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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5729790  366 LKRHIRS--HTGE--RPFQC--SLCSYASRDTYKLKRHMRTHSGEKPYECYI--CHARFTQSGTMK---MHILQKHTENV 434
Cdd:COG5048 305 LTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLNNEppqSLQQYKDLKND 384

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5729790  435 AKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGK--KCRYCDAVFHERYALIQHQKSHKNEKRFKCDQC 500
Cdd:COG5048 385 KKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSIL 452

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 5729790    509 HMIMHKRTHTGEKPYACSHCDKTFRQ 534
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

C2H2-type zinc-finger domain;

                          10        20
                  ....*....|....*....|....*
gi 5729790    351 FKCSMCDYASVEVSKLKRHIRSHTG 375
Cdd:pfam13909   1 YKCSQCDYSTAWKSNLKRHLRKHTG 25

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5729790  366 LKRHIRS--HTGE--RPFQC--SLCSYASRDTYKLKRHMRTHSGEKPYECYI--CHARFTQSGTMK---MHILQKHTENV 434
Cdd:COG5048 305 LTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLNNEppqSLQQYKDLKND 384

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5729790  435 AKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGK--KCRYCDAVFHERYALIQHQKSHKNEKRFKCDQC 500
Cdd:COG5048 385 KKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSIL 452

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 5729790    280 NLDRHMKSHTDERPHKCHLCGRAFRT 305
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

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
                ....*....|....*....|....*....|...
gi 5729790  468 KCRYCDAVFHERYALIQHQKShkneKRFKCDQC 500
Cdd:cd20908   3 WCYYCDREFDDEKILIQHQKA----KHFKCHIC 31

C2H2-type zinc-finger domain;

                          10        20
                  ....*....|....*....|....*
gi 5729790    351 FKCSMCDYASVEVSKLKRHIRSHTG 375
Cdd:pfam13909   1 YKCSQCDYSTAWKSNLKRHLRKHTG 25

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5729790  366 LKRHIRS--HTGE--RPFQC--SLCSYASRDTYKLKRHMRTHSGEKPYECYI--CHARFTQSGTMK---MHILQKHTENV 434
Cdd:COG5048 305 LTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLNNEppqSLQQYKDLKND 384

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5729790  435 AKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGK--KCRYCDAVFHERYALIQHQKSHKNEKRFKCDQC 500
Cdd:COG5048 385 KKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSIL 452

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*.
gi 5729790    280 NLDRHMKSHTDERPHKCHLCGRAFRT 305
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26

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
                ....*....|....*....|....*....|...
gi 5729790  468 KCRYCDAVFHERYALIQHQKShkneKRFKCDQC 500
Cdd:cd20908   3 WCYYCDREFDDEKILIQHQKA----KHFKCHIC 31

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|..
gi 5729790    366 LKRHIRSHTGERPFQCSLCSYA 387
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKS 23

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 5729790    309 LRNHLNTHTGTRPHKCPDCDMAFVT 333
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26

Bacterial Peptidase A24 N-terminal domain; This family is found at the N-terminus of the pre-pilin peptidases (pfam01478). It's function has not been specifically determined; however some of the family have been characterized as bifunctional, and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in, but their role was incorrectly ascribed.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 5729790    438 HCPHCDTVIaRKSDLGVHLrkqhSYIEQGKKCRYCDAVFHERYALI 483
Cdd:pfam06750  29 HCPSCGHRL-RWYDNIPVL----SWLLLRGRCRYCGAKISIRYPLV 69

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 5729790  265 TFQCELCSYTcPRRSNLDRHMKSHTDERPHKCHLCGRAFRTvtllrnhlnthtgtrPHKCPDC---DMAFVTSG 335
Cdd:cd18804  45 SVLCRDCGYV-PECPNCDVSMTYHKSTNKLKCHYCGYQEPI---------------PKQCPECgseDLVFKGIG 102