GapMind for catabolism of small carbon sources

 

Protein WP_079646278.1 in Sphingomonas histidinilytica UM2

Annotation: NCBI__GCF_900167915.1:WP_079646278.1

Length: 252 amino acids

Source: GCF_900167915.1 in NCBI

Candidate for 51 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 95% 157.5 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 95% 157.5 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-glutamate catabolism gltL med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 95% 157.5 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 84% 152.5 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 40% 82% 139.4 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 91% 162.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 94% 155.6 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 94% 155.6 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-arginine catabolism artP lo ABC transporter for L-Arginine, putative ATPase component (characterized) 38% 95% 152.1 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 91% 150.6 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 88% 150.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 36% 98% 148.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 95% 146.4 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 92% 145.6 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 92% 145.6 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 88% 145.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 88% 145.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 88% 145.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 88% 145.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 39% 88% 145.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 35% 74% 144.4 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 99% 143.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 34% 98% 141.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 66% 138.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 137.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 64% 137.1 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 65% 135.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 69% 131.3 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 94% 131 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 34% 62% 131 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 34% 57% 126.3 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
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) 34% 75% 124.8 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 67% 120.2 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 101.7 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 199.5

Sequence Analysis Tools

View WP_079646278.1 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

MADTPKILLEGVRKAFGGNAVLDGVDLAIERGESMVIIGQSGSGKSVMLKCILGLIRPDR
GAIRVDGEDLMAMSARELETARAKFGMLFQGSALFDSLPIWRNVTFALTQGRLRDSAKMR
KIAAENLERVGLGSEVLDLRPSELSGGMQKRVALARAIAPRPEIIFFDEPTTGLDPIRAD
VINDLIVELVEELGVTALTITHDMASARKIAHRVAMLYQGRIVWSGPRDRLYDSGNPYVD
QFVQGRAEGPIR

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