HHsearch alignment for GI: 254780995 and conserved domain: TIGR00195
>TIGR00195 exoDNase_III exodeoxyribonuclease III; InterPro: IPR000097 DNA damaging agents such as the antitumor drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity. This family contains members of AP endonuclease family 1. Except for Rrp1 and arp, these enzymes are proteins of about 300 amino-acid residues. Rrp1 and arp both contain additional and unrelated sequences in their N-terminal section (about 400 residues for Rrp1 and 270 for arp). The proteins contain glutamate which has been shown , in the Escherichia coli enzyme to bind a divalent metal ion such as magnesium or manganese.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005622 intracellular.
Probab=99.83 E-value=3.4e-21 Score=133.51 Aligned_cols=111 Identities=19% Similarity=0.220 Sum_probs=87.1
Q ss_pred HHHHHHHHHHHHCCCCC-EEEEEECCCCCCCCCCCCHH---------------------HHHCCCCC----CCHHHCCC-
Q ss_conf 99999999985116998-89996147776883100278---------------------76326554----10000257-
Q gi|254780995|r 6 GEWLKKWADQKIKTGIP-FVIAGDFNRKINSIGDTDDF---------------------WQKMDPDG----LLIRFPQE- 58 (125)
Q Consensus 6 ~~~L~~~i~~~~~~~~p-vIi~GDFN~~~~~~~~~~~~---------------------~~~l~~~~----~~~~~~~~- 58 (125)
T Consensus 141 ~~~l~~yl~~~~~~~~p~v~~CGD~NiAp~eiDl~~P~~nrnRWL~~GKCSF~~~ER~~~~~~l~~Gn~vDtFR~~~p~~ 220 (281)
T TIGR00195 141 LEALQNYLEKLRDKDKPEVIICGDFNIAPEEIDLHSPDENRNRWLHAGKCSFLPEEREWLDRLLEAGNFVDTFRKFNPDK 220 (281)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCC
T ss_conf 99999999998636898899976778898613567885111331333321388899999999986006133200005688
Q ss_pred CCCCCCCCCCCC-CCCCCCCCCCHHHHCCCCCCC--EEEEECCCCCCCCCCCCCCCCCEEEEE
Q ss_conf 676871038875-543335521012100257321--154302474112586788756499999
Q gi|254780995|r 59 KESTCNVIKRNK-SSLDYFVIDRDNKNFLIDNSF--SIVSYDQSDLDTRRSKLSTHCPLTIEY 118 (125)
Q Consensus 59 ~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~SDH~PV~~~l 118 (125)
T Consensus 221 ~~~YtWwdYR~~Ga~drN~--GWRID~~l~s~~L~~~~~~~~I~~d~rg~EKPSDH~Pv~l~~ 281 (281)
T TIGR00195 221 EGAYTWWDYRTRGARDRNR--GWRIDYFLVSEPLKERCVDCLIDKDVRGSEKPSDHCPVVLEI 281 (281)
T ss_pred CCCCCEEECCCCCCCCCCC--HHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEC
T ss_conf 8940033113368502462--243355330848988898764121300168888756526658