Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_10350 AO356_10350 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_10350 Length = 759 Score = 298 bits (764), Expect = 6e-85 Identities = 205/619 (33%), Positives = 319/619 (51%), Gaps = 39/619 (6%) Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQ-- 293 E E + T++ LA A ++ + + + GV S G+A G V Sbjct: 137 EGEEAFLVTMSAQLAGVIAHAEATGSISGLGRQGKGIQEAKFVGVPGSPGAAVGTAVVML 196 Query: 294 -------VAERTLEMPEFAADQQLERESLE--RALMHATQALQRLRDNAAGEAQADIFKA 344 V ++T+ + A+ L + ++E RA M A A +L E +A +F Sbjct: 197 PPADLDVVPDKTIT--DINAELGLFKTAIEGVRADMRALSA--KLATQLRPEERA-LFDV 251 Query: 345 HQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQR 404 + +L+D SL + +I G+ A A F+ + L ERA D+ D+G+R Sbjct: 252 YLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLRERASDVKDLGRR 311 Query: 405 VLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARAL 464 +L + PD IL++E+LTP+ + GK+ G +V G SHVAILARA+ Sbjct: 312 LLAYLQQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAGLVSVLGSGNSHVAILARAM 371 Query: 465 GLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENA 524 G+P V GL S G ++++D GE++ +P+ + +Q ++++Q Sbjct: 372 GIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVEEEKQLSLGLDALR 431 Query: 525 ARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTY 584 VT DGH + N LA+ +A GAEG+GL R+E + PS EQ Y Sbjct: 432 DLPCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQRFPSEKEQLAIY 491 Query: 585 SAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRA 644 A PQ + +R+LD+GGDK L+Y P+ E NPFLG RGIR+ L+ P++ Q RA Sbjct: 492 REQLAAFHPQP-VTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTLDHPEIFLVQARA 549 Query: 645 IL-SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE------------LPKLGI 691 +L +S GL L I+LPM+S EL EEAL L R +P +G+ Sbjct: 550 MLKASEGLNNLRILLPMISGTHEL--------EEALHLIHRAWGEVRDEGTDVPMPPVGV 601 Query: 692 MIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIAST 751 MIE+PAA A +VDF S+G+NDLTQY LA+DR++PR+A D HP+VL+ + + Sbjct: 602 MIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQALQNV 661 Query: 752 VKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAI 811 V+ AHA GK V +CG +A + A LL+ +G D LS++ +P +K +R++ LS Q + Sbjct: 662 VRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSKAQEL 721 Query: 812 AHQVLGLESAEQVREALSV 830 +V+ +++ + + +L + Sbjct: 722 LAEVMTIDNPQVIHSSLQL 740 Lambda K H 0.318 0.132 0.370 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1255 Number of extensions: 56 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 844 Length of database: 759 Length adjustment: 41 Effective length of query: 803 Effective length of database: 718 Effective search space: 576554 Effective search space used: 576554 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory