GapMind for catabolism of small carbon sources

 

Protein WP_091524012.1 in Flavobacterium ummariense DS-12

Annotation: NCBI__GCF_900115115.1:WP_091524012.1

Length: 312 amino acids

Source: GCF_900115115.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 33% 77% 158.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 139.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 139.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 139.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 88% 139.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
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) 33% 62% 136.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 69% 132.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 69% 132.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 31% 71% 130.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
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) 34% 81% 124.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
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) 34% 81% 124.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 31% 64% 120.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 105.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 93% 96.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 36% 172.2

Sequence Analysis Tools

View WP_091524012.1 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

MLQVNQLSFSYNNSQILSDVSFQLKAGNSYALIGASGSGKSTLLKLVYGLLDADSGSIFW
NEKQILGPAYHLVPGMDYMKYLAQDFDLMPFVSVAENVGRFLSNFYLKEKKNRVDELLEL
VDMTEFANVKAKFLSGGQMQRTALARVLALEPEFLLLDEPFSHIDPFQKRELATQLFQYC
KQKGITILFTSHTPEEALMYADEILVLQNGILIEKDIPQNIYENPKNEYIARLTGDVNII
PANYFDLNINEVLYVRPHELQISNDGSEVKIKHSYFTGKNYLIYAVLNDLEICFVHKTAL
QPNERVYVSVLK

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