GapMind for catabolism of small carbon sources

 

Protein WP_055437409.1 in Lacinutrix algicola AKS293

Annotation: NCBI__GCF_001418085.1:WP_055437409.1

Length: 247 amino acids

Source: GCF_001418085.1 in NCBI

Candidate for 61 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 37% 94% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-glutamate catabolism gltL 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) 37% 94% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 97% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 37% 86% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 91% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 91% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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) 36% 81% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 36% 97% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 36% 97% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-proline catabolism opuBA lo 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) 41% 50% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 92% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 139 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 78% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 78% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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) 37% 74% 136 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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) 36% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 96% 131 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 58% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 62% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 35% 55% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 57% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 84% 127.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 57% 124.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 57% 124.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 83% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 62% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 74% 123.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 34% 57% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 79% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 54% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 34% 57% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 69% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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% 97% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 60% 117.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 60% 117.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 66% 111.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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) 32% 83% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 36% 53% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
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) 32% 56% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 68% 107.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 233.8

Sequence Analysis Tools

View WP_055437409.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSKEIIKIEDLKREFTMGAETVRALRGISFDIKEGEFVTIMGSSGSGKSTMLNILGCLDQ
PTSGLYEIDGVSVKDLSRNELATIRNEKIGFIFQSYNLLARTSAIENVELPLLYNSKVST
EERRKRAIEALKKVGLGERLDHTPAQLSGGQQQRVAIARSLVNNPVMLLADEATGNLDTR
TAYEIMSIFQELNEQGITIAFVTHEEDIATFSSRTIVLKDGNIIQDNKNENVQSAKVELA
KLPKQDD

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