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