# List of top-scoring protein chains for t2k-100-30-alpha 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 1rxxA 421 4.66e-04 1jdw 423 1.53e-02 1jdw d.126.1.2 41129 1s9rA 410 1.89e-01 1lxyA 409 2.67e-01 1tdj 514 2.79e-01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1m0dA 138 3.29e-01 c.52.1.17 74354 1fzrA 138 5.63e-01 1fzrA c.52.1.17 33336 1nnlA 225 7.45e-01 c.108.1.4 85906 1ej6A 1289 8.50e-01 i.7.1.1 45967 1m41A 380 8.88e-01 c.1.16.4 78595 1h70A 255 9.08e-01 1h70A d.126.1.3 60711 1vhwA 253 9.86e-01 1fztA 211 1.18e+00 1qhfA c.60.1.1 60158 1f6dA 376 1.54e+00 1f6dA c.87.1.3 35467 1o5oA 221 1.58e+00 1ks2A 219 1.75e+00 c.35.1.2 72908 d.58.40.1 72909 1lkzA 219 1.80e+00 c.35.1.2 73991 d.58.40.1 73992 1kutA 230 1.92e+00 d.143.1.1 73017 1o8bA 219 1.94e+00 c.35.1.2 81180 d.58.40.1 81181 1jb7B 260 1.95e+00 1otcB b.40.4.3 62839 1bcpC 199 2.01e+00 1bcpB b.40.2.1 25121 d.169.1.2 42430 1qgvA 142 2.31e+00 1qgvA c.47.1.8 33056 1otcB 260 2.47e+00 1otcB b.40.4.3 25310 1ctn 540 2.55e+00 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1nxjA 183 2.63e+00 c.8.7.1 86382 1e19A 314 2.72e+00 1b7bA c.73.1.1 34967 4bcl 366 2.73e+00 4bcl b.75.1.1 27968 1id0A 152 2.97e+00 d.122.1.3 66111 1ebbA 202 3.10e+00 c.60.1.1 64900 1ecpA 238 3.19e+00 1ecpA c.56.2.1 33775 1k9sA 237 3.20e+00 c.56.2.1 68359 1vgvA 384 3.23e+00 1h2eA 207 3.27e+00 c.60.1.1 70857 1heiA 451 3.62e+00 1heiA c.37.1.14 32463 c.37.1.14 32464 1dqaC 467 3.66e+00 1dqaA d.58.20.1 39366 d.179.1.1 42587 1bs0A 384 3.82e+00 1bs0A c.67.1.4 34490 1mwpA 96 3.91e+00 1mwpA d.170.2.1 42453 1fbtA 190 4.05e+00 1bif c.60.1.4 34004 8ohm 435 4.13e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 1edqA 540 4.72e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1pk9A 237 4.78e+00 1k9tA 540 4.80e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1dqaA 467 5.01e+00 1dqaA d.58.20.1 39364 d.179.1.1 42585 1pbgA 468 5.07e+00 1e70M c.1.8.4 28946 1sviA 195 5.08e+00 1j08A 226 5.33e+00 c.47.1.2 83855 c.47.1.2 83856 1hc7A 477 5.61e+00 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 3pbgA 468 5.73e+00 1e70M c.1.8.4 28951 1bif 469 5.90e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1hw8A 467 6.11e+00 1dqaA d.58.20.1 61298 d.179.1.1 61299 1bzyA 217 6.20e+00 1qk3A c.61.1.1 34071 1hlrA 907 6.30e+00 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 3bamB 213 6.33e+00 1bam c.52.1.3 33289 2bifA 469 6.46e+00 1bif c.37.1.7 31963 c.60.1.4 34009 1gci 269 6.75e+00 1gci c.41.1.1 32503 1sep 261 6.82e+00 1oaa c.2.1.2 29830 3bifA 468 7.02e+00 1bif c.37.1.7 31962 c.60.1.4 34008 1obfO 335 7.16e+00 c.2.1.3 86768 d.81.1.1 86769 1j1nA 492 7.25e+00 c.94.1.1 83978 1si7A 369 7.54e+00 1fwyA 331 7.62e+00 1fwyA b.81.1.4 28064 c.68.1.5 34522 1oaa 259 7.72e+00 1oaa c.2.1.2 29829 1f6kA 293 7.79e+00 1nal3 c.1.10.1 29081 1bg7 176 7.88e+00 2fha a.25.1.1 16686 1hv9A 456 8.07e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1f3rB 257 8.24e+00 1f3rB b.1.1.1 20417 b.1.1.1 20416 1pg6A 243 8.26e+00 1ekgA 127 8.35e+00 1dlxA d.82.2.1 40021 2fha 183 8.37e+00 2fha a.25.1.1 16674 1b37B 472 9.02e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1f74A 293 9.18e+00 1nal3 c.1.10.1 29079 1vhxA 150 9.48e+00 1pydA 556 9.54e+00 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1fxlA 167 9.58e+00 1b7fA d.58.7.1 39183 d.58.7.1 39184 1fcqA 350 9.64e+00 c.1.8.9 65006 1id1A 153 9.65e+00 1id1A c.2.1.9 62286 1dosA 358 9.70e+00 1dosA c.1.10.2 29175 3bamA 213 9.82e+00 1bam c.52.1.3 33288 1onxA 390 9.93e+00 b.92.1.7 87176 c.1.9.13 87177 1oi1A 221 1.01e+01 b.34.9.3 87037 b.34.9.3 87038 1ji8A 111 1.03e+01 d.203.1.1 66733 1kwhA 492 1.03e+01 c.94.1.1 68876 1egzA 291 1.05e+01 7a3hA c.1.8.3 28828 1k77A 260 1.05e+01 c.1.15.5 72096 1szwA 379 1.06e+01 1b5qA 472 1.09e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1cl1A 395 1.11e+01 1cl2A c.67.1.3 34395 1rwiA 270 1.11e+01 1b37A 472 1.11e+01 1b37B c.3.1.2 30389 d.16.1.5 37953 1kafA 108 1.12e+01 d.199.1.1 68372 1pvdA 537 1.12e+01 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1kte 105 1.14e+01 1kte c.47.1.1 32771 1g61A 228 1.15e+01 1g61A d.126.1.1 41126 1hymA 45 1.15e+01 1hymA d.40.1.1 38581 1kmnD 424 1.16e+01 1adjA c.51.1.1 33185 d.104.1.1 40734 1b57A 358 1.19e+01 1dosA c.1.10.2 29177 1v93A 296 1.23e+01 1fc4A 401 1.25e+01 1bs0A c.67.1.4 59760 1ao8 162 1.26e+01 3dfr c.71.1.1 34883 1onwA 390 1.29e+01 b.92.1.7 87172 c.1.9.13 87173 1fs0E 138 1.29e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 2sniI 83 1.31e+01 2sniI d.40.1.1 38573 1bs9 207 1.31e+01 1bs9 c.23.9.1 31330 1g66A 207 1.31e+01 1bs9 c.23.9.1 31329 1ah2 269 1.35e+01 1gci c.41.1.1 32542 1dpgA 485 1.38e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1e58A 249 1.40e+01 1qhfA c.60.1.1 59262 1pg4A 652 1.42e+01 e.23.1.1 88067 1nnmA 652 1.42e+01 1a8y 367 1.44e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1n2eA 300 1.44e+01 c.26.1.4 85268 3pgk 416 1.44e+01 16pk c.86.1.1 35451 1qrdA 273 1.45e+01 1d4aA c.23.5.3 31217 1eemA 241 1.47e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1mopA 300 1.52e+01 c.26.1.4 85035 1kamA 194 1.53e+01 c.26.1.3 72254 1m6dA 214 1.55e+01 d.3.1.1 84849 1qgxA 357 1.56e+01 1qgxA e.7.1.1 42973 1ka1A 357 1.56e+01 e.7.1.1 68369 1riqA 465 1.57e+01 2ms2A 129 1.58e+01 1msc d.85.1.1 40049 1i60A 278 1.59e+01 c.1.15.4 71118 1p27B 106 1.61e+01 1fy2A 229 1.61e+01 1fyeA c.23.16.4 31478 2dpg 485 1.61e+01 1dpgA c.2.1.3 30076 d.81.1.5 39991 1mzhA 225 1.62e+01 c.1.10.1 79698 1kzhA 555 1.62e+01 c.89.1.1 73361 1egpA 45 1.64e+01 1egpA d.40.1.1 38561 1fxjA 331 1.65e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1fha 183 1.67e+01 2fha a.25.1.1 16675 1hl9A 449 1.68e+01 1d4aA 273 1.69e+01 1d4aA c.23.5.3 31219 1gzgA 337 1.71e+01 c.1.10.3 70805 1hdiA 413 1.72e+01 16pk c.86.1.1 60964 1iz0A 302 1.76e+01 b.35.1.2 83821 c.2.1.1 83822 1diiC 80 1.78e+01 1diiC a.3.1.1 15925 1bq3B 246 1.79e+01 1qhfA c.60.1.1 33979 1hgxA 183 1.80e+01 1tc1A c.61.1.1 34027 1qpbA 563 1.81e+01 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1fyeA 229 1.82e+01 1fyeA c.23.16.4 31477 1vjqA 79 1.85e+01 1nddA 76 1.87e+01 1ubi d.15.1.1 37599 1a8l 226 1.89e+01 1a8l c.47.1.2 32777 c.47.1.2 32778 1ogqA 313 1.91e+01 c.10.2.8 86996 1jjiA 311 1.93e+01 c.69.1.2 66766 1h77A 605 1.93e+01 1l9xA 315 1.94e+01 c.23.16.1 73762 1q0pA 223 1.95e+01 1ypcI 64 1.97e+01 2sniI d.40.1.1 38570 1kbqA 273 1.97e+01 c.23.5.3 68391 1nh9A 87 2.02e+01 1sjyA 159 2.08e+01 1qauA 112 2.09e+01 1qauA b.36.1.1 24779 1uxoA 192 2.11e+01 1nx8A 273 2.11e+01 b.82.2.8 86374 1nwzA 125 2.12e+01 d.110.3.1 86370 3pyp 125 2.12e+01 3pyp d.110.3.1 40897 2phy 125 2.13e+01 3pyp d.110.3.1 40901 1rcd 173 2.14e+01 2fha a.25.1.1 16687 1f8yA 157 2.14e+01 1f8xA c.23.14.1 31395 3phy 125 2.15e+01 3pyp d.110.3.1 40904 1kekA 1231 2.15e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1qhtA 775 2.17e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1h1dA 221 2.17e+01 c.66.1.1 83452 1uae 419 2.18e+01 1uae d.68.2.2 39574 1nddD 76 2.18e+01 1ubi d.15.1.1 37602 1a3k 137 2.19e+01 1a3k b.29.1.3 24218 1k5cA 335 2.21e+01 b.80.1.3 72076 1vid 221 2.22e+01 1vid c.66.1.1 34178 1jhb 106 2.22e+01 1kte c.47.1.1 32772 1k4nA 192 2.23e+01 d.32.1.5 72059 1qlwA 328 2.24e+01 1qlwA c.69.1.15 34722 1coaI 64 2.25e+01 2sniI d.40.1.1 38574 1g2iA 166 2.25e+01 1g2iA c.23.16.2 31438 1f8xA 157 2.25e+01 1f8xA c.23.14.1 31397 1g86A 142 2.26e+01 b.29.1.3 70161 1ufhA 180 2.26e+01 d.108.1.1 88485 1ubi 76 2.27e+01 1ubi d.15.1.1 37584 1j6nA 303 2.28e+01 c.79.1.1 71594 1g5cA 170 2.28e+01 1g5cA c.53.2.1 60264 1nmoA 247 2.30e+01 1m6yA 301 2.31e+01 a.60.13.1 78716 c.66.1.23 78717 1iugA 352 2.32e+01 1lw6I 64 2.36e+01 d.40.1.1 74294 1l6rA 227 2.36e+01 c.108.1.10 77768 1o6dA 163 2.41e+01 1bwzA 274 2.41e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1ubq 76 2.45e+01 1ubi d.15.1.1 37585 1iw7C 1119 2.46e+01 e.29.1.1 71474 1b4kA 337 2.49e+01 1b4kA c.1.10.3 29184 1cw0A 155 2.50e+01 1vsrA c.52.1.15 33333 1ehiA 377 2.50e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1ipaA 274 2.53e+01 c.116.1.1 71254 d.79.3.3 71255 1hdkA 141 2.55e+01 b.29.1.3 65807 1no5A 114 2.56e+01 1qhfA 240 2.57e+01 1qhfA c.60.1.1 33960 1ivg 388 2.57e+01 2qwc b.68.1.1 27578 1hka 158 2.60e+01 1hka d.58.30.1 39433 2rslA 140 2.61e+01 2rslA c.53.1.1 33345 1ogwA 76 2.64e+01 d.15.1.1 87001 1cf9A 753 2.68e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1q7hA 153 2.71e+01 1f5sA 211 2.71e+01 1f5sA c.108.1.4 59656 1dkiA 371 2.71e+01 1dkiA d.3.1.1 37090 1eucB 396 2.74e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1qj4A 257 2.75e+01 1qj4A c.69.1.20 34796 1l7mA 211 2.75e+01 c.108.1.4 73664 1v4vA 376 2.75e+01 1bolA 222 2.77e+01 1bolA d.124.1.1 41120 1o4vA 183 2.77e+01 c.23.8.1 86628 1yasA 257 2.78e+01 1qj4A c.69.1.20 34801 1dat 174 2.78e+01 2fha a.25.1.1 16677 2prf 125 2.79e+01 3nul d.110.1.1 40887 1dxy 333 2.79e+01 1dxy c.2.1.4 30094 c.23.12.1 31354 1b6tA 159 2.79e+01 1b6tA c.26.1.3 31600 1s4qA 228 2.84e+01 1gqzA 274 2.89e+01 d.21.1.1 83311 d.21.1.1 83312 1aew 174 2.89e+01 2fha a.25.1.1 16676 1axj 122 2.91e+01 1axj b.45.1.1 25749 1ly7A 121 2.93e+01 d.82.2.1 74339 1o6zA 303 2.95e+01 c.2.1.5 81107 d.162.1.1 81108 1jqbA 351 2.95e+01 b.35.1.2 77151 c.2.1.1 77152 1glv 303 2.95e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1uspA 139 2.96e+01 1httA 423 2.98e+01 1adjA c.51.1.1 33178 d.104.1.1 40727 1q77A 138 2.99e+01 1j5xA 342 2.99e+01 c.80.1.1 71591 1esgA 213 3.00e+01 1bam c.52.1.3 33286 1fnsA 196 3.00e+01 1auq c.62.1.1 34136 1hrnA 337 3.03e+01 1smrA b.50.1.2 26869 1mc0A 368 3.07e+01 d.110.2.1 78937 d.110.2.1 78938 1qe5A 266 3.09e+01 1b8oA c.56.2.1 33784 1lzlA 323 3.10e+01 c.69.1.2 78306 1o58A 303 3.10e+01 1eumA 165 3.14e+01 1eumA a.25.1.1 59507 1he2A 206 3.14e+01 1he2A c.2.1.2 60966 1bzsA 165 3.14e+01 1hfc d.92.1.11 40348 1lcl 142 3.15e+01 1lcl b.29.1.3 24216 1iv8A 720 3.19e+01 b.71.1.1 76842 c.1.8.1 76843 1hl8A 449 3.20e+01 1qavB 115 3.20e+01 1qauA b.36.1.1 24780 1qjcA 158 3.20e+01 1b6tA c.26.1.3 63328 1g6oA 330 3.21e+01 1g6oA c.37.1.11 32430 1nnwA 252 3.25e+01 d.159.1.5 80674 1qp2A 70 3.26e+01 1pse b.34.4.2 24596 1oakA 196 3.27e+01 1auq c.62.1.1 34138 1uc2A 481 3.29e+01 1gp1A 198 3.29e+01 1gp1A c.47.1.10 33059 1rl6A 177 3.30e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1irp 153 3.31e+01 1irp b.42.1.2 25559 1rkd 309 3.31e+01 1rkd c.72.1.1 34928 1eqnA 321 3.35e+01 1dd9A e.13.1.1 43256 1lkyA 77 3.36e+01 a.60.1.1 73985 1vjoA 393 3.37e+01 1gt91 357 3.37e+01 1j0aA 325 3.40e+01 c.79.1.1 83871 1r2rA 248 3.41e+01 1poiB 260 3.43e+01 1poiB c.63.1.3 34155 1bam 213 3.46e+01 1bam c.52.1.3 33285 1bcpB 199 3.52e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1hztA 190 3.52e+01 1i9aA d.113.1.2 61459 1em8A 147 3.55e+01 1rqpA 299 3.58e+01 1iqpA 327 3.62e+01 a.80.1.1 62649 c.37.1.20 62650 1ji7A 89 3.63e+01 a.60.1.1 71682 1e5rA 290 3.64e+01 1e5rA b.82.2.4 59276 1otfA 62 3.65e+01 1otfA d.80.1.1 39820 1b0pA 1231 3.67e+01 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 2abk 211 3.68e+01 2abk a.96.1.1 18743 1konA 249 3.70e+01 e.39.1.1 72823 1g2qA 187 3.71e+01 c.61.1.1 65117 1p2fA 220 3.76e+01 a.4.6.1 87720 c.23.1.1 87721 1eqoA 158 3.77e+01 1hka d.58.30.1 39432 1dd9A 338 3.82e+01 1dd9A e.13.1.1 43254 1jenA 267 3.82e+01 1jenA 1gw9A 388 3.85e+01 c.1.15.3 70658 1oatA 439 3.90e+01 2dkb c.67.1.4 34461 1ijbA 202 3.90e+01 c.62.1.1 71229 1bt0A 76 3.91e+01 1ubi d.15.1.1 37607 1f2rI 100 3.92e+01 1c9fA d.15.2.1 37641 1utiA 58 3.93e+01 1n00A 321 3.94e+01 a.65.1.1 85241 1npdA 288 3.95e+01 c.2.1.7 80681 c.58.1.5 80682 1pz1A 333 3.98e+01 1n7hA 381 3.99e+01 c.2.1.2 80250