# List of top-scoring protein chains for t2k-100-30-alpha 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 1rz3A 201 3.21e-02 c.37.1.6 -7048 1aye 401 2.48e-01 1aye c.56.5.1 33824 d.58.3.1 39065 1jhnA 424 2.56e-01 b.29.1.12 70060 b.104.1.1 66722 1dkxA 219 3.40e-01 1dkzA unknown_sccs -446 unknown_sccs -3061 1dkzA 219 3.99e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1ixmA 192 5.93e-01 1ixmA d.123.1.1 41114 1ixmB 192 7.87e-01 1ixmA d.123.1.1 41115 1dxgA 36 9.80e-01 1dxgA g.41.5.2 45247 1fzvA 132 1.17e+00 1vpfA g.17.1.1 60159 1ggrA 168 1.19e+00 1gpr b.84.3.1 28279 1aoeA 192 1.66e+00 1aoeA c.71.1.1 34923 1fggA 261 1.99e+00 1fggA c.68.1.7 34576 1ovaA 386 2.09e+00 1ovaA e.1.1.1 42619 1b88A 114 2.43e+00 1tcrA b.1.1.1 20608 1kwsA 261 2.53e+00 c.68.1.7 73083 1d5mB 192 3.02e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1o54A 277 3.04e+00 c.66.1.13 -8095 1aohA 147 3.13e+00 1aohA b.2.2.2 22401 1f3z 161 3.13e+00 1gpr b.84.3.1 28273 1rhfA 182 3.14e+00 b.1.1.1 -2335 b.1.1.4 -2684 1qhuA 460 3.18e+00 1qhuA b.66.1.1 27530 b.66.1.1 27531 1hxn 219 3.22e+00 1hxn b.66.1.1 27529 1js8A 394 3.64e+00 a.86.1.1 67219 b.112.1.1 67220 1gq2A 555 3.86e+00 c.2.1.7 70308 c.58.1.3 70309 1pytA 94 3.90e+00 1pytA d.58.3.1 39064 1uhgA 385 3.90e+00 e.1.1.1 88491 1mexL 213 3.92e+00 b.1.1.1 -2124 b.1.1.2 -2352 1dbqA 289 4.22e+00 1qpzA c.93.1.1 35666 1hfuA 503 4.62e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1pdgC 109 4.63e+00 1pdgA g.17.1.1 44750 12e8L 214 4.65e+00 8fabA b.1.1.1 20268 b.1.1.2 21268 1a65A 504 4.68e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1hxkA 1015 4.91e+00 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1qwnA 1045 5.05e+00 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1htyA 1015 5.22e+00 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1ejeA 192 5.31e+00 1ejeA b.45.1.2 25757 1hwwA 1015 5.34e+00 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1bvp1 349 5.98e+00 1bvp1 1q2wA 308 6.01e+00 b.47.1.4 88355 1oz2A 331 6.23e+00 b.34.9.3 -3597 b.34.9.3 -3598 b.34.9.3 -3599 2fbjL 213 6.37e+00 8fabA b.1.1.1 19850 b.1.1.2 20954 1a3lL 217 6.49e+00 8fabA b.1.1.1 20240 b.1.1.2 21252 1m42A 102 6.99e+00 b.1.18.17 78597 1ux6A 350 7.20e+00 unknown_sccs -3451 unknown_sccs -12886 1rurL 217 7.33e+00 b.1.1.1 -2094 b.1.1.2 -2389 1cauA 181 7.35e+00 1dgwA b.82.1.2 28102 1dgwA 178 7.37e+00 1dgwA b.82.1.2 28090 1snzA 344 7.41e+00 b.30.5.4 -3496 1pdgA 109 7.44e+00 1pdgA g.17.1.1 44748 1mjuL 219 7.54e+00 b.1.1.1 -2083 b.1.1.2 -2360 1bpr 191 7.88e+00 1dkzA unknown_sccs 43319 1glaF 168 8.03e+00 1gpr b.84.3.1 28274 1hyxL 216 8.08e+00 8fabA b.1.1.1 20166 b.1.1.2 21190 1a2vA 655 8.28e+00 1a2vA b.30.2.1 24416 d.17.2.1 38059 d.17.2.1 38060 1forL 210 8.44e+00 8fabA b.1.1.1 19988 b.1.1.2 21044 1v7oA 165 8.67e+00 unknown_sccs -10249 1qtfA 246 8.68e+00 1agjA b.47.1.1 25830 1cs8A 316 8.75e+00 1cs8A d.3.1.1 37065 1tetL 216 9.23e+00 32c2A b.1.1.1 19902 b.1.1.2 20996 1qd6C 240 9.54e+00 1qd5A 1dqqA 214 9.55e+00 8fabA b.1.1.1 20420 b.1.1.2 21390 1eta1 127 9.73e+00 1etb1 1q6hA 224 9.76e+00 d.26.1.1 -9487 1mkkA 96 9.89e+00 g.17.1.1 79240 1mlbA 214 1.01e+01 8fabA b.1.1.1 20050 b.1.1.2 21092 1a87 321 1.04e+01 1a87 f.1.1.1 43380 1ahsA 126 1.05e+01 1ahsA b.19.1.1 23794 1v84A 253 1.06e+01 1mup 166 1.07e+01 1mup b.60.1.1 27133 1fp5A 222 1.07e+01 1f6aB b.1.1.2 21530 b.1.1.2 21531 1se8A 301 1.08e+01 1q9rA 219 1.09e+01 b.1.1.1 -2109 b.1.1.2 -2375 1e6oL 212 1.09e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 1c8oA 300 1.15e+01 1c8oA e.1.1.1 42677 1aohB 147 1.18e+01 1aohA b.2.2.2 22402 1gg3A 279 1.19e+01 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1jp4A 308 1.21e+01 1jp4A e.7.1.1 63223 1etb1 127 1.22e+01 1etb1 1ospL 214 1.26e+01 32c2A b.1.1.1 20116 b.1.1.2 21146 1b1cA 181 1.27e+01 1amoA c.23.5.2 31212 1wetA 340 1.28e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1qpzA 340 1.31e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1cfyA 143 1.33e+01 1cof d.109.1.2 40858 1budA 197 1.33e+01 1atlA d.92.1.9 40328 1o0pA 104 1.34e+01 d.58.7.1 86535 1bj7 156 1.34e+01 1bj7 b.60.1.1 27113 1uvqB 198 1.34e+01 b.1.1.2 -2659 d.19.1.1 -9348 1neu 124 1.41e+01 1neu b.1.1.1 19704 1m2tB 263 1.41e+01 b.42.2.1 84762 b.42.2.1 84763 1ttbA 127 1.46e+01 1etb1 b.3.4.1 22543 1ycsA 199 1.49e+01 1tupA b.2.5.2 22433 1q72L 218 1.57e+01 b.1.1.1 -2071 b.1.1.2 -2347 1olrA 224 1.59e+01 b.29.1.11 -3489 1flrL 219 1.61e+01 8fabA b.1.1.1 19904 b.1.1.2 20998 1s3iA 310 1.64e+01 b.46.1.1 -4111 c.65.1.1 -8042 1lkcA 364 1.66e+01 c.67.1.1 73978 1cof 143 1.66e+01 1cof d.109.1.2 40860 1i8dA 213 1.74e+01 b.43.4.3 61953 b.43.4.3 61954 1sacA 204 1.75e+01 1sacA b.29.1.5 24237 1tupA 219 1.76e+01 1tupA b.2.5.2 22434 1kb5A 115 1.76e+01 1tvdA b.1.1.1 20611 1tsrA 219 1.77e+01 1tupA b.2.5.2 22437 1f41A 127 1.80e+01 1etb1 b.3.4.1 22539 1f56A 91 1.80e+01 2cbp b.6.1.1 22896 32c2A 217 1.83e+01 32c2A b.1.1.1 20438 b.1.1.2 21404 2mllB 255 1.88e+01 1abrB b.42.2.1 25567 b.42.2.1 25568 1nnwA 252 1.95e+01 d.159.1.5 80674 1m93B 245 1.95e+01 1uypA 432 1.95e+01 unknown_sccs -3480 unknown_sccs -4554 3chy 128 1.96e+01 3chy c.23.1.1 31038 1qauA 112 1.96e+01 1qauA b.36.1.1 24779 1nlbL 220 1.97e+01 b.1.1.1 80623 b.1.1.2 80624 1uolA 219 1.98e+01 b.2.5.2 -2886 1g7rA 594 1.98e+01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1nepA 130 2.00e+01 b.1.18.7 80440 1e6mA 128 2.02e+01 3chy c.23.1.1 31039 1f86A 115 2.05e+01 1etb1 b.3.4.1 59689 1qd5A 275 2.05e+01 1qd5A f.4.2.1 43748 1mwyA 73 2.07e+01 d.58.17.1 79616 1utwA 432 2.08e+01 1k7jA 206 2.10e+01 d.115.1.1 72103 1vybA 238 2.11e+01 1souA 194 2.13e+01 2rhe 114 2.17e+01 8fabA b.1.1.1 20523 1mcpL 220 2.22e+01 8fabA b.1.1.1 19858 b.1.1.2 20958 1qy1A 174 2.22e+01 b.60.1.1 -4445 1pxfA 111 2.26e+01 b.40.4.4 88341 2phlA 397 2.30e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1s2dA 167 2.30e+01 c.23.14.1 -6469 1gpqA 135 2.35e+01 d.233.1.1 83295 1sh8A 154 2.37e+01 1r13A 148 2.38e+01 d.169.1.1 -11646 h.1.1.1 -12895 1ospH 218 2.42e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 1jeqB 565 2.43e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1gtxA 472 2.44e+01 1gtxA 1lkzA 219 2.46e+01 unknown_sccs 73991 d.58.40.1 73992 1dgrC 178 2.47e+01 1dgwA b.82.1.2 28100 1cq3A 233 2.48e+01 1cq3A b.27.1.1 23923 1vpwA 340 2.49e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1jbeA 128 2.50e+01 3chy c.23.1.1 62845 1rz1A 161 2.54e+01 b.45.1.2 -4088 1hxxA 340 2.60e+01 2omf f.4.3.1 61385 1lfpA 249 2.61e+01 e.39.1.1 73885 1i06A 180 2.61e+01 1mup b.60.1.1 27131 1b6sA 355 2.61e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1ew3A 159 2.62e+01 1mup b.60.1.1 27114 1l1zA 274 2.62e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1r2zA 274 2.66e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 2chsA 127 2.67e+01 2chsA d.79.1.2 39764 1h6tA 291 2.68e+01 b.1.18.15 65686 c.10.2.1 65687 1ac6A 110 2.72e+01 1tcrA b.1.1.1 20606 1iz0A 302 2.73e+01 b.35.1.2 83821 c.2.1.1 83822 1iw7C 1119 2.74e+01 e.29.1.1 71474 1dzfA 215 2.75e+01 1dzfA c.52.3.1 33344 d.78.1.1 39753 1hnnA 282 2.78e+01 c.66.1.15 65895 1qfhA 212 2.79e+01 1qfhA b.1.18.10 21893 b.1.18.10 21894 1hh2P 344 2.79e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1pvtA 238 2.83e+01 c.74.1.1 -8444 1qavB 115 2.84e+01 1qauA b.36.1.1 24780 1cz3A 168 2.86e+01 1d1gA c.71.1.1 34891 1jv4A 162 2.87e+01 b.60.1.1 67343 1fg9C 245 2.87e+01 1jrhI b.1.2.1 22060 b.1.2.1 22061 1qubA 319 2.90e+01 1qubA g.18.1.1 44863 g.18.1.1 44864 g.18.1.1 44865 g.18.1.1 44866 g.18.1.1 44867 1dl5A 317 2.91e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1a3qA 285 2.93e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1i05A 180 2.95e+01 1mup b.60.1.1 27130 1gy9A 283 2.96e+01 b.82.2.5 70742 1fxzA 476 2.98e+01 b.82.1.2 65059 b.82.1.2 65060 1muhA 481 3.00e+01 c.55.3.4 79485 1jrkA 156 3.00e+01 d.113.1.1 71827 1pkhA 204 3.03e+01 b.85.4.1 -5053 1fo0A 116 3.08e+01 1tvdA b.1.1.1 20610 1s5lE 84 3.09e+01 2cavA 445 3.12e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1lc5A 364 3.13e+01 c.67.1.1 73827 1d1gA 168 3.21e+01 1d1gA c.71.1.1 34889 1itvA 195 3.21e+01 b.66.1.1 76791 1nfiA 301 3.23e+01 1a3qA b.1.18.1 21942 b.2.5.3 22455 1p35A 299 3.35e+01 1p35A b.28.1.1 23925 2iadB 205 3.36e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 2pleA 105 3.38e+01 1qadA d.93.1.1 40522 1k2eA 156 3.40e+01 d.113.1.1 72010 1nnsA 326 3.40e+01 c.88.1.1 85910 1jhsA 188 3.46e+01 d.107.1.1 84172 1vppV 102 3.46e+01 1vpfA g.17.1.1 44753 1dp0A 1023 3.46e+01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 2fnbA 95 3.46e+01 2fnbA b.1.2.1 21979 2pabA 127 3.49e+01 1etb1 b.3.4.1 22597 1eq6A 189 3.49e+01 1eq6A d.107.1.1 40796 1cd9B 215 3.49e+01 1cto b.1.2.1 22041 b.1.2.1 22042 1nfiC 301 3.51e+01 b.1.18.1 21943 b.2.5.3 22456 1f0cA 305 3.51e+01 1c8oA e.1.1.1 42676 1kyaA 499 3.53e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1s71A 316 3.53e+01 1sgvA 316 3.53e+01 b.122.1.1 -5120 unknown_sccs -10148 1rwhA 757 3.60e+01 a.102.3.2 -1340 b.24.1.1 -3300 b.30.5.2 -3508 1m5zA 91 3.66e+01 b.36.1.1 78676 1jopA 155 3.66e+01 b.82.2.7 84187 1iz6A 138 3.69e+01 b.34.5.2 76976 b.40.4.5 76977 1v5xA 203 3.75e+01 c.1.2.4 -5169 1vkdA 338 3.77e+01 1oi1A 221 3.80e+01 b.34.9.3 87037 b.34.9.3 87038 1bix 287 3.82e+01 1bix d.151.1.1 41781 1gm6A 175 3.88e+01 b.60.1.1 70272 1nezG 128 3.88e+01 b.1.1.1 85592 1r6lA 239 3.91e+01 d.14.1.4 -9057 d.101.1.1 -10747 1grj 158 3.93e+01 1grj a.2.1.1 15691 d.26.1.2 38433 1f3iA 481 4.00e+01 1b7eA