# 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 1dyqA 234 2.00e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 5.41e-01 2rslA c.53.1.1 33345 2fclA 169 7.59e-01 1sqsA 242 1.05e+00 c.23.5.5 98968 1repC 251 1.07e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1m93A 55 1.21e+00 e.1.1.1 91235 1qhlA 227 1.99e+00 1qhlA c.37.1.12 32382 2bg5A 324 2.72e+00 1ydmA 187 3.29e+00 1ex0A 731 3.44e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1regX 122 3.44e+00 1regX d.58.27.1 39406 2g9iA 249 3.67e+00 1y96B 85 3.70e+00 1zpvA 91 4.23e+00 1iz5A 249 4.35e+00 d.131.1.2,d.131.1.2 83834,83835 1v0lA 313 4.41e+00 c.1.8.3 108207 2afbA 351 4.43e+00 1d2oA 187 4.57e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1c7qA 445 4.62e+00 2pgi c.80.1.2 35307 2cxcA 144 4.84e+00 2b7eA 59 5.05e+00 1c52 131 5.18e+00 1c52 a.3.1.1 15810 1kqpA 271 5.20e+00 c.26.2.1 72883 1hdoA 206 5.47e+00 1he2A c.2.1.2 60965 1s55A 156 5.55e+00 1e0tA 470 6.68e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2flsA 132 7.00e+00 1b25A 619 7.41e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 1a53 247 7.47e+00 1a53 c.1.2.4 28564 1exg 110 7.53e+00 1exg b.2.2.1 22387 1sek 378 8.38e+00 1sek e.1.1.1 42675 1vkuA 100 8.39e+00 a.28.1.1 108690 2gmqA 118 8.51e+00 1zruA 264 8.80e+00 1o1zA 234 8.80e+00 c.1.18.3 86555 1o6dA 163 9.25e+00 c.116.1.3 92567 2fgtA 417 9.56e+00 1m4jA 142 9.81e+00 d.109.1.2 78602 1h72C 296 1.02e+01 d.14.1.5,d.58.26.1 60712,60713 1m07A 111 1.05e+01 d.5.1.1 78328 1qavA 90 1.06e+01 1qauA b.36.1.1 24777 1n8kA 374 1.09e+01 b.35.1.2,c.2.1.1 80298,80299 1i6lA 328 1.12e+01 c.26.1.1 66041 1bn8A 420 1.12e+01 1pcl b.80.1.1 28022 1a99A 344 1.14e+01 1pot c.94.1.1 35812 1o0yA 260 1.20e+01 c.1.10.1 80756 1tf1A 198 1.21e+01 d.110.2.2 106826 1b56 135 1.21e+01 1hmt b.60.1.2 27183 1t0hA 132 1.25e+01 b.34.2.1 106207 1bia 321 1.26e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1xwvA 129 1.27e+01 1t0aA 159 1.31e+01 1s0pA 176 1.37e+01 a.192.1.1 98300 1qlmA 316 1.42e+01 1qlmA d.147.1.1 41765 2aefA 234 1.50e+01 1u3wA 374 1.52e+01 1vqoL 165 1.52e+01 1nijA 318 1.52e+01 c.37.1.10,d.237.1.1 85741,85742 1xcbA 211 1.59e+01 a.4.5.38,c.2.1.12 109552,109553 2cygA 312 1.61e+01 2gfgA 193 1.62e+01 1qzgA 187 1.65e+01 b.40.4.3 96643 1idk 359 1.65e+01 1qcxA b.80.1.2 28025 1wwhA 119 1.68e+01 1vcvA 226 1.69e+01 1ej0A 180 1.71e+01 1ej0A c.66.1.2 34179 1wu3I 161 1.72e+01 1gyxA 76 1.72e+01 d.80.1.1 76387 1i8fA 81 1.73e+01 1i8fA b.38.1.1 61959 1qy1A 174 1.74e+01 b.60.1.1 96568 1s9rA 410 1.76e+01 d.126.1.4 98758 1ois 223 1.77e+01 1a36A e.15.1.1 43267 1s50A 259 1.79e+01 2etxA 209 1.80e+01 1dkuA 317 1.83e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1wrjA 156 1.84e+01 2asbA 251 1.86e+01 1fh9A 312 1.89e+01 1taxA c.1.8.3 28913 2fbyA 205 1.91e+01 1ydyA 356 1.92e+01 1zthA 258 1.95e+01 2bwfA 77 2.01e+01 1ma3A 253 2.02e+01 c.31.1.5 78883 5nul 138 2.02e+01 5nul c.23.5.1 31191 1p3dA 475 2.04e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2amhA 207 2.06e+01 1vjpA 394 2.08e+01 c.2.1.3,d.81.1.3 100828,100829 1tt8A 164 2.21e+01 1oj4A 283 2.23e+01 d.14.1.5,d.58.26.5 93083,93084 2bo4A 397 2.32e+01 1nf3C 128 2.34e+01 b.36.1.1 85596 1xkrA 206 2.34e+01 2gw6A 123 2.34e+01 1svpA 161 2.36e+01 1svpA b.47.1.3 26384 1vjjA 692 2.37e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1juvA 193 2.40e+01 c.71.1.1 90912 4uagA 437 2.42e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1cfr 285 2.46e+01 1cfr c.52.1.7 33312 1zndA 174 2.47e+01 1vddA 228 2.50e+01 e.49.1.1 108519 1oa2A 218 2.54e+01 b.29.1.11 86721 1hqz1 141 2.65e+01 1zp4A 304 2.75e+01 1z5sD 83 2.87e+01 1nu4A 97 2.88e+01 d.58.7.1 80731 1qi9A 556 2.88e+01 1qhbA a.111.1.2 19053 1ukuA 102 2.90e+01 d.58.5.2 99533 1qopB 396 2.92e+01 2tysB c.79.1.1 35270 1vr7A 142 3.00e+01 1o58A 303 3.01e+01 c.79.1.1 92491 1nf2A 268 3.13e+01 c.108.1.10 91849 1epwA 1290 3.15e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1wlyA 333 3.16e+01 2aq4A 434 3.18e+01 1xdpA 687 3.18e+01 1hm9A 468 3.20e+01 b.81.1.4,c.68.1.5 65866,65867 1rwzA 245 3.22e+01 d.131.1.2,d.131.1.2 98005,98006 1qhtA 775 3.22e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1bdfA 235 3.24e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1nq6A 302 3.27e+01 c.1.8.3 92046 1xn5A 146 3.27e+01 1jy5A 212 3.29e+01 d.124.1.1 71940 2fh7A 595 3.29e+01 1gxqA 106 3.35e+01 a.4.6.1 70721 1h6lA 353 3.39e+01 b.68.3.1 60687 1quqB 121 3.43e+01 1quqB b.40.4.3 25305 2fcjA 119 3.47e+01 1kshA 186 3.54e+01 c.37.1.8 72914 1fg7A 356 3.57e+01 1gewA c.67.1.1 59819 1yiyA 429 3.61e+01 1g7nA 131 3.63e+01 b.60.1.2 83274 1vbuA 328 3.66e+01 1cojA 212 3.68e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2b2aA 199 3.73e+01 1cf7B 95 3.77e+01 1cf7B a.4.5.17 16152 1z90A 469 3.79e+01 1sr4B 261 3.81e+01 d.151.1.1 105949 1b43A 340 3.82e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1e9rA 437 3.89e+01 c.37.1.11 64827 1i8dA 213 3.91e+01 b.43.4.3,b.43.4.3 61953,61954 1u55A 188 4.03e+01 d.278.1.1 107677 1pyfA 312 4.04e+01 c.1.7.1 95334 1kq1A 77 4.07e+01 b.38.1.2 72848 1je0A 236 4.09e+01 c.56.2.1 66581 1xklA 273 4.10e+01 1ns5A 155 4.12e+01 c.116.1.3 80705 1luzA 88 4.12e+01 b.40.4.5 74271 1ur1A 378 4.12e+01 c.1.8.3 99804 1x8dA 104 4.15e+01 1xtoA 311 4.16e+01 1n8jA 186 4.17e+01 c.47.1.10 85401 1tygB 87 4.19e+01 d.15.3.2 107455 1b0uA 262 4.25e+01 1b0uA c.37.1.12 32370 1xyiA 66 4.25e+01 1uc7A 125 4.26e+01 c.47.1.1 99163 1ft5A 211 4.31e+01 1bvb a.138.1.3 19681 1udc 338 4.34e+01 1xel c.2.1.2 29785 1rwrA 301 4.37e+01 b.80.1.11 97990 2f6hX 419 4.43e+01 1wohA 305 4.43e+01 c.42.1.1 109446 2cq2A 114 4.45e+01 1yb2A 275 4.64e+01 1fzqA 181 4.68e+01 1hurA c.37.1.8 32060 2g5dA 422 4.69e+01 1gntA 553 4.69e+01 e.26.1.1 70290 1zetA 388 4.77e+01 1yoaA 159 4.77e+01 1fhgA 154 4.78e+01 1tlk b.1.1.4 21706 2tpt 440 4.78e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1l1sA 113 4.78e+01 c.114.1.1 73484 2fn0A 437 4.81e+01 1m12A 84 4.82e+01 a.64.1.1 84745 1h09A 338 4.82e+01 b.109.1.1,c.1.8.8 83420,83421 1whvA 100 4.87e+01 1vknA 351 4.87e+01 c.2.1.3,d.81.1.1 108676,108677 1in0A 163 4.90e+01 d.58.49.1,d.58.49.1 83694,83695 1f9vA 347 4.99e+01 1bg2 c.37.1.9 59745 1ve0A 134 5.00e+01 2as9A 210 5.07e+01 1u7eB 154 5.09e+01 1xvqA 175 5.09e+01 1i1rB 181 5.20e+01 1i1rB a.26.1.1 61548 1g291 372 5.22e+01 1g291 1o69A 394 5.22e+01 c.67.1.4 92560 1v30A 124 5.25e+01 1vbvA 105 5.30e+01 1gs5A 258 5.32e+01 c.73.1.2 70395 2fkcA 247 5.35e+01 1r6xA 395 5.37e+01 b.122.1.3,c.26.1.5 97167,97168 1ob8A 135 5.39e+01 1xfcA 384 5.44e+01 1zhvA 134 5.45e+01 2ftzA 284 5.47e+01 1wfeA 86 5.47e+01 1bby 69 5.50e+01 2bby a.4.5.15 16149 1pbjA 125 5.51e+01 d.37.1.1,d.37.1.1 94414,94415 2a41C 32 5.55e+01 2aioA 269 5.67e+01 1y43B 173 5.70e+01 1tiqA 180 5.71e+01 d.108.1.1 107010 1bg6 359 5.71e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1njhA 119 5.72e+01 b.128.1.1 85787 1jp4A 308 5.73e+01 1jp4A e.7.1.1 63223 2trcP 217 5.74e+01 1b9yC c.47.1.6 33051 1duvG 333 5.82e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1cq3A 233 5.85e+01 1cq3A b.27.1.1 23923 1no5A 114 5.87e+01 d.218.1.5 92014 1yizA 429 6.03e+01 1r6jA 82 6.11e+01 b.36.1.1 97151 1ze3C 205 6.11e+01 1ljoA 77 6.14e+01 b.38.1.1 73941 2dfkA 402 6.15e+01 1iwmA 186 6.16e+01 b.125.1.2 83758 2f42A 179 6.21e+01 1ghhA 81 6.27e+01 1ghhA d.57.1.1 38940 1eceA 358 6.27e+01 1eceA c.1.8.3 28813 1y96A 86 6.30e+01 1cxc 124 6.48e+01 1ycc a.3.1.1 15890 1khbA 625 6.50e+01 c.91.1.1,c.109.1.1 68606,68607 1uxzA 131 6.52e+01 b.18.1.10 100170 1a8q 274 6.53e+01 1brt c.69.1.12 34702 1zpsA 138 6.54e+01 2ptd 298 6.57e+01 2plc c.1.18.2 29605 1ee6A 197 6.58e+01 1ee6A b.80.1.1 28024 1k38A 254 6.66e+01 e.3.1.1 84303 1ok7A 366 6.67e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1ta8A 332 6.73e+01 1s14A 194 6.76e+01 d.122.1.2 98329 1uc2A 481 6.77e+01 d.261.1.1 99161 1z7aA 308 6.79e+01 1c7gA 456 6.82e+01 c.67.1.2 90415 1azsA 220 6.92e+01 1azsA d.58.29.1 39416 1du9A 28 6.93e+01 g.3.7.2 44148 1q3lA 69 6.94e+01 1josA 128 6.95e+01 d.52.7.1 84191 2hvm 273 6.95e+01 1cnv c.1.8.5 28985 1qg8A 255 7.04e+01 1qg8A c.68.1.1 34505 2gh1A 301 7.06e+01 2gk3A 256 7.10e+01 1id0A 152 7.12e+01 d.122.1.3 66111 1wy6A 172 7.20e+01 8rucI 123 7.24e+01 1rboC d.73.1.1 39629 1yg6A 193 7.25e+01 1ll2A 333 7.26e+01 c.68.1.14 74005 2cxaA 256 7.31e+01 2av5A 120 7.42e+01 1ukkA 142 7.44e+01 d.227.1.1 99491 2a1xA 308 7.49e+01 1wpuA 147 7.50e+01 1wouA 123 7.54e+01 c.47.1.16 109471 2biiA 424 7.57e+01 1hrkA 359 7.63e+01 1hrkA c.92.1.1 61228 1wmqA 147 7.75e+01 1y2tA 142 7.87e+01 2g6tA 306 7.97e+01 1sbyA 254 7.97e+01 1dj7B 75 7.98e+01 1dj7B b.34.4.3 24598 2bz6L 53 8.01e+01 1rfeA 162 8.10e+01 1w94A 156 8.13e+01 1qqp1 213 8.14e+01 1qqp1 1w9zA 283 8.20e+01 2a15A 139 8.35e+01 1wmhA 89 8.36e+01 1ri5A 298 8.43e+01 c.66.1.34 97502 1tdzA 272 8.46e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1vfsA 386 8.48e+01 b.49.2.2,c.1.6.1 108584,108585 2ftrA 108 8.53e+01 2ga9D 469 8.59e+01 1mwwA 128 8.60e+01 d.80.1.4 91483 1v93A 296 8.77e+01 c.1.23.1 100532 1mixA 206 8.77e+01 a.11.2.1,b.55.1.5 79166,79167 1r6lA 239 8.80e+01 d.14.1.4,d.101.1.1 97153,97154 1of5A 221 8.84e+01 d.17.4.2 86933 1whsA 255 8.88e+01 1ivyA c.69.1.5 34649 1kkhA 317 8.95e+01 d.14.1.5,d.58.26.3 72645,72646 1gd1O 334 8.95e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2trxA 108 8.99e+01 1thx c.47.1.1 32719