NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958668594|ref|XP_038945325|]
View 

uncharacterized protein LOC304336 isoform X1 [Rattus norvegicus]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12204268)

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:0003677|GO:0008270|GO:0005515|GO:0001217|GO:0003700
PubMed:  8183940|22803940|2023909|8183939|8183940|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 smart00349
krueppel associated box;
43-102 5.34e-30

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 112.30  E-value: 5.34e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594   43 VSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLVWLGYCLVKPELISKLEKGFEPW 102
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
425-697 7.41e-11

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 65.10  E-value: 7.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 425 RKCSKAFYHNSLLSQYQTAHTTEQQSDCKELMKIYFYISSLTqHHRPHTLEKPYGCNDCMKTFSHKSQLARHQRTHTGEK 504
Cdd:COG5048   175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSS-DQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDS 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 505 PHECKECRKAFCHKSHLTRHQGIHAPEKPyeckeckksfyLRSQLTQHQrthtgekpfeCKECQKAFFRNSHLTQHQ--K 582
Cdd:COG5048   254 SSSASESPRSSLPTASSQSSSPNESDSSS-----------EKGFSLPIK----------SKQCNISFSRSSPLTRHLrsV 312

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 583 IHTGE--KPHKCKE--CGNAFARKSHLTQHQKTHTGERPYECKECR-------KAFSRKSQLMQHETTHTGERAYEC--K 649
Cdd:COG5048   313 NHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNssskfspLLNNEPPQSLQQYKDLKNDKKSETlsN 392

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958668594 650 ECRKTFYLKAYLTRHQVIHKSEKP--FECKKCGKAFSRKSYLTRHQKTHK 697
Cdd:COG5048   393 SCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHT 442
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
43-102 5.34e-30

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 112.30  E-value: 5.34e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594   43 VSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLVWLGYCLVKPELISKLEKGFEPW 102
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 42-83 2.17e-21

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 87.53  E-value: 2.17e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958668594  42 LVSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLVWLG 83
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 43-80 4.62e-17

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 74.89  E-value: 4.62e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958668594  43 VSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLV 80
Cdd:cd07765     1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLV 38
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
425-697 7.41e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 65.10  E-value: 7.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 425 RKCSKAFYHNSLLSQYQTAHTTEQQSDCKELMKIYFYISSLTqHHRPHTLEKPYGCNDCMKTFSHKSQLARHQRTHTGEK 504
Cdd:COG5048   175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSS-DQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDS 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 505 PHECKECRKAFCHKSHLTRHQGIHAPEKPyeckeckksfyLRSQLTQHQrthtgekpfeCKECQKAFFRNSHLTQHQ--K 582
Cdd:COG5048   254 SSSASESPRSSLPTASSQSSSPNESDSSS-----------EKGFSLPIK----------SKQCNISFSRSSPLTRHLrsV 312

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 583 IHTGE--KPHKCKE--CGNAFARKSHLTQHQKTHTGERPYECKECR-------KAFSRKSQLMQHETTHTGERAYEC--K 649
Cdd:COG5048   313 NHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNssskfspLLNNEPPQSLQQYKDLKNDKKSETlsN 392

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958668594 650 ECRKTFYLKAYLTRHQVIHKSEKP--FECKKCGKAFSRKSYLTRHQKTHK 697
Cdd:COG5048   393 SCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHT 442
zf-H2C2_2 pfam13465
Zinc-finger double domain;
493-515 3.91e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.91e-04
                          10        20
                  ....*....|....*....|...
gi 1958668594 493 LARHQRTHTGEKPHECKECRKAF 515
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
43-102 5.34e-30

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 112.30  E-value: 5.34e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594   43 VSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLVWLGYCLVKPELISKLEKGFEPW 102
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 42-83 2.17e-21

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 87.53  E-value: 2.17e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958668594  42 LVSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLVWLG 83
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 43-80 4.62e-17

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 74.89  E-value: 4.62e-17
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958668594  43 VSFEDVAVDFTWQEWQELDAVQRTLYRDVMLENYRSLV 80
Cdd:cd07765     1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLV 38
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
425-697 7.41e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 65.10  E-value: 7.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 425 RKCSKAFYHNSLLSQYQTAHTTEQQSDCKELMKIYFYISSLTqHHRPHTLEKPYGCNDCMKTFSHKSQLARHQRTHTGEK 504
Cdd:COG5048   175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSS-DQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDS 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 505 PHECKECRKAFCHKSHLTRHQGIHAPEKPyeckeckksfyLRSQLTQHQrthtgekpfeCKECQKAFFRNSHLTQHQ--K 582
Cdd:COG5048   254 SSSASESPRSSLPTASSQSSSPNESDSSS-----------EKGFSLPIK----------SKQCNISFSRSSPLTRHLrsV 312

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 583 IHTGE--KPHKCKE--CGNAFARKSHLTQHQKTHTGERPYECKECR-------KAFSRKSQLMQHETTHTGERAYEC--K 649
Cdd:COG5048   313 NHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNssskfspLLNNEPPQSLQQYKDLKNDKKSETlsN 392

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958668594 650 ECRKTFYLKAYLTRHQVIHKSEKP--FECKKCGKAFSRKSYLTRHQKTHK 697
Cdd:COG5048   393 SCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKIHT 442
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
476-636 7.03e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 52.39  E-value: 7.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 476 KPYGCNDCMKTFSHKSQLARHQRT--HTGE--KPHECKE--CRKAFCHKSHLTRHQGIHAPEKPYECKEC-------KKS 542
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLnssskfsPLL 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 543 FYLRSQLTQHQRTHTGEKPFEC--KECQKAFFRNSHLTQHQKIHTGEKPH--KCKECGNAFARKSHLTQHQKTHTGERPY 618
Cdd:COG5048   368 NNEPPQSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447

                         170
                  ....*....|....*...
gi 1958668594 619 ECkECRKAFSRKSQLMQH 636
Cdd:COG5048   448 LC-SILKSFRRDLDLSNH 464
zf-H2C2_2 pfam13465
Zinc-finger double domain;
493-515 3.91e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.91e-04
                          10        20
                  ....*....|....*....|...
gi 1958668594 493 LARHQRTHTGEKPHECKECRKAF 515
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
604-629 4.57e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 4.57e-04
                          10        20
                  ....*....|....*....|....*.
gi 1958668594 604 HLTQHQKTHTGERPYECKECRKAFSR 629
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
576-601 4.85e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 4.85e-04
                          10        20
                  ....*....|....*....|....*.
gi 1958668594 576 HLTQHQKIHTGEKPHKCKECGNAFAR 601
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 674-696 6.36e-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: 6.36e-04
                          10        20
                  ....*....|....*....|...
gi 1958668594 674 FECKKCGKAFSRKSYLTRHQKTH 696
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
476-564 6.43e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 42.76  E-value: 6.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958668594 476 KPYGCNDCMKTFSHKSQLARHQRTHTGEKPHECKECrkafchkshltrhqgihapekpyeckECKKSFYLRSQLTQHQRT 555
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYS--------------------------GCDKSFSRPLELSRHLRT 85


                  ....*....
gi 1958668594 556 HTGEKPFEC 564
Cdd:COG5048    86 HHNNPSDLN 94
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
532-590 6.54e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 42.76  E-value: 6.54e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958668594 532 KPYECKECKKSFYLRSQLTQHQRTHTGEKPFEC--KECQKAFFRNSHLTQHQKIHTGEKPH 590
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSD 92
zf-H2C2_2 pfam13465
Zinc-finger double domain;
549-571 1.29e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.58  E-value: 1.29e-03
                          10        20
                  ....*....|....*....|...
gi 1958668594 549 LTQHQRTHTGEKPFECKECQKAF 571
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
560-613 1.48e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 41.61  E-value: 1.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958668594 560 KPFECKECQKAFFRNSHLTQHQKIHTGEKPHKC--KECGNAFARKSHLTQHQKTHT 613
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHH 87
 
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