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Conserved domains on  [gi|1039013965|gb|ANM63631|]
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integrator complex subunit [Arabidopsis thaliana]

Protein Classification

integrator complex subunit 9( domain architecture ID 11039990)

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

Gene Ontology:  GO:0032039|GO:0016180|GO:0005634
PubMed:  16239144

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 101-280 1.53e-20

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.


The actual alignment was detected with superfamily member cd16294:

Pssm-ID: 451500 [Multi-domain]  Cd Length: 166  Bit Score: 89.09  E-value: 1.53e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 101 SFIDIVLISNPMGLLGLPFLTQNPGFFAKIYMTEVTAKIGQLMMEDIVSmhkefrcfhgpdnssfpgwiknldseqvpal 180
Cdd:cd16294    42 STVDVILISNYHCMLALPFITEYTGFTGVVYATEPTVQIGRLLMEELVQ------------------------------- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 181 lkkvvfgesgddlgswmrlyslddiesCMKKVQGVKFAEEVCYNGTLIIKALSSGLDIGACNWLINGPNGSLSYVSDSIF 260
Cdd:cd16294    91 ---------------------------ALSKIQLVGYSQKLDLFGAVQVTALSSGYCLGSSNWVIQSHYEKISYVSGSSV 143

                         170       180
                  ....*....|....*....|
gi 1039013965 261 VSHHARSFDFHGLKETDVLI 280
Cdd:cd16294   144 LTTHPQPMDQTSLKNSDVLI 163
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 375-475 2.54e-19

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: 84.13  E-value: 2.54e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965  375 KVPIFVISSVAEELLAYTNTIPEWLCEQRQEKLISGE--PSFGHLKFIKNKKIHLfpaihspnLITSWQEPCIVFASHWS 452
Cdd:smart01027  19 NVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFEQGRnpFDFKNLKFVKSLEESK--------RLNDYKGPKVIIASSGM 90

                           90       100
                   ....*....|....*....|...
gi 1039013965  453 LRLGPSVQLLQRWRGDPKSLLVL 475
Cdd:smart01027  91 LTGGRSRHYLKRLAPDPRNTVIL 113
 
Name Accession Description Interval E-value
Int9-like_MBL-fold cd16294
integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain; Integrator is a ...
 101-280 1.53e-20

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: 89.09  E-value: 1.53e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 101 SFIDIVLISNPMGLLGLPFLTQNPGFFAKIYMTEVTAKIGQLMMEDIVSmhkefrcfhgpdnssfpgwiknldseqvpal 180
Cdd:cd16294    42 STVDVILISNYHCMLALPFITEYTGFTGVVYATEPTVQIGRLLMEELVQ------------------------------- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 181 lkkvvfgesgddlgswmrlyslddiesCMKKVQGVKFAEEVCYNGTLIIKALSSGLDIGACNWLINGPNGSLSYVSDSIF 260
Cdd:cd16294    91 ---------------------------ALSKIQLVGYSQKLDLFGAVQVTALSSGYCLGSSNWVIQSHYEKISYVSGSSV 143

                         170       180
                  ....*....|....*....|
gi 1039013965 261 VSHHARSFDFHGLKETDVLI 280
Cdd:cd16294   144 LTTHPQPMDQTSLKNSDVLI 163
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 375-475 2.54e-19

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: 84.13  E-value: 2.54e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965  375 KVPIFVISSVAEELLAYTNTIPEWLCEQRQEKLISGE--PSFGHLKFIKNKKIHLfpaihspnLITSWQEPCIVFASHWS 452
Cdd:smart01027  19 NVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFEQGRnpFDFKNLKFVKSLEESK--------RLNDYKGPKVIIASSGM 90

                           90       100
                   ....*....|....*....|...
gi 1039013965  453 LRLGPSVQLLQRWRGDPKSLLVL 475
Cdd:smart01027  91 LTGGRSRHYLKRLAPDPRNTVIL 113
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 375-475 2.27e-06

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: 46.74  E-value: 2.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 375 KVPIFVISSVAEELLAYTNTIPEWLCEQRQEKLISGEPSfghlkfiknKKIHLFPaihspnlitswqEPCIVFASHWSLR 454
Cdd:pfam10996  19 KIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSES---------KAINEGK------------GPKVIIASSGMLE 77

                          90       100
                  ....*....|....*....|.
gi 1039013965 455 LGPSVQLLQRWRGDPKSLLVL 475
Cdd:pfam10996  78 GGRSRHHLKHWAPDPKNTVIF 98
 
Name Accession Description Interval E-value
Int9-like_MBL-fold cd16294
integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain; Integrator is a ...
 101-280 1.53e-20

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: 89.09  E-value: 1.53e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 101 SFIDIVLISNPMGLLGLPFLTQNPGFFAKIYMTEVTAKIGQLMMEDIVSmhkefrcfhgpdnssfpgwiknldseqvpal 180
Cdd:cd16294    42 STVDVILISNYHCMLALPFITEYTGFTGVVYATEPTVQIGRLLMEELVQ------------------------------- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 181 lkkvvfgesgddlgswmrlyslddiesCMKKVQGVKFAEEVCYNGTLIIKALSSGLDIGACNWLINGPNGSLSYVSDSIF 260
Cdd:cd16294    91 ---------------------------ALSKIQLVGYSQKLDLFGAVQVTALSSGYCLGSSNWVIQSHYEKISYVSGSSV 143

                         170       180
                  ....*....|....*....|
gi 1039013965 261 VSHHARSFDFHGLKETDVLI 280
Cdd:cd16294   144 LTTHPQPMDQTSLKNSDVLI 163
Beta-Casp smart01027
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 375-475 2.54e-19

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: 84.13  E-value: 2.54e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965  375 KVPIFVISSVAEELLAYTNTIPEWLCEQRQEKLISGE--PSFGHLKFIKNKKIHLfpaihspnLITSWQEPCIVFASHWS 452
Cdd:smart01027  19 NVPIYLDSPMAARATEIYKSYPEWMSDEIRKRFEQGRnpFDFKNLKFVKSLEESK--------RLNDYKGPKVIIASSGM 90

                           90       100
                   ....*....|....*....|...
gi 1039013965  453 LRLGPSVQLLQRWRGDPKSLLVL 475
Cdd:smart01027  91 LTGGRSRHYLKRLAPDPRNTVIL 113
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 100-280 3.62e-13

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: 68.51  E-value: 3.62e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 100 ASFIDIVLISNP--MGLLGLPFLTQNPGFFAKIYMTEVTAKIGQLMMEDIVsmhkefrcfhgpdnssfpgwiknldseqv 177
Cdd:cd07734    47 PPEIDAILISHFhlDHCGALPYLFRGFIFRGPIYATHPTVALGRLLLEDYV----------------------------- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 178 pallkkvvfgESGDDLGSWMRLYSLDDIESCMKKVQGVKFAEEVCYNGTLIIKALSSGLDIGACNWLINGPNGSLSYVSD 257
Cdd:cd07734    98 ----------KSAERIGQDQSLYTPEDIEEALKHIVPLGYGQSIDLFPALSLTAYNAGHVLGAAMWEIQIYGEKLVYTGD 167

                         170       180
                  ....*....|....*....|....*.
gi 1039013965 258 SIFV-SHH--ARSFDFHGLketDVLI 280
Cdd:cd07734   168 FSNTeDRLlpAASILPPRP---DLLI 190
CPSF3-like_MBL-fold cd16292
cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; ...
 99-245 3.75e-07

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: 51.05  E-value: 3.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965  99 EASFIDIVLIS----NPMGllGLPFLTQNPGFFAKIYMTEVTAKIGQLMMEDIVSmhkefrcfhgpdnssfpgwIKNLDS 174
Cdd:cd16292    49 DLSEIDLLLIThfhlDHCG--ALPYFLQKTNFKGRVFMTHPTKAIYKWLLSDYVR-------------------VSNISS 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1039013965 175 EQvpallkkvvfgesgddlgswmRLYSLDDIESCMKKVQGVKFAEEVCYNGtliIK--ALSSGLDIGACNWLI 245
Cdd:cd16292   108 DE---------------------MLYTETDLEASMDKIETIDFHQEVEVNG---IKftAYNAGHVLGAAMFMV 156
INTS11-like_MBL-fold cd16291
Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain; ...
 100-257 1.05e-06

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: 49.95  E-value: 1.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 100 ASFIDIVLISN-PMGLLG-LPFLTQNPGFFAKIYMTEVTAKIGQLMMEDivsmhkefrcfhgpdnssfpgwiknldseqv 177
Cdd:cd16291    53 TEHIDCVIISHfHLDHCGaLPYFTEVVGYDGPIYMTHPTKAICPILLED------------------------------- 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 178 palLKKVVFGESGDDlgswmRLYSLDDIESCMKKVQGVKFAEEVCYNGTLIIKALSSGLDIGACNWLINGPNGSLSYVSD 257
Cdd:cd16291   102 ---YRKIAVERKGET-----NFFTSQMIKDCMKKVIAVNLHETVQVDDELEIKAYYAGHVLGAAMFYVRVGDESVVYTGD 173
Beta-Casp pfam10996
Beta-Casp domain; The beta-CASP domain is found C terminal to the beta-lactamase domain in ...
 375-475 2.27e-06

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: 46.74  E-value: 2.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039013965 375 KVPIFVISSVAEELLAYTNTIPEWLCEQRQEKLISGEPSfghlkfiknKKIHLFPaihspnlitswqEPCIVFASHWSLR 454
Cdd:pfam10996  19 KIPIYLDSPLAIKATEVYRRYPEYLDDEARHFVISKSES---------KAINEGK------------GPKVIIASSGMLE 77

                          90       100
                  ....*....|....*....|.
gi 1039013965 455 LGPSVQLLQRWRGDPKSLLVL 475
Cdd:pfam10996  78 GGRSRHHLKHWAPDPKNTVIF 98
 
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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