GapMind for catabolism of small carbon sources

 

Protein WP_036260776.1 in Methylocapsa aurea KYG T

Annotation: NCBI__GCF_000746085.1:WP_036260776.1

Length: 322 amino acids

Source: GCF_000746085.1 in NCBI

Candidate for 70 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 48% 80% 225.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 44% 84% 188 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 41% 86% 175.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 80% 190.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 41% 63% 184.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 82% 181.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 82% 181.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 69% 181.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 69% 181.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 40% 66% 181 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 75% 180.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 33% 84% 179.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 70% 175.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 61% 174.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 72% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 85% 172.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 83% 172.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 63% 170.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 36% 77% 168.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 39% 63% 168.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 40% 64% 166 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 64% 165.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 64% 165.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 64% 165.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 64% 162.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 67% 161.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 33% 84% 161 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 74% 158.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 83% 146.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 98% 144.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 91% 142.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 36% 99% 140.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 90% 139.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 37% 90% 139.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 95% 137.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 95% 137.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 34% 93% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 34% 97% 137.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
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) 35% 92% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
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) 35% 92% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
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) 35% 92% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
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) 35% 92% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
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) 35% 92% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 69% 136.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 66% 134.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 66% 134.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 66% 134.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 66% 134.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 78% 127.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 74% 127.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 300.1

Sequence Analysis Tools

View WP_036260776.1 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

MIELREVSKSFGGALAVDNLSLRIEGGAFFVLIGPSGCGKSTVLRMINAMISCDRGKIEI
GGQDIAKLDPVTLRRGIGYVIQSGGLFPHWTIKDNIAAVPRLLGWSDARCAERLDEIVAM
LRIDPALLPRYPRQLSGGQQQRIGVARALAADPDVILMDEPFAALDPVSRADLQEELRRL
HAQSCKTIVFVTHDMDEALRLATHMAVMNKGALVQTGAPAEIMLRPADQFVRAFLGGDNL
PLRLLEFTPVQDRLRSGSKLGRIFGQGVGAGAGETIAASASLKAALTLMLARGCDHLDVE
DESGARLGEIHAADIIAGDDAR

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