GapMind for catabolism of small carbon sources

 

Protein WP_053938622.1 in Amantichitinum ursilacus IGB-41

Annotation: NCBI__GCF_001294205.1:WP_053938622.1

Length: 498 amino acids

Source: GCF_001294205.1 in NCBI

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 63% 99% 639 aldehyde dehydrogenase 56% 537.0
L-arginine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 63% 99% 639 aldehyde dehydrogenase 56% 537.0
L-citrulline catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 63% 99% 639 aldehyde dehydrogenase 56% 537.0
putrescine catabolism puuC hi 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 63% 99% 639 aldehyde dehydrogenase 56% 537.0
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 53% 99% 523.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
ethanol catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-threonine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
thymidine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 98% 422.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 45% 92% 406 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 363.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 363.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 363.2 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 351.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 351.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 37% 95% 310.1 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 100% 293.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 99% 287.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 99% 287.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 99% 287.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 37% 99% 287.3 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 283.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 283.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 283.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 283.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 32% 95% 248.4 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 241.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 241.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 241.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 241.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 97% 241.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 235.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 235.7 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 81% 234.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 81% 234.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 81% 234.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 81% 234.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 35% 81% 234.6 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 95% 214.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 95% 214.5 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 63% 639.0

Sequence Analysis Tools

View WP_053938622.1 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

MSQTKDFAYWRHLAEGLQIEGRALIDGEFTAAASGKTFDCISPIDGKLLTQVAWCGEADV
DHTVAIARQRFESGVWSDLNPRQRKEIMLRWAELIRVHADEIALLETLDAGKPIGDTTTV
DVPGAAYTVQWYAEAIDKAGGEVAPVDYHLVGLVTRQPIGVVAAVVPWNFPILMAAWKFG
PALAAGNSVILKPSEKSPLSALRVAQLALEAGIPPGVFNVLPGFGDTGKLLALHMDVDCL
AFTGSTFVGKQLMQHSGQSNLKRVWLELGGKSPNIIMPDCPDMARAARSAAGAIFYNMGE
MCTAGSRLLVHRSVKDEFIKALIAEAAAYKPGNPLDPATSMGAIVDHIQLERVMSYIETG
KGEATLLLGGGRTLTETGGYYIEPTIFDVASQEARVAAEEIFGPVLSVITFDTLDEAIAL
ANASEYGLAAAIWTADLTTAHEAARRLRAGTVWVNCYDEGGDMNFPFGGFKQSGNGRDKS
LHALDKYTELKSTLIRLR

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