GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1248 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1248 ABC-2 type transport system ATP-binding protein

Length: 315 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 96% 120.2 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 92% 116.7 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 92% 105.9 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8
myo-inositol catabolism iatA lo Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 31% 57% 93.6 uncharacterized ABC transporter ATP-binding protein yadG 43% 238.8

Sequence Analysis Tools

View N515DRAFT_1248 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

MTEQATPTPHAVSVRGISKTYKGGFQALKSIDLDIRRGEIFALLGPNGAGKTTLISIICG
IVKPSAGTVSADGHDVLRDYRLTRAKIGLVPQELSTDAFETVWAAVRFSRGLFGRARDDR
HIEKVLRDLSLWEKKDAKIMTLSGGMKRRVLIAKALAHEPSILFLDEPTAGVDVELRHDM
WEMVRRLRATGVTVILTTHYIEEAEEMADRVGVITRGELILVEDKRALMRKLGKKQLSIS
LKSPIQALPQGLDEYALELADDGATITYTFDAQGEDTGIAVLLRKLGDRGVDFKDLHTLE
SSLEDIFVSLVRGTR

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