Protein WP_055444491.1 in Lacinutrix himadriensis E4-9a
Annotation: NCBI__GCF_001418105.1:WP_055444491.1
Length: 259 amino acids
Source: GCF_001418105.1 in NCBI
Candidate for 33 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) | 40% | 92% | 162.2 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
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) | 40% | 92% | 162.2 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 97% | 162.5 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 97% | 162.5 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 38% | 90% | 156 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-arginine catabolism | artP | lo | 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) | 35% | 96% | 146.7 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-histidine catabolism | hisP | lo | 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) | 35% | 96% | 146.7 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-lysine catabolism | hisP | lo | 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) | 35% | 96% | 146.7 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 82% | 143.3 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 82% | 143.3 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 60% | 142.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 35% | 84% | 139.4 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 33% | 94% | 137.5 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 57% | 136.7 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 35% | 68% | 134 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 35% | 68% | 134 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 35% | 68% | 134 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 35% | 62% | 129.8 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 31% | 57% | 125.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 62% | 124 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 62% | 124 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 32% | 81% | 122.1 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 57% | 120.6 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 57% | 120.6 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 33% | 57% | 120.6 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 31% | 54% | 120.6 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
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) | 32% | 73% | 117.9 | Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 | 37% | 168.7 |
Sequence Analysis Tools
View WP_055444491.1 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
MNTGQNNSKAIENIETKSVMLEIKDLRKSFGDNAVLNGFNLKLYEGENLVIMGKSGSGKS
VMIKCLVGLLQADSGSIKIMDQEINTLNQKDLNILRTEIGFLFQGSALYDSMTVRENLEF
PLRRHKTRFKDASNMDELVTEALESVGLLHTVDLMPAELSGGMKRRIALARTLILKPKII
LYDEPTSGLDPITSKEIIALMRSIQKQYKTSSLIITHDVDCARVVSERIVLLVDGVNYVE
GTYSELSTSTDAQVKAFFK
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