# List of top-scoring protein chains for t2k-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 1ihp 438 2.45e-02 1ihp c.60.1.2 33993 6gsvA 217 7.27e-02 1b8xA a.45.1.1,c.47.1.5 17633,32925 1efcA 393 1.14e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1efuA 385 2.68e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 2c4jA 218 2.75e-01 1xw5A 217 2.75e-01 1tbmA 326 2.79e-01 a.211.1.2 106744 1eemA 241 3.32e-01 1eemA a.45.1.1,c.47.1.5 17717,33011 1b4pA 217 5.16e-01 a.45.1.1,c.47.1.5 83158,83159 1cr6B 554 5.16e-01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1qfxA 460 5.61e-01 1qfxA c.60.1.2 33994 1qwoA 442 6.89e-01 c.60.1.2 104620 1bd8 156 7.68e-01 1bd8 d.211.1.1 19157 1zd3A 555 8.03e-01 1zejA 293 8.50e-01 2myo 118 8.51e-01 2myo d.211.1.1 19175 1myo 118 9.69e-01 2myo d.211.1.1 19174 1axdA 209 1.06e+00 1gnwA a.45.1.1,c.47.1.5 17730,33024 1vj5A 555 1.13e+00 c.108.1.2,c.69.1.11 100799,100800 1sz2A 332 1.20e+00 2furA 209 1.21e+00 1q18A 332 1.33e+00 c.55.1.7,c.55.1.7 104470,104471 1zv1A 65 1.50e+00 1etu 394 1.71e+00 1efcA c.37.1.8 64737 2fiyA 309 1.77e+00 1trrA 107 1.92e+00 1jhgA a.4.12.1 19017 1x1fA 149 2.14e+00 2wrpR 107 2.30e+00 1jhgA a.4.12.1 19010 1ufaA 520 3.05e+00 a.8.3.3,c.6.2.4 99329,99330 1jhgA 101 3.19e+00 1jhgA a.4.12.1 19009 1im5A 180 3.36e+00 c.33.1.3 66211 1y3nA 490 3.67e+00 1w1oA 534 3.73e+00 d.58.32.4,d.145.1.1 109071,109072 1jpaA 312 3.77e+00 d.144.1.7 67011 1m98A 317 3.79e+00 a.175.1.1,d.17.4.6 78866,78867 1ohfA 644 4.03e+00 b.121.4.8 93014 1llmC 88 4.89e+00 g.37.1.1,g.37.1.1 91059,91060 1p4dA 330 5.27e+00 d.89.1.5 94101 2fu4A 83 5.35e+00 2b1eA 564 5.57e+00 1x6vA 630 6.01e+00 1ni3A 392 6.10e+00 c.37.1.8,d.15.10.2 80531,80532 1n45A 233 6.26e+00 a.132.1.1 79981 2occH 85 6.34e+00 2occH a.51.1.1 17796 1gumA 222 7.09e+00 1pgtA a.45.1.1,c.47.1.5 17683,32977 1o5hA 214 7.13e+00 a.191.1.1 92497 1fhuA 320 7.19e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1fsu 492 7.22e+00 1auk c.76.1.2 35032 2iu5A 195 7.99e+00 2afwA 329 8.08e+00 1xmeA 568 8.20e+00 1ycsB 239 8.32e+00 1ycsB d.211.1.1,b.34.2.1 19155,24553 1sszA 34 8.83e+00 j.35.1.1 105999 1qrjB 199 9.50e+00 1qrjB a.28.3.1 16952 1rh9A 373 9.52e+00 1nd7A 374 9.75e+00 d.148.1.1 91817 1rcsA 105 1.01e+01 1jhgA a.4.12.1 19025 1d5wC 126 1.02e+01 1dbwA c.23.1.1 31101 1z00B 84 1.02e+01 1hp5A 512 1.03e+01 1hp4A c.1.8.6,d.92.2.1 61113,61114 1rxqA 178 1.04e+01 a.213.1.1 105118 1zboA 210 1.04e+01 2ccmA 191 1.10e+01 1yw0A 276 1.13e+01 1ad3A 452 1.15e+01 1ad3A c.82.1.1 35335 2mev2 256 1.16e+01 1aym2 1hdiA 413 1.17e+01 16pk c.86.1.1 60964 1b8aA 438 1.17e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1gewA 356 1.20e+01 1gewA c.67.1.1 60470 1jb0I 38 1.21e+01 1jb0I f.23.17.1 62826 1ds1A 324 1.24e+01 1drtA b.82.2.2 28127 1dryA 324 1.26e+01 1drtA b.82.2.2 28128 2gsvA 80 1.28e+01 1hp4A 512 1.28e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1jakA 512 1.28e+01 c.1.8.6,d.92.2.1 66472,66473 1whrA 124 1.28e+01 2aclB 244 1.31e+01 1ppjF 110 1.31e+01 f.27.1.1 104262 1n1jA 93 1.36e+01 a.22.1.3 79813 1h3nA 878 1.44e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1e08A 371 1.49e+01 i.4.1.1 45914 1mzbA 136 1.52e+01 a.4.5.42 91497 2fqmA 75 1.62e+01 1yy7A 213 1.70e+01 1xioA 261 1.70e+01 1v54H 85 1.74e+01 a.51.1.1 100329 1f7uA 607 1.77e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1eia 207 1.77e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1fg7A 356 1.78e+01 1gewA c.67.1.1 59819 1dbwA 126 1.79e+01 1dbwA c.23.1.1 31095 1jhdA 396 1.81e+01 b.122.1.3,c.26.1.5 66712,66713 2aplA 157 1.95e+01 1yozA 116 1.99e+01 2aawA 222 2.02e+01 1kpsB 171 2.03e+01 a.118.12.1 68787 1pa7A 130 2.05e+01 a.40.1.1 94410 2lefA 86 2.06e+01 2lefA a.21.1.1 16433 1s6lA 212 2.07e+01 1dckA 126 2.10e+01 1dbwA c.23.1.1 31097 1v9jA 113 2.11e+01 d.52.6.1 100542 1x74A 360 2.14e+01 1x91A 153 2.15e+01 1tw9A 206 2.16e+01 a.45.1.1,c.47.1.5 107381,107382 3crxA 343 2.27e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1vi0A 206 2.27e+01 a.4.1.9,a.121.1.1 100720,100721 1drtA 324 2.33e+01 1drtA b.82.2.2 28130 1z2nX 324 2.35e+01 1b35A 260 2.35e+01 1b35A b.121.4.1 23333 1w07A 659 2.37e+01 1kbuA 349 2.38e+01 a.60.9.1,d.163.1.1 72284,72285 1ewfA 456 2.38e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 1bp1 456 2.39e+01 1bp1 d.83.1.1,d.83.1.1 40026,40027 1bgp 309 2.41e+01 1bgp a.93.1.1 18690 1i9gA 280 2.43e+01 c.66.1.13 62090 1r6uA 437 2.47e+01 c.26.1.1 97163 1hmy 327 2.49e+01 6mhtA c.66.1.26 34229 1hg2A 289 2.50e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1qd9A 124 2.52e+01 1qu9A d.79.1.1 39758 1jae 471 2.52e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1gulA 222 2.55e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1jk8B 190 2.57e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 1br1B 150 2.61e+01 1wdcC a.39.1.5 17309 1cn4C 166 2.69e+01 1eerA a.26.1.2 16847 1t5oA 351 2.70e+01 c.124.1.5 106459 1n0qA 93 2.70e+01 k.37.1.1 79754 2a2fX 325 2.72e+01 1jmtB 28 2.72e+01 2aheA 267 2.76e+01 4crxA 322 2.78e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1zrzA 364 2.79e+01 1repC 251 2.80e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1okcA 297 2.81e+01 f.42.1.1 93248 1h6zA 913 2.81e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2f96A 224 2.83e+01 1m65A 245 2.85e+01 c.6.3.1 84847 2g6tA 306 2.86e+01 1qq8A 214 2.92e+01 1qq8A 2db0A 253 2.94e+01 1ehkA 562 2.94e+01 1ehkA f.24.1.1 43624 1skf 262 3.05e+01 1skf e.3.1.1 42684 1hf8A 289 3.07e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1tkeA 224 3.10e+01 1es5A 262 3.16e+01 1skf e.3.1.1 42679 2c30A 321 3.16e+01 1esiA 262 3.19e+01 1skf e.3.1.1 42682 2es9A 115 3.21e+01 1fjxA 327 3.22e+01 6mhtA c.66.1.26 34228 1wm5A 208 3.22e+01 1qmzB 259 3.23e+01 1vin a.74.1.1,a.74.1.1 18338,18339 1hg5A 289 3.27e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1t7rA 269 3.29e+01 a.123.1.1 106635 1n1jB 97 3.36e+01 a.22.1.3 79814 1vqoI 162 3.36e+01 3mhtA 327 3.40e+01 6mhtA c.66.1.26 34234 1qcrF 103 3.41e+01 1be3F f.27.1.1 43676 1lghA 56 3.45e+01 1lghA f.3.1.1 43733 1mun 225 3.51e+01 1mun a.96.1.2 18744 1mgpA 313 3.57e+01 c.119.1.1 79098 1z6uA 150 3.57e+01 1tf5A 844 3.65e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1hz4A 373 3.67e+01 a.118.8.2 65960 1crxA 322 3.67e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1ozhA 566 3.68e+01 c.31.1.3,c.36.1.5,c.36.1.9 93833,93834,93835 1r6wA 322 3.71e+01 c.1.11.2,d.54.1.1 97165,97166 1g7oA 215 3.72e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1h2vC 771 3.73e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1noyA 388 3.76e+01 1clqA c.55.3.5 33713 2c7pA 327 3.85e+01 1ufzA 83 3.85e+01 a.5.9.1 107821 2esnA 310 3.86e+01 1fhvA 323 3.88e+01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1pd21 199 3.88e+01 1pd21 1dnpA 471 3.89e+01 1qnf a.99.1.1,c.28.1.1 18775,31630 1xikA 375 3.89e+01 1xikA a.25.1.2 16784 1zq9A 285 3.94e+01 1ugpA 203 3.99e+01 d.149.1.1 107831 1s72I 162 4.00e+01 a.4.7.1 105328 1wovA 250 4.01e+01 1pgtA 210 4.01e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1vin 268 4.11e+01 1vin a.74.1.1,a.74.1.1 18354,18355 1ireA 204 4.13e+01 d.149.1.1 76769 1hh8A 213 4.14e+01 1e96B a.118.8.1 61042 1xo0A 324 4.15e+01 1muyA 225 4.18e+01 1mun a.96.1.2 18745 2bbrA 195 4.19e+01 1otsA 465 4.19e+01 f.20.1.1 87415 1d6gA 47 4.22e+01 1d6gA g.33.1.1 44976 1myf 153 4.23e+01 1a6m a.1.1.2 15147 1b74A 254 4.27e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 2b1xA 470 4.27e+01 1b48A 221 4.28e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1q87A 221 4.32e+01 e.47.1.1 96192 2beiA 170 4.33e+01 1r4wA 226 4.34e+01 c.47.1.13 97050 1m3uA 264 4.38e+01 c.1.12.8 84784 1gqeA 365 4.40e+01 e.38.1.1 70351 1y88A 199 4.45e+01 1n3gA 113 4.53e+01 d.204.1.1 79962 1vzoA 355 4.59e+01 d.144.1.7 108971 1b73A 254 4.59e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1es2A 262 4.60e+01 1skf e.3.1.1 42680 2fgtA 417 4.61e+01 1sra 151 4.65e+01 1sra a.39.1.3 17190 1im8A 244 4.65e+01 c.66.1.14 66212 1fxtA 149 4.68e+01 d.20.1.1 65055 1aj5A 173 4.68e+01 1alvA a.39.1.8 17367 1ewqA 765 4.69e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1s7jA 262 4.69e+01 d.21.1.2 98647 1n3kA 130 4.73e+01 a.77.1.4 79965 2cchB 260 4.78e+01 6mhtA 327 4.78e+01 6mhtA c.66.1.26 34226 1qh4A 380 4.88e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 8ohm 435 4.92e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1sheA 103 4.95e+01 d.274.1.1 105551 2bo9A 308 4.99e+01 1ddzA 496 5.01e+01 1ddzA c.53.2.1,c.53.2.1 33372,33373 1ihbA 162 5.01e+01 1bd8 d.211.1.1 19161 1wmmA 145 5.03e+01 1lfpA 249 5.03e+01 e.39.1.1 73885 1i7dA 659 5.03e+01 1d6mA e.10.1.1 61886 1m6kA 251 5.07e+01 e.3.1.1 78695 1uohA 226 5.07e+01 d.211.1.1 99690 2afaA 425 5.08e+01 1be3F 110 5.09e+01 1be3F f.27.1.1 43668 1z6gA 218 5.11e+01 2g62A 325 5.11e+01 1vjrA 271 5.16e+01 c.108.1.14 100832 1nozA 388 5.17e+01 1clqA c.55.3.5 33715 1x31D 99 5.18e+01 1ordA 730 5.24e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1huvA 380 5.33e+01 c.1.4.1 61277 1nkl 78 5.34e+01 1nkl a.64.1.1 18140 2dfkA 402 5.35e+01 1t92A 116 5.35e+01 1biqA 375 5.38e+01 1xikA a.25.1.2 16786 1p4cA 380 5.43e+01 c.1.4.1 94100 1kfuS 184 5.43e+01 a.39.1.8 68574 1m6nA 802 5.43e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 78697,78698,78699,78700 1fzyA 149 5.55e+01 d.20.1.1 65072 1pq1A 196 5.56e+01 f.1.4.1 94986 1v9mA 323 5.58e+01 f.40.1.1 100543 1se7A 83 5.60e+01 1ylqA 96 5.62e+01 2a2rA 210 5.70e+01 1mp8A 281 5.71e+01 d.144.1.7 91384 1ap7 168 5.80e+01 1bd8 d.211.1.1 19170 2f1sA 186 5.89e+01 18gsA 210 5.94e+01 1pgtA a.45.1.1,c.47.1.5 17528,32822 1qs2A 401 6.00e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 2b33A 140 6.03e+01 1rzsA 61 6.06e+01 a.35.1.2 105139 1buyA 166 6.12e+01 1eerA a.26.1.2 16848 1kpkA 473 6.12e+01 f.20.1.1 68776 1ngnA 155 6.19e+01 a.96.1.2 85697 1j8mF 297 6.21e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1j8yF 297 6.22e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1k6iA 352 6.23e+01 c.2.1.2 68223 1qv1A 195 6.24e+01 a.39.1.5 96347 1r5zA 323 6.32e+01 f.40.1.1 97135 1iq0A 592 6.34e+01 a.27.1.1,c.26.1.1,d.67.2.1 66257,66258,66259 2fpmA 322 6.37e+01 2bykB 128 6.38e+01 1kplA 473 6.43e+01 f.20.1.1 68782 2atjA 308 6.46e+01 1bgp a.93.1.1 18675 1heiA 451 6.47e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1ynfA 458 6.52e+01 1bccF 109 6.59e+01 1be3F f.27.1.1 43700 1us5A 314 6.61e+01 c.94.1.1 99856 1z3eB 73 6.75e+01 1alvA 173 6.80e+01 1alvA a.39.1.8 17370 1wucA 250 6.81e+01 1m32A 366 6.91e+01 c.67.1.3 78508 1qo7A 394 6.91e+01 1qo7A c.69.1.11 34697 1a1iA 90 6.93e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1acp 77 6.94e+01 1acp a.28.1.1 16931 2b7aA 293 6.96e+01 1z63A 500 7.03e+01 2gdjA 264 7.03e+01 1qu9A 128 7.08e+01 1qu9A d.79.1.1 39755 1qu9C 128 7.08e+01 1qu9A d.79.1.1 39757 1dtdA 303 7.11e+01 1aye c.56.5.1 33823 2adoA 196 7.13e+01 1t8kA 77 7.16e+01 a.28.1.1 106666 1l0iA 78 7.17e+01 a.28.1.1 77643 1g2fC 90 7.31e+01 k.12.1.1 60222 1deuA 277 7.34e+01 1theB d.3.1.1 37085 1mg2D 155 7.42e+01 a.3.1.1 79062 2mtaC 147 7.43e+01 2mtaC a.3.1.1 15908 1sphA 88 7.57e+01 1ptf d.94.1.1 40544 1xjzA 233 7.58e+01 1kinA 366 7.62e+01 1a5y 330 7.66e+01 1pty c.45.1.2 32673 1s72N 187 7.67e+01 c.55.4.1 105333 2etxA 209 7.71e+01 1t1uA 639 7.73e+01 2c5rA 67 7.78e+01 1pgjA 478 7.84e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1v1rA 400 7.89e+01 c.36.1.11 108272 1tu7A 208 8.00e+01 2f4mB 61 8.06e+01 1vls 146 8.09e+01 1vls a.24.2.1 16532 2spo 154 8.16e+01 1a6m a.1.1.2 15053 1mym 154 8.20e+01 1a6m a.1.1.2 15054 1x23A 155 8.23e+01 1fx8A 281 8.30e+01 f.19.1.1 43651 1n1fA 159 8.32e+01 a.26.1.3 79803 1gdeA 389 8.41e+01 c.67.1.1 60456 1e6iA 121 8.46e+01 1b91A a.29.2.1 16969 1mlo 154 8.50e+01 1a6m a.1.1.2 15085 2grrB 170 8.53e+01 1zvzA 279 8.56e+01 1s5lX 50 8.58e+01 1fehA 574 8.59e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1scfA 273 8.62e+01 1exzA a.26.1.2 16873 1b06A 210 8.63e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1h9eA 56 8.64e+01 1h9eA a.140.1.1 60825 7atjA 308 8.66e+01 1bgp a.93.1.1 18673 1xfsA 178 8.66e+01 d.129.3.5 109589 1ituA 369 8.71e+01 c.1.9.7 71423 1aisB 200 8.72e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 2ch0A 133 8.82e+01 1es4A 262 8.83e+01 1skf e.3.1.1 42683 1tqyB 415 8.86e+01 c.95.1.1,c.95.1.1 107247,107248 1b4jL 214 8.95e+01 8fabA b.1.1.1,b.1.1.2 20308,21300