RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972434   30 WSVNICGKKKWLFFPPGEEEALRDCHGNLPYDVTSTEL--LDTHLYPKI--QHHSLPIEVIQEPGEMVFVPSGWHHQVYN 105
Cdd:pfam02373  24 NYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLlhLNTIISPKQlrENGIPVYRFVQKPGEFVFTFPGWYHQVFN 103

                          90
                  ....*....|.
gi 568972434  106 LDDTISINHNW 116
Cdd:pfam02373 104 LGFNIAEAVNF 114

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972434   30 WSVNICGKKKWLFFPPGEEEALRDCHGNLPYDVTSTEL--LDTHLYPKI--QHHSLPIEVIQEPGEMVFVPSGWHHQVYN 105
Cdd:pfam02373  24 NYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLlhLNTIISPKQlrENGIPVYRFVQKPGEFVFTFPGWYHQVFN 103

                          90
                  ....*....|.
gi 568972434  106 LDDTISINHNW 116
Cdd:pfam02373 104 LGFNIAEAVNF 114

nucleotide-binding domain (NBD) of the actin-related protein 8 (Arp8)-like subfamily; The Arp8-like family includes Arp8, also called actin-like protein 8, from vertebrates and fungi. Human Arp8 is encoded by the ACTR8 gene and is also known as INO80 complex subunit N. It plays an important role in the functional organization of mitotic chromosomes. Arp8 exhibits low basal ATPase activity, and is unable to polymerize. It is probably a core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication, and probably DNA repair. it is required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage. Arp8 strongly prefers nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting it may act as a nucleosome recognition module within the complex. This subfamily also contains Arabidopsis thaliana Arp9.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972434  20 GAPDIFRSFSWSVNICGkkkwlfFPPgeeealRDCHGNLPYDvtsTELLDtHLYPKIQHHSLPIEVIQEPGEMVFVPSG- 98
Cdd:cd10206  266 GGDDITRCFLWLLRRSG------FPY------RECNLNSPLD---FLLLE-RLKETYCTLDQDDIGVQLHEFYVREPGQp 329

                         90       100
                 ....*....|....*....|..
gi 568972434  99 ---WHHQVYNLDDTI--SINHN 115
Cdd:cd10206  330 tlkYQFKLLPLDEAIvqSILSC 351

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972434   30 WSVNICGKKKWLFFPPGEEEALRDCHGNLPYDVTSTEL--LDTHLYPKI--QHHSLPIEVIQEPGEMVFVPSGWHHQVYN 105
Cdd:pfam02373  24 NYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLlhLNTIISPKQlrENGIPVYRFVQKPGEFVFTFPGWYHQVFN 103

                          90
                  ....*....|.
gi 568972434  106 LDDTISINHNW 116
Cdd:pfam02373 104 LGFNIAEAVNF 114

Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];

                         10        20
                 ....*....|....*....|....*.
gi 568972434  84 EVIQEPGEMVFVPSGWHHQVYNLDDT 109
Cdd:COG4101   89 RVVTEPGDFIFIPPGVPHQEINLSDT 114