# List of top-scoring protein chains for t2k-100-30-bys-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 2f8aA 208 7.50e-37 1gp1A 198 2.97e-36 1gp1A c.47.1.10 33059 1st9A 143 1.99e-18 c.47.1.10 98987 2f9sA 151 3.22e-18 1jfuA 186 1.25e-16 c.47.1.10 62940 1xzoA 174 3.41e-11 1kngA 156 4.80e-11 c.47.1.10 72777 1z5yE 149 1.97e-10 1lu4A 136 6.20e-09 c.47.1.10 91124 1xvwA 160 8.01e-09 1zzoA 136 8.53e-09 2fy6A 143 1.91e-08 1qk8A 146 2.05e-08 1ewxA c.47.1.10 33061 1ewxA 146 2.78e-08 1ewxA c.47.1.10 33062 1o6jA 150 6.80e-08 c.47.1.10 81089 1o8xA 146 8.84e-08 c.47.1.10 86681 2b7kA 200 3.39e-07 1nw2A 105 8.85e-07 c.47.1.1 92215 1i5gA 144 1.01e-06 1ewxA c.47.1.10 61784 1qmvA 197 1.05e-06 1qq2A c.47.1.10 33066 1aiu 105 1.38e-06 1erv c.47.1.1 32746 1t00A 112 1.52e-06 1nswA 105 1.70e-06 c.47.1.1 92097 1thx 115 2.32e-06 1thx c.47.1.1 32732 2cvbA 188 2.61e-06 1erv 105 4.32e-06 1erv c.47.1.1 32743 1qq2A 199 7.33e-06 1qq2A c.47.1.10 33064 1wmjA 130 9.87e-06 2trxA 108 1.09e-05 1thx c.47.1.1 32719 1v98A 140 2.67e-05 1faaA 124 3.10e-05 1erv c.47.1.1 32738 1fb6A 105 3.66e-05 1thx c.47.1.1 32739 1mdiA 105 3.68e-05 1erv c.47.1.1 32755 1kebA 108 4.18e-05 c.47.1.1 77341 1f9mA 112 4.90e-05 1erv c.47.1.1 32736 1w4vA 119 7.29e-05 1uvzA 119 8.35e-05 1dbyA 107 9.43e-05 1thx c.47.1.1 32734 1r26A 125 1.91e-04 c.47.1.1 96847 1zyeA 220 2.28e-04 1erw 105 2.66e-04 1erv c.47.1.1 32745 1tof 112 4.67e-04 1erv c.47.1.1 32733 1erzA 303 8.31e-04 1erzA d.160.1.2 59498 1x0rA 249 8.77e-04 2f51A 118 1.33e-03 1uf5A 303 1.35e-03 d.160.1.2 107808 1mek 120 4.99e-03 1erv c.47.1.2 32775 2b5eA 504 5.09e-03 1qxhA 167 5.95e-03 c.47.1.10 96528 2a4vA 159 9.85e-03 1uc7A 125 1.06e-02 c.47.1.1 99163 1psqA 163 1.08e-02 c.47.1.10 88283 1xvqA 175 1.12e-02 1n8jA 186 2.28e-02 c.47.1.10 85401 1emsA 440 4.90e-02 1emsA d.13.1.1,d.160.1.1 37520,42086 1ionA 243 6.67e-02 c.37.1.10 62633 1eejA 216 7.74e-02 1eejA c.47.1.9,d.17.3.1 33057,38071 1f1uA 323 7.93e-02 d.32.1.3,d.32.1.3 83200,83201 1ovqA 138 8.85e-02 c.55.3.8 93607 1nu0A 138 1.07e-01 c.55.3.8 92165 1j08A 226 1.79e-01 c.47.1.2,c.47.1.2 83855,83856 1xccA 220 2.49e-01 1g3qA 237 3.17e-01 1hyqA c.37.1.10 60237 1ac1A 189 3.98e-01 1fvkA c.47.1.13 90326 1senA 164 4.08e-01 c.47.1.1 105465 1jfrA 262 4.17e-01 1jfrA c.69.1.16 34724 1ecsA 126 4.50e-01 1ecsA d.32.1.2 59407 1fp4A 492 4.51e-01 c.92.2.3 76187 1t3bA 211 4.58e-01 c.47.1.9,d.17.3.1 106341,106342 1sxrA 183 5.04e-01 d.118.1.1 106101 1jr7A 311 5.05e-01 b.82.2.3 63255 2fomB 185 5.47e-01 1kk1A 410 5.83e-01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1va4A 279 6.23e-01 c.69.1.12 108458 1aod 289 6.53e-01 2plc c.1.18.2 29615 1cjbA 231 6.94e-01 1qk3A c.61.1.1 34079 2a5lA 200 7.83e-01 1fvkA 189 7.89e-01 1fvkA c.47.1.13 90351 1dsbA 189 7.90e-01 1fvkA c.47.1.13 90347 2bl1A 172 7.92e-01 1kbqA 273 8.01e-01 c.23.5.3 68391 1q98A 165 8.42e-01 c.47.1.10 96253 1dbrA 231 8.47e-01 1qk3A c.61.1.1 34041 1a8l 226 8.76e-01 1a8l c.47.1.2,c.47.1.2 32777,32778 1d4aA 273 8.95e-01 1d4aA c.23.5.3 31219 1skoA 143 9.01e-01 d.110.7.1 105676 1qbgA 272 9.15e-01 1d4aA c.23.5.3 31227 2f2lX 167 9.29e-01 2abbA 364 1.01e+00 1uf3A 228 1.01e+00 d.159.1.6 99317 1qk4A 233 1.03e+00 1qk3A c.61.1.1 34037 1yvoA 172 1.03e+00 1vyrA 364 1.05e+00 c.1.4.1 108906 2plc 274 1.12e+00 2plc c.1.18.2 29614 1gvoA 364 1.13e+00 c.1.4.1 76357 1z7gA 217 1.15e+00 1vicA 262 1.16e+00 c.68.1.13 100756 2minA 491 1.18e+00 1qguA c.92.2.3 35609 1bzyA 217 1.18e+00 1qk3A c.61.1.1 34071 1fo5A 85 1.20e+00 1fo5A c.47.1.1 59922 1s0uA 408 1.24e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1qrdA 273 1.29e+00 1d4aA c.23.5.3 31217 8ohm 435 1.35e+00 1heiA c.37.1.14,c.37.1.14 32469,32470 1xm7A 195 1.35e+00 1t5bA 201 1.35e+00 c.23.5.3 106433 1vflA 356 1.39e+00 1vypX 364 1.42e+00 c.1.4.1 108905 1cozA 129 1.49e+00 1cozA c.26.1.2 31598 2essA 248 1.55e+00 1fsgA 233 1.58e+00 1qk3A c.61.1.1 34029 1cp2A 269 1.63e+00 1cp2A c.37.1.10 32269 1bykA 255 1.66e+00 1bykA c.93.1.1 35706 1kllA 130 1.67e+00 d.32.1.2 72720 1jlwA 219 1.68e+00 a.45.1.1,c.47.1.5 71741,71742 1acvA 189 1.69e+00 1fvkA c.47.1.13 90328 1f1xA 322 1.70e+00 d.32.1.3,d.32.1.3 83208,83209 1df9A 191 1.72e+00 1befA b.47.1.3 26420 2cokA 113 1.82e+00 2gd1O 334 1.82e+00 1dssG c.2.1.3,d.81.1.1 29978,39893 1befA 181 1.85e+00 1befA b.47.1.3 26419 1a4mA 349 1.85e+00 1a4mA c.1.9.1 29014 1vpqA 273 1.89e+00 1vhxA 150 1.89e+00 c.55.3.8 100712 1nfkA 325 1.90e+00 1a3qA b.1.18.1,b.2.5.3 21929,22444 1xg5A 279 2.09e+00 2his 312 2.11e+00 1taxA c.1.8.3 28918 2dvh 79 2.30e+00 1c53 a.3.1.1 15803 2cybA 323 2.42e+00 1hh1A 143 2.51e+00 1gefA c.52.1.18 61036 1q6hA 224 2.52e+00 d.26.1.1 95975 1tp9A 162 2.52e+00 1tikA 213 2.55e+00 c.23.5.3 107003 1wouA 123 2.59e+00 c.47.1.16 109471 1qf9A 194 2.74e+00 1zin c.37.1.1 31848 3minC 491 2.75e+00 1qguA c.92.2.3 35607 1hbq 183 2.81e+00 1aqb b.60.1.1 27078 1xhfA 123 2.82e+00 1tv8A 340 2.88e+00 c.1.28.3 107352 1unqA 125 2.96e+00 b.55.1.1 107968 1h10A 125 2.98e+00 b.55.1.1 83446 1pj5A 830 3.00e+00 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1c14A 262 3.02e+00 1eny c.2.1.2 29927 1vlmA 219 3.10e+00 c.66.1.41 108836 1m1nA 491 3.10e+00 c.92.2.3 78417 1hmpA 217 3.13e+00 1qk3A c.61.1.1 34075 1ewjA 126 3.20e+00 1ecsA d.32.1.2 59526 1vmeA 410 3.23e+00 c.23.5.1,d.157.1.3 108893,108894 1gh2A 107 3.30e+00 1erv c.47.1.1 60515 1vs0A 310 3.36e+00 2b18A 164 3.38e+00 1w1iE 357 3.40e+00 c.1.9.1 109051 1y9zA 441 3.48e+00 2akrA 285 3.50e+00 1zx1A 231 3.50e+00 1wsrA 375 3.52e+00 1y2qA 143 3.63e+00 1qk3A 233 3.66e+00 1qk3A c.61.1.1 34031 1ag9A 175 3.74e+00 1rcf c.23.5.1 31178 1j3wA 163 3.74e+00 d.110.7.1 90833 1sg0A 230 3.75e+00 2b9wA 424 3.75e+00 1zh5A 195 3.75e+00 1fkx 349 3.77e+00 1a4mA c.1.9.1 29018 1wmhA 89 3.78e+00 1xf1A 926 3.84e+00 1yzfA 195 3.87e+00 1vpdA 299 3.99e+00 1kjnA 157 4.01e+00 c.115.1.1 72614 1hlrA 907 4.10e+00 1vlbA 907 4.10e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1vjnA 220 4.11e+00 d.157.1.4 100825 1h61A 364 4.17e+00 1oyc c.1.4.1 60657 2h1tA 188 4.37e+00 5ukdA 194 4.39e+00 1zin c.37.1.1 31851 1obfO 335 4.44e+00 c.2.1.3,d.81.1.1 86768,86769 1a23 189 4.49e+00 1fvkA c.47.1.13 90319 1u3aA 189 4.49e+00 1v6cA 441 4.55e+00 1heiA 451 4.60e+00 1heiA c.37.1.14,c.37.1.14 32463,32464 1ij8A 128 4.62e+00 b.61.1.1 62480 1wbiA 129 4.65e+00 1nqnA 122 4.65e+00 b.61.1.1 86042 1uxaA 194 4.71e+00 b.21.1.1 108091 1l9gA 192 4.77e+00 c.18.1.2 84568 2f2lA 167 4.86e+00 1wd5A 208 4.87e+00 8rucI 123 4.89e+00 1rboC d.73.1.1 39629 1rboC 123 4.97e+00 1rboC d.73.1.1 39634 2bzsA 236 5.04e+00 1ufoA 238 5.06e+00 c.69.1.27 99344 2rslA 140 5.06e+00 2rslA c.53.1.1 33345 1vd2A 89 5.11e+00 d.15.2.2 108517 1c53 79 5.27e+00 1c53 a.3.1.1 15801 1vetA 124 5.39e+00 d.110.7.1 108553 1vjrA 271 5.43e+00 c.108.1.14 100832 1q6uA 245 5.47e+00 d.26.1.1 95998 1xo1A 291 5.62e+00 1exnA a.60.7.1,c.120.1.2 18086,33356 1wznA 252 5.79e+00 1umdA 367 5.80e+00 c.36.1.11 99599 1h9sA 140 5.99e+00 1b9mA b.40.6.2,b.40.6.2 60843,60844 1hmy 327 6.02e+00 6mhtA c.66.1.26 34229 1nkiA 135 6.06e+00 d.32.1.2 91941 2c1lA 358 6.07e+00 1fhdA 312 6.08e+00 1taxA c.1.8.3 28915 1lqpA 135 6.10e+00 d.32.1.2 78151 1u0tA 307 6.14e+00 e.52.1.1 107567 1si7A 369 6.16e+00 d.265.1.4 98883 2b0tA 738 6.23e+00 1szwA 379 6.28e+00 d.265.1.4 99047 2c0cA 362 6.35e+00 1qh8A 478 6.44e+00 1qguA c.92.2.3 35633 1m2bA 110 6.45e+00 c.47.1.11 78474 1qadA 111 6.51e+00 1qadA d.93.1.1 40498 2fp7B 172 6.74e+00 2bbsA 290 6.82e+00 1vl8A 267 6.90e+00 c.2.1.2 108733 1vbkA 307 7.07e+00 1qsgA 265 7.08e+00 1eny c.2.1.2 29935 1l5zA 155 7.16e+00 c.23.1.1 77722 1qnrA 344 7.23e+00 1qnoA c.1.8.3 28834 1y55X 126 7.24e+00 1xc3A 302 7.29e+00 2fhzA 109 7.33e+00 1qg6A 261 7.41e+00 1eny c.2.1.2 29919 1s8nA 205 7.53e+00 c.23.1.1 105374 1b9mA 265 7.57e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1vyoA 128 7.67e+00 1wryA 121 7.72e+00 1ve3A 227 7.85e+00 1cd1A 315 8.07e+00 1cd1A b.1.1.2,d.19.1.1 21579,38155 1s1fA 406 8.11e+00 1tjyA 316 8.11e+00 c.93.1.1 107062 1e4fT 419 8.14e+00 1e4fT c.55.1.1,c.55.1.1 33453,33454 2axoA 270 8.17e+00 1h54A 754 8.22e+00 a.102.1.4,b.30.5.3 60634,60635 1m2dA 110 8.24e+00 c.47.1.11 78476 1m98A 317 8.41e+00 a.175.1.1,d.17.4.6 78866,78867 1hztA 190 8.45e+00 1i9aA d.113.1.2 61459 1h54B 754 8.45e+00 a.102.1.4,b.30.5.3 60636,60637 1amj 754 8.53e+00 1amj c.8.2.1,c.83.1.1 30725,35401 1wcdJ 441 8.62e+00 2ez9A 603 8.69e+00 1zu4A 320 8.73e+00 1yobA 179 8.79e+00 1kt6A 183 8.83e+00 b.60.1.1 84466 1qguA 478 8.98e+00 1qguA c.92.2.3 35625 1hbp 183 9.07e+00 1aqb b.60.1.1 27079 1f89A 291 9.10e+00 d.160.1.1 64988 1wehA 171 9.16e+00 1ro5A 201 9.28e+00 d.108.1.3 105023 2cz2A 223 9.31e+00 1rbp 182 9.34e+00 1aqb b.60.1.1 27085 1hgxA 183 9.37e+00 1tc1A c.61.1.1 34027 1y0zA 330 9.46e+00 1h9oA 112 9.48e+00 1qadA d.93.1.1 60837 1gym 298 9.52e+00 2plc c.1.18.2 29606 1ur1A 378 9.79e+00 c.1.8.3 99804 2ptd 298 9.81e+00 2plc c.1.18.2 29605 2ae2A 260 9.97e+00 1bdb c.2.1.2 29945 1lst 239 1.00e+01 1lst c.94.1.1 35755 1fh9A 312 1.04e+01 1taxA c.1.8.3 28913 1k8tA 510 1.04e+01 e.41.1.1 68316 1aqb 183 1.05e+01 1aqb b.60.1.1 27084 1dvh 79 1.05e+01 1c53 a.3.1.1 15802 1ixkA 315 1.07e+01 c.66.1.38 90716 1im8A 244 1.08e+01 c.66.1.14 66212 1ju2A 536 1.09e+01 c.3.1.2,d.16.1.1 77169,77170 1n9lA 109 1.09e+01 d.110.3.6 85468 1h1lA 481 1.09e+01 c.92.2.3 70851 1e5dA 402 1.10e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1qnoA 344 1.10e+01 1qnoA c.1.8.3 28838 2bgiA 272 1.10e+01 1svcP 365 1.11e+01 1a3qA b.1.18.1,b.2.5.3 21924,22443 1egzA 291 1.12e+01 7a3hA c.1.8.3 28828 1n3lA 372 1.13e+01 c.26.1.1 79966 1r7aA 504 1.13e+01 b.71.1.1,c.1.8.1 97192,97193 1ghtA 105 1.16e+01 2rslA c.53.1.1 60526 1fp3A 402 1.17e+01 1fp3A a.102.1.3 18842 1f5sA 211 1.18e+01 1f5sA c.108.1.4 59656 1s95A 333 1.18e+01 d.159.1.3 105375 1zuwA 272 1.18e+01 1rz3A 201 1.24e+01 c.37.1.6 98132 1zd7A 159 1.26e+01 1cqzA 554 1.27e+01 1cr6B c.69.1.11,c.108.1.2 34689,43339 2bgcA 238 1.27e+01 1gskA 513 1.27e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 2d09A 407 1.28e+01 2tmkA 216 1.29e+01 3tmkA c.37.1.1 31928 1mkyA 439 1.30e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1x84A 189 1.33e+01 1pea 385 1.36e+01 1pea c.93.1.1 35662 1a76 326 1.37e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1vrvA 101 1.37e+01 3tmkA 216 1.38e+01 3tmkA c.37.1.1 31920 2furA 209 1.38e+01 1add 349 1.38e+01 1a4mA c.1.9.1 29020 1s5lA 344 1.39e+01 1xfuA 747 1.40e+01 1gtxA 472 1.42e+01 1gtxA 1q7fA 286 1.43e+01 b.68.9.1 96036 1t0iA 191 1.43e+01 c.23.5.4 106209 1aba 87 1.45e+01 1aba c.47.1.1 32760 1l7mA 211 1.47e+01 c.108.1.4 73664 1u6tA 121 1.48e+01 5abp 306 1.49e+01 8abp c.93.1.1 35651 1wosA 364 1.51e+01 b.44.2.1,d.250.1.1 109468,109469 1gxuA 91 1.52e+01 d.58.10.1 76378 1geeA 261 1.55e+01 c.2.1.2 90509 1up6A 416 1.55e+01 c.2.1.5,d.162.1.2 107976,107977 1abe 306 1.55e+01 8abp c.93.1.1 35648 1gcoA 261 1.56e+01 1ybvA c.2.1.2 29884 1mjhA 162 1.57e+01 1mjhA c.26.2.4 31639 1oj7A 408 1.57e+01 e.22.1.2 103971 1x1nA 524 1.58e+01 1z5lA 285 1.59e+01 2bznA 351 1.59e+01 1dgjA 907 1.59e+01 1alo a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 17909,37694,38585,41415 2d0eA 407 1.60e+01 3mhtA 327 1.61e+01 6mhtA c.66.1.26 34234 1tu6A 215 1.62e+01 d.3.1.1 107318 1j97A 211 1.62e+01 1f5sA c.108.1.4 62753 1poxA 585 1.63e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1m5wA 243 1.63e+01 c.1.24.1 84836 1wdxA 69 1.65e+01 1j3gA 187 1.66e+01 d.118.1.1 77075 2bzgA 232 1.66e+01 1pch 88 1.68e+01 1ptf d.94.1.1 40564 1s2kA 206 1.68e+01 b.29.1.20 98389 1h8eG 272 1.70e+01 1e79G c.49.2.1 60756 1hyvA 166 1.70e+01 1b9dA c.55.3.2 61424 2bwqA 129 1.70e+01 1t6cA 315 1.71e+01 c.55.1.8,c.55.1.8 106558,106559 1qqcA 773 1.71e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1gdtA 183 1.71e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 2ar9A 278 1.77e+01 1wzcA 249 1.77e+01 1zxuA 217 1.79e+01 2aviA 128 1.79e+01 1swuA b.61.1.1 27411 6acn 754 1.81e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1egr 85 1.81e+01 1kte c.47.1.1 32765 1xi7A 61 1.83e+01 2cmuA 342 1.85e+01 1i9aA 182 1.85e+01 1i9aA d.113.1.2 62082 1hrhA 136 1.86e+01 1rthA c.55.3.1 33577 1kxoA 184 1.86e+01 b.60.1.1 84475 1xwtA 405 1.86e+01 2bkxA 242 1.86e+01 1lba 146 1.87e+01 1lba d.118.1.1 41062 1x92A 199 1.87e+01 2aa4A 289 1.87e+01 1obpA 159 1.87e+01 1obpA 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8.73e+01 1pdc 45 8.73e+01 g.14.1.2 44667 1wvhA 134 8.76e+01 1f43A 61 8.76e+01 1akhA a.4.1.1 15982 2a97A 439 8.76e+01 1f02T 66 8.79e+01 1f02T j.67.1.1 46360 1tluA 130 8.88e+01 d.156.1.2 107139 1itcA 516 8.90e+01 b.3.1.1,c.1.8.1 83705,83706 1nnlA 225 8.93e+01 c.108.1.4 85906 1x24A 180 8.95e+01 1oz7A 131 8.96e+01 d.169.1.1 93806 1mbyA 88 8.98e+01 d.223.1.1 78931 1tc5A 194 8.99e+01 c.110.1.1 106752 1m7xA 617 8.99e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1hslA 238 8.99e+01 1lst c.94.1.1 35804