# 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 2.36e-01 3seb b.40.2.2,d.15.6.1 59140,59141 1m93A 55 8.70e-01 e.1.1.1 91235 1hyuA 521 1.02e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1sqsA 242 1.11e+00 c.23.5.5 98968 1zynA 202 1.11e+00 1repC 251 1.49e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1y96B 85 1.52e+00 2fclA 169 1.87e+00 2ewrA 170 1.89e+00 2myr 501 2.40e+00 2afbA 351 2.75e+00 1iz5A 249 2.78e+00 d.131.1.2,d.131.1.2 83834,83835 1ockA 412 2.87e+00 c.117.1.1 86802 1xewY 172 3.05e+00 1ycyA 71 3.06e+00 2bg5A 324 3.49e+00 1c52 131 3.72e+00 1c52 a.3.1.1 15810 2rslA 140 4.26e+00 2rslA c.53.1.1 33345 1j5vA 351 4.40e+00 c.72.1.1 71585 1k38A 254 4.59e+00 e.3.1.1 84303 1yiyA 429 5.65e+00 1xn5A 146 5.76e+00 1a0rP 245 5.81e+00 1b9yC c.47.1.6 33054 1e4mM 501 6.07e+00 1e70M c.1.8.4 59226 2pil 159 6.18e+00 2pil d.24.1.1 38376 1hqz1 141 6.22e+00 1vr7A 142 6.24e+00 1tluA 130 6.42e+00 d.156.1.2 107139 1of8A 370 6.91e+00 c.1.10.4 92819 2cxcA 144 7.34e+00 1sr4B 261 8.04e+00 d.151.1.1 105949 2fgtA 417 8.57e+00 1lwjA 441 8.61e+00 b.71.1.1,c.1.8.1 74303,74304 1fl2A 310 8.61e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1qi9A 556 8.62e+00 1qhbA a.111.1.2 19053 1pnsC 206 8.64e+00 i.1.1.1 88170 1urnA 97 9.58e+00 1urnA d.58.7.1 39153 1fhgA 154 9.85e+00 1tlk b.1.1.4 21706 2fkcA 247 1.12e+01 1d2oA 187 1.13e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1wmhB 86 1.15e+01 1o0pA 104 1.17e+01 d.58.7.1 86535 2g9iA 249 1.23e+01 1e9rA 437 1.23e+01 c.37.1.11 64827 1tlk 154 1.26e+01 1tlk b.1.1.4 21707 2amhA 207 1.30e+01 1rfeA 162 1.31e+01 2gmqA 118 1.34e+01 1quqB 121 1.37e+01 1quqB b.40.4.3 25305 1iqaA 160 1.43e+01 b.22.1.1 71274 1wcdJ 441 1.50e+01 1s55A 156 1.50e+01 1uekA 275 1.51e+01 d.14.1.5,d.58.26.5 88483,88484 1bia 321 1.52e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1oiaA 95 1.56e+01 d.58.7.1 87051 1fw9A 164 1.57e+01 1fw9A d.190.1.1 60059 1tt8A 164 1.57e+01 1c7qA 445 1.69e+01 2pgi c.80.1.2 35307 1ft5A 211 1.70e+01 1bvb a.138.1.3 19681 1m4jA 142 1.72e+01 d.109.1.2 78602 2g5dA 422 1.75e+01 1h72C 296 1.77e+01 d.14.1.5,d.58.26.1 60712,60713 1qhlA 227 1.79e+01 1qhlA c.37.1.12 32382 1ynmA 247 1.81e+01 1kqpA 271 1.84e+01 c.26.2.1 72883 1wouA 123 1.84e+01 c.47.1.16 109471 1b25A 619 1.93e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1vjpA 394 1.97e+01 c.2.1.3,d.81.1.3 100828,100829 2b7eA 59 1.97e+01 2gh1A 301 2.01e+01 1fsz 372 2.01e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1nf3C 128 2.03e+01 b.36.1.1 85596 1jfbA 404 2.06e+01 a.104.1.1 66624 1f24A 402 2.07e+01 1rom a.104.1.1 18953 1evuA 731 2.10e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1ve0A 134 2.12e+01 2aefA 234 2.15e+01 1fwkA 296 2.16e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1pbgA 468 2.18e+01 1e70M c.1.8.4 28946 1w2iA 91 2.21e+01 d.58.10.1 109127 1zhrA 238 2.29e+01 1ih8A 271 2.32e+01 2nsyA c.26.2.1 62377 1wrjA 156 2.34e+01 1v0lA 313 2.35e+01 c.1.8.3 108207 1yizA 429 2.37e+01 1od8A 313 2.37e+01 c.1.8.3 86838 1ex0A 731 2.38e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1fjgC 239 2.38e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1luzA 88 2.40e+01 b.40.4.5 74271 1o1zA 234 2.43e+01 c.1.18.3 86555 1zhmA 238 2.46e+01 1wspA 84 2.46e+01 2culA 232 2.47e+01 1no5A 114 2.49e+01 d.218.1.5 92014 1te7A 103 2.55e+01 1juvA 193 2.58e+01 c.71.1.1 90912 1id0A 152 2.59e+01 d.122.1.3 66111 1e0wA 313 2.66e+01 1taxA c.1.8.3 59150 1o9gA 250 2.67e+01 c.66.1.29 86692 1qlmA 316 2.71e+01 1qlmA d.147.1.1 41765 1zhpA 238 2.79e+01 1cojA 212 2.81e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1ep3B 262 2.81e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1nu4A 97 2.83e+01 d.58.7.1 80731 1wmhA 89 2.84e+01 1qopB 396 2.86e+01 2tysB c.79.1.1 35270 2dfkA 402 2.88e+01 1gd1O 334 2.90e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2adoA 196 3.00e+01 1vcvA 226 3.01e+01 1n8kA 374 3.06e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 3.06e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 2d9rA 104 3.13e+01 1jhsA 188 3.13e+01 d.107.1.1 84172 1eceA 358 3.13e+01 1eceA c.1.8.3 28813 1bby 69 3.14e+01 2bby a.4.5.15 16149 2ohxA 374 3.22e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 2aq4A 434 3.22e+01 1woqA 267 3.23e+01 c.55.1.10,c.55.1.10 109462,109463 2awpA 198 3.24e+01 2g6tA 306 3.25e+01 1xfcA 384 3.30e+01 1nijA 318 3.32e+01 c.37.1.10,d.237.1.1 85741,85742 1f0cA 305 3.34e+01 1c8oA e.1.1.1 42676 1vkuA 100 3.37e+01 a.28.1.1 108690 1ri7A 171 3.40e+01 a.4.5.32,d.58.4.2 97504,97505 1mo9A 523 3.43e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 2etxA 209 3.44e+01 1bdfA 235 3.45e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1smlA 269 3.46e+01 1smlA d.157.1.1 42053 1xx9A 238 3.52e+01 1cby 259 3.57e+01 1cby d.103.1.1 40705 1rh9A 373 3.61e+01 1xtoA 311 3.64e+01 2a15A 139 3.68e+01 1enwA 114 3.69e+01 1enwA a.5.4.1 16291 1vddA 228 3.69e+01 e.49.1.1 108519 1sq9A 397 3.74e+01 b.69.4.1 105889 1d1gA 168 3.75e+01 1d1gA c.71.1.1 34889 1vicA 262 3.75e+01 c.68.1.13 100756 2gfgA 193 3.75e+01 1x74A 360 3.76e+01 1z6gA 218 3.77e+01 1pbjA 125 3.78e+01 d.37.1.1,d.37.1.1 94414,94415 1ma3A 253 3.81e+01 c.31.1.5 78883 1hdoA 206 3.85e+01 1he2A c.2.1.2 60965 1b5tA 275 3.87e+01 1b5tA c.1.23.1 29676 1vr4A 103 3.88e+01 1xttA 216 3.89e+01 1h7zA 194 3.90e+01 1qhvA b.21.1.1 60733 1toaA 313 3.93e+01 1toaA c.92.2.2 35598 1r6jA 82 3.98e+01 b.36.1.1 97151 1tiqA 180 4.00e+01 d.108.1.1 107010 2aioA 269 4.04e+01 1r5jA 337 4.05e+01 c.77.1.5 97097 1vbvA 105 4.15e+01 1ny4A 82 4.16e+01 b.40.4.5 92316 1qx4A 274 4.18e+01 b.43.4.2,c.25.1.1 104624,104625 1nteA 82 4.19e+01 b.36.1.1 86163 1wluA 136 4.20e+01 1ri5A 298 4.28e+01 c.66.1.34 97502 1o0yA 260 4.31e+01 c.1.10.1 80756 1ve6A 582 4.34e+01 1wlyA 333 4.37e+01 1fzqA 181 4.38e+01 1hurA c.37.1.8 32060 1duvG 333 4.47e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1kjwA 295 4.48e+01 b.34.2.1,c.37.1.1 68643,68644 1xel 338 4.56e+01 1xel c.2.1.2 29786 1udc 338 4.61e+01 1xel c.2.1.2 29785 2b4rO 345 4.65e+01 2gw6A 123 4.69e+01 1o58A 303 4.72e+01 c.79.1.1 92491 1sn4A 64 4.74e+01 1aho g.3.7.1 44136 2hvm 273 4.76e+01 1cnv c.1.8.5 28985 2bo4A 397 4.80e+01 1i8fA 81 4.83e+01 1i8fA b.38.1.1 61959 1exg 110 4.84e+01 1exg b.2.2.1 22387 1wu3I 161 4.89e+01 1ml8A 134 4.90e+01 d.227.1.2 85013 1f2tB 148 4.95e+01 1f2tB 1j1yA 136 4.95e+01 d.38.1.5 90776 1jy1A 464 4.98e+01 d.136.1.3,d.136.1.3 67438,67439 1ri6A 343 4.99e+01 b.69.11.1 97503 1dkuA 317 5.02e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1wyxA 69 5.05e+01 1s0pA 176 5.17e+01 a.192.1.1 98300 1hm9A 468 5.20e+01 b.81.1.4,c.68.1.5 65866,65867 1qg8A 255 5.25e+01 1qg8A c.68.1.1 34505 1z52A 470 5.29e+01 1icxA 155 5.35e+01 d.129.3.1 71191 1pyfA 312 5.37e+01 c.1.7.1 95334 1vi1A 345 5.39e+01 c.77.1.4 100724 1t0hA 132 5.40e+01 b.34.2.1 106207 1wkqA 164 5.42e+01 c.97.1.2 109393 8rucI 123 5.46e+01 1rboC d.73.1.1 39629 1ydmA 187 5.47e+01 1w9zA 283 5.51e+01 1ydyA 356 5.52e+01 1s50A 259 5.54e+01 1ej6D 418 5.58e+01 i.7.1.1 45970 1eq6A 189 5.69e+01 1eq6A d.107.1.1 40796 1larA 575 5.69e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1ip9A 85 5.70e+01 1ip9A d.15.2.2 62638 1e0tA 470 5.74e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1es6A 296 5.74e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1xcbA 211 5.78e+01 a.4.5.38,c.2.1.12 109552,109553 1t8qA 336 5.88e+01 c.1.18.3 106669 1f9vA 347 5.93e+01 1bg2 c.37.1.9 59745 1ur1A 378 5.96e+01 c.1.8.3 99804 1vqoI 162 5.99e+01 1fjgB 256 6.04e+01 1fjfB c.23.15.1 31400 1uwzA 136 6.07e+01 c.97.1.1 108081 1zc1A 208 6.09e+01 1bg6 359 6.12e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1ylqA 96 6.14e+01 1jtkA 136 6.15e+01 c.97.1.1 71862 1b33N 67 6.15e+01 1b33N d.30.1.1 38459 1u46A 291 6.23e+01 d.144.1.7 107656 1k0fA 277 6.24e+01 c.92.2.2 71974 1ll2A 333 6.31e+01 c.68.1.14 74005 1uurA 473 6.34e+01 a.47.1.1,b.2.5.5,d.93.1.1 100016,100017,100018 1ltlA 279 6.36e+01 b.40.4.11 84701 1xvqA 175 6.38e+01 2amyA 246 6.42e+01 1g291 372 6.58e+01 1g291 1vhxA 150 6.59e+01 c.55.3.8 100712 2fh7A 595 6.61e+01 1vphA 149 6.64e+01 1g97A 459 6.72e+01 1fwyA b.81.1.4,c.68.1.5 60394,60395 1zpvA 91 6.88e+01 1xdpA 687 6.89e+01 1z4rA 168 6.92e+01 1kqzA 273 6.99e+01 c.1.8.5 68844 3seb 238 7.03e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2akoA 251 7.19e+01 1vfsA 386 7.22e+01 b.49.2.2,c.1.6.1 108584,108585 1omzA 293 7.24e+01 c.68.1.15 87093 1ej0A 180 7.24e+01 1ej0A c.66.1.2 34179 1cfr 285 7.26e+01 1cfr c.52.1.7 33312 1o98A 511 7.35e+01 c.105.1.1,c.76.1.3 86684,86685 1qysA 106 7.36e+01 k.41.1.1 96603 1p42A 270 7.39e+01 d.14.1.7,d.14.1.7 87754,87755 1zp4A 304 7.41e+01 1zpsA 138 7.46e+01 1mk0A 97 7.47e+01 d.226.1.1 79216 2frnA 278 7.53e+01 1yg6A 193 7.53e+01 1gyxA 76 7.63e+01 d.80.1.1 76387 1bn8A 420 7.69e+01 1pcl b.80.1.1 28022 1azo 232 7.76e+01 1azo c.52.1.14 33329 2ab5A 269 7.86e+01 1x23A 155 7.88e+01 1yy7A 213 7.91e+01 1s72N 187 7.95e+01 c.55.4.1 105333 1vhh 162 7.95e+01 1vhh d.65.1.2 39550 2dddA 225 7.96e+01 1yr2A 741 7.96e+01 1i7pA 274 7.96e+01 b.43.4.2,c.25.1.1 66048,66049 1ta3B 303 7.96e+01 c.1.8.3 106732 1xkrA 206 8.03e+01 1xhfA 123 8.12e+01 2cygA 312 8.13e+01 1vqoN 187 8.15e+01 1pvtA 238 8.16e+01 c.74.1.1 95189 1xubA 298 8.16e+01 4pfk 319 8.18e+01 3pfk c.89.1.1 35582 1shsA 147 8.21e+01 1shsA b.15.1.1 23675 1uc7A 125 8.22e+01 c.47.1.1 99163 2d1pA 140 8.24e+01 1d4tA 104 8.26e+01 1d4tA d.93.1.1 40537 1bueA 265 8.27e+01 1btl e.3.1.1 42727 2bpa1 426 8.40e+01 2bpa1 1gadO 330 8.40e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 2f5gA 133 8.41e+01 1u9cA 224 8.44e+01 1kwiA 101 8.50e+01 d.17.1.3 77564 1kshA 186 8.50e+01 c.37.1.8 72914 1wojA 214 8.59e+01 1i6lA 328 8.59e+01 c.26.1.1 66041 1ztxL 212 8.63e+01 1gewA 356 8.67e+01 1gewA c.67.1.1 60470 1ede 310 8.71e+01 1b6g c.69.1.8 34662 1sek 378 8.73e+01 1sek e.1.1.1 42675 1pfkA 320 8.75e+01 3pfk c.89.1.1 35575 1a53 247 8.80e+01 1a53 c.1.2.4 28564 1igs 248 8.81e+01 1a53 c.1.2.4 28565 1n8jA 186 8.88e+01 c.47.1.10 85401 1tw0A 157 8.91e+01 2bbkL 125 8.93e+01 2bbkL g.21.1.1 44882 1fg7A 356 8.93e+01 1gewA c.67.1.1 59819 1aq0A 306 8.94e+01 1aq0A c.1.8.3 28842