GapMind for catabolism of small carbon sources

 

Protein WP_008236514.1 in Imtechella halotolerans K1

Annotation: NCBI__GCF_000260835.1:WP_008236514.1

Length: 313 amino acids

Source: GCF_000260835.1 in NCBI

Candidate for 27 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 PotG aka B0855, component of Putrescine porter (characterized) 34% 72% 160.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 95% 154.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 71% 150.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
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) 36% 71% 147.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 70% 145.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 70% 145.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 32% 63% 144.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 63% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 32% 78% 137.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 65% 136.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 30% 80% 132.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 63% 132.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
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) 31% 65% 127.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
trehalose catabolism malK 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) 31% 65% 127.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 105.5 Fe(3+)-transporting ATPase; EC 3.6.3.30 32% 166.0

Sequence Analysis Tools

View WP_008236514.1 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

MLSIQNISFSYNNTPVLNQLSLDIIPGEHLSIIGASGCGKSTLLKLIYGLLTPSDGNLYW
NEKKLLGPDFNIVPGEDDMKYLAQDFGLMPFITASENIGKYLSNFYPIKKKKRIFELLEM
VGMAEYANVKAQFLSGGQQQRIALAQVLAQEPKVLLLDEPFSHIDNFQKNTLRRDLFHHL
KSSKITCLVATHDATDALSFADNVLVLKDGKKIAYNTPKELYLNPGSTYTASLFGDVNTI
DAQLFFPDRKGFLWIYPHQLKVKEDSKLRVKVLDNYFSGNGYLIKGISKGKILFFLHHTS
IPSGSETGLCLNR

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