GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_4232 in Dyella japonica UNC79MFTsu3.2

Annotation: FitnessBrowser__Dyella79:N515DRAFT_4232

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

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

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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 (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