GapMind for catabolism of small carbon sources

 

Protein WP_029134446.1 in Sedimenticola selenatireducens DSM 17993

Annotation: NCBI__GCF_000428045.1:WP_029134446.1

Length: 480 amino acids

Source: GCF_000428045.1 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
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 98% 317.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 98% 317.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 42% 94% 314.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 97% 341.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 97% 341.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 97% 341.3 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 39% 88% 324.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 39% 88% 324.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
putrescine catabolism gabD lo Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) 39% 88% 324.7 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 91% 316.6 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 96% 311.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 305.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 305.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 38% 94% 305.8 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 297.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 297.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 297.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 98% 297.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 274.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 274.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 274.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 274.2 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 241.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 241.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 241.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 241.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 241.9 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 32% 95% 223.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 213.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 213.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 213.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 213.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 96% 213.4 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 94% 191 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 94% 191 3-succinoylsemialdehyde-pyridine dehydrogenase; SAPD; EC 1.2.1.83 53% 508.8

Sequence Analysis Tools

View WP_029134446.1 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

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Sequence

MLDKRTFYINGQWVDPIKPVELEVINPSTEEPCATIALGGQADTDAAVAAARNAFGDWSQ
SDREQRLALLEKLAEIYQARSNEMAEAISSEMGAPISLAKTAQCGAGIWHIKNFIRALKT
FEFERRLGPHAPNDRILLEPVGVCGLITPWNWPMNQVTLKVIPALATGCTLVLKPSEISP
LSAMLFAEMIDQAGFPPGVFNLVNGDGAGVGSQLTAHPDVDMISFTGSTRAGIAISKSAA
DTVKRVSLELGGKGANLVFADADENAIKRGLRHCFNNSGQSCNAPTRMLVQRPLYQQAVE
TAAQLAEGTAVDHSANEGRHIGPVVSQAQYDKIQRLIQQGTDEGARLVAGGPGRPEGIDR
GYFVRPTVFADVGQDMQIAREEIFGPVLSITPFDSEEEAITIANDTVYGLTNYIQTQDSA
RAKRVARQLRSGMVEINGHSPGAGSPFGGYKQSGNGREGGVWGLEEFLEVKAVSGWPSEE

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