# List of top-scoring protein chains for t2k-100-30-alpha 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 1jogA 146 1.03e-21 a.24.16.2 77142 1dgmA 363 1.58e-01 1bx4A c.72.1.1 34936 1buoA 121 2.60e-01 1buoA d.42.1.1 38631 1k6wA 426 2.70e-01 b.92.1.2 68236 c.1.9.5 68237 1pa7A 130 5.34e-01 a.40.1.1 -896 1mb3A 124 6.80e-01 c.23.1.1 78907 2cxbA 124 7.24e-01 1ycc a.3.1.1 15891 1dk8A 147 8.10e-01 1agrE a.91.1.1 18548 1cxc 124 9.50e-01 1ycc a.3.1.1 15890 1m5tA 124 9.86e-01 c.23.1.1 78660 1s7zA 117 1.07e+00 unknown_sccs -344 1im4A 221 1.38e+00 unknown_sccs 62581 1fp4A 492 1.60e+00 c.92.2.3 76187 1o3uA 135 1.69e+00 a.24.16.3 86615 1e6yB 433 1.70e+00 1mroB a.89.1.1 18535 d.58.31.2 39453 2minA 491 1.72e+00 1qguA c.92.2.3 35609 1m1nA 491 1.72e+00 c.92.2.3 78417 1r8iA 213 1.87e+00 unknown_sccs -411 1aua 296 1.98e+00 1aua a.5.3.1 16290 c.13.1.1 30882 3minC 491 2.01e+00 1qguA c.92.2.3 35607 1i58A 189 2.17e+00 1b3qA d.122.1.3 61773 1rxxA 421 2.25e+00 unknown_sccs -10982 2sas 185 2.32e+00 2sas a.39.1.5 17258 1nnwA 252 2.44e+00 d.159.1.5 80674 1l8qA 324 2.59e+00 a.4.12.2 77809 c.37.1.20 77810 1q08A 99 2.83e+00 a.6.1.3 -381 1ah7 245 2.89e+00 1ah7 a.124.1.1 19339 1h5rA 293 3.54e+00 c.68.1.6 65623 1qhhA 167 4.18e+00 1pjr c.37.1.19 32393 1qbqA 333 4.20e+00 1ft1A a.118.6.1 19187 1liiA 363 4.37e+00 c.72.1.1 73921 1ezfA 340 4.48e+00 1ezfA a.128.1.2 19440 1au7A 146 4.81e+00 1au7A a.4.1.1 15995 a.35.1.1 17021 1au1A 166 4.83e+00 1ifa a.26.1.3 16889 1nksA 194 4.92e+00 1nksA c.37.1.1 31886 1qzzA 374 4.95e+00 a.4.5.29 -277 c.66.1.12 -8045 1auiB 169 5.16e+00 1auiB a.39.1.5 17325 1a0p 290 5.36e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1jcqA 382 5.60e+00 a.118.6.1 66504 1rmi 160 5.61e+00 1ifa a.26.1.3 16891 1b4eA 323 5.61e+00 1b4kA c.1.10.3 29186 1cxzB 86 5.61e+00 1cxzB a.2.6.1 15705 1i8jA 323 5.70e+00 1b4kA c.1.10.3 61968 1l6sA 323 5.95e+00 c.1.10.3 73627 1gkpA 458 5.96e+00 b.92.1.3 70231 c.1.9.6 70232 1jvsA 400 6.05e+00 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1snnA 227 6.33e+00 1jcrA 377 6.54e+00 a.118.6.1 66506 1q0qA 406 6.67e+00 1jipA 403 6.74e+00 a.104.1.1 66748 1udxA 416 6.90e+00 b.117.1.1 -3546 c.37.1.8 -7101 unknown_sccs -9009 1d8dA 377 6.98e+00 1ft1A a.118.6.1 19185 1dt6A 473 6.99e+00 1dt6A a.104.1.1 18977 1miwA 404 7.09e+00 a.173.1.1 79162 d.218.1.4 79163 1j09A 468 7.27e+00 a.97.1.1 77025 c.26.1.1 77026 1pq9A 253 7.29e+00 a.123.1.1 -1687 3lynA 136 7.32e+00 1lis a.19.1.1 16413 1ld8A 382 7.43e+00 a.118.6.1 73838 1hrkA 359 7.45e+00 1hrkA c.92.1.1 61228 1ek0A 170 7.53e+00 1ctqA c.37.1.8 32076 2lisA 136 7.76e+00 1lis a.19.1.1 16405 1h5vA 304 7.87e+00 c.1.8.3 70898 1lis 136 8.15e+00 1lis a.19.1.1 16406 1fjgD 209 8.36e+00 1c05A d.66.1.2 39553 1hyqA 263 8.48e+00 1hyqA c.37.1.10 61412 1qwgA 251 8.52e+00 unknown_sccs -5678 1oxa 403 8.94e+00 1f4tA a.104.1.1 18965 1kk8B 139 9.15e+00 a.39.1.5 77430 1pvyA 227 9.35e+00 d.115.1.2 -10937 1a3h 300 9.39e+00 7a3hA c.1.8.3 28819 1j6oA 268 9.49e+00 c.1.9.12 77088 1im8A 244 9.82e+00 c.66.1.14 66212 1hg2A 289 9.93e+00 1hg5A unknown_sccs -401 unknown_sccs -1630 1h16A 759 1.01e+01 c.7.1.1 76462 7a3hA 303 1.02e+01 7a3hA c.1.8.3 28817 3crxA 343 1.03e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1jnyA 435 1.04e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1cm5A 759 1.04e+01 1cm5A c.7.1.1 30671 1mp4A 292 1.04e+01 c.68.1.6 79376 1hf8A 289 1.04e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1kbuA 349 1.07e+01 a.60.9.1 72284 d.163.1.1 72285 1k5hA 398 1.07e+01 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1wdcB 156 1.09e+01 1wdcB a.39.1.5 17302 1fmjA 351 1.10e+01 c.37.1.5 59879 1ft1A 377 1.11e+01 1ft1A a.118.6.1 19186 1f74A 293 1.11e+01 1nal3 c.1.10.1 29079 1mxgA 435 1.12e+01 b.71.1.1 85193 c.1.8.1 85194 1rx0A 393 1.13e+01 a.29.3.1 -742 e.6.1.1 -11858 2tct 207 1.14e+01 2tct a.4.1.9 16063 a.121.1.1 19240 1e4yA 214 1.19e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1ukz 203 1.19e+01 1zin c.37.1.1 31840 1f6kA 293 1.20e+01 1nal3 c.1.10.1 29081 1oasA 322 1.20e+01 1oasA c.79.1.1 35293 1gumA 222 1.24e+01 1pgtA a.45.1.1 17683 c.47.1.5 32977 1hg5A 289 1.27e+01 1hg5A unknown_sccs -400 unknown_sccs -1629 1f44A 324 1.27e+01 a.60.9.1 64982 d.163.1.1 64983 1dat 174 1.29e+01 2fha a.25.1.1 16677 1jae 471 1.30e+01 1smd b.71.1.1 27773 c.1.8.1 28760 1crxA 322 1.32e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1l3lA 234 1.34e+01 a.4.6.2 73541 d.110.5.1 73542 1t7pA 698 1.34e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1fpoA 171 1.34e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1okrA 123 1.35e+01 unknown_sccs -235 4crxA 322 1.36e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1mvoA 136 1.37e+01 c.23.1.1 79513 1gulA 222 1.39e+01 1pgtA a.45.1.1 17675 c.47.1.5 32969 1k8tA 510 1.40e+01 e.41.1.1 68316 1q1aA 289 1.44e+01 c.31.1.5 -6781 1rktA 205 1.45e+01 a.4.1.9 -210 a.121.1.1 -1663 1pufB 73 1.46e+01 a.4.1.1 -192 1dr8B 344 1.48e+01 1cnzA c.77.1.1 35052 1a6r 471 1.51e+01 3gcb d.3.1.1 37033 1i36A 264 1.53e+01 a.100.1.8 71108 c.2.1.6 71109 1b72B 87 1.54e+01 1akhA a.4.1.1 16001 1jj2B 337 1.56e+01 1ffkB b.43.3.2 63086 1s72B 338 1.56e+01 1thfD 253 1.58e+01 1thfD c.1.2.1 28535 1gxqA 106 1.60e+01 a.4.6.1 70721 1or7A 194 1.61e+01 a.4.13.2 87332 a.177.1.1 87333 1g59A 468 1.62e+01 a.97.1.1 60257 c.26.1.1 60258 1aew 174 1.63e+01 2fha a.25.1.1 16676 1aqm 453 1.63e+01 1smd b.71.1.1 27717 c.1.8.1 28704 1gkzA 388 1.64e+01 a.29.5.1 65268 d.122.1.4 65269 1oxkB 134 1.64e+01 c.23.1.1 -6411 1g94A 448 1.65e+01 b.71.1.1 65169 c.1.8.1 65170 1p9bA 442 1.70e+01 c.37.1.10 -7115 1v54E 109 1.71e+01 a.118.11.1 -1652 1akhA 61 1.77e+01 1akhA a.4.1.1 15980 2igd 61 1.80e+01 2igd d.15.7.1 37821 2pflA 759 1.80e+01 1cm5A c.7.1.1 30675 1alvA 173 1.81e+01 1alvA a.39.1.8 17370 1igd 61 1.82e+01 2igd d.15.7.1 37822 1mc3A 296 1.82e+01 c.68.1.6 78943 2fokA 579 1.82e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1tmy 120 1.85e+01 1dbwA c.23.1.1 31083 1pgx 83 1.86e+01 2igd d.15.7.1 37823 1bp3A 191 1.90e+01 1huw a.26.1.1 16838 1b0b 142 1.90e+01 2fal a.1.1.2 15010 1cjcA 460 1.91e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1pjr 724 1.92e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1fcjA 322 1.92e+01 1oasA c.79.1.1 35289 1f7uA 607 1.95e+01 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1vh7A 265 1.99e+01 c.1.2.1 -5159 1gln 468 2.01e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1su8A 636 2.02e+01 e.26.1.2 -12015 1paqA 189 2.02e+01 unknown_sccs -1557 5eau 548 2.02e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1jjyA 636 2.02e+01 1jjyA 1aoy 78 2.05e+01 1aoy a.4.5.3 16087 1bk5A 422 2.05e+01 1bk5A a.118.1.1 19130 3pflA 759 2.08e+01 1cm5A c.7.1.1 30673 1mx3A 347 2.09e+01 c.2.1.4 79638 c.23.12.1 79639 1oj7A 408 2.09e+01 1moh 142 2.11e+01 1flp a.1.1.2 15012 1eq1A 166 2.12e+01 a.63.1.1 64910 1b43A 340 2.12e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1jfkA 134 2.12e+01 a.39.1.5 66639 1gkxA 388 2.14e+01 a.29.5.1 65266 d.122.1.4 65267 1izmA 184 2.19e+01 unknown_sccs -1233 1gr8A 412 2.23e+01 1ockA 412 2.23e+01 c.117.1.1 86802 3gcb 470 2.23e+01 3gcb d.3.1.1 37032 1lvaA 258 2.24e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1iqpA 327 2.24e+01 a.80.1.1 62649 c.37.1.20 62650 1na3A 91 2.25e+01 k.38.1.1 85481 1flp 142 2.26e+01 1flp a.1.1.2 15011 1uiiA 83 2.27e+01 1akeA 214 2.27e+01 1zin c.37.1.1 31905 g.41.2.1 45185 1sqsA 242 2.31e+01 unknown_sccs -6433 1vhzA 198 2.35e+01 d.113.1.1 -10897 1cby 259 2.39e+01 1cby d.103.1.1 40705 1eqfA 280 2.44e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1d3uB 201 2.46e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 2cblA 305 2.47e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1jcrB 437 2.47e+01 a.102.4.3 66507 3kvt 115 2.47e+01 1t1dA d.42.1.2 38642 6gsvA 217 2.53e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1a76 326 2.53e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 1zin 217 2.54e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1e8gA 560 2.58e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1ns1A 73 2.59e+01 1ail a.16.1.1 16382 1e7uA 961 2.59e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1ee4A 423 2.63e+01 1ee4A a.118.1.1 19128 1k3yA 221 2.63e+01 a.45.1.1 77245 c.47.1.5 77246 1rkpA 326 2.64e+01 a.125.1.1 -1729 1iw7C 1119 2.65e+01 e.29.1.1 71474 1ccwA 137 2.66e+01 1be1 c.23.6.1 31238 1idm 343 2.66e+01 1cnzA c.77.1.1 35035 1gcb 454 2.68e+01 3gcb d.3.1.1 37034 1ail 73 2.70e+01 1ail a.16.1.1 16381 1qltA 560 2.73e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1k3lA 221 2.75e+01 a.45.1.1 77229 c.47.1.5 77230 2occE 109 2.78e+01 2occE a.118.11.1 19224 1afrA 345 2.79e+01 1afrA a.25.1.2 16805 1yrnA 61 2.80e+01 1akhA a.4.1.1 15981 1apyA 162 2.81e+01 1apyA d.153.1.5 42004 1oi6A 205 2.84e+01 1f08A 148 2.86e+01 1f08A d.89.1.2 59564 16vpA 366 2.89e+01 16vpA d.180.1.1 42601 1r5pA 108 2.89e+01 unknown_sccs -7487 1brlA 355 2.93e+01 1lucA c.1.16.1 29553 1a7tA 232 2.97e+01 1a7tA d.157.1.1 42041 1go3F 107 2.99e+01 a.60.8.2 65407 1oa4A 222 3.02e+01 b.29.1.11 86731 1d8dB 437 3.05e+01 1ft1B a.102.4.3 18866 1m5yA 408 3.07e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1ku1A 230 3.08e+01 a.118.3.1 72996 1qqiA 104 3.10e+01 1opc a.4.6.1 16233 1jigA 146 3.12e+01 a.25.1.1 71685 1oi7A 288 3.15e+01 c.2.1.8 87049 c.23.4.1 87050 1f6fA 199 3.21e+01 1f6fA a.26.1.1 16839 1uaaA 673 3.23e+01 1pjr c.37.1.19 32401 c.37.1.19 32402 1gseA 221 3.23e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1b8xA 280 3.24e+01 1b8xA a.45.1.1 17739 c.47.1.5 33033 1scmB 145 3.25e+01 1wdcB a.39.1.5 17304 1vaoA 560 3.26e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1brwA 433 3.29e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1cs1C 386 3.29e+01 1ibjA c.67.1.3 34401 1qrjB 199 3.29e+01 1qrjB a.28.3.1 16952 1aq6A 253 3.29e+01 1qq5A c.108.1.1 43331 1knqA 175 3.30e+01 c.37.1.17 72786 2mysB 166 3.32e+01 1wdcB a.39.1.5 17308 1de6A 426 3.34e+01 1de5A c.1.15.2 29398 1ofnA 205 3.35e+01 b.82.1.1 -4830 1j99A 293 3.37e+01 c.37.1.5 71618 1ngvA 534 3.40e+01 c.111.1.2 85698 1e8xA 961 3.40e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1vpwA 340 3.41e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1b47A 304 3.41e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 5eat 548 3.46e+01 5eat a.102.4.1 18853 a.128.1.3 19445 1dgsA 667 3.47e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 2gsq 202 3.48e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1qlaA 656 3.49e+01 1qlaA a.7.3.1 16328 c.3.1.4 30427 d.168.1.1 42310 1isiA 265 3.49e+01 e.4.1.1 71394 1icrA 217 3.50e+01 1vfrA d.90.1.1 62274 1hssA 124 3.58e+01 1bea a.52.1.2 17819 1dbqA 289 3.59e+01 1qpzA c.93.1.1 35666 1oq9A 363 3.61e+01 a.25.1.2 87257 1lehA 364 3.63e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1a8y 367 3.64e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1dl2A 511 3.65e+01 1dl2A a.102.2.1 18844 1d8wA 426 3.67e+01 1de5A c.1.15.2 29394 1eupA 403 3.70e+01 1rom a.104.1.1 18967 1g60A 260 3.71e+01 c.66.1.11 70151 1hw1A 239 3.71e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1h40A 71 3.74e+01 1d1qA 161 3.77e+01 1dg9A c.44.1.1 32642 1s0aA 429 3.79e+01 c.67.1.4 -8201 1qj5A 429 3.82e+01 1dtyA c.67.1.4 34493 1js8A 394 3.84e+01 a.86.1.1 67219 b.112.1.1 67220 1dugA 234 3.86e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1m6kA 251 3.89e+01 e.3.1.1 78695 1hh8A 213 3.99e+01 1e96B a.118.8.1 61042 1ufbA 127 3.99e+01 a.24.16.3 -635 1g8iA 190 3.99e+01 1rec a.39.1.5 60363