GapMind for catabolism of small carbon sources

 

Protein WP_079650634.1 in Sphingomonas histidinilytica UM2

Annotation: NCBI__GCF_900167915.1:WP_079650634.1

Length: 252 amino acids

Source: GCF_900167915.1 in NCBI

Candidate for 79 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) 45% 73% 193.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 91% 165.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 89% 162.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 89% 162.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-glutamate catabolism gltL med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 89% 162.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 58% 166 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 75% 161 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 63% 160.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 63% 160.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 156.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 156.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 39% 63% 156.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 156 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 156 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 45% 66% 155.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 83% 154.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 40% 57% 152.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 68% 152.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 85% 152.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 63% 152.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 68% 152.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 92% 151 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 92% 151 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 92% 151 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 92% 151 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 92% 151 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 93% 150.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 54% 148.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 36% 76% 147.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 34% 94% 147.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 37% 68% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 35% 64% 144.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 63% 144.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-maltose catabolism thuK 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) 36% 68% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 36% 68% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 38% 61% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 37% 86% 143.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 141.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 141.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-asparagine catabolism glnQ lo 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) 36% 96% 140.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 62% 140.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 35% 70% 139.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 61% 139.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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) 35% 81% 138.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 59% 137.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 66% 137.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 80% 136 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 95% 135.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 95% 135.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 59% 135.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 64% 135.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 70% 134.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 78% 134.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 35% 56% 130.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
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% 71% 125.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 70% 124 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 54% 122.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 54% 122.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 54% 122.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 54% 122.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 78% 120.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 93% 117.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 112.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 112.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 95% 112.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 32% 93% 110.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 90% 95.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 90% 95.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 92% 94.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 50% 221.1

Sequence Analysis Tools

View WP_079650634.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MISFDHVGKHYAGRRVLDDVSLTIERGSFVALVGASGAGKTTLLKTINRLVEIDTGAIAI
EGRDIAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGMPREERAARVAELLDL
VALPADLAARHPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRAL
HDVMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGAGDPRIEAMIAVARR
SAARLDALAAGR

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