GapMind for catabolism of small carbon sources

 

Protein WP_041416363.1 in Shewanella halifaxensis HAW-EB4

Annotation: NCBI__GCF_000019185.1:WP_041416363.1

Length: 874 amino acids

Source: GCF_000019185.1 in NCBI

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism acn hi Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 80% 100% 1392.5
L-isoleucine catabolism acn hi acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99) (TIGR02333) 100% 1754.8
propionate catabolism acn hi Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 80% 100% 1392.5
propionate catabolism acn hi acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99) (TIGR02333) 100% 1754.8
L-threonine catabolism acn hi Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 80% 100% 1392.5
L-threonine catabolism acn hi acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99) (TIGR02333) 100% 1754.8
L-valine catabolism acn hi Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 80% 100% 1392.5
L-valine catabolism acn hi acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99) (TIGR02333) 100% 1754.8
citrate catabolism acn hi 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 83% 99% 1445.3
L-isoleucine catabolism acnD hi 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 83% 99% 1445.3 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 45% 743.0
propionate catabolism acnD hi 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 83% 99% 1445.3 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 45% 743.0
L-threonine catabolism acnD hi 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 83% 99% 1445.3 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 45% 743.0
L-valine catabolism acnD hi 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 83% 99% 1445.3 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 45% 743.0

Sequence Analysis Tools

View WP_041416363.1 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

MNTNYRKPLPGSDLDYFDTEAAVNAISPGAYAKLPYSSRVYAENLVRRCSPESLSDCLSQ
IIHRKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIADKGGDPSKVNPVVPTQLIVDH
SLAVEHAGFEKDAFEKNRAIEDRRNQDRFHFINWTKTAFENIDVIQPGNGIMHQINLEKM
SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRPSYMRLPDIVGV
ELVGKRQSGITATDIVLAITEFLRNEKVVSTYLEFFGEGAANLTLGDRATISNMTPEFGA
TAAMFYIDDKTIDYLKLTGRDDKQVKLVETYAKQAGLWADSLQDAEYERVLRFDLSSVGR
NIAGPSNPHRRVATADLAAKGISGYLDSELEEAGLMPDGACIIAAITSCTNTSNPRNVIA
AGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEDANLLTELEALGFGIVGFACTTCNG
MSGALDPVIQQEVIDRDLYTTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRF
DIEKDVLGQDSNGNDILLKDLWPSDEEIDAVIAQSVKPEQFRKVYEPMFDLKVDYGDDNE
LKVNPQYEWRPQSTYIRRPPYWEGALAGERTMKGMRPLAVLGDNITTDHLSPSNAIMLDS
AAGAYLHKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVTQLGKNGEVEVKQGSF
ARIEPEGAESRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGF
ERIHRTNLVGMGVLPLEFTNGANRHTYQIDGTETYDVLGERTPGAHLTVIMTRSNGEVAE
IPVKCRLDTAEEVSIYEAGGILQRFAQDFLESST

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