GapMind for catabolism of small carbon sources

 

Protein WP_042204389.1 in Nitratifractor salsuginis DSM 16511

Annotation: NCBI__GCF_000186245.1:WP_042204389.1

Length: 242 amino acids

Source: GCF_000186245.1 in NCBI

Candidate for 73 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bztD hi BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 74% 92% 365.5 ABC transporter for D-Alanine, ATPase component 70% 351.3
L-aspartate catabolism bztD hi BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 74% 92% 365.5 ABC transporter for D-Alanine, ATPase component 70% 351.3
L-glutamate catabolism gltL hi BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 74% 92% 365.5 ABC transporter for D-Alanine, ATPase component 70% 351.3
L-asparagine catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-aspartate catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-glutamate catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-leucine catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-proline catabolism aapP med 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) 73% 93% 363.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 70% 95% 351.3 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 61% 93% 305.4 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 64% 100% 304.3 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 64% 100% 304.3 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 61% 100% 288.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 61% 100% 288.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 60% 92% 281.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 60% 92% 281.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 57% 100% 273.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 53% 96% 261.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-asparagine catabolism glnQ med 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) 54% 98% 259.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 53% 98% 253.4 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 49% 99% 243.8 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 49% 94% 243 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 49% 94% 241.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-citrulline catabolism PS417_17605 med 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) 49% 91% 233.8 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 72% 172.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 39% 56% 166.4 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 68% 162.2 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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% 55% 161.8 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 81% 157.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 63% 157.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 64% 154.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 64% 154.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 63% 154.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 35% 62% 153.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 64% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 64% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 37% 63% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 64% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 61% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 64% 152.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 63% 152.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 34% 67% 146.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 37% 81% 146.4 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 61% 146 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 66% 146 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 55% 145.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 144.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 37% 61% 143.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 72% 142.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 62% 142.5 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 35% 61% 139.4 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 60% 138.3 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 60% 137.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 62% 133.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 97% 130.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 97% 130.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 30% 65% 127.9 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 35% 88% 126.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 31% 64% 126.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 77% 126.7 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 33% 80% 123.6 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 56% 122.1 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
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) 31% 57% 121.3 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 70% 119 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 70% 109 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 62% 107.8 BztD, component of Glutamate/glutamine/aspartate/asparagine porter 74% 365.5

Sequence Analysis Tools

View WP_042204389.1 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

MIQLQNVNKWYGDFHVLKDINLDVKKGEIVVVAGPSGSGKSTMIRCINRLEEYQEGSIKV
NGIEVNNDVKNLRQVRSNVAMVFQHFNLFPHLTILENLTLAPVWVYKKPKKEAIETAMHY
LEKVNIAEQANKYPNQLSGGQQQRVAIARALCKNPDIMLFDEPTSALDPEMIGEVLDVMM
KLAEEGKTMVTVTHEMGFARKVADRVIFMDAGQIVEENDPETFFHHPESERLKLFLQQIL
NH

This GapMind analysis is from Apr 09 2024. 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