# 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 1top 162 3.71e-02 1ncx a.39.1.5 17223 1npyA 271 8.89e-02 c.2.1.7 85995 c.58.1.5 85996 1q0uA 219 2.83e-01 c.37.1.19 -7205 1kgdA 180 3.41e-01 c.37.1.1 68582 1nt4A 391 4.51e-01 c.60.1.2 -7942 1ggzA 148 4.61e-01 a.39.1.5 70176 1qdeA 224 4.83e-01 1qvaA c.37.1.19 32410 1vi2A 300 5.95e-01 c.2.1.7 -5960 c.58.1.5 -6366 1pg4A 652 6.43e-01 e.23.1.1 88067 1j6pA 418 6.75e-01 b.92.1.4 77089 c.1.9.9 77090 1p1mA 406 7.40e-01 b.92.1.4 87696 c.1.9.9 87697 1s96A 219 8.38e-01 c.37.1.1 -6972 1lf6A 684 9.23e-01 a.102.1.5 77918 b.30.5.5 77919 1wm1A 317 1.05e+00 1hv9A 456 1.06e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1efyA 350 1.06e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1qtrA 317 1.15e+00 1qtrA c.69.1.7 34660 1nf2A 268 1.19e+00 c.108.1.10 -6842 1k9uA 78 1.21e+00 a.39.1.10 84348 1g7fA 298 1.54e+00 1pty c.45.1.2 60330 1hqkA 154 1.63e+00 c.16.1.1 65902 1f5jA 199 1.69e+00 1axkA b.29.1.11 24342 1fgs 428 1.70e+00 1fgs c.59.1.2 33959 c.72.2.2 34962 1a4iA 301 1.72e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 3htsB 102 1.92e+00 2hts a.4.5.22 16175 1g8iA 190 1.96e+00 1rec a.39.1.5 60363 1qtwA 285 2.04e+00 1qumA c.1.15.1 29392 1ex7A 186 2.18e+00 1gky c.37.1.1 59537 1jhfA 202 2.22e+00 a.4.5.2 63057 b.87.1.1 63058 1kjwA 295 2.34e+00 b.34.2.1 68643 c.37.1.1 68644 1gnlA 544 2.36e+00 e.26.1.1 70287 1czaN 917 2.38e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1smlA 269 2.43e+00 1smlA d.157.1.1 42053 1gky 187 2.53e+00 1gky c.37.1.1 31839 1g4yR 148 2.70e+00 1cll a.39.1.5 60252 1mwwA 128 3.04e+00 unknown_sccs -10451 1aerA 205 3.14e+00 1aerA d.166.1.1 42249 1cc1S 283 3.20e+00 2frvA e.19.1.1 43313 1ef1A 294 3.30e+00 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1g2iA 166 3.35e+00 1g2iA c.23.16.2 31438 1jx2B 315 3.42e+00 c.37.1.8 67404 1s29A 92 3.50e+00 unknown_sccs -315 1auiB 169 3.50e+00 1auiB a.39.1.5 17325 1lfpA 249 3.52e+00 e.39.1.1 73885 1b8aA 438 3.92e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1iyeA 309 3.99e+00 e.17.1.1 83786 2liv 344 3.99e+00 2liv c.93.1.1 35708 1qxhA 167 4.35e+00 c.47.1.10 -7496 1qcsA 211 4.52e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 1o66A 275 4.68e+00 c.1.12.8 -5590 1mup 166 4.98e+00 1mup b.60.1.1 27133 1fxjA 331 4.99e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1sgoA 139 5.06e+00 unknown_sccs -10487 1k0sA 151 5.26e+00 b.40.7.1 67969 4pep 326 5.33e+00 1smrA b.50.1.2 26843 1ok7A 366 5.38e+00 3psg 370 5.50e+00 1smrA b.50.1.2 26841 1plq 258 5.81e+00 1plq d.131.1.2 41388 d.131.1.2 41389 1wdcC 156 5.83e+00 1wdcC a.39.1.5 17317 1b5fA 239 6.17e+00 1smrA b.50.1.2 26836 1t9kA 347 6.56e+00 1uiuA 502 6.67e+00 c.94.1.1 -8674 1igwA 434 6.93e+00 c.1.12.7 62370 1sxjE 354 6.96e+00 1s6cA 183 7.17e+00 a.39.1.5 -858 1se0A 116 7.57e+00 g.52.1.1 -12841 1i2aA 219 8.11e+00 e.24.1.1 -12012 1hc7A 477 8.19e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 1mrzA 293 8.22e+00 b.43.5.1 -4048 c.26.1.3 -6616 1g57A 217 8.29e+00 1g57A d.115.1.2 60253 2polA 366 8.32e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1h4vB 421 8.37e+00 1adjA c.51.1.1 60624 d.104.1.1 60625 1lfwA 470 8.57e+00 c.56.5.4 77942 d.58.19.1 77943 1ptvA 321 8.75e+00 1pty c.45.1.2 32665 1adjA 421 8.78e+00 1adjA c.51.1.1 33188 d.104.1.1 40737 1s4qA 228 9.00e+00 c.37.1.1 -6975 1jv4A 162 9.07e+00 b.60.1.1 67343 1m45A 148 9.16e+00 a.39.1.5 78598 1euhA 475 9.20e+00 1euhA c.82.1.1 35369 1xypA 190 9.29e+00 1axkA b.29.1.11 24327 1lucB 324 9.30e+00 1lucA c.1.16.1 29548 1i1kA 309 9.55e+00 1daaA e.17.1.1 61533 1kq3A 376 9.66e+00 e.22.1.2 68790 1larA 575 9.72e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1mmiA 366 9.73e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1qh7A 207 9.74e+00 1axkA b.29.1.11 24317 1op3H 225 9.78e+00 b.1.1.1 87208 b.1.1.2 87209 1e0cA 271 9.90e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1kgsA 225 1.02e+01 a.4.6.1 68596 c.23.1.1 68597 1p9qC 256 1.07e+01 1n0uA 842 1.08e+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 1gxrA 337 1.13e+01 b.69.4.1 70722 1otgA 125 1.16e+01 1otgA d.80.1.2 39831 1jlnA 297 1.17e+01 1pty c.45.1.2 63172 1sy6A 204 1.18e+01 1i05A 180 1.18e+01 1mup b.60.1.1 27130 1e5dA 402 1.19e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1hk9A 74 1.19e+01 b.38.1.2 83541 1vjqA 79 1.21e+01 unknown_sccs -13478 1kwmA 402 1.21e+01 c.56.5.1 73079 d.58.3.1 73080 1ir6A 424 1.29e+01 c.107.1.2 71342 1qamA 244 1.34e+01 2ercA c.66.1.24 34220 1brt 277 1.36e+01 1brt c.69.1.12 34699 1i06A 180 1.36e+01 1mup b.60.1.1 27131 1f6yA 262 1.38e+01 1f6yA c.1.21.2 29673 1kxqE 120 1.38e+01 b.1.1.1 73171 1m7xA 617 1.39e+01 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1broA 277 1.40e+01 1brt c.69.1.12 34700 1l4uA 176 1.41e+01 c.37.1.2 73568 1pvxA 194 1.42e+01 1axkA b.29.1.11 24341 1f9zA 135 1.44e+01 1qipA d.32.1.1 38484 1qopA 268 1.47e+01 2tysA c.1.2.4 28570 2tysA 268 1.48e+01 2tysA c.1.2.4 28572 2shpA 525 1.48e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1nzoA 363 1.49e+01 b.105.1.1 -2933 e.3.1.1 -11784 1g3qA 237 1.49e+01 1hyqA c.37.1.10 60237 1sdjA 310 1.56e+01 d.21.1.2 -9420 d.21.1.2 -9421 1hqz1 141 1.56e+01 1avsA 90 1.57e+01 1cll a.39.1.5 17226 1cc8A 73 1.57e+01 1cc8A d.58.17.1 39343 1yna 194 1.60e+01 1axkA b.29.1.11 24335 1f02T 66 1.61e+01 1f02T j.67.1.1 46360 1vhrA 184 1.69e+01 1vhrA c.45.1.1 32651 1mb3A 124 1.69e+01 c.23.1.1 78907 1psuA 140 1.70e+01 d.38.1.5 88285 1knwA 425 1.72e+01 b.49.2.3 -4274 c.1.6.1 -5229 1tuc 63 1.73e+01 1tuc b.34.2.1 24492 1v95A 130 1.73e+01 1kafA 108 1.74e+01 d.199.1.1 68372 1dp4A 435 1.76e+01 1dp4A c.93.1.1 35710 1eq9A 222 1.77e+01 5ptp b.47.1.2 26068 1imbA 277 1.77e+01 1imbA e.7.1.1 42957 1h6fA 193 1.78e+01 b.2.5.4 70901 1b9hA 388 1.80e+01 1b9hA c.67.1.4 34488 1vid 221 1.80e+01 1vid c.66.1.1 34178 1cd8 114 1.82e+01 1cd8 b.1.1.1 19714 2hhmA 276 1.83e+01 1imbA e.7.1.1 42955 1m32A 366 1.84e+01 c.67.1.3 78508 1p9kA 79 1.84e+01 unknown_sccs -10238 1bmqB 88 1.85e+01 1pauB 1rewC 135 1.85e+01 g.7.1.3 -12531 1l4iA 206 1.86e+01 b.1.11.1 73564 b.7.2.1 73565 1pa1A 310 1.87e+01 c.45.1.2 -7332 1k4iA 233 1.88e+01 d.115.1.2 72056 1nhkL 144 1.89e+01 1npk d.58.6.1 39142 1d2sA 170 1.89e+01 1d2sA b.29.1.4 24221 1mi8A 158 1.89e+01 b.86.1.2 -5061 1g5hA 454 1.92e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1hfuA 503 1.93e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1gx5A 536 1.94e+01 e.8.1.4 70682 1bt0A 76 1.95e+01 1ubi d.15.1.1 37607 1g6sA 427 1.96e+01 1eps d.68.2.2 39584 1g2yA 32 2.01e+01 unknown_sccs 17003 1dhr 241 2.01e+01 1dhr c.2.1.2 29832 1din 236 2.02e+01 1din c.69.1.9 34682 1dcs 311 2.03e+01 1dcs b.82.2.1 28124 1pf5A 131 2.09e+01 d.79.1.1 -10368 1uisA 231 2.09e+01 d.22.1.1 -9450 1f5fA 205 2.09e+01 1d2sA b.29.1.4 24222 1apyB 141 2.11e+01 1apyB 1el4A 195 2.12e+01 1ej3A a.39.1.5 59453 1dq3A 454 2.14e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1eaiC 61 2.18e+01 1eaiC g.22.1.1 44894 1r6dA 337 2.20e+01 c.2.1.2 -5757 1iugA 352 2.22e+01 c.67.1.3 -8176 2lbp 346 2.23e+01 2liv c.93.1.1 35709 1h4gA 207 2.23e+01 b.29.1.11 70863 1fa8A 135 2.28e+01 1qipA d.32.1.1 38486 1pxwA 128 2.29e+01 d.79.3.1 -10406 1epwA 1290 2.31e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1usgA 346 2.31e+01 c.93.1.1 -8635 1n0xL 215 2.32e+01 b.1.1.1 -2063 b.1.1.2 -2429 1ift 263 2.33e+01 1mrj d.165.1.1 42211 1c7gA 456 2.33e+01 c.67.1.2 -8153 1i8kB 124 2.35e+01 b.1.1.1 71131 1h1dA 221 2.38e+01 c.66.1.1 83452 1g8mA 593 2.38e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1gtvA 214 2.39e+01 c.37.1.1 70537 1c2pA 576 2.43e+01 1quvA e.8.1.4 43117 1nmeA 146 2.44e+01 c.17.1.1 85874 1q35A 320 2.45e+01 c.94.1.1 -8658 1q1rA 431 2.45e+01 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1v2xA 194 2.47e+01 c.116.1.1 -6704 1qxoA 388 2.49e+01 unknown_sccs -11161 1hyxH 224 2.51e+01 1igtB b.1.1.1 20167 b.1.1.2 21191 1twdA 256 2.52e+01 1pqhA 143 2.54e+01 b.52.2.1 -4318 1ugmA 125 2.54e+01 1r7lA 110 2.54e+01 1oi2A 366 2.56e+01 c.32.1.2 87039 d.79.2.2 87040 1qy1A 174 2.56e+01 b.60.1.1 -4445 1uurA 473 2.63e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1a7w 69 2.63e+01 1a7w a.22.1.2 16477 1gmxA 108 2.71e+01 c.46.1.3 65355 1rwyA 109 2.74e+01 a.39.1.4 -825 1nrvA 105 2.74e+01 d.93.1.1 86126 1k1xA 659 2.75e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1f4qA 165 2.76e+01 1alvA a.39.1.8 17360 1ipaA 274 2.76e+01 c.116.1.1 71254 d.79.3.3 71255 1jl3A 139 2.77e+01 c.44.1.1 66826 1sbxA 106 2.78e+01 1q9jA 422 2.81e+01 1gt91 357 2.83e+01 1al3 324 2.84e+01 1al3 c.94.1.1 35835 1ixmA 192 2.84e+01 1ixmA d.123.1.1 41114 1p5fA 189 2.84e+01 c.23.16.2 -6508 1aqb 183 2.87e+01 1aqb b.60.1.1 27084 1g0hA 252 2.90e+01 1dk4A e.7.1.1 60171 1h1yA 228 2.91e+01 c.1.2.2 76506 1sedA 117 2.94e+01 1p57B 255 2.99e+01 b.47.1.2 -4248 1jk7A 323 3.00e+01 1auiA d.159.1.3 63144 1k6wA 426 3.02e+01 b.92.1.2 68236 c.1.9.5 68237 2gmfA 127 3.03e+01 2gmfA a.26.1.2 16849 1qfjA 232 3.04e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1uq5A 263 3.04e+01 d.165.1.1 -11555 1a65A 504 3.08e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1fpzA 212 3.10e+01 1fpzA c.45.1.1 59976 1scuA 288 3.14e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1lktA 104 3.15e+01 1lktA b.90.1.1 28398 1guqA 348 3.15e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 1vhsA 175 3.16e+01 d.108.1.1 -10794 1cseE 274 3.19e+01 1gci c.41.1.1 32481 2bbkH 355 3.20e+01 2bbkH b.69.2.1 27634 1g5bA 221 3.21e+01 1g5bA d.159.1.3 60261 1k20A 310 3.24e+01 c.107.1.1 68027 1jbwA 428 3.24e+01 c.59.1.2 62860 c.72.2.2 62861 1exrA 148 3.28e+01 1cll a.39.1.5 17299 1qh3A 260 3.29e+01 1qh5A d.157.1.2 42059 1j1yA 136 3.30e+01 d.38.1.5 -9671 1dbtA 239 3.31e+01 1dbtA c.1.2.3 28539 1mmsA 140 3.36e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 1ha3A 405 3.37e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1ikpA 613 3.38e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1qtoA 122 3.42e+01 1bylA d.32.1.2 38494 1dfmA 223 3.43e+01 1d2iA c.52.1.5 33295 1hcv 117 3.45e+01 1igtB b.1.1.1 20514 1hdr 244 3.47e+01 1dhr c.2.1.2 29837 1rk8A 165 3.47e+01 d.58.7.1 -10018 1abrA 251 3.47e+01 1mrj d.165.1.1 42196 1kqrA 179 3.48e+01 b.29.1.14 72886 1qkkA 155 3.48e+01 1dbwA c.23.1.1 31104 1qh5A 260 3.49e+01 1qh5A d.157.1.2 42057 1nxiA 132 3.51e+01 d.58.47.1 86381 1pz5B 220 3.51e+01 b.1.1.1 -2215 b.1.1.2 -2545 1rliA 184 3.52e+01 unknown_sccs -6438 1mu5A 471 3.54e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1ujnA 348 3.55e+01 e.22.1.1 -11998 1cm9A 74 3.57e+01 1b3aA d.9.1.1 37405 1iktA 120 3.60e+01 d.106.1.1 66188 1kk8B 139 3.62e+01 a.39.1.5 77430 1rypC 244 3.63e+01 1rypC d.153.1.4 41934 1p42A 270 3.64e+01 d.14.1.7 87754 d.14.1.7 87755 1f46A 140 3.67e+01 1f46A d.129.4.1 59643 1afb1 154 3.67e+01 1rtm1 1qyaA 307 3.69e+01 1o97D 320 3.71e+01 c.26.2.3 81233 c.31.1.2 81234 1gk8I 140 3.77e+01 d.73.1.1 65242 1g6oA 330 3.81e+01 1g6oA c.37.1.11 32430 1gnwA 211 3.83e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1fjmA 330 3.95e+01 1auiA d.159.1.3 42082 1ojaA 520 3.96e+01 c.3.1.2 -6000 d.16.1.5 -9220 1bvyF 191 3.96e+01 1bvyF c.23.5.1 31207