GapMind for catabolism of small carbon sources

 

Protein WP_057508189.1 in Stenotrophomonas chelatiphaga DSM 21508

Annotation: NCBI__GCF_001431535.1:WP_057508189.1

Length: 892 amino acids

Source: GCF_001431535.1 in NCBI

Candidate for 21 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) 52% 80% 840.5
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-citrulline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-proline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 80% 840.5
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 33% 60% 131 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
4-hydroxybenzoate catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 53% 125.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-tryptophan catabolism nbaE lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 53% 125.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-tryptophan catabolism praB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 53% 125.2 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 59% 122.1 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-arginine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 61% 113.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
L-citrulline catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 61% 113.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6
putrescine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 61% 113.6 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 54% 873.6

Sequence Analysis Tools

View WP_057508189.1 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

MNAPTLSPAAPGFTPPADALLSPELPASPSPFRQAITDAWLKDEATHVSELLAQARLPAD
EQAQVQALAADLVARVRVRAKDQGAIEAFMRQYDLGSEEGVLLMCVAEALLRIPDQDTAD
KLIRDKLADADWKKHMGGSDSVLVNASTWGLMLTGKLVQINDVTRADVPGAFKRLMGRVG
EPVIRLAVRQAMKIMGHQFVMGRTIGEALERSHKGDNASYRYSFDMLGEGALTMKDALRY
LEDYRRAIHAIGGDHKARGGRPEGDVNNAPGISIKLSALYPRYEHAKRARVLQDLVPGVL
ELAQLAKSYGIGCTVDAEEADRLELSLDIIDAVFSDASLAGWDGFGVVVQAYQKRTPYTI
DFLADMARRNGRRLQVRLVKGAYWDAEIKRAQIEGYPGYPVFTRKQNTDVSYLACAKRLF
GHSDAIYPMFATHNAHTIAAIRTIAKGGVYEHQKLHGMGDDLYAEVVPADRLGLPCRVYA
PVGSHEDLLPYLVRRLLENGANSSFVNRITDDRVAIAELVRDPVEMVSAFAAVSPSNIAH
PKIPLPVNLLRSQNHDRNNSMGINLANDNALRALAEQLNAAVKPWTAAPLVPGATVTGAS
LPVTNPADTRQVVGHWQAADAATVQKALANAVAAQPAWNRTPATSRAAILEHAADQLEAR
IAEFMALCVKEAGKSLPDGVAEVREAVDFLRYYAKQAREQFAHAEKLPSPTGESNELQLH
GRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTNLIGYYAVKLLLDAGVPEGV
LQFLPGDGATVGAALTADPRVAGVAFTGSTDTARAINRAMAARDAAIGVLIAETGGQNAF
IADSSALPEQLVKDAIGSAFTSAGQRCSAARVLFVQDDIADKVMTMLAGRGE

This GapMind analysis is from Apr 09 2024. 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