Protein WP_011033306.1 in Methanosarcina mazei Go1
Annotation: NCBI__GCF_000007065.1:WP_011033306.1
Length: 263 amino acids
Source: GCF_000007065.1 in NCBI
Candidate for 13 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | Ac3H11_2560 | hi | ABC transporter for L-Histidine, ATPase component (characterized) | 51% | 97% | 260.4 | Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- | 48% | 226.1 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 43% | 63% | 182.6 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 41% | 58% | 174.5 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 64% | 172.6 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| 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) | 40% | 60% | 169.9 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 61% | 167.2 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 42% | 61% | 167.2 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 57% | 164.1 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 40% | 57% | 162.2 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 36% | 62% | 156.8 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 41% | 50% | 154.5 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 91% | 152.1 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 38% | 55% | 122.1 | ABC transporter for L-Histidine, ATPase component | 51% | 260.4 |
Sequence Analysis Tools
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
MEVRDCDVKMGRVSVKNVSRIFTKKEDGSGTEALHNISFDVQDGEFICLLGPSGCGKTTL
LRITAGLETLTSGEITLNGVPITGPDPKRGMVFQQYSLFPWRTVIDNITFGLEMQGIDKT
RARKQVEKYLELVGLEQFKNSYPHELSGGMQQRAAIARALANEPEVLLMDEPFGALDAQT
RNVLQDELLKIWEQKHVTFLFVTHSVDEAVVLSDRIIVMTSRPGRIKEIVKVEIPRPRSR
TSPEVNRLRDHILKLLEEERFTR
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