# 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 1lktA 104 5.52e-01 1lktA b.90.1.1 28398 1m93C 41 2.33e+00 1vjfA 180 3.13e+00 d.116.1.1 100809 1tp6A 128 3.66e+00 d.17.4.12 107184 2f4qA 346 3.83e+00 1uh6A 100 4.17e+00 d.15.1.1 99394 1yx1A 264 4.21e+00 2c3vA 102 4.49e+00 1qavB 115 4.72e+00 1qauA b.36.1.1 24780 2a2pA 129 4.79e+00 1cqyA 99 5.36e+00 1b9zA b.3.1.1 22527 1u0tA 307 5.51e+00 e.52.1.1 107567 1cdq 77 5.91e+00 1cds g.7.1.3 44459 1tqzA 133 6.90e+00 1cds 77 6.97e+00 1cds g.7.1.3 44461 1qauA 112 7.29e+00 1qauA b.36.1.1 24779 2fhxA 246 7.99e+00 1h4rA 314 8.12e+00 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1v74A 107 8.21e+00 d.243.1.1 100442 2cvzA 289 8.35e+00 1zkdA 387 8.36e+00 1dcjA 81 8.71e+00 1dcjA d.68.3.3 59115 1ui0A 205 9.03e+00 c.18.1.2 99411 1bywA 110 1.03e+01 1bywA d.110.3.6 40912 1ijqA 316 1.06e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1wm3A 72 1.09e+01 1vr9A 213 1.12e+01 1byrA 155 1.14e+01 1byrA d.136.1.1 41450 1eagA 342 1.17e+01 1eagA b.50.1.2 26826 1eg9A 449 1.22e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 1.22e+01 b.33.1.2,d.129.3.3 81162,81163 1ndoA 449 1.23e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1a0k 131 1.27e+01 3nul d.110.1.1 40892 2go8A 122 1.30e+01 1n9lA 109 1.31e+01 d.110.3.6 85468 1e39A 571 1.40e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1m64A 571 1.46e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1yp2A 451 1.47e+01 1pczA 191 1.49e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1e19A 314 1.49e+01 1b7bA c.73.1.1 34967 1kssA 571 1.55e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1yqtA 538 1.55e+01 2fh5A 185 1.56e+01 1p2hA 571 1.56e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1qjdA 571 1.56e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1q9iA 571 1.58e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 1.60e+01 1isaA 192 1.60e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1iscA 192 1.60e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1lj1A 571 1.61e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1m7xA 617 1.61e+01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1mkeA 152 1.71e+01 b.55.1.4 79231 1vkiA 181 1.72e+01 d.116.1.1 108664 1lgpA 116 1.80e+01 b.26.1.2 73890 1bpv 112 1.81e+01 1bpv b.1.2.1 22071 3nul 130 1.83e+01 3nul d.110.1.1 40891 1qq2A 199 1.85e+01 1qq2A c.47.1.10 33064 1qhoA 686 1.89e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 3ezmA 101 1.93e+01 3ezmA b.89.1.1 28395 1obr 326 1.94e+01 1aye c.56.5.2 33828 1bf4A 63 1.97e+01 1azpA b.34.13.1 37461 1l9gA 192 2.10e+01 c.18.1.2 84568 2cr5A 109 2.12e+01 2gk3A 256 2.14e+01 1b9zA 516 2.15e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1mi0A 65 2.18e+01 d.15.7.1 79135 2gcc 70 2.23e+01 2gcc d.10.1.2 37484 1lv9A 77 2.23e+01 d.9.1.1 78233 1yaxA 153 2.24e+01 1wgoA 123 2.27e+01 1xqaA 113 2.31e+01 1emwA 88 2.32e+01 1emwA d.27.1.1 38448 1cv8 174 2.32e+01 1cv8 d.3.1.1 37089 1tyyA 339 2.33e+01 1gpeA 587 2.36e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 5bcaA 516 2.41e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1qmvA 197 2.43e+01 1qq2A c.47.1.10 33066 1ln1A 214 2.44e+01 d.129.3.2 74038 1ttwA 138 2.46e+01 d.198.1.1 107308 1vq2A 193 2.51e+01 1vemA 516 2.56e+01 1cor 82 2.57e+01 451c a.3.1.1 15903 1itcA 516 2.58e+01 b.3.1.1,c.1.8.1 83705,83706 2gw6A 123 2.60e+01 2dchX 216 2.61e+01 1b8iB 63 2.65e+01 1akhA a.4.1.1 16011 1voqa 90 2.72e+01 1c8cA 64 2.93e+01 1azpA b.34.13.1 59084 1cs0C 1073 3.01e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1jj2R 84 3.02e+01 1ffkP d.12.1.1 63103 1s72S 85 3.03e+01 d.12.1.1 105338 1keeG 1073 3.03e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1c3oG 1073 3.03e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 1bxwA 172 3.09e+01 1bxwA f.4.1.1 43743 1l4sA 112 3.10e+01 d.204.1.1 77693 2cu3A 64 3.10e+01 1jdbB 1073 3.12e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1c3oC 1073 3.17e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1xc3A 302 3.19e+01 1h8eG 272 3.28e+01 1e79G c.49.2.1 60756 2dg5B 190 3.36e+01 1kjvA 284 3.42e+01 b.1.1.2,d.19.1.1 77421,77422 1p6oA 161 3.45e+01 c.97.1.2 94185 1lwdA 413 3.45e+01 c.77.1.1 78265 1bxrA 1073 3.46e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18570,31499,31697,31698,41542,41543 1h7mA 102 3.47e+01 d.79.3.1 83485 1txkA 498 3.48e+01 b.1.18.2,b.30.5.9 107425,107426 2dln 306 3.49e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1y9wA 140 3.51e+01 1omiA 248 3.54e+01 b.82.3.3,a.4.5.4 87079,87080 1uaqA 158 3.58e+01 c.97.1.2 88386 1iow 306 3.64e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1lq9A 112 3.72e+01 d.58.4.3 78129 1xfsA 178 3.75e+01 d.129.3.5 109589 1tiiD 99 3.79e+01 1tiiD b.40.2.1 24965 1n3gA 113 3.80e+01 d.204.1.1 79962 1ru3A 732 3.82e+01 e.26.1.3 97835 1l0oA 150 3.88e+01 d.122.1.3 73403 1z2mA 155 3.91e+01 1qb5D 99 3.96e+01 b.40.2.1 88357 1x54A 434 4.02e+01 1qjpA 171 4.03e+01 1bxwA f.4.1.1 43742 1u14A 172 4.04e+01 c.51.4.3 107579 1keeE 1073 4.06e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 1c3oE 1073 4.07e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1fjgP 88 4.11e+01 1emwA d.27.1.1 38444 1wrvA 308 4.21e+01 1d3uA 181 4.25e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1vcdA 126 4.28e+01 1ct5A 256 4.31e+01 1ct5A c.1.6.2 28663 2bjbA 462 4.32e+01 1pm1X 180 4.33e+01 b.60.1.1 104189 1ay2 159 4.39e+01 2pil d.24.1.1 38377 1mtpB 43 4.44e+01 1yarH 217 4.45e+01 1te7A 103 4.47e+01 2pil 159 4.49e+01 2pil d.24.1.1 38376 1th8A 145 4.50e+01 d.122.1.3 106908 1xewY 172 4.59e+01 1nrlA 316 4.66e+01 a.123.1.1 92091 1ry9A 145 4.76e+01 d.198.1.1 98094 1ne9A 335 4.77e+01 d.108.1.4,d.108.1.4 91839,91840 1d4tA 104 4.78e+01 1d4tA d.93.1.1 40537 1nzjA 298 4.79e+01 c.26.1.1 92377 1w41A 101 4.80e+01 1ntr 124 4.83e+01 1dbwA c.23.1.1 31092 1gyxA 76 4.86e+01 d.80.1.1 76387 1tm0A 350 4.93e+01 d.21.1.3 107147 1w9hA 427 4.96e+01 1zip 217 5.03e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1cch 82 5.04e+01 451c a.3.1.1 15902 1ebdA 455 5.05e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1azqA 66 5.05e+01 1azpA b.34.13.1 37469 1jtkA 136 5.08e+01 c.97.1.1 71862 2bgiA 272 5.10e+01 1a5r 103 5.12e+01 1a5r d.15.1.1 37597 1uwzA 136 5.27e+01 c.97.1.1 108081 1ryaA 160 5.30e+01 d.113.1.5 105122 2a8eA 220 5.31e+01 1onqA 283 5.42e+01 b.1.1.2,d.19.1.1 93365,93366 1pufB 73 5.42e+01 a.4.1.1 95132 1b54 257 5.43e+01 1ct5A c.1.6.2 28664 2bmoA 447 5.49e+01 1kq1A 77 5.54e+01 b.38.1.2 72848 1xvqA 175 5.62e+01 1j7gA 144 5.87e+01 c.110.1.1 84130 1zin 217 5.96e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2hglA 136 5.99e+01 2fq9A 225 6.00e+01 1e79G 272 6.05e+01 1e79G c.49.2.1 33158 1nqcA 217 6.10e+01 d.3.1.1 86024 1vjvA 415 6.12e+01 d.3.1.9 108632 1vetA 124 6.14e+01 d.110.7.1 108553 1ffyA 917 6.23e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 6.23e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1mzbA 136 6.25e+01 a.4.5.42 91497 1aisA 182 6.27e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1jnuA 104 6.33e+01 d.110.3.6 71762 1xxqA 161 6.45e+01 2he7A 283 6.59e+01 1htjF 210 6.65e+01 1htjF a.91.1.1 61254 1iujA 106 6.67e+01 d.58.4.5 90701 2gclA 261 6.67e+01 1jofA 365 6.69e+01 b.69.10.1 71775 1huxA 270 6.69e+01 1huxA c.55.1.5 61278 1f2tB 148 6.78e+01 1f2tB 2gjdA 157 6.79e+01 1zyeA 220 6.79e+01 2gaiA 633 6.94e+01 1xrkA 124 6.94e+01 1sqeA 109 7.00e+01 d.58.4.5 105908 1dmhA 311 7.00e+01 1dmhA b.3.6.1 22633 1u58A 253 7.01e+01 1lyxA 248 7.03e+01 c.1.1.1 78304 1d4oA 184 7.17e+01 1d4oA c.31.1.4 31748 1ap8 213 7.31e+01 1ap8 d.86.1.1 40151 1nofA 383 7.34e+01 b.71.1.2,c.1.8.3 92020,92021 1tlfA 301 7.41e+01 1tlfA c.93.1.1 35687 1h8cA 82 7.45e+01 1h8cA d.15.1.2 37608 1kllA 130 7.47e+01 d.32.1.2 72720 1tzaA 134 7.53e+01 b.1.23.1 107468 1o5xA 248 7.60e+01 c.1.1.1 92528 1yhfA 115 7.66e+01 1ifqA 138 7.66e+01 1ifqA d.110.4.1 62350 1gmuA 143 7.81e+01 b.107.1.1,d.58.38.1 65335,65336 2bzuA 181 7.86e+01 2c4xA 260 7.99e+01 1dg9A 157 8.10e+01 1dg9A c.44.1.1 32637 1peeA 180 8.13e+01 b.60.1.1 104126 1pjxA 314 8.17e+01 b.68.6.1 104167 2ghrA 302 8.17e+01 2fkcA 247 8.21e+01 1kyfA 247 8.22e+01 b.1.10.1,d.105.1.1 73220,73221 1qx4A 274 8.23e+01 b.43.4.2,c.25.1.1 104624,104625 1r4kA 169 8.25e+01 b.34.14.1 96997 1svjA 156 8.26e+01 d.220.1.1 106049 1hn2A 159 8.26e+01 b.60.1.1 65890 1w6sA 599 8.31e+01 1gt1A 159 8.37e+01 b.60.1.1 90515 1mdbA 539 8.39e+01 e.23.1.1 79008 1p57A 114 8.42e+01 d.170.1.2 94125 1obpA 159 8.43e+01 1obpA b.60.1.1 27092 2fikA 287 8.43e+01 1am2 199 8.62e+01 1am2 b.86.1.2 28381 1jmxA 494 8.63e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1pdnC 128 8.70e+01 6paxA a.4.1.5 16047 1uhvA 500 8.72e+01 b.71.1.2,c.1.8.3 99402,99403 1f5sA 211 8.74e+01 1f5sA c.108.1.4 59656 1j97A 211 8.74e+01 1f5sA c.108.1.4 62753 1m13A 316 8.75e+01 a.123.1.1 84746 1l7mA 211 8.84e+01 c.108.1.4 73664 1phr 157 8.84e+01 1dg9A c.44.1.1 32635 16pk 415 8.85e+01 16pk c.86.1.1 35454