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Conserved domains on  [gi|63054460|ref|NP_588409|]
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zf-CCCH type zinc finger protein [Schizosaccharomyces pombe]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 86-379 1.77e-54

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


:

Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 185.46  E-value: 1.77e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460  86 PKCALSHALPGNTNLPNGTSTNTMASMAANGGASSVASKQMGANQISPSLSSKTMKNPADKANNTTATDVRGNTATSPYF 165
Cdd:COG5084   1 EKNVCSFAIDGKCNLGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 166 PFSRSPGRHSgNSTINGMMTTPnflSSGVNSRSVDEFNNSSSGFPSSLNGIPIASpPLATSPTSFSLASSASSTNLGGSK 245
Cdd:COG5084  81 NFNSIRGSRL-STPNNHVNPVL---SSSVVCKFFLRGLCKSGFSCEFLHEYDLRS-SQGPPCRSFSLKGSCSSGPSCGYS 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 246 GLLfqQMTSENNRDYFSRRPTLLNTYGNRCSSTDTLSSLSRLTSqdPLKASLPLQSPPLAPKTGVSLSRPRLTLDQSLGN 325
Cdd:COG5084 156 HID--PDSFAGNCDQYSGATYGFCPLGASCKFSHTLKRVSYGSS--PCGNYTPPFSPPGTPSESVSSWGYGKGTSCSLSH 231

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 63054460 326 LSLGSGINQRRQVPRSNSYAGAFPSVVSASLPTKVDLNHQMDVSDEEQRFLSTP 379
Cdd:COG5084 232 PSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
ZnF_C3H1 smart00356
zinc finger;
43-67 5.17e-07

zinc finger;


:

Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 46.08  E-value: 5.17e-07
                           10        20
                   ....*....|....*....|....*
gi 63054460     43 QHVPCKFFRNGTCTAGENCPFSHSL 67
Cdd:smart00356   3 KTELCKFFKRGYCPRGDRCKFAHPL 27
ZnF_C3H1 smart00356
zinc finger;
72-92 7.63e-06

zinc finger;


:

Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.62  E-value: 7.63e-06
                           10        20
                   ....*....|....*....|.
gi 63054460     72 PICKYFLKGNCKFGPKCALSH 92
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 86-379 1.77e-54

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 185.46  E-value: 1.77e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460  86 PKCALSHALPGNTNLPNGTSTNTMASMAANGGASSVASKQMGANQISPSLSSKTMKNPADKANNTTATDVRGNTATSPYF 165
Cdd:COG5084   1 EKNVCSFAIDGKCNLGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 166 PFSRSPGRHSgNSTINGMMTTPnflSSGVNSRSVDEFNNSSSGFPSSLNGIPIASpPLATSPTSFSLASSASSTNLGGSK 245
Cdd:COG5084  81 NFNSIRGSRL-STPNNHVNPVL---SSSVVCKFFLRGLCKSGFSCEFLHEYDLRS-SQGPPCRSFSLKGSCSSGPSCGYS 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 246 GLLfqQMTSENNRDYFSRRPTLLNTYGNRCSSTDTLSSLSRLTSqdPLKASLPLQSPPLAPKTGVSLSRPRLTLDQSLGN 325
Cdd:COG5084 156 HID--PDSFAGNCDQYSGATYGFCPLGASCKFSHTLKRVSYGSS--PCGNYTPPFSPPGTPSESVSSWGYGKGTSCSLSH 231

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 63054460 326 LSLGSGINQRRQVPRSNSYAGAFPSVVSASLPTKVDLNHQMDVSDEEQRFLSTP 379
Cdd:COG5084 232 PSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
ZnF_C3H1 smart00356
zinc finger;
43-67 5.17e-07

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 46.08  E-value: 5.17e-07
                           10        20
                   ....*....|....*....|....*
gi 63054460     43 QHVPCKFFRNGTCTAGENCPFSHSL 67
Cdd:smart00356   3 KTELCKFFKRGYCPRGDRCKFAHPL 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 47-65 5.61e-06

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 42.79  E-value: 5.61e-06
                          10
                  ....*....|....*....
gi 63054460    47 CKFFRNGTCTAGENCPFSH 65
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
72-92 7.63e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.62  E-value: 7.63e-06
                           10        20
                   ....*....|....*....|.
gi 63054460     72 PICKYFLKGNCKFGPKCALSH 92
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 47-92 2.10e-05

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 43.60  E-value: 2.10e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 63054460    47 CKFFRNGTCTAGENCPFSH---SLETErPICKYFLKGNCkFGPKCALSH 92
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHceaALGNE-TVCTLWQEGRC-FRPVCRFRH 54
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 72-92 2.29e-05

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 41.03  E-value: 2.29e-05
                          10        20
                  ....*....|....*....|.
gi 63054460    72 PICKYFLKGNCKFGPKCALSH 92
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
 
Name Accession Description Interval E-value
YTH1 COG5084
Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin ...
 86-379 1.77e-54

Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only];


Pssm-ID: 227416 [Multi-domain]  Cd Length: 285  Bit Score: 185.46  E-value: 1.77e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460  86 PKCALSHALPGNTNLPNGTSTNTMASMAANGGASSVASKQMGANQISPSLSSKTMKNPADKANNTTATDVRGNTATSPYF 165
Cdd:COG5084   1 EKNVCSFAIDGKCNLGSGCTYNHSNYTSLNDGLQSVSSKYMGAKQISPSLSSPTFKNKANLMQNTNDNFVPGNTVACISR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 166 PFSRSPGRHSgNSTINGMMTTPnflSSGVNSRSVDEFNNSSSGFPSSLNGIPIASpPLATSPTSFSLASSASSTNLGGSK 245
Cdd:COG5084  81 NFNSIRGSRL-STPNNHVNPVL---SSSVVCKFFLRGLCKSGFSCEFLHEYDLRS-SQGPPCRSFSLKGSCSSGPSCGYS 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 63054460 246 GLLfqQMTSENNRDYFSRRPTLLNTYGNRCSSTDTLSSLSRLTSqdPLKASLPLQSPPLAPKTGVSLSRPRLTLDQSLGN 325
Cdd:COG5084 156 HID--PDSFAGNCDQYSGATYGFCPLGASCKFSHTLKRVSYGSS--PCGNYTPPFSPPGTPSESVSSWGYGKGTSCSLSH 231

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 63054460 326 LSLGSGINQRRQVPRSNSYAGAFPSVVSASLPTKVDLNHQMDVSDEEQRFLSTP 379
Cdd:COG5084 232 PSLNIDIQQPQTAPSRKDSGGTNPIGASSEIGSEADGNMQNSISGSGDSEEIEE 285
ZnF_C3H1 smart00356
zinc finger;
43-67 5.17e-07

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 46.08  E-value: 5.17e-07
                           10        20
                   ....*....|....*....|....*
gi 63054460     43 QHVPCKFFRNGTCTAGENCPFSHSL 67
Cdd:smart00356   3 KTELCKFFKRGYCPRGDRCKFAHPL 27
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 47-65 5.61e-06

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 42.79  E-value: 5.61e-06
                          10
                  ....*....|....*....
gi 63054460    47 CKFFRNGTCTAGENCPFSH 65
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
72-92 7.63e-06

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 42.62  E-value: 7.63e-06
                           10        20
                   ....*....|....*....|.
gi 63054460     72 PICKYFLKGNCKFGPKCALSH 92
Cdd:smart00356   5 ELCKFFKRGYCPRGDRCKFAH 25
zf-CCCH_3 pfam15663
Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically ...
 47-92 2.10e-05

Zinc-finger containing family; zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length.


Pssm-ID: 464787 [Multi-domain]  Cd Length: 110  Bit Score: 43.60  E-value: 2.10e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 63054460    47 CKFFRNGTCTAGENCPFSH---SLETErPICKYFLKGNCkFGPKCALSH 92
Cdd:pfam15663   8 CYFFYYSTCTKGDSCPFRHceaALGNE-TVCTLWQEGRC-FRPVCRFRH 54
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 72-92 2.29e-05

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 41.03  E-value: 2.29e-05
                          10        20
                  ....*....|....*....|.
gi 63054460    72 PICKYFLKGNCKFGPKCALSH 92
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 74-92 1.56e-04

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 38.94  E-value: 1.56e-04
                          10
                  ....*....|....*....
gi 63054460    74 CKYFLKGNCKFGPKCALSH 92
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
44-66 2.01e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.71  E-value: 2.01e-04
                          10        20
                  ....*....|....*....|....
gi 63054460    44 HVPCKFF-RNGTCTAGENCPFSHS 66
Cdd:pfam00642   3 TELCRFFlRTGYCKYGDRCKFAHG 26
zf-CCCH_2 pfam14608
RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented ...
 46-65 2.18e-04

RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented by fingers 5-7 of Nab2. Nab2 ZnF5-7 are zinc-fingers of the type C-x8-C-x5-C-x3-H. Nab2 ZnFs function in the generation of export-competent mRNPs. Mab2 is a conserved polyadenosine-RNA-binding Zn finger protein required for both mRNA export and polyadenylation regulation and becomes attached to the mRNP after splicing and during or immediately after polyadenylation. The three ZnFs, 5-7, have almost identical folds and, most unusually, associate with one another to form a single coherent structural unit. ZnF5-7 bind to eight consecutive adenines, and chemical shift perturbations identify residues on each finger that interact with RNA.


Pssm-ID: 464217  Cd Length: 19  Bit Score: 38.26  E-value: 2.18e-04
                          10        20
                  ....*....|....*....|
gi 63054460    46 PCKFFrnGTCTAGENCPFSH 65
Cdd:pfam14608   1 PCRFG--GNCTFGPKCPFSH 18
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 45-65 2.81e-04

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 37.95  E-value: 2.81e-04
                          10        20
                  ....*....|....*....|.
gi 63054460    45 VPCKFFRNGTCTAGENCPFSH 65
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
zf-CCCH_2 pfam14608
RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented ...
 73-93 8.19e-04

RNA-binding, Nab2-type zinc finger; This is an unusual zinc-finger family, and is represented by fingers 5-7 of Nab2. Nab2 ZnF5-7 are zinc-fingers of the type C-x8-C-x5-C-x3-H. Nab2 ZnFs function in the generation of export-competent mRNPs. Mab2 is a conserved polyadenosine-RNA-binding Zn finger protein required for both mRNA export and polyadenylation regulation and becomes attached to the mRNP after splicing and during or immediately after polyadenylation. The three ZnFs, 5-7, have almost identical folds and, most unusually, associate with one another to form a single coherent structural unit. ZnF5-7 bind to eight consecutive adenines, and chemical shift perturbations identify residues on each finger that interact with RNA.


Pssm-ID: 464217  Cd Length: 19  Bit Score: 36.72  E-value: 8.19e-04
                          10        20
                  ....*....|....*....|.
gi 63054460    73 ICKYFlkGNCKFGPKCALSHA 93
Cdd:pfam14608   1 PCRFG--GNCTFGPKCPFSHP 19
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
71-92 2.41e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 35.63  E-value: 2.41e-03
                          10        20
                  ....*....|....*....|...
gi 63054460    71 RPICKYFLK-GNCKFGPKCALSH 92
Cdd:pfam00642   3 TELCRFFLRtGYCKYGDRCKFAH 25
 
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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