NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|568980060|ref|XP_006516134|]
View 

cleavage and polyadenylation specificity factor subunit 2 isoform X1 [Mus musculus]

Protein Classification

CPSF2-like_MBL-fold and Beta-Casp domain-containing protein( domain architecture ID 10888779)

protein containing domains CPSF2-like_MBL-fold, Beta-Casp, RMMBL, and CPSF100_C

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 7-204 1.24e-126

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: 376.09  E-value: 1.24e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   7 LTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFSVDIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGLNCAIYA 86
Cdd:cd16293    1 FTPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  87 TIPVYKMGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKDG 166
Cdd:cd16293   81 TLPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDS 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 568980060 167 eEEIVYAVDFNHKREIHLNGCSLEMLS--RPSLLITDSFN 204
Cdd:cd16293  161 -EDIVYAVDWNHKKERHLNGAVLDSFGglRPSLLITDADN 199
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 608-779 2.01e-63

Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex.


:

Pssm-ID: 463836  Cd Length: 162  Bit Score: 209.43  E-value: 2.01e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  608 VRLKDSLVSSLQFCKAKDAELAWIDGVLDMRvskvdtgvILEEGELKDDGEDSEMQVDAPSDSsamaQQKAMKSLFGEDE 687
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLDRA--------ALEEGAAEEEEEEEDEEEENANKK----QKLEQFSLKDDDE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  688 KELGEETEIIPTLEPLPPHEVP-GHQSVFMNEPRLSDFKQVLLREGIQAEFVG-GVLVCNNQVAVRRTETGRIGLEGCLC 765
Cdd:pfam13299  69 KESKESKDSIPTLDPLPSNLAPaVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGeGTLVCNGTVAVRKTETGRIEIEGVGG 148

                         170
                  ....*....|....
gi 568980060  766 QDFYRIRDLLYEQY 779
Cdd:pfam13299 149 PTFYAVRRLIYEQL 162
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-368 1.58e-28

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: 110.71  E-value: 1.58e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   243 VLELAQLLDQIWRTKdaGLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEdKRNNPFQFRHLSLCHGLSD---LAR 319
Cdd:smart01027   1 TQELLLILEELWREG--ELPNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEEskrLND 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 568980060   320 VPSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFL 368
Cdd:smart01027  78 YKGPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 528-591 2.66e-13

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: 64.95  E-value: 2.66e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568980060  528 SIEIKARVTYID-YEGRSDGDSIKKIINQMKPRQLIIVHGPPEASQDLAECCRAFGGkdIKVYMP 591
Cdd:pfam07521   1 GIPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELG--IEVFVP 63
 
Name Accession Description Interval E-value
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 7-204 1.24e-126

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: 376.09  E-value: 1.24e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   7 LTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFSVDIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGLNCAIYA 86
Cdd:cd16293    1 FTPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  87 TIPVYKMGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKDG 166
Cdd:cd16293   81 TLPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDS 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 568980060 167 eEEIVYAVDFNHKREIHLNGCSLEMLS--RPSLLITDSFN 204
Cdd:cd16293  161 -EDIVYAVDWNHKKERHLNGAVLDSFGglRPSLLITDADN 199
Lactamase_B_6 pfam16661
Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase ...
 22-199 7.75e-88

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


Pssm-ID: 406948  Cd Length: 192  Bit Score: 275.24  E-value: 7.75e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   22 LLQVDEFRFLLDCGWDEHFSV-DIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGK----LGLNCAIYATIPVYKMGQM 96
Cdd:pfam16661   1 LLEFDNVRILLDPGWDGSFSYeSDLKYLEKILPEVDLILLSHPTLEHLGAYPLLYYKfgshLGSNIPVYATLPVANLGRV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   97 FMYDLYQSRHN--TEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKdGEEEIVYAV 174
Cdd:pfam16661  81 STYDLYASRGIlgPYDSSELDLDDIDAAFDKIKTLKYSQTVDLKGKFDGLTITPYNSGHTLGGTIWKISK-NSEKIVYAV 159

                         170       180       190
                  ....*....|....*....|....*....|...
gi 568980060  175 DFNHKREIHLNGCS--------LEMLSRPSLLI 199
Cdd:pfam16661 160 DWNHTKDSHLNGASlldstgkpLESLVRPTALI 192
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 608-779 2.01e-63

Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex.


Pssm-ID: 463836  Cd Length: 162  Bit Score: 209.43  E-value: 2.01e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  608 VRLKDSLVSSLQFCKAKDAELAWIDGVLDMRvskvdtgvILEEGELKDDGEDSEMQVDAPSDSsamaQQKAMKSLFGEDE 687
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLDRA--------ALEEGAAEEEEEEEDEEEENANKK----QKLEQFSLKDDDE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  688 KELGEETEIIPTLEPLPPHEVP-GHQSVFMNEPRLSDFKQVLLREGIQAEFVG-GVLVCNNQVAVRRTETGRIGLEGCLC 765
Cdd:pfam13299  69 KESKESKDSIPTLDPLPSNLAPaVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGeGTLVCNGTVAVRKTETGRIEIEGVGG 148

                         170
                  ....*....|....
gi 568980060  766 QDFYRIRDLLYEQY 779
Cdd:pfam13299 149 PTFYAVRRLIYEQL 162
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-368 1.58e-28

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: 110.71  E-value: 1.58e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   243 VLELAQLLDQIWRTKdaGLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEdKRNNPFQFRHLSLCHGLSD---LAR 319
Cdd:smart01027   1 TQELLLILEELWREG--ELPNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEEskrLND 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 568980060   320 VPSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFL 368
Cdd:smart01027  78 YKGPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 6-391 3.99e-28

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


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 117.60  E-value: 3.99e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   6 KLTTLSGVQEESALCYLLQVDEFRFLLDCGWD--------EHFSVDIIDslrkhvhqIDAVLLSHP--DplHLGALPFAV 75
Cdd:COG1236    2 KLTFLGAAGEVTGSCYLLETGGTRILIDCGLFqggkernwPPFPFRPSD--------VDAVVLTHAhlD--HSGALPLLV 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  76 gKLGLNCAIYATIPVYK-MGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLkgkgHGLSITPLPAGHM 154
Cdd:COG1236   72 -KEGFRGPIYATPATADlARILLGDSAKIQEEEAEAEPLYTEEDAERALELFQTVDYGEPFEI----GGVRVTFHPAGHI 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 155 IGGTIWKIvKDGEEEIVYAVDFNHKREIHLNGcsLEMLSRPSLLITDSfnaTY---VQPRRKQRDEQLLTNVLETLRGDG 231
Cdd:COG1236  147 LGSAQVEL-EVGGKRIVFSGDYGREDDPLLAP--PEPVPPADVLITES---TYgdrLHPPREEVEAELAEWVRETLARGG 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 232 NVLI---AVdtaGRVLELAQLLDQIWRTKDA--------GLGVYSLALLnnvsynvvefsksqvewmsDKLMRCFEDKRN 300
Cdd:COG1236  221 TVLIpafAL---GRAQELLYLLRELKKEGRLpdipiyvsGMAIRATEIY-------------------RRHGEYLRDEAQ 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 301 NPFQFRHLSLCHGLSDLARV--PSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNptekvte 378
Cdd:COG1236  279 DPFALPNLRFVTSVEESKALnrKGPAIIIAPSGMLTGGRILHHLKRFLWDPRNTILFVGYQAEGTLGRRLLRG------- 351

                        410
                 ....*....|...
gi 568980060 379 ielRKRVKLEGKE 391
Cdd:COG1236  352 ---AKEVKIFGEE 361
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-366 8.46e-20

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: 85.26  E-value: 8.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  243 VLELAQLLDQIWRTKDagLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEDKRNNpfqfrhlslchglSDLARVPS 322
Cdd:pfam10996   1 AQELLYLLDELWREGR--LPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSES-------------KAINEGKG 65

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 568980060  323 PKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLAR 366
Cdd:pfam10996  66 PKVIIASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 528-591 2.66e-13

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: 64.95  E-value: 2.66e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568980060  528 SIEIKARVTYID-YEGRSDGDSIKKIINQMKPRQLIIVHGPPEASQDLAECCRAFGGkdIKVYMP 591
Cdd:pfam07521   1 GIPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELG--IEVFVP 63
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 20-182 1.95e-08

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 54.48  E-value: 1.95e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060    20 CYLLQVDEFRFLLDCGWDEhfSVDIIDSLRKH-VHQIDAVLLSHPDPLHLGALPFAVGKlgLNCAIYATipvyKMGQMFM 98
Cdd:smart00849   2 SYLVRDDGGAILIDTGPGE--AEDLLAELKKLgPKKIDAIILTHGHPDHIGGLPELLEA--PGAPVYAP----EGTAELL 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060    99 YDLYQSRHNTEDFtlftlddvDAAFDKIQQLKFSQIVNLkgKGHGLSITPLPaGHMIGGTiwkIVKDGEEEIVYAVDFNH 178
Cdd:smart00849  74 KDLLALLGELGAE--------AEPAPPDRTLKDGDELDL--GGGELEVIHTP-GHTPGSI---VLYLPEGKILFTGDLLF 139


                   ....
gi 568980060   179 KREI 182
Cdd:smart00849 140 AGGD 143
 
Name Accession Description Interval E-value
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 7-204 1.24e-126

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: 376.09  E-value: 1.24e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   7 LTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFSVDIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGLNCAIYA 86
Cdd:cd16293    1 FTPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  87 TIPVYKMGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKDG 166
Cdd:cd16293   81 TLPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDS 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 568980060 167 eEEIVYAVDFNHKREIHLNGCSLEMLS--RPSLLITDSFN 204
Cdd:cd16293  161 -EDIVYAVDWNHKKERHLNGAVLDSFGglRPSLLITDADN 199
Lactamase_B_6 pfam16661
Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase ...
 22-199 7.75e-88

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


Pssm-ID: 406948  Cd Length: 192  Bit Score: 275.24  E-value: 7.75e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   22 LLQVDEFRFLLDCGWDEHFSV-DIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGK----LGLNCAIYATIPVYKMGQM 96
Cdd:pfam16661   1 LLEFDNVRILLDPGWDGSFSYeSDLKYLEKILPEVDLILLSHPTLEHLGAYPLLYYKfgshLGSNIPVYATLPVANLGRV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   97 FMYDLYQSRHN--TEDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGKGHGLSITPLPAGHMIGGTIWKIVKdGEEEIVYAV 174
Cdd:pfam16661  81 STYDLYASRGIlgPYDSSELDLDDIDAAFDKIKTLKYSQTVDLKGKFDGLTITPYNSGHTLGGTIWKISK-NSEKIVYAV 159

                         170       180       190
                  ....*....|....*....|....*....|...
gi 568980060  175 DFNHKREIHLNGCS--------LEMLSRPSLLI 199
Cdd:pfam16661 160 DWNHTKDSHLNGASlldstgkpLESLVRPTALI 192
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 608-779 2.01e-63

Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex.


Pssm-ID: 463836  Cd Length: 162  Bit Score: 209.43  E-value: 2.01e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  608 VRLKDSLVSSLQFCKAKDAELAWIDGVLDMRvskvdtgvILEEGELKDDGEDSEMQVDAPSDSsamaQQKAMKSLFGEDE 687
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLDRA--------ALEEGAAEEEEEEEDEEEENANKK----QKLEQFSLKDDDE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  688 KELGEETEIIPTLEPLPPHEVP-GHQSVFMNEPRLSDFKQVLLREGIQAEFVG-GVLVCNNQVAVRRTETGRIGLEGCLC 765
Cdd:pfam13299  69 KESKESKDSIPTLDPLPSNLAPaVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGeGTLVCNGTVAVRKTETGRIEIEGVGG 148

                         170
                  ....*....|....
gi 568980060  766 QDFYRIRDLLYEQY 779
Cdd:pfam13299 149 PTFYAVRRLIYEQL 162
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-368 1.58e-28

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: 110.71  E-value: 1.58e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   243 VLELAQLLDQIWRTKdaGLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEdKRNNPFQFRHLSLCHGLSD---LAR 319
Cdd:smart01027   1 TQELLLILEELWREG--ELPNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEEskrLND 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 568980060   320 VPSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFL 368
Cdd:smart01027  78 YKGPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 8-202 1.82e-28

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: 112.81  E-value: 1.82e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   8 TTLSGVQEESALCYLLQVDEFRFLLDCGWDeHFSVDI---IDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGLNCAI 84
Cdd:cd07734    1 TPLGGGQEVGRSCFLVEFKGRTVLLDCGMN-PGKEDPeacLPQFELLPPEIDAILISHFHLDHCGALPYLFRGFIFRGPI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  85 YATIPVYKMGQMFMYDLYQSRHNT-EDFTLFTLDDVDAAFDKIQQLKFSQIVNLKGkghGLSITPLPAGHMIGGTIWKIV 163
Cdd:cd07734   80 YATHPTVALGRLLLEDYVKSAERIgQDQSLYTPEDIEEALKHIVPLGYGQSIDLFP---ALSLTAYNAGHVLGAAMWEIQ 156

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 568980060 164 KDGeEEIVYAVDFNHKREIHLNGCSLeMLSRPSLLITDS 202
Cdd:cd07734  157 IYG-EKLVYTGDFSNTEDRLLPAASI-LPPRPDLLITES 193
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 6-391 3.99e-28

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


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 117.60  E-value: 3.99e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   6 KLTTLSGVQEESALCYLLQVDEFRFLLDCGWD--------EHFSVDIIDslrkhvhqIDAVLLSHP--DplHLGALPFAV 75
Cdd:COG1236    2 KLTFLGAAGEVTGSCYLLETGGTRILIDCGLFqggkernwPPFPFRPSD--------VDAVVLTHAhlD--HSGALPLLV 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  76 gKLGLNCAIYATIPVYK-MGQMFMYDLYQSRHNTEDFTLFTLDDVDAAFDKIQQLKFSQIVNLkgkgHGLSITPLPAGHM 154
Cdd:COG1236   72 -KEGFRGPIYATPATADlARILLGDSAKIQEEEAEAEPLYTEEDAERALELFQTVDYGEPFEI----GGVRVTFHPAGHI 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 155 IGGTIWKIvKDGEEEIVYAVDFNHKREIHLNGcsLEMLSRPSLLITDSfnaTY---VQPRRKQRDEQLLTNVLETLRGDG 231
Cdd:COG1236  147 LGSAQVEL-EVGGKRIVFSGDYGREDDPLLAP--PEPVPPADVLITES---TYgdrLHPPREEVEAELAEWVRETLARGG 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 232 NVLI---AVdtaGRVLELAQLLDQIWRTKDA--------GLGVYSLALLnnvsynvvefsksqvewmsDKLMRCFEDKRN 300
Cdd:COG1236  221 TVLIpafAL---GRAQELLYLLRELKKEGRLpdipiyvsGMAIRATEIY-------------------RRHGEYLRDEAQ 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060 301 NPFQFRHLSLCHGLSDLARV--PSPKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLARFLIDNptekvte 378
Cdd:COG1236  279 DPFALPNLRFVTSVEESKALnrKGPAIIIAPSGMLTGGRILHHLKRFLWDPRNTILFVGYQAEGTLGRRLLRG------- 351

                        410
                 ....*....|...
gi 568980060 379 ielRKRVKLEGKE 391
Cdd:COG1236  352 ---AKEVKIFGEE 361
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-366 8.46e-20

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: 85.26  E-value: 8.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  243 VLELAQLLDQIWRTKDagLGVYSLALLNNVSYNVVEFSKSQVEWMSDKLMRCFEDKRNNpfqfrhlslchglSDLARVPS 322
Cdd:pfam10996   1 AQELLYLLDELWREGR--LPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSES-------------KAINEGKG 65

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 568980060  323 PKVVLASQPDLECGFSRDLFIQWCQDPKNSIILTYRTTPGTLAR 366
Cdd:pfam10996  66 PKVIIASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
TTHA0252-CPSF-like_MBL-fold cd16295
Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; ...
 7-177 1.89e-16

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: 78.27  E-value: 1.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   7 LTTLSGVQEESALCYLLQVDEFRFLLDCG------------WDEhFSVDIidslrkhvHQIDAVLLSHPDPLHLGALPFA 74
Cdd:cd16295    1 LTFLGAAREVTGSCYLLETGGKRILLDCGlfqggkeleelnNEP-FPFDP--------KEIDAVILTHAHLDHSGRLPLL 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  75 VgKLGLNCAIYATIPVYKMGQMFMYD-LYQSRHNTEDFT---LFTLDDVDAAFDKIQQLKFSQIVNLkgkGHGLSITPLP 150
Cdd:cd16295   72 V-KEGFRGPIYATPATKDLAELLLLDsAKIQEEEAEHPPaepLYTEEDVEKALKHFRPVEYGEPFEI---GPGVKVTFYD 147

                        170       180
                 ....*....|....*....|....*..
gi 568980060 151 AGHMIGGTIWKIVKDGEEEIVYAVDFN 177
Cdd:cd16295  148 AGHILGSASVELEIGGGKRILFSGDLG 174
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 5-202 2.17e-15

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: 75.31  E-value: 2.17e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   5 IKLTTLSGVQEESALCYLLQVDEFRFLLDCGWDEHFS-------VDIIDslrkhVHQIDAVLLSHPDPLHLGALPFAVGK 77
Cdd:cd16292    1 LEITPLGAGQEVGRSCVILEFKGKTIMLDCGIHPGYSglaslpfFDEID-----LSEIDLLLITHFHLDHCGALPYFLQK 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  78 LGLNCAIYATIPVYKMGQMFMYDLYQ-SRHNTEDFtLFTLDDVDAAFDKIQQLKFSQIVNLKgkghGLSITPLPAGHMIG 156
Cdd:cd16292   76 TNFKGRVFMTHPTKAIYKWLLSDYVRvSNISSDEM-LYTETDLEASMDKIETIDFHQEVEVN----GIKFTAYNAGHVLG 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 568980060 157 GTIWKIVKDGeEEIVYAVDFNHKREIHLNGCSLEMLsRPSLLITDS 202
Cdd:cd16292  151 AAMFMVEIAG-VRVLYTGDYSREEDRHLPAAEIPPI-KPDVLIVES 194
INTS11-like_MBL-fold cd16291
Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain; ...
 20-202 3.83e-14

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: 71.91  E-value: 3.83e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  20 CYLLQVDEFRFLLDCGW------DEHFSV-DIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGLNCAIYATIPVYK 92
Cdd:cd16291   14 CILVTIGGKNIMFDCGMhmgyndERRFPDfSYISQNGPFTEHIDCVIISHFHLDHCGALPYFTEVVGYDGPIYMTHPTKA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  93 MGQMFMYD---LYQSRHNTEDFtlFTLDDVDAAFDKIQQLKFSQIVNLKGkghGLSITPLPAGHMIGGTIWKiVKDGEEE 169
Cdd:cd16291   94 ICPILLEDyrkIAVERKGETNF--FTSQMIKDCMKKVIAVNLHETVQVDD---ELEIKAYYAGHVLGAAMFY-VRVGDES 167

                        170       180       190
                 ....*....|....*....|....*....|...
gi 568980060 170 IVYAVDFNHKREIHLNGCSLEMLsRPSLLITDS 202
Cdd:cd16291  168 VVYTGDYNMTPDRHLGAAWIDRL-RPDLLITES 199
Int9-like_MBL-fold cd16294
integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain; Integrator is a ...
 5-172 3.83e-14

integrator subunit 9, 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 Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74). 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: 293852 [Multi-domain]  Cd Length: 166  Bit Score: 70.99  E-value: 3.83e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   5 IKLTTLSGvqEESALCYLLQVDEFRFLLDCGWDEHFSVDIIDslrkhVHQIDAVLLShpDPLHLGALPFAVGKLGLNCAI 84
Cdd:cd16294    1 MKLYCLSG--HPTLPCNVLKFKSTTIMLDCGLDCPPETELID-----LSTVDVILIS--NYHCMLALPFITEYTGFTGVV 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  85 YATIPVYKMGQMFMYDLYQsrhntedftlftlddvdaAFDKIQQLKFSQIVNLKGkghGLSITPLPAGHMIGGTIWkIVK 164
Cdd:cd16294   72 YATEPTVQIGRLLMEELVQ------------------ALSKIQLVGYSQKLDLFG---AVQVTALSSGYCLGSSNW-VIQ 129


                 ....*...
gi 568980060 165 DGEEEIVY 172
Cdd:cd16294  130 SHYEKISY 137
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 528-591 2.66e-13

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: 64.95  E-value: 2.66e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568980060  528 SIEIKARVTYID-YEGRSDGDSIKKIINQMKPRQLIIVHGPPEASQDLAECCRAFGGkdIKVYMP 591
Cdd:pfam07521   1 GIPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELG--IEVFVP 63
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 20-182 1.95e-08

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 54.48  E-value: 1.95e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060    20 CYLLQVDEFRFLLDCGWDEhfSVDIIDSLRKH-VHQIDAVLLSHPDPLHLGALPFAVGKlgLNCAIYATipvyKMGQMFM 98
Cdd:smart00849   2 SYLVRDDGGAILIDTGPGE--AEDLLAELKKLgPKKIDAIILTHGHPDHIGGLPELLEA--PGAPVYAP----EGTAELL 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060    99 YDLYQSRHNTEDFtlftlddvDAAFDKIQQLKFSQIVNLkgKGHGLSITPLPaGHMIGGTiwkIVKDGEEEIVYAVDFNH 178
Cdd:smart00849  74 KDLLALLGELGAE--------AEPAPPDRTLKDGDELDL--GGGELEVIHTP-GHTPGSI---VLYLPEGKILFTGDLLF 139


                   ....
gi 568980060   179 KREI 182
Cdd:smart00849 140 AGGD 143
RNaseZ_short-form-like_MBL-fold cd07716
uncharacterized bacterial subgroup of Ribonuclease Z, short form; MBL-fold metallo-hydrolase ...
 20-91 5.71e-07

uncharacterized bacterial subgroup of Ribonuclease Z, short form; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. Members of this bacterial 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: 293802 [Multi-domain]  Cd Length: 175  Bit Score: 50.13  E-value: 5.71e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568980060  20 CYLLQVDEFRFLLDCGWdehfsvDIIDSLRKHV--HQIDAVLLS--HPDplH---LGALPFAVgKLGLNCAIYATIPVY 91
Cdd:cd07716   20 GYLLEADGFRILLDCGS------GVLSRLQRYIdpEDLDAVVLShlHPD--HcadLGVLQYAR-RYHPRGARKPPLPLY 89
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 20-207 5.84e-07

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 51.43  E-value: 5.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  20 CYLLQVDEFRFLLDCGwdehFSV-DIIDSLRKHVHQIDAVLLSHPDPLHL-GALPFAVGKLGLNCAIYATIPVYK-MGQM 96
Cdd:COG1235   37 SILVEADGTRLLIDAG----PDLrEQLLRLGLDPSKIDAILLTHEHADHIaGLDDLRPRYGPNPIPVYATPGTLEaLERR 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  97 F--MYDLYQSRHNTEDFTL---FTLDDvdaafdkiqqlkfsqivnlkgkghgLSITPLPAGHMIGGTI-WKIvKDGEEEI 170
Cdd:COG1235  113 FpyLFAPYPGKLEFHEIEPgepFEIGG-------------------------LTVTPFPVPHDAGDPVgYRI-EDGGKKL 166

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 568980060 171 VYAVDFNhkreiHLNGCSLEMLSRPSLLItdsFNATY 207
Cdd:COG1235  167 AYATDTG-----YIPEEVLELLRGADLLI---LDATY 195
RnjA COG0595
mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];
20-87 1.10e-06

mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440360 [Multi-domain]  Cd Length: 553  Bit Score: 51.99  E-value: 1.10e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568980060  20 CYLLQVDEFRFLLDCGW----DEHFSVDII----DSLRKHVHQIDAVLLSHP--DplHLGALPFAVGKlgLNCAIYAT 87
Cdd:COG0595   21 MYVYEYDDDIIIVDCGLkfpeDEMPGVDLVipdiSYLEENKDKIKGIVLTHGheD--HIGALPYLLKE--LNVPVYGT 94
RNaseJ_MBL-fold cd07714
RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a ...
 20-87 5.87e-06

RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a prokaryotic ribonuclease which plays a key part in RNA processing and in RNA degradation. It can act as an endonuclease which is specific for single-stranded regions of RNA irrespective of their sequence or location, and as a processive 5' exonuclease which only acts on substrates having a single phosphate or a hydroxyl at the 5' end. Many bacterial species have only one RNase J, but some, such as Bacillus subtilis, have two. 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: 293800 [Multi-domain]  Cd Length: 248  Bit Score: 48.56  E-value: 5.87e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568980060  20 CYLLQVDEFRFLLDCGW----DEHFSVDII----DSLRKHVHQIDAVLLSHP--DplHLGALPFAVGKlgLNCAIYAT 87
Cdd:cd07714   13 MYVVEYDDDIIIIDCGLkfpdEDMPGVDYIipdfSYLEENKDKIKGIFITHGheD--HIGALPYLLPE--LNVPIYAT 86
Lactamase_B pfam00753
Metallo-beta-lactamase superfamily;
20-210 1.04e-05

Metallo-beta-lactamase superfamily;


Pssm-ID: 425851 [Multi-domain]  Cd Length: 196  Bit Score: 46.98  E-value: 1.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   20 CYLLQVDEFRFLLDCGWDEHFSVD-IIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKlgLNCAIYATIPVYKMGQMFM 98
Cdd:pfam00753   8 SYLIEGGGGAVLIDTGGSAEAALLlLLAALGLGPKDIDAVILTHGHFDHIGGLGELAEA--TDVPVIVVAEEARELLDEE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060   99 YDLYQSRHNTEDFTLFTLDDVDAAFDKiqqlkfsQIVNLKGKGHGLSITPLPAGHMIggtiwkIVKDGEEEIVYAVDFNH 178
Cdd:pfam00753  86 LGLAASRLGLPGPPVVPLPPDVVLEEG-------DGILGGGLGLLVTHGPGHGPGHV------VVYYGGGKVLFTGDLLF 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 568980060  179 KREIHLNGC----------SLEMLSRPSLLITDSFNATYVQP 210
Cdd:pfam00753 153 AGEIGRLDLplggllvlhpSSAESSLESLLKLAKLKAAVIVP 194
GloB COG0491
Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General ...
 20-86 3.95e-05

Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General function prediction only];


Pssm-ID: 440257 [Multi-domain]  Cd Length: 215  Bit Score: 45.45  E-value: 3.95e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568980060  20 CYLLQVDEFRFLLDCGWDEHFSVDIIDSLRKHVHQIDAVLLSHPDPLHLGALPFAVGKLGlnCAIYA 86
Cdd:COG0491   17 SYLIVGGDGAVLIDTGLGPADAEALLAALAALGLDIKAVLLTHLHPDHVGGLAALAEAFG--APVYA 81
metallo-hydrolase-like_MBL-fold cd06262
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 20-173 5.78e-04

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; 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 which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, 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 which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


Pssm-ID: 293792 [Multi-domain]  Cd Length: 188  Bit Score: 41.50  E-value: 5.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568980060  20 CYLLQVDEFR-FLLDCGWDEHfsVDIIDSLRKHVHQIDAVLLSH--PDplHLGALPFAVGKLGlncaiyatIPVYkMGQM 96
Cdd:cd06262   12 CYLVSDEEGEaILIDPGAGAL--EKILEAIEELGLKIKAILLTHghFD--HIGGLAELKEAPG--------APVY-IHEA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568980060  97 FMYDLYQSRHNTEDFTLFTLDDVDAafdkIQQLKFSQIVNLkgKGHGLSITPLPaGHMIGGTIWKIvkdGEEEIVYA 173
Cdd:cd06262   79 DAELLEDPELNLAFFGGGPLPPPEP----DILLEDGDTIEL--GGLELEVIHTP-GHTPGSVCFYI---EEEGVLFT 145
ComEC COG2333
DNA uptake channel protein ComEC C-terminal domain, metallo-beta-lactamase superfamily ...
 31-78 6.56e-04

DNA uptake channel protein ComEC C-terminal domain, metallo-beta-lactamase superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441904 [Multi-domain]  Cd Length: 253  Bit Score: 42.15  E-value: 6.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568980060  31 LLDCGWDEHFSV---DIIDSLRKH-VHQIDAVLLSHPDPLHLGALP-----FAVGKL 78
Cdd:COG2333   25 LIDTGPRPSFDAgerVVLPYLRALgIRRLDLLVLTHPDADHIGGLAavleaFPVGRV 81
ElaC COG1234
Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];
20-73 7.76e-04

Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440847 [Multi-domain]  Cd Length: 250  Bit Score: 42.10  E-value: 7.76e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568980060  20 CYLLQVDEFRFLLDCGwdEHfsvdIIDSLRKH---VHQIDAVLLSHPDPLHLGALPF 73
Cdd:COG1234   21 SYLLEAGGERLLIDCG--EG----TQRQLLRAgldPRDIDAIFITHLHGDHIAGLPG 71
ComA-like_MBL-fold cd07731
Competence protein ComA, ComEC and related proteins; MBL-fold metallo hydrolase domain; This ...
 18-78 1.94e-03

Competence protein ComA, ComEC and related proteins; MBL-fold metallo hydrolase domain; This subgroup includes proteins required for natural transformation competence including Neisseria gonorrhoeae ComA, Pseudomonas stutzeri ComA, Bacillus subtilis ComEC (also known as ComE operon protein 3) and Haemophilus influenza ORF2 encoded by the rec-2 gene, as well as Escherichia coli YcaI which does not mediate spontaneous plasmid transformation on nutrient-containing agar plates. It also includes the phosphorylcholine esterase (Pce) domain of choline-binding protein e from streptococcus pneumonia. 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: 293817 [Multi-domain]  Cd Length: 179  Bit Score: 39.81  E-value: 1.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568980060  18 ALCYLLQVDEFRFLLDCGWDEHFSVD-IIDSLR-KHVHQIDAVLLSHPDPLHLGALP-----FAVGKL 78
Cdd:cd07731   10 GDAILIQTPGKTILIDTGPRDSFGEDvVVPYLKaRGIKKLDYLILTHPDADHIGGLDavlknFPVKEV 77
RNaseZ_MBL-fold cd16272
Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as ...
 20-75 3.51e-03

Ribonuclease Z; MBL-fold metallo-hydrolase domain; The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. It includes the C-terminus of human ELAC2 and Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. 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: 293830 [Multi-domain]  Cd Length: 180  Bit Score: 39.17  E-value: 3.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 568980060  20 CYLLQVDEFRFLLDCGWDEHFSVDIIDslrKHVHQIDAVLLS--HPDplHLGALPFAV 75
Cdd:cd16272   19 SYLLETGGTRILLDCGEGTVYRLLKAG---VDPDKLDAIFLShfHLD--HIGGLPTLL 71
metallo-hydrolase-like_MBL-fold cd07740
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 20-73 3.88e-03

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain; 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) from which this fold was named are only a small fraction of the activities which are 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: 293826 [Multi-domain]  Cd Length: 194  Bit Score: 39.16  E-value: 3.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 568980060  20 CYLLQVDEFRFLLDCGwdehfsVDIIDSLRK---HVHQIDAVLLSHPDPLHLGALPF 73
Cdd:cd07740   18 CFHVASEAGRFLIDCG------ASSLIALKRagiDPNAIDAIFITHLHGDHFGGLPF 68
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH