krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 118918411   285 VTFDDVAVHFSEQEWGNLSEWQKELYKNVMRGNYESLVSMDYAISKPDLMSQMERGERP 343
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411    7 SPLSFPSVPQEETLRQAPAGlPRETLFQSRVLPPKEIPS-------LSPTIPRQGSLPQTSSAPKQETSGR-MPHVLQKG 78
Cdd:pfam03154 207 PPQGSPATSQPPNQTQSTAA-PHTLIQQTPTLHPQRLPSphpplqpMTQPPPPSQVSPQPLPQPSLHGQMPpMPHSLQTG 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411   79 PSLLCSAASEQETSLQGPLASQEGTQYPPPAAAEQEVSlLSHSPHHQEAPvHSPEAPEKDPLTLSPtVPETDMDPLLQSP 158
Cdd:pfam03154 286 PSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQ-RIHTPPSQSQL-QSQQPPREQPLPPAP-LSMPHIKPPPTTP 362

                  ....*..
gi 118918411  159 VSQKDTP 165
Cdd:pfam03154 363 IPQLPNP 369

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 118918411   285 VTFDDVAVHFSEQEWGNLSEWQKELYKNVMRGNYESLVSMDYAISKPDLMSQMERGERP 343
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 118918411 285 VTFDDVAVHFSEQEWGNLSEWQKELYKNVMRGNYESLVSM 324
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 118918411  708 HLLRHQRTHTGERPFKCPECEKSFS 732
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 118918411 696 CSLCGKSFSRPSHLLRHQRTHTgerpFKCPECEKSFSEKSKLTNHC-RVHSRER---PHACP 753
Cdd:cd20908    4 CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHClQVHKETLtkvPNALP 61

ISL3 family transposase;

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 118918411 742 RVHSRERPHACPECGKS--FIRKHHlleHRRIH---TGERP---------YHCAECGKRFTQK 790
Cdd:NF033550   3 EAELTRGDATCPECGKPsrRVHDTG---KRRIRhlpIFGRPvylelrvrrFKCPECGKTFTEE 62

krueppel associated box;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 118918411   285 VTFDDVAVHFSEQEWGNLSEWQKELYKNVMRGNYESLVSMDYAISKPDLMSQMERGERP 343
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 118918411 285 VTFDDVAVHFSEQEWGNLSEWQKELYKNVMRGNYESLVSM 324
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 118918411  708 HLLRHQRTHTGERPFKCPECEKSFS 732
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

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.

                          10        20
                  ....*....|....*....|...
gi 118918411  694 FICSLCGKSFSRPSHLLRHQRTH 716
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411   16 QEETLRQAPAGLPRETLFQSRVLPPKeipslSPTIPRQGSlPQTSSAPKQETSGRMPHVL-QKGPSL----LCSAASEQE 90
Cdd:pfam03154 177 QSGAASPPSPPPPGTTQAATAGPTPS-----APSVPPQGS-PATSQPPNQTQSTAAPHTLiQQTPTLhpqrLPSPHPPLQ 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411   91 TSLQGPLASQEGTQYPPPAAAEQEVSLLSHSPHHQEAPVHSPEAPEKDPLTLSPTVPETDMDPLLQSPVSQKDTPFQISS 170
Cdd:pfam03154 251 PMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPS 330

                         170
                  ....*....|....*...
gi 118918411  171 AVQ-------KEQPLPTA 181
Cdd:pfam03154 331 QSQlqsqqppREQPLPPA 348

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 118918411 693 SFICSLCGKSFSRPSHLLRHQRTHTGERPFKC--PECEKSFSEKSKLTNHCRVHS 745
Cdd:COG5048   33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHH 87

DNA translocase FtsK; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411    6 SSPLSFPSVPQEETLRQAPAGLPRETLFQSRVLPPKEIPSlsptiPRQGSLPQTSSAPKQETSGRMPHVLQKGPSLlcsA 85
Cdd:PRK10263  741 HEPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQ-----PQQPVAPQPQYQQPQQPVAPQPQYQQPQQPV---A 812

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 118918411   86 ASEQETSLQGPLASQEGTQYPPPAAAEQEVSLLSHS---PHHQEAPVHSPEA--PEKDPLTLSPT-VPETDMDPLLQSP- 158
Cdd:PRK10263  813 PQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTLLHPllmRNGDSRPLHKPTTplPSLDLLTPPPSeVEPVDTFALEQMAr 892

                         170       180
                  ....*....|....*....|....*....
gi 118918411  159 -VSQKDTPFQISSAVQKEQPLPTaeITRL 186
Cdd:PRK10263  893 lVEARLADFRIKADVVNYSPGPV--ITRF 919

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.

                          10        20
                  ....*....|....*....|...
gi 118918411  750 HACPECGKSFIRKHHLLEHRRIH 772
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

C2H2-type zinc-finger domain;

                          10        20
                  ....*....|....*....|....*
gi 118918411  636 YKCPECDSSFSHKSSLTKHQITHTG 660
Cdd:pfam13909   1 YKCSQCDYSTAWKSNLKRHLRKHTG 25

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.

                          10        20
                  ....*....|....*....|...
gi 118918411  778 YHCAECGKRFTQKHHLLEHQRAH 800
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

CpXC protein; This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 118918411  637 KCPECDSSFSHksslTKHQITHTGERP-------------YTCPECKKSFRLHISLVIHQR 684
Cdd:pfam14353   2 TCPKCGKEFEA----EVWTSINADEDPelkekvldgslfsFTCPKCGASFRLEYPLLYHDP 58

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.

                          10        20
                  ....*....|....*....|...
gi 118918411  546 FTCMECGKSFRLKINLIIHQRNH 568
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23