# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1xubA 298 8.51e-04 1u1wA 298 1.10e-03 1tm0A 350 1.84e-03 d.21.1.3 107147 1w61A 414 1.91e-03 2gkeA 274 5.44e-03 1gqzA 274 8.16e-03 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 1.67e-02 1bwzA d.21.1.1,d.21.1.1 38337,38338 1t6kA 278 2.18e-02 1ym5A 300 1.38e-01 1o0pA 104 6.20e-01 d.58.7.1 86535 1vdkA 466 6.32e-01 a.127.1.1 100561 1o17A 345 6.74e-01 a.46.2.1,c.27.1.1 80765,80766 1p3dA 475 6.78e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gqyA 475 6.92e-01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1d0iA 156 1.54e+00 2dhqA c.23.13.1 31383 1dklA 410 1.75e+00 1dklA c.60.1.2 33996 1j6uA 469 1.99e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1wc3A 219 2.00e+00 1dkmA 410 2.14e+00 1dklA c.60.1.2 34000 1hcz 252 2.86e+00 1hcz b.2.6.1,b.84.2.2 22464,28250 1ab8A 220 2.89e+00 1azsA d.58.29.1 39414 1azsB 212 2.97e+00 1azsA d.58.29.1 39423 1dkqA 410 3.00e+00 1dklA c.60.1.2 33998 1gtzA 156 3.22e+00 c.23.13.1 70539 2pcfB 250 3.25e+00 1hcz i.4.1.1 45911 1xtqA 177 3.86e+00 1sdjA 310 4.58e+00 d.21.1.2,d.21.1.2 98807,98808 1g7sA 594 4.92e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1uurA 473 5.21e+00 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ycoA 279 5.33e+00 1wekA 217 5.57e+00 1uag 437 6.35e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 3uagA 437 6.38e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 4uagA 437 6.81e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 2fnaA 357 6.93e+00 1z5hA 780 7.72e+00 1qx4A 274 7.72e+00 b.43.4.2,c.25.1.1 104624,104625 1eo9A 209 7.74e+00 3pchA b.3.6.1 22731 2azpA 318 7.80e+00 1i7pA 274 8.44e+00 b.43.4.2,c.25.1.1 66048,66049 1jihA 531 8.47e+00 d.240.1.1,e.8.1.7 90374,90375 1fl9A 161 8.60e+00 c.37.1.18 70137 1mxmA 254 8.76e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1ov3A 138 1.02e+01 b.34.2.1,b.34.2.1 87451,87452 1ug1A 92 1.03e+01 b.34.2.1 99360 2cy2A 174 1.04e+01 1on3A 523 1.05e+01 c.14.1.4,c.14.1.4 87107,87108 1vquA 374 1.21e+01 2b61A 377 1.21e+01 1mqvA 125 1.22e+01 a.24.3.2 79415 1abbA 828 1.23e+01 1a8i c.87.1.4 35536 5gcnA 166 1.25e+01 1yghA d.108.1.1 40807 1wtaA 275 1.26e+01 1bvqA 141 1.27e+01 1bvqA d.38.1.1 38542 1u9yA 284 1.29e+01 1vh5A 148 1.31e+01 d.38.1.5 100642 1xhkA 187 1.32e+01 1cjtA 217 1.37e+01 1azsA d.58.29.1 39419 1umkA 275 1.38e+01 2f23A 156 1.46e+01 2aioA 269 1.47e+01 1oe4A 247 1.49e+01 c.18.1.3 86895 2fvhA 120 1.52e+01 2b6eA 146 1.59e+01 2myr 501 1.60e+01 1fjgR 88 1.65e+01 1fjfR a.4.8.1 16252 1rzuA 485 1.65e+01 c.87.1.8 105140 1lo7A 141 1.67e+01 d.38.1.1 74144 2b3nA 159 1.82e+01 2g84A 197 1.83e+01 1pyoA 167 1.89e+01 c.17.1.1 95370 1h2rL 534 1.90e+01 1h2rL e.18.1.1 43298 1ubkL 534 1.93e+01 e.18.1.1 88422 1smlA 269 1.94e+01 1smlA d.157.1.1 42053 1o0iA 138 1.95e+01 d.38.1.5 86532 1clqA 903 1.97e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1h8lA 380 2.00e+01 b.3.2.1,c.56.5.1 65737,65738 1c8kA 842 2.02e+01 1a8i c.87.1.4 35491 2tdt 274 2.05e+01 3tdt b.81.1.2 28054 1a8i 842 2.09e+01 1a8i c.87.1.4 35490 2b5wA 357 2.11e+01 1h2aL 567 2.12e+01 1h2rL e.18.1.1 43299 1y9wA 140 2.14e+01 1wuiL 534 2.17e+01 2gjgA 248 2.19e+01 1xttA 216 2.20e+01 1h65A 270 2.21e+01 c.37.1.8 65640 3tdt 274 2.24e+01 3tdt b.81.1.2 28053 1yqfA 203 2.25e+01 1mjc 69 2.32e+01 1mjc b.40.4.5 25319 2aliA 158 2.39e+01 1fzkA 274 2.47e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 2govA 195 2.50e+01 1gzqA 300 2.52e+01 b.1.1.2,d.19.1.1 70818,70819 1sr8A 298 2.52e+01 e.54.1.1 105959 1h9dB 134 2.57e+01 2jhbA b.54.1.1 60822 1gmuA 143 2.57e+01 b.107.1.1,d.58.38.1 65335,65336 1t7vA 278 2.58e+01 1gv3A 248 2.63e+01 a.2.11.1,d.44.1.1 70585,70586 2af4C 333 2.63e+01 1ih7A 903 2.68e+01 1clqA c.55.3.5,e.8.1.1 62375,62376 1tafB 70 2.68e+01 1tafB a.22.1.3 16482 1z94A 147 2.70e+01 1u55A 188 2.79e+01 d.278.1.1 107677 1izmA 184 2.81e+01 a.199.1.1 90725 2bw8A 227 2.83e+01 1wpgA 994 2.83e+01 1c0aA 585 2.92e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1g5cA 170 2.95e+01 1g5cA c.53.2.1 60264 1tdtA 259 2.97e+01 3tdt b.81.1.2 28055 1dlhB 188 2.98e+01 1iakB b.1.1.2,d.19.1.1 21598,38172 1dmhA 311 2.98e+01 1dmhA b.3.6.1 22633 1g9oA 91 3.09e+01 1pdr b.36.1.1 60400 1lylA 504 3.14e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1kgqA 274 3.15e+01 b.81.1.2 72447 1h0bA 256 3.15e+01 b.29.1.11 83422 1h5uA 842 3.18e+01 1a8i c.87.1.4 60655 1y8qA 346 3.23e+01 1qstA 160 3.29e+01 1yghA d.108.1.1 40804 1mngA 203 3.37e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1onqA 283 3.50e+01 b.1.1.2,d.19.1.1 93365,93366 1lk2A 274 3.51e+01 b.1.1.2,d.19.1.1 91056,91057 1mroC 247 3.57e+01 1mroC d.58.31.1 39437 1s7jA 262 3.61e+01 d.21.1.2 98647 1culA 217 3.63e+01 1azsA d.58.29.1 39417 1z54A 132 3.63e+01 1e6qM 501 3.64e+01 1e70M c.1.8.4 28920 1y791 680 3.69e+01 1bx2B 191 3.75e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1ah0 316 3.83e+01 1frb c.1.7.1 28685 1eulA 994 3.84e+01 1eulA 1hbnC 248 3.84e+01 1mroC d.58.31.1 60902 1u7nA 336 3.86e+01 c.77.1.4 107726 1yozA 116 3.87e+01 1iuhA 198 3.95e+01 d.61.1.2 83711 1bupA 386 3.95e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1ba1 386 3.96e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1kay 381 3.97e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1hpm 386 3.98e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1a8l 226 4.07e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1f2rI 100 4.11e+01 1c9fA d.15.2.1 37641 1jj2P 95 4.13e+01 1ffkN b.34.5.1 63101 1s72Q 96 4.14e+01 b.34.5.1 105336 1gmwA 143 4.17e+01 b.107.1.1,d.58.38.1 65347,65348 1vqoQ 96 4.22e+01 1ycdA 243 4.33e+01 1eriA 276 4.40e+01 1ckqA c.52.1.1 33231 1cl8A 276 4.40e+01 1ckqA c.52.1.1 33230 1ixlA 131 4.48e+01 d.38.1.5 90717 1dat 174 4.58e+01 2fha a.25.1.1 16677 1ckqA 276 4.60e+01 1ckqA c.52.1.1 33229 1fjgK 129 4.61e+01 1fjfK c.55.4.1 33733 1ewqA 765 4.66e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1nnsA 326 4.68e+01 c.88.1.1 85910 1azsA 220 4.78e+01 1azsA d.58.29.1 39416 1ng2A 193 4.80e+01 b.34.2.1,b.34.2.1 85660,85661 1kr7A 110 4.89e+01 a.1.1.4 72890 1qpsA 261 4.89e+01 1ckqA c.52.1.1 33234 1o70A 324 5.08e+01 b.118.1.1,b.118.1.1 81115,81116 1k0eA 453 5.09e+01 d.161.1.1 67938 1g7pA 274 5.17e+01 b.1.1.2,d.19.1.1 70153,70154 1g7rA 594 5.19e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 2ghsA 326 5.21e+01 1x88A 359 5.24e+01 2hrvA 142 5.28e+01 2hrvA b.47.1.4 26429 1e4mM 501 5.38e+01 1e70M c.1.8.4 59226 1poxA 585 5.45e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1atr 386 5.45e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1ats 386 5.47e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1prxA 224 5.48e+01 1prxA c.47.1.10 33076 7catA 506 5.53e+01 1cf9A e.5.1.1 42781 1rxr 83 5.59e+01 2nllB g.39.1.2 45114 1od3A 168 5.65e+01 b.18.1.10 86825 1hg2A 289 5.66e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1g7tA 594 5.73e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1tx4B 178 5.80e+01 1ctqA c.37.1.8 32045 1w77A 228 5.82e+01 1kpuA 274 5.89e+01 b.1.1.2,d.19.1.1 84456,84457 1ofzA 312 6.00e+01 b.68.8.1 86978 1su4A 994 6.07e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1aqdB 198 6.07e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 2a8yA 270 6.09e+01 1ig8A 486 6.16e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1e1oA 504 6.20e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1k8kD 300 6.22e+01 d.198.2.1,d.198.2.1 68309,68310 1sg6A 393 6.27e+01 e.22.1.1 105522 1jx4A 352 6.27e+01 d.240.1.1,e.8.1.7 90378,90379 1e70M 501 6.27e+01 1e70M c.1.8.4 28926 1i92A 91 6.31e+01 1pdr b.36.1.1 61990 1rylA 167 6.32e+01 d.276.1.1 105124 1fzoA 274 6.33e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1wnlA 235 6.38e+01 1j0hA 588 6.38e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1ndh 272 6.42e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1u0kA 288 6.47e+01 d.21.1.2,d.21.1.2 107547,107548 1zq1C 633 6.51e+01 1lox 662 6.53e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1fsfA 266 6.56e+01 c.124.1.1 65047 2cfaA 217 6.62e+01 1nmeB 92 6.63e+01 1b65A 375 6.64e+01 1b65A d.154.1.1 42020 1b47A 304 6.82e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 2aneA 125 6.84e+01 1l5oA 356 6.89e+01 c.39.1.1 77711 1jyhA 157 6.93e+01 d.60.1.3 71956 1l0wA 580 7.05e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1q1rA 431 7.12e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1d0sA 356 7.14e+01 1d0vA c.39.1.1 32477 1j9lA 247 7.19e+01 c.106.1.1 62762 1g1kA 143 7.19e+01 1aohA b.2.2.2 22404 2h4uA 145 7.26e+01 1pwt 61 7.27e+01 1tud b.34.2.1 24490 1jh8A 356 7.29e+01 c.39.1.1 63052 1prxB 224 7.34e+01 1prxA c.47.1.10 33077 1vl2A 421 7.39e+01 c.26.2.1,d.210.1.1 108708,108709 1j9jA 247 7.41e+01 c.106.1.1 62758 1eg9A 449 7.50e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1nscA 390 7.56e+01 2qwc b.68.1.1 27591 1ilyA 90 7.56e+01 c.55.4.1 71245 2b0tA 738 7.58e+01 1ndoA 449 7.58e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1vhtA 218 7.59e+01 c.37.1.1 100700 2bywA 418 7.61e+01 1ek4A 418 7.65e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1k24A 253 7.69e+01 f.4.4.2 72002 1hsbA 270 7.70e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 1ah4 315 7.72e+01 1frb c.1.7.1 28684 1hzdA 272 7.81e+01 c.14.1.3 65969 1josA 128 7.92e+01 d.52.7.1 84191 1cur 155 7.97e+01 1rcy b.6.1.1 23021 1deaA 266 7.97e+01 1deaA c.124.1.1 31760 1wqwA 235 8.00e+01 2fsjA 346 8.02e+01 1o7nA 449 8.03e+01 b.33.1.2,d.129.3.3 81162,81163 1kqfA 1015 8.04e+01 b.52.2.2,c.81.1.1 72871,72872 1pjcA 361 8.04e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1q0pA 223 8.07e+01 c.62.1.1 95507 1j5eK 129 8.13e+01 c.55.4.1 71554 2tmp 127 8.14e+01 1br9 b.40.3.1 25236 1dp4A 435 8.17e+01 1dp4A c.93.1.1 35710 1gutA 68 8.21e+01 b.40.6.1 65576 1pfsA 78 8.25e+01 1pfsA b.40.4.7 25391 1fi4A 416 8.30e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 2cx7A 130 8.31e+01 1y0hA 105 8.32e+01 1jug 125 8.36e+01 3lzt d.2.1.2 36587 1itwA 741 8.41e+01 c.77.1.2 76793 1ri5A 298 8.42e+01 c.66.1.34 97502 1dd8A 406 8.43e+01 1dd8A c.95.1.1,c.95.1.1 35932,35933 1yt5A 258 8.48e+01 2a35A 215 8.60e+01 1a8z 153 8.61e+01 1rcy b.6.1.1 23020 2h0bA 184 8.71e+01 1kkcA 221 8.74e+01 a.2.11.1,d.44.1.1 68660,68661 2bduA 297 8.79e+01 1u04A 771 8.81e+01 b.34.14.1,c.55.3.10 107539,107540 2cxcA 144 8.85e+01 1k8kE 178 8.85e+01 a.148.1.1 68311 1rcy 151 8.87e+01 1rcy b.6.1.1 23018 1yphC 131 8.89e+01 1a3z 155 8.89e+01 1rcy b.6.1.1 23019 1g2bA 62 9.00e+01 1tud b.34.2.1 24488