# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1lgtA 297 6.31e-16 d.32.1.3 77956 d.32.1.3 77957 1lkdA 297 7.08e-16 d.32.1.3 78059 d.32.1.3 78060 1han 297 7.76e-16 1han d.32.1.3 38506 d.32.1.3 38507 1lqpA 135 1.37e-14 d.32.1.2 78151 1nkiA 135 1.85e-14 d.32.1.2 -9544 1dhy 292 5.19e-14 1han d.32.1.3 38504 d.32.1.3 38505 1kw3B 292 5.56e-14 d.32.1.3 77549 d.32.1.3 77550 1gdgA 293 1.22e-13 1f1uA 323 3.36e-13 d.32.1.3 83200 d.32.1.3 83201 1f1xA 322 1.21e-12 d.32.1.3 83208 d.32.1.3 83209 1fa8A 135 7.25e-12 1qipA d.32.1.1 38486 1f9zA 135 7.28e-12 1qipA d.32.1.1 38484 1mpyA 307 7.66e-12 1mpyA d.32.1.3 38508 d.32.1.3 38509 1qipA 183 7.23e-11 1qipA d.32.1.1 38470 1r9cA 139 7.99e-11 d.32.1.2 -9557 1bh5A 183 1.79e-10 1qipA d.32.1.1 38476 1kllA 130 2.21e-09 d.32.1.2 72720 1jc4A 148 5.17e-09 1jc4A d.32.1.4 62863 1ecsA 126 9.61e-08 1ecsA d.32.1.2 59407 1ewjA 126 1.99e-07 1ecsA d.32.1.2 59526 1qtoA 122 7.31e-06 1bylA d.32.1.2 38494 1bylA 125 8.32e-06 1bylA d.32.1.2 38495 1cjxA 357 9.96e-05 1cjxA d.32.1.3 38516 d.32.1.3 38517 1j5yA 187 1.11e-01 a.4.5.1 71592 d.94.2.1 71593 1cyx 205 1.14e-01 1cyx b.6.1.2 23023 1sjyA 159 1.88e-01 d.113.1.1 -10908 1hztA 190 4.26e-01 1i9aA d.113.1.2 61459 1st9A 143 5.67e-01 c.47.1.10 -7503 1cyw 205 5.80e-01 1cyx b.6.1.2 23024 1dynA 125 5.98e-01 1dynA b.55.1.1 26955 1ejdA 419 7.36e-01 1uae d.68.2.2 39576 1uae 419 7.52e-01 1uae d.68.2.2 39574 1ipaA 274 7.62e-01 c.116.1.1 71254 d.79.3.3 71255 1a0i 348 8.59e-01 1a0i b.40.4.6 25363 d.142.2.1 41577 1mh1 186 8.97e-01 1eesA c.37.1.8 32002 1i9aA 182 9.72e-01 1i9aA d.113.1.2 62082 1g0sA 209 1.09e+00 1g0sA d.113.1.1 60187 1qqgA 264 1.16e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1a8p 258 1.20e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 2dynA 122 1.30e+00 1dynA b.55.1.1 26957 1tx4B 178 1.43e+00 1ctqA c.37.1.8 32045 1m7bA 184 1.49e+00 c.37.1.8 74572 1kmqA 184 1.72e+00 c.37.1.8 84412 1lfwA 470 1.72e+00 c.56.5.4 77942 d.58.19.1 77943 1a3yA 149 2.08e+00 1obpA b.60.1.1 27110 1cmkE 350 2.36e+00 1cdkA d.144.1.7 41623 1dzkA 157 2.49e+00 1obpA b.60.1.1 27096 1i9gA 280 2.65e+00 c.66.1.13 62090 1m0dA 138 2.67e+00 c.52.1.17 74354 1fokA 568 2.73e+00 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1g4uS 383 2.74e+00 1g4uS a.24.11.1 16643 c.45.1.2 32691 1gkuB 1054 2.80e+00 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 2fokA 579 2.89e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1k6zA 141 2.91e+00 d.198.1.1 68247 1fftB 315 3.11e+00 1cyx b.6.1.2 23025 f.17.2.1 43628 1aje 194 3.13e+00 1ctqA c.37.1.8 32071 1akr 147 3.48e+00 1rcf c.23.5.1 31152 1k4nA 192 3.54e+00 d.32.1.5 72059 1vkxA 273 3.64e+00 1a3qA b.1.18.1 21941 b.2.5.3 22454 1iv0A 98 3.67e+00 unknown_sccs -7667 1jkeA 145 3.75e+00 c.110.1.1 66791 1l1qA 186 3.76e+00 c.61.1.1 77653 1bu5A 147 3.81e+00 5nul c.23.5.1 31155 1q7lA 198 3.89e+00 c.56.5.4 -7886 1ycsA 199 4.08e+00 1tupA b.2.5.2 22433 1tsrA 219 4.20e+00 1tupA b.2.5.2 22437 1tupA 219 4.20e+00 1tupA b.2.5.2 22434 1t95A 240 4.20e+00 1k6iA 352 4.31e+00 c.2.1.2 68223 1uj6A 227 4.33e+00 1j9jA 247 4.45e+00 c.106.1.1 62758 1p9qC 256 4.57e+00 1v93A 296 4.67e+00 c.1.23.1 -5654 1jx4A 352 5.12e+00 unknown_sccs -10188 unknown_sccs -11898 1bd3A 243 5.23e+00 1bd3A c.61.1.1 34098 1mjgM 729 5.53e+00 e.26.1.3 79204 1vkmA 297 5.65e+00 1kmmA 424 5.73e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1uolA 219 5.76e+00 b.2.5.2 -2886 1cg2A 393 6.06e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1j8mF 297 6.14e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1nxzA 246 6.34e+00 b.122.1.2 86391 c.116.1.5 86392 1j7gA 144 6.42e+00 c.110.1.1 84130 1jykA 254 6.50e+00 c.68.1.13 67458 2fx2 147 6.51e+00 1rcf c.23.5.1 31158 1o54A 277 6.82e+00 c.66.1.13 -8095 1gqyA 475 6.90e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1f4pA 147 7.03e+00 5nul c.23.5.1 59651 1ew3A 159 7.08e+00 1mup b.60.1.1 27114 1g4wR 383 7.11e+00 1g4uS a.24.11.1 16644 c.45.1.2 32692 2fcr 173 7.45e+00 1rcf c.23.5.1 31151 1j9lA 247 7.79e+00 c.106.1.1 62762 1oaoC 729 7.79e+00 e.26.1.3 86746 1vhyA 257 8.19e+00 b.122.1.2 -5129 c.116.1.5 -6705 1jbuH 254 8.27e+00 5ptp b.47.1.2 62856 1fc6A 388 8.35e+00 1fc6A b.36.1.3 64738 c.14.1.2 64739 1j9eA 147 8.57e+00 c.23.5.1 62756 1ipiA 123 8.69e+00 c.52.1.18 66255 1gheA 177 9.17e+00 d.108.1.1 76222 1fa0A 537 9.19e+00 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1eq0A 158 9.34e+00 d.58.30.1 64909 1iknA 286 9.86e+00 1a3qA b.1.18.1 21936 b.2.5.3 22449 1v0wA 506 9.90e+00 1f0iA 504 9.91e+00 1f0iA d.136.1.2 59566 d.136.1.2 59567 1thtA 305 1.00e+01 1thtA c.69.1.13 34711 1mu5A 471 1.00e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 8abp 306 1.01e+01 8abp c.93.1.1 35647 1b00A 127 1.01e+01 3chy c.23.1.1 31122 1eluB 390 1.04e+01 1elqA c.67.1.3 34435 1eluA 390 1.05e+01 1elqA c.67.1.3 34434 1elqA 390 1.05e+01 1elqA c.67.1.3 34436 1mqsA 671 1.10e+01 e.25.1.1 79414 1oywA 523 1.10e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1om0A 274 1.10e+01 c.1.8.5 87058 1is8K 84 1.13e+01 d.205.1.1 66331 1j8yF 297 1.18e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1floA 422 1.20e+01 1floA a.60.9.1 18106 d.163.1.1 42166 1uz5A 402 1.25e+01 b.85.6.1 -5029 b.103.1.1 -5069 c.57.1.2 -7902 1viuA 203 1.25e+01 d.113.1.1 -10889 1fzrA 138 1.27e+01 1fzrA c.52.1.17 33336 1eiwA 111 1.28e+01 1eiwA c.23.3.1 31130 1heiA 451 1.29e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1nxiA 132 1.31e+01 d.58.47.1 86381 1r72A 211 1.32e+01 unknown_sccs -215 unknown_sccs -5981 1e0tA 470 1.34e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1k6xA 352 1.35e+01 c.2.1.2 68238 1fggA 261 1.35e+01 1fggA c.68.1.7 34576 1kwsA 261 1.35e+01 c.68.1.7 73083 1ctf 74 1.35e+01 1ctf d.45.1.1 38759 1p8kZ 254 1.36e+01 d.95.2.1 -10648 d.95.2.1 -10649 1mkaA 171 1.36e+01 1mkaA d.38.1.2 38543 1qwgA 251 1.37e+01 unknown_sccs -5678 1sqgA 429 1.39e+01 1ryaA 160 1.39e+01 1gdtA 183 1.40e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1nm2A 317 1.46e+01 c.19.1.1 80654 d.58.23.1 80655 1r4xA 275 1.48e+01 unknown_sccs -2846 unknown_sccs -10776 1cjbA 231 1.52e+01 1qk3A c.61.1.1 34079 1dd9A 338 1.55e+01 1dd9A e.13.1.1 43254 1pwgA 349 1.56e+01 1p3dA 475 1.61e+01 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1qmvA 197 1.61e+01 1qq2A c.47.1.10 33066 1aisA 182 1.62e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1ax4A 467 1.63e+01 1ax4A c.67.1.2 34391 1ghtA 105 1.64e+01 2rslA c.53.1.1 60526 3pte 349 1.64e+01 3pte e.3.1.1 42687 1tplA 426 1.65e+01 1ax4A c.67.1.2 34387 1cyu 98 1.66e+01 1stfI d.17.1.2 38004 1eqnA 321 1.66e+01 1dd9A e.13.1.1 43256 1n0uA 842 1.67e+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 1j5eK 129 1.68e+01 c.55.4.1 71554 1k1gA 131 1.70e+01 d.51.1.1 68015 1pk9A 237 1.71e+01 c.56.2.1 -7734 1fukA 165 1.74e+01 1fukA c.37.1.19 32409 1drmA 131 1.77e+01 1drmA d.110.3.2 40908 1lopA 164 1.78e+01 2cpl b.62.1.1 27510 1hrdA 449 1.85e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1hskA 326 1.90e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1oejA 193 1.90e+01 unknown_sccs -4461 1kvkA 395 1.91e+01 d.14.1.5 73060 d.58.26.3 73061 1gefA 123 1.92e+01 1gefA c.52.1.18 60465 1cdkA 350 1.92e+01 1cdkA d.144.1.7 41620 1pzdA 322 1.92e+01 unknown_sccs -2848 unknown_sccs -10778 1lswA 131 1.93e+01 d.110.3.2 78181 1tbd 134 1.95e+01 2tbd d.89.1.1 40240 1b6sA 355 1.95e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1j1lA 290 1.95e+01 unknown_sccs -4877 1b6rA 355 1.95e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1obpA 159 1.96e+01 1obpA b.60.1.1 27092 1omwA 689 1.97e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1o5oA 221 1.98e+01 c.61.1.1 -7954 1cxlA 686 2.00e+01 1cxlA b.1.18.2 21829 b.3.1.1 22498 b.71.1.1 27736 c.1.8.1 28723 1hruA 188 2.00e+01 1hruA d.115.1.1 40926 2tbd 134 2.01e+01 2tbd d.89.1.1 40241 1onjA 61 2.03e+01 g.7.1.1 -12530 1mplA 349 2.06e+01 e.3.1.1 79387 1p5tA 127 2.08e+01 b.55.1.2 -4368 1ne9A 335 2.13e+01 d.108.1.4 -10805 d.108.1.4 -10806 1jl0A 334 2.13e+01 1jenA d.156.1.1 63155 1e6mA 128 2.13e+01 3chy c.23.1.1 31039 1i19A 561 2.14e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1j5xA 342 2.15e+01 c.80.1.1 71591 1ot1A 686 2.15e+01 b.1.18.2 87392 b.3.1.1 87393 b.71.1.1 87394 c.1.8.1 87395 1k89 449 2.16e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1hr6B 443 2.17e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1d3cA 686 2.19e+01 1cxlA b.1.18.2 21827 b.3.1.1 22496 b.71.1.1 27734 c.1.8.1 28721 1iq4A 179 2.20e+01 1iq4A d.77.1.1 62641 1g61A 228 2.22e+01 1g61A d.126.1.1 41126 1ruxA 951 2.22e+01 1dhx 1mzbA 136 2.25e+01 unknown_sccs -266 1bby 69 2.25e+01 2bby a.4.5.15 16149 1uw4A 91 2.26e+01 unknown_sccs -10038 1nbaA 264 2.31e+01 1nbaA unknown_sccs 31753 1ecpA 238 2.31e+01 1ecpA c.56.2.1 33775 1vhcA 224 2.35e+01 c.1.10.1 -5488 1drqA 131 2.35e+01 1drmA 1msk 331 2.36e+01 1msk d.173.1.1 42495 1mb3A 124 2.36e+01 c.23.1.1 78907 1kmnD 424 2.37e+01 1adjA c.51.1.1 33185 d.104.1.1 40734 1rkqA 282 2.37e+01 c.108.1.10 -6847 2rslA 140 2.40e+01 2rslA c.53.1.1 33345 1jdw 423 2.41e+01 1jdw d.126.1.2 41129 1aa8A 347 2.43e+01 1an9A 1bgvA 449 2.45e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1j31A 262 2.46e+01 d.160.1.2 -11473 1hn0A 1021 2.49e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 1k9sA 237 2.50e+01 c.56.2.1 68359 1qr7A 350 2.50e+01 1qr7A c.1.10.4 29191 1bt4A 362 2.54e+01 1bjnA c.67.1.4 34468 1fa0B 537 2.55e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1jfuA 186 2.55e+01 c.47.1.10 62940 1hvbA 349 2.57e+01 3pte e.3.1.1 42686 2bby 69 2.58e+01 2bby a.4.5.15 16148 1jg5A 83 2.58e+01 d.205.1.1 66666 1przA 252 2.61e+01 unknown_sccs -10158 1fnmA 691 2.64e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1n6zA 105 2.70e+01 unknown_sccs 85369 1cvrA 435 2.71e+01 1cvrA b.1.18.12 21949 c.17.1.2 31006 1wwaX 109 2.73e+01 1wwcA b.1.1.4 21775 1gqwA 283 2.73e+01 b.82.2.5 70377 1httA 423 2.74e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1gy9A 283 2.75e+01 b.82.2.5 70742 2scuB 388 2.76e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1g0oA 283 2.78e+01 1ybvA c.2.1.2 60181 1qwkA 317 2.80e+01 c.1.7.1 -5237 1qhqA 140 2.82e+01 1qhqA b.6.1.1 63326 1prxA 224 2.86e+01 1prxA c.47.1.10 33076 1g7rA 594 2.88e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1jscA 630 2.89e+01 c.31.1.3 67224 c.36.1.5 67225 c.36.1.9 67226 1ddeA 338 2.90e+01 1dd9A e.13.1.1 43255 2mbr 340 2.93e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1uxy 340 2.94e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1r7lA 110 2.94e+01 1j6uA 469 2.95e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1ybvA 283 2.98e+01 1ybvA c.2.1.2 29948 1v9fA 325 3.02e+01 1apmE 350 3.04e+01 1cdkA d.144.1.7 41628 1qb4A 883 3.08e+01 c.1.12.3 74640 1fiy 883 3.08e+01 1fiy c.1.12.3 29307 1lst 239 3.08e+01 1lst c.94.1.1 35755 1eesA 178 3.08e+01 1eesA c.37.1.8 32073 1ua4A 455 3.14e+01 c.72.1.3 -8416 1ocvA 125 3.17e+01 d.17.4.3 86810 1r61A 207 3.18e+01 unknown_sccs -6086 1ge9A 184 3.22e+01 1dd5A d.67.3.1 60463 3ladA 476 3.22e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1o63A 219 3.25e+01 c.94.1.1 -8691 1qh5A 260 3.25e+01 1qh5A d.157.1.2 42057 1vhwA 253 3.26e+01 c.56.2.1 -7765 1rvkA 382 3.26e+01 c.1.11.2 -5568 d.54.1.1 -9826 1q8iA 783 3.27e+01 c.55.3.5 -7635 e.8.1.1 -11885 1o57A 291 3.29e+01 unknown_sccs -249 c.61.1.1 -7960 1p41A 291 3.29e+01 1ur1A 378 3.30e+01 c.1.8.3 -5311 5tmpA 213 3.32e+01 5tmpA c.37.1.1 31931 1qjgA 125 3.36e+01 1opy d.17.4.3 38102 1o20A 427 3.36e+01 c.82.1.1 86556 1h75A 81 3.38e+01 1h75A c.47.1.1 60716 1okrA 123 3.41e+01 unknown_sccs -235 1vj1A 363 3.43e+01 b.35.1.2 -3728 c.2.1.1 -5752 1d5wC 126 3.47e+01 1dbwA c.23.1.1 31101 1nrzA 164 3.48e+01 c.38.1.1 86131 1kwgA 645 3.48e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1kwkA 645 3.49e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1l6wA 220 3.50e+01 c.1.10.1 73632 1fjgK 129 3.50e+01 1fjfK c.55.4.1 33733 1fvgA 199 3.51e+01 1fvaA d.58.28.1 39408 1g7tA 594 3.51e+01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1ng0A 253 3.54e+01 b.121.4.7 80475 1j6zA 376 3.54e+01 1yagA c.55.1.1 62667 c.55.1.1 62668 1gmiA 136 3.56e+01 b.7.1.1 65309 1jyaA 130 3.58e+01 d.198.1.1 67453 1jqnA 883 3.60e+01 c.1.12.3 77159 1dywA 173 3.61e+01 2cpl b.62.1.1 27505 1sviA 195 3.65e+01 1prxB 224 3.67e+01 1prxA c.47.1.10 33077 1qnrA 344 3.68e+01 1qnoA c.1.8.3 28834 1rrpB 134 3.70e+01 1rrpB b.55.1.3 26995 1adjA 421 3.71e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1gveA 327 3.71e+01 c.1.7.1 70597 1muhA 481 3.76e+01 c.55.3.4 79485 1ebpA 211 3.77e+01 1eerB b.1.2.1 22023 b.1.2.1 22024 1qnoA 344 3.81e+01 1qnoA c.1.8.3 28838 1mla 309 3.86e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1hkvA 453 3.87e+01 b.49.2.3 83559 c.1.6.1 83560 2sns 149 3.88e+01 1snc b.40.1.1 24860 1euhA 475 3.91e+01 1euhA c.82.1.1 35369 1ebaA 215 3.91e+01 1eerB b.1.2.1 22015 b.1.2.1 22016 1gox 370 3.92e+01 1gox c.1.4.1 28607 1f3iA 481 3.95e+01 1b7eA 1dckA 126 3.95e+01 1dbwA c.23.1.1 31097 1vk6A 269 3.97e+01 unknown_sccs -10923 unknown_sccs -10924 1atzB 189 3.97e+01 1atzA c.62.1.1 34133 1j3vA 289 3.99e+01 a.100.1.1 -1303 c.2.1.6 -5947