GapMind for catabolism of small carbon sources

 

Protein 8501186 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1920 ABC transporter related (RefSeq)

Length: 249 amino acids

Source: Miya in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 60% 99% 294.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 60% 99% 294.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 58% 100% 279.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 58% 100% 279.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 58% 100% 279.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 94% 277.7 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 94% 277.7 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 58% 92% 276.6 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 58% 92% 276.6 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 54% 96% 270.8 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 55% 98% 265.8 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 54% 94% 256.9 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 254.6 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 254.6 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 49% 97% 242.3 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 50% 89% 238 glutamine ABC transporter, ATP-binding protein GlnQ 63% 295.8

Sequence Analysis Tools

View 8501186 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKTCESPMIEIRNLHKRFGQNEVLRGIDLTVCPGEVVVIIGPSGSGKSTALRCINRLEEI
TSGKVVVDGHDLYDPATDINYVRTEAGMVFQQFNLFPHMSVLHNVTLGPIRVRRTPRAEA
DRLGLALLEKVGLADKATAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVG
EVLEVMRALALEGMTMVIVTHEMGFAREVADRVIFIDQGRIQEEGPPDEFFSAPKNPRLR
EFLGRVRHA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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