Protein WP_012674002.1 in Sulfurihydrogenibium azorense Az-Fu1
Annotation: NCBI__GCF_000021545.1:WP_012674002.1
Length: 254 amino acids
Source: GCF_000021545.1 in NCBI
Candidate for 15 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 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) | 34% | 64% | 136.3 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| 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) | 34% | 64% | 136.3 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 95% | 135.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 95% | 135.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 36% | 95% | 135.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 31% | 66% | 132.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-arginine catabolism | artP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 132.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 132.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| L-lysine catabolism | hisP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 92% | 132.1 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 59% | 130.6 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 72% | 117.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 33% | 61% | 115.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 33% | 61% | 115.5 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 31% | 55% | 109.4 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 89% | 99.8 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 66% | 335.9 |
Sequence Analysis Tools
View WP_012674002.1 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
MAENLKMEVKNLNFYYSGNKLALKNINMPIYEKKITALIGPSGCGKTTLLRCFNRMHDLY
PGNRYEGEILLDGKNILDKDVDLMELRTKVGMVFQKPTPFPMSIFENIAYGLKLQGIKNK
TELKDRVEQALKEAALWEEVKDRLDTSAFGLSGGQQQRLCIARTIAVKPEVILFDEPTSA
LDPISTAKIEELIVELKKNHTIIIVTHNMQQAARVSDYTAFMYLGELIEFDSTDIIFTKP
NKKLTEDYISGRFG
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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