GapMind for catabolism of small carbon sources

 

Protein 8501039 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1775 acetate/CoA ligase (RefSeq)

Length: 667 amino acids

Source: Miya in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
4-hydroxybenzoate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
L-lactate catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
L-lactate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
acetate catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
acetate catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
2'-deoxyinosine catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
2'-deoxyinosine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
2-deoxy-D-ribose catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
2-deoxy-D-ribose catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
ethanol catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
ethanol catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
L-threonine catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
L-threonine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
thymidine catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
thymidine catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
L-tryptophan catabolism acs hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 58% 98% 754.6
L-tryptophan catabolism acs hi acs: acetate--CoA ligase (EC 6.2.1.1) (TIGR02188) 100% 996.2
propionate catabolism prpE hi Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized) 59% 96% 750.7

Sequence Analysis Tools

View 8501039 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

MSQNKSDKIESMMDEKRLFAPPAAPSGDRRRPHVNGMDEYLAHRERADKDPEGFWGDRAR
QLLDWFTPWDKVMDADMNEPRIEWFKGATLNVAYNCLDRHLVNGRRNKAAIIWQGEPEDD
VRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALYMPMIPELAVAMLACARIGAVHSIVFA
GFSAVSLQNRIQDCEAKVVVTADAVLRAGRSIPLKVNVDEALKDCPSVERVVVVDRAHSN
CAMREGRDMWWHEAMADRTLDTSCPCAKMDSEDMLFILYTSGSTGKPKGVVHTTGGYLAY
AAHTTQWVFDLHDDDVYWCTADIGWITGHSYIVYGPLALGGTTLMFEGVPSWPGPDRFWH
IVEKFRVNIFYTAPTVIRALMREGAHWTQKHDLSSLRVLGSVGEPINPEAWMWYHEHIGH
SRLPIVDTWWQTETGGIMISALPYATTLKPGSATMPLPGIDAAVVKADGTPCGPNEGGHL
VVRKPWPGMLRGVFGSPERYKSTYFERFPGMYESGDGARTDEDGYTWVMGRLDDVINVSG
HRMGTAEVESALVSHPAVAEAAVVGMPHAIKGEAIYAYVTLSAGTEETEELRAALRTWVR
KEIGPIATPEVIQFAEGLPKTRSGKIMRRILRKIASGAGSDFGDTSTLADPGVVQDLIEG
RVQLTGH

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