NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2462499425|ref|XP_054189221|]
View 

zinc finger protein 558 isoform X2 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 18089471)

KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development and in regulating viral replication and transcription

CATH:  3.30.160.60|1.10.287.1360
Gene Ontology:  GO:0005515|GO:0008270|GO:0003677|GO:0006355|GO:0001217|GO:0003700
PubMed:  8183940|22803940|2023909|8183939|10748030|27867147|28765213|11361095|30718982|10940247
SCOP:  4003583|4002243

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
KRAB super family cl42959
krueppel associated box;
1-29 2.03e-08

krueppel associated box;


The actual alignment was detected with superfamily member smart00349:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 50.28  E-value: 2.03e-08
                           10        20
                   ....*....|....*....|....*....
gi 2462499425    1 MLENCRNLASLGCRVNKPSLISQLEQDKK 29
Cdd:smart00349  30 MLENYSNLVSLGFQVPKPDLISQLEQGEE 58
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
91-327 2.15e-05

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.84  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425  91 STKSNLTQHKRIHTGEKPYDCSQCGKSFSSRSYLTIHKRIHNGEKPYECNHCGKAFSDPSSLRLHLRIHTGEKPYECNQC 170
Cdd:COG5048   181 SSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASES 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 171 FHVFRTSCNLKSHKRIHTGE-------NHHECNQCGKAFSTRSSLTGHN--SIHTGE--KPYEC--HDCGKTFRKSSYLT 237
Cdd:COG5048   261 PRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSCpySLCGKLFSRNDALK 340

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 238 QHVRTHTGEKPYECNEC-------GKSFSSSFSLTVHKRIHTGEKPYECSD--CGKAFNNLSAVKKHLRTHTGEKPYECN 308
Cdd:COG5048   341 RHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPYNCK 420

                         250       260
                  ....*....|....*....|.
gi 2462499425 309 --HCGKSFTSNSYLSVHKRIH 327
Cdd:COG5048   421 npPCSKSFNRHYNLIPHKKIH 441
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
1-29 2.03e-08

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 50.28  E-value: 2.03e-08
                           10        20
                   ....*....|....*....|....*....
gi 2462499425    1 MLENCRNLASLGCRVNKPSLISQLEQDKK 29
Cdd:smart00349  30 MLENYSNLVSLGFQVPKPDLISQLEQGEE 58
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
91-327 2.15e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.84  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425  91 STKSNLTQHKRIHTGEKPYDCSQCGKSFSSRSYLTIHKRIHNGEKPYECNHCGKAFSDPSSLRLHLRIHTGEKPYECNQC 170
Cdd:COG5048   181 SSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASES 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 171 FHVFRTSCNLKSHKRIHTGE-------NHHECNQCGKAFSTRSSLTGHN--SIHTGE--KPYEC--HDCGKTFRKSSYLT 237
Cdd:COG5048   261 PRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSCpySLCGKLFSRNDALK 340

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 238 QHVRTHTGEKPYECNEC-------GKSFSSSFSLTVHKRIHTGEKPYECSD--CGKAFNNLSAVKKHLRTHTGEKPYECN 308
Cdd:COG5048   341 RHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPYNCK 420

                         250       260
                  ....*....|....*....|.
gi 2462499425 309 --HCGKSFTSNSYLSVHKRIH 327
Cdd:COG5048   421 npPCSKSFNRHYNLIPHKKIH 441
zf-H2C2_2 pfam13465
Zinc-finger double domain;
235-260 1.71e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 1.71e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425 235 YLTQHVRTHTGEKPYECNECGKSFSS 260
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
1-29 2.03e-08

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 50.28  E-value: 2.03e-08
                           10        20
                   ....*....|....*....|....*....
gi 2462499425    1 MLENCRNLASLGCRVNKPSLISQLEQDKK 29
Cdd:smart00349  30 MLENYSNLVSLGFQVPKPDLISQLEQGEE 58
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
91-327 2.15e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.84  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425  91 STKSNLTQHKRIHTGEKPYDCSQCGKSFSSRSYLTIHKRIHNGEKPYECNHCGKAFSDPSSLRLHLRIHTGEKPYECNQC 170
Cdd:COG5048   181 SSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASES 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 171 FHVFRTSCNLKSHKRIHTGE-------NHHECNQCGKAFSTRSSLTGHN--SIHTGE--KPYEC--HDCGKTFRKSSYLT 237
Cdd:COG5048   261 PRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSCpySLCGKLFSRNDALK 340

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 238 QHVRTHTGEKPYECNEC-------GKSFSSSFSLTVHKRIHTGEKPYECSD--CGKAFNNLSAVKKHLRTHTGEKPYECN 308
Cdd:COG5048   341 RHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPYNCK 420

                         250       260
                  ....*....|....*....|.
gi 2462499425 309 --HCGKSFTSNSYLSVHKRIH 327
Cdd:COG5048   421 npPCSKSFNRHYNLIPHKKIH 441
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
107-172 8.94e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 43.92  E-value: 8.94e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462499425 107 KPYDCSQCGKSFSSRSYLTIHKRIHNGEKPYECNH--CGKAFSDPSSLRLHLRIHTGEKPYECNQCFH 172
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNSKSLP 99
zf-H2C2_2 pfam13465
Zinc-finger double domain;
235-260 1.71e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 1.71e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425 235 YLTQHVRTHTGEKPYECNECGKSFSS 260
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
93-324 2.28e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 42.76  E-value: 2.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425  93 KSNLTQHKRIHTGEKPYDCSQCG----KSFSSRSYLTIHKRIHNGEKPYECNHCG--KAFSDPSSLRLHLRIHTG-EKPY 165
Cdd:COG5048   211 IPSSSSDQNLENSSSSLPLTTNSqlspKSLLSQSPSSLSSSDSSSSASESPRSSLptASSQSSSPNESDSSSEKGfSLPI 290

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 166 ECNQCFHVFRTSCNLKSHKR--IHTGENH--HEC--NQCGKAFSTRSSLTGHNSIHTGEKPYECH--DCGKTFRKSSY-- 235
Cdd:COG5048   291 KSKQCNISFSRSSPLTRHLRsvNHSGESLkpFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKllNSSSKFSPLLNne 370

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 236 ---LTQHVRTHTGEKPYEC--NECGKSFSSSFSLTVHKRIHTGEKPYEC--SDCGKAFNNLSAVKKHLRTHTGEKPYECN 308
Cdd:COG5048   371 ppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCknPPCSKSFNRHYNLIPHKKIHTNHAPLLCS 450

                         250
                  ....*....|....*.
gi 2462499425 309 HCGKSFTSNSYLSVHK 324
Cdd:COG5048   451 ILKSFRRDLDLSNHGK 466
zf-H2C2_2 pfam13465
Zinc-finger double domain;
95-120 3.33e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.35  E-value: 3.33e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425  95 NLTQHKRIHTGEKPYDCSQCGKSFSS 120
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
291-316 3.67e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.35  E-value: 3.67e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425 291 AVKKHLRTHTGEKPYECNHCGKSFTS 316
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 245-300 7.66e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 40.86  E-value: 7.66e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462499425 245 GEKPYECN--ECGKSFSSSFSLTVHKR-------------------IHTGEKPYECSDCGKAFNNLSAVKKHlRTHT 300
Cdd:COG5189   346 DGKPYKCPveGCNKKYKNQNGLKYHMLhghqnqklhenpspekmniFSAKDKPYRCEVCDKRYKNLNGLKYH-RKHS 421
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 141-244 8.37e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 40.86  E-value: 8.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 141 HCGKAFSDPSSLRLHLRihtGEKPYECN--QCFHVFRTSCNLKSHKRihtgenHHECNQcgkAFSTRSSLTGHNSIHTGE 218
Cdd:COG5189   329 HGGERNIDTPSRMLKVK---DGKPYKCPveGCNKKYKNQNGLKYHML------HGHQNQ---KLHENPSPEKMNIFSAKD 396

                          90       100
                  ....*....|....*....|....*.
gi 2462499425 219 KPYECHDCGKTFRKSSYLTQHvRTHT 244
Cdd:COG5189   397 KPYRCEVCDKRYKNLNGLKYH-RKHS 421
zf-H2C2_2 pfam13465
Zinc-finger double domain;
179-204 9.79e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 9.79e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425 179 NLKSHKRIHTGENHHECNQCGKAFST 204
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
263-288 9.98e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 9.98e-04
                          10        20
                  ....*....|....*....|....*.
gi 2462499425 263 SLTVHKRIHTGEKPYECSDCGKAFNN 288
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
79-327 2.38e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.68  E-value: 2.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425  79 KLNECNQCFKVFSTKSNLTQHKRIHTGEKPYDCSQ--CGKSFSSRSYLTIHKRIHNGEKPYECNHCG------KAFSDPS 150
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNSKSLplsnskASSSSLS 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 151 SLRLHLRIHTGEKPYECNQCFHVFRTS---------------CNLKSHKRIHTGENHHECNQ---CGKAFSTRSSLTGHN 212
Cdd:COG5048   112 SSSSNSNDNNLLSSHSLPPSSRDPQLPdllsisnlrnnplpgNNSSSVNTPQSNSLHPPLPAnslSKDPSSNLSLLISSN 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462499425 213 SIHTGEKPYECHDCGKTFRKSSYLTQHVRTH------------------------TGEKPYECNECGKSFSSSFSLTVHK 268
Cdd:COG5048   192 VSTSIPSSSENSPLSSSYSIPSSSSDQNLENsssslplttnsqlspksllsqspsSLSSSDSSSSASESPRSSLPTASSQ 271

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462499425 269 RIH----------TGEKPYECSDCGKAFNNLSAVKKHLRT--HTGE--KPYECNH--CGKSFTSNSYLSVHKRIH 327
Cdd:COG5048   272 SSSpnesdsssekGFSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLH 346
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 221-243 4.22e-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: 34.20  E-value: 4.22e-03
                          10        20
                  ....*....|....*....|...
gi 2462499425 221 YECHDCGKTFRKSSYLTQHVRTH 243
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 137-159 5.83e-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: 33.81  E-value: 5.83e-03
                          10        20
                  ....*....|....*....|...
gi 2462499425 137 YECNHCGKAFSDPSSLRLHLRIH 159
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH