# 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 6.63e-04 1u1wA 298 8.49e-04 1tm0A 350 1.32e-03 d.21.1.3 107147 1w61A 414 2.22e-03 1t6kA 278 1.59e-02 2gkeA 274 2.22e-02 1gqzA 274 3.69e-02 d.21.1.1,d.21.1.1 83311,83312 1bwzA 274 9.04e-02 1bwzA d.21.1.1,d.21.1.1 38337,38338 1ym5A 300 1.24e-01 1p3dA 475 2.94e-01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1gqyA 475 3.02e-01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1o0pA 104 4.07e-01 d.58.7.1 86535 1vdkA 466 5.90e-01 a.127.1.1 100561 1d0iA 156 9.71e-01 2dhqA c.23.13.1 31383 1wc3A 219 1.54e+00 1j6uA 469 1.58e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1dklA 410 1.74e+00 1dklA c.60.1.2 33996 1gtzA 156 2.00e+00 c.23.13.1 70539 1dkmA 410 2.13e+00 1dklA c.60.1.2 34000 1qx4A 274 2.32e+00 b.43.4.2,c.25.1.1 104624,104625 1dkqA 410 2.89e+00 1dklA c.60.1.2 33998 1ab8A 220 3.11e+00 1azsA d.58.29.1 39414 1i7pA 274 3.23e+00 b.43.4.2,c.25.1.1 66048,66049 1g7sA 594 3.49e+00 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25712,25713,31032,32147 1mxmA 254 3.51e+00 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1sdjA 310 3.70e+00 d.21.1.2,d.21.1.2 98807,98808 1azsB 212 3.97e+00 1azsA d.58.29.1 39423 1umkA 275 4.47e+00 1uag 437 4.67e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 3uagA 437 4.68e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 4uagA 437 4.96e+00 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1clqA 903 5.19e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 1uurA 473 5.23e+00 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ycoA 279 5.40e+00 1hcz 252 6.02e+00 1hcz b.2.6.1,b.84.2.2 22464,28250 2azpA 318 6.53e+00 1o17A 345 6.56e+00 a.46.2.1,c.27.1.1 80765,80766 2pcfB 250 6.65e+00 1hcz i.4.1.1 45911 1wekA 217 7.12e+00 1ih7A 903 7.23e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 2fnaA 357 7.24e+00 1on3A 523 7.50e+00 c.14.1.4,c.14.1.4 87107,87108 1h2rL 534 8.43e+00 1h2rL e.18.1.1 43298 1ubkL 534 8.53e+00 e.18.1.1 88422 1wuiL 534 9.33e+00 1vh5A 148 9.67e+00 d.38.1.5 100642 1bvqA 141 9.69e+00 1bvqA d.38.1.1 38542 1ug1A 92 9.85e+00 b.34.2.1 99360 1jihA 531 1.02e+01 d.240.1.1,e.8.1.7 90374,90375 1pyoA 167 1.06e+01 c.17.1.1 95370 1abbA 828 1.09e+01 1a8i c.87.1.4 35536 2b6eA 146 1.11e+01 1mqvA 125 1.17e+01 a.24.3.2 79415 1fl9A 161 1.25e+01 c.37.1.18 70137 1xttA 216 1.25e+01 1h2aL 567 1.29e+01 1h2rL e.18.1.1 43299 1u9yA 284 1.31e+01 1lo7A 141 1.33e+01 d.38.1.1 74144 1gv3A 248 1.37e+01 a.2.11.1,d.44.1.1 70585,70586 1o0iA 138 1.41e+01 d.38.1.5 86532 1h65A 270 1.42e+01 c.37.1.8 65640 2b5wA 357 1.43e+01 1y9wA 140 1.44e+01 1vquA 374 1.47e+01 1wtaA 275 1.49e+01 2b3nA 159 1.51e+01 1g9oA 91 1.52e+01 1pdr b.36.1.1 60400 1oe4A 247 1.52e+01 c.18.1.3 86895 2b61A 377 1.53e+01 1cjtA 217 1.56e+01 1azsA d.58.29.1 39419 2g84A 197 1.60e+01 1sr8A 298 1.62e+01 e.54.1.1 105959 5gcnA 166 1.64e+01 1yghA d.108.1.1 40807 2tdt 274 1.66e+01 3tdt b.81.1.2 28054 1xtqA 177 1.66e+01 1t7vA 278 1.67e+01 1fjgR 88 1.70e+01 1fjfR a.4.8.1 16252 1xhkA 187 1.71e+01 1c8kA 842 1.79e+01 1a8i c.87.1.4 35491 1ov3A 138 1.79e+01 b.34.2.1,b.34.2.1 87451,87452 3tdt 274 1.82e+01 3tdt b.81.1.2 28053 1a8i 842 1.92e+01 1a8i c.87.1.4 35490 2cy2A 174 1.98e+01 1mngA 203 2.01e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1c0aA 585 2.02e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1yqfA 203 2.03e+01 2aliA 158 2.09e+01 1tafB 70 2.12e+01 1tafB a.22.1.3 16482 1mjc 69 2.14e+01 1mjc b.40.4.5 25319 2aioA 269 2.18e+01 1g5cA 170 2.18e+01 1g5cA c.53.2.1 60264 2govA 195 2.25e+01 1u55A 188 2.27e+01 d.278.1.1 107677 1tdtA 259 2.38e+01 3tdt b.81.1.2 28055 1bupA 386 2.41e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1iuhA 198 2.42e+01 d.61.1.2 83711 1kay 381 2.42e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 1ba1 386 2.42e+01 1ba1 c.55.1.1,c.55.1.1 33387,33388 1hpm 386 2.43e+01 1ba1 c.55.1.1,c.55.1.1 33381,33382 1i92A 91 2.45e+01 1pdr b.36.1.1 61990 1h8lA 380 2.49e+01 b.3.2.1,c.56.5.1 65737,65738 1kgqA 274 2.58e+01 b.81.1.2 72447 1lylA 504 2.59e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1yozA 116 2.62e+01 1wpgA 994 2.68e+01 1h5uA 842 2.73e+01 1a8i c.87.1.4 60655 2af4C 333 2.80e+01 1izmA 184 2.83e+01 a.199.1.1 90725 1onqA 283 2.92e+01 b.1.1.2,d.19.1.1 93365,93366 1dlhB 188 2.93e+01 1iakB b.1.1.2,d.19.1.1 21598,38172 1y8qA 346 3.00e+01 1smlA 269 3.04e+01 1smlA d.157.1.1 42053 1bx2B 191 3.09e+01 1iakB b.1.1.2,d.19.1.1 21610,38184 1atr 386 3.19e+01 1ba1 c.55.1.1,c.55.1.1 33421,33422 1ndh 272 3.22e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1y791 680 3.24e+01 1fzkA 274 3.26e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 1g7rA 594 3.43e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25716,25717,31034,32149 2ghsA 326 3.51e+01 1mroC 247 3.57e+01 1mroC d.58.31.1 39437 1eulA 994 3.60e+01 1eulA 1yzhA 214 3.63e+01 1f2rI 100 3.63e+01 1c9fA d.15.2.1 37641 1s7jA 262 3.68e+01 d.21.1.2 98647 1itwA 741 3.73e+01 c.77.1.2 76793 1u7nA 336 3.80e+01 c.77.1.4 107726 2fvhA 120 3.88e+01 1ats 386 3.91e+01 1ba1 c.55.1.1,c.55.1.1 33423,33424 1od3A 168 4.01e+01 b.18.1.10 86825 1nnsA 326 4.02e+01 c.88.1.1 85910 1g7tA 594 4.04e+01 1g7rA b.43.3.1,b.43.3.1,c.20.1.1,c.37.1.8 25714,25715,31033,32148 1ewqA 765 4.07e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1hbnC 248 4.07e+01 1mroC d.58.31.1 60902 1hg2A 289 4.07e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1prxA 224 4.14e+01 1prxA c.47.1.10 33076 1eriA 276 4.19e+01 1ckqA c.52.1.1 33231 1rsy 152 4.19e+01 1rsy b.7.1.2 23192 1culA 217 4.23e+01 1azsA d.58.29.1 39417 1dat 174 4.37e+01 2fha a.25.1.1 16677 1cl8A 276 4.37e+01 1ckqA c.52.1.1 33230 1fjgK 129 4.39e+01 1fjfK c.55.4.1 33733 1gzqA 300 4.39e+01 b.1.1.2,d.19.1.1 70818,70819 1w77A 228 4.44e+01 1lk2A 274 4.48e+01 b.1.1.2,d.19.1.1 91056,91057 1b65A 375 4.49e+01 1b65A d.154.1.1 42020 1srqA 341 4.51e+01 e.55.1.1 105967 1de6A 426 4.52e+01 1de5A c.1.15.2 29398 1ckqA 276 4.54e+01 1ckqA c.52.1.1 33229 1dp4A 435 4.55e+01 1dp4A c.93.1.1 35710 1de5A 426 4.55e+01 1de5A c.1.15.2 29402 2b0tA 738 4.58e+01 1aorA 605 4.64e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1e1oA 504 4.66e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1qpsA 261 4.73e+01 1ckqA c.52.1.1 33234 1lox 662 4.79e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1qstA 160 4.88e+01 1yghA d.108.1.1 40804 1ng2A 193 4.88e+01 b.34.2.1,b.34.2.1 85660,85661 1ycdA 243 4.89e+01 1ixlA 131 4.91e+01 d.38.1.5 90717 1zq1C 633 4.94e+01 1rylA 167 4.95e+01 d.276.1.1 105124 1rxr 83 5.01e+01 2nllB g.39.1.2 45114 1ah0 316 5.01e+01 1frb c.1.7.1 28685 1kr7A 110 5.06e+01 a.1.1.4 72890 1l0wA 580 5.08e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1poxA 585 5.14e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1jx4A 352 5.24e+01 d.240.1.1,e.8.1.7 90378,90379 1k0eA 453 5.35e+01 d.161.1.1 67938 1q1rA 431 5.37e+01 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 1z5hA 780 5.40e+01 1azsA 220 5.42e+01 1azsA d.58.29.1 39416 2cx7A 130 5.46e+01 1l5oA 356 5.52e+01 c.39.1.1 77711 1d0sA 356 5.64e+01 1d0vA c.39.1.1 32477 1u0kA 288 5.64e+01 d.21.1.2,d.21.1.2 107547,107548 1tx4B 178 5.66e+01 1ctqA c.37.1.8 32045 1pzsA 208 5.70e+01 b.1.8.1 104397 1kqfA 1015 5.77e+01 b.52.2.2,c.81.1.1 72871,72872 1a8l 226 5.82e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1kkcA 221 5.87e+01 a.2.11.1,d.44.1.1 68660,68661 1prxB 224 5.90e+01 1prxA c.47.1.10 33077 1fsfA 266 5.91e+01 c.124.1.1 65047 1jh8A 356 5.95e+01 c.39.1.1 63052 1k8kD 300 6.00e+01 d.198.2.1,d.198.2.1 68309,68310 1vl2A 421 6.06e+01 c.26.2.1,d.210.1.1 108708,108709 2fsjA 346 6.17e+01 2aneA 125 6.31e+01 1ri5A 298 6.34e+01 c.66.1.34 97502 1ksr 100 6.44e+01 1qfhA b.1.18.10 21897 1b47A 304 6.49e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1aqdB 198 6.56e+01 1iakB b.1.1.2,d.19.1.1 21586,38160 1g7pA 274 6.56e+01 b.1.1.2,d.19.1.1 70153,70154 1nmeB 92 6.66e+01 2cxcA 144 6.71e+01 1yt5A 258 6.82e+01 1pfsA 78 6.83e+01 1pfsA b.40.4.7 25391 1k8kE 178 6.84e+01 a.148.1.1 68311 1su4A 994 6.84e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 98993,98994,98995,98996 1p5zB 263 6.84e+01 c.37.1.1 87815 1isaA 192 6.91e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1jyhA 157 6.94e+01 d.60.1.3 71956 1d0vA 356 6.95e+01 1d0vA c.39.1.1 32476 1wnlA 235 6.96e+01 1iscA 192 6.96e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1gutA 68 6.99e+01 b.40.6.1 65576 1j5eK 129 7.00e+01 c.55.4.1 71554 1deaA 266 7.08e+01 1deaA c.124.1.1 31760 1sg6A 393 7.16e+01 e.22.1.1 105522 1z54A 132 7.20e+01 1k24A 253 7.21e+01 f.4.4.2 72002 1a8z 153 7.28e+01 1rcy b.6.1.1 23020 1a3z 155 7.30e+01 1rcy b.6.1.1 23019 1aipE 405 7.31e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1josA 128 7.32e+01 d.52.7.1 84191 1rcy 151 7.38e+01 1rcy b.6.1.1 23018 1y0hA 105 7.40e+01 1y2tA 142 7.48e+01 1k3xA 262 7.51e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1lghB 45 7.58e+01 1lghB f.3.1.1 43734 1jug 125 7.58e+01 3lzt d.2.1.2 36587 1qjtA 99 7.59e+01 1eh2 a.39.1.6 17335 1q0pA 223 7.73e+01 c.62.1.1 95507 1ig8A 486 7.77e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1svr 114 7.86e+01 1svy d.109.1.1 40833 2calA 154 7.88e+01 1ilyA 90 7.91e+01 c.55.4.1 71245 1ntvA 152 7.92e+01 b.55.1.2 86168 1e30A 155 7.96e+01 1rcy b.6.1.1 23016 1tp5A 119 7.98e+01 1gpwB 201 7.99e+01 c.23.16.1 65461 1j0hA 588 8.09e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1kpuA 274 8.13e+01 b.1.1.2,d.19.1.1 84456,84457 1ek4A 418 8.14e+01 1dd8A c.95.1.1,c.95.1.1 59436,59437 1l7aA 318 8.19e+01 c.69.1.25 77772 2bywA 418 8.19e+01 1hzdA 272 8.29e+01 c.14.1.3 65969 1o70A 324 8.30e+01 b.118.1.1,b.118.1.1 81115,81116 1j9lA 247 8.30e+01 c.106.1.1 62762 1evhA 112 8.40e+01 1evhA b.55.1.4 26997 1f08A 148 8.41e+01 1f08A d.89.1.2 59564 1j9jA 247 8.46e+01 c.106.1.1 62758 1z94A 147 8.47e+01 2c7pA 327 8.52e+01 1wqwA 235 8.58e+01 1urvA 190 8.60e+01 1ut0A 190 8.60e+01 a.1.1.2 108012 1csp 67 8.65e+01 1mjc b.40.4.5 25321 1wlsA 328 8.75e+01 2a8yA 270 8.82e+01 1jvnA 555 8.84e+01 c.1.2.1,c.23.16.1 67355,67356 1ffkE 119 8.86e+01 1ffkE d.79.3.1 39812 1k9vF 201 8.87e+01 c.23.16.1 68365 1gpb 842 8.89e+01 1a8i c.87.1.4 35478 2a6aA 218 8.95e+01 1fzoA 274 8.99e+01 1agdA b.1.1.2,d.19.1.1 60155,60156