# List of top-scoring protein chains for t2k-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 1.51e-01 1esfA 233 3.07e-01 3seb b.40.2.2,d.15.6.1 25146,37735 2ewrA 170 5.28e-01 1hyuA 521 5.37e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2fclA 169 5.78e-01 1dyqA 234 6.03e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1igs 248 8.77e-01 1a53 c.1.2.4 28565 1a53 247 9.12e-01 1a53 c.1.2.4 28564 2rslA 140 1.20e+00 2rslA c.53.1.1 33345 1ma3A 253 1.20e+00 c.31.1.5 78883 1agnA 373 1.22e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 1ghtA 105 1.58e+00 2rslA c.53.1.1 60526 1ge8A 249 1.92e+00 1plq d.131.1.2,d.131.1.2 41398,41399 1gdtA 183 2.41e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1juk 248 2.80e+00 1a53 c.1.2.4 28567 2fvtA 135 2.94e+00 1d2pA 373 3.08e+00 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1m93A 55 3.23e+00 e.1.1.1 91235 1iz5A 249 3.28e+00 d.131.1.2,d.131.1.2 83834,83835 1pnsC 206 3.39e+00 i.1.1.1 88170 2c3zA 222 3.84e+00 1qzgA 187 4.19e+00 b.40.4.3 96643 1souA 194 4.45e+00 c.124.1.6 105858 1fjgC 239 4.62e+00 1fjfC d.52.3.1,d.53.1.1 38831,38839 1sqsA 242 5.29e+00 c.23.5.5 98968 1thg 544 5.66e+00 1thg c.69.1.17 34763 1zpvA 91 5.87e+00 2b33A 140 5.96e+00 1repC 251 6.10e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1j5eC 239 6.22e+00 d.52.3.1,d.53.1.1 71544,71545 1q59A 172 6.75e+00 f.1.4.1 95881 1u2xA 474 7.06e+00 c.72.1.3 107622 1my6A 199 7.23e+00 a.2.11.1,d.44.1.1 85232,85233 2pil 159 7.26e+00 2pil d.24.1.1 38376 1xwvA 129 8.21e+00 1d2oA 187 8.71e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 2aioA 269 8.92e+00 1he2A 206 9.23e+00 1he2A c.2.1.2 60966 1a0rP 245 9.31e+00 1b9yC c.47.1.6 33054 1smlA 269 9.31e+00 1smlA d.157.1.1 42053 1qhlA 227 9.35e+00 1qhlA c.37.1.12 32382 1exg 110 9.36e+00 1exg b.2.2.1 22387 1c52 131 9.47e+00 1c52 a.3.1.1 15810 1focA 132 9.57e+00 1c52 a.3.1.1 15812 1fl2A 310 1.01e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1f13A 731 1.01e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1ydmA 187 1.03e+01 2bg5A 324 1.03e+01 1gm6A 175 1.05e+01 b.60.1.1 70272 1ej0A 180 1.07e+01 1ej0A c.66.1.2 34179 1hdoA 206 1.08e+01 1he2A c.2.1.2 60965 1ay2 159 1.14e+01 2pil d.24.1.1 38377 1gguA 731 1.14e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1evuA 731 1.19e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1regX 122 1.20e+01 1regX d.58.27.1 39406 2flsA 132 1.26e+01 2ifeA 100 1.26e+01 1tig d.68.1.1 39567 1fieA 731 1.27e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 2b7eA 59 1.28e+01 1jhfA 202 1.38e+01 a.4.5.2,b.87.1.1 63057,63058 2axwA 134 1.40e+01 1ggtB 731 1.42e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1zruA 264 1.43e+01 1ex0A 731 1.45e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ockA 412 1.45e+01 c.117.1.1 86802 1od8A 313 1.45e+01 c.1.8.3 86838 1v0lA 313 1.45e+01 c.1.8.3 108207 1qrkA 731 1.48e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1sek 378 1.49e+01 1sek e.1.1.1 42675 2cxcA 144 1.54e+01 5gcnA 166 1.54e+01 1yghA d.108.1.1 40807 1e0wA 313 1.58e+01 1taxA c.1.8.3 59150 1adl 131 1.61e+01 1hmt b.60.1.2 27186 1mm4A 170 1.63e+01 f.4.1.2 79294 2nsyA 271 1.64e+01 2nsyA c.26.2.1 31612 1ycyA 71 1.65e+01 1nijA 318 1.71e+01 c.37.1.10,d.237.1.1 85741,85742 1kqpA 271 1.71e+01 c.26.2.1 72883 1epwA 1290 1.71e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2d1uA 104 1.72e+01 1nsyA 271 1.73e+01 2nsyA c.26.2.1 31614 2bsdA 264 1.74e+01 1wmhA 89 1.74e+01 1lid 131 1.76e+01 1hmt b.60.1.2 27184 1g7nA 131 1.77e+01 b.60.1.2 83274 1vr0A 247 1.78e+01 1b0zA 445 1.90e+01 2pgi c.80.1.2 35309 2pgi 445 1.90e+01 2pgi c.80.1.2 35308 1j5vA 351 1.96e+01 c.72.1.1 71585 1ih8A 271 1.97e+01 2nsyA c.26.2.1 62377 2cygA 312 2.00e+01 1bib 321 2.06e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 2awpA 198 2.10e+01 2g9iA 249 2.11e+01 1lwjA 441 2.17e+01 b.71.1.1,c.1.8.1 74303,74304 1nxiA 132 2.29e+01 d.58.47.1 86381 1aogA 485 2.33e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1m07A 111 2.33e+01 d.5.1.1 78328 1xyfA 436 2.36e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1a3wA 500 2.39e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 5nul 138 2.39e+01 5nul c.23.5.1 31191 2gfgA 193 2.40e+01 1plr 258 2.43e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1v30A 124 2.49e+01 1kshA 186 2.57e+01 c.37.1.8 72914 1rwiA 270 2.59e+01 b.68.9.1 97987 1g8lA 411 2.61e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1c7qA 445 2.65e+01 2pgi c.80.1.2 35307 2fvx 138 2.75e+01 5nul c.23.5.1 31200 1y96B 85 2.77e+01 1tf1A 198 2.79e+01 d.110.2.2 106826 1t64A 377 2.80e+01 c.42.1.2 106543 1b65A 375 2.86e+01 1b65A d.154.1.1 42020 2a2pA 129 2.91e+01 1ab0 131 2.93e+01 1hmt b.60.1.2 27190 1ee2A 373 2.96e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1fp1D 372 2.97e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1t8qA 336 2.99e+01 c.1.18.3 106669 1a9v 129 3.02e+01 1a9v b.1.18.7 21946 2gw6A 123 3.03e+01 1ktjA 129 3.06e+01 b.1.18.7 72974 1b25A 619 3.11e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1xedA 117 3.12e+01 1o58A 303 3.13e+01 c.79.1.1 92491 2fox 138 3.16e+01 5nul c.23.5.1 31197 3nll 138 3.18e+01 5nul c.23.5.1 31206 1qdlB 195 3.19e+01 1qdlB c.23.16.1 31437 1sr4B 261 3.20e+01 d.151.1.1 105949 1d2rB 326 3.24e+01 1d2rB c.26.1.1 31573 1eceA 358 3.29e+01 1eceA c.1.8.3 28813 1fpqA 372 3.31e+01 1fpqA a.4.5.29,c.66.1.12 59947,59948 1v5tA 90 3.37e+01 d.15.1.1 108385 1hetA 374 3.37e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 2gmqA 118 3.38e+01 1n8kA 374 3.40e+01 b.35.1.2,c.2.1.1 80298,80299 1c8oA 300 3.43e+01 1c8oA e.1.1.1 42677 1o6dA 163 3.48e+01 c.116.1.3 92567 1heuA 374 3.52e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1mg2B 131 3.56e+01 g.21.1.1 79060 1e0tA 470 3.56e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2apsA 162 3.57e+01 1yaiA b.1.8.1 22298 3pbgA 468 3.57e+01 1e70M c.1.8.4 28951 1xhfA 123 3.61e+01 1bc4 111 3.63e+01 1onc d.5.1.1 37279 1vddA 228 3.64e+01 e.49.1.1 108519 1grvB 182 3.67e+01 c.61.1.1 76322 1t0hA 132 3.67e+01 b.34.2.1 106207 1iqaA 160 3.71e+01 b.22.1.1 71274 1d2rA 326 3.73e+01 1d2rB c.26.1.1 31572 1axeA 374 3.77e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1pyfA 312 3.79e+01 c.1.7.1 95334 1bxlA 181 3.79e+01 1maz f.1.4.1 43396 1n91A 108 3.82e+01 d.206.1.1 80326 1a71A 374 3.83e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1h72C 296 3.84e+01 d.14.1.5,d.58.26.1 60712,60713 2aefA 234 3.87e+01 1s55A 156 3.87e+01 1b56 135 3.93e+01 1hmt b.60.1.2 27183 1o0pA 104 3.93e+01 d.58.7.1 86535 2ohxA 374 3.94e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1h8vA 218 3.98e+01 2nlrA b.29.1.11 60795 1oa2A 218 3.99e+01 b.29.1.11 86721 1vfsA 386 4.10e+01 b.49.2.2,c.1.6.1 108584,108585 1y96A 86 4.12e+01 1bn8A 420 4.14e+01 1pcl b.80.1.1 28022 1zthA 258 4.15e+01 1bia 321 4.19e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1audA 101 4.19e+01 1urnA d.58.7.1 39156 2afbA 351 4.20e+01 1urnA 97 4.21e+01 1urnA d.58.7.1 39153 1axgA 374 4.24e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 2bspA 420 4.29e+01 1pcl b.80.1.1 28023 2bwfA 77 4.33e+01 2his 312 4.48e+01 1taxA c.1.8.3 28918 1c0dA 358 4.52e+01 1eceA c.1.8.3 28815 1fh9A 312 4.66e+01 1taxA c.1.8.3 28913 1vdc 333 4.67e+01 1trb c.3.1.5,c.3.1.5 30545,30546 1plq 258 4.72e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1wu3I 161 4.74e+01 1qi9A 556 4.78e+01 1qhbA a.111.1.2 19053 1u3wA 374 4.81e+01 1s50A 259 4.82e+01 1h2cA 140 4.82e+01 b.31.1.1 83462 1fhdA 312 4.84e+01 1taxA c.1.8.3 28915 1r5lA 262 4.87e+01 a.5.3.1,c.13.1.1 97099,97100 1a99A 344 4.87e+01 1pot c.94.1.1 35812 2fh7A 595 4.87e+01 1pbgA 468 4.88e+01 1e70M c.1.8.4 28946 2bbkL 125 4.89e+01 2bbkL g.21.1.1 44882 1tzaA 134 4.91e+01 b.1.23.1 107468 1nu4A 97 4.92e+01 d.58.7.1 80731 1ri7A 171 4.96e+01 a.4.5.32,d.58.4.2 97504,97505 1cx0A 95 4.98e+01 1urnA d.58.7.1 39158 1r5jA 337 4.99e+01 c.77.1.5 97097 1m5oC 100 4.99e+01 d.58.7.1 78654 1ddf 127 5.00e+01 1ddf a.77.1.2 18423 1dg3A 592 5.01e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1iscA 192 5.03e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1rmi 160 5.06e+01 1ifa a.26.1.3 16891 1tlk 154 5.07e+01 1tlk b.1.1.4 21707 8adh 374 5.08e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1isaA 192 5.11e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 2fgtA 417 5.13e+01 1u6bA 98 5.15e+01 d.58.7.1 107703 1ble 163 5.15e+01 1ble c.38.1.1 32475 1i6lA 328 5.15e+01 c.26.1.1 66041 1i6kA 328 5.17e+01 c.26.1.1 66040 1ecfB 504 5.25e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1s0pA 176 5.27e+01 a.192.1.1 98300 1ryjA 70 5.29e+01 d.15.3.2 98104 1gh6A 114 5.31e+01 a.2.3.1 65191 1vkuA 100 5.32e+01 a.28.1.1 108690 1dkrA 317 5.34e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1xdpA 687 5.41e+01 1zp4A 304 5.42e+01 1vd2A 89 5.52e+01 d.15.2.2 108517 1vqzA 341 5.52e+01 1sfnA 246 5.56e+01 b.82.1.11 105496 1hm9A 468 5.64e+01 b.81.1.4,c.68.1.5 65866,65867 1ois 223 5.65e+01 1a36A e.15.1.1 43267 1vcvA 226 5.71e+01 1yr2A 741 5.73e+01 1pls 113 5.73e+01 1pls b.55.1.1 26965 2amhA 207 5.74e+01 1lufA 343 5.80e+01 d.144.1.7 78223 1nf3C 128 5.84e+01 b.36.1.1 85596 1o0yA 260 5.88e+01 c.1.10.1 80756 1v04A 355 5.93e+01 b.68.6.2 100240 1t9bA 677 5.98e+01 2as9A 210 5.99e+01 1x8dA 104 6.03e+01 1gyxA 76 6.04e+01 d.80.1.1 76387 1uag 437 6.04e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1n99A 166 6.05e+01 b.36.1.1,b.36.1.1 85459,85460 1kal 29 6.05e+01 g.3.3.1 44077 1xcbA 211 6.10e+01 a.4.5.38,c.2.1.12 109552,109553 2f4mA 295 6.10e+01 1wspA 84 6.15e+01 2fj6A 82 6.20e+01 1cf7A 76 6.23e+01 1cf7B a.4.5.17 16151 1zhvA 134 6.23e+01 1wrjA 156 6.32e+01 1qavA 90 6.35e+01 1qauA b.36.1.1 24777 1cc1S 283 6.41e+01 2frvA e.19.1.1 43313 1a6zA 275 6.56e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1id0A 152 6.58e+01 d.122.1.3 66111 4uagA 437 6.61e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 2adbA 148 6.62e+01 1f0cA 305 6.68e+01 1c8oA e.1.1.1 42676 1wwhA 119 6.71e+01 1umuB 116 6.71e+01 1umuA b.87.1.1 28383 1oiaA 95 6.73e+01 d.58.7.1 87051 1xnaA 183 6.75e+01 1xnaA b.18.1.8 23773 1fht 116 6.80e+01 1urnA d.58.7.1 39157 1af8 86 6.80e+01 2af8 a.28.1.1 16932 1rwrA 301 6.83e+01 b.80.1.11 97990 1vm6A 228 6.85e+01 c.2.1.3,d.81.1.3 108876,108877 1p8kZ 254 6.87e+01 d.95.2.1,d.95.2.1 94361,94362 1xyiA 66 6.88e+01 1fwkA 296 6.93e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1ghr 306 7.02e+01 1aq0A c.1.8.3 28844 1xkiA 162 7.04e+01 1tiqA 180 7.13e+01 d.108.1.1 107010 1lxyA 409 7.15e+01 d.126.1.4 91154 1wjbA 55 7.17e+01 1wjcA a.4.10.1 16265 2bby 69 7.17e+01 2bby a.4.5.15 16148 1qa5A 58 7.17e+01 1qa5A j.52.1.1 46335 2b3wA 168 7.19e+01 1larA 575 7.26e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1fecA 490 7.31e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1u1hA 765 7.39e+01 c.1.22.2,c.1.22.2 107580,107581 1ponB 36 7.42e+01 1ponB 1p5vA 235 7.45e+01 b.1.11.1,b.7.2.1 87812,87813 1fhgA 154 7.58e+01 1tlk b.1.1.4 21706 1ifa 158 7.58e+01 1ifa a.26.1.3 16892 1culA 217 7.61e+01 1azsA d.58.29.1 39417 1es6A 296 7.63e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1p3dA 475 7.66e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1i8fA 81 7.68e+01 1i8fA b.38.1.1 61959 2b2aA 199 7.70e+01 1dkuA 317 7.70e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1irxA 523 7.71e+01 a.97.1.2,c.26.1.1 71378,71379 1whvA 100 7.74e+01 1fc2D 224 7.86e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1b5tA 275 7.89e+01 1b5tA c.1.23.1 29676 1b43A 340 7.90e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1jlxA 304 7.91e+01 1jlyA b.42.3.1,b.42.3.1 25583,25584 1ygs 234 7.92e+01 1ygs b.26.1.1 23907 1acmA 310 7.97e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 2alzA 390 7.98e+01 1v7wA 807 7.99e+01 a.102.1.4,b.30.5.3 108411,108412 1ydyA 356 7.99e+01 2snv 151 8.06e+01 1svpA b.47.1.3 26394 1bc9 200 8.10e+01 1pbv a.118.3.1 19180 1u1jA 765 8.14e+01 c.1.22.2,c.1.22.2 107590,107591 1q48A 134 8.18e+01 d.224.1.2 95783 1qlmA 316 8.18e+01 1qlmA d.147.1.1 41765 1fc1A 224 8.22e+01 1igtB b.1.1.2,b.1.1.2 21520,21521 1ekxA 311 8.25e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1vi7A 217 8.26e+01 d.14.1.11,d.58.11.2 100740,100741 1wvqA 167 8.26e+01 1gewA 356 8.35e+01 1gewA c.67.1.1 60470 1xdnA 277 8.37e+01 1vmaA 306 8.40e+01 a.24.13.1,c.37.1.10 108887,108888 1hqz9 141 8.43e+01 1ljoA 77 8.43e+01 b.38.1.1 73941 2nadA 393 8.44e+01 2nadA c.2.1.4,c.23.12.1 30090,31350 1r9gA 216 8.53e+01 c.23.16.1 97258 1quqB 121 8.55e+01 1quqB b.40.4.3 25305 1ztsA 139 8.66e+01 1qopB 396 8.77e+01 2tysB c.79.1.1 35270 8atcA 310 8.82e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1s9rA 410 8.84e+01 d.126.1.4 98758