GapMind for catabolism of small carbon sources

 

Protein WP_026090354.1 in Salinicoccus carnicancri Crm

Annotation: NCBI__GCF_000330705.1:WP_026090354.1

Length: 247 amino acids

Source: GCF_000330705.1 in NCBI

Candidate for 47 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 Arginine transport ATP-binding protein ArtM (characterized) 48% 100% 235.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 46% 94% 230.7 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 49% 94% 225.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 46% 96% 223.8 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-lysine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 46% 96% 223.8 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 46% 97% 223.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 47% 89% 221.9 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 47% 98% 221.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 47% 98% 221.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 48% 99% 219.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 48% 99% 219.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 43% 97% 215.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 45% 94% 212.6 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 44% 92% 209.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 46% 99% 208.8 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 46% 99% 208.8 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 44% 93% 208.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 44% 93% 208.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 44% 93% 208.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 44% 93% 208.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
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) 44% 93% 208.4 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 45% 86% 205.7 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 45% 86% 205.7 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 44% 85% 199.1 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 44% 85% 199.1 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 64% 155.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 96% 134 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 96% 134 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 96% 134 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 31% 93% 125.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 93% 122.9 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 93% 122.9 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 93% 122.9 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 90% 122.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 90% 122.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 90% 122.5 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 91% 121.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 91% 121.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 91% 121.3 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 95% 118.6 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 95% 118.6 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 95% 118.6 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 108.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 108.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 108.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 108.2 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 64% 102.8 L-cystine import ATP-binding protein TcyN; EC 7.4.2.- 57% 278.1

Sequence Analysis Tools

View WP_026090354.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MLSLRNLKLSFDGSQVLDDINLDVKKGEVVTLIGPSGTGKTSLLRCINLLERPDSGFISL
GGLDYDYSRISKKEALNLRRKTAMVFQQYNLFKNKTAIENVMDAQMVVQKKSRKEAYEKS
MQELKRVGLEAKVDAYPSQLSGGQQQRVSIARALAVEPEVILFDEPTSALDPELVGEVLK
SIEEVAKSGMTIMLVTHEMSFARDISDKIVFMDKGRIAESGTPEEIFSQSTNTRTQQFLN
KFYTAVH

This GapMind analysis is from Sep 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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