GapMind for catabolism of small carbon sources

 

Protein WP_012467210.1 in Chlorobium limicola DSM 245

Annotation: NCBI__GCF_000020465.1:WP_012467210.1

Length: 328 amino acids

Source: GCF_000020465.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 91% 117.5 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 34% 50% 116.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 115.2 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 115.2 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 115.2 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 115.2 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 115.2 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 88% 102.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 102.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 95% 90.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 95% 90.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 95% 90.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 95% 90.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 95% 90.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 30% 87% 87 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 36% 185.7

Sequence Analysis Tools

View WP_012467210.1 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

MSTMSGPAIRAKGLEKRFGDVRAVQGVDIEVAPGELFGFLGPNGAGKTTAMTMLTGLSRP
DAGSIEIGGVDCSKNPKAAQHLIGVVPDESNLYPELSGFENLCFSGALYGMRRDERRRKA
SELLDLFDLGDAASRKFSGYSKGMKRRLVIAAAIMHDPPLLFLDEPTSGIDVASSPYDTP
HCLSDLHRNGVTIFMTTHFIDEAERLCDRIAFIVNGRIVRTDTVERLLQPVQGRYALTVS
FSDAAKVPLMDLERAFPLLEFHMLPGGELRVESGEALKTGALVRFLEEAGAEVTEAKKRV
LSLEDVFVEITGIGAGRMEKEKEGRGRR

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