GapMind for catabolism of small carbon sources

 

Protein BWI76_RS19710 in Klebsiella michiganensis M5al

Annotation: BWI76_RS19710 NupC/NupG family nucleoside CNT transporter

Length: 416 amino acids

Source: Koxy in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2'-deoxyinosine catabolism nupC hi Concentrative nucleoside transporter, CNT, of 418 aas and 12 TMSs. A repeat-swapped model of VcCNT predicts that nucleoside transport occurs via a mechanism involving an elevator-like substrate binding domain movement across the membrane (characterized) 52% 100% 424.1 Broadly selective nucleoside:Na+ cotransporter, hfCNT (transports uridine, thymidine, inosine, 3'-azido-3'deoxythymidine, 2'3'dideoxycytidine, and 2'3'dideoxyinosine) (Na+/uridine = 2) 34% 265.8
thymidine catabolism nupC hi Nucleoside permease; Flags: Precursor (characterized, see rationale) 50% 100% 416 Nucleoside permease NupC 45% 354.4
thymidine catabolism Slc28a3 lo Broadly selective nucleoside:Na+ cotransporter, hfCNT (transports uridine, thymidine, inosine, 3'-azido-3'deoxythymidine, 2'3'dideoxycytidine, and 2'3'dideoxyinosine) (Na+/uridine = 2) (characterized) 34% 60% 265.8 Putative nucleoside permease NupX 87% 721.8

Sequence Analysis Tools

View BWI76_RS19710 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MDIMRSLLGMVVLLAIAFALSVNKKRISIRTVGAALLLQIVIGGVMLYFPPGKWLVEQAA
LGVHKVMSYSDAGSAFIFGSLVGPKMDVLFDGAGFIFAFRVLPAIIFVTALISLLYYLGV
MGLLIRILGGIFQKALNISKIESFVAVTTIFLGQNEIPAIVKPFINKLNRNELFTAICSG
MASIAGSMMIGYAGMGVPIDYLLAASLMAIPGGILFARMLSPATEASQVTFDNLSFSETP
PKSVIEAAASGAMTGLKIAAGVATVVMAFVAIIALLNGIIGGIGGWFGFGHATLEGIFGF
LLAPLAWIMGVDWSDATLAGSLIGQKLAINEFVAYLNFSPYLQSGGNLDVKTVAIISFAL
CGFANFGSIGVVVGAFSAISPQRAPEIAQLGLRALAAATLSNLMSATIAGFFIGLA

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, 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