Protein WP_012468536.1 in Geobacter lovleyi SZ
Annotation: NCBI__GCF_000020385.1:WP_012468536.1
Length: 350 amino acids
Source: GCF_000020385.1 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-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 57% | 161.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 86% | 156.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 87% | 152.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 33% | 79% | 152.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 31% | 84% | 152.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 37% | 60% | 151.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 35% | 69% | 149.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 37% | 60% | 143.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 31% | 86% | 142.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 31% | 86% | 142.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 70% | 138.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 61% | 136.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 31% | 77% | 134 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
| 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) | 30% | 79% | 133.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 183.7 |
Sequence Analysis Tools
View WP_012468536.1 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
MELQLQLRKQQGDFALELDLKVSGERIGIFGPSGSGKSTLVNLLAGLARPDAGQILLDGQ
PLFDSSNRINLLPHRRRIALVFQQHGLFPHLTVRKNLLYGYQRCPAAERRIELAEVAEVL
EITDLMGQMPDTLSGGQSQRVALGRAILASPRLLLMDEPLSALDDDLRYRIIPYLNLVSE
RFRIPFVFISHSLVEMRLMADQVAVLEKGQLAGVVAPEELARQRMGQSASGYINLLELGM
PEEQEGLLAFPWAGQELLLSGGAGTEPGTFELSSRDIILCKRHPDAISARNLLPCMVRSL
FESGKKTGIELDCNGSSLVAEVVPAAAQELQITPGSTVWAAIKASAFRRL
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