HHsearch alignment for GI: 254780454 and conserved domain: cd00577

>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Probab=99.03  E-value=3.3e-07  Score=62.72  Aligned_cols=205  Identities=19%  Similarity=0.275  Sum_probs=142.9

Q ss_pred             EEEEEEEECCCCCEEEEEEECCEEEEEEEEECCCCC------CCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCC-C--
Q ss_conf             011667761787348999853415766664357875------3310000010001222210277646433133455-3--
Q gi|254780454|r  157 LNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQI------AKMPSIIVPRKAVGEILRILSSKDSSVKVSLSES-R--  227 (385)
Q Consensus       157 L~Gv~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~------~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~-~--  227 (385)
T Consensus        20 ~~e~~~~~~~~G--i~i~~~D~s~v~lv~~~L~~~~F~~Y~~~~~~~~gv~~~~L~kiLk~~~~~-d~l~l~~~~~~~l~   96 (248)
T cd00577          20 VDEANFDITEDG--ISLQAMDSSHVALVSLFLPKELFEEYRCDEEISLGVNLKSLLKILKCAGNE-DCVTLRADDEDPLK   96 (248)
T ss_pred             HCCEEEEEECCE--EEEEEECCCCEEEEEEEECHHHCEEEECCCCEEEEEEHHHHHHHHHHHCCC-CEEEEEECCCCCEE
T ss_conf             581999990785--799999999779999997743190781499889999989999998642489-71899963799179


Q ss_pred             EEEECC----EEEEEEEECCCCCCCCCCCCC-CCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCC
Q ss_conf             010025----069998512665532210135-556617998489988889887410123555302565176599998078
Q gi|254780454|r  228 IHLNIE----SLSMSVRLIDGEFPNYQNVIP-CSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNP  302 (385)
Q Consensus       228 i~~~~~----~~~~~srLi~g~yPdy~~vip-~~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~  302 (385)
T Consensus        97 i~~~~~~~~~~~~~~l~l~d~~~~~~~~--p~~e~~~~i~~~s~~~~~~~~~l~~~~d----~v~i~~~~~~~~~~~~gd  170 (248)
T cd00577          97 ILFESSKGDVTSEFSLKLMDIDSEQLPI--PELEYDATVTLPSDELKDIVRDLESISD----SVTISASKDGFKFSAEGE  170 (248)
T ss_pred             EEEEECCCCEEEEEEEECCCCCCCCCCC--CCCCCCEEEEECHHHHHHHHHHHHHHCC----CEEEEEECCEEEEEEEEC
T ss_conf             9999579867999995033676446789--8766568999719999999999996099----499999399899999944


Q ss_pred             CCEEEEEEE-E-------EEECCCCEEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             732689999-9-------89628843999638899889873575334663389996589875899437765444555667
Q gi|254780454|r  303 DMGKAIESM-N-------VYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKV  374 (385)
Q Consensus       303 e~g~~~e~i-~-------~~~~G~~~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~  374 (385)
T Consensus       171 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~yL~~~~k~~~l----s~~V~i~~~~~-~Pl~l~y~~~~-------~~  237 (248)
T cd00577         171 -LGGASVTLLPKDSDLLVTIECSEPVSSTYSLKYLKDFTKAAPL----SDKVTLSFGSD-GPLSLEFKIAD-------GG  237 (248)
T ss_pred             -CCCEEEEEEECCCCEEEEEECCCCEEEEEEHHHHHHHHHHHCC----CCEEEEEECCC-CCEEEEEECCC-------CE
T ss_conf             -8857999930898606898549736899989999998625046----98799997699-77899999289-------80


Q ss_pred             CEEEEEEEE
Q ss_conf             637998321
Q gi|254780454|r  375 NAFYVLMPM  383 (385)
Q Consensus       375 ~~~~liMPv  383 (385)
T Consensus       238 ~i~f~lAP~  246 (248)
T cd00577         238 HLTFYLAPK  246 (248)
T ss_pred             EEEEEECCC
T ss_conf             999998644