GapMind for catabolism of small carbon sources

 

Protein WP_079556595.1 in Alkalitalea saponilacus SC/BZ-SP2

Annotation: NCBI__GCF_002201795.1:WP_079556595.1

Length: 229 amino acids

Source: GCF_002201795.1 in NCBI

Candidate for 52 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 41% 90% 159.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 41% 90% 155.2 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 39% 89% 164.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 60% 161 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 60% 161 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 60% 161 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 60% 161 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 39% 56% 159.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 39% 56% 159.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 91% 154.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 91% 154.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 64% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 64% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 154.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 35% 67% 153.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 64% 152.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 84% 149.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 84% 149.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 56% 147.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 56% 146.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 64% 146.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 37% 56% 146.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 37% 54% 146.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 59% 146 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 90% 145.6 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 90% 145.6 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 58% 143.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 58% 142.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 58% 142.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 33% 67% 141 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 61% 136 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 57% 132.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 38% 79% 125.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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% 74% 119.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 64% 119 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 73% 117.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
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) 36% 73% 117.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 54% 115.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 69% 115.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 41% 194.5

Sequence Analysis Tools

View WP_079556595.1 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

MKTVIKTTNLQKIYNNSVAPVKAVNNISLEFQEGEFTAIVGPSGSGKTTFLNLIGGLDKP
TGGEIYIDGTEISTMKESELFDFRLRNIGFVFQSYNLIPVLTAKENVSFIMLLQKRSKAE
MEQRATEMLEQVGLSDKLNSRPNQLSGGQQQRVAVARALASKPKFVLADEPTANLDTESA
FNLLDIMEKLNKEENITLIFSTHDQRVIERAGRVITLVDGSVSKDEVIS

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