GapMind for catabolism of small carbon sources

 

Protein WP_017868004.1 in Lactobacillus pobuzihii E100301

Annotation: NCBI__GCF_000349725.1:WP_017868004.1

Length: 244 amino acids

Source: GCF_000349725.1 in NCBI

Candidate for 52 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) 57% 100% 284.6 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 60% 282.7
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) 60% 97% 282.7 Arginine transport ATP-binding protein ArtM 57% 284.6
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) 60% 97% 282.7 Arginine transport ATP-binding protein ArtM 57% 284.6
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 54% 92% 259.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 54% 92% 259.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 50% 98% 256.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-lysine catabolism hisP med ABC transporter for L-Lysine, ATPase component (characterized) 50% 96% 255 Arginine transport ATP-binding protein ArtM 57% 284.6
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 97% 254.6 Arginine transport ATP-binding protein ArtM 57% 284.6
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) 50% 96% 252.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 50% 94% 250.8 Arginine transport ATP-binding protein ArtM 57% 284.6
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) 49% 90% 239.6 Arginine transport ATP-binding protein ArtM 57% 284.6
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 49% 94% 236.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 44% 80% 157.9 Arginine transport ATP-binding protein ArtM 57% 284.6
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 67% 160.2 Arginine transport ATP-binding protein ArtM 57% 284.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 67% 160.2 Arginine transport ATP-binding protein ArtM 57% 284.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 70% 159.5 Arginine transport ATP-binding protein ArtM 57% 284.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 70% 159.5 Arginine transport ATP-binding protein ArtM 57% 284.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 72% 154.1 Arginine transport ATP-binding protein ArtM 57% 284.6
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 76% 140.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 91% 131.3 Arginine transport ATP-binding protein ArtM 57% 284.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 62% 127.5 Arginine transport ATP-binding protein ArtM 57% 284.6
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 94% 125.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 125.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 125.2 Arginine transport ATP-binding protein ArtM 57% 284.6
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) 30% 98% 125.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 125.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-alanine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-serine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-threonine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 91% 122.9 Arginine transport ATP-binding protein ArtM 57% 284.6
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 89% 122.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 92% 112.1 Arginine transport ATP-binding protein ArtM 57% 284.6
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 85% 110.5 Arginine transport ATP-binding protein ArtM 57% 284.6
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 97% 110.2 Arginine transport ATP-binding protein ArtM 57% 284.6
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 97% 110.2 Arginine transport ATP-binding protein ArtM 57% 284.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 84% 104 Arginine transport ATP-binding protein ArtM 57% 284.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 84% 104 Arginine transport ATP-binding protein ArtM 57% 284.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 84% 104 Arginine transport ATP-binding protein ArtM 57% 284.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 84% 104 Arginine transport ATP-binding protein ArtM 57% 284.6

Sequence Analysis Tools

View WP_017868004.1 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

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Sequence

MSELLQIQNLKKSFGKNEILTDINETVSKGEVVCVVGPSGAGKSTFLRCLNVLEHPTDGK
IIFEGQDLTQISEKQLNNLRQKMGMVFQNFNLFPNMTVLGNIIAAPMKVKGQTQEEAEKK
ARELLDRIGLADKADQYPASLSGGQSQRVAIVRALAMDPEVMLFDEPTSALDPEMVGEVL
EVMKDLANSGMTMVVVTHEMGFAREVADRIWLMADGYIQESGKPSEIFEKPQTKRGQEFL
SKVL

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