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Conserved domains on  [gi|915404364|ref|WP_050787502|]
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phage holin family protein [Rhodococcus jostii]

Protein Classification

phage holin family protein( domain architecture ID 11146795)

uncharacterized phage holin family protein may function in the transport of murein hydrolases (endolysins) across the cytoplasmic membrane to the cell wall where these enzymes hydrolyze the cell wall polymer as a prelude to cell lysis; contains a type I phosphodiesterase/nucleotide pyrophosphatase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
11-134 5.32e-18

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


:

Pssm-ID: 441553  Cd Length: 116  Bit Score: 80.13  E-value: 5.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  11 LVEFFVLWGSSALALIVLDRILGGITLDrssftpipTLPAALVLALVFGLLNAALWPVIMRFMSWIGPVLLFVGVFLAGG 90
Cdd:COG1950    1 MMRFLIRWLVNALALLIAAYLLPGIEVD--------SFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINA 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 915404364  91 VMMLLTLYLVPVASVDQLSDAFVLAALLSLFTSVVSGAIASRSD 134
Cdd:COG1950   73 LMLWLAAWLVPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
ALP_like super family cl23718
alkaline phosphatases and sulfatases; This family includes alkaline phosphatases and ...
 162-429 2.97e-07

alkaline phosphatases and sulfatases; This family includes alkaline phosphatases and sulfatases. Alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. Both alkaline phosphatase and sulfatase are essential for human metabolism. Deficiency of individual enzyme cause genetic diseases.


The actual alignment was detected with superfamily member pfam01663:

Pssm-ID: 474031 [Multi-domain]  Cd Length: 343  Bit Score: 52.81  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  162 LLCIQIDGLGYDVLRRaiaDGVTPGLAKLVRETHRlVPWHTD---------WSSQ-TGatqlgvLHGSNHNVPAFRWYDK 231
Cdd:pfam01663   1 LLVISLDGFRADYLDR---FELTPNLAALAKEGVS-APNLTPvfptltfpnHYTLvTG------LYPGSHGIVGNTFYDP 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  232 TTERISVFSNpADNEQRELERTG-IPGLLAHDGASRGNLFTGGAHdnvlvvsrmrgarlgggAGYSDYFADPASalrtsi 310
Cdd:pfam01663  71 KTGEYLVFVI-SDPEDPRWWQGEpIWDTAAKAGVRAAALFWPGSE-----------------VDYSTYYGTPPR------ 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  311 rmvaELQRELRQSLrqkrkdiqprvprggvyPFVRAFATVLATDVAAAAVVGDLIKGRSVVYVDLIGYDEVSHHSGISRP 390
Cdd:pfam01663 127 ----YLKDDYNNSV-----------------PFEDRVDTAVLQTWLDLPFADVAAERPDLLLVYLEEPDYAGHRYGPDSP 185

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 915404364  391 ETLAVLTKLDDVIEMLLAVVAQA--DRPYRVVVLSDHGQSQ 429
Cdd:pfam01663 186 EVEDALRRVDRAIGDLLEALDERglFEDTNVIVVSDHGMTP 226
 
Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
11-134 5.32e-18

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


Pssm-ID: 441553  Cd Length: 116  Bit Score: 80.13  E-value: 5.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  11 LVEFFVLWGSSALALIVLDRILGGITLDrssftpipTLPAALVLALVFGLLNAALWPVIMRFMSWIGPVLLFVGVFLAGG 90
Cdd:COG1950    1 MMRFLIRWLVNALALLIAAYLLPGIEVD--------SFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINA 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 915404364  91 VMMLLTLYLVPVASVDQLSDAFVLAALLSLFTSVVSGAIASRSD 134
Cdd:COG1950   73 LMLWLAAWLVPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
Phage_holin_4_2 pfam04020
Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane ...
 14-124 2.59e-16

Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organizms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases.


Pssm-ID: 461132 [Multi-domain]  Cd Length: 105  Bit Score: 74.72  E-value: 2.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364   14 FFVLWGSSALALIVLDRILGGITldrssftpIPTLPAALVLALVFGLLNAALWPVIMRFMSWIGPVLLFVGVFLAGGVMM 93
Cdd:pfam04020   3 FLIRWLVNALALLVVAYLLPGIE--------VDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALML 74

                          90       100       110
                  ....*....|....*....|....*....|.
gi 915404364   94 LLTLYLVPVASVDQLSDAFVLAALLSLFTSV 124
Cdd:pfam04020  75 LLASWLVPGFSVDGFWAALLGALVLSIVSSL 105
Phosphodiest pfam01663
Type I phosphodiesterase / nucleotide pyrophosphatase; This family consists of ...
 162-429 2.97e-07

Type I phosphodiesterase / nucleotide pyrophosphatase; This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyze the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity. The alignment encompasses the active site. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum.


Pssm-ID: 396300 [Multi-domain]  Cd Length: 343  Bit Score: 52.81  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  162 LLCIQIDGLGYDVLRRaiaDGVTPGLAKLVRETHRlVPWHTD---------WSSQ-TGatqlgvLHGSNHNVPAFRWYDK 231
Cdd:pfam01663   1 LLVISLDGFRADYLDR---FELTPNLAALAKEGVS-APNLTPvfptltfpnHYTLvTG------LYPGSHGIVGNTFYDP 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  232 TTERISVFSNpADNEQRELERTG-IPGLLAHDGASRGNLFTGGAHdnvlvvsrmrgarlgggAGYSDYFADPASalrtsi 310
Cdd:pfam01663  71 KTGEYLVFVI-SDPEDPRWWQGEpIWDTAAKAGVRAAALFWPGSE-----------------VDYSTYYGTPPR------ 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  311 rmvaELQRELRQSLrqkrkdiqprvprggvyPFVRAFATVLATDVAAAAVVGDLIKGRSVVYVDLIGYDEVSHHSGISRP 390
Cdd:pfam01663 127 ----YLKDDYNNSV-----------------PFEDRVDTAVLQTWLDLPFADVAAERPDLLLVYLEEPDYAGHRYGPDSP 185

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 915404364  391 ETLAVLTKLDDVIEMLLAVVAQA--DRPYRVVVLSDHGQSQ 429
Cdd:pfam01663 186 EVEDALRRVDRAIGDLLEALDERglFEDTNVIVVSDHGMTP 226
AtaC COG1524
c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase, AlkP superfamily [Signal ...
 167-428 3.28e-05

c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase, AlkP superfamily [Signal transduction mechanisms];


Pssm-ID: 441133 [Multi-domain]  Cd Length: 370  Bit Score: 46.66  E-value: 3.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 167 IDGLGYDVLRRAIadgvTPGLAKLVRETHRLVPWHTDWSSQTG---ATQL-GVLHGsNHNVPAFRWYDKTTERISVFSNP 242
Cdd:COG1524   31 VDGLRADLLERAH----APNLAALAARGVYARPLTSVFPSTTApahTTLLtGLYPG-EHGIVGNGWYDPELGRVVNSLSW 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 243 ADNEQRELERTGIPGLLAHdgasrgnlftggAHDNVLVVSRMrgarlgggagYSDYFADPASALRTSirmvaelqrelrq 322
Cdd:COG1524  106 VEDGFGSNSLLPVPTIFER------------ARAAGLTTAAV----------FWPSFEGSGLIDAAR------------- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 323 slrqkrkdiqPRVPRGGVYPFVRAFATVLATDVAAaavvgDLIK--GRSVVYVDLIGYDEVSHHSGISRPETLAVLTKLD 400
Cdd:COG1524  151 ----------PYPYDGRKPLLGNPAADRWIAAAAL-----ELLRegRPDLLLVYLPDLDYAGHRYGPDSPEYRAALREVD 215

                        250       260       270
                 ....*....|....*....|....*....|
gi 915404364 401 DVIEMLLAVVAQADRP--YRVVVLSDHGQS 428
Cdd:COG1524  216 AALGRLLDALKARGLYegTLVIVTADHGMV 245
Enpp cd16018
Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin; Ecto-nucleotide ...
 379-432 3.38e-04

Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin; Ecto-nucleotide pyrophosphatases/phosphodiesterases (ENPPs) hydrolyze 5'-phosphodiester bonds in nucleotides and their derivatives, resulting in the release of 5'-nucleotide monophosphates. ENPPs have multiple physiological roles, including nucleotide recycling, modulation of purinergic receptor signaling, regulation of extracellular pyrophosphate levels, stimulation of cell motility, and possible roles in regulation of insulin receptor (IR) signaling and activity of ecto-kinases. The eukaryotic ENPP family contains at least five members that have different tissue distribution and physiological roles.


Pssm-ID: 293742 [Multi-domain]  Cd Length: 267  Bit Score: 42.96  E-value: 3.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 915404364 379 DEVSHHSGISRPETLAVLTKLDDVIEMLLAVVAQAD--RPYRVVVLSDHGQSQGAT 432
Cdd:cd16018  168 DSAGHKYGPDSPEVNEALKRVDRRLGYLIEALKERGllDDTNIIVVSDHGMTDVGT 223
 
Name Accession Description Interval E-value
YvlD COG1950
Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];
11-134 5.32e-18

Uncharacterized membrane protein YvlD, DUF360 family [Function unknown];


Pssm-ID: 441553  Cd Length: 116  Bit Score: 80.13  E-value: 5.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  11 LVEFFVLWGSSALALIVLDRILGGITLDrssftpipTLPAALVLALVFGLLNAALWPVIMRFMSWIGPVLLFVGVFLAGG 90
Cdd:COG1950    1 MMRFLIRWLVNALALLIAAYLLPGIEVD--------SFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINA 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 915404364  91 VMMLLTLYLVPVASVDQLSDAFVLAALLSLFTSVVSGAIASRSD 134
Cdd:COG1950   73 LMLWLAAWLVPGFHVDGFWAALLGALVLSIVSSLLSSLLGDDKD 116
Phage_holin_4_2 pfam04020
Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane ...
 14-124 2.59e-16

Mycobacterial 4 TMS phage holin, superfamily IV; These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organizms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases.


Pssm-ID: 461132 [Multi-domain]  Cd Length: 105  Bit Score: 74.72  E-value: 2.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364   14 FFVLWGSSALALIVLDRILGGITldrssftpIPTLPAALVLALVFGLLNAALWPVIMRFMSWIGPVLLFVGVFLAGGVMM 93
Cdd:pfam04020   3 FLIRWLVNALALLVVAYLLPGIE--------VDSFGTALIAALVLGLLNALVKPILVLLTLPLTILTLGLFLLVINALML 74

                          90       100       110
                  ....*....|....*....|....*....|.
gi 915404364   94 LLTLYLVPVASVDQLSDAFVLAALLSLFTSV 124
Cdd:pfam04020  75 LLASWLVPGFSVDGFWAALLGALVLSIVSSL 105
Phosphodiest pfam01663
Type I phosphodiesterase / nucleotide pyrophosphatase; This family consists of ...
 162-429 2.97e-07

Type I phosphodiesterase / nucleotide pyrophosphatase; This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyze the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity. The alignment encompasses the active site. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum.


Pssm-ID: 396300 [Multi-domain]  Cd Length: 343  Bit Score: 52.81  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  162 LLCIQIDGLGYDVLRRaiaDGVTPGLAKLVRETHRlVPWHTD---------WSSQ-TGatqlgvLHGSNHNVPAFRWYDK 231
Cdd:pfam01663   1 LLVISLDGFRADYLDR---FELTPNLAALAKEGVS-APNLTPvfptltfpnHYTLvTG------LYPGSHGIVGNTFYDP 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  232 TTERISVFSNpADNEQRELERTG-IPGLLAHDGASRGNLFTGGAHdnvlvvsrmrgarlgggAGYSDYFADPASalrtsi 310
Cdd:pfam01663  71 KTGEYLVFVI-SDPEDPRWWQGEpIWDTAAKAGVRAAALFWPGSE-----------------VDYSTYYGTPPR------ 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364  311 rmvaELQRELRQSLrqkrkdiqprvprggvyPFVRAFATVLATDVAAAAVVGDLIKGRSVVYVDLIGYDEVSHHSGISRP 390
Cdd:pfam01663 127 ----YLKDDYNNSV-----------------PFEDRVDTAVLQTWLDLPFADVAAERPDLLLVYLEEPDYAGHRYGPDSP 185

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 915404364  391 ETLAVLTKLDDVIEMLLAVVAQA--DRPYRVVVLSDHGQSQ 429
Cdd:pfam01663 186 EVEDALRRVDRAIGDLLEALDERglFEDTNVIVVSDHGMTP 226
AtaC COG1524
c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase, AlkP superfamily [Signal ...
 167-428 3.28e-05

c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase, AlkP superfamily [Signal transduction mechanisms];


Pssm-ID: 441133 [Multi-domain]  Cd Length: 370  Bit Score: 46.66  E-value: 3.28e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 167 IDGLGYDVLRRAIadgvTPGLAKLVRETHRLVPWHTDWSSQTG---ATQL-GVLHGsNHNVPAFRWYDKTTERISVFSNP 242
Cdd:COG1524   31 VDGLRADLLERAH----APNLAALAARGVYARPLTSVFPSTTApahTTLLtGLYPG-EHGIVGNGWYDPELGRVVNSLSW 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 243 ADNEQRELERTGIPGLLAHdgasrgnlftggAHDNVLVVSRMrgarlgggagYSDYFADPASALRTSirmvaelqrelrq 322
Cdd:COG1524  106 VEDGFGSNSLLPVPTIFER------------ARAAGLTTAAV----------FWPSFEGSGLIDAAR------------- 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 915404364 323 slrqkrkdiqPRVPRGGVYPFVRAFATVLATDVAAaavvgDLIK--GRSVVYVDLIGYDEVSHHSGISRPETLAVLTKLD 400
Cdd:COG1524  151 ----------PYPYDGRKPLLGNPAADRWIAAAAL-----ELLRegRPDLLLVYLPDLDYAGHRYGPDSPEYRAALREVD 215

                        250       260       270
                 ....*....|....*....|....*....|
gi 915404364 401 DVIEMLLAVVAQADRP--YRVVVLSDHGQS 428
Cdd:COG1524  216 AALGRLLDALKARGLYegTLVIVTADHGMV 245
Enpp cd16018
Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin; Ecto-nucleotide ...
 379-432 3.38e-04

Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin; Ecto-nucleotide pyrophosphatases/phosphodiesterases (ENPPs) hydrolyze 5'-phosphodiester bonds in nucleotides and their derivatives, resulting in the release of 5'-nucleotide monophosphates. ENPPs have multiple physiological roles, including nucleotide recycling, modulation of purinergic receptor signaling, regulation of extracellular pyrophosphate levels, stimulation of cell motility, and possible roles in regulation of insulin receptor (IR) signaling and activity of ecto-kinases. The eukaryotic ENPP family contains at least five members that have different tissue distribution and physiological roles.


Pssm-ID: 293742 [Multi-domain]  Cd Length: 267  Bit Score: 42.96  E-value: 3.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 915404364 379 DEVSHHSGISRPETLAVLTKLDDVIEMLLAVVAQAD--RPYRVVVLSDHGQSQGAT 432
Cdd:cd16018  168 DSAGHKYGPDSPEVNEALKRVDRRLGYLIEALKERGllDDTNIIVVSDHGMTDVGT 223
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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