# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1g79A 218 7.21e-45 1ci0A b.45.1.1 25752 1dnlA 199 9.12e-45 1ci0A b.45.1.1 25753 1nrgA 261 9.90e-37 b.45.1.1 80694 1t9mA 214 2.11e-33 1ty9A 222 7.43e-32 1ci0A 228 6.58e-30 1ci0A b.45.1.1 25750 1rfeA 162 2.45e-20 2fhqA 141 1.45e-17 1vl7A 157 1.97e-15 b.45.1.1 108732 2asfA 137 9.20e-14 2fg9A 178 1.59e-13 2aq6A 147 1.61e-12 1w9aA 147 7.69e-12 2furA 209 1.17e-11 1xxoA 147 1.66e-11 2arzA 247 7.04e-09 1xhnA 184 1.31e-08 1axj 122 1.48e-08 1axj b.45.1.1 25749 1flmA 122 8.97e-08 1axj b.45.1.1 25747 1w3oA 216 4.24e-07 1ejeA 192 5.17e-04 1ejeA b.45.1.2 25757 1obpA 159 2.89e-02 1obpA b.60.1.1 27092 1ylnA 252 3.37e-02 1hn2A 159 3.89e-02 b.60.1.1 65890 1gt1A 159 3.90e-02 b.60.1.1 90515 1quqB 121 7.30e-02 1quqB b.40.4.3 25305 2d37A 176 9.90e-02 1ibvB 229 1.64e-01 1pyaB 228 1.86e-01 1pyaB 1twfK 120 3.16e-01 1wocA 103 3.62e-01 1ha1 184 3.93e-01 1ha1 d.58.7.1,d.58.7.1 39147,39148 2cn3A 737 4.92e-01 2bgiA 272 5.09e-01 1i50K 120 6.04e-01 d.74.3.2 61765 1rz1A 161 6.30e-01 b.45.1.2 98124 1sva1 361 6.35e-01 1vpsA 1nnjA 271 7.23e-01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1sxvA 172 7.85e-01 2fo3A 125 8.04e-01 1tdzA 272 8.41e-01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1wi1A 126 8.44e-01 1m1hA 248 8.79e-01 b.114.1.1,d.58.42.1 78415,78416 1x8dA 104 1.07e+00 1mxgA 435 1.12e+00 b.71.1.1,c.1.8.1 85193,85194 1yoaA 159 1.42e+00 1zavA 180 1.45e+00 2c60A 111 1.49e+00 1wgbA 159 1.50e+00 1feuA 206 1.51e+00 1feuA b.53.1.1 59801 1r1bA 59 1.52e+00 1r1bA a.16.1.3 16396 2coqA 108 1.58e+00 1d2dA 59 1.68e+00 1r1bA a.16.1.3 16397 1rocA 155 1.75e+00 b.1.22.1 97673 1txyA 104 1.86e+00 1xewX 182 2.19e+00 1vhtA 218 2.20e+00 c.37.1.1 100700 2cwzA 141 2.21e+00 1gp2G 71 2.26e+00 1tbgE a.137.3.1 19635 1vheA 373 2.27e+00 b.49.3.1,c.56.5.4 100669,100670 1xneA 113 2.37e+00 2cr9A 139 2.44e+00 1pjjA 271 2.47e+00 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1l3kA 196 2.51e+00 d.58.7.1,d.58.7.1 73539,73540 1zxfA 155 2.56e+00 2fvgA 340 2.69e+00 2bgcA 238 2.80e+00 1pguA 615 2.90e+00 b.69.4.1,b.69.4.1 88069,88070 1bax 94 3.00e+00 1bax a.61.1.3 18133 1uzxA 169 3.05e+00 d.20.1.2 100238 1v1qA 134 3.06e+00 1sjyA 159 3.11e+00 d.113.1.1 98900 1wj9A 211 3.11e+00 1t5hX 504 3.14e+00 e.23.1.1 106449 2f4mA 295 3.21e+00 2fp8A 322 3.33e+00 2cwsA 237 3.35e+00 1vqoD 177 3.38e+00 1byqA 228 3.82e+00 1yer d.122.1.1 41100 2a6sA 84 3.96e+00 1ri6A 343 3.97e+00 b.69.11.1 97503 2fe7A 166 4.01e+00 2bcjB 340 4.03e+00 1k3xA 262 4.27e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1b8aA 438 4.29e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1khqA 212 4.61e+00 d.3.1.1 90964 1rg9A 383 4.75e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1ex2A 189 5.00e+00 1ex2A c.51.4.2 33225 1j5yA 187 5.05e+00 a.4.5.1,d.94.2.1 71592,71593 1vrbA 342 5.14e+00 1a0rB 340 5.37e+00 1tbgA b.69.4.1 27658 1vs0A 310 5.39e+00 1m5q1 130 5.64e+00 1ywsA 82 5.65e+00 2ew0A 192 5.76e+00 1h7zA 194 5.79e+00 1qhvA b.21.1.1 60733 1asyA 490 5.89e+00 1b8aA b.40.4.1,d.104.1.1 25242,40763 1qhlA 227 6.04e+00 1qhlA c.37.1.12 32382 1dcuA 357 6.21e+00 1frpA e.7.1.1 42943 1n3bA 216 6.32e+00 c.37.1.1 79959 1xkpC 143 6.36e+00 1k0gA 453 6.58e+00 d.161.1.1 67940 1f0iA 504 6.63e+00 1f0iA d.136.1.2,d.136.1.2 59566,59567 1dkxA 219 6.64e+00 1dkzA a.8.4.1,b.130.1.1 90339,90340 1z4xA 532 6.74e+00 1ughI 82 6.81e+00 1ugiA d.17.5.1 38133 1yer 228 6.82e+00 1yer d.122.1.1 41101 1dfuP 94 7.05e+00 1dfuP b.53.1.1 26936 1v0wA 506 7.20e+00 d.136.1.2,d.136.1.2 108220,108221 1g60A 260 7.24e+00 c.66.1.11 70151 1ppn 212 7.30e+00 1cs8A d.3.1.1 37004 1gotB 340 7.31e+00 1tbgA b.69.4.1 27648 1z4vA 532 7.42e+00 1l1zA 274 7.51e+00 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1yuwA 554 7.58e+00 2f9dA 125 7.74e+00 1e5pA 151 7.77e+00 1bj7 b.60.1.1 59272 1sfe 180 7.91e+00 1sfe a.4.2.1,c.55.7.1 16073,33748 1nb9A 147 8.17e+00 b.43.5.1 85515 1tbgA 340 8.25e+00 1tbgA b.69.4.1 27649 1ysjA 404 8.34e+00 1ew3A 159 8.36e+00 1mup b.60.1.1 27114 1r2zA 274 8.55e+00 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 2u2fA 85 8.56e+00 2u2fA d.58.7.1 39167 1rowA 109 8.75e+00 b.1.11.2 97676 1gm6A 175 8.85e+00 b.60.1.1 70272 1dkzA 219 9.24e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 1ugiA 84 9.27e+00 1ugiA d.17.5.1 38125 1g6nA 210 9.38e+00 2cgpA a.4.5.4,b.82.3.2 16100,28139 1gtkA 313 9.39e+00 c.94.1.1,d.50.2.1 76346,76347 2cohA 202 9.68e+00 1mxiA 160 1.01e+01 c.116.1.1 79646 1xkiA 162 1.05e+01 1mjc 69 1.06e+01 1mjc b.40.4.5 25319 1mxb 383 1.07e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41329,41330,41331 1zboA 210 1.09e+01 1k4fA 248 1.10e+01 e.3.1.1 68138 1icxA 155 1.11e+01 d.129.3.1 71191 1uylA 236 1.14e+01 d.122.1.1 108147 1ipwA 175 1.15e+01 2prd b.40.5.1 25427 1y0vH 146 1.16e+01 1wexA 104 1.17e+01 1zo0A 126 1.18e+01 1fzkA 274 1.20e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 2f4pA 147 1.23e+01 1kpf 126 1.27e+01 1kpf d.13.1.1 37507 1m40A 263 1.29e+01 e.3.1.1 74437 1zybA 232 1.32e+01 1wvhA 134 1.36e+01 1widA 130 1.36e+01 1fjgJ 105 1.36e+01 1fjfJ d.58.15.1 39330 1y0yA 353 1.37e+01 1aazA 87 1.39e+01 1aba c.47.1.1 32761 1tuhA 156 1.42e+01 d.17.4.11 107345 1dm9A 133 1.43e+01 1dm9A d.66.1.3 39560 1k0eA 453 1.45e+01 d.161.1.1 67938 1fzoA 274 1.48e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1i0rA 169 1.48e+01 1i0rA b.45.1.2 61489 1ww7A 160 1.52e+01 1kpuA 274 1.53e+01 b.1.1.2,d.19.1.1 84456,84457 1qy6A 274 1.55e+01 b.47.1.1 96574 1am1 213 1.56e+01 1yer d.122.1.1 41095 1omiA 248 1.56e+01 b.82.3.3,a.4.5.4 87079,87080 1i0sA 169 1.57e+01 1i0rA b.45.1.2 61491 1fxlA 167 1.60e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1c0aA 585 1.61e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1xuvA 178 1.61e+01 1wi6A 88 1.62e+01 1ygs 234 1.64e+01 1ygs b.26.1.1 23907 1tvjA 166 1.65e+01 1bbpA 173 1.69e+01 1bbpA b.60.1.1 27147 1tmcA 175 1.71e+01 1agdA d.19.1.1 38258 1rypD 241 1.72e+01 1rypD d.153.1.4 41935 1qm9A 198 1.76e+01 1qm9A d.58.7.1,d.58.7.1 39207,39208 1fqgA 263 1.77e+01 1btl e.3.1.1 42699 1vhsA 175 1.77e+01 d.108.1.1 100698 1eaxA 241 1.79e+01 b.47.1.2 64889 1fljA 260 1.79e+01 2cba b.74.1.1 27954 1mxa 383 1.80e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41326,41327,41328 1dkiA 371 1.82e+01 1dkiA d.3.1.1 37090 1kxoA 184 1.82e+01 b.60.1.1 84475 1fmk 452 1.83e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1p27B 106 1.86e+01 d.58.7.1 93908 1q5qA 259 1.89e+01 d.153.1.4 95904 2cgpA 210 1.92e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1zglB 192 1.92e+01 1jhdA 396 1.93e+01 b.122.1.3,c.26.1.5 66712,66713 1aba 87 1.94e+01 1aba c.47.1.1 32760 1ukgA 252 2.01e+01 b.29.1.1 99489 1j58A 385 2.01e+01 b.82.1.2 71531 1y4hA 188 2.01e+01 1n3oA 252 2.04e+01 b.29.1.1 79967 1d1rA 116 2.06e+01 1d1rA d.64.1.1 39548 4rhn 115 2.06e+01 1kpf d.13.1.1 37495 1duzA 275 2.06e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 1btl 263 2.09e+01 1btl e.3.1.1 42691 1aoeA 192 2.09e+01 1aoeA c.71.1.1 34923 1qk8A 146 2.12e+01 1ewxA c.47.1.10 33061 1nogA 177 2.13e+01 a.25.2.2 85923 1v4pA 157 2.15e+01 1ermA 263 2.16e+01 1btl e.3.1.1 42690 2bf6A 449 2.17e+01 1ndk 155 2.18e+01 1npk d.58.6.1 39118 1lk2A 274 2.20e+01 b.1.1.2,d.19.1.1 91056,91057 1pfl 139 2.21e+01 1pne d.110.1.1 40877 1uunA 184 2.21e+01 f.6.1.2 100012 1ol0A 121 2.24e+01 b.1.1.1 93296 1g7pA 274 2.24e+01 b.1.1.2,d.19.1.1 70153,70154 1pda 315 2.26e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1z94A 147 2.28e+01 1zg2A 107 2.28e+01 2av1A 275 2.29e+01 9pap 212 2.33e+01 1cs8A d.3.1.1 37006 1whxA 111 2.37e+01 2pil 159 2.37e+01 2pil d.24.1.1 38376 1cwvA 492 2.39e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1obwA 175 2.41e+01 2prd b.40.5.1 25416 1k8kD 300 2.42e+01 d.198.2.1,d.198.2.1 68309,68310 1q3iA 214 2.44e+01 d.220.1.1 104524 2fnjA 226 2.46e+01 1npk 154 2.46e+01 1npk d.58.6.1 39099 1ry9A 145 2.48e+01 d.198.1.1 98094 2d0oA 610 2.48e+01 1z0pA 84 2.51e+01 1qbiA 454 2.52e+01 1c9uA b.68.2.1 27619 1n87A 56 2.54e+01 g.44.1.2 85390 1dixA 208 2.55e+01 1bk7A d.124.1.1 41122 1ay2 159 2.56e+01 2pil d.24.1.1 38377 1pxvA 183 2.56e+01 d.3.1.1 95301 1cv8 174 2.57e+01 1cv8 d.3.1.1 37089 1c9uA 454 2.62e+01 1c9uA b.68.2.1 27623 1dhn 121 2.62e+01 1dhn d.96.1.3 40663 1udiI 83 2.62e+01 1ugiA d.17.5.1 38124 1xn9A 101 2.63e+01 1u00A 227 2.64e+01 1fofA 246 2.67e+01 1fofA e.3.1.1 42763 1x88A 359 2.69e+01 1vpbA 451 2.75e+01 1xfsA 178 2.77e+01 d.129.3.5 109589 1x74A 360 2.79e+01 1san 62 2.83e+01 2hddA a.4.1.1 16008 1owfA 99 2.87e+01 a.55.1.1 87487 1ihfA 99 2.88e+01 1huuA a.55.1.1 17893 1p8cA 145 2.93e+01 a.152.1.2 94354 1g33A 73 2.94e+01 a.39.1.4 65121 2cfxA 144 2.94e+01 2bvbA 137 3.01e+01 1o7kA 131 3.02e+01 d.189.1.1 81144 1irsA 112 3.06e+01 1qqgA b.55.1.2 26991 1ewxA 146 3.06e+01 1ewxA c.47.1.10 33062 1ahdP 68 3.08e+01 2hddA a.4.1.1 16006 1ubdC 124 3.10e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1 45053,45054,45055,45056 1vkdA 338 3.10e+01 b.67.2.4 108644 1ft9A 222 3.14e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 2cwkA 160 3.15e+01 2pviA 157 3.16e+01 3pviA c.52.1.6 33302 1eur 365 3.17e+01 1eut b.68.1.1 27607 2occG 84 3.22e+01 2occG f.23.2.1 43522 1d8hA 311 3.24e+01 1d8iA d.63.1.1 39544 1i40A 175 3.25e+01 b.40.5.1 66024 1h4rA 314 3.27e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1o8xA 146 3.38e+01 c.47.1.10 86681 1pytA 94 3.44e+01 1pytA d.58.3.1 39064 1o4rA 108 3.44e+01 d.93.1.1 92469 1so7A 382 3.46e+01 1gceA 364 3.50e+01 1gceA e.3.1.1 42738 2cioA 212 3.52e+01 1jeiA 53 3.52e+01 1jeiA a.140.1.1 62918 1k55A 246 3.53e+01 e.3.1.1 68156 2gq1A 332 3.55e+01 1kk8B 139 3.58e+01 a.39.1.5 77430 1m3iA 471 3.58e+01 f.9.1.1 91178 1e3uA 246 3.60e+01 1fofA e.3.1.1 42755 1k3sA 113 3.60e+01 d.198.1.1 68120 1nt0A 286 3.61e+01 b.23.1.1,b.23.1.1,g.3.11.1 86143,86144,86145 2a1vA 144 3.61e+01 2av7A 275 3.67e+01 2g64A 140 3.69e+01 1mdbA 539 3.72e+01 e.23.1.1 79008 2bayA 61 3.73e+01 1l0wA 580 3.78e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1am2 199 3.78e+01 1am2 b.86.1.2 28381 1sxl 97 3.81e+01 1b7fA d.58.7.1 39180 1enxA 190 3.88e+01 1axkA b.29.1.11 24325 1ga0A 364 3.90e+01 1gceA e.3.1.1 60410 1xfoA 357 3.91e+01 1tif 78 3.91e+01 1tif d.15.8.1 37836 2sttA 96 3.91e+01 1awcA a.4.5.21 16163 1wvqA 167 3.97e+01 2g7lA 243 3.97e+01 2bnkA 67 4.00e+01 1cokA 68 4.03e+01 1cokA a.60.1.2 17945 1fsz 372 4.06e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1p5tA 127 4.12e+01 b.55.1.2 94148 2fbyA 205 4.20e+01 1at0 145 4.20e+01 1at0 b.86.1.1 28374 1xypA 190 4.22e+01 1axkA b.29.1.11 24327 1cruA 454 4.23e+01 1c9uA b.68.2.1 27617 2fug1 438 4.24e+01 1b1gA 75 4.24e+01 1psrA a.39.1.1 17151 1go4A 205 4.27e+01 d.135.1.1 70292 1g0uE 234 4.31e+01 d.153.1.4 41950 1nnwA 252 4.32e+01 d.159.1.5 80674 1zwyA 185 4.35e+01 1u58A 253 4.35e+01 2bsjA 133 4.44e+01 2sak 121 4.45e+01 2sak d.15.5.1 37711 1hdmA 201 4.46e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2bjfA 329 4.47e+01 1anu 138 4.49e+01 1aohA b.2.2.2 22403 1yphC 131 4.49e+01 1tz0A 114 4.52e+01 d.58.4.5 107463 1kawA 135 4.52e+01 3ullA b.40.4.3 25288 1nziA 159 4.56e+01 b.23.1.1,g.3.11.1 86449,86450 1zc1A 208 4.58e+01 1yr2A 741 4.62e+01 1onhA 364 4.64e+01 e.3.1.1 93357 1jhnA 424 4.71e+01 b.104.1.1,b.29.1.12 66722,70060 2g0qA 173 4.75e+01 1memA 215 4.75e+01 1cs8A d.3.1.1 37069 1sacA 204 4.80e+01 1sacA b.29.1.5 24237 1k5nA 276 4.80e+01 b.1.1.2,d.19.1.1 77266,77267 1dun 134 4.85e+01 1dun b.85.4.1 28371 2bgzA 299 4.87e+01 1d8iA 311 4.93e+01 1d8iA d.63.1.1 39541 2c3gA 98 4.99e+01 1tu6A 215 5.00e+01 d.3.1.1 107318 1kpeA 126 5.04e+01 1kpf d.13.1.1 37508 1erxA 184 5.06e+01 1np1A b.60.1.1 27164 2fblA 153 5.10e+01 1ydwA 362 5.11e+01 1ah6 220 5.13e+01 1yer d.122.1.1 41094 1tkeA 224 5.13e+01 2ag5A 246 5.19e+01 1qf6A 642 5.20e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 2bkqA 212 5.20e+01 1m2oA 768 5.20e+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 1fwkA 296 5.21e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1shaA 104 5.21e+01 1fmk d.93.1.1 40424 2azeA 155 5.21e+01 1hsbA 270 5.22e+01 1agdA b.1.1.2,d.19.1.1 20736,38257 2bwrA 401 5.23e+01 1v54G 85 5.25e+01 f.23.2.1 100328 1j1uA 306 5.27e+01 c.26.1.1 83980 1shbA 104 5.32e+01 1fmk d.93.1.1 40425 1jn5B 250 5.32e+01 d.17.4.2 66922 1c8uA 285 5.33e+01 1c8uA 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