# List of top-scoring protein chains for T0303.t2k-w0.5 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 1jud 232 3.40e-20 1qq5A c.108.1.1 43325 1zrn 232 4.71e-20 1qq5A c.108.1.1 43323 2ah5A 210 2.63e-19 2fdrA 229 3.36e-19 2gfhA 260 3.88e-18 1te2A 226 3.89e-18 c.108.1.6 106792 1x42A 232 1.66e-17 1aq6A 253 2.13e-17 1qq5A c.108.1.1 43331 1qq5A 253 2.49e-17 1qq5A c.108.1.1 43327 1qq7A 253 7.73e-17 1qq5A c.108.1.1 43329 1o08A 221 1.17e-16 c.108.1.6 86525 1l7mA 211 1.03e-14 c.108.1.4 73664 1j97A 211 3.32e-14 1f5sA c.108.1.4 62753 1l7pA 211 4.04e-14 c.108.1.4 73670 1rqlA 267 5.49e-14 c.108.1.3 97750 2fi1A 190 7.43e-14 1rdfA 267 9.24e-14 c.108.1.3 104884 1fezA 256 1.03e-13 1fezA c.108.1.3 43343 1swvA 267 2.75e-13 2b0cA 206 6.12e-13 2b8eA 273 1.40e-12 1qyiA 384 5.07e-12 c.108.1.13 96595 1vjrA 271 2.24e-10 c.108.1.14 100832 1pw5A 253 7.44e-10 c.108.1.14 95199 1zd3A 555 1.07e-09 1cr6A 554 1.72e-09 1cr6B c.69.1.11,c.108.1.2 34687,43337 1zjjA 263 1.99e-09 1yv9A 264 2.07e-09 1nnlA 225 5.23e-09 c.108.1.4 85906 1l8lA 225 6.52e-09 c.108.1.4 84562 1wviA 257 3.88e-08 1ys9A 254 4.45e-08 2c4nA 250 4.54e-08 1ydfA 257 7.13e-08 1u7pA 164 1.23e-07 1zs9A 261 1.90e-07 1wr8A 231 3.22e-06 2g80A 253 4.34e-06 1nf2A 268 9.00e-06 c.108.1.10 91849 1ymqA 261 1.53e-05 1k1eA 180 1.62e-05 c.108.1.5 67995 2feaA 236 1.88e-05 1yj5A 383 2.04e-05 1wpgA 994 5.28e-05 1rkuA 206 7.26e-05 c.108.1.11 97627 2bdeA 470 1.16e-04 2b30A 301 1.25e-04 1nrwA 288 1.83e-04 c.108.1.10 86128 1rkqA 282 3.10e-04 c.108.1.10 97621 1rlmA 271 3.42e-04 1z5gA 214 3.48e-04 1z88A 214 5.57e-04 2b82A 211 1.36e-03 1rmtA 212 1.36e-03 1rloA 271 1.88e-03 1q92A 197 1.08e-02 c.108.1.8 96250 1ltqA 301 1.91e-02 c.108.1.9,c.37.1.1 78208,78209 2g09A 297 2.22e-02 1mhsA 920 3.04e-02 i.18.1.1 79130 1l6rA 227 4.94e-02 c.108.1.10 77768 2g07A 297 6.98e-02 1z4mA 197 7.68e-02 2amyA 246 9.59e-02 1s2oA 244 1.06e-01 1xviA 275 1.16e-01 1pz1A 333 1.57e-01 c.1.7.1 95390 1hg3A 225 1.86e-01 1hg3A c.1.1.1 61025 1wv2A 265 2.02e-01 1t9zA 197 2.31e-01 c.108.1.16 106728 1wzcA 249 4.66e-01 2fueA 262 4.94e-01 1pyfA 312 5.20e-01 c.1.7.1 95334 1ly1A 181 6.79e-01 c.37.1.1 74334 1y8aA 332 7.40e-01 1ynpA 317 7.52e-01 1xpjA 126 9.99e-01 1ta0A 197 1.11e+00 c.108.1.16 106729 1u02A 239 2.01e+00 c.108.1.15 107538 2b61A 377 2.08e+00 1vbjA 281 2.11e+00 1bc3 319 4.67e+00 1avc a.65.1.1 18175 1tj7A 457 4.80e+00 1z6zA 282 4.86e+00 1bc1 319 4.95e+00 1avc a.65.1.1 18173 1avhA 320 5.11e+00 1avc a.65.1.1 18159 1anxA 319 5.12e+00 1avc a.65.1.1 18161 1hve 319 5.87e+00 1avc a.65.1.1 18156 1hvd 319 6.14e+00 1avc a.65.1.1 18154 1bcy 319 6.49e+00 1avc a.65.1.1 18172 1hvf 319 7.04e+00 1avc a.65.1.1 18155 1oc2A 348 7.06e+00 c.2.1.2 92765 1bcw 319 7.60e+00 1avc a.65.1.1 18176 1n41A 319 7.63e+00 a.65.1.1 79978 1i86A 389 7.66e+00 c.95.1.2,c.95.1.2 66068,66069 1jk0A 419 8.75e+00 a.25.1.2 63142 1frb 315 8.84e+00 1frb c.1.7.1 28665 1smqA 399 8.86e+00 a.25.1.2 105766 2ran 316 8.97e+00 1avc a.65.1.1 18170 1n42A 319 9.01e+00 a.65.1.1 79979 1n44A 319 9.12e+00 a.65.1.1 79980 1a8b 318 9.21e+00 1avc a.65.1.1 18171 1d6hA 387 9.23e+00 1bi5A c.95.1.2,c.95.1.2 36005,36006 1bc0 319 9.24e+00 1avc a.65.1.1 18174 1cmlA 389 9.35e+00 1bi5A c.95.1.2,c.95.1.2 35989,35990 1bi5A 389 9.40e+00 1bi5A c.95.1.2,c.95.1.2 35985,35986 1bq6A 388 9.40e+00 1bi5A c.95.1.2,c.95.1.2 35987,35988 1d6iA 388 9.50e+00 1bi5A c.95.1.2,c.95.1.2 36001,36002 1i88A 389 9.96e+00 c.95.1.2,c.95.1.2 66070,66071 1i8bA 389 1.01e+01 c.95.1.2,c.95.1.2 66078,66079 1bcz 319 1.02e+01 1avc a.65.1.1 18177 1yo8A 634 1.12e+01 1i89A 389 1.13e+01 c.95.1.2,c.95.1.2 66074,66075 1u0vA 393 1.13e+01 1fzrA 138 1.16e+01 1fzrA c.52.1.17 33336 1chwA 389 1.21e+01 1bi5A c.95.1.2,c.95.1.2 35997,35998 1hqmC 1119 1.23e+01 i.8.1.1 45974 1ynjC 1119 1.23e+01 1m0dA 138 1.28e+01 c.52.1.17 74354 1uekA 275 1.33e+01 d.14.1.5,d.58.26.5 88483,88484 1jwxA 389 1.38e+01 c.95.1.2,c.95.1.2 71920,71921 1pnuC 197 1.57e+01 i.1.1.1 88200 2a6hC 1119 1.57e+01 1vorF 198 1.58e+01 1nwyC 204 1.67e+01 i.1.1.2 86347 1nkwC 205 1.68e+01 i.1.1.2 80588 1vctA 205 1.74e+01 1c9wA 315 1.83e+01 1frb c.1.7.1 28699 1i6vC 1118 1.94e+01 e.29.1.1 61856 1l9uC 1118 1.94e+01 i.8.1.1 73750 1qrhA 261 1.98e+01 1ckqA c.52.1.1 33232 1e32A 458 2.00e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1ha0A 494 2.01e+01 1hgeA b.19.1.2,h.3.1.1 23824,45697 2ftwA 521 2.03e+01 1qriA 261 2.05e+01 1ckqA c.52.1.1 33233 1xbtA 193 2.17e+01 2fgeA 995 2.18e+01 1xyr1 232 2.25e+01 1qpsA 261 2.28e+01 1ckqA c.52.1.1 33234 1rjdA 334 2.36e+01 c.66.1.37 97558 1bw0A 416 2.38e+01 1bw0A c.67.1.1 34385 1h6fA 193 2.39e+01 b.2.5.4 70901 2ctwA 109 2.40e+01 1nbaA 264 2.41e+01 1nbaA c.33.1.3 31753 1j3nA 408 2.41e+01 c.95.1.1,c.95.1.1 84074,84075 1jzdA 220 2.41e+01 c.47.1.9,d.17.3.1 84257,84258 2cw1A 65 2.43e+01 1dgi1 288 2.44e+01 1w4rA 195 2.45e+01 1teeA 393 2.46e+01 c.95.1.2 106811 1hxs1 302 2.48e+01 1ar71 302 2.48e+01 1pov1 1pov1 302 2.49e+01 1pov1 1ar61 302 2.51e+01 1pov1 1cydA 244 2.51e+01 1cydA c.2.1.2 29825 1al21 302 2.53e+01 1pov1 2b3oA 532 2.53e+01 1jzoA 216 2.54e+01 c.47.1.9,d.17.3.1 84267,84268 1eejA 216 2.55e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1t6mA 299 2.56e+01 1vpqA 273 2.60e+01 2czrA 226 2.62e+01 1jjfA 268 2.65e+01 c.69.1.2 66765 1cl8A 276 2.65e+01 1ckqA c.52.1.1 33230 1ahr 146 2.66e+01 1cll a.39.1.5 17287 2c7bA 311 2.74e+01 1xfxO 149 2.79e+01 1y6wA 148 2.81e+01 2c4xA 260 2.81e+01 1hzjA 348 2.81e+01 1xel c.2.1.2 61450 1i3kA 348 2.81e+01 1xel c.2.1.2 61595 1ek6A 348 2.84e+01 1xel c.2.1.2 29800 3cln 148 2.85e+01 1cll a.39.1.5 17286 1o1zA 234 2.86e+01 c.1.18.3 86555 1jt2A 268 2.91e+01 c.69.1.2 71858 1gs5A 258 2.96e+01 c.73.1.2 70395 1ffyA 917 3.00e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1w8jA 766 3.06e+01 1v2xA 194 3.06e+01 c.116.1.1 100274 2ctqA 112 3.06e+01 1mxeA 148 3.10e+01 a.39.1.5 79644 2bkhB 149 3.10e+01 1oojA 149 3.10e+01 a.39.1.5 87198 1id1A 153 3.17e+01 1id1A c.2.1.9 62286 1px5A 349 3.30e+01 a.160.1.2,d.218.1.6 95277,95278 1rjwA 339 3.33e+01 b.35.1.2,c.2.1.1 97582,97583 1iq8A 582 3.37e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1nb4A 570 3.48e+01 e.8.1.4 85509 1ocp 67 3.50e+01 1au7A a.4.1.1 15999 1w7jA 795 3.55e+01 1n7vA 555 3.56e+01 b.126.1.1 85377 1n7uA 554 3.57e+01 b.126.1.1 85376 2be6A 150 3.64e+01 1k93D 144 3.66e+01 a.39.1.5 68330 1y0vH 146 3.67e+01 2f3yA 148 3.68e+01 1iq5A 149 3.69e+01 a.39.1.5 62643 1prwA 149 3.69e+01 a.39.1.5 95062 1fehA 574 3.71e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1cdmA 144 3.74e+01 1cll a.39.1.5 17270 1cdlA 147 3.75e+01 1cll a.39.1.5 17272 2dfsA 1080 3.87e+01 1tedA 393 3.95e+01 c.95.1.2 106807 1tolA 222 4.00e+01 1g3p b.37.1.1,d.212.1.1 24790,39587 1j0gA 92 4.02e+01 d.15.1.6 90740 1wxsA 90 4.04e+01 2g5cA 281 4.10e+01 1dgkN 917 4.19e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33487,33488,33489,33490 1czaN 917 4.19e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1uwkA 557 4.19e+01 e.51.1.1 108065 1qg8A 255 4.20e+01 1qg8A c.68.1.1 34505 1w1uA 557 4.21e+01 e.51.1.1 109079 1qrqA 325 4.23e+01 1qrqA c.1.7.1 28667 2bb3A 221 4.28e+01 1hgxA 183 4.30e+01 1tc1A c.61.1.1 34027 1uwlA 557 4.31e+01 e.51.1.1 108067 1lngA 87 4.31e+01 d.201.1.1 74045 1hkbA 917 4.33e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 4pfk 319 4.33e+01 3pfk c.89.1.1 35582 1l9aA 87 4.34e+01 d.201.1.1 73710 1v47A 349 4.36e+01 b.122.1.3,c.26.1.5 100292,100293 1qhaA 917 4.43e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1exbA 332 4.49e+01 1qrqA c.1.7.1 28666 2a79A 333 4.51e+01 1wi3A 71 4.57e+01 1mvoA 136 4.86e+01 c.23.1.1 79513 1dt9A 437 5.08e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1p4xA 250 5.11e+01 a.4.5.28,a.4.5.28 87784,87785 1lhpA 312 5.15e+01 c.72.1.5 77960 1an7A 136 5.21e+01 1seiA d.140.1.1 41465 1mrqA 323 5.24e+01 c.1.7.1 91445 2dexX 671 5.28e+01 1x13A 401 5.37e+01 1zsxA 347 5.40e+01 1wdaA 670 5.53e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1eo1A 124 5.55e+01 1eo1A c.55.5.1 33739 1fjgH 138 5.55e+01 1seiA d.140.1.1 41468 1os5A 576 5.60e+01 e.8.1.4 93475 1wd8A 670 5.64e+01 b.2.9.1,b.6.1.6,d.126.1.5 109237,109238,109239 1csjA 531 5.65e+01 1quvA e.8.1.4 43120 1xsjA 778 5.69e+01 1we5A 772 5.69e+01 2f2hA 773 5.69e+01 1s05A 129 5.70e+01 a.24.3.2 98254 2ax0A 580 5.73e+01 1adwA 123 5.77e+01 1bqk b.6.1.1 22893 1gx6A 531 5.79e+01 e.8.1.4 70683 1c2pA 576 5.79e+01 1quvA e.8.1.4 43117 1gx5A 536 5.79e+01 e.8.1.4 70682 1quvA 578 5.82e+01 1quvA e.8.1.4 43119 1nhuA 578 5.89e+01 e.8.1.4 85723 2f2oA 179 5.89e+01 1zxxA 319 5.91e+01 1qs7A 145 5.93e+01 k.21.1.1 88373 1vrkA 148 5.93e+01 1cll k.21.1.1 46451 1qtxA 148 5.97e+01 k.21.1.1 88375 1vl8A 267 6.01e+01 c.2.1.2 108733 2b0aA 186 6.13e+01 1ogqA 313 6.21e+01 c.10.2.8 86996 1xb0A 108 6.41e+01 1mtoA 319 6.54e+01 c.89.1.1 79458 1xb4A 202 6.55e+01 1ihiA 323 6.60e+01 c.1.7.1 66142 1op2A 234 6.60e+01 b.47.1.2 104020 1j96A 323 6.61e+01 c.1.7.1 71616 1xjbA 325 6.69e+01 6pfkA 319 6.70e+01 3pfk c.89.1.1 35583 1x94A 191 6.75e+01 c.80.1.3 109522 1eerA 166 6.76e+01 1eerA a.26.1.2 16846 1b0uA 262 6.97e+01 1b0uA c.37.1.12 32370 1us5A 314 7.08e+01 c.94.1.1 99856 1m9lA 199 7.10e+01 c.10.3.1 84903 1dv1A 449 7.12e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1rf6A 427 7.14e+01 d.68.2.2 97366 1ds9A 198 7.15e+01 1ds9A c.10.3.1 30879 1dv2A 452 7.18e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1mo2A 294 7.19e+01 c.69.1.22 79331 1i10A 331 7.33e+01 3ldh c.2.1.5,d.162.1.1 61499,61500 1kezA 300 7.33e+01 c.69.1.22 68546 1yfsA 465 7.35e+01 1clm 148 7.37e+01 1cll a.39.1.5 17301 1exrA 148 7.37e+01 1cll a.39.1.5 17299 1b74A 254 7.42e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1l7yA 94 7.47e+01 d.15.1.6 73676 1yvuA 706 7.69e+01 1rxwA 336 7.73e+01 a.60.7.1,c.120.1.2 98059,98060 1ispA 181 7.77e+01 c.69.1.18 76778 1nw9A 98 7.81e+01 g.52.1.1 86293 1uufA 369 7.92e+01 b.35.1.2,c.2.1.1 100006,100007 1k8kD 300 7.93e+01 d.198.2.1,d.198.2.1 68309,68310 2briA 225 8.04e+01 1q5mA 322 8.07e+01 c.1.7.1 104539 1op0A 234 8.14e+01 b.47.1.2 104019 2bmuA 226 8.14e+01 1q13A 323 8.16e+01 1urhA 280 8.16e+01 c.46.1.2,c.46.1.2 99829,99830 2fiqA 420 8.18e+01 1sjpA 504 8.35e+01 1t4mA 181 8.43e+01 1e3oC 160 8.45e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1g3fA 117 8.49e+01 1g3fA g.52.1.1 45378 2brxA 244 8.49e+01 1f9xA 120 8.52e+01 1g3fA g.52.1.1 59748 1im5A 180 8.54e+01 c.33.1.3 66211 1ma3A 253 8.55e+01 c.31.1.5 78883 1sviA 195 8.55e+01 c.37.1.8 106048 1gzkA 315 8.68e+01 d.144.1.7 83406 1j5wA 298 8.72e+01 d.104.1.1 71589 1g73C 121 8.82e+01 1g3fA g.52.1.1 45375 2bdwA 362 8.86e+01 1dcnA 433 8.89e+01 1auwA a.127.1.1 19420