GapMind for catabolism of small carbon sources

 

Protein 207735 in Desulfovibrio vulgaris Hildenborough

Annotation: MicrobesOnline__882:207735

Length: 551 amino acids

Source: 882 in MicrobesOnline

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
propionate catabolism prpE med Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized) 43% 94% 454.1 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
4-hydroxybenzoate catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
L-lactate catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
acetate catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
2'-deoxyinosine catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
2-deoxy-D-ribose catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
ethanol catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
L-threonine catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
thymidine catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
L-tryptophan catabolism acs lo 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized) 40% 94% 367.5 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0
4-hydroxybenzoate catabolism hcl lo Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized) 33% 97% 234.2 medium-chain acyl-CoA ligase (EC 6.2.1.2) 53% 604.0

Sequence Analysis Tools

View 207735 at MicrobesOnline

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

MDKLTFASYDEFLRVFSLDAPETFNFAFDVLDAMANETPDRLAIAHVDDAGVRRDYTFAW
LADASARLANALKARGVRKGHRVMLVLHRRIEFWVSMLALHRLGAVAIPAPAQLTPKDIV
FRVERAQVRAVIVDDGITDRIEAARPDCPTLSVLVQCGGTPLPDGWCDYEALCADASPSF
PRPTAPDELACGEDPLLIFFSSGTTGMPKMVEHVHTYPLGHLVTGMYWHDLRPGDLHLTV
ADTGWGKAVWGKFYGQWMAGAAVFVYDFRGKFDPEALLDVVAKNGVTTFCAPPTVYRFLV
RADLSRYDLSKLRHCTTAGELLNESVFHGWKAATGLSIYEGYGQTETTLQIATLSCMEAK
PGSIGRPMPGWGITLLDHEGKECPTGEEGEICIRISDGLPVGLFRGYVEDAEKTASVMFD
GYYHTGDKAWMDEDGYLWFLGRVDDLIKSSGYRIGPFEVESALVAHPAVVEAAVTGVPDP
LRGQAVKATIVLAAGYEAGEVLTKELQDHVKKVTAPYKYPRIVEYVAELPKTISGKIKRA
EIRQRDSEKSA

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