Family Search for PF16378 (DUF4988)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF16378 hits 5 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
BT_RS16855 PL29 family lyase N-terminal domain-containing protein from Bacteroides thetaiotaomicron VPI-5482
BT3329, BT_3329 hypothetical protein from Bacteroides thetaiotaomicron VPI-5482
Aligns to 25:207 / 645 (28.4%), covers 100.0% of PF16378, 199.4 bits
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...family nutrient uptake outer memb. protein 2.6 0.001 BT_RS16820 BT3322 Redoxin family protein 2.9 0.005 BT_RS16855 BT3329 DUF4988 domain-containing protein 11.1 to 5.3 0 to 4E-07 BT_RS16930 to 45 BT3344 to 47 DUF4973 domain-containing protein, RagB/SusD family nutrient uptake outer memb. protein, TonB-dependent receptor, IPT/TIG domain-containing...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...nutrient uptake outer memb. protein 2.6 0.001 BT_RS16820 BT3322 Redoxin family protein 2.9 0.005 BT_RS16855 BT3329 DUF4988 domain-containing protein 11.1 to 5.3 0 to 4E-07 BT_RS16930 to 45 BT3344 to 47 DUF4973 domain-containing protein, RagB/SusD family nutrient uptake outer memb. protein, TonB-dependent receptor, IPT/TIG domain-containing protein...”
- Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species
Overbeeke, Frontiers in microbiology 2022 - “...in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders, suggesting that cooperative degradation as well as...”
- “...et al., 2018 ) and interacts together with the predicted surface glycan binding proteins (SGBP) BT_3329 and BT_3330 at the outer membrane. The BT_3328 lyase has been shown to prefer larger molecules with a high degree of polymerization ( Ndeh et al., 2018 ). Since the...”
- Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries
Rawat, Gut microbes 2022 - “...cell surface glycan-binding protein (SGBP) (BT3331) and a SusC-like TonB-dependent transporter (BT3332). Other surface proteins, BT3329 and BT3330, are also proven to be SGBPs. 69 Within the PUL, four PLs are encoded, viz . BT3324, BT3328, BT3350, and the distal BT4410. Among them, BT3324 and BT3350...”
- “...gut. The surface-localized BT3328-PL29 dissimilates extracellular CS to produce oligomers, which are bound by SGBPs: BT3329, BT3330, and BT3332 (SusD-like), and internalized by BT3331-SusC-like transporter. These oligomers are processed by three periplasmic PLs (BT3324-PL8, BT3350-PL8, and BT4410-PL33) and BT3349-4-O-sulfatase (S1_27). The disaccharide products of these CS...”
- Host glycan utilization within the Bacteroidetes Sus-like paradigm
Brown, Glycobiology 2021 - “...et al. 2018). CS/DS/HA recognition requires two SGBPs, BT3329 and BT3330, likely due to the greater diversity in monosaccharides and sulfation of these...”
- “...the SusCDlike complex with help from two SGBP proteins, BT3329 and BT3330. Once imported, a suite of PL enzymes, a GH88, and three sulfatases depolymerize and...”
- Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus
Ndeh, Nature communications 2020 - “...susC ), a hybrid two-component sensor (BT3334 HTCS ) and two proteins of unknown function (BT3329 and BT3330). The non-PUL encoded genes, BT1596-S1_9 2S-sulf and BT4410 PL33 , encode a 2-O sulfatase and a hyaluronidase, respectively (Fig. 1a, b ). A paradigm for how PULs organise...”
- “...to enter cytoplasmic metabolic pathways. Extracellular glycan binding and degradation Two genes of unknown function BT3329 and BT3330 exist within PUL CS/DS/HA . Both proteins had no enzymatic activity against any GAG substrates. However, they were shown to exhibit binding by isothermal titration calorimetry (ITC). Both...”
- The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29
Ndeh, The Journal of biological chemistry 2018 - “...of B. thetaiotaomicron, three of such genes BT_3328, BT_3329 and BT_3330 (all of unknown function) appear in a distinct operon (BT_332830) conserved in several...”
- Species-specific dynamic responses of gut bacteria to a mammalian glycan
Raghavan, Journal of bacteriology 2015 - “...B. thetaiotaomicron CS PUL includes three genes (BT3328, BT3329, and BT3330) encoding proteins of unknown function predicted to localize to the outer membrane....”
BT3328 hyaluronic acid endo-lyase (PL29) from Bacteroides thetaiotaomicron VPI-5482
BT3328, BT_3328 hypothetical protein from Bacteroides thetaiotaomicron VPI-5482
WP_008767539 DUF4955 domain-containing protein from Bacteroides thetaiotaomicron
Aligns to 25:206 / 868 (21.0%), covers 97.3% of PF16378, 111.8 bits
- mutant phenotype: Specifically important in carbon source Hyaluronic acid sodium salt from Streptococcus equi. In vitro, it also degrades other glycosaminoglycans such as chondroitin sulfate and dermatan sulfate (PMCID:PMC6240882), but it is not important for utilizing chondroitin sulfate. We do not have fitness data for dermatan sulfate.
- Human Gut Microbiota and Drug Metabolism
Pant, Microbial ecology 2023 - “...the genome of gut bacteria Bacteroides cellulosilyticus [ 137 ]. Another study reported a gene (BT_3328) encoding a novel polysaccharide lyase, BtCDH from B. thetaiotaomicron , capable of degrading the dermatan sulfate, chondroitin sulfate, and hyaluronic acid of glycosaminoglycans, an important player in hostmicrobial interactions [...”
- Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species
Overbeeke, Frontiers in microbiology 2022 - “...act on both compounds. We propose that in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders,...”
- “...et al., 2014 ). Additionally, a novel surface lyase with a high affinity for CS (BT_3328) has recently been identified ( Ndeh et al., 2018 , 2020 ). Although B . theta PUL architecture for CS and HA degradation has been well-studied, the ability of other...”
- Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries
Rawat, Gut microbes 2022 - “...proven to be SGBPs. 69 Within the PUL, four PLs are encoded, viz . BT3324, BT3328, BT3350, and the distal BT4410. Among them, BT3324 and BT3350 belong to polysaccharide lyase family 8 (PL8), whereas BT3328 and BT4410 belong to PL29 and PL33 families, respectively. 80 ,...”
- “...periplasm. However, Ndeh et al., 2018 101 showed the presence of a surface-localized polysaccharide lyase (BT3328), which was identified as the founding member of the PL29 family. BT3328-PL29 was shown to cleave CS, DS, and HA through endolytic -elimination. Product analysis revealed that a series of...”
- Host glycan utilization within the Bacteroidetes Sus-like paradigm
Brown, Glycobiology 2021 - “...pair and a single extracellular enzyme, a PL29-family BT3328, the first identified in this family (Ndeh et al. 2018). CS/DS/HA recognition requires two SGBPs,...”
- Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments
Liu, Cell reports 2021 - “...given that only CS contains sulfated sugars. The polysaccharide lyase family PL29 enzyme encoded by BT3328 was only important for fitness on HA, despite the activity of this enzyme against both HA and CS in vitro ( Ndeh et al., 2018 ). The first GAG utilization...”
- Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus
Ndeh, Nature communications 2020 - “...PL33 are upregulated 4 , 13 . PUL CS/DS/HA encodes three PLs (BT3324 PL8 , BT3328 PL29 and BT3350 PL8 ), one GH88 (BT3348 GH88 ), 2-O-sulfatases (BT3333-S1_15 6S-sulf and BT3349-S1_27 4S-sulf) , a single SusC/D-like transporter system (BT3331 susD -BT3332 susC ), a hybrid two-component...”
- “...measurable affinity, similar to that of BT3329 SGBP (Supplementary Table 1 ). The surface lyase, BT3328 PL29 , showed its highest enzymatic activity and affinity against CS-A>CS-C>HA and little activity on DS, differing from previous data 18 . End point assays, the total number of glycosidic...”
- The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29
Ndeh, The Journal of biological chemistry 2018 - “...Here, we investigated a gene of unknown function (BT_3328) from the chondroitin sulfate (CS) utilization locus of B. thetaiotaomicron. NMR and UV spectroscopic...”
- “...CS PUL of B. thetaiotaomicron, three of such genes BT_3328, BT_3329 and BT_3330 (all of unknown function) appear in a distinct operon (BT_332830) conserved in...”
- Species-specific dynamic responses of gut bacteria to a mammalian glycan
Raghavan, Journal of bacteriology 2015 - “...the B. thetaiotaomicron CS PUL includes three genes (BT3328, BT3329, and BT3330) encoding proteins of unknown function predicted to localize to the outer...”
- The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29.
Ndeh, The Journal of biological chemistry 2018 - GeneRIF: BtCDH is a cell surfacae glucosaminoglycan-degrading polysaccharide lyase from the PL29 family.
BF3767 Hypothetical protein from Bacteroides fragilis YCH46
Aligns to 153:312 / 721 (22.2%), covers 62.6% of PF16378, 60.4 bits
EDO10800.1 corn-bran specific endo-β-1,4-xylanase (BACOVA_03433) (EC 3.2.1.8) (see protein)
BACOVA_03433 hypothetical protein from Bacteroides ovatus ATCC 8483
Aligns to 52:219 / 947 (17.7%), covers 87.9% of PF16378, 54.0 bits
- Glycan complexity dictates microbial resource allocation in the large intestine
Rogowski, Nature communications 2015 - “...data indicated that BACOVA_03419 (GH3), BACOVA_03421 (GH43), BACOVA_03431 (inactive GH10, see later results), BACOVA_03432 (GH30), BACOVA_03433 (GH98) and BACOVA_04390 (GH10) were presented on the surface of B. ovatus ( Fig. 3 ). The only lipoprotein facing the periplasm was the GH43 enzyme BACOVA_03425. These conclusions were...”
- “...surface trimming' of complex xylans. Three of the surface enzymes (BACOVA_04390 GH10, BACOVA_03432 GH30 and BACOVA_03433 GH98 ( Fig. 3a,b ) exhibited endo activity and therefore are likely involved in cleaving the xylan backbone before importing into the periplasm. Studies on recombinant BACOVA_04390 GH10 showed that...”
BT2486 hypothetical protein from Bacteroides thetaiotaomicron VPI-5482
Aligns to 24:152 / 1016 (12.7%), covers 64.8% of PF16378, 40.3 bits
Or search for genetic data about PF16378 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory