# 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 2ah5A 210 1.64e-04 2go7A 207 1.13e-01 1dioA 554 4.79e-01 1dioA c.1.19.3 29656 1eexA 554 4.91e-01 1dioA c.1.19.3 29650 1e19A 314 7.93e-01 1b7bA c.73.1.1 34967 2aebA 322 9.67e-01 1zkrA 153 1.69e+00 2f2eA 146 1.73e+00 1is8A 230 1.82e+00 d.96.1.1 66321 1cfe 135 2.02e+00 1cfe d.111.1.1 40913 1wusA 180 2.77e+00 1a59 378 2.77e+00 1aj8A a.103.1.1 18902 1jnyA 435 3.27e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2b49A 287 3.47e+00 1x3lA 440 3.60e+00 2fnaA 357 3.73e+00 1sf8A 126 3.90e+00 d.271.1.1 105472 1t5oA 351 4.00e+00 c.124.1.5 106459 1wteA 272 4.06e+00 1sgmA 191 4.08e+00 a.4.1.9,a.121.1.1 105537,105538 1pu6A 218 4.19e+00 a.96.1.5 95123 2coiA 386 4.22e+00 2f1kA 279 4.42e+00 2a5kA 307 4.69e+00 1dt4A 73 4.95e+00 1dt4A d.51.1.1 38799 1smbA 154 4.98e+00 d.111.1.1 105756 1y1pA 342 5.29e+00 1ujmA 342 5.58e+00 1kzyC 259 5.60e+00 c.15.1.4,c.15.1.4 73383,73384 1ft9A 222 6.01e+00 1ft9A a.4.5.4,b.82.3.1 16107,28131 1i2aA 219 6.11e+00 e.24.1.1 90660 1puoA 170 6.43e+00 a.101.1.1,a.101.1.1 95134,95135 1ekfA 365 6.43e+00 1ekfA e.17.1.1 59445 1pysA 350 6.61e+00 1pysA d.104.1.1 40775 1vp8A 201 6.63e+00 2fp1A 166 6.76e+00 1kt8A 365 6.78e+00 e.17.1.1 77531 1ktaA 365 7.04e+00 e.17.1.1 77533 2f6lA 166 7.14e+00 1dk0A 188 7.24e+00 1b2vA d.35.1.1 38530 1rxdA 159 7.25e+00 1zckA 154 7.39e+00 1e68A 70 7.43e+00 1e68A a.64.2.1 18144 1d3vA 323 7.44e+00 1d3vA c.42.1.1 32559 1b8zA 90 7.50e+00 1huuA a.55.1.1 17902 1ezwA 349 7.70e+00 1ezwA c.1.16.3 29558 1q6aA 107 7.89e+00 a.186.1.1 95966 2bsxA 253 7.95e+00 1vhtA 218 8.01e+00 c.37.1.1 100700 1q2wA 308 8.05e+00 b.47.1.4 88355 2amdA 311 8.07e+00 1b7yA 350 8.18e+00 1pysA d.104.1.1 40776 1aa2 108 8.20e+00 1bkrA a.40.1.1 17395 1y8qB 640 8.31e+00 2a1hA 365 8.32e+00 18gsA 210 8.34e+00 1pgtA a.45.1.1,c.47.1.5 17528,32822 2a2fX 325 8.35e+00 1rlaA 323 8.50e+00 1d3vA c.42.1.1 32561 1miwA 404 8.70e+00 a.173.1.1,d.218.1.4 79162,79163 1nxuA 333 8.78e+00 c.122.1.1 86389 1bkrA 109 8.95e+00 1bkrA a.40.1.1 17394 1t2bA 397 8.98e+00 1t3tA 1303 9.76e+00 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 1aqwA 209 1.01e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1kekA 1231 1.02e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 68524,68525,68526,68527,68528 1wa8B 95 1.05e+01 1rh6A 55 1.07e+01 a.6.1.7 104935 1x24A 180 1.14e+01 1dtjA 76 1.15e+01 1dt4A d.51.1.1 38800 1wy9A 147 1.16e+01 1v2zA 111 1.19e+01 a.186.1.1 108300 1sqwA 188 1.21e+01 1ks9A 291 1.21e+01 a.100.1.7,c.2.1.6 68857,68858 1sly 618 1.26e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 1t5yA 190 1.26e+01 b.122.1.1,d.17.6.3 106495,106496 1lx8A 55 1.29e+01 a.6.1.7 84734 1q1gA 276 1.29e+01 c.56.2.1 95574 1uc8A 280 1.33e+01 c.30.1.6,d.142.1.7 99165,99166 1txdA 385 1.34e+01 a.87.1.1,b.55.1.1 107422,107423 1oaoA 674 1.35e+01 e.26.1.2 86744 2es4D 332 1.36e+01 17gsA 210 1.39e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 2fiyA 309 1.40e+01 1b3bA 415 1.40e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1ukz 203 1.42e+01 1zin c.37.1.1 31840 1fqvJ 149 1.50e+01 1fqvD a.157.1.1,d.42.1.1 19266,38670 1o06A 20 1.52e+01 j.105.1.1 86524 2gh1A 301 1.54e+01 1b0pA 1231 1.56e+01 c.36.1.8,c.36.1.12,c.48.1.3,c.64.1.1,d.58.1.5 31831,31832,33104,34157,39003 1pgtA 210 1.56e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1uedA 406 1.60e+01 a.104.1.1 99256 1lbkA 208 1.60e+01 a.45.1.1,c.47.1.5 73809,73810 2bykB 128 1.62e+01 1z9hA 290 1.64e+01 1q1fA 151 1.66e+01 a.1.1.2 104476 1rcuA 195 1.69e+01 c.129.1.1 97295 1ihgA 370 1.74e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1fqvD 149 1.80e+01 1fqvD a.157.1.1,d.42.1.1 19263,38667 1gvjA 146 1.93e+01 a.4.5.21 90525 1odoA 408 1.96e+01 a.104.1.1 92783 1nktA 922 1.98e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 85830,85831,85832,85833 1g8lA 411 1.98e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1cz4A 185 2.01e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1cjsA 219 2.01e+01 1cjsA e.24.1.1 43354 1b2vA 188 2.04e+01 1b2vA d.35.1.1 38532 1cnt3 187 2.09e+01 1cnt3 1syxB 86 2.10e+01 1g2cA 52 2.10e+01 1g2cA h.3.2.1 45767 1jeqA 609 2.13e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 2g38B 198 2.15e+01 1xviA 275 2.16e+01 1n3bA 216 2.17e+01 c.37.1.1 79959 1g2cK 52 2.20e+01 1g2cK h.3.2.1 45772 1g2cO 52 2.20e+01 1g2cO h.3.2.1 45774 1e4yA 214 2.25e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1kzuB 41 2.26e+01 1kzuB f.3.1.1 43728 1lkyA 77 2.27e+01 a.60.1.1 73985 1vqwA 457 2.28e+01 2cxxA 190 2.31e+01 1vhxA 150 2.34e+01 c.55.3.8 100712 1z5nA 242 2.34e+01 1zclA 180 2.35e+01 1ji7A 89 2.37e+01 a.60.1.1 71682 1b0nA 111 2.39e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1ybzA 91 2.43e+01 1vsgA 364 2.49e+01 1vsgA h.4.1.1 45782 1z5oA 242 2.50e+01 1nkzB 41 2.54e+01 f.3.1.1 80612 1kv4A 42 2.55e+01 j.4.1.3 73051 1c3wA 222 2.56e+01 1c3wA f.13.1.1 43405 2ccjA 205 2.59e+01 1m0kA 262 2.61e+01 f.13.1.1 78344 1g2cQ 52 2.63e+01 1g2cQ h.3.2.1 45775 1zmtA 254 2.66e+01 1h3lA 87 2.66e+01 a.177.1.1 76639 2ffjA 300 2.71e+01 1pwxA 254 2.77e+01 c.2.1.2 95262 1pm6A 72 2.79e+01 a.6.1.7 94894 1g2cI 52 2.85e+01 1g2cI h.3.2.1 45771 1zzkA 82 2.87e+01 1cg5B 141 2.95e+01 1cg5B a.1.1.2 15585 2c3mA 1231 2.97e+01 1b33A 160 2.98e+01 1qgwC a.1.1.3 15649 1o82A 70 2.99e+01 a.64.2.1 92630 1l7vA 326 3.01e+01 f.22.1.1 73672 2eu9A 355 3.02e+01 2grrB 170 3.05e+01 1t0qB 330 3.06e+01 a.25.1.2 106221 1jjvA 206 3.11e+01 c.37.1.1 71698 1j5kA 89 3.11e+01 d.51.1.1 71565 1x6vA 630 3.13e+01 1cnt2 187 3.19e+01 1cnt3 1u3dA 509 3.24e+01 a.99.1.1,c.28.1.1 107638,107639 1d3uB 201 3.25e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1ecmA 109 3.27e+01 1ecmA a.130.1.1 19492 1rypF 233 3.28e+01 1rypF d.153.1.4 41937 1hnr 47 3.29e+01 1hnr a.155.1.1 17896 1nu7D 282 3.37e+01 a.8.6.1,a.8.6.1 92191,92192 1ir6A 424 3.53e+01 c.107.1.2 71342 1kbjA 412 3.61e+01 c.1.4.1 72280 1sz2A 332 3.63e+01 1glqA 209 3.64e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 2g7sA 194 3.64e+01 1oj6A 151 3.65e+01 a.1.1.2 93088 1zccA 248 3.70e+01 2at9 247 3.71e+01 1c3wA f.13.1.1 43427 1qsaA 618 3.72e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1rkbA 173 3.74e+01 1ka8A 100 3.76e+01 a.4.5.20 72241 1jalA 363 3.80e+01 c.37.1.8,d.15.10.2 84138,84139 1wuiL 534 3.81e+01 2a1dD 329 3.83e+01 1h2aL 567 3.83e+01 1h2rL e.18.1.1 43299 1ubkL 534 3.85e+01 e.18.1.1 88422 1odkA 235 3.86e+01 c.56.2.1 86863 1f07A 321 3.94e+01 1ezwA c.1.16.3 59560 2cw6A 298 3.96e+01 3vub 101 3.97e+01 3vub b.34.6.1 24613 2bw3A 534 3.98e+01 1qusA 322 4.00e+01 1ltm d.2.1.6 36991 1oqcA 125 4.06e+01 a.24.15.1 87264 1h2rL 534 4.08e+01 1h2rL e.18.1.1 43298 1jysA 242 4.10e+01 c.56.2.1 77216 1ltm 320 4.10e+01 1ltm d.2.1.6 36992 1r0dA 206 4.12e+01 a.216.1.1 104715 1akeA 214 4.17e+01 1zin c.37.1.1,g.41.2.1 31905,45185 1wzzA 334 4.20e+01 1latA 82 4.23e+01 2nllB g.39.1.2 45122 2cdnA 201 4.24e+01 1kgbA 231 4.28e+01 f.13.1.1 68581 1uxtA 501 4.29e+01 c.82.1.1 108125 1ntr 124 4.29e+01 1dbwA c.23.1.1 31092 1z6gA 218 4.31e+01 1k4nA 192 4.34e+01 d.32.1.5 72059 1hlvA 131 4.39e+01 a.4.1.7,a.4.1.7 65854,65855 1bde 35 4.41e+01 1bde j.11.1.1 46142 2aqwA 332 4.43e+01 1gdvA 85 4.43e+01 1ctj a.3.1.1 60458 1dc7A 124 4.51e+01 1dbwA c.23.1.1 31093 1azwA 313 4.57e+01 1qtrA c.69.1.7 34658 1mejA 223 4.66e+01 c.65.1.1 79029 1gyfA 62 4.67e+01 1gyfA d.76.1.1 39749 1xocA 520 4.68e+01 1meoA 209 4.74e+01 c.65.1.1 79035 1e3mA 800 4.79e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1g0uE 234 4.81e+01 d.153.1.4 41950 1gmuA 143 4.83e+01 b.107.1.1,d.58.38.1 65335,65336 1rxwA 336 4.84e+01 a.60.7.1,c.120.1.2 98059,98060 1vfrA 218 4.85e+01 1vfrA d.90.1.1 40247 1u55A 188 4.88e+01 d.278.1.1 107677 1lkxA 697 4.89e+01 c.37.1.9 73981 1w41A 101 4.91e+01 1srrA 124 5.03e+01 1dz3A c.23.1.1 31110 1fj7A 101 5.08e+01 1fj7A d.58.7.1 39209 2cfuA 658 5.13e+01 1jwwA 80 5.20e+01 d.58.17.1 71919 1lmzA 187 5.33e+01 a.96.1.4 74037 1dbhA 354 5.33e+01 1awe a.87.1.1,b.55.1.1 18514,26967 2awdA 323 5.37e+01 2fbqA 235 5.55e+01 1nnsA 326 5.65e+01 c.88.1.1 85910 1aa7A 158 5.74e+01 1aa7A a.95.1.1 18741 1nwmX 142 5.76e+01 a.7.8.1 86301 1psdA 409 5.78e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1fcbA 511 5.79e+01 1gox c.1.4.1,d.120.1.1 28620,41087 1wosA 364 5.89e+01 b.44.2.1,d.250.1.1 109468,109469 1nu5A 370 5.89e+01 c.1.11.2,d.54.1.1 92183,92184 2gtsA 86 5.92e+01 1su8A 636 5.93e+01 e.26.1.2 98999 1qcwA 410 6.00e+01 1gox c.1.4.1 28622 1yzfA 195 6.10e+01 1fn9A 365 6.13e+01 1fn9A d.196.1.1 59894 1tksA 204 6.14e+01 d.115.1.2 107114 1spgB 147 6.19e+01 1cg5B a.1.1.2 15588 1vhqA 232 6.19e+01 c.23.16.2 100696 1vekA 84 6.23e+01 1i58A 189 6.24e+01 1b3qA d.122.1.3 61773 2bgiA 272 6.26e+01 1unlD 208 6.29e+01 2axtJ 40 6.30e+01 1ztdA 133 6.33e+01 1sc6A 404 6.36e+01 1gydB 315 6.50e+01 b.67.2.1 70751 2ccmA 191 6.51e+01 1q0vA 81 6.52e+01 j.105.1.1 95514 1xqoA 256 6.58e+01 2f02A 323 6.59e+01 1ybxA 143 6.62e+01 1pysB 785 6.68e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1ppjG 81 6.72e+01 f.23.13.1 104263 1jjyA 636 6.78e+01 1jjyA 2afcA 168 6.80e+01 1a48 306 6.89e+01 1a48 d.143.1.1 41590 1xkyA 301 6.93e+01 1q18A 332 6.93e+01 c.55.1.7,c.55.1.7 104470,104471 1cnt1 187 6.94e+01 1cnt3 1pbyA 489 6.94e+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 6.96e+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 2fdrA 229 6.97e+01 1mhdA 132 7.06e+01 1mhdA d.164.1.1 42175 2ch4A 320 7.06e+01 1cd9C 175 7.11e+01 1bgc a.26.1.1 16816 1r5qA 102 7.17e+01 a.186.1.1 97103 1w6tA 444 7.18e+01 1fnnA 389 7.29e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1a2vA 655 7.33e+01 1a2vA b.30.2.1,d.17.2.1,d.17.2.1 24416,38059,38060 1h2vC 771 7.34e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1oy1A 228 7.37e+01 c.23.16.2 87548 1i7wA 538 7.42e+01 3bct a.118.1.1 61909 1aisB 200 7.45e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1ywfA 296 7.45e+01 1tafA 68 7.47e+01 1tafA a.22.1.3 16481 1oeyA 83 7.51e+01 d.15.2.2 92800 1bh9B 89 7.52e+01 1bh9B a.22.1.3 16485 1xnfA 275 7.53e+01 1allB 161 7.61e+01 1qgwC a.1.1.3 15648 1ku1A 230 7.62e+01 a.118.3.1 72996 1hjzA 192 7.63e+01 c.50.1.2 83520 1ppjJ 62 7.64e+01 f.23.14.1 104266 1jf9A 408 7.67e+01 1c0nA c.67.1.3 62931 1z67A 135 7.68e+01 1y10A 407 7.68e+01 1m5yA 408 7.73e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1jfiA 98 7.74e+01 1jfiA a.22.1.3 62936 1n1jA 93 7.80e+01 a.22.1.3 79813 1jj2U 70 7.86e+01 1ffkS a.2.2.1 63106 1hqoA 258 7.88e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1s72V 71 7.90e+01 a.2.2.1 105341 1tm9A 137 7.93e+01 a.225.1.1 107150 1yyvA 131 7.99e+01 1qguB 519 8.00e+01 1qguB c.92.2.3 35626 1qhqA 140 8.02e+01 1qhqA b.6.1.1 63326 1wcwA 261 8.03e+01 1p3jA 217 8.03e+01 c.37.1.1,g.41.2.1 94022,94023 1qh8B 519 8.11e+01 1qguB c.92.2.3 35634 1bal 51 8.15e+01 1bbl a.9.1.1 16357 1v54A 514 8.20e+01 f.24.1.1 100321 2a8kA 108 8.22e+01 1vgoA 253 8.24e+01 1lfkA 398 8.29e+01 a.104.1.1 77926 1gln 468 8.29e+01 1gln a.97.1.1,c.26.1.1 18752,31588 2b99A 156 8.30e+01 1elrA 131 8.37e+01 1a17 a.118.8.1 19209 1ux8A 132 8.39e+01 1c0nA 406 8.39e+01 1c0nA c.67.1.3 34433 1scmA 60 8.40e+01 1wdcA 1m6sA 347 8.42e+01 c.67.1.1 78701 1jg8A 347 8.42e+01 1jg8A c.67.1.1 62946 1l0lG 81 8.43e+01 f.23.13.1 84493 1jh6A 189 8.43e+01 d.61.1.1 66707 1fa8A 135 8.44e+01 1qipA d.32.1.1 38486 1z83A 196 8.51e+01 1kp0A 402 8.53e+01 c.55.2.1,d.127.1.1 72834,72835 1vpc 45 8.56e+01 1vpc j.11.1.1 46138 1dgsA 667 8.70e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1zynA 202 8.81e+01 2occA 514 8.84e+01 2occA f.24.1.1 43518 2a07F 93 8.92e+01 1x42A 232 8.95e+01 1ju3A 583 8.96e+01 b.18.1.13,c.69.1.21 67300,67301