HHsearch alignment for GI: 254780288 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=100.00  E-value=0  Score=589.09  Aligned_cols=258  Identities=35%  Similarity=0.631  Sum_probs=250.9

Q ss_pred             CEEEEEEECCHHHHHHHH--HHHHHHHCCCEEEEEEEECCHHHCCHHHHHHCCCEEEEEEC--CCCCCEEEEEEECCEE-
Q ss_conf             079987103188889989--99998728988999856579445897787328978999304--7765148987403137-
Q gi|254780288|r    4 VTVATWNVNSIRARIHNL--AAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQ--KSYNGVAILSKYQPIE-   78 (281)
Q Consensus         4 lrI~TwNinglr~r~~~l--~~~l~~~~pDIi~LQEvk~~~~~~~~~~~~~~gy~~~~~~~--k~~~GvaIlsk~~~~~-   78 (281)
T Consensus         1 mK~iSwNVNGlRAr~~~~dFl~~~~~~~pDilClQEtKv~~e~~P~~~~~~~GYh~f~~~~~~KGy~GVA~~sk~EP~~d   80 (281)
T TIGR00195         1 MKLISWNVNGLRARLHKGDFLDWLKENKPDILCLQETKVADEQFPRELFEEEGYHVFFSGAKKKGYSGVAIFSKEEPLSD   80 (281)
T ss_pred             CCEEEECCCHHHHHCCHHHHHHHHCCCCCCEEECCCCCCCCCCCCHHHHHHCCCEEEECCCEEECCCCEEEEECCCCHHH
T ss_conf             95578602235533004358888423899587320101456677878997649817873642336430799862688588


Q ss_pred             EEECCCCCCC-------CCCCCEECCCCCCCCCEEEEEEEECCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH-HH
Q ss_conf             8632555644-------3233010110002320799963104667-8544310123677776553322232014760-00
Q gi|254780288|r   79 IVTHLPGDDL-------DVQARFIEATFTINTQTLRIGNLYLPHG-NPITSTKYDDKISWIKRFLRFASQRLELEEP-LI  149 (281)
Q Consensus        79 v~~~~~~~~~-------d~~~R~i~~~i~~~~~~i~v~n~y~P~g-~~~~~~~~~~k~~~~~~l~~~l~~~~~~~~~-vI  149 (281)
T Consensus        81 V~~G~~~e~~PaltGdlD~e~R~I~a~~~~~~G~~Tv~N~Y~PnGES~~~~~k~~YKl~w~~~l~~yl~~~~~~~~p~v~  160 (281)
T TIGR00195        81 VRYGFGVEEEPALTGDLDAEGRVITAEFDGFLGLLTVVNGYFPNGESRLDSEKLPYKLQWLEALQNYLEKLRDKDKPEVI  160 (281)
T ss_pred             HHCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             60367887765332761216717999757830248999866559843001455788999999999999998636898899


Q ss_pred             HHHHCCCCCCCCCCHHHHHCCC---CCC---CCHHHHHHHHHCCCCC-HHHHCCCCCCC-CCCEECCCCCCC-CCCCCCC
Q ss_conf             0110146867420000121048---734---4634556532103310-00000133788-872003578767-5255777
Q gi|254780288|r  150 FAGDYNIIPQPHDCYNPIIWEN---DAC---FTLEVRQSFQKLQNMG-FTDAIRATHDT-HHLYSFWDYYAD-SWSKNKG  220 (281)
Q Consensus       150 i~GDFN~a~~~~D~~~~~~~~~---~~~---~~~~er~~~~~l~~~g-l~D~~r~~~~~-~~~yT~~~~~~~-~~~~n~G  220 (281)
T Consensus       161 ~CGD~NiAp~eiDl~~P~~nrnRWL~~GKCSF~~~ER~~~~~~l~~Gn~vDtFR~~~p~~~~~YtWwdYR~~Ga~drN~G  240 (281)
T TIGR00195       161 ICGDFNIAPEEIDLHSPDENRNRWLHAGKCSFLPEEREWLDRLLEAGNFVDTFRKFNPDKEGAYTWWDYRTRGARDRNRG  240 (281)
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCEEECCCCCCCCCCCH
T ss_conf             97677889861356788511133133332138889999999998600613320000568889400331133685024622


Q ss_pred             CEEEEEEECHHHHHHHHCEEEECHHHCCCCCCCCCCEEEEE
Q ss_conf             13569994778983332028712220686767622199999
Q gi|254780288|r  221 IRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSL  261 (281)
Q Consensus       221 ~RID~il~s~~l~~~v~~~~I~~~~~~~~~~SDH~Pv~~~l  261 (281)
T Consensus       241 WRID~~l~s~~L~~~~~~~~I~~d~rg~EKPSDH~Pv~l~~  281 (281)
T TIGR00195       241 WRIDYFLVSEPLKERCVDCLIDKDVRGSEKPSDHCPVVLEI  281 (281)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEC
T ss_conf             43355330848988898764121300168888756526658