GapMind for catabolism of small carbon sources

 

Protein HSERO_RS05835 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS05835 arginine ABC transporter ATP-binding protein

Length: 242 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med L-Arginine ABC transporter, ATPase component (characterized) 56% 97% 266.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 54% 98% 264.6 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 54% 98% 264.6 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 55% 97% 263.1 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 256.9 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 256.9 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 56% 96% 256.9 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 56% 96% 256.9 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 54% 100% 255.4 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 54% 100% 255.4 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 54% 93% 255.4 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 57% 89% 254.6 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 53% 93% 254.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 53% 93% 254.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 53% 93% 254.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 53% 93% 254.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 53% 93% 254.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 91% 252.7 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 91% 252.7 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 52% 94% 250.4 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 54% 94% 249.2 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9

Sequence Analysis Tools

View HSERO_RS05835 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

MIEVKRISKCFGRHEVLKDVSLSVAQGEVVCLIGPSGSGKSTVLRCINGLESYERGDILI
DGQRVDRDGPDIHRLRTRVGMVFQRFNLFPHRTVLENVTEGPIYVNGLARAQARSEAMSL
LDKVGLAARCDAYPAQLSGGQQQRVAIARSLAMQPEAILFDEPTSALDPELVGEVLAVMR
TLAADGMTMIVVTHEMGFAREVADRVCFLHSGSIVESGAAAQVLAEPQHARTQDFLRRVI
GK

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