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
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
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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