GapMind for catabolism of small carbon sources

 

Protein 352309 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

Length: 549 amino acids

Source: Btheta in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribonate catabolism aacS hi Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 44% 95% 487.6 Acyl-CoA ligase SID4; Siderophore biosynthesis cluster protein SID4; EC 6.2.1.- 41% 387.5
2-deoxy-D-ribose catabolism aacS hi Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 44% 95% 487.6 Acyl-CoA ligase SID4; Siderophore biosynthesis cluster protein SID4; EC 6.2.1.- 41% 387.5
L-leucine catabolism aacS hi Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 44% 95% 487.6 Acyl-CoA ligase SID4; Siderophore biosynthesis cluster protein SID4; EC 6.2.1.- 41% 387.5
L-phenylalanine catabolism aacS hi Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 44% 95% 487.6 Acyl-CoA ligase SID4; Siderophore biosynthesis cluster protein SID4; EC 6.2.1.- 41% 387.5
L-tyrosine catabolism aacS hi Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized) 44% 95% 487.6 Acyl-CoA ligase SID4; Siderophore biosynthesis cluster protein SID4; EC 6.2.1.- 41% 387.5
phenylacetate catabolism paaK lo phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 30% 67% 164.5 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
L-phenylalanine catabolism paaK lo phenylacetate-CoA ligase (EC 6.2.1.30) (characterized) 30% 67% 164.5 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
4-hydroxybenzoate catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
L-lactate catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
acetate catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
2'-deoxyinosine catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
2-deoxy-D-ribose catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
ethanol catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
L-threonine catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
thymidine catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6
L-tryptophan catabolism acs lo Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized) 31% 64% 142.9 Acetoacetate--CoA ligase (EC 6.2.1.16) 44% 487.6

Sequence Analysis Tools

View 352309 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

MQLFERTLGQWLEHWAEETPDKEYIVYSDRNLRFTWSQLNQRVDDMAKGLIAVGVERGTH
VGIWAANVPDWLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDF
VQMTYTMLPELKTCERGHLKSERFPYMKNVIYVGQEKHRGMYNTAEILLLGNNVEDDRLT
ELKSKVDCHDVVNMQYTSGTTGFPKGVMLTHYNIANNGFLTGEHMKFTADDKLCCCVPLF
HCFGVVLATMNCLTHGCTQVMVERFDPLVVLASIHKERCTALYGVPTMFIAELHHPMFDL
FDMSCLRTGIMAGSLCPVELMKQVEEKMYMKVTSVYGLTEAAPGMTATRIDDSFDVRCNT
VGRDFEFTEVRVIDPETGEECPVGVQGEMCNRGYNTMKGYYKNPEATAEVIDKDNFLHSG
DLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDVQVAGIPSKKYGEAV
GAFIILQEGVEMHESDVRDFCKNKISRYKIPKYVFFVKEFPMTGSGKIQKFRLKDLGLQL
CKEQGIEII

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