GapMind for catabolism of small carbon sources

 

Protein WP_200770545.1 in Sulfurivirga caldicuralii DSM 17737

Annotation: NCBI__GCF_900141795.1:WP_200770545.1

Length: 649 amino acids

Source: GCF_900141795.1 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-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 34% 88% 125.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 30% 80% 123.6 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 31% 100% 110.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 31% 100% 110.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 31% 100% 110.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 31% 100% 110.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 30% 96% 109.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 30% 96% 109.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 30% 96% 109.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 89% 103.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 89% 103.2 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 33% 96% 100.1 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 94% 95.5 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 91% 94 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 91% 94 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 91% 94 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 91% 94 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 30% 96% 92.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 30% 96% 92.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7
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) 30% 96% 92.8 Probable multidrug ABC transporter ATP-binding protein YbhF 41% 391.7

Sequence Analysis Tools

View WP_200770545.1 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

MSDVAAPSAKMASGQTGAMDSQQSAAMIRLQGVVKRYRKTTALRGVDLTVARGQLFGLIG
PDGAGKSSLMHIVAGVLAQDAGEVVVNGVAIRDERSAEAVKAQLGLMPQGLGLNLYPTLS
VEENLRFFADLHAIPPEVVSQRIEQLLAMTQMSRFRDRRMQHLSGGMKQKLGLMCTLIHE
PQLIILDEPTTGVDPISRQAFWELLNQLVRERALTALVSTAYMDEAARFDTLALMHDGLI
LEQGPPDSLAAGQAATVLWFSAAARDTLRPCLQDFSAMRLRMEAGQLRAWLPQTQREALV
QKLDSPPVRETPPTLEDLFMAAVGAPHDLTFDWAPPPPASAPVEIRADGLVRRFGDFTAV
DHVSLQVRAGEIFGLLGANGAGKSTLIRMLTGILLPTAGSGEVAGQPLGKAARQVRQRIG
YMSQQFSLYPQLSVLENLRLFGRIYGLRRRQLQQRIEWGLDWTGLVTDKNEAAGRLPLGK
RQRLALLAAILHEPEVLFLDEPTSGVDPLGRQQFWGLLHTLVRKEGVALLVTTHAMNEAE
NCHNLALMRQGRVVASGSPRQLRSTVRSRFGEVYALRVDDTARALATLRQRGWLAFAQGR
EVHVFVAGDDASLGRLKAQLDEAGCVISAIERVEPTMEEVFVSMIEGTA

This GapMind analysis is from Apr 09 2024. 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