GapMind for catabolism of small carbon sources

 

Protein WP_092053392.1 in Desulfuromonas acetexigens DSM 1397

Annotation: NCBI__GCF_900111775.1:WP_092053392.1

Length: 229 amino acids

Source: GCF_900111775.1 in NCBI

Candidate for 30 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 med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 84% 158.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 42% 90% 152.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 40% 85% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-arginine catabolism artP med L-Arginine ABC transporter, ATPase component (characterized) 41% 82% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 84% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 84% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 40% 84% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 40% 81% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 141.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 141.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 91% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 91% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 55% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 55% 130.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 35% 73% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 83% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 210.7

Sequence Analysis Tools

View WP_092053392.1 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

MAFIEINGLSKHYPSRAGVVAALDGIDLSIDEGTFLGVMGPSGSGKSTFLSLIGGLCHPT
AGTIRVDGIDIFRLPAEQLADFRREYLGFVFQSFNLVPYLTALENVMLPLTVKKLANAEK
RERAYQVLERVGLKARAGHLPGELSGGEQERVAIARALVNRPPLILADEPTGSLDTATAA
SIMDLFAELNGEGQTIVMVTHNPETRGNFHRTLLLRDGRVAGESLATAA

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