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Conserved domains on  [gi|15237845|ref|NP_197776|]
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cleavage and polyadenylation specificity factor 100 [Arabidopsis thaliana]

Protein Classification

cleavage and polyadenylation specificity factor subunit 2; integrator complex subunit 9( domain architecture ID 13007184)

cleavage and polyadenylation specificity factor (CPSF) subunit 2, 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| integrator complex subunit 9 is a component of the Integrator complex, a complex involved in the transcription of small nuclear RNAs (snRNA) and their 3'-box-dependent processing

Graphical summary

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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; ...
 8-203 2.13e-113

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: 340.65  E-value: 2.13e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   8 TPLCGVYNENPLSYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSAPVYAT 87
Cdd:cd16293   2 TPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYAT 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  88 EPVHRLGLLTMYDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAPHVAGHMLGGSIWRITKDGE 167
Cdd:cd16293  82 LPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDSE 161

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15237845 168 DVIYAVDYNHRKERHLNGTVLQSF--VRPAVLITDAYH 203
Cdd:cd16293 162 DIVYAVDWNHKKERHLNGAVLDSFggLRPSLLITDADN 199
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-366 3.24e-31

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: 118.41  E-value: 3.24e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    243 VLELLLILEQHWSQRGF-SFPIYFLTYVSSSTIDYVKSFLEWMSDSISKSFEtSRDNAFLLRHVTLLINKTDLD--NAPP 319
Cdd:smart01027   1 TQELLLILEELWREGELpNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEESKrlNDYK 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 15237845    320 GPKVVLASMASLEAGFAREIFVEWANDPRNLVLFTETGQFGTLARML 366
Cdd:smart01027  80 GPKVIIASSGMLTGGRSRHYLKRLAPDPRNTVILTGYQAEGTLGRKL 126
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 610-736 7.69e-25

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: 101.57  E-value: 7.69e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   610 VQLSEKLMSNVIFKKLGDSEVAWVDSEV-------------------------------------------GKTERDMRS 646
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLdraaleegaaeeeeeeedeeeenankkqkleqfslkdddekesKESKDSIPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   647 LLPMPG--AASPHKPVLVGDLKIADFKQFLSSKGVQVEFAGGGALRCGEYVTLRKVGpTGqkggasgpqQILIEGPLCED 724
Cdd:pfam13299  81 LDPLPSnlAPAVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGEGTLVCNGTVAVRKTE-TG---------RIEIEGVGGPT 150

                         170
                  ....*....|..
gi 15237845   725 YYKIRDYLYSQF 736
Cdd:pfam13299 151 FYAVRRLIYEQL 162
RMMBL super family cl38234
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 533-593 2.90e-05

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.


The actual alignment was detected with superfamily member pfam07521:

Pssm-ID: 462191 [Multi-domain]  Cd Length: 63  Bit Score: 42.22  E-value: 2.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237845   533 VTVSCSLVKMD-YEGRSDGRSIKSMIAHVSPLKLVLVHAIAEATEHLKQHCLNNICPHVYAP 593
Cdd:pfam07521   2 IPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELGIEVFVP 63
 
Name Accession Description Interval E-value
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 8-203 2.13e-113

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: 340.65  E-value: 2.13e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   8 TPLCGVYNENPLSYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSAPVYAT 87
Cdd:cd16293   2 TPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYAT 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  88 EPVHRLGLLTMYDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAPHVAGHMLGGSIWRITKDGE 167
Cdd:cd16293  82 LPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDSE 161

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15237845 168 DVIYAVDYNHRKERHLNGTVLQSF--VRPAVLITDAYH 203
Cdd:cd16293 162 DIVYAVDWNHKKERHLNGAVLDSFggLRPSLLITDADN 199
Lactamase_B_6 pfam16661
Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase ...
 22-198 5.59e-70

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


Pssm-ID: 406948  Cd Length: 192  Bit Score: 227.09  E-value: 5.59e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    22 LVSIDGFNFLIDCGWNDLFD-TSLLEPLSRVASTIDAVLLSHPDTLHIGALPY----AMKQLGLSAPVYATEPVHRLGLL 96
Cdd:pfam16661   1 LLEFDNVRILLDPGWDGSFSyESDLKYLEKILPEVDLILLSHPTLEHLGAYPLlyykFGSHLGSNIPVYATLPVANLGRV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    97 TMYDQFLSRKQV--SDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAPHVAGHMLGGSIWRITKDGEDVIYAVD 174
Cdd:pfam16661  81 STYDLYASRGILgpYDSSELDLDDIDAAFDKIKTLKYSQTVDLKGKFDGLTITPYNSGHTLGGTIWKISKNSEKIVYAVD 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 15237845   175 YNHRKERHLNGT--------VLQSFVRPAVLI 198
Cdd:pfam16661 161 WNHTKDSHLNGAslldstgkPLESLVRPTALI 192
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 20-367 1.20e-32

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


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 130.69  E-value: 1.20e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHP--DtlHIGALPYAMKQlGLSAPVYATEPVHRLGLLT 97
Cdd:COG1236  16 CYLLETGGTRILIDCGLFQGGKERNWPPFPFRPSDVDAVVLTHAhlD--HSGALPLLVKE-GFRGPIYATPATADLARIL 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  98 MYDQ-FLSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLsgkgEGIVIAPHVAGHMLGGSIWRITKDGEDVIYAVDYN 176
Cdd:COG1236  93 LGDSaKIQEEEAEAEPLYTEEDAERALELFQTVDYGEPFEI----GGVRVTFHPAGHILGSAQVELEVGGKRIVFSGDYG 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845 177 HRKerhlngtvlQSFVRPAVLITDAyHALYT-------NQTARQQRDKEFLDTISKHLEVGGNVLLPVDTAGRVLELLLI 249
Cdd:COG1236 169 RED---------DPLLAPPEPVPPA-DVLITestygdrLHPPREEVEAELAEWVRETLARGGTVLIPAFALGRAQELLYL 238

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845 250 LEQHWSQRGFS-FPIyfltYVS---SSTIDYVKSFLEWMSDSIsksfetsrDNAFLLRHVTlLINKTDLDNA--PPGPKV 323
Cdd:COG1236 239 LRELKKEGRLPdIPI----YVSgmaIRATEIYRRHGEYLRDEA--------QDPFALPNLR-FVTSVEESKAlnRKGPAI 305

                       330       340       350       360
                ....*....|....*....|....*....|....*....|....*.
gi 15237845 324 VLASMASLEAGFAREIFVEWANDPRNLVLFteTG--QFGTLARMLQ 367
Cdd:COG1236 306 IIAPSGMLTGGRILHHLKRFLWDPRNTILF--VGyqAEGTLGRRLL 349
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-366 3.24e-31

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: 118.41  E-value: 3.24e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    243 VLELLLILEQHWSQRGF-SFPIYFLTYVSSSTIDYVKSFLEWMSDSISKSFEtSRDNAFLLRHVTLLINKTDLD--NAPP 319
Cdd:smart01027   1 TQELLLILEELWREGELpNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEESKrlNDYK 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 15237845    320 GPKVVLASMASLEAGFAREIFVEWANDPRNLVLFTETGQFGTLARML 366
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 ...
 243-364 4.54e-25

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: 100.28  E-value: 4.54e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   243 VLELLLILEQHWSQ-RGFSFPIYFLTYVSSSTIDYVKSFLEWMSDSISKSFETSRDNAFLlrhvtllinktdldNAPPGP 321
Cdd:pfam10996   1 AQELLYLLDELWREgRLPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSESKAI--------------NEGKGP 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 15237845   322 KVVLASMASLEAGFAREIFVEWANDPRNLVLFTETGQFGTLAR 364
Cdd:pfam10996  67 KVIIASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 610-736 7.69e-25

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: 101.57  E-value: 7.69e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   610 VQLSEKLMSNVIFKKLGDSEVAWVDSEV-------------------------------------------GKTERDMRS 646
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLdraaleegaaeeeeeeedeeeenankkqkleqfslkdddekesKESKDSIPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   647 LLPMPG--AASPHKPVLVGDLKIADFKQFLSSKGVQVEFAGGGALRCGEYVTLRKVGpTGqkggasgpqQILIEGPLCED 724
Cdd:pfam13299  81 LDPLPSnlAPAVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGEGTLVCNGTVAVRKTE-TG---------RIEIEGVGGPT 150

                         170
                  ....*....|..
gi 15237845   725 YYKIRDYLYSQF 736
Cdd:pfam13299 151 FYAVRRLIYEQL 162
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 20-174 4.52e-09

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: 56.41  E-value: 4.52e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845     20 SYLVSIDGFNFLIDCGWNDLFDtsLLEPLSRV-ASTIDAVLLSHPDTLHIGALPYAMKQLGlsAPVYATEPVHRLglltM 98
Cdd:smart00849   2 SYLVRDDGGAILIDTGPGEAED--LLAELKKLgPKKIDAIILTHGHPDHIGGLPELLEAPG--APVYAPEGTAEL----L 73

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237845     99 YDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLTysqnyhlsgkGEGIVIApHVAGHMLGGSIWRItkDGEDVIYAVD 174
Cdd:smart00849  74 KDLLALLGELGAEAEPAPPDRTLKDGDELDLG----------GGELEVI-HTPGHTPGSIVLYL--PEGKILFTGD 136
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 533-593 2.90e-05

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: 42.22  E-value: 2.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237845   533 VTVSCSLVKMD-YEGRSDGRSIKSMIAHVSPLKLVLVHAIAEATEHLKQHCLNNICPHVYAP 593
Cdd:pfam07521   2 IPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELGIEVFVP 63
PRK11921 PRK11921
anaerobic nitric oxide reductase flavorubredoxin;
14-87 5.12e-03

anaerobic nitric oxide reductase flavorubredoxin;


Pssm-ID: 237023 [Multi-domain]  Cd Length: 394  Bit Score: 40.06  E-value: 5.12e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237845   14 YNenplSYLVSiDGFNFLIDCGWNDlFDTSLLEPLSRVA--STIDAVLLSHPDTLHIGALPYAMKQLGlSAPVYAT 87
Cdd:PRK11921  33 YN----SYLIK-DEKTVLIDTVWQP-FAKEFVENLKKEIdlDKIDYIVANHGEIDHSGALPELMKEIP-DTPIYCT 101
 
Name Accession Description Interval E-value
CPSF2-like_MBL-fold cd16293
cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; ...
 8-203 2.13e-113

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: 340.65  E-value: 2.13e-113
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   8 TPLCGVYNENPLSYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSAPVYAT 87
Cdd:cd16293   2 TPLSGAGDESPLCYLLEIDDVTILLDCGWDESFDMEYLESLKRIAPTIDAVLLSHPDLEHLGALPYLVGKLGLTCPVYAT 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  88 EPVHRLGLLTMYDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAPHVAGHMLGGSIWRITKDGE 167
Cdd:cd16293  82 LPVHKMGRMFMYDLYQSRGLEEDFNLFTLDDVDEAFDRITQLKYSQPVNLRGKGDGLTITAYNAGHTLGGTIWKITKDSE 161

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15237845 168 DVIYAVDYNHRKERHLNGTVLQSF--VRPAVLITDAYH 203
Cdd:cd16293 162 DIVYAVDWNHKKERHLNGAVLDSFggLRPSLLITDADN 199
Lactamase_B_6 pfam16661
Metallo-beta-lactamase superfamily domain; This family is part of the metallo-beta-lactamase ...
 22-198 5.59e-70

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


Pssm-ID: 406948  Cd Length: 192  Bit Score: 227.09  E-value: 5.59e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    22 LVSIDGFNFLIDCGWNDLFD-TSLLEPLSRVASTIDAVLLSHPDTLHIGALPY----AMKQLGLSAPVYATEPVHRLGLL 96
Cdd:pfam16661   1 LLEFDNVRILLDPGWDGSFSyESDLKYLEKILPEVDLILLSHPTLEHLGAYPLlyykFGSHLGSNIPVYATLPVANLGRV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    97 TMYDQFLSRKQV--SDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAPHVAGHMLGGSIWRITKDGEDVIYAVD 174
Cdd:pfam16661  81 STYDLYASRGILgpYDSSELDLDDIDAAFDKIKTLKYSQTVDLKGKFDGLTITPYNSGHTLGGTIWKISKNSEKIVYAVD 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 15237845   175 YNHRKERHLNGT--------VLQSFVRPAVLI 198
Cdd:pfam16661 161 WNHTKDSHLNGAslldstgkPLESLVRPTALI 192
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 8-199 6.39e-33

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: 125.52  E-value: 6.39e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   8 TPLCGVYNENPLSYLVSIDGFNFLIDCGWNDLFDT--SLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSAPVY 85
Cdd:cd07734   1 TPLGGGQEVGRSCFLVEFKGRTVLLDCGMNPGKEDpeACLPQFELLPPEIDAILISHFHLDHCGALPYLFRGFIFRGPIY 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  86 ATEPVHRLGLLTMYDQF-LSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGkgeGIVIAPHVAGHMLGGSIWRITK 164
Cdd:cd07734  81 ATHPTVALGRLLLEDYVkSAERIGQDQSLYTPEDIEEALKHIVPLGYGQSIDLFP---ALSLTAYNAGHVLGAAMWEIQI 157

                       170       180       190
                ....*....|....*....|....*....|....*
gi 15237845 165 DGEDVIYAVDYNHRKERHLNGTVLqSFVRPAVLIT 199
Cdd:cd07734 158 YGEKLVYTGDFSNTEDRLLPAASI-LPPRPDLLIT 191
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 20-367 1.20e-32

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


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 130.69  E-value: 1.20e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHP--DtlHIGALPYAMKQlGLSAPVYATEPVHRLGLLT 97
Cdd:COG1236  16 CYLLETGGTRILIDCGLFQGGKERNWPPFPFRPSDVDAVVLTHAhlD--HSGALPLLVKE-GFRGPIYATPATADLARIL 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  98 MYDQ-FLSRKQVSDFDLFTLDDIDSAFQNVIRLTYSQNYHLsgkgEGIVIAPHVAGHMLGGSIWRITKDGEDVIYAVDYN 176
Cdd:COG1236  93 LGDSaKIQEEEAEAEPLYTEEDAERALELFQTVDYGEPFEI----GGVRVTFHPAGHILGSAQVELEVGGKRIVFSGDYG 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845 177 HRKerhlngtvlQSFVRPAVLITDAyHALYT-------NQTARQQRDKEFLDTISKHLEVGGNVLLPVDTAGRVLELLLI 249
Cdd:COG1236 169 RED---------DPLLAPPEPVPPA-DVLITestygdrLHPPREEVEAELAEWVRETLARGGTVLIPAFALGRAQELLYL 238

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845 250 LEQHWSQRGFS-FPIyfltYVS---SSTIDYVKSFLEWMSDSIsksfetsrDNAFLLRHVTlLINKTDLDNA--PPGPKV 323
Cdd:COG1236 239 LRELKKEGRLPdIPI----YVSgmaIRATEIYRRHGEYLRDEA--------QDPFALPNLR-FVTSVEESKAlnRKGPAI 305

                       330       340       350       360
                ....*....|....*....|....*....|....*....|....*.
gi 15237845 324 VLASMASLEAGFAREIFVEWANDPRNLVLFteTG--QFGTLARMLQ 367
Cdd:COG1236 306 IIAPSGMLTGGRILHHLKRFLWDPRNTILF--VGyqAEGTLGRRLL 349
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 243-366 3.24e-31

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: 118.41  E-value: 3.24e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    243 VLELLLILEQHWSQRGF-SFPIYFLTYVSSSTIDYVKSFLEWMSDSISKSFEtSRDNAFLLRHVTLLINKTDLD--NAPP 319
Cdd:smart01027   1 TQELLLILEELWREGELpNVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEESKrlNDYK 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 15237845    320 GPKVVLASMASLEAGFAREIFVEWANDPRNLVLFTETGQFGTLARML 366
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 ...
 243-364 4.54e-25

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: 100.28  E-value: 4.54e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   243 VLELLLILEQHWSQ-RGFSFPIYFLTYVSSSTIDYVKSFLEWMSDSISKSFETSRDNAFLlrhvtllinktdldNAPPGP 321
Cdd:pfam10996   1 AQELLYLLDELWREgRLPKIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSESKAI--------------NEGKGP 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 15237845   322 KVVLASMASLEAGFAREIFVEWANDPRNLVLFTETGQFGTLAR 364
Cdd:pfam10996  67 KVIIASSGMLEGGRSRHHLKHWAPDPKNTVIFTGYQAEGTLGR 109
CPSF100_C pfam13299
Cleavage and polyadenylation factor 2 C-terminal; This family lies at the C-terminus of many ...
 610-736 7.69e-25

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: 101.57  E-value: 7.69e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   610 VQLSEKLMSNVIFKKLGDSEVAWVDSEV-------------------------------------------GKTERDMRS 646
Cdd:pfam13299   1 VKLSDSLVSSLKWQKVRGLEVAWVTGRLdraaleegaaeeeeeeedeeeenankkqkleqfslkdddekesKESKDSIPT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   647 LLPMPG--AASPHKPVLVGDLKIADFKQFLSSKGVQVEFAGGGALRCGEYVTLRKVGpTGqkggasgpqQILIEGPLCED 724
Cdd:pfam13299  81 LDPLPSnlAPAVHQPLFVGDLRLSDLKKLLQSAGHTAEFRGEGTLVCNGTVAVRKTE-TG---------RIEIEGVGGPT 150

                         170
                  ....*....|..
gi 15237845   725 YYKIRDYLYSQF 736
Cdd:pfam13299 151 FYAVRRLIYEQL 162
INTS11-like_MBL-fold cd16291
Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain; ...
 22-201 7.59e-23

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: 96.95  E-value: 7.59e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  22 LVSIDGFNFLIDCG----WND---LFDTSLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSAPVYATEPVHRLG 94
Cdd:cd16291  16 LVTIGGKNIMFDCGmhmgYNDerrFPDFSYISQNGPFTEHIDCVIISHFHLDHCGALPYFTEVVGYDGPIYMTHPTKAIC 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  95 LLTMYDQ---FLSRKQVSDFdlFTLDDIDSAFQNVIRLTYSQNYHLsgkGEGIVIAPHVAGHMLGGSIWRITKDGEDVIY 171
Cdd:cd16291  96 PILLEDYrkiAVERKGETNF--FTSQMIKDCMKKVIAVNLHETVQV---DDELEIKAYYAGHVLGAAMFYVRVGDESVVY 170

                       170       180       190
                ....*....|....*....|....*....|
gi 15237845 172 AVDYNHRKERHLnGTVLQSFVRPAVLITDA 201
Cdd:cd16291 171 TGDYNMTPDRHL-GAAWIDRLRPDLLITES 199
TTHA0252-CPSF-like_MBL-fold cd16295
Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; ...
 20-183 2.99e-21

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: 92.14  E-value: 2.99e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGwndLF------DTSLLEPLSRVASTIDAVLLSHPDTLHIGALPYAMKQlGLSAPVYATEPVHRL 93
Cdd:cd16295  14 CYLLETGGKRILLDCG---LFqggkelEELNNEPFPFDPKEIDAVILTHAHLDHSGRLPLLVKE-GFRGPIYATPATKDL 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  94 GLLTMYD-QFLSRKQVSDFD---LFTLDDIDSAFQNVIRLTYSQNYHLsgkGEGIVIAPHVAGHMLGGSIWRIT-KDGED 168
Cdd:cd16295  90 AELLLLDsAKIQEEEAEHPPaepLYTEEDVEKALKHFRPVEYGEPFEI---GPGVKVTFYDAGHILGSASVELEiGGGKR 166

                       170
                ....*....|....*
gi 15237845 169 VIYAVDYNhRKERHL 183
Cdd:cd16295 167 ILFSGDLG-RKNTPL 180
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 5-201 2.46e-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: 74.93  E-value: 2.46e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   5 VQVTPLcGVYNENPLS-YLVSIDGFNFLIDCG------------WNDLFDtslleplsrvASTIDAVLLSHPDTLHIGAL 71
Cdd:cd16292   1 LEITPL-GAGQEVGRScVILEFKGKTIMLDCGihpgysglaslpFFDEID----------LSEIDLLLITHFHLDHCGAL 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  72 PYAMKQLGLSAPVYATEPVHRLGLLTMYDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLtysqNYHLSGKGEGIVIAPHVA 151
Cdd:cd16292  70 PYFLQKTNFKGRVFMTHPTKAIYKWLLSDYVRVSNISSDEMLYTETDLEASMDKIETI----DFHQEVEVNGIKFTAYNA 145

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 15237845 152 GHMLGGSIWRITKDGEDVIYAVDYNHRKERHLNGTVLQSfVRPAVLITDA 201
Cdd:cd16292 146 GHVLGAAMFMVEIAGVRVLYTGDYSREEDRHLPAAEIPP-IKPDVLIVES 194
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 20-174 4.52e-09

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: 56.41  E-value: 4.52e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845     20 SYLVSIDGFNFLIDCGWNDLFDtsLLEPLSRV-ASTIDAVLLSHPDTLHIGALPYAMKQLGlsAPVYATEPVHRLglltM 98
Cdd:smart00849   2 SYLVRDDGGAILIDTGPGEAED--LLAELKKLgPKKIDAIILTHGHPDHIGGLPELLEAPG--APVYAPEGTAEL----L 73

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237845     99 YDQFLSRKQVSDFDLFTLDDIDSAFQNVIRLTysqnyhlsgkGEGIVIApHVAGHMLGGSIWRItkDGEDVIYAVD 174
Cdd:smart00849  74 KDLLALLGELGAEAEPAPPDRTLKDGDELDLG----------GGELEVI-HTPGHTPGSIVLYL--PEGKILFTGD 136
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 20-177 4.73e-09

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


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 57.98  E-value: 4.73e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGwNDLFDTSLLEPLSrvASTIDAVLLSHPDTLHI-GALPYAMKQLGLSAPVYATEPVHRlGLLTM 98
Cdd:COG1235  37 SILVEADGTRLLIDAG-PDLREQLLRLGLD--PSKIDAILLTHEHADHIaGLDDLRPRYGPNPIPVYATPGTLE-ALERR 112

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  99 YDQF-------LSRKQVSDFDLFTLDDID-SAFQnvirltysqnyhlsgkgegiviAPHVAGHMLGgsiWRITKDGEDVI 170
Cdd:COG1235 113 FPYLfapypgkLEFHEIEPGEPFEIGGLTvTPFP----------------------VPHDAGDPVG---YRIEDGGKKLA 167


                ....*..
gi 15237845 171 YAVDYNH 177
Cdd:COG1235 168 YATDTGY 174
Int9-like_MBL-fold cd16294
integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain; Integrator is a ...
 29-171 2.35e-08

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: 54.04  E-value: 2.35e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  29 NFLIDCGWNDLFDTSLLEplsrvASTIDAVLLShpDTLHIGALPYAMKQLGLSAPVYATEPVHRLGLLTMYD--QFLSRK 106
Cdd:cd16294  23 TIMLDCGLDCPPETELID-----LSTVDVILIS--NYHCMLALPFITEYTGFTGVVYATEPTVQIGRLLMEElvQALSKI 95

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15237845 107 QVsdfdlftlddidsafqnvirLTYSQNYHLSGkgeGIVIAPHVAGHMLGGSIWRITKDGEDVIY 171
Cdd:cd16294  96 QL--------------------VGYSQKLDLFG---AVQVTALSSGYCLGSSNWVIQSHYEKISY 137
metallo-hydrolase-like_MBL-fold cd06262
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 12-172 2.33e-07

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: 51.52  E-value: 2.33e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  12 GVYNENplSYLVSID-GFNFLIDCGWNDLfdTSLLEPLSRVASTIDAVLLSH--PDtlHIGALPYAMKQLGlsAPVYATE 88
Cdd:cd06262   6 GPLQTN--CYLVSDEeGEAILIDPGAGAL--EKILEAIEELGLKIKAILLTHghFD--HIGGLAELKEAPG--APVYIHE 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  89 PvhrlglltmydqflsrkqvsDFDLFTLDDIDSAFQNVIRLTYSQNYHLSGKGEGIVIAP------HVAGHMLGGSIWRI 162
Cdd:cd06262  78 A--------------------DAELLEDPELNLAFFGGGPLPPPEPDILLEDGDTIELGGleleviHTPGHTPGSVCFYI 137

                       170
                ....*....|
gi 15237845 163 tkDGEDVIYA 172
Cdd:cd06262 138 --EEEGVLFT 145
GloB COG0491
Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General ...
 20-118 4.93e-07

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: 51.23  E-value: 4.93e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSH--PDtlHIGALPYAMKQLGlsAPVYATEPVHRLGLLT 97
Cdd:COG0491  17 SYLIVGGDGAVLIDTGLGPADAEALLAALAALGLDIKAVLLTHlhPD--HVGGLAALAEAFG--APVYAHAAEAEALEAP 92

                        90       100
                ....*....|....*....|.
gi 15237845  98 MYDQFLSRKQVSDFDLFTLDD 118
Cdd:COG0491  93 AAGALFGREPVPPDRTLEDGD 113
Lactamase_B pfam00753
Metallo-beta-lactamase superfamily;
20-172 8.30e-07

Metallo-beta-lactamase superfamily;


Pssm-ID: 425851 [Multi-domain]  Cd Length: 196  Bit Score: 50.06  E-value: 8.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    20 SYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVA-STIDAVLLSHPDTLHIGALPYAMKQLGlsAPVYATEPVHRLGLLTM 98
Cdd:pfam00753   8 SYLIEGGGGAVLIDTGGSAEAALLLLLAALGLGpKDIDAVILTHGHFDHIGGLGELAEATD--VPVIVVAEEARELLDEE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15237845    99 YDQFLSRKQVSDFDLFTLDDIDSAFQnvirltysqnyhLSGKGEGIVIAPHVAGHMLGGSIWRITKDGEDVIYA 172
Cdd:pfam00753  86 LGLAASRLGLPGPPVVPLPPDVVLEE------------GDGILGGGLGLLVTHGPGHGPGHVVVYYGGGKVLFT 147
RNaseZ_short-form-like_MBL-fold cd07716
uncharacterized bacterial subgroup of Ribonuclease Z, short form; MBL-fold metallo-hydrolase ...
 20-118 2.48e-06

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: 48.21  E-value: 2.48e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGwndlfdTSLLEPLSRVA--STIDAVLLS--HPD-TLHIGALPYAMK--QLGLSA---PVYA-TE 88
Cdd:cd07716  20 GYLLEADGFRILLDCG------SGVLSRLQRYIdpEDLDAVVLShlHPDhCADLGVLQYARRyhPRGARKpplPLYGpAG 93

                        90       100       110
                ....*....|....*....|....*....|
gi 15237845  89 PVHRLGLLTMYDQFlsrkqvsdFDLFTLDD 118
Cdd:cd07716  94 PAERLAALYGLEDV--------FDFHPIEP 115
Lactamase_B_2 pfam12706
Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and ...
 29-174 4.39e-06

Beta-lactamase superfamily domain; This family is part of the beta-lactamase superfamily and is related to pfam00753.


Pssm-ID: 432732 [Multi-domain]  Cd Length: 196  Bit Score: 48.07  E-value: 4.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845    29 NFLIDCGWnDLF--DTSLLEPLSRVASTIDAVLLSHPDTLHIGALPyAMKQlGLSAPVYATEPVHRlgLLTMYDQFLSRK 106
Cdd:pfam12706   2 RILIDPGP-DLRqqALPALQPGRLRDDPIDAVLLTHDHYDHLAGLL-DLRE-GRPRPLYAPLGVLA--HLRRNFPYLFLL 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15237845   107 QVSDFDLFTLdDIDSAFQ---NVIRLTYSQNYHLSGKGEGIVIAPhVAGhmlggsiWRITKDGEDVIYAVD 174
Cdd:pfam12706  77 EHYGVRVHEI-DWGESFTvgdGGLTVTATPARHGSPRGLDPNPGD-TLG-------FRIEGPGKRVYYAGD 138
RMMBL pfam07521
Zn-dependent metallo-hydrolase RNA specificity domain; The metallo-beta-lactamase fold ...
 533-593 2.90e-05

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: 42.22  E-value: 2.90e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237845   533 VTVSCSLVKMD-YEGRSDGRSIKSMIAHVSPLKLVLVHAIAEATEHLKQHCLNNICPHVYAP 593
Cdd:pfam07521   2 IPVRARIETIDgFSGHADRRELLELIKGLKPKPIVLVHGEPRALLALAELLKEELGIEVFVP 63
ComA-like_MBL-fold cd07731
Competence protein ComA, ComEC and related proteins; MBL-fold metallo hydrolase domain; This ...
 19-78 3.53e-05

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: 45.20  E-value: 3.53e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237845  19 LSYLVSIDGFNFLIDCGWNDLFDTSLLEP--LSRVASTIDAVLLSHPDTLHIGALPYAMKQL 78
Cdd:cd07731  11 DAILIQTPGKTILIDTGPRDSFGEDVVVPylKARGIKKLDYLILTHPDADHIGGLDAVLKNF 72
DHPS-like_MBL-fold cd07713
Methanocaldococcus jannaschii dihydropteroate synthase, Thermoanaerobacter tengcongensis Tflp, ...
 12-86 5.08e-05

Methanocaldococcus jannaschii dihydropteroate synthase, Thermoanaerobacter tengcongensis Tflp, and related proteins; MBL-fold metallo hydrolase domain; This subgroup includes Methanocaldococcus jannaschii 7,8-dihydropterin-6-methyl-4-(beta-D-ribofuranosyl)-aminobenzene-5'-phosphate synthase (EC 2.5.1.15), a folate biosynthetic enzyme also known as dihydropteroate synthase and 7,8 dihydropteroate synthase. Thermoanaerobacter tengcongensis Tflp is a ferredoxin-like member. 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: 293799  Cd Length: 269  Bit Score: 45.69  E-value: 5.08e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  12 GVYNENPLSYLVSIDGFNFLIDCGWNDLFdtslLEPLSRV---ASTIDAVLLSHP--DtlHIGALPYAMKQLGlSAPVYA 86
Cdd:cd07713  14 GLLAEHGLSLLIETEGKKILFDTGQSGVL----LHNAKKLgidLSDIDAVVLSHGhyD--HTGGLKALLELNP-KAPVYA 86
ComEC COG2333
DNA uptake channel protein ComEC C-terminal domain, metallo-beta-lactamase superfamily ...
 22-108 2.96e-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: 43.31  E-value: 2.96e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  22 LVSIDGFNFLIDCGWNDLFDT--SLLEPL--SRVASTIDAVLLSHPDTLHIGALPYAMKQLGLSApVYATEPVHRLGLLT 97
Cdd:COG2333  16 IRTPDGKTILIDTGPRPSFDAgeRVVLPYlrALGIRRLDLLVLTHPDADHIGGLAAVLEAFPVGR-VLVSGPPDTSETYE 94

                        90
                ....*....|.
gi 15237845  98 MYDQFLSRKQV 108
Cdd:COG2333  95 RLLEALKEKGI 105
RnjA COG0595
mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];
21-88 4.37e-04

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


Pssm-ID: 440360 [Multi-domain]  Cd Length: 553  Bit Score: 43.51  E-value: 4.37e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  21 YLVSIDGFNFLIDCGW----NDLF-------DTS-LLEPLSRvastIDAVLLSHP--DtlHIGALPYAMKQLGlsAPVYA 86
Cdd:COG0595  22 YVYEYDDDIIIVDCGLkfpeDEMPgvdlvipDISyLEENKDK----IKGIVLTHGheD--HIGALPYLLKELN--VPVYG 93


                ..
gi 15237845  87 TE 88
Cdd:COG0595  94 TP 95
RNaseJ_MBL-fold cd07714
RNAaseJ, MBL-fold metallo-hydrolase domain; RNase J, also called Ribonuclease J, is a ...
 21-88 1.24e-03

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: 41.24  E-value: 1.24e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  21 YLVSIDGFNFLIDCGW----NDLF-------DTSLLEplsRVASTIDAVLLSHP--DtlHIGALPYAMKQLGlsAPVYAT 87
Cdd:cd07714  14 YVVEYDDDIIIIDCGLkfpdEDMPgvdyiipDFSYLE---ENKDKIKGIFITHGheD--HIGALPYLLPELN--VPIYAT 86


                .
gi 15237845  88 E 88
Cdd:cd07714  87 P 87
YycJ-like_MBL-fold cd07733
uncharacterized subgroup which includes Bacillus subtilis YycJ and related proteins; MBL-fold ...
 20-118 2.04e-03

uncharacterized subgroup which includes Bacillus subtilis YycJ and related proteins; MBL-fold metallo hydrolase domain; Includes the uncharacterized Bacillus subtilis YycJ protein. 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. 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: 293819 [Multi-domain]  Cd Length: 151  Bit Score: 39.17  E-value: 2.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845  20 SYLVSIDGFNFLIDCGWNDLFDTSLLEPLSRVASTIDAVLLSHPDTLHI-GALPYAMKqlgLSAPVYATEpvhrlGLLTM 98
Cdd:cd07733  11 CTYLETEDGKLLIDAGLSGRKITGRLAEIGRDPEDIDAILVTHEHADHIkGLGVLARK---YNVPIYATA-----GTLRA 82

                        90       100
                ....*....|....*....|
gi 15237845  99 YDQFLSRKQVSDFDLFTLDD 118
Cdd:cd07733  83 MERKVGLIDVDQKQIFEPGE 102
metallo-hydrolase-like_MBL-fold cd16279
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo; ...
 2-119 3.98e-03

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo; 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. Some members of this subgroup are named as octanoyltransferase (also known as lipoate-protein ligase B).


Pssm-ID: 293837 [Multi-domain]  Cd Length: 193  Bit Score: 38.99  E-value: 3.98e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237845   2 GTSVQVtP----LCGV-YNENP------LSYLVSIDGFNFLIDCGwNDLFDTSLLEPLSRvastIDAVLLSHP--DtlHI 68
Cdd:cd16279   9 GTSSGV-PvigcDCGVcDSSDPknrrlrSSILIETGGKNILIDTG-PDFRQQALRAGIRK----LDAVLLTHAhaD--HI 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237845  69 GAL----PYAMKQLGlSAPVYATEPVHRlGLLTMYDQF-----------LSRKQVSDFDLFTLDDI 119
Cdd:cd16279  81 HGLddlrPFNRLQQR-PIPVYASEETLD-DLKRRFPYFfaatggggvpkLDLHIIEPDEPFTIGGL 144
PRK11921 PRK11921
anaerobic nitric oxide reductase flavorubredoxin;
14-87 5.12e-03

anaerobic nitric oxide reductase flavorubredoxin;


Pssm-ID: 237023 [Multi-domain]  Cd Length: 394  Bit Score: 40.06  E-value: 5.12e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237845   14 YNenplSYLVSiDGFNFLIDCGWNDlFDTSLLEPLSRVA--STIDAVLLSHPDTLHIGALPYAMKQLGlSAPVYAT 87
Cdd:PRK11921  33 YN----SYLIK-DEKTVLIDTVWQP-FAKEFVENLKKEIdlDKIDYIVANHGEIDHSGALPELMKEIP-DTPIYCT 101
 
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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