Protein WP_019386899.1 in Arenitalea lutea P7-3-5
Annotation: NCBI__GCF_000283015.1:WP_019386899.1
Length: 303 amino acids
Source: GCF_000283015.1 in NCBI
Candidate for 36 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 34% | 67% | 149.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 34% | 63% | 141.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 70% | 138.7 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
L-proline catabolism | opuBA | lo | 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) | 35% | 76% | 138.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 74% | 137.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 74% | 137.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 74% | 137.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 74% | 137.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 69% | 136 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 71% | 133.3 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 60% | 132.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 71% | 132.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 73% | 130.6 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 32% | 63% | 130.6 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 70% | 129.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 70% | 129.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 70% | 129.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 70% | 129.8 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-cellobiose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-glucose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
lactose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
sucrose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
trehalose catabolism | gtsD | 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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
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) | 31% | 60% | 129.4 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 62% | 127.9 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 31% | 81% | 102.1 | Fe(3+)-transporting ATPase; EC 3.6.3.30 | 38% | 159.1 |
Sequence Analysis Tools
View WP_019386899.1 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
MLIVKNLKFSYKKTAVLKNISFDANQGENVAIIGESGSGKSTLLKVLYGEYDLDEGHIFW
NDNEILGPKFNLVVGYDFMKYVAQEFDLMPFITVEENIGKFLSRFYPEEKHRRTQELIEV
VELTEFAKTKVKTLSGGQKQRVALARALAKQPEIILLDEPFSHIDNFKKQSLRRSVFKYL
KDNHITCIVATHDKEDVLGYADQMIVLNNNKIAVKDTPEQLYKHPKTPLVASFFGEFNVI
NNQIYYAHQLEVVNDSELKMTVTNAYYKGHYFLIEAELNGEHMFFEHPKSLKPGTEICLA
IKK
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