# List of top-scoring protein chains for t04-100-30-str2-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 1zq9A 285 1.89e-24 1j8uA 325 2.85e-01 d.178.1.1 71611 1yadA 221 2.91e-01 1mvwC 147 4.31e-01 i.15.1.1 79525 4pah 308 4.49e-01 4pah d.178.1.1 42576 1yf3A 259 5.01e-01 1ynuA 473 7.28e-01 1xclA 235 7.70e-01 2a0kA 161 8.41e-01 2f2tA 161 8.41e-01 1m7yA 435 9.93e-01 c.67.1.4 78761 2f62A 161 1.23e+00 2fz4A 237 1.31e+00 1b8gA 429 1.48e+00 1b8gA c.67.1.4 34499 1vsd 152 1.71e+00 1cxqA c.55.3.2 33625 1ujmA 342 1.98e+00 1dk0A 188 2.14e+00 1b2vA d.35.1.1 38530 1y1pA 342 2.16e+00 1q0sA 259 2.48e+00 c.66.1.28 95509 2f4lA 297 2.57e+00 1o1zA 234 2.61e+00 c.1.18.3 86555 1hlvA 131 2.65e+00 a.4.1.7,a.4.1.7 65854,65855 1y88A 199 2.83e+00 1jalA 363 3.17e+00 c.37.1.8,d.15.10.2 84138,84139 1a7s 221 3.22e+00 1a7s b.47.1.2 26284 1mlwA 301 3.31e+00 d.178.1.1 79289 1j6pA 418 3.34e+00 b.92.1.4,c.1.9.9 77089,77090 1v97A 1332 3.50e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1cnzA 363 3.63e+00 1cnzA c.77.1.1 35061 1cxqA 162 3.99e+00 1cxqA c.55.3.2 33621 1scuA 288 4.10e+00 2scuA c.2.1.8,c.23.4.1 30307,31135 1p1mA 406 4.19e+00 b.92.1.4,c.1.9.9 87696,87697 1ockA 412 4.35e+00 c.117.1.1 86802 2ah5A 210 4.50e+00 1y1xA 191 4.72e+00 1y82A 157 4.92e+00 1o1xA 155 5.12e+00 c.121.1.1 86553 1w7jB 151 5.19e+00 1vbuA 328 5.20e+00 1i4wA 353 5.29e+00 c.66.1.24 66028 1xg7A 250 5.73e+00 1xqoA 256 5.80e+00 1vljA 407 5.87e+00 e.22.1.2 108832 1x0vA 354 6.10e+00 2ax3A 502 6.23e+00 1x3sA 195 6.23e+00 1dp3A 55 6.32e+00 1dp3A a.55.1.2 59128 1eljA 381 6.32e+00 4mbp c.94.1.1 35791 1fo4A 1332 6.44e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1p1cA 199 6.55e+00 c.66.1.16 87669 1q0rA 298 6.56e+00 c.69.1.28 95508 1ooeA 236 6.91e+00 c.2.1.2 87196 2btoA 473 7.02e+00 1fiqC 763 7.28e+00 1fiqC d.41.1.1,d.133.1.1 38588,41418 1top 162 7.38e+00 1ncx a.39.1.5 17223 2fm9A 215 7.45e+00 1qyrA 252 7.57e+00 c.66.1.24 104657 2prd 174 7.79e+00 2prd b.40.5.1 25435 1byrA 155 7.84e+00 1byrA d.136.1.1 41450 1zk8A 183 8.10e+00 1q8cA 151 8.22e+00 a.79.1.2 96202 1nxuA 333 8.30e+00 c.122.1.1 86389 2ethA 154 8.32e+00 1twfA 1733 8.78e+00 1ctj 89 8.85e+00 1ctj a.3.1.1 15798 1m65A 245 8.95e+00 c.6.3.1 84847 1rp4A 389 9.14e+00 a.227.1.1 105027 1vqtA 213 9.24e+00 1fnnA 389 9.38e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 1senA 164 9.40e+00 c.47.1.1 105465 1riqA 465 9.65e+00 a.203.1.1,d.104.1.1 97516,97517 1p57B 255 9.69e+00 b.47.1.2 94126 1wwiA 148 1.04e+01 1rrmA 386 1.04e+01 e.22.1.2 105081 1wy1A 172 1.05e+01 1yfsA 465 1.05e+01 1zcoA 262 1.10e+01 2ch4A 320 1.14e+01 1lqtA 456 1.16e+01 c.3.1.1,c.4.1.1 74198,74199 2f06A 144 1.16e+01 1g8kA 825 1.20e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1im5A 180 1.23e+01 c.33.1.3 66211 1v0dA 329 1.24e+01 d.4.1.7 108204 2cw6A 298 1.28e+01 1vl5A 260 1.33e+01 c.66.1.41 108720 1jb9A 316 1.42e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1sczA 233 1.43e+01 c.43.1.1 98802 1cy5A 97 1.46e+01 1cy5A a.77.1.3 18430 1eg7A 557 1.52e+01 1eg7A c.37.1.10 32241 1h8dH 260 1.53e+01 5ptp 1lvaA 258 1.53e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ea9C 583 1.53e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 2astA 159 1.56e+01 1xhcA 367 1.57e+01 1i58A 189 1.60e+01 1b3qA d.122.1.3 61773 1fhdA 312 1.62e+01 1taxA c.1.8.3 28915 2g0wA 296 1.68e+01 1tl9A 339 1.68e+01 2bjfA 329 1.68e+01 1dqzA 280 1.69e+01 1dqyA c.69.1.3 34638 2fywA 267 1.71e+01 1x3zA 335 1.72e+01 1eo1A 124 1.78e+01 1eo1A c.55.5.1 33739 1yzyA 413 1.81e+01 1fexA 59 1.84e+01 a.4.1.3 59803 1kwfA 363 1.86e+01 a.102.1.2 73078 1o6dA 163 1.87e+01 c.116.1.3 92567 1f20A 435 1.89e+01 b.43.4.1,c.25.1.4 64932,64933 1hkhA 279 1.90e+01 c.69.1.12 90628 1ox0A 430 1.92e+01 c.95.1.1,c.95.1.1 87495,87496 1oxjA 173 1.94e+01 a.60.1.2,a.118.1.13 87517,87518 1dvoA 152 1.99e+01 1dvoA a.136.1.1 19623 1v96A 149 1.99e+01 2b34A 199 2.02e+01 1v5vA 401 2.04e+01 1bueA 265 2.07e+01 1btl e.3.1.1 42727 1opjA 293 2.15e+01 d.144.1.7 87230 1sfxA 109 2.21e+01 a.4.5.50 105505 1sh7A 284 2.25e+01 1ek6A 348 2.28e+01 1xel c.2.1.2 29800 1xsjA 778 2.30e+01 1zu4A 320 2.31e+01 2gsaA 432 2.32e+01 2gsaA c.67.1.4 34446 1yqtA 538 2.34e+01 1t3cA 421 2.38e+01 d.92.1.7 106343 1cx4A 305 2.40e+01 b.82.3.2,b.82.3.2 59099,59100 1oa4A 222 2.45e+01 b.29.1.11 86731 1muwA 386 2.45e+01 c.1.15.3 79495 1fcyA 236 2.49e+01 2lbd a.123.1.1 19282 1cjcA 460 2.49e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1p35A 299 2.50e+01 1p35A b.28.1.1 23925 1gcvB 136 2.51e+01 1cg5B a.1.1.2 15589 2fhpA 187 2.53e+01 1dugA 234 2.57e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1t4hA 290 2.61e+01 d.144.1.7 106420 2f2hA 773 2.64e+01 1tqyA 424 2.64e+01 c.95.1.1,c.95.1.1 107245,107246 1qpcA 279 2.65e+01 1fgkA d.144.1.7 41685 1eq2A 310 2.65e+01 1eq2A c.2.1.2 29814 1ton 235 2.67e+01 5ptp b.47.1.2 26307 1zgzA 122 2.68e+01 1g6hA 257 2.86e+01 1gajA c.37.1.12 60318 1lj9A 144 2.87e+01 a.4.5.28 78035 1g3qA 237 2.91e+01 1hyqA c.37.1.10 60237 1xrtA 467 2.92e+01 2bjcA 62 2.97e+01 1vj1A 363 3.10e+01 b.35.1.2,c.2.1.1 100794,100795 1wmbA 260 3.10e+01 1sd4A 126 3.10e+01 a.4.5.39 105428 1rloA 271 3.10e+01 1qwgA 251 3.12e+01 c.1.27.1 96473 1dcs 311 3.19e+01 1dcs b.82.2.1 28124 2cb2A 318 3.22e+01 1cjgA 62 3.27e+01 1pru a.35.1.5 17112 2b9lA 394 3.29e+01 2ff4A 388 3.30e+01 1nrfA 262 3.32e+01 e.3.1.1 92086 1pq4A 291 3.38e+01 c.92.2.2 94995 1ta9A 450 3.39e+01 1fnc 314 3.39e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 2byjA 439 3.40e+01 1ddgA 374 3.41e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1luaA 287 3.47e+01 c.2.1.7,c.58.1.4 78216,78217 1w33A 181 3.54e+01 1zrn 232 3.55e+01 1qq5A c.108.1.1 43323 1n9dA 199 3.57e+01 a.26.1.1 85464 1o0yA 260 3.58e+01 c.1.10.1 80756 1fnd 314 3.60e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1rd5A 262 3.60e+01 1mgtA 174 3.63e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1jeoA 180 3.64e+01 c.80.1.3 66611 1jy5A 212 3.65e+01 d.124.1.1 71940 1qcwA 410 3.66e+01 1gox c.1.4.1 28622 1ju2A 536 3.66e+01 c.3.1.2,d.16.1.1 77169,77170 1j09A 468 3.67e+01 a.97.1.1,c.26.1.1 77025,77026 2eutA 294 3.70e+01 1vzqH 250 3.71e+01 1tzzA 392 3.71e+01 1kfuL 699 3.72e+01 a.39.1.8,b.14.1.1,d.3.1.3 68571,68572,68573 1korA 400 3.72e+01 c.26.2.1,d.210.1.1 72824,72825 1oz9A 150 3.79e+01 d.92.1.15 93808 1a4pA 96 3.84e+01 1b4cA a.39.1.2 17176 1t8qA 336 3.84e+01 c.1.18.3 106669 2azqA 311 3.85e+01 2amhA 207 3.89e+01 1kbjA 412 3.90e+01 c.1.4.1 72280 1pvmA 184 3.91e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1veaA 148 3.92e+01 d.275.1.1 108529 1sgwA 214 3.93e+01 c.37.1.12 105541 1bn7A 294 3.94e+01 1bn6A c.69.1.8 34677 1xvjA 109 3.95e+01 1vquA 374 4.00e+01 1h3nA 878 4.02e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1bx1A 314 4.08e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1lwjA 441 4.09e+01 b.71.1.1,c.1.8.1 74303,74304 1ebdC 41 4.09e+01 1ebdC a.9.1.1 16355 1cem 363 4.13e+01 1cem a.102.1.2 18826 2gfnA 209 4.14e+01 1jdrA 294 4.14e+01 1ryc a.93.1.1 62908 1s5lA 344 4.16e+01 1yrbA 262 4.18e+01 1np8A 159 4.19e+01 a.39.1.8 92022 1amp 291 4.22e+01 1amp c.56.5.4 33837 2c5aA 379 4.22e+01 2bylA 439 4.27e+01 1mkrA 294 4.28e+01 a.93.1.1 84997 1ydyA 356 4.32e+01 2ew2A 316 4.34e+01 1yqfA 203 4.36e+01 1u46A 291 4.38e+01 d.144.1.7 107656 1fh9A 312 4.40e+01 1taxA c.1.8.3 28913 1ihgA 370 4.41e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1z8gA 372 4.41e+01 1b5tA 275 4.43e+01 1b5tA c.1.23.1 29676 2rslA 140 4.43e+01 2rslA c.53.1.1 33345 1ydwA 362 4.51e+01 1j1hA 144 4.51e+01 b.111.1.1 77056 1sb8A 352 4.51e+01 c.2.1.2 105410 1lokA 291 4.55e+01 c.56.5.4 78122 1vpqA 273 4.59e+01 1jv4A 162 4.61e+01 b.60.1.1 67343 2a74A 643 4.69e+01 1mwyA 73 4.71e+01 d.58.17.1 79616 2furA 209 4.75e+01 1iugA 352 4.76e+01 c.67.1.3 90699 1paqA 189 4.79e+01 a.118.1.14 94413 1j75A 67 4.79e+01 a.4.5.19 62673 1z82A 335 4.79e+01 1i06A 180 4.79e+01 1mup b.60.1.1 27131 1h8eD 482 4.79e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1vjpA 394 4.81e+01 c.2.1.3,d.81.1.3 100828,100829 1i05A 180 4.86e+01 1mup b.60.1.1 27130 1zndA 174 4.87e+01 1qy1A 174 4.88e+01 b.60.1.1 96568 1s2wA 295 4.88e+01 c.1.12.7 98407 1u6rA 380 4.89e+01 1l7vA 326 4.89e+01 f.22.1.1 73672 1cf9A 753 4.92e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1fiuA 286 4.92e+01 1fiuA c.52.1.10 33317 1zbyA 294 4.98e+01 1cyj 90 5.02e+01 1ctj a.3.1.1 15805 1i50K 120 5.05e+01 d.74.3.2 61765 1z53A 294 5.13e+01 2bvlA 543 5.17e+01 2c07A 285 5.30e+01 1i50A 1733 5.31e+01 e.29.1.2 61754 2anpA 291 5.32e+01 1rlmB 271 5.44e+01 1ni4B 341 5.48e+01 c.36.1.7,c.48.1.2 85729,85730 1efnB 152 5.51e+01 1efnB d.102.1.1 40699 2f7fA 494 5.56e+01 1fobA 334 5.58e+01 c.1.8.3 83255 1lwdA 413 5.58e+01 c.77.1.1 78265 1fs1B 141 5.59e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1rwyA 109 5.66e+01 a.39.1.4 98002 1m8jA 181 5.67e+01 c.26.1.3 84875 2f3yA 148 5.71e+01 1jl2A 156 5.72e+01 c.55.3.1 66822 1f1eA 154 5.79e+01 a.22.1.2 64927 1bob 320 5.80e+01 1bob d.108.1.1 40816 1mr7A 209 5.85e+01 b.81.1.3 91430 1xuuA 349 5.86e+01 2aj2A 208 5.86e+01 3xis 387 5.87e+01 4xis c.1.15.3 29423 2f6kA 307 5.87e+01 1qh4A 380 5.88e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1ioj 57 5.89e+01 1ioj j.39.1.1 46293 4xis 387 5.90e+01 4xis c.1.15.3 29421 1f0nA 285 5.91e+01 1dqyA c.69.1.3 34636 1ejxA 100 5.93e+01 d.8.1.1 83182 1xfxA 777 5.94e+01 1jdpA 441 5.94e+01 c.93.1.1 62906 1vkwA 218 5.96e+01 d.90.1.2 108695 1cnv 299 5.99e+01 1cnv c.1.8.5 28989 1kyqA 274 6.03e+01 c.2.1.11,e.37.1.1 73281,73282 1d3gA 367 6.07e+01 1d3gA c.1.4.1 28600 1ji1A 637 6.09e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1huw 166 6.11e+01 1huw a.26.1.1 16831 1zthA 258 6.12e+01 1i7dA 659 6.14e+01 1d6mA e.10.1.1 61886 1wvfA 520 6.19e+01 1rlmA 271 6.24e+01 1uarA 285 6.28e+01 c.46.1.2,c.46.1.2 107762,107763 2b0mA 393 6.28e+01 1mlg 154 6.29e+01 1a6m a.1.1.2 15104 2his 312 6.33e+01 1taxA c.1.8.3 28918 1gpeA 587 6.35e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1jmsA 381 6.35e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1mym 154 6.37e+01 1a6m a.1.1.2 15054 2ba2A 85 6.39e+01 1gw0A 559 6.48e+01 b.6.1.3,b.6.1.3,b.6.1.3 70623,70624,70625 1ispA 181 6.48e+01 c.69.1.18 76778 1a3aA 148 6.51e+01 1a3aA d.112.1.1 40917 1x31D 99 6.56e+01 1iw7C 1119 6.59e+01 e.29.1.1 71474 1ofdA 1520 6.64e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1i6wA 181 6.65e+01 1i6wA c.69.1.18 61859 2fe8A 315 6.66e+01 2cwxA 430 6.75e+01 1rijA 25 6.75e+01 k.32.1.1 104951 2f4mA 295 6.77e+01 1qy6A 274 6.81e+01 b.47.1.1 96574 1it2A 146 6.95e+01 a.1.1.2 66365 1uh4A 637 6.97e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1fehA 574 7.01e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2hvm 273 7.13e+01 1cnv c.1.8.5 28985 1tvlA 454 7.16e+01 c.1.16.4 107366 2g7gA 213 7.16e+01 1j30A 144 7.18e+01 a.25.1.1 90806 1wstA 417 7.19e+01 1xd8A 289 7.21e+01 1qe3A 489 7.22e+01 2bce c.69.1.1 34630 1mszA 86 7.32e+01 d.68.7.1 79428 1twfK 120 7.34e+01 1wmqA 147 7.36e+01 1kx5B 102 7.36e+01 a.22.1.1 77594 1j5vA 351 7.42e+01 c.72.1.1 71585 2b33A 140 7.44e+01 2nlrA 234 7.45e+01 2nlrA b.29.1.11 24344 1w9pA 433 7.47e+01 2anxA 146 7.49e+01 2f9lA 199 7.53e+01 1mtyB 384 7.58e+01 1mtyB a.25.1.2 16740 2mgb 154 7.60e+01 1a6m a.1.1.2 15102 1izcA 339 7.62e+01 c.1.12.5 83838 2pii 112 7.63e+01 2pii d.58.5.1 39071 1vjvA 415 7.66e+01 d.3.1.9 108632 1xahA 354 7.69e+01 1gln 468 7.71e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1bbpA 173 7.72e+01 1bbpA b.60.1.1 27147 1sglA 209 7.74e+01 d.124.1.1 105536 2spl 154 7.78e+01 1a6m a.1.1.2 15047 1ru3A 732 7.91e+01 e.26.1.3 97835 1pymA 295 7.91e+01 1pymA c.1.12.7 29308 1qfjA 232 7.92e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1uxtA 501 7.95e+01 c.82.1.1 108125 1xbbA 291 8.00e+01 1q16C 225 8.07e+01 f.21.3.1 95549 1omhA 293 8.07e+01 d.89.1.5 93348 1ojrA 274 8.13e+01 c.74.1.1 93147 1mup 166 8.13e+01 1mup b.60.1.1 27133 1hr6B 443 8.14e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1pjr 724 8.15e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 2b6nA 278 8.19e+01 1nu5A 370 8.20e+01 c.1.11.2,d.54.1.1 92183,92184 1qgoA 264 8.26e+01 1qgoA c.92.1.2 35596 1guxB 152 8.26e+01 1guxB a.74.1.3 18389 1ncs 47 8.26e+01 1ncs g.37.1.1 45040 1i50C 318 8.33e+01 d.74.3.1,d.181.1.1 61756,61757 1r6oC 106 8.34e+01 1wdkC 390 8.37e+01 c.95.1.1,c.95.1.1 109258,109259 1mod 154 8.40e+01 1a6m a.1.1.2 15107 1w36B 1180 8.42e+01 1s50A 259 8.46e+01 1pyoB 105 8.46e+01 5pal 109 8.49e+01 1a75A a.39.1.4 17215 1on2A 142 8.51e+01 a.4.5.24,a.76.1.1 87103,87104 1qgrA 876 8.54e+01 1qgrA a.118.1.1 19119 1ky3A 182 8.54e+01 c.37.1.8 73193 1q0vA 81 8.55e+01 j.105.1.1 95514 103m 154 8.55e+01 1a6m a.1.1.2 15124 1qqeA 292 8.58e+01 1qqeA a.118.8.1 19210 1orvA 728 8.59e+01 b.70.3.1,c.69.1.24 87354,87355 1l2tA 235 8.60e+01 c.37.1.12 73514 1tn4 159 8.62e+01 1ncx a.39.1.5 17248 1wmhB 86 8.63e+01 1mll 154 8.64e+01 1a6m a.1.1.2 15057 1lxa 262 8.65e+01 1lxa b.81.1.1 28052 1f75A 249 8.67e+01 1f75A c.101.1.1 59662 1avsA 90 8.68e+01 1cll a.39.1.5 17226 1i5nA 146 8.71e+01 1i5nA a.24.10.3 61805 1ls9A 91 8.72e+01 a.3.1.1 78177 1r1dA 247 8.74e+01 c.69.1.29 96813 1zjkA 403 8.76e+01 1br1B 150 8.86e+01 1wdcC a.39.1.5 17309 2c3zA 222 8.88e+01 1twfC 318 8.90e+01