HHsearch alignment for GI: 254780130 and conserved domain: TIGR00603
>TIGR00603 rad25 DNA repair helicase rad25; InterPro: IPR001161 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XP group B (XP-B) give rise to both XP and Cockayne syndrome . The DNA/RNA helicase domain IPR001650 from INTERPRO is also present in this group of proteins.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=98.46 E-value=3.6e-07 Score=59.22 Aligned_cols=125 Identities=19% Similarity=0.291 Sum_probs=93.4
Q ss_pred CHHHHHHHHHHHH--HC-CCCCEEEHHHHHHH----HHHHHHHHHCC-CCHHHHHHHHHHHH-CCCCCEEEECHHHHHHH
Q ss_conf 7234334999986--14-89971105789999----99987653047-78234899999972-78986999721443233
Q gi|254780130|r 52 HDEKIKALEVIIE--KA-NAAPIIVAYHFNSD----LARLQKAFPQG-RTLDKDPCTIQEWN-EGKIPLLFAHPASCGHG 122 (205)
Q Consensus 52 ~~~Kl~~l~~ii~--~~-~~~kviVf~~f~~~----l~~l~~~~~~~-~~~~~r~~~i~~f~-~~~~~Vll~~~~a~g~G 122 (205)
T Consensus 494 NP~KFrACqFLI~fHE~~RgDKIIVFsDNVfAL~~YA~kl~KpfIYGpTsq~ER~~IL~nF~~n~~vnTIF~S-KVGDtS 572 (756)
T TIGR00603 494 NPNKFRACQFLIRFHERQRGDKIIVFSDNVFALKEYAIKLGKPFIYGPTSQQERMQILQNFKHNPKVNTIFLS-KVGDTS 572 (756)
T ss_pred CCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHCCCCEEECCCCHHHHHHHHHHCCCCCCCCEEEEE-EECCCC
T ss_conf 8644357789888854148885899424478999999873896540798713799998621558864568984-302775
Q ss_pred HHHHHHCCEEEEECCCCCHHHHH-HHHHHHHHHHHHCCC------CCCCEEEEEEEECCCHHH
Q ss_conf 22432067589726899988802-255557666542026------577539999983889589
Q gi|254780130|r 123 LNLQYGGNILVFFSLWWDLEEHQ-QMIERIGVTRQRQAG------FKRAVFVYYLIAQNTIDE 178 (205)
Q Consensus 123 lnL~~a~~~vI~~~~~~n~~~~~-Qa~~Ri~~~r~hR~G------Q~~~v~v~~l~~~~tiEe 178 (205)
T Consensus 573 iDlPE-AnvlIQiSSH~GSRRQEAQRLGRILRAK~~~~~r~aggkE~YNAFFYSLVS~DTqEm 634 (756)
T TIGR00603 573 IDLPE-ANVLIQISSHYGSRRQEAQRLGRILRAKKKSDARMAGGKEEYNAFFYSLVSKDTQEM 634 (756)
T ss_pred CCCCC-CCEEEEEEECCCCHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCEEEEECCCCCCEEE
T ss_conf 14221-426776532677403687641320167875133313776442201210134451465