# List of top-scoring protein chains for t04-100-30-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 2gfgA 193 3.31e-01 1y2qA 143 3.73e-01 1mp9A 198 5.05e-01 d.129.1.1,d.129.1.1 91385,91386 1vpjA 192 1.60e+00 1v5vA 401 1.97e+00 1xqaA 113 2.06e+00 1ckv 141 2.09e+00 1ckv d.137.1.1 41452 1qhtA 775 2.32e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1s69A 124 2.64e+00 a.1.1.1 105305 1ockA 412 2.65e+00 c.117.1.1 86802 1u94A 356 2.67e+00 c.37.1.11,d.48.1.1 107743,107744 1ofuA 320 2.78e+00 c.32.1.1,d.79.2.1 86972,86973 1vmbA 140 3.14e+00 1gntA 553 3.31e+00 e.26.1.1 70290 1e2uA 553 3.38e+00 1e1dA e.26.1.1 43362 1atiA 505 3.47e+00 1atiA c.51.1.1,d.104.1.1 33196,40745 1aisA 182 3.58e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1j8yF 297 3.71e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1obbA 480 3.94e+00 c.2.1.5,d.162.1.2 86760,86761 1rtxA 123 4.25e+00 a.1.1.1 97827 1tqjA 230 4.34e+00 c.1.2.2 107228 1tzjA 338 4.68e+00 1vgjA 184 4.72e+00 2reb 352 4.74e+00 2reb c.37.1.11,d.48.1.1 32282,38767 1dlyA 164 5.06e+00 1dlyA a.1.1.1 14983 1sesA 421 5.37e+00 1sesA a.2.7.1,d.104.1.1 15710,40710 1gx5A 536 5.47e+00 e.8.1.4 70682 1vetB 125 5.57e+00 d.110.7.1 108554 1ubeA 349 5.73e+00 c.37.1.11,d.48.1.1 88412,88413 1gnlA 544 5.86e+00 e.26.1.1 70287 1dtwB 342 5.92e+00 1qs0B c.36.1.7,c.48.1.2 31828,33102 1wqaA 455 6.14e+00 1fx2A 235 6.66e+00 1fx2A d.58.29.1 39430 1mjhA 162 6.75e+00 1mjhA c.26.2.4 31639 1us5A 314 6.81e+00 c.94.1.1 99856 1gudA 288 6.95e+00 c.93.1.1 83326 1vkhA 273 7.17e+00 c.69.1.32 108662 1nx8A 273 7.52e+00 b.82.2.8 86374 1cliA 345 7.75e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 1fvuB 125 7.97e+00 1ixxB d.169.1.1 42346 2bb6A 414 8.34e+00 1v6tA 255 8.88e+00 1rp4A 389 8.93e+00 a.227.1.1 105027 1twuA 139 1.04e+01 d.32.1.8 107413 1q9jA 422 1.15e+01 c.43.1.2,c.43.1.2 104590,104591 2abwA 227 1.16e+01 1nf9A 207 1.24e+01 c.33.1.3 85631 1eziA 228 1.26e+01 1eyrA c.68.1.13 34512 1fyeA 229 1.26e+01 1fyeA c.23.16.4 31477 1avyA 74 1.32e+01 1avyB h.1.17.1 45656 1e8pA 46 1.35e+01 g.55.1.1 59385 1rpxA 230 1.35e+01 1rpxA c.1.2.2 28536 1rpjA 288 1.36e+01 2dri c.93.1.1 35656 1c2pA 576 1.37e+01 1quvA e.8.1.4 43117 1vhwA 253 1.40e+01 c.56.2.1 100706 1kyqA 274 1.42e+01 c.2.1.11,e.37.1.1 73281,73282 1zetA 388 1.44e+01 1xzoA 174 1.49e+01 1qs0B 338 1.50e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2bfdB 345 1.50e+01 1b24A 188 1.53e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1qtoA 122 1.60e+01 1bylA d.32.1.2 38494 2gf6A 135 1.62e+01 1v37A 177 1.63e+01 1n3yA 198 1.66e+01 c.62.1.1 79976 1u9iA 519 1.69e+01 1nv8A 284 1.75e+01 c.66.1.30 86224 1yj7A 171 1.76e+01 1olsB 342 1.78e+01 c.36.1.7,c.48.1.2 93332,93333 1zin 217 1.78e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1x7yB 342 1.79e+01 1rthA 560 1.79e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1v1rB 342 1.90e+01 c.36.1.7,c.48.1.2 108273,108274 1z92B 219 1.91e+01 2g0cA 76 1.94e+01 1rz3A 201 1.94e+01 c.37.1.6 98132 1c7gA 456 1.99e+01 c.67.1.2 90415 2acvA 463 2.00e+01 1vr6A 350 2.01e+01 1ymqA 261 2.06e+01 1vdxA 184 2.16e+01 2b4gA 317 2.16e+01 1cc8A 73 2.17e+01 1cc8A d.58.17.1 39343 1ylxA 103 2.18e+01 1jv1A 505 2.23e+01 c.68.1.5 71892 1skoB 130 2.27e+01 d.110.7.1 105677 1x6vA 630 2.31e+01 1nf8A 207 2.38e+01 c.33.1.3 85630 1pvgA 418 2.40e+01 d.14.1.3,d.122.1.2 95161,95162 1xp8A 366 2.41e+01 1rzmA 338 2.44e+01 c.1.10.4 105137 1iae 200 2.44e+01 1iae d.92.1.8 40311 1j98A 157 2.44e+01 1j98A d.185.1.2 62755 1xi1A 575 2.48e+01 1vrtA 560 2.54e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 2asfA 137 2.62e+01 1g6hA 257 2.62e+01 1gajA c.37.1.12 60318 1oltA 457 2.65e+01 c.1.28.2 93334 1oo0B 110 2.65e+01 d.58.7.1 87183 1e25A 282 2.68e+01 1e25A e.3.1.1 42731 1ezwA 349 2.76e+01 1ezwA c.1.16.3 29558 1sffA 426 2.76e+01 c.67.1.4 105482 1jg5A 83 2.79e+01 d.205.1.1 66666 1fm0E 150 2.80e+01 1fmaE d.41.5.1 38629 1hfoA 113 2.82e+01 d.80.1.3 61006 1ufkA 254 2.84e+01 c.66.1.39 99340 1a73A 163 2.92e+01 1a73A d.4.1.3 37145 1uheA 97 2.92e+01 1lfpA 249 2.96e+01 e.39.1.1 73885 1knyA 253 2.97e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 2b5iD 217 3.00e+01 1xmxA 385 3.02e+01 1p3jA 217 3.04e+01 c.37.1.1,g.41.2.1 94022,94023 1b5eA 246 3.12e+01 1b5eA d.117.1.1 41056 1aky 221 3.13e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1jx6A 342 3.14e+01 c.93.1.1 67406 2b4vA 468 3.15e+01 1r89A 437 3.16e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1nonA 179 3.17e+01 c.61.1.1 103868 2h3bA 494 3.22e+01 1zip 217 3.26e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1rhcA 330 3.27e+01 c.1.16.3 97468 2fuvA 549 3.31e+01 1vhoA 346 3.36e+01 b.49.3.1,c.56.5.4 100694,100695 1u14A 172 3.37e+01 c.51.4.3 107579 1gxjA 186 3.42e+01 d.215.1.1 70707 1iab 200 3.44e+01 1iae d.92.1.8 40312 1j0dA 341 3.45e+01 c.79.1.1 83902 2alzA 390 3.46e+01 2fcr 173 3.49e+01 1rcf c.23.5.1 31151 1f5aA 513 3.49e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1t3nA 388 3.53e+01 d.240.1.1,e.8.1.7 106363,106364 1pv9A 348 3.61e+01 c.55.2.1,d.127.1.1 95157,95158 2f2hA 773 3.65e+01 2gjsA 176 3.65e+01 1r8eA 278 3.73e+01 a.6.1.3,d.60.1.1 104843,104844 1w66A 232 3.79e+01 1xfjA 261 3.80e+01 d.194.1.2 109585 1h75A 81 3.84e+01 1h75A c.47.1.1 60716 1j34B 123 3.89e+01 d.169.1.1 84049 1rm6A 769 3.90e+01 1x13A 401 3.95e+01 1d2sA 170 3.97e+01 1d2sA b.29.1.4 24221 1ii7A 333 3.97e+01 1ii7A d.159.1.4 62415 1wryA 121 4.00e+01 1eudB 396 4.04e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 2bjiA 277 4.06e+01 1jyhA 157 4.06e+01 d.60.1.3 71956 1a8p 258 4.10e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1tk9A 188 4.13e+01 c.80.1.3 107082 1f5fA 205 4.17e+01 1d2sA b.29.1.4 24222 1rcf 169 4.20e+01 1rcf c.23.5.1 31170 1zghA 260 4.22e+01 1louA 101 4.26e+01 1ris d.58.14.1 39323 2cdnA 201 4.27e+01 1vypX 364 4.30e+01 c.1.4.1 108905 1lssA 140 4.36e+01 c.2.1.9 74246 1gvoA 364 4.38e+01 c.1.4.1 76357 1yvkA 163 4.45e+01 1oboA 169 4.48e+01 c.23.5.1 86776 1xg9A 260 4.48e+01 1w25A 459 4.49e+01 1qj2C 285 4.53e+01 1qj2C 2ca6A 386 4.55e+01 1y1pA 342 4.57e+01 1kafA 108 4.58e+01 d.199.1.1 68372 1ymkA 175 4.59e+01 1ow1A 195 4.66e+01 b.131.1.3 93625 1q79A 514 4.68e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1g5hA 454 4.71e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1c7sA 858 4.75e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1g0uG 252 4.75e+01 d.153.1.4 41952 1lc5A 364 4.81e+01 c.67.1.1 73827 1wy2A 351 4.83e+01 1h61A 364 4.85e+01 1oyc c.1.4.1 60657 1xb4A 202 4.85e+01 1vyrA 364 4.85e+01 c.1.4.1 108906 2a2kA 175 4.86e+01 2abbA 364 4.88e+01 1j6pA 418 4.91e+01 b.92.1.4,c.1.9.9 77089,77090 1yhtA 367 5.01e+01 1vm8A 534 5.03e+01 1cg2A 393 5.04e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1ujmA 342 5.06e+01 1gnd 447 5.07e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 1wy7A 207 5.10e+01 1ox3A 109 5.10e+01 h.1.17.1 93668 1qqcA 773 5.11e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1fsz 372 5.13e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 8abp 306 5.15e+01 8abp c.93.1.1 35647 1e3jA 352 5.25e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1tikA 213 5.25e+01 c.23.5.3 107003 2ci1A 275 5.26e+01 1p1mA 406 5.32e+01 b.92.1.4,c.1.9.9 87696,87697 1rypA 243 5.33e+01 1pmaA d.153.1.4 41932 1qb0A 211 5.33e+01 1c25 c.46.1.1 32699 2atxA 194 5.38e+01 1wvfA 520 5.42e+01 1gwyA 175 5.45e+01 b.97.1.1 83356 1xviA 275 5.45e+01 1hqkA 154 5.46e+01 c.16.1.1 65902 1t5bA 201 5.47e+01 c.23.5.3 106433 1cnt1 187 5.51e+01 1cnt3 1xgsA 295 5.51e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1mugA 168 5.59e+01 1mugA c.18.1.2 31030 1x3zA 335 5.60e+01 1sw5B 275 5.62e+01 c.94.1.1 106070 1qnaA 200 5.64e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1ur5A 309 5.66e+01 c.2.1.5,d.162.1.1 99807,99808 1vljA 407 5.66e+01 e.22.1.2 108832 1yrgA 385 5.68e+01 1yrgA c.10.1.2 30854 1luaA 287 5.78e+01 c.2.1.7,c.58.1.4 78216,78217 1p5fA 189 5.80e+01 c.23.16.2 94142 1r9wA 145 5.84e+01 d.89.1.2 97264 1evxA 162 5.88e+01 1a73A d.4.1.3 37149 1w5fA 353 5.90e+01 1f2dA 341 5.91e+01 1f2dA c.79.1.1 35298 1s0yA 76 5.93e+01 d.80.1.1 98314 1q5qA 259 5.95e+01 d.153.1.4 95904 1x67A 146 5.96e+01 1u7iA 136 5.96e+01 d.32.1.7 107724 1t3kA 152 5.96e+01 c.46.1.1 106357 1cd8 114 6.00e+01 1cd8 b.1.1.1 19714 1jj2S 119 6.09e+01 1ffkQ b.34.5.1 63104 1s72T 120 6.09e+01 b.34.5.1 105339 2fp4B 395 6.14e+01 1wvcA 259 6.14e+01 1jh6A 189 6.16e+01 d.61.1.1 66707 1jayA 212 6.21e+01 c.2.1.6 66478 1ooeA 236 6.27e+01 c.2.1.2 87196 1nvmB 312 6.29e+01 c.2.1.3,d.81.1.1 86251,86252 1dlwA 116 6.32e+01 1dlyA a.1.1.1 14982 1o94A 729 6.39e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2f4nA 273 6.44e+01 1gefA 123 6.46e+01 1gefA c.52.1.18 60465 1p57A 114 6.54e+01 d.170.1.2 94125 1djqA 729 6.56e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1vqoT 120 6.58e+01 1y8qA 346 6.62e+01 1ebdC 41 6.77e+01 1ebdC a.9.1.1 16355 1ys4A 354 6.78e+01 2bkyX 89 6.91e+01 1qgxA 357 6.94e+01 1qgxA e.7.1.1 42973 1v60A 123 6.94e+01 1ka1A 357 6.97e+01 e.7.1.1 68369 1p1lA 102 7.00e+01 d.58.5.2 87695 1eqoA 158 7.08e+01 1hka 1oz9A 150 7.15e+01 d.92.1.15 93808 1jqlB 140 7.18e+01 c.37.1.20 63234 1d5tA 433 7.19e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 2culA 232 7.23e+01 1xhvA 257 7.27e+01 c.52.1.19 109597 1am7A 158 7.31e+01 1am7A d.2.1.4 36981 1gcb 454 7.35e+01 3gcb d.3.1.1 37034 1n9lA 109 7.38e+01 d.110.3.6 85468 1hyeA 313 7.49e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1f9yA 158 7.54e+01 d.58.30.1 83249 2g7zA 282 7.55e+01 5abp 306 7.55e+01 8abp c.93.1.1 35651 1et0A 269 7.59e+01 1et0A e.17.1.1 43289 1iow 306 7.64e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1gy7A 125 7.68e+01 d.17.4.2 70738 1md6A 154 7.69e+01 b.42.1.2 91242 2polA 366 7.69e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1ne9A 335 7.71e+01 d.108.1.4,d.108.1.4 91839,91840 1kc6A 257 7.72e+01 c.52.1.19 68419 1b8zA 90 7.75e+01 1huuA a.55.1.1 17902 1chuA 540 7.76e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ju2A 536 7.83e+01 c.3.1.2,d.16.1.1 77169,77170 1tzfA 259 7.88e+01 c.68.1.13 107476 1zxiF 288 7.91e+01 1hd2A 161 7.95e+01 c.47.1.10 60962 2amyA 246 7.96e+01 1jg1A 235 8.03e+01 c.66.1.7 66661 1za7A 165 8.05e+01 1xr4A 509 8.05e+01 1usgA 346 8.08e+01 c.93.1.1 99864 1ecsA 126 8.16e+01 1ecsA d.32.1.2 59407 1xa3A 437 8.16e+01 1uroA 367 8.19e+01 1uroA c.1.22.1 29675 1i88A 389 8.19e+01 c.95.1.2,c.95.1.2 66070,66071 1g3qA 237 8.21e+01 1hyqA c.37.1.10 60237 1r5mA 425 8.21e+01 1ugjA 141 8.28e+01 b.41.1.3 107826 1ekgA 127 8.31e+01 1dlxA d.82.2.1 40021 1i2kA 269 8.35e+01 e.17.1.1 90661 2c5aA 379 8.36e+01 1ewkA 490 8.37e+01 1ewkA c.93.1.1 35712 2ez6A 221 8.51e+01 1jnuA 104 8.56e+01 d.110.3.6 71762 2bh1A 250 8.61e+01 1k0rA 366 8.65e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1u6tA 121 8.69e+01 1djnA 729 8.72e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1tljA 213 8.72e+01 d.282.1.1 107126 2audA 257 8.73e+01 2tmdA 729 8.76e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1b1cA 181 8.76e+01 1amoA c.23.5.2 31212 1kk1A 410 8.89e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1xtqA 177 8.96e+01 1bykA 255 8.98e+01 1bykA c.93.1.1 35706