# List of top-scoring protein chains for t2k-100-30-bys-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 1wolA 122 4.26e-20 1ufbA 127 1.27e-15 a.24.16.3 99331 1o3uA 135 3.50e-13 a.24.16.3 86615 1wwpA 119 1.81e-01 1h1wA 289 2.59e-01 d.144.1.7 83460 1uu3A 310 3.67e-01 d.144.1.7 99999 1knzA 164 4.71e-01 e.34.1.1 68709 3grx 82 5.51e-01 1aba c.47.1.1 32769 1k47A 337 7.36e-01 d.14.1.5,d.58.26.4 72040,72041 2ag5A 246 7.84e-01 1a17 166 7.89e-01 1a17 a.118.8.1 19206 1na3A 91 7.96e-01 k.38.1.1 85481 1xrhA 351 8.96e-01 1wkbA 810 1.04e+00 2frvB 536 1.12e+00 1h2rL e.18.1.1 43291 1v3wA 173 1.34e+00 b.81.1.5 100291 1ugpB 226 1.68e+00 b.34.4.4 107832 1ireB 228 1.75e+00 b.34.4.4 76770 2cfuA 658 1.96e+00 2avpA 70 2.36e+00 1e2aA 105 2.80e+00 1e2aA a.7.2.1 16322 2evrA 246 3.11e+00 2e2aA 105 3.18e+00 a.7.2.1 88499 1ca1 370 3.32e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 1ji6A 589 3.38e+00 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1ouvA 273 3.48e+00 a.118.18.1 93570 1khoA 370 4.57e+00 a.124.1.1,b.12.1.3 72489,72490 2crbA 97 4.68e+00 1atg 231 4.82e+00 1atg c.94.1.1 35834 1p4xA 250 4.92e+00 a.4.5.28,a.4.5.28 87784,87785 1elwA 118 4.94e+00 1a17 a.118.8.1 19207 1eg7A 557 5.18e+00 1eg7A c.37.1.10 32241 1mvoA 136 5.45e+00 c.23.1.1 79513 16vpA 366 5.61e+00 16vpA d.180.1.1 42601 1u5dA 108 5.63e+00 1u60A 310 6.16e+00 e.3.1.2 107692 1b8aA 438 6.40e+00 1b8aA b.40.4.1,d.104.1.1 25244,40765 1x6vA 630 6.57e+00 1kbqA 273 6.80e+00 c.23.5.3 68391 1qbgA 272 6.92e+00 1d4aA c.23.5.3 31227 2a61A 145 6.99e+00 1d4aA 273 7.03e+00 1d4aA c.23.5.3 31219 1hu4A 288 7.35e+00 1hu4A 1wtyA 119 7.70e+00 1n5dA 288 7.91e+00 c.2.1.2 80030 1usmA 80 8.38e+00 d.74.1.1 99876 1siqA 392 8.75e+00 a.29.3.1,e.6.1.1 105585,105586 2g0qA 173 8.92e+00 1x9mA 698 9.05e+00 1l7bA 92 9.95e+00 c.15.1.2 91053 1dlc 584 1.01e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1q52A 314 1.05e+01 c.14.1.3 95846 1s5lE 84 1.06e+01 1frvB 536 1.10e+01 1h2rL e.18.1.1 43296 1oh0A 131 1.12e+01 d.17.4.3 87004 1t7pA 698 1.16e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1zq4A 693 1.18e+01 2anxA 146 1.19e+01 1hhsA 664 1.19e+01 1hi0P e.8.1.6 61045 1h2bA 359 1.21e+01 b.35.1.2,c.2.1.1 90543,90544 1vqoD 177 1.22e+01 1y21A 282 1.29e+01 1kr7A 110 1.29e+01 a.1.1.4 72890 1uvjA 664 1.29e+01 e.8.1.6 100045 1p2xA 159 1.30e+01 a.40.1.1 104062 1ntfA 282 1.32e+01 d.151.1.2 92104 1swxA 209 1.33e+01 a.224.1.1 106075 1mmoB 384 1.36e+01 1mtyB a.25.1.2 16768 1yn9A 169 1.44e+01 1f1eA 154 1.47e+01 a.22.1.2 64927 1hi0P 664 1.47e+01 1hi0P e.8.1.6 61051 1lox 662 1.47e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1e7uA 961 1.47e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1dmmA 131 1.47e+01 1opy d.17.4.3 38114 1mtyB 384 1.54e+01 1mtyB a.25.1.2 16740 2chgA 226 1.58e+01 1si6X 282 1.61e+01 1gs5A 258 1.62e+01 c.73.1.2 70395 1jf0A 195 1.65e+01 1ej3A a.39.1.5 62926 1opy 131 1.70e+01 1opy d.17.4.3 38113 1dd5A 185 1.72e+01 1dd5A d.67.3.1 39564 1uwkA 557 1.75e+01 e.51.1.1 108065 1sauA 115 1.77e+01 1wcrA 103 1.78e+01 1a2xA 159 1.81e+01 1ncx a.39.1.5 17251 1s6cA 183 1.83e+01 a.39.1.5 98594 1f16A 192 1.87e+01 1f16A f.1.4.1 43400 1j30A 144 1.87e+01 a.25.1.1 90806 1kamA 194 1.92e+01 c.26.1.3 72254 1srrA 124 1.93e+01 1dz3A c.23.1.1 31110 1e8xA 961 2.00e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1rkbA 173 2.06e+01 1ea2A 131 2.08e+01 d.17.4.3 64860 1wt4A 73 2.09e+01 1x92A 199 2.14e+01 1wbeA 209 2.24e+01 1wd6A 123 2.25e+01 2ab0A 205 2.32e+01 1ap6A 198 2.33e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1qwiA 143 2.37e+01 d.227.1.1 96474 2g03A 194 2.41e+01 1e9rA 437 2.43e+01 c.37.1.11 64827 1xg2B 153 2.45e+01 1fz1C 389 2.48e+01 1mtyB a.25.1.2 16746 1ht6A 405 2.51e+01 b.71.1.1,c.1.8.1 83629,83630 1azo 232 2.51e+01 1azo c.52.1.14 33329 1vzjA 40 2.52e+01 1lo7A 141 2.54e+01 d.38.1.1 74144 1jchA 551 2.54e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1jchC 551 2.55e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1eexA 554 2.56e+01 1dioA c.1.19.3 29650 1eriA 276 2.57e+01 1ckqA c.52.1.1 33231 2genA 197 2.62e+01 1xdfA 157 2.64e+01 1ckqA 276 2.66e+01 1ckqA c.52.1.1 33229 1abmA 198 2.67e+01 1avmA 1bvqA 141 2.69e+01 1bvqA d.38.1.1 38542 1aua 296 2.75e+01 1aua a.5.3.1,c.13.1.1 16290,30882 2bcgG 453 2.79e+01 1oshA 232 2.82e+01 a.123.1.1 93496 1tfjA 219 2.82e+01 1np8A 159 2.85e+01 a.39.1.8 92022 1qpsA 261 2.89e+01 1ckqA c.52.1.1 33234 1cl8A 276 2.89e+01 1ckqA c.52.1.1 33230 1dioA 554 2.91e+01 1dioA c.1.19.3 29656 1c1gD 284 2.92e+01 1c1gA h.1.5.1 45576 1d7mA 101 2.99e+01 1d7mA h.1.10.1 45628 1sl8A 191 3.00e+01 1pl4A 198 3.05e+01 a.2.11.1,d.44.1.1 94854,94855 1lxjA 104 3.05e+01 d.58.48.1 84736 1jcdA 52 3.08e+01 h.1.16.1 84157 2thiA 379 3.10e+01 2thiA c.94.1.1 35794 1am9A 82 3.11e+01 1am9A a.38.1.1 17140 2ghpA 292 3.13e+01 1ww8A 439 3.22e+01 1ge9A 184 3.26e+01 1dd5A d.67.3.1 60463 1yrnA 61 3.26e+01 1akhA a.4.1.1 15981 1i60A 278 3.31e+01 c.1.15.4 71118 1tkjA 284 3.33e+01 1sflA 238 3.39e+01 1x6mA 196 3.43e+01 1tf9A 284 3.47e+01 1qq9A 284 3.47e+01 1xjo c.56.5.4 33841 1t98A 287 3.52e+01 1xq8A 140 3.52e+01 1cjcA 460 3.56e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1mngA 203 3.57e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1ywfA 296 3.57e+01 1o04A 500 3.60e+01 c.82.1.1 86508 1brwA 433 3.65e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1zesA 125 3.65e+01 1kcxA 518 3.69e+01 b.92.1.3,c.1.9.6 90953,90954 1ydwA 362 3.69e+01 1w3iA 293 3.70e+01 c.1.10.1 109152 2b5eA 504 3.71e+01 2fq4A 192 3.76e+01 1zybA 232 3.78e+01 2djkA 133 3.79e+01 1c1gB 284 3.81e+01 1c1gB h.1.5.1 45574 1mo0A 275 3.83e+01 c.1.1.1 79329 1e8yA 966 3.84e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1woyA 500 3.85e+01 1qhdA 398 3.87e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1ycdA 243 3.94e+01 1nlwB 76 3.96e+01 a.38.1.1 80634 1xjo 284 3.98e+01 1xjo c.56.5.4 33843 1yozA 116 4.00e+01 2b0tA 738 4.01e+01 1n0nA 199 4.05e+01 a.2.11.1,d.44.1.1 79750,79751 1ukvG 453 4.07e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1o63A 219 4.08e+01 c.94.1.1 92540 1bxkA 355 4.10e+01 1bxkA c.2.1.2 29803 1pmzA 86 4.17e+01 a.39.1.10 104195 1sfjA 238 4.22e+01 1c1gC 284 4.26e+01 1c1gA h.1.5.1 45575 1qo0D 196 4.27e+01 1qo0D c.23.1.3 31125 1wmaA 276 4.40e+01 1c1gA 284 4.47e+01 1c1gA h.1.5.1 45573 1o1xA 155 4.48e+01 c.121.1.1 86553 1mnaA 298 4.48e+01 c.69.1.22 79322 1p5sA 203 4.49e+01 a.40.1.1 94147 1obs 267 4.52e+01 1mrj d.165.1.1 42213 2as0A 396 4.53e+01 2axtE 84 4.59e+01 1hfoA 113 4.64e+01 d.80.1.3 61006 1tph1 247 4.64e+01 1amk 1g6nA 210 4.65e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1om2A 95 4.75e+01 1om2A a.23.4.1 16520 1tzvA 142 4.76e+01 a.79.1.1 107526 1ewqA 765 4.76e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1m12A 84 4.80e+01 a.64.1.1 84745 2bjdA 101 4.81e+01 1jj2D 176 4.84e+01 1ffkD d.77.1.1 63088 1be3F 110 4.91e+01 1be3F f.27.1.1 43668 1ze3D 125 4.94e+01 1ppjF 110 4.95e+01 f.27.1.1 104262 1kk9A 221 4.99e+01 d.115.1.1 77432 1n97A 389 5.01e+01 a.104.1.1 80335 1a8h 500 5.04e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 163l 164 5.09e+01 1l92 d.2.1.3 36658 1b5l 172 5.13e+01 1b5l a.26.1.3 16900 1yc9A 442 5.14e+01 1rljA 139 5.17e+01 c.23.5.7 104983 1w5cE 84 5.19e+01 1avqA 228 5.21e+01 1avqA c.52.1.13 33326 2bf9A 36 5.21e+01 1rz4A 226 5.27e+01 a.4.5.53,a.118.1.18 105131,105132 1k7jA 206 5.28e+01 d.115.1.1 72103 1fxlA 167 5.34e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 2cgpA 210 5.39e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1t0qA 498 5.42e+01 a.25.1.2 106220 1wjgA 137 5.56e+01 1uquA 482 5.57e+01 c.87.1.6 99796 1uqtA 482 5.59e+01 c.87.1.6 99794 1ift 263 5.66e+01 1mrj d.165.1.1 42211 1kfnA 56 5.78e+01 h.1.16.1 72422 1qc9A 276 5.81e+01 1ckqA c.52.1.1 33235 1d3yA 301 5.81e+01 1d3yA e.12.1.1 43252 256bA 106 5.82e+01 256bA a.24.3.1 16539 1bccF 109 5.82e+01 1be3F f.27.1.1 43700 1jajA 174 5.86e+01 d.218.1.2 66471 1apc 106 5.93e+01 256bA a.24.3.1 16543 1sctB 151 5.93e+01 3sdhA a.1.1.2 15003 1jgjA 217 5.94e+01 1c3wA f.13.1.1 62952 1d7kA 421 5.99e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1izmA 184 6.01e+01 a.199.1.1 90725 1ej3A 191 6.05e+01 1ej3A a.39.1.5 17259 1uocA 289 6.06e+01 c.55.3.9 99686 2ayuA 417 6.06e+01 1zgmA 248 6.07e+01 1is1A 185 6.15e+01 d.67.3.1 83704 1kfuS 184 6.17e+01 a.39.1.8 68574 2f4lA 297 6.19e+01 1vbiA 344 6.19e+01 1b00A 127 6.23e+01 3chy c.23.1.1 31122 2f9fA 177 6.30e+01 2cyjA 118 6.38e+01 1akhA 61 6.41e+01 1akhA a.4.1.1 15980 1alvA 173 6.42e+01 1alvA a.39.1.8 17370 1o1zA 234 6.48e+01 c.1.18.3 86555 1ic8A 194 6.48e+01 a.4.1.1,a.35.1.1 76740,76741 1x79B 112 6.51e+01 1r2rA 248 6.54e+01 c.1.1.1 96875 1nhyA 219 6.54e+01 a.45.1.1,c.47.1.5 80520,80521 2gtrA 261 6.55e+01 1uhkA 191 6.57e+01 1tueB 218 6.58e+01 b.91.1.1 107324 1jagA 241 6.61e+01 c.37.1.1 66463 1n6zA 105 6.62e+01 d.263.1.1 85369 1cg5B 141 6.63e+01 1cg5B a.1.1.2 15585 1a8y 367 6.73e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1hw5A 210 6.82e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1fts 295 6.85e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 2g7gA 213 6.92e+01 1z8oA 404 7.03e+01 1jfaA 374 7.04e+01 a.128.1.5 66622 1wn0A 145 7.04e+01 1rxwA 336 7.18e+01 a.60.7.1,c.120.1.2 98059,98060 1qmqA 414 7.18e+01 1phd a.104.1.1 18907 1kiyA 374 7.18e+01 a.128.1.5 72555 1v7nV 163 7.19e+01 a.26.1.2 100476 1osa 148 7.32e+01 1cll a.39.1.5 17300 1owfA 99 7.32e+01 a.55.1.1 87487 1ihfA 99 7.33e+01 1huuA a.55.1.1 17893 1iujA 106 7.34e+01 d.58.4.5 90701 1aszB 490 7.37e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2fywA 267 7.41e+01 1j57A 143 7.48e+01 d.221.1.1 77079 2aelA 374 7.51e+01 1asyA 490 7.61e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1gw5S 142 7.64e+01 d.110.4.2 70633 1b8dA 164 7.66e+01 1cpcA a.1.1.3 15665 3thiA 371 7.68e+01 2thiA c.94.1.1 35792 1lis 136 7.69e+01 1lis a.19.1.1 16406 2lisA 136 7.69e+01 1lis a.19.1.1 16405 1ppt 36 7.87e+01 1ppt j.6.1.1 46089 2eshA 118 7.91e+01 1exrA 148 7.92e+01 1cll a.39.1.5 17299 2coiA 386 7.99e+01 1ag9A 175 7.99e+01 1rcf c.23.5.1 31178 1tw9A 206 8.00e+01 a.45.1.1,c.47.1.5 107381,107382 1mek 120 8.01e+01 1erv c.47.1.2 32775 1gzsB 165 8.02e+01 a.168.1.1 76425 1jf2A 195 8.10e+01 1ej3A a.39.1.5 62930 1z2iA 358 8.13e+01 1evsA 187 8.14e+01 1evsA a.26.1.1 16845 1rrmA 386 8.20e+01 e.22.1.2 105081 1wy1A 172 8.27e+01 3mddA 385 8.28e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 2fcwA 109 8.36e+01 1fioA 196 8.43e+01 1fioA a.47.2.1 17773 1ymtA 246 8.49e+01 1kyoC 385 8.52e+01 f.32.1.1,f.21.1.2 75904,75905 1peh 35 8.54e+01 1peh j.14.1.1 46151 1ltlA 279 8.56e+01 b.40.4.11 84701 1y8tA 324 8.60e+01 1fmeA 28 8.65e+01 k.12.1.1 59878 1w7lA 422 8.71e+01 c.67.1.1 109226 1a36A 592 8.79e+01 1a36A a.2.8.1,d.163.1.2,e.15.1.1 15715,42173,43266 1r0kA 388 8.81e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1gumA 222 8.82e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 1a3aC 148 8.86e+01 1a3aA d.112.1.1 40919 1ekeA 230 8.89e+01 1ekeA c.55.3.1 33572 1cw0A 155 8.91e+01 1vsrA c.52.1.15 33333 1qwvA 142 8.93e+01 a.39.2.1 96506 1ahr 146 8.98e+01 1cll a.39.1.5 17287 1i8oA 114 8.98e+01 1ycc a.3.1.1 61979 1ann 318 9.00e+01 1avc a.65.1.1 18151