GapMind for catabolism of small carbon sources

 

Protein WP_085635425.1 in Marivita geojedonensis DPG-138

Annotation: NCBI__GCF_002115805.1:WP_085635425.1

Length: 274 amino acids

Source: GCF_002115805.1 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-isoleucine catabolism livF hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) 42% 183.0
L-leucine catabolism livF hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) 42% 183.0
L-phenylalanine catabolism livF hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 43% 199.1
L-proline catabolism HSERO_RS00900 hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-serine catabolism Ac3H11_1692 hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-tyrosine catabolism Ac3H11_1692 hi ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 213.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-valine catabolism livF hi High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 46% 100% 199.5 NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) 42% 183.0
L-alanine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 46% 100% 199.5 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 43% 199.1
L-serine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 46% 100% 199.5 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 43% 199.1
L-threonine catabolism braG med High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 46% 100% 199.5 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 43% 199.1
L-arginine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-glutamate catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-histidine catabolism braG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 98% 193.4 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
D-alanine catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 44% 98% 193 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-proline catabolism AZOBR_RS08250 med Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 44% 98% 193 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-isoleucine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 42% 94% 183 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-leucine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 42% 94% 183 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-proline catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 42% 94% 183 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-valine catabolism natE med NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 42% 94% 183 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5
L-histidine catabolism natE med NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 40% 98% 172.2 High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine 46% 199.5

Sequence Analysis Tools

View WP_085635425.1 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

MLDATRTDETLLEVNNIEVIYNHVILVLKGVSLSVKKGGITALLGGNGAGKTTTLKAISN
LLHSERGEVTKGSIIYQGERVQDLDPAALVKRGVIQVMEGRHCFGHLTVEENLLTGAYTR
KDGKGAIEADLQMVYDYFPRLKERRKSQAGYTSGGEQQMTAIGRALMSRPETILLDEPSM
GLAPQLVEQIFEIVKSVNENEGVSFLLAEQNTNVALHYAHQGYILENGRVVMDGPAAELR
ENPDVKEFYLGMSDEGRKSFRDVRSYRRRKRWLA

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