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Conserved domains on  [gi|1972267430|ref|NP_001379313|]
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poly(A)-specific ribonuclease [Caenorhabditis elegans]

Protein Classification

CCR4-Not complex 3'-5'-exoribonuclease subunit Ccr4( domain architecture ID 11469374)

CCR4-Not complex 3'-5'-exoribonuclease subunit Ccr4 acts as the catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 213-559 0e+00

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: 548.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd09097     1 VMCYNVLCDKYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMKK--ASTSENMLNRVMPRDNIGLCAVLKIKESVYANKflgrmq 370
Cdd:cd09097    81 TMSEAERKHVDGCAIFFKTSKFKLVEKHLIEFNQLAMANadAEGSEDMLNRVMTKDNIALIVVLEARETSYEGN------ 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 371 ipmndnvVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKKYQITQQQVPVLICGDFNSLPDSGVFEYLSK 450
Cdd:cd09097   155 -------KGQLLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKFSRYPYEDSADIPLVVCGDFNSLPDSGVYELLSN 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 451 GQITRRHMDLKSFRDDSCLekftnstDKNVISHPLRLDSACD-INSIPFTNYTLDFKGMIDYIFATPQSLARLGILGPFD 529
Cdd:cd09097   228 GSVSPNHPDFKEDPYGEYL-------TASGLTHSFKLKSAYAnLGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLGPPD 300

                         330       340       350
                  ....*....|....*....|....*....|
gi 1972267430 530 PQWVQsNKILGFPHPHVASDHIPIMAQYAI 559
Cdd:cd09097   301 EDWYL-NKVVGLPNPHFPSDHIALLAEFRI 329
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
59-160 2.84e-27

Leucine-rich repeat (LRR) protein [Transcription];


:

Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 114.65  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  59 TELEIHG-RVKNLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLR 137
Cdd:COG4886   116 ESLDLSGnQLTDLPEELANLTNLKELDLSNNQLTDLPEPLGNLTNLKSLDLSNNQLTDLPEELGNLTNLKELDLSNNQIT 195

                          90       100
                  ....*....|....*....|...
gi 1972267430 138 VLPYELGKLFRIQTLGLQGNPLS 160
Cdd:COG4886   196 DLPEPLGNLTNLEELDLSGNQLT 218
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 213-559 0e+00

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: 548.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd09097     1 VMCYNVLCDKYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMKK--ASTSENMLNRVMPRDNIGLCAVLKIKESVYANKflgrmq 370
Cdd:cd09097    81 TMSEAERKHVDGCAIFFKTSKFKLVEKHLIEFNQLAMANadAEGSEDMLNRVMTKDNIALIVVLEARETSYEGN------ 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 371 ipmndnvVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKKYQITQQQVPVLICGDFNSLPDSGVFEYLSK 450
Cdd:cd09097   155 -------KGQLLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKFSRYPYEDSADIPLVVCGDFNSLPDSGVYELLSN 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 451 GQITRRHMDLKSFRDDSCLekftnstDKNVISHPLRLDSACD-INSIPFTNYTLDFKGMIDYIFATPQSLARLGILGPFD 529
Cdd:cd09097   228 GSVSPNHPDFKEDPYGEYL-------TASGLTHSFKLKSAYAnLGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLGPPD 300

                         330       340       350
                  ....*....|....*....|....*....|
gi 1972267430 530 PQWVQsNKILGFPHPHVASDHIPIMAQYAI 559
Cdd:cd09097   301 EDWYL-NKVVGLPNPHFPSDHIALLAEFRI 329
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
186-559 3.72e-75

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 244.29  E-value: 3.72e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 186 INTHPPPERNWVMIRH-----ADPERPIATFTVLCYNVLCDKYATVNQYSYCpSWALNWEYRKGLIIKEIRTYEADVITL 260
Cdd:COG5239     1 GPDPDFPRRELDFIQRpflsiGHYAEKDTDFTIMTYNVLAQTYATRKMYPYS-GWALKWSYRSRLLLQELLYYNADILCL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 261 QEVETEQFRTLFQPELKQLGYAGIFEAKSR-AKTMGEEERKYVDGCAIFWKVD----KFDMDKQ--YLFEFSSVAMKKAS 333
Cdd:COG5239    80 QEVDAEDFEDFWKDQLGKLGYDGIFIPKERkVKWMIDYDTTKVDGCAIFLKRFidssKLGLILAvtHLFWHPYGYYERFR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 334 TSENMLNRVMPRDNIglcavlkikesVYANKFLGRMQIPmndnvVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRV 413
Cdd:COG5239   160 QTYILLNRIGEKDNI-----------AWVCLFVGLFNKE-----PGDTPYVANTHLPWDPKYRDVKLIQCSLLYRELKKV 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 414 LEEVSKKYQI-----TQQQVPVLICGDFNSLPDSGVFEYLSKGQItrrhmdlkSFRDDSCLEKFTNSTDKNVISHPLRLD 488
Cdd:COG5239   224 LKEELNDDKEegdikSYPEVDILITGDFNSLRASLVYKFLVTSQI--------QLHESLNGRDFSLYSVGYKFVHPENLK 295

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972267430 489 SACDINSIPFTNYTLDFKGMIDYIFATPQSLARL-GILGPFDPQWvqSNKILGFPHPHVASDHIPIMAQYAI 559
Cdd:COG5239   296 SDNSKGELGFTNWTPGFKGVIDYIFYHGGLLTRQtGLLGVVEGEY--ASKVIGLPNMPFPSDHIPLLAEFAS 365
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 189-557 1.75e-73

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 246.56  E-value: 1.75e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 189 HPPPeRNWVMIRHADPERPIA---------TFTVLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVIT 259
Cdd:PLN03144  225 SPTP-RRLIQVNGLDGMGHLDldgrtssagTFTVLSYNILSDLYATSDMYSYCPPWALSWTYRRQNLLREIVGYRADILC 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 260 LQEVETEQFRTLFQPELKQLGYAGIFEAKSraktmGE--EERKYV-DGCAIFWKVDKFDMDKQYLFEFSSVAMkkaSTSE 336
Cdd:PLN03144  304 LQEVQSDHFEEFFAPELDKHGYQALYKKKT-----TEvyTGNTYViDGCATFFRRDRFSLVKKYEVEFNKAAQ---SLTE 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 337 NM---------LNRVMpRDNIGLCAVLKIKESVYANKFLGRMQIpmndnvvgnpLVVATAHIHWDPEFCDVKLVQsmmlT 407
Cdd:PLN03144  376 ALipsaqkkaaLNRLL-KDNVALIVVLEAKFGNQGADNGGKRQL----------LCVANTHIHANQELKDVKLWQ----V 440

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 408 HEVSRVLEEVSKKYQItqqqvPVLICGDFNSLPDSGVFEYLSKGQITRRHMDLKS-----FRDDSCLE-------KFTNS 475
Cdd:PLN03144  441 HTLLKGLEKIAASADI-----PMLVCGDFNSVPGSAPHCLLATGKVDPLHPDLAVdplgiLRPASKLThqlplvsAYSSF 515

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 476 TDKNVISHPL-----RLDSAcdINSIPFTNYTLDFKGMIDYIFATPQSLARLGILGPFDPQWVQsnKILGFPHPHVASDH 550
Cdd:PLN03144  516 ARMPGSGSGLeqqrrRMDPA--TNEPLFTNCTRDFIGTLDYIFYTADSLTVESLLELLDEESLR--KDTALPSPEWSSDH 591


                  ....*..
gi 1972267430 551 IPIMAQY 557
Cdd:PLN03144  592 IALLAEF 598
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
59-160 2.84e-27

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 114.65  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  59 TELEIHG-RVKNLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLR 137
Cdd:COG4886   116 ESLDLSGnQLTDLPEELANLTNLKELDLSNNQLTDLPEPLGNLTNLKSLDLSNNQLTDLPEELGNLTNLKELDLSNNQIT 195

                          90       100
                  ....*....|....*....|...
gi 1972267430 138 VLPYELGKLFRIQTLGLQGNPLS 160
Cdd:COG4886   196 DLPEPLGNLTNLEELDLSGNQLT 218
LRR_8 pfam13855
Leucine rich repeat;
78-136 1.80e-09

Leucine rich repeat;


Pssm-ID: 404697 [Multi-domain]  Cd Length: 61  Bit Score: 53.68  E-value: 1.80e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972267430  78 THLSALFLNNNGLTRLPPEI-AQLTNLTMLDISNNKLRSL-PTELGDMISLCHLYLNNNQL 136
Cdd:pfam13855   1 PNLRSLDLSNNRLTSLDDGAfKGLSNLKVLDLSNNLLTTLsPGAFSGLPSLRYLDLSGNRL 61
PLN00113 PLN00113
leucine-rich repeat receptor-like protein kinase; Provisional
 72-165 1.97e-07

leucine-rich repeat receptor-like protein kinase; Provisional


Pssm-ID: 215061 [Multi-domain]  Cd Length: 968  Bit Score: 54.08  E-value: 1.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  72 PSLWQLTHLSALFLNNNGLT-RLPPEIAQLTNLTMLDISNNKLR-SLPTELGDMISLCHLYLNNNQLR-VLPYELGKLFR 148
Cdd:PLN00113  254 SSLGNLKNLQYLFLYQNKLSgPIPPSIFSLQKLISLDLSDNSLSgEIPELVIQLQNLEILHLFSNNFTgKIPVALTSLPR 333

                          90
                  ....*....|....*..
gi 1972267430 149 IQTLGLQGNPLSPEISK 165
Cdd:PLN00113  334 LQVLQLWSNKFSGEIPK 350
PPP1R42 cd21340
protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 ...
 68-139 1.06e-06

protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 (PPP1R42), also known as leucine-rich repeat-containing protein 67 (lrrc67) or testis leucine-rich repeat (TLRR) protein, plays a role in centrosome separation. PPP1R42 has been shown to interact with the well-conserved signaling protein phosphatase-1 (PP1) and thereby increasing PP1's activity, which counters centrosome separation. Inhibition of PPP1R42 expression increases the number of centrosomes per cell while its depletion reduces the activity of PP1 leading to activation of NEK2, the kinase responsible for phosphorylation of centrosomal linker proteins promoting centrosome separation.


Pssm-ID: 411060 [Multi-domain]  Cd Length: 220  Bit Score: 49.78  E-value: 1.06e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972267430  68 KNLS--PSLWQLTHLSALFLNNNGLTRLPPeIAQLTNLTMLDISNNKLRSLPtELGDMISLCHLYLNNNQLRVL 139
Cdd:cd21340    12 KNITkiDNLSLCKNLKVLYLYDNKITKIEN-LEFLTNLTHLYLQNNQIEKIE-NLENLVNLKKLYLGGNRISVV 83
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 216-438 1.26e-05

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: 46.06  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 216 YNVLCDkyatvnqysycPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKsraktmg 295
Cdd:pfam03372   3 WNVNGG-----------NADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPG------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 296 eeERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMkkastsenmlnrvmprdniglcavlkikesvyankflgRMQIPMND 375
Cdd:pfam03372  65 --GGGGGGGVAILSRYPLSSVILVDLGEFGDPAL--------------------------------------RGAIAPFA 104

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1972267430 376 NVVGNPLVVATAHIHWDPefcdvklvqsmmLTHEVSRVLEEVSKKYQITQQQVPVLICGDFNS 438
Cdd:pfam03372 105 GVLVVPLVLTLAPHASPR------------LARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 213-559 0e+00

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: 548.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd09097     1 VMCYNVLCDKYATRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMKK--ASTSENMLNRVMPRDNIGLCAVLKIKESVYANKflgrmq 370
Cdd:cd09097    81 TMSEAERKHVDGCAIFFKTSKFKLVEKHLIEFNQLAMANadAEGSEDMLNRVMTKDNIALIVVLEARETSYEGN------ 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 371 ipmndnvVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKKYQITQQQVPVLICGDFNSLPDSGVFEYLSK 450
Cdd:cd09097   155 -------KGQLLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAEKFSRYPYEDSADIPLVVCGDFNSLPDSGVYELLSN 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 451 GQITRRHMDLKSFRDDSCLekftnstDKNVISHPLRLDSACD-INSIPFTNYTLDFKGMIDYIFATPQSLARLGILGPFD 529
Cdd:cd09097   228 GSVSPNHPDFKEDPYGEYL-------TASGLTHSFKLKSAYAnLGELPFTNYTPDFKGVIDYIFYSADTLSVLGLLGPPD 300

                         330       340       350
                  ....*....|....*....|....*....|
gi 1972267430 530 PQWVQsNKILGFPHPHVASDHIPIMAQYAI 559
Cdd:cd09097   301 EDWYL-NKVVGLPNPHFPSDHIALLAEFRI 329
Deadenylase_CCR4b cd10312
C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit ...
 213-556 2.43e-140

C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit 6-like; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4b, also known as CCR4-NOT transcription complex subunit 6-like (CNOT6L). 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, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b. CCR4b associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4b exhibits Mg2+-dependent deadenylase activity with strict specificity for poly (A) RNA as substrate. CCR4b is mainly localized in the cytoplasm. It regulates cell growth and influences cell cycle progression by regulating p27/Kip1 mRNA levels. It contributes to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197339  Cd Length: 348  Bit Score: 411.34  E-value: 2.43e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd10312     1 VMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMKKASTSENMLNRVMPRDNIGLCAVLKIKESVYAnkfLGRMQIP 372
Cdd:cd10312    81 IMSEQERKHVDGCAIFFKTEKFSLVQKHTVEFNQVAMANSEGSEAMLNRVMTKDNIGVAVVLEVHKELFG---AGMKPIH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 373 MNDNVVgnpLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKKY---QITQQQVPVLICGDFNSLPDSGVFEYLS 449
Cdd:cd10312   158 AADKQL---LIVANAHMHWDPEYSDVKLIQTMMFVSELKNILEKASSRPgspTADPNSIPLVLCADLNSLPDSGVVEYLS 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 450 KGQITRRHMDLKSFRDDSCLEKFT----NSTDKNVISHPLRLDSACDINSIPFTNYTLDFKGMIDYIFATPQSLARLGIL 525
Cdd:cd10312   235 NGGVADNHKDFKELRYNECLMNFScngkNGSSEGRITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVL 314

                         330       340       350
                  ....*....|....*....|....*....|.
gi 1972267430 526 GPFDPQWVQSNKILGFPHPHVASDHIPIMAQ 556
Cdd:cd10312   315 GPLDPQWLVENNITGCPHPHIPSDHFSLLTQ 345
Deadenylase_CCR4a cd10313
C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; ...
 213-556 3.75e-123

C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4a, also known as CCR4-NOT transcription complex subunit 6 (CNOT6). 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, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a and CCR4b (also called CNOT6-like or CNOT6L). CCR4a associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4a 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 of various P-body components. It also plays a role in cellular responses to DNA damage, by regulating Chk2 activity.


Pssm-ID: 197340  Cd Length: 350  Bit Score: 367.45  E-value: 3.75e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd10313     1 VMCYNVLCDKYATRQLYGYCPSWALNWDYRKKAIMQEILSCNADIISLQEVETEQYYSFFLVELKERGYNGFFSPKSRAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMKKASTSENMLNRVMPRDNIGLCAVLKI-KESVYANKflGRMQI 371
Cdd:cd10313    81 TMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAVLLELrKELIEMSS--GKPHL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 372 PMNDNVvgnpLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKKYQIT----QQQVPVLICGDFNSLPDSGVFEY 447
Cdd:cd10313   159 GMEKQL----ILVANAHMHWDPEYSDVKLVQTMMFLSEVKNIIDKASRSLKSSvlgeTGTIPLVLCADLNSLPDSGVVEY 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 448 LSKGQITRRHMDLKSFRDDSCLEKFT----NSTDKNVISHPLRLDSACDINSIPFTNYTLDFKGMIDYIFATPQSLARLG 523
Cdd:cd10313   235 LSTGGVETNHKDFKELRYNESLTNFScngkNGTTNGRITHGFKLKSAYENGLMPYTNYTFDFKGIIDYIFYSKPQLNTLG 314

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1972267430 524 ILGPFDPQWVQSNKILGFPHPHVASDHIPIMAQ 556
Cdd:cd10313   315 ILGPLDHHWLVENNISGCPHPLIPSDHFSLFAQ 347
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
186-559 3.72e-75

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 244.29  E-value: 3.72e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 186 INTHPPPERNWVMIRH-----ADPERPIATFTVLCYNVLCDKYATVNQYSYCpSWALNWEYRKGLIIKEIRTYEADVITL 260
Cdd:COG5239     1 GPDPDFPRRELDFIQRpflsiGHYAEKDTDFTIMTYNVLAQTYATRKMYPYS-GWALKWSYRSRLLLQELLYYNADILCL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 261 QEVETEQFRTLFQPELKQLGYAGIFEAKSR-AKTMGEEERKYVDGCAIFWKVD----KFDMDKQ--YLFEFSSVAMKKAS 333
Cdd:COG5239    80 QEVDAEDFEDFWKDQLGKLGYDGIFIPKERkVKWMIDYDTTKVDGCAIFLKRFidssKLGLILAvtHLFWHPYGYYERFR 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 334 TSENMLNRVMPRDNIglcavlkikesVYANKFLGRMQIPmndnvVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRV 413
Cdd:COG5239   160 QTYILLNRIGEKDNI-----------AWVCLFVGLFNKE-----PGDTPYVANTHLPWDPKYRDVKLIQCSLLYRELKKV 223

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 414 LEEVSKKYQI-----TQQQVPVLICGDFNSLPDSGVFEYLSKGQItrrhmdlkSFRDDSCLEKFTNSTDKNVISHPLRLD 488
Cdd:COG5239   224 LKEELNDDKEegdikSYPEVDILITGDFNSLRASLVYKFLVTSQI--------QLHESLNGRDFSLYSVGYKFVHPENLK 295

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972267430 489 SACDINSIPFTNYTLDFKGMIDYIFATPQSLARL-GILGPFDPQWvqSNKILGFPHPHVASDHIPIMAQYAI 559
Cdd:COG5239   296 SDNSKGELGFTNWTPGFKGVIDYIFYHGGLLTRQtGLLGVVEGEY--ASKVIGLPNMPFPSDHIPLLAEFAS 365
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 189-557 1.75e-73

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 246.56  E-value: 1.75e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 189 HPPPeRNWVMIRHADPERPIA---------TFTVLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVIT 259
Cdd:PLN03144  225 SPTP-RRLIQVNGLDGMGHLDldgrtssagTFTVLSYNILSDLYATSDMYSYCPPWALSWTYRRQNLLREIVGYRADILC 303

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 260 LQEVETEQFRTLFQPELKQLGYAGIFEAKSraktmGE--EERKYV-DGCAIFWKVDKFDMDKQYLFEFSSVAMkkaSTSE 336
Cdd:PLN03144  304 LQEVQSDHFEEFFAPELDKHGYQALYKKKT-----TEvyTGNTYViDGCATFFRRDRFSLVKKYEVEFNKAAQ---SLTE 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 337 NM---------LNRVMpRDNIGLCAVLKIKESVYANKFLGRMQIpmndnvvgnpLVVATAHIHWDPEFCDVKLVQsmmlT 407
Cdd:PLN03144  376 ALipsaqkkaaLNRLL-KDNVALIVVLEAKFGNQGADNGGKRQL----------LCVANTHIHANQELKDVKLWQ----V 440

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 408 HEVSRVLEEVSKKYQItqqqvPVLICGDFNSLPDSGVFEYLSKGQITRRHMDLKS-----FRDDSCLE-------KFTNS 475
Cdd:PLN03144  441 HTLLKGLEKIAASADI-----PMLVCGDFNSVPGSAPHCLLATGKVDPLHPDLAVdplgiLRPASKLThqlplvsAYSSF 515

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 476 TDKNVISHPL-----RLDSAcdINSIPFTNYTLDFKGMIDYIFATPQSLARLGILGPFDPQWVQsnKILGFPHPHVASDH 550
Cdd:PLN03144  516 ARMPGSGSGLeqqrrRMDPA--TNEPLFTNCTRDFIGTLDYIFYTADSLTVESLLELLDEESLR--KDTALPSPEWSSDH 591


                  ....*..
gi 1972267430 551 IPIMAQY 557
Cdd:PLN03144  592 IALLAEF 598
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
59-160 2.84e-27

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 114.65  E-value: 2.84e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  59 TELEIHG-RVKNLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLR 137
Cdd:COG4886   116 ESLDLSGnQLTDLPEELANLTNLKELDLSNNQLTDLPEPLGNLTNLKSLDLSNNQLTDLPEELGNLTNLKELDLSNNQIT 195

                          90       100
                  ....*....|....*....|...
gi 1972267430 138 VLPYELGKLFRIQTLGLQGNPLS 160
Cdd:COG4886   196 DLPEPLGNLTNLEELDLSGNQLT 218
Deadenylase cd09082
C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains ...
 213-558 1.54e-25

C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains the C-terminal catalytic domains of the deadenylases, CCR4 and 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 the 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. Saccharomyces cerevisiae 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. The deadenylase activities of Ccr4p and nocturnin differ: nocturnin degrades poly(A), Ccr4p degrades both poly(A) and single-stranded DNA, and in contrast to Ccr4p, nocturnin appears to function in a highly processive manner. 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: 197316 [Multi-domain]  Cd Length: 348  Bit Score: 108.21  E-value: 1.54e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATVNQYSYCPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRAK 292
Cdd:cd09082     1 VMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 TMGEEERKYVDGCAIFWKVDKFDMDKQYLFEFSS-VAMKKASTSENMLNRVMPRDNIGLCAVLKIKESVYANKflgrmqi 371
Cdd:cd09082    81 IMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQvAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGM------- 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 372 PMNDNVVGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLE---EVSKKYQITQQQVPVLICGDFNSLPDSGVFEYL 448
Cdd:cd09082   154 KPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEkasSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYL 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 449 SKGQitrrhMDLKSFRddSCLEKFTNSTDKNVISHPLRLDSACDINS-IPFTNYTLDFKGMI----------DYIFATPQ 517
Cdd:cd09082   234 SNGG-----VADNHKD--FKELRYNECLMNFSCNGKNGSSEGRITHGfQLKSAYENNLMPYTnytfdfkgviDYIFYSKT 306

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 1972267430 518 SL---ARLGILGPFDPQWVQSNKILGFPHPhvaSDHIPIMAQYA 558
Cdd:cd09082   307 HMnvlGVLGPLDPQWLVENNITGCPHPHIP---SDHFSLLTQLE 347
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
59-165 4.02e-25

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 108.10  E-value: 4.02e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  59 TELEIHG-RVKNLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLR 137
Cdd:COG4886   139 KELDLSNnQLTDLPEPLGNLTNLKSLDLSNNQLTDLPEELGNLTNLKELDLSNNQITDLPEPLGNLTNLEELDLSGNQLT 218

                          90       100       110
                  ....*....|....*....|....*....|
gi 1972267430 138 VLPYELGKLFRIQTLGLQGNPLS--PEISK 165
Cdd:COG4886   219 DLPEPLANLTNLETLDLSNNQLTdlPELGN 248
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
72-160 8.89e-24

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 104.25  E-value: 8.89e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  72 PSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLRVLPYELGKLFRIQT 151
Cdd:COG4886   107 EELSNLTNLESLDLSGNQLTDLPEELANLTNLKELDLSNNQLTDLPEPLGNLTNLKSLDLSNNQLTDLPEELGNLTNLKE 186


                  ....*....
gi 1972267430 152 LGLQGNPLS 160
Cdd:COG4886   187 LDLSNNQIT 195
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 213-557 3.45e-23

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: 98.71  E-value: 3.45e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 213 VLCYNVLCDKYATvnqysycpswalnweyRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKSRak 292
Cdd:cd08372     1 VASYNVNGLNAAT----------------RASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSGPSR-- 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 293 tmgeeeRKYVDGCAIFWKVDKFDMDKQYLFEFssvamkkastsenmlNRVMPRDNIGLCAVLKIKesvyankflgrmqip 372
Cdd:cd08372    63 ------KEGYEGVAILSKTPKFKIVEKHQYKF---------------GEGDSGERRAVVVKFDVH--------------- 106

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 373 mndnvvGNPLVVATAHIHWDPEFCDVKLVQSMMLTHEVSRVLEEVSKkyqitqqqvPVLICGDFNSLPDSGVFEYLSKgq 452
Cdd:cd08372   107 ------DKELCVVNAHLQAGGTRADVRDAQLKEVLEFLKRLRQPNSA---------PVVICGDFNVRPSEVDSENPSS-- 169

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 453 itrrhmdlksfrddsclekftnstdKNVISHPLRLDSACDINSIPFTNYT--LDFKGMIDYIFATPQSLARlgilgpfdp 530
Cdd:cd08372   170 -------------------------MLRLFVALNLVDSFETLPHAYTFDTymHNVKSRLDYIFVSKSLLPS--------- 215

                         330       340
                  ....*....|....*....|....*...
gi 1972267430 531 qwVQSNKILGFPH-PHVASDHIPIMAQY 557
Cdd:cd08372   216 --VKSSKILSDAArARIPSDHYPIEVTL 241
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 232-558 2.56e-21

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: 94.41  E-value: 2.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 232 CPSWALNWEYRKGLIIKEIRTYEADVITLQEVEteQFRTLFQPELKQLGYAGIFEAKSRAKTMGEEERKYVDGCAIFWKV 311
Cdd:cd09096    22 CPCEALKWEERKYLILEEILTYDPDILCLQEVD--HYKDTLQPLLSRLGYQGTFFPKPDSPCLYIENNNGPDGCALFFRK 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 312 DKFDMDKqylfefssvamkkasTSENMLNRVMPRDN-IGLCAVLKIKESvyankflgrmqipmndnvvGNPLVVATAHIH 390
Cdd:cd09096   100 DRFELVN---------------TEKIRLSAMTLKTNqVAIACTLRCKET-------------------GREICLAVTHLK 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 391 WDPEFCDVKLVQSMMLTHEVSRVLEEVSkkyqitqqqVPVLICGDFNSLPDSGVFEYLSkgqitrrhmdlksfrddscle 470
Cdd:cd09096   146 ARTGWERLRSEQGKDLLQNLQSFIEGAK---------IPLIICGDFNAEPTEPVYKTFS--------------------- 195

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 471 kftnstdknviSHPLRLDSACDINSI------PFTNYTLDFKG----MIDYIFATPQSL---ARLGILGpfdpqwVQSNK 537
Cdd:cd09096   196 -----------NSSLNLNSAYKLLSAdgqsepPYTTWKIRTSGecrhTLDYIFYSKDALsveQLLDLPT------EEQIG 258

                         330       340
                  ....*....|....*....|.
gi 1972267430 538 ILGFPHPHVASDHIPIMAQYA 558
Cdd:cd09096   259 PNRLPSFNYPSDHLSLVCDFS 279
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
53-187 1.72e-16

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 81.90  E-value: 1.72e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  53 GRSTRWTELEIHG-RVKNLSPSLWQLTHLSALFLNNNGLTRLPpEIAQLTNLTMLDISNNKLRSLPtELGDMISLCHLYL 131
Cdd:COG4886   202 GNLTNLEELDLSGnQLTDLPEPLANLTNLETLDLSNNQLTDLP-ELGNLTNLEELDLSNNQLTDLP-PLANLTNLKTLDL 279

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1972267430 132 NNNQLRVLpyELGKLFRIQTLGLQGNPLSPEISKIYHETNGAQKILQFLLDHLTIN 187
Cdd:COG4886   280 SNNQLTDL--KLKELELLLGLNSLLLLLLLLNLLELLILLLLLTTLLLLLLLLKGL 333
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 212-555 9.68e-14

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: 71.48  E-value: 9.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 212 TVLCYNVLCDkyatvnqysyCPSWALN-WEYRKGLIIKEIRTYEADVITLQEVETEQFRtlfqpELKQL--GYAGIFEAK 288
Cdd:cd09083     1 RVMTFNIRYD----------NPSDGENsWENRKDLVAELIKFYDPDIIGTQEALPHQLA-----DLEELlpEYDWIGVGR 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 289 SRAKTMGEeerkyvdGCAIFWKVDKFDMDKQYLFEFSSVAMKKASTS-ENMLNRVmprdniglC--AVLKIKESvyankf 365
Cdd:cd09083    66 DDGKEKGE-------FSAIFYRKDRFELLDSGTFWLSETPDVVGSKGwDAALPRI--------CtwARFKDKKT------ 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 366 lgrmqipmndnvvGNPLVVATAHIhwDPEfCDVKLVQSMMLthevsrVLEEVSKkyqiTQQQVPVLICGDFNSLPDSGVF 445
Cdd:cd09083   125 -------------GKEFYVFNTHL--DHV-GEEAREESAKL------ILERIKE----IAGDLPVILTGDFNAEPDSEPY 178

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 446 EYLSKGQitrrhmdlksFRDdsclekfTNSTDKNVISHPlrldsacdINSipFTNYTLDFKGM-IDYIFATPQslarlgi 524
Cdd:cd09083   179 KTLTSGG----------LKD-------ARDTAATTDGGP--------EGT--FHGFKGPPGGSrIDYIFVSPG------- 224

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1972267430 525 lgpFDPQWVQ--SNKILGfphpHVASDHIPIMA 555
Cdd:cd09083   225 ---VKVLSYEilTDRYDG----RYPSDHFPVVA 250
LRR_8 pfam13855
Leucine rich repeat;
78-136 1.80e-09

Leucine rich repeat;


Pssm-ID: 404697 [Multi-domain]  Cd Length: 61  Bit Score: 53.68  E-value: 1.80e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972267430  78 THLSALFLNNNGLTRLPPEI-AQLTNLTMLDISNNKLRSL-PTELGDMISLCHLYLNNNQL 136
Cdd:pfam13855   1 PNLRSLDLSNNRLTSLDDGAfKGLSNLKVLDLSNNLLTTLsPGAFSGLPSLRYLDLSGNRL 61
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
59-187 3.78e-09

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 59.18  E-value: 3.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  59 TELEIHG-RVKNLsPSLWQLTHLSALFLNNNGLTRLPPEiAQLTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNNQLR 137
Cdd:COG4886   231 ETLDLSNnQLTDL-PELGNLTNLEELDLSNNQLTDLPPL-ANLTNLKTLDLSNNQLTDLKLKELELLLGLNSLLLLLLLL 308

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1972267430 138 VLPYELGKLFRIQTLGLQGNPLSPEISKIYHETNGAQKILQFLLDHLTIN 187
Cdd:COG4886   309 NLLELLILLLLLTTLLLLLLLLKGLLVTLTTLALSLSLLALLTLLLLLNL 358
LRR COG4886
Leucine-rich repeat (LRR) protein [Transcription];
32-160 2.03e-08

Leucine-rich repeat (LRR) protein [Transcription];


Pssm-ID: 443914 [Multi-domain]  Cd Length: 414  Bit Score: 56.87  E-value: 2.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  32 KTLTNGMSRVHRVLTEDEIASGRSTRWTELEIHGRVKNLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNN 111
Cdd:COG4886    27 LLLLLLLLLALLLLSLLSLLLLLTLLLSLLLRDLLLSSLLLLLSLLLLLLLSLLLLSLLLLGLTDLGDLTNLTELDLSGN 106

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1972267430 112 KlrslptELGDMISLCHLYLNNNQLRVLPYELGKLFRIQTLGLQGNPLS 160
Cdd:COG4886   107 E------ELSNLTNLESLDLSGNQLTDLPEELANLTNLKELDLSNNQLT 149
LRR_8 pfam13855
Leucine rich repeat;
101-159 4.50e-08

Leucine rich repeat;


Pssm-ID: 404697 [Multi-domain]  Cd Length: 61  Bit Score: 49.83  E-value: 4.50e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972267430 101 TNLTMLDISNNKLRSLPTE-LGDMISLCHLYLNNNQLRVL-PYELGKLFRIQTLGLQGNPL 159
Cdd:pfam13855   1 PNLRSLDLSNNRLTSLDDGaFKGLSNLKVLDLSNNLLTTLsPGAFSGLPSLRYLDLSGNRL 61
PLN00113 PLN00113
leucine-rich repeat receptor-like protein kinase; Provisional
 72-165 1.97e-07

leucine-rich repeat receptor-like protein kinase; Provisional


Pssm-ID: 215061 [Multi-domain]  Cd Length: 968  Bit Score: 54.08  E-value: 1.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  72 PSLWQLTHLSALFLNNNGLT-RLPPEIAQLTNLTMLDISNNKLR-SLPTELGDMISLCHLYLNNNQLR-VLPYELGKLFR 148
Cdd:PLN00113  254 SSLGNLKNLQYLFLYQNKLSgPIPPSIFSLQKLISLDLSDNSLSgEIPELVIQLQNLEILHLFSNNFTgKIPVALTSLPR 333

                          90
                  ....*....|....*..
gi 1972267430 149 IQTLGLQGNPLSPEISK 165
Cdd:PLN00113  334 LQVLQLWSNKFSGEIPK 350
PLN03150 PLN03150
hypothetical protein; Provisional
 80-163 2.25e-07

hypothetical protein; Provisional


Pssm-ID: 178695 [Multi-domain]  Cd Length: 623  Bit Score: 53.67  E-value: 2.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  80 LSALFLNNNGLT-RLPPEIAQLTNLTMLDISNNKLR-SLPTELGDMISLCHLYLNNNQLR-VLPYELGKLFRIQTLGLQG 156
Cdd:PLN03150  420 IDGLGLDNQGLRgFIPNDISKLRHLQSINLSGNSIRgNIPPSLGSITSLEVLDLSYNSFNgSIPESLGQLTSLRILNLNG 499


                  ....*..
gi 1972267430 157 NPLSPEI 163
Cdd:PLN03150  500 NSLSGRV 506
PPP1R42 cd21340
protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 ...
 68-139 1.06e-06

protein phosphatase 1 regulatory subunit 42; Protein phosphatase 1 regulatory subunit 42 (PPP1R42), also known as leucine-rich repeat-containing protein 67 (lrrc67) or testis leucine-rich repeat (TLRR) protein, plays a role in centrosome separation. PPP1R42 has been shown to interact with the well-conserved signaling protein phosphatase-1 (PP1) and thereby increasing PP1's activity, which counters centrosome separation. Inhibition of PPP1R42 expression increases the number of centrosomes per cell while its depletion reduces the activity of PP1 leading to activation of NEK2, the kinase responsible for phosphorylation of centrosomal linker proteins promoting centrosome separation.


Pssm-ID: 411060 [Multi-domain]  Cd Length: 220  Bit Score: 49.78  E-value: 1.06e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972267430  68 KNLS--PSLWQLTHLSALFLNNNGLTRLPPeIAQLTNLTMLDISNNKLRSLPtELGDMISLCHLYLNNNQLRVL 139
Cdd:cd21340    12 KNITkiDNLSLCKNLKVLYLYDNKITKIEN-LEFLTNLTHLYLQNNQIEKIE-NLENLVNLKKLYLGGNRISVV 83
PLN00113 PLN00113
leucine-rich repeat receptor-like protein kinase; Provisional
 49-165 2.88e-06

leucine-rich repeat receptor-like protein kinase; Provisional


Pssm-ID: 215061 [Multi-domain]  Cd Length: 968  Bit Score: 50.62  E-value: 2.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  49 EIASGRSTRWTELEIHGRVKNLSPSLWQLTHLSALFLNNNGLT-RLPPEIAQLTNLTMLDISNNKLR-SLPTELGDMISL 126
Cdd:PLN00113  159 DIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVgQIPRELGQMKSLKWIYLGYNNLSgEIPYEIGGLTSL 238

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1972267430 127 CHLYL-NNNQLRVLPYELGKLFRIQTLGLQGNPLSPEISK 165
Cdd:PLN00113  239 NHLDLvYNNLTGPIPSSLGNLKNLQYLFLYQNKLSGPIPP 278
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 216-438 1.26e-05

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: 46.06  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 216 YNVLCDkyatvnqysycPSWALNWEYRKGLIIKEIRTYEADVITLQEVETEQFRTLFQPELKQLGYAGIFEAKsraktmg 295
Cdd:pfam03372   3 WNVNGG-----------NADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPG------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 296 eeERKYVDGCAIFWKVDKFDMDKQYLFEFSSVAMkkastsenmlnrvmprdniglcavlkikesvyankflgRMQIPMND 375
Cdd:pfam03372  65 --GGGGGGGVAILSRYPLSSVILVDLGEFGDPAL--------------------------------------RGAIAPFA 104

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1972267430 376 NVVGNPLVVATAHIHWDPefcdvklvqsmmLTHEVSRVLEEVSKKYQITQQQVPVLICGDFNS 438
Cdd:pfam03372 105 GVLVVPLVLTLAPHASPR------------LARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
PLN00113 PLN00113
leucine-rich repeat receptor-like protein kinase; Provisional
 77-165 4.46e-05

leucine-rich repeat receptor-like protein kinase; Provisional


Pssm-ID: 215061 [Multi-domain]  Cd Length: 968  Bit Score: 46.76  E-value: 4.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  77 LTHLSALFLNNNGLT-RLPPEIAQLTNLTMLDISNNKLRS-LPTELGDMISLCHLYLNNNQLR-VLPYELGKLFRIQTLG 153
Cdd:PLN00113  139 IPNLETLDLSNNMLSgEIPNDIGSFSSLKVLDLGGNVLVGkIPNSLTNLTSLEFLTLASNQLVgQIPRELGQMKSLKWIY 218

                          90
                  ....*....|..
gi 1972267430 154 LQGNPLSPEISK 165
Cdd:PLN00113  219 LGYNNLSGEIPY 230
LRR_8 pfam13855
Leucine rich repeat;
59-113 1.18e-04

Leucine rich repeat;


Pssm-ID: 404697 [Multi-domain]  Cd Length: 61  Bit Score: 40.20  E-value: 1.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1972267430  59 TELEI-HGRVKNLSPSLWQ-LTHLSALFLNNNGLTRLPPE-IAQLTNLTMLDISNNKL 113
Cdd:pfam13855   4 RSLDLsNNRLTSLDDGAFKgLSNLKVLDLSNNLLTTLSPGaFSGLPSLRYLDLSGNRL 61
LRR_4 pfam12799
Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a ...
 78-118 1.66e-04

Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.


Pssm-ID: 463713 [Multi-domain]  Cd Length: 44  Bit Score: 39.15  E-value: 1.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1972267430  78 THLSALFLNNNGLTRLPPeIAQLTNLTMLDIS-NNKLRSLPT 118
Cdd:pfam12799   1 PNLEVLDLSNNQITDIPP-LAKLPNLETLDLSgNNKITDLSD 41
PRK15370 PRK15370
type III secretion system effector E3 ubiquitin transferase SlrP;
63-160 2.05e-04

type III secretion system effector E3 ubiquitin transferase SlrP;


Pssm-ID: 185268 [Multi-domain]  Cd Length: 754  Bit Score: 44.30  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  63 IHGRVKNLSPSLWQLTHLSALF--------LNNNGLTRLPPEIAqlTNLTMLDISNNKLRSLPTELGDMISLCHLYLNNn 134
Cdd:PRK15370  218 LQGNIKTLYANSNQLTSIPATLpdtiqemeLSINRITELPERLP--SALQSLDLFHNKISCLPENLPEELRYLSVYDNS- 294

                          90       100
                  ....*....|....*....|....*.
gi 1972267430 135 qLRVLPYELGKlfRIQTLGLQGNPLS 160
Cdd:PRK15370  295 -IRTLPAHLPS--GITHLNVQSNSLT 317
PRK15387 PRK15387
type III secretion system effector E3 ubiquitin transferase SspH2;
80-179 2.17e-04

type III secretion system effector E3 ubiquitin transferase SspH2;


Pssm-ID: 185285 [Multi-domain]  Cd Length: 788  Bit Score: 44.38  E-value: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  80 LSALFLNNNGLTRLPPEIAQLTNLTmldISNNKLRSLPTELGDMISLChlyLNNNQLRVLPYELGKLFRIQTLGLQGNPL 159
Cdd:PRK15387  384 LKELIVSGNRLTSLPVLPSELKELM---VSGNRLTSLPMLPSGLLSLS---VYRNQLTRLPESLIHLSSETTVNLEGNPL 457

                          90       100
                  ....*....|....*....|....
gi 1972267430 160 SPEISKIYHETNGAQ----KILQF 179
Cdd:PRK15387  458 SERTLQALREITSAPgysgPIIRF 481
nSMase cd09078
Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological ...
 422-555 2.20e-03

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: 40.40  E-value: 2.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 422 QITQQQVPVLICGDFNslpdsgvFEYLSKGQITRRHMDLKSFRDDSCLEKF--TNSTDKnvishplrldsaCDINSIPFT 499
Cdd:cd09078   162 KNIPDNEPVIIAGDFN-------VDKRSSRDEYDDMLEQLHDYNAPEPITAgeTPLTWD------------PGTNLLAKY 222

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430 500 NYTLDFKGMIDYIFATPQSL----ARLGILGPFDPQWvqsNKILGFPHPHVaSDHIPIMA 555
Cdd:cd09078   223 NYPGGGGERLDYILYSNDHLqpssWSNEVEVPKSPTW---SVTNGYTFADL-SDHYPVSA 278
LRR_4 pfam12799
Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a ...
 101-136 2.67e-03

Leucine Rich repeats (2 copies); Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.


Pssm-ID: 463713 [Multi-domain]  Cd Length: 44  Bit Score: 36.07  E-value: 2.67e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1972267430 101 TNLTMLDISNNKLRSLPtELGDMISLCHLYLNNNQL 136
Cdd:pfam12799   1 PNLEVLDLSNNQITDIP-PLAKLPNLETLDLSGNNK 35
PLN00113 PLN00113
leucine-rich repeat receptor-like protein kinase; Provisional
 69-169 4.21e-03

leucine-rich repeat receptor-like protein kinase; Provisional


Pssm-ID: 215061 [Multi-domain]  Cd Length: 968  Bit Score: 40.22  E-value: 4.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430  69 NLSPSLWQLTHLSALFLNNNGLTRLPPEIAQLTNLTMLDISNNKLR-SLPTELGDMISLCHLYLNNNQLR-VLPYELGKL 146
Cdd:PLN00113  443 RINSRKWDMPSLQMLSLARNKFFGGLPDSFGSKRLENLDLSRNQFSgAVPRKLGSLSELMQLKLSENKLSgEIPDELSSC 522

                          90       100
                  ....*....|....*....|...
gi 1972267430 147 FRIQTLGLQGNPLSPEISKIYHE 169
Cdd:PLN00113  523 KKLVSLDLSHNQLSGQIPASFSE 545
PLN03210 PLN03210
Resistant to P. syringae 6; Provisional
 65-168 7.16e-03

Resistant to P. syringae 6; Provisional


Pssm-ID: 215633 [Multi-domain]  Cd Length: 1153  Bit Score: 39.47  E-value: 7.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267430   65 GRVKNLSPSLWQLTH-LSALFLNNN-GLTRLPPEIAQLTNLTMLDISNNK-LRSLPT--ELGDMISL----C-------- 127
Cdd:PLN03210   764 ERVQPLTPLMTMLSPsLTRLFLSDIpSLVELPSSIQNLHKLEHLEIENCInLETLPTgiNLESLESLdlsgCsrlrtfpd 843

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1972267430  128 ------HLYLNNNQLRVLPYELGKLFRIQTLGLQG-NPL---SPEISKIYH 168
Cdd:PLN03210   844 istnisDLNLSRTGIEEVPWWIEKFSNLSFLDMNGcNNLqrvSLNISKLKH 894
 
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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