# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1l5aA 436 1.78e-04 c.43.1.2 75923 c.43.1.2 75924 1o7fA 469 1.09e-01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1jn5A 140 3.02e-01 d.17.4.2 66921 1jkgA 140 3.93e-01 d.17.4.2 66795 1je5A 206 4.14e-01 1je5A b.40.4.7 62909 1foeA 377 5.79e-01 1foeA a.87.1.1 18517 b.55.1.1 26969 1ryp2 233 6.03e-01 1ryp2 1ki1B 352 6.06e-01 a.87.1.1 72497 b.55.1.1 72498 1b7yA 350 7.37e-01 1pysA d.104.1.1 40776 1pysA 350 9.49e-01 1pysA d.104.1.1 40775 1icxA 155 1.23e+00 d.129.3.1 71191 1g0u1 266 1.31e+00 1oejA 193 1.32e+00 1f1sA 814 1.46e+00 a.102.3.2 64928 b.1.18.2 64929 b.24.1.1 64930 b.30.5.2 64931 1f5aA 513 1.48e+00 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1e7uA 961 1.86e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1k8kA 418 2.36e+00 c.55.1.1 68305 c.55.1.1 68306 1hjp 203 2.45e+00 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1jhnA 424 3.23e+00 b.29.1.12 70060 b.104.1.1 66722 1a15A 67 3.32e+00 1a15A d.9.1.1 37451 1fa0B 537 3.90e+00 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1rgs 288 4.04e+00 1rgs b.82.3.2 28146 b.82.3.2 28147 1qgvA 142 4.16e+00 1qgvA c.47.1.8 33056 1nhs 447 4.19e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1o0iA 138 4.24e+00 1nhp 447 4.32e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1regX 122 4.63e+00 1regX d.58.27.1 39406 1lenA 181 4.87e+00 1led b.29.1.1 24032 1qg7A 67 4.91e+00 1a15A d.9.1.1 37449 1joa 447 4.96e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1g4mA 393 5.22e+00 b.1.18.11 65143 b.1.18.11 65144 1o57A 291 5.32e+00 1p41A 291 5.32e+00 1ffyA 917 5.79e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 5.79e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1f3rB 257 5.85e+00 1f3rB b.1.1.1 20416 b.1.1.1 20417 1hcz 252 6.33e+00 1hcz b.2.6.1 22464 b.84.2.2 28250 1i1iP 681 6.71e+00 1i1iP d.92.1.5 40297 1qf6A 642 6.72e+00 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1f4qA 165 7.09e+00 1alvA a.39.1.8 17360 1bgp 309 7.27e+00 1bgp a.93.1.1 18690 1fxlA 167 7.34e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1bh5A 183 7.38e+00 1qipA d.32.1.1 38476 1jjoC 261 7.78e+00 1ar0A 127 8.40e+00 1ounA d.17.4.2 38092 1rhi3 236 8.54e+00 1aym3 2pcfB 250 8.61e+00 1hcz i.4.1.1 45911 1f2nA 238 8.92e+00 1f2nA b.10.1.2 23291 1qddA 144 9.33e+00 1qddA d.169.1.1 42324 1e2wA 251 9.48e+00 1hcz b.2.6.1 22466 b.84.2.2 28252 1dmuA 299 9.76e+00 1dmuA c.52.1.4 33294 1qqp3 220 9.97e+00 1qqp3 2pvaA 345 9.97e+00 3pvaA d.153.1.3 41850 1ounA 127 1.00e+01 1ounA d.17.4.2 38090 1b12A 248 1.02e+01 1b12A b.87.1.2 28388 1cqxA 403 1.03e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1bbt3 220 1.04e+01 1qqp3 1hh2P 344 1.09e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1k4jA 230 1.15e+01 d.108.1.3 72057 1qipA 183 1.15e+01 1qipA d.32.1.1 38470 1qk3A 233 1.16e+01 1qk3A c.61.1.1 34031 1fh6A 282 1.16e+01 1fh6A d.183.1.1 42609 1m5yA 408 1.20e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1a8h 500 1.25e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1amj 754 1.28e+01 1amj c.8.2.1 30725 c.83.1.1 35401 1cx4A 305 1.30e+01 b.82.3.2 59099 b.82.3.2 59100 1kzfA 230 1.30e+01 d.108.1.3 73354 3dapA 320 1.31e+01 1dapA c.2.1.3 30051 d.81.1.3 39966 1a4kA 217 1.32e+01 8fabA b.1.1.1 20236 b.1.1.2 21248 1jmuB 666 1.35e+01 1i58A 189 1.37e+01 1b3qA d.122.1.3 61773 1ge8A 249 1.38e+01 1plq d.131.1.2 41398 d.131.1.2 41399 8acn 754 1.38e+01 1amj c.8.2.1 30724 c.83.1.1 35400 4rhv3 236 1.40e+01 1aym3 1gwmA 153 1.41e+01 7icd 416 1.42e+01 1iso c.77.1.1 35072 1j6wA 175 1.43e+01 1j98A d.185.1.2 62663 1gy6A 127 1.51e+01 d.17.4.2 70736 1k94A 165 1.52e+01 a.39.1.8 68333 1qqgA 264 1.52e+01 1qqgA b.55.1.2 26987 b.55.1.2 26988 1hq8A 123 1.54e+01 1b6e d.169.1.1 61127 1guqA 348 1.55e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 1k8wA 327 1.56e+01 d.58.35.2 68317 d.58.35.2 68318 1e8xA 961 1.58e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1njkA 156 1.61e+01 1ekrA 161 1.63e+01 1ekrA d.58.21.1 39380 1dttA 560 1.63e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1gg3A 279 1.65e+01 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1h6dA 433 1.69e+01 c.2.1.3 65656 d.81.1.5 65657 1gupA 348 1.69e+01 1guqA d.13.1.2 37534 d.13.1.2 37535 2ltnA 181 1.77e+01 1led b.29.1.1 24024 1vfrA 218 1.79e+01 1vfrA d.90.1.1 40247 2bpa1 426 1.80e+01 2bpa1 1lnh 857 1.81e+01 1yge a.119.1.1 19237 b.12.1.1 23637 1f06A 320 1.82e+01 1dapA c.2.1.3 59556 d.81.1.3 59557 1b0jA 754 1.85e+01 1amj c.8.2.1 30719 c.83.1.1 35395 1dapA 320 1.88e+01 1dapA c.2.1.3 30053 d.81.1.3 39968 3pcgA 200 1.91e+01 3pchA b.3.6.1 22647 1lvl 458 1.93e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1gztA 115 1.93e+01 b.115.1.1 76428 1gw5M 435 1.93e+01 b.2.7.1 70631 d.110.4.2 70632 1lkvX 232 1.93e+01 a.118.14.1 73980 1i4nA 251 1.97e+01 c.1.2.4 71114 1iso 416 2.02e+01 1iso c.77.1.1 35065 1jk0B 345 2.03e+01 a.25.1.2 63143 1iz5A 249 2.06e+01 3pvaA 335 2.06e+01 3pvaA d.153.1.3 41854 7acn 754 2.09e+01 1amj c.8.2.1 30717 c.83.1.1 35393 1c96A 753 2.09e+01 1amj c.8.2.1 30727 c.83.1.1 35403 6acn 754 2.10e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1gqeA 365 2.11e+01 e.38.1.1 70351 1el6B 219 2.18e+01 1el6B d.182.1.1 42607 3pchA 200 2.20e+01 3pchA b.3.6.1 22653 1o0pA 104 2.20e+01 2pcdA 200 2.22e+01 3pchA b.3.6.1 22665 1e43A 483 2.22e+01 1bli b.71.1.1 59217 c.1.8.1 59218 1azo 232 2.25e+01 1azo c.52.1.14 33329 1epaA 164 2.25e+01 1epaA b.60.1.1 27128 1l1qA 186 2.25e+01 c.61.1.1 77653 1hw7A 255 2.26e+01 1i7fA d.193.1.1 61297 1o5hA 214 2.30e+01 1oxcA 114 2.34e+01 1fv0A 121 2.36e+01 a.133.1.2 70147 2fnbA 95 2.40e+01 2fnbA b.1.2.1 21979 3pmgA 561 2.41e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 1ggwA 140 2.42e+01 1ggwA a.39.1.5 60490 1drmA 131 2.43e+01 1drmA d.110.3.2 40908 1qj8A 148 2.48e+01 1qj8A f.4.1.1 43744 1c5cL 214 2.53e+01 32c2A b.1.1.1 20474 b.1.1.2 21438 1kpmA 121 2.64e+01 a.133.1.2 72844 1aipE 405 2.66e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1jb2A 127 2.71e+01 d.17.4.2 71624 1dgsA 667 2.77e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1cjcA 460 2.78e+01 1cjcA c.3.1.1 30319 c.4.1.1 30604 1b6rA 355 2.80e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1mmiA 366 2.87e+01 1brwA 433 2.89e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1lswA 131 2.89e+01 d.110.3.2 78181 1l7iL 214 2.91e+01 b.1.1.1 73658 b.1.1.2 73659 3cla 213 2.93e+01 3cla c.43.1.1 32610 2hmiA 558 2.94e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1avqA 228 2.94e+01 1avqA c.52.1.13 33326 1a6wL 109 3.05e+01 1mfa b.1.1.1 20252 1cuk 203 3.05e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1kb9B 352 3.05e+01 d.185.1.1 77313 d.185.1.1 77314 1pb1A 416 3.06e+01 1aisA 182 3.06e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1iicA 422 3.10e+01 1nmtA d.108.1.2 62422 d.108.1.2 62423 1m22A 503 3.14e+01 c.117.1.1 78464 1hbyA 123 3.15e+01 7rsa d.5.1.1 60936 1of4A 179 3.15e+01 1rthA 560 3.24e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1go3E 187 3.34e+01 b.40.4.5 65406 1a36A 592 3.35e+01 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1mfa 247 3.37e+01 1mfa b.1.1.1 19888 b.1.1.1 19889 1jvwA 167 3.42e+01 d.26.1.1 71907 1epbA 164 3.46e+01 1epaA b.60.1.1 27126 1as4A 341 3.50e+01 1sek e.1.1.1 42623 1gvzA 237 3.52e+01 b.47.1.2 76360 1hxpA 348 3.56e+01 1guqA d.13.1.2 37530 d.13.1.2 37531 1b35A 260 3.56e+01 1b35A b.10.1.3 23333 1n99A 166 3.64e+01 1drqA 131 3.64e+01 1drmA 1rbp 182 3.64e+01 1aqb b.60.1.1 27085 1b6sA 355 3.64e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1mkiA 330 3.68e+01 1a6uL 108 3.69e+01 1mfa b.1.1.1 20254 1a6vL 110 3.70e+01 1mfa b.1.1.1 20256 1et9A 204 3.76e+01 1an8 b.40.2.2 25204 d.15.6.1 37793 1j7iA 264 3.79e+01 1j7iA d.144.1.6 62694 1nvvS 481 3.79e+01 1hdmB 193 3.79e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1zin 217 3.80e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1awcA 110 3.92e+01 1awcA a.4.5.21 16167 1i69A 219 3.94e+01 c.94.1.1 61825 1mv3A 213 3.94e+01 1iuz 98 3.95e+01 1plc b.6.1.1 22861 1h9oA 112 3.96e+01 1qadA d.93.1.1 60837 1ezvB 352 3.97e+01 1ezvB d.185.1.1 59543 d.185.1.1 59544 1fwxA 595 3.99e+01 b.6.1.4 60069 b.69.3.1 60070