# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 2ah5A 210 1.57e-03 1pu6A 218 2.75e-01 a.96.1.5 95123 1t5oA 351 3.11e-01 c.124.1.5 106459 1e19A 314 4.01e-01 1b7bA c.73.1.1 34967 2f2eA 146 8.85e-01 2go7A 207 1.32e+00 1eexA 554 2.59e+00 1dioA c.1.19.3 29650 18gsA 210 2.63e+00 1pgtA a.45.1.1,c.47.1.5 17528,32822 1lbkA 208 2.64e+00 a.45.1.1,c.47.1.5 73809,73810 1aqwA 209 2.75e+00 1pgtA a.45.1.1,c.47.1.5 17517,32811 1z9hA 290 2.80e+00 1dioA 554 2.86e+00 1dioA c.1.19.3 29656 1sf8A 126 2.89e+00 d.271.1.1 105472 17gsA 210 2.90e+00 1pgtA a.45.1.1,c.47.1.5 17524,32818 2ng1 293 3.28e+00 1ng1 a.24.13.1,c.37.1.10 16962,32273 1wusA 180 3.41e+00 1pgtA 210 3.89e+00 1pgtA a.45.1.1,c.47.1.5 17515,32809 1uc8A 280 4.17e+00 c.30.1.6,d.142.1.7 99165,99166 1wy0A 342 6.02e+00 2a5vA 213 6.66e+00 1ym3A 215 6.67e+00 1ecmA 109 7.02e+00 1ecmA a.130.1.1 19492 1r0dA 206 7.34e+00 a.216.1.1 104715 1dmtA 696 7.34e+00 1dmtA d.92.1.4 40296 189l 164 7.78e+00 1l92 d.2.1.3 36960 1cfe 135 7.84e+00 1cfe d.111.1.1 40913 2b49A 287 8.13e+00 2cbiA 594 8.42e+00 1glqA 209 8.58e+00 1pgtA a.45.1.1,c.47.1.5 17588,32882 1r1hA 696 8.69e+00 d.92.1.4 104756 2fnaA 357 9.33e+00 2gk3A 256 9.78e+00 1ls1A 295 1.02e+01 a.24.13.1,c.37.1.10 78170,78171 1fjeB 175 1.02e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1ekfA 365 1.04e+01 1ekfA e.17.1.1 59445 2a1hA 365 1.05e+01 1ffh 294 1.05e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 2f1kA 279 1.07e+01 1ktaA 365 1.09e+01 e.17.1.1 77533 1xnfA 275 1.09e+01 1kt8A 365 1.09e+01 e.17.1.1 77531 1jpnA 296 1.11e+01 a.24.13.1,c.37.1.10 67039,67040 1fj7A 101 1.12e+01 1fj7A d.58.7.1 39209 111l 164 1.15e+01 1l92 d.2.1.3 36661 1miwA 404 1.16e+01 a.173.1.1,d.218.1.4 79162,79163 2coiA 386 1.27e+01 1pysA 350 1.35e+01 1pysA d.104.1.1 40775 1ng1 294 1.38e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1y8qB 640 1.39e+01 2fp1A 166 1.40e+01 2f6lA 166 1.40e+01 1dk5A 322 1.48e+01 1dk5A a.65.1.1 18192 1nxuA 333 1.50e+01 c.122.1.1 86389 1rypF 233 1.54e+01 1rypF d.153.1.4 41937 1ppjB 439 1.55e+01 d.185.1.1,d.185.1.1 104254,104255 2bykB 128 1.57e+01 2f7tA 227 1.67e+01 1oj6A 151 1.70e+01 a.1.1.2 93088 1sgmA 191 1.71e+01 a.4.1.9,a.121.1.1 105537,105538 1g0uE 234 1.74e+01 d.153.1.4 41950 1q1fA 151 1.78e+01 a.1.1.2 104476 1txdA 385 1.82e+01 a.87.1.1,b.55.1.1 107422,107423 1aj6 219 1.85e+01 1aj6 d.122.1.2 41106 1aa2 108 1.99e+01 1bkrA a.40.1.1 17395 1es4A 262 1.99e+01 1skf e.3.1.1 42683 2g7sA 194 1.99e+01 1a59 378 1.99e+01 1aj8A a.103.1.1 18902 1bkrA 109 2.03e+01 1bkrA a.40.1.1 17394 1is8A 230 2.07e+01 d.96.1.1 66321 1ezfA 340 2.07e+01 1ezfA a.128.1.2 19440 1skf 262 2.08e+01 1skf e.3.1.1 42684 1es5A 262 2.10e+01 1skf e.3.1.1 42679 2gtsA 86 2.11e+01 2at9 247 2.14e+01 1c3wA f.13.1.1 43427 1esiA 262 2.14e+01 1skf e.3.1.1 42682 1vqwA 457 2.19e+01 1es2A 262 2.22e+01 1skf e.3.1.1 42680 1lx8A 55 2.25e+01 a.6.1.7 84734 1vgoA 253 2.27e+01 1ygtA 111 2.30e+01 1jqSB 32 2.31e+01 1jqsB 32 2.31e+01 i.1.1.1 63238 1rh6A 55 2.35e+01 a.6.1.7 104935 1f16A 192 2.40e+01 1f16A f.1.4.1 43400 1pm6A 72 2.42e+01 a.6.1.7 94894 1sly 618 2.43e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 2axtJ 40 2.45e+01 1kzuB 41 2.45e+01 1kzuB f.3.1.1 43728 1nkzB 41 2.45e+01 f.3.1.1 80612 1qsaA 618 2.46e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1o06A 20 2.47e+01 j.105.1.1 86524 1r8sE 203 2.48e+01 a.118.3.1 97248 1wy9A 147 2.49e+01 2cdnA 201 2.65e+01 192l 164 2.73e+01 1l92 d.2.1.3 36815 1zkrA 153 2.75e+01 1kpsB 171 2.78e+01 a.118.12.1 68787 2a07F 93 2.78e+01 1d6mA 653 2.85e+01 1d6mA e.10.1.1 43248 1ft9A 222 2.86e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 2ffjA 300 2.93e+01 1nhyA 219 2.96e+01 a.45.1.1,c.47.1.5 80520,80521 1ihgA 370 2.98e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2ccjA 205 2.98e+01 1b3bA 415 2.99e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1ukz 203 3.01e+01 1zin c.37.1.1 31840 1mpgA 282 3.03e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1z6gA 218 3.06e+01 1b7yA 350 3.13e+01 1pysA d.104.1.1 40776 2fgeA 995 3.13e+01 174lA 164 3.14e+01 1l92 d.2.1.3 36956 2grrB 170 3.23e+01 1rv3A 483 3.25e+01 c.67.1.4 105101 1q6aA 107 3.27e+01 a.186.1.1 95966 1c3wA 222 3.29e+01 1c3wA f.13.1.1 43405 1q1vA 70 3.29e+01 a.159.4.1 104479 1i7dA 659 3.32e+01 1d6mA e.10.1.1 61886 1k0dA 260 3.38e+01 a.45.1.1,c.47.1.5 67930,67931 1m0kA 262 3.40e+01 f.13.1.1 78344 1kgbA 231 3.40e+01 f.13.1.1 68581 1izmA 184 3.42e+01 a.199.1.1 90725 1wa8B 95 3.45e+01 1hqoA 258 3.51e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1r8mE 203 3.53e+01 a.118.3.1 97242 1y1pA 342 3.54e+01 1v2zA 111 3.57e+01 a.186.1.1 108300 1sz2A 332 3.60e+01 1vhtA 218 3.62e+01 c.37.1.1 100700 1np3A 338 3.62e+01 a.100.1.2,c.2.1.6 85946,85947 2a2fX 325 3.64e+01 1l0lG 81 3.66e+01 f.23.13.1 84493 1latA 82 3.67e+01 2nllB g.39.1.2 45122 1pbv 195 3.68e+01 1pbv a.118.3.1 19179 2bsxA 253 3.76e+01 1b8zA 90 3.77e+01 1huuA a.55.1.1 17902 1cg5B 141 3.77e+01 1cg5B a.1.1.2 15585 1g6wA 261 3.78e+01 1hqoA a.45.1.1,c.47.1.5 17751,33045 1yvrA 538 3.84e+01 2aqwA 332 3.87e+01 1ujmA 342 3.87e+01 1ys7A 233 3.91e+01 1zccA 248 3.93e+01 1q1oA 98 3.98e+01 d.15.2.2 95596 1g2cK 52 4.01e+01 1g2cK h.3.2.1 45772 1cnsA 243 4.02e+01 1cnsA d.2.1.1 36241 1aisB 200 4.04e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1dxjA 242 4.04e+01 1cnsA d.2.1.1 36244 1unlD 208 4.05e+01 1x3lA 440 4.07e+01 171l 164 4.11e+01 1l92 d.2.1.3 36962 1alvA 173 4.27e+01 1alvA a.39.1.8 17370 2baa 243 4.31e+01 1cnsA d.2.1.1 36243 1vhnA 318 4.33e+01 c.1.4.1 100693 1jeqA 609 4.46e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1g59A 468 4.47e+01 a.97.1.1,c.26.1.1 60257,60258 169lA 164 4.52e+01 1l92 d.2.1.3 36963 1wzzA 334 4.52e+01 1rcuA 195 4.54e+01 c.129.1.1 97295 2a5kA 307 4.56e+01 1io1A 398 4.58e+01 1io1A e.32.1.1 62611 1qusA 322 4.59e+01 1ltm d.2.1.6 36991 1ireB 228 4.60e+01 b.34.4.4 76770 1ugpB 226 4.60e+01 b.34.4.4 107832 2amdA 311 4.61e+01 1mq4A 272 4.62e+01 d.144.1.7 91391 2bnkA 67 4.62e+01 1j09A 468 4.65e+01 a.97.1.1,c.26.1.1 77025,77026 1bsg 266 4.68e+01 1btl e.3.1.1 42729 3vub 101 4.70e+01 3vub b.34.6.1 24613 1pq1A 196 4.79e+01 f.1.4.1 94986 1e9rA 437 4.95e+01 c.37.1.11 64827 1kv4A 42 4.99e+01 j.4.1.3 73051 1g2cQ 52 5.02e+01 1g2cQ h.3.2.1 45775 1ltm 320 5.14e+01 1ltm d.2.1.6 36992 1ku1A 230 5.16e+01 a.118.3.1 72996 1smbA 154 5.18e+01 d.111.1.1 105756 1jjrA 151 5.20e+01 a.140.2.1 66772 1szt 68 5.29e+01 1aikN h.3.2.1 45725 1zwwA 256 5.32e+01 2ci1A 275 5.34e+01 1ufiA 64 5.34e+01 a.30.4.1 99336 1w36C 1122 5.35e+01 152l 164 5.39e+01 1l92 d.2.1.3 36904 1f3mA 80 5.40e+01 1f3mA j.66.1.1 46358 2bw3A 534 5.44e+01 1jj2U 70 5.46e+01 1ffkS a.2.2.1 63106 1t2bA 397 5.50e+01 1s72V 71 5.52e+01 a.2.2.1 105341 1vqoV 71 5.52e+01 1l0lB 439 5.60e+01 d.185.1.1,d.185.1.1 84484,84485 1maz 221 5.62e+01 1maz f.1.4.1 43393 2aorA 223 5.80e+01 1be3B 439 5.82e+01 1be3B d.185.1.1,d.185.1.1 58952,58953 1ozjA 144 5.82e+01 d.164.1.1 93846 1b48A 221 5.85e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1odoA 408 5.91e+01 a.104.1.1 92783 1jgsA 138 5.92e+01 a.4.5.28 66683 1q1gA 276 5.92e+01 c.56.2.1 95574 2es4D 332 5.95e+01 1nu5A 370 6.00e+01 c.1.11.2,d.54.1.1 92183,92184 172l 164 6.01e+01 1l92 d.2.1.3 36905 2erbA 125 6.13e+01 1d3uB 201 6.14e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1l58 164 6.17e+01 1l92 d.2.1.3 36635 1x58A 62 6.17e+01 1b4pA 217 6.27e+01 a.45.1.1,c.47.1.5 83158,83159 1bhdA 118 6.30e+01 1bkrA a.40.1.1 17398 1hssA 124 6.31e+01 1bea a.52.1.2 17819 5ukdA 194 6.31e+01 1zin c.37.1.1 31851 1jwwA 80 6.35e+01 d.58.17.1 71919 1zckA 154 6.35e+01 1rxdA 159 6.36e+01 1bj4A 470 6.37e+01 1bj4A c.67.1.4 34479 2a2dA 478 6.37e+01 126l 164 6.47e+01 1l92 d.2.1.3 36699 1o82A 70 6.52e+01 a.64.2.1 92630 1b0nA 111 6.55e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 177l 164 6.55e+01 1l92 d.2.1.3 36958 1dw0A 112 6.60e+01 1dw0A a.3.1.1 15911 1mxmA 254 6.69e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 142l 164 6.69e+01 1l92 d.2.1.3 36874 1oz9A 150 6.70e+01 d.92.1.15 93808 1qf9A 194 6.75e+01 1zin c.37.1.1 31848 180lA 164 6.84e+01 1l92 d.2.1.3 36867 128l 164 6.96e+01 1l92 d.2.1.3 36634 1mhdA 132 6.97e+01 1mhdA d.164.1.1 42175 1k8qA 377 7.01e+01 c.69.1.6 72177 1h05A 146 7.02e+01 c.23.13.1 76433 1pbyA 489 7.07e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1jjuA 489 7.07e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1jf9A 408 7.07e+01 1c0nA c.67.1.3 62931 173l 164 7.08e+01 1l92 d.2.1.3 36728 2dhqA 146 7.12e+01 2dhqA c.23.13.1 31382 1gks 78 7.21e+01 1cc5 a.3.1.1 15909 1ap4 89 7.25e+01 1ncx a.39.1.5 17253 2gx9A 129 7.25e+01 2bcqA 335 7.28e+01 160l 164 7.36e+01 1l92 d.2.1.3 36748 123l 164 7.39e+01 1l92 d.2.1.3 36697 1q18A 332 7.41e+01 c.55.1.7,c.55.1.7 104470,104471 143l 164 7.43e+01 1l92 d.2.1.3 36857 1rztA 331 7.50e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1t3tA 1303 7.55e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1wteA 272 7.59e+01 107l 164 7.63e+01 1l92 d.2.1.3 36690 163l 164 7.65e+01 1l92 d.2.1.3 36658 1k8kG 151 7.67e+01 a.118.13.1 68313 138l 164 7.67e+01 1l92 d.2.1.3 36679 129l 164 7.70e+01 1l92 d.2.1.3 36660 1af3 196 7.71e+01 1maz f.1.4.1 43397 149l 164 7.71e+01 1l92 d.2.1.3 36959 118l 164 7.75e+01 1l92 d.2.1.3 36642 1a91 79 7.78e+01 1a91 f.17.1.1 43635 2cosA 54 7.78e+01 1ffkS 70 7.82e+01 1ffkS a.2.2.1 15692 1vhqA 232 7.82e+01 c.23.16.2 100696 2aq4A 434 7.87e+01 157l 164 7.88e+01 1l92 d.2.1.3 36717 147l 164 7.91e+01 1l92 d.2.1.3 36864 1qloA 34 7.96e+01 1qloA j.35.1.1 46281 167lA 164 7.96e+01 1l92 d.2.1.3 36937 1e68A 70 7.96e+01 1e68A a.64.2.1 18144 1gln 468 7.97e+01 1gln a.97.1.1,c.26.1.1 18752,31588 130l 164 8.03e+01 1l92 d.2.1.3 36638 159l 164 8.09e+01 1l92 d.2.1.3 36682 1l92 164 8.11e+01 1l92 d.2.1.3 36629 119l 164 8.11e+01 1l92 d.2.1.3 36622 1t7lA 766 8.11e+01 145l 164 8.15e+01 1l92 d.2.1.3 36860 166l 164 8.19e+01 1l92 d.2.1.3 36681 131l 164 8.22e+01 1l92 d.2.1.3 36685 1e3mA 800 8.24e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 2b7nA 273 8.24e+01 1lw9A 164 8.27e+01 d.2.1.3 84727 175lA 164 8.27e+01 1l92 d.2.1.3 36924 1aj5A 173 8.28e+01 1alvA a.39.1.8 17367 1dlwA 116 8.29e+01 1dlyA a.1.1.1 14982 2a2cA 478 8.30e+01 6gsvA 217 8.31e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1t9kA 347 8.33e+01 c.124.1.5 106721 162l 164 8.33e+01 1l92 d.2.1.3 36749 1po5A 476 8.36e+01 a.104.1.1 94963 1b6iA 164 8.38e+01 1l92 d.2.1.3 36945 1qzzA 374 8.42e+01 a.4.5.29,c.66.1.12 96719,96720 164l 164 8.48e+01 1l92 d.2.1.3 36714 1ntr 124 8.50e+01 1dbwA c.23.1.1 31092 1se7A 83 8.58e+01 1np8A 159 8.64e+01 a.39.1.8 92022 125l 164 8.66e+01 1l92 d.2.1.3 36672 156l 164 8.71e+01 1l92 d.2.1.3 36709 1sf9A 128 8.72e+01 b.34.15.1 98831 2aebA 322 8.80e+01 199l 164 8.82e+01 1l92 d.2.1.3 36855 2fiqA 420 8.84e+01 161l 164 8.86e+01 1l92 d.2.1.3 36636 1elrA 131 8.87e+01 1a17 a.118.8.1 19209 1ihoA 283 8.87e+01 1ihoA c.26.1.4 62390 1bh9B 89 8.89e+01 1bh9B a.22.1.3 16485 1ohmA 44 8.90e+01 j.106.1.1 93025 109l 164 8.91e+01 1l92 d.2.1.3 36781 122l 164 8.93e+01 1l92 d.2.1.3 36667 1wb9A 800 8.95e+01 1r71A 178 8.96e+01 a.4.14.1 104823 1oy1A 228 8.99e+01 c.23.16.2 87548