# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1mzeA 351 2.74e-20 b.82.2.6 79694 1h2kA 349 4.07e-20 b.82.2.6 76572 2cavA 445 1.05e-06 1dgwA b.82.1.2 28094 b.82.1.2 28095 1j58A 385 1.71e-06 b.82.1.2 71531 1cawB 184 1.07e-05 1caxB b.82.1.2 28113 1cauB 184 2.97e-05 1caxB b.82.1.2 28103 1fi2A 201 6.60e-05 1fi2A b.82.1.2 59845 1caxB 184 1.16e-04 1caxB b.82.1.2 28105 2phlA 397 2.21e-04 1dgwA b.82.1.2 28082 b.82.1.2 28083 2arcA 164 3.89e-04 2arcA b.82.4.1 28148 1fxzA 476 4.37e-04 b.82.1.2 65059 b.82.1.2 65060 2arcB 164 7.39e-04 2arcA b.82.4.1 28149 2aacA 177 7.69e-04 2arcA b.82.4.1 28150 1od5A 492 1.16e-03 b.82.1.2 86832 b.82.1.2 86833 1qwrA 319 1.23e-02 b.82.1.3 -4880 1mrzA 293 1.48e-02 b.43.5.1 -4048 c.26.1.3 -6616 1qxrA 189 2.68e-02 b.82.1.7 -4834 1plzA 189 4.15e-02 b.82.1.7 88160 1e5rA 290 4.63e-02 1e5rA b.82.2.4 59276 1h1iC 350 5.60e-02 b.82.1.5 76471 1h1iD 350 8.34e-02 b.82.1.5 76472 1h1iB 350 8.76e-02 b.82.1.5 76470 1juhA 350 9.08e-02 b.82.1.5 71884 1pbuA 162 1.00e-01 d.58.46.1 88030 1lr5A 163 1.10e-01 b.82.1.2 74215 1dgrC 178 2.54e-01 1dgwA b.82.1.2 28100 1dgwA 178 3.97e-01 1dgwA b.82.1.2 28090 1cauA 181 6.86e-01 1dgwA b.82.1.2 28102 1o4tA 133 7.57e-01 b.82.1.9 86622 1iznB 277 9.21e-01 e.43.1.2 83848 1jihA 531 9.43e-01 unknown_sccs -10212 unknown_sccs -11922 1iejA 332 1.05e+00 1nnt c.94.1.2 62328 1ofnA 205 1.07e+00 b.82.1.1 -4830 1q15A 503 1.29e+00 c.26.2.1 -6625 d.153.1.1 -11400 1oi6A 205 1.49e+00 1nnt 328 1.58e+00 1nnt c.94.1.2 35884 1l0wA 580 1.58e+00 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1bia 321 2.03e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1nxmA 197 2.10e+00 b.82.1.1 86385 1i4wA 353 2.20e+00 c.66.1.24 66028 1g55A 343 2.35e+00 1g55A c.66.1.26 34247 1ifqA 138 2.40e+00 1ifqA d.110.4.1 62350 1ey2A 471 2.40e+00 1ey2A b.82.1.4 28116 1jhnA 424 2.88e+00 b.29.1.12 70060 b.104.1.1 66722 1tfaA 329 2.96e+00 1nnt c.94.1.2 35880 1shwA 138 2.98e+00 1gnuA 117 3.21e+00 d.15.1.3 65403 1dzrA 183 3.34e+00 1dzrA b.82.1.1 28076 1gttA 429 3.38e+00 d.177.1.1 70529 d.177.1.1 70530 1i7oA 429 3.69e+00 1i7oA d.177.1.1 61893 d.177.1.1 61894 1a16 440 3.83e+00 1az9 c.55.2.1 33548 d.127.1.1 41165 1nftA 329 3.83e+00 1nnt c.94.1.2 35881 1gskA 513 3.92e+00 b.6.1.3 83314 b.6.1.3 83315 b.6.1.3 83316 1eybA 471 3.99e+00 1ey2A b.82.1.4 28115 1upiA 225 4.39e+00 b.82.1.1 -4823 1rm8A 169 4.82e+00 d.92.1.11 -10584 1crwG 333 5.54e+00 1dssG c.2.1.3 30026 d.81.1.1 39941 1ep0A 185 5.61e+00 1dzrA b.82.1.1 28080 1ptf 88 5.72e+00 1ptf d.94.1.1 40549 1ugmA 125 5.89e+00 1jplA 171 5.94e+00 a.118.9.2 67027 1o1yA 239 6.00e+00 c.23.16.1 86554 1k8kC 372 6.22e+00 b.69.4.1 68308 1jhsA 188 6.50e+00 d.107.1.1 84172 1mu5A 471 7.13e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1sq9A 397 7.17e+00 1rc6A 261 7.37e+00 unknown_sccs -4868 1k8kD 300 7.56e+00 d.198.2.1 68309 d.198.2.1 68310 1l5xA 280 7.90e+00 c.106.1.1 77718 1aba 87 8.41e+00 1aba c.47.1.1 32760 1qwgA 251 8.59e+00 unknown_sccs -5678 2rveA 244 8.59e+00 1rvaA c.52.1.2 33283 1k8kF 168 8.72e+00 d.198.2.1 68312 1ft9A 222 9.55e+00 1ft9A a.4.5.4 16107 b.82.3.1 28131 1bib 321 9.77e+00 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1eonA 245 9.92e+00 1rvaA c.52.1.2 33238 1eq6A 189 1.06e+01 1eq6A d.107.1.1 40796 1sx5A 244 1.13e+01 c.52.1.2 -7551 1k8tA 510 1.13e+01 e.41.1.1 68316 1augA 215 1.19e+01 1a2zA c.56.4.1 33798 1mhqA 148 1.19e+01 a.118.9.2 84973 1ns5A 155 1.20e+01 c.116.1.3 80705 1uok 558 1.21e+01 1uok b.71.1.1 27801 c.1.8.1 28788 1uetA 437 1.22e+01 unknown_sccs -1144 unknown_sccs -9798 unknown_sccs -10058 1s5pA 235 1.23e+01 c.31.1.5 -6774 1t0yA 122 1.24e+01 d.15.1.1 -9151 1eo6A 117 1.26e+01 1eo6A d.15.1.3 37609 1dssG 333 1.28e+01 1dssG c.2.1.3 30022 d.81.1.1 39937 1rvaA 244 1.37e+01 1rvaA c.52.1.2 33240 2rslA 140 1.40e+01 2rslA c.53.1.1 33345 1a8e 329 1.42e+01 1cb6A c.94.1.2 35888 1b77A 228 1.42e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1qhdA 398 1.49e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1jssA 224 1.50e+01 d.129.3.2 71844 1d4tA 104 1.53e+01 1d4tA d.93.1.1 40537 1pzxA 289 1.54e+01 c.119.1.1 -8623 1az9 457 1.54e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1b12A 248 1.56e+01 1b12A b.87.1.2 28388 1be3B 439 1.59e+01 1be3B d.185.1.1 58952 d.185.1.1 58953 1spuB 727 1.60e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1kn9A 249 1.67e+01 b.87.1.2 68699 1bxlA 181 1.68e+01 1maz f.1.4.1 43396 1elt 236 1.73e+01 5ptp b.47.1.2 26281 2viuA 328 1.75e+01 1hgeA b.19.1.2 23797 1trb 320 1.77e+01 1trb c.3.1.5 30529 c.3.1.5 30530 2cb5A 453 1.84e+01 3gcb d.3.1.1 37035 1evhA 112 1.84e+01 1evhA b.55.1.4 26997 1dgrM 93 1.86e+01 1caxB b.82.1.2 28101 1hdkA 141 1.89e+01 b.29.1.3 65807 1rlkA 117 1.89e+01 unknown_sccs -7526 7aatA 401 1.90e+01 1ajsA c.67.1.1 34250 1p32A 209 1.91e+01 1p32A d.25.1.1 38379 3hmgA 328 2.00e+01 1hgeA b.19.1.2 23825 1c4oA 664 2.04e+01 1d2mA c.37.1.19 32415 c.37.1.19 32416 1f75A 249 2.05e+01 1f75A c.101.1.1 59662 1gdtA 183 2.05e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1dctA 324 2.07e+01 6mhtA c.66.1.26 34244 1d3kA 329 2.10e+01 1nnt c.94.1.2 35889 1jqfA 334 2.12e+01 c.94.1.2 67086 1dgrW 93 2.12e+01 1caxB 1g5cA 170 2.15e+01 1g5cA c.53.2.1 60264 1ny6A 267 2.18e+01 c.37.1.20 -7221 1d6zA 727 2.20e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1gw0A 559 2.24e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1bob 320 2.27e+01 1bob d.108.1.1 40816 1v9fA 325 2.29e+01 1vkdA 338 2.36e+01 1oeyJ 107 2.37e+01 d.15.2.2 -9168 1pex 207 2.37e+01 1gen b.66.1.1 27540 1n8fA 350 2.39e+01 c.1.10.4 85397 1ksfX 758 2.40e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1j5rA 371 2.42e+01 1gxrA 337 2.43e+01 b.69.4.1 70722 1hgeA 328 2.44e+01 1hgeA b.19.1.2 23816 1g60A 260 2.44e+01 c.66.1.11 70151 1lct 333 2.50e+01 1cb6A c.94.1.2 35836 1d3hA 367 2.53e+01 1d3gA c.1.4.1 28601 1gg1A 350 2.57e+01 1qr7A c.1.10.4 29187 1e8cA 498 2.58e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1erjA 393 2.60e+01 1erjA b.69.4.1 27660 1squA 155 2.62e+01 unknown_sccs -10229 1pfjA 108 2.62e+01 1btu 240 2.63e+01 5ptp b.47.1.2 26241 1kc6A 257 2.70e+01 c.52.1.19 68419 1g4yR 148 2.71e+01 1cll a.39.1.5 60252 1ibxB 145 2.73e+01 1c9fA d.15.2.1 62232 1lcl 142 2.74e+01 1lcl b.29.1.3 24216 1ryoA 327 2.75e+01 c.94.1.2 -8708 1oroA 213 2.77e+01 1opr c.61.1.1 34093 1eulA 994 2.78e+01 1eulA 1jqlB 140 2.79e+01 c.37.1.20 63234 1r9lA 309 2.88e+01 c.94.1.1 -8700 1smvA 260 2.94e+01 1smvA b.121.4.7 23288 1umsA 174 2.94e+01 1hfc d.92.1.11 40368 1m12A 84 2.97e+01 a.64.1.1 84745 1gvkB 240 3.00e+01 b.47.1.2 70610 1agx 331 3.01e+01 4pgaA c.88.1.1 35564 1gpr 162 3.02e+01 1gpr b.84.3.1 28267 1cdy 178 3.05e+01 1cdy b.1.1.1 19719 b.1.1.3 21658 1o91A 178 3.11e+01 b.22.1.1 -3282 1bykA 255 3.13e+01 1bykA c.93.1.1 35706 1tiyA 164 3.18e+01 1g86A 142 3.18e+01 b.29.1.3 70161 1ujkA 147 3.21e+01 a.118.9.2 -1623 1mkmA 249 3.26e+01 a.4.5.33 79242 d.110.2.2 79243 1jwgA 147 3.28e+01 a.118.9.2 71911 2mev2 256 3.31e+01 1aym2 1ezoA 370 3.33e+01 4mbp c.94.1.1 59539 1ignA 246 3.37e+01 1ignA a.4.1.6 16048 a.4.1.6 16049 1przA 252 3.37e+01 unknown_sccs -10158 1qj2C 285 3.39e+01 1qj2C 1o2dA 371 3.45e+01 e.22.1.2 86591 1f2rI 100 3.48e+01 1c9fA d.15.2.1 37641 1jffB 445 3.50e+01 c.32.1.1 62934 d.79.2.1 62935 1v7wA 807 3.53e+01 1qhhA 167 3.53e+01 1pjr c.37.1.19 32393 1pv9A 348 3.53e+01 c.55.2.1 -7610 d.127.1.1 -11000 1qf5A 431 3.54e+01 1adeA c.37.1.10 32212 1pv5A 264 3.61e+01 unknown_sccs -10182 1oo0A 147 3.75e+01 d.232.1.1 87182 1gpmA 525 3.78e+01 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1qfrA 89 3.81e+01 1ptf d.94.1.1 40552 1qr7A 350 3.91e+01 1qr7A c.1.10.4 29191 1lh0A 213 3.91e+01 c.61.1.1 73896 1o8bA 219 3.93e+01 unknown_sccs 81180 d.58.40.1 81181 1cur 155 3.94e+01 1rcy b.6.1.1 23021