# List of top-scoring protein chains for t04-100-30-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 1dyqA 234 2.90e-01 3seb b.40.2.2,d.15.6.1 59140,59141 2ewrA 170 6.79e-01 2fclA 169 7.31e-01 2rslA 140 7.98e-01 2rslA c.53.1.1 33345 1zynA 202 8.09e-01 1pnsC 206 1.01e+00 i.1.1.1 88170 1fjgC 239 1.31e+00 1fjfC d.52.3.1,d.53.1.1 38831,38839 1sqsA 242 1.67e+00 c.23.5.5 98968 1repC 251 1.78e+00 1repC a.4.5.10,a.4.5.10 16125,16126 1hyuA 521 2.02e+00 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1m93A 55 2.14e+00 e.1.1.1 91235 1evuA 731 3.08e+00 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1qhlA 227 3.21e+00 1qhlA c.37.1.12 32382 1ex0A 731 3.30e+00 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 90465,90466,90467,90468 1ycyA 71 4.02e+00 2bg5A 324 4.11e+00 1exg 110 4.37e+00 1exg b.2.2.1 22387 1a0rP 245 4.37e+00 1b9yC c.47.1.6 33054 1hdoA 206 4.79e+00 1he2A c.2.1.2 60965 1y96B 85 5.10e+00 2flsA 132 5.31e+00 2g9iA 249 5.45e+00 1ydmA 187 5.70e+00 1regX 122 5.88e+00 1regX d.58.27.1 39406 1od8A 313 5.93e+00 c.1.8.3 86838 1v0lA 313 5.95e+00 c.1.8.3 108207 2pil 159 6.30e+00 2pil d.24.1.1 38376 1e0wA 313 6.32e+00 1taxA c.1.8.3 59150 1d2oA 187 6.36e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1zpvA 91 6.74e+00 1iz5A 249 6.84e+00 d.131.1.2,d.131.1.2 83834,83835 2cxcA 144 6.85e+00 1c7qA 445 7.16e+00 2pgi c.80.1.2 35307 2afbA 351 7.47e+00 1igs 248 7.58e+00 1a53 c.1.2.4 28565 1d2rA 326 7.79e+00 1d2rB c.26.1.1 31572 1kqpA 271 8.40e+00 c.26.2.1 72883 1a53 247 8.40e+00 1a53 c.1.2.4 28564 2b7eA 59 8.44e+00 1c52 131 8.65e+00 1c52 a.3.1.1 15810 1g7nA 131 8.77e+00 b.60.1.2 83274 1ih8A 271 8.88e+00 2nsyA c.26.2.1 62377 1lwjA 441 9.65e+00 b.71.1.1,c.1.8.1 74303,74304 1ej0A 180 9.79e+00 1ej0A c.66.1.2 34179 1m07A 111 1.02e+01 d.5.1.1 78328 1s55A 156 1.05e+01 1iqaA 160 1.07e+01 b.22.1.1 71274 1zruA 264 1.08e+01 1e0tA 470 1.09e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1lid 131 1.09e+01 1hmt b.60.1.2 27184 1b25A 619 1.11e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 1xwvA 129 1.13e+01 2b33A 140 1.13e+01 2bsdA 264 1.15e+01 1b56 135 1.18e+01 1hmt b.60.1.2 27183 1t8qA 336 1.19e+01 c.1.18.3 106669 2gmqA 118 1.19e+01 1i6lA 328 1.30e+01 c.26.1.1 66041 1o1zA 234 1.31e+01 c.1.18.3 86555 1sek 378 1.33e+01 1sek e.1.1.1 42675 1vkuA 100 1.38e+01 a.28.1.1 108690 1nijA 318 1.40e+01 c.37.1.10,d.237.1.1 85741,85742 1pbgA 468 1.48e+01 1e70M c.1.8.4 28946 1o6dA 163 1.51e+01 c.116.1.3 92567 2fgtA 417 1.53e+01 1o0pA 104 1.58e+01 d.58.7.1 86535 1a99A 344 1.59e+01 1pot c.94.1.1 35812 1j5vA 351 1.60e+01 c.72.1.1 71585 1tf1A 198 1.61e+01 d.110.2.2 106826 1hetA 374 1.66e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1n8kA 374 1.66e+01 b.35.1.2,c.2.1.1 80298,80299 1bn8A 420 1.69e+01 1pcl b.80.1.1 28022 1r5jA 337 1.70e+01 c.77.1.5 97097 1qavA 90 1.72e+01 1qauA b.36.1.1 24777 1bia 321 1.75e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1o0yA 260 1.87e+01 c.1.10.1 80756 1t0hA 132 1.93e+01 b.34.2.1 106207 1kshA 186 2.01e+01 c.37.1.8 72914 1x8dA 104 2.02e+01 2ohxA 374 2.11e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 1fl2A 310 2.13e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1s0pA 176 2.13e+01 a.192.1.1 98300 1h72C 296 2.20e+01 d.14.1.5,d.58.26.1 60712,60713 1u3wA 374 2.25e+01 1v04A 355 2.35e+01 b.68.6.2 100240 2aefA 234 2.40e+01 1qzgA 187 2.44e+01 b.40.4.3 96643 1zthA 258 2.44e+01 2cygA 312 2.45e+01 1ma3A 253 2.45e+01 c.31.1.5 78883 1xhfA 123 2.53e+01 1vqoL 165 2.54e+01 1qlmA 316 2.58e+01 1qlmA d.147.1.1 41765 1s9rA 410 2.60e+01 d.126.1.4 98758 2etxA 209 2.61e+01 1ois 223 2.61e+01 1a36A e.15.1.1 43267 1t0aA 159 2.61e+01 1xttA 216 2.63e+01 1i8fA 81 2.66e+01 1i8fA b.38.1.1 61959 1vcvA 226 2.66e+01 1s50A 259 2.67e+01 1fh9A 312 2.67e+01 1taxA c.1.8.3 28913 1idk 359 2.73e+01 1qcxA b.80.1.2 28025 1wwhA 119 2.73e+01 1vjpA 394 2.75e+01 c.2.1.3,d.81.1.3 100828,100829 1fhdA 312 2.75e+01 1taxA c.1.8.3 28915 1gyxA 76 2.75e+01 d.80.1.1 76387 1xcbA 211 2.77e+01 a.4.5.38,c.2.1.12 109552,109553 2fbyA 205 2.80e+01 2his 312 2.82e+01 1taxA c.1.8.3 28918 1dkuA 317 2.83e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1wu3I 161 2.84e+01 2gfgA 193 2.85e+01 1qy1A 174 2.88e+01 b.60.1.1 96568 2bwfA 77 2.89e+01 1vjjA 692 2.94e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1wrjA 156 2.94e+01 1ydyA 356 2.95e+01 1ml9A 302 3.01e+01 b.85.7.1 79282 1quqB 121 3.01e+01 1quqB b.40.4.3 25305 2aioA 269 3.06e+01 5nul 138 3.15e+01 5nul c.23.5.1 31191 1plq 258 3.18e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1smlA 269 3.20e+01 1smlA d.157.1.1 42053 2amhA 207 3.26e+01 1xn5A 146 3.32e+01 1w9zA 283 3.37e+01 1xkiA 162 3.38e+01 1o58A 303 3.39e+01 c.79.1.1 92491 1juvA 193 3.40e+01 c.71.1.1 90912 2adoA 196 3.41e+01 1h8vA 218 3.44e+01 2nlrA b.29.1.11 60795 4uagA 437 3.45e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1rwzA 245 3.50e+01 d.131.1.2,d.131.1.2 98005,98006 1oa2A 218 3.50e+01 b.29.1.11 86721 1u2xA 474 3.58e+01 c.72.1.3 107622 1f0cA 305 3.62e+01 1c8oA e.1.1.1 42676 2bo4A 397 3.63e+01 1vr7A 142 3.63e+01 2asbA 251 3.66e+01 1vddA 228 3.67e+01 e.49.1.1 108519 1umuA 116 3.68e+01 1umuA b.87.1.1 28382 1nf3C 128 3.73e+01 b.36.1.1 85596 1tt8A 164 3.76e+01 1fw9A 164 3.77e+01 1fw9A d.190.1.1 60059 1vm6A 228 3.79e+01 c.2.1.3,d.81.1.3 108876,108877 1jj2K 164 3.83e+01 1ffkJ c.12.1.1 63096 1m4jA 142 3.83e+01 d.109.1.2 78602 1q8hA 49 3.84e+01 g.32.1.1 96207 1epwA 1290 3.87e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2gw6A 123 3.88e+01 1nu4A 97 3.89e+01 d.58.7.1 80731 1qi9A 556 3.89e+01 1qhbA a.111.1.2 19053 1cfr 285 3.93e+01 1cfr c.52.1.7 33312 1tlk 154 3.95e+01 1tlk b.1.1.4 21707 1zp4A 304 3.96e+01 1rwrA 301 3.97e+01 b.80.1.11 97990 1hqz1 141 4.00e+01 1i06A 180 4.01e+01 1mup b.60.1.1 27131 1sfnA 246 4.01e+01 b.82.1.11 105496 1ztxL 212 4.06e+01 1xkrA 206 4.07e+01 1zndA 174 4.09e+01 1gewA 356 4.15e+01 1gewA c.67.1.1 60470 1urnA 97 4.17e+01 1urnA d.58.7.1 39153 1z5sD 83 4.23e+01 1fwkA 296 4.23e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 1aq0A 306 4.26e+01 1aq0A c.1.8.3 28842 2b2aA 199 4.26e+01 1svpA 161 4.34e+01 1svpA b.47.1.3 26384 1jv4A 162 4.35e+01 b.60.1.1 67343 1u1hA 765 4.40e+01 c.1.22.2,c.1.22.2 107580,107581 1ygs 234 4.43e+01 1ygs b.26.1.1 23907 1nq6A 302 4.44e+01 c.1.8.3 92046 1qopB 396 4.45e+01 2tysB c.79.1.1 35270 1ukuA 102 4.47e+01 d.58.5.2 99533 2fh7A 595 4.52e+01 1u1jA 765 4.53e+01 c.1.22.2,c.1.22.2 107590,107591 1mup 166 4.55e+01 1mup b.60.1.1 27133 1s72L 165 4.57e+01 c.12.1.1 105331 1nf2A 268 4.58e+01 c.108.1.10 91849 1r9gA 216 4.58e+01 c.23.16.1 97258 1bdfA 235 4.61e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1ta8A 332 4.61e+01 1oj4A 283 4.61e+01 d.14.1.5,d.58.26.5 93083,93084 1ktjA 129 4.63e+01 b.1.18.7 72974 1h6lA 353 4.65e+01 b.68.3.1 60687 2c3zA 222 4.76e+01 2aq4A 434 4.82e+01 1sr4B 261 4.87e+01 d.151.1.1 105949 1cf7B 95 4.88e+01 1cf7B a.4.5.17 16152 1larA 575 4.88e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1qhtA 775 4.89e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1jy5A 212 4.89e+01 d.124.1.1 71940 1fg7A 356 4.91e+01 1gewA c.67.1.1 59819 1kq1A 77 4.96e+01 b.38.1.2 72848 1cojA 212 4.96e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1xx4A 261 4.98e+01 1yiyA 429 5.00e+01 1r6xA 395 5.03e+01 b.122.1.3,c.26.1.5 97167,97168 1udc 338 5.03e+01 1xel c.2.1.2 29785 1shsA 147 5.09e+01 1shsA b.15.1.1 23675 2cq2A 114 5.11e+01 1gxqA 106 5.16e+01 a.4.6.1 70721 1htjF 210 5.20e+01 1htjF a.91.1.1 61254 1xdpA 687 5.25e+01 1xel 338 5.34e+01 1xel c.2.1.2 29786 1vi7A 217 5.35e+01 d.14.1.11,d.58.11.2 100740,100741 1u6bA 98 5.35e+01 d.58.7.1 107703 1id0A 152 5.35e+01 d.122.1.3 66111 2fcjA 119 5.37e+01 1mkp 144 5.48e+01 1vhrA c.45.1.1 32654 1yoaA 159 5.50e+01 1njhA 119 5.52e+01 b.128.1.1 85787 1ri7A 171 5.55e+01 a.4.5.32,d.58.4.2 97504,97505 1i05A 180 5.56e+01 1mup b.60.1.1 27130 2amyA 246 5.56e+01 1wlyA 333 5.69e+01 1f0lA 535 5.70e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1u55A 188 5.70e+01 d.278.1.1 107677 1hm9A 468 5.79e+01 b.81.1.4,c.68.1.5 65866,65867 1fzqA 181 5.83e+01 1hurA c.37.1.8 32060 2ffeA 311 5.84e+01 1ur1A 378 5.91e+01 c.1.8.3 99804 1xfcA 384 5.96e+01 1pyfA 312 5.97e+01 c.1.7.1 95334 1b43A 340 5.97e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 2as9A 210 6.00e+01 2alzA 390 6.01e+01 1luzA 88 6.05e+01 b.40.4.5 74271 1of8A 370 6.10e+01 c.1.10.4 92819 1n8jA 186 6.11e+01 c.47.1.10 85401 1je0A 236 6.15e+01 c.56.2.1 66581 1ns5A 155 6.17e+01 c.116.1.3 80705 1xyiA 66 6.17e+01 1wohA 305 6.23e+01 c.42.1.1 109446 1z90A 469 6.30e+01 4pfk 319 6.31e+01 3pfk c.89.1.1 35582 1tygB 87 6.33e+01 d.15.3.2 107455 1vbuA 328 6.36e+01 1fhgA 154 6.44e+01 1tlk b.1.1.4 21706 1xklA 273 6.44e+01 1hjxA 362 6.48e+01 c.1.8.5,d.26.3.1 83512,83513 1t3nA 388 6.48e+01 d.240.1.1,e.8.1.7 106363,106364 1uc7A 125 6.60e+01 c.47.1.1 99163 1qorA 327 6.63e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1i8dA 213 6.71e+01 b.43.4.3,b.43.4.3 61953,61954 1o69A 394 6.72e+01 c.67.1.4 92560 1ft5A 211 6.75e+01 1bvb a.138.1.3 19681 1zetA 388 6.78e+01 2f6hX 419 6.81e+01 1l1sA 113 6.83e+01 c.114.1.1 73484 1jx7A 117 6.85e+01 c.114.1.1 77195 1f9vA 347 6.91e+01 1bg2 c.37.1.9 59745 1xtoA 311 6.94e+01 1txvB 440 6.98e+01 1b0uA 262 7.00e+01 1b0uA c.37.1.12 32370 1whvA 100 7.02e+01 1b5tA 275 7.02e+01 1b5tA c.1.23.1 29676 1p3dA 475 7.06e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1k0rA 366 7.08e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 67961,67962,67963,67964 1m12A 84 7.15e+01 a.64.1.1 84745 1wgbA 159 7.30e+01 1rf6A 427 7.32e+01 d.68.2.2 97366 2ftzA 284 7.38e+01 1xvqA 175 7.38e+01 1pbjA 125 7.43e+01 d.37.1.1,d.37.1.1 94414,94415 1g291 372 7.43e+01 1g291 1i1rB 181 7.48e+01 1i1rB a.26.1.1 61548 2polA 366 7.55e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1vknA 351 7.71e+01 c.2.1.3,d.81.1.1 108676,108677 1uxzA 131 7.72e+01 b.18.1.10 100170 1duvG 333 7.79e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1yb2A 275 7.81e+01 1eceA 358 7.81e+01 1eceA c.1.8.3 28813 1in0A 163 7.84e+01 d.58.49.1,d.58.49.1 83694,83695 2b4rO 345 7.86e+01 1vfsA 386 7.87e+01 b.49.2.2,c.1.6.1 108584,108585 2g5dA 422 7.89e+01 1bby 69 7.90e+01 2bby a.4.5.15 16149 1ri6A 343 7.98e+01 b.69.11.1 97503 2cxaA 256 8.00e+01 1zhvA 134 8.06e+01 1ve0A 134 8.07e+01 1e9rA 437 8.08e+01 c.37.1.11 64827 1vbvA 105 8.09e+01 1tiqA 180 8.10e+01 d.108.1.1 107010 2bbkL 125 8.12e+01 2bbkL g.21.1.1 44882 2adcA 229 8.19e+01 2tpt 440 8.20e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1v30A 124 8.20e+01 2fn0A 437 8.21e+01 1ob8A 135 8.31e+01 1egaA 301 8.37e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 1yizA 429 8.40e+01 1ljoA 77 8.53e+01 b.38.1.1 73941 1cq3A 233 8.54e+01 1cq3A b.27.1.1 23923 1su0B 159 8.55e+01 d.224.1.2 106015 1nteA 82 8.56e+01 b.36.1.1 86163 2bz6L 53 8.58e+01 1gntA 553 8.61e+01 e.26.1.1 70290 1bg6 359 8.63e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1no5A 114 8.67e+01 d.218.1.5 92014 1e2uA 553 8.70e+01 1e1dA e.26.1.1 43362 1bo1A 416 8.70e+01 1bo1A d.143.1.2 41591 1tluA 130 8.71e+01 d.156.1.2 107139 1y96A 86 8.72e+01 1y43B 173 8.73e+01 16pk 415 8.73e+01 16pk c.86.1.1 35454 1iwmA 186 8.76e+01 b.125.1.2 83758 1wspA 84 8.78e+01 2a41C 32 8.78e+01 2trcP 217 8.81e+01 1b9yC c.47.1.6 33051 1a8q 274 8.85e+01 1brt c.69.1.12 34702 1nnjA 271 8.96e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1gs5A 258 8.96e+01 c.73.1.2 70395