# 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 1y8qA 346 4.93e-02 2cybA 323 2.70e-01 1zu0A 529 3.68e-01 1wm3A 72 9.64e-01 1a99A 344 9.80e-01 1pot c.94.1.1 35812 1brwA 433 1.05e+00 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1xgsA 295 1.13e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 2d5cA 263 1.22e+00 1jg5A 83 1.41e+00 d.205.1.1 66666 1r3eA 309 1.43e+00 b.122.1.1,d.265.1.2 96907,96908 1e5dA 402 1.49e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1t0hB 224 1.57e+00 c.37.1.1 106208 2mhr 118 1.72e+00 2mhr a.24.4.1 16581 1vmiA 355 1.95e+00 1is8K 84 2.19e+00 d.205.1.1 66331 1gefA 123 2.24e+00 1gefA c.52.1.18 60465 1edoA 244 2.56e+00 1ybvA c.2.1.2 29896 2faoA 309 2.59e+00 2cy0A 263 2.60e+00 1yqfA 203 2.62e+00 1o0xA 262 2.65e+00 d.127.1.1 80755 1a7e 118 2.67e+00 2mhr a.24.4.1 16583 1nrfA 262 2.82e+00 e.3.1.1 92086 1nseA 444 2.91e+00 1nseA d.174.1.1 42534 1j3mA 129 2.95e+00 d.129.7.1 103836 1y9kA 157 2.97e+00 1w41A 101 3.00e+00 1d0cA 444 3.04e+00 d.174.1.1 64769 5nseA 444 3.06e+00 d.174.1.1 74644 1d1vA 444 3.09e+00 1nseA d.174.1.1 59101 1h7mA 102 3.11e+00 d.79.3.1 83485 1j34B 123 3.30e+00 d.169.1.1 84049 2gtqA 867 3.37e+00 1n3lA 372 3.38e+00 c.26.1.1 79966 2matA 264 3.45e+00 1c24A d.127.1.1 41146 1wxdA 263 3.46e+00 1xnzA 264 3.85e+00 2czrA 226 3.87e+00 1v8gA 329 3.88e+00 a.46.2.1,c.27.1.1 100505,100506 2fb0A 94 4.34e+00 1sgvA 316 4.42e+00 b.122.1.1,d.265.1.2 98858,98859 2fi0A 81 4.43e+00 1qo7A 394 4.54e+00 1qo7A c.69.1.11 34697 1jzuA 157 4.89e+00 b.60.1.1 84271 1j1uA 306 4.99e+00 c.26.1.1 83980 1mjhB 162 5.02e+00 1mjhA c.26.2.4 31640 1xocA 520 5.04e+00 1q5yA 85 5.28e+00 d.58.18.4 95950 3il8 72 5.31e+00 1tvxA d.9.1.1 37356 1n9lA 109 5.35e+00 d.110.3.6 85468 1ffkI 194 5.36e+00 1ffkI d.12.1.2 37494 1t3lA 337 5.51e+00 b.34.2.1,c.37.1.1 106358,106359 1c24A 263 5.52e+00 1c24A d.127.1.1 41148 1ixxB 123 5.69e+00 1ixxB d.169.1.1 42336 1o4vA 183 5.78e+00 c.23.8.1 86628 1yemA 179 5.87e+00 1r1dA 247 6.02e+00 c.69.1.29 96813 1gmlA 178 6.05e+00 c.8.5.2 70273 1jq4A 98 6.16e+00 d.15.4.2 67083 1obbA 480 6.42e+00 c.2.1.5,d.162.1.2 86760,86761 1va4A 279 6.46e+00 c.69.1.12 108458 2ggcA 263 6.55e+00 1u46A 291 6.55e+00 d.144.1.7 107656 1ed5A 444 6.65e+00 1nseA d.174.1.1 42530 1w6uA 302 6.84e+00 4matA 278 7.03e+00 1c24A d.127.1.1 41150 1tqhA 247 7.16e+00 c.69.1.29 107225 1vp8A 201 7.18e+00 2aqjA 538 7.37e+00 3grx 82 7.66e+00 1aba c.47.1.1 32769 1qwgA 251 7.85e+00 c.1.27.1 96473 1iukA 140 7.86e+00 c.2.1.8 83712 1ipiA 123 7.94e+00 c.52.1.18 66255 2drpA 66 8.07e+00 2drpA g.37.1.1,g.37.1.1 45026,45027 1fukA 165 8.16e+00 1fukA c.37.1.19 32409 1lx7A 253 8.25e+00 c.56.2.1 74329 1vd4A 62 8.36e+00 2cvlA 124 8.44e+00 1hh1A 143 8.51e+00 1gefA c.52.1.18 61036 2ew8A 249 8.64e+00 1pfkA 320 8.69e+00 3pfk c.89.1.1 35575 1t6aA 126 8.78e+00 d.129.8.1 106555 1a5r 103 8.84e+00 1a5r d.15.1.1 37597 1nzjA 298 8.90e+00 c.26.1.1 92377 1ldjA 760 8.91e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1xuuA 349 9.00e+00 1a94A 99 9.25e+00 1fmb b.50.1.1 26599 3lck 271 9.35e+00 1fmk d.144.1.7 41686 1mjhA 162 9.50e+00 1mjhA c.26.2.4 31639 1k2eA 156 9.54e+00 d.113.1.1 72010 1rxyA 253 1.01e+01 c.56.2.1 98065 2a9fA 398 1.01e+01 1w6tA 444 1.08e+01 1b24A 188 1.11e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1f2aA 215 1.12e+01 1cs8A d.3.1.1 37040 2fhzA 109 1.13e+01 1u7iA 136 1.13e+01 d.32.1.7 107724 1tl0D 103 1.15e+01 1icwA 72 1.15e+01 1tvxA d.9.1.1 37357 1tit 98 1.15e+01 1tit b.1.1.4 21716 1f5sA 211 1.16e+01 1f5sA c.108.1.4 59656 1whi 122 1.16e+01 1whi b.39.1.1 24810 1s68A 249 1.19e+01 d.142.2.4 98591 1j97A 211 1.20e+01 1f5sA c.108.1.4 62753 1wyuA 438 1.20e+01 1a9xA 1058 1.20e+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 18550,31479,31657,31658,41502,41503 1rqlA 267 1.21e+01 c.108.1.3 97750 1cqa 133 1.21e+01 3nul d.110.1.1 40890 1k26A 156 1.21e+01 d.113.1.1 72003 1ooeA 236 1.22e+01 c.2.1.2 87196 1l7mA 211 1.22e+01 c.108.1.4 73664 2dtr 226 1.24e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2fulA 178 1.25e+01 1tzbA 302 1.25e+01 c.80.1.1 107470 1c0wA 225 1.27e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1crkA 380 1.31e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1x9iA 302 1.33e+01 1f1xA 322 1.35e+01 d.32.1.3,d.32.1.3 83208,83209 1sauA 115 1.35e+01 1ab6A 125 1.35e+01 3chy c.23.1.1 31054 1uohA 226 1.36e+01 d.211.1.1 99690 1h75A 81 1.37e+01 1h75A c.47.1.1 60716 1qpcA 279 1.37e+01 1fgkA d.144.1.7 41685 1vjeA 166 1.38e+01 d.185.1.2 100807 1jv4A 162 1.39e+01 b.60.1.1 67343 1fe0A 68 1.42e+01 1cc8A d.58.17.1 39345 1g0oA 283 1.43e+01 1ybvA c.2.1.2 60181 2d4pA 141 1.43e+01 1d3zA 76 1.43e+01 1ubi d.15.1.1 37592 1nddD 76 1.44e+01 1ubi d.15.1.1 37602 1rfzA 168 1.45e+01 a.195.1.1 97411 1xmpA 170 1.46e+01 1vquA 374 1.47e+01 2b8tA 223 1.49e+01 1reqD 637 1.50e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1wu7A 434 1.55e+01 1xqaA 113 1.57e+01 1aim 215 1.57e+01 1cs8A d.3.1.1 37044 1ubq 76 1.57e+01 1ubi d.15.1.1 37585 2eryA 172 1.58e+01 1vk8A 106 1.59e+01 d.58.48.1 108636 1ubi 76 1.60e+01 1ubi d.15.1.1 37584 2c71A 216 1.60e+01 1gy8A 397 1.60e+01 c.2.1.2 83376 1wurA 220 1.61e+01 1wj9A 211 1.61e+01 1f1uA 323 1.62e+01 d.32.1.3,d.32.1.3 83200,83201 1f52A 468 1.64e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1ybvA 283 1.64e+01 1ybvA c.2.1.2 29948 1g6oA 330 1.65e+01 1g6oA c.37.1.11 32430 1ww8A 439 1.67e+01 1u8zA 168 1.67e+01 1dazC 99 1.67e+01 1hvc b.50.1.1 26501 1vqoU 66 1.67e+01 1me4A 215 1.70e+01 d.3.1.1 79023 1me3A 215 1.70e+01 d.3.1.1 79022 1wvfA 520 1.70e+01 1ht6A 405 1.71e+01 b.71.1.1,c.1.8.1 83629,83630 1jrkA 156 1.72e+01 d.113.1.1 71827 1zlqA 502 1.75e+01 1k1tA 99 1.77e+01 b.50.1.1 71995 1om4A 422 1.78e+01 d.174.1.1 87067 7reqB 637 1.78e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 2a0jA 149 1.78e+01 1aaqA 99 1.80e+01 1fmb b.50.1.1 26688 1k8wA 327 1.80e+01 b.122.1.1,d.265.1.2 83094,90388 1uiuA 502 1.80e+01 c.94.1.1 99434 2bkqA 212 1.80e+01 1j8rA 196 1.81e+01 1j8rA b.2.3.3 62745 1xmrA 243 1.83e+01 1i05A 180 1.85e+01 1mup b.60.1.1 27130 2fblA 153 1.88e+01 1jm1A 204 1.88e+01 b.33.1.1 71745 1jnrB 150 1.89e+01 d.58.1.5 66969 2a14A 263 1.90e+01 1jg1A 235 1.91e+01 c.66.1.7 66661 1mat 264 1.91e+01 1c24A d.127.1.1 41152 1k3fA 253 1.92e+01 c.56.2.1 68105 1ab5A 125 1.93e+01 3chy c.23.1.1 31056 1oahA 519 1.95e+01 a.138.1.3 86736 1an8 208 1.95e+01 1an8 b.40.2.2,d.15.6.1 25202,37791 1o4wA 147 1.97e+01 c.120.1.1 86629 1o22A 170 1.98e+01 d.238.1.1 86557 1nv8A 284 1.99e+01 c.66.1.30 86224 1reqB 637 1.99e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1gnkA 112 2.01e+01 2pii d.58.5.1 39073 2fvhA 120 2.02e+01 2gcfA 73 2.04e+01 1e0bA 68 2.04e+01 1e0bA b.34.13.2 37476 1v7rA 186 2.05e+01 c.51.4.1 100482 2bkrA 212 2.07e+01 1id3B 102 2.08e+01 a.22.1.1 66113 5hvpA 99 2.08e+01 1fmb b.50.1.1 26605 1m2oA 768 2.09e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1mi0A 65 2.10e+01 d.15.7.1 79135 1oz9A 150 2.12e+01 d.92.1.15 93808 1p6oA 161 2.13e+01 c.97.1.2 94185 1innA 166 2.16e+01 1j98A d.185.1.2 62608 1lufA 343 2.17e+01 d.144.1.7 78223 1difA 99 2.18e+01 1fmb b.50.1.1 26503 6pfkA 319 2.20e+01 3pfk c.89.1.1 35583 1bi0 226 2.21e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 1aw7A 194 2.22e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1kzkA 99 2.22e+01 b.50.1.1 73371 1fmb 104 2.23e+01 1fmb b.50.1.1 26777 2ethA 154 2.24e+01 1t6t1 118 2.24e+01 1hcxA 127 2.26e+01 b.109.1.1 65800 1yzhA 214 2.27e+01 1ta0A 197 2.27e+01 c.108.1.16 106729 2gsfA 373 2.28e+01 1mwyA 73 2.29e+01 d.58.17.1 79616 2bzoB 79 2.29e+01 1wosA 364 2.29e+01 b.44.2.1,d.250.1.1 109468,109469 1ny1A 240 2.32e+01 c.6.2.3 86395 1vchA 175 2.34e+01 1gvmA 136 2.36e+01 b.109.1.1 70612 1jbeA 128 2.36e+01 3chy c.23.1.1 62845 1b3rA 431 2.38e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1vhzA 198 2.38e+01 d.113.1.1 100718 1q9uA 130 2.40e+01 d.129.7.1 96314 1u11A 182 2.40e+01 c.23.8.1 107576 1uaqA 158 2.43e+01 c.97.1.2 88386 1mmvB 419 2.45e+01 d.174.1.1 91318 1j7nA 776 2.46e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1eh9A 558 2.46e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 2frnA 278 2.50e+01 1g65K 211 2.52e+01 d.153.1.4 41907 1yspA 181 2.54e+01 1mlwA 301 2.56e+01 d.178.1.1 79289 1nx8A 273 2.56e+01 b.82.2.8 86374 1rvv1 154 2.57e+01 1rvv1 1rvvA 154 2.57e+01 1rvv1 c.16.1.1 30927 1nh0A 99 2.57e+01 b.50.1.1 91869 1axaA 99 2.57e+01 1hvc b.50.1.1 26633 2fexA 188 2.59e+01 1heiA 451 2.64e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1ktbA 405 2.65e+01 b.71.1.1,c.1.8.1 72960,72961 2f20A 240 2.65e+01 1tfe 145 2.65e+01 1tfe d.43.1.1 38680 1omp 370 2.66e+01 4mbp c.94.1.1 35778 2culA 232 2.67e+01 2fwtA 125 2.67e+01 1v25A 541 2.68e+01 e.23.1.1 108275 1hywA 68 2.69e+01 1hywA d.186.1.1 61425 1yagA 375 2.71e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1hvc 203 2.73e+01 1hvc b.50.1.1 26614 1nbwA 607 2.76e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1ctqA 166 2.76e+01 1ctqA c.37.1.8 31965 2b0cA 206 2.77e+01 2a7oA 112 2.77e+01 1a7aA 432 2.78e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1k8hA 133 2.78e+01 b.111.1.1 72176 2cwoA 197 2.81e+01 2bgcA 238 2.81e+01 1ogwA 76 2.82e+01 d.15.1.1 87001 1c3oE 1073 2.83e+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 1nrwA 288 2.86e+01 c.108.1.10 86128 1htrB 329 2.89e+01 1smrA 2f1kA 279 2.89e+01 1dq3A 454 2.94e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1cz3A 168 2.94e+01 1d1gA c.71.1.1 34891 1uetA 437 2.95e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1np6A 174 2.98e+01 c.37.1.10 85954 1a81A 254 2.98e+01 1a81A d.93.1.1,d.93.1.1 40507,40508 1vljA 407 2.98e+01 e.22.1.2 108832 1ytvA 366 2.99e+01 2avnA 260 3.00e+01 1jykA 254 3.05e+01 c.68.1.13 67458 1y7tA 327 3.05e+01 1wehA 171 3.05e+01 1j6zA 376 3.05e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1konA 249 3.05e+01 e.39.1.1 72823 1qo2A 241 3.08e+01 1qo2A c.1.2.1 28533 1mpb 370 3.08e+01 4mbp c.94.1.1 35780 1srb 21 3.08e+01 j.28.1.1 46201 2b3yA 888 3.08e+01 1qysA 106 3.09e+01 k.41.1.1 96603 1atnA 373 3.09e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 1swvA 267 3.10e+01 3seb 238 3.11e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2ao0A 324 3.11e+01 1yzyA 413 3.11e+01 1keeE 1073 3.13e+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 1j7nB 776 3.15e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 2fn2 59 3.18e+01 1e8bA g.14.1.2 44668 1v6tA 255 3.18e+01 1z08A 170 3.19e+01 1ml4A 308 3.20e+01 c.78.1.1,c.78.1.1 79255,79256 1d1gA 168 3.20e+01 1d1gA c.71.1.1 34889 1z5yE 149 3.22e+01 1juvA 193 3.22e+01 c.71.1.1 90912 1crn 46 3.22e+01 1cbn g.13.1.1 44622 2f5gA 133 3.25e+01 1a9mA 99 3.25e+01 1hvc b.50.1.1 26642 1ovoA 56 3.25e+01 2ovo g.68.1.1 44697 1xt9A 212 3.26e+01 1ffkR 66 3.26e+01 1ffkR g.39.1.6 45152 1jdbB 1073 3.26e+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 1b1bA 140 3.28e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 1a7lA 389 3.28e+01 4mbp c.94.1.1 35787 1amf 233 3.30e+01 1wod c.94.1.1 35833 1wod 233 3.30e+01 1wod c.94.1.1 35832 8ohm 435 3.31e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1r89A 437 3.35e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2pfkA 320 3.35e+01 3pfk c.89.1.1 35577 1n13B 113 3.37e+01 3tss 194 3.38e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1t4hA 290 3.40e+01 d.144.1.7 106420 1yqdA 366 3.42e+01 1fx7A 230 3.42e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1sgpI 51 3.45e+01 2ovo g.68.1.1 44678 1r0rI 51 3.48e+01 g.68.1.1 96736 1e25A 282 3.50e+01 1e25A e.3.1.1 42731 2d8sA 80 3.52e+01 1fviA 297 3.54e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1bi6H 41 3.54e+01 1bi6H g.3.12.1 44340 1mh3A 421 3.56e+01 a.4.1.1,c.94.1.1 79112,79113 1bmdA 327 3.56e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1a6jA 163 3.57e+01 1a6jA d.112.1.1 40915 1je3A 97 3.57e+01 d.68.3.3 71637 2ae0X 345 3.57e+01 1mxiA 160 3.58e+01 c.116.1.1 79646 1jo0A 98 3.61e+01 d.68.4.1 77140 2bkrB 77 3.62e+01 1lgr 468 3.63e+01 1lgr d.15.9.1,d.128.1.1 37837,41167 1jj2T 66 3.63e+01 1ffkR g.39.1.6 63105 1s72U 66 3.63e+01 g.39.1.6 105340 1wuaA 375 3.64e+01 1v93A 296 3.66e+01 c.1.23.1 100532 1a0i 348 3.66e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1b02A 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