GapMind for catabolism of small carbon sources

 

Protein WP_065398591.1 in Chryseobacterium arthrosphaerae CC-VM-7

Annotation: NCBI__GCF_001684965.1:WP_065398591.1

Length: 342 amino acids

Source: GCF_001684965.1 in NCBI

Candidate for 76 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 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 44% 96% 263.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 40% 99% 184.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 42% 96% 184.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 42% 96% 184.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 75% 173.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 94% 171.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 72% 170.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 37% 95% 170.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 37% 95% 170.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 98% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 67% 165.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 39% 62% 165.2 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 162.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 162.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 162.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 84% 162.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 98% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 92% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 98% 159.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 98% 159.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 94% 158.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 91% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 91% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 88% 156.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 94% 156 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 95% 156 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 35% 54% 154.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 94% 149.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 81% 145.6 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 73% 143.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 30% 81% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 30% 81% 141.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 33% 95% 139.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 86% 137.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 78% 137.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 32% 65% 136.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 31% 80% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 35% 90% 134.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 32% 72% 134 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 99% 131.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 99% 131.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 99% 131.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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% 79% 127.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 32% 88% 125.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
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) 32% 88% 125.9 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 31% 53% 124.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 98% 124.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 86% 121.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 114.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 114.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 114.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 88% 114.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 56% 105.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 51% 351.3

Sequence Analysis Tools

View WP_065398591.1 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

Fitness BLAST: loading...

Sequence

MIEIRNISKTFHQKNQSFKALDKVSLNIEKGDIVGIIGFSGAGKSTLIRTVNLLERPDEG
QIIINGKDFTKLNSRQLAEERKKIGMIFQHFNLLSSRTVFDNVALPLELDHTGKEQINRK
VNELLKIVGLEEKANDYPRSLSGGQKQRVAIARALANDPHLLLCDEATSALDPATTQSIL
QLLRDINQRLGITILLITHEMEVIKTVCNHVAVIDKGKLLTKGTLSEIISDKEHPVIRQF
INSDIMTLPQELNNRLQKEPKEGLFPLVEIELNENISVEQILSTLYNQYKIPYKLLKADV
EYFGNSNFGKLLLQLQGEAEENQQAIYYLNQNKIQNTVKGYA

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