GapMind for catabolism of small carbon sources

 

Protein WP_110207765.1 in Nocardioides daejeonensis MJ31

Annotation: NCBI__GCF_003194585.1:WP_110207765.1

Length: 412 amino acids

Source: GCF_003194585.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA med BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 48% 95% 355.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-proline catabolism proV med glycine betaine/l-proline transport atp-binding protein prov (characterized) 45% 99% 328.6 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 55% 96% 287 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 54% 96% 285 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 94% 157.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 94% 157.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-glutamate catabolism gltL med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 94% 157.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 74% 171.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 33% 83% 170.2 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 58% 161.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 68% 159.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 68% 159.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 58% 157.5 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-asparagine catabolism glnQ lo 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) 36% 98% 152.9 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 34% 67% 152.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 76% 149.8 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 65% 141 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 65% 139.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 65% 139.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 65% 139.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 65% 139.4 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 89% 138.7 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 91% 136.7 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 91% 136.7 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 31% 98% 136.7 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 48% 360.5

Sequence Analysis Tools

View WP_110207765.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSLIELSGVHKIFGKRPQRALARLQSGATREELRADGITAAVIDASFTVDPGQIFVVMGL
SGSGKSTLIRMVNGLLEPTSGSVVVAGEDLARLDARKLRRARREKVSMVFQHFALLPHRT
VGENAAYALKVKGMNRSDRQRQAEQALEMVGLGGWGGSLPGDLSGGMRQRVGLARALAAG
TEVMLMDEAFSALDPLIRREMQDQLIELQNQLGKTILFITHDLNEAMRLGDRIAMMRDGR
IVQQGTAEQILNDPANDYVAQFVQDVDRTKVLTAASIMERPVAVLGAGQGPRAAHKLMRE
NQLNALMVVDRQHNLRGLITEATAAEAVKTGQESLDGLVTPAHQVTPDTCVADLFTAAAE
RPEPLAVVEGTKLAGVIARVTLLSALGNLNGSETAAGELVSAGSATTDGGQA

This GapMind analysis is from Sep 24 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:

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