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Conserved domains on  [gi|145334817|ref|NP_001078754|]
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Calcium-binding endonuclease/exonuclease/phosphatase family [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 32-247 2.05e-09

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member cd09096:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 280  Bit Score: 58.20  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  32 NILApiyKRLS-HKDQSLRESDNRAYWLGRNHRIIDWLLYERSSIICLQEFwvgnEELVNLYEKRLGDAGYLSYKLG--- 107
Cdd:cd09096    6 NILA---QALGeGKDGFVRCPCEALKWEERKYLILEEILTYDPDILCLQEV----DHYKDTLQPLLSRLGYQGTFFPkpd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 108 ------RTNNRGDGLLTAVHKDYFRVVNSRDLLFNDCGDRVAQllhVELVPPYSQYDAHQEVLIVNTHLlfPHDSTLSIV 181
Cdd:cd09096   79 spclyiENNNGPDGCALFFRKDRFELVNTEKIRLSAMTLKTNQ---VAIACTLRCKETGREICLAVTHL--KARTGWERL 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145334817 182 RLQQVYKILQYVESYQKEVNlspMPIILCGDWNGSKRGHVYKFLRSQGFvsSYDTAHRYTDSDAHK 247
Cdd:cd09096  154 RSEQGKDLLQNLQSFIEGAK---IPLIICGDFNAEPTEPVYKTFSNSSL--NLNSAYKLLSADGQS 214
FRQ1 super family cl34916
Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];
277-373 8.04e-06

Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5126:

Pssm-ID: 444056 [Multi-domain]  Cd Length: 137  Bit Score: 45.17  E-value: 8.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 277 KTSWSEAVFGMFRYLLRRASLTAEDAFAFLKTDNDGdHITFMGFCETLRQLnltghcnGLTTKEIKDLWTQADIDGNGLL 356
Cdd:COG5126   49 RISREEFVAGMESLFEATVEPFARAAFDLLDTDGDG-KISADEFRRLLTAL-------GVSEEEADELFARLDTDGDGKI 120

                         90
                 ....*....|....*..
gi 145334817 357 DYKEFQQrIWNQTWSEQ 373
Cdd:COG5126  121 SFEEFVA-AVRDYYTPD 136
 
Name Accession Description Interval E-value
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 32-247 2.05e-09

C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197330 [Multi-domain]  Cd Length: 280  Bit Score: 58.20  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  32 NILApiyKRLS-HKDQSLRESDNRAYWLGRNHRIIDWLLYERSSIICLQEFwvgnEELVNLYEKRLGDAGYLSYKLG--- 107
Cdd:cd09096    6 NILA---QALGeGKDGFVRCPCEALKWEERKYLILEEILTYDPDILCLQEV----DHYKDTLQPLLSRLGYQGTFFPkpd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 108 ------RTNNRGDGLLTAVHKDYFRVVNSRDLLFNDCGDRVAQllhVELVPPYSQYDAHQEVLIVNTHLlfPHDSTLSIV 181
Cdd:cd09096   79 spclyiENNNGPDGCALFFRKDRFELVNTEKIRLSAMTLKTNQ---VAIACTLRCKETGREICLAVTHL--KARTGWERL 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145334817 182 RLQQVYKILQYVESYQKEVNlspMPIILCGDWNGSKRGHVYKFLRSQGFvsSYDTAHRYTDSDAHK 247
Cdd:cd09096  154 RSEQGKDLLQNLQSFIEGAK---IPLIICGDFNAEPTEPVYKTFSNSSL--NLNSAYKLLSADGQS 214
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 30-214 3.07e-08

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 52.99  E-value: 3.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  30 TFNIlapiykrlsHKDQSLRESDNRaywlgrnHRIIDWLLYERSSIICLQEFwvgneelvnlyekrlgdaGYLSyklgrt 109
Cdd:COG3568   12 TYNI---------RYGLGTDGRADL-------ERIARVIRALDPDVVALQEN------------------AILS------ 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 110 nnRgdglltavhkdyFRVVNSRDLLFNDCGDRVAQLLHVELVPPysqydaHQEVLIVNTHLlfphDSTLSIVRLQQVYKI 189
Cdd:COG3568   52 --R------------YPIVSSGTFDLPDPGGEPRGALWADVDVP------GKPLRVVNTHL----DLRSAAARRRQARAL 107

                        170       180
                 ....*....|....*....|....*
gi 145334817 190 LQYVESYQKevnlsPMPIILCGDWN 214
Cdd:COG3568  108 AELLAELPA-----GAPVILAGDFN 127
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 52-214 3.17e-07

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 50.30  E-value: 3.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817   52 DNRAYWLGRNHRIIDWLLYERSSIICLQEFWVGNEELVNLYEKRLGdaGYLSYKLGRTNNRGDGLLTAVHKDYFRVVNSR 131
Cdd:pfam03372  10 ADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYG--GFLSYGGPGGGGGGGGVAILSRYPLSSVILVD 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  132 DLLFNDCGDRVAQLLHVELVPpysqydahqevlIVNTHLLFPHDSTLSIVRLQQVYKILQYVESYQKevnlSPMPIILCG 211
Cdd:pfam03372  88 LGEFGDPALRGAIAPFAGVLV------------VPLVLTLAPHASPRLARDEQRADLLLLLLALLAP----RSEPVILAG 151


                  ...
gi 145334817  212 DWN 214
Cdd:pfam03372 152 DFN 154
FRQ1 COG5126
Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];
277-373 8.04e-06

Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];


Pssm-ID: 444056 [Multi-domain]  Cd Length: 137  Bit Score: 45.17  E-value: 8.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 277 KTSWSEAVFGMFRYLLRRASLTAEDAFAFLKTDNDGdHITFMGFCETLRQLnltghcnGLTTKEIKDLWTQADIDGNGLL 356
Cdd:COG5126   49 RISREEFVAGMESLFEATVEPFARAAFDLLDTDGDG-KISADEFRRLLTAL-------GVSEEEADELFARLDTDGDGKI 120

                         90
                 ....*....|....*..
gi 145334817 357 DYKEFQQrIWNQTWSEQ 373
Cdd:COG5126  121 SFEEFVA-AVRDYYTPD 136
EFh cd00051
EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal ...
 299-365 1.24e-03

EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.


Pssm-ID: 238008 [Multi-domain]  Cd Length: 63  Bit Score: 37.14  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334817 299 AEDAFAFLKTDNDGdHITFmgfcETLRQLnLTGHCNGLTTKEIKDLWTQADIDGNGLLDYKEFQQRI 365
Cdd:cd00051    2 LREAFRLFDKDGDG-TISA----DELKAA-LKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62
EF-hand_7 pfam13499
EF-hand domain pair;
299-365 3.23e-03

EF-hand domain pair;


Pssm-ID: 463900 [Multi-domain]  Cd Length: 67  Bit Score: 36.08  E-value: 3.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145334817  299 AEDAFAFLKTDNDGdHITFmgfcETLRQLnLTGHCNG--LTTKEIKDLWTQADIDGNGLLDYKEFQQRI 365
Cdd:pfam13499   4 LKEAFKLLDSDGDG-YLDV----EELKKL-LRKLEEGepLSDEEVEELFKEFDLDKDGRISFEEFLELY 66
 
Name Accession Description Interval E-value
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 32-247 2.05e-09

C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197330 [Multi-domain]  Cd Length: 280  Bit Score: 58.20  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  32 NILApiyKRLS-HKDQSLRESDNRAYWLGRNHRIIDWLLYERSSIICLQEFwvgnEELVNLYEKRLGDAGYLSYKLG--- 107
Cdd:cd09096    6 NILA---QALGeGKDGFVRCPCEALKWEERKYLILEEILTYDPDILCLQEV----DHYKDTLQPLLSRLGYQGTFFPkpd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 108 ------RTNNRGDGLLTAVHKDYFRVVNSRDLLFNDCGDRVAQllhVELVPPYSQYDAHQEVLIVNTHLlfPHDSTLSIV 181
Cdd:cd09096   79 spclyiENNNGPDGCALFFRKDRFELVNTEKIRLSAMTLKTNQ---VAIACTLRCKETGREICLAVTHL--KARTGWERL 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145334817 182 RLQQVYKILQYVESYQKEVNlspMPIILCGDWNGSKRGHVYKFLRSQGFvsSYDTAHRYTDSDAHK 247
Cdd:cd09096  154 RSEQGKDLLQNLQSFIEGAK---IPLIICGDFNAEPTEPVYKTFSNSSL--NLNSAYKLLSADGQS 214
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 30-237 1.78e-08

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 54.92  E-value: 1.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  30 TFNIlapiykRLSHKDqslrESDNRayWLGRNHRIIDWLLYERSSIICLQEfwvGNEELVNLYEKRLGDagYLSYKLGRT 109
Cdd:cd09083    4 TFNI------RYDNPS----DGENS--WENRKDLVAELIKFYDPDIIGTQE---ALPHQLADLEELLPE--YDWIGVGRD 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 110 NNRGDGLLTAV--HKDYFRVVNSRDLLFNDCGDrvaqllhvelVPPYSQYDAH----------------QEVLIVNTHll 171
Cdd:cd09083   67 DGKEKGEFSAIfyRKDRFELLDSGTFWLSETPD----------VVGSKGWDAAlprictwarfkdkktgKEFYVFNTH-- 134

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 145334817 172 FPHDSTLSivRLQQVYKILQYVESYQKevnlsPMPIILCGDWNGSKRGHVYKFLRSQGFVSSYDTA 237
Cdd:cd09083  135 LDHVGEEA--REESAKLILERIKEIAG-----DLPVILTGDFNAEPDSEPYKTLTSGGLKDARDTA 193
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 30-214 3.07e-08

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 52.99  E-value: 3.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  30 TFNIlapiykrlsHKDQSLRESDNRaywlgrnHRIIDWLLYERSSIICLQEFwvgneelvnlyekrlgdaGYLSyklgrt 109
Cdd:COG3568   12 TYNI---------RYGLGTDGRADL-------ERIARVIRALDPDVVALQEN------------------AILS------ 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 110 nnRgdglltavhkdyFRVVNSRDLLFNDCGDRVAQLLHVELVPPysqydaHQEVLIVNTHLlfphDSTLSIVRLQQVYKI 189
Cdd:COG3568   52 --R------------YPIVSSGTFDLPDPGGEPRGALWADVDVP------GKPLRVVNTHL----DLRSAAARRRQARAL 107

                        170       180
                 ....*....|....*....|....*
gi 145334817 190 LQYVESYQKevnlsPMPIILCGDWN 214
Cdd:COG3568  108 AELLAELPA-----GAPVILAGDFN 127
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 57-232 7.96e-08

C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197331 [Multi-domain]  Cd Length: 329  Bit Score: 53.85  E-value: 7.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  57 WLGRNHRIIDWLLYERSSIICLQEfwVGNEELVNLYEKRLGDAGY--LSYKLGRTNNRG-------DGLLTAVHKDYFRV 127
Cdd:cd09097   27 WDYRKQNILKEILSYNADILCLQE--VETDQYEDFFLPELKQHGYdgVFKPKSRAKTMSeaerkhvDGCAIFFKTSKFKL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 128 VNSRDLLFNDCG-------------------DRVAQLLHVELVPPYSQYDAHQEVLIVNTHLLFPHDstLSIVRLQQVYK 188
Cdd:cd09097  105 VEKHLIEFNQLAmanadaegsedmlnrvmtkDNIALIVVLEARETSYEGNKGQLLIVANTHIHWDPE--FSDVKLVQTMM 182

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334817 189 ILQYVESYQKEVNLSP------MPIILCGDWNGSKRGHVYKFLrSQGFVS 232
Cdd:cd09097  183 LLEELEKIAEKFSRYPyedsadIPLVVCGDFNSLPDSGVYELL-SNGSVS 231
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 52-214 3.17e-07

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 50.30  E-value: 3.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817   52 DNRAYWLGRNHRIIDWLLYERSSIICLQEFWVGNEELVNLYEKRLGdaGYLSYKLGRTNNRGDGLLTAVHKDYFRVVNSR 131
Cdd:pfam03372  10 ADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYG--GFLSYGGPGGGGGGGGVAILSRYPLSSVILVD 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  132 DLLFNDCGDRVAQLLHVELVPpysqydahqevlIVNTHLLFPHDSTLSIVRLQQVYKILQYVESYQKevnlSPMPIILCG 211
Cdd:pfam03372  88 LGEFGDPALRGAIAPFAGVLV------------VPLVLTLAPHASPRLARDEQRADLLLLLLALLAP----RSEPVILAG 151


                  ...
gi 145334817  212 DWN 214
Cdd:pfam03372 152 DFN 154
FRQ1 COG5126
Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];
277-373 8.04e-06

Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms];


Pssm-ID: 444056 [Multi-domain]  Cd Length: 137  Bit Score: 45.17  E-value: 8.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 277 KTSWSEAVFGMFRYLLRRASLTAEDAFAFLKTDNDGdHITFMGFCETLRQLnltghcnGLTTKEIKDLWTQADIDGNGLL 356
Cdd:COG5126   49 RISREEFVAGMESLFEATVEPFARAAFDLLDTDGDG-KISADEFRRLLTAL-------GVSEEEADELFARLDTDGDGKI 120

                         90
                 ....*....|....*..
gi 145334817 357 DYKEFQQrIWNQTWSEQ 373
Cdd:COG5126  121 SFEEFVA-AVRDYYTPD 136
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 75-228 6.07e-04

Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine; Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid "second messenger" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197312 [Multi-domain]  Cd Length: 280  Bit Score: 41.56  E-value: 6.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  75 IICLQE-FwvGNEELVNLYEKRLGDAGYLSYKLGRTNNRGD------GLLTAVHkdyFRVVNSRDLLFNDCG--DRVAQ- 144
Cdd:cd09078   39 VVVLQEvF--DARARKRLLNGLKKEYPYQTDVVGRSPSGWSsklvdgGVVILSR---YPIVEKDQYIFPNGCgaDCLAAk 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 145 -LLHVELVPPYSQYdahqeVLIVNTHLLFPHDSTLS-IVRLQQVYKILQYVESYQKEVNlspMPIILCGDWN---GSKRG 219
Cdd:cd09078  114 gVLYAKINKGGTKV-----YHVFGTHLQASDGSCLDrAVRQKQLDELRAFIEEKNIPDN---EPVIIAGDFNvdkRSSRD 185


                 ....*....
gi 145334817 220 HVYKFLRSQ 228
Cdd:cd09078  186 EYDDMLEQL 194
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 62-233 9.28e-04

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 40.74  E-value: 9.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  62 HRIIDWLLYERSSIICLQEFWvgNEELVNLYEKRLGDAGYLSYKLGRTNNRGDGLLTAVHKdyFRVVNSRDLLFNDCGDR 141
Cdd:cd09084   19 DKILDFIKKQDPDILCLQEYY--GSEGDKDDDLRLLLKGYPYYYVVYKSDSGGTGLAIFSK--YPILNSGSIDFPNTNNN 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 142 VAQllhVELVPPysqydaHQEVLIVNTHL----LFPHDSTLS---IVRLQQVYKILQ-----------YVESYQKEVNLS 203
Cdd:cd09084   95 AIF---ADIRVG------GDTIRVYNVHLesfrITPSDKELYkeeKKAKELSRNLLRklaeafkrraaQADLLAADIAAS 165

                        170       180       190
                 ....*....|....*....|....*....|...
gi 145334817 204 PMPIILCGDWNGSKRGHVYKFLRSQ---GFVSS 233
Cdd:cd09084  166 PYPVIVCGDFNDTPASYVYRTLKKGltdAFVEA 198
EFh cd00051
EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal ...
 299-365 1.24e-03

EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.


Pssm-ID: 238008 [Multi-domain]  Cd Length: 63  Bit Score: 37.14  E-value: 1.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334817 299 AEDAFAFLKTDNDGdHITFmgfcETLRQLnLTGHCNGLTTKEIKDLWTQADIDGNGLLDYKEFQQRI 365
Cdd:cd00051    2 LREAFRLFDKDGDG-TISA----DELKAA-LKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 152-232 1.68e-03

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 40.07  E-value: 1.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 152 PPYSQY----DAHQEVLIVNTHLLFPHDSTLSIV--RLQQVYKILQYVESYQKEvnLSPMPIILCGDWNGSKRGHVYKFL 225
Cdd:cd10283  111 PPYAAKfksgGTGFDFTLVNVHLKSGGSSKSGQGakRVAEAQALAEYLKELADE--DPDDDVILLGDFNIPADEDAFKAL 188


                 ....*..
gi 145334817 226 RSQGFVS 232
Cdd:cd10283  189 TKAGFKS 195
EFh_PI-PLC cd15898
EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4. ...
 305-362 1.69e-03

EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes; PI-PLC isozymes are signaling enzymes that hydrolyze the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. This family corresponds to the four EF-hand motifs containing PI-PLC isozymes, including PI-PLC-beta (1-4), -gamma (1-2), -delta (1,3,4), -epsilon (1), -zeta (1), eta (1-2). Lower eukaryotes such as yeast and slime molds contain only delta-type isozymes. In contrast, other types of isoforms present in higher eukaryotes. This family also includes 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase 1 (PLC1) from fungi. Some homologs from plants contain only two atypical EF-hand motifs and they are not included. All PI-PLC isozymes except sperm-specific PI-PLC-zeta share a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. PI-PLC-zeta lacks the PH domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Most of EF-hand motifs found in PI-PLCs consist of a helix-loop-helix structure, but lack residues critical to metal binding. Moreover, the EF-hand region of most of PI-PLCs may have an important regulatory function, but it has yet to be identified. However, PI-PLC-zeta is a key exception. It is responsible for Ca2+ oscillations in fertilized oocytes and exhibits a high sensitivity to Ca2+ mediated through its EF-hand domain. In addition, PI-PLC-eta2 shows a canonical EF-loop directing Ca2+-sensitivity and thus can amplify transient Ca2+ signals. Also it appears that PI-PLC-delta1 can regulate the binding of PH domain to PIP2 in a Ca2+-dependent manner through its functionally important EF-hand domains. PI-PLCs can be activated by a variety of extracellular ligands, such as growth factors, hormones, cytokines and lipids. Their activation has been implicated in tumorigenesis and/or metastasis linked to migration, proliferation, growth, inflammation, angiogenesis and actin cytoskeleton reorganization. PI-PLC-beta isozymes are activated by G-protein coupled receptor (GPCR) through different mechanisms. However, PI-PLC-gamma isozymes are activated by receptor tyrosine kinase (RTK), such as Rho and Ras GTPases. In contrast, PI-PLC-epsilon are activated by both GPCR and RTK. PI-PLC-delta1 and PLC-eta 1 are activated by GPCR-mediated calcium mobilization. The activation mechanism for PI-PLC-zeta remains unclear.


Pssm-ID: 320029 [Multi-domain]  Cd Length: 137  Bit Score: 38.42  E-value: 1.69e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 145334817 305 FLKTDNDGDHitFMGFCET---LRQLNLTghcngLTTKEIKDLWTQADIDGNGLLDYKEFQ 362
Cdd:cd15898    6 WIKADKDGDG--KLSLKEIkklLKRLNIR-----VSEKELKKLFKEVDTNGDGTLTFDEFE 59
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 60-241 1.86e-03

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 39.77  E-value: 1.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817  60 RNHRIIDWLLYERSSIICLQEfwVGNEELVNLYEKRLGDAGYLSYKLGRTNNRG-DGLLTAVHKDYFRVVNSRDLLFN-- 136
Cdd:cd08372   14 RASGIARWVRELDPDIVCLQE--VKDSQYSAVALNQLLPEGYHQYQSGPSRKEGyEGVAILSKTPKFKIVEKHQYKFGeg 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334817 137 DCGDRVAQLLHVELvppysqydAHQEVLIVNTHLlfPHDSTLSIVRLQQVYKILQYVESYQKEVNLspmPIILCGDWNGS 216
Cdd:cd08372   92 DSGERRAVVVKFDV--------HDKELCVVNAHL--QAGGTRADVRDAQLKEVLEFLKRLRQPNSA---PVVICGDFNVR 158

                        170       180       190
                 ....*....|....*....|....*....|...
gi 145334817 217 KR--------GHVYKFLRSQGFVSSYDTAHRYT 241
Cdd:cd08372  159 PSevdsenpsSMLRLFVALNLVDSFETLPHAYT 191
EF-hand_7 pfam13499
EF-hand domain pair;
299-365 3.23e-03

EF-hand domain pair;


Pssm-ID: 463900 [Multi-domain]  Cd Length: 67  Bit Score: 36.08  E-value: 3.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145334817  299 AEDAFAFLKTDNDGdHITFmgfcETLRQLnLTGHCNG--LTTKEIKDLWTQADIDGNGLLDYKEFQQRI 365
Cdd:pfam13499   4 LKEAFKLLDSDGDG-YLDV----EELKKL-LRKLEEGepLSDEEVEELFKEFDLDKDGRISFEEFLELY 66
EFh_PI-PLCdelta cd16202
EF-hand motif found in phosphoinositide phospholipase C delta (PI-PLC-delta); PI-PLC-delta ...
 304-363 4.01e-03

EF-hand motif found in phosphoinositide phospholipase C delta (PI-PLC-delta); PI-PLC-delta isozymes represent a class of metazoan PI-PLCs that are some of the most sensitive to calcium among all PLCs. Their activation is modulated by intracellular calcium ion concentration, phospholipids, polyamines, and other proteins, such as RhoAGAP. Like other PI-PLC isozymes, PI-PLC-delta isozymes contain a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1, 3 and 4). PI-PLC-delta1 is relatively well characterized. It is activated by high calcium levels generated by other PI-PLC family members, and therefore functions as a calcium amplifier within the cell. Different PI-PLC-delta isozymes have different tissue distribution and different subcellular locations. PI-PLC-delta1 is mostly a cytoplasmic protein, PI-PLC-delta3 is located in the membrane, and PI-PLC-delta4 is predominantly detected in the cell nucleus. PI-PLC-delta isozymes is evolutionarily conserved even in non-mammalian species, such as yeast, slime molds and plants.


Pssm-ID: 320032 [Multi-domain]  Cd Length: 140  Bit Score: 37.59  E-value: 4.01e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 145334817 304 AFLKTDNDGDhiTFMGF---CETLRQLNLtghcnGLTTKEIKDLWTQADIDGNGLLDYKEFQQ 363
Cdd:cd16202    5 QFRKADKNGD--GKLSFkecKKLLKKLNV-----KVDKDYAKKLFQEADTSGEDVLDEEEFVQ 60
EF-hand_1 pfam00036
EF hand; The EF-hands can be divided into two classes: signalling proteins and buffering ...
 340-363 7.18e-03

EF hand; The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.


Pssm-ID: 425435 [Multi-domain]  Cd Length: 29  Bit Score: 33.91  E-value: 7.18e-03
                          10        20
                  ....*....|....*....|....
gi 145334817  340 EIKDLWTQADIDGNGLLDYKEFQQ 363
Cdd:pfam00036   1 ELKEIFRLFDKDGDGKIDFEEFKE 24
 
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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