GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_4232 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Length: 1074 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-arginine catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 696.3
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-arginine catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 696.3
L-citrulline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-citrulline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 696.3
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-citrulline catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 696.3
L-proline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 56% 83% 1088.9
L-proline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 696.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 92% 197.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 92% 197.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 32% 95% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 89% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 89% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 89% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 89% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-tryptophan catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 32% 95% 173.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 31% 95% 171 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 93% 170.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-arginine catabolism patD lo Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 31% 95% 160.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-citrulline catabolism patD lo Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 31% 95% 160.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
putrescine catabolism patD lo Gamma-aminobutyraldehyde dehydrogenase; ABALDH; EC 1.2.1.19; 1-pyrroline dehydrogenase; 4-aminobutanal dehydrogenase; 5-aminopentanal dehydrogenase; EC 1.2.1.- (uncharacterized) 31% 95% 160.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-arginine catabolism gabD lo Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 31% 99% 156.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
L-citrulline catabolism gabD lo Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 31% 99% 156.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9
putrescine catabolism gabD lo Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized) 31% 99% 156.8 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 56% 1088.9

Sequence Analysis Tools

View N515DRAFT_4232 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

MRPFCHNTYNCGIPCASPAHRHPVTQPILSPELPTGAEPARARITAAWLRDETEAVNDLL
VQASLPPVEREKVIDLAADLVTRVRARAKDQSAVESFMRQYDLSSEEGVLLMCVAEALLR
IPDKATADKLIRDKLGDANWKKHLGQSESLFVNASTWGLMLTGKLVNLAGDIRHDFTGAL
RRLVGRAGEPAIRLAVRQAMRIMGHQFVMGRTIGEALDRCAQKEYAVYRYSYDMLGESAL
TSETAERYQQDYRNAIAAIGARGPFANHTDAPSISVKLSALHPRYEVAKRELARRDLTAK
LLELSQLAMKHGIALSVDAEEADRLELSLDILGDVFAHPSLAGWNGLGIVVQAYSKRTPF
VIDWLIETARGSGRRWYVRLVKGAYWDAEVKRAQENGLPGYPVYTRKPNTDVSYLACARK
LFDAGIELIYPQFATHNAHTIAAVHHLAKGRPYEYQRLHGMGTDLYAEVIGAQNLNVPCR
VYAPVGTHEDLLPYLVRRLLENGANTSFVNRVVDESLPVRELVADPCETVRSFASIPHPR
IPLPVNLYGELRKNSMGVNFSNDNELKALAETVNAKSGPWTATPLVPGATSAGATVQVTN
PADRRQVVGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFI
ALCVREAGKGLPDAIAEIREAADFLRYYATMARRYFGQPEQLPGPTGESNQLFLNGRGVF
VCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAGVPADVLQYLP
GDGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGGQNAMIADSS
ALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTD
VGPVIDEDARKILVDHAARMDQEAKKIGEVALDPATTGNGTFFAPRAYEIPGLATLTREI
FGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNRNQI
GAVVGVQPFGGEGLSGTGPKAGGPHYLFRFAGERTLTINTTAAGGNASLLTIGE

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