# 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 1xngA 268 3.35e-02 1dq3A 454 2.25e-01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1eylA 186 8.44e-01 1wba b.42.4.1 25593 1d2eA 397 1.09e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1l1jA 239 1.15e+00 b.47.1.1 84516 1kk1A 410 1.34e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1han 297 1.48e+00 1han d.32.1.3,d.32.1.3 38506,38507 1lkdA 297 1.51e+00 d.32.1.3,d.32.1.3 78059,78060 1zn8A 180 2.42e+00 1z0sA 278 2.50e+00 1suwA 249 2.59e+00 e.52.1.1 106027 1yhfA 115 2.93e+00 2asi 360 3.26e+00 2rmpA b.50.1.2 26824 1llwA 1520 3.38e+00 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1rzfL 213 3.49e+00 b.1.1.1,b.1.1.2 98152,98153 1nezG 128 3.51e+00 b.1.1.1 85592 1lgtA 297 3.60e+00 d.32.1.3,d.32.1.3 77956,77957 1e3aB 560 3.80e+00 1ajqB 1zvnA 99 4.51e+00 1gnhA 206 4.68e+00 1sacA b.29.1.5 24252 1b09A 206 4.81e+00 1sacA b.29.1.5 24247 1bqhG 129 4.87e+00 1cd8 b.1.1.1 19715 1xzoA 174 5.39e+00 2bynA 227 6.89e+00 1efuA 385 7.11e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1ofdA 1520 7.53e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2bcjB 340 7.79e+00 1gm7B 557 7.82e+00 1gk9B 557 7.90e+00 1gkfB 557 7.97e+00 1gpmA 525 8.15e+00 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ajqB 557 8.50e+00 1ajqB 1hq3D 103 9.00e+00 1aoiB a.22.1.1 16464 1tzyD 103 9.00e+00 a.22.1.1 107533 1cgt 684 9.50e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21815,22484,27722,28709 1gm9B 557 9.65e+00 1aoiB 87 9.92e+00 1aoiB a.22.1.1 16470 1aoiF 87 1.06e+01 1aoiB a.22.1.1 16471 1gotB 340 1.07e+01 1tbgA b.69.4.1 27648 1ifrA 121 1.17e+01 b.1.16.1 71203 1suh 146 1.18e+01 1edhA b.1.6.1 22206 1kx5B 102 1.19e+01 a.22.1.1 77594 1cb8A 678 1.19e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1gg4A 452 1.21e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1lvwA 295 1.23e+01 c.68.1.6 84723 1s0uA 408 1.25e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1tnrA 144 1.27e+01 2tnfA b.22.1.1 23867 1riqA 465 1.31e+01 a.203.1.1,d.104.1.1 97516,97517 1w2tA 432 1.32e+01 1qmeA 702 1.33e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1id3B 102 1.37e+01 a.22.1.1 66113 1air 353 1.49e+01 1air b.80.1.1 28018 2pec 353 1.49e+01 1air b.80.1.1 28019 3ait 74 1.52e+01 1hoe b.5.1.1 22835 1jmcA 246 1.52e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1olrA 224 1.53e+01 b.29.1.11 93330 1tlyA 278 1.57e+01 f.4.6.1 107143 1f89A 291 1.57e+01 d.160.1.1 64988 2rspB 124 1.59e+01 2rspB b.50.1.1 26772 1pnkB 557 1.68e+01 1ajqB 1bhgA 613 1.68e+01 1bhgA b.1.4.1,b.18.1.5,c.1.8.3 22161,23766,28889 2a2pA 129 1.73e+01 1tbgA 340 1.75e+01 1tbgA b.69.4.1 27649 1b3mA 389 1.77e+01 1b3mA 1efcA 393 1.79e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1gt1A 159 1.86e+01 b.60.1.1 90515 1hm2A 700 1.87e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1eujA 166 1.89e+01 1eujA b.40.4.4 25316 1xl3C 92 1.94e+01 1yfsA 465 1.94e+01 1ih8A 271 1.97e+01 2nsyA c.26.2.1 62377 2cokA 113 2.02e+01 2acaA 189 2.03e+01 1h6yA 170 2.08e+01 b.18.1.7 70904 1xe1A 116 2.10e+01 b.43.3.1 109571 1yu2A 381 2.14e+01 1yu1A 381 2.16e+01 1i8nA 126 2.16e+01 1i8nA g.10.1.2 61976 1iloA 77 2.16e+01 c.47.1.1 66205 1yu3A 381 2.16e+01 1yu0A 381 2.19e+01 1p5dX 463 2.22e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1yu4A 381 2.23e+01 2rmpA 361 2.23e+01 2rmpA b.50.1.2 26825 1r8nA 185 2.23e+01 b.42.4.1 104851 2d13A 227 2.23e+01 1goh 639 2.35e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1f3lA 321 2.40e+01 1g6q2 c.66.1.6 59630 1el5A 389 2.42e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1ojqA 212 2.53e+01 d.166.1.1 93146 1r6vA 671 2.53e+01 1jkfA 533 2.55e+01 c.2.1.3,d.81.1.3 71700,71701 1f6fB 210 2.55e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 1liuA 528 2.55e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 1hn2A 159 2.57e+01 b.60.1.1 65890 1obpA 159 2.66e+01 1obpA b.60.1.1 27092 1a65A 504 2.67e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1zeqX 84 2.71e+01 1p1jA 533 2.84e+01 c.2.1.3,d.81.1.3 87687,87688 1l9fA 389 2.84e+01 c.3.1.2,d.16.1.3 73716,73717 1sz6B 263 2.85e+01 1hfuA 503 2.94e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1wckA 220 3.00e+01 1a6wL 109 3.04e+01 1mfa b.1.1.1 20252 1s6lA 212 3.07e+01 1ru8A 232 3.11e+01 c.26.2.1 97849 1a6vL 110 3.13e+01 1mfa b.1.1.1 20256 2b3nA 159 3.36e+01 1tul 108 3.36e+01 1tul b.85.5.1 28373 1m4vA 204 3.42e+01 b.40.2.2,d.15.6.1 74459,74460 2ait 74 3.44e+01 1hoe b.5.1.1 22837 1u2fA 90 3.46e+01 1u2fA d.58.7.1 39168 1pmzA 86 3.48e+01 a.39.1.10 104195 1jkiA 533 3.49e+01 c.2.1.3,d.81.1.3 71704,71705 1yfqA 342 3.51e+01 1y7mA 164 3.58e+01 2def 147 3.60e+01 1bs4A d.167.1.1 42305 1oaqL 120 3.63e+01 b.1.1.1 92708 1cto 109 3.65e+01 1cto b.1.2.1 22054 2ms2A 129 3.65e+01 1msc d.85.1.1 40049 1e79D 482 3.71e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1dyoA 160 3.76e+01 1dyoA b.18.1.7 23771 1aq3A 129 3.77e+01 1msc d.85.1.1 40079 1hgxA 183 3.88e+01 1tc1A c.61.1.1 34027 1gof 639 3.89e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1yer 228 3.90e+01 1yer d.122.1.1 41101 1qcsA 211 3.98e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1yg9A 330 4.01e+01 1vrmA 325 4.02e+01 1zkkA 167 4.05e+01 2fimA 276 4.28e+01 1wdcB 156 4.35e+01 1wdcB a.39.1.5 17302 1fs0E 138 4.36e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1pxfA 111 4.48e+01 b.40.4.4 88341 2gpzA 111 4.49e+01 1xnkA 196 4.49e+01 1fl0A 171 4.55e+01 1eujA b.40.4.4 25315 1k2yX 463 4.56e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1qwdA 177 4.66e+01 b.60.1.1 96471 1xcbA 211 4.72e+01 a.4.5.38,c.2.1.12 109552,109553 1h9sA 140 4.73e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1m2xA 223 4.75e+01 d.157.1.1 84764 1zljA 78 4.89e+01 1ybiA 288 4.95e+01 1i9bA 217 5.05e+01 1i9bA b.96.1.1 62084 1fvuB 125 5.12e+01 1ixxB d.169.1.1 42346 1oa2A 218 5.21e+01 b.29.1.11 86721 2aotA 292 5.30e+01 1gpwB 201 5.32e+01 c.23.16.1 65461 1a6uL 108 5.33e+01 1mfa b.1.1.1 20254 2ck3D 482 5.38e+01 1yhpA 212 5.40e+01 1am1 213 5.47e+01 1yer d.122.1.1 41095 1amw 214 5.47e+01 1yer d.122.1.1 41093 1j83A 180 5.50e+01 b.18.1.12 66430 1ah6 220 5.50e+01 1yer d.122.1.1 41094 2brcA 214 5.52e+01 1eu1A 780 5.52e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1nukA 183 5.53e+01 1nukA b.18.1.4 23721 1jqeA 292 5.64e+01 c.66.1.19 71789 1sb2A 133 5.70e+01 1onxA 390 5.73e+01 b.92.1.7,c.1.9.13 87176,87177 1zp7A 206 5.73e+01 1cdb 105 5.76e+01 1qa9A b.1.1.1 19744 1aorA 605 5.78e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1pguA 615 5.80e+01 b.69.4.1,b.69.4.1 88069,88070 1kz8A 337 5.87e+01 e.7.1.1 77633 1cojA 212 5.87e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2nsyA 271 5.88e+01 2nsyA c.26.2.1 31612 1nsyA 271 5.89e+01 2nsyA c.26.2.1 31614 1zkiA 133 5.89e+01 1hnf 182 5.91e+01 1qa9A b.1.1.1,b.1.1.3 19741,21680 1kqpA 271 6.03e+01 c.26.2.1 72883 1b9mA 265 6.03e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1kk8B 139 6.07e+01 a.39.1.5 77430 1h8vA 218 6.13e+01 2nlrA b.29.1.11 60795 1h8eD 482 6.14e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1rznA 205 6.16e+01 1c5cH 215 6.16e+01 1igtB b.1.1.1,b.1.1.2 20475,21439 1lrwA 600 6.16e+01 b.70.1.1 91111 1g0uL 241 6.17e+01 d.153.1.4 41894 1o88A 353 6.26e+01 b.80.1.1 81178 1rsy 152 6.27e+01 1rsy b.7.1.2 23192 2cyeA 133 6.30e+01 1v70A 105 6.33e+01 1uowA 159 6.35e+01 b.7.1.2 107975 2pdd 43 6.35e+01 1ebdC a.9.1.1 16358 1ebdC 41 6.36e+01 1ebdC a.9.1.1 16355 1psuA 140 6.37e+01 d.38.1.5 88285 2asuB 234 6.38e+01 1wh0A 134 6.39e+01 1pne 140 6.49e+01 1pne d.110.1.1 40866 1qa9A 102 6.53e+01 1qa9A b.1.1.1 19742 2ew2A 316 6.59e+01 2fvgA 340 6.61e+01 1y6hA 177 6.63e+01 2fs2A 151 6.67e+01 1fxzA 476 6.71e+01 b.82.1.2,b.82.1.2 65059,65060 1v0eA 666 6.78e+01 1uypA 432 6.85e+01 b.29.1.19,b.67.2.3 100176,100177 1eft 405 6.89e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1u24A 337 6.92e+01 1lktA 104 6.93e+01 1lktA b.90.1.1 28398 1uylA 236 7.04e+01 d.122.1.1 108147 1byqA 228 7.19e+01 1yer d.122.1.1 41100 1tie 172 7.27e+01 1wba b.42.4.1 25592 1tmxA 293 7.28e+01 1tif 78 7.29e+01 1tif d.15.8.1 37836 1wj2A 78 7.31e+01 1scmB 145 7.46e+01 1wdcB a.39.1.5 17304 1nqeA 594 7.51e+01 f.4.3.3 86027 1h1iB 350 7.57e+01 b.82.1.5 76470 1hpgA 187 7.60e+01 1qq4A b.47.1.1 25813 1wy5A 317 7.61e+01 1h1aA 191 7.69e+01 b.29.1.11 83450 1w85I 49 7.85e+01 1n4xH 120 7.89e+01 b.1.1.1 85324 2sga 181 7.90e+01 1qq4A b.47.1.1 25808 1eo9A 209 7.92e+01 3pchA b.3.6.1 22731 1wruA 379 7.97e+01 3pnp 289 8.00e+01 1b8oA c.56.2.1 33763 1gya 105 8.11e+01 1qa9A b.1.1.1 19745 1erjA 393 8.33e+01 1erjA b.69.4.1 27660 1kmmA 424 8.40e+01 1adjA c.51.1.1,d.104.1.1 33174,40723 2rspA 124 8.40e+01 2rspB b.50.1.1 26771 1e8pA 46 8.51e+01 g.55.1.1 59385 1sznA 417 8.54e+01 b.71.1.1,c.1.8.1 106162,106163 1hlvA 131 8.56e+01 a.4.1.7,a.4.1.7 65854,65855 2fcbA 173 8.58e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 1k3iA 656 8.60e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 2gaeA 346 8.61e+01 1tbuA 118 8.64e+01 1dkgA 197 8.76e+01 1dkgA b.73.1.1,h.1.9.1 27812,45626 1h1iD 350 8.87e+01 b.82.1.5 76472 1r26A 125 8.89e+01 c.47.1.1 96847 2gjgA 248 8.91e+01