# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1nxmA 197 1.18e-01 b.82.1.1 86385 1tqzA 133 6.74e-01 3nul 130 1.37e+00 3nul d.110.1.1 40891 1yprA 125 1.38e+00 3nul d.110.1.1 40888 1z90A 469 1.48e+00 1a0k 131 1.76e+00 3nul d.110.1.1 40892 1fxzA 476 2.71e+00 b.82.1.2,b.82.1.2 65059,65060 1xrtA 467 4.53e+00 1ojqA 212 5.17e+00 d.166.1.1 93146 1lxdA 100 5.57e+00 1lfdA d.15.1.5 37624 2oneA 436 5.79e+00 4enl c.1.11.1,d.54.1.1 29203,38847 1cqa 133 5.80e+00 3nul d.110.1.1 40890 2al2A 436 5.85e+00 1prq 125 5.94e+00 3nul d.110.1.1 40883 2al1A 436 6.04e+00 1acf 125 7.04e+00 3nul d.110.1.1 40882 1juhA 350 7.17e+00 b.82.1.5 71884 2ffsA 157 7.70e+00 1llnA 262 7.71e+00 d.165.1.1 84625 1oneA 436 7.72e+00 4enl c.1.11.1,d.54.1.1 29200,38844 4enl 436 8.19e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1eur 365 9.06e+00 1eut b.68.1.1 27607 1m98A 317 9.34e+00 a.175.1.1,d.17.4.6 78866,78867 1bqnA 558 9.58e+00 1rthA c.55.3.1,e.8.1.2 33599,43064 1tq5A 242 9.65e+00 1ue1A 164 9.90e+00 b.40.4.3 99243 1icfI 65 1.06e+01 1icfI g.28.1.1 44958 1apa 266 1.07e+01 1qi7A d.165.1.1 42205 1fvuB 125 1.14e+01 1ixxB d.169.1.1 42346 1dynA 125 1.17e+01 1dynA b.55.1.1 26955 1u9aA 160 1.21e+01 1u9aA d.20.1.1 38333 1vqoQ 96 1.24e+01 1jj2P 95 1.24e+01 1ffkN b.34.5.1 63101 1s72Q 96 1.24e+01 b.34.5.1 105336 1u2cA 246 1.25e+01 b.1.6.2,d.272.1.1 107610,107611 2fuvA 549 1.26e+01 2cr9A 139 1.29e+01 2pia 321 1.33e+01 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1dmzA 158 1.34e+01 1qu5A b.26.1.2 23921 1cv8 174 1.38e+01 1cv8 d.3.1.1 37089 1wwrA 171 1.38e+01 1xfsA 178 1.43e+01 d.129.3.5 109589 2bepA 159 1.47e+01 1bqnB 430 1.51e+01 1rthA e.8.1.2 43065 2grrA 161 1.52e+01 2rgf 97 1.53e+01 1lfdA d.15.1.5 37627 1h1iD 350 1.55e+01 b.82.1.5 76472 1h1iB 350 1.63e+01 b.82.1.5 76470 2dynA 122 1.67e+01 1dynA b.55.1.1 26957 1h1iC 350 1.71e+01 b.82.1.5 76471 1bh5A 183 1.74e+01 1qipA d.32.1.1 38476 1qipA 183 1.74e+01 1qipA d.32.1.1 38470 1a3s 160 1.81e+01 1u9aA d.20.1.1 38335 1hcxA 127 1.81e+01 b.109.1.1 65800 1h8gA 95 1.88e+01 b.109.1.1 65735 1c1bB 440 1.91e+01 1rthA e.8.1.2 43077 1fa8A 135 1.91e+01 1qipA d.32.1.1 38486 2awaA 390 2.03e+01 1fkoB 440 2.05e+01 1rthA e.8.1.2 43095 1df7A 159 2.06e+01 3dfr c.71.1.1 34885 1f9zA 135 2.07e+01 1qipA d.32.1.1 38484 1zn6A 227 2.08e+01 1qcxA 359 2.08e+01 1qcxA b.80.1.2 28028 1rpmA 278 2.10e+01 2shpA c.45.1.2 32679 1woqA 267 2.12e+01 c.55.1.10,c.55.1.10 109462,109463 1yfuA 174 2.18e+01 1q8bA 105 2.21e+01 d.58.4.6 96201 1ffkN 95 2.27e+01 1ffkN b.34.5.1 24606 1eetB 427 2.34e+01 1rthA e.8.1.2 43079 1b7aA 186 2.34e+01 1a44 b.17.1.1 23705 2frnA 278 2.36e+01 2cn3A 737 2.53e+01 1a44 185 2.53e+01 1a44 b.17.1.1 23704 1khdA 345 2.59e+01 a.46.2.1,c.27.1.1 77400,77401 1vrtA 560 2.59e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1s4bP 674 2.61e+01 d.92.1.5 105252 1dx5I 118 2.62e+01 1dx5I g.3.11.1,g.3.11.1,g.3.11.1 44302,44303,44304 2as0A 396 2.74e+01 1yh6A 179 2.77e+01 1tzfA 259 2.78e+01 c.68.1.13 107476 1y71A 130 2.86e+01 1khiA 176 2.97e+01 b.34.5.2,b.40.4.5 77408,77409 1ps2 60 3.00e+01 2pspA g.16.1.1 44746 1j9jA 247 3.01e+01 c.106.1.1 62758 1j9lA 247 3.05e+01 c.106.1.1 62762 1baoA 110 3.09e+01 1b20A d.1.1.2 36187 1bngA 110 3.14e+01 1b20A d.1.1.2 36184 1j1qA 261 3.14e+01 d.165.1.1 90768 1v0aA 178 3.14e+01 1eo1A 124 3.18e+01 1eo1A c.55.5.1 33739 1a2pA 110 3.22e+01 1b20A d.1.1.2 36140 1banA 110 3.23e+01 1b20A d.1.1.2 36197 1gikA 261 3.26e+01 d.165.1.1 90513 1raxA 115 3.32e+01 1lfdA d.15.1.5 37626 2bryA 497 3.32e+01 1pot 325 3.34e+01 1pot c.94.1.1 35807 1mugA 168 3.35e+01 1mugA c.18.1.2 31030 1hmpA 217 3.39e+01 1qk3A c.61.1.1 34075 1eut 605 3.44e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21891,23712,27609 1vplA 256 3.44e+01 1ijtA 128 3.45e+01 1bfg b.42.1.1 62510 1dq3A 454 3.46e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1zc3B 113 3.48e+01 1euu 605 3.56e+01 1eut b.1.18.2,b.18.1.1,b.68.1.1 21892,23713,27610 1jf0A 195 3.58e+01 1ej3A a.39.1.5 62926 1kf6A 602 3.59e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1lvoA 302 3.69e+01 b.47.1.4 74284 1lcyA 325 3.73e+01 b.36.1.4,b.47.1.1 73834,73835 1fk9A 543 3.74e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1xtoA 311 3.76e+01 1ywsA 82 3.83e+01 1rthA 560 3.86e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 2ampA 304 3.91e+01 1b2sA 110 4.08e+01 1b20A d.1.1.2 36213 1b3sA 110 4.08e+01 1b20A d.1.1.2 36229 1kyqA 274 4.09e+01 c.2.1.11,e.37.1.1 73281,73282 1ts9A 102 4.11e+01 2f5tX 233 4.12e+01 1q8fA 313 4.13e+01 c.70.1.1 96203 2apsA 162 4.22e+01 1yaiA b.1.8.1 22298 1wcqA 601 4.23e+01 1lfdA 87 4.25e+01 1lfdA d.15.1.5 37622 1b2zA 110 4.26e+01 1b20A d.1.1.2 36216 1w8oA 601 4.28e+01 2d93A 134 4.28e+01 1ucyE 109 4.34e+01 1ucyE 1z7gA 217 4.37e+01 1yhfA 115 4.41e+01 1dloA 556 4.41e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 1mh0A 287 4.42e+01 b.47.1.2 79110 1cjtA 217 4.52e+01 1azsA d.58.29.1 39419 1zmyA 142 4.52e+01 1prr 173 4.54e+01 1prs b.11.1.1,b.11.1.1 23623,23624 1brhA 110 4.62e+01 1b20A d.1.1.2 36151 1brnL 110 4.63e+01 1b20A d.1.1.2 36143 2prf 125 4.66e+01 3nul d.110.1.1 40887 1sqjA 789 4.68e+01 b.69.13.1,b.69.13.1 105918,105919 1qndA 123 4.73e+01 1qndA d.106.1.1 40794 1jvsA 400 4.74e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1gvmA 136 4.76e+01 b.109.1.1 70612 1npsA 88 4.84e+01 1prs b.11.1.1 23622 1hniB 427 4.86e+01 1rthA e.8.1.2 43045 2biwA 490 4.87e+01 1h0hB 214 4.88e+01 d.58.1.5 76437 1csyA 112 4.89e+01 1lckA d.93.1.1 40519 1bnr 110 4.91e+01 1b20A d.1.1.2 36206 1fjgE 162 4.92e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 2cy2A 174 5.03e+01 2fymA 431 5.04e+01 1nziA 159 5.09e+01 b.23.1.1,g.3.11.1 86449,86450 1hmvB 440 5.10e+01 1rthA e.8.1.2 43047 1azsA 220 5.24e+01 1azsA d.58.29.1 39416 2gjdA 157 5.25e+01 1vmeA 410 5.27e+01 c.23.5.1,d.157.1.3 108893,108894 1b35A 260 5.34e+01 1b35A b.121.4.1 23333 1fkoA 543 5.38e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 1syxB 86 5.42e+01 2gupA 292 5.45e+01 1s6lA 212 5.46e+01 1upqA 123 5.46e+01 1j5eE 161 5.60e+01 d.14.1.1,d.50.1.2 71547,71548 1ap8 213 5.67e+01 1ap8 d.86.1.1 40151 1i3zA 103 5.71e+01 d.93.1.1 83667 1culA 217 5.82e+01 1azsA d.58.29.1 39417 1gyfA 62 5.92e+01 1gyfA d.76.1.1 39749 1y4hA 188 5.94e+01 1a62 130 6.03e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1zq4A 693 6.06e+01 1mxgA 435 6.11e+01 b.71.1.1,c.1.8.1 85193,85194 2b7yA 182 6.16e+01 1ug1A 92 6.16e+01 b.34.2.1 99360 8kme2 259 6.18e+01 1ucyE 1yopA 83 6.25e+01 1rypH 205 6.29e+01 d.153.1.4 41876 1cojA 212 6.29e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1i1iP 681 6.34e+01 1i1iP d.92.1.5 40297 2adgB 222 6.42e+01 2ftwA 521 6.51e+01 1d6aB 262 6.51e+01 1qi7A d.165.1.1 42198 1qciA 262 6.52e+01 1qi7A d.165.1.1 42201 1o5uA 101 6.57e+01 b.82.1.8 92518 2phlA 397 6.58e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1f6fB 210 6.69e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1ark 60 6.75e+01 1bb9 b.34.2.1 24473 1yliA 153 6.77e+01 1mvfD 82 6.77e+01 b.129.1.1 85143 1k5hA 398 6.77e+01 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1qv1A 195 6.78e+01 a.39.1.5 96347 2cf8H 257 6.79e+01 1q8iA 783 6.81e+01 c.55.3.5,e.8.1.1 96208,96209 1oqkA 97 6.81e+01 b.137.1.1 93419 1j58A 385 6.87e+01 b.82.1.2 71531 1jf2A 195 7.04e+01 1ej3A a.39.1.5 62930 1vzqH 250 7.05e+01 1iw7C 1119 7.05e+01 e.29.1.1 71474 1hniA 558 7.05e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 1olzA 663 7.07e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 1j9aA 184 7.10e+01 c.55.3.5 84135 1xygD 359 7.15e+01 1el4A 195 7.25e+01 1ej3A a.39.1.5 59453 2cz1A 206 7.28e+01 1ewqA 765 7.30e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1glcG 501 7.32e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1zo2A 129 7.35e+01 1cyx 205 7.36e+01 1cyx b.6.1.2 23023 1fnmA 691 7.37e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 2bf6A 449 7.37e+01 2fa8A 105 7.41e+01 1m1fA 110 7.41e+01 b.34.6.2 78401 1p7gA 222 7.49e+01 a.2.11.1,d.44.1.1 94223,94224 1ty0A 211 7.50e+01 b.40.2.2,d.15.6.1 107440,107441 1b21A 110 7.58e+01 1b20A d.1.1.2 36219 1ctt 294 7.63e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1rnbA 110 7.64e+01 1b20A d.1.1.2 36196 1eysH 259 7.65e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1b20A 110 7.71e+01 1b20A d.1.1.2 36207 1dgrN 79 7.74e+01 1caxB 1dgrV 79 7.74e+01 1caxB b.82.1.2 28099 1p5zB 263 7.77e+01 c.37.1.1 87815 1cyw 205 7.77e+01 1cyx b.6.1.2 23024 1ahtH 259 7.91e+01 5ptp 2c4bA 143 7.94e+01 1vk0A 206 7.99e+01 c.55.3.5 100839 1f89A 291 8.15e+01 d.160.1.1 64988 1lckA 175 8.20e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 1h8dH 260 8.20e+01 5ptp 1iuaA 83 8.21e+01 g.35.1.1 71438 1ydwA 362 8.23e+01 1vr1H 261 8.25e+01 5ptp 1e9iA 431 8.31e+01 c.1.11.1,d.54.1.1 64818,64819 1pxvA 183 8.37e+01 d.3.1.1 95301 1c5lH 259 8.39e+01 5ptp 1dttA 560 8.45e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1dm0A 287 8.47e+01 1dm0A d.165.1.2 42227 1jtdB 273 8.48e+01 b.69.5.2 67265 1dloB 427 8.72e+01 1rthA e.8.1.2 43041 1t7vA 278 8.76e+01 1jmsA 381 8.81e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1wba 175 8.82e+01 1wba b.42.4.1 25591 2avtA 378 8.86e+01 1ri6A 343 8.89e+01 b.69.11.1 97503 1vkdA 338 8.90e+01 b.67.2.4 108644 1qz8A 113 8.95e+01 b.140.1.1 96619