Protein WP_019556634.1 in Thiomicrorhabdus arctica DSM 13458
Annotation: NCBI__GCF_000381085.1:WP_019556634.1
Length: 309 amino acids
Source: GCF_000381085.1 in NCBI
Candidate for 37 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) | 48% | 94% | 237.7 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 212.2 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 42% | 63% | 174.9 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 41% | 64% | 173.3 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 39% | 61% | 170.2 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 61% | 160.2 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 61% | 160.2 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 60% | 156.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 60% | 156.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 60% | 156.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 60% | 156.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| 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) | 38% | 61% | 156 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 42% | 52% | 156 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| 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) | 38% | 61% | 156 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 37% | 69% | 155.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 91% | 155.2 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| 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) | 38% | 96% | 154.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 39% | 57% | 153.3 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 35% | 68% | 151 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 39% | 95% | 150.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-glutamate catabolism | gltL | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 39% | 95% | 150.6 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| 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) | 37% | 62% | 149.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 68% | 149.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 62% | 149.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 58% | 149.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 37% | 56% | 149.4 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 58% | 147.9 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 77% | 147.9 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 54% | 146.7 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 34% | 65% | 146.4 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 36% | 65% | 144.1 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| 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) | 36% | 56% | 142.1 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 79% | 119.8 | ABC transporter for L-Histidine, ATPase component | 48% | 237.7 |
Sequence Analysis Tools
View WP_019556634.1 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
MTNKTQVEQQSHPLNSWQTAEIQDRNERILKRPKTLEVKGLDKSFEHKGKTNKVLNKIDF
TAYKREFICVVGPSGCGKSTLARLIAGLETQEAGHILVDGKHVTEPGPDRGMVFQSYSLF
PWMSVKHNVMFGLTQSGMSRNSAESEAFQWIDLVGLTPFLDAYPHQLSGGMKQRVAIIRA
LANQPKILLMDEPFAALDPQNRLKMQQYLLEIWQNIDITVFFITHDLDEAIYLADRILVL
DANPGQVREVLNVPLPRPRAEDTLLSPAFMATKDYLETLVHPPQPELDFEEKLSMVRLVS
VNAQVPDIF
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