# 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 1zynA 202 8.38e-02 1igs 248 1.45e-01 1a53 c.1.2.4 28565 1a53 247 1.61e-01 1a53 c.1.2.4 28564 1hyuA 521 2.17e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2c3zA 222 5.56e-01 1dyqA 234 5.92e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2rslA 140 8.23e-01 2rslA c.53.1.1 33345 2ewrA 170 1.04e+00 2fclA 169 1.18e+00 1pnsC 206 1.19e+00 i.1.1.1 88170 1sqsA 242 1.42e+00 c.23.5.5 98968 1fjgC 239 1.58e+00 1fjfC d.52.3.1,d.53.1.1 38831,38839 2aioA 269 2.04e+00 1smlA 269 2.15e+00 1smlA d.157.1.1 42053 2fvtA 135 2.82e+00 2flsA 132 2.94e+00 1m93A 55 3.18e+00 e.1.1.1 91235 2g9iA 249 3.55e+00 1hdoA 206 3.55e+00 1he2A c.2.1.2 60965 1thg 544 3.58e+00 1thg c.69.1.17 34763 1ma3A 253 3.83e+00 c.31.1.5 78883 1q59A 172 3.91e+00 f.1.4.1 95881 1repC 251 4.18e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1zpvA 91 4.25e+00 1a0rP 245 4.48e+00 1b9yC c.47.1.6 33054 1qhlA 227 4.80e+00 1qhlA c.37.1.12 32382 1ycyA 71 5.32e+00 1evuA 731 5.63e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1od8A 313 5.84e+00 c.1.8.3 86838 1v0lA 313 5.86e+00 c.1.8.3 108207 1regX 122 5.96e+00 1regX d.58.27.1 39406 2bg5A 324 6.00e+00 1e0wA 313 6.48e+00 1taxA c.1.8.3 59150 1ex0A 731 6.82e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ej0A 180 7.01e+00 1ej0A c.66.1.2 34179 1qzgA 187 7.07e+00 b.40.4.3 96643 2pil 159 7.34e+00 2pil d.24.1.1 38376 2cxcA 144 7.35e+00 1zruA 264 7.51e+00 1exg 110 7.73e+00 1exg b.2.2.1 22387 2bsdA 264 7.81e+00 1c7qA 445 8.01e+00 2pgi c.80.1.2 35307 1souA 194 8.05e+00 c.124.1.6 105858 1iz5A 249 8.60e+00 d.131.1.2,d.131.1.2 83834,83835 1kqpA 271 9.03e+00 c.26.2.1 72883 1tf1A 198 9.11e+00 d.110.2.2 106826 1g7nA 131 9.41e+00 b.60.1.2 83274 1fl2A 310 9.45e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 2gmqA 118 9.70e+00 1y96B 85 9.71e+00 1vr0A 247 9.92e+00 1kshA 186 9.96e+00 c.37.1.8 72914 1ih8A 271 1.00e+01 2nsyA c.26.2.1 62377 1v30A 124 1.18e+01 1o6dA 163 1.20e+01 c.116.1.3 92567 1t8qA 336 1.21e+01 c.1.18.3 106669 1m07A 111 1.24e+01 d.5.1.1 78328 2bwfA 77 1.34e+01 2axwA 134 1.36e+01 1s55A 156 1.42e+01 1iqaA 160 1.51e+01 b.22.1.1 71274 1eceA 358 1.52e+01 1eceA c.1.8.3 28813 1zthA 258 1.55e+01 1jhfA 202 1.55e+01 a.4.5.2,b.87.1.1 63057,63058 1lwjA 441 1.56e+01 b.71.1.1,c.1.8.1 74303,74304 2b7eA 59 1.63e+01 1d2rA 326 1.64e+01 1d2rB c.26.1.1 31572 1lid 131 1.64e+01 1hmt b.60.1.2 27184 2amhA 207 1.64e+01 2b33A 140 1.64e+01 1yr2A 741 1.65e+01 1vkuA 100 1.66e+01 a.28.1.1 108690 1b65A 375 1.67e+01 1b65A d.154.1.1 42020 1ydmA 187 1.67e+01 1xkrA 206 1.70e+01 1r5jA 337 1.73e+01 c.77.1.5 97097 1nijA 318 1.73e+01 c.37.1.10,d.237.1.1 85741,85742 1t0hA 132 1.84e+01 b.34.2.1 106207 1b56 135 1.85e+01 1hmt b.60.1.2 27183 1pbgA 468 1.90e+01 1e70M c.1.8.4 28946 1d2oA 187 1.91e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1wrjA 156 1.94e+01 1s50A 259 1.96e+01 1sek 378 1.96e+01 1sek e.1.1.1 42675 1b25A 619 1.97e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1u2xA 474 1.98e+01 c.72.1.3 107622 2aefA 234 1.99e+01 2his 312 2.00e+01 1taxA c.1.8.3 28918 1v5tA 90 2.03e+01 d.15.1.1 108385 1a99A 344 2.10e+01 1pot c.94.1.1 35812 1r5lA 262 2.12e+01 a.5.3.1,c.13.1.1 97099,97100 1fh9A 312 2.16e+01 1taxA c.1.8.3 28913 1fhdA 312 2.22e+01 1taxA c.1.8.3 28915 1i6lA 328 2.23e+01 c.26.1.1 66041 1vddA 228 2.24e+01 e.49.1.1 108519 1h72C 296 2.26e+01 d.14.1.5,d.58.26.1 60712,60713 1g8lA 411 2.28e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1n8kA 374 2.31e+01 b.35.1.2,c.2.1.1 80298,80299 1rwiA 270 2.33e+01 b.68.9.1 97987 1hetA 374 2.34e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1o0pA 104 2.36e+01 d.58.7.1 86535 1nf3C 128 2.40e+01 b.36.1.1 85596 1i8fA 81 2.41e+01 1i8fA b.38.1.1 61959 1epwA 1290 2.42e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1qi9A 556 2.48e+01 1qhbA a.111.1.2 19053 2cq2A 114 2.53e+01 1h8vA 218 2.57e+01 2nlrA b.29.1.11 60795 1quqB 121 2.58e+01 1quqB b.40.4.3 25305 1y96A 86 2.61e+01 1qy1A 174 2.63e+01 b.60.1.1 96568 2d1uA 104 2.64e+01 1oa2A 218 2.65e+01 b.29.1.11 86721 1mm4A 170 2.69e+01 f.4.1.2 79294 1wwhA 119 2.70e+01 1sfnA 246 2.70e+01 b.82.1.11 105496 1vl4A 447 2.72e+01 d.283.1.1 108718 1e0tA 470 2.75e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1c52 131 2.76e+01 1c52 a.3.1.1 15810 1vm6A 228 2.77e+01 c.2.1.3,d.81.1.3 108876,108877 1w9zA 283 2.78e+01 2awpA 198 2.78e+01 1wmhA 89 2.78e+01 1o0yA 260 2.79e+01 c.1.10.1 80756 1ta8A 332 2.81e+01 1kq1A 77 2.83e+01 b.38.1.2 72848 1t0aA 159 2.87e+01 1ydyA 356 2.90e+01 1bn8A 420 2.92e+01 1pcl b.80.1.1 28022 2cygA 312 2.97e+01 1u3wA 374 2.97e+01 2ohxA 374 2.98e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1xwvA 129 3.01e+01 2fbyA 205 3.01e+01 1ddf 127 3.05e+01 1ddf a.77.1.2 18423 2b3wA 168 3.15e+01 1my6A 199 3.15e+01 a.2.11.1,d.44.1.1 85232,85233 1h6lA 353 3.16e+01 b.68.3.1 60687 2a2pA 129 3.18e+01 1wvqA 167 3.18e+01 1vfsA 386 3.19e+01 b.49.2.2,c.1.6.1 108584,108585 1bia 321 3.27e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1h2cA 140 3.34e+01 b.31.1.1 83462 1nxiA 132 3.34e+01 d.58.47.1 86381 1j5vA 351 3.39e+01 c.72.1.1 71585 1juvA 193 3.39e+01 c.71.1.1 90912 1cfr 285 3.51e+01 1cfr c.52.1.7 33312 1xhfA 123 3.58e+01 2tpt 440 3.59e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1o58A 303 3.59e+01 c.79.1.1 92491 1n91A 108 3.60e+01 d.206.1.1 80326 4pfk 319 3.61e+01 3pfk c.89.1.1 35582 1xfcA 384 3.63e+01 1ble 163 3.65e+01 1ble c.38.1.1 32475 1tzaA 134 3.65e+01 b.1.23.1 107468 2bbkL 125 3.70e+01 2bbkL g.21.1.1 44882 1xdpA 687 3.71e+01 1f0cA 305 3.72e+01 1c8oA e.1.1.1 42676 1t64A 377 3.73e+01 c.42.1.2 106543 1xedA 117 3.75e+01 1zndA 174 3.75e+01 1m4jA 142 3.76e+01 d.109.1.2 78602 5nul 138 3.77e+01 5nul c.23.5.1 31191 1jv4A 162 3.77e+01 b.60.1.1 67343 1rf6A 427 3.78e+01 d.68.2.2 97366 1qhtA 775 3.87e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1oj4A 283 3.89e+01 d.14.1.5,d.58.26.5 93083,93084 1vcvA 226 3.92e+01 2afbA 351 3.93e+01 1i06A 180 3.97e+01 1mup b.60.1.1 27131 1vbuA 328 4.02e+01 1qavA 90 4.03e+01 1qauA b.36.1.1 24777 1wu3I 161 4.04e+01 1s9rA 410 4.04e+01 d.126.1.4 98758 1o1zA 234 4.09e+01 c.1.18.3 86555 1ois 223 4.16e+01 1a36A e.15.1.1 43267 1tt8A 164 4.21e+01 1fw9A 164 4.21e+01 1fw9A d.190.1.1 60059 2bo4A 397 4.21e+01 1ml9A 302 4.21e+01 b.85.7.1 79282 1i05A 180 4.31e+01 1mup b.60.1.1 27130 1r9gA 216 4.32e+01 c.23.16.1 97258 2gfgA 193 4.37e+01 1fp1D 372 4.38e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1shsA 147 4.39e+01 1shsA b.15.1.1 23675 2g0uA 92 4.41e+01 2fgtA 417 4.43e+01 2f4mA 295 4.45e+01 1u1hA 765 4.53e+01 c.1.22.2,c.1.22.2 107580,107581 1xcbA 211 4.53e+01 a.4.5.38,c.2.1.12 109552,109553 1xkiA 162 4.53e+01 1mup 166 4.55e+01 1mup b.60.1.1 27133 1ockA 412 4.61e+01 c.117.1.1 86802 1nq6A 302 4.70e+01 c.1.8.3 92046 1p5vA 235 4.72e+01 b.1.11.1,b.7.2.1 87812,87813 1ztxL 212 4.76e+01 1z0wA 207 4.84e+01 2gw6A 123 4.86e+01 1bdfA 235 4.87e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2fcjA 119 4.88e+01 2b2aA 199 4.91e+01 1a8i 842 4.93e+01 1a8i c.87.1.4 35490 1ee6A 197 4.95e+01 1ee6A b.80.1.1 28024 1fwkA 296 4.96e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1udc 338 5.01e+01 1xel c.2.1.2 29785 1zhvA 134 5.02e+01 1qopB 396 5.10e+01 2tysB c.79.1.1 35270 1xttA 216 5.13e+01 1rwrA 301 5.14e+01 b.80.1.11 97990 2gkeA 274 5.19e+01 1tlk 154 5.21e+01 1tlk b.1.1.4 21707 1gqzA 274 5.21e+01 d.21.1.1,d.21.1.1 83311,83312 1xdnA 277 5.28e+01 1umuA 116 5.33e+01 1umuA b.87.1.1 28382 1ljoA 77 5.33e+01 b.38.1.1 73941 2fj6A 82 5.41e+01 1u1jA 765 5.42e+01 c.1.22.2,c.1.22.2 107590,107591 1cojA 212 5.46e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1xel 338 5.46e+01 1xel c.2.1.2 29786 1qlmA 316 5.48e+01 1qlmA d.147.1.1 41765 1vjjA 692 5.53e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 16pk 415 5.63e+01 16pk c.86.1.1 35454 1s0pA 176 5.64e+01 a.192.1.1 98300 1xyiA 66 5.64e+01 1urnA 97 5.66e+01 1urnA d.58.7.1 39153 1vdc 333 5.68e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1uc7A 125 5.70e+01 c.47.1.1 99163 1cf7B 95 5.73e+01 1cf7B a.4.5.17 16152 1aq0A 306 5.82e+01 1aq0A c.1.8.3 28842 1idk 359 5.84e+01 1qcxA b.80.1.2 28025 1xx4A 261 5.86e+01 1je0A 236 5.91e+01 c.56.2.1 66581 2amyA 246 5.94e+01 1n8jA 186 5.96e+01 c.47.1.10 85401 1plq 258 6.01e+01 1plq d.131.1.2,d.131.1.2 41388,41389 2cdpA 160 6.01e+01 1jx7A 117 6.02e+01 c.114.1.1 77195 1xnaA 183 6.03e+01 1xnaA b.18.1.8 23773 2fh7A 595 6.03e+01 1ijgA 309 6.06e+01 1fouA e.27.1.1 62493 1u6tA 121 6.07e+01 2etxA 209 6.14e+01 1uc2A 481 6.19e+01 d.261.1.1 99161 1v7wA 807 6.25e+01 a.102.1.4,b.30.5.3 108411,108412 1es6A 296 6.26e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1wlyA 333 6.30e+01 1qa5A 58 6.34e+01 1qa5A j.52.1.1 46335 1nf2A 268 6.36e+01 c.108.1.10 91849 1omzA 293 6.36e+01 c.68.1.15 87093 1s6lA 212 6.45e+01 1gewA 356 6.45e+01 1gewA c.67.1.1 60470 1nu4A 97 6.47e+01 d.58.7.1 80731 1vqzA 341 6.51e+01 1l2tA 235 6.55e+01 c.37.1.12 73514 1v04A 355 6.63e+01 b.68.6.2 100240 1l1sA 113 6.64e+01 c.114.1.1 73484 1pbjA 125 6.81e+01 d.37.1.1,d.37.1.1 94414,94415 2axpA 173 6.82e+01 1vi7A 217 6.88e+01 d.14.1.11,d.58.11.2 100740,100741 1t9bA 677 6.88e+01 1mkp 144 6.88e+01 1vhrA c.45.1.1 32654 1vqoL 165 6.91e+01 1id0A 152 7.00e+01 d.122.1.3 66111 1dkuA 317 7.03e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1cc1S 283 7.05e+01 2frvA e.19.1.1 43313 2a6hA 315 7.06e+01 2as9A 210 7.10e+01 1u6bA 98 7.12e+01 d.58.7.1 107703 1f9vA 347 7.21e+01 1bg2 c.37.1.9 59745 1cq3A 233 7.22e+01 1cq3A b.27.1.1 23923 2bm5A 186 7.29e+01 1fg7A 356 7.33e+01 1gewA c.67.1.1 59819 1tq5A 242 7.42e+01 1b43A 340 7.43e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1nnjA 271 7.47e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1h5uA 842 7.51e+01 1a8i c.87.1.4 60655 1u55A 188 7.54e+01 d.278.1.1 107677 1vmaA 306 7.60e+01 a.24.13.1,c.37.1.10 108887,108888 1rwzA 245 7.64e+01 d.131.1.2,d.131.1.2 98005,98006 1f0lA 535 7.70e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1gyxA 76 7.72e+01 d.80.1.1 76387 1egaA 301 7.85e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1iwmA 186 7.89e+01 b.125.1.2 83758 1vknA 351 7.90e+01 c.2.1.3,d.81.1.1 108676,108677 1ugiA 84 7.91e+01 1ugiA d.17.5.1 38125 2polA 366 7.95e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1yiyA 429 7.96e+01 1ukuA 102 8.01e+01 d.58.5.2 99533 2trcP 217 8.03e+01 1b9yC c.47.1.6 33051 1b93A 152 8.04e+01 1b93A c.24.1.2 31507 1tygB 87 8.06e+01 d.15.3.2 107455 1fhgA 154 8.08e+01 1tlk b.1.1.4 21706 1x8dA 104 8.15e+01 1ywlA 96 8.17e+01 1q3iA 214 8.18e+01 d.220.1.1 104524 1u7eB 154 8.23e+01 1larA 575 8.30e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1ns5A 155 8.30e+01 c.116.1.3 80705 1ea9C 583 8.37e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 2pooA 355 8.37e+01 1qlgA b.68.3.1 27626 1pm1X 180 8.44e+01 b.60.1.1 104189 1uheA 97 8.47e+01 2ga9D 469 8.50e+01 2adoA 196 8.51e+01 1pjjA 271 8.60e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1q48A 134 8.62e+01 d.224.1.2 95783 2alzA 390 8.62e+01 1wohA 305 8.62e+01 c.42.1.1 109446 1hm9A 468 8.62e+01 b.81.1.4,c.68.1.5 65866,65867 1zetA 388 8.67e+01 1vjpA 394 8.67e+01 c.2.1.3,d.81.1.3 100828,100829 1tdzA 272 8.72e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 2aq4A 434 8.72e+01 1luzA 88 8.73e+01 b.40.4.5 74271 1ztsA 139 8.78e+01 1gs5A 258 8.79e+01 c.73.1.2 70395 1xseA 295 8.82e+01 1sr4B 261 8.82e+01 d.151.1.1 105949 1txvB 440 8.88e+01 1duvG 333 8.90e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1jp4A 308 8.90e+01 1jp4A e.7.1.1 63223 2ez6A 221 8.92e+01 1i1rB 181 8.98e+01 1i1rB a.26.1.1 61548