GapMind for catabolism of small carbon sources

 

Protein CCNA_01506 in Caulobacter crescentus NA1000

Annotation: CCNA_01506 cystine transport ATP-binding protein

Length: 246 amino acids

Source: Caulo in FitnessBrowser

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 52% 97% 235.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 52% 97% 235.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 95% 234.2 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 95% 234.2 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 95% 234.2 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 52% 98% 230.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 52% 98% 230.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 48% 99% 224.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 50% 92% 222.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 50% 92% 222.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 49% 94% 221.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 48% 96% 221.1 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 48% 89% 212.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 48% 94% 211.5 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 47% 92% 211.1 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 46% 93% 208.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 46% 93% 208.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 46% 93% 208.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 46% 93% 208.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
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) 46% 93% 208.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 46% 90% 205.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 46% 90% 205.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 47% 93% 204.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 43% 98% 202.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 43% 98% 202.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 70% 155.2 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 65% 146.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 65% 146.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 65% 146.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 65% 146.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 69% 146 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 69% 146 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 61% 138.3 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 60% 127.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 61% 279.6

Sequence Analysis Tools

View CCNA_01506 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

MSAIDAKSLKKSFGDTPVLAGVDLAVVPGEVVAIIGPSGSGKSTLLRCLAGLEPLNDGDL
TIAGVAAGGKTPLAKALNGRVGFVFQSFNLFPHRTALENVIEGPIVVRREDPAKARAKGL
ALLEKVGLADRVDAYPSALSGGQQQRCAIARALAMDPEVILFDEPTSALDPELVGEVLAV
IRDLAAEKRTMVIVTHQMDFARDVAERTIFMDGGVIVEQGPSRQLLASPREERTRRFLAR
SGVLQP

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