GapMind for catabolism of small carbon sources

 

Protein CCNA_01905 in Caulobacter crescentus NA1000

Annotation: CCNA_01905 urea carboxylase

Length: 1207 amino acids

Source: Caulo in FitnessBrowser

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-leucine catabolism liuB med methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized) 44% 91% 411.8 urea carboxylase (EC 6.3.4.6) 59% 1365.9
L-isoleucine catabolism pccA med Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 48% 70% 406 urea carboxylase (EC 6.3.4.6) 59% 1365.9
propionate catabolism pccA med Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 48% 70% 406 urea carboxylase (EC 6.3.4.6) 59% 1365.9
L-threonine catabolism pccA med Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 48% 70% 406 urea carboxylase (EC 6.3.4.6) 59% 1365.9
L-valine catabolism pccA med Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized) 48% 70% 406 urea carboxylase (EC 6.3.4.6) 59% 1365.9
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) 40% 86% 327 urea carboxylase (EC 6.3.4.6) 59% 1365.9
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) 40% 86% 327 urea carboxylase (EC 6.3.4.6) 59% 1365.9
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) 40% 86% 327 urea carboxylase (EC 6.3.4.6) 59% 1365.9
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) 40% 86% 327 urea carboxylase (EC 6.3.4.6) 59% 1365.9

Sequence Analysis Tools

View CCNA_01905 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MFDKVLIANRGAIACRIIRTLRAMGVKSVAVFSDADAGSLHVSMADEAVRLGPAPAAESY
LRADLVLAAAQATGAQAIHPGYGFLSESAAFAQACEDAGVTFIGPSADNIRAFGLKHTAR
DLAQAHGVPLAPGTDLLTDPAAALAAAQRIGFPVILKATAGGGGIGMRVCESAEAVEEAF
AAVRRLATGNFSDGGVFLERYVHKARHIEVQVFGDGAGRVAALGERDCSLQRRNQKVVEE
TPAPGLPAATRTALLDAAVRLAKAANYRSAGTVEFLYDADRDDFFFLEVNTRLQVEHGVT
EQVTGVDLVEWMVRGAAGDFSFLDTPPPAPRGAAIQVRLYAEDPAQDYRPSAGVLTEVAF
PEGVRADGWVVDGTEVSAFYDPMLAKLIVIAEHRPAAVAALQAALDATRLAGIETNLDWL
RTVTRSQPFVSGEVSTRALETIAWAPDTIQVLSGGPATTVQDWPGRRGYWDVGVPPSGPM
DALAFRLGNRLLANPDDAAGLEITALGPTLKFNRPATLCLTGARFDARLDGVAVEPYTPF
DVRPGQTLKIGRVVEAGLRGYLLLRGGLDVPTYLGSRSTFTLGGFGGHAGRNLTAGDVLR
LLPAPEAPPGALDEPLRPALTKTWTIRVLPGPHGAPDFFTPADVAMIGGTDWKVHYNSNR
TGVRLVGPKPEWARRDGGEAGLHPSNIHDNAYAIGAIDFTGDMPIILGPDGPSLGGFVCP
FVIIEADLWKAGQLAPGDTVRFAVVDDPTAAAALETQEALIAQLGAAPPRPAPAVIDVEA
SPILRELPQDGHRPRVLYRRQGDQHLLVEYGPIVLDLELRLRIHALLLDLQAQALEGVID
LTPGIRSLQVHYDSRRLSQARLLDILVAAEDRLGGLDDFEIPSRVVHLPLSWKDPAIYQT
IDKYMQAVRDDAPWCPDNIEFIRRVNGLNGIDDVQKIVFDARYLVMGLGDVYLGAPVATP
VDPRHRLVTTKYNPARTWTPPNVVGIGGAYMCIYGMEGPGGYQLFGRTIQVWNTWRQTDA
FTDGKPWLLRFFDQIRFFPVSAEELVEWRRDFPLGRRAIRIEEETFRLSDYRRLLAENAE
SIAAFQSRRQAAFDAERADWEAKGEFARVEALSGVAEADDAVAAVEVPAGADLVEAPLGG
NVWKVLVEPGQAVEAGAVIAIIEAMKAECDVATPTAGVVSAVYAQPGQPIAAGAPVIAVT
PVAEAAA

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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