# 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 1.06e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1dyqA 234 1.96e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2ewrA 170 2.87e-01 2fclA 169 3.09e-01 1d2pA 373 3.54e-01 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1agnA 373 3.74e-01 2ohxA b.35.1.2,c.2.1.1 24737,29753 2rslA 140 4.01e-01 2rslA c.53.1.1 33345 1zynA 202 4.09e-01 1ghtA 105 5.40e-01 2rslA c.53.1.1 60526 1gdtA 183 6.19e-01 2rslA a.4.1.2,c.53.1.1 16021,33348 1d2oA 187 6.47e-01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1ge8A 249 7.54e-01 1plq d.131.1.2,d.131.1.2 41398,41399 1pnsC 206 9.26e-01 i.1.1.1 88170 1hyuA 521 1.15e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1sqsA 242 1.23e+00 c.23.5.5 98968 1repC 251 1.40e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1fjgC 239 1.42e+00 1fjfC d.52.3.1,d.53.1.1 38831,38839 1j5eC 239 1.55e+00 d.52.3.1,d.53.1.1 71544,71545 1m93A 55 1.63e+00 e.1.1.1 91235 1iz5A 249 1.81e+00 d.131.1.2,d.131.1.2 83834,83835 1focA 132 2.04e+00 1c52 a.3.1.1 15812 1c52 131 2.48e+00 1c52 a.3.1.1 15810 2bg5A 324 2.64e+00 2b33A 140 2.79e+00 1xwvA 129 2.84e+00 1ydmA 187 3.09e+00 5gcnA 166 3.23e+00 1yghA d.108.1.1 40807 1a0rP 245 4.25e+00 1b9yC c.47.1.6 33054 1lwjA 441 5.46e+00 b.71.1.1,c.1.8.1 74303,74304 1a3wA 500 5.86e+00 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1wspA 84 5.87e+00 1qhlA 227 5.98e+00 1qhlA c.37.1.12 32382 2afbA 351 6.01e+00 1y96B 85 6.24e+00 1f13A 731 6.73e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 1vjpA 394 6.88e+00 c.2.1.3,d.81.1.3 100828,100829 1fieA 731 7.48e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21879,22167,22168,37109 1ex0A 731 7.69e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1aogA 485 7.81e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1evuA 731 8.02e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ggtB 731 8.04e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21882,22173,22174,37112 1gguA 731 8.19e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21885,22179,22180,37115 2snv 151 8.21e+00 1svpA b.47.1.3 26394 1zpvA 91 8.29e+00 2nsyA 271 8.59e+00 2nsyA c.26.2.1 31612 2b7eA 59 9.14e+00 1nsyA 271 9.20e+00 2nsyA c.26.2.1 31614 1svpA 161 9.37e+00 1svpA b.47.1.3 26384 1d2rB 326 9.52e+00 1d2rB c.26.1.1 31573 1kqpA 271 9.57e+00 c.26.2.1 72883 1d2rA 326 9.63e+00 1d2rB c.26.1.1 31572 2fox 138 9.68e+00 5nul c.23.5.1 31197 1ycyA 71 9.75e+00 1regX 122 9.89e+00 1regX d.58.27.1 39406 1ih8A 271 9.94e+00 2nsyA c.26.2.1 62377 1j5vA 351 9.97e+00 c.72.1.1 71585 1gm6A 175 1.02e+01 b.60.1.1 70272 1dkrA 317 1.02e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 5nul 138 1.05e+01 5nul c.23.5.1 31191 1e0tA 470 1.05e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1qrkA 731 1.05e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21889,22187,22188,37119 2fvx 138 1.08e+01 5nul c.23.5.1 31200 1ma3A 253 1.10e+01 c.31.1.5 78883 1ri7A 171 1.12e+01 a.4.5.32,d.58.4.2 97504,97505 2gfgA 193 1.13e+01 2fgtA 417 1.16e+01 1b25A 619 1.16e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 3pbgA 468 1.21e+01 1e70M c.1.8.4 28951 2pil 159 1.22e+01 2pil d.24.1.1 38376 1xhfA 123 1.23e+01 1exg 110 1.24e+01 1exg b.2.2.1 22387 1bib 321 1.24e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1ee2A 373 1.27e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1n8kA 374 1.28e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 1.28e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1v0lA 313 1.29e+01 c.1.8.3 108207 1od8A 313 1.29e+01 c.1.8.3 86838 1a71A 374 1.29e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1dkuA 317 1.30e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1heuA 374 1.30e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1e0wA 313 1.32e+01 1taxA c.1.8.3 59150 3nll 138 1.35e+01 5nul c.23.5.1 31206 1nijA 318 1.45e+01 c.37.1.10,d.237.1.1 85741,85742 1s0pA 176 1.45e+01 a.192.1.1 98300 1ktjA 129 1.47e+01 b.1.18.7 72974 1vkuA 100 1.49e+01 a.28.1.1 108690 1t8qA 336 1.51e+01 c.1.18.3 106669 1axeA 374 1.58e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1axgA 374 1.63e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1b0zA 445 1.67e+01 2pgi c.80.1.2 35309 2pgi 445 1.67e+01 2pgi c.80.1.2 35308 2ohxA 374 1.70e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1i6lA 328 1.71e+01 c.26.1.1 66041 1u3wA 374 1.72e+01 1i6kA 328 1.73e+01 c.26.1.1 66040 2g9iA 249 1.73e+01 1ibsA 317 1.80e+01 c.61.1.2,c.61.1.2 66107,66108 2flsA 132 1.80e+01 1c8oA 300 1.81e+01 1c8oA e.1.1.1 42677 1m07A 111 1.83e+01 d.5.1.1 78328 1nu4A 97 1.84e+01 d.58.7.1 80731 1qlmA 316 1.85e+01 1qlmA d.147.1.1 41765 1xyfA 436 1.85e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1o6dA 163 1.87e+01 c.116.1.3 92567 1cf7A 76 1.90e+01 1cf7B a.4.5.17 16151 1gyxA 76 1.95e+01 d.80.1.1 76387 1epwA 1290 1.97e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1a99A 344 1.99e+01 1pot c.94.1.1 35812 1audA 101 2.00e+01 1urnA d.58.7.1 39156 8adh 374 2.01e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1sek 378 2.04e+01 1sek e.1.1.1 42675 1zp4A 304 2.04e+01 1he2A 206 2.06e+01 1he2A c.2.1.2 60966 1vcvA 226 2.06e+01 1qdlB 195 2.08e+01 1qdlB c.23.16.1 31437 2gw6A 123 2.13e+01 1idk 359 2.15e+01 1qcxA b.80.1.2 28025 1m5oC 100 2.18e+01 d.58.7.1 78654 1pbgA 468 2.18e+01 1e70M c.1.8.4 28946 2cxcA 144 2.20e+01 1ld4A 264 2.20e+01 i.6.1.1 77886 1urnA 97 2.21e+01 1urnA d.58.7.1 39153 1ay2 159 2.23e+01 2pil d.24.1.1 38377 1wrjA 156 2.23e+01 1hdoA 206 2.28e+01 1he2A c.2.1.2 60965 2gmqA 118 2.35e+01 1a9v 129 2.36e+01 1a9v b.1.18.7 21946 1qavA 90 2.36e+01 1qauA b.36.1.1 24777 1cx0A 95 2.40e+01 1urnA d.58.7.1 39158 1c7qA 445 2.41e+01 2pgi c.80.1.2 35307 1rmi 160 2.47e+01 1ifa a.26.1.3 16891 2ifeA 100 2.56e+01 1tig d.68.1.1 39567 1qvaA 223 2.56e+01 1qvaA c.37.1.19 32411 1pyfA 312 2.57e+01 c.1.7.1 95334 1wu3I 161 2.59e+01 1u6bA 98 2.61e+01 d.58.7.1 107703 1u2xA 474 2.64e+01 c.72.1.3 107622 1plr 258 2.64e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1uag 437 2.65e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30653,33954,34957 1hqz9 141 2.68e+01 1s55A 156 2.69e+01 1iqaA 160 2.70e+01 b.22.1.1 71274 1ois 223 2.70e+01 1a36A e.15.1.1 43267 4uagA 437 2.77e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1vddA 228 2.78e+01 e.49.1.1 108519 1gh6A 114 2.81e+01 a.2.3.1 65191 2cygA 312 2.81e+01 1jfbA 404 2.87e+01 a.104.1.1 66624 1p3dA 475 2.87e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1qzgA 187 2.89e+01 b.40.4.3 96643 1o1zA 234 2.97e+01 c.1.18.3 86555 1sr4B 261 2.97e+01 d.151.1.1 105949 1bn8A 420 2.98e+01 1pcl b.80.1.1 28022 1hqz1 141 2.99e+01 1h72C 296 3.07e+01 d.14.1.5,d.58.26.1 60712,60713 1b56 135 3.11e+01 1hmt b.60.1.2 27183 1bia 321 3.11e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1bc4 111 3.14e+01 1onc d.5.1.1 37279 1u1jA 765 3.15e+01 c.1.22.2,c.1.22.2 107590,107591 1tiqA 180 3.17e+01 d.108.1.1 107010 2alzA 390 3.19e+01 2bspA 420 3.23e+01 1pcl b.80.1.1 28023 1u1hA 765 3.26e+01 c.1.22.2,c.1.22.2 107580,107581 1cf7B 95 3.26e+01 1cf7B a.4.5.17 16152 1wwhA 119 3.27e+01 1a53 247 3.29e+01 1a53 c.1.2.4 28564 1r5jA 337 3.38e+01 c.77.1.5 97097 1s50A 259 3.40e+01 1oiaA 95 3.41e+01 d.58.7.1 87051 1ydyA 356 3.41e+01 1cmnA 402 3.44e+01 1rom a.104.1.1 18958 1o0yA 260 3.47e+01 c.1.10.1 80756 1xn5A 146 3.51e+01 1rom 403 3.56e+01 1rom a.104.1.1 18963 1i5pA 633 3.59e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2etxA 209 3.66e+01 1qorA 327 3.66e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1fht 116 3.67e+01 1urnA d.58.7.1 39157 1ca1 370 3.75e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1tlk 154 3.76e+01 1tlk b.1.1.4 21707 1qopB 396 3.76e+01 2tysB c.79.1.1 35270 1quqB 121 3.83e+01 1quqB b.40.4.3 25305 2bby 69 3.89e+01 2bby a.4.5.15 16148 1shsA 147 3.90e+01 1shsA b.15.1.1 23675 1grvB 182 3.90e+01 c.61.1.1 76322 1xklA 273 3.92e+01 1t0hA 132 3.92e+01 b.34.2.1 106207 1gqyA 475 3.97e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 2wsyB 396 3.97e+01 2tysB c.79.1.1 35288 1mk0A 97 3.98e+01 d.226.1.1 79216 1igs 248 3.98e+01 1a53 c.1.2.4 28565 2g6tA 306 4.05e+01 2adoA 196 4.15e+01 2fh7A 595 4.18e+01 2tysB 397 4.23e+01 2tysB c.79.1.1 35272 1pczA 191 4.24e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1f0cA 305 4.28e+01 1c8oA e.1.1.1 42676 1ygs 234 4.28e+01 1ygs b.26.1.1 23907 1plq 258 4.32e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1f76A 336 4.33e+01 c.1.4.1 76160 1t0aA 159 4.37e+01 1i8dA 213 4.40e+01 b.43.4.3,b.43.4.3 61953,61954 1t3nA 388 4.40e+01 d.240.1.1,e.8.1.7 106363,106364 1b5tA 275 4.47e+01 1b5tA c.1.23.1 29676 1f24A 402 4.51e+01 1rom a.104.1.1 18953 1xcbA 211 4.52e+01 a.4.5.38,c.2.1.12 109552,109553 1ifa 158 4.53e+01 1ifa a.26.1.3 16892 1snlA 103 4.54e+01 a.39.1.7 105820 1nf3C 128 4.54e+01 b.36.1.1 85596 2aefA 234 4.56e+01 1i4vA 115 4.68e+01 1umuA b.87.1.1 61734 1dj7B 75 4.68e+01 1dj7B b.34.4.3 24598 2amhA 207 4.70e+01 1umuB 116 4.74e+01 1umuA b.87.1.1 28383 1y43B 173 4.75e+01 1bvb 211 4.79e+01 1bvb a.138.1.3 19683 2apsA 162 4.79e+01 1yaiA b.1.8.1 22298 1hm9A 468 4.81e+01 b.81.1.4,c.68.1.5 65866,65867 1i8fA 81 4.85e+01 1i8fA b.38.1.1 61959 1cfr 285 4.89e+01 1cfr c.52.1.7 33312 1tf1A 198 4.90e+01 d.110.2.2 106826 2as9A 210 4.91e+01 1ft5A 211 4.93e+01 1bvb a.138.1.3 19681 1ej0A 180 4.96e+01 1ej0A c.66.1.2 34179 1o58A 303 4.98e+01 c.79.1.1 92491 1zetA 388 5.12e+01 1o8uA 257 5.15e+01 c.14.1.3 81194 1bby 69 5.15e+01 2bby a.4.5.15 16149 1p8kZ 254 5.16e+01 d.95.2.1,d.95.2.1 94361,94362 8rucI 123 5.20e+01 1rboC d.73.1.1 39629 1wjbA 55 5.27e+01 1wjcA a.4.10.1 16265 1qoxN 449 5.29e+01 1qoxN c.1.8.4 28978 1k8yB 396 5.34e+01 c.79.1.1 72184 2asbA 251 5.37e+01 1larA 575 5.39e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1hbxA 92 5.40e+01 1mnmA d.88.1.1 60930 1fhgA 154 5.45e+01 1tlk b.1.1.4 21706 1cbg 490 5.45e+01 1e70M c.1.8.4 28933 1fwkA 296 5.49e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1m4jA 142 5.49e+01 d.109.1.2 78602 1xdpA 687 5.50e+01 2f42A 179 5.50e+01 1wjcA 47 5.54e+01 1wjcA a.4.10.1 16261 1acmA 310 5.56e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1a50B 396 5.63e+01 2tysB c.79.1.1 35280 1k38A 254 5.69e+01 e.3.1.1 84303 1ghr 306 5.71e+01 1aq0A c.1.8.3 28844 1e6yA 569 5.83e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1as4A 341 5.89e+01 1sek e.1.1.1 42623 1zruA 264 5.91e+01 1zthA 258 5.92e+01 1h09A 338 5.95e+01 b.109.1.1,c.1.8.8 83420,83421 1pkn 530 5.95e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 8atcA 310 5.98e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 3kar 346 5.98e+01 1bg2 c.37.1.9 32198 1uteA 313 5.98e+01 1uteA d.159.1.1 42078 1vi7A 217 6.04e+01 d.14.1.11,d.58.11.2 100740,100741 1cc1L 498 6.07e+01 1h2rL e.18.1.1 43301 1diwA 441 6.13e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1knaA 69 6.14e+01 b.34.13.2 72771 1rboC 123 6.15e+01 1rboC d.73.1.1 39634 1ponB 36 6.19e+01 1ponB 1no5A 114 6.21e+01 d.218.1.5 92014 1q3lA 69 6.26e+01 1ll2A 333 6.26e+01 c.68.1.14 74005 1v5nA 89 6.27e+01 g.49.1.3 108380 1ztxL 212 6.32e+01 1ap0 73 6.33e+01 1ap0 b.34.13.2 37475 2bz6L 53 6.40e+01 1ekxA 311 6.40e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1pnsB 234 6.43e+01 i.1.1.1 88169 1aokA 122 6.44e+01 1poa a.133.1.2 19560 1z90A 469 6.48e+01 1vr7A 142 6.50e+01 1szoA 257 6.50e+01 c.14.1.3 106164 1at1A 310 6.53e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 2b2aA 199 6.58e+01 1rwrA 301 6.61e+01 b.80.1.11 97990 1n99A 166 6.62e+01 b.36.1.1,b.36.1.1 85459,85460 1culA 217 6.62e+01 1azsA d.58.29.1 39417 2av5A 120 6.67e+01 1vjjA 692 6.73e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1ur1A 378 6.73e+01 c.1.8.3 99804 1vqoL 165 6.80e+01 2bwfA 77 6.86e+01 2a1xA 308 6.88e+01 1o69A 394 6.91e+01 c.67.1.4 92560 1j5eB 256 6.94e+01 c.23.15.1 71543 1fjgB 256 6.95e+01 1fjfB c.23.15.1 31400 1fzqA 181 6.96e+01 1hurA c.37.1.8 32060 1mkp 144 6.98e+01 1vhrA c.45.1.1 32654 1xyiA 66 7.00e+01 2adbA 148 7.09e+01 1fyvA 161 7.10e+01 1fyvA c.23.2.1 31127 1b43A 340 7.15e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2bo4A 397 7.18e+01 2bsdA 264 7.19e+01 1fw9A 164 7.28e+01 1fw9A d.190.1.1 60059 1tt8A 164 7.28e+01 1c7gA 456 7.28e+01 c.67.1.2 90415 1f9vA 347 7.33e+01 1bg2 c.37.1.9 59745 1whvA 100 7.40e+01 1htjF 210 7.40e+01 1htjF a.91.1.1 61254 1g97A 459 7.42e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1g0dA 695 7.49e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 60166,60167,60168,60169 1nteA 82 7.57e+01 b.36.1.1 86163 1njhA 119 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d.126.1.4 91154 1pvtA 238 8.58e+01 c.74.1.1 95189 1wmqA 147 8.61e+01 2his 312 8.62e+01 1taxA c.1.8.3 28918 2aq8A 269 8.65e+01 1fc2D 224 8.71e+01 1igtB b.1.1.2,b.1.1.2 21516,21517 1y96A 86 8.78e+01 1oa2A 218 8.81e+01 b.29.1.11 86721 1cvwL 55 8.85e+01 1hcgB g.3.11.1 44211 2gh1A 301 8.85e+01 2aq4A 434 8.91e+01 2scuB 388 8.92e+01 2scuB c.23.4.1,d.142.1.4 31141,41562