GapMind for catabolism of small carbon sources

 

Protein WP_015334118.1 in Fibrella aestuarina BUZ 2

Annotation: NCBI__GCF_000331105.1:WP_015334118.1

Length: 221 amino acids

Source: GCF_000331105.1 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
L-arginine catabolism artP lo 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) 37% 88% 146 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-histidine catabolism hisP lo 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) 37% 88% 146 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-lysine catabolism hisP lo 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) 37% 88% 146 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 86% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 89% 117.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 89% 117.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 89% 117.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 89% 117.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-isoleucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 36% 86% 116.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-leucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 36% 86% 116.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 36% 86% 116.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-valine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 36% 86% 116.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 34% 87% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 34% 87% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 34% 87% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 86% 107.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 86% 107.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 86% 107.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 91% 97.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 91% 97.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 48% 208.4

Sequence Analysis Tools

View WP_015334118.1 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

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Sequence

MPILHATNLRRAYGPLPVLNDVSLSIDAGEVVSIVGASGAGKSTLLHILGTLDRPDGGSV
TLAGQDVFSLTDKQLARFRNEQIGFVFQFHNLLPEFTALENVAIPGFIGGRDEKAVRQRA
AELLSRLGLADRQQHFPAQLSGGEQQRVAVARALINQPAVVFADEPSGNLDSRNAEELHQ
LFFDLRDTFGQTFIIVTHNETLAMLADRSITLRDGHVVKTE

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