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Conserved domains on  [gi|1402371412|ref|NP_001351301|]
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cleavage and polyadenylation specificity factor subunit 3 isoform 2 [Mus musculus]

Protein Classification

CPSF3/YSH1 family protein( domain architecture ID 11441009)

CPSF3/YSH1 family protein is a component of the cleavage and polyadenylation specificity factor (CPSF) complex that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition; belongs to the metallo-beta-lactamase superfamily

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CPSF73-100_C pfam11718
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal ...
 359-562 4.32e-90

Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.


:

Pssm-ID: 463330  Cd Length: 204  Bit Score: 275.92  E-value: 4.32e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 359 QRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKLTGDVEELEIQEK-PALKVFKSITVV 437
Cdd:pfam11718   1 QLVSGVLVKKDFNYHLMAPEDLREYTGLSTTTVTQRQSIPLSASFSLLRWHLEQMFGDVEELEDKEGkPTLRVMGCVTVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 438 QEPGMVVLEWLANPSNDMYADTVTTVILEVQSNP---KIRKGAVQKVSKKLEMHVYSKRLEVMLQDIFGEDCVS-VKDDS 513
Cdd:pfam11718  81 VEKGEVTLEWEGNPVNDMIADSVLAVLLSVESSPasvKLSELPLRNPHAESDPEERIERLIMLLEAQFGEDCVIeLPKVP 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1402371412 514 VLSVTVDGKTANINLETRAVECEegsedDESLREMVELAAQRLYEALTP 562
Cdd:pfam11718 161 GLEVTVDGKVANIDLETLEVECE-----DEVLKDRVETVVERAVEAVAP 204
COG1782 super family cl34358
Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General ...
 2-336 1.13e-82

Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General function prediction only];


The actual alignment was detected with superfamily member COG1782:

Pssm-ID: 441388 [Multi-domain]  Cd Length: 460  Bit Score: 265.45  E-value: 1.13e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA-GIKFWCYHAGHVLGAAMFMIEIAG--VKLLYTGDFSRQEDRhLM--AAEIPNI 76
Cdd:COG1782   124 LYTEKDVEKALKHFITLDYGEVTDIApDIKLTFYNAGHILGSAIVHLHIGDglHNIVFSGDLGRGKTP-LLrpPTPFPRA 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  77 kpDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHpELHDIPIYYASSLAK 156
Cdd:COG1782   203 --DTLIMESTYGGRLHPSREEAEEELAKVINETIERGGKVLIPAFAVGRTQEILYVLNELMREG-KIPEVPVYLDSPMAI 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 157 KCMAVYQTYVNAMNDKIRKQININ-NPFVFKHISNLKSMDHFDDI----GPSVVMASPGMIQNGLSRELFESWCTDKRNG 231
Cdd:COG1782   280 EATAIHTAYPEYLDEELRDLIFKGeNPFLFENLHYVESVEESKEIndsdEPAIIIATSGMLTGGRILHHLKHLAPDPKNT 359

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 232 VIIAGYCVEGTLAKHIMSEPEEItTMSGQKLPLKMSVDYI-SFSAHTDYQQTSEFIRAL--KPPHVILVHGEQNEMARLK 308
Cdd:COG1782   360 ILFVGYQAEGTLGRRLLDGAKEV-KIFGETIPVRAEVETIdGFSGHADRNELLNWLRRLkpKPKKVFLVHGEPEAAEALA 438

                         330       340
                  ....*....|....*....|....*...
gi 1402371412 309 AALIREYedndevHIEVHNPRNTEAVTL 336
Cdd:COG1782   439 SSIRKKL------GIEVVIPENLETIRL 460
 
Name Accession Description Interval E-value
CPSF73-100_C pfam11718
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal ...
 359-562 4.32e-90

Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.


Pssm-ID: 463330  Cd Length: 204  Bit Score: 275.92  E-value: 4.32e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 359 QRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKLTGDVEELEIQEK-PALKVFKSITVV 437
Cdd:pfam11718   1 QLVSGVLVKKDFNYHLMAPEDLREYTGLSTTTVTQRQSIPLSASFSLLRWHLEQMFGDVEELEDKEGkPTLRVMGCVTVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 438 QEPGMVVLEWLANPSNDMYADTVTTVILEVQSNP---KIRKGAVQKVSKKLEMHVYSKRLEVMLQDIFGEDCVS-VKDDS 513
Cdd:pfam11718  81 VEKGEVTLEWEGNPVNDMIADSVLAVLLSVESSPasvKLSELPLRNPHAESDPEERIERLIMLLEAQFGEDCVIeLPKVP 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1402371412 514 VLSVTVDGKTANINLETRAVECEegsedDESLREMVELAAQRLYEALTP 562
Cdd:pfam11718 161 GLEVTVDGKVANIDLETLEVECE-----DEVLKDRVETVVERAVEAVAP 204
COG1782 COG1782
Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General ...
 2-336 1.13e-82

Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General function prediction only];


Pssm-ID: 441388 [Multi-domain]  Cd Length: 460  Bit Score: 265.45  E-value: 1.13e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA-GIKFWCYHAGHVLGAAMFMIEIAG--VKLLYTGDFSRQEDRhLM--AAEIPNI 76
Cdd:COG1782   124 LYTEKDVEKALKHFITLDYGEVTDIApDIKLTFYNAGHILGSAIVHLHIGDglHNIVFSGDLGRGKTP-LLrpPTPFPRA 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  77 kpDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHpELHDIPIYYASSLAK 156
Cdd:COG1782   203 --DTLIMESTYGGRLHPSREEAEEELAKVINETIERGGKVLIPAFAVGRTQEILYVLNELMREG-KIPEVPVYLDSPMAI 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 157 KCMAVYQTYVNAMNDKIRKQININ-NPFVFKHISNLKSMDHFDDI----GPSVVMASPGMIQNGLSRELFESWCTDKRNG 231
Cdd:COG1782   280 EATAIHTAYPEYLDEELRDLIFKGeNPFLFENLHYVESVEESKEIndsdEPAIIIATSGMLTGGRILHHLKHLAPDPKNT 359

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 232 VIIAGYCVEGTLAKHIMSEPEEItTMSGQKLPLKMSVDYI-SFSAHTDYQQTSEFIRAL--KPPHVILVHGEQNEMARLK 308
Cdd:COG1782   360 ILFVGYQAEGTLGRRLLDGAKEV-KIFGETIPVRAEVETIdGFSGHADRNELLNWLRRLkpKPKKVFLVHGEPEAAEALA 438

                         330       340
                  ....*....|....*....|....*...
gi 1402371412 309 AALIREYedndevHIEVHNPRNTEAVTL 336
Cdd:COG1782   439 SSIRKKL------GIEVVIPENLETIRL 460
CPSF73-100_C smart01098
This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the ...
 357-563 1.77e-63

This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins; The exact function of this domain is not known.


Pssm-ID: 215023  Cd Length: 212  Bit Score: 207.27  E-value: 1.77e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  357 QGQRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKL------TGDVEELEIQEKPALKV 430
Cdd:smart01098   1 EGQIISGILVKKDFNYDLLLPSDLDLRTDLSTSTIIQRQTIPLPSSASLLLVLLELMfefgfvEEDVDEEEKKEKAALIV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  431 FKSITVVQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNP---KIRKGAVQKVSKKLEMHVYSKRLEVMLQDIFGEDCV 507
Cdd:smart01098  81 MGDVTVTYSGHMLVLEWESSPVNDMDADSDSAIILLISSEPspaKVKSSSKSKHHHHNDEEFREKLIEILLKEQFGDGVV 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1402371412  508 SVKDDSVLSVTVDGKTANINLETRAVECeegsEDDESLREMVELAAQRLYEALTPV 563
Cdd:smart01098 161 NVEEGEDLKVTVDGKTANIDLETLKVVE----EDDESLVERLEELLERIRLTLLPI 212
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 1-85 2.66e-57

cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain; CPSF3 (also known as cleavage and polyadenylation specificity factor 73 kDa subunit/CPSF-73) functions as a 3' endonuclease in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and in 3' end processing of metazoan histone pre-mRNAs. This subgroup also contains the yeast homolog of CPSF-73, Ysh1/Brr5 which has roles in mRNA and snoRNA synthesis. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain, and a RMMBL domain (RNA-metabolizing metallo-beta-lactamase). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293850  Cd Length: 194  Bit Score: 190.10  E-value: 2.66e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   1 MLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDI 80
Cdd:cd16292   110 MLYTETDLEASMDKIETIDFHQEVEVNGIKFTAYNAGHVLGAAMFMVEIAGVRVLYTGDYSREEDRHLPAAEIPPIKPDV 189


                  ....*
gi 1402371412  81 LIIES 85
Cdd:cd16292   190 LIVES 194
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 126-247 2.85e-45

Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.


Pssm-ID: 214983 [Multi-domain]  Cd Length: 126  Bit Score: 155.78  E-value: 2.85e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  126 AQELLLILDEYWQNHpELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQINI-NNPFVFKHISNLKSMDHFDDI---- 200
Cdd:smart01027   1 TQELLLILEELWREG-ELPNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFEQgRNPFDFKNLKFVKSLEESKRLndyk 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1402371412  201 GPSVVMASPGMIQNGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHI 247
Cdd:smart01027  80 GPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 126-245 1.01e-34

Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.


Pssm-ID: 463203  Cd Length: 109  Bit Score: 126.47  E-value: 1.01e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 126 AQELLLILDEYWQNHpELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQIninnpfvfkhISNLKSMDHFDDIGPSVV 205
Cdd:pfam10996   1 AQELLYLLDELWREG-RLPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFV----------ISKSESKAINEGKGPKVI 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1402371412 206 MASPGMIQNGLSRELFESWCTDKRNGVIIAGYCVEGTLAK 245
Cdd:pfam10996  70 IASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
 
Name Accession Description Interval E-value
CPSF73-100_C pfam11718
Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal ...
 359-562 4.32e-90

Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term; This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.


Pssm-ID: 463330  Cd Length: 204  Bit Score: 275.92  E-value: 4.32e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 359 QRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKLTGDVEELEIQEK-PALKVFKSITVV 437
Cdd:pfam11718   1 QLVSGVLVKKDFNYHLMAPEDLREYTGLSTTTVTQRQSIPLSASFSLLRWHLEQMFGDVEELEDKEGkPTLRVMGCVTVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 438 QEPGMVVLEWLANPSNDMYADTVTTVILEVQSNP---KIRKGAVQKVSKKLEMHVYSKRLEVMLQDIFGEDCVS-VKDDS 513
Cdd:pfam11718  81 VEKGEVTLEWEGNPVNDMIADSVLAVLLSVESSPasvKLSELPLRNPHAESDPEERIERLIMLLEAQFGEDCVIeLPKVP 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1402371412 514 VLSVTVDGKTANINLETRAVECEegsedDESLREMVELAAQRLYEALTP 562
Cdd:pfam11718 161 GLEVTVDGKVANIDLETLEVECE-----DEVLKDRVETVVERAVEAVAP 204
COG1782 COG1782
Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General ...
 2-336 1.13e-82

Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General function prediction only];


Pssm-ID: 441388 [Multi-domain]  Cd Length: 460  Bit Score: 265.45  E-value: 1.13e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA-GIKFWCYHAGHVLGAAMFMIEIAG--VKLLYTGDFSRQEDRhLM--AAEIPNI 76
Cdd:COG1782   124 LYTEKDVEKALKHFITLDYGEVTDIApDIKLTFYNAGHILGSAIVHLHIGDglHNIVFSGDLGRGKTP-LLrpPTPFPRA 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  77 kpDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHpELHDIPIYYASSLAK 156
Cdd:COG1782   203 --DTLIMESTYGGRLHPSREEAEEELAKVINETIERGGKVLIPAFAVGRTQEILYVLNELMREG-KIPEVPVYLDSPMAI 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 157 KCMAVYQTYVNAMNDKIRKQININ-NPFVFKHISNLKSMDHFDDI----GPSVVMASPGMIQNGLSRELFESWCTDKRNG 231
Cdd:COG1782   280 EATAIHTAYPEYLDEELRDLIFKGeNPFLFENLHYVESVEESKEIndsdEPAIIIATSGMLTGGRILHHLKHLAPDPKNT 359

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 232 VIIAGYCVEGTLAKHIMSEPEEItTMSGQKLPLKMSVDYI-SFSAHTDYQQTSEFIRAL--KPPHVILVHGEQNEMARLK 308
Cdd:COG1782   360 ILFVGYQAEGTLGRRLLDGAKEV-KIFGETIPVRAEVETIdGFSGHADRNELLNWLRRLkpKPKKVFLVHGEPEAAEALA 438

                         330       340
                  ....*....|....*....|....*...
gi 1402371412 309 AALIREYedndevHIEVHNPRNTEAVTL 336
Cdd:COG1782   439 SSIRKKL------GIEVVIPENLETIRL 460
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 2-301 2.90e-81

RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 260.12  E-value: 2.90e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNiKPDIL 81
Cdd:COG1236   109 LYTEEDAERALELFQTVDYGEPFEIGGVRVTFHPAGHILGSAQVELEVGGKRIVFSGDYGREDDPLLAPPEPVP-PADVL 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  82 IIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHpELHDIPIyYASSLAKKCMAV 161
Cdd:COG1236   188 ITESTYGDRLHPPREEVEAELAEWVRETLARGGTVLIPAFALGRAQELLYLLRELKKEG-RLPDIPI-YVSGMAIRATEI 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 162 YQTYVNAMNDKIRkqininNPFVFKHISNLKSMDH---FDDIGPSVVMASPGMIQNGLSRELFESWCTDKRNGVIIAGYC 238
Cdd:COG1236   266 YRRHGEYLRDEAQ------DPFALPNLRFVTSVEEskaLNRKGPAIIIAPSGMLTGGRILHHLKRFLWDPRNTILFVGYQ 339

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1402371412 239 VEGTLAKHIMSEPEEItTMSGQKLPLKMSVD-YISFSAHTDYQQTSEFIRALKPP-HVILVHGEQ 301
Cdd:COG1236   340 AEGTLGRRLLRGAKEV-KIFGEEVPVRARVErLFGLSAHADWDELLEWIKATGKPeRVFLVHGEP 403
CPSF73-100_C smart01098
This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the ...
 357-563 1.77e-63

This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins; The exact function of this domain is not known.


Pssm-ID: 215023  Cd Length: 212  Bit Score: 207.27  E-value: 1.77e-63
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  357 QGQRVSGILVKRNFNYHILSPCDLSNYTDLAMSTVKQTQAIPYTGPFYLLYYQLQKL------TGDVEELEIQEKPALKV 430
Cdd:smart01098   1 EGQIISGILVKKDFNYDLLLPSDLDLRTDLSTSTIIQRQTIPLPSSASLLLVLLELMfefgfvEEDVDEEEKKEKAALIV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  431 FKSITVVQEPGMVVLEWLANPSNDMYADTVTTVILEVQSNP---KIRKGAVQKVSKKLEMHVYSKRLEVMLQDIFGEDCV 507
Cdd:smart01098  81 MGDVTVTYSGHMLVLEWESSPVNDMDADSDSAIILLISSEPspaKVKSSSKSKHHHHNDEEFREKLIEILLKEQFGDGVV 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1402371412  508 SVKDDSVLSVTVDGKTANINLETRAVECeegsEDDESLREMVELAAQRLYEALTPV 563
Cdd:smart01098 161 NVEEGEDLKVTVDGKTANIDLETLKVVE----EDDESLVERLEELLERIRLTLLPI 212
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 1-85 2.66e-57

cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain; CPSF3 (also known as cleavage and polyadenylation specificity factor 73 kDa subunit/CPSF-73) functions as a 3' endonuclease in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and in 3' end processing of metazoan histone pre-mRNAs. This subgroup also contains the yeast homolog of CPSF-73, Ysh1/Brr5 which has roles in mRNA and snoRNA synthesis. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain, and a RMMBL domain (RNA-metabolizing metallo-beta-lactamase). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293850  Cd Length: 194  Bit Score: 190.10  E-value: 2.66e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   1 MLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDI 80
Cdd:cd16292   110 MLYTETDLEASMDKIETIDFHQEVEVNGIKFTAYNAGHVLGAAMFMVEIAGVRVLYTGDYSREEDRHLPAAEIPPIKPDV 189


                  ....*
gi 1402371412  81 LIIES 85
Cdd:cd16292   190 LIVES 194
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 126-247 2.85e-45

Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.


Pssm-ID: 214983 [Multi-domain]  Cd Length: 126  Bit Score: 155.78  E-value: 2.85e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412  126 AQELLLILDEYWQNHpELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQINI-NNPFVFKHISNLKSMDHFDDI---- 200
Cdd:smart01027   1 TQELLLILEELWREG-ELPNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFEQgRNPFDFKNLKFVKSLEESKRLndyk 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1402371412  201 GPSVVMASPGMIQNGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHI 247
Cdd:smart01027  80 GPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 126-245 1.01e-34

Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains.


Pssm-ID: 463203  Cd Length: 109  Bit Score: 126.47  E-value: 1.01e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412 126 AQELLLILDEYWQNHpELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQIninnpfvfkhISNLKSMDHFDDIGPSVV 205
Cdd:pfam10996   1 AQELLYLLDELWREG-RLPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFV----------ISKSESKAINEGKGPKVI 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1402371412 206 MASPGMIQNGLSRELFESWCTDKRNGVIIAGYCVEGTLAK 245
Cdd:pfam10996  70 IASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 2-85 1.52e-34

Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; CPSF3 (cleavage and polyadenylation specificity factor subunit 3; also known as cleavage and polyadenylation specificity factor 73 kDa subunit, CPSF-73) and CPSF2 (also known as cleavage and polyadenylation specificity factor 100 kDa subunit /CPSF-100) are components of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. CPSF3 functions as a 3' endonuclease. Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)), and Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74) are subunits of Integrator, a metazoan-specific multifunctional protein complex composed of 14 subunits. Integrator has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293820 [Multi-domain]  Cd Length: 193  Bit Score: 128.99  E-value: 1.52e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA-GIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDI 80
Cdd:cd07734   109 LYTPEDIEEALKHIVPLGYGQSIDLFpALSLTAYNAGHVLGAAMWEIQIYGEKLVYTGDFSNTEDRLLPAASILPPRPDL 188


                  ....*
gi 1402371412  81 LIIES 85
Cdd:cd07734   189 LITES 193
INTS11-like_MBL-fold cd16291
Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain; ...
 2-85 9.36e-25

Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain; Integrator is a metazoan-specific multisubunit, multifunctional protein complex composed of 14 subunits named Int1-Int14 (Integrator subunits). This subgroup includes Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)). Integrator complex has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293849  Cd Length: 199  Bit Score: 101.95  E-value: 9.36e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEV-AGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDI 80
Cdd:cd16291   115 FFTSQMIKDCMKKVIAVNLHETVQVdDELEIKAYYAGHVLGAAMFYVRVGDESVVYTGDYNMTPDRHLGAAWIDRLRPDL 194


                  ....*
gi 1402371412  81 LIIES 85
Cdd:cd16291   195 LITES 199
TTHA0252-CPSF-like_MBL-fold cd16295
Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; ...
 2-85 7.99e-20

Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; Includes the archaeal cleavage and polyadenylation specificity factors (CPSFs) such as Methanothermobacter thermautotrophicus MTH1203, and Pyrococcus horikoshii PH1404. In addition to the MBL-fold metallo-hydrolase nuclease and the beta-CASP domains, members of this subgroup contain two contiguous KH domains. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293853 [Multi-domain]  Cd Length: 197  Bit Score: 87.51  E-value: 7.99e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA-GIKFWCYHAGHVLGAAMFMIEI-AGVKLLYTGDFSRQEDRhLMAAEIPNIKPD 79
Cdd:cd16295   113 LYTEEDVEKALKHFRPVEYGEPFEIGpGVKVTFYDAGHILGSASVELEIgGGKRILFSGDLGRKNTP-LLRDPAPPPEAD 191


                  ....*.
gi 1402371412  80 ILIIES 85
Cdd:cd16295   192 YLIMES 197
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 261-328 1.82e-11

Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. This, the fifth motif, appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 which are involved in the processing of mRNA. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases.


Pssm-ID: 462191 [Multi-domain]  Cd Length: 63  Bit Score: 59.56  E-value: 1.82e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1402371412 261 KLPLKMSVDYIS-FSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALIREYedndevHIEVHNP 328
Cdd:pfam07521   1 GIPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEEL------GIEVFVP 63
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 2-85 1.78e-05

cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; MBL-fold metallo-hydrolase domain; CPSF2, also known as cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF-100), is a component of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. This subgroup includes Ydh1p, the yeast homolog of CPSF2. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293851  Cd Length: 199  Bit Score: 45.97  E-value: 1.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   2 LYTETDLEESMDKIETINFHEVKEVA----GIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNI- 76
Cdd:cd16293   107 LFTLDDVDEAFDRITQLKYSQPVNLRgkgdGLTITAYNAGHTLGGTIWKITKDSEDIVYAVDWNHKKERHLNGAVLDSFg 186

                          90
                  ....*....|.
gi 1402371412  77 --KPDILIIES 85
Cdd:cd16293   187 glRPSLLITDA 197
metallo-hydrolase-like_MBL-fold cd07732
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 15-84 1.69e-04

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain; Includes functionally uncharacterized Enterococcus faecalis EF2904. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry.


Pssm-ID: 293818 [Multi-domain]  Cd Length: 202  Bit Score: 42.98  E-value: 1.69e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1402371412  15 IETINFHEVKEVAGIKFWCYHAGH-VLGAAMFMIEIAGVKLLYTGDF----SRQEDRHLMAAEIPNiKPDILIIE 84
Cdd:cd07732   128 IRVFESGKSFTIGDFTVTPYLVDHsAPGAYAFLIEAPGKRIFYTGDFrfhgRKPELTEAFVEKAPK-NIDVLLME 201
Lactamase_B_6 pfam16661
Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase ...
 7-82 4.75e-03

Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase superfamily.


Pssm-ID: 406948  Cd Length: 192  Bit Score: 38.35  E-value: 4.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402371412   7 DLEESMDKIETINFHEVKEV----AGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPN------- 75
Cdd:pfam16661 104 DIDAAFDKIKTLKYSQTVDLkgkfDGLTITPYNSGHTLGGTIWKISKNSEKIVYAVDWNHTKDSHLNGASLLDstgkple 183


                  ....*....
gi 1402371412  76 --IKPDILI 82
Cdd:pfam16661 184 slVRPTALI 192
 
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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