GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1085 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1085 D-methionine transport system ATP-binding protein

Length: 336 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 69 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 hi Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 71% 100% 458.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 52% 310.5
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 45% 100% 188.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 98% 176.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 98% 176.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 41% 99% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 41% 97% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 41% 99% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-glutamate catabolism gltL 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) 41% 97% 171.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 42% 82% 171 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 40% 93% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 42% 82% 166.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 88% 164.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 74% 182.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 39% 76% 167.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 40% 93% 167.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 93% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 93% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 93% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 93% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 40% 93% 166.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 39% 97% 163.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 94% 161.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 39% 96% 157.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 36% 62% 154.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 152.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 152.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 94% 152.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 99% 152.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 99% 152.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 93% 143.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 35% 80% 143.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-proline catabolism opuBA lo 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) 37% 73% 142.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 89% 141.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 30% 91% 141 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 36% 80% 140.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 31% 80% 140.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 88% 139.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 72% 138.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 62% 137.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 62% 137.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 64% 137.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 64% 137.9 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 35% 61% 137.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 80% 136.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 32% 75% 136.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 65% 135.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 65% 133.3 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 59% 132.1 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 32% 71% 129.8 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 72% 126.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 78% 124.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 73% 123.6 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 61% 121.7 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 30% 65% 115.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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) 31% 61% 115.2 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
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% 90% 114.4 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-alanine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-leucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-proline catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-serine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-threonine catabolism braF lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 86% 110.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8

Sequence Analysis Tools

View N515DRAFT_1085 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGG
SILIDGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKA
RVDELLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASV
LELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRR
FVNEALPEEAAGELAPYTHVPGRILRLSFRGEATWTPALGRVARDTGVDFNILAGRIDRI
KDLPYGQLTLAMQGSGVDQALVALRAAGIEIEELNR

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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