254781190

 Score =  292 bits (748), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 132/233 (56%), Positives = 169/233 (72%)

Query: 1   MVATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAP 60
           + +  +D     GFG +CG+G  P+YAFD+D  DE+  + F + F+   G PI R+GQ P
Sbjct: 41  LSSEKIDKLPACGFGFVCGVGEQPLYAFDIDSKDEKTANTFKDTFEILHGTPIVRIGQKP 100

Query: 61  KTLMLFRMQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVE 120
           K L+ FRM +  +KK+K+ E  QGHL+ L  GQ FVAYNIHPKT++ YTW+  PH  KVE
Sbjct: 101 KILIPFRMNKEGIKKKKTTESTQGHLDILGCGQYFVAYNIHPKTKKEYTWTTPPHRFKVE 160

Query: 121 ELPLLTPDEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGEE 180
           + PLL+ ++VEY F+FF  IT P  K+K     SK W ++NNR+YTN EI AFLSCFGEE
Sbjct: 161 DTPLLSEEDVEYLFKFFQEITVPLVKDKKSIIPSKTWTNNNNRQYTNREITAFLSCFGEE 220

Query: 181 FYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           FYNGSHDEWIPVVMA+H+ETRGS++GKEI R W K G TYDE++FN KWD+FD
Sbjct: 221 FYNGSHDEWIPVVMAVHHETRGSSKGKEIARRWSKQGSTYDEENFNYKWDTFD 273

Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  292 bits (747), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 132/233 (56%), Positives = 169/233 (72%)

Query: 1   MVATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAP 60
           + +  +D     GFG +CG+G  P+YAFD+D  DE+  + F + F+   G PI R+GQ P
Sbjct: 41  LSSEKIDKLPACGFGFVCGVGEQPLYAFDIDSKDEKTANTFKDTFEILHGTPIVRIGQKP 100

Query: 61  KTLMLFRMQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVE 120
           K L+ FRM +  +KK+K+ E  QGHL+ L  GQ FVAYNIHPKT++ YTW+  PH  KVE
Sbjct: 101 KILIPFRMNKEGIKKKKTTESTQGHLDILGCGQYFVAYNIHPKTKKEYTWTTPPHRFKVE 160

Query: 121 ELPLLTPDEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGEE 180
           + PLL+ ++VEY F+FF  IT P  K+K     SK W ++NNR+YTN EI AFLSCFGEE
Sbjct: 161 DTPLLSEEDVEYLFKFFQEITVPLVKDKKSIIPSKTWTNNNNRQYTNREITAFLSCFGEE 220

Query: 181 FYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           FYNGSHDEWIPVVMA+H+ETRGS++GKEI R W K G TYDE++FN KWD+FD
Sbjct: 221 FYNGSHDEWIPVVMAVHHETRGSSKGKEIARRWSKQGSTYDEENFNYKWDTFD 273

Species: Liberibacter phage SC1
Genus: 
Family: Podoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses

 Score =  256 bits (654), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/233 (53%), Positives = 164/233 (70%)

Query: 1   MVATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAP 60
           + + ++D     GFG++CG+G  P+YAFD+D  DE+  + F + F+   G PI R+GQ P
Sbjct: 41  LSSEEIDKLPACGFGLVCGVGEQPLYAFDIDSKDEKTTNNFKDTFEILHGTPIVRIGQKP 100

Query: 61  KTLMLFRMQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVE 120
           K L+ FRM +  +KK+K+ E  QGHL+ L YGQ FVAYNIHP T+  YTW+  PH  K E
Sbjct: 101 KILIPFRMDKDGVKKKKTPESPQGHLDILGYGQYFVAYNIHPITKEEYTWTTPPHRFKAE 160

Query: 121 ELPLLTPDEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGEE 180
           +LPLL+ ++VE F + F   TTP  K K   K  K+ K++NNR YTN EI AFLSCF E+
Sbjct: 161 DLPLLSKEDVECFSKAFQDFTTPLVKAKKSIKPVKLGKNNNNRYYTNREITAFLSCFNED 220

Query: 181 FYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           FYNGSHD+WIPV+MA+H+ETRGS +G++I R W K G TYDE +FN KWD+FD
Sbjct: 221 FYNGSHDDWIPVIMAVHHETRGSDKGQDIARRWSKQGSTYDEANFNYKWDTFD 273

Species: Liberibacter phage SC2
Genus: 
Family: Podoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 98/166 (59%), Positives = 120/166 (72%)

Query: 68  MQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVEELPLLTP 127
           M +  +KK+++ +  QGHL+ L  GQ FVAYNIHPKT+  YTW+  P A K EELPLL+ 
Sbjct: 1   MAKAGIKKKQTPKSQQGHLDILGGGQYFVAYNIHPKTKEEYTWTTPPDAFKAEELPLLSE 60

Query: 128 DEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGEEFYNGSHD 187
           ++VE+ FEFF   TTP  K K   K  K   +  NRRYTN EI AFLSCFGEEF NG+HD
Sbjct: 61  EDVEHLFEFFKESTTPVVKAKKEIKSPKEGNTKGNRRYTNREITAFLSCFGEEFTNGTHD 120

Query: 188 EWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           EWIPVVMAIH+ET+GS EGKE+ R W K G +YDE++FN KW +FD
Sbjct: 121 EWIPVVMAIHHETQGSHEGKELARRWSKRGSSYDEENFNYKWSTFD 166

Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  206 bits (523), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 98/166 (59%), Positives = 120/166 (72%)

Query: 68  MQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVEELPLLTP 127
           M +  +KK+++ +  QGHL+ L  GQ FVAYNIHPKT+  YTW+  P A K EELPLL+ 
Sbjct: 1   MAKAGIKKKQTPKSQQGHLDILGGGQYFVAYNIHPKTKEEYTWTTPPDAFKAEELPLLSE 60

Query: 128 DEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGEEFYNGSHD 187
           ++VE+ FEFF   TTP  K K   K  K   +  NRRYTN EI AFLSCFGEEF NG+HD
Sbjct: 61  EDVEHLFEFFKESTTPVVKAKKEIKSPKEGNTKGNRRYTNREITAFLSCFGEEFTNGTHD 120

Query: 188 EWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           EWIPVVMAIH+ET+GS EGKE+ R W K G +YDE++FN KW +FD
Sbjct: 121 EWIPVVMAIHHETQGSHEGKELARRWSKRGSSYDEENFNYKWSTFD 166

Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score =  111 bits (278), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 78/250 (31%), Positives = 110/250 (44%), Gaps = 24/250 (9%)

Query: 3   ATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAPKT 62
           A D+  Y  +G G+LCG G  PV A DVD  D ++  RF    Q   G    RVG APK 
Sbjct: 41  AADLTRYPEHGVGVLCGQGAQPVVAIDVDTTDAELAARFVAWCQEHLGATCERVGNAPKI 100

Query: 63  LMLFRMQETNLKKQKSE--EKIQG---HLEFLAYGQQFVAYNIHPKTQRAYTWSI---AP 114
           L+ +R +     K      E + G    LE L  GQQFVAY++HP T R Y W+      
Sbjct: 101 LLAYRAESEGWGKATGAWFEDLAGDRHRLEVLGKGQQFVAYHVHPDTGRPYEWTDFFGGL 160

Query: 115 HALKVEELPLLTPDEVEYFFEFFDTITTP-----RDKEKSYRKLSKIWKSHNNRRYTN-- 167
            A++  +LP++T  +VE   + F+ +            KS   L+   +      Y    
Sbjct: 161 DAMRASDLPVITEAQVEEALQVFEAMAEECGLARVTGSKSRTGLTSAPEDDPLMAYEPPV 220

Query: 168 ----IEIRAFLSCFGEEFYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTY-DE 222
                E R  ++    E Y    D W+ V M++H+E  GS E   +  EW      Y   
Sbjct: 221 GIDLAEARRLVAYVDNEDY----DTWLKVGMSLHHEFDGSGEALALWDEWSATASNYASS 276

Query: 223 KSFNAKWDSF 232
           +    +WDSF
Sbjct: 277 EDVARRWDSF 286

Species: Bordetella phage BPP-1
Genus: Bpp-1-like viruses
Family: Podoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses

 Score = 88.2 bits (217), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 104/240 (43%), Gaps = 26/240 (10%)

Query: 17  LCGIG--THPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAPKTLMLFRMQETNLK 74
           L G+G  T      D+D+ DE       N      G    RVG+AP+ L+LFR  E   K
Sbjct: 72  LAGVGFLTKNTPGVDIDISDEGFAKHMENFVHENFGMAPVRVGRAPRRLLLFRCTEPFSK 131

Query: 75  KQKS----EEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTW--SIAPHALKVEELPLLTPD 128
              S    E      +E LA GQQFVA++IHP T+R Y W    +P  ++  ELP+L   
Sbjct: 132 VNSSVYLDEWGEAQKVEILANGQQFVAFHIHPDTKRPYEWLYKQSPLDIEASELPVLRRV 191

Query: 129 EVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRY------------TNI---EIRAF 173
           + +   + F+     R      R  +   +S +                T+I   E+ A 
Sbjct: 192 DAQAIVDEFEKQAKLRGWTLKKRSRTAPERSESGGEIDYDDPFAADVAKTDIGEDELHAK 251

Query: 174 LSCFGEEFYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
           L    +      ++ W+ V MA+ ++  G   G E+  EW +    YD K  +AKW SFD
Sbjct: 252 LLLVPDA---DDYETWVNVGMALFHQYDGHERGLELWHEWSETADNYDAKELDAKWKSFD 308

Species: Burkholderia phage BcepNazgul
Genus: 
Family: Siphoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 106/233 (45%), Gaps = 26/233 (11%)

Query: 15  GILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCG-KPISRVGQAPKTLMLFRMQETNL 73
           G++CG     +   D+DVLD     R         G  P+SR+G+APK L+ FR      
Sbjct: 95  GLVCG----DLIGVDIDVLDRDHAHRLTFIATEMLGMSPLSRIGRAPKILLAFRTDAPFD 150

Query: 74  KKQKSE----EKIQGHLEFLAYGQQFVAYNIHPKTQRAYTW-SIAPHALKVEELPLLTPD 128
           K Q SE    +     +E LA GQQFV + IHP T+  Y W   +P  + + ELP+++ D
Sbjct: 151 KVQTSEFHMLDGTVARVEVLATGQQFVGFGIHPDTKAPYHWPECSPLDVSLHELPVVSQD 210

Query: 129 EVEYFFE----FF-----DTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFLSCFGE 179
               F      +F      T +  R+ ++  RK + + +     R    E  A +S   +
Sbjct: 211 RCAAFISAAEGYFRKVGGQTTSDRREIDREGRKAAGLKQKEAPSRELIEEAVAHIS--ND 268

Query: 180 EFYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSF 232
           E     +D+WI V +A+ Y   GS +G+++   W       D      KWDSF
Sbjct: 269 EL---PYDDWIKVGLAL-YAALGS-DGRDLWETWSAEASKNDPAYSAEKWDSF 316

Species: Rhodobacterales bacterium Y4I
Genus: 
Family: 
Order: Rhodobacterales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score = 83.6 bits (205), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/252 (28%), Positives = 108/252 (42%), Gaps = 41/252 (16%)

Query: 6   VDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAPKTLML 65
            + Y  NG GIL    T    A D+DV DE  V    +      G+   R+G+ PK L L
Sbjct: 54  AERYTKNGIGIL----TKYTPAVDIDVYDEDAVAHMADWVLENVGRAPCRIGREPKKLFL 109

Query: 66  FRMQETNLKKQKS----EEKIQGH-LEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALK-- 118
           FR  E+   K KS    ++  Q H +E LA GQQFVAY IHP T R Y W    + L   
Sbjct: 110 FRT-ESPFSKVKSGVWEDDFGQRHAVEILADGQQFVAYGIHPDTNRDYYWLDDENPLNNA 168

Query: 119 ----VEELPLLTPDEVEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIRAFL 174
               +EE+ L T  E+   F+ +        KE+ +  + +    +      + E   + 
Sbjct: 169 ADFDLEEISLDTAREIAAEFDRY-------AKEQGWTMVKRPMNGYEAIGTADEE--DWA 219

Query: 175 SCFGEEFYNGSHDE----------------WIPVVMAIHYETRGSAEGKEIVREWCKLGR 218
           +  G   ++G++++                +I V+ A+    R   E K I REW     
Sbjct: 220 ATAGIRKWDGTYEDLRDLVMKYPNPEDYENYIKVLAALQISCRDQDEAKSIAREWAMQAH 279

Query: 219 TYDEKSFNAKWD 230
            +D+  F  KWD
Sbjct: 280 NFDDGDFEYKWD 291

Species: Staphylococcus phage SA1
Genus: 
Family: Myoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses

 Score = 77.8 bits (190), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 62/218 (28%), Positives = 92/218 (42%), Gaps = 35/218 (16%)

Query: 19  GIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCG--KPISRVGQAPKTLMLFRMQETNLKKQ 76
           G+ T  + A DVD  D  + D+      +  G  +   RVG+APK L +F+  E   K  
Sbjct: 63  GVLTGDIVAVDVDAPDAAIADQLIARLMAIPGAKRAPYRVGKAPKCLFIFKATEPRRKAS 122

Query: 77  KSEEKIQG---HLEFLAYGQQFVAYNIHPKTQRAYTWSIA-PHALKVEELPLLTPDEVEY 132
             E  I G    +E L  GQQFVAY  H +T   Y WS   P ++ + +LP +TPD V+ 
Sbjct: 123 TGEYLIGGSKCQVEILGQGQQFVAYGNHAETGLPYVWSNGEPLSIPLHDLPEITPDAVDA 182

Query: 133 FFEFFDTIT----TPRDKEKSYRKLSK----IWKSHNNRRYTNIEIRAFLSCFGEEFYNG 184
           F    D I     TP  K+   R+  +     W+  N+    N                 
Sbjct: 183 FLADADAILAKAGTPMKKKSEPRQQGRGADTFWQRVNSAALDNT---------------- 226

Query: 185 SHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDE 222
             D W+P + +   +  G+   +   +E   LGR  +E
Sbjct: 227 --DRWVPSLFSSARKEAGTGAWRITSKE---LGRDLEE 259

Species: Sinorhizobium medicae
Genus: Sinorhizobium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 2/50 (4%)

Query: 184 GSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD 233
             +D W+ V MA+ +E     EG E+  EW      YD      KWDSF 
Sbjct: 13  DDYDSWLRVGMALKHEF--GEEGLELWDEWSAKSSKYDPGECERKWDSFK 60

This alpha helical domain is found at the C terminal of primases. Length = 74

Probab=99.85  E-value=1.4e-20  Score=137.70  Aligned_cols=120  Identities=13%  Similarity=0.079  Sum_probs=83.2

Q ss_pred             CHHHHHCCCCCCEEEEECCCCCCEEEEEEECCCHHHHHHHHH--HHHHHCCCCEEEECCCCCEEEEEECCCCCCCCCCCC
Q ss_conf             237875186168899707884888999954898467899999--776408986298678895399984474312433577
Q gi|254781190|r    2 VATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNN--EFQSCCGKPISRVGQAPKTLMLFRMQETNLKKQKSE   79 (233)
Q Consensus         2 va~~~~~~p~~giGi~~G~~s~~l~~iDiD~~d~~~~~~~~~--~~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~~~   79 (233)
T Consensus        30 i~~w~~~~p~~niGi~~G~--sglvviDiD~~~~~~~-~~~~~~~~~~l~~~t~~~~T~~gG~H~~f~~p~~~~~~~-~~  105 (152)
T cd04859          30 IEAWWRDGPDANIGLRTGP--SGLVVIDIDVKHDGAA-ALAALAELGKLPPLTLTVRTGSGGRHLYFRVPDGVPVKS-VK  105 (152)
T ss_pred             HHHHHHHCCCCCEEEECCC--CCEEEEECCCCCCCHH-HHHHHHHCCCCCCCCEEEECCCCCEEEEEECCCCCCCCC-CC
T ss_conf             9999985998448888288--8779997326776346-899877615778777478869994499998999862233-22


Q ss_pred             CCCCCCEEEEECCCEEEECCCCCCCCCCEEEECCCCCCCHHHCCCCCHHHHH
Q ss_conf             7676635898458328953668888884574216776882236768999999
Q gi|254781190|r   80 EKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVEELPLLTPDEVE  131 (233)
Q Consensus        80 ~~~~~~iEi~~~g~q~V~~g~hp~Tg~~Y~W~~~~~~~~~~~lP~~~~~~l~  131 (233)
T Consensus       106 ~~~~~~vDir~~g~yvV~pPS~~~~g~~y~~~~---~~---~~~~~P~wl~~  151 (152)
T cd04859         106 GKGGPGIDIRGGGGYVVAPPSVHPGGGYYVWKS---TV---DPAPAPEWLLD  151 (152)
T ss_pred             CCCCCCEEEEECCCEEECCCCCCCCCCEEEECC---CC---CCCCCCHHHHC
T ss_conf             476786789835988981786848964698089---99---86678867863

These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.

Probab=99.78  E-value=6.8e-18  Score=122.21  Aligned_cols=117  Identities=15%  Similarity=0.091  Sum_probs=77.4

Q ss_pred             CHHHHHCCCCCCEEEEECCCCCCEEEEEEECCCHHHHHHHHHHHH--HHCCCCEEEECCCCCEEEEEECCCCCCCCCCC-
Q ss_conf             237875186168899707884888999954898467899999776--40898629867889539998447431243357-
Q gi|254781190|r    2 VATDVDHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQ--SCCGKPISRVGQAPKTLMLFRMQETNLKKQKS-   78 (233)
Q Consensus         2 va~~~~~~p~~giGi~~G~~s~~l~~iDiD~~d~~~~~~~~~~~~--~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~~-   78 (233)
T Consensus        37 i~~w~~~~p~~nigv~~g~--~~lvviDiD~~~~~~--~l~~l~~~~~~lp~t~~~~T~~gG~H~~fr~p~~~~~~~~~~  112 (161)
T pfam09250        37 IRRWWARNPGANIGLPTGR--SGLVVLDVDTKAGGD--ALAALERAGGPLPPTLVVRTPSGGRHLYFRVPDGPELKRNLL  112 (161)
T ss_pred             HHHHHHCCCCCCEEEECCC--CCEEEEECCCCCCHH--HHHHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCC
T ss_conf             9999860999528887089--857999576765448--999999854888886168889997799997788864367522


Q ss_pred             --CCCCCCCEEEEECC-CEEEECCCCCCCCCCEEEECCCCCCCHHHCCC
Q ss_conf             --77676635898458-32895366888888457421677688223676
Q gi|254781190|r   79 --EEKIQGHLEFLAYG-QQFVAYNIHPKTQRAYTWSIAPHALKVEELPL  124 (233)
Q Consensus        79 --~~~~~~~iEi~~~g-~q~V~~g~hp~Tg~~Y~W~~~~~~~~~~~lP~  124 (233)
T Consensus       113 ~~~~~~~~gvDir~~g~~yvv~ppS~~~~g-~Y~w~~~-~~~~~~~~P~  159 (161)
T pfam09250       113 FAKDGGGGGIDIRAGGGGYVVAPPSVHPGG-PYEWTGG-TPLPPAPAPE  159 (161)
T ss_pred             CCCCCCCCCEEEECCCCCEEEECCCCCCCE-EEEEECC-CCCCCCCCCC
T ss_conf             102678998798538962899579537983-2898159-9888778988

Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.

Probab=99.09  E-value=1.9e-10  Score=79.23  Aligned_cols=91  Identities=14%  Similarity=0.153  Sum_probs=65.2

Q ss_pred             CHHHHHCCCCCCEEEEECCC----CCCEEEEEEECCCH---HHHHHHHHHHHHHCC-----CCEEEECCCCCEEEEEECC
Q ss_conf             23787518616889970788----48889999548984---678999997764089-----8629867889539998447
Q gi|254781190|r    2 VATDVDHYVYNGFGILCGIG----THPVYAFDVDVLDE---QVVDRFNNEFQSCCG-----KPISRVGQAPKTLMLFRMQ   69 (233)
Q Consensus         2 va~~~~~~p~~giGi~~G~~----s~~l~~iDiD~~d~---~~~~~~~~~~~~~~~-----~~~~~~g~~~~~~~lfr~~   69 (233)
T Consensus        29 ~~~w~~~~~~~~i~~~~~~~~~~~~~~~lv~DlD~~~~~~~~~~~~~a~~~~~ll~~~~~~~~~~~TG~-~G~H~~~~~-  106 (136)
T cd00525          29 ILAWLANLPPGNIGLSLGRYDKLWKPDLLVFDLDPDDYDCWEDVKEAALLLRELLDEDGLNTLVVTSGS-RGLHVYVRL-  106 (136)
T ss_pred             HHHHHHHCCCEEEECCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCC-CEEEEEEEC-
T ss_conf             999886338575017766567567998799826899999899999999999999988499554374389-834999976-


Q ss_pred             CCCCCCCCCCCCCCCCEEEEEC--CCEEEECCCCCC-CCCCEEE
Q ss_conf             4312433577767663589845--832895366888-8884574
Q gi|254781190|r   70 ETNLKKQKSEEKIQGHLEFLAY--GQQFVAYNIHPK-TQRAYTW  110 (233)
Q Consensus        70 ~~~~~~~~~~~~~~~~iEi~~~--g~q~V~~g~hp~-Tg~~Y~W  110 (233)
T Consensus       107 ----------------iD~~~~~~~~~~v~p~S~~~~~~~~p~~  134 (136)
T cd00525         107 ----------------IDIRVNARGRLLVAPPSVHPRPGGPPSW  134 (136)
T ss_pred             ----------------CHHHCCCCCCEEECCCCCCCCCCCCCCC
T ss_conf             ----------------4564357897276365566899897877

The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the pri

Probab=99.70  E-value=2.4e-17  Score=119.05  Aligned_cols=60  Identities=33%  Similarity=0.591  Sum_probs=55.0

Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC
Q ss_conf             99999973580013567457999998763027886226799999861388998678999862079
Q gi|254781190|r  169 EIRAFLSCFGEEFYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEKSFNAKWDSFD  233 (233)
Q Consensus       169 ~a~~~L~~i~~~~~~~dyd~W~~vg~AL~~~~~~~~~~l~lw~~WS~~~~~y~~~~~~~~W~sF~  233 (233)
T Consensus         1 ~~~~~L~~i~~~---~dy~~W~~vG~aL~~~~--~~~~~~lw~~wS~~~~ky~~~~~~~~W~sf~   60 (74)
T pfam08707         1 DAREALDFIPPR---DDYDSWLRVGMALKHEF--GEEGLELWDEWSAKSSKYDPGECERKWDSFK   60 (74)
T ss_pred             CHHHHHHCCCCC---CCHHHHHHHHHHHHHCC--CHHHHHHHHHHHCCCCCCCHHHHHHHHHHCC
T ss_conf             988997238986---88899999999998266--6579999999974656588378999998377

This alpha helical domain is found at the C terminal of primases.

Probab=90.01  E-value=0.98  Score=23.31  Aligned_cols=50  Identities=12%  Similarity=0.182  Sum_probs=29.8

Q ss_pred             CCCEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEECCCC-CEEEEEECCCC
Q ss_conf             488899995489846789999977640898629867889-53999844743
Q gi|254781190|r   22 THPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAP-KTLMLFRMQET   71 (233)
Q Consensus        22 s~~l~~iDiD~~d~~~~~~~~~~~~~~~~~~~~~~g~~~-~~~~lfr~~~~   71 (233)
T Consensus        30 ~sgli~lDiD~l~~ee~~~~r~~l~~dp~t~~~FvSpSG~GvKi~V~~~~~   80 (136)
T pfam08800        30 YNGLVCLDVDHLAKEELERVKQKAAALPYTVLAFISSSGRGVKIWVRFDRP   80 (136)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEEECCC
T ss_conf             688089982899989999999998469948999985799879999997577

This presumed domain is found at the N-terminus of VirE proteins.

Probab=99.68  E-value=1.5e-17  Score=119.01  Aligned_cols=105  Identities=9%  Similarity=0.080  Sum_probs=68.7

Q ss_pred             HHHHHCCCCC-CEEEEECCCCCCEEEEEEECCCHHHHHHH---HHHHHHHCCCCEEEECCCCCEEEEEECCCCCCCCCCC
Q ss_conf             3787518616-88997078848889999548984678999---9977640898629867889539998447431243357
Q gi|254781190|r    3 ATDVDHYVYN-GFGILCGIGTHPVYAFDVDVLDEQVVDRF---NNEFQSCCGKPISRVGQAPKTLMLFRMQETNLKKQKS   78 (233)
Q Consensus         3 a~~~~~~p~~-giGi~~G~~s~~l~~iDiD~~d~~~~~~~---~~~~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~~   78 (233)
                      ..+++++|.+ ||||+||+ + ++++||||..  .....+   ..+.+.+..+++++++ .++.|+||+.++.+..+...
T Consensus        47 ~~w~~~~p~~~NiGI~tG~-s-glvViDiD~~--~~~~~~~~~~~l~~~~~~T~~v~Tp-sGG~HlYf~~~~~p~~~~~~  121 (216)
T 1ro2_A           47 QRFLKMIEEGYNYAIPGGQ-K-GMVIMDFESK--EKLKAWIGESALEELCRKTLCTNTV-HGGIHIYVLSNDIPPHKINP  121 (216)
T ss_dssp             HHHHHHHHHTCEEEEESSG-G-GEEEEEESCH--HHHHHHHCHHHHHHHHHHSCEEECT-TSCEEEEEECSCCCSSCCCC
T ss_pred             HHHHHHCCCCCEEEEECCC-C-CEEEEECCCC--CHHHHHHHHHHHHHCCCCCEEEECC-CCEEEEEEECCCCCCCCCCC
T ss_conf             9999859975559998178-8-8899978885--2066665556666208886699889-98589999778878554365


Q ss_pred             C--CCCCCCEEEEECCCEEEECCC-----C-CCCCCCEEEEC
Q ss_conf             7--767663589845832895366-----8-88888457421
Q gi|254781190|r   79 E--EKIQGHLEFLAYGQQFVAYNI-----H-PKTQRAYTWSI  112 (233)
Q Consensus        79 ~--~~~~~~iEi~~~g~q~V~~g~-----h-p~Tg~~Y~W~~  112 (233)
                      .  ......||||+.|+|||+|||     | +.++.+|+|.+
T Consensus       122 ~~~~~g~~~iDir~~ggYVVaPgS~i~h~~~~~~~~~~~~~~  163 (216)
T 1ro2_A          122 LFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQN  163 (216)
T ss_dssp             SEESSSSEEEEEECTTCEEECTTCEEEGGGCCSTTCTTTTCS
T ss_pred             CEECCCCCEEEEEECCCEEEECCEECCCCCCCCCCCCCCCCC
T ss_conf             332389844899716988995581035666787777745787

Probab=99.56  E-value=6.7e-15  Score=103.69  Aligned_cols=100  Identities=11%  Similarity=0.143  Sum_probs=62.0

Q ss_pred             HHHHHCCCCC-CEEEEECCCCCCEEEEEEECCCHHHHHHHH--HHHHHHCCCCEEEECCCCCEEEEEECCCCCC-CCCCC
Q ss_conf             3787518616-889970788488899995489846789999--9776408986298678895399984474312-43357
Q gi|254781190|r    3 ATDVDHYVYN-GFGILCGIGTHPVYAFDVDVLDEQVVDRFN--NEFQSCCGKPISRVGQAPKTLMLFRMQETNL-KKQKS   78 (233)
Q Consensus         3 a~~~~~~p~~-giGi~~G~~s~~l~~iDiD~~d~~~~~~~~--~~~~~~~~~~~~~~g~~~~~~~lfr~~~~~~-~~~~~   78 (233)
                      ..+++.+|.+ ||||+||+  +|+++||||..  .....+.  .-+..++..+....+..||.|+||+.++.+. +.+..
T Consensus        51 ~~Ww~~~P~a~NIGI~TG~--sGLVVLDiD~k--eg~~~~~~~~~L~~li~~T~~VkTPSGG~HLYfr~~e~Pp~k~~p~  126 (335)
T 3m1m_A           51 QRFLKMIEEGYNYAIPGGQ--KGLVILDFESK--EKLKAWIGESALEELCRKTLCTNTVHGGIHIYVLSNDIPPHKINPL  126 (335)
T ss_dssp             HHHHHHHHTTCEEEEESSG--GGEEEEEESCH--HHHHHHHCHHHHHHHHHHSCEEECTTSCEEEEEECSSCCSSCEEEE
T ss_pred             HHHHHHCCCCCEEEEECCC--CCEEEEECCCC--CCHHHHHHHHHHHHCCCCCEEEECCCCCEEEEEECCCCCHHHCCCC
T ss_conf             9999749875548997288--88899989786--4224554345666317787699899991899997899882322654


Q ss_pred             CCC-CCCCEEEEECCCEEEECCC-----CCCCCC
Q ss_conf             776-7663589845832895366-----888888
Q gi|254781190|r   79 EEK-IQGHLEFLAYGQQFVAYNI-----HPKTQR  106 (233)
Q Consensus        79 ~~~-~~~~iEi~~~g~q~V~~g~-----hp~Tg~  106 (233)
                      ... ....+||++.|+|||+|||     |++|.+
T Consensus       127 ~~~~G~gviDirs~ggYVVaPGS~inh~~~~~~k  160 (335)
T 3m1m_A          127 FEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDK  160 (335)
T ss_dssp             EEETTEEEEEEECTTCEEECTTCEEEGGGCCSTT
T ss_pred             CCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCC
T ss_conf             2247874277854897898882020455666667

Probab=96.22  E-value=0.012  Score=33.03  Aligned_cols=59  Identities=12%  Similarity=0.088  Sum_probs=37.9

Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHH-HHHHHHHHC
Q ss_conf             999997358001356745799999876302788622679999986138899867-899986207
Q gi|254781190|r  170 IRAFLSCFGEEFYNGSHDEWIPVVMAIHYETRGSAEGKEIVREWCKLGRTYDEK-SFNAKWDSF  232 (233)
Q Consensus       170 a~~~L~~i~~~~~~~dyd~W~~vg~AL~~~~~~~~~~l~lw~~WS~~~~~y~~~-~~~~~W~sF  232 (233)
                      ....+.....   +.+|.+|.-+ ++|.+.-.+.+....+..++|...+++++. ...+.|.+|
T Consensus       228 ~~~l~~r~~g---d~S~~D~~~a-~~l~~~G~t~d~ia~Ai~~~sp~~~~~~~~~~~dya~rt~  287 (323)
T 3h20_A          228 MAGLVKRFGD---DLSKCDFIAA-QKLASRGRSAEEIGKAMAEASPALAERKPGHEADYIERTV  287 (323)
T ss_dssp             HHHHHHHCTT---CHHHHHHHHH-HHHHHTTCCHHHHHHHHHHHCHHHHTCC--CHHHHHHHHH
T ss_pred             HHCCHHHHCC---CCHHHHHHHH-HHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
T ss_conf             4310222058---8218799999-9999947999999999986281334357553247999999

class: Alpha and beta proteins (a+b)
fold: Prim-pol domain
superfamily: Prim-pol domain
family: Bifunctional DNA primase/polymerase N-terminal domain
domain: Bifunctional DNA primase/polymerase N-terminal domain
species: Archaeon Sulfolobus islandicus [TaxId: 43080]

Probab=99.70  E-value=4.4e-18  Score=120.68  Aligned_cols=105  Identities=10%  Similarity=0.066  Sum_probs=69.8

Q ss_pred             HHHHHCCCCC-CEEEEECCCCCCEEEEEEECCCHHHHHHHH---HHHHHHCCCCEEEECCCCCEEEEEECCCCCCCCCCC
Q ss_conf             3787518616-889970788488899995489846789999---977640898629867889539998447431243357
Q gi|254781190|r    3 ATDVDHYVYN-GFGILCGIGTHPVYAFDVDVLDEQVVDRFN---NEFQSCCGKPISRVGQAPKTLMLFRMQETNLKKQKS   78 (233)
Q Consensus         3 a~~~~~~p~~-giGi~~G~~s~~l~~iDiD~~d~~~~~~~~---~~~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~~   78 (233)
                      ..+++++|.+ ||||+||. + |+++||||..  .....+.   .+...+..+.+++++ .+++|+||+.++.+..+...
T Consensus        47 ~~w~~~~p~~~NiGi~~G~-s-glVViDiD~~--~~~~~~~~~~~l~~~~~~T~~v~Tp-sGG~HlYf~~~e~p~~~~~~  121 (210)
T d1ro0a_          47 QRFLKMIEEGYNYAIPGGQ-K-GMVIMDFESK--EKLKAWIGESALEELCRKTLCTNTV-HGGIHIYVLSNDIPPHKINP  121 (210)
T ss_dssp             HHHHHHHHTTCEEEEESSG-G-GEEEEEESCH--HHHHHHHCHHHHHHHHHHSCEEECT-TSCEEEEEECSSCCSSCCCC
T ss_pred             HHHHHHCCCCCEEEEECCC-C-CEEEEECCCC--HHHHHHHHHHHHHCCCCCCEEEECC-CCCEEEEEECCCCCCCCCCC
T ss_conf             9998749875548996377-7-7899987882--3455541004554348887599879-99189999878877542134


Q ss_pred             C--CCCCCCEEEEECCCEEEECCC-----CCCC-CCCEEEEC
Q ss_conf             7--767663589845832895366-----8888-88457421
Q gi|254781190|r   79 E--EKIQGHLEFLAYGQQFVAYNI-----HPKT-QRAYTWSI  112 (233)
Q Consensus        79 ~--~~~~~~iEi~~~g~q~V~~g~-----hp~T-g~~Y~W~~  112 (233)
                      .  ......|||++.|+|||+|||     |++| +.+|+|.+
T Consensus       122 ~~~~~g~~~iDir~~g~yVv~PpS~~~h~h~~~~~~~~~~~~  163 (210)
T d1ro0a_         122 LFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQN  163 (210)
T ss_dssp             SEEETTEEEEEEECTTCEEECTTCEEEGGGCCSTTCTTTTCS
T ss_pred             CEECCCCCEEEEEEECCEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             466178735889700898995574246635677777641555

Probab=99.78  E-value=9.5e-20  Score=132.51  Aligned_cols=135  Identities=11%  Similarity=0.132  Sum_probs=89.9

Q ss_pred             CHHHHHCCCCC-CEEEEECCCCCCEEEEEEECCCHHHHHHHHHH---HHHHCCCCEEEECCCCCEEEEEECCCCCCCCCC
Q ss_conf             23787518616-88997078848889999548984678999997---764089862986788953999844743124335
Q gi|254781190|r    2 VATDVDHYVYN-GFGILCGIGTHPVYAFDVDVLDEQVVDRFNNE---FQSCCGKPISRVGQAPKTLMLFRMQETNLKKQK   77 (233)
Q Consensus         2 va~~~~~~p~~-giGi~~G~~s~~l~~iDiD~~d~~~~~~~~~~---~~~~~~~~~~~~g~~~~~~~lfr~~~~~~~~~~   77 (233)
                      |..++..+|.+ ||||.||.  .++++||+|.  ......+..+   ...+..++.++++ ++++|+|||+|+....+..
T Consensus        46 i~~w~~~~p~~~nigi~~G~--~~~vviD~D~--~~g~~~~~~l~~~~~~l~~t~~~~T~-~gG~h~~f~~p~~~~~~~~  120 (216)
T 1ro2_A           46 KQRFLKMIEEGYNYAIPGGQ--KGMVIMDFES--KEKLKAWIGESALEELCRKTLCTNTV-HGGIHIYVLSNDIPPHKIN  120 (216)
T ss_dssp             HHHHHHHHHHTCEEEEESSG--GGEEEEEESC--HHHHHHHHCHHHHHHHHHHSCEEECT-TSCEEEEEECSCCCSSCCC
T ss_pred             HHHHHHHCCCCCEEEEECCC--CCEEEEECCC--CCHHHHHHHHHHHHHCCCCCEEEECC-CCCEEEEEECCCCCCCCCC
T ss_conf             99999849975659996487--7789998888--52034442224566238886489858-9917999976888865315


Q ss_pred             C--CCCCCCCEEEEECCCEEEECCC----CCCCCCCEEEECCCCC---CCHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             7--7767663589845832895366----8888884574216776---8822367689999999997544201
Q gi|254781190|r   78 S--EEKIQGHLEFLAYGQQFVAYNI----HPKTQRAYTWSIAPHA---LKVEELPLLTPDEVEYFFEFFDTIT  141 (233)
Q Consensus        78 ~--~~~~~~~iEi~~~g~q~V~~g~----hp~Tg~~Y~W~~~~~~---~~~~~lP~~~~~~l~~~~~~~~~~~  141 (233)
                      .  ......+||||+.|+|+|+|||    ||.||+.|+|..++..   .+...++.+....+..+........
T Consensus       121 ~~~~~~~~~gvdir~~g~~vV~ppS~~~~~~~~g~~Y~w~~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~  193 (216)
T 1ro2_A          121 PLFEENGKGIIDLQSYNSYVLGLGSCVNHLHCTTDKCPWKEQNYTTCYTLYNELKEISKVDLKSLLRFLAEKG  193 (216)
T ss_dssp             CSEESSSSEEEEEECTTCEEECTTCEEEGGGCCSTTCTTTTCSCEEECEESSSCCCCEECCHHHHHHHHHHHH
T ss_pred             CCEECCCCCEEEEEECCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             5443278842889836988996361046646787766524566556676743335554255367899999877