GapMind for catabolism of small carbon sources

 

Protein WP_017220578.1 in Moritella dasanensis ArB 0140

Annotation: NCBI__GCF_000276805.1:WP_017220578.1

Length: 487 amino acids

Source: GCF_000276805.1 in NCBI

Candidate for 37 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacF hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 53% 99% 516.2
D-galacturonate catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 53% 99% 516.2
D-glucuronate catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 53% 99% 516.2
D-xylose catabolism dopDH hi 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 53% 99% 516.2
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 98% 305.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 98% 305.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 35% 98% 305.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 302.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 302.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 302.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 302.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 96% 294.3 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 96% 294.3 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
putrescine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 96% 294.3 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 95% 270 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 95% 270 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 33% 94% 263.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 33% 94% 263.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 33% 94% 263.8 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 256.5 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 256.5 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 256.5 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 256.5 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 256.5 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 99% 250 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 99% 250 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 99% 250 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 99% 250 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 31% 97% 240.4 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 95% 239.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 95% 239.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 95% 239.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 95% 239.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 95% 239.6 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 31% 87% 237.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 95% 211.1 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 95% 211.1 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 53% 516.2

Sequence Analysis Tools

View WP_017220578.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTTQTQRIQAESSLYIGGEWQAGVSTVANINPSDISQNLGNFAQASTAQVHQAISAAKHA
QPTWEKTPLEQKQAVLQGIGDELIARCDELGRLLSSEEGKPFLEGRGEIYRAGQFFQYFA
AEVLRQIGDSAASVRPGVTVEVTREAVGVVAIISPWNFPTATAAWKIAPALAFGNSVIWK
PANLTPASAVALTEIIHRQGLPAGTFNLVLGSGSEVGNVLINSTEVNGVSFTGSVDTGRK
IAAATAPNFVRCQLEMGSKNALIVADDADINIAVEATIAGSFSGAGQKCTASSRLVVMDG
IHDAYVEALIKRMSQLKVGHALEDGVFMGPVVDGKQLDANLAWIDTARQSGGELAFGGER
LSMEHEGFYMSPTLFINTKNDWSVNQEEVFAPMASVIRVADLEEAIATTNDTRFGLTSGI
ITQSLRTSTLFKQQAQTGCVMVNLPTAGTDYHVPFGGRKESSFGPREQGQYAKEFYTVVK
TAYQRAY

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