HHsearch alignment for GI: 255764477 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=96.20  E-value=0.0044  Score=39.77  Aligned_cols=35  Identities=23%  Similarity=0.427  Sum_probs=29.4

Q ss_pred             EEEEECCCCCCHHHHHH-HHHHCCCEEEEHHHHHHH
Q ss_conf             99988886667899999-999779869990499999
Q gi|255764477|r    3 IIGLTGSIGTGKTTVAE-FLKKEKIPVISSDDIVDK   37 (199)
Q Consensus         3 iIgitG~igSGKStv~~-~l~~~G~~v~~aD~i~~~   37 (199)
T Consensus       371 ~V~~VGlPG~GKS~F~~~~l~~~GY~~VN~DTLGS~  406 (526)
T TIGR01663       371 VVVAVGLPGAGKSTFLKKFLVSAGYKIVNADTLGST  406 (526)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCCCEEECCCCCCCH
T ss_conf             899843899857788885403578558715456722