Protein WP_072910078.1 in Malonomonas rubra DSM 5091
Annotation: NCBI__GCF_900142125.1:WP_072910078.1
Length: 244 amino acids
Source: GCF_900142125.1 in NCBI
Candidate for 35 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | glnQ | med | 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) | 60% | 97% | 285.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-glutamate catabolism | gltL | med | 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) | 60% | 97% | 285.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 59% | 100% | 280.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 62% | 88% | 279.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 62% | 88% | 279.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 58% | 99% | 278.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 58% | 99% | 278.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 57% | 92% | 270 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 61% | 86% | 263.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-asparagine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 60% | 86% | 263.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-aspartate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 60% | 86% | 263.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-glutamate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 60% | 86% | 263.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-leucine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 60% | 86% | 263.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-proline catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 60% | 86% | 263.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 60% | 84% | 261.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 60% | 84% | 261.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 58% | 90% | 260.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 56% | 91% | 247.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 52% | 99% | 246.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 52% | 99% | 246.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 51% | 94% | 243.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | hisP | med | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 50% | 93% | 234.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 49% | 97% | 227.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 48% | 89% | 223.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-citrulline catabolism | PS417_17605 | med | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 50% | 87% | 213.8 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 41% | 72% | 183.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 41% | 56% | 167.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| 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) | 42% | 58% | 164.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 87% | 155.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 64% | 148.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 64% | 148.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 62% | 148.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 40% | 78% | 141.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| 2'-deoxyinosine catabolism | nupA | lo | Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) | 32% | 51% | 127.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 31% | 94% | 125.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 62% | 291.2 |
Sequence Analysis Tools
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
MIKTVDLKKIFTGRGTEVRAVDGVTTHIKSGEVVVVIGPSGSGKSTYLRCLNGLETLTDG
HIMIDGIDLADKKTDLNKVRREVGMVFQQFNLFPHKTVLDNIILAQQVVRKRNRKEAEDK
ARQLLKKVGIADKESVYPGHLSGGQQQRVAIARALAMDPKIMLFDEPTSALDPEMVGEVL
DVMKQLAREGMTMVVVTHEMGFAREVADRVIFMDHGKLVEEGTPEHFFTEPREERAKDFL
RQVL
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