HHsearch alignment for GI: 254780847 and conserved domain: TIGR01663
>TIGR01663 PNK-3'Pase polynucleotide kinase 3'-phosphatase; InterPro: IPR006550 These sequences represent the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3'-phosphates is essential for the further processing of the break by DNA polymerases , . The central phosphatase domain is a member of the IIIA subfamily (IPR006549 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by IPR006551 from INTERPRO. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. .
Probab=94.01 E-value=0.047 Score=33.74 Aligned_cols=92 Identities=26% Similarity=0.334 Sum_probs=58.4
Q ss_pred CEEEEECCCEEEE------------CC-CCCCCHHHHHHHHHHCCCCEEEECCC-----CC-CHHHHHHH----HHHCCC
Q ss_conf 9999927443231------------88-14862799999999879819998598-----99-95899998----751277
Q gi|254780847|r 16 DVILCDVWGVLHN------------GQ-KFLPGTIPALKEARENGLKVILFTNS-----PR-PSASVISQ----IQSLGS 72 (282)
Q Consensus 16 d~~lfD~DGvL~~------------g~-~~ipgA~e~l~~L~~~g~~~~~lTN~-----s~-~~~~~~~~----L~~lG~ 72 (282)
T Consensus 169 K~AGyDlDGT~I~T~SG~VFP~~~~DW~I~yPE~P~KL~~L~~~GyK~~~FTNQ~~I~RGK~~~~~FK~K~~~~V~KLGV 248 (526)
T TIGR01663 169 KVAGYDLDGTLIKTKSGKVFPKNTDDWRILYPEVPRKLKELEKDGYKLVLFTNQGSIARGKLNLDDFKVKVKAVVEKLGV 248 (526)
T ss_pred CEEEEECCCCEEECCCCEECCCCCCCCEEECCCCCHHHHHHHHCCCEEEEEECCCCEECCCCCHHHHHHHHHHHHHHCCC
T ss_conf 34424257736731343020688886578456544578887418827999845773001555656766688888986189
Q ss_pred CCHHCCCCCCHH------HHHHHHHHHHC--------CCCCCCCCCCHHH
Q ss_conf 700001356879------99999998531--------6545438725212
Q gi|254780847|r 73 SSQFWDDIITSG------DLTHHLLVEES--------HNIFFIGPQRDYA 108 (282)
Q Consensus 73 ~~~~~d~I~ts~------~~~~~~l~~~~--------~~v~viG~~~~~~ 108 (282)
T Consensus 249 P~QVl-~A~~~GlYRKP~TGMW~HL~~~~NDG~~I~~~~~~FVGDAAGRP 297 (526)
T TIGR01663 249 PIQVL-VAIGDGLYRKPLTGMWDHLKEEANDGVEISIDDSIFVGDAAGRP 297 (526)
T ss_pred CEEEE-EECCCCCCCCCCCHHHHHHHHHCCCCCEEECCCEEEECCCCCCC
T ss_conf 76887-65068720277520478988753688123117757871667888