GapMind for catabolism of small carbon sources

 

Protein WP_078716392.1 in Desulfovibrio gracilis DSM 16080

Annotation: NCBI__GCF_900167125.1:WP_078716392.1

Length: 1001 amino acids

Source: GCF_900167125.1 in NCBI

Candidate for 51 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 50% 99% 521.9
L-arginine catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 100% 697.1
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 50% 99% 521.9
L-arginine catabolism rocA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 100% 697.1
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 50% 99% 521.9
L-citrulline catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 100% 697.1
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 50% 99% 521.9
L-citrulline catabolism rocA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 100% 697.1
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 50% 99% 521.9
L-proline catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 100% 697.1
L-arginine catabolism put1 med Proline dehydrogenase; PRODH; DrPRODH; Proline oxidase; EC 1.5.5.2 (characterized) 31% 97% 123.6
L-citrulline catabolism put1 med Proline dehydrogenase; PRODH; DrPRODH; Proline oxidase; EC 1.5.5.2 (characterized) 31% 97% 123.6
L-proline catabolism put1 med Proline dehydrogenase; PRODH; DrPRODH; Proline oxidase; EC 1.5.5.2 (characterized) 31% 97% 123.6
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 95% 272.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 95% 272.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 95% 272.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 34% 95% 272.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 255.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 255.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 98% 255.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 88% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 88% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 33% 94% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 35% 88% 246.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 94% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 94% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 34% 94% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 97% 240.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 34% 97% 240.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
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) 33% 94% 235.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
4-hydroxybenzoate catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
2'-deoxyinosine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
2-deoxy-D-ribose catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
ethanol catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-threonine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
thymidine catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-tryptophan catabolism adh lo Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized) 32% 94% 235 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 95% 233.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 95% 233.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 31% 95% 233.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 31% 98% 229.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 88% 218.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 88% 218.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 88% 218.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 88% 218.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 33% 88% 218.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 208 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 208 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 208 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 98% 208 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 208 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 91% 200.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 91% 200.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 50% 521.9

Sequence Analysis Tools

View WP_078716392.1 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

MNRSAQETSIRDTGRAFFESIRGEAPSVFNKGFWTGKVMDWAMKNEDFKVQLFRFVDVLP
YLNTTDNLTRHIEEYFSGEDAEIPSVLKWGAGKSTGIIGNLAGKVMGKAIRSNIEGMARQ
FIVGQNTKEALKGMKKLRKDGFAFTVDLLGEATVSEEESEAYMNGYLELLDAVAGEQASW
AALGGNGDLDWGYAPKVNVSVKPSALYSQSKPVDVEGSVQGILARLKPIYRKVREMNGFL
CIDMEALKYKEMTLELFKRLREDPEFVDYPHLSIVLQAYLKDTDKDLDELIAWVREKNLP
IGIRLVKGAYWDEETVIALQSGWPVPVWTNKAESDMSYERNSKKILENSDLIYFQCGSHN
VRTISYVFETAKALDVPEDRYEFQVLYGMAEPVRKGLQNVAKRVRLYCPYGELIPGMAYL
VRRLLENTANESFLRQSFAEGEEVDRLMENPEETLKRELAAKCAPEETDSKGLDAPFRND
ELIDFTIPGNRHAFPEAIATVRAAKGKTYPLCIGGKDVETEKFIQSSNPADPDEVLGRIC
QAGQGEIDQAIAAAESALPAWRDTEPRERAEVILRAAAIMRRRQFELSAWQVLEVGKQWD
QAFHDVGEAIDFMEYYARDMVRLGKPRRMGRAPGEHNQLFYQAKGIAAVISPWNFPLAIS
TGMVSANIVVGNPVIYKPSNLAPIIGYGLVEIFREAGLPDGVFNYCPGSSRDMGDYLVEH
PKVAVISFTGSEAVGLRIQEKAAKVQPGQTHCKRVVAEMGGKNAIIVDDDADLDLAVLHI
LYSAFGFQGQKCSACSRVIVVEDIYDRFIERLTKAAECIKIGPSEDPANYMGPVVDASAQ
QKILEYIDLAAKEGTILVKRSVPEKGCYVPLTIVTDIEPQHRIAQEEIFGPVLAVMRAKD
FDQAIDWANATRFALTGGVFSRSPKHLDQARREFRVGNLYLNRNNTGALVERQPFGGFKM
SGVGSKTGGPDYLIQLMDPRCVTENTMRRGFTPIEEGEMWV

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