RPSBLAST alignment for GI: 254781076 and conserved domain: cd07181
>gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with two other accessory proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. Length = 216
Score = 70.7 bits (174), Expect = 3e-13
Identities = 57/188 (30%), Positives = 79/188 (42%), Gaps = 40/188 (21%)
Query: 28 GIDEVGRGALAGPVVVAAIILDPNN----IPFGINDSKKISHKKREELYEKITSSA---- 79
GIDE GRG + GP+V + G DSK ++ +KREEL++KI +
Sbjct: 2 GIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALG 61
Query: 80 -IISISSASHQYIDKH--NIHKATLDAIYH--AVENLQVIPRSALIDGRSIPE---DL-- 129
I S QYI K L+ I H A+ + +S L G ++ E D
Sbjct: 62 WATRILSP--QYISAKMLARTKYNLNEISHDAAIG----LIKSVLDKGVNVTEVYVDTVG 115
Query: 130 -------------PCQAFAVI-KGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDS 175
P F V K DS+ ++AASI+AKVTRDR ++ D
Sbjct: 116 PPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRALKNWQFDEYLIDPDG 175
Query: 176 HV--GYPT 181
GYP+
Sbjct: 176 DFGSGYPS 183