Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate GFF3793 Psest_3862 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__psRCH2:GFF3793 Length = 757 Score = 279 bits (713), Expect = 5e-79 Identities = 187/574 (32%), Positives = 295/574 (51%), Gaps = 10/574 (1%) Query: 285 GETLAPNTLAGVCAAPGVAVGK-LVRWDDADIDP-PEKANGTSAAESRLLDKAIATVDAD 342 G+ + G+ APG VG LV AD+D P+K AE L + A+ V AD Sbjct: 170 GKGIQETRFIGIPGAPGAGVGTALVVLPPADLDVVPDKHIDNIDAELTLFEAALEAVRAD 229 Query: 343 LDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIAI 402 + + + E +F V+ ++L+D L +I G+ A A R+ +R + Sbjct: 230 MRNLSEKLATQMRKEERALFDVYLMMLDDSALGGEVTKVIRTGQWAQGALRQVVREHVRR 289 Query: 403 LTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSR 462 ++DA L ERA+D++DI +R+L L T P++ +L +EE +P+ L + + Sbjct: 290 FEMMDDAYLRERASDVKDIGRRLLSYLQEARQQTLTYPDKTILVSEELSPAMLGEVPEGK 349 Query: 463 VTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTELD 522 + +V G + SH AILAR GIP ++ D ++ +G +++V+ G + P ++ Sbjct: 350 LVGMVSVLGSSNSHVAILARAMGIPTVMGAVDLPYSKVDGIELIVDGYRGEIITNPGKVL 409 Query: 523 VERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVGLL 582 E+ + + + E + T DG I + N L D A E GA+ VGL Sbjct: 410 REQYEVLAEQERQLSEGLDVLRELPCETIDGHRIPLWVNTGLLADVVRAQERGAEGVGLY 469 Query: 583 RTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNPAL 642 RTE+ F+ + P+ E Y+ ++A +R+LD+G DK + Y + E NP L Sbjct: 470 RTEVPFMIKERFPSEKEQMAIYREQLEAFHPLPVTMRSLDIGGDKCLPYFPIKEE-NPFL 528 Query: 643 GLRGIRLAQVRPDLLDDQLRGLL-AVQPLGAVRILLPMVTDVGELIRIRKRIDEFARELG 701 G RGIR+ P++ Q R +L A L +RILLPM++ +GEL I E+ Sbjct: 529 GWRGIRVTLDHPEIFLLQTRAMLKASAGLNNLRILLPMISGIGELEEALHLIHRAWCEV- 587 Query: 702 RTEPIEV-----GVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQA 756 R E ++V GVMIEVP+A L +LA+ DF+S+G+NDLTQY LA+DR +A Sbjct: 588 RDEGLDVHMPPVGVMIEVPAAVYLTRELARQVDFISVGSNDLTQYLLAVDRNNPRVADLY 647 Query: 757 DGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGIK 816 D LHPAVL + V+ A GK V +CG +AGDP A LL+ +G LS++ ++P +K Sbjct: 648 DYLHPAVLEALQRVVKEAHSEGKPVSICGEMAGDPAAAVLLLAMGFDSLSMNATNLPKVK 707 Query: 817 ARVRNLDYQLCRQRAQDALALESAQAVRAASRET 850 +R + +Q + L+S Q +++ + T Sbjct: 708 WLLRQISMDTAQQLLARVMLLDSPQVIQSTVQLT 741 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: 1222 Number of extensions: 61 Number of successful extensions: 6 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: 854 Length of database: 757 Length adjustment: 41 Effective length of query: 813 Effective length of database: 716 Effective search space: 582108 Effective search space used: 582108 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