# List of top-scoring protein chains for T0279.t04-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 1jr2A 286 9.77e-24 c.113.1.1 67111 1e1cA 727 9.45e-01 1reqA c.1.19.1 29636 c.23.6.1 31263 1reqA 727 9.50e-01 1reqA c.1.19.1 29620 c.23.6.1 31247 5reqA 727 9.50e-01 1reqA c.1.19.1 29632 c.23.6.1 31259 1q7bA 244 1.03e+00 c.2.1.2 -5826 1gz5A 456 1.06e+00 c.87.1.6 76406 1uqtA 482 1.06e+00 c.87.1.6 -8593 1cg2A 393 1.07e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1q7cA 244 1.09e+00 c.2.1.2 -5830 1jud 232 1.19e+00 1qq5A c.108.1.1 43325 1ru3A 732 1.29e+00 e.26.1.3 -12021 1b74A 254 1.51e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1pqhA 143 2.46e+00 b.52.2.1 -4318 1b1cA 181 3.31e+00 1amoA c.23.5.2 31212 1r2rA 248 3.65e+00 c.1.1.1 -5147 1htiA 248 4.04e+00 1amk c.1.1.1 28455 1typA 487 4.05e+00 3grs c.3.1.5 30509 c.3.1.5 30510 d.87.1.1 40186 1tytB 486 4.06e+00 3grs c.3.1.5 30515 c.3.1.5 30516 d.87.1.1 40189 1tytA 487 4.06e+00 3grs c.3.1.5 30513 c.3.1.5 30514 d.87.1.1 40188 2tprA 490 4.16e+00 3grs c.3.1.5 30505 c.3.1.5 30506 d.87.1.1 40184 1fecA 490 4.23e+00 3grs c.3.1.5 30489 c.3.1.5 30490 d.87.1.1 40176 1pt1A 143 4.47e+00 b.52.2.1 -4322 1uc8A 280 4.98e+00 unknown_sccs -6718 unknown_sccs -11230 1tib 269 5.10e+00 3tgl c.69.1.17 34738 1jcuA 208 5.28e+00 d.115.1.1 71634 1uc9A 280 5.40e+00 unknown_sccs -6720 unknown_sccs -11232 1ja1A 622 5.70e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1ja0A 620 5.77e+00 1amoA b.43.4.1 62798 c.23.5.2 62799 c.25.1.4 62800 1j9zA 622 5.77e+00 1amoA b.43.4.1 62792 c.23.5.2 62793 c.25.1.4 62794 1p5dX 463 5.93e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1amoA 615 5.98e+00 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1pqfA 143 5.99e+00 b.52.2.1 -4316 1ou5A 448 6.01e+00 a.173.1.1 87445 d.218.1.4 87446 1n5dA 288 6.11e+00 c.2.1.2 80030 1be1 137 6.24e+00 1be1 c.23.6.1 31237 1mjgM 729 6.46e+00 e.26.1.3 79204 1oaoC 729 6.48e+00 e.26.1.3 86746 1k2yX 463 6.60e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1zrn 232 6.66e+00 1qq5A c.108.1.1 43323 1gt6A 269 6.78e+00 c.69.1.17 76342 1ma9B 376 7.17e+00 c.55.1.1 78890 c.55.1.1 78891 1qz5A 375 7.20e+00 c.55.1.1 -7590 c.55.1.1 -7591 1atnA 373 7.21e+00 1yagA c.55.1.1 33437 c.55.1.1 33438 1lcuA 371 7.23e+00 c.55.1.1 73830 c.55.1.1 73831 1j6zA 376 7.23e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1jbqA 435 7.28e+00 1oasA c.79.1.1 62850 1esvA 377 7.29e+00 1yagA c.55.1.1 33433 c.55.1.1 33434 1m54A 363 7.31e+00 c.79.1.1 74463 1ng1 294 8.16e+00 1ng1 a.24.13.1 16961 c.37.1.10 32272 1ls1A 295 8.17e+00 a.24.13.1 78170 c.37.1.10 78171 1jpnA 296 8.17e+00 a.24.13.1 67039 c.37.1.10 67040 1o87A 297 8.18e+00 a.24.13.1 -619 c.37.1.10 -7117 1q7zA 566 8.45e+00 c.1.21.2 -5638 c.1.26.1 -5666 2ng1 293 9.19e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 1ffh 294 9.20e+00 1ng1 a.24.13.1 16960 c.37.1.10 32271 1rj9B 300 9.30e+00 a.24.13.1 -621 c.37.1.10 -7119 1vhnA 318 9.52e+00 c.1.4.1 -5209 1jflA 228 9.52e+00 c.78.2.1 71656 c.78.2.1 71657 1fjhA 257 1.02e+01 1fjhB c.2.1.2 29870 1v8dA 235 1.02e+01 1i60A 278 1.03e+01 c.1.15.4 71118 2ffhA 425 1.05e+01 1ng1 a.24.13.1 16965 a.36.1.1 17122 c.37.1.10 32276 1uohA 226 1.08e+01 d.211.1.1 -9572 1qymA 227 1.09e+01 d.211.1.1 -9573 1m0sA 219 1.12e+01 unknown_sccs 78351 d.58.40.1 78352 1nhr 447 1.12e+01 1nhp c.3.1.5 30553 c.3.1.5 30554 d.87.1.1 40198 1npx 447 1.14e+01 1nhp c.3.1.5 30557 c.3.1.5 30558 d.87.1.1 40200 1nhs 447 1.14e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1nhq 447 1.15e+01 1nhp c.3.1.5 30551 c.3.1.5 30552 d.87.1.1 40197 1nhp 447 1.15e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1ixrA 191 1.15e+01 a.60.2.1 76925 b.40.4.2 76926 1iugA 352 1.21e+01 c.67.1.3 -8176 1dliA 402 1.21e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1p85M 117 1.23e+01 i.1.1.1 87882 1onfA 500 1.28e+01 c.3.1.5 87141 c.3.1.5 87142 d.87.1.1 87143 1mo0A 275 1.29e+01 c.1.1.1 79329 2pfkC 320 1.30e+01 3pfk c.89.1.1 35579 1pfkA 320 1.31e+01 3pfk c.89.1.1 35575 1tzbA 302 1.32e+01 1f8wA 447 1.32e+01 1nhp c.3.1.5 30561 c.3.1.5 30562 d.87.1.1 40202 1uch 230 1.37e+01 1uch d.3.1.6 37129 1edoA 244 1.38e+01 1ybvA c.2.1.2 29896 1h2hA 241 1.42e+01 c.2.1.3 83058 d.81.1.3 70861 1pw5A 253 1.48e+01 unknown_sccs -6852 1uelA 95 1.49e+01 d.15.1.1 -9137 1i3kA 348 1.52e+01 1xel c.2.1.2 61595 1o98A 511 1.52e+01 c.105.1.1 86684 c.76.1.3 86685 1moq 368 1.57e+01 1moq c.80.1.1 35302 1d4xA 375 1.57e+01 1yagA c.55.1.1 59107 c.55.1.1 59108 1vjrA 271 1.57e+01 unknown_sccs -6853 1m72A 272 1.58e+01 c.17.1.1 -7927 1nfiE 213 1.62e+01 1iknD d.211.1.1 19172 1p1aA 85 1.62e+01 1dq3A 454 1.65e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1mjhA 162 1.68e+01 1mjhA c.26.2.4 31639 1v4lB 125 1.72e+01 d.169.1.1 -11630 1oznA 285 1.73e+01 c.10.2.7 87621 1bia 321 1.73e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1i2sA 282 1.73e+01 e.3.1.1 71104 1p8tA 285 1.73e+01 c.10.2.7 87982 1iknD 236 1.74e+01 1iknD d.211.1.1 19171 1m6yA 301 1.78e+01 a.60.13.1 78716 c.66.1.23 78717 4blmA 265 1.79e+01 1btl e.3.1.1 42721 1vjqA 79 1.79e+01 unknown_sccs -13478 1j5pA 253 1.79e+01 c.2.1.3 83092 d.81.1.3 71577 2dldA 337 1.82e+01 1dxy c.2.1.4 30099 c.23.12.1 31359 1qh8A 478 1.83e+01 1qguA c.92.2.3 35633 1jqeA 292 1.83e+01 c.66.1.19 71789 1hzjA 348 1.84e+01 1xel c.2.1.2 61450 1h1lA 481 1.84e+01 c.92.2.3 70851 1o99A 511 1.86e+01 c.105.1.1 81235 c.76.1.3 81236 1srvA 145 1.88e+01 1derA c.8.5.1 30817 1iirA 415 1.91e+01 1iirA c.87.1.5 62453 1f2jA 370 1.91e+01 1fbaA c.1.10.1 29154 1dljA 402 1.94e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1f1jA 305 2.03e+01 1pauA c.17.1.1 59596 1ek6A 348 2.05e+01 1xel c.2.1.2 29800 1hp1A 516 2.06e+01 d.114.1.1 70976 d.159.1.2 70977 1oi8A 532 2.07e+01 2btfA 375 2.08e+01 1yagA c.55.1.1 33429 c.55.1.1 33430 1v54H 85 2.11e+01 a.51.1.1 -979 1dgnA 89 2.17e+01 1dgnA a.77.1.3 18436 1jqdA 292 2.28e+01 c.66.1.19 71787 1e0tA 470 2.39e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1kp0A 402 2.42e+01 c.55.2.1 72834 d.127.1.1 72835 1o1xA 155 2.42e+01 c.121.1.1 86553 1pgvA 197 2.44e+01 c.10.1.1 88073 1j4aA 333 2.44e+01 c.2.1.4 71502 c.23.12.1 71503 1id1A 153 2.45e+01 1id1A c.2.1.9 62286 1pczA 191 2.47e+01 1ytbA d.129.1.1 41292 d.129.1.1 41293 1e6vA 553 2.49e+01 1mroA a.89.1.1 18527 d.58.31.2 39445 1qv9A 283 2.49e+01 unknown_sccs -6888 1ush 550 2.51e+01 1ush d.114.1.1 40923 d.159.1.2 42079 1hpuA 525 2.51e+01 d.114.1.1 70979 d.159.1.2 70980 1jcfA 344 2.52e+01 c.55.1.1 62878 c.55.1.1 62879 1oidA 532 2.54e+01 1j49A 333 2.55e+01 c.2.1.4 71498 c.23.12.1 71499 1h4vB 421 2.58e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1aisA 182 2.61e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1o4sA 389 2.63e+01 c.67.1.1 86620 1d9sA 136 2.63e+01 1bd8 i.11.1.1 46013 1d3uA 181 2.64e+01 1ytbA d.129.1.1 41290 d.129.1.1 41291 1qnlA 385 2.64e+01 1pea c.93.1.1 35665 1rypF 233 2.65e+01 1rypF d.153.1.4 41937 1fntF 234 2.65e+01 1ccwB 483 2.66e+01 1cb7B c.1.19.2 29646 1kvu 338 2.70e+01 1xel c.2.1.2 29794 1pwhA 327 2.72e+01 c.79.1.1 -8524 1npyA 271 2.73e+01 c.2.1.7 85995 c.58.1.5 85996 1g0uE 234 2.74e+01 d.153.1.4 41950 1udc 338 2.75e+01 1xel c.2.1.2 29785 1pyqA 144 2.81e+01 b.52.2.1 -4314 1pea 385 2.85e+01 1pea c.93.1.1 35662 1gqfA 265 2.94e+01 c.17.1.1 65470 1mzbA 136 2.97e+01 unknown_sccs -266 1p3jA 217 3.05e+01 c.37.1.1 -6996 g.41.2.1 -12769 1bed 181 3.07e+01 1fvkA unknown_sccs -7444 1we3A 543 3.09e+01 1axkA 394 3.12e+01 1axkA b.29.1.2 24181 b.29.1.11 24315 1o13A 136 3.16e+01 c.55.5.1 80762 1ngvA 534 3.17e+01 c.111.1.2 85698 1db3A 372 3.21e+01 1db3A c.2.1.2 29813 1j0dA 341 3.21e+01 c.79.1.1 83902 1i5eA 209 3.22e+01 c.61.1.1 71116 1pt0A 144 3.25e+01 b.52.2.1 -4320 1bd3A 243 3.26e+01 1bd3A c.61.1.1 34098 1iukA 140 3.30e+01 c.2.1.8 83712 1ei1A 391 3.30e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1d8lA 149 3.34e+01 1hjp a.60.2.1 17948 b.40.4.2 25267 1udb 338 3.38e+01 1xel c.2.1.2 29787 1lrkA 338 3.40e+01 c.2.1.2 74225 1v47A 349 3.42e+01 b.122.1.3 -5127 c.26.1.5 -6622 1r4mA 529 3.44e+01 c.111.1.2 -8276 1fs0G 230 3.47e+01 1fs0G c.49.2.1 59999 1hjp 203 3.49e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1j2rA 199 3.50e+01 unknown_sccs -6799 1cuk 203 3.53e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1k1xA 659 3.55e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1f2dA 341 3.58e+01 1f2dA c.79.1.1 35298 1ee0A 402 3.59e+01 1bi5A c.95.1.2 36007 c.95.1.2 36008 2liv 344 3.60e+01 2liv c.93.1.1 35708 1o20A 427 3.62e+01 c.82.1.1 86556 1nf1A 333 3.63e+01 1nf1A a.116.1.2 19110 1umdB 324 3.64e+01 c.36.1.7 -6929 c.48.1.2 -7539 1t0iA 191 3.66e+01 1pjtA 457 3.72e+01 c.2.1.11 -5908 c.90.1.1 -8615 e.37.1.1 -12008 1e96A 192 3.73e+01 1ctqA c.37.1.8 32007 1i4tD 192 3.73e+01 c.37.1.8 61731 1a0dA 440 3.75e+01 1a0cA c.1.15.3 29533 1dz3A 130 3.76e+01 1dz3A c.23.1.1 31105 1g71A 347 3.78e+01 1g71A unknown_sccs 43268 1iq7A 345 3.81e+01 c.94.1.2 66261 1o5xA 248 3.89e+01 c.1.1.1 -5157 1knzA 164 3.92e+01 e.34.1.1 68709 1e2jA 331 3.95e+01 1qhiA c.37.1.1 31874 1e2kA 331 3.95e+01 1qhiA c.37.1.1 31854 1p77A 272 3.96e+01 c.2.1.7 -5965 c.58.1.5 -6371 1e2lA 331 3.97e+01 1qhiA c.37.1.1 31872 1e0uA 470 3.99e+01 1a49A b.58.1.1 27072 c.1.12.1 29300 c.49.1.1 33154 1a9y 338 3.99e+01 1xel c.2.1.2 29789 1kmcA 303 4.00e+01 c.17.1.1 68690