HHsearch alignment for GI: 254780834 and conserved domain: TIGR01391
>TIGR01391 dnaG DNA primase; InterPro: IPR006295 DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. The C-terminal region of these proteins is poorly conserved between species. In Escherichia coli, primase (DnaG) interacts with the replicative DnaB helicase, single-stranded DNA binding protein (SSB), and DNA polymerase III holoenzyme , , , . Although DnaG is capable of synthesizing 60-nucleotide-long primers in vitro this primer length is restrained to 11 (±1) nucleotides in the context of the replisome . Members of this entry are homologs of DnaG and have been identified in all prokaryotes, as well as in several bacteriophage. On the basis of sequence analysis, these proteins appear structurally distinct from primases known to act in archaeal, eukaryotic replication or to either of the two subunits, p50 and p60, of the heterodimeric eukaryotic DNA primase (IPR002755 from INTERPRO). DnaG has been shown by proteolysis to comprise three structural domains: a 12-kD NH2-terminal Zn2+-binding domain (ZBD), a 36-kD core domain containing the polymerase region, and a 15-kD COOH-terminal DnaB-interaction domain (DnaB-ID) , .; GO: 0003896 DNA primase activity, 0006269 DNA replication synthesis of RNA primer.
Probab=100.00 E-value=0 Score=702.79 Aligned_cols=413 Identities=44% Similarity=0.749 Sum_probs=391.3
Q ss_pred CCCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHC
Q ss_conf 87888999998748888875412221015887777755753458888587879817897467136888878989989885
Q gi|254780834|r 2 NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALL 81 (648)
Q Consensus 2 ~i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~ 81 (648)
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~-----~~~~cPfh~~~~ps~~~~~~~~~~~cfgc~~~G~~~~f~~~~~ 75 (424)
T TIGR01391 1 RIPEEVIDELKERVDIVDLVSEYVKLKKKGKN-----YVGLCPFHHEKTPSFSVSPEKGFYHCFGCGAGGDAIKFLMEIE 75 (424)
T ss_pred CCCHHHHHHHHHHCCHHHHHHHHHHHHCCCCC-----CEEECCCCCCCCCCEEEECCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf 97467899998620057776544311004774-----0453365455676224301335355530466660577777761
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCHHH------HHHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHCCCCHHHH
Q ss_conf 9997999999999818858776820367------778899999999999999999732677-757899998506885351
Q gi|254780834|r 82 GCSFIESVQRLAAIAGVPLPVVDPKIEK------KEKIQTDLIRLIEVATDFFHHSLKNAR-DKRLHYYLDERGIDSHAI 154 (648)
Q Consensus 82 ~~~f~ea~~~la~~~gi~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~a~~yl~~Rg~~~~~~ 154 (648)
T Consensus 76 ~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~yl~~rg~~~~~~ 154 (424)
T TIGR01391 76 GLSFVEAVKELAKRAGLDLPLEK-ESEKSPDKAEEKSERKELLELLELAAEFFKNELKNTPEGNRALDYLLSRGLSDETI 154 (424)
T ss_pred CCCHHHHHHHHHHHHCCCCCHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHH
T ss_conf 57678999999987377321000-22210233343335678999999999999987520101468899998628888789
Q ss_pred CCCCCCCCCCCCCHHHHHHHCC-CCCHHHHHHHCCCEECCCC-CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCE
Q ss_conf 0124422567741034554205-9973452320121003465-4100001671688897077858885010014655300
Q gi|254780834|r 155 EMFKLGYAPDSRYSLREHLRQK-GFSEEKIIEAGLLIDGDNS-ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVK 232 (648)
Q Consensus 155 ~~f~lG~ap~~~~~l~~~l~~~-~~~~~~~~~~gl~~~~~~~-~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~K 232 (648)
T Consensus 155 ~~f~~G~~p~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~f~~r~~~p~~~~~g~~~~fggr~~~-~~~~k 233 (424)
T TIGR01391 155 SRFGLGYAPDNWDFLLDFLENKKGFDLELLLEAGLLVKKENGDQKYYDRFRNRIIFPIHDPKGKVVGFGGRALG-DEKPK 233 (424)
T ss_pred HHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHCCCCEECCCCCCHHHHHHHCEEEEEEECCCCCEEEECCCCCC-CCCCC
T ss_conf 87403677552467888763201555567865033000145541023222220254433367865540430015-66663
Q ss_pred ECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHH
Q ss_conf 10387676535210110817888864331000023567870899714388999874355421134321366267898851
Q gi|254780834|r 233 YLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWK 312 (648)
Q Consensus 233 YlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r 312 (648)
T Consensus 234 y~n~p~~~~~~k~~~l~~~~~~~~~~~~----------~~~~~~~eG~~d~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~ 303 (424)
T TIGR01391 234 YLNSPETPLFKKGELLYGLDKARKEIRK----------EKELLLVEGYMDVIALHQAGIKNAVASLGTALTEEHLKLLKR 303 (424)
T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHHHC----------CCEEEEECCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 1156533000010356546677776512----------660688602567788765055402444312201789999863
Q ss_pred CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHH-CCCHHHHHHHHHHH
Q ss_conf 26818996178866225777888888777536973067525788888899720366889988641-49927999999985
Q gi|254780834|r 313 LSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVE-SLPLVDMLWKRETE 391 (648)
Q Consensus 313 ~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~-A~~l~dFl~~~l~~ 391 (648)
T Consensus 304 ~~~~~~~~~dgd~aG~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~dpd~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 383 (424)
T TIGR01391 304 YADEIILCFDGDSAGLKAALRALELLLPLGKDGISVKVVLLPGGKDPDELLRKEGAEALKKLLENGSLPLIEFLLEYLLS 383 (424)
T ss_pred CCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 25727898557412378899999987641256622789865777887999862047889999741664079999998730
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 3023314579999999998854179989999999999999
Q gi|254780834|r 392 NRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDR 431 (648)
Q Consensus 392 ~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~ 431 (648)
T Consensus 384 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 423 (424)
T TIGR01391 384 GYNLDSPEEKAKLLEELLPLLKKLPDPLLRDSYLQKLAEL 423 (424)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf 1355435689999999988875202157899999998750