# List of top-scoring protein chains for t04-100-30-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 1dvoA 152 6.48e-21 1dvoA a.136.1.1 19623 1llfA 534 4.29e-01 c.69.1.17 78094 1cleA 534 4.41e-01 1thg c.69.1.17 34771 1x8bA 289 7.30e-01 1uj8A 77 7.34e-01 1apyB 141 8.10e-01 1apyB 1zx0A 236 8.23e-01 1v7cA 351 9.12e-01 c.79.1.1 100446 1yumA 242 1.07e+00 1jj2C 246 1.20e+00 1ffkC c.22.1.1 63087 1s72C 246 1.21e+00 c.22.1.1 105321 1svfB 38 1.22e+00 1svfB h.3.2.1 45764 1thg 544 1.23e+00 1thg c.69.1.17 34763 2anuA 255 1.32e+00 2c8mA 262 1.74e+00 1z1dA 103 1.76e+00 1yr2A 741 1.83e+00 1ve3A 227 1.93e+00 1pmzA 86 1.99e+00 a.39.1.10 104195 1gvnA 90 2.18e+00 a.8.2.1 76353 1vqoC 246 2.22e+00 1iscA 192 2.47e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1z5hA 780 2.58e+00 1mzbA 136 2.78e+00 a.4.5.42 91497 2ga1A 106 3.02e+00 2flsA 132 3.22e+00 1fo1A 271 3.29e+00 1fo1A c.10.2.3,d.58.7.2 30869,39213 2ffsA 157 3.34e+00 1w0mA 226 3.42e+00 c.1.1.1 109027 1bg1A 722 3.66e+00 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 2c1cA 312 3.74e+00 1qhtA 775 4.08e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1dpuA 99 4.09e+00 1dpuA a.4.5.16 16150 1usyA 275 4.20e+00 1lcyA 325 4.50e+00 b.36.1.4,b.47.1.1 73834,73835 1vl8A 267 4.68e+00 c.2.1.2 108733 1efyA 350 4.79e+00 1a26 a.41.1.1,d.166.1.2 17413,42275 1pbjA 125 4.91e+00 d.37.1.1,d.37.1.1 94414,94415 2arsA 262 5.00e+00 1tu5A 746 5.01e+00 1k9uA 78 5.06e+00 a.39.1.10 84348 1fgkA 310 5.68e+00 1fgkA d.144.1.7 41693 1gvkB 240 5.73e+00 b.47.1.2 70610 1ki1B 352 5.88e+00 a.87.1.1,b.55.1.1 72497,72498 1jksA 294 5.95e+00 d.144.1.7 71710 1uby 367 5.96e+00 1uby a.128.1.1 19435 1f53A 84 6.13e+00 1f53A b.11.1.4 23632 1jqgA 433 6.40e+00 c.56.5.1,d.58.3.1 71791,71792 1wraA 308 6.91e+00 2bibA 547 7.58e+00 2cxxA 190 7.63e+00 1zupA 315 7.71e+00 1tn4 159 7.99e+00 1ncx a.39.1.5 17248 1v3wA 173 8.37e+00 b.81.1.5 100291 1z7aA 308 8.63e+00 1nekD 115 8.65e+00 f.21.2.2 80432 2c30A 321 8.82e+00 1lv7A 257 9.26e+00 c.37.1.20 78232 1wyuB 474 9.38e+00 1w33A 181 9.82e+00 1pvmA 184 1.00e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1yirA 408 1.03e+01 1ucrA 78 1.04e+01 a.4.5.45 99188 2fafA 608 1.04e+01 2gsfA 373 1.09e+01 1u9iA 519 1.10e+01 1qnjA 240 1.10e+01 5ptp b.47.1.2 26238 1hw1A 239 1.11e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1o50A 157 1.11e+01 d.37.1.1,d.37.1.1 92478,92479 1rykA 69 1.11e+01 a.60.11.1 98105 1yp2A 451 1.13e+01 1bc8C 93 1.13e+01 1awcA a.4.5.21 16168 1jpaA 312 1.14e+01 d.144.1.7 67011 1umnA 165 1.15e+01 a.25.1.1 99607 1kgnA 329 1.17e+01 a.25.1.2 68584 1q5dA 419 1.18e+01 a.104.1.1 95891 1v4xB 146 1.28e+01 a.1.1.2 108364 1p3qQ 54 1.32e+01 a.5.2.4 87748 1ggzA 148 1.36e+01 a.39.1.5 70176 2erbA 125 1.38e+01 1ymtA 246 1.43e+01 1w61A 414 1.48e+01 2bitX 165 1.49e+01 2evaA 307 1.50e+01 1yllA 200 1.51e+01 1no1A 126 1.52e+01 a.179.1.1 85913 1qvbA 481 1.53e+01 1qvbA c.1.8.4 28983 1vgjA 184 1.54e+01 2g39A 497 1.55e+01 2aq9A 262 1.56e+01 1te2A 226 1.58e+01 c.108.1.6 106792 3pviA 157 1.60e+01 3pviA c.52.1.6 33300 1oxwA 373 1.60e+01 c.19.1.3 87539 1p4cA 380 1.61e+01 c.1.4.1 94100 1g8iA 190 1.61e+01 1rec a.39.1.5 60363 1hwxA 501 1.62e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 2bh8A 101 1.63e+01 2fswA 107 1.65e+01 2es4D 332 1.70e+01 2pviA 157 1.76e+01 3pviA c.52.1.6 33302 1obr 326 1.82e+01 1aye c.56.5.2 33828 1r5lA 262 1.82e+01 a.5.3.1,c.13.1.1 97099,97100 1ufbA 127 1.83e+01 a.24.16.3 99331 1q60A 99 1.83e+01 1pgyA 47 1.85e+01 a.5.2.1 94696 2ghsA 326 1.85e+01 1vm7A 311 1.85e+01 c.72.1.1 108884 1gotG 73 1.86e+01 1tbgE a.137.3.1 19629 1knyA 253 1.91e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1hlvA 131 1.95e+01 a.4.1.7,a.4.1.7 65854,65855 1eyhA 144 1.98e+01 1eduA a.118.9.1 19214 2fneA 117 2.00e+01 1nz0A 118 2.00e+01 d.14.1.2 86433 1ufaA 520 2.02e+01 a.8.3.3,c.6.2.4 99329,99330 1ld8A 382 2.02e+01 a.118.6.1 73838 1p94A 76 2.08e+01 a.43.1.3 94380 1ji0A 240 2.13e+01 c.37.1.12 71665 1p4fA 293 2.13e+01 d.144.1.7 104063 1z9bA 135 2.17e+01 1dszB 85 2.17e+01 2nllB g.39.1.2 45108 1vdxA 184 2.17e+01 1g71A 347 2.17e+01 1g71A d.264.1.1 43268 1a78A 134 2.29e+01 1c1lA b.29.1.3 24212 2d9iA 96 2.29e+01 1quqB 121 2.31e+01 1quqB b.40.4.3 25305 1ov9A 50 2.32e+01 a.155.1.1 93591 2acvA 463 2.35e+01 1lxa 262 2.36e+01 1lxa b.81.1.1 28052 1n5nA 180 2.37e+01 d.167.1.1 85336 1awsA 164 2.38e+01 2cpl b.62.1.1 27431 1awqA 164 2.42e+01 2cpl b.62.1.1 27461 1vloA 381 2.47e+01 b.44.2.1,d.250.1.1 108838,108839 1yasA 257 2.51e+01 1qj4A c.69.1.20 34801 1iukA 140 2.51e+01 c.2.1.8 83712 1o5zA 442 2.52e+01 c.59.1.2,c.72.2.2 92530,92531 1eswA 500 2.55e+01 1cwyA c.1.8.1 59500 1gp6A 356 2.56e+01 b.82.2.1 65441 1lj9A 144 2.57e+01 a.4.5.28 78035 2fazA 78 2.59e+01 1kk8B 139 2.60e+01 a.39.1.5 77430 1qc7A 101 2.62e+01 1qc7A a.118.14.1 18456 2scpA 174 2.67e+01 2scpA a.39.1.5 17256 2iv2X 715 2.69e+01 1r5zA 323 2.69e+01 f.40.1.1 97135 2c07A 285 2.70e+01 1qj4A 257 2.71e+01 1qj4A c.69.1.20 34796 1wdcB 156 2.72e+01 1wdcB a.39.1.5 17302 2bl2A 156 2.80e+01 1eluA 390 2.81e+01 1elqA c.67.1.3 34434 1ohlA 342 2.84e+01 c.1.10.3 87035 1a0i 348 2.85e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1elqA 390 2.85e+01 1elqA c.67.1.3 34436 1xxqA 161 2.87e+01 1xknA 355 2.88e+01 1mkmA 249 2.88e+01 a.4.5.33,d.110.2.2 79242,79243 1qhfA 240 2.89e+01 1qhfA c.60.1.1 33960 1tn6A 382 2.91e+01 1aa6 715 2.94e+01 2napA b.52.2.2,c.81.1.1 26916,35324 1qkrA 188 2.95e+01 1qkrA a.24.9.1 16628 2bk9A 153 2.98e+01 1y9zA 441 3.00e+01 1v6cA 441 3.01e+01 1uox 296 3.09e+01 1uox 1qczA 169 3.15e+01 1qczA c.23.8.1 31276 1vlpA 441 3.16e+01 d.41.2.2,d.41.2.3 108840,108841 1dqaA 467 3.20e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 2a9fA 398 3.28e+01 1sxjE 354 3.29e+01 a.80.1.1,c.37.1.20 106089,106090 1ji8A 111 3.30e+01 d.203.1.1 66733 1yndA 165 3.31e+01 1x3kA 152 3.32e+01 1mveA 243 3.34e+01 b.29.1.2 85140 1mba 147 3.35e+01 2fal a.1.1.2 15149 2cpl 165 3.35e+01 2cpl b.62.1.1 27420 1sgmA 191 3.37e+01 a.4.1.9,a.121.1.1 105537,105538 1je8A 82 3.37e+01 a.4.6.2 77108 1ydiA 263 3.38e+01 1bolA 222 3.39e+01 1bolA d.124.1.1 41120 1o7kA 131 3.41e+01 d.189.1.1 81144 1g0oA 283 3.48e+01 1ybvA c.2.1.2 60181 1em9A 154 3.49e+01 1d1dA a.73.1.1 18333 1my6A 199 3.49e+01 a.2.11.1,d.44.1.1 85232,85233 1y0mA 61 3.50e+01 1bf2 750 3.51e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1ig5A 75 3.51e+01 4icb a.39.1.1 62363 1h7nA 342 3.51e+01 1b4kA c.1.10.3 60726 2ae2A 260 3.55e+01 1bdb c.2.1.2 29945 1wmiA 90 3.55e+01 2f57A 317 3.55e+01 1iznB 277 3.56e+01 e.43.1.2 83848 1b0nA 111 3.56e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1xuqA 212 3.59e+01 1j24A 143 3.59e+01 c.52.1.20 84008 2gyqA 175 3.61e+01 1g5gA 481 3.62e+01 f.12.1.1,h.3.2.1 65155,65156 1xclA 235 3.64e+01 1uzcA 71 3.67e+01 a.159.2.1 100222 1g2yA 32 3.74e+01 a.34.2.1 17003 1r2fA 319 3.75e+01 1r2fA a.25.1.2 16800 1rkuA 206 3.76e+01 c.108.1.11 97627 1m4lA 307 3.79e+01 c.56.5.1 78604 1z6gA 218 3.80e+01 1rec 201 3.82e+01 1rec a.39.1.5 17326 2ctc 307 3.83e+01 1aye c.56.5.1 33802 1wwiA 148 3.94e+01 1y1nA 291 3.94e+01 1r6vA 671 4.06e+01 1xriA 151 4.06e+01 1qavA 90 4.11e+01 1qauA b.36.1.1 24777 2aaxA 275 4.12e+01 1ywpA 64 4.13e+01 1dbhA 354 4.17e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1ctf 74 4.17e+01 1ctf d.45.1.1 38759 2b7aA 293 4.20e+01 1yp5A 58 4.25e+01 1yxmA 303 4.33e+01 1ldfA 281 4.33e+01 f.19.1.1 73845 1izmA 184 4.33e+01 a.199.1.1 90725 1yf3A 259 4.35e+01 2ci9A 102 4.39e+01 1sknP 92 4.40e+01 1sknP a.37.1.1 17127 1o9gA 250 4.43e+01 c.66.1.29 86692 1r4uA 301 4.47e+01 d.96.1.4,d.96.1.4 97047,97048 2fp7B 172 4.51e+01 2gujA 155 4.51e+01 1g4yR 148 4.52e+01 1cll a.39.1.5 60252 1erd 40 4.53e+01 1erd a.10.1.1 16362 1v54E 109 4.61e+01 a.118.11.1 100326 1mwpA 96 4.63e+01 1mwpA d.170.2.1 42453 1wrrA 301 4.66e+01 1f7lA 121 4.66e+01 1f7lA d.150.1.2 59666 1m1hA 248 4.77e+01 b.114.1.1,d.58.42.1 78415,78416 1ybhA 590 4.80e+01 1rkeA 262 4.81e+01 a.24.9.1,a.24.9.1 97608,97609 2b3hA 329 4.82e+01 1v63A 101 4.83e+01 a.21.1.1 108391 2go7A 207 4.85e+01 4icb 76 4.88e+01 4icb a.39.1.1 17145 1d8dA 377 4.91e+01 1ft1A a.118.6.1 19185 1ornA 226 4.93e+01 a.96.1.1 87342 1vg5A 73 5.00e+01 2awpA 198 5.04e+01 1a58 177 5.09e+01 2cpl b.62.1.1 27495 1wmmA 145 5.10e+01 1us5A 314 5.12e+01 c.94.1.1 99856 1j5sA 463 5.16e+01 c.1.9.8 71580 1z3eA 132 5.17e+01 1rzjG 321 5.17e+01 d.172.1.1 98200 1vdwA 254 5.19e+01 e.7.1.1 100569 2ct9A 208 5.21e+01 1vp7A 100 5.22e+01 2b5hA 200 5.23e+01 1u55A 188 5.24e+01 d.278.1.1 107677 1g8mA 593 5.27e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1j75A 67 5.38e+01 a.4.5.19 62673 1k3rA 268 5.40e+01 b.40.4.10,c.116.1.2 72018,72019 2bjqA 345 5.40e+01 1odkA 235 5.44e+01 c.56.2.1 86863 1q0gA 117 5.45e+01 a.24.22.1 104428 1wmuB 146 5.51e+01 a.1.1.2 109417 1v8eA 224 5.53e+01 1vdnA 162 5.55e+01 1vkpA 383 5.56e+01 d.126.1.6 108686 2essA 248 5.59e+01 2bhwA 232 5.61e+01 1exrA 148 5.63e+01 1cll a.39.1.5 17299 1zfjA 491 5.64e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1t9kA 347 5.64e+01 c.124.1.5 106721 2bzoB 79 5.67e+01 1r6wA 322 5.73e+01 c.1.11.2,d.54.1.1 97165,97166 1yvhA 329 5.75e+01 1sup 275 5.79e+01 1gci c.41.1.1 32510 1mldA 314 5.83e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1h3nA 878 5.83e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1yh6A 179 5.84e+01 1p1cA 199 5.84e+01 c.66.1.16 87669 2atfA 200 5.85e+01 1z9eA 127 5.86e+01 1tueA 212 5.91e+01 c.37.1.20 107323 2mcm 112 5.92e+01 2mcm b.1.7.1 22207 1qu9A 128 5.92e+01 1qu9A d.79.1.1 39755 1udh 244 5.95e+01 3eugA c.18.1.1 31015 1hv9A 456 6.04e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1ugpB 226 6.05e+01 b.34.4.4 107832 1xwrA 97 6.12e+01 1cpcA 162 6.14e+01 1cpcA a.1.1.3 15643 1oh0A 131 6.14e+01 d.17.4.3 87004 1odfA 290 6.16e+01 c.37.1.6 92782 1f1uA 323 6.16e+01 d.32.1.3,d.32.1.3 83200,83201 1ulyA 192 6.23e+01 1t6sA 162 6.24e+01 2fu4A 83 6.24e+01 1eca 136 6.27e+01 1flp a.1.1.2 15209 1u2pA 163 6.28e+01 1ugxA 133 6.29e+01 1oywA 523 6.29e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 1s3aA 102 6.32e+01 1zs4A 83 6.34e+01 2ct8A 497 6.36e+01 1t6uA 117 6.39e+01 a.24.22.1 106584 1kzyC 259 6.43e+01 c.15.1.4,c.15.1.4 73383,73384 1ykhB 132 6.47e+01 1wn5A 130 6.48e+01 1um0A 365 6.49e+01 d.258.1.1 107942 1zwwA 256 6.50e+01 2ffcA 353 6.50e+01 1yruB 74 6.52e+01 2occE 109 6.59e+01 2occE a.118.11.1 19224 1jp4A 308 6.67e+01 1jp4A e.7.1.1 63223 1ieaA 192 6.70e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 1otsA 465 6.70e+01 f.20.1.1 87415 1nqkA 381 6.75e+01 c.1.16.4 92050 1a04A 215 6.84e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1kjwA 295 6.89e+01 b.34.2.1,c.37.1.1 68643,68644 1ireB 228 6.90e+01 b.34.4.4 76770 1yaiA 151 6.97e+01 1yaiA b.1.8.1 22289 1lw6E 281 6.98e+01 c.41.1.1 74293 1uehA 253 6.99e+01 c.101.1.1 99259 1pufB 73 7.06e+01 a.4.1.1 95132 1kq6A 141 7.08e+01 d.189.1.1 91020 1qzgA 187 7.09e+01 b.40.4.3 96643 1xteA 154 7.11e+01 1f1xA 322 7.11e+01 d.32.1.3,d.32.1.3 83208,83209 1uwcA 261 7.14e+01 c.69.1.17 100101 2cblA 305 7.21e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17380,17774,40528 1s4bP 674 7.21e+01 d.92.1.5 105252 2aaoA 166 7.30e+01 2g0wA 296 7.31e+01 2gl5A 410 7.33e+01 1lx7A 253 7.41e+01 c.56.2.1 74329 1vd6A 224 7.42e+01 1h0pA 182 7.45e+01 b.62.1.1 76450 1rkbA 173 7.45e+01 1is1A 185 7.45e+01 d.67.3.1 83704 1spgA 144 7.45e+01 1abwA a.1.1.2 15409 1jpyA 137 7.47e+01 g.17.1.6 67065 2aplA 157 7.47e+01 2bo9A 308 7.50e+01 1n97A 389 7.50e+01 a.104.1.1 80335 1rxyA 253 7.52e+01 c.56.2.1 98065 2gwdA 449 7.54e+01 1tvoA 368 7.59e+01 1b67A 68 7.61e+01 1a7w a.22.1.2 16474 12asA 330 7.74e+01 12asA d.104.1.1 40783 1qo7A 394 7.74e+01 1qo7A c.69.1.11 34697 1rq6A 62 7.76e+01 1ud0A 113 7.79e+01 a.8.4.1 99198 1j7gA 144 7.83e+01 c.110.1.1 84130 1m26A 133 7.86e+01 1i0dA 332 7.97e+01 1pscA c.1.9.3 61487 1q6uA 245 7.98e+01 d.26.1.1 95998 1dekA 241 7.98e+01 1dekA c.37.1.1 31842 1bkb 136 8.00e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1okhA 46 8.05e+01 g.13.1.1 93253 1wm3A 72 8.07e+01 1pcfA 66 8.08e+01 1pcfA d.18.1.1 38142 1pujA 282 8.09e+01 c.37.1.8 88294 1f4qA 165 8.11e+01 1alvA a.39.1.8 17360 1qsgA 265 8.16e+01 1eny c.2.1.2 29935 2d37A 176 8.16e+01 1ys1X 320 8.21e+01 1pa7A 130 8.22e+01 a.40.1.1 94410 1u6mA 199 8.22e+01 1vk9A 151 8.23e+01 c.139.1.1 108640 2a72A 146 8.23e+01 1to2E 281 8.24e+01 1k94A 165 8.30e+01 a.39.1.8 68333 2bjhA 260 8.31e+01 1d2rA 326 8.43e+01 1d2rB c.26.1.1 31572 1qj2C 285 8.45e+01 1qj2C 1xtnA 120 8.51e+01 1gbs 185 8.54e+01 153l d.2.1.5 36986 1tp5A 119 8.58e+01 1t01A 255 8.65e+01 a.24.9.1,a.24.9.1 106188,106189 1fnoA 417 8.65e+01 d.58.19.1,c.56.5.4 70145,75841 1xbbA 291 8.65e+01 7fd1A 106 8.69e+01 1a6l d.58.1.2 38953 1xahA 354 8.73e+01 1cruA 454 8.82e+01 1c9uA b.68.2.1 27617 1yyqA 374 8.82e+01 1qi7A 253 8.88e+01 1qi7A d.165.1.1 42210 1q3oA 109 8.93e+01 b.36.1.1 95700 1blxA 326 8.93e+01 1hcl d.144.1.7 41596 1q8dA 108 8.96e+01 a.228.1.1 104554