.83e+01 c.98.2.1 72797 c.91.1.2 72798 1qisA 396 1.88e+01 1ajsA c.67.1.1 34284 1v9kA 228 1.90e+01 1nu5A 370 1.92e+01 c.1.11.2 -5565 d.54.1.1 -9823 1l3kA 196 1.93e+01 d.58.7.1 73539 d.58.7.1 73540 1is1A 185 1.94e+01 d.67.3.1 83704 1mai 131 1.95e+01 1mai b.55.1.1 26951 1e42A 258 1.96e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1f6bA 198 1.96e+01 c.37.1.8 64986 1mkaA 171 1.98e+01 1mkaA d.38.1.2 38543 1r8sA 164 2.02e+01 c.37.1.8 -7082 1e58A 249 2.05e+01 1qhfA c.60.1.1 59262 1f0iA 504 2.08e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1p4kA 295 2.11e+01 d.153.1.5 87772 1v0wA 506 2.13e+01 1oi7A 288 2.13e+01 c.2.1.8 87049 c.23.4.1 87050 1cf2O 337 2.14e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1oj4A 283 2.15e+01 d.14.1.5 -9088 d.58.26.5 -10133 1gkpA 458 2.20e+01 b.92.1.3 70231 c.1.9.6 70232 1bbpA 173 2.22e+01 1bbpA b.60.1.1 27147 2fmr 65 2.24e+01 2fmr d.51.1.1 38808 1a8p 258 2.25e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1egiA 147 2.28e+01 1eggA d.169.1.1 42331 1tc5A 194 2.29e+01 1ovlA 271 2.29e+01 a.123.1.1 87455 1qlpA 394 2.29e+01 1ovaA e.1.1.1 42628 1c1yB 77 2.30e+01 1c1yB d.15.1.5 37618 1rxxA 421 2.31e+01 unknown_sccs -10982 1ugpB 226 2.32e+01 1nj4A 363 2.33e+01 b.105.1.1 80545 e.3.1.1 80546 1ireB 228 2.35e+01 b.34.4.4 76770 1j3wA 163 2.41e+01 unknown_sccs -10870 1lylA 504 2.41e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1st9A 143 2.47e+01 c.47.1.10 -7503 1kngA 156 2.47e+01 c.47.1.10 72777 1sphA 88 2.48e+01 1ptf d.94.1.1 40544 1korA 400 2.49e+01 c.26.2.1 72824 d.210.1.1 72825 1faoA 126 2.51e+01 1faoA b.55.1.1 26974 1ub0A 258 2.53e+01 c.72.1.2 88394 1ccwB 483 2.54e+01 1cb7B c.1.19.2 29646 1nqjA 119 2.55e+01 b.23.2.1 86031 1p3dA 475 2.55e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 2fcr 173 2.56e+01 1rcf c.23.5.1 31151 1r4xA 275 2.58e+01 unknown_sccs -2846 unknown_sccs -10776 1mq4A 272 2.61e+01 d.144.1.7 -11349 1uq5A 263 2.64e+01 d.165.1.1 -11555 1vhyA 257 2.71e+01 b.122.1.2 -5129 c.116.1.5 -6705 1f20A 435 2.73e+01 b.43.4.1 64932 c.25.1.4 64933 1nb8A 353 2.79e+01 d.3.1.9 80385 1mwqA 101 2.83e+01 unknown_sccs -9962 1h3nA 878 2.83e+01 a.27.1.1 76641 b.51.1.1 76642 c.26.1.1 76643 1hdkA 141 2.85e+01 b.29.1.3 65807 3nul 130 2.91e+01 3nul d.110.1.1 40891 1r0pA 312 2.93e+01 d.144.1.7 -11377 1nxiA 132 2.96e+01 d.58.47.1 86381 1l5aA 436 2.96e+01 c.43.1.2 75923 c.43.1.2 75924 1gadO 330 2.98e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 1q7bA 244 3.00e+01 c.2.1.2 -5826 3psg 370 3.04e+01 1smrA b.50.1.2 26841 1d4xA 375 3.05e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1nr4A 71 3.09e+01 d.9.1.1 -8957 1lfpA 249 3.10e+01 e.39.1.1 73885 1bm9A 122 3.10e+01 1bm9A a.4.5.7 16116 1k8kD 300 3.11e+01 d.198.2.1 68309 d.198.2.1 68310 1kafA 108 3.15e+01 d.199.1.1 68372 1n3hA 207 3.16e+01 b.55.1.2 -4350 1mplA 349 3.18e+01 e.3.1.1 79387 1ha1 184 3.20e+01 1ha1 d.58.7.1 39147 d.58.7.1 39148 1qyiA 384 3.25e+01 unknown_sccs -6836 1us8A 147 3.27e+01 c.37.1.12 -7194 1di2A 69 3.27e+01 1di2A d.50.1.1 38780 1pytA 94 3.29e+01 1pytA d.58.3.1 39064 1na3A 91 3.34e+01 k.38.1.1 85481 1hjxA 362 3.36e+01 c.1.8.5 83512 d.26.3.1 83513 1oywA 523 3.39e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1ndh 272 3.39e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1ttzA 87 3.41e+01 1f7lA 121 3.42e+01 1f7lA d.150.1.2 59666 1vjfA 180 3.43e+01 d.116.1.1 -10941 1fiqC 763 3.43e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1l7mA 211 3.46e+01 c.108.1.4 73664 1iow 306 3.46e+01 1iow c.30.1.2 31713 d.142.1.1 41481 1m2eA 135 3.48e+01 c.23.1.5 78478 1fqtA 112 3.49e+01 1fqtA b.33.1.1 24441 1gr3A 160 3.51e+01 b.22.1.1 65476 1i7pA 274 3.52e+01 b.43.4.2 66048 c.25.1.1 66049 1j97A 211 3.52e+01 1f5sA c.108.1.4 62753 1mr3F 181 3.55e+01 c.37.1.8 79422 1v7rA 186 3.56e+01 c.51.4.1 -7546 1dp0A 1023 3.59e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1ddgA 374 3.62e+01 1amoA b.43.4.1 25671 c.25.1.4 31559 1roaA 122 3.62e+01 1jz8A 1023 3.64e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1ub3A 220 3.64e+01 c.1.10.1 88395 1jpaA 312 3.66e+01 d.144.1.7 67011 1i50B 1224 3.71e+01 e.29.1.1 61755 1e4fT 419 3.73e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1ax4A 467 3.73e+01 1ax4A c.67.1.2 34391 1bykA 255 3.74e+01 1bykA c.93.1.1 35706 1avmA 201 3.74e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1mi3A 322 3.78e+01 c.1.7.1 -5257 1b0b 142 3.79e+01 2fal a.1.1.2 15010 1ek8A 185 3.80e+01 1ek8A d.67.3.1 59444 1vf7A 369 3.84e+01 1naqA 112 3.86e+01 d.58.5.2 -9984 1opd 85 3.86e+01 1ptf d.94.1.1 40560 1cl1A 395 3.89e+01 1cl2A c.67.1.3 34395 1o3yA 166 3.94e+01 c.37.1.8 86618 1hvbA 349 3.97e+01 3pte e.3.1.1 42686