# List of top-scoring protein chains for t06-100-30-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 2fhqA 141 6.08e-10 1dnlA 199 8.97e-10 1ci0A b.45.1.1 25753 1g79A 218 1.30e-09 1ci0A b.45.1.1 25752 1rfeA 162 1.03e-08 1nrgA 261 1.21e-08 b.45.1.1 80694 1ty9A 222 1.58e-08 1vl7A 157 1.12e-07 b.45.1.1 108732 2fg9A 178 2.09e-07 2aq6A 147 1.06e-06 2furA 209 8.51e-06 1w9aA 147 9.49e-06 2asfA 137 2.67e-05 1xhnA 184 1.05e-04 2arzA 247 4.98e-03 1ejeA 192 4.80e-02 1ejeA b.45.1.2 25757 1flmA 122 1.50e-01 1axj b.45.1.1 25747 2f6kA 307 2.05e-01 1tr8A 102 2.72e-01 2a1fA 247 3.47e-01 1jyhA 157 4.02e-01 d.60.1.3 71956 1pvmA 184 7.31e-01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ye8A 178 7.45e-01 2ahuA 531 1.14e+00 1l0wA 580 1.44e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1vc1A 110 1.46e+00 c.13.2.1 108493 1mjfA 281 1.58e+00 c.66.1.17 79198 1zybA 232 1.67e+00 2bneA 241 1.70e+00 1r4pB 70 1.83e+00 b.40.2.1 97026 1zt3A 80 2.14e+00 2fcjA 119 2.20e+00 1vpkA 378 2.24e+00 1zkjA 359 2.38e+00 1d2fA 390 2.41e+00 1d2fA c.67.1.3 34411 1wzoA 246 2.43e+00 1a7j 290 2.60e+00 1a7j c.37.1.6 31952 1kb0A 677 2.60e+00 a.3.1.6,b.70.1.1 68378,68379 1yc5A 246 2.61e+00 2g09A 297 2.76e+00 2f15A 96 2.79e+00 3thiA 371 3.09e+00 2thiA c.94.1.1 35792 1jwqA 179 3.37e+00 c.56.5.6 90921 1i0rA 169 3.42e+00 1i0rA b.45.1.2 61489 1byyA 53 3.93e+00 j.12.1.1 46147 1rgzA 363 4.09e+00 e.3.1.1 97457 1zd9A 188 4.16e+00 1ywqA 200 4.28e+00 1vlyA 338 4.32e+00 b.44.2.1,d.250.1.1 108871,108872 1x72A 334 4.56e+00 d.126.1.6 109495 1t77A 414 4.57e+00 1v54B 227 4.92e+00 b.6.1.2,f.17.2.1 100322,100323 1udzA 182 5.17e+00 b.51.1.1 99239 1c8uA 285 5.41e+00 1c8uA d.38.1.3,d.38.1.3 38547,38548 1vggA 161 5.58e+00 2d0iA 333 5.75e+00 1wnyA 186 5.81e+00 1z2wA 192 6.09e+00 1v0wA 506 6.24e+00 d.136.1.2,d.136.1.2 108220,108221 1p80A 753 6.55e+00 c.23.16.3,e.5.1.1 94337,94338 1i24A 404 6.76e+00 c.2.1.2 83663 2av5A 120 7.01e+00 1x6zA 123 7.28e+00 1x0pA 143 7.36e+00 1h5uA 842 7.61e+00 1a8i c.87.1.4 60655 2cmuA 342 7.63e+00 1qtnA 164 7.78e+00 1pauA c.17.1.1 30999 1et9A 204 7.96e+00 1an8 b.40.2.2,d.15.6.1 25204,37793 2chnA 716 8.15e+00 1cliA 345 8.35e+00 1cliA d.79.4.1,d.139.1.1 39816,41459 2a4hA 126 8.58e+00 1di6A 195 8.65e+00 1di6A c.57.1.1 33863 1j5pA 253 8.79e+00 d.81.1.3,c.2.1.3 71577,83092 2f4qA 346 8.85e+00 1a92A 50 8.92e+00 1a92A h.4.6.1 45791 1dlfH 124 8.95e+00 1igtB b.1.1.1 20383 1oflA 481 9.08e+00 b.80.1.4 103934 1ni4B 341 9.16e+00 c.36.1.7,c.48.1.2 85729,85730 1rgyA 360 9.86e+00 e.3.1.1 97456 1w6sA 599 9.97e+00 1e4iA 447 1.05e+01 1e70M c.1.8.4 59225 2dcnA 311 1.10e+01 1gweA 503 1.15e+01 e.5.1.1 70667 1vrmA 325 1.17e+01 3sil 379 1.29e+01 3sil b.68.1.1 27542 2fj8A 125 1.32e+01 2azeA 155 1.34e+01 1kb9D 246 1.36e+01 a.3.1.3,f.23.11.1 77317,77318 1pfo 500 1.39e+01 1pfo f.9.1.1 43826 1gzcA 239 1.40e+01 b.29.1.1 70803 2bwrA 401 1.44e+01 4pgaA 337 1.47e+01 4pgaA c.88.1.1 35565 1j2gA 319 1.51e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 3pcgA 200 1.52e+01 3pchA b.3.6.1 22647 1nmeA 146 1.55e+01 c.17.1.1 85874 1ei5A 520 1.55e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 2g6fX 59 1.56e+01 1sl4A 155 1.62e+01 d.169.1.1 105710 1r0vA 305 1.65e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1u02A 239 1.67e+01 c.108.1.15 107538 2ghsA 326 1.70e+01 1pbyA 489 1.74e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1pz5B 220 1.75e+01 b.1.1.1,b.1.1.2 95403,95404 1gd1O 334 1.79e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2fdiA 211 1.80e+01 1kgdA 180 1.82e+01 c.37.1.1 68582 1zx5A 300 1.84e+01 1bouB 302 1.86e+01 1bouB c.56.6.1 33859 1sd4A 126 1.91e+01 a.4.5.39 105428 1zdzA 302 1.92e+01 1mjnA 179 1.93e+01 c.62.1.1 79210 1mp9A 198 1.93e+01 d.129.1.1,d.129.1.1 91385,91386 1nynA 131 1.94e+01 d.235.1.1 86410 2bgiA 272 1.97e+01 2bv2A 83 1.97e+01 1ln1A 214 1.97e+01 d.129.3.2 74038 1ksiA 642 1.99e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1o50A 157 2.11e+01 d.37.1.1,d.37.1.1 92478,92479 1zxtA 76 2.12e+01 2ffyA 358 2.13e+01 1npsA 88 2.13e+01 1prs b.11.1.1 23622 1pmi 440 2.13e+01 1pmi b.82.1.3 28114 1qwdA 177 2.14e+01 b.60.1.1 96471 1ofdA 1520 2.14e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2erfA 209 2.15e+01 1vpjA 192 2.15e+01 1od3A 168 2.16e+01 b.18.1.10 86825 1xphA 150 2.16e+01 1ylnA 252 2.16e+01 2eu9A 355 2.18e+01 1of5A 221 2.18e+01 d.17.4.2 86933 1st9A 143 2.20e+01 c.47.1.10 98987 1z4eA 153 2.23e+01 1zd7A 159 2.25e+01 1tfr 305 2.26e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1uuhA 159 2.31e+01 d.169.1.4 100008 1gskA 513 2.33e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1gtfA 74 2.34e+01 b.82.5.1 70460 2fp4B 395 2.34e+01 1r3dA 264 2.34e+01 1uu3A 310 2.37e+01 d.144.1.7 99999 2bjrA 368 2.38e+01 1g5cA 170 2.39e+01 1g5cA c.53.2.1 60264 1yvcA 70 2.47e+01 1f7uA 607 2.48e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1jjdA 55 2.49e+01 1jjdA g.46.1.1 63116 1g7nA 131 2.52e+01 b.60.1.2 83274 1vkbA 161 2.56e+01 d.269.1.1 108643 1vgyA 393 2.57e+01 c.56.5.4,d.58.19.1 100620,100621 1u7iA 136 2.58e+01 d.32.1.7 107724 1pg4A 652 2.60e+01 e.23.1.1 88067 1r2zA 274 2.71e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1hw7A 255 2.72e+01 1i7fA d.193.1.1 61297 1uyjA 296 2.73e+01 f.8.1.2 108143 1xw3A 110 2.74e+01 1f6bA 198 2.81e+01 c.37.1.8 64986 1z5bA 469 2.86e+01 1up9A 107 2.91e+01 1j1lA 290 2.91e+01 b.82.1.12 90766 1c1lA 136 2.95e+01 1c1lA b.29.1.3 24219 1mf7A 194 2.97e+01 c.62.1.1 84937 1a4iA 301 2.99e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1uzxA 169 3.08e+01 d.20.1.2 100238 1o8xA 146 3.10e+01 c.47.1.10 86681 1rocA 155 3.10e+01 b.1.22.1 97673 1xdfA 157 3.11e+01 1xjcA 169 3.11e+01 2fwuA 157 3.11e+01 2ajgA 196 3.14e+01 1i7wB 151 3.16e+01 1i7wB j.71.1.1 61910 1qh5A 260 3.17e+01 1qh5A d.157.1.2 42057 1r6xA 395 3.20e+01 b.122.1.3,c.26.1.5 97167,97168 1rttA 193 3.25e+01 c.23.5.4 105098 1gudA 288 3.35e+01 c.93.1.1 83326 1ojrA 274 3.41e+01 c.74.1.1 93147 2bw2A 140 3.42e+01 2bb3A 221 3.44e+01 1lr7A 74 3.47e+01 g.3.11.3,g.68.1.1 84679,84680 1jubA 311 3.49e+01 c.1.4.1 90908 1sx5A 244 3.51e+01 c.52.1.2 99023 2cfxA 144 3.52e+01 1ti6B 274 3.53e+01 b.3.5.1,d.58.1.5 106976,106977 2feaA 236 3.54e+01 1wm1A 317 3.56e+01 c.69.1.7 109405 1u7bA 261 3.60e+01 2cu3A 64 3.65e+01 1c0pA 363 3.67e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1u0kA 288 3.69e+01 d.21.1.2,d.21.1.2 107547,107548 1jysA 242 3.69e+01 c.56.2.1 77216 1z0wA 207 3.70e+01 1wj5A 120 3.74e+01 1mkmA 249 3.75e+01 a.4.5.33,d.110.2.2 79242,79243 1wj9A 211 3.78e+01 1cseI 71 3.88e+01 1egpA d.40.1.1 38559 2bhgA 209 3.94e+01 1jalA 363 3.95e+01 c.37.1.8,d.15.10.2 84138,84139 1y4tA 322 3.98e+01 2giyA 191 4.06e+01 1ash 150 4.09e+01 1ash a.1.1.2 15622 1u7nA 336 4.10e+01 c.77.1.4 107726 1hgxA 183 4.11e+01 1tc1A c.61.1.1 34027 1dbwA 126 4.12e+01 1dbwA c.23.1.1 31095 1uypA 432 4.14e+01 b.29.1.19,b.67.2.3 100176,100177 2ch4A 320 4.16e+01 1wdtA 665 4.17e+01 1zsyA 357 4.21e+01 1jnyA 435 4.22e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2d37A 176 4.26e+01 1iz6A 138 4.30e+01 b.34.5.2,b.40.4.5 76976,76977 1xg4A 295 4.34e+01 1bco 327 4.40e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1vbwA 68 4.40e+01 1rsy 152 4.40e+01 1rsy b.7.1.2 23192 1uv7A 110 4.41e+01 d.67.4.1 100040 2b06A 155 4.43e+01 1vjgA 218 4.47e+01 c.23.10.6 100810 1nwwA 149 4.47e+01 d.17.4.8 86306 2ayuA 417 4.48e+01 1uwvA 433 4.49e+01 b.40.4.12,c.66.1.40 100128,100129 1u04A 771 4.52e+01 b.34.14.1,c.55.3.10 107539,107540 1t0qA 498 4.53e+01 a.25.1.2 106220 1cfr 285 4.54e+01 1cfr c.52.1.7 33312 2f9sA 151 4.55e+01 8dfr 189 4.56e+01 1aoeA c.71.1.1 34895 1g5hA 454 4.58e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1yfsA 465 4.58e+01 1pe9A 361 4.59e+01 b.80.1.1 94595 1j5sA 463 4.61e+01 c.1.9.8 71580 1vcaA 202 4.61e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 1i2mA 216 4.61e+01 1byuA c.37.1.8 61568 1mpxA 615 4.62e+01 b.18.1.13,c.69.1.21 85041,85042 1iu8A 206 4.65e+01 c.56.4.1 71436 1wqaA 455 4.69e+01 1bw0A 416 4.73e+01 1bw0A c.67.1.1 34385 1rp0A 284 4.74e+01 1q52A 314 4.78e+01 c.14.1.3 95846 1wr8A 231 4.78e+01 1v5vA 401 4.85e+01 1brwA 433 4.85e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1khdA 345 4.90e+01 a.46.2.1,c.27.1.1 77400,77401 1viaA 175 4.91e+01 c.37.1.2 100754 1nf2A 268 4.91e+01 c.108.1.10 91849 1u14A 172 4.95e+01 c.51.4.3 107579 1ollA 188 4.97e+01 b.1.1.4,b.1.1.4 93313,93314 1e5pA 151 4.97e+01 1bj7 b.60.1.1 59272 1qbjA 81 4.98e+01 1qbjA a.4.5.19 16155 1q4rA 112 4.99e+01 d.58.4.4 95823 1ubkS 267 4.99e+01 e.19.1.1 88423 1cbs 137 5.03e+01 1hmt b.60.1.2 27201 1fyeA 229 5.04e+01 1fyeA c.23.16.4 31477 1pzxA 289 5.06e+01 c.119.1.1 95484 1fqtA 112 5.07e+01 1fqtA b.33.1.1 24441 1y0zA 330 5.08e+01 1wuiS 267 5.11e+01 1o4tA 133 5.11e+01 b.82.1.9 86622 1zirA 173 5.11e+01 2bitX 165 5.14e+01 1f9yA 158 5.14e+01 d.58.30.1 83249 1s12A 94 5.14e+01 2b8nA 429 5.15e+01 1pjxA 314 5.16e+01 b.68.6.1 104167 1yoaA 159 5.19e+01 1svmA 377 5.20e+01 1d1gA 168 5.32e+01 1d1gA c.71.1.1 34889 1i4uA 181 5.33e+01 b.60.1.1 61732 1jjtA 228 5.35e+01 1a7tA d.157.1.1 63139 1qo2A 241 5.35e+01 1qo2A c.1.2.1 28533 1e19A 314 5.36e+01 1b7bA c.73.1.1 34967 1rliA 184 5.40e+01 c.23.5.6 97647 1iab 200 5.40e+01 1iae d.92.1.8 40312 1wcdJ 441 5.41e+01 1d2mA 665 5.42e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1vqqA 646 5.45e+01 1zavA 180 5.46e+01 1or0B 528 5.47e+01 1vr4A 103 5.63e+01 1bteA 97 5.64e+01 1bteA g.7.1.3 44463 1iooA 196 5.68e+01 d.124.1.1 71250 1yzsA 121 5.68e+01 2b0oE 301 5.77e+01 1m98A 317 5.80e+01 a.175.1.1,d.17.4.6 78866,78867 1q8dA 108 5.81e+01 a.228.1.1 104554 1lp9E 194 5.82e+01 b.1.1.1,b.1.1.2 91086,91087 1lzlA 323 5.82e+01 c.69.1.2 78306 1vbvA 105 5.83e+01 1cdzA 96 5.83e+01 1cdzA c.15.1.1 30925 1qw1A 121 5.83e+01 2arpF 152 5.84e+01 2ae5B 528 5.86e+01 1jksA 294 5.91e+01 d.144.1.7 71710 2gibA 103 5.92e+01 1ehiA 377 5.96e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1v2xA 194 5.98e+01 c.116.1.1 100274 2b3gA 123 5.98e+01 1epuA 591 5.99e+01 1dn1A e.25.1.1 43358 1oi0A 124 6.08e+01 c.97.3.1 93045 1n9pA 207 6.13e+01 b.1.18.16 80343 2gefA 217 6.14e+01 1vckA 115 6.16e+01 1kngA 156 6.19e+01 c.47.1.10 72777 1kdxB 28 6.22e+01 1kewA 361 6.24e+01 c.2.1.2 68544 1q40B 219 6.27e+01 d.17.4.2 95771 1qhtA 775 6.28e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1knqA 175 6.30e+01 c.37.1.17 72786 1tig 94 6.36e+01 1tig d.68.1.1 39566 1dxy 333 6.40e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1orc 71 6.41e+01 1orc a.35.1.2 17054 1ux8A 132 6.44e+01 2fgeA 995 6.58e+01 1xeuA 263 6.58e+01 1lm8V 160 6.60e+01 b.3.3.1 74035 1m1hA 248 6.61e+01 b.114.1.1,d.58.42.1 78415,78416 1q1fA 151 6.62e+01 a.1.1.2 104476 1txlA 215 6.62e+01 b.60.1.4 107429 1y13A 181 6.62e+01 1wxiA 275 6.64e+01 2eifA 136 6.72e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1k20A 310 6.77e+01 c.107.1.1 68027 1zo2A 129 6.78e+01 2f4pA 147 6.79e+01 2f8yA 223 6.82e+01 1b3aA 67 6.83e+01 1b3aA d.9.1.1 37410 1qopB 396 6.91e+01 2tysB c.79.1.1 35270 1hy7A 173 6.93e+01 d.92.1.11 65957 1mtpB 43 6.93e+01 1o59A 355 6.94e+01 b.18.1.22,b.18.1.22 92495,92496 1im5A 180 6.95e+01 c.33.1.3 66211 1tif 78 6.96e+01 1tif d.15.8.1 37836 1f74A 293 6.99e+01 1nal3 c.1.10.1 29079 1ugiA 84 6.99e+01 1ugiA d.17.5.1 38125 1iqrA 420 7.04e+01 a.99.1.1,c.28.1.1 66275,66276 1ekjA 221 7.11e+01 1ekjB c.53.2.1 33364 2aefA 234 7.12e+01 1wy2A 351 7.15e+01 1vliA 385 7.24e+01 b.85.1.1,c.1.10.6 108830,108831 1fxkC 133 7.32e+01 1fxkC a.2.5.1 15702 1gy8A 397 7.33e+01 c.2.1.2 83376 1yloA 348 7.33e+01 1w2tA 432 7.35e+01 1bupA 386 7.41e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1gntA 553 7.75e+01 e.26.1.1 70290 1mkiA 330 7.79e+01 e.3.1.2 84994 2bc4A 211 7.81e+01 1heiA 451 7.81e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1si6X 282 7.83e+01 1j09A 468 7.86e+01 a.97.1.1,c.26.1.1 77025,77026 1v8qA 85 7.88e+01 b.84.4.1 108428 1ejfA 125 7.90e+01 1ejfA b.15.1.2 23683 1hrhA 136 7.97e+01 1rthA c.55.3.1 33577 1al3 324 7.97e+01 1al3 c.94.1.1 35835 1zbqA 327 8.00e+01 2cdcA 366 8.00e+01 1v4pA 157 8.04e+01 1z0nA 96 8.06e+01 1sc3A 178 8.08e+01 c.17.1.1 105416 2fgtA 417 8.15e+01 1zfjA 491 8.19e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1mb3A 124 8.20e+01 c.23.1.1 78907 2ai4A 119 8.28e+01 1n9lA 109 8.28e+01 d.110.3.6 85468 2g58A 121 8.28e+01 2conA 79 8.43e+01 1bkzA 135 8.43e+01 1a3k b.29.1.3 24202 1c7qA 445 8.46e+01 2pgi c.80.1.2 35307 1mtzA 293 8.47e+01 c.69.1.7 79467 1eaxA 241 8.47e+01 b.47.1.2 64889 2b4yA 271 8.49e+01 1b8dA 164 8.57e+01 1cpcA a.1.1.3 15665 1dgwX 79 8.57e+01 1caxB b.82.1.2 28091 1o9yA 84 8.60e+01 b.139.1.1 92692 2cy2A 174 8.69e+01 1l5pA 93 8.69e+01 d.15.4.1 73598 1nb9A 147 8.71e+01 b.43.5.1 85515 1q32A 544 8.73e+01 d.136.1.3,d.136.1.3 104507,104508 1o98A 511 8.74e+01 c.105.1.1,c.76.1.3 86684,86685 1o7dE 126 8.76e+01 1x75A 132 8.76e+01 1z84A 351 8.78e+01 1uc7A 125 8.80e+01 c.47.1.1 99163 1wsrA 375 8.99e+01