# List of top-scoring protein chains for t2k-100-30-str2-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 2.22e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1esfA 233 3.10e-01 3seb b.40.2.2,d.15.6.1 25146,37735 1m93A 55 6.74e-01 e.1.1.1 91235 1zynA 202 9.56e-01 1sqsA 242 9.68e-01 c.23.5.5 98968 1hyuA 521 9.75e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1repC 251 1.22e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1ge8A 249 1.25e+00 1plq d.131.1.2,d.131.1.2 41398,41399 1agnA 373 1.25e+00 2ohxA b.35.1.2,c.2.1.1 24737,29753 1y96B 85 1.56e+00 1gdtA 183 2.10e+00 2rslA a.4.1.2,c.53.1.1 16021,33348 1hqz9 141 2.15e+00 2fclA 169 2.21e+00 1xewY 172 2.24e+00 2ewrA 170 2.24e+00 2afbA 351 2.32e+00 2myr 501 2.69e+00 2bg5A 324 2.70e+00 1ycyA 71 3.01e+00 1ockA 412 3.12e+00 c.117.1.1 86802 1c52 131 3.16e+00 1c52 a.3.1.1 15810 1iz5A 249 3.25e+00 d.131.1.2,d.131.1.2 83834,83835 1j5vA 351 3.94e+00 c.72.1.1 71585 1k38A 254 4.34e+00 e.3.1.1 84303 2rslA 140 4.50e+00 2rslA c.53.1.1 33345 5gcnA 166 4.72e+00 1yghA d.108.1.1 40807 1hqz1 141 4.78e+00 1d2pA 373 4.91e+00 1d2oA b.3.5.1,b.3.5.1,b.3.5.1,b.3.5.1 22629,22630,22631,22632 1yiyA 429 5.24e+00 1a0rP 245 5.68e+00 1b9yC c.47.1.6 33054 1pnsC 206 6.05e+00 i.1.1.1 88170 1e9rA 437 6.11e+00 c.37.1.11 64827 1vr7A 142 6.14e+00 1xn5A 146 6.15e+00 1tluA 130 6.44e+00 d.156.1.2 107139 1e70M 501 6.59e+00 1e70M c.1.8.4 28926 1e4mM 501 6.60e+00 1e70M c.1.8.4 59226 1e6qM 501 6.88e+00 1e70M c.1.8.4 28920 2cxcA 144 6.94e+00 2fgtA 417 7.21e+00 2pil 159 7.34e+00 2pil d.24.1.1 38376 1ay2 159 7.44e+00 2pil d.24.1.1 38377 1j5eC 239 7.82e+00 d.52.3.1,d.53.1.1 71544,71545 1iqaA 160 7.84e+00 b.22.1.1 71274 1s55A 156 8.28e+00 1lwjA 441 8.50e+00 b.71.1.1,c.1.8.1 74303,74304 1h72C 296 9.24e+00 d.14.1.5,d.58.26.1 60712,60713 1qi9A 556 9.27e+00 1qhbA a.111.1.2 19053 1fwkA 296 9.32e+00 1fwkA d.14.1.5,d.58.26.1 37576,39398 1fhgA 154 9.39e+00 1tlk b.1.1.4 21706 1fw9A 164 9.77e+00 1fw9A d.190.1.1 60059 1tt8A 164 9.77e+00 2fkcA 247 1.08e+01 1urnA 97 1.10e+01 1urnA d.58.7.1 39153 2ifeA 100 1.13e+01 1tig d.68.1.1 39567 1fht 116 1.15e+01 1urnA d.58.7.1 39157 1wmhB 86 1.16e+01 1bib 321 1.23e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1tlk 154 1.24e+01 1tlk b.1.1.4 21707 2g9iA 249 1.28e+01 2amhA 207 1.28e+01 1cx0A 95 1.33e+01 1urnA d.58.7.1 39158 1d2oA 187 1.39e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 2wsyB 396 1.45e+01 2tysB c.79.1.1 35288 1bia 321 1.47e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1m5oC 100 1.53e+01 d.58.7.1 78654 1vjpA 394 1.54e+01 c.2.1.3,d.81.1.3 100828,100829 1sr4B 261 1.56e+01 d.151.1.1 105949 1hfbA 370 1.60e+01 c.1.10.4 76706 1gnf 46 1.61e+01 1gatA g.39.1.1 45107 1of8A 370 1.64e+01 c.1.10.4 92819 1fsz 372 1.69e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1ft5A 211 1.71e+01 1bvb a.138.1.3 19681 1uekA 275 1.71e+01 d.14.1.5,d.58.26.5 88483,88484 2g5dA 422 1.76e+01 1nf3C 128 1.77e+01 b.36.1.1 85596 1kqpA 271 1.80e+01 c.26.2.1 72883 1nsyA 271 1.81e+01 2nsyA c.26.2.1 31614 1kvs 338 1.81e+01 1xel c.2.1.2 29799 1quqB 121 1.81e+01 1quqB b.40.4.3 25305 1rfeA 162 1.82e+01 1c7qA 445 1.82e+01 2pgi c.80.1.2 35307 1ynmA 247 1.83e+01 1qhlA 227 1.85e+01 1qhlA c.37.1.12 32382 2tysB 397 1.86e+01 2tysB c.79.1.1 35272 1bvb 211 1.86e+01 1bvb a.138.1.3 19683 1b0zA 445 1.90e+01 2pgi c.80.1.2 35309 2pgi 445 1.90e+01 2pgi c.80.1.2 35308 2b7eA 59 1.91e+01 1b25A 619 1.93e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1fjgC 239 1.93e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1wouA 123 1.93e+01 c.47.1.16 109471 1ve0A 134 1.95e+01 1wcdJ 441 1.96e+01 1oiaA 95 1.97e+01 d.58.7.1 87051 1bksB 397 2.00e+01 2tysB c.79.1.1 35285 1zhrA 238 2.11e+01 2aefA 234 2.11e+01 2gmqA 118 2.14e+01 2gh1A 301 2.15e+01 1a50B 396 2.16e+01 2tysB c.79.1.1 35280 1pbgA 468 2.24e+01 1e70M c.1.8.4 28946 2culA 232 2.25e+01 1zhmA 238 2.26e+01 1v0lA 313 2.28e+01 c.1.8.3 108207 1k8yB 396 2.29e+01 c.79.1.1 72184 1jfbA 404 2.29e+01 a.104.1.1 66624 1ih8A 271 2.29e+01 2nsyA c.26.2.1 62377 1od8A 313 2.29e+01 c.1.8.3 86838 1f24A 402 2.30e+01 1rom a.104.1.1 18953 1yizA 429 2.30e+01 1wrjA 156 2.33e+01 2nsyA 271 2.34e+01 2nsyA c.26.2.1 31612 1qlmA 316 2.39e+01 1qlmA d.147.1.1 41765 1no5A 114 2.40e+01 d.218.1.5 92014 3pbgA 468 2.45e+01 1e70M c.1.8.4 28951 1audA 101 2.46e+01 1urnA d.58.7.1 39156 1luzA 88 2.50e+01 b.40.4.5 74271 1focA 132 2.54e+01 1c52 a.3.1.1 15812 1ee2A 373 2.55e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1e0wA 313 2.59e+01 1taxA c.1.8.3 59150 1zhpA 238 2.61e+01 1qopB 396 2.82e+01 2tysB c.79.1.1 35270 2adoA 196 2.82e+01 1o1zA 234 2.83e+01 c.1.18.3 86555 1aogA 485 2.87e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1vkuA 100 2.89e+01 a.28.1.1 108690 1gh6A 114 2.95e+01 a.2.3.1 65191 1woqA 267 2.95e+01 c.55.1.10,c.55.1.10 109462,109463 1te7A 103 2.97e+01 2dfkA 402 2.99e+01 1wmhA 89 3.01e+01 1m4jA 142 3.01e+01 d.109.1.2 78602 1f0cA 305 3.03e+01 1c8oA e.1.1.1 42676 1n99A 166 3.09e+01 b.36.1.1,b.36.1.1 85459,85460 2aq4A 434 3.10e+01 1nu4A 97 3.13e+01 d.58.7.1 80731 1vcvA 226 3.13e+01 1ghtA 105 3.13e+01 2rslA c.53.1.1 60526 2d9rA 104 3.19e+01 1cojA 212 3.20e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1n8kA 374 3.22e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 3.23e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 8adh 374 3.24e+01 2ohxA b.35.1.2,c.2.1.1 24690,29706 1c8oA 300 3.27e+01 1c8oA e.1.1.1 42677 1r6jA 82 3.27e+01 b.36.1.1 97151 2etxA 209 3.27e+01 1jhsA 188 3.29e+01 d.107.1.1 84172 1axgA 374 3.29e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1a71A 374 3.29e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1ri7A 171 3.29e+01 a.4.5.32,d.58.4.2 97504,97505 1juvA 193 3.31e+01 c.71.1.1 90912 1heuA 374 3.31e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 1xx9A 238 3.32e+01 1id0A 152 3.33e+01 d.122.1.3 66111 1toaA 313 3.35e+01 1toaA c.92.2.2 35598 2ohxA 374 3.36e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1x74A 360 3.36e+01 1axeA 374 3.36e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1o9gA 250 3.38e+01 c.66.1.29 86692 1bby 69 3.38e+01 2bby a.4.5.15 16149 2bby 69 3.40e+01 2bby a.4.5.15 16148 1ifa 158 3.41e+01 1ifa a.26.1.3 16892 1ep3B 262 3.55e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 2g6tA 306 3.55e+01 1xtoA 311 3.56e+01 1xfcA 384 3.60e+01 1nteA 82 3.64e+01 b.36.1.1 86163 1xyfA 436 3.65e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1ny4A 82 3.67e+01 b.40.4.5 92316 2gw6A 123 3.68e+01 2a15A 139 3.70e+01 2gfgA 193 3.76e+01 1h7zA 194 3.85e+01 1qhvA b.21.1.1 60733 1enwA 114 3.89e+01 1enwA a.5.4.1 16291 1b5tA 275 3.90e+01 1b5tA c.1.23.1 29676 1d1gA 168 3.91e+01 1d1gA c.71.1.1 34889 1tiqA 180 3.99e+01 d.108.1.1 107010 1r5jA 337 4.04e+01 c.77.1.5 97097 1vddA 228 4.05e+01 e.49.1.1 108519 1vicA 262 4.06e+01 c.68.1.13 100756 2udpA 338 4.06e+01 1xel c.2.1.2 29791 1wspA 84 4.07e+01 1mu7A 485 4.11e+01 d.136.1.3,d.136.1.3 79475,79476 1cby 259 4.16e+01 1cby d.103.1.1 40705 1z52A 470 4.19e+01 1rh9A 373 4.24e+01 1eceA 358 4.31e+01 1eceA c.1.8.3 28813 1wlyA 333 4.33e+01 1c0dA 358 4.36e+01 1eceA c.1.8.3 28815 1ma3A 253 4.46e+01 c.31.1.5 78883 1he2A 206 4.46e+01 1he2A c.2.1.2 60966 1hdoA 206 4.47e+01 1he2A c.2.1.2 60965 1rmi 160 4.48e+01 1ifa a.26.1.3 16891 1udb 338 4.54e+01 1xel c.2.1.2 29787 1a9y 338 4.54e+01 1xel c.2.1.2 29789 1ri5A 298 4.54e+01 c.66.1.34 97502 1sn4A 64 4.54e+01 1aho g.3.7.1 44136 1xel 338 4.55e+01 1xel c.2.1.2 29786 1cz3A 168 4.55e+01 1d1gA c.71.1.1 34891 1i8fA 81 4.55e+01 1i8fA b.38.1.1 61959 1a9z 338 4.57e+01 1xel c.2.1.2 29795 1bdfA 235 4.60e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1pbjA 125 4.60e+01 d.37.1.1,d.37.1.1 94414,94415 1duvG 333 4.61e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1wluA 136 4.64e+01 1udc 338 4.64e+01 1xel c.2.1.2 29785 1wu3I 161 4.66e+01 1o0yA 260 4.68e+01 c.1.10.1 80756 1tbrR 103 4.81e+01 1tbrR g.68.1.1,g.68.1.1 44707,44708 1sq9A 397 4.86e+01 b.69.4.1 105889 1gd1O 334 4.95e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2bo4A 397 5.00e+01 1e0tA 470 5.14e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1fzqA 181 5.18e+01 1hurA c.37.1.8 32060 1dkuA 317 5.18e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2hvm 273 5.19e+01 1cnv c.1.8.5 28985 1xvqA 175 5.23e+01 1jy1A 464 5.35e+01 d.136.1.3,d.136.1.3 67438,67439 1h09A 338 5.36e+01 b.109.1.1,c.1.8.8 83420,83421 1ip9A 85 5.40e+01 1ip9A d.15.2.2 62638 1vi1A 345 5.43e+01 c.77.1.4 100724 1xcbA 211 5.43e+01 a.4.5.38,c.2.1.12 109552,109553 2b4rO 345 5.44e+01 1wyxA 69 5.47e+01 2awpA 198 5.49e+01 1icxA 155 5.51e+01 d.129.3.1 71191 1s0pA 176 5.51e+01 a.192.1.1 98300 1pyfA 312 5.51e+01 c.1.7.1 95334 1fl2A 310 5.53e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1uwzA 136 5.61e+01 c.97.1.1 108081 1z6gA 218 5.61e+01 1ml8A 134 5.64e+01 d.227.1.2 85013 1preB 470 5.64e+01 1preA d.169.1.2,f.8.1.1 42438,43825 2gd1O 334 5.66e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1b33N 67 5.73e+01 1b33N d.30.1.1 38459 1vfsA 386 5.75e+01 b.49.2.2,c.1.6.1 108584,108585 1ve6A 582 5.75e+01 1hm9A 468 5.77e+01 b.81.1.4,c.68.1.5 65866,65867 1jtkA 136 5.79e+01 c.97.1.1 71862 1k0fA 277 5.86e+01 c.92.2.2 71974 1ydmA 187 5.87e+01 1f2tB 148 5.89e+01 1f2tB 1j1yA 136 5.89e+01 d.38.1.5 90776 1ydyA 356 5.96e+01 1ej6D 418 5.97e+01 i.7.1.1 45970 1kjwA 295 5.98e+01 b.34.2.1,c.37.1.1 68643,68644 1jxmA 301 6.05e+01 b.34.2.1,c.37.1.1 67420,67421 1bg6 359 6.08e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 2c7hA 86 6.09e+01 1ur1A 378 6.09e+01 c.1.8.3 99804 1qg8A 255 6.14e+01 1qg8A c.68.1.1 34505 1eq6A 189 6.16e+01 1eq6A d.107.1.1 40796 1u46A 291 6.19e+01 d.144.1.7 107656 1f13A 731 6.24e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 2dldA 337 6.33e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1zc1A 208 6.35e+01 1fjgB 256 6.38e+01 1fjfB c.23.15.1 31400 1s50A 259 6.39e+01 1qx4A 274 6.39e+01 b.43.4.2,c.25.1.1 104624,104625 1t8qA 336 6.46e+01 c.1.18.3 106669 1kk9A 221 6.55e+01 d.115.1.1 77432 1ylqA 96 6.57e+01 1ep2B 261 6.60e+01 1ep2B b.43.4.2,c.25.1.3 25666,31556 1uurA 473 6.67e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1qdlB 195 6.73e+01 1qdlB c.23.16.1 31437 1f9vA 347 6.81e+01 1bg2 c.37.1.9 59745 1xdpA 687 6.87e+01 1ll2A 333 6.87e+01 c.68.1.14 74005 1p8kZ 254 6.91e+01 d.95.2.1,d.95.2.1 94361,94362 1vr4A 103 7.00e+01 3seb 238 7.08e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1vm6A 228 7.10e+01 c.2.1.3,d.81.1.3 108876,108877 1zpvA 91 7.16e+01 2amyA 246 7.19e+01 1pk9A 237 7.19e+01 c.56.2.1 94823 1jjgA 102 7.37e+01 b.40.4.5 71696 1d0sA 356 7.40e+01 1d0vA c.39.1.1 32477 1yr2A 741 7.43e+01 1zpsA 138 7.46e+01 8rucI 123 7.49e+01 1rboC d.73.1.1 39629 1gyxA 76 7.49e+01 d.80.1.1 76387 1rboC 123 7.50e+01 1rboC d.73.1.1 39634 1g97A 459 7.53e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1ejjA 511 7.54e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1vqoI 162 7.59e+01 1z4rA 168 7.59e+01 1ck9A 104 7.59e+01 1ck9A d.79.3.1 39806 1g291 372 7.60e+01 1g291 1wjcA 47 7.64e+01 1wjcA a.4.10.1 16261 1kqzA 273 7.68e+01 c.1.8.5 68844 1wqaA 455 7.69e+01 1k7jA 206 7.71e+01 d.115.1.1 72103 2asbA 251 7.74e+01 1evuA 731 7.74e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1o0pA 104 7.79e+01 d.58.7.1 86535 1preA 470 7.79e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1cf7A 76 7.85e+01 1cf7B a.4.5.17 16151 1vphA 149 7.86e+01 1mk0A 97 7.86e+01 d.226.1.1 79216 1shsA 147 7.87e+01 1shsA b.15.1.1 23675 2f5gA 133 7.90e+01 1kqyA 273 7.90e+01 c.1.8.5 68843 1cfr 285 7.93e+01 1cfr c.52.1.7 33312 1o98A 511 7.97e+01 c.105.1.1,c.76.1.3 86684,86685 1vhxA 150 7.99e+01 c.55.3.8 100712 2dddA 225 8.07e+01 2akoA 251 8.13e+01 1wkqA 164 8.15e+01 c.97.1.2 109393 1t0aA 159 8.16e+01 1ll0A 339 8.21e+01 c.68.1.14 73995 1yg6A 193 8.22e+01 1qlwA 328 8.23e+01 1qlwA c.69.1.15 34722 1se4 239 8.27e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1f76A 336 8.29e+01 c.1.4.1 76160 1bdmB 327 8.33e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 1k0rA 366 8.36e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1p42A 270 8.36e+01 d.14.1.7,d.14.1.7 87754,87755 1zp4A 304 8.44e+01 1qysA 106 8.45e+01 k.41.1.1 96603 1o58A 303 8.48e+01 c.79.1.1 92491 1xhfA 123 8.50e+01 1bn8A 420 8.58e+01 1pcl b.80.1.1 28022 1qayA 428 8.61e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 2d1pA 140 8.62e+01 3kar 346 8.65e+01 1bg2 c.37.1.9 32198 1vhh 162 8.67e+01 1vhh d.65.1.2 39550 1uc7A 125 8.78e+01 c.47.1.1 99163 1ltlA 279 8.80e+01 b.40.4.11 84701 2fn0A 437 8.87e+01 2frnA 278 8.89e+01 2fvx 138 8.90e+01 5nul c.23.5.1 31200 1larA 575 8.92e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1exmA 405 8.93e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131