GapMind for catabolism of small carbon sources

 

Protein WP_073950325.1 in Streptomyces kebangsaanensis SUK12

Annotation: NCBI__GCF_001906585.1:WP_073950325.1

Length: 511 amino acids

Source: GCF_001906585.1 in NCBI

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 50% 98% 469.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 387.5
L-citrulline catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 50% 98% 469.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 387.5
L-lysine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 50% 98% 469.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 387.5
putrescine catabolism patD hi aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 50% 98% 469.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 387.5
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 369.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 369.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-tryptophan catabolism nbaE med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 40% 93% 356.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized) 42% 94% 353.2 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism gabD med Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized) 41% 98% 293.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-citrulline catabolism gabD med Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized) 41% 98% 293.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
putrescine catabolism gabD med Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized) 41% 98% 293.9 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 96% 334 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 96% 334 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 96% 334 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 38% 96% 334 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 329.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 329.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 94% 329.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 38% 99% 294.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 38% 99% 294.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 38% 99% 294.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 38% 99% 294.3 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 250 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 250 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 250 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 250 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 34% 95% 250 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 85% 245.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 85% 245.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 85% 245.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 85% 245.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 85% 245.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 34% 96% 230.7 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 94% 223.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 33% 98% 211.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 33% 98% 211.8 aminobutyraldehyde dehydrogenase (EC 1.2.1.19) 50% 469.5

Sequence Analysis Tools

View WP_073950325.1 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

MQNPGNAAQDRFPAQNRFADGAQYIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDV
DAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDV
PGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLP
AIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMV
SFTGSTAVGKRVAEIATASVKRLHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDC
TAATRAYVQRPLYEEFVARTAALMETVRLGDPFAPGTDLGPLISHVHRDRVAGFVDRARA
YARVVTGGEAPQGELKNGAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLA
NDTAYGLAASAWSRDVYRANRATREIKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSY
SFEEYTQIKHVMFDNTAVARKDWHRTIFGDR

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