GapMind for catabolism of small carbon sources

 

Protein WP_008537164.1 in Megamonas funiformis YIT 11815

Annotation: NCBI__GCF_000245775.1:WP_008537164.1

Length: 353 amino acids

Source: GCF_000245775.1 in NCBI

Candidate for 62 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 47% 100% 297.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 44% 100% 198.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 44% 100% 198.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-glutamate catabolism gltL med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 44% 100% 198.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 40% 100% 196.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
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) 41% 98% 179.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 86% 176 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 93% 175.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 93% 175.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 92% 171 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 92% 171 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 42% 62% 190.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 92% 177.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-asparagine catabolism aapP lo 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) 39% 93% 176.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-aspartate catabolism aapP lo 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) 39% 93% 176.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-glutamate catabolism aapP lo 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) 39% 93% 176.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-leucine catabolism aapP lo 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) 39% 93% 176.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-proline catabolism aapP lo 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) 39% 93% 176.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 39% 56% 175.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 94% 174.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 97% 174.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 39% 94% 172.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 90% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 90% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 97% 167.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 62% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 62% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 62% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 62% 162.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 93% 160.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 30% 86% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 32% 94% 157.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 38% 87% 156.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-citrulline catabolism PS417_17605 lo 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) 36% 89% 154.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 35% 92% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 35% 92% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 63% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 69% 144.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 69% 144.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 32% 77% 143.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 82% 142.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 66% 138.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 66% 138.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 85% 104.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 50% 342.0

Sequence Analysis Tools

View WP_008537164.1 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

MIKLKNIVKTYDTPNGSVHALKDINLEIKRGEIYGIIGLSGAGKSTLVRCINMLERPTSG
NVIVNGKDLTTMTESQLREARKDIGMIFQHFNLLSTSTVYDNIAFPLKLAGKSKEEIKAK
VEPLLKLVGLENKAHQYPSQLSGGQKQRVGIARALANDTKVLLCDEATSALDPQTTKAIL
ELIRDINKKLQLTVVVITHEMQVIKDLCDKVAVLDHGVIAENGTVLEIFTNPKEPITKEF
MSVLSSNELPAAYRNGKVHKEYIKDATMLLRLTFIGESADNPVIAGLIRKFPELDISILF
GDLSQIQMVQFGRMIIGLDGKEDQIKDAIKSLMEQDLKVEVIGYVQRRTHATA

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