# 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 1csbB 205 7.19e-02 1theB 1theA 260 9.37e-02 1theB d.3.1.1 37056 1theB 260 1.25e-01 1theB d.3.1.1 37057 1b1jA 123 1.78e-01 7rsa d.5.1.1 37298 1gmyA 261 2.39e-01 d.3.1.1 76236 1un3A 123 3.10e-01 d.5.1.1 99646 1k59A 123 3.20e-01 d.5.1.1 72073 1kn0A 212 3.23e-01 d.50.1.3 77444 1b1iA 123 4.18e-01 7rsa d.5.1.1 37295 1b1eA 123 5.06e-01 7rsa d.5.1.1 37300 2gxfA 142 5.61e-01 1hbyA 123 6.94e-01 7rsa d.5.1.1 60936 1v8hA 107 9.36e-01 1ekgA 127 1.02e+00 1dlxA d.82.2.1 40021 1agi 125 1.20e+00 7rsa d.5.1.1 37303 2bgcA 238 1.24e+00 1j9bA 141 1.48e+00 c.47.1.12 66459 1a4yB 123 1.67e+00 7rsa d.5.1.1 37296 1s3cA 141 1.71e+00 1hh2P 344 1.77e+00 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 2cavA 445 1.88e+00 1dgwA b.82.1.2,b.82.1.2 28094,28095 1xfsA 178 1.97e+00 d.129.3.5 109589 1i3uA 127 2.18e+00 1gc1H b.1.1.1 61636 2bibA 547 2.19e+00 1bmfA 510 2.60e+00 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1dq3A 454 2.74e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1tif 78 2.80e+00 1tif d.15.8.1 37836 1xovA 326 2.84e+00 2cokA 113 2.84e+00 1oh0A 131 2.89e+00 d.17.4.3 87004 1ly7A 121 2.94e+00 d.82.2.1 74339 1aoiB 87 3.77e+00 1aoiB a.22.1.1 16470 1aoiF 87 4.09e+00 1aoiB a.22.1.1 16471 1opy 131 4.10e+00 1opy d.17.4.3 38113 2f1fA 164 4.34e+00 1wsrA 375 4.52e+00 1dmmA 131 4.54e+00 1opy d.17.4.3 38114 1j7nA 776 4.72e+00 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1hq3D 103 4.76e+00 1aoiB a.22.1.1 16464 1y9wA 140 4.83e+00 1ea2A 131 4.91e+00 d.17.4.3 64860 1tzyD 103 5.52e+00 a.22.1.1 107533 1cauA 181 5.88e+00 1dgwA b.82.1.2 28102 1id3B 102 6.13e+00 a.22.1.1 66113 1lfpA 249 6.51e+00 e.39.1.1 73885 1ru8A 232 6.52e+00 c.26.2.1 97849 1gio 125 6.54e+00 7rsa d.5.1.1 37304 1u69A 163 6.63e+00 d.32.1.7 107699 2bwkA 121 6.72e+00 2fk9A 157 6.99e+00 2scuB 388 7.04e+00 2scuB c.23.4.1,d.142.1.4 31141,41562 1kx5B 102 7.04e+00 a.22.1.1 77594 1eqnA 321 7.14e+00 1dd9A e.13.1.1 43256 1iloA 77 7.22e+00 c.47.1.1 66205 2fug5 207 7.27e+00 2arhA 203 7.37e+00 1oj5A 132 7.49e+00 d.110.3.8 93087 1kkeA 210 7.57e+00 b.21.1.2,b.83.1.2 68669,68670 1b6vA 124 8.10e+00 7rsa d.5.1.1 37286 2c4bA 143 8.13e+00 1vj7A 393 8.18e+00 a.211.1.1,d.218.1.8 100801,100802 1dzaA 129 8.25e+00 7rsa d.5.1.1 37275 1eal 127 8.28e+00 1hmt b.60.1.2 27227 1tp6A 128 8.52e+00 d.17.4.12 107184 2ck3A 510 8.95e+00 1gxuA 91 9.20e+00 d.58.10.1 76378 1a5p 124 9.28e+00 7rsa d.5.1.1 37201 1lfo 128 9.32e+00 1hmt b.60.1.2 27223 1yezA 68 9.37e+00 1dgwA 178 9.86e+00 1dgwA b.82.1.2 28090 1el5A 389 9.88e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1lj5A 379 9.88e+00 e.1.1.1 73928 2gfaA 119 1.01e+01 1opoA 348 1.07e+01 b.121.4.7 87240 1hbp 183 1.09e+01 1aqb b.60.1.1 27079 1rbp 182 1.09e+01 1aqb b.60.1.1 27085 1omiA 248 1.10e+01 b.82.3.3,a.4.5.4 87079,87080 1r0pA 312 1.10e+01 d.144.1.7 96734 1fwp 139 1.10e+01 1eayC d.58.24.1 39396 1y96A 86 1.11e+01 1ux2A 212 1.13e+01 b.96.1.1 100132 1yqfA 203 1.21e+01 2bj7A 138 1.22e+01 1rq6A 62 1.22e+01 1e79A 510 1.24e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1qsgA 265 1.24e+01 1eny c.2.1.2 29935 1io1A 398 1.25e+01 1io1A e.32.1.1 62611 2f1lA 187 1.26e+01 1qwdA 177 1.27e+01 b.60.1.1 96471 1a9eA 277 1.37e+01 1agdA b.1.1.2,d.19.1.1 20757,38268 1p9qC 256 1.39e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 3sxlA 184 1.41e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1dgrC 178 1.46e+01 1dgwA b.82.1.2 28100 1b3mA 389 1.46e+01 1b3mA 1j7nB 776 1.49e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 2ca6A 386 1.51e+01 1x99A 145 1.52e+01 1rzmA 338 1.52e+01 c.1.10.4 105137 1gheA 177 1.53e+01 d.108.1.1 76222 2apqA 139 1.56e+01 1dxkA 227 1.59e+01 1a7tA d.157.1.1 42036 2blnA 305 1.62e+01 1louA 101 1.65e+01 1ris d.58.14.1 39323 2bj0A 203 1.66e+01 1uw6A 211 1.66e+01 b.96.1.1 100079 1mc3A 296 1.68e+01 c.68.1.6 78943 1banA 110 1.74e+01 1b20A d.1.1.2 36197 1yrgA 385 1.77e+01 1yrgA c.10.1.2 30854 1l9fA 389 1.78e+01 c.3.1.2,d.16.1.3 73716,73717 1hbq 183 1.81e+01 1aqb b.60.1.1 27078 1hyxH 224 1.87e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1rifA 282 1.89e+01 c.37.1.23 97507 1vqoT 120 1.90e+01 1bb8 71 1.90e+01 2bb8 d.10.1.1 37478 1i9bA 217 1.93e+01 1i9bA b.96.1.1 62084 1brhA 110 1.99e+01 1b20A d.1.1.2 36151 2d27A 149 2.02e+01 1h8eA 510 2.03e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 2bc2B 227 2.07e+01 1a7tA d.157.1.1 42032 1a7cA 379 2.08e+01 1sek e.1.1.1 42660 1aqb 183 2.09e+01 1aqb b.60.1.1 27084 1ebdC 41 2.10e+01 1ebdC a.9.1.1 16355 1r13A 148 2.17e+01 d.169.1.1,h.1.1.1 96782,96783 1kskA 234 2.17e+01 d.66.1.5,d.265.1.3 72920,90389 1xjcA 169 2.18e+01 2g3aA 152 2.21e+01 1b3qA 379 2.22e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1tmcA 175 2.26e+01 1agdA d.19.1.1 38258 1vlqA 337 2.27e+01 c.69.1.25 108848 1l0qA 391 2.30e+01 b.1.3.1,b.69.2.3 77644,77645 2d13A 227 2.33e+01 1pvyA 227 2.34e+01 d.115.1.2 95195 2bynA 227 2.36e+01 1uv6A 210 2.36e+01 b.96.1.1 100030 1a2pA 110 2.37e+01 1b20A d.1.1.2 36140 1hilB 220 2.40e+01 1igtB b.1.1.1,b.1.1.2 19787,20897 1mhnA 59 2.40e+01 b.34.9.1 84964 1b7fA 168 2.42e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1rnbA 110 2.45e+01 1b20A d.1.1.2 36196 1icxA 155 2.45e+01 d.129.3.1 71191 1baoA 110 2.46e+01 1b20A d.1.1.2 36187 1k3eA 156 2.52e+01 d.198.1.1 68103 1lgpA 116 2.53e+01 b.26.1.2 73890 1kt6A 183 2.55e+01 b.60.1.1 84466 1lyvA 306 2.55e+01 c.45.1.2 74348 1a8vA 121 2.61e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1g5cA 170 2.62e+01 1g5cA c.53.2.1 60264 1mqoA 227 2.63e+01 d.157.1.1 103846 1yioA 208 2.66e+01 1k4nA 192 2.66e+01 d.32.1.5 72059 1hup 141 2.71e+01 1rtm1 d.169.1.1,h.1.1.1 42354,45422 1b2zA 110 2.72e+01 1b20A d.1.1.2 36216 1qqcA 773 2.78e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1snnA 227 2.78e+01 d.115.1.2 105821 1gl0I 35 2.79e+01 g.4.1.1 65271 1pil 112 2.79e+01 2pii d.58.5.1 39072 1a5q 124 2.81e+01 7rsa d.5.1.1 37258 1ha1 184 2.83e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 2a8kA 108 2.84e+01 1yts 278 2.85e+01 1ytw c.45.1.2 32690 1xk7A 408 2.86e+01 1a1oA 276 2.86e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 2bypA 214 2.86e+01 1zt2B 212 2.88e+01 1whsB 153 2.90e+01 1whtB 1s6lA 212 2.91e+01 1g5vA 88 2.92e+01 1g5vA b.34.9.1 60292 1uuzA 137 2.93e+01 d.233.1.1 100024 1y88A 199 2.96e+01 1vfgA 390 2.97e+01 a.173.1.1,d.218.1.4 108570,108571 1vl5A 260 3.01e+01 c.66.1.41 108720 1gouA 116 3.02e+01 d.1.1.2 65429 2bb8 71 3.03e+01 2bb8 d.10.1.1 37480 1b2sA 110 3.03e+01 1b20A d.1.1.2 36213 1l7bA 92 3.09e+01 c.15.1.2 91053 1ul7A 102 3.15e+01 d.129.6.1 99540 1bcsB 160 3.17e+01 1whtB 1dy5A 124 3.20e+01 7rsa d.5.1.1 37163 1glv 303 3.24e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 2f91B 35 3.25e+01 1yr4B 35 3.25e+01 1whtB 153 3.25e+01 1whtB 1konA 249 3.26e+01 e.39.1.1 72823 1t95A 240 3.29e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1w85I 49 3.30e+01 1yptA 305 3.33e+01 1ytw c.45.1.2 32686 2ey4C 82 3.34e+01 1lniA 96 3.37e+01 d.1.1.2 74046 1nnxA 109 3.38e+01 b.40.10.1 92013 1vsrA 136 3.38e+01 1vsrA c.52.1.15 33332 2g6fX 59 3.38e+01 1ytw 306 3.38e+01 1ytw c.45.1.2 32689 1aazA 87 3.38e+01 1aba c.47.1.1 32761 1l3kA 196 3.42e+01 d.58.7.1,d.58.7.1 73539,73540 1cojA 212 3.44e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1pmzA 86 3.45e+01 a.39.1.10 104195 1oaqH 121 3.48e+01 b.1.1.1 92707 1qg6A 261 3.48e+01 1eny c.2.1.2 29919 1bngA 110 3.48e+01 1b20A d.1.1.2 36184 1o4wA 147 3.49e+01 c.120.1.1 86629 1zybA 232 3.49e+01 1mqkH 127 3.50e+01 b.1.1.1 85053 2pii 112 3.52e+01 2pii d.58.5.1 39071 1dg6A 191 3.54e+01 1d4vB b.22.1.1 23883 1vkcA 158 3.55e+01 1wy5A 317 3.57e+01 1han 297 3.59e+01 1han d.32.1.3,d.32.1.3 38506,38507 1s72T 120 3.63e+01 b.34.5.1 105339 1zvnA 99 3.64e+01 2ch4A 320 3.65e+01 1f9aA 168 3.66e+01 1f9aA c.26.1.3 31602 1a1nA 276 3.68e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 1bw8A 321 3.71e+01 1bw8A b.2.7.1 22482 1e01A 48 3.77e+01 1e01A 1b69A 69 3.77e+01 2bb8 d.10.1.1 37479 1cw0A 155 3.79e+01 1vsrA c.52.1.15 33333 1mw7A 240 3.87e+01 e.39.1.1 79557 2ak5A 64 3.88e+01 1x1rA 178 3.89e+01 1aba 87 3.91e+01 1aba c.47.1.1 32760 1jl0A 334 3.97e+01 1jenA d.156.1.1 63155 1i58A 189 4.01e+01 1b3qA d.122.1.3 61773 1xfxA 777 4.03e+01 1gy6A 127 4.04e+01 d.17.4.2 70736 1bxxA 285 4.05e+01 1bw8A b.2.7.1 22483 2fdoA 94 4.05e+01 1q5yA 85 4.06e+01 d.58.18.4 95950 1k2yX 463 4.07e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ut7A 171 4.07e+01 b.143.1.1 99906 1yp8A 33 4.09e+01 2f86B 143 4.10e+01 2bl0C 142 4.11e+01 1gsoA 431 4.14e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1klo 162 4.17e+01 1klo g.3.11.2,g.3.11.2,g.3.11.2 44326,44327,44328 2ghpA 292 4.17e+01 1xkpB 124 4.18e+01 1jj2S 119 4.18e+01 1ffkQ b.34.5.1 63104 1b20A 110 4.20e+01 1b20A d.1.1.2 36207 1nycA 111 4.20e+01 b.61.2.2 92336 1xa3A 437 4.22e+01 2g76A 335 4.22e+01 1a0oD 134 4.23e+01 1eayC d.58.24.1 39391 1txvB 440 4.23e+01 1mt6A 280 4.23e+01 b.76.2.1,b.85.7.1 79446,79447 1v6tA 255 4.24e+01 7rsa 124 4.26e+01 7rsa d.5.1.1 37165 2d4qA 257 4.26e+01 2bxxA 134 4.27e+01 1rnd 124 4.33e+01 7rsa d.5.1.1 37178 1f3mC 297 4.34e+01 1hcl d.144.1.7 41677 1xh3A 276 4.47e+01 1pm3A 78 4.52e+01 b.41.1.2 94889 1e19A 314 4.58e+01 1b7bA c.73.1.1 34967 2dhqA 146 4.58e+01 2dhqA c.23.13.1 31382 1yrgB 385 4.59e+01 1yrgA c.10.1.2 30855 1ef1A 294 4.61e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1lb2B 84 4.62e+01 a.60.3.1 77871 1h9eA 56 4.63e+01 1h9eA a.140.1.1 60825 1f0zA 66 4.65e+01 1f0zA d.15.3.2 37644 2bc2A 227 4.67e+01 1a7tA d.157.1.1 42031 2basA 431 4.68e+01 1v88A 130 4.69e+01 b.55.1.1 108423 1widA 130 4.69e+01 1ytn 306 4.74e+01 1ytw c.45.1.2 32688 1i8kB 124 4.74e+01 b.1.1.1 71131 1j7gA 144 4.76e+01 c.110.1.1 84130 1gd8A 118 4.76e+01 d.188.1.1 60445 1uheA 97 4.78e+01 1kpeA 126 4.79e+01 1kpf d.13.1.1 37508 1adqH 225 4.85e+01 1igtB b.1.1.1,b.1.1.2 20273,21273 1brnL 110 4.86e+01 1b20A d.1.1.2 36143 2av7A 275 4.89e+01 1ywqA 200 4.91e+01 1ecsA 126 4.92e+01 1ecsA d.32.1.2 59407 1xer 103 4.93e+01 1xer d.58.1.3 38990 1njhA 119 4.93e+01 b.128.1.1 85787 1e0gA 48 4.93e+01 1e01A d.7.1.1 37325 1wfxA 186 4.95e+01 2g7jA 124 4.97e+01 1ohpA 125 5.01e+01 2d1uA 104 5.07e+01 2pdd 43 5.10e+01 1ebdC a.9.1.1 16358 1ugpB 226 5.12e+01 b.34.4.4 107832 1r26A 125 5.17e+01 c.47.1.1 96847 1h7mA 102 5.24e+01 d.79.3.1 83485 1a1mA 278 5.24e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1zpwX 90 5.24e+01 1ar0A 127 5.26e+01 1ounA d.17.4.2 38092 1ckv 141 5.26e+01 1ckv d.137.1.1 41452 1s28A 132 5.29e+01 d.198.1.1 105223 1rwsA 77 5.29e+01 d.15.3.2 97991 1jguH 217 5.30e+01 b.1.1.1,b.1.1.2 66688,66689 1sqhA 312 5.33e+01 d.108.1.5 98966 2czrA 226 5.37e+01 1nf2A 268 5.38e+01 c.108.1.10 91849 1mr4A 47 5.39e+01 g.3.7.5 91429 2bvpA 276 5.40e+01 1keiA 316 5.42e+01 d.92.1.2 77349 1duzA 275 5.43e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 1yu2A 381 5.45e+01 2cdpA 160 5.46e+01 1hsbA 270 5.47e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 1jyoA 130 5.48e+01 d.198.1.1 67483 1kao 167 5.48e+01 1ctqA c.37.1.8 32014 3pvaA 335 5.51e+01 3pvaA d.153.1.3 41854 1kllA 130 5.53e+01 d.32.1.2 72720 1t0fA 276 5.55e+01 1aiu 105 5.55e+01 1erv c.47.1.1 32746 1xfuA 747 5.58e+01 1b3sA 110 5.59e+01 1b20A d.1.1.2 36229 1bymA 97 5.60e+01 1bi0 b.34.1.2 24458 1aw8B 91 5.61e+01 1aw8B 1korA 400 5.67e+01 c.26.2.1,d.210.1.1 72824,72825 1san 62 5.68e+01 2hddA a.4.1.1 16008 1p5hA 428 5.68e+01 c.123.1.1 87802 2dlbA 80 5.72e+01 1usuA 260 5.72e+01 d.14.1.8 99885 1pvxA 194 5.72e+01 1axkA b.29.1.11 24341 1b21A 110 5.75e+01 1b20A d.1.1.2 36219 1hjrA 158 5.76e+01 1hjrA c.55.3.6 33727 1erw 105 5.79e+01 1erv c.47.1.1 32745 1szhA 161 5.82e+01 a.226.1.1 106157 2a5jA 191 5.83e+01 1ris 101 5.85e+01 1ris d.58.14.1 39314 1f1zA 273 5.90e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1ewjA 126 5.97e+01 1ecsA d.32.1.2 59526 1scmB 145 5.98e+01 1wdcB a.39.1.5 17304 1ddeA 338 5.98e+01 1dd9A e.13.1.1 43255 1mszA 86 5.99e+01 d.68.7.1 79428 1wu7A 434 6.02e+01 1gvp 87 6.03e+01 1gvp b.40.4.7 25369 1w4tA 299 6.03e+01 1mkeA 152 6.04e+01 b.55.1.4 79231 1u2fA 90 6.04e+01 1u2fA d.58.7.1 39168 1uovA 159 6.08e+01 b.7.1.2 107974 1lkdA 297 6.17e+01 d.32.1.3,d.32.1.3 78059,78060 1ounA 127 6.19e+01 1ounA d.17.4.2 38090 1rsy 152 6.21e+01 1rsy b.7.1.2 23192 1k07A 263 6.21e+01 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