GapMind for catabolism of small carbon sources

 

Protein WP_093427604.1 in Thiohalospira halophila HL 3

Annotation: NCBI__GCF_900112605.1:WP_093427604.1

Length: 397 amino acids

Source: GCF_900112605.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proV hi Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 60% 99% 465.3 OtaA, component of The salt-induced glycine betaine OtaABC transporter 51% 386.0
L-proline catabolism opuBA med 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) 49% 96% 375.6 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 58% 95% 302.8 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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) 55% 96% 289.7 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 41% 87% 167.2 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 41% 58% 180.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 62% 177.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 62% 177.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 61% 177.6 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 73% 176 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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) 38% 61% 175.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 82% 170.2 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 85% 164.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 93% 163.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine 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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 86% 162.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 84% 158.7 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 84% 158.7 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 65% 157.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 69% 157.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 65% 157.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 93% 156.4 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 93% 156.4 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 60% 156.4 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 91% 156 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 91% 156 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 97% 155.2 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 83% 154.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 83% 154.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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) 34% 96% 152.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 78% 152.1 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 90% 149.8 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 95% 147.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 91% 146.4 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 94% 140.6 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 31% 96% 137.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 35% 70% 137.9 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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) 34% 88% 137.5 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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) 32% 78% 129.8 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 94% 129.4 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 67% 126.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
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% 125.6 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 90% 121.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 90% 121.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 90% 121.3 Glycine betaine/choline transport system ATP-binding protein OusV 60% 467.6

Sequence Analysis Tools

View WP_093427604.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTDKIVVENLYKIFGPDPDEAFELMDQGQDKDAIFEKTGNTVGVKDANFAIQEGEVFVIM
GLSGSGKSTMVRLLNRLIEPTRGSVKVDGHDVTKMSRKELIELRRRDMSMVFQSFALLPH
RTVLENTAFGLEISGADRAKREERALEALETVGLKSNANSYPSELSGGMQQRVGLARALA
VDPSILLMDEAFSALDPLIRTEMQDELISLQEKHARTVVFISHDLDEAMRIGDRIAIMQG
GEVVQVGTPEEIVTNPANDYVRSFFYGVDVSQVFSAGDIARRDAVTVIERPGVDVNTALQ
QLKRATSDAAVILDKNQKYLGMISVDSLMEAMKGEGETRYAEAFLKDIETAGQDMPLTDV
LSMVAAARWPVPVVDDNGRYLGVISRKALLETLDRTG

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