GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_3888 in Pseudomonas fluorescens FW300-N1B4

Annotation: Aconitate hydratase (EC 4.2.1.3)

Length: 913 amino acids

Source: pseudo1_N1B4 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
citrate catabolism acn hi Aconitate hydratase (EC 4.2.1.3) (characterized) 71% 99% 1315.1
citrate catabolism acn hi acnA: aconitate hydratase 1 (EC 4.2.1.3) (TIGR01341) 100% 1420.2
L-isoleucine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 69% 99% 1244.2
propionate catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 69% 99% 1244.2
L-threonine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 69% 99% 1244.2
L-valine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 69% 99% 1244.2
L-isoleucine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 48% 54% 438.7 Aconitate hydratase (EC 4.2.1.3) 71% 1315.1
propionate catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 48% 54% 438.7 Aconitate hydratase (EC 4.2.1.3) 71% 1315.1
L-threonine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 48% 54% 438.7 Aconitate hydratase (EC 4.2.1.3) 71% 1315.1
L-valine catabolism acnD lo 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 48% 54% 438.7 Aconitate hydratase (EC 4.2.1.3) 71% 1315.1

Sequence Analysis Tools

View Pf1N1B4_3888 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPSLDSLKTLKTLQVDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTG
ADLKAIAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPL
SPVDLVIDHSVMVDKYASASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGIC
HQVNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
PVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADR
ATIANMAPEYGATCGFFPVDEVTLEYLRLSGRTPQTVKLVEAYSKTQGLWRLPGKEPVFT
DSLALDMGSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQFKPSSKEEGRLESEGGGGVA
VGNADLIGEADYHHEGSTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLKR
KPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIEKAIQK
ADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDKDGHP
VYLRDIWPSTKEIADAVTQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDSTYIQ
HPPFFDDIGGPAPVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPR
DFNSYGSRRGNHQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMRYQASG
TPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQN
RKSLNLTGKETLDILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAG
GILHYVLRQLIAS

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