Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF5270 PS417_26985 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__WCS417:GFF5270 Length = 759 Score = 278 bits (711), Expect = 9e-79 Identities = 183/576 (31%), Positives = 300/576 (52%), Gaps = 22/576 (3%) Query: 285 GETLAPNTLAGVCAAPGVAVGK-LVRWDDADIDP-PEKANGTSAAESRLLDKAIATVDAD 342 G+ + GV +PG AVG +V AD+D P+K AE +L A+ V AD Sbjct: 170 GKGIQEAKFVGVPGSPGAAVGTAVVMLPPADLDVVPDKTVSDIDAEIKLFKTALEGVRAD 229 Query: 343 LDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAI 402 + + + E +F V++++L+D +L + + +I G+ A A R+ + + Sbjct: 230 MRNLSNKLATQLRPEERALFDVYQMMLDDASLGNEVKTVIKTGQWAQGALRQVVTDHVNR 289 Query: 403 LTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSR 462 ++D L ERA+D+RD+ +R+L L T P+ +L +EE T + L + + Sbjct: 290 FEMMDDDYLRERASDVRDLGRRLLAKLQEDRTTNLVYPDNTILVSEELTATMLGEVPEGK 349 Query: 463 VTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELD 522 + LV G SH AILAR GIP ++ + D +A +G ++V+ G + P+E+ Sbjct: 350 LVGLVSVLGSGNSHVAILARAMGIPTVMGLVDLPYAKVDGIGMIVDGHRGEVFTNPSEV- 408 Query: 523 VERARLERTRLADVREANRRTS-------QQAAVTSDGRAIEVAANIATLDDAKTAVENG 575 R + A+V E ++ + + VT+DG + + N L D A + G Sbjct: 409 ------LRKQYAEVVEEEKQLALGLDSLRELPCVTTDGHRVPLLVNTGLLADVARAQQRG 462 Query: 576 ADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLP 635 A+ VGL RTE+ F+ P+ E Y+ + A +R+LD+G DK + Y + Sbjct: 463 AEGVGLYRTEVPFMINQRFPSEKEQLAIYREQLQAFHPLPVTMRSLDIGGDKSLSYFPIK 522 Query: 636 PEPNPALGLRGIRLAQVRPDLLDDQLRGLL-AVQPLGAVRILLPMVTDVGEL---IRIRK 691 E NP LG RGIR+ P++ Q R +L A + L +RILLPM++ EL + + Sbjct: 523 -EDNPFLGWRGIRVTLDHPEIFLVQTRAMLKASEGLNNLRILLPMISGTHELEEALHLIH 581 Query: 692 RIDEFARELGRTEPIE-VGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQA 750 R R+ G P+ +GVMIE+P+A A +LA+ DFLS+G+NDLTQY LA+DR Sbjct: 582 RAWGEVRDEGADVPMPPIGVMIEIPAAVYQAKELARQVDFLSVGSNDLTQYLLAVDRNNP 641 Query: 751 DLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPV 810 +A D LHPAVL+ + V+ A GK V +CG +AGDP A LL+ +G LS++ Sbjct: 642 RVADLYDYLHPAVLQALQHVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNAT 701 Query: 811 SVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAA 846 ++P +K +R ++ + + + + +++ Q + ++ Sbjct: 702 NLPKVKWMLRQVELSMAKDLLAELMTIDNPQVIHSS 737 Lambda K H 0.317 0.133 0.371 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: 1274 Number of extensions: 59 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 854 Length of database: 759 Length adjustment: 41 Effective length of query: 813 Effective length of database: 718 Effective search space: 583734 Effective search space used: 583734 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: 56 (26.2 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