GapMind for catabolism of small carbon sources

 

Protein GFF2473 in Pseudomonas stutzeri RCH2

Annotation: Psest_2521 aconitate hydratase 1

Length: 891 amino acids

Source: psRCH2 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 A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 70% 99% 1248
citrate catabolism acn hi acnA: aconitate hydratase 1 (EC 4.2.1.3) (TIGR01341) 100% 1420
L-isoleucine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 70% 99% 1248
propionate catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 70% 99% 1248
L-threonine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 70% 99% 1248
L-valine catabolism acn hi Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) 70% 99% 1248
L-isoleucine catabolism acnD med 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 99% 728.8 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 70% 1248.0
propionate catabolism acnD med 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 99% 728.8 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 70% 1248.0
L-threonine catabolism acnD med 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 99% 728.8 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 70% 1248.0
L-valine catabolism acnD med 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) 45% 99% 728.8 Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 70% 1248.0

Sequence Analysis Tools

View GFF2473 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

MPSLDSLKCRRSLEVAGKTYHYYSLPDAAAQLGDISRLPTSLKVLLENLLRWEDNQTVRA
DDLKSLVSWLDTRSSTMEIQYRPARVLMQDFTGVPAVVDLAAMRDAVAKAGGDPQKINPL
SPVDLVIDHSVMVDRFGSDQAFEQNVEIEMQRNGERYEFLRWGQQAFDNFAVVPPGTGIC
HQVNLEYLGQVVWTREENGETFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
PVSMLIPEVIGFRLTGKLNEGVTATDLVLTVTQMLRKHGVVGKFVEFYGPGLDHLPLADR
ATIGNMAPEYGATCGFFPVDQVTIDYLRLTGRNEERIALVEAYSKAQGMWRDSNSPAPEF
TATLELDLSQVRPSVAGPKRPQDRVTLGDIGANFDLLLETSGRQQQADTDFAVAAEQFQL
KHGAVVIAAITSCTNTSNPNVLMAAGLVAKKAIERGLQRKPWVKTSLAPGSKVVTDYLER
AGLTRYLDELGFNLVGYGCTTCIGNSGPLPDAIGQAITDNDLIVSSVLSGNRNFEGRVHP
LVKANWLASPPLVVAFALAGTTRIDMDREPLGYDAQNQPVYLKDIWPSSAEIAEAVARID
GEMFRSRYADVFSGDEHWQKIPVSAGDTYAWNANSSYVQNPPYFEDIGQPPTPPADVENA
RVLAVFGDSITTDHISPAGNIKASSPAGLYLQSLGVAPEDFNSYGSRRGNHEVMMRGTFA
NIRIRNEMLGGEEGGNTLYQPSGEKLSIYDAAMRYQAEGVPLVVIAGKEYGTGSSRDWAA
KGTNLLGVKAVIAESFERIHRSNLIGMGVLALQFVNDQTRQSLGLNGMEKLSIRGLDADI
KPRQMLTVDVERADGSRDSFQVLSRIDTLNEVQYFKAGGILHYVLRQLIAH

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