GapMind for catabolism of small carbon sources

 

Protein 207710 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU2226 acetyl-CoA carboxylase, biotin carboxylase, putative

Length: 471 amino acids

Source: 882 in MicrobesOnline

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism pccA lo propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized) 33% 58% 234.2 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
propionate catabolism pccA lo propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized) 33% 58% 234.2 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-threonine catabolism pccA lo propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized) 33% 58% 234.2 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-valine catabolism pccA lo propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized) 33% 58% 234.2 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-leucine catabolism liuB lo Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized) 36% 65% 231.5 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-isoleucine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 33% 81% 206.1 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
propionate catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 33% 81% 206.1 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-threonine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 33% 81% 206.1 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0
L-valine catabolism pccA1 lo acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 33% 81% 206.1 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 37% 265.0

Sequence Analysis Tools

View 207710 at MicrobesOnline

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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MQTNDHKVLVANRGEIATRIVRACHRLGLEFTCVYTAEDAASGHVRLARELGGANSLYRV
SSYHDANELLAVADDAGCTAVHPGYGFFAEDYRFARRVAQRERKLIFIGPSWRVIRELGD
KINTKRLARSLGVPTVPGSDKPIYDELEAEKVAQSLYEFQEQQGIRRPLVLVKASAGGGG
MGIEEVYDLDLFKSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQIVSDRTGRNPVHF
GTRNCSIQSIGLQKRIEVAPGFDPTSIEYGFDAAQVLRDITYHSLAMARKVGYDNVGTWE
WIVTRDGHPFLMEVNTRIQVENGVSARIARVNGQEVDLIAEQIRIGLGQPLGYGQEDITF
EGVGIEYRLIAEDPDNRFTPWVGRIDAFGWPEEDWARMYTHVPTEEPYDIPTEFDPNLAL
AIIWGKDLEEVKRRGVSFLEGLTLQGQNKAGDELRSNVNFLRDNTGRILRF

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, the preprint on GapMind for carbon sources, 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