# List of top-scoring protein chains for T0288.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.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 2fneA 117 6.91e-11 1um7A 113 1.30e-10 b.36.1.1 99579 1rgrA 99 1.39e-10 b.36.1.1 104931 1kefA 93 1.65e-10 b.36.1.1 72369 1zokA 93 2.50e-10 1iu0A 91 2.60e-10 b.36.1.1 83707 2bygA 117 2.60e-10 1d5gA 96 2.86e-10 b.36.1.1 70080 1wfvA 103 2.98e-10 1gm1A 94 3.02e-10 b.36.1.1 70271 1vj6A 102 3.02e-10 1tp5A 119 3.68e-10 1whaA 105 4.22e-10 2fe5A 94 4.50e-10 1uewA 114 4.78e-10 b.36.1.1 99281 1be9A 119 4.88e-10 1pdr b.36.1.1 24774 2fcfA 103 5.49e-10 1qlcA 95 7.35e-10 1qauA b.36.1.1 24776 1pdr 99 8.25e-10 1pdr b.36.1.1 24771 1wf8A 107 1.18e-09 1uezA 101 1.28e-09 b.36.1.1 99286 1z87A 263 1.50e-09 1qavA 90 1.51e-09 1qauA b.36.1.1 24777 1uhpA 107 1.52e-09 b.36.1.1 99400 1z86A 87 1.56e-09 1ueqA 123 1.70e-09 b.36.1.1 99271 2pdzA 86 1.72e-09 1pdr b.36.1.1 24778 1uf1A 128 1.79e-09 b.36.1.1 99288 1gq5A 91 1.89e-09 b.36.1.1 76274 1gq4A 90 1.91e-09 b.36.1.1 70340 1i92A 91 2.07e-09 1pdr b.36.1.1 61990 1g9oA 91 2.08e-09 1pdr b.36.1.1 60400 1n7eA 97 2.53e-09 b.36.1.1 91691 1q7xA 108 2.96e-09 b.36.1.1 96059 1um1A 110 2.98e-09 b.36.1.1 99578 1x5qA 110 3.20e-09 1oziA 99 3.22e-09 b.36.1.1 93845 1x6dA 119 3.47e-09 1ihjA 98 5.31e-09 1pdr b.36.1.1 62382 1ujuA 111 6.08e-09 b.36.1.1 99469 1uepA 103 1.28e-08 b.36.1.1 99270 1wi2A 104 1.39e-08 1t2mA 101 1.40e-08 1xz9A 101 1.45e-08 2f0aA 98 1.87e-08 1l6oA 95 1.88e-08 b.36.1.1 84534 1qavB 115 2.86e-08 1qauA b.36.1.1 24780 1vb7A 94 2.90e-08 b.36.1.1 108474 1b8qA 127 2.93e-08 1qauA b.36.1.1 24781 1qauA 112 3.03e-08 1qauA b.36.1.1 24779 1mc7A 95 3.15e-08 b.36.1.1 91241 2csjA 117 3.52e-08 1x5nA 114 3.56e-08 1i16 130 4.10e-08 1i16 b.36.1.2 24787 1wg6A 127 4.17e-08 1q3oA 109 4.23e-08 b.36.1.1 95700 1v5lA 103 4.32e-08 b.36.1.1 108378 1va8A 113 4.47e-08 1wf7A 103 6.12e-08 1wh1A 124 6.25e-08 1kwaA 88 6.61e-08 1kwaA b.36.1.1 24772 1x8sA 102 6.87e-08 1ry4A 128 7.07e-08 b.36.1.1 98085 2cssA 121 7.16e-08 1rzxA 98 7.62e-08 b.36.1.1 98236 1x5rA 112 9.14e-08 1p1dA 196 1.02e-07 b.36.1.1,b.36.1.1 93896,93897 1wi4A 109 1.05e-07 1x45A 98 1.14e-07 1rgwA 85 1.22e-07 b.36.1.1 97455 1zubA 114 1.23e-07 1wjlA 90 1.30e-07 1u3bA 185 1.31e-07 1u37A 89 1.34e-07 1n7tA 103 1.49e-07 b.36.1.1 80275 1mfgA 95 1.53e-07 b.36.1.1 79043 1wfgA 131 1.62e-07 1nf3C 128 1.69e-07 b.36.1.1 85596 1uitA 117 1.77e-07 b.36.1.1 99433 2cs5A 119 1.86e-07 1v62A 117 1.90e-07 b.36.1.1 108390 1ujdA 117 2.23e-07 b.36.1.1 99454 1p1eA 101 2.23e-07 b.36.1.1 93898 1v5qA 122 2.27e-07 b.36.1.1 108383 1ufxA 103 4.38e-07 b.36.1.1 99359 1w9eA 166 4.75e-07 1ujvA 96 6.55e-07 b.36.1.1 99470 1whdA 100 1.67e-06 2f5yA 91 2.28e-06 1u39A 80 2.37e-06 1y7nA 90 2.42e-06 1m5zA 91 2.70e-06 b.36.1.1 78676 1v6bA 118 4.10e-06 b.36.1.1 108394 1wifA 126 8.67e-06 1r6jA 82 1.35e-05 b.36.1.1 97151 1obxA 79 1.78e-05 b.36.1.1 86783 1fc6A 388 3.09e-05 1fc6A b.36.1.3,c.14.1.2 64738,64739 1fc9A 388 4.00e-05 1fc6A b.36.1.3,c.14.1.2 64742,64743 1vaeA 111 9.72e-05 b.36.1.1 108466 1lcyA 325 3.19e-03 b.36.1.4,b.47.1.1 73834,73835 1ky9A 448 4.22e-03 b.36.1.4,b.47.1.1 73198,73199 1sotA 320 8.00e-03 b.36.1.4,b.47.1.1 105852,105853 1sozA 314 8.00e-03 b.36.1.4,b.47.1.1 105859,105860 1te0A 318 8.00e-03 1y8tA 324 6.64e-01 1nvjA 140 5.56e+00 d.41.5.1 86243 1fm0E 150 5.62e+00 1fmaE d.41.5.1 38629 1zn8A 180 8.28e+00 1fn4B 218 8.65e+00 b.1.1.1,b.1.1.2 59886,59887 2bh4X 134 9.03e+00 2bgvX 134 9.51e+00 1ao0A 459 1.23e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1gph1 465 1.24e+01 1ecfB 1m54A 363 1.36e+01 c.79.1.1 74463 1db3A 372 1.46e+01 1db3A c.2.1.2 29813 1jbqA 435 1.48e+01 1oasA c.79.1.1 62850 1x6vA 630 1.72e+01 1lnzA 342 1.83e+01 b.117.1.1,c.37.1.8 78112,78113 1gljO 501 1.85e+01 1glcG c.55.1.4,c.55.1.4 33525,33526 1sw2A 275 1.86e+01 c.94.1.1 106064 1sw5A 275 1.86e+01 c.94.1.1 106069 1glaG 501 1.87e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1bu6O 501 1.88e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1oroA 213 2.01e+01 1opr c.61.1.1 34093 1rlw 126 2.33e+01 1rlw b.7.1.1 23177 1yq8A 191 2.34e+01 1repC 251 2.38e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1jalA 363 2.42e+01 c.37.1.8,d.15.10.2 84138,84139 1mhsA 920 2.45e+01 i.18.1.1 79130 1bci 138 2.50e+01 1rlw b.7.1.1 23180 1oxxK 353 2.54e+01 b.40.6.3,c.37.1.12 93715,93716 1oxsC 353 2.55e+01 b.40.6.3,c.37.1.12 87519,87520 1kk1A 410 2.69e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1dms 781 2.76e+01 1dmr b.52.2.2,c.81.1.1 26906,35314 1mzvA 235 3.21e+01 c.61.1.1 91502 1uc2A 481 3.30e+01 d.261.1.1 99161 1bx4A 345 3.36e+01 1bx4A c.72.1.1 34935 1uuhA 159 3.59e+01 d.169.1.4 100008 1qgc4 438 3.64e+01 1igtB 2a6tA 271 3.65e+01 1bnlA 178 3.65e+01 1koe d.169.1.5 42444 155c 135 3.69e+01 1ycc a.3.1.1 15900 1yb2A 275 3.71e+01 1hgu 191 3.80e+01 1huw a.26.1.1 16837 1csp 67 3.80e+01 1mjc b.40.4.5 25321 1koe 172 3.82e+01 1koe d.169.1.5 42448 1dy1A 188 3.87e+01 1koe d.169.1.5 42450 1dl6A 58 4.16e+01 1dl6A g.41.3.1 45207 1rlyA 60 4.16e+01 g.41.3.1 104988 1t6t1 118 4.18e+01 1vorL 132 4.18e+01 1e18A 823 4.30e+01 1dmr b.52.2.2,c.81.1.1 26907,35315 1e61A 823 4.32e+01 1dmr b.52.2.2,c.81.1.1 26908,35316 1dmr 823 4.32e+01 1dmr b.52.2.2,c.81.1.1 26904,35312 4dmr 823 4.33e+01 1dmr b.52.2.2,c.81.1.1 26905,35313 1p99A 295 4.38e+01 c.94.1.1 94384 1mjc 69 4.39e+01 1mjc b.40.4.5 25319 1cot 129 4.41e+01 1ycc a.3.1.1 15899 1yg9A 330 4.42e+01 1qb7A 236 4.65e+01 1qb7A c.61.1.1 34087 1nkwI 134 4.68e+01 i.1.1.2 80594 1wveC 80 4.71e+01 1mkmA 249 4.76e+01 a.4.5.33,d.110.2.2 79242,79243 2d4pA 141 4.92e+01 1zz1A 369 5.23e+01 2ahsA 295 5.33e+01 1lvoA 302 5.43e+01 b.47.1.4 74284 1yj5C 143 5.46e+01 2ampA 304 5.47e+01 1dxrH 258 5.48e+01 6prcH b.41.1.1,f.23.10.1 25456,43433 1prcH 259 5.49e+01 6prcH b.41.1.1,f.23.10.1 25460,43445 1wscA 230 5.68e+01 1r13A 148 5.74e+01 d.169.1.1,h.1.1.1 96782,96783 1tis 286 5.88e+01 1bkpA d.117.1.1 41040 1usyA 275 5.90e+01 1kk3A 410 6.07e+01 b.43.3.1,b.44.1.1,c.37.1.8 72640,72641,72642 1yjmA 110 6.33e+01 1n2tA 386 6.48e+01 c.67.1.3 79858 1figH 216 6.54e+01 1igtB b.1.1.1,b.1.1.2 19923,21017 1kjyB 36 6.70e+01 1hkvA 453 6.74e+01 b.49.2.3,c.1.6.1 83559,83560 1t3qB 788 6.86e+01 d.41.1.1,d.133.1.1 106369,106370 2bwfA 77 6.87e+01 1usyC 275 7.47e+01 1e6vC 258 7.93e+01 1mroC d.58.31.1 39439 1ot2A 686 7.93e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87396,87397,87398,87399 2bhtA 303 8.02e+01 1ot1A 686 8.03e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1lluA 342 8.17e+01 b.35.1.2,c.2.1.1 91064,91065 1hvyA 288 8.21e+01 1bkpA d.117.1.1 41049 2brfA 110 8.22e+01 2fbwD 103 8.23e+01 1hzwA 290 8.24e+01 1bkpA d.117.1.1 61464 1k2pA 263 8.39e+01 d.144.1.7 72012 1x4pA 66 8.41e+01 1s9pA 227 8.41e+01 a.123.1.1 105384 1ypvA 313 8.49e+01 1kv6A 230 8.50e+01 a.123.1.1 77546 3hhrA 190 8.53e+01 1huw a.26.1.1 16835 1hwgA 191 8.57e+01 1huw a.26.1.1 16834 1ju6A 313 8.61e+01 d.117.1.1 63289 1huw 191 8.64e+01 1huw a.26.1.1 16831 2bh8A 101 8.99e+01