# 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 5.04e-02 1ncx a.39.1.5 17223 1iybA 208 3.45e-01 d.124.1.1 -10977 1ggzA 148 4.25e-01 a.39.1.5 70176 1nt4A 391 9.80e-01 c.60.1.2 -7942 1s29A 92 9.81e-01 unknown_sccs -315 1pg4A 652 1.02e+00 e.23.1.1 88067 1gnlA 544 1.23e+00 e.26.1.1 70287 1auiB 169 1.64e+00 1auiB a.39.1.5 17325 1qfjA 232 2.26e+00 1qfjA b.43.4.2 25655 c.25.1.1 31545 1vi2A 300 2.41e+00 c.2.1.7 -5960 c.58.1.5 -6366 1i2aA 219 2.52e+00 e.24.1.1 -12012 1wdcC 156 2.66e+00 1wdcC a.39.1.5 17317 1qtrA 317 2.89e+00 1qtrA c.69.1.7 34660 1czaN 917 2.96e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1mup 166 3.09e+00 1mup b.60.1.1 27133 1efyA 350 3.45e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1q0uA 219 3.61e+00 c.37.1.19 -7205 1npyA 271 3.73e+00 c.2.1.7 85995 c.58.1.5 85996 1jv4A 162 4.37e+00 b.60.1.1 67343 1f4qA 165 4.43e+00 1alvA a.39.1.8 17360 1g7fA 298 4.55e+00 1pty c.45.1.2 60330 1i05A 180 4.62e+00 1mup b.60.1.1 27130 1wm1A 317 4.87e+00 1avsA 90 4.91e+00 1cll a.39.1.5 17226 1nowA 507 5.12e+00 c.1.8.6 85936 d.92.2.1 85937 1g4yR 148 5.14e+00 1cll a.39.1.5 60252 1g8iA 190 5.17e+00 1rec a.39.1.5 60363 1lf6A 684 5.46e+00 a.102.1.5 77918 b.30.5.5 77919 2sas 185 5.51e+00 2sas a.39.1.5 17258 1m45A 148 5.98e+00 a.39.1.5 78598 1f5jA 199 6.05e+00 1axkA b.29.1.11 24342 1i06A 180 6.30e+00 1mup b.60.1.1 27131 1k9uA 78 6.35e+00 a.39.1.10 84348 1din 236 6.38e+00 1din c.69.1.9 34682 1a4iA 301 6.55e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 1rwzA 245 6.68e+00 d.131.1.2 -11106 d.131.1.2 -11107 1larA 575 6.76e+00 1larA c.45.1.2 32693 c.45.1.2 32694 1k4iA 233 6.82e+00 d.115.1.2 72056 1qcsA 211 7.00e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 2shpA 525 7.42e+00 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1g2rA 100 7.82e+00 1g2rA d.192.1.1 60231 1ojaA 520 8.16e+00 c.3.1.2 -6000 d.16.1.5 -9220 3cla 213 8.25e+00 3cla c.43.1.1 32610 1smlA 269 8.47e+00 1smlA d.157.1.1 42053 1sc3B 88 8.66e+00 1pqhA 143 9.56e+00 b.52.2.1 -4318 1uurA 473 9.59e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1qy1A 174 1.01e+01 b.60.1.1 -4445 1dp4A 435 1.03e+01 1dp4A c.93.1.1 35710 1sgoA 139 1.05e+01 unknown_sccs -10487 3htsB 102 1.09e+01 2hts a.4.5.22 16175 1uiuA 502 1.09e+01 c.94.1.1 -8674 1wdkC 390 1.11e+01 1fgs 428 1.12e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1pvxA 194 1.13e+01 1axkA b.29.1.11 24341 1b8aA 438 1.18e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1l4iA 206 1.19e+01 b.1.11.1 73564 b.7.2.1 73565 1e0cA 271 1.19e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1aerA 205 1.21e+01 1aerA d.166.1.1 42249 1b5fA 239 1.22e+01 1smrA b.50.1.2 26836 1ptvA 321 1.26e+01 1pty c.45.1.2 32665 1seiA 130 1.33e+01 1seiA d.140.1.1 41463 1cqxA 403 1.36e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1hqz1 141 1.42e+01 1op3H 225 1.50e+01 b.1.1.1 87208 b.1.1.2 87209 1lam 484 1.50e+01 1lam c.56.5.3 33829 c.50.1.1 33166 1fdr 248 1.50e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1tuc 63 1.50e+01 1tuc b.34.2.1 24492 1g57A 217 1.60e+01 1g57A d.115.1.2 60253 1s6cA 183 1.62e+01 a.39.1.5 -858 1ir6A 424 1.63e+01 c.107.1.2 71342 1nxiA 132 1.65e+01 d.58.47.1 86381 1xypA 190 1.67e+01 1axkA b.29.1.11 24327 1ok7A 366 1.72e+01 1iyeA 309 1.79e+01 e.17.1.1 83786 1s3eA 520 1.82e+01 c.3.1.2 -6022 d.16.1.5 -9242 1bmqB 88 1.93e+01 1pauB 1yna 194 1.94e+01 1axkA b.29.1.11 24335 1k94A 165 2.00e+01 a.39.1.8 68333 2polA 366 2.00e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1cseE 274 2.02e+01 1gci c.41.1.1 32481 1ecsA 126 2.02e+01 1ecsA d.32.1.2 59407 1kgdA 180 2.11e+01 c.37.1.1 68582 1enfA 212 2.11e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1rwyA 109 2.16e+01 a.39.1.4 -825 1el4A 195 2.18e+01 1ej3A a.39.1.5 59453 1mmsA 140 2.25e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 1g5bA 221 2.27e+01 1g5bA d.159.1.3 60261 1f02T 66 2.28e+01 1f02T j.67.1.1 46360 1djnA 729 2.31e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1ov3A 138 2.32e+01 b.34.2.1 87451 b.34.2.1 87452 1vk1A 242 2.37e+01 1wdnA 226 2.39e+01 1lst c.94.1.1 35816 1kk8B 139 2.45e+01 a.39.1.5 77430 1d7yA 408 2.51e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1gt91 357 2.52e+01 1m32A 366 2.56e+01 c.67.1.3 78508 1kqrA 179 2.57e+01 b.29.1.14 72886 1t1gA 364 2.59e+01 1epwA 1290 2.61e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1qr0A 228 2.62e+01 1qr0A d.150.1.1 59038 d.150.1.1 59039 1rl6A 177 2.65e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 2cb5A 453 2.68e+01 3gcb d.3.1.1 37035 1c7gA 456 2.71e+01 c.67.1.2 -8153 1lucB 324 2.75e+01 1lucA c.1.16.1 29548 2tmdA 729 2.80e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1nhp 447 2.87e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1p9kA 79 2.90e+01 unknown_sccs -10238 1pa1A 310 2.99e+01 c.45.1.2 -7332 1qh7A 207 3.04e+01 1axkA b.29.1.11 24317 1plq 258 3.06e+01 1plq d.131.1.2 41388 d.131.1.2 41389 1dfmA 223 3.07e+01 1d2iA c.52.1.5 33295 1mmiA 366 3.09e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1o94A 729 3.11e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1n46A 258 3.15e+01 a.123.1.1 85315 1m7xA 617 3.18e+01 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1rewC 135 3.24e+01 g.7.1.3 -12531 2liv 344 3.26e+01 2liv c.93.1.1 35708 1r0rE 274 3.35e+01 c.41.1.1 -7293 1kcvH 217 3.37e+01 b.1.1.1 72315 b.1.1.2 72316 1jk7A 323 3.39e+01 1auiA d.159.1.3 63144 1uufA 369 3.41e+01 b.35.1.2 -3706 c.2.1.1 -5730 1nmeB 92 3.55e+01 1iugA 352 3.63e+01 c.67.1.3 -8176 1bg2 325 3.69e+01 1bg2 c.37.1.9 32189 1r7lA 110 3.73e+01 1eq9A 222 3.76e+01 5ptp b.47.1.2 26068 1skoB 130 3.83e+01 2apr 325 3.86e+01 2er7E b.50.1.2 26819 3aprE 325 3.88e+01 2er7E b.50.1.2 26820 1q9jA 422 3.92e+01 1m1hA 248 3.98e+01 b.114.1.1 78415 d.58.42.1 78416