# 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 1vybA 238 1.87e+00 d.151.1.1 108897 1pjcA 361 1.89e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1pk9A 237 2.00e+00 c.56.2.1 94823 2fg9A 178 2.02e+00 1cqa 133 2.14e+00 3nul d.110.1.1 40890 1pjbA 361 2.16e+00 1sayA c.2.1.4,c.23.12.2 30103,31363 1sayA 361 2.39e+00 1sayA c.2.1.4,c.23.12.2 30102,31362 1okjA 251 2.50e+00 c.55.1.9,c.55.1.9 103998,103999 1k9sA 237 2.86e+00 c.56.2.1 68359 1i1dA 161 3.23e+00 1i21A d.108.1.1 61526 1vhmA 195 3.48e+00 d.110.2.1 100691 1jysA 242 3.52e+00 c.56.2.1 77216 1ecpA 238 3.76e+00 1ecpA c.56.2.1 33775 1i21A 159 3.95e+00 1i21A d.108.1.1 61549 1i12A 160 4.15e+00 1i21A d.108.1.1 61515 2d4pA 141 4.17e+00 1z5nA 242 4.22e+00 1kyhA 276 4.26e+00 c.72.1.4 73222 1y5eA 169 5.05e+00 1a0k 131 5.33e+00 3nul d.110.1.1 40892 1z5oA 242 5.73e+00 1gw5S 142 6.00e+00 d.110.4.2 70633 1vc1A 110 6.06e+00 c.13.2.1 108493 1wyzA 242 6.14e+00 1a8s 273 6.21e+00 1brt c.69.1.12 34710 1vk1A 242 6.41e+00 d.268.1.2 108634 1qysA 106 6.58e+00 k.41.1.1 96603 1v37A 177 6.69e+00 2cxcA 144 7.47e+00 3nul 130 7.60e+00 3nul d.110.1.1 40891 1pkp 150 8.53e+00 1pkp d.14.1.1,d.50.1.2 37551,38787 1i5gA 144 1.24e+01 1ewxA c.47.1.10 61784 1ub3A 220 1.41e+01 c.1.10.1 88395 1vhwA 253 1.48e+01 c.56.2.1 100706 1je0A 236 1.48e+01 c.56.2.1 66581 1wy1A 172 1.49e+01 1lnqA 336 1.50e+01 c.2.1.9,f.14.1.1 74049,74050 2aefA 234 1.53e+01 1ezm 301 1.56e+01 1hyt d.92.1.2 58980 1c4oA 664 1.57e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1o89A 345 1.60e+01 b.35.1.2,c.2.1.1 92644,92645 2avnA 260 1.61e+01 1nv8A 284 1.66e+01 c.66.1.30 86224 1e79G 272 1.68e+01 1e79G c.49.2.1 33158 1keiA 316 1.84e+01 d.92.1.2 77349 1tfr 305 1.88e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1v9sA 208 1.90e+01 1v74B 87 2.08e+01 a.24.20.1 100443 2plc 274 2.10e+01 2plc c.1.18.2 29614 1o6jA 150 2.12e+01 c.47.1.10 81089 1n6zA 105 2.22e+01 d.263.1.1 85369 2bl1A 172 2.29e+01 1id1A 153 2.35e+01 1id1A c.2.1.9 62286 1uae 419 2.39e+01 1uae d.68.2.2 39574 1hyt 316 2.40e+01 1hyt d.92.1.2 59005 1ve3A 227 2.42e+01 1pz7A 204 2.43e+01 b.29.1.4 95405 1raxA 115 2.43e+01 1lfdA d.15.1.5 37626 1aod 289 2.49e+01 2plc c.1.18.2 29615 1vk8A 106 2.51e+01 d.58.48.1 108636 1tfuA 157 2.55e+01 c.26.1.3 106859 1tiqA 180 2.58e+01 d.108.1.1 107010 2bh1X 96 2.60e+01 1e5dA 402 2.65e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1q7zA 566 2.67e+01 c.1.21.2,c.1.26.1 96090,96091 1m6yA 301 2.68e+01 a.60.13.1,c.66.1.23 78716,78717 2g0qA 173 2.71e+01 1kdj 102 2.73e+01 1plc b.6.1.1 22864 1lx7A 253 2.73e+01 c.56.2.1 74329 2es7A 142 2.74e+01 8tlnE 316 2.84e+01 1hyt d.92.1.2 59075 1vr5A 547 2.87e+01 2nsyA 271 2.91e+01 2nsyA c.26.2.1 31612 1dbwA 126 2.93e+01 1dbwA c.23.1.1 31095 1ec7A 446 2.97e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1vjeA 166 3.02e+01 d.185.1.2 100807 2dg5A 366 3.03e+01 1bqg 451 3.06e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1lssA 140 3.06e+01 c.2.1.9 74246 1u4gA 301 3.06e+01 d.92.1.2 107670 1rxyA 253 3.07e+01 c.56.2.1 98065 1ws6A 171 3.10e+01 1innA 166 3.17e+01 1j98A d.185.1.2 62608 1kzhA 555 3.18e+01 c.89.1.1 73361 1khyA 148 3.23e+01 a.174.1.1 77410 1jj7A 260 3.26e+01 c.37.1.12 63114 1hnuA 280 3.44e+01 1hnoA c.14.1.3 61096 1yvoA 172 3.48e+01 1chrA 370 3.49e+01 1mucA c.1.11.2,d.54.1.1 29252,38896 1t0qA 498 3.55e+01 a.25.1.2 106220 2tmnE 316 3.65e+01 1hyt d.92.1.2 59055 1h75A 81 3.70e+01 1h75A c.47.1.1 60716 1t94A 459 3.75e+01 d.240.1.1,e.8.1.7 106701,106702 1k3fA 253 3.80e+01 c.56.2.1 68105 1zotA 358 3.83e+01 1fm0D 81 3.86e+01 1fmaD d.15.3.1 37642 1eayC 74 3.86e+01 1eayC d.58.24.1 39386 1yruA 364 3.96e+01 2cdnA 201 4.00e+01 1bxkA 355 4.04e+01 1bxkA c.2.1.2 29803 1ygmA 118 4.07e+01 1iieA 75 4.07e+01 1iieA a.109.1.1 19039 1ew4A 106 4.11e+01 1ew4A d.82.2.1 40023 1yrtA 364 4.15e+01 1gp6A 356 4.22e+01 b.82.2.1 65441 1a9nA 176 4.23e+01 1a9nA c.10.2.4 30875 2f5xA 312 4.29e+01 1jdfA 447 4.30e+01 c.1.11.2,d.54.1.1 62897,62898 1m2xA 223 4.35e+01 d.157.1.1 84764 1iz1A 294 4.36e+01 a.4.5.37,c.94.1.1 83823,83824 1a41 234 4.41e+01 1a41 d.163.1.2 42174 1gp4A 356 4.41e+01 b.82.2.1 65439 2rgf 97 4.43e+01 1lfdA d.15.1.5 37627 1s72E 178 4.47e+01 d.141.1.1,d.141.1.1 105323,105324 1jj2E 177 4.49e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1wapA 75 4.54e+01 1wapA b.82.5.1 28153 1kqpA 271 4.58e+01 c.26.2.1 72883 1vr6A 350 4.59e+01 1va4A 279 4.60e+01 c.69.1.12 108458 1usgA 346 4.65e+01 c.93.1.1 99864 1us5A 314 4.65e+01 c.94.1.1 99856 1a0p 290 4.67e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 6tmnE 316 4.73e+01 1hyt d.92.1.2 59071 2az2A 73 4.75e+01 1wozA 177 4.76e+01 1x24A 180 4.79e+01 1sviA 195 4.85e+01 c.37.1.8 106048 1kpgA 287 4.85e+01 c.66.1.18 68735 2ffcA 353 4.99e+01 2ck3D 482 5.06e+01 1othA 321 5.08e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1s6yA 450 5.08e+01 c.2.1.5,d.162.1.2 105314,105315 1iab 200 5.09e+01 1iae d.92.1.8 40312 1hnoA 280 5.11e+01 1hnoA c.14.1.3 61095 1j24A 143 5.14e+01 c.52.1.20 84008 1i4yA 114 5.15e+01 2mhr a.24.4.1 61738 1k8kA 418 5.18e+01 c.55.1.1,c.55.1.1 68305,68306 1uirA 314 5.21e+01 c.66.1.17 99429 1ne2A 200 5.27e+01 c.66.1.32 85586 2liv 344 5.30e+01 2liv c.93.1.1 35708 1ockA 412 5.31e+01 c.117.1.1 86802 1i7qB 193 5.31e+01 1qdlB c.23.16.1 61902 1llp 343 5.34e+01 1arv a.93.1.1 18578 2lbp 346 5.42e+01 2liv c.93.1.1 35709 1tidB 119 5.43e+01 c.13.2.1 107000 1ryiA 382 5.44e+01 1nsyA 271 5.53e+01 2nsyA c.26.2.1 31614 1vp8A 201 5.57e+01 1m9nA 613 5.58e+01 c.24.1.3,c.97.2.1 78870,78871 1tt7A 330 5.59e+01 1uaaA 673 5.63e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1e79D 482 5.63e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 1zejA 293 5.70e+01 2bfwA 200 5.72e+01 2bhuA 602 5.74e+01 2a2nA 176 5.76e+01 1ih8A 271 5.87e+01 2nsyA c.26.2.1 62377 1lxdA 100 5.87e+01 1lfdA d.15.1.5 37624 1qlmA 316 5.87e+01 1qlmA d.147.1.1 41765 2ax3A 502 5.89e+01 2bsyA 278 5.90e+01 1yvkA 163 6.01e+01 1g8mA 593 6.06e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1vbkA 307 6.14e+01 1sqiA 393 6.17e+01 d.32.1.3,d.32.1.3 105914,105915 1sc3B 88 6.18e+01 1kp9B 287 6.20e+01 c.66.1.18 68734 1bu8A 452 6.25e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1dckA 126 6.25e+01 1dbwA c.23.1.1 31097 1vg0A 650 6.26e+01 c.3.1.3,d.16.1.6 108596,108597 2dddA 225 6.28e+01 1b4bA 71 6.39e+01 1b4aA d.74.2.1 39718 1914 232 6.40e+01 1914 d.49.1.1,d.49.1.1 83028,83029 1f7wA 144 6.47e+01 1f46A d.129.4.1 59679 1m1cA 680 6.49e+01 e.42.1.1 78395 1yw5A 177 6.51e+01 1cn2 67 6.51e+01 1aho g.3.7.1 44129 1tcoA 375 6.53e+01 1auiA d.159.1.3 42084 2g39A 497 6.54e+01 1ki9A 192 6.54e+01 c.37.1.1 84404 2f6eA 127 6.54e+01 1iibA 106 6.56e+01 1iibA c.44.2.1 32648 1ejdA 419 6.63e+01 1uae d.68.2.2 39576 1emvA 86 6.63e+01 1cei a.28.2.1 16944 1wstA 417 6.65e+01 1idsA 207 6.72e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1sbp 310 6.77e+01 1sbp c.94.1.1 35760 1qlpA 394 6.78e+01 1ovaA e.1.1.1 42628 1yzhA 214 6.79e+01 1j8mF 297 6.82e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1jfvA 131 6.83e+01 c.44.1.1 66654 1r77A 103 6.84e+01 1sjiA 350 6.91e+01 1vqoE 178 6.95e+01 2d1yA 256 6.95e+01 1ru8A 232 6.97e+01 c.26.2.1 97849 1ve5A 311 6.97e+01 1wzuA 300 7.06e+01 1z4rA 168 7.06e+01 1xt8A 292 7.09e+01 2f1wA 158 7.11e+01 1zu1A 127 7.12e+01 2fl4A 149 7.16e+01 1pydA 556 7.19e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1iy8A 267 7.21e+01 c.2.1.2 83774 1xo7A 166 7.25e+01 830cA 168 7.26e+01 1ck7A d.92.1.11 40400 1pvdA 537 7.29e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31737,31777,31778 1qg9A 21 7.29e+01 j.35.1.1 46275 2cx6A 90 7.32e+01 1xkqA 280 7.33e+01 1rzuA 485 7.33e+01 c.87.1.8 105140 1v98A 140 7.38e+01 1p9rA 418 7.41e+01 c.37.1.11 94399 2az0A 73 7.45e+01 2bkaA 242 7.45e+01 2fbwD 103 7.46e+01 1uuyA 167 7.46e+01 c.57.1.1 108059 1z4eA 153 7.50e+01 2h88D 103 7.54e+01 2bmfA 451 7.56e+01 1ef8A 261 7.57e+01 1ef8A c.14.1.3 30921 1r5jA 337 7.62e+01 c.77.1.5 97097 1ypfA 336 7.62e+01 1pvgA 418 7.66e+01 d.14.1.3,d.122.1.2 95161,95162 2fvx 138 7.67e+01 5nul c.23.5.1 31200 1xmiA 291 7.72e+01 1ast 200 7.73e+01 1iae d.92.1.8 40310 1aszB 490 7.76e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1an9A 340 7.78e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1skyE 473 7.80e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1hsbB 99 7.85e+01 1agdB b.1.1.2 20737 1j8yF 297 7.87e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1kqzA 273 7.92e+01 c.1.8.5 68844 1hxhA 253 7.92e+01 c.2.1.2 76725 1m1hA 248 7.94e+01 b.114.1.1,d.58.42.1 78415,78416 1zd9A 188 7.99e+01 1iae 200 8.10e+01 1iae d.92.1.8 40311 1zesA 125 8.16e+01 1eueA 86 8.18e+01 1cyo d.120.1.1 59504 1ujmA 342 8.18e+01 2brfA 110 8.19e+01 1i2oA 316 8.20e+01 1onrA c.1.10.1 61574 1ng4A 390 8.25e+01 c.3.1.2,d.16.1.3 85666,85667 1xc3A 302 8.25e+01 1on0A 158 8.31e+01 d.108.1.1 87095 1fmaD 81 8.32e+01 1fmaD d.15.3.1 37643 1tufA 434 8.40e+01 b.49.2.3,c.1.6.1 107335,107336 1aw5 326 8.40e+01 1b4kA c.1.10.3 29181 1jljA 189 8.48e+01 c.57.1.1 63169 1zclA 180 8.49e+01 1yx0A 159 8.51e+01 2f4iA 197 8.54e+01 1icwA 72 8.59e+01 1tvxA d.9.1.1 37357 1nu5A 370 8.62e+01 c.1.11.2,d.54.1.1 92183,92184 1wosA 364 8.63e+01 b.44.2.1,d.250.1.1 109468,109469 1y13A 181 8.67e+01 2b7aA 293 8.68e+01 1wmbA 260 8.80e+01 1zjjA 263 8.83e+01 1chuA 540 8.91e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ebfA 358 8.91e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1b1cA 181 8.99e+01 1amoA c.23.5.2 31212