# List of top-scoring protein chains for t04-100-30-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 2.08e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1m93A 55 6.11e-01 e.1.1.1 91235 1zynA 202 8.58e-01 1sqsA 242 8.69e-01 c.23.5.5 98968 1hyuA 521 8.75e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1repC 251 1.08e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1y96B 85 1.38e+00 2fclA 169 1.94e+00 1xewY 172 1.97e+00 2ewrA 170 1.97e+00 2afbA 351 2.03e+00 2myr 501 2.34e+00 2bg5A 324 2.35e+00 1ycyA 71 2.62e+00 1ockA 412 2.71e+00 c.117.1.1 86802 1c52 131 2.75e+00 1c52 a.3.1.1 15810 1iz5A 249 2.82e+00 d.131.1.2,d.131.1.2 83834,83835 1j5vA 351 3.41e+00 c.72.1.1 71585 1k38A 254 3.74e+00 e.3.1.1 84303 2rslA 140 3.87e+00 2rslA c.53.1.1 33345 1hqz1 141 4.11e+00 1yiyA 429 4.49e+00 1a0rP 245 4.86e+00 1b9yC c.47.1.6 33054 1pnsC 206 5.17e+00 i.1.1.1 88170 1e9rA 437 5.22e+00 c.37.1.11 64827 1vr7A 142 5.24e+00 1xn5A 146 5.25e+00 1tluA 130 5.49e+00 d.156.1.2 107139 1e4mM 501 5.62e+00 1e70M c.1.8.4 59226 2cxcA 144 5.90e+00 2fgtA 417 6.13e+00 2pil 159 6.23e+00 2pil d.24.1.1 38376 1iqaA 160 6.65e+00 b.22.1.1 71274 1s55A 156 7.01e+00 1lwjA 441 7.19e+00 b.71.1.1,c.1.8.1 74303,74304 1h72C 296 7.80e+00 d.14.1.5,d.58.26.1 60712,60713 1qi9A 556 7.83e+00 1qhbA a.111.1.2 19053 1fwkA 296 7.87e+00 1fwkA d.14.1.5,d.58.26.1 37576,39398 1fhgA 154 7.93e+00 1tlk b.1.1.4 21706 1fw9A 164 8.24e+00 1fw9A d.190.1.1 60059 1tt8A 164 8.24e+00 2fkcA 247 9.12e+00 1urnA 97 9.27e+00 1urnA d.58.7.1 39153 1wmhB 86 9.72e+00 1tlk 154 1.04e+01 1tlk b.1.1.4 21707 2g9iA 249 1.07e+01 2amhA 207 1.07e+01 1d2oA 187 1.16e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1bia 321 1.22e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1vjpA 394 1.28e+01 c.2.1.3,d.81.1.3 100828,100829 1sr4B 261 1.30e+01 d.151.1.1 105949 1of8A 370 1.37e+01 c.1.10.4 92819 1fsz 372 1.40e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1ft5A 211 1.42e+01 1bvb a.138.1.3 19681 1uekA 275 1.42e+01 d.14.1.5,d.58.26.5 88483,88484 2g5dA 422 1.46e+01 1nf3C 128 1.47e+01 b.36.1.1 85596 1kqpA 271 1.49e+01 c.26.2.1 72883 1quqB 121 1.50e+01 1quqB b.40.4.3 25305 1rfeA 162 1.51e+01 1c7qA 445 1.51e+01 2pgi c.80.1.2 35307 1ynmA 247 1.52e+01 1qhlA 227 1.53e+01 1qhlA c.37.1.12 32382 2b7eA 59 1.59e+01 1b25A 619 1.60e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1fjgC 239 1.60e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1wouA 123 1.60e+01 c.47.1.16 109471 1ve0A 134 1.62e+01 1wcdJ 441 1.62e+01 1oiaA 95 1.63e+01 d.58.7.1 87051 1zhrA 238 1.74e+01 2aefA 234 1.74e+01 2gmqA 118 1.77e+01 2gh1A 301 1.78e+01 1pbgA 468 1.85e+01 1e70M c.1.8.4 28946 2culA 232 1.86e+01 1zhmA 238 1.87e+01 1v0lA 313 1.88e+01 c.1.8.3 108207 1jfbA 404 1.89e+01 a.104.1.1 66624 1ih8A 271 1.89e+01 2nsyA c.26.2.1 62377 1od8A 313 1.89e+01 c.1.8.3 86838 1f24A 402 1.90e+01 1rom a.104.1.1 18953 1yizA 429 1.90e+01 1wrjA 156 1.92e+01 1qlmA 316 1.97e+01 1qlmA d.147.1.1 41765 1no5A 114 1.98e+01 d.218.1.5 92014 1luzA 88 2.06e+01 b.40.4.5 74271 1e0wA 313 2.13e+01 1taxA c.1.8.3 59150 1zhpA 238 2.15e+01 1qopB 396 2.31e+01 2tysB c.79.1.1 35270 2adoA 196 2.32e+01 1o1zA 234 2.32e+01 c.1.18.3 86555 1vkuA 100 2.37e+01 a.28.1.1 108690 1woqA 267 2.42e+01 c.55.1.10,c.55.1.10 109462,109463 1te7A 103 2.44e+01 2dfkA 402 2.45e+01 1wmhA 89 2.46e+01 1m4jA 142 2.47e+01 d.109.1.2 78602 1f0cA 305 2.48e+01 1c8oA e.1.1.1 42676 2aq4A 434 2.53e+01 1nu4A 97 2.56e+01 d.58.7.1 80731 1vcvA 226 2.56e+01 2d9rA 104 2.61e+01 1cojA 212 2.62e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1n8kA 374 2.63e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 2.64e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1r6jA 82 2.67e+01 b.36.1.1 97151 2etxA 209 2.67e+01 1jhsA 188 2.69e+01 d.107.1.1 84172 1ri7A 171 2.69e+01 a.4.5.32,d.58.4.2 97504,97505 1juvA 193 2.70e+01 c.71.1.1 90912 1xx9A 238 2.71e+01 1id0A 152 2.72e+01 d.122.1.3 66111 1toaA 313 2.73e+01 1toaA c.92.2.2 35598 2ohxA 374 2.74e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1x74A 360 2.75e+01 1o9gA 250 2.76e+01 c.66.1.29 86692 1bby 69 2.76e+01 2bby a.4.5.15 16149 1ep3B 262 2.89e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 2g6tA 306 2.90e+01 1xtoA 311 2.91e+01 1xfcA 384 2.94e+01 1nteA 82 2.96e+01 b.36.1.1 86163 1ny4A 82 2.99e+01 b.40.4.5 92316 2gw6A 123 3.00e+01 2a15A 139 3.02e+01 2gfgA 193 3.06e+01 1h7zA 194 3.13e+01 1qhvA b.21.1.1 60733 1enwA 114 3.17e+01 1enwA a.5.4.1 16291 1b5tA 275 3.17e+01 1b5tA c.1.23.1 29676 1d1gA 168 3.19e+01 1d1gA c.71.1.1 34889 1tiqA 180 3.24e+01 d.108.1.1 107010 1r5jA 337 3.28e+01 c.77.1.5 97097 1vddA 228 3.29e+01 e.49.1.1 108519 1vicA 262 3.30e+01 c.68.1.13 100756 1wspA 84 3.31e+01 1cby 259 3.38e+01 1cby d.103.1.1 40705 1z52A 470 3.40e+01 1rh9A 373 3.44e+01 1eceA 358 3.50e+01 1eceA c.1.8.3 28813 1wlyA 333 3.52e+01 1ma3A 253 3.62e+01 c.31.1.5 78883 1hdoA 206 3.63e+01 1he2A c.2.1.2 60965 1ri5A 298 3.68e+01 c.66.1.34 97502 1sn4A 64 3.68e+01 1aho g.3.7.1 44136 1xel 338 3.69e+01 1xel c.2.1.2 29786 1i8fA 81 3.69e+01 1i8fA b.38.1.1 61959 1bdfA 235 3.73e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1pbjA 125 3.73e+01 d.37.1.1,d.37.1.1 94414,94415 1duvG 333 3.74e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1wluA 136 3.76e+01 1udc 338 3.76e+01 1xel c.2.1.2 29785 1wu3I 161 3.78e+01 1o0yA 260 3.80e+01 c.1.10.1 80756 1sq9A 397 3.93e+01 b.69.4.1 105889 1gd1O 334 4.00e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2bo4A 397 4.05e+01 1e0tA 470 4.16e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1fzqA 181 4.19e+01 1hurA c.37.1.8 32060 1dkuA 317 4.19e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 2hvm 273 4.19e+01 1cnv c.1.8.5 28985 1xvqA 175 4.22e+01 1jy1A 464 4.32e+01 d.136.1.3,d.136.1.3 67438,67439 1h09A 338 4.33e+01 b.109.1.1,c.1.8.8 83420,83421 1ip9A 85 4.36e+01 1ip9A d.15.2.2 62638 1vi1A 345 4.38e+01 c.77.1.4 100724 1xcbA 211 4.38e+01 a.4.5.38,c.2.1.12 109552,109553 2b4rO 345 4.39e+01 1wyxA 69 4.41e+01 2awpA 198 4.43e+01 1icxA 155 4.45e+01 d.129.3.1 71191 1s0pA 176 4.45e+01 a.192.1.1 98300 1pyfA 312 4.45e+01 c.1.7.1 95334 1fl2A 310 4.46e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1uwzA 136 4.52e+01 c.97.1.1 108081 1z6gA 218 4.52e+01 1ml8A 134 4.55e+01 d.227.1.2 85013 1b33N 67 4.62e+01 1b33N d.30.1.1 38459 1vfsA 386 4.63e+01 b.49.2.2,c.1.6.1 108584,108585 1ve6A 582 4.64e+01 1hm9A 468 4.65e+01 b.81.1.4,c.68.1.5 65866,65867 1jtkA 136 4.67e+01 c.97.1.1 71862 1k0fA 277 4.72e+01 c.92.2.2 71974 1ydmA 187 4.73e+01 1f2tB 148 4.75e+01 1f2tB 1j1yA 136 4.75e+01 d.38.1.5 90776 1ydyA 356 4.80e+01 1ej6D 418 4.81e+01 i.7.1.1 45970 1kjwA 295 4.82e+01 b.34.2.1,c.37.1.1 68643,68644 1bg6 359 4.89e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 2c7hA 86 4.90e+01 1ur1A 378 4.90e+01 c.1.8.3 99804 1qg8A 255 4.95e+01 1qg8A c.68.1.1 34505 1eq6A 189 4.96e+01 1eq6A d.107.1.1 40796 1u46A 291 4.98e+01 d.144.1.7 107656 1zc1A 208 5.11e+01 1fjgB 256 5.13e+01 1fjfB c.23.15.1 31400 1s50A 259 5.13e+01 1qx4A 274 5.13e+01 b.43.4.2,c.25.1.1 104624,104625 1t8qA 336 5.19e+01 c.1.18.3 106669 1ylqA 96 5.28e+01 1uurA 473 5.36e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1f9vA 347 5.47e+01 1bg2 c.37.1.9 59745 1xdpA 687 5.51e+01 1ll2A 333 5.51e+01 c.68.1.14 74005 1p8kZ 254 5.54e+01 d.95.2.1,d.95.2.1 94361,94362 1vr4A 103 5.62e+01 3seb 238 5.68e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1vm6A 228 5.70e+01 c.2.1.3,d.81.1.3 108876,108877 1zpvA 91 5.74e+01 2amyA 246 5.76e+01 1yr2A 741 5.95e+01 1zpsA 138 5.98e+01 8rucI 123 6.00e+01 1rboC d.73.1.1 39629 1gyxA 76 6.00e+01 d.80.1.1 76387 1g97A 459 6.03e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1vqoI 162 6.07e+01 1z4rA 168 6.07e+01 1g291 372 6.09e+01 1g291 1kqzA 273 6.15e+01 c.1.8.5 68844 1wqaA 455 6.16e+01 1k7jA 206 6.17e+01 d.115.1.1 72103 2asbA 251 6.20e+01 1evuA 731 6.20e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1o0pA 104 6.23e+01 d.58.7.1 86535 1preA 470 6.24e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1vphA 149 6.29e+01 1mk0A 97 6.29e+01 d.226.1.1 79216 1shsA 147 6.30e+01 1shsA b.15.1.1 23675 2f5gA 133 6.32e+01 1cfr 285 6.34e+01 1cfr c.52.1.7 33312 1o98A 511 6.37e+01 c.105.1.1,c.76.1.3 86684,86685 1vhxA 150 6.39e+01 c.55.3.8 100712 2dddA 225 6.45e+01 2akoA 251 6.50e+01 1wkqA 164 6.51e+01 c.97.1.2 109393 1t0aA 159 6.52e+01 1yg6A 193 6.57e+01 1qlwA 328 6.58e+01 1qlwA c.69.1.15 34722 1k0rA 366 6.67e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1p42A 270 6.68e+01 d.14.1.7,d.14.1.7 87754,87755 1zp4A 304 6.74e+01 1qysA 106 6.75e+01 k.41.1.1 96603 1o58A 303 6.77e+01 c.79.1.1 92491 1xhfA 123 6.79e+01 1bn8A 420 6.85e+01 1pcl b.80.1.1 28022 2d1pA 140 6.88e+01 1vhh 162 6.92e+01 1vhh d.65.1.2 39550 1uc7A 125 7.00e+01 c.47.1.1 99163 1ltlA 279 7.02e+01 b.40.4.11 84701 2fn0A 437 7.08e+01 2frnA 278 7.09e+01 1larA 575 7.12e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1exmA 405 7.12e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1ta3B 303 7.22e+01 c.1.8.3 106732 1es6A 296 7.23e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1mo9A 523 7.28e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1wojA 214 7.29e+01 1vp2A 208 7.31e+01 1d4tA 104 7.35e+01 1d4tA d.93.1.1 40537 2cygA 312 7.43e+01 1s72N 187 7.45e+01 c.55.4.1 105333 1kwiA 101 7.51e+01 d.17.1.3 77564 1gadO 330 7.54e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1sek 378 7.62e+01 1sek e.1.1.1 42675 1vqoN 187 7.64e+01 1xubA 298 7.67e+01 4pfk 319 7.68e+01 3pfk c.89.1.1 35582 1ztxL 212 7.75e+01 1ha3A 405 7.80e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1bueA 265 7.82e+01 1btl e.3.1.1 42727 1tw0A 157 7.83e+01 2ab5A 269 7.87e+01 2fh7A 595 7.91e+01 1pfkA 320 7.93e+01 3pfk c.89.1.1 35575 1ys4A 354 7.93e+01 1di2A 69 7.96e+01 1di2A d.50.1.1 38780 1omzA 293 8.03e+01 c.68.1.15 87093 1u3wA 374 8.14e+01 1aohA 147 8.18e+01 1aohA b.2.2.2 22401 2gvkA 317 8.18e+01 1eqjA 511 8.19e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1kk8B 139 8.24e+01 a.39.1.5 77430 1n8jA 186 8.24e+01 c.47.1.10 85401 1ede 310 8.36e+01 1b6g c.69.1.8 34662 1aq0A 306 8.42e+01 1aq0A c.1.8.3 28842 1nnjA 271 8.43e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1j1vA 94 8.67e+01 a.4.12.2 83981 1pjjA 271 8.72e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1gewA 356 8.80e+01 1gewA c.67.1.1 60470 5nul 138 8.81e+01 5nul c.23.5.1 31191 1eijA 80 8.83e+01 1eijA a.5.6.1 16298 2f6hX 419 8.85e+01 1y7tA 327 8.85e+01 1fg7A 356 8.85e+01 1gewA c.67.1.1 59819 1u1wA 298 8.88e+01 1bmdA 327 8.91e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 2bw3A 534 8.97e+01 1gqzA 274 8.99e+01 d.21.1.1,d.21.1.1 83311,83312 1plq 258 8.99e+01 1plq d.131.1.2,d.131.1.2 41388,41389