# List of top-scoring protein chains for t2k-100-30-bys-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 2fhqA 141 1.28e-13 1dnlA 199 5.19e-12 1ci0A b.45.1.1 25753 1g79A 218 6.86e-12 1ci0A b.45.1.1 25752 1nrgA 261 6.43e-09 b.45.1.1 80694 1rfeA 162 2.60e-08 2fg9A 178 1.08e-07 1t9mA 214 1.96e-07 1ty9A 222 1.18e-06 2asfA 137 1.07e-05 1ci0A 228 1.07e-05 1ci0A b.45.1.1 25750 2aq6A 147 5.18e-05 1w9aA 147 8.56e-05 1xxoA 147 9.04e-05 1vl7A 157 1.08e-04 b.45.1.1 108732 1flmA 122 6.85e-04 1axj b.45.1.1 25747 2furA 209 9.88e-04 1axj 122 1.05e-03 1axj b.45.1.1 25749 1w3oA 216 4.72e-03 1ejeA 192 1.49e-02 1ejeA b.45.1.2 25757 1xhnA 184 4.18e-02 2arzA 247 4.77e-02 2bgiA 272 8.26e-02 1ww7A 160 1.77e+00 2f4iA 197 4.69e+00 1nnt 328 6.36e+00 1nnt c.94.1.2 35884 2ag5A 246 6.66e+00 1vmeA 410 6.89e+00 c.23.5.1,d.157.1.3 108893,108894 1j58A 385 9.11e+00 b.82.1.2 71531 1a8p 258 9.38e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 2c1lA 358 9.49e+00 1tfaA 329 9.55e+00 1nnt c.94.1.2 35880 1w66A 232 9.91e+00 1ipd 345 1.12e+01 1cnzA c.77.1.1 35038 1wd6A 123 1.18e+01 1zt3A 80 1.18e+01 1p3wA 404 1.21e+01 c.67.1.3 87752 1f6bA 198 1.25e+01 c.37.1.8 64986 1pse 69 1.26e+01 1pse b.34.4.2 24595 1ye8A 178 1.36e+01 1xaa 345 1.37e+01 1cnzA c.77.1.1 35033 1iejA 332 1.38e+01 1nnt c.94.1.2 62328 1nftA 329 1.41e+01 1nnt c.94.1.2 35881 1j5kA 89 1.41e+01 d.51.1.1 71565 1me4A 215 1.44e+01 d.3.1.1 79023 2fcjA 119 1.49e+01 1aim 215 1.51e+01 1cs8A d.3.1.1 37044 1r8sA 164 1.52e+01 c.37.1.8 97247 1d8yA 605 1.52e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1rz3A 201 1.56e+01 c.37.1.6 98132 1vrtA 560 1.58e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1ujqA 305 1.59e+01 c.1.12.7 99463 1y0yA 353 1.61e+01 1e5dA 402 1.69e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1ofuA 320 1.75e+01 c.32.1.1,d.79.2.1 86972,86973 1jeyA 609 1.81e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1i24A 404 1.81e+01 c.2.1.2 83663 1bbpA 173 1.83e+01 1bbpA b.60.1.1 27147 1zzkA 82 1.92e+01 1qx4A 274 1.92e+01 b.43.4.2,c.25.1.1 104624,104625 1fsz 372 2.00e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1dttA 560 2.05e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1s2wA 295 2.06e+01 c.1.12.7 98407 2g1uA 155 2.07e+01 1fivA 113 2.11e+01 1fmb b.50.1.1 26764 4fiv 113 2.15e+01 1fmb b.50.1.1 26762 1me3A 215 2.15e+01 d.3.1.1 79022 1vimA 200 2.22e+01 c.80.1.3 100758 1f2aA 215 2.23e+01 1cs8A d.3.1.1 37040 2fauA 341 2.24e+01 1xfkA 336 2.25e+01 1div 149 2.25e+01 1div d.99.1.1,d.100.1.1 40692,40693 1n9lA 109 2.33e+01 d.110.3.6 85468 2hmiA 558 2.35e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 1a8q 274 2.35e+01 1brt c.69.1.12 34702 2etjA 250 2.36e+01 1k0mA 241 2.37e+01 a.45.1.1,c.47.1.5 67949,67950 1rq2A 382 2.50e+01 c.32.1.1,d.79.2.1 105048,105049 1rthA 560 2.51e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1fts 295 2.54e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1g6aA 271 2.63e+01 1btl e.3.1.1 42704 1pjr 724 2.66e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1fnuA 221 2.67e+01 3seb b.40.2.2,d.15.6.1 25212,37801 2abqA 306 2.69e+01 2b6hA 192 2.73e+01 2bvfA 459 2.77e+01 1o5oA 221 2.83e+01 c.61.1.1 92509 2bznA 351 2.90e+01 1pvtA 238 2.93e+01 c.74.1.1 95189 1eetA 557 2.95e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1i9zA 347 2.95e+01 1i9yA d.151.1.2 62102 1hrhA 136 3.03e+01 1rthA c.55.3.1 33577 1ko3A 230 3.11e+01 d.157.1.1 90974 1tr8A 102 3.12e+01 2b4yA 271 3.13e+01 1jeqA 609 3.19e+01 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1hurA 180 3.21e+01 1hurA c.37.1.8 32052 1vmaA 306 3.22e+01 a.24.13.1,c.37.1.10 108887,108888 1pguA 615 3.28e+01 b.69.4.1,b.69.4.1 88069,88070 1x88A 359 3.32e+01 2bw3A 534 3.34e+01 1ndh 272 3.40e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1zd7A 159 3.40e+01 1fkoA 543 3.50e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 1vpmA 169 3.52e+01 1i7pA 274 3.52e+01 b.43.4.2,c.25.1.1 66048,66049 1xfoA 357 3.53e+01 1klnA 605 3.63e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1iu8A 206 3.67e+01 c.56.4.1 71436 2a5sA 284 3.70e+01 1fk9A 543 3.70e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1wsrA 375 3.71e+01 1i9yA 347 3.73e+01 1i9yA d.151.1.2 62101 1k0nA 241 3.74e+01 a.45.1.1,c.47.1.5 67953,67954 1wj9A 211 3.81e+01 1khbA 625 3.82e+01 c.91.1.1,c.109.1.1 68606,68607 2fivA 116 3.83e+01 1fmb b.50.1.1 26766 1sxgA 280 3.85e+01 1q0bA 367 3.88e+01 c.37.1.9 95502 1p5tA 127 3.88e+01 b.55.1.2 94148 2ay1A 394 3.89e+01 1ajsA c.67.1.1 34357 3fivA 116 3.95e+01 1fmb b.50.1.1 26768 1vi6A 208 3.96e+01 c.23.15.1 100736 1txgA 335 3.97e+01 1nszA 347 4.03e+01 b.30.5.4 80724 1qm4A 396 4.06e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 2c6qA 351 4.12e+01 1gal 583 4.19e+01 1gpeA c.3.1.2,d.16.1.1 30386,37950 2bwqA 129 4.20e+01 1dzkA 157 4.21e+01 1obpA b.60.1.1 27096 1qp2A 70 4.23e+01 1pse b.34.4.2 24596 2azeA 155 4.38e+01 1vphA 149 4.53e+01 1kijA 390 4.59e+01 d.14.1.3,d.122.1.2 72514,72515 1mmuA 347 4.60e+01 b.30.5.4 79303 2dpmA 284 4.62e+01 2dpmA c.66.1.28 34246 1l7jA 347 4.68e+01 b.30.5.4 73660 1idm 343 4.72e+01 1cnzA c.77.1.1 35035 1ybiA 288 4.78e+01 1rznA 205 4.79e+01 2bwrA 401 4.95e+01 1bywA 110 5.00e+01 1bywA d.110.3.6 40912 1k7jA 206 5.01e+01 d.115.1.1 72103 1uarA 285 5.06e+01 c.46.1.2,c.46.1.2 107762,107763 1zvkA 358 5.13e+01 1vpjA 192 5.15e+01 1ho1A 242 5.17e+01 1ho1A c.1.24.1 61097 2f15A 96 5.22e+01 1gv9A 260 5.32e+01 b.29.1.13 70596 1lyxA 248 5.33e+01 c.1.1.1 78304 1ejjA 511 5.36e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1gw5M 435 5.38e+01 b.2.7.1,d.110.4.2 70631,70632 1kuuA 202 5.40e+01 d.153.2.1 73019 1a3yA 149 5.42e+01 1obpA b.60.1.1 27110 1tvjA 166 5.42e+01 1qrrA 394 5.48e+01 1qrrA c.2.1.2 29824 1snzA 344 5.53e+01 b.30.5.4 98930 1j27A 102 5.65e+01 d.58.50.1 90778 1hniA 558 5.66e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 1wr8A 231 5.66e+01 1v9sA 208 5.69e+01 1umkA 275 5.72e+01 1udzA 182 5.78e+01 b.51.1.1 99239 1ehaA 558 5.79e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1tgrA 52 5.82e+01 2bduA 297 5.84e+01 1oo0A 147 5.93e+01 d.232.1.1 87182 1wnyA 186 5.96e+01 2f46A 156 6.09e+01 2myr 501 6.10e+01 1zq4A 693 6.11e+01 2g09A 297 6.14e+01 2f0aA 98 6.14e+01 1y3nA 490 6.21e+01 2a4vA 159 6.22e+01 1xtoA 311 6.27e+01 1wk8A 194 6.28e+01 1xv5A 401 6.28e+01 1mkyA 439 6.30e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1o5xA 248 6.37e+01 c.1.1.1 92528 1zp7A 206 6.47e+01 1s72S 85 6.51e+01 d.12.1.1 105338 1l7jB 347 6.58e+01 b.30.5.4 73661 1jj2R 84 6.62e+01 1ffkP d.12.1.1 63103 1dr8B 344 6.75e+01 1cnzA c.77.1.1 35052 1o98A 511 6.81e+01 c.105.1.1,c.76.1.3 86684,86685 1v0wA 506 6.90e+01 d.136.1.2,d.136.1.2 108220,108221 1kkcA 221 6.92e+01 a.2.11.1,d.44.1.1 68660,68661 1y81A 138 6.93e+01 1rl4A 188 6.94e+01 d.167.1.1 97636 1agqA 135 7.01e+01 1agqA g.17.1.2 44789 1z0mA 96 7.02e+01 1gph1 465 7.11e+01 1ecfB 1jvsA 400 7.13e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1w8oA 601 7.19e+01 1i31A 314 7.19e+01 1bw8A b.2.7.1 22481 1nv8A 284 7.20e+01 c.66.1.30 86224 2etvA 346 7.24e+01 1eqjA 511 7.26e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 2fgtA 417 7.28e+01 1hmvA 560 7.29e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 2aebA 322 7.36e+01 1tidB 119 7.38e+01 c.13.2.1 107000 2g39A 497 7.40e+01 1lvoA 302 7.42e+01 b.47.1.4 74284 1eu3A 210 7.53e+01 1an8 b.40.2.2,d.15.6.1 25206,37795 1x3lA 440 7.57e+01 1t1jA 125 7.60e+01 c.137.1.1 106249 1wcqA 601 7.61e+01 2b59A 187 7.67e+01 2rslA 140 7.74e+01 2rslA c.53.1.1 33345 1gca 309 7.74e+01 1gca c.93.1.1 35659 1rf8B 100 7.80e+01 a.210.1.1 97371 2arpA 116 7.89e+01 1an7A 136 7.90e+01 1seiA d.140.1.1 41465 1eur 365 7.90e+01 1eut b.68.1.1 27607 1ksyA 154 7.90e+01 d.89.1.2 72948 1cz3A 168 7.90e+01 1d1gA c.71.1.1 34891 1tzfA 259 7.90e+01 c.68.1.13 107476 1u0tA 307 7.92e+01 e.52.1.1 107567 1kz1A 159 7.93e+01 c.16.1.1 73318 2f62A 161 7.99e+01 1g4fA 86 8.02e+01 1qubA g.18.1.1 44873 1z0nA 96 8.03e+01 1b00A 127 8.08e+01 3chy c.23.1.1 31122 1fwxA 595 8.08e+01 b.6.1.4,b.69.3.1 60069,60070 2f2tA 161 8.08e+01 1ejbA 168 8.21e+01 1rvv1 c.16.1.1 59417 1o3yA 166 8.22e+01 c.37.1.8 86618 1pfxL 146 8.26e+01 1cfi g.3.11.1,g.3.11.1,g.32.1.1 44207,44208,44973 1wvcA 259 8.32e+01 1g5qA 181 8.40e+01 1g5qA c.34.1.1 60288 1bqnA 558 8.43e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 2a0kA 161 8.44e+01 1z41A 338 8.47e+01 1t71A 281 8.48e+01 1db3A 372 8.50e+01 1db3A c.2.1.2 29813 1x6oA 174 8.52e+01 b.34.5.2,b.40.4.5 109493,109494 1mqeA 207 8.56e+01 d.113.1.1 91394 2gkeA 274 8.62e+01 1rzrA 332 8.62e+01 1lp9E 194 8.78e+01 b.1.1.1,b.1.1.2 91086,91087 1o89A 345 8.78e+01 b.35.1.2,c.2.1.1 92644,92645 1f2tB 148 8.79e+01 1f2tB 2d93A 134 8.80e+01 1vm6A 228 8.85e+01 c.2.1.3,d.81.1.3 108876,108877 1b7gO 340 8.92e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907