# List of top-scoring protein chains for t04-100-30-alpha-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 2ap1A 327 1.22e-03 1yrvA 169 1.09e-01 1jl5A 454 1.75e-01 c.10.2.6 66830 1gd8A 118 2.14e-01 d.188.1.1 60445 1g0uG 252 2.19e-01 d.153.1.4 41952 1rqlA 267 2.23e-01 c.108.1.3 97750 1rypA 243 2.59e-01 1pmaA d.153.1.4 41932 1xqaA 113 3.17e-01 1eqfA 280 4.09e-01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1ufiA 64 4.45e-01 a.30.4.1 99336 1jy2O 56 5.01e-01 h.1.8.1 67441 1exrA 148 5.21e-01 1cll a.39.1.5 17299 1fezA 256 5.55e-01 1fezA c.108.1.3 43343 1kvkA 395 7.56e-01 d.14.1.5,d.58.26.3 73060,73061 1swvA 267 8.90e-01 1ggzA 148 9.19e-01 a.39.1.5 70176 1r85A 379 1.23e+00 c.1.8.3 104839 1rdfA 267 1.32e+00 c.108.1.3 104884 2fi9A 128 1.42e+00 1xttA 216 1.44e+00 2h88C 140 1.48e+00 1kr4A 125 1.49e+00 d.58.5.2 72889 1b7yA 350 1.69e+00 1pysA d.104.1.1 40776 1nepA 130 1.89e+00 b.1.18.7 80440 2a5lA 200 1.94e+00 1h2kA 349 1.98e+00 b.82.2.6 76572 1u08A 386 2.08e+00 c.67.1.1 107543 1v5sA 126 2.23e+00 d.129.6.1 108384 1w0bA 102 2.39e+00 a.7.11.1 108985 1yirA 408 2.44e+00 1r0pA 312 2.45e+00 d.144.1.7 96734 1omrA 201 2.47e+00 a.39.1.5 93349 1zoyC 140 2.55e+00 1zclA 180 2.63e+00 1zd9A 188 2.74e+00 1x24A 180 2.76e+00 1rec 201 2.76e+00 1rec a.39.1.5 17326 1kshA 186 2.78e+00 c.37.1.8 72914 1nvvS 481 2.96e+00 a.117.1.1 86279 1sziA 247 3.13e+00 a.24.23.1 106159 1sz2A 332 3.23e+00 1q18A 332 3.28e+00 c.55.1.7,c.55.1.7 104470,104471 2bjkA 516 3.59e+00 2b20A 403 3.64e+00 1u9aA 160 3.68e+00 1u9aA d.20.1.1 38333 1fseA 74 3.74e+00 1fseA a.4.6.2 60000 1uzbA 516 3.76e+00 c.82.1.1 100220 1wzvA 155 4.12e+00 1kveB 77 4.59e+00 1kveB 1stzA 338 4.71e+00 a.4.5.51,d.110.2.3 106009,106010 2fjlA 150 4.86e+00 1hzxA 349 5.08e+00 1f88A f.13.1.2 61466 1yx1A 264 5.19e+00 1lre 81 5.29e+00 1lre a.13.1.1 16376 1pysA 350 5.52e+00 1pysA d.104.1.1 40775 1ul7A 102 5.58e+00 d.129.6.1 99540 1ajsA 412 5.58e+00 1ajsA c.67.1.1 34276 2fbwC 141 5.73e+00 1o5iA 249 5.77e+00 c.2.1.2 92499 2a3qA 170 5.80e+00 1l9hA 349 5.93e+00 f.13.1.2 73720 1z5bA 469 6.28e+00 1wp5A 323 6.31e+00 1u19A 349 6.43e+00 1w77A 228 6.55e+00 1pwxA 254 6.60e+00 c.2.1.2 95262 1ujwB 135 6.61e+00 h.4.9.1 99472 1a8y 367 6.74e+00 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1w2xA 758 6.78e+00 c.14.1.4,c.14.1.4 109134,109135 1wg8A 285 6.83e+00 1opjA 293 7.05e+00 d.144.1.7 87230 1v54E 109 7.49e+00 a.118.11.1 100326 1bhdA 118 7.65e+00 1bkrA a.40.1.1 17398 2ffsA 157 7.77e+00 1ov2A 99 7.81e+00 a.13.1.1 93580 2dfkA 402 7.86e+00 1qgtA 149 7.99e+00 1qgtA a.62.1.1 18135 1wf9A 107 8.12e+00 1ty0A 211 8.36e+00 b.40.2.2,d.15.6.1 107440,107441 2occE 109 8.57e+00 2occE a.118.11.1 19224 1top 162 8.64e+00 1ncx a.39.1.5 17223 2bpsA 81 8.85e+00 2ajrA 331 9.14e+00 1uxtA 501 9.32e+00 c.82.1.1 108125 2f3yA 148 9.67e+00 2bwfA 77 9.97e+00 1sxjE 354 1.02e+01 a.80.1.1,c.37.1.20 106089,106090 2fupA 168 1.02e+01 1elqA 390 1.05e+01 1elqA c.67.1.3 34436 2afdA 88 1.07e+01 1k4nA 192 1.08e+01 d.32.1.5 72059 1prs 173 1.12e+01 1prs b.11.1.1,b.11.1.1 23625,23626 1fthA 122 1.13e+01 d.150.1.2 60028 1otsA 465 1.13e+01 f.20.1.1 87415 2grrA 161 1.13e+01 1nrjA 158 1.13e+01 d.110.4.4 86124 1a8d 452 1.16e+01 1a8d b.29.1.6,b.42.4.2 24262,25607 1zmtA 254 1.20e+01 1jggA 60 1.22e+01 2hddA a.4.1.1 62950 1gqeA 365 1.22e+01 e.38.1.1 70351 1q2hA 69 1.22e+01 a.34.4.1 104498 1s1qA 145 1.23e+01 d.20.1.2 98351 1g4yR 148 1.23e+01 1cll a.39.1.5 60252 1p5fA 189 1.25e+01 c.23.16.2 94142 1r59O 505 1.31e+01 1lkkA 105 1.31e+01 1lckA d.93.1.1 40412 1xawA 140 1.33e+01 2feaA 236 1.33e+01 1z8uA 102 1.33e+01 1yovA 537 1.35e+01 1eluA 390 1.37e+01 1elqA c.67.1.3 34434 1xdfA 157 1.40e+01 2g8lA 299 1.41e+01 1c44A 123 1.41e+01 1qndA d.106.1.1 40795 1lvfA 110 1.44e+01 a.47.2.1 74280 1fus 106 1.45e+01 9rnt d.1.1.4 36050 1ytw 306 1.46e+01 1ytw c.45.1.2 32689 1nvpD 108 1.48e+01 a.32.1.1,b.56.1.1 92213,92214 2b6hA 192 1.48e+01 1gg3A 279 1.49e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1z6uA 150 1.50e+01 1jfbA 404 1.50e+01 a.104.1.1 66624 2gokA 429 1.53e+01 1na6A 404 1.54e+01 b.142.1.1,c.52.1.22 91748,91749 1akz 223 1.54e+01 3eugA c.18.1.1 31007 1cuk 203 1.56e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1a17 166 1.60e+01 1a17 a.118.8.1 19206 2a0iA 330 1.64e+01 2g0uA 92 1.64e+01 1ofgA 381 1.64e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1ytfD 121 1.65e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1kllA 130 1.65e+01 d.32.1.2 72720 1jsdA 319 1.65e+01 b.19.1.2 63258 1y01A 102 1.66e+01 1innA 166 1.67e+01 1j98A d.185.1.2 62608 1w9yA 319 1.73e+01 1hn0A 1021 1.73e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 2db9A 149 1.74e+01 1rxdA 159 1.74e+01 1vhnA 318 1.74e+01 c.1.4.1 100693 1r1qA 100 1.76e+01 d.93.1.1 104763 7aatA 401 1.78e+01 1ajsA c.67.1.1 34250 1ev0A 58 1.80e+01 1ev0A d.71.1.1 39594 1gkzA 388 1.85e+01 a.29.5.1,d.122.1.4 65268,65269 1a92A 50 1.87e+01 1a92A h.4.6.1 45791 1nh2D 121 1.87e+01 a.32.1.1,b.56.1.1 91876,91877 1zckA 154 1.91e+01 1lmeA 176 1.91e+01 d.167.1.1 84629 1nkpB 83 1.94e+01 a.38.1.1 80574 1td6A 306 1.95e+01 1bs0A 384 1.98e+01 1bs0A c.67.1.4 34490 1g8iA 190 1.99e+01 1rec a.39.1.5 60363 1zb1A 392 2.00e+01 1h6dA 433 2.00e+01 c.2.1.3,d.81.1.5 65656,65657 2f46A 156 2.05e+01 1mlwA 301 2.06e+01 d.178.1.1 79289 1wgxA 73 2.07e+01 1qqgA 264 2.07e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1wdtA 665 2.08e+01 1ww8A 439 2.11e+01 1ei7A 158 2.16e+01 1rmvA a.24.5.1 16584 1zczA 464 2.19e+01 2f6uA 234 2.20e+01 2cglA 489 2.22e+01 1yf9A 171 2.22e+01 1q1vA 70 2.23e+01 a.159.4.1 104479 1mu5A 471 2.25e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1lyvA 306 2.25e+01 c.45.1.2 74348 1dj7A 117 2.25e+01 1dj7A g.36.1.1 44997 1uj8A 77 2.29e+01 1gpjA 404 2.29e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1vjeA 166 2.30e+01 d.185.1.2 100807 1p5zB 263 2.31e+01 c.37.1.1 87815 2fa8A 105 2.32e+01 1s4kA 120 2.38e+01 a.35.1.6 105254 1ztpA 251 2.43e+01 1n82A 331 2.43e+01 c.1.8.3 91703 1wpaA 114 2.45e+01 1r62A 160 2.45e+01 d.122.1.3 104816 1wmhA 89 2.47e+01 2d81A 318 2.47e+01 1p8xA 344 2.50e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1t7lA 766 2.51e+01 1f24A 402 2.55e+01 1rom a.104.1.1 18953 1iapA 211 2.58e+01 a.91.1.1 62119 1mkfA 382 2.60e+01 b.116.1.1 79232 2h1nA 567 2.64e+01 1zwwA 256 2.65e+01 1gu7A 364 2.68e+01 b.35.1.2,c.2.1.1 83321,83322 1wl9A 440 2.72e+01 2aobA 99 2.73e+01 2fh1A 344 2.75e+01 1u2eA 289 2.75e+01 1uuhA 159 2.79e+01 d.169.1.4 100008 1rtwA 220 2.79e+01 a.132.1.3 97823 2gp5A 349 2.85e+01 1rrmA 386 2.91e+01 e.22.1.2 105081 1o3yA 166 2.91e+01 c.37.1.8 86618 1lm8B 118 2.97e+01 d.15.1.1 74033 1o26A 232 2.97e+01 d.207.1.1 86566 1gttA 429 3.01e+01 d.177.1.1,d.177.1.1 70529,70530 1v9mA 323 3.01e+01 f.40.1.1 100543 1glcG 501 3.11e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 2ahqA 76 3.17e+01 1z08A 170 3.18e+01 2carA 196 3.20e+01 1w32A 348 3.21e+01 1b3uA 588 3.22e+01 1b3uA a.118.1.2 19135 2d2sA 235 3.27e+01 1avsA 90 3.29e+01 1cll a.39.1.5 17226 1yzyA 413 3.31e+01 1az9 457 3.33e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1vpqA 273 3.33e+01 1cpcA 162 3.33e+01 1cpcA a.1.1.3 15643 1aj8A 371 3.34e+01 1aj8A a.103.1.1 18900 1qksA 567 3.37e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1ail 73 3.38e+01 1ail a.16.1.1 16381 2bh8A 101 3.38e+01 1vctA 205 3.43e+01 2c43A 323 3.47e+01 1fcdA 401 3.48e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 2g7zA 282 3.48e+01 2bydA 323 3.50e+01 1dofA 403 3.51e+01 1c3cA a.127.1.1 19429 1jpzA 473 3.51e+01 a.104.1.1 67069 1fa0A 537 3.54e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1ug0A 88 3.55e+01 a.217.1.1 107822 1ni9A 338 3.58e+01 e.7.1.2 85739 1k24A 253 3.59e+01 f.4.4.2 72002 1o0yA 260 3.59e+01 c.1.10.1 80756 1yg2A 179 3.61e+01 1jnrB 150 3.64e+01 d.58.1.5 66969 1n13B 113 3.66e+01 1xbsA 149 3.67e+01 1go4A 205 3.78e+01 d.135.1.1 70292 1z21A 112 3.85e+01 1fgyA 127 3.94e+01 1faoA b.55.1.1 26976 1go4E 100 3.96e+01 h.1.22.1 70296 1vmiA 355 3.98e+01 1wrmA 165 3.99e+01 1sjiA 350 4.00e+01 1lyxA 248 4.04e+01 c.1.1.1 78304 1pq4A 291 4.06e+01 c.92.2.2 94995 1jyrA 96 4.07e+01 d.93.1.1 71969 1xn9A 101 4.09e+01 1r5zA 323 4.09e+01 f.40.1.1 97135 1o7fA 469 4.10e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 1s0yB 71 4.10e+01 d.80.1.1 98315 2d1yA 256 4.13e+01 1l6kA 77 4.13e+01 h.6.1.1 77724 1vcbA 118 4.19e+01 1vcbA d.15.1.1 37603 2bwvA 440 4.21e+01 1x91A 153 4.23e+01 1uyrA 737 4.25e+01 c.14.1.4,c.14.1.4 100188,100189 1hfoA 113 4.25e+01 d.80.1.3 61006 1a4iA 301 4.30e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1pmmA 466 4.36e+01 c.67.1.6 94901 1ek8A 185 4.39e+01 1ek8A d.67.3.1 59444 1yf2A 425 4.39e+01 1eg3A 261 4.46e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1ln1A 214 4.47e+01 d.129.3.2 74038 1fi2A 201 4.50e+01 1fi2A b.82.1.2 59845 1a6i 217 4.51e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1clxA 347 4.56e+01 1taxA c.1.8.3 28899 1xjzA 233 4.59e+01 1szoA 257 4.60e+01 c.14.1.3 106164 1sk4A 163 4.62e+01 d.118.1.1 105664 1pmi 440 4.65e+01 1pmi b.82.1.3 28114 1pz4A 116 4.66e+01 d.106.1.1 95400 1div 149 4.68e+01 1div d.99.1.1,d.100.1.1 40692,40693 1xtnA 120 4.70e+01 1bjwA 382 4.78e+01 1bjwA c.67.1.1 34349 1qsdA 106 4.80e+01 1qsdA a.7.5.1 16335 2et1A 201 4.82e+01 1ylmA 144 4.83e+01 1tvlA 454 4.83e+01 c.1.16.4 107366 2fj6A 82 4.90e+01 2gmyA 153 4.92e+01 1zndA 174 4.93e+01 2anwA 241 4.93e+01 1tuoA 464 4.97e+01 1jfmA 174 4.98e+01 d.19.1.1 66640 1tn4 159 4.98e+01 1ncx a.39.1.5 17248 1z6oM 191 5.00e+01 1fzyA 149 5.01e+01 d.20.1.1 65072 1qy1A 174 5.02e+01 b.60.1.1 96568 1mjc 69 5.03e+01 1mjc b.40.4.5 25319 1q5yA 85 5.04e+01 d.58.18.4 95950 2f6lA 166 5.07e+01 1ufzA 83 5.10e+01 a.5.9.1 107821 1s9kD 53 5.14e+01 1ia9A 280 5.15e+01 1ia9A d.144.1.5 62113 2fp1A 166 5.20e+01 1hl9A 449 5.24e+01 b.71.1.3,c.1.8.11 90650,90651 1w23A 360 5.24e+01 1uzcA 71 5.27e+01 a.159.2.1 100222 1xkrA 206 5.32e+01 1rgxA 114 5.36e+01 g.77.1.1 104932 1nbwA 607 5.37e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1sxrA 183 5.43e+01 d.118.1.1 106101 1neyA 247 5.46e+01 c.1.1.1 80449 1f20A 435 5.47e+01 b.43.4.1,c.25.1.4 64932,64933 1jj2L 194 5.47e+01 1ffkI d.12.1.2 63097 2b7kA 200 5.56e+01 1w6sB 74 5.63e+01 1t3jA 96 5.65e+01 h.4.16.1 106356 2fcjA 119 5.65e+01 2f60K 64 5.71e+01 1x1iA 752 5.74e+01 1d8hA 311 5.75e+01 1d8iA d.63.1.1 39544 1ym3A 215 5.76e+01 1ni5A 433 5.78e+01 c.26.2.5,d.229.1.1 80533,80534 1jchA 551 5.80e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1lbeA 258 5.85e+01 1lbeA e.4.1.1 42773 1esmA 316 5.95e+01 1esmA c.37.1.6 31953 1zfpE 98 5.96e+01 1griA d.93.1.1 40465 1nfp 228 5.98e+01 1nfp c.1.16.2 29555 1xteA 154 6.03e+01 1pytA 94 6.06e+01 1pytA d.58.3.1 39064 2aeuA 374 6.08e+01 1ux8A 132 6.09e+01 1f8vA 355 6.17e+01 2bbvA b.121.4.4 23329 2gqrA 237 6.17e+01 1a02F 56 6.22e+01 1a02F h.1.3.1 45534 1ois 223 6.22e+01 1a36A e.15.1.1 43267 2gkpA 167 6.25e+01 1u7kA 131 6.27e+01 1jv4A 162 6.27e+01 b.60.1.1 67343 1n2zA 245 6.36e+01 c.92.2.2 79865 1b5pA 385 6.39e+01 c.67.1.1 90403 1onwA 390 6.39e+01 b.92.1.7,c.1.9.13 87172,87173 2fnjB 118 6.51e+01 1f5aA 513 6.52e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1sfe 180 6.53e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 2ex0A 399 6.55e+01 1fzqA 181 6.56e+01 1hurA c.37.1.8 32060 1ziwA 680 6.56e+01 1f2eA 201 6.57e+01 1a0fA a.45.1.1,c.47.1.5 17745,33039 1v60A 123 6.57e+01 1m3qA 317 6.60e+01 a.96.1.3,d.129.1.2 91184,91185 1l8nA 679 6.67e+01 c.1.8.10,d.92.2.2 84564,84565 1naqA 112 6.68e+01 d.58.5.2 91761 4icb 76 6.69e+01 4icb a.39.1.1 17145 1wxcB 134 6.70e+01 2ga1A 106 6.71e+01 1rr7A 129 6.73e+01 a.4.1.14 105075 1u8xX 472 6.76e+01 c.2.1.5,d.162.1.2 107741,107742 1o5xA 248 6.82e+01 c.1.1.1 92528 1nmeB 92 6.82e+01 1cnt1 187 6.83e+01 1cnt3 1w7bA 339 6.85e+01 1n45A 233 6.91e+01 a.132.1.1 79981 1o5kA 306 6.93e+01 c.1.10.1 92504 1xiuA 230 6.94e+01 1miuA 738 6.99e+01 a.170.1.1,a.171.1.1,b.40.4.3,b.40.4.3,b.40.4.3 79153,79154,79155,79156,79157 1yz4A 160 7.00e+01 1aqm 453 7.07e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1vqoM 195 7.08e+01 1bu7A 455 7.16e+01 1bu7A a.104.1.1 18937 1wdcC 156 7.18e+01 1wdcC a.39.1.5 17317 1mup 166 7.22e+01 1mup b.60.1.1 27133 1wc9A 169 7.25e+01 1jr7A 311 7.26e+01 b.82.2.3 63255 1s2xA 206 7.27e+01 a.47.3.1 105229 1wx1A 335 7.28e+01 1eyvA 156 7.29e+01 1eyvA 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