HHsearch alignment for GI: 254780129 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=99.91 E-value=1.4e-25 Score=166.10 Aligned_cols=160 Identities=20% Similarity=0.326 Sum_probs=132.2
Q ss_pred CCCCCHHHHHHHH-HHHHCCC---CEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 8713489999999-9996798---19996899988999999999997408994899723310137889999851553460
Q gi|254780129|r 2 HLVLKPHQIVMVN-WLLSHDR---CALWASMGSGKTVSVLFALSTIKILDPRPVLIIAPLRVAQYVWKDEVERWSAFSDM 77 (220)
Q Consensus 2 ~~~Lrp~Q~~a~~-~~~~~~~---~~l~~~~G~GKT~~ai~~~~~~~~~~~~~~LIi~P~s~~~~~W~~e~~~~~~~~~~ 77 (220)
T Consensus 267 ~t~~RPYQEKSLrsKMFGNGRARSGiIVLPCGAGKsLVGvTAACTvk----Ks~lVLctS~VSV~QW~~QFk~WSti~d~ 342 (756)
T TIGR00603 267 TTVLRPYQEKSLRSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVK----KSVLVLCTSAVSVEQWKQQFKLWSTIDDS 342 (756)
T ss_pred CCCCCCCHHHHCCCCCCCCCCCCCCCEECCCCCCCCHHHHHHHEEEE----EEEEEEECCCHHHHHHHHHHHHCCCCCCC
T ss_conf 77889751110444566786110551776778883112254420231----00789726710088999887522688735
Q ss_pred EEEEEECCCCCCCCCCCCCCCEEEECHHHHHCCC---------CCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 6998611210112234567662786566731000---------0000024720000251220136543320369999999
Q gi|254780129|r 78 TVSSLIGSERQRIKALNTPAHLYIINFENIPWLV---------KMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGK 148 (220)
Q Consensus 78 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~---------~~~~~~~~~~~iIiDEaH~~kn~~~~~~~k~~k~l~~ 148 (220)
T Consensus 343 ~IcrFTSD~Ke~~---~~~~gv~vsTYsMva~t~kRS~es~k~m~~l~~rEWGl~~LDEVHvv-------PA~mFRrVlt 412 (756)
T TIGR00603 343 QICRFTSDAKEKF---HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVV-------PAAMFRRVLT 412 (756)
T ss_pred CCCCCCCCCCCCC---CCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCC-------CCCCCCCHHH
T ss_conf 5110252135762---66533588733000247543188999999970687317986110103-------5001660101
Q ss_pred HHHCCCCEEEEECCCCCCC--CHHHHHHHHHHH-CC
Q ss_conf 8513798799831653248--889999999982-88
Q gi|254780129|r 149 VAFSKVKRFIELTGTPSPN--GLIDLWGQIWFL-DK 181 (220)
Q Consensus 149 ~~~~~~~~~l~LTgTPi~n--~~~el~~ll~~l-~p 181 (220)
T Consensus 413 ~~~aHcK--LGLTATLvREDdKI~D----LNFLIGP 442 (756)
T TIGR00603 413 IVQAHCK--LGLTATLVREDDKIQD----LNFLIGP 442 (756)
T ss_pred HHHHHHC--CCCCEEEECCCCCCCC----CCCCCCC
T ss_conf 4433200--1432110011143031----2213572