GapMind for catabolism of small carbon sources

 

Protein WP_078211525.1 in Flavobacterium sp. LM5

Annotation: NCBI__GCF_002017945.1:WP_078211525.1

Length: 393 amino acids

Source: GCF_002017945.1 in NCBI

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism fadA hi 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized) 53% 100% 389.4 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-isoleucine catabolism fadA med acetyl-CoA C-acyltransferase (EC 2.3.1.16) (TIGR01930) 100% 448.3 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
4-hydroxybenzoate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-arginine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-citrulline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
2-deoxy-D-ribonate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
2-deoxy-D-ribose catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-leucine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-lysine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
phenylacetate catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-phenylalanine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-proline catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
L-tyrosine catabolism atoB med Probable acetyl-CoA acyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized) 44% 99% 300.8 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) 44% 288.9
phenylacetate catabolism paaJ1 med 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized) 43% 90% 295 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
L-phenylalanine catabolism paaJ1 med 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized) 43% 90% 295 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
4-hydroxybenzoate catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 42% 100% 287.3 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
phenylacetate catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 42% 100% 287.3 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
L-phenylalanine catabolism paaJ2 med 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale) 42% 100% 287.3 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
4-hydroxybenzoate catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 100% 282.3 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
L-tryptophan catabolism pcaF med β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized) 43% 100% 282.3 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
4-hydroxybenzoate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 268.5 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
phenylacetate catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 268.5 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4
L-phenylalanine catabolism pimB lo 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized) 39% 100% 268.5 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 53% 389.4

Sequence Analysis Tools

View WP_078211525.1 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

MKTAYIVKAYRTAVGKAPKGVFRFKRPDELAAETIQYMMNELPDFDKTRIDDVMVGNAMP
EAEQGLNVGRLISLMGLKVDDVPGVTVNRYCASGLETIGMATAKIQSGMAHCIIAGGAES
MSYIPMGGYKPTPDYKVAAAGHEDYYWGMGLTSEAVAKQFNISRADQDEFAFQSHNKALK
AQAEGKFDNQIVPITVEQTFINENGKKETKSYVVTKDEGPRAGTSLEALAGLRPVFAADG
SVTAGNSSQMSDGAAFVLVMSEEMVKELNIQPIARLVNFASAGVEPRIMGIGPVKAIPKA
LKQAGLTLNDIDLIELNEAFASQALAVTRELNLNPDIINVNGGAIALGHPLGCTGAKLSV
QLFDEMKRRGNKYGIVSMCVGTGQGSAGIFELV

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