# List of top-scoring protein chains for T0330.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 2ah5A 210 3.05e-23 2fdrA 229 3.33e-23 1te2A 226 2.78e-21 c.108.1.6 106792 2gfhA 260 2.73e-19 1o08A 221 6.99e-19 c.108.1.6 86525 2go7A 207 1.07e-18 1x42A 232 1.20e-17 1l7mA 211 2.48e-16 c.108.1.4 73664 1j97A 211 1.04e-15 1f5sA c.108.1.4 62753 1l7pA 211 1.45e-15 c.108.1.4 73670 1rqlA 267 5.98e-15 c.108.1.3 97750 1jud 232 6.59e-15 1qq5A c.108.1.1 43325 2fi1A 190 8.68e-15 1zrn 232 8.80e-15 1qq5A c.108.1.1 43323 1rdfA 267 1.11e-14 c.108.1.3 104884 1fezA 256 2.16e-14 1fezA c.108.1.3 43343 1swvA 267 3.64e-14 1qyiA 384 6.97e-13 c.108.1.13 96595 1aq6A 253 1.15e-12 1qq5A c.108.1.1 43331 1qq5A 253 1.28e-12 1qq5A c.108.1.1 43327 1qq7A 253 5.85e-12 1qq5A c.108.1.1 43329 2b0cA 206 1.35e-10 1nnlA 225 1.88e-10 c.108.1.4 85906 1l8lA 225 2.04e-10 c.108.1.4 84562 1vjrA 271 5.33e-10 c.108.1.14 100832 1zjjA 263 2.16e-09 1pw5A 253 2.18e-09 c.108.1.14 95199 1zd3A 555 5.42e-09 2c4nA 250 6.60e-09 1cr6A 554 7.90e-09 1cr6B c.69.1.11,c.108.1.2 34687,43337 1yv9A 264 3.61e-08 1u7pA 164 1.92e-07 1ydfA 257 2.12e-07 1wviA 257 2.57e-07 1ys9A 254 2.61e-07 1wr8A 231 4.55e-06 1nf2A 268 1.62e-05 c.108.1.10 91849 2b8eA 273 1.65e-05 2feaA 236 1.81e-05 1yj5A 383 1.13e-04 1q92A 197 1.36e-04 c.108.1.8 96250 1rkuA 206 1.45e-04 c.108.1.11 97627 1z5gA 214 2.76e-04 1k1eA 180 3.73e-04 c.108.1.5 67995 1z88A 214 3.84e-04 1ymqA 261 4.22e-04 1nrwA 288 1.03e-03 c.108.1.10 86128 1z4mA 197 1.11e-03 2b82A 211 1.20e-03 1rmtA 212 1.20e-03 2g09A 297 1.66e-03 2g07A 297 2.52e-03 1zs9A 261 3.71e-03 1rlmA 271 4.73e-03 1l6rA 227 5.30e-03 c.108.1.10 77768 2g80A 253 1.73e-02 1rloA 271 1.89e-02 2b30A 301 2.02e-02 1rkqA 282 5.28e-02 c.108.1.10 97621 1hg3A 225 5.87e-02 1hg3A c.1.1.1 61025 1s2oA 244 9.39e-02 1ltqA 301 9.66e-02 c.108.1.9,c.37.1.1 78208,78209 2bdeA 470 4.10e-01 1ly1A 181 4.81e-01 c.37.1.1 74334 1xviA 275 5.48e-01 2amyA 246 7.95e-01 1wv2A 265 1.15e+00 1wzcA 249 1.15e+00 1y8aA 332 1.35e+00 1vctA 205 2.06e+00 1wpgA 994 2.20e+00 1pyfA 312 2.48e+00 c.1.7.1 95334 1oc2A 348 3.16e+00 c.2.1.2 92765 1uufA 369 4.12e+00 b.35.1.2,c.2.1.1 100006,100007 2a6hC 1119 4.40e+00 1pz1A 333 4.56e+00 c.1.7.1 95390 1j0hA 588 5.16e+00 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1ynjC 1119 5.89e+00 1hqmC 1119 5.93e+00 i.8.1.1 45974 1l9uC 1118 6.57e+00 i.8.1.1 73750 1i6vC 1118 6.60e+00 e.29.1.1 61856 1iq8A 582 6.88e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 2fueA 262 6.97e+00 1u02A 239 7.14e+00 c.108.1.15 107538 1j0jA 588 7.32e+00 b.1.18.2,b.71.1.1,c.1.8.1 77039,77040,77041 1zw6A 166 8.91e+00 1smaA 588 9.21e+00 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21854,27781,28768 521p 166 9.62e+00 1ctqA c.37.1.8 31992 1w8jA 766 1.18e+01 1w7jA 795 1.20e+01 1tkjA 284 1.21e+01 1agp 166 1.25e+01 1ctqA c.37.1.8 31985 1nhr 447 1.26e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30553,30554,40198 1nhq 447 1.26e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30551,30552,40197 1nhp 447 1.27e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1npx 447 1.27e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30557,30558,40200 1b74A 254 1.28e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1nhs 447 1.28e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1lf0A 166 1.33e+01 c.37.1.8 77913 1nvvQ 166 1.39e+01 c.37.1.8 86277 1ctqA 166 1.40e+01 1ctqA c.37.1.8 31965 1rvdA 166 1.41e+01 1ctqA c.37.1.8 31974 421p 166 1.42e+01 1ctqA c.37.1.8 31983 1kzhA 555 1.43e+01 c.89.1.1 73361 2c5lA 173 1.45e+01 6q21A 171 1.49e+01 1ctqA c.37.1.8 31979 221p 166 1.50e+01 1ctqA c.37.1.8 31987 2q21 171 1.50e+01 1ctqA c.37.1.8 31986 2ev0A 142 1.51e+01 2evwX 166 1.54e+01 621p 166 1.57e+01 1ctqA c.37.1.8 31988 821p 166 1.57e+01 1ctqA c.37.1.8 31969 1on2A 142 1.61e+01 a.4.5.24,a.76.1.1 87103,87104 1gviA 588 1.61e+01 b.1.18.2,b.71.1.1,c.1.8.1 70604,70605,70606 2ctqA 112 1.62e+01 2dfsA 1080 1.68e+01 1z78A 215 1.72e+01 2erfA 209 1.73e+01 1za4A 251 1.74e+01 1wxsA 90 1.75e+01 1j0gA 92 1.75e+01 d.15.1.6 90740 721p 166 1.78e+01 1ctqA c.37.1.8 31975 4q21 189 1.80e+01 1ctqA c.37.1.8 31978 1fehA 574 1.81e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1iaqA 166 1.85e+01 1ctqA c.37.1.8 62120 1lj8A 493 1.86e+01 a.100.1.9,c.2.1.6 90392,90393 1f8wA 447 1.91e+01 1nhp c.3.1.5,c.3.1.5,d.87.1.1 30561,30562,40202 1l7yA 94 1.99e+01 d.15.1.6 73676 1n82A 331 2.08e+01 c.1.8.3 91703 1id1A 153 2.16e+01 1id1A c.2.1.9 62286 1p6bA 336 2.31e+01 c.1.9.3 94163 2go1A 401 2.33e+01 1lfdB 167 2.34e+01 1ctqA c.37.1.8 31976 2nacA 393 2.35e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 1ma3A 253 2.45e+01 c.31.1.5 78883 1kgnA 329 2.48e+01 a.25.1.2 68584 1xj0A 166 2.53e+01 1xcmA 167 2.56e+01 1jah 166 2.69e+01 1ctqA c.37.1.8 31972 1xpjA 126 2.71e+01 1gro 416 2.78e+01 1iso c.77.1.1 35079 2gsdA 402 2.92e+01 1uumA 372 3.00e+01 c.1.4.1 100010 1kcxA 518 3.02e+01 b.92.1.3,c.1.9.6 90953,90954 1cs6A 382 3.06e+01 1cs6A b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21760,21761,21762,21763 1v4vA 376 3.09e+01 c.87.1.3 100313 1o1zA 234 3.09e+01 c.1.18.3 86555 1qw7A 336 3.13e+01 2gwrA 238 3.16e+01 1t9zA 197 3.23e+01 c.108.1.16 106728 1dnv 437 3.27e+01 1dnv b.121.5.3 23332 2c7bA 311 3.47e+01 1r30A 369 3.51e+01 c.1.28.1 96895 1stzA 338 3.59e+01 a.4.5.51,d.110.2.3 106009,106010 1d6iA 388 3.63e+01 1bi5A c.95.1.2,c.95.1.2 36001,36002 1klzA 247 3.69e+01 c.1.2.3 72731 1ys4A 354 3.77e+01 1wekA 217 3.83e+01 1ihp 438 4.13e+01 1ihp c.60.1.2 33993 1wyuA 438 4.18e+01 1i86A 389 4.20e+01 c.95.1.2,c.95.1.2 66068,66069 1uasA 362 4.22e+01 b.71.1.1,c.1.8.1 88388,88389 1nw9A 98 4.25e+01 g.52.1.1 86293 1xb0A 108 4.37e+01 3ezaA 249 4.37e+01 1zymA a.60.10.1,c.8.1.2 18112,30707 1ztmA 490 4.37e+01 1d6hA 387 4.38e+01 1bi5A c.95.1.2,c.95.1.2 36005,36006 1ktbA 405 4.40e+01 b.71.1.1,c.1.8.1 72960,72961 2c2nA 339 4.43e+01 1bq6A 388 4.45e+01 1bi5A c.95.1.2,c.95.1.2 35987,35988 1bi5A 389 4.46e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1pta 327 4.48e+01 1pscA c.1.9.3 29064 1adwA 123 4.50e+01 1bqk b.6.1.1 22893 1dpmA 329 4.50e+01 1pscA c.1.9.3 29062 1eywA 331 4.51e+01 1pscA c.1.9.3 29057 1px5A 349 4.52e+01 a.160.1.2,d.218.1.6 95277,95278 1i0dA 332 4.52e+01 1pscA c.1.9.3 61487 1jgmA 336 4.54e+01 1pscA c.1.9.3 62953 1zymA 258 4.55e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1e32A 458 4.56e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1eza 259 4.57e+01 1zymA a.60.10.1,c.8.1.2 18113,30708 1cmlA 389 4.57e+01 1bi5A c.95.1.2,c.95.1.2 35989,35990 1g3fA 117 4.66e+01 1g3fA g.52.1.1 45378 1f9xA 120 4.70e+01 1g3fA g.52.1.1 59748 1pscA 365 4.72e+01 1pscA c.1.9.3 29058 1i88A 389 4.76e+01 c.95.1.2,c.95.1.2 66070,66071 1g73C 121 4.81e+01 1g3fA g.52.1.1 45375 1i3kA 348 4.83e+01 1xel c.2.1.2 61595 1i89A 389 4.90e+01 c.95.1.2,c.95.1.2 66074,66075 1n19A 154 4.94e+01 b.1.8.1 79795 1km6A 247 5.04e+01 c.1.2.3 72742 1sosA 154 5.07e+01 1mfmA b.1.8.1 22249 1hv8A 367 5.17e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1chwA 389 5.19e+01 1bi5A c.95.1.2,c.95.1.2 35997,35998 1clkA 387 5.24e+01 4xis c.1.15.3 29438 1urhA 280 5.25e+01 c.46.1.2,c.46.1.2 99829,99830 1dfvA 177 5.31e+01 1nglA b.60.1.1 27144 1yc5A 246 5.33e+01 1nglA 179 5.37e+01 1nglA b.60.1.1 27146 1pmy 123 5.39e+01 1bqk b.6.1.1 22888 1ek6A 348 5.49e+01 1xel c.2.1.2 29800 1n18A 154 5.51e+01 b.1.8.1 79785 1hzjA 348 5.53e+01 1xel c.2.1.2 61450 1dwqA 262 5.53e+01 1qj4A c.69.1.20 34808 1jwxA 389 5.56e+01 c.95.1.2,c.95.1.2 71920,71921 1sjpA 504 5.58e+01 1l3nA 153 5.61e+01 b.1.8.1 73549 1xs3A 80 5.62e+01 1azvA 153 5.62e+01 1mfmA b.1.8.1 22247 1i1nA 226 5.73e+01 c.66.1.7 71102 1i8bA 389 5.74e+01 c.95.1.2,c.95.1.2 66078,66079 1hgxA 183 5.77e+01 1tc1A c.61.1.1 34027 1e9pB 151 5.85e+01 1mfmA b.1.8.1 22216 2almA 431 5.91e+01 1xbtA 193 6.00e+01 1tx4A 198 6.02e+01 1tx4A a.116.1.1 19098 1vqvA 306 6.04e+01 1tdhA 364 6.04e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1pnuC 197 6.07e+01 i.1.1.1 88200 1vorF 198 6.09e+01 1dwoA 262 6.12e+01 1qj4A c.69.1.20 34804 1h6fA 193 6.15e+01 b.2.5.4 70901 2ftsA 419 6.16e+01 1t3eA 421 6.17e+01 b.85.6.1,b.103.1.1,c.57.1.2 106348,106349,106350 1uxmA 153 6.17e+01 b.1.8.1 100157 1p1vA 153 6.21e+01 b.1.8.1 93900 1hl4A 154 6.22e+01 b.1.8.1 83587 1q47A 495 6.22e+01 b.69.12.1 104532 1sxeA 97 6.23e+01 a.60.1.1 106080 1ynpA 317 6.34e+01 1tj7A 457 6.35e+01 1jzdA 220 6.37e+01 c.47.1.9,d.17.3.1 84257,84258 1w4rA 195 6.43e+01 1funA 153 6.44e+01 1mfmA b.1.8.1 22259 1uxlA 153 6.45e+01 b.1.8.1 100147 1efpA 307 6.46e+01 1efvA c.26.2.3,c.31.1.2 31635,31729 1eb8A 262 6.47e+01 c.69.1.20 64896 1rtg 210 6.47e+01 1gen b.66.1.1 27537 1nwyC 204 6.55e+01 i.1.1.2 86347 1nkwC 205 6.58e+01 i.1.1.2 80588 1q77A 138 6.59e+01 c.26.2.4 96023 1t2bA 397 6.59e+01 1jzoA 216 6.61e+01 c.47.1.9,d.17.3.1 84267,84268 1gen 218 6.64e+01 1gen b.66.1.1 27536 2c9vA 153 6.66e+01 1u0vA 393 6.68e+01 1ozuA 153 6.73e+01 b.1.8.1 87630 1zcoA 262 6.83e+01 3sodB 152 6.83e+01 1ox0A 430 6.87e+01 c.95.1.1,c.95.1.1 87495,87496 1q0eA 152 6.88e+01 b.1.8.1 95504 1msk 331 6.90e+01 1msk d.173.1.1 42495 1wi3A 71 6.90e+01 1cbjA 151 6.91e+01 1mfmA b.1.8.1 22213 1t6mA 299 6.91e+01 1we5A 772 6.97e+01 1j3nA 408 6.97e+01 c.95.1.1,c.95.1.1 84074,84075 2f2hA 773 6.97e+01 1xsjA 778 6.99e+01 1eejA 216 7.05e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1dt9A 437 7.09e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1ypwA 806 7.17e+01 2absA 383 7.19e+01 1r7rA 816 7.27e+01 b.52.2.3,c.37.1.20,c.37.1.20,d.31.1.1 97203,97204,97205,97206 1s05A 129 7.31e+01 a.24.3.2 98254 1u4nA 310 7.31e+01 1w5eA 364 7.32e+01 1w5bA 364 7.33e+01 2fnaA 357 7.34e+01 1smqA 399 7.38e+01 a.25.1.2 105766 1fsz 372 7.40e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1ve2A 235 7.45e+01 1jk0A 419 7.45e+01 a.25.1.2 63142 1nz8A 119 7.51e+01 d.58.42.1 92363 1qzpA 68 7.52e+01 a.14.1.1 96654 1e9oB 152 7.79e+01 1mfmA b.1.8.1 22228 1qzfA 521 7.79e+01 c.71.1.1,d.117.1.1 96633,96634 1zv6A 68 7.79e+01 1e9oA 152 7.81e+01 1mfmA b.1.8.1 22227 1e9qB 151 7.81e+01 1mfmA b.1.8.1 22218 2d2jA 329 7.83e+01 1e9qA 151 7.83e+01 1mfmA b.1.8.1 22217 1klyA 247 7.88e+01 c.1.2.3 72730 1qmrA 159 7.88e+01 1bv1 d.129.3.1 41314 1uc2A 481 7.88e+01 d.261.1.1 99161 1km5A 247 7.89e+01 c.1.2.3 72741 1xq6A 253 7.93e+01 2b8nA 429 7.94e+01 1mo2A 294 7.96e+01 c.69.1.22 79331 1cb4A 151 7.99e+01 1mfmA b.1.8.1 22236 1kezA 300 7.99e+01 c.69.1.22 68546 2avnA 260 8.02e+01 1k2yX 463 8.07e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1lepA 99 8.13e+01 1lepA b.35.1.1 24649 1evqA 310 8.14e+01 1jkmA c.69.1.2 34635 1sg6A 393 8.16e+01 e.22.1.1 105522 2fkfA 462 8.23e+01 1p5dX 463 8.23e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1i10A 331 8.26e+01 3ldh c.2.1.5,d.162.1.1 61499,61500 1qt1A 387 8.37e+01 4xis c.1.15.3 29436 1wcgA 464 8.46e+01 1dv2A 452 8.53e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1c02A 166 8.57e+01 1qspA a.24.10.2 16633 1wy2A 351 8.58e+01 2fkmX 462 8.61e+01 1oxy 628 8.65e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18486,18497,21862 2bkcA 156 8.73e+01 1ukxA 137 8.74e+01 d.20.1.3 107919 1x89A 178 8.76e+01 1ll1 628 8.77e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1bw0A 416 8.78e+01 1bw0A c.67.1.1 34385 2atvA 196 8.78e+01 1lla 628 8.81e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1p2fA 220 8.85e+01 a.4.6.1,c.23.1.1 87720,87721 1idn1 190 8.85e+01 1ido 1zosA 230 8.86e+01 1l6mA 180 8.87e+01 b.60.1.1 84531 1n9zA 192 8.94e+01 c.62.1.1 85478 1dv1A 449 8.99e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1an7A 136 9.00e+01 1seiA d.140.1.1 41465 1e6jP 210 9.00e+01 1ak4C a.28.3.1,a.73.1.1 16956,18323