# 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 1eztA 166 3.50e-30 1agrE a.91.1.1 18541 1agrE 205 8.45e-30 1agrE a.91.1.1 18538 1fqiA 147 2.87e-28 1agrE a.91.1.1 18542 2a72A 146 3.17e-28 2bt2A 161 3.74e-28 1agrH 205 3.84e-28 1agrE a.91.1.1 18539 1dk8A 147 1.31e-22 1agrE a.91.1.1 18548 1omwA 689 6.33e-13 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1htjF 210 7.56e-12 1htjF a.91.1.1 61254 1iapA 211 3.04e-05 a.91.1.1 62119 1wixA 164 1.27e-01 1mnaA 298 2.10e-01 c.69.1.22 79322 1wvfA 520 3.96e-01 2b0jA 358 1.25e+00 1qlaA 656 1.33e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1txuA 273 1.42e+00 a.222.1.1 107439 1td6A 306 1.56e+00 1lj8A 493 1.70e+00 a.100.1.9,c.2.1.6 90392,90393 1eco 136 1.71e+00 1flp a.1.1.2 15208 1eca 136 1.74e+00 1flp a.1.1.2 15209 1ecd 136 1.74e+00 1flp a.1.1.2 15211 1abbA 828 1.76e+00 1a8i c.87.1.4 35536 1aw9 216 1.89e+00 1gnwA a.45.1.1,c.47.1.5 17736,33030 1wa5B 530 2.33e+00 1znbA 232 2.50e+00 1a7tA d.157.1.1 42039 1y3nA 490 2.60e+00 1c3cA 429 2.72e+00 1c3cA a.127.1.1 19425 2bs3A 656 3.11e+00 1il6 185 3.20e+00 1alu a.26.1.1 16827 1gkuB 1054 3.26e+00 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1a7tA 232 3.32e+00 1a7tA d.157.1.1 42041 1n8vA 112 3.77e+00 a.118.21.1 85457 1bk5A 422 3.96e+00 1bk5A a.118.1.1 19130 1mpxA 615 4.12e+00 b.18.1.13,c.69.1.21 85041,85042 1k3yA 221 4.23e+00 a.45.1.1,c.47.1.5 77245,77246 1k3lA 221 4.65e+00 a.45.1.1,c.47.1.5 77229,77230 1n5uA 585 4.91e+00 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 1c8kA 842 5.11e+00 1a8i c.87.1.4 35491 2an9A 207 5.18e+00 1alu 186 5.38e+00 1alu a.26.1.1 16826 1bj5 585 5.51e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19369,19370,19371 1bq3B 246 5.53e+00 1qhfA c.60.1.1 33979 1d3uB 201 5.56e+00 1aisB a.74.1.2,a.74.1.2 18386,18387 1p32C 209 5.63e+00 1p32A d.25.1.1 38381 1a8i 842 6.05e+00 1a8i c.87.1.4 35490 1gpb 842 6.10e+00 1a8i c.87.1.4 35478 1b48A 221 6.40e+00 1pgtA a.45.1.1,c.47.1.5 17703,32997 1g5hA 454 6.41e+00 1g5hA c.51.1.1,d.104.1.1 60270,60271 1p32A 209 6.45e+00 1p32A d.25.1.1 38379 1ngnA 155 6.53e+00 a.96.1.2 85697 1edg 380 6.55e+00 1edg c.1.8.3 28807 1ha2A 585 6.70e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 60866,60867,60868 1h5uA 842 6.72e+00 1a8i c.87.1.4 60655 1bk6A 422 7.27e+00 1bk5A a.118.1.1 19133 1fs7A 485 7.28e+00 1qdbA a.138.1.3 19691 1x6mA 196 7.33e+00 1aszB 490 7.41e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 2bxkA 585 7.48e+00 1aisB 200 7.79e+00 1aisB a.74.1.2,a.74.1.2 18384,18385 1ao6A 585 7.82e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19354,19355,19356 1e7aA 585 7.97e+00 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19360,19361,19362 1lk3A 160 8.08e+00 a.26.1.3 73950 1iw7C 1119 8.17e+00 e.29.1.1 71474 1gseA 221 8.48e+00 1pgtA a.45.1.1,c.47.1.5 17667,32961 1f3aA 222 8.58e+00 1pgtA a.45.1.1,c.47.1.5 17701,32995 1p2fA 220 8.63e+00 a.4.6.1,c.23.1.1 87720,87721 1nznA 126 8.82e+00 a.118.8.1 92382 1qahA 136 8.96e+00 d.79.1.1 96338 2a6hC 1119 9.17e+00 2aw5A 541 9.45e+00 1ee4A 423 9.59e+00 1ee4A a.118.1.1 19128 1ignA 246 9.81e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 1f3lA 321 9.87e+00 1g6q2 c.66.1.6 59630 1uor 585 1.01e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19396,19397,19398 1oniA 137 1.02e+01 d.79.1.1 87144 1wbpA 397 1.05e+01 2b3oA 532 1.20e+01 1f2dA 341 1.20e+01 1f2dA c.79.1.1 35298 2a0mA 316 1.23e+01 1x3kA 152 1.27e+01 1j0dA 341 1.32e+01 c.79.1.1 83902 1iygA 133 1.38e+01 a.118.8.1 76947 1eljA 381 1.38e+01 4mbp c.94.1.1 35791 1qlaC 256 1.41e+01 1qlaC f.21.2.1 43722 1j1nA 492 1.41e+01 c.94.1.1 83978 1ofuA 320 1.42e+01 c.32.1.1,d.79.2.1 86972,86973 1bucA 383 1.45e+01 3mdeA a.29.3.1,e.6.1.1 16590,42851 1m2aA 110 1.49e+01 c.47.1.11 78472 2pviA 157 1.50e+01 3pviA c.52.1.6 33302 1dmtA 696 1.52e+01 1dmtA d.92.1.4 40296 1isiA 265 1.53e+01 e.4.1.1 71394 1eh2 106 1.54e+01 1eh2 a.39.1.6 17339 1b25A 619 1.55e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1z2lA 423 1.55e+01 1ct9A 553 1.56e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1klnA 605 1.57e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1qguB 519 1.62e+01 1qguB c.92.2.3 35626 1n08A 163 1.65e+01 b.43.5.1 79730 1eu8A 409 1.72e+01 1eu8A c.94.1.1 59502 1k8kG 151 1.73e+01 a.118.13.1 68313 1hl2A 297 1.74e+01 c.1.10.1 83581 1r1hA 696 1.75e+01 d.92.1.4 104756 1qhfA 240 1.76e+01 1qhfA c.60.1.1 33960 1ks8A 433 1.77e+01 a.102.1.2 77519 1lj2A 110 1.79e+01 h.1.13.2 73926 1av1A 201 1.83e+01 1av1A h.5.1.1 45796 1ieaB 228 1.84e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1cd1A 315 1.84e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1imbA 277 1.87e+01 1imbA e.7.1.1 42957 3pviA 157 1.87e+01 3pviA c.52.1.6 33300 2cunA 410 1.92e+01 1s96A 219 1.94e+01 c.37.1.1 98740 1mq4A 272 1.97e+01 d.144.1.7 91391 1u2xA 474 2.01e+01 c.72.1.3 107622 1m2bA 110 2.01e+01 c.47.1.11 78474 1eyuA 157 2.03e+01 3pviA c.52.1.6 33304 2bs3C 256 2.05e+01 1kwhA 492 2.07e+01 c.94.1.1 68876 1e4eA 343 2.09e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1ez3A 127 2.15e+01 1dn1B a.47.2.1 17768 1s2xA 206 2.21e+01 a.47.3.1 105229 1z1lA 345 2.24e+01 1uetA 437 2.27e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1kx9A 112 2.28e+01 a.118.21.1 77602 1ush 550 2.29e+01 1ush d.114.1.1,d.159.1.2 40923,42079 1qh8B 519 2.30e+01 1qguB c.92.2.3 35634 1pvuA 154 2.33e+01 3pviA c.52.1.6 33306 1h6dA 433 2.36e+01 c.2.1.3,d.81.1.5 65656,65657 1io2A 213 2.38e+01 1ekeA c.55.3.1 62612 1zip 217 2.43e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1qb7A 236 2.49e+01 1qb7A c.61.1.1 34087 1y6nL 145 2.52e+01 1gq2A 555 2.53e+01 c.2.1.7,c.58.1.3 70308,70309 1fdyA 297 2.56e+01 1nal3 c.1.10.1 29071 1hr6A 475 2.60e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1rlr 761 2.64e+01 1rlr a.98.1.1,c.7.1.2 18753,30679 2f2gA 221 2.67e+01 1omoA 322 2.73e+01 c.2.1.13 104017 1vf1A 229 2.75e+01 1hp1A 516 2.81e+01 d.114.1.1,d.159.1.2 70976,70977 1pytA 94 2.82e+01 1pytA d.58.3.1 39064 1vgvA 384 2.83e+01 c.87.1.3 100608 1u58A 253 2.84e+01 1xx4A 261 2.85e+01 1qazA 351 2.92e+01 1qazA a.102.3.1 18848 1qzmA 94 2.95e+01 c.37.1.20 96651 1cem 363 2.97e+01 1cem a.102.1.2 18826 1c7qA 445 3.02e+01 2pgi c.80.1.2 35307 1eueA 86 3.06e+01 1cyo d.120.1.1 59504 1ln1A 214 3.07e+01 d.129.3.2 74038 1ej0A 180 3.13e+01 1ej0A c.66.1.2 34179 2hhmA 276 3.19e+01 1imbA e.7.1.1 42955 2akrA 285 3.28e+01 1f6dA 376 3.34e+01 1f6dA c.87.1.3 35467 2pgi 445 3.37e+01 2pgi c.80.1.2 35308 1b0zA 445 3.39e+01 2pgi c.80.1.2 35309 2f8mA 244 3.42e+01 1l8nA 679 3.51e+01 c.1.8.10,d.92.2.2 84564,84565 1hzdA 272 3.55e+01 c.14.1.3 65969 1imdA 277 3.62e+01 1imbA e.7.1.1 42968 1q4mA 221 3.63e+01 a.132.1.3 95805 1v9mA 323 3.64e+01 f.40.1.1 100543 1ibrB 462 3.64e+01 1qgrA a.118.1.1 19120 1pqzA 238 3.67e+01 b.1.1.2,d.19.1.1 104297,104298 1au1A 166 3.73e+01 1ifa a.26.1.3 16889 1u7nA 336 3.77e+01 c.77.1.4 107726 2fbmA 291 3.79e+01 1ws9A 387 3.86e+01 1dcfA 136 3.86e+01 1dcfA c.23.1.2 31124 2fw2A 260 3.87e+01 2g5dA 422 3.88e+01 1zpdA 568 3.96e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1z5lA 285 3.97e+01 1zq4A 693 3.99e+01 1h1yA 228 3.99e+01 c.1.2.2 76506 1hcuA 503 4.00e+01 a.102.2.1 65796 1xm8A 254 4.03e+01 1qq2A 199 4.04e+01 1qq2A c.47.1.10 33064 1u13A 455 4.07e+01 a.104.1.1 107578 1u6rA 380 4.08e+01 1kbjA 412 4.13e+01 c.1.4.1 72280 1ug3A 339 4.17e+01 1o5oA 221 4.18e+01 c.61.1.1 92509 1z5hA 780 4.18e+01 1sqeA 109 4.32e+01 d.58.4.5 105908 1dat 174 4.35e+01 2fha a.25.1.1 16677 1nu7D 282 4.35e+01 a.8.6.1,a.8.6.1 92191,92192 2ilk 160 4.38e+01 2ilk a.26.1.3 16885 1d9cA 121 4.43e+01 1d9cA a.26.1.3 16901 2azjA 289 4.47e+01 1v9sA 208 4.47e+01 1ne9A 335 4.56e+01 d.108.1.4,d.108.1.4 91839,91840 1gtxA 472 4.64e+01 1gtxA 1ir3A 306 4.64e+01 1fmk d.144.1.7 41702 2cx9A 387 4.66e+01 1zoyA 622 4.67e+01 1fcdA 401 4.68e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1yoyA 175 4.70e+01 1ej5A 107 4.71e+01 1ej5A a.68.1.1 18268 1jf4A 147 4.74e+01 a.1.1.2 71643 2btzA 394 4.79e+01 1kwfA 363 4.81e+01 a.102.1.2 73078 1x8vA 455 4.82e+01 1ilk 151 4.86e+01 2ilk a.26.1.3 16886 2bf9A 36 4.87e+01 1yyqA 374 4.88e+01 1jkvA 266 4.88e+01 a.25.1.3 71719 1wstA 417 4.95e+01 1o9iA 266 4.99e+01 a.25.1.3 92671 1aw5 326 4.99e+01 1b4kA c.1.10.3 29181 2d68A 82 5.00e+01 1aew 174 5.03e+01 2fha a.25.1.1 16676 1qo7A 394 5.04e+01 1qo7A c.69.1.11 34697 1e6wA 260 5.04e+01 1e6wA c.2.1.2 59326 1ynbA 173 5.07e+01 1k0nA 241 5.10e+01 a.45.1.1,c.47.1.5 67953,67954 1lmb3 92 5.10e+01 1lmb3 1zin 217 5.13e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2f5tX 233 5.19e+01 1jfkA 134 5.21e+01 a.39.1.5 66639 2a1dD 329 5.24e+01 1xc3A 302 5.28e+01 1qmvA 197 5.31e+01 1qq2A c.47.1.10 33066 1jv1A 505 5.33e+01 c.68.1.5 71892 2fytA 340 5.33e+01 1bqbA 301 5.34e+01 1hyt d.92.1.2 58962 1aky 221 5.39e+01 1zin c.37.1.1,g.41.2.1 31896,45197 2bjiA 277 5.43e+01 1i50A 1733 5.48e+01 e.29.1.2 61754 1nal1 297 5.52e+01 1nal3 2b7aA 293 5.53e+01 2bfxA 284 5.56e+01 1mo2A 294 5.57e+01 c.69.1.22 79331 1aqwA 209 5.57e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 2d29A 387 5.62e+01 1wtyA 119 5.63e+01 1lliA 92 5.64e+01 1lmb3 a.35.1.2 17025 1xwmA 217 5.66e+01 1vllA 334 5.72e+01 c.2.1.13 108834 2lhb 149 5.72e+01 2fal a.1.1.2 15597 1lwjA 441 5.79e+01 b.71.1.1,c.1.8.1 74303,74304 1gqaA 130 5.95e+01 a.24.3.2 76275 1ann 318 5.97e+01 1avc a.65.1.1 18151 1ykuA 136 6.02e+01 2ebn 289 6.03e+01 2ebn c.1.8.5 28990 1dovA 181 6.04e+01 1dovA a.24.9.1 16627 1gwiA 411 6.10e+01 a.104.1.1 76364 1aq0A 306 6.10e+01 1aq0A c.1.8.3 28842 1j2rA 199 6.16e+01 c.33.1.3 90788 2dfkA 402 6.19e+01 1fqyA 269 6.23e+01 1fqyA f.19.1.1 43649 1fezA 256 6.25e+01 1fezA c.108.1.3 43343 1lbkA 208 6.27e+01 a.45.1.1,c.47.1.5 73809,73810 1wovA 250 6.29e+01 1sumB 235 6.33e+01 a.7.12.1 106025 1y6iA 233 6.39e+01 1k9dA 679 6.40e+01 c.1.8.10,d.92.2.2 77292,77293 1jbwA 428 6.40e+01 c.59.1.2,c.72.2.2 62860,62861 1d8yA 605 6.42e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 2beiA 170 6.44e+01 1ltdA 506 6.46e+01 1gox c.1.4.1,d.120.1.1 28618,41086 2agcA 162 6.48e+01 2kfnA 605 6.54e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1jk0B 345 6.63e+01 a.25.1.2 63143 1uumA 372 6.69e+01 c.1.4.1 100010 1ps1A 337 6.74e+01 1ps1A a.128.1.4 19450 2dpg 485 6.75e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1asyA 490 6.80e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1gtmA 419 6.89e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1pv9A 348 6.89e+01 c.55.2.1,d.127.1.1 95157,95158 2c12A 439 6.93e+01 1dpgA 485 6.97e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 2b33A 140 7.00e+01 1awpA 92 7.06e+01 1cyo d.120.1.1 41071 1xg7A 250 7.07e+01 1n9dA 199 7.14e+01 a.26.1.1 85464 1x9bA 53 7.14e+01 1irk 306 7.15e+01 1fmk d.144.1.7 41703 1jm6A 407 7.16e+01 a.29.5.1,d.122.1.4 66876,66877 1o1zA 234 7.25e+01 c.1.18.3 86555 1dn1B 267 7.28e+01 1dn1B a.47.2.1 17771 1r2fA 319 7.29e+01 1r2fA a.25.1.2 16800 1bh6A 274 7.32e+01 1gci c.41.1.1 32487 1ohvA 472 7.35e+01 c.67.1.4 93031 1br0A 120 7.35e+01 a.47.2.1 17772 1alvA 173 7.42e+01 1alvA a.39.1.8 17370 1gycA 499 7.43e+01 b.6.1.3,b.6.1.3,b.6.1.3 70748,70749,70750 1ar1A 558 7.51e+01 2occA f.24.1.1 43618 1qcwA 410 7.58e+01 1gox c.1.4.1 28622 1vf6A 83 7.62e+01 a.194.1.1 100600 1kfd 605 7.62e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1xzpB 150 7.77e+01 1fcbA 511 7.77e+01 1gox c.1.4.1,d.120.1.1 28620,41087 1n97A 389 7.80e+01 a.104.1.1 80335 1kobA 387 7.81e+01 1tkiA d.144.1.7 41640 1vrpA 381 7.81e+01 1twfA 1733 7.81e+01 1r5zA 323 7.82e+01 f.40.1.1 97135 1un8A 552 7.94e+01 c.119.1.2,a.208.1.1 103806,99661 1zb1A 392 7.95e+01 1x0rA 249 7.99e+01 1goiA 499 7.99e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1tzvA 142 8.00e+01 a.79.1.1 107526 1aq5A 47 8.05e+01 1aq5A h.1.6.1 45577 1ofgA 381 8.06e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1t3qC 288 8.09e+01 d.87.2.1,d.145.1.3 106371,106372 1pmzA 86 8.14e+01 a.39.1.10 104195 1preA 470 8.18e+01 1preA d.169.1.2,f.8.1.1 42437,43824 17gsA 210 8.20e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 1csc 433 8.22e+01 1csh a.103.1.1 18886 1ujkA 147 8.32e+01 a.118.9.2 99457 1xjjA 644 8.40e+01 1hsm 79 8.44e+01 1cktA a.21.1.1 16421 1c7nA 399 8.46e+01 1d2fA c.67.1.3 34413 1r88A 280 8.49e+01 c.69.1.3 97219 1e6pA 499 8.50e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1nal3 297 8.65e+01 1nal3 1t46A 313 8.67e+01 d.144.1.7 106397 1jqfA 334 8.68e+01 c.94.1.2 67086 1bc3 319 8.73e+01 1avc a.65.1.1 18175 1iktA 120 8.75e+01 d.106.1.1 66188 1p99A 295 8.80e+01 c.94.1.1 94384 1m98A 317 8.81e+01 a.175.1.1,d.17.4.6 78866,78867 1ayl 541 8.81e+01 1ayl c.91.1.1,c.109.1.1 64718,64719 1obdA 306 8.82e+01 d.143.1.1 86767 1w98B 283 8.82e+01 1a48 306 8.87e+01 1a48 d.143.1.1 41590 1y0bA 197 8.90e+01 1k0mA 241 8.96e+01 a.45.1.1,c.47.1.5 67949,67950 1d3kA 329 8.97e+01 1nnt c.94.1.2 35889