# List of top-scoring protein chains for T0324.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 2fdrA 229 1.68e-22 1te2A 226 2.69e-22 c.108.1.6 106792 2ah5A 210 7.81e-22 1x42A 232 5.64e-21 2gfhA 260 5.82e-21 1o08A 221 1.71e-20 c.108.1.6 86525 2go7A 207 1.33e-19 1jud 232 8.56e-18 1qq5A c.108.1.1 43325 1zrn 232 1.03e-17 1qq5A c.108.1.1 43323 2fi1A 190 7.60e-17 1aq6A 253 3.77e-15 1qq5A c.108.1.1 43331 1qq5A 253 3.82e-15 1qq5A c.108.1.1 43327 1rqlA 267 5.28e-15 c.108.1.3 97750 1rdfA 267 1.03e-14 c.108.1.3 104884 1qq7A 253 1.64e-14 1qq5A c.108.1.1 43329 1fezA 256 1.95e-14 1fezA c.108.1.3 43343 1swvA 267 2.33e-14 2b0cA 206 4.41e-14 1qyiA 384 1.29e-13 c.108.1.13 96595 1l7mA 211 3.76e-12 c.108.1.4 73664 1j97A 211 1.76e-11 1f5sA c.108.1.4 62753 1l7pA 211 1.89e-11 c.108.1.4 73670 1cr6A 554 2.02e-11 1cr6B c.69.1.11,c.108.1.2 34687,43337 1vjrA 271 2.56e-11 c.108.1.14 100832 1zd3A 555 3.69e-11 1pw5A 253 9.96e-11 c.108.1.14 95199 2c4nA 250 1.74e-10 1yv9A 264 3.03e-10 1ys9A 254 1.13e-09 1ydfA 257 1.15e-09 1zjjA 263 1.37e-09 1wviA 257 1.45e-09 1nnlA 225 1.59e-07 c.108.1.4 85906 1l8lA 225 1.90e-07 c.108.1.4 84562 1u7pA 164 3.06e-07 1wr8A 231 9.04e-06 1nf2A 268 1.19e-05 c.108.1.10 91849 1yj5A 383 1.21e-05 2b8eA 273 2.05e-05 1zs9A 261 3.40e-05 2feaA 236 4.08e-05 1ymqA 261 5.36e-05 2g80A 253 2.14e-04 1nrwA 288 2.79e-04 c.108.1.10 86128 2b30A 301 5.19e-04 1rkqA 282 7.49e-04 c.108.1.10 97621 1rlmA 271 7.77e-04 1q92A 197 1.13e-03 c.108.1.8 96250 1rkuA 206 1.53e-03 c.108.1.11 97627 1k1eA 180 1.54e-03 c.108.1.5 67995 2bdeA 470 2.14e-03 1z88A 214 2.57e-03 1z5gA 214 2.58e-03 1rloA 271 5.42e-03 1z4mA 197 6.81e-03 2b82A 211 1.06e-02 1rmtA 212 1.06e-02 2g09A 297 1.17e-02 2g07A 297 1.34e-02 2amyA 246 1.69e-01 1hg3A 225 1.88e-01 1hg3A c.1.1.1 61025 1l6rA 227 2.05e-01 c.108.1.10 77768 1ltqA 301 2.05e-01 c.108.1.9,c.37.1.1 78208,78209 1xviA 275 2.10e-01 1s2oA 244 4.46e-01 1t9zA 197 6.87e-01 c.108.1.16 106728 1gs5A 258 8.61e-01 c.73.1.2 70395 1pz1A 333 1.12e+00 c.1.7.1 95390 1ta0A 197 1.69e+00 c.108.1.16 106729 1pyfA 312 1.88e+00 c.1.7.1 95334 1ly1A 181 2.02e+00 c.37.1.1 74334 1oc2A 348 3.05e+00 c.2.1.2 92765 2fueA 262 3.32e+00 1wpgA 994 4.21e+00 1o1zA 234 5.21e+00 c.1.18.3 86555 1xpjA 126 6.15e+00 1wv2A 265 6.23e+00 1u02A 239 6.71e+00 c.108.1.15 107538 1wzcA 249 8.77e+00 1gen 218 9.60e+00 1gen b.66.1.1 27536 1rtg 210 9.76e+00 1gen b.66.1.1 27537 1vctA 205 1.03e+01 1px5A 349 1.04e+01 a.160.1.2,d.218.1.6 95277,95278 1nhr 447 1.05e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30553,30554,40198 2a6hC 1119 1.09e+01 1y8aA 332 1.14e+01 1vbjA 281 1.21e+01 1nhs 447 1.22e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1adwA 123 1.25e+01 1bqk b.6.1.1 22893 1npx 447 1.27e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30557,30558,40200 1d6iA 388 1.28e+01 1bi5A c.95.1.2,c.95.1.2 36001,36002 1nhq 447 1.29e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30551,30552,40197 1e3oC 160 1.39e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1nhp 447 1.43e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1i89A 389 1.45e+01 c.95.1.2,c.95.1.2 66074,66075 1f8wA 447 1.48e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30561,30562,40202 1i86A 389 1.58e+01 c.95.1.2,c.95.1.2 66068,66069 1uekA 275 1.62e+01 d.14.1.5,d.58.26.5 88483,88484 1i8bA 389 1.64e+01 c.95.1.2,c.95.1.2 66078,66079 1ynpA 317 1.69e+01 1ynjC 1119 1.71e+01 1hqmC 1119 1.72e+01 i.8.1.1 45974 1i88A 389 1.76e+01 c.95.1.2,c.95.1.2 66070,66071 1op0A 234 1.78e+01 b.47.1.2 104019 1d6hA 387 1.81e+01 1bi5A c.95.1.2,c.95.1.2 36005,36006 1tj7A 457 1.81e+01 1ck7A 631 1.84e+01 1ck7A b.66.1.1,g.14.1.2,g.14.1.2,g.14.1.2,a.20.1.2,d.92.1.11 27538,44674,44675,44676,58969,58970 1bq6A 388 1.84e+01 1bi5A c.95.1.2,c.95.1.2 35987,35988 1bi5A 389 1.85e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1cmlA 389 1.86e+01 1bi5A c.95.1.2,c.95.1.2 35989,35990 1b74A 254 1.86e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1op2A 234 1.87e+01 b.47.1.2 104020 1chwA 389 1.93e+01 1bi5A c.95.1.2,c.95.1.2 35997,35998 1l9uC 1118 1.99e+01 i.8.1.1 73750 1i6vC 1118 2.00e+01 e.29.1.1 61856 1fehA 574 2.01e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1an7A 136 2.03e+01 1seiA d.140.1.1 41465 1cs6A 382 2.04e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1fjgH 138 2.07e+01 1seiA d.140.1.1 41468 1pnuC 197 2.13e+01 i.1.1.1 88200 1vorF 198 2.14e+01 1xyr1 232 2.20e+01 1nwyC 204 2.22e+01 i.1.1.2 86347 1nkwC 205 2.22e+01 i.1.1.2 80588 1ar61 302 2.34e+01 1pov1 1xbtA 193 2.39e+01 1ar71 302 2.39e+01 1pov1 1al21 302 2.39e+01 1pov1 1dgi1 288 2.40e+01 2c7bA 311 2.44e+01 1hxs1 302 2.44e+01 1pov1 302 2.45e+01 1pov1 2b8nA 429 2.47e+01 1jwxA 389 2.56e+01 c.95.1.2,c.95.1.2 71920,71921 1xsjA 778 2.59e+01 1we5A 772 2.59e+01 2f2hA 773 2.59e+01 1uj2A 252 2.62e+01 c.37.1.6 99452 1hyuA 521 2.66e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1d5mB 192 2.75e+01 1iakB b.1.1.2,d.19.1.1 21618,38192 1xrjA 261 2.78e+01 1uasA 362 2.80e+01 b.71.1.1,c.1.8.1 88388,88389 1w4rA 195 2.81e+01 1d5zB 192 2.84e+01 1iakB b.1.1.2,d.19.1.1 21620,38194 2czrA 226 3.25e+01 1gviA 588 3.36e+01 b.1.18.2,b.71.1.1,c.1.8.1 70604,70605,70606 1mo2A 294 3.36e+01 c.69.1.22 79331 1urhA 280 3.38e+01 c.46.1.2,c.46.1.2 99829,99830 1u0vA 393 3.39e+01 1wxsA 90 3.40e+01 1kezA 300 3.41e+01 c.69.1.22 68546 1xb0A 108 3.41e+01 1j0gA 92 3.41e+01 d.15.1.6 90740 1jzdA 220 3.42e+01 c.47.1.9,d.17.3.1 84257,84258 2ctwA 109 3.42e+01 1dt9A 437 3.44e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1jzoA 216 3.52e+01 c.47.1.9,d.17.3.1 84267,84268 1w8jA 766 3.57e+01 1w7jA 795 3.61e+01 2ctqA 112 3.66e+01 1eejA 216 3.72e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 2ldxA 331 3.74e+01 1fzrA 138 3.87e+01 1fzrA c.52.1.17 33336 1o4xA 167 3.91e+01 a.4.1.1,a.35.1.1 92470,92471 1smaA 588 3.99e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21854,27781,28768 1cqtA 163 4.03e+01 1au7A a.4.1.1,a.35.1.1 15992,17018 1bw0A 416 4.04e+01 1bw0A c.67.1.1 34385 1ek6A 348 4.06e+01 1xel c.2.1.2 29800 1j96A 323 4.10e+01 c.1.7.1 71616 1ihiA 323 4.10e+01 c.1.7.1 66142 1xg4A 295 4.10e+01 1xjbA 325 4.11e+01 1mumA 295 4.15e+01 c.1.12.7 85108 1ujqA 305 4.18e+01 c.1.12.7 99463 1vrbA 342 4.20e+01 1ydhA 216 4.27e+01 1m0dA 138 4.28e+01 c.52.1.17 74354 1gt0C 159 4.37e+01 a.4.1.1,a.35.1.1 76335,76336 2dfsA 1080 4.37e+01 1vl2A 421 4.41e+01 c.26.2.1,d.210.1.1 108708,108709 1i3kA 348 4.41e+01 1xel c.2.1.2 61595 2gwrA 238 4.47e+01 1s05A 129 4.53e+01 a.24.3.2 98254 1z0sA 278 4.60e+01 1octC 156 4.64e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1v6aA 332 4.67e+01 2cw1A 65 4.71e+01 1l7yA 94 4.72e+01 d.15.1.6 73676 1o3uA 135 4.72e+01 a.24.16.3 86615 1xnfA 275 4.74e+01 1l5zA 155 4.75e+01 c.23.1.1 77722 1o54A 277 4.78e+01 c.66.1.13 92482 1tv8A 340 4.80e+01 c.1.28.3 107352 1t2fA 333 4.82e+01 c.2.1.5,d.162.1.1 99088,99089 1i0zA 333 4.82e+01 3ldh c.2.1.5,d.162.1.1 61495,61496 1smqA 399 4.93e+01 a.25.1.2 105766 1hzjA 348 4.94e+01 1xel c.2.1.2 61450 2fb2A 340 4.96e+01 1jk0A 419 4.98e+01 a.25.1.2 63142 1mrqA 323 4.99e+01 c.1.7.1 91445 1qkkA 155 5.01e+01 1dbwA c.23.1.1 31104 1t6mA 299 5.04e+01 1zy8A 474 5.13e+01 1rymA 212 5.19e+01 c.56.3.1 98106 1i10A 331 5.19e+01 3ldh c.2.1.5,d.162.1.1 61499,61500 1a7aA 432 5.19e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1li4A 432 5.27e+01 c.2.1.4,c.23.12.3 84616,84617 2bjfA 329 5.33e+01 2hrpH 226 5.35e+01 1igtB b.1.1.1,b.1.1.2 20171,21195 1e32A 458 5.40e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1xwfA 431 5.45e+01 1b3rA 431 5.49e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1wekA 217 5.55e+01 1b35A 260 5.57e+01 1b35A b.121.4.1 23333 1c9wA 315 5.62e+01 1frb c.1.7.1 28699 1zmdA 474 5.69e+01 1ktbA 405 5.79e+01 b.71.1.1,c.1.8.1 72960,72961 1q6uA 245 5.90e+01 d.26.1.1 95998 1zrzA 364 5.95e+01 1losA 224 5.97e+01 c.1.2.3 74157 1d4fA 431 5.99e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1fv1B 190 6.05e+01 1iakB b.1.1.2,d.19.1.1 21606,38180 1nw9A 98 6.07e+01 g.52.1.1 86293 1ocp 67 6.13e+01 1au7A a.4.1.1 15999 1ma3A 253 6.15e+01 c.31.1.5 78883 1zglB 192 6.15e+01 2f3oA 776 6.19e+01 1i94H 138 6.20e+01 1seiA d.140.1.1 61999 1kz7A 353 6.25e+01 a.87.1.1,b.55.1.1 73333,73334 1rj2A 353 6.29e+01 a.87.1.1,b.55.1.1 104954,104955 1lb1A 353 6.30e+01 a.87.1.1,b.55.1.1 73784,73785 1kzgA 353 6.30e+01 a.87.1.1,b.55.1.1 73355,73356 1g3fA 117 6.54e+01 1g3fA g.52.1.1 45378 1f9xA 120 6.62e+01 1g3fA g.52.1.1 59748 1dwqA 262 6.65e+01 1qj4A c.69.1.20 34808 1pmy 123 6.73e+01 1bqk b.6.1.1 22888 1gro 416 6.75e+01 1iso c.77.1.1 35079 1g73C 121 6.75e+01 1g3fA g.52.1.1 45375 1aj8A 371 6.89e+01 1aj8A a.103.1.1 18900 1y1uA 585 6.94e+01 1n82A 331 6.98e+01 c.1.8.3 91703 2ftsA 419 7.00e+01 1t3eA 421 7.07e+01 b.85.6.1,b.103.1.1,c.57.1.2 106348,106349,106350 1dl6A 58 7.17e+01 1dl6A g.41.3.1 45207 1lhpA 312 7.21e+01 c.72.1.5 77960 1jcuA 208 7.26e+01 d.115.1.1 71634 1t2nA 181 7.28e+01 1rlyA 60 7.31e+01 g.41.3.1 104988 1oxy 628 7.36e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18486,18497,21862 2fx0A 201 7.36e+01 2ev0A 142 7.41e+01 1ll1 628 7.42e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1e0uA 470 7.42e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27072,29300,33154 1kgnA 329 7.43e+01 a.25.1.2 68584 1r5vB 185 7.47e+01 b.1.1.2,d.19.1.1 97118,97119 1pkyA 470 7.60e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27068,29296,33150 1ry8A 323 7.62e+01 1s1pA 331 7.71e+01 c.1.7.1 98350 1lla 628 7.71e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1on2A 142 7.74e+01 a.4.5.24,a.76.1.1 87103,87104 1ispA 181 7.75e+01 c.69.1.18 76778 1iebB 227 7.97e+01 1iakB b.1.1.2,d.19.1.1 21636,38210 1e0tA 470 7.99e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1t4mA 181 8.04e+01 1j0hA 588 8.25e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1ktdB 215 8.25e+01 b.1.1.2,d.19.1.1 72966,72967 1klyA 247 8.25e+01 c.1.2.3 72730 1b0uA 262 8.35e+01 1b0uA c.37.1.12 32370 2fvzA 273 8.39e+01 1kt2B 213 8.45e+01 b.1.1.2,d.19.1.1 72953,72954 2bmuA 226 8.51e+01 2briA 225 8.57e+01 1dnv 437 8.58e+01 1dnv b.121.5.3 23332 1klzA 247 8.61e+01 c.1.2.3 72731 1fngB 224 8.69e+01 1iakB b.1.1.2,d.19.1.1 59906,59907 1j0jA 588 8.70e+01 b.1.18.2,b.71.1.1,c.1.8.1 77039,77040,77041 1a6aB 187 8.74e+01 1iakB b.1.1.2,d.19.1.1 21616,38190 1ieaB 228 8.80e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 1fneB 224 8.85e+01 1iakB b.1.1.2,d.19.1.1 59898,59899 1ve2A 235 8.90e+01 2greA 349 8.93e+01 1re3B 313 8.95e+01 d.171.1.1,h.1.8.1 104892,104893 1rynA 202 8.97e+01 c.56.3.1 98107