# List of top-scoring protein chains for t04-100-40-40-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 1theA 260 4.84e-02 1theB d.3.1.1 37056 1gmyA 261 6.97e-02 d.3.1.1 76236 1ru8A 232 4.69e-01 c.26.2.1 97849 1un3A 123 6.98e-01 d.5.1.1 99646 1agi 125 1.13e+00 7rsa d.5.1.1 37303 1j9bA 141 1.42e+00 c.47.1.12 66459 1s3cA 141 1.63e+00 2bibA 547 1.71e+00 1ekgA 127 2.04e+00 1dlxA d.82.2.1 40021 2bgcA 238 2.37e+00 1el5A 389 2.56e+00 1b3mA c.3.1.2,d.16.1.3 30369,37937 1a4yB 123 2.92e+00 7rsa d.5.1.1 37296 1oh0A 131 3.00e+00 d.17.4.3 87004 2gxfA 142 3.32e+00 2cokA 113 3.56e+00 1gxuA 91 3.58e+00 d.58.10.1 76378 1iloA 77 3.95e+00 c.47.1.1 66205 1vj7A 393 4.10e+00 a.211.1.1,d.218.1.8 100801,100802 1yqfA 203 4.51e+00 1v8hA 107 4.54e+00 2bj0A 203 4.58e+00 1xfsA 178 4.66e+00 d.129.3.5 109589 1ux2A 212 4.68e+00 b.96.1.1 100132 1qwdA 177 5.25e+00 b.60.1.1 96471 1dq3A 454 5.35e+00 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1kx5B 102 5.40e+00 a.22.1.1 77594 1uw6A 211 5.46e+00 b.96.1.1 100079 2blnA 305 5.49e+00 1hq3D 103 5.60e+00 1aoiB a.22.1.1 16464 1tif 78 5.69e+00 1tif d.15.8.1 37836 1qqcA 773 6.30e+00 1tgoA c.55.3.5,e.8.1.1 33724,43013 1dmmA 131 6.39e+00 1opy d.17.4.3 38114 1tzyD 103 6.52e+00 a.22.1.1 107533 2f1fA 164 6.57e+00 2fug5 207 6.64e+00 1y96A 86 6.88e+00 2d13A 227 7.00e+00 1omiA 248 7.26e+00 b.82.3.3,a.4.5.4 87079,87080 2bwkA 121 7.65e+00 1uv6A 210 7.67e+00 b.96.1.1 100030 1i9bA 217 7.72e+00 1i9bA b.96.1.1 62084 2g76A 335 7.87e+00 1opy 131 8.00e+00 1opy d.17.4.3 38113 1zvnA 99 8.06e+00 1wsrA 375 8.09e+00 1dzaA 129 8.19e+00 7rsa d.5.1.1 37275 1wfxA 186 8.64e+00 2gfaA 119 8.70e+00 1mqoA 227 9.18e+00 d.157.1.1 103846 2b4hA 254 9.26e+00 2d27A 149 9.88e+00 2bynA 227 9.97e+00 1rzmA 338 1.04e+01 c.1.10.4 105137 1hyxH 224 1.08e+01 1igtB b.1.1.1,b.1.1.2 20167,21191 1ut7A 171 1.10e+01 b.143.1.1 99906 2arhA 203 1.11e+01 2dhqA 146 1.13e+01 2dhqA c.23.13.1 31382 2bypA 214 1.13e+01 1a7cA 379 1.14e+01 1sek e.1.1.1 42660 2basA 431 1.14e+01 2ck3A 510 1.17e+01 1yu2A 381 1.17e+01 1vqoT 120 1.19e+01 1io1A 398 1.20e+01 1io1A e.32.1.1 62611 2fk9A 157 1.20e+01 2apqA 139 1.21e+01 1j7gA 144 1.22e+01 c.110.1.1 84130 1tp6A 128 1.23e+01 d.17.4.12 107184 2a7mA 250 1.23e+01 1yllA 200 1.25e+01 1hh2P 344 1.27e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1e79A 510 1.27e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18269,26434,32314 1l0qA 391 1.31e+01 b.1.3.1,b.69.2.3 77644,77645 1ul7A 102 1.34e+01 d.129.6.1 99540 2g6fX 59 1.34e+01 1r26A 125 1.35e+01 c.47.1.1 96847 1n4xH 120 1.37e+01 b.1.1.1 85324 1txvB 440 1.37e+01 1r13A 148 1.38e+01 d.169.1.1,h.1.1.1 96782,96783 1g5cA 170 1.39e+01 1g5cA c.53.2.1 60264 1jkeA 145 1.39e+01 c.110.1.1 66791 1nf2A 268 1.41e+01 c.108.1.10 91849 2ak5A 64 1.43e+01 3pvaA 335 1.44e+01 3pvaA d.153.1.3 41854 1xk7A 408 1.45e+01 2c4bA 143 1.46e+01 1j7nA 776 1.50e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1hbq 183 1.51e+01 1aqb b.60.1.1 27078 1v6tA 255 1.51e+01 2bl0C 142 1.52e+01 1p5dX 463 1.61e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1whsB 153 1.61e+01 1whtB 1go3E 187 1.65e+01 b.40.4.5,d.230.1.1 83054,83055 1esl 162 1.68e+01 1esl d.169.1.1,g.3.11.1 42353,44225 2ca6A 386 1.68e+01 1yu1A 381 1.70e+01 1mvfA 135 1.71e+01 b.1.1.1 85141 2d1uA 104 1.74e+01 1a8vA 121 1.74e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1s72T 120 1.75e+01 b.34.5.1 105339 1nciA 110 1.78e+01 1edhA b.1.6.1 22191 1zt2B 212 1.79e+01 1l7bA 92 1.81e+01 c.15.1.2 91053 1jj2S 119 1.82e+01 1ffkQ b.34.5.1 63104 1dxrH 258 1.82e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1h8eA 510 1.87e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 60738,60739,60740 1k2yX 463 1.88e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1yu4A 381 1.89e+01 1yu0A 381 1.92e+01 1lfpA 249 1.94e+01 e.39.1.1 73885 1mhnA 59 1.94e+01 b.34.9.1 84964 1m98A 317 1.95e+01 a.175.1.1,d.17.4.6 78866,78867 1x99A 145 1.96e+01 1jguH 217 2.00e+01 b.1.1.1,b.1.1.2 66688,66689 1upiA 225 2.01e+01 b.82.1.1 99757 2g7jA 124 2.02e+01 1kskA 234 2.03e+01 d.66.1.5,d.265.1.3 72920,90389 1zxkA 98 2.03e+01 1whtB 153 2.04e+01 1whtB 1wcwA 261 2.12e+01 1g71A 347 2.13e+01 1g71A d.264.1.1 43268 1eylA 186 2.15e+01 1wba b.42.4.1 25593 1u2fA 90 2.17e+01 1u2fA d.58.7.1 39168 1wy5A 317 2.19e+01 2f1lA 187 2.22e+01 1yrgA 385 2.23e+01 1yrgA c.10.1.2 30854 1opoA 348 2.25e+01 b.121.4.7 87240 1jqeA 292 2.25e+01 c.66.1.19 71789 1mszA 86 2.27e+01 d.68.7.1 79428 1xa3A 437 2.31e+01 2cveA 191 2.33e+01 1oaqH 121 2.35e+01 b.1.1.1 92707 1jr5A 90 2.37e+01 a.150.1.1 67113 1h05A 146 2.37e+01 c.23.13.1 76433 1ol0A 121 2.39e+01 b.1.1.1 93296 1dd9A 338 2.39e+01 1dd9A e.13.1.1 43254 1qsgA 265 2.42e+01 1eny c.2.1.2 29935 1ha1 184 2.45e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1k07A 263 2.47e+01 d.157.1.1 77218 1vl5A 260 2.49e+01 c.66.1.41 108720 1kt6A 183 2.50e+01 b.60.1.1 84466 2ai4A 119 2.52e+01 1xovA 326 2.53e+01 1yezA 68 2.54e+01 1dcfA 136 2.56e+01 1dcfA c.23.1.2 31124 2ghpA 292 2.57e+01 1o6sB 105 2.57e+01 b.1.6.1 81096 1p9qC 256 2.57e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2fyxA 143 2.60e+01 1guiA 155 2.60e+01 b.18.1.14 76351 1w4tA 299 2.61e+01 1bymA 97 2.62e+01 1bi0 b.34.1.2 24458 1yu3A 381 2.62e+01 1fh0A 221 2.64e+01 1cs8A d.3.1.1 59832 1wd7A 261 2.67e+01 1u0qA 125 2.69e+01 1a4pA 96 2.71e+01 1b4cA a.39.1.2 17176 1ht6A 405 2.71e+01 b.71.1.1,c.1.8.1 83629,83630 1rwsA 77 2.72e+01 d.15.3.2 97991 2pvaA 345 2.72e+01 3pvaA d.153.1.3 41850 1ckv 141 2.72e+01 1ckv d.137.1.1 41452 1z5bA 469 2.73e+01 1aqb 183 2.77e+01 1aqb b.60.1.1 27084 2f5gA 133 2.79e+01 1rifA 282 2.80e+01 c.37.1.23 97507 1pvyA 227 2.82e+01 d.115.1.2 95195 1f15A 218 2.84e+01 1f15B b.121.4.5 23320 1hilB 220 2.91e+01 1igtB b.1.1.1,b.1.1.2 19787,20897 1lb2B 84 3.00e+01 a.60.3.1 77871 1l3kA 196 3.02e+01 d.58.7.1,d.58.7.1 73539,73540 1zybA 232 3.07e+01 2msbA 115 3.09e+01 1rtm1 d.169.1.1 42355 1jl0A 334 3.15e+01 1jenA d.156.1.1 63155 1k8kC 372 3.16e+01 b.69.4.1 68308 1aba 87 3.17e+01 1aba c.47.1.1 32760 2a6mA 155 3.18e+01 1ebdC 41 3.29e+01 1ebdC a.9.1.1 16355 1o4wA 147 3.30e+01 c.120.1.1 86629 1i8kB 124 3.31e+01 b.1.1.1 71131 1xer 103 3.32e+01 1xer d.58.1.3 38990 1u69A 163 3.34e+01 d.32.1.7 107699 1qo3C 137 3.34e+01 1qo3C d.169.1.1 42350 3daaA 277 3.35e+01 1daaA e.17.1.1 43272 1mw7A 240 3.35e+01 e.39.1.1 79557 1lyvA 306 3.35e+01 c.45.1.2 74348 1u6tA 121 3.39e+01 1j1xH 114 3.46e+01 b.1.1.1 77063 1i4uA 181 3.46e+01 b.60.1.1 61732 1yioA 208 3.46e+01 1y9wA 140 3.47e+01 1svpA 161 3.48e+01 1svpA b.47.1.3 26384 1odkA 235 3.49e+01 c.56.2.1 86863 1feuA 206 3.52e+01 1feuA b.53.1.1 59801 1nz0A 118 3.52e+01 d.14.1.2 86433 1snnA 227 3.54e+01 d.115.1.2 105821 2bc2A 227 3.54e+01 1a7tA d.157.1.1 42031 1jbeA 128 3.56e+01 3chy c.23.1.1 62845 1rzhH 260 3.61e+01 b.41.1.1,f.23.10.1 98162,98163 1jm1A 204 3.61e+01 b.33.1.1 71745 1qxoA 388 3.65e+01 d.258.1.1 96539 1jp4A 308 3.68e+01 1jp4A e.7.1.1 63223 1v32A 101 3.69e+01 a.42.1.1 100277 1p5hA 428 3.72e+01 c.123.1.1 87802 1rtm1 149 3.73e+01 1rtm1 1dg6A 191 3.76e+01 1d4vB b.22.1.1 23883 1q5yA 85 3.79e+01 d.58.18.4 95950 1w85I 49 3.87e+01 1l7mA 211 3.88e+01 c.108.1.4 73664 1memA 215 3.93e+01 1cs8A d.3.1.1 37069 1m2xA 223 3.95e+01 d.157.1.1 84764 1qw1A 121 3.95e+01 2ey4C 82 3.98e+01 1lj5A 379 4.01e+01 e.1.1.1 73928 1mqkH 127 4.01e+01 b.1.1.1 85053 1louA 101 4.02e+01 1ris d.58.14.1 39323 1jjtA 228 4.03e+01 1a7tA d.157.1.1 63139 1ywqA 200 4.04e+01 1uu1A 335 4.04e+01 c.67.1.1 99993 1qhtA 775 4.07e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 2cq2A 114 4.08e+01 1erw 105 4.11e+01 1erv c.47.1.1 32745 2bj7A 138 4.13e+01 1h7mA 102 4.16e+01 d.79.3.1 83485 1aiu 105 4.21e+01 1erv c.47.1.1 32746 1p5vA 235 4.21e+01 b.1.11.1,b.7.2.1 87812,87813 1e79H 146 4.22e+01 1e79H a.2.10.1,b.93.1.1 15721,28438 1gheA 177 4.23e+01 d.108.1.1 76222 2bvpA 276 4.23e+01 1uv7A 110 4.24e+01 d.67.4.1 100040 1vr5A 547 4.24e+01 1mkyA 439 4.25e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 2a15A 139 4.26e+01 1s6cA 183 4.27e+01 a.39.1.5 98594 1x1rA 178 4.31e+01 1tu6A 215 4.34e+01 d.3.1.1 107318 1dgwA 178 4.37e+01 1dgwA b.82.1.2 28090 1rq6A 62 4.38e+01 2bvcA 486 4.42e+01 1xfpA 142 4.44e+01 b.1.1.1 109587 1nycA 111 4.44e+01 b.61.2.2 92336 1vfgA 390 4.45e+01 a.173.1.1,d.218.1.4 108570,108571 1mp9A 198 4.46e+01 d.129.1.1,d.129.1.1 91385,91386 1f9aA 168 4.46e+01 1f9aA c.26.1.3 31602 2a9mL 110 4.47e+01 1kkeA 210 4.49e+01 b.21.1.2,b.83.1.2 68669,68670 1iq4A 179 4.57e+01 1iq4A d.77.1.1 62641 1vlqA 337 4.59e+01 c.69.1.25 108848 1bb8 71 4.61e+01 2bb8 d.10.1.1 37478 1vkcA 158 4.62e+01 1f3mC 297 4.62e+01 1hcl d.144.1.7 41677 1sqhA 312 4.62e+01 d.108.1.5 98966 1g1tA 157 4.64e+01 d.169.1.1,g.3.11.1 65104,65105 1i50A 1733 4.68e+01 e.29.1.2 61754 1wp5A 323 4.69e+01 1npeA 267 4.69e+01 b.68.5.1 92032 1vr6A 350 4.79e+01 2pii 112 4.81e+01 2pii d.58.5.1 39071 1x0pA 143 4.85e+01 1v5vA 401 4.88e+01 1fe0A 68 4.88e+01 1cc8A d.58.17.1 39345 2a8jA 420 4.90e+01 1ef1A 294 4.94e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2adgB 222 4.96e+01 2g6bA 180 4.96e+01 1qg3A 195 4.97e+01 1qg3A b.1.2.1,b.1.2.1 21993,21994 1t2jA 116 5.04e+01 1dy5A 124 5.04e+01 7rsa d.5.1.1 37163 1rdo1 113 5.06e+01 1rtm1 1i58A 189 5.07e+01 1b3qA d.122.1.3 61773 1wdcC 156 5.09e+01 1wdcC a.39.1.5 17317 1y7mA 164 5.11e+01 1s6lA 212 5.11e+01 1xjcA 169 5.13e+01 1oz9A 150 5.25e+01 d.92.1.15 93808 1jopA 155 5.28e+01 b.82.2.7 84187 1gy6A 127 5.28e+01 d.17.4.2 70736 1tu1A 148 5.29e+01 d.107.1.3 107316 1k4nA 192 5.33e+01 d.32.1.5 72059 1x31C 206 5.34e+01 2ch4A 320 5.34e+01 2aq4A 434 5.35e+01 1p7tA 731 5.37e+01 c.1.13.1 94319 1p0hA 318 5.39e+01 d.108.1.1 93866 1lb6A 160 5.39e+01 b.8.1.1 73798 1fw9A 164 5.39e+01 1fw9A d.190.1.1 60059 2gjgA 248 5.40e+01 1cojA 212 5.41e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1u0sA 86 5.41e+01 d.58.24.1 107565 1jssA 224 5.44e+01 d.129.3.2 71844 1o4sA 389 5.45e+01 c.67.1.1 86620 1qovH 260 5.45e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1jmxB 349 5.45e+01 b.69.2.2 66906 2al6A 375 5.51e+01 1ospO 257 5.53e+01 1ospO b.76.1.1 27971 2aioA 269 5.61e+01 1l8rA 101 5.65e+01 a.6.1.4 73700 3chy 128 5.65e+01 3chy c.23.1.1 31038 1aoy 78 5.65e+01 1aoy a.4.5.3 16087 1rpjA 288 5.67e+01 2dri c.93.1.1 35656 1ytw 306 5.67e+01 1ytw c.45.1.2 32689 2au3A 407 5.67e+01 1ffyA 917 5.69e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1korA 400 5.70e+01 c.26.2.1,d.210.1.1 72824,72825 2f8yA 223 5.75e+01 1nmeA 146 5.76e+01 c.17.1.1 85874 1r0pA 312 5.80e+01 d.144.1.7 96734 1t4oA 117 5.81e+01 d.50.1.1 106425 1u7lA 392 5.83e+01 2aotA 292 5.84e+01 1h4rA 314 5.85e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1b74A 254 5.87e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1hgxA 183 5.90e+01 1tc1A c.61.1.1 34027 2a9mH 126 5.91e+01 1j97A 211 5.95e+01 1f5sA c.108.1.4 62753 2g3aA 152 5.95e+01 2amyA 246 5.96e+01 1qexA 288 5.96e+01 1qexA b.32.1.1 24425 1slqA 278 5.98e+01 f.47.1.1 105719 1a62 130 5.99e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1sbxA 106 6.00e+01 a.6.1.4 105414 1uuzA 137 6.03e+01 d.233.1.1 100024 1ni5A 433 6.07e+01 c.26.2.5,d.229.1.1 80533,80534 1xwsA 313 6.11e+01 1a2yB 116 6.13e+01 1gc1H b.1.1.1 19927 1mu5A 471 6.15e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1w4vA 119 6.16e+01 1tp5A 119 6.18e+01 1kpeA 126 6.18e+01 1kpf d.13.1.1 37508 1usuA 260 6.20e+01 d.14.1.8 99885 1a2pA 110 6.20e+01 1b20A d.1.1.2 36140 1dun 134 6.21e+01 1dun b.85.4.1 28371 2fomB 185 6.22e+01 1qwvA 142 6.24e+01 a.39.2.1 96506 1gouA 116 6.24e+01 d.1.1.2 65429 1wwkA 307 6.24e+01 1n0xH 230 6.25e+01 b.1.1.1,b.1.1.2 91528,91529 1g79A 218 6.34e+01 1ci0A b.45.1.1 25752 1smlA 269 6.36e+01 1smlA d.157.1.1 42053 1fxlA 167 6.38e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1erv 105 6.39e+01 1erv c.47.1.1 32743 1jogA 146 6.43e+01 a.24.16.2 77142 2bu3A 254 6.44e+01 1nox 205 6.51e+01 1nox d.90.1.1 40242 1tuzA 118 6.52e+01 1suwA 249 6.53e+01 e.52.1.1 106027 1kafA 108 6.56e+01 d.199.1.1 68372 2bbkH 355 6.61e+01 2bbkH b.69.2.1 27634 1pm3A 78 6.62e+01 b.41.1.2 94889 1jenA 267 6.64e+01 1jenA 2cdpA 160 6.65e+01 1ti6B 274 6.66e+01 b.3.5.1,d.58.1.5 106976,106977 1uacH 114 6.66e+01 b.1.1.1 99132 2fauA 341 6.67e+01 2a5jA 191 6.70e+01 2f2gA 221 6.73e+01 1dp7P 76 6.74e+01 1dp7P a.4.5.20 16159 1uv4A 293 6.75e+01 1l4dB 122 6.76e+01 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