GapMind for catabolism of small carbon sources

 

Protein WP_012408912.1 in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Annotation: NCBI__GCF_000020025.1:WP_012408912.1

Length: 248 amino acids

Source: GCF_000020025.1 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
4-hydroxybenzoate catabolism badH med BadH (characterized) 41% 99% 177.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
phenylacetate catabolism badH med BadH (characterized) 41% 99% 177.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-phenylalanine catabolism badH med BadH (characterized) 41% 99% 177.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 42% 98% 172.6 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-rhamnose catabolism LRA5 med 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 41% 95% 157.9 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 39% 98% 160.6 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
D-sorbitol (glucitol) catabolism sdh lo Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized) 37% 99% 156 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 54% 141.7 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase (characterized) 35% 99% 136.3 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
D-galactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 35% 96% 122.1 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
lactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 35% 96% 122.1 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 95% 118.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 95% 118.2 3-oxoacyl-[acyl-carrier-protein] reductase; 3-ketoacyl-acyl carrier protein reductase; EC 1.1.1.100 76% 368.6

Sequence Analysis Tools

View WP_012408912.1 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

MTLLQGKVAIVTGASRGIGKAIAIELASQGAIAVVNYASSSAAAEAVVTEITAVGGQAIA
IQADVSKGDQVDALVNAVMEKFSRVDILVNNAGITRDTLLLRLKPEDWQAVIDLNLTGVF
LCTRAVSKIMLKQRSGRIINITSVAGQMGNPGQSNYSAAKAGVIGFTKSVAKELATRGIT
VNAVAPGFITTDMTSDLNNPEDILKYIPLGRFGQPEEVAGMVRFLAADPAANYITGQVFN
VDGGMVMA

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