GapMind for catabolism of small carbon sources

 

Protein WP_007691018.1 in Halococcus hamelinensis 100A6

Annotation: NCBI__GCF_000336675.1:WP_007691018.1

Length: 367 amino acids

Source: GCF_000336675.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 46% 78% 245.7 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 34% 98% 144.4 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 97% 142.5 BitD, component of The iron transporter, BitABCDEF 45% 266.5
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) 33% 100% 141.7 BitD, component of The iron transporter, BitABCDEF 45% 266.5
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) 33% 100% 141.7 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 98% 140.2 BitD, component of The iron transporter, BitABCDEF 45% 266.5
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) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
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) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
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) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 117.9 BitD, component of The iron transporter, BitABCDEF 45% 266.5
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 84% 111.3 BitD, component of The iron transporter, BitABCDEF 45% 266.5

Sequence Analysis Tools

View WP_007691018.1 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

MAAVSERGPADTNPTGVELDDVTVRFGDVAALRDVSLAVEDGEFFTLVGPSGCGKTTTLR
AIAGFETPATGAVRIGGREMGGVPPEDRNVGVVFQNYALFPHLSVRENVGYGLRFHDPPG
EVTTRERVDDLLSLVDMADMAERDPDALSGGQQQRVALARALAPGPDVLLLDEPLSALDA
RLRERLRVTLKAIQRDLEITTIYVTHDQAEALAVSDRVAVVNDGRIEQVDTPERVYREPA
SRFVAEFVGDNNRFEAEITGTDPPRASVDGLDVTLPNASDVSAGRPVTLCVRPEAIRVTD
GDVGSSGAAATTMTATVESREFLGDAYRLHCRWNDRSVLVKTGGRRPPEGTVRLAFDTDD
VQVLTDE

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