GapMind for catabolism of small carbon sources

 

Protein WP_017731511.1 in Nafulsella turpanensis ZLM-10

Annotation: NCBI__GCF_000346615.1:WP_017731511.1

Length: 343 amino acids

Source: GCF_000346615.1 in NCBI

Candidate for 62 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 95% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 95% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 30% 88% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 95% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 95% 168.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 97% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 32% 90% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 33% 92% 152.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 88% 151.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 88% 151.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 31% 96% 149.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 31% 96% 148.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 82% 147.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 30% 88% 146.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 31% 75% 142.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 92% 141.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 92% 141.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 33% 76% 139.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 30% 82% 138.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 31% 74% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 71% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 30% 91% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 33% 82% 136.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 30% 90% 134.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 93% 130.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 93% 130.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 93% 130.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 87% 129.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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) 33% 90% 128.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 67% 127.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 67% 127.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 67% 127.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 33% 80% 124.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
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% 80% 124.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 76% 115.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-alanine catabolism braG lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-isoleucine catabolism natE lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-leucine catabolism natE lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-proline catabolism natE lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-serine catabolism braG lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-threonine catabolism braG lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-valine catabolism natE lo NatE, 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) 33% 93% 107.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 97% 105.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.1

Sequence Analysis Tools

View WP_017731511.1 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

MIEIRQLRKRFEGKEQDILQEMNLSLGEGEIVGLVGSSGSGKTTLLRLLAGLEEPSAGTI
LFRGMPVAGPSQQLVAGHPSIRIVHQDFELAHRLSVYENVAQKLRHLHPEEQQERALELL
EVCHLGALAYTFVEQLSGGEKQRLALARTLAEAPELLLLDEPFSNLDPPLKEDIKEKLFS
YIREQGIAAILVSHDPKDALPLADRFWVLEQGKLVQQGSPREVYYRSASPEVARLFGKIN
LVKKEVLMEVLKGDALDFLQKLPAGSVVGIRPDVVQVMAEKESHLLGVVKSMSFSGIHSE
TSILIGEILIISCYQPGYYTAKPGEVLGLMLKPEHLQVWSAKD

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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