# List of top-scoring protein chains for T0459.t2k-w0.5 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.soe.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 2hztA 107 1.37e-16 1yyvA 131 8.76e-16 a.4.5.69 124254 1z7uA 112 9.06e-16 a.4.5.69 124672 2fswA 107 1.16e-15 a.4.5.69 134042 2f2eA 146 1.47e-14 a.4.5.69 132808 2p4wA 202 2.79e-05 a.4.5.64 139495 3bpvA 138 7.54e-04 1ub9A 100 7.67e-04 a.4.5.28 99159 3bpxA 148 7.78e-04 2pfbA 153 1.82e-03 2pexA 153 1.85e-03 1r22A 122 3.05e-03 a.4.5.5 104777 1i1gA 141 3.74e-03 a.4.5.32,d.58.4.2 65982,65983 2a61A 145 3.81e-03 a.4.5.28 126187 2fbhA 146 4.32e-03 a.4.5.28 133245 1r1tA 122 5.34e-03 a.4.5.5 104769 2ethA 154 5.92e-03 a.4.5.28 132358 1z91A 147 7.22e-03 a.4.5.28 124736 1sfxA 109 9.33e-03 a.4.5.50 105505 3bj6A 152 1.35e-02 3cjnA 162 1.35e-02 2jscA 118 1.38e-02 2d1hA 109 1.63e-02 a.4.5.50 131125 2hr3A 147 1.76e-02 a.4.5.28 136678 1ku9A 152 2.28e-02 a.4.5.36 77544 2oqgA 114 2.57e-02 2fbiA 142 2.66e-02 a.4.5.28 133246 2eshA 118 3.32e-02 a.4.5.61 132325 2gxgA 146 5.77e-02 3b73A 111 5.89e-02 1lj9A 144 6.47e-02 a.4.5.28 78035 2fbkA 181 9.91e-02 a.4.5.28 133247 1lnwA 147 1.03e-01 a.4.5.28 78104 2co5A 99 1.15e-01 2b0lA 102 1.15e-01 a.4.5.66 127641 2v7fA 150 1.27e-01 1r1uA 106 1.29e-01 a.4.5.5 104771 2p5vA 162 1.49e-01 1xmaA 145 1.56e-01 a.4.5.61 115477 3ctaA 230 1.57e-01 2e7xA 150 1.58e-01 2pmhA 150 1.58e-01 2yx4A 150 1.58e-01 2efpA 150 1.59e-01 2pn6A 150 1.69e-01 2e1cA 171 1.74e-01 3cdhA 155 1.86e-01 1j75A 67 1.99e-01 a.4.5.19 62673 2bv6A 142 2.98e-01 1s3jA 155 3.40e-01 a.4.5.28 98437 2cyyA 151 3.50e-01 a.4.5.32,d.58.4.2 131028,131029 2o0mA 345 3.67e-01 2h09A 155 3.76e-01 2cg4A 152 6.10e-01 a.4.5.32,d.58.4.2 130417,130418 3bddA 142 6.63e-01 1yg2A 179 7.51e-01 a.4.5.61 116681 1wj5A 120 7.97e-01 a.4.5.59 114692 1ucrA 78 8.41e-01 a.4.5.45 99188 2oz6A 207 1.00e+00 1i1sA 96 1.06e+00 1bjaA a.4.5.9 16124 1bjaA 95 1.12e+00 1bjaA a.4.5.9 16122 2e1nA 138 1.24e+00 1fztA 211 1.25e+00 1qhfA c.60.1.1 60158 2nyiA 195 1.26e+00 1uhnA 189 1.56e+00 a.39.1.5 99399 2nnnA 140 1.77e+00 2heoA 67 1.83e+00 2zfdA 226 1.88e+00 2gqqA 163 1.89e+00 1mzbA 136 2.07e+00 a.4.5.42 91497 1e2xA 243 2.33e+00 1e2xA a.4.5.6,a.78.1.1 16113,18443 1hw1A 239 2.36e+00 1e2xA a.4.5.6,a.78.1.1 16111,18441 1mkmA 249 2.80e+00 a.4.5.33,d.110.2.2 79242,79243 2qvoA 95 2.84e+00 2rjbA 455 3.58e+00 1zg3A 358 3.92e+00 1zgaA 357 3.93e+00 1zgjA 354 3.95e+00 1jzoA 216 4.09e+00 c.47.1.9,d.17.3.1 84267,84268 1jzdA 220 4.13e+00 c.47.1.9,d.17.3.1 84257,84258 3c7jA 237 4.21e+00 1eejA 216 4.34e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 3boqA 160 4.46e+00 1r7jA 95 4.48e+00 a.4.5.49 104836 2pg4A 95 4.52e+00 1jgsA 138 4.62e+00 a.4.5.28 66683 2rdpA 150 4.97e+00 2dbbA 151 5.28e+00 3broA 141 5.44e+00 2cfxA 144 5.59e+00 a.4.5.32,d.58.4.2 130395,130396 2e0zA 345 5.64e+00 2f3xA 157 5.84e+00 d.38.1.5 132901 1s6jA 87 6.13e+00 a.39.1.5 112042 1v2yA 105 6.40e+00 d.15.1.1 100275 2fa5A 162 6.64e+00 2ia0A 171 7.48e+00 2p8tA 200 7.61e+00 1pknA 530 8.12e+00 b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1f5tA 121 8.57e+00 1bi0 a.4.5.24,a.76.1.1 16203,18409 1s6iA 188 8.79e+00 a.39.1.5 105310 1bw6A 56 9.17e+00 1bw6A a.4.1.7 16052 2jtvA 65 9.53e+00 1r36A 140 9.64e+00 a.4.5.21 111675 2nnyA 171 9.65e+00 2hgcA 102 9.98e+00 1k78B 110 1.00e+01 a.4.5.21 68257 1o5lA 213 1.00e+01 b.82.3.2 92506 2qz8A 149 1.05e+01 2dkpA 128 1.06e+01 2b4xI 427 1.06e+01 1b1bA 140 1.08e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 2b4xL 427 1.14e+01 e.1.1.1 127867 1jvqI 432 1.14e+01 e.1.1.1 84232 1dzhI 432 1.14e+01 1ovaA e.1.1.1 42652 1dzgI 432 1.14e+01 1ovaA e.1.1.1 42656 1oyhI 432 1.14e+01 e.1.1.1 93727 2hijI 432 1.15e+01 2sttA 96 1.16e+01 1awcA a.4.5.21 16163 1tbxA 99 1.17e+01 a.4.5.48 106748 2gd4C 443 1.20e+01 2g50A 530 1.20e+01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1f3wA 530 1.20e+01 b.58.1.1,c.1.12.1,c.49.1.1 64934,64935,64936 1a49A 530 1.21e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1f3xA 530 1.21e+01 b.58.1.1,c.1.12.1,c.49.1.1 64958,64959,64960 2fu4A 83 1.23e+01 1md0A 141 1.23e+01 a.4.5.21 79000 1q74A 303 1.25e+01 c.134.1.1 96019 1u2wA 122 1.25e+01 a.4.5.5 119487 1gvjA 146 1.26e+01 a.4.5.21 90525 1t6t1 118 1.26e+01 3bjaA 139 1.27e+01 1q7tA 328 1.27e+01 c.134.1.1 96057 2nyxA 168 1.29e+01 2obpA 96 1.30e+01 2isyA 157 1.30e+01 a.4.5.24,a.76.1.1 137612,137613 1tw3A 360 1.30e+01 a.4.5.29,c.66.1.12 107373,107374 1y0uA 96 1.30e+01 a.4.5.5 116310 1zjhA 548 1.32e+01 3bjfA 518 1.32e+01 3bjtA 530 1.32e+01 1t5aA 567 1.33e+01 1pkmA 530 1.34e+01 b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1g8iA 190 1.37e+01 1rec a.39.1.5 60363 1mdmB 161 1.43e+01 a.4.5.21 79012 1xcvA 139 1.45e+01 a.4.5.24,a.76.1.1 121862,121863 2vbwA 150 1.51e+01 1xdpA 687 1.63e+01 a.7.15.1,d.322.1.2,d.136.1.4,d.136.1.4 121896,121897,121898,121899 1vqyA 116 1.64e+01 d.58.4.13 120418 2ra5A 247 1.64e+01 1t98A 287 1.77e+01 a.4.5.65,a.47.6.1 119196,119197 2omzB 105 1.80e+01 1q1hA 110 1.84e+01 a.4.5.41 95580 1ulyA 192 1.87e+01 a.4.5.58 113297 2omxB 108 1.88e+01 3gpdG 334 1.91e+01 1dssG c.2.1.3,d.81.1.1 30029,39944 2ivmA 150 1.98e+01 1g3yA 226 2.02e+01 a.4.5.24,a.76.1.1,b.34.1.2 65136,65137,65138 2h41A 95 2.10e+01 2jc7A 244 2.11e+01 2pq8A 278 2.11e+01 2givA 295 2.18e+01 d.108.1.1 135253 1g3tA 226 2.19e+01 a.4.5.24,a.76.1.1,b.34.1.2 65127,65128,65129 2dqlA 115 2.20e+01 1c0wA 225 2.21e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 2dtrA 226 2.21e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1xn7A 78 2.28e+01 a.4.5.62 115576 1fx7A 230 2.28e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2omwB 105 2.29e+01 2fnaA 357 2.29e+01 a.4.5.11,c.37.1.20 133809,133810 1zybA 232 2.30e+01 a.4.5.4,b.82.3.2 125815,125816 2qq9A 226 2.31e+01 2tdxA 226 2.33e+01 a.4.5.24,a.76.1.1 16201,18407 1fwzA 226 2.34e+01 a.4.5.24,a.76.1.1,b.34.1.2 60077,60078,60079 2qqbA 226 2.35e+01 2qqaA 226 2.36e+01 1p92A 226 2.39e+01 a.4.5.24,a.76.1.1,b.34.1.2 104085,104086,104087 2ev0A 142 2.50e+01 a.4.5.24,a.76.1.1 132413,132414 1on2A 142 2.56e+01 a.4.5.24,a.76.1.1 87103,87104 1a79A 171 2.58e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1in6A 334 2.58e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1duxC 94 2.60e+01 1awcA a.4.5.21 16170 2oczA 231 2.63e+01 2zkrp 196 2.64e+01 2cqzA 177 2.70e+01 1in4A 334 2.70e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1in7A 334 2.72e+01 1hqcA a.4.5.11,c.37.1.20 62603,62604 1j7kA 334 2.75e+01 1hqcA a.4.5.11,c.37.1.20 62695,62696 1in8A 334 2.75e+01 1hqcA a.4.5.11,c.37.1.20 62605,62606 1in5A 334 2.76e+01 1hqcA a.4.5.11,c.37.1.20 62599,62600 1s58A 554 2.82e+01 b.121.5.2 105262 2r4fA 441 2.86e+01 1dqaA 467 2.91e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1suhA 146 3.00e+01 b.1.6.1 22206 2pjpA 121 3.02e+01 1fu5A 111 3.12e+01 1qadA d.93.1.1 40505 1r9wA 145 3.19e+01 d.89.1.2 97264 1v4rA 102 3.23e+01 a.4.5.6 119835 2o72A 213 3.26e+01 2hhjA 267 3.29e+01 c.60.1.1 136497 2v79A 135 3.55e+01 1edwA 26 3.57e+01 j.35.1.1 46241 1oo3A 111 3.63e+01 d.93.1.1 87184 1hh2P 344 3.64e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 2ha1A 201 3.65e+01 1l2fA 369 3.75e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 91044,91045,91046,91047 2r5jA 423 3.90e+01 1wp9A 494 3.91e+01 c.37.1.19,c.37.1.19 121143,121144 1g2hA 61 3.91e+01 1g2hA a.4.1.12 60224 1zgdA 312 3.93e+01 1cg1A 431 4.13e+01 1adeA c.37.1.10 32223 1cg3A 431 4.16e+01 1adeA c.37.1.10 32219 1cg4A 431 4.24e+01 1adeA c.37.1.10 32228 1fliA 98 4.24e+01 1awcA a.4.5.21 16160 1qf5A 431 4.24e+01 1adeA c.37.1.10 32212 1kkbA 432 4.24e+01 c.37.1.10 72643 1yzbA 182 4.25e+01 2aukA 190 4.37e+01 2agaA 190 4.38e+01 2b5tI 432 4.52e+01 e.1.1.1 127905 1bc8C 93 4.57e+01 1awcA a.4.5.21 16168 1q1pA 212 4.70e+01 b.1.6.1,b.1.6.1 95597,95598 3cymA 440 4.70e+01 2dosA 176 4.73e+01 1ff5A 219 4.78e+01 1edhA b.1.6.1,b.1.6.1 22202,22203 1edhA 226 4.88e+01 1edhA b.1.6.1,b.1.6.1 22198,22199 2hl6A 260 5.01e+01 c.69.1.17 136561 1uwcA 261 5.01e+01 c.69.1.17 100101 2oolA 337 5.14e+01 1uswA 260 5.14e+01 c.69.1.17 99895 1mgqA 83 5.19e+01 b.38.1.1 79099 2o03A 131 5.31e+01 1hlvA 131 5.41e+01 a.4.1.7,a.4.1.7 65854,65855 1b9mA 265 5.45e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2ftcN 96 5.47e+01 3bg9A 718 5.50e+01 3bg3A 718 5.50e+01 1o7lA 262 5.50e+01 a.4.5.8,b.40.6.2,b.40.6.2 81147,81148,81149 2rkhA 180 5.54e+01 1o1yA 239 5.82e+01 c.23.16.1 86554 2vcyA 344 5.88e+01 1hbxG 157 5.94e+01 1awcA a.4.5.21 60934 2qdxA 257 5.94e+01 1i6xA 209 5.96e+01 a.4.5.4,b.82.3.2 83673,83674 1z68A 719 5.99e+01 1attA 429 6.17e+01 1ovaA e.1.1.1 42638 2nn4A 72 6.22e+01 1a8pA 258 6.43e+01 b.43.4.2,c.25.1.1 25654,31544 1jriA 85 6.55e+01 b.38.1.1 67121 1jbmA 86 6.57e+01 b.38.1.1 84143 1lojA 87 6.59e+01 b.38.1.1 84650 2cw6A 298 6.71e+01 1j9aA 184 6.87e+01 c.55.3.5 84135 1zynA 202 6.87e+01 c.47.1.2,c.47.1.2 125838,125839 2do7A 101 6.95e+01 2dluA 111 7.06e+01 1i5zA 209 7.07e+01 a.4.5.4,b.82.3.2 83669,83670 1hw5A 210 7.08e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1g6nA 210 7.09e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1pqnA 127 7.09e+01 c.47.1.8 95025 2ek5A 129 7.10e+01 2iugA 120 7.23e+01 1j6uA 469 7.30e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1o3sA 200 7.32e+01 a.4.5.4,b.82.3.2 86609,86610 2jfbA 164 7.35e+01 2pefA 373 7.50e+01 1zrzA 364 7.52e+01 2vh4A 381 7.56e+01 1zx4A 192 7.58e+01 2peeA 387 7.61e+01 1c7qA 445 7.64e+01 2pgi c.80.1.2 35307 2ntzA 192 7.66e+01 2pnaA 104 7.75e+01 d.93.1.1 40501 1o3tA 200 7.76e+01 a.4.5.4,b.82.3.2 86611,86612 1fmvA 761 7.77e+01 1lvk b.34.3.1,c.37.1.9 24580,32177 1vomA 762 7.78e+01 b.34.3.1,c.37.1.9 24577,32174 1mmaA 762 7.80e+01 b.34.3.1,c.37.1.9 24587,32184 2akaA 776 7.83e+01 1jx2A 776 7.83e+01 b.34.3.1,c.37.1.9 67402,67403 1d0yA 761 7.83e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1yv3A 762 7.83e+01 1w9iA 770 7.85e+01 1w9jA 770 7.85e+01 1w9kA 770 7.87e+01 1w9lA 770 7.87e+01 1bdgA 451 7.88e+01 c.55.1.3,c.55.1.3 33461,33462 2r2zA 93 7.91e+01