GapMind for catabolism of small carbon sources

 

Protein WP_043918238.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043918238.1

Length: 349 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 100% 340.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 100% 340.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 51% 96% 334 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 52% 92% 314.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-maltose catabolism malK_Sm med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 46% 100% 309.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
trehalose catabolism malK med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 46% 100% 309.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 48% 99% 305.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 46% 96% 304.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 296.2 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 42% 73% 184.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 100% 150.2 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 100% 150.2 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 52% 345.5

Sequence Analysis Tools

View WP_043918238.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MAEIKLKNVTKRWGDFVGVQAFDLDIADREFLVLLGPSGCGKTTTMRMIAGLEDPTAGDI
YIGDRRVNDLDPKDRDIAMVFQSYGLYPNLTVYENIRFPLKVRKVPQAEHEERVMRASAM
VELDDFLHRKPAALSGGQRQRVALARAIVRTPQVFLMDEPLSNLDAKLRVSTRAQIKNLS
HELKVTTIYVTHDQIEAMTLADRVVVMKAGIVQQVGTPTEIYDQPQNTFVAGFIGSPAMN
LMAGEIRDGTFHSENATIPGVSGPPGKVICGFRAEDASVAEEGQGELRAPVYSMELLGDS
TMVTVRTGRDLVAVKAPKEFRAEIKAPFAAHIPAEICHVFDAESGERVV

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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