GapMind for catabolism of small carbon sources

 

Protein 8501416 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Length: 1013 amino acids

Source: Miya in FitnessBrowser

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) 46% 99% 477.6
L-arginine catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 98% 665.9
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 46% 99% 477.6
L-arginine catabolism rocA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 98% 665.9
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 46% 99% 477.6
L-citrulline catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 98% 665.9
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 46% 99% 477.6
L-citrulline catabolism rocA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 98% 665.9
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 46% 99% 477.6
L-proline catabolism putA hi pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) 98% 665.9
L-arginine catabolism put1 med Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized) 30% 93% 124.8
L-citrulline catabolism put1 med Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized) 30% 93% 124.8
L-proline catabolism put1 med Proline dehydrogenase; PRODH; Proline oxidase; TtPRODH; EC 1.5.5.2 (characterized) 30% 93% 124.8
L-arabinose catabolism xacF lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 36% 95% 277.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
D-galacturonate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 36% 95% 277.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
D-glucuronate catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 36% 95% 277.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
D-xylose catabolism dopDH lo 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 36% 95% 277.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
4-hydroxybenzoate catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
2'-deoxyinosine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
2-deoxy-D-ribose catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
ethanol catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-threonine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
thymidine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-tryptophan catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 97% 247.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 97% 245 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
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) 34% 98% 241.5 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 33% 91% 238.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 33% 93% 238 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 33% 93% 238 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 33% 93% 238 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 33% 95% 235.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 33% 95% 235.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 33% 95% 235.3 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 95% 234.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 95% 234.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 95% 234.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 95% 234.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 93% 229.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 93% 229.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 93% 229.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 33% 93% 229.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 218.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 218.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 218.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 218.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 218.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 91% 201.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 91% 201.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 94% 201.4 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) 46% 477.6

Sequence Analysis Tools

View 8501416 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MEQHLDARIVERGKEFFKSISGEAPSIFNKGFWTGKVMDWAMQNEGFKVQLFRFVDVLPY
LNTSEALTRHIREYFSADGADVPPVLKWGAGAAGFGGAFTGMLMGKFIRSNIEGMARTFI
IGENTKEAIKGLAKLRKEGFAFTVDLLGEATVSEEEADAYRDGYLEVLDAISREHAKWAP
LTDSTGSTTGPDASQDWGHTPKVNVSIKPSALYSQAKPGDVEGSVQGILSRLVPIYRKIV
EMGGFLCIDMEQLKYREMTLELFKRLRTMPEFRDYPHLSIVLQAYLRCTEHDLDELLAWG
RAERLPFGIRLVKGAYWDYETVMAKQNGWEIPVWTRKPESDICYEKLARRILENNDLVYF
ACASHNVRTISTVMETARALNVPAHRYEFQVLYGMAEPVRKGLKNVAGRVRLYCPYGELI
PGMAYLVRRLLENTANESFLRQSFVDGAELERLLENPQATLERELAAAPPPRSTPAAQPG
IDGLPPFVNESMLDLTIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPA
KPAEVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFELSAW
QVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVI
APWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRS
SVMGDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDD
ADLDEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANY
MGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIF
GPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAM
VERQPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTENTMRRGFAPIEEDDDWIG

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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