GapMind for catabolism of small carbon sources

 

Protein WP_109939631.1 in Methanospirillum stamsii Pt1

Annotation: NCBI__GCF_003173335.1:WP_109939631.1

Length: 378 amino acids

Source: GCF_003173335.1 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 opuBA med 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) 50% 72% 226.1 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 42% 83% 177.6 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 82% 172.9 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 39% 59% 175.6 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 43% 59% 174.1 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 32% 93% 158.3 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 33% 78% 156 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 36% 89% 143.3 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 36% 89% 143.3 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 37% 91% 138.3 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 31% 98% 125.9 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 65% 120.9 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 89% 115.2 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 55% 111.3 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 66% 108.6 Glycine betaine transporter, ATP-binding protein, component of The glycine betaine uptake porter, GbpABCD 45% 290.4

Sequence Analysis Tools

View WP_109939631.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIGTRGGNIRLFDTITSLDLTGVSKWYNNSCAVSYLTLSIQGGELITLIGGSGSGKTTTL
KMINRLIEPDSGEILINGQNFLSFNPVALRRSIGYVIQQIGLFPHMSVAENISIPLTLGK
VHQDRIRNRIDELLTLVSLSPDTFRDRKPSELSGGQQQRVGLARALAADPPLLLMDEPFG
ALDPLLRRQLQEEFLRIKKSLGKTIIFVTHDIDEAFLLSDRIAVLREGSLHALTTPPELL
VAAQNDPYLALLTGGDRLCRIRTAPVQVLCVDPGEVYFCSDTQEIPRLQSAIQRKEIRVA
VITPPDGRLYAILPDDEITTGGENKSPLVRLSPETTIQEALFKFSRSSARVAILSEHNEG
PVILLEDLIRFLSGAKQA

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