# 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 1esfA 233 1.57e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1dyqA 234 2.63e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2ewrA 170 3.22e-01 2fclA 169 3.44e-01 1d2pA 373 5.29e-01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 2rslA 140 5.77e-01 2rslA c.53.1.1 33345 1zynA 202 6.14e-01 1agnA 373 6.37e-01 2ohxA b.35.1.2,c.2.1.1 24737,29753 1ghtA 105 8.46e-01 2rslA c.53.1.1 60526 1gdtA 183 8.74e-01 2rslA a.4.1.2,c.53.1.1 16021,33348 1d2oA 187 9.39e-01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1ge8A 249 1.17e+00 1plq d.131.1.2,d.131.1.2 41398,41399 1pnsC 206 1.62e+00 i.1.1.1 88170 1hyuA 521 1.69e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1sqsA 242 1.78e+00 c.23.5.5 98968 1repC 251 2.13e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1xwvA 129 2.42e+00 1fjgC 239 2.50e+00 1fjfC d.52.3.1,d.53.1.1 38831,38839 1m93A 55 2.65e+00 e.1.1.1 91235 1iz5A 249 2.65e+00 d.131.1.2,d.131.1.2 83834,83835 1j5eC 239 2.69e+00 d.52.3.1,d.53.1.1 71544,71545 1focA 132 3.32e+00 1c52 a.3.1.1 15812 2bg5A 324 3.63e+00 1c52 131 4.03e+00 1c52 a.3.1.1 15810 2b33A 140 4.59e+00 5gcnA 166 4.71e+00 1yghA d.108.1.1 40807 1ydmA 187 4.73e+00 1f13A 731 5.17e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1wspA 84 5.65e+00 1a0rP 245 5.79e+00 1b9yC c.47.1.6 33054 1exg 110 5.83e+00 1exg b.2.2.1 22387 1fieA 731 5.92e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 1evuA 731 5.98e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1gguA 731 6.18e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 1ex0A 731 6.56e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ggtB 731 6.92e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1lwjA 441 7.17e+00 b.71.1.1,c.1.8.1 74303,74304 1qrkA 731 7.74e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 1d2rB 326 8.02e+00 1d2rB c.26.1.1 31573 1y96B 85 8.17e+00 1qhlA 227 8.22e+00 1qhlA c.37.1.12 32382 1vjpA 394 8.98e+00 c.2.1.3,d.81.1.3 100828,100829 1d2rA 326 9.13e+00 1d2rB c.26.1.1 31572 2afbA 351 9.40e+00 1a3wA 500 9.57e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 2ifeA 100 9.76e+00 1tig d.68.1.1 39567 1ktjA 129 1.02e+01 b.1.18.7 72974 2apsA 162 1.04e+01 1yaiA b.1.8.1 22298 1ma3A 253 1.09e+01 c.31.1.5 78883 1nijA 318 1.12e+01 c.37.1.10,d.237.1.1 85741,85742 1zpvA 91 1.14e+01 2nsyA 271 1.20e+01 2nsyA c.26.2.1 31612 2flsA 132 1.24e+01 1ycyA 71 1.25e+01 1gm6A 175 1.27e+01 b.60.1.1 70272 1nsyA 271 1.29e+01 2nsyA c.26.2.1 31614 1aogA 485 1.32e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 2b7eA 59 1.33e+01 1kqpA 271 1.33e+01 c.26.2.1 72883 2snv 151 1.34e+01 1svpA b.47.1.3 26394 1ih8A 271 1.38e+01 2nsyA c.26.2.1 62377 1dkrA 317 1.43e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1regX 122 1.43e+01 1regX d.58.27.1 39406 5nul 138 1.47e+01 5nul c.23.5.1 31191 1a9v 129 1.48e+01 1a9v b.1.18.7 21946 1he2A 206 1.49e+01 1he2A c.2.1.2 60966 1v0lA 313 1.49e+01 c.1.8.3 108207 1od8A 313 1.50e+01 c.1.8.3 86838 1j5vA 351 1.50e+01 c.72.1.1 71585 2fvx 138 1.51e+01 5nul c.23.5.1 31200 1bib 321 1.52e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1i6lA 328 1.52e+01 c.26.1.1 66041 1i6kA 328 1.53e+01 c.26.1.1 66040 1m07A 111 1.53e+01 d.5.1.1 78328 1ri7A 171 1.54e+01 a.4.5.32,d.58.4.2 97504,97505 1b25A 619 1.54e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2pil 159 1.55e+01 2pil d.24.1.1 38376 1o0pA 104 1.57e+01 d.58.7.1 86535 2fox 138 1.57e+01 5nul c.23.5.1 31197 1e0wA 313 1.58e+01 1taxA c.1.8.3 59150 2fgtA 417 1.61e+01 1e0tA 470 1.61e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1svpA 161 1.63e+01 1svpA b.47.1.3 26384 3pbgA 468 1.65e+01 1e70M c.1.8.4 28951 1xhfA 123 1.67e+01 1hdoA 206 1.67e+01 1he2A c.2.1.2 60965 1adl 131 1.69e+01 1hmt b.60.1.2 27186 1ee2A 373 1.71e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 2gfgA 193 1.73e+01 1n8kA 374 1.73e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 1.74e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1a71A 374 1.75e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1heuA 374 1.75e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1dkuA 317 1.78e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1g7nA 131 1.79e+01 b.60.1.2 83274 1lid 131 1.82e+01 1hmt b.60.1.2 27184 3nll 138 1.90e+01 5nul c.23.5.1 31206 1s0pA 176 1.95e+01 a.192.1.1 98300 1t8qA 336 1.98e+01 c.1.18.3 106669 2g9iA 249 2.01e+01 1nu4A 97 2.11e+01 d.58.7.1 80731 1b0zA 445 2.12e+01 2pgi c.80.1.2 35309 2pgi 445 2.12e+01 2pgi c.80.1.2 35308 1axeA 374 2.12e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1axgA 374 2.15e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1audA 101 2.16e+01 1urnA d.58.7.1 39156 1epwA 1290 2.16e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1m5oC 100 2.25e+01 d.58.7.1 78654 1ej0A 180 2.26e+01 1ej0A c.66.1.2 34179 1u3wA 374 2.26e+01 1vkuA 100 2.26e+01 a.28.1.1 108690 2ohxA 374 2.27e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1urnA 97 2.29e+01 1urnA d.58.7.1 39153 1xyfA 436 2.34e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1a99A 344 2.36e+01 1pot c.94.1.1 35812 1cf7A 76 2.37e+01 1cf7B a.4.5.17 16151 1ibsA 317 2.42e+01 c.61.1.2,c.61.1.2 66107,66108 1cx0A 95 2.47e+01 1urnA d.58.7.1 39158 2cxcA 144 2.49e+01 1b56 135 2.50e+01 1hmt b.60.1.2 27183 1zp4A 304 2.50e+01 1o6dA 163 2.50e+01 c.116.1.3 92567 1bc4 111 2.51e+01 1onc d.5.1.1 37279 1xn5A 146 2.60e+01 8adh 374 2.62e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1u6bA 98 2.63e+01 d.58.7.1 107703 1gyxA 76 2.64e+01 d.80.1.1 76387 1ay2 159 2.65e+01 2pil d.24.1.1 38377 2gmqA 118 2.69e+01 1fl2A 310 2.72e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1sek 378 2.73e+01 1sek e.1.1.1 42675 1qdlB 195 2.73e+01 1qdlB c.23.16.1 31437 1u2xA 474 2.77e+01 c.72.1.3 107622 1vcvA 226 2.79e+01 1c8oA 300 2.84e+01 1c8oA e.1.1.1 42677 1pbgA 468 2.85e+01 1e70M c.1.8.4 28946 1quqB 121 2.89e+01 1quqB b.40.4.3 25305 1a53 247 2.93e+01 1a53 c.1.2.4 28564 1qlmA 316 2.98e+01 1qlmA d.147.1.1 41765 2gw6A 123 2.98e+01 1c7qA 445 3.01e+01 2pgi c.80.1.2 35307 1idk 359 3.03e+01 1qcxA b.80.1.2 28025 1ab0 131 3.03e+01 1hmt b.60.1.2 27190 1wrjA 156 3.04e+01 1qavA 90 3.11e+01 1qauA b.36.1.1 24777 1igs 248 3.12e+01 1a53 c.1.2.4 28565 1sr4B 261 3.14e+01 d.151.1.1 105949 1uag 437 3.16e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1ld4A 264 3.17e+01 i.6.1.1 77886 1rmi 160 3.17e+01 1ifa a.26.1.3 16891 1bia 321 3.26e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1ois 223 3.26e+01 1a36A e.15.1.1 43267 2cygA 312 3.27e+01 1wu3I 161 3.28e+01 1x8dA 104 3.32e+01 1v04A 355 3.34e+01 b.68.6.2 100240 4uagA 437 3.34e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1pyfA 312 3.36e+01 c.1.7.1 95334 1oiaA 95 3.39e+01 d.58.7.1 87051 1qvaA 223 3.41e+01 1qvaA c.37.1.19 32411 1umuB 116 3.42e+01 1umuA b.87.1.1 28383 1qzgA 187 3.46e+01 b.40.4.3 96643 1plr 258 3.49e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1gh6A 114 3.56e+01 a.2.3.1 65191 1vddA 228 3.57e+01 e.49.1.1 108519 1jfbA 404 3.58e+01 a.104.1.1 66624 1hqz9 141 3.60e+01 1bn8A 420 3.74e+01 1pcl b.80.1.1 28022 1o1zA 234 3.76e+01 c.1.18.3 86555 1fht 116 3.77e+01 1urnA d.58.7.1 39157 1ca1 370 3.77e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1t0hA 132 3.82e+01 b.34.2.1 106207 1cf7B 95 3.86e+01 1cf7B a.4.5.17 16152 2alzA 390 3.90e+01 1grvB 182 3.93e+01 c.61.1.1 76322 1hqz1 141 3.93e+01 2bspA 420 3.96e+01 1pcl b.80.1.1 28023 1i4vA 115 3.96e+01 1umuA b.87.1.1 61734 1tiqA 180 3.99e+01 d.108.1.1 107010 1tlk 154 4.02e+01 1tlk b.1.1.4 21707 1pczA 191 4.12e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2as9A 210 4.15e+01 1s50A 259 4.15e+01 1v5nA 89 4.18e+01 g.49.1.3 108380 1s55A 156 4.24e+01 1iqaA 160 4.26e+01 b.22.1.1 71274 1cmnA 402 4.29e+01 1rom a.104.1.1 18958 1ydyA 356 4.30e+01 1o0yA 260 4.40e+01 c.1.10.1 80756 1wwhA 119 4.41e+01 1rom 403 4.41e+01 1rom a.104.1.1 18963 2etxA 209 4.42e+01 1u1jA 765 4.44e+01 c.1.22.2,c.1.22.2 107590,107591 1u1hA 765 4.53e+01 c.1.22.2,c.1.22.2 107580,107581 1tf1A 198 4.55e+01 d.110.2.2 106826 2bby 69 4.62e+01 2bby a.4.5.15 16148 1p8kZ 254 4.69e+01 d.95.2.1,d.95.2.1 94361,94362 1r5jA 337 4.73e+01 c.77.1.5 97097 1qorA 327 4.74e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2fh7A 595 4.77e+01 1qopB 396 4.77e+01 2tysB c.79.1.1 35270 1kal 29 4.87e+01 g.3.3.1 44077 1o58A 303 4.92e+01 c.79.1.1 92491 1xklA 273 4.94e+01 2g6tA 306 5.00e+01 2adoA 196 5.02e+01 2wsyB 396 5.05e+01 2tysB c.79.1.1 35288 1xttA 216 5.10e+01 1zruA 264 5.27e+01 1f24A 402 5.32e+01 1rom a.104.1.1 18953 2tysB 397 5.34e+01 2tysB c.79.1.1 35272 2bz6L 53 5.35e+01 1i5pA 633 5.35e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2nadA 393 5.38e+01 2nadA c.2.1.4,c.23.12.1 30090,31350 1mk0A 97 5.39e+01 d.226.1.1 79216 1kshA 186 5.40e+01 c.37.1.8 72914 1mg2B 131 5.40e+01 g.21.1.1 79060 1h72C 296 5.41e+01 d.14.1.5,d.58.26.1 60712,60713 1t3nA 388 5.42e+01 d.240.1.1,e.8.1.7 106363,106364 1fhgA 154 5.51e+01 1tlk b.1.1.4 21706 1b5tA 275 5.52e+01 1b5tA c.1.23.1 29676 1ygs 234 5.54e+01 1ygs b.26.1.1 23907 1ifa 158 5.60e+01 1ifa a.26.1.3 16892 1larA 575 5.68e+01 1larA c.45.1.2,c.45.1.2 32693,32694 2amhA 207 5.69e+01 1rwrA 301 5.73e+01 b.80.1.11 97990 1snlA 103 5.74e+01 a.39.1.7 105820 1njhA 119 5.75e+01 b.128.1.1 85787 1vjjA 692 5.78e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1plq 258 5.80e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1p3dA 475 5.81e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2aefA 234 5.82e+01 1shsA 147 5.82e+01 1shsA b.15.1.1 23675 1cfr 285 5.87e+01 1cfr c.52.1.7 33312 1a6zA 275 5.88e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1bby 69 5.88e+01 2bby a.4.5.15 16149 1zthA 258 5.88e+01 8rucI 123 5.90e+01 1rboC d.73.1.1 39629 1wjbA 55 5.92e+01 1wjcA a.4.10.1 16265 1i8fA 81 5.99e+01 1i8fA b.38.1.1 61959 1nf3C 128 6.03e+01 b.36.1.1 85596 1acmA 310 6.10e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1hm9A 468 6.17e+01 b.81.1.4,c.68.1.5 65866,65867 1umuA 116 6.20e+01 1umuA b.87.1.1 28382 1o8uA 257 6.21e+01 c.14.1.3 81194 1bvb 211 6.25e+01 1bvb a.138.1.3 19683 2b2aA 199 6.27e+01 1xkiA 162 6.28e+01 1y43B 173 6.30e+01 1f0cA 305 6.30e+01 1c8oA e.1.1.1 42676 1zetA 388 6.32e+01 2bsdA 264 6.40e+01 1ft5A 211 6.41e+01 1bvb a.138.1.3 19681 8atcA 310 6.44e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1f76A 336 6.49e+01 c.1.4.1 76160 2a0fA 310 6.51e+01 1dj7B 75 6.52e+01 1dj7B b.34.4.3 24598 1hbxA 92 6.53e+01 1mnmA d.88.1.1 60930 1xcbA 211 6.55e+01 a.4.5.38,c.2.1.12 109552,109553 1ghr 306 6.66e+01 1aq0A c.1.8.3 28844 1k8yB 396 6.68e+01 c.79.1.1 72184 1ay9A 108 6.72e+01 1umuA b.87.1.1 28384 1uteA 313 6.80e+01 1uteA d.159.1.1 42078 1of8A 370 6.81e+01 c.1.10.4 92819 1vr7A 142 6.83e+01 1rboC 123 6.84e+01 1rboC d.73.1.1 39634 1ekxA 311 6.84e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1wjcA 47 6.90e+01 1wjcA a.4.10.1 16261 1a50B 396 7.04e+01 2tysB c.79.1.1 35280 2f42A 179 7.05e+01 1e6yA 569 7.05e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1at1A 310 7.11e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1cbg 490 7.13e+01 1e70M c.1.8.4 28933 1cvwL 55 7.22e+01 1hcgB g.3.11.1 44211 1fzqA 181 7.31e+01 1hurA c.37.1.8 32060 1gqyA 475 7.31e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1pvtA 238 7.38e+01 c.74.1.1 95189 1aokA 122 7.41e+01 1poa a.133.1.2 19560 1diwA 441 7.42e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1p9rA 418 7.42e+01 c.37.1.11 94399 1hfbA 370 7.44e+01 c.1.10.4 76706 1ri6A 343 7.45e+01 b.69.11.1 97503 1ztxL 212 7.45e+01 1o69A 394 7.45e+01 c.67.1.4 92560 2ffeA 311 7.54e+01 1knaA 69 7.54e+01 b.34.13.2 72771 1t0aA 159 7.55e+01 1n99A 166 7.57e+01 b.36.1.1,b.36.1.1 85459,85460 1ll2A 333 7.58e+01 c.68.1.14 74005 1ur1A 378 7.62e+01 c.1.8.3 99804 1no5A 114 7.62e+01 d.218.1.5 92014 1xdpA 687 7.67e+01 1k38A 254 7.68e+01 e.3.1.1 84303 1ponB 36 7.69e+01 1ponB 3kar 346 7.70e+01 1bg2 c.37.1.9 32198 1qoxN 449 7.72e+01 1qoxN c.1.8.4 28978 2adbA 148 7.72e+01 1q3lA 69 7.75e+01 1z90A 469 7.77e+01 1ap0 73 7.78e+01 1ap0 b.34.13.2 37475 1pnsB 234 7.83e+01 i.1.1.1 88169 1szoA 257 7.89e+01 c.14.1.3 106164 2av5A 120 7.97e+01 2bbkL 125 8.02e+01 2bbkL g.21.1.1 44882 2bwfA 77 8.04e+01 1as4A 341 8.09e+01 1sek e.1.1.1 42623 1xx4A 261 8.11e+01 1culA 217 8.12e+01 1azsA d.58.29.1 39417 1pkn 530 8.24e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 1i8dA 213 8.28e+01 b.43.4.3,b.43.4.3 61953,61954 1vi7A 217 8.30e+01 d.14.1.11,d.58.11.2 100740,100741 1fjgB 256 8.39e+01 1fjfB c.23.15.1 31400 1j5eB 256 8.41e+01 c.23.15.1 71543 1f9vA 347 8.43e+01 1bg2 c.37.1.9 59745 2b4rO 345 8.45e+01 1xyiA 66 8.46e+01 3uagA 437 8.46e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30652,33953,34956 1whvA 100 8.50e+01 2bo4A 397 8.63e+01 1mkp 144 8.77e+01 1vhrA c.45.1.1 32654 1htjF 210 8.82e+01 1htjF a.91.1.1 61254 1fh9A 312 8.82e+01 1taxA c.1.8.3 28913 2a1xA 308 8.82e+01 1vqoL 165 8.88e+01 1d3uA 181 8.89e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 2myr 501 8.92e+01 1rwzA 245 8.99e+01 d.131.1.2,d.131.1.2 98005,98006