# 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 1hyuA 521 1.42e-01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1ockA 412 1.56e-01 c.117.1.1 86802 1zynA 202 1.87e-01 1dyqA 234 2.68e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2aioA 269 2.93e-01 1smlA 269 4.04e-01 1smlA d.157.1.1 42053 1souA 194 6.39e-01 c.124.1.6 105858 1m93A 55 8.05e-01 e.1.1.1 91235 2bg5A 324 9.64e-01 1a53 247 1.26e+00 1a53 c.1.2.4 28564 1igs 248 1.27e+00 1a53 c.1.2.4 28565 2c3zA 222 1.47e+00 1yiyA 429 1.82e+00 1iz5A 249 1.91e+00 d.131.1.2,d.131.1.2 83834,83835 2myr 501 2.06e+00 2d1uA 104 2.17e+00 1fl2A 310 2.72e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 2fvtA 135 2.89e+00 1sqsA 242 2.90e+00 c.23.5.5 98968 1vfsA 386 2.99e+00 b.49.2.2,c.1.6.1 108584,108585 1qi9A 556 3.06e+00 1qhbA a.111.1.2 19053 1repC 251 3.66e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1qhlA 227 4.20e+00 1qhlA c.37.1.12 32382 1sr4B 261 4.63e+00 d.151.1.1 105949 1eceA 358 4.77e+00 1eceA c.1.8.3 28813 1e4mM 501 5.14e+00 1e70M c.1.8.4 59226 1tzaA 134 5.29e+00 b.1.23.1 107468 2a2pA 129 5.45e+00 2aefA 234 5.49e+00 2fclA 169 5.67e+00 2ewrA 170 5.67e+00 1fhgA 154 6.19e+00 1tlk b.1.1.4 21706 2rslA 140 6.41e+00 2rslA c.53.1.1 33345 1xn5A 146 6.58e+00 1v0lA 313 7.04e+00 c.1.8.3 108207 1rwiA 270 7.09e+00 b.68.9.1 97987 1q59A 172 7.27e+00 f.1.4.1 95881 1e0wA 313 7.39e+00 1taxA c.1.8.3 59150 1od8A 313 7.57e+00 c.1.8.3 86838 2g9iA 249 7.73e+00 1g8lA 411 7.82e+00 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1a0rP 245 8.02e+00 1b9yC c.47.1.6 33054 1of8A 370 8.05e+00 c.1.10.4 92819 1jhfA 202 8.17e+00 a.4.5.2,b.87.1.1 63057,63058 1ma3A 253 8.22e+00 c.31.1.5 78883 1hqz1 141 8.22e+00 1y96B 85 8.47e+00 1pnsC 206 8.66e+00 i.1.1.1 88170 1k38A 254 8.67e+00 e.3.1.1 84303 1j5vA 351 8.72e+00 c.72.1.1 71585 1tlk 154 8.77e+00 1tlk b.1.1.4 21707 1h72C 296 8.80e+00 d.14.1.5,d.58.26.1 60712,60713 1t9bA 677 8.98e+00 1xfcA 384 9.06e+00 1hdoA 206 9.28e+00 1he2A c.2.1.2 60965 1xewY 172 9.34e+00 1wmhA 89 9.81e+00 1cc1S 283 1.02e+01 2frvA e.19.1.1 43313 1my6A 199 1.03e+01 a.2.11.1,d.44.1.1 85232,85233 2dfkA 402 1.03e+01 1c7qA 445 1.09e+01 2pgi c.80.1.2 35307 1vr0A 247 1.10e+01 1fwkA 296 1.11e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1pbgA 468 1.11e+01 1e70M c.1.8.4 28946 1lwjA 441 1.12e+01 b.71.1.1,c.1.8.1 74303,74304 1wouA 123 1.19e+01 c.47.1.16 109471 1nxiA 132 1.24e+01 d.58.47.1 86381 1ej0A 180 1.25e+01 1ej0A c.66.1.2 34179 2d1pA 140 1.27e+01 1es6A 296 1.27e+01 1es6A b.31.1.1,b.31.1.1 83048,83049 1o0pA 104 1.30e+01 d.58.7.1 86535 1o58A 303 1.32e+01 c.79.1.1 92491 1ycyA 71 1.37e+01 1o1zA 234 1.37e+01 c.1.18.3 86555 1bia 321 1.40e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2fgtA 417 1.41e+01 1vc4A 254 1.42e+01 c.1.2.4 100557 2a15A 139 1.43e+01 2amhA 207 1.43e+01 1e9rA 437 1.45e+01 c.37.1.11 64827 2culA 232 1.45e+01 1fw9A 164 1.47e+01 1fw9A d.190.1.1 60059 1tt8A 164 1.47e+01 1woqA 267 1.48e+01 c.55.1.10,c.55.1.10 109462,109463 2f4mA 295 1.50e+01 1nijA 318 1.51e+01 c.37.1.10,d.237.1.1 85741,85742 1ft5A 211 1.51e+01 1bvb a.138.1.3 19681 1wcdJ 441 1.56e+01 2pil 159 1.57e+01 2pil d.24.1.1 38376 1ur1A 378 1.63e+01 c.1.8.3 99804 1xkrA 206 1.67e+01 1plq 258 1.71e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1yizA 429 1.76e+01 2cygA 312 1.79e+01 1pyfA 312 1.83e+01 c.1.7.1 95334 1d2oA 187 1.84e+01 1d2oA b.3.5.1,b.3.5.1 22625,22626 1mkaA 171 1.84e+01 1mkaA d.38.1.2 38543 1c52 131 1.85e+01 1c52 a.3.1.1 15810 1wrjA 156 1.85e+01 1lqtA 456 1.90e+01 c.3.1.1,c.4.1.1 74198,74199 1xcbA 211 1.98e+01 a.4.5.38,c.2.1.12 109552,109553 2bbkL 125 2.00e+01 2bbkL g.21.1.1 44882 1toaA 313 2.04e+01 1toaA c.92.2.2 35598 1wmhB 86 2.08e+01 1regX 122 2.15e+01 1regX d.58.27.1 39406 1n8kA 374 2.18e+01 b.35.1.2,c.2.1.1 80298,80299 1hetA 374 2.18e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 2b7eA 59 2.19e+01 1u9cA 224 2.22e+01 1bdfA 235 2.23e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2ohxA 374 2.23e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1vr7A 142 2.24e+01 2awpA 198 2.27e+01 1sek 378 2.28e+01 1sek e.1.1.1 42675 2afbA 351 2.29e+01 1fjgC 239 2.31e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1tluA 130 2.32e+01 d.156.1.2 107139 2bo4A 397 2.33e+01 1db3A 372 2.34e+01 1db3A c.2.1.2 29813 1gwmA 153 2.35e+01 b.18.1.19 83348 1nf3C 128 2.37e+01 b.36.1.1 85596 1wlyA 333 2.45e+01 2gmqA 118 2.46e+01 2cxcA 144 2.49e+01 1r5jA 337 2.50e+01 c.77.1.5 97097 1quqB 121 2.53e+01 1quqB b.40.4.3 25305 1v30A 124 2.57e+01 1iqaA 160 2.60e+01 b.22.1.1 71274 2polA 366 2.66e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1s55A 156 2.67e+01 1fzyA 149 2.68e+01 d.20.1.1 65072 1tr9A 341 2.71e+01 1vicA 262 2.78e+01 c.68.1.13 100756 1gewA 356 2.82e+01 1gewA c.67.1.1 60470 1u1wA 298 2.82e+01 1fg7A 356 2.83e+01 1gewA c.67.1.1 59819 1bby 69 2.87e+01 2bby a.4.5.15 16149 1zthA 258 2.91e+01 1vjpA 394 2.94e+01 c.2.1.3,d.81.1.3 100828,100829 1id0A 152 2.95e+01 d.122.1.3 66111 1rh9A 373 3.00e+01 1pbjA 125 3.00e+01 d.37.1.1,d.37.1.1 94414,94415 2axpA 173 3.01e+01 1xubA 298 3.01e+01 1b25A 619 3.05e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1ddf 127 3.06e+01 1ddf a.77.1.2 18423 1m4jA 142 3.06e+01 d.109.1.2 78602 1vddA 228 3.11e+01 e.49.1.1 108519 2axwA 134 3.12e+01 1wb4A 297 3.12e+01 1ri5A 298 3.14e+01 c.66.1.34 97502 1gklA 297 3.18e+01 c.69.1.2 65250 1dljA 402 3.22e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 1u2xA 474 3.24e+01 c.72.1.3 107622 1uekA 275 3.28e+01 d.14.1.5,d.58.26.5 88483,88484 1r6jA 82 3.32e+01 b.36.1.1 97151 1e0tA 470 3.34e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1kwiA 101 3.35e+01 d.17.1.3 77564 1uc7A 125 3.47e+01 c.47.1.1 99163 1o98A 511 3.51e+01 c.105.1.1,c.76.1.3 86684,86685 1azo 232 3.55e+01 1azo c.52.1.14 33329 1oiaA 95 3.62e+01 d.58.7.1 87051 1flcA 432 3.63e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1ve6A 582 3.66e+01 1urnA 97 3.69e+01 1urnA d.58.7.1 39153 1nteA 82 3.71e+01 b.36.1.1 86163 1fzqA 181 3.73e+01 1hurA c.37.1.8 32060 1eqjA 511 3.76e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1h7zA 194 3.76e+01 1qhvA b.21.1.1 60733 1vcvA 226 3.80e+01 1f0cA 305 3.82e+01 1c8oA e.1.1.1 42676 1o9gA 250 3.87e+01 c.66.1.29 86692 1vhxA 150 3.91e+01 c.55.3.8 100712 1b5tA 275 3.92e+01 1b5tA c.1.23.1 29676 1f9vA 347 3.97e+01 1bg2 c.37.1.9 59745 1zhrA 238 4.02e+01 2g0uA 92 4.07e+01 1juvA 193 4.13e+01 c.71.1.1 90912 1zhmA 238 4.15e+01 1o0yA 260 4.17e+01 c.1.10.1 80756 1jx7A 117 4.19e+01 c.114.1.1 77195 1omzA 293 4.20e+01 c.68.1.15 87093 1nwwA 149 4.22e+01 d.17.4.8 86306 1kqpA 271 4.25e+01 c.26.2.1 72883 2gh1A 301 4.27e+01 1vi1A 345 4.29e+01 c.77.1.4 100724 2fj6A 82 4.31e+01 1xedA 117 4.31e+01 1d1gA 168 4.32e+01 1d1gA c.71.1.1 34889 1t64A 377 4.34e+01 c.42.1.2 106543 1h2cA 140 4.34e+01 b.31.1.1 83462 2g5dA 422 4.35e+01 1aq0A 306 4.39e+01 1aq0A c.1.8.3 28842 1jtkA 136 4.42e+01 c.97.1.1 71862 1rwzA 245 4.44e+01 d.131.1.2,d.131.1.2 98005,98006 1uwzA 136 4.46e+01 c.97.1.1 108081 1fr3A 67 4.48e+01 1fr3A b.40.6.1 25436 1luzA 88 4.54e+01 b.40.4.5 74271 1mo9A 523 4.54e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1c7nA 399 4.55e+01 1d2fA c.67.1.3 34413 1ob8A 135 4.57e+01 1fsz 372 4.57e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1qo2A 241 4.57e+01 1qo2A c.1.2.1 28533 1xx9A 238 4.58e+01 1zhpA 238 4.66e+01 1jlyA 304 4.66e+01 1jlyA b.42.3.1,b.42.3.1 25587,25588 2fh7A 595 4.68e+01 1d0vA 356 4.75e+01 1d0vA c.39.1.1 32476 4pfk 319 4.77e+01 3pfk c.89.1.1 35582 1s50A 259 4.78e+01 1ny4A 82 4.80e+01 b.40.4.5 92316 1udc 338 4.81e+01 1xel c.2.1.2 29785 1cq3A 233 4.83e+01 1cq3A b.27.1.1 23923 1ri6A 343 4.83e+01 b.69.11.1 97503 1xvqA 175 4.89e+01 1ecpA 238 4.91e+01 1ecpA c.56.2.1 33775 1un7A 400 4.92e+01 b.92.1.5,c.1.9.10 99657,99658 1duvG 333 4.92e+01 1othA c.78.1.1,c.78.1.1 35228,35229 2d9rA 104 4.93e+01 1uheA 97 4.93e+01 1xel 338 4.97e+01 1xel c.2.1.2 29786 1mixA 206 4.99e+01 a.11.2.1,b.55.1.5 79166,79167 1nq6A 302 5.00e+01 c.1.8.3 92046 1i8fA 81 5.05e+01 1i8fA b.38.1.1 61959 1l5oA 356 5.09e+01 c.39.1.1 77711 1ih8A 271 5.14e+01 2nsyA c.26.2.1 62377 1p5vA 235 5.16e+01 b.1.11.1,b.7.2.1 87812,87813 1wyxA 69 5.17e+01 1vd2A 89 5.21e+01 d.15.2.2 108517 1cjbA 231 5.24e+01 1qk3A c.61.1.1 34079 1wluA 136 5.27e+01 1larA 575 5.35e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1qwnA 1045 5.37e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1m7vA 363 5.41e+01 d.174.1.1 78748 1mmiA 366 5.42e+01 d.131.1.1,d.131.1.1,d.131.1.1 91309,91310,91311 1xttA 216 5.44e+01 1bn8A 420 5.44e+01 1pcl b.80.1.1 28022 1z52A 470 5.52e+01 2hvm 273 5.53e+01 1cnv c.1.8.5 28985 1x6mA 196 5.55e+01 1y9aA 360 5.56e+01 1k9sA 237 5.60e+01 c.56.2.1 68359 1ll2A 333 5.62e+01 c.68.1.14 74005 1xseA 295 5.66e+01 2aq4A 434 5.73e+01 1h6zA 913 5.79e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1ta3B 303 5.80e+01 c.1.8.3 106732 1w7lA 422 5.82e+01 c.67.1.1 109226 1no5A 114 5.84e+01 d.218.1.5 92014 1rf6A 427 5.86e+01 d.68.2.2 97366 1thg 544 5.90e+01 1thg c.69.1.17 34763 1k77A 260 5.91e+01 c.1.15.5 72096 2a9dA 372 5.92e+01 1bg6 359 5.98e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 2ewcA 126 5.98e+01 1v5tA 90 6.03e+01 d.15.1.1 108385 1htyA 1015 6.04e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1y1oA 203 6.06e+01 1oa2A 218 6.11e+01 b.29.1.11 86721 1tiqA 180 6.11e+01 d.108.1.1 107010 1u46A 291 6.11e+01 d.144.1.7 107656 1s6lA 212 6.11e+01 2gfgA 193 6.12e+01 1wu3I 161 6.15e+01 1t6kA 278 6.18e+01 1qlmA 316 6.18e+01 1qlmA d.147.1.1 41765 1j1yA 136 6.19e+01 d.38.1.5 90776 1pqxA 91 6.21e+01 d.267.1.1 104296 1vr4A 103 6.26e+01 1jy1A 464 6.26e+01 d.136.1.3,d.136.1.3 67438,67439 1h8vA 218 6.30e+01 2nlrA b.29.1.11 60795 1z6gA 218 6.30e+01 1gd1O 334 6.32e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1pxeA 63 6.44e+01 g.73.1.1 95286 2c7hA 86 6.49e+01 1ri7A 171 6.51e+01 a.4.5.32,d.58.4.2 97504,97505 1ysjA 404 6.52e+01 1yzxA 226 6.58e+01 1sn4A 64 6.66e+01 1aho g.3.7.1 44136 1p42A 270 6.66e+01 d.14.1.7,d.14.1.7 87754,87755 1g60A 260 6.76e+01 c.66.1.11 70151 1k0fA 277 6.79e+01 c.92.2.2 71974 1ede 310 6.80e+01 1b6g c.69.1.8 34662 1wspA 84 6.82e+01 1exg 110 6.84e+01 1exg b.2.2.1 22387 1rsy 152 6.86e+01 1rsy b.7.1.2 23192 1qlwA 328 6.93e+01 1qlwA c.69.1.15 34722 1rfeA 162 7.01e+01 1jjzA 29 7.01e+01 g.3.3.1 71699 1qhvA 195 7.04e+01 1qhvA b.21.1.1 23842 1u3wA 374 7.04e+01 1zp4A 304 7.07e+01 1x74A 360 7.14e+01 2ptd 298 7.23e+01 2plc c.1.18.2 29605 1q48A 134 7.28e+01 d.224.1.2 95783 2bl9A 238 7.28e+01 1w9zA 283 7.29e+01 1k7hA 476 7.32e+01 c.76.1.1 72101 1cby 259 7.34e+01 1cby d.103.1.1 40705 1evuA 731 7.34e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1kqzA 273 7.34e+01 c.1.8.5 68844 1g6gA 127 7.37e+01 1g6gA b.26.1.2 23916 1yqcA 170 7.38e+01 2czrA 226 7.42e+01 1gqzA 274 7.42e+01 d.21.1.1,d.21.1.1 83311,83312 1vkuA 100 7.45e+01 a.28.1.1 108690 1xkqA 280 7.46e+01 1r7aA 504 7.48e+01 b.71.1.1,c.1.8.1 97192,97193 1a8q 274 7.56e+01 1brt c.69.1.12 34702 1ylqA 96 7.59e+01 1ggzA 148 7.66e+01 a.39.1.5 70176 2aqjA 538 7.76e+01 1preA 470 7.84e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1ns5A 155 7.92e+01 c.116.1.3 80705 1ok7A 366 7.93e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1yc5A 246 7.96e+01 1wqaA 455 7.96e+01 1xyiA 66 8.00e+01 2g50A 530 8.02e+01 1hm9A 468 8.05e+01 b.81.1.4,c.68.1.5 65866,65867 1yg6A 193 8.11e+01 1acx 108 8.11e+01 2mcm b.1.7.1 22211 1yy7A 213 8.11e+01 1ydmA 187 8.12e+01 1o57A 291 8.17e+01 a.4.5.40,c.61.1.1 92483,92484 1soxA 466 8.20e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1kz7A 353 8.20e+01 a.87.1.1,b.55.1.1 73333,73334 2akoA 251 8.22e+01 1vqoI 162 8.29e+01 1ep3B 262 8.33e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 2c1gA 431 8.34e+01 1g66A 207 8.37e+01 1bs9 c.69.1.30 31329 1ecfA 504 8.38e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1vetA 124 8.42e+01 d.110.7.1 108553 1ex0A 731 8.42e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1m4zA 238 8.44e+01 b.34.12.1 78630 1t8qA 336 8.46e+01 c.1.18.3 106669 1zc1A 208 8.49e+01 2bypA 214 8.49e+01 1k0rA 366 8.56e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1kblA 873 8.69e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ps9A 671 8.77e+01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1tuoA 464 8.78e+01 2gzqA 200 8.83e+01 2asbA 251 8.90e+01 2b3wA 168 8.98e+01 1u6tA 121 8.98e+01 1vbuA 328 9.00e+01