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Conserved domains on  [gi|544711245|ref|NP_001269862|]
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zinc finger protein 341 isoform 1 [Homo sapiens]

Protein Classification

C2H2-type zinc finger protein( domain architecture ID 11472214)

Cys2His2 (C2H2)-type zinc finger protein may be involved in transcriptional regulation

CATH:  3.30.160.60
Gene Ontology:  GO:0008270|GO:0003677
PubMed:  11361095|22803940
SCOP:  4003583

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
323-729 7.17e-09

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 323 KCSYCDKSfTKNFDLQQH----IRSHTGEKPFQCIACGRAFAQKSNVKKHMQTHKvwppgHSGGTVSRNSVTVQVMALNP 398
Cdd:COG5048   32 RPDSCPNC-TDSFSRLEHltrhIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRT-----HHNNPSDLNSKSLPLSNSKA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 399 SRQEDEESTGLGQPLPGAPQPqalstageeeGDKPESKQVVLIDSSYLCQFCPSKFSTYFqLKSHMTQHKNEQVYKCVVK 478
Cdd:COG5048  106 SSSSLSSSSSNSNDNNLLSSH----------SLPPSSRDPQLPDLLSISNLRNNPLPGNN-SSSVNTPQSNSLHPPLPAN 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 479 SCAQTFPKLDTFLEHIKSHQEELSYRCHLCGKDFPSLYDLGVHQYSHSLLPQHSPKKDNAVYKCVKCVNKYSTpealehh 558
Cdd:COG5048  175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSS------- 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 559 lqtATHNFPCPHCQKVFPCERYLRRH----------LPTHGSGGRFKCQVCKKFFRREHYLKLH--AHIHSGE--KPYKC 624
Cdd:COG5048  248 ---LSSSDSSSSASESPRSSLPTASSqssspnesdsSSEKGFSLPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSC 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 625 --SVCESAFNRKDKLKRHMLIHEPFKKYKCPFSTHTGCSKEFNRPDKLKAHILSHSGMKLHK--CAL--CSKSFSRRAHL 698
Cdd:COG5048  325 pySLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKseTLSnsCIRNFKRDSNL 404

                        410       420       430
                 ....*....|....*....|....*....|...
gi 544711245 699 AEHQRAHT--GNYKFRCAGCAKGFSRHKYLKDH 729
Cdd:COG5048  405 SLHIITHLsfRPYNCKNPPCSKSFNRHYNLIPH 437
KREPA super family cl49620
Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, ...
 237-374 2.50e-03

Kinetoplastid RNA Editing Protein A (KREPA); The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, respectively) proteins are components of the RNA editing complex of parasitic protozoans such as Trypanosoma and Leishmania species. These parasites have a uniquely organized mitochondrial genome, the kinetoplast. Most kinetoplast-transcribed mRNAs are cryptic and encode multiple subunits for the electron transport chain following maturation through a uridine insertion/deletion process called RNA editing. KREPAs participate in the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. The editosome, a high molecular mass enzyme complex, carries out the reaction with the help of critical enzymes and structural proteins. Five related editosome proteins KREPA1 (TbMP81), KREPA2 (TbMP63), KREPA3 (TbMP42), KREPA4 (TbMP24), KREPA5 (TbMP19), and KREPA6 (TbMP18) play critical roles in the structure and auxiliary functions of the editing process without any predicted catalytic function. The KREPA1, KREPA2, and KREPA3 proteins contain C2H2 zinc finger motifs and KREPA4 and KREPA6, contain RNA-binding domains but all have a conserved C-terminal sequences that resemble an oligonucleotide-binding (OB)-fold domain. Thus, this group of five proteins is likely to be involved in protein-protein and/or protein-RNA interactions. RNA editing is crucial for the parasite's survival in both its bloodstream and procyclic form life cycle stages which allows the parasite to adapt to its environment and maintain its viability.


The actual alignment was detected with superfamily member cd23959:

Pssm-ID: 483960 [Multi-domain]  Cd Length: 424  Bit Score: 41.39  E-value: 2.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 237 ALGMQPYPPLEVPNQCVEPPV----YPTPTVYSPGKQGFKPKGPNPAAPMTSATGGTVATFDSPatlktrrakgarglPE 312
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVsaspFATATDTAPSSGAPDGFPAEASAPSPFAAPASAASFPAA--------------PV 236

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544711245 313 AAGKPKAQKLKCSYCDKSFTKNFDLQQHIRSHTGEKPfqciacgrafaQKSNVKKHMQTHKV 374
Cdd:cd23959  237 ANGEAATPTHACTICGKAFSTHEGLRMHSKAKHGVEL-----------EKAKTAKRKKRRSV 287
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
323-729 7.17e-09

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 323 KCSYCDKSfTKNFDLQQH----IRSHTGEKPFQCIACGRAFAQKSNVKKHMQTHKvwppgHSGGTVSRNSVTVQVMALNP 398
Cdd:COG5048   32 RPDSCPNC-TDSFSRLEHltrhIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRT-----HHNNPSDLNSKSLPLSNSKA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 399 SRQEDEESTGLGQPLPGAPQPqalstageeeGDKPESKQVVLIDSSYLCQFCPSKFSTYFqLKSHMTQHKNEQVYKCVVK 478
Cdd:COG5048  106 SSSSLSSSSSNSNDNNLLSSH----------SLPPSSRDPQLPDLLSISNLRNNPLPGNN-SSSVNTPQSNSLHPPLPAN 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 479 SCAQTFPKLDTFLEHIKSHQEELSYRCHLCGKDFPSLYDLGVHQYSHSLLPQHSPKKDNAVYKCVKCVNKYSTpealehh 558
Cdd:COG5048  175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSS------- 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 559 lqtATHNFPCPHCQKVFPCERYLRRH----------LPTHGSGGRFKCQVCKKFFRREHYLKLH--AHIHSGE--KPYKC 624
Cdd:COG5048  248 ---LSSSDSSSSASESPRSSLPTASSqssspnesdsSSEKGFSLPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSC 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 625 --SVCESAFNRKDKLKRHMLIHEPFKKYKCPFSTHTGCSKEFNRPDKLKAHILSHSGMKLHK--CAL--CSKSFSRRAHL 698
Cdd:COG5048  325 pySLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKseTLSnsCIRNFKRDSNL 404

                        410       420       430
                 ....*....|....*....|....*....|...
gi 544711245 699 AEHQRAHT--GNYKFRCAGCAKGFSRHKYLKDH 729
Cdd:COG5048  405 SLHIITHLsfRPYNCKNPPCSKSFNRHYNLIPH 437
zf-H2C2_2 pfam13465
Zinc-finger double domain;
336-361 4.83e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 43.51  E-value: 4.83e-06
                          10        20
                  ....*....|....*....|....*.
gi 544711245  336 DLQQHIRSHTGEKPFQCIACGRAFAQ 361
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 321-373 3.05e-05

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 42.93  E-value: 3.05e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 544711245 321 KLKCSYCDKSFTKNFDLQQHIRSHTgekpFQCIACGRAFAQKSNVKKHMQT-HK 373
Cdd:cd20908    1 KPWCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCLQvHK 50
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 237-374 2.50e-03

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 41.39  E-value: 2.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 237 ALGMQPYPPLEVPNQCVEPPV----YPTPTVYSPGKQGFKPKGPNPAAPMTSATGGTVATFDSPatlktrrakgarglPE 312
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVsaspFATATDTAPSSGAPDGFPAEASAPSPFAAPASAASFPAA--------------PV 236

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544711245 313 AAGKPKAQKLKCSYCDKSFTKNFDLQQHIRSHTGEKPfqciacgrafaQKSNVKKHMQTHKV 374
Cdd:cd23959  237 ANGEAATPTHACTICGKAFSTHEGLRMHSKAKHGVEL-----------EKAKTAKRKKRRSV 287
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
323-729 7.17e-09

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 323 KCSYCDKSfTKNFDLQQH----IRSHTGEKPFQCIACGRAFAQKSNVKKHMQTHKvwppgHSGGTVSRNSVTVQVMALNP 398
Cdd:COG5048   32 RPDSCPNC-TDSFSRLEHltrhIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRT-----HHNNPSDLNSKSLPLSNSKA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 399 SRQEDEESTGLGQPLPGAPQPqalstageeeGDKPESKQVVLIDSSYLCQFCPSKFSTYFqLKSHMTQHKNEQVYKCVVK 478
Cdd:COG5048  106 SSSSLSSSSSNSNDNNLLSSH----------SLPPSSRDPQLPDLLSISNLRNNPLPGNN-SSSVNTPQSNSLHPPLPAN 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 479 SCAQTFPKLDTFLEHIKSHQEELSYRCHLCGKDFPSLYDLGVHQYSHSLLPQHSPKKDNAVYKCVKCVNKYSTpealehh 558
Cdd:COG5048  175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSS------- 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 559 lqtATHNFPCPHCQKVFPCERYLRRH----------LPTHGSGGRFKCQVCKKFFRREHYLKLH--AHIHSGE--KPYKC 624
Cdd:COG5048  248 ---LSSSDSSSSASESPRSSLPTASSqssspnesdsSSEKGFSLPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSC 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 625 --SVCESAFNRKDKLKRHMLIHEPFKKYKCPFSTHTGCSKEFNRPDKLKAHILSHSGMKLHK--CAL--CSKSFSRRAHL 698
Cdd:COG5048  325 pySLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKseTLSnsCIRNFKRDSNL 404

                        410       420       430
                 ....*....|....*....|....*....|...
gi 544711245 699 AEHQRAHT--GNYKFRCAGCAKGFSRHKYLKDH 729
Cdd:COG5048  405 SLHIITHLsfRPYNCKNPPCSKSFNRHYNLIPH 437
zf-H2C2_2 pfam13465
Zinc-finger double domain;
336-361 4.83e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 43.51  E-value: 4.83e-06
                          10        20
                  ....*....|....*....|....*.
gi 544711245  336 DLQQHIRSHTGEKPFQCIACGRAFAQ 361
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 321-373 3.05e-05

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 42.93  E-value: 3.05e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 544711245 321 KLKCSYCDKSFTKNFDLQQHIRSHTgekpFQCIACGRAFAQKSNVKKHMQT-HK 373
Cdd:cd20908    1 KPWCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCLQvHK 50
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
441-608 2.10e-04

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 44.69  E-value: 2.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 441 IDSSYLCQFCPSKFSTYFQLKSHM--TQHKNE--QVYKCVVKSCAQTFPKLDTFLEHIKSHQEELSYRCHL--CGKDFPS 514
Cdd:COG5048  286 FSLPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSP 365

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 515 LYDLGVHQY-SHSLLPQHSPKKDNAVYKCVK-CVNKYSTPEALEHHLQTATHNFPCPHCQKVFPCERYLRRHLPTHGSGG 592
Cdd:COG5048  366 LLNNEPPQSlQQYKDLKNDKKSETLSNSCIRnFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHA 445

                        170
                 ....*....|....*.
gi 544711245 593 RFKCQVCKKFFRREHY 608
Cdd:COG5048  446 PLLCSILKSFRRDLDL 461
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 323-344 8.28e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 37.28  E-value: 8.28e-04
                          10        20
                  ....*....|....*....|..
gi 544711245  323 KCSYCDKSFTKNFDLQQHIRSH 344
Cdd:pfam00096   2 KCPDCGKSFSRKSNLKRHLRTH 23
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 237-374 2.50e-03

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 41.39  E-value: 2.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 237 ALGMQPYPPLEVPNQCVEPPV----YPTPTVYSPGKQGFKPKGPNPAAPMTSATGGTVATFDSPatlktrrakgarglPE 312
Cdd:cd23959  171 AAQQSSASPGEVASPFASGTVsaspFATATDTAPSSGAPDGFPAEASAPSPFAAPASAASFPAA--------------PV 236

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544711245 313 AAGKPKAQKLKCSYCDKSFTKNFDLQQHIRSHTGEKPfqciacgrafaQKSNVKKHMQTHKV 374
Cdd:cd23959  237 ANGEAATPTHACTICGKAFSTHEGLRMHSKAKHGVEL-----------EKAKTAKRKKRRSV 287
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
316-510 3.43e-03

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.83  E-value: 3.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 316 KPKAQKLKCSYCDKSFTKNFDLQQHIRS--HTGE--KPFQC--IACGRAFAQKSNVKKHMQTHkvwppghsggtvsrnsv 389
Cdd:COG5048  284 KGFSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLH----------------- 346

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 390 tvqvMALNPSRQEDEESTGLGQPLPGAPQPQALSTAGEEEGDKPESKQVvlidssylcQFCPSKFSTYFQLKSHMTQHKN 469
Cdd:COG5048  347 ----TSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLS---------NSCIRNFKRDSNLSLHIITHLS 413

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 544711245 470 EQVYKCVVKSCAQTFPKLDTFLEHIKSHQEELSYRCHLCGK 510
Cdd:COG5048  414 FRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
COG5236 COG5236
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
555-682 3.92e-03

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227561 [Multi-domain]  Cd Length: 493  Bit Score: 40.77  E-value: 3.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544711245 555 LEHHLQTATHNFPCPHC---QKVFPCE------RYLRRH----LPTHGSGGRFKCQVCKKFFrrehYLKLHAHIHSGEKP 621
Cdd:COG5236  169 LKKHYKAQHGFVLCSECignKKDFWNEirlfrsSTLRDHknggLEEEGFKGHPLCIFCKIYF----YDDDELRRHCRLRH 244

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544711245 622 YKCSVCESA-------FNRKDKLKRHmlihepFKK--YKCPFST-HTGCSKEFNRPDKLKAHILSHSGMKL 682
Cdd:COG5236  245 EACHICDMVgpiryqyFKSYEDLEAH------FRNahYCCTFQTcRVGKCYVFPYHTELLEHLTRFHKVNA 309
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 683-705 5.61e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 5.61e-03
                          10        20
                  ....*....|....*....|...
gi 544711245  683 HKCALCSKSFSRRAHLAEHQRAH 705
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 622-644 6.44e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 6.44e-03
                          10        20
                  ....*....|....*....|...
gi 544711245  622 YKCSVCESAFNRKDKLKRHMLIH 644
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
637-666 7.81e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.65  E-value: 7.81e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 544711245  637 LKRHMLIHEPFKKYKCPFsthtgCSKEFNR 666
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPE-----CGKSFKS 26
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
503-525 7.92e-03

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 34.53  E-value: 7.92e-03
                          10        20
                  ....*....|....*....|...
gi 544711245  503 YRCHLCGKDFPSLYDLGVHQYSH 525
Cdd:pfam13912   2 HECSECGKSFPSYQALGGHKKSH 24
 
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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