Protein WP_019866661.1 in Methylovulum miyakonense HT12
Annotation: NCBI__GCF_000384075.1:WP_019866661.1
Length: 584 amino acids
Source: GCF_000384075.1 in NCBI
Candidate for 23 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 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 97% | 183 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 59% | 143.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 59% | 143.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 87% | 143.3 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 38% | 57% | 139.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 56% | 138.3 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-maltose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 55% | 136.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 55% | 136.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 55% | 136.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| trehalose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 55% | 136.7 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 36% | 62% | 136.3 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 37% | 56% | 134.8 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 59% | 130.6 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| 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) | 36% | 58% | 130.6 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 59% | 130.6 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 59% | 130.6 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| 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) | 36% | 58% | 130.6 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 34% | 57% | 130.2 | ABC transporter for nitrate, ATPase component | 63% | 693.7 |
Sequence Analysis Tools
View WP_019866661.1 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
MTAATKLKLVHPAMTEQPKSPSNDPELPLVELVNVCKSYGEGKNKASILKNINLSIKDGE
FIAIVGFSGSGKTTLISTLAGLIQADSGAVLKQGKPITAPGPDRGVVFQNYSLMPWLTVF
ENVALAVDEIFKDWPADKRRAHTEKYVRMVNLGAAMDKMPAELSGGMRQRVNVARALAAN
PDILLLDEPLSALDALTRGNLQDEILSIWEQEKKTVILITNDVDEAIYMADRVIPLNPGP
DATFGPDFPVTIARPRDRTALNHNEEFKRLRAEITQYLMAIGMEKAQDTLGDKVILPNVR
PNTSNDWKNDSSALKPEQDNLGKARYLEFSQLSKIYPKPSGNGTVKVVDGFDLKMKKGEF
ISIIGHSGCGKSTVLSMAAGLTSISEGGIILDNREVDSAGPDKGVVFQAPSLFPWLTAFE
NVMLGVDKVYPHAKKSEREDIVEYYLTRVGLGDALRKKAGDMSNGMRQRVGIARAFALSP
KLLLLDEPFGMLDSLTRWELQEVLMEVWERTHVTAIVVTHDVDEAILLADRVVMMTNGPH
AKIGKIQEIDLPRPRSRKALLAHDDYYRYRESILTFLTECDHTH
This GapMind analysis is from Apr 09 2024. 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