GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_2303 in Pseudomonas fluorescens FW300-N1B4

Annotation: Dihydroxy-acid dehydratase (EC 4.2.1.9)

Length: 613 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
D-xylose catabolism xad lo xylonate dehydratase (EC 4.2.1.82) (characterized) 31% 80% 210.7 dihydroxyacid dehydratase 75% 919.8
L-arabinose catabolism xacD lo L-arabonate dehydratase (EC 4.2.1.25) (characterized) 33% 61% 192.6 dihydroxyacid dehydratase 75% 919.8
D-cellobiose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
D-gluconate catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
D-glucose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
lactose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
D-maltose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
sucrose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8
trehalose catabolism edd lo Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized) 34% 50% 157.9 dihydroxyacid dehydratase 75% 919.8

Sequence Analysis Tools

View Pf1N1B4_2303 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

MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV
AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS
NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLASHGLDLVDAMVIAADSSASDEKVA
EYERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIVEL
CKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRDID
RLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEGIA
KWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEGGL
AVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRYEG
PKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVQ
DGDKVLIDIPNRSINLLISDEEMAARRAEQDKKGWKPVEVRPRKVTTALKAYALLATSAD
KGAVRNKAMLDGL

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