C-terminal fragment of effector protein VpdB; This model represents the C-terminal fragment of ...
14-299
3.09e-50
C-terminal fragment of effector protein VpdB; This model represents the C-terminal fragment of the effector protein VpdB that binds the Legionella pneumophila Dot/Icm type IVB coupling protein (T4CP) complex which includes IcmS, IcmW, and LvgA. These L. pneumophila proteins are known to selectively assist the export of a subclass of effectors. The effector protein VpdB, like other L. pneumophila effectors VpdA, VpdC and VpdD, is a homolog of phospholipase A (PLA) patatin-like enzymes. However, VpdB does not appear to be involved in phospholipid metabolism. The structure reveals interactions between LvgA and a linear motif in the C-terminus of VpdB. This binding interface of LvgA also interacts with the C-terminal region of three additional L. pneumophila effectors, SidH, SetA, and PieA.
The actual alignment was detected with superfamily member TIGR04379:
Pssm-ID: 421976 Cd Length: 290 Bit Score: 167.83 E-value: 3.09e-50
myo-inosose-2 dehydratase; Members of this family include the enzyme myo-inosose-2 dehydratase, ...
14-299
3.09e-50
myo-inosose-2 dehydratase; Members of this family include the enzyme myo-inosose-2 dehydratase, product of the gene iolE, as found in inositol utilization cassettes in many species. [Energy metabolism, Sugars]
Pssm-ID: 275172 Cd Length: 290 Bit Score: 167.83 E-value: 3.09e-50
Xylose isomerase-like TIM barrel; This TIM alpha/beta barrel structure is found in xylose ...
46-284
3.83e-24
Xylose isomerase-like TIM barrel; This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae.
Pssm-ID: 426164 [Multi-domain] Cd Length: 248 Bit Score: 98.21 E-value: 3.83e-24
AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester ...
39-270
3.53e-06
AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar.
Pssm-ID: 237986 Cd Length: 279 Bit Score: 47.70 E-value: 3.53e-06
cobamide remodeling phosphodiesterase CbiR; Rare cobamides, analogs of B12 with critical ...
176-270
1.28e-03
cobamide remodeling phosphodiesterase CbiR; Rare cobamides, analogs of B12 with critical differences in the lower ligand, can become available for a salvage-like pathway to B12 biosynthesis through the action of enzymes that cleave the lower ligand. Members of this family are CbiR, a phosphodiesterase, which joins CbiZ, a previously discovered amidohydrolase, in the guild of cobamide remodeling enzymes.
Pssm-ID: 469174 Cd Length: 249 Bit Score: 39.54 E-value: 1.28e-03
myo-inosose-2 dehydratase; Members of this family include the enzyme myo-inosose-2 dehydratase, ...
14-299
3.09e-50
myo-inosose-2 dehydratase; Members of this family include the enzyme myo-inosose-2 dehydratase, product of the gene iolE, as found in inositol utilization cassettes in many species. [Energy metabolism, Sugars]
Pssm-ID: 275172 Cd Length: 290 Bit Score: 167.83 E-value: 3.09e-50
Xylose isomerase-like TIM barrel; This TIM alpha/beta barrel structure is found in xylose ...
46-284
3.83e-24
Xylose isomerase-like TIM barrel; This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae.
Pssm-ID: 426164 [Multi-domain] Cd Length: 248 Bit Score: 98.21 E-value: 3.83e-24
AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester ...
39-270
3.53e-06
AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar.
Pssm-ID: 237986 Cd Length: 279 Bit Score: 47.70 E-value: 3.53e-06
C-terminal fragment of effector protein VpdB; This model represents the C-terminal fragment of ...
184-273
9.89e-04
C-terminal fragment of effector protein VpdB; This model represents the C-terminal fragment of the effector protein VpdB that binds the Legionella pneumophila Dot/Icm type IVB coupling protein (T4CP) complex which includes IcmS, IcmW, and LvgA. These L. pneumophila proteins are known to selectively assist the export of a subclass of effectors. The effector protein VpdB, like other L. pneumophila effectors VpdA, VpdC and VpdD, is a homolog of phospholipase A (PLA) patatin-like enzymes. However, VpdB does not appear to be involved in phospholipid metabolism. The structure reveals interactions between LvgA and a linear motif in the C-terminus of VpdB. This binding interface of LvgA also interacts with the C-terminal region of three additional L. pneumophila effectors, SidH, SetA, and PieA.
Pssm-ID: 408997 Cd Length: 126 Bit Score: 38.42 E-value: 9.89e-04
cobamide remodeling phosphodiesterase CbiR; Rare cobamides, analogs of B12 with critical ...
176-270
1.28e-03
cobamide remodeling phosphodiesterase CbiR; Rare cobamides, analogs of B12 with critical differences in the lower ligand, can become available for a salvage-like pathway to B12 biosynthesis through the action of enzymes that cleave the lower ligand. Members of this family are CbiR, a phosphodiesterase, which joins CbiZ, a previously discovered amidohydrolase, in the guild of cobamide remodeling enzymes.
Pssm-ID: 469174 Cd Length: 249 Bit Score: 39.54 E-value: 1.28e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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