# List of top-scoring protein chains for t06-100-30-bys-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 1svmA 377 6.96e-02 2db0A 253 1.03e-01 1edg 380 2.77e-01 1edg c.1.8.3 28807 1ugpA 203 3.82e-01 d.149.1.1 107831 256bA 106 4.69e-01 256bA a.24.3.1 16539 1z5hA 780 5.72e-01 1odfA 290 7.37e-01 c.37.1.6 92782 2gshA 414 7.98e-01 2a97A 439 9.02e-01 1t1uA 639 1.07e+00 1h1dA 221 1.09e+00 c.66.1.1 83452 1otvA 259 1.36e+00 a.132.1.4 93526 1jy5A 212 2.02e+00 d.124.1.1 71940 1dd9A 338 2.08e+00 1dd9A e.13.1.1 43254 2cosA 54 2.23e+00 1hssA 124 2.34e+00 1bea a.52.1.2 17819 1g8iA 190 2.76e+00 1rec a.39.1.5 60363 1psrA 100 2.81e+00 1psrA a.39.1.2 17180 1dzkA 157 2.92e+00 1obpA b.60.1.1 27096 1zgyA 272 2.93e+00 1avsA 90 3.08e+00 1cll a.39.1.5 17226 1e8gA 560 3.19e+00 1qltA d.58.32.1,d.145.1.1 39455,41718 1zkdA 387 3.22e+00 1k9uA 78 3.28e+00 a.39.1.10 84348 1k8kA 418 3.38e+00 c.55.1.1,c.55.1.1 68305,68306 1yz4A 160 3.65e+00 1xnfA 275 4.13e+00 1e7lA 157 4.45e+00 1en7A a.140.4.1,d.4.1.5 64728,64729 2cw6A 298 4.48e+00 1ff9A 450 4.72e+00 1ff9A c.2.1.3,d.81.1.2 30039,39954 1hnjA 317 4.83e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 1qv1A 195 4.88e+00 a.39.1.5 96347 1lfkA 398 5.00e+00 a.104.1.1 77926 1ls1A 295 5.16e+00 a.24.13.1,c.37.1.10 78170,78171 1apyB 141 5.19e+00 1apyB 2a3qA 170 5.35e+00 1gnwA 211 5.37e+00 1gnwA a.45.1.1,c.47.1.5 17727,33021 2ap1A 327 5.48e+00 1l7mA 211 5.71e+00 c.108.1.4 73664 1l3iA 192 6.41e+00 c.66.1.22 77676 1a6s 87 6.60e+00 1a6s a.61.1.4 18134 1zpyA 95 6.66e+00 1j55A 95 6.70e+00 a.39.1.2 77078 1sgmA 191 6.78e+00 a.4.1.9,a.121.1.1 105537,105538 1oe4A 247 7.12e+00 c.18.1.3 86895 2fwhA 134 7.38e+00 1oksA 56 7.50e+00 a.8.5.1 93271 1s6cA 183 7.71e+00 a.39.1.5 98594 2bo3A 94 7.76e+00 1ir6A 424 7.97e+00 c.107.1.2 71342 2czdA 208 8.04e+00 2gb7A 305 8.05e+00 1uc7A 125 8.30e+00 c.47.1.1 99163 1y10A 407 8.47e+00 1b79A 119 8.72e+00 1b79A a.81.1.1 18451 1l1qA 186 8.78e+00 c.61.1.1 77653 1i2aA 219 9.02e+00 e.24.1.1 90660 1fp2A 352 9.03e+00 1fpxA a.4.5.29,c.66.1.12 59941,59942 1rr7A 129 9.27e+00 a.4.1.14 105075 1rvkA 382 9.63e+00 c.1.11.2,d.54.1.1 97928,97929 1jogA 146 9.76e+00 a.24.16.2 77142 2fcjA 119 1.00e+01 1zchA 255 1.00e+01 1np3A 338 1.00e+01 a.100.1.2,c.2.1.6 85946,85947 2fpqA 444 1.04e+01 1pfvA 551 1.06e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1h99A 224 1.07e+01 a.142.1.1,a.142.1.1 60814,60815 1pmi 440 1.07e+01 1pmi b.82.1.3 28114 1m5iA 125 1.09e+01 h.4.13.1 78648 2fbnA 198 1.10e+01 2c46A 241 1.10e+01 1zt2B 212 1.12e+01 1tkkA 366 1.13e+01 c.1.11.2,d.54.1.1 107089,107090 1v4vA 376 1.15e+01 c.87.1.3 100313 1czaN 917 1.16e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1w6sB 74 1.20e+01 1me8A 503 1.25e+01 c.1.5.1 79028 1auiB 169 1.27e+01 1auiB a.39.1.5 17325 1f9yA 158 1.27e+01 d.58.30.1 83249 1idrA 136 1.36e+01 1dlyA a.1.1.1 62301 1eu1A 780 1.37e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1rcwA 231 1.38e+01 a.132.1.4 97299 1wmaA 276 1.39e+01 1zs9A 261 1.41e+01 1hp1A 516 1.48e+01 d.114.1.1,d.159.1.2 70976,70977 1ei6A 406 1.50e+01 c.76.1.4 90443 1cg5A 141 1.52e+01 1abwA a.1.1.2 15406 1u61A 138 1.53e+01 a.149.1.1 107696 1m0uA 249 1.54e+01 a.45.1.1,c.47.1.5 78359,78360 1jjfA 268 1.55e+01 c.69.1.2 66765 7aatA 401 1.55e+01 1ajsA c.67.1.1 34250 1z8oA 404 1.57e+01 1np6A 174 1.58e+01 c.37.1.10 85954 1u5tB 169 1.59e+01 a.4.5.54,a.4.5.54 107686,107687 1twyA 290 1.73e+01 1bf5A 545 1.73e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1rrzA 86 1.73e+01 a.7.10.1 105086 1on3A 523 1.75e+01 c.14.1.4,c.14.1.4 87107,87108 1i7nA 309 1.86e+01 c.30.1.5,d.142.1.3 83681,83682 1hb6A 86 1.88e+01 a.11.1.1 70959 1uhnA 189 1.94e+01 a.39.1.5 99399 1j5wA 298 1.95e+01 d.104.1.1 71589 1wy9A 147 1.98e+01 1q8cA 151 1.99e+01 a.79.1.2 96202 1wiwA 290 2.01e+01 1xwmA 217 2.03e+01 2amxA 376 2.05e+01 1gtzA 156 2.07e+01 c.23.13.1 70539 2csbA 519 2.09e+01 2aqjA 538 2.09e+01 1u04A 771 2.09e+01 b.34.14.1,c.55.3.10 107539,107540 1mhnA 59 2.12e+01 b.34.9.1 84964 1zczA 464 2.19e+01 2vhbA 146 2.20e+01 2vhbA a.1.1.2 15629 1qwgA 251 2.26e+01 c.1.27.1 96473 2gl5A 410 2.27e+01 1uz3A 102 2.31e+01 2au3A 407 2.31e+01 2bl0C 142 2.33e+01 1w68A 390 2.33e+01 a.25.1.2 109216 1wx1A 335 2.33e+01 2gi3A 476 2.38e+01 2d13A 227 2.39e+01 1lr7A 74 2.40e+01 g.3.11.3,g.68.1.1 84679,84680 1s0yA 76 2.40e+01 d.80.1.1 98314 1lbu 213 2.41e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1ctj 89 2.42e+01 1ctj a.3.1.1 15798 1wkbA 810 2.44e+01 1dzaA 129 2.47e+01 7rsa d.5.1.1 37275 2f6mB 109 2.50e+01 1pmzA 86 2.55e+01 a.39.1.10 104195 1vi0A 206 2.56e+01 a.4.1.9,a.121.1.1 100720,100721 1sz2A 332 2.56e+01 1vk4A 298 2.57e+01 c.72.1.1 100850 1dkzA 219 2.57e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1ztcA 221 2.59e+01 1wmwA 330 2.66e+01 1vb5A 276 2.68e+01 1uanA 227 2.69e+01 c.134.1.1 99135 1xouB 95 2.69e+01 1rljA 139 2.72e+01 c.23.5.7 104983 1ztsA 139 2.72e+01 1te5A 257 2.75e+01 d.153.1.1 106795 1rxwA 336 2.75e+01 a.60.7.1,c.120.1.2 98059,98060 1vlaA 150 2.80e+01 d.227.1.2 108735 1q1rA 431 2.80e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1nmeA 146 2.80e+01 c.17.1.1 85874 1nbwA 607 2.81e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1zroA 602 2.81e+01 2a61A 145 2.88e+01 1nh2D 121 2.88e+01 a.32.1.1,b.56.1.1 91876,91877 2b0oE 301 2.97e+01 1h2sA 225 3.03e+01 f.13.1.1 76578 1mexH 215 3.04e+01 b.1.1.1,b.1.1.2 91257,91258 1p80A 753 3.10e+01 c.23.16.3,e.5.1.1 94337,94338 1wu7A 434 3.11e+01 2anuA 255 3.26e+01 1uarA 285 3.28e+01 c.46.1.2,c.46.1.2 107762,107763 1yge 839 3.29e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1fpoA 171 3.29e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 1cby 259 3.33e+01 1cby d.103.1.1 40705 1rqtA 37 3.34e+01 a.108.1.1 97771 1wy6A 172 3.36e+01 1pcfA 66 3.42e+01 1pcfA d.18.1.1 38142 1yfsA 465 3.44e+01 1mqoA 227 3.45e+01 d.157.1.1 103846 1vefA 395 3.49e+01 1unkA 87 3.53e+01 1cei a.28.2.1 16935 1tv8A 340 3.53e+01 c.1.28.3 107352 2be4A 272 3.53e+01 1u4bA 580 3.56e+01 c.55.3.5,e.8.1.1 107664,107665 2b4wA 315 3.57e+01 2g7sA 194 3.58e+01 1tu9A 134 3.58e+01 a.1.1.2 107320 1f2vA 219 3.60e+01 1f2vA c.23.17.1 59627 1gweA 503 3.60e+01 e.5.1.1 70667 1ex0A 731 3.61e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1u09A 476 3.63e+01 e.8.1.4 107545 1wdjA 187 3.68e+01 1r0mA 375 3.69e+01 c.1.11.2,d.54.1.1 104747,104748 1kzyC 259 3.72e+01 c.15.1.4,c.15.1.4 73383,73384 1fpzA 212 3.75e+01 1fpzA c.45.1.1 59976 1uedA 406 3.75e+01 a.104.1.1 99256 1yqtA 538 3.79e+01 1lla 628 3.82e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1j1bA 420 3.84e+01 d.144.1.7 90758 1z2aA 168 3.84e+01 1ulyA 192 3.86e+01 2f0aA 98 3.92e+01 1pxqA 35 3.92e+01 j.5.1.2 104382 2bk9A 153 3.92e+01 1su8A 636 3.93e+01 e.26.1.2 98999 1z8sA 146 3.93e+01 1u55A 188 3.95e+01 d.278.1.1 107677 1epwA 1290 3.96e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1j8uA 325 3.96e+01 d.178.1.1 71611 1c44A 123 3.97e+01 1qndA d.106.1.1 40795 1p2xA 159 3.97e+01 a.40.1.1 104062 2bl0B 145 4.01e+01 1dv1A 449 4.13e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1on2A 142 4.18e+01 a.4.5.24,a.76.1.1 87103,87104 2czvC 120 4.18e+01 1k66A 149 4.19e+01 c.23.1.1 90941 1n4qB 377 4.23e+01 a.102.4.3 91636 1w19A 160 4.24e+01 2aa4A 289 4.24e+01 1fyhB 229 4.25e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1ygmA 118 4.25e+01 2a3nA 355 4.26e+01 1r1hA 696 4.30e+01 d.92.1.4 104756 1v4pA 157 4.31e+01 2ga1A 106 4.33e+01 1jfzA 154 4.39e+01 a.149.1.1 66655 1ois 223 4.42e+01 1a36A e.15.1.1 43267 2fk8A 318 4.44e+01 1e0eA 55 4.44e+01 1wjcA a.4.10.1 59147 1eueA 86 4.45e+01 1cyo d.120.1.1 59504 1gnlA 544 4.51e+01 e.26.1.1 70287 2iu5A 195 4.51e+01 1ji1A 637 4.52e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1rz4A 226 4.54e+01 a.4.5.53,a.118.1.18 105131,105132 1vhtA 218 4.59e+01 c.37.1.1 100700 1m0kA 262 4.62e+01 f.13.1.1 78344 1chuA 540 4.64e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1h0hA 977 4.66e+01 b.52.2.2,c.81.1.1 76435,76436 1rtwA 220 4.71e+01 a.132.1.3 97823 2akzA 439 4.71e+01 1jkxA 212 4.73e+01 c.65.1.1 66813 1k2eA 156 4.76e+01 d.113.1.1 72010 1eyvA 156 4.76e+01 1eyvA a.79.1.1 18446 1l3eB 101 4.78e+01 g.53.1.1 73536 1oq9A 363 4.79e+01 a.25.1.2 87257 1s0pA 176 4.81e+01 a.192.1.1 98300 2fkiA 126 4.95e+01 1pprM 312 5.01e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1yy7A 213 5.03e+01 1h7zA 194 5.03e+01 1qhvA b.21.1.1 60733 1ctf 74 5.07e+01 1ctf d.45.1.1 38759 1nijA 318 5.11e+01 c.37.1.10,d.237.1.1 85741,85742 1qh8A 478 5.12e+01 1qguA c.92.2.3 35633 1xl7A 612 5.12e+01 1wlsA 328 5.16e+01 1wm1A 317 5.16e+01 c.69.1.7 109405 1iruK 201 5.16e+01 d.153.1.4 71362 1sauA 115 5.20e+01 1j2jB 45 5.24e+01 a.7.8.1 84017 2b1fA 34 5.31e+01 1w9yA 319 5.36e+01 2b8iA 77 5.36e+01 1tr8A 102 5.39e+01 1j24A 143 5.40e+01 c.52.1.20 84008 1w3iA 293 5.41e+01 c.1.10.1 109152 1hfoA 113 5.41e+01 d.80.1.3 61006 2axiA 115 5.43e+01 2gwfB 134 5.51e+01 1qo7A 394 5.56e+01 1qo7A c.69.1.11 34697 1g4wR 383 5.57e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1r9jA 673 5.57e+01 1u6eA 335 5.58e+01 2cp8A 54 5.67e+01 2gsq 202 5.70e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1a3aA 148 5.72e+01 1a3aA d.112.1.1 40917 1zq9A 285 5.77e+01 1tif 78 5.79e+01 1tif d.15.8.1 37836 1rxqA 178 5.83e+01 a.213.1.1 105118 2aaoA 166 5.88e+01 1v7wA 807 5.88e+01 a.102.1.4,b.30.5.3 108411,108412 1v71A 323 5.98e+01 1yk4A 52 6.00e+01 1ejgA 46 6.00e+01 1cbn g.13.1.1 44618 1j1qA 261 6.03e+01 d.165.1.1 90768 2hddA 61 6.08e+01 2hddA a.4.1.1 15971 1iro 54 6.17e+01 1rb9 g.41.5.1 45223 2f8xM 63 6.23e+01 1vkwA 218 6.33e+01 d.90.1.2 108695 1x46A 150 6.33e+01 1jb0I 38 6.35e+01 1jb0I f.23.17.1 62826 3nul 130 6.38e+01 3nul d.110.1.1 40891 1ad1A 266 6.38e+01 1aj2 c.1.21.1 29668 2as0A 396 6.40e+01 2bg9A 370 6.45e+01 1obbA 480 6.53e+01 c.2.1.5,d.162.1.2 86760,86761 1uh4A 637 6.56e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1v7nV 163 6.59e+01 a.26.1.2 100476 2b7uA 257 6.63e+01 1wu9A 80 6.74e+01 1iu4A 331 6.81e+01 d.3.1.8 71430 1v1aA 309 6.87e+01 c.72.1.1 100249 1zc6A 305 6.88e+01 2arpF 152 6.89e+01 1wn5A 130 7.00e+01 1l7vA 326 7.02e+01 f.22.1.1 73672 2bwfA 77 7.02e+01 1cr1A 296 7.03e+01 1cr1A c.37.1.11 32286 1q5dA 419 7.05e+01 a.104.1.1 95891 1v54A 514 7.05e+01 f.24.1.1 100321 1wvfA 520 7.07e+01 1n97A 389 7.11e+01 a.104.1.1 80335 1v54G 85 7.12e+01 f.23.2.1 100328 1r9lA 309 7.15e+01 c.94.1.1 97262 1r6fA 310 7.21e+01 e.46.1.1 97149 1wu3I 161 7.25e+01 1e5kA 201 7.39e+01 1fr9A c.68.1.8 34578 1lehA 364 7.40e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1lj9A 144 7.53e+01 a.4.5.28 78035 1brfA 53 7.54e+01 1rb9 g.41.5.1 45236 5csmA 256 7.60e+01 5csmA a.130.1.2 19494 1yoeA 322 7.63e+01 1o2dA 371 7.66e+01 e.22.1.2 86591 1wxiA 275 7.67e+01 1j6rA 214 7.71e+01 d.173.1.2 71598 1sszA 34 7.74e+01 j.35.1.1 105999 1wa8A 99 7.81e+01 1j8fA 323 7.83e+01 1j8fA c.31.1.5 62738 2cvcA 545 7.85e+01 2fbwA 621 7.85e+01 1wy0A 342 7.86e+01 1uwcA 261 7.90e+01 c.69.1.17 100101 1x3mA 415 7.92e+01 2bg5A 324 7.95e+01 2ahqA 76 8.00e+01 1k6kA 143 8.03e+01 a.174.1.1 77274 2bgcA 238 8.24e+01 2gfnA 209 8.31e+01 1uocA 289 8.34e+01 c.55.3.9 99686 1zarA 282 8.37e+01 1f1eA 154 8.38e+01 a.22.1.2 64927 1bea 127 8.44e+01 1bea a.52.1.2 17826 1dtdB 61 8.45e+01 1dtvA g.30.1.1 44962 1o5zA 442 8.47e+01 c.59.1.2,c.72.2.2 92530,92531 1o26A 232 8.50e+01 d.207.1.1 86566 1t15A 214 8.52e+01 c.15.1.3,c.15.1.3 99067,99068 1dkmA 410 8.52e+01 1dklA c.60.1.2 34000 2h3bA 494 8.52e+01 1iow 306 8.53e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1ni4B 341 8.55e+01 c.36.1.7,c.48.1.2 85729,85730 1mijA 152 8.59e+01 a.4.1.1 79150 1gsoA 431 8.62e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1gw5S 142 8.62e+01 d.110.4.2 70633 1pufB 73 8.68e+01 a.4.1.1 95132 1jayA 212 8.70e+01 c.2.1.6 66478 1obdA 306 8.80e+01 d.143.1.1 86767 1wstA 417 8.84e+01 1iv3A 152 8.86e+01 d.79.5.1 76828 1gqvA 135 8.96e+01 d.5.1.1 70376 1df4A 68 8.99e+01 1aikN h.3.2.1 45719