# 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 4.27e-01 1lktA b.90.1.1 28398 1m93C 41 1.28e+00 2f4qA 346 1.74e+00 1vjfA 180 1.98e+00 d.116.1.1 100809 1tp6A 128 2.05e+00 d.17.4.12 107184 1yx1A 264 2.42e+00 2c3vA 102 2.92e+00 1qavB 115 3.36e+00 1qauA b.36.1.1 24780 1cqyA 99 3.50e+00 1b9zA b.3.1.1 22527 2go8A 122 4.28e+00 1qauA 112 5.37e+00 1qauA b.36.1.1 24779 1v74A 107 5.78e+00 d.243.1.1 100442 1uh6A 100 5.86e+00 d.15.1.1 99394 1cdq 77 5.98e+00 1cds g.7.1.3 44459 2a2pA 129 6.13e+00 1dcjA 81 6.17e+00 1dcjA d.68.3.3 59115 2cvzA 289 6.49e+00 1tqzA 133 7.04e+00 1u0tA 307 7.14e+00 e.52.1.1 107567 1cds 77 7.23e+00 1cds g.7.1.3 44461 1h4rA 314 7.52e+00 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1byrA 155 7.57e+00 1byrA d.136.1.1 41450 1zkdA 387 7.62e+00 1m7xA 617 7.69e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 2fhxA 246 7.74e+00 1bywA 110 8.00e+00 1bywA d.110.3.6 40912 1mkeA 152 8.98e+00 b.55.1.4 79231 1wm3A 72 9.94e+00 1ijqA 316 1.06e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1ui0A 205 1.10e+01 c.18.1.2 99411 1vr9A 213 1.14e+01 1yp2A 451 1.16e+01 1qq2A 199 1.21e+01 1qq2A c.47.1.10 33064 1yqtA 538 1.24e+01 1vq2A 193 1.28e+01 1pczA 191 1.29e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1b8iB 63 1.29e+01 1akhA a.4.1.1 16011 1isaA 192 1.32e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1iscA 192 1.33e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1vkiA 181 1.34e+01 d.116.1.1 108664 1a0k 131 1.35e+01 3nul d.110.1.1 40892 1qhoA 686 1.36e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1obr 326 1.42e+01 1aye c.56.5.2 33828 3ezmA 101 1.48e+01 3ezmA b.89.1.1 28395 1eagA 342 1.51e+01 1eagA b.50.1.2 26826 1wgoA 123 1.58e+01 1eg9A 449 1.62e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 1.62e+01 b.33.1.2,d.129.3.3 81162,81163 1ndoA 449 1.65e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1bpv 112 1.69e+01 1bpv b.1.2.1 22071 2fh5A 185 1.72e+01 1e39A 571 1.73e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1b9zA 516 1.74e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1n9lA 109 1.78e+01 d.110.3.6 85468 1cor 82 1.78e+01 451c a.3.1.1 15903 1m64A 571 1.80e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1lgpA 116 1.81e+01 b.26.1.2 73890 1kssA 571 1.88e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1p2hA 571 1.88e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1qjdA 571 1.88e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1q9iA 571 1.91e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 1.93e+01 1lj1A 571 1.93e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1e19A 314 1.95e+01 1b7bA c.73.1.1 34967 1xqaA 113 1.96e+01 1qmvA 197 1.96e+01 1qq2A c.47.1.10 33066 1omiA 248 1.97e+01 b.82.3.3,a.4.5.4 87079,87080 3nul 130 2.04e+01 3nul d.110.1.1 40891 1emwA 88 2.04e+01 1emwA d.27.1.1 38448 1yaxA 153 2.05e+01 1xfsA 178 2.09e+01 d.129.3.5 109589 1tyyA 339 2.10e+01 5bcaA 516 2.16e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1itcA 516 2.18e+01 b.3.1.1,c.1.8.1 83705,83706 1vemA 516 2.19e+01 1bxwA 172 2.22e+01 1bxwA f.4.1.1 43743 2gcc 70 2.24e+01 2gcc d.10.1.2 37484 1lv9A 77 2.25e+01 d.9.1.1 78233 1jj2R 84 2.41e+01 1ffkP d.12.1.1 63103 1s72S 85 2.41e+01 d.12.1.1 105338 1x54A 434 2.42e+01 2d1uA 104 2.52e+01 1l9gA 192 2.58e+01 c.18.1.2 84568 1y9wA 140 2.65e+01 1bf4A 63 2.67e+01 1azpA b.34.13.1 37461 1ebdA 455 2.67e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 2ghrA 302 2.68e+01 1h7mA 102 2.76e+01 d.79.3.1 83485 1pufB 73 2.80e+01 a.4.1.1 95132 1qjpA 171 2.81e+01 1bxwA f.4.1.1 43742 1cv8 174 2.85e+01 1cv8 d.3.1.1 37089 1vetA 124 2.96e+01 d.110.7.1 108553 1kjvA 284 2.97e+01 b.1.1.2,d.19.1.1 77421,77422 1ln1A 214 3.00e+01 d.129.3.2 74038 1lwdA 413 3.05e+01 c.77.1.1 78265 1p6oA 161 3.08e+01 c.97.1.2 94185 1gpeA 587 3.14e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1uaqA 158 3.17e+01 c.97.1.2 88386 2bjbA 462 3.18e+01 2cr5A 109 3.21e+01 1ne9A 335 3.23e+01 d.108.1.4,d.108.1.4 91839,91840 1l4sA 112 3.25e+01 d.204.1.1 77693 1voqa 90 3.26e+01 1cs0C 1073 3.28e+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 1c3oG 1073 3.30e+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 1keeG 1073 3.30e+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 2dg5B 190 3.32e+01 1ry9A 145 3.32e+01 d.198.1.1 98094 1ffyA 917 3.33e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 3.33e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1mi0A 65 3.38e+01 d.15.7.1 79135 1txkA 498 3.38e+01 b.1.18.2,b.30.5.9 107425,107426 1jdbB 1073 3.40e+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 3.40e+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 1lq9A 112 3.41e+01 d.58.4.3 78129 2gk3A 256 3.49e+01 2dln 306 3.50e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1jofA 365 3.65e+01 b.69.10.1 71775 1j09A 468 3.67e+01 a.97.1.1,c.26.1.1 77025,77026 1c8cA 64 3.68e+01 1azpA b.34.13.1 59084 1nrlA 316 3.68e+01 a.123.1.1 92091 1wrvA 308 3.71e+01 1bxrA 1073 3.71e+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 1iow 306 3.78e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1onqA 283 3.80e+01 b.1.1.2,d.19.1.1 93365,93366 1d3uA 181 3.80e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1w9hA 427 3.82e+01 1oshA 232 3.90e+01 a.123.1.1 93496 1l0oA 150 3.93e+01 d.122.1.3 73403 1xewY 172 3.93e+01 1cch 82 3.98e+01 451c a.3.1.1 15902 2cu3A 64 3.99e+01 1te7A 103 4.04e+01 1fjgP 88 4.05e+01 1emwA d.27.1.1 38444 1h8cA 82 4.10e+01 1h8cA d.15.1.2 37608 1n3gA 113 4.12e+01 d.204.1.1 79962 1cuk 203 4.13e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1zip 217 4.17e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1b72B 87 4.18e+01 1akhA a.4.1.1 16001 1tlfA 301 4.20e+01 1tlfA c.93.1.1 35687 1ttwA 138 4.32e+01 d.198.1.1 107308 1vcdA 126 4.33e+01 1xc3A 302 4.37e+01 1th8A 145 4.38e+01 d.122.1.3 106908 1skoA 143 4.39e+01 d.110.7.1 105676 1h8eG 272 4.41e+01 1e79G c.49.2.1 60756 2gw6A 123 4.41e+01 1vjvA 415 4.44e+01 d.3.1.9 108632 1xrkA 124 4.54e+01 1keeE 1073 4.67e+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 4.72e+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 1svjA 156 4.74e+01 d.220.1.1 106049 1u14A 172 4.74e+01 c.51.4.3 107579 1kllA 130 4.78e+01 d.32.1.2 72720 1nzjA 298 4.79e+01 c.26.1.1 92377 1htjF 210 4.82e+01 1htjF a.91.1.1 61254 1kq1A 77 4.85e+01 b.38.1.2 72848 1gyxA 76 4.85e+01 d.80.1.1 76387 1sqeA 109 4.90e+01 d.58.4.5 105908 1tm0A 350 4.93e+01 d.21.1.3 107147 1wh5A 80 4.94e+01 1w41A 101 4.95e+01 1bhe 376 5.01e+01 1bhe b.80.1.3 28030 1xxqA 161 5.04e+01 1mtpB 43 5.06e+01 1xvqA 175 5.14e+01 1ka9H 200 5.14e+01 c.23.16.1 77308 1huxA 270 5.21e+01 1huxA c.55.1.5 61278 1efaA 333 5.23e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1d4oA 184 5.27e+01 1d4oA c.31.1.4 31748 1yarH 217 5.34e+01 2a8eA 220 5.35e+01 1qx4A 274 5.39e+01 b.43.4.2,c.25.1.1 104624,104625 1zin 217 5.40e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1tzaA 134 5.41e+01 b.1.23.1 107468 1ri9A 102 5.44e+01 b.34.2.1 97506 1f2tB 148 5.47e+01 1f2tB 1ct5A 256 5.52e+01 1ct5A c.1.6.2 28663 1jtkA 136 5.54e+01 c.97.1.1 71862 1ryaA 160 5.60e+01 d.113.1.5 105122 1ttzA 87 5.62e+01 c.47.1.1 107309 1uwzA 136 5.63e+01 c.97.1.1 108081 1jyeA 349 5.63e+01 c.93.1.1 67455 1nofA 383 5.67e+01 b.71.1.2,c.1.8.3 92020,92021 2gclA 261 5.72e+01 1yhfA 115 5.81e+01 1ifqA 138 5.82e+01 1ifqA d.110.4.1 62350 1m13A 316 5.83e+01 a.123.1.1 84746 1r1qA 100 5.89e+01 d.93.1.1 104763 1aisA 182 5.98e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1ay2 159 6.06e+01 2pil d.24.1.1 38377 1pnkB 557 6.09e+01 1ajqB 1dmhA 311 6.13e+01 1dmhA b.3.6.1 22633 1a5r 103 6.23e+01 1a5r d.15.1.1 37597 2pil 159 6.26e+01 2pil d.24.1.1 38376 1gm9B 557 6.28e+01 1gm7B 557 6.30e+01 1e3aB 560 6.32e+01 1ajqB 1ajqB 557 6.34e+01 1ajqB 1gk9B 557 6.34e+01 1gkfB 557 6.35e+01 1azqA 66 6.46e+01 1azpA b.34.13.1 37469 1a79A 171 6.48e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1whzA 70 6.49e+01 1iujA 106 6.51e+01 d.58.4.5 90701 1d4tA 104 6.51e+01 1d4tA d.93.1.1 40537 1u58A 253 6.51e+01 1e79G 272 6.53e+01 1e79G c.49.2.1 33158 1kyfA 247 6.65e+01 b.1.10.1,d.105.1.1 73220,73221 1pm1X 180 6.71e+01 b.60.1.1 104189 1w6sA 599 6.75e+01 2bzuA 181 6.77e+01 1mdbA 539 6.78e+01 e.23.1.1 79008 1uocA 289 6.81e+01 c.55.3.9 99686 1ru3A 732 6.84e+01 e.26.1.3 97835 1a15A 67 6.84e+01 1a15A d.9.1.1 37451 1z2mA 155 6.92e+01 1hn2A 159 6.95e+01 b.60.1.1 65890 1obpA 159 6.95e+01 1obpA b.60.1.1 27092 1tiiD 99 7.07e+01 1tiiD b.40.2.1 24965 1b54 257 7.14e+01 1ct5A c.1.6.2 28664 1jmxA 494 7.17e+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 1gt1A 159 7.21e+01 b.60.1.1 90515 1bu6O 501 7.26e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1qb5D 99 7.33e+01 b.40.2.1 88357 1pdnC 128 7.36e+01 6paxA a.4.1.5 16047 1pjxA 314 7.39e+01 b.68.6.1 104167 1lyxA 248 7.42e+01 c.1.1.1 78304 2gaiA 633 7.43e+01 1vqoS 85 7.47e+01 1hjp 203 7.48e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1zxmA 400 7.48e+01 2a25A 193 7.57e+01 2db9A 149 7.59e+01 2bgiA 272 7.70e+01 2bmoA 447 7.79e+01 1k2fA 190 7.80e+01 b.8.1.2 68054 1gmuA 143 7.82e+01 b.107.1.1,d.58.38.1 65335,65336 1m65A 245 7.83e+01 c.6.3.1 84847 1am2 199 7.83e+01 1am2 b.86.1.2 28381 1uasA 362 7.92e+01 b.71.1.1,c.1.8.1 88388,88389 1o5xA 248 7.93e+01 c.1.1.1 92528 2d2mD 145 8.01e+01 1ap8 213 8.13e+01 1ap8 d.86.1.1 40151 2crvA 120 8.15e+01 1gtkA 313 8.17e+01 c.94.1.1,d.50.2.1 76346,76347 1ndh 272 8.24e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 2c4xA 260 8.30e+01 1zyeA 220 8.33e+01 1j7gA 144 8.37e+01 c.110.1.1 84130 1hdj 77 8.40e+01 1bqz a.2.3.1 15696 1r4kA 169 8.40e+01 b.34.14.1 96997 1ku1A 230 8.46e+01 a.118.3.1 72996 1wzcA 249 8.49e+01 1jidA 128 8.67e+01 d.201.1.1 66735 1lrwA 600 8.73e+01 b.70.1.1 91111 16pk 415 8.77e+01 16pk c.86.1.1 35454 2fq9A 225 8.78e+01 1pvmA 184 8.79e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1nqcA 217 8.82e+01 d.3.1.1 86024 1y88A 199 8.90e+01 1sur 215 8.97e+01 1sur c.26.2.2 31620