GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_4352 in Pseudomonas fluorescens FW300-N1B4

Annotation: Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)

Length: 380 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 61% 96% 424.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 42% 255.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 87% 204.1 PotG aka B0855, component of Putrescine porter 61% 424.9
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 80% 137.1 PotG aka B0855, component of Putrescine porter 61% 424.9

Sequence Analysis Tools

View Pf1N1B4_4352 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

MANASSIYRKALEGHQAPKKVLVKVDRVTKKFDETTAVDDVSLEIHQGEIFALLGGSGSG
KSTLLRMLAGFERPTEGRILLDGVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLK
QDRLPASEIDARVEEMLRLVHMTQYARRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPM
GALDKKLRSQMQLELVEIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPVDI
YEAPVSRMVCEFIGNVNAFDGTVVEDLEGHAIIHSPDLEQKIYVGHGVSTSVQDKSITYA
IRPEKMLVSTLKPETRYNWSEGKVHDIAYLGGHSVFYVELPGGKIVQSFMANAERRGARP
TWDDQVYVWWEDDSGVVLRS

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