GapMind for catabolism of small carbon sources

 

Protein WP_008496179.1 in Planococcus halocryophilus Or1

Annotation: NCBI__GCF_000342445.1:WP_008496179.1

Length: 330 amino acids

Source: GCF_000342445.1 in NCBI

Candidate for 48 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) 42% 100% 262.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 44% 81% 195.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 44% 81% 195.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 33% 78% 200.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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% 179.1 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
trehalose catabolism thuK 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% 179.1 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 34% 90% 177.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 35% 77% 172.6 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 35% 77% 171 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 70% 168.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 70% 168.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 31% 92% 168.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-cellobiose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-glucose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
lactose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-maltose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
sucrose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
sucrose 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
trehalose catabolism gtsD 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) 39% 62% 167.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 65% 165.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 99% 161 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 67% 159.8 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 65% 159.1 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 64% 156 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 90% 155.6 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 90% 155.6 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 90% 155.6 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 87% 155.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 74% 153.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 34% 65% 148.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 34% 65% 148.3 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 57% 147.9 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 65% 145.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
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) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 97% 118.2 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 104.4 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 104.4 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 104.4 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 101.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 101.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 101.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 101.7 Osmoprotectant import ATP-binding protein OsmV; EC 7.6.2.- 49% 306.6

Sequence Analysis Tools

View WP_008496179.1 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

MISFKNVTKRYGEEIVAVNDVDFTVEEGKIVVLLGPSGCGKTTLLRMVNRLESISEGEII
INNENSKDLDAIELRRKIGYVIQSNGLFPNMTIEENVMLVPDLLGWSKKEKRERFEYLMK
LIGLDAKDYGKRFPHELSGGQQQRIGVVRALAADPPVMLMDEPFGALDPIIRDKIQEEFL
QIQREVKKTILFVSHDIDEAIKMADKIVLLRNGEIMQFDTPSKMLSHPKNEFVSQFFGKD
RAIKSLSLHTVEDLQTIIGLGPVDESIQDTKTINIHQDLRNTLSMLMNQEADQVVVKNDQ
DENIGTITIDLVQKYLHFEIKGKMSASQEG

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