Protein WP_028313154.1 in Desulfatibacillum aliphaticivorans DSM 15576
Annotation: NCBI__GCF_000429905.1:WP_028313154.1
Length: 248 amino acids
Source: GCF_000429905.1 in NCBI
Candidate for 28 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) | 45% | 93% | 228.4 | CynD, component of Bispecific cyanate/nitrite transporter | 49% | 213.4 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 41% | 62% | 166 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 43% | 51% | 165.6 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 45% | 57% | 164.9 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 45% | 57% | 164.9 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 40% | 64% | 163.3 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 40% | 58% | 157.1 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 59% | 156.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 39% | 70% | 156.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 39% | 59% | 155.2 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 41% | 58% | 155.2 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 39% | 59% | 155.2 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 57% | 153.7 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 40% | 58% | 151.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 53% | 151.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 42% | 56% | 151.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 95% | 147.9 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 41% | 57% | 147.9 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
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) | 41% | 53% | 146.4 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 70% | 145.2 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 91% | 138.7 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 33% | 53% | 93.6 | ABC transporter for L-Histidine, ATPase component | 45% | 228.4 |
Sequence Analysis Tools
View WP_028313154.1 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
MLELTNVAKMYSNINGERIEAVEGLSLNIEENEMVCLVGRSGCGKTTTLRLIAGLESPSR
GRISLRGKKVEGPAAERCVVFQRYTLFPWRSVLANVAFGLEMQGVSKKEREAAALKYLGL
VGLEDQAKAYPPELSGGMQQRVAVARALAADPEVLLMDEPFGALDAQTRNVLQQELMRIW
RADQKTIVFVTHDIQEAVLLADRVVVMQGPPGRIREIMDCSLPRPRDRNSQEFTGMCDRI
HALLEGAD
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