GapMind for catabolism of small carbon sources

 

Protein WP_008635292.1 in Bizionia argentinensis JUB59

Annotation: NCBI__GCF_000224335.1:WP_008635292.1

Length: 928 amino acids

Source: GCF_000224335.1 in NCBI

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
citrate catabolism acn hi Aconitate hydratase (EC 4.2.1.3) (characterized) 53% 99% 994.6 2-methylisocitrate dehydratase (EC 4.2.1.99) 48% 887.5
citrate catabolism acn med acnA: aconitate hydratase 1 (EC 4.2.1.3) (TIGR01341) 100% 1302.1 2-methylisocitrate dehydratase (EC 4.2.1.99) 48% 887.5
L-isoleucine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 50% 99% 943.3
propionate catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 50% 99% 943.3
L-threonine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 50% 99% 943.3
L-valine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 50% 99% 943.3
L-isoleucine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 55% 417.5 Aconitate hydratase (EC 4.2.1.3) 53% 994.6
propionate catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 55% 417.5 Aconitate hydratase (EC 4.2.1.3) 53% 994.6
L-threonine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 55% 417.5 Aconitate hydratase (EC 4.2.1.3) 53% 994.6
L-valine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 55% 417.5 Aconitate hydratase (EC 4.2.1.3) 53% 994.6

Sequence Analysis Tools

View WP_008635292.1 at NCBI

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

MDKDIYHIKKTLHINGKESYYFSLVELQKQGHDISKMPFSIRILLENALRNYDDFAVTKE
NIETLLNWKPKGSDKDIPFKPARVLMQDFTGVPAVVDIAALRTEVARKGKNPDSINPLIP
VDLVIDHSVQVDYFGTDYAYQRNIDEEYKRNQERYQFLKWAQNSFDNFTVVPPGMGICHQ
INLEYLSKGVIERNGEIFPDSLVGTDSHTPMVNGIGVVAWGVGGIEAEAAILGQPLYFIM
PEVIGLKLTGKLPLGSTATDLVLTIANLLRKRGVVGKFVEVFGPGLDYLSVPDRATIGNM
SPEFGSTITYFPIDDKTLEYMRQSNRSEAQINLVETYCKANMLWRENENKITYTDVVELD
VSSIVPTVAGPKRPQDKILLKDFKNKFIELLDDSFNRKYISQKDREIEKSITRFDNEGGD
LPVPEPKTKPQLLETETKEKDGLKTVWITRGQEKFMLSDGAVAIAAITSCTNTSNPFVMV
GAGLVAKKAREHGLDVKPWVKTSLAPGSKVVTDYLEKADLMKDLEALRFHLAGYGCTSCI
GNSGPLPQQIAKAIDEHNLVVTSVLSGNRNFEARIHPQVKMNFLMSPMLVVAYAIAGRVD
IDLINEPISYDINQEPVYLKDIWPTDDEINAVLSRVLSPLDFKKNYDEIFEGNEIWRNLE
VPKGKLYDWNESSTYIKEIPFFKGISDEPEPLQNIENAKALLVLGDSITTDHISPAGAFN
ENSAAGKYLLSKGVAKSDFNSYGSRRGNDEVMVRGTFANVRIKNKLAKKEGGYTKFLPTG
EEMTVFDAAEKYRESNTPLVVLVGKEYGSGSSRDWAAKGTFLLGIKAVLAESYERIHRSN
LVGLGVLPLEYKNGDTAESLGIIGTENFTFCGITEDIKPLKEVEITATDENGKEIKFKAI
ARLDSAIEIEYYRNGGILQYVLRQFLKA

This GapMind analysis is from Sep 24 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