Psyllid ID: psy15222

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440----
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
cHHHHHHHHHHHcccHHHHHHHHHccccHHHHHHcccccccccHHHHHHHHHccccHHHHHHcccccccccccccccccccccccccccccccEEEEEcccccEEEEccccccccccccccccccccccccccccccHHHHHHHcHHcccEEEEEcHHHHHHHHHcccccEEccccccccHHHHHHHHHccccEEEEEcccHHHHHHHHHHHHHHHcccccccEEEEEEccccccccHHHHHHcHHHHHHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHcccHHHHHccHHHHHHHHHcccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccc
cHHHHHHHHHHHHccHHHHHHHHHccccHHHHHHHccccccccHHHHHHHccccHHHHHHHHcccEEEccccccccccccccccEEccccccEEEEEEccccEEEEEccEEccccccccccccccccHHcccHHHHHHHHHHHHcccccEEEEEEcHHHHHHHHHHcccHEEEEccccccHHHHHHHHHHcccEEEEEcccHHHHHHHHHHHHHHHHHcccccEEEEEEccccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHcHHHHHHcccccHHHHHccccccHHHHHHHHHHHHHccccccHHHHHHHHHHcHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHc
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNlgyapnewnALNKVFLdynnintlasSGLVVDKIINkvnqspviekykrydrfrgrimfpikntdgqiigfggrlikdsneakyinspetplfhksnelyglfeaknaiEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKflflpdkydpdsyirKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYpslineinsedmIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
micasdfykiqlknskEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVdkiinkvnqspviekykrydrFRGRImfpikntdgqiiGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYAtddkiikflflpdkydpdSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFkintssikhktieKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTlldaiykdrksvv
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQagrraarraLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPlssslrfkiisslskiikvsFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
**CASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYK******
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINK*******EKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIIL**********EKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSF********************************IMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKS**
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKII***NQSP**EKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKIN**************QPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
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MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQDNFEYSIEIAKKTLLDAIYKDRKSVV
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query444 2.2.26 [Sep-21-2011]
P57028590 DNA primase OS=Neisseria yes N/A 0.745 0.561 0.406 1e-71
P57029590 DNA primase OS=Neisseria yes N/A 0.745 0.561 0.406 3e-71
Q9I5W0 664 DNA primase OS=Pseudomona yes N/A 0.716 0.478 0.403 9e-64
P0A119 660 DNA primase OS=Pseudomona yes N/A 0.707 0.475 0.378 3e-59
P0A118 660 DNA primase OS=Pseudomona yes N/A 0.707 0.475 0.378 3e-59
Q8FDG5581 DNA primase OS=Escherichi yes N/A 0.576 0.440 0.409 4e-58
P0ABS7581 DNA primase OS=Shigella f yes N/A 0.576 0.440 0.409 7e-58
P0ABS5581 DNA primase OS=Escherichi N/A N/A 0.576 0.440 0.409 7e-58
P0ABS6581 DNA primase OS=Escherichi N/A N/A 0.576 0.440 0.409 7e-58
P07362581 DNA primase OS=Salmonella yes N/A 0.581 0.444 0.406 5e-57
>sp|P57028|PRIM_NEIMA DNA primase OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=dnaG PE=3 SV=1 Back     alignment and function desciption
 Score =  270 bits (691), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 144/354 (40%), Positives = 216/354 (61%), Gaps = 23/354 (6%)

Query: 3   CASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLAS 62
            A+DFY  QLK +  A  +L KRGL+ E+I  + LGYAP+ W  L +VF  Y N   L  
Sbjct: 123 AAADFYAQQLKFNPAAKAYLDKRGLSAEVIAHYGLGYAPDGWQPLTQVFQPYPN-TALVD 181

Query: 63  SGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYIN 122
           +G+V+D             + + YDRFR RIMFPI+N  GQ+IGFGGR++ DS + KY+N
Sbjct: 182 TGMVIDN------------EGRHYDRFRHRIMFPIRNPRGQVIGFGGRVLDDS-KPKYLN 228

Query: 123 SPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTST 182
           SP+TPLF K   LYGL+E + A++++G +L+ EGYMDV+ L+QFG    VA LGTA T+ 
Sbjct: 229 SPDTPLFDKGKNLYGLYEGRAAVKEAGRILVVEGYMDVVALAQFGVGYGVAALGTATTAE 288

Query: 183 HIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRK 242
           H+K ++   +SI F FDGD AGR+AA RALE  L    DDK + FLFLP+++DPDSYIR 
Sbjct: 289 HVKILMRQADSIYFCFDGDSAGRKAAWRALENALPQLKDDKSLHFLFLPEEHDPDSYIRA 348

Query: 243 FGYKIFSKKVL-EAMSLLQFFLEEIILNYNLKTIKD-IEKSKYNIEYLFKIIPLSSSLRF 300
           +G   F   +L ++  L ++F E +    +L T +   E  K +   L +I   + +L +
Sbjct: 349 YGKAQFEDALLNQSKPLSEYFWEHLSDGIHLNTQEGKAELVKTSSPLLAQIT--APALAY 406

Query: 301 KIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKN--IQPICIEYQIMKLLI 352
            +   LS+++ +   + +NL ++       + +++KN  + PI ++  +M  L+
Sbjct: 407 LLKQRLSELVGI---DPDNLAQLLGQEAPKRHVKQKNYKLPPISVKQPVMPTLV 457
DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks during chromosomal DNA synthesis.
Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) (taxid: 122587)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: -
>sp|P57029|PRIM_NEIMB DNA primase OS=Neisseria meningitidis serogroup B (strain MC58) GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|Q9I5W0|PRIM_PSEAE DNA primase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|P0A119|PRIM_PSEPU DNA primase OS=Pseudomonas putida GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|P0A118|PRIM_PSEPK DNA primase OS=Pseudomonas putida (strain KT2440) GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|Q8FDG5|PRIM_ECOL6 DNA primase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|P0ABS7|PRIM_SHIFL DNA primase OS=Shigella flexneri GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|P0ABS5|PRIM_ECOLI DNA primase OS=Escherichia coli (strain K12) GN=dnaG PE=1 SV=1 Back     alignment and function description
>sp|P0ABS6|PRIM_ECO57 DNA primase OS=Escherichia coli O157:H7 GN=dnaG PE=3 SV=1 Back     alignment and function description
>sp|P07362|PRIM_SALTY DNA primase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=dnaG PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query444
340786216 598 DNA primase [Collimonas fungivorans Ter3 0.966 0.717 0.431 1e-108
399017720 602 DNA primase, catalytic core [Herbaspiril 0.972 0.717 0.422 1e-108
300310202 598 DNA primase [Herbaspirillum seropedicae 0.970 0.720 0.429 1e-106
409404649 598 DNA primase [Herbaspirillum sp. GW103] g 0.970 0.720 0.432 1e-105
152979908 599 DNA primase [Janthinobacterium sp. Marse 0.966 0.716 0.443 1e-102
398836333 599 DNA primase, catalytic core [Herbaspiril 0.963 0.714 0.419 1e-101
134093712 602 DNA primase [Herminiimonas arsenicoxydan 0.966 0.712 0.432 1e-101
445499115 589 DNA primase DnaG [Janthinobacterium sp. 0.952 0.718 0.421 9e-98
427400731 598 DNA primase [Massilia timonae CCUG 45783 0.959 0.712 0.402 4e-97
395763825 589 DNA primase [Janthinobacterium lividum P 0.930 0.701 0.436 6e-97
>gi|340786216|ref|YP_004751681.1| DNA primase [Collimonas fungivorans Ter331] gi|340551483|gb|AEK60858.1| DNA primase [Collimonas fungivorans Ter331] Back     alignment and taxonomy information
 Score =  397 bits (1020), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 190/440 (43%), Positives = 292/440 (66%), Gaps = 11/440 (2%)

Query: 1   MICASDFYKIQLKNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTL 60
           M  A DFY+  L+++  A+++LK+RGL  E+  +F LGY+P+ W++L +VF DY     L
Sbjct: 120 MSAACDFYRQHLRSAPNAVDYLKRRGLTGEVAAKFGLGYSPDNWDSLRQVFPDYE-ATAL 178

Query: 61  ASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKY 120
             SGLV+D+   + N        KRYDRFR RIMFPI+NT GQ+IGFGGR++ DS E KY
Sbjct: 179 VESGLVIDRTDEEGN------NRKRYDRFRDRIMFPIRNTKGQVIGFGGRVL-DSGEPKY 231

Query: 121 INSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACT 180
           +NSPETPLF K +ELYGLFEA+ AI  +GYVL+TEGYMDV+ L+Q GF Q VA LGTACT
Sbjct: 232 LNSPETPLFQKGSELYGLFEARQAIRDAGYVLVTEGYMDVVALAQLGFPQAVATLGTACT 291

Query: 181 STHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 240
            TH+ K+L  T+ ++FSFDGD+AGR+AARRAL+ CL +ATD+K+IKFLFLP ++DPDS++
Sbjct: 292 PTHVHKLLRQTDHVVFSFDGDRAGRKAARRALDACLPHATDNKVIKFLFLPQEHDPDSFV 351

Query: 241 RKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRF 300
           R+ G + F +++ +AM L QF L E+    +L T +   +++Y+ + L +++P  SSLR 
Sbjct: 352 REMGAEAFERQIHDAMPLSQFLLNEVTAEADLSTSEGRARAQYDAKPLMQLMP-PSSLRL 410

Query: 301 KIISSLSKIIKVSFNEINNLFKINT--SSIKHKTIEKKNIQPICIEYQIMKLLISYPSLI 358
           +I+  L+++ + + NEI +LF++    +S +          P+ +E QI++LL+++P+  
Sbjct: 411 QIVRGLAQLTQSTPNEIESLFELAKPIASARRAPPRSNRPPPVGLERQIIRLLVAHPAFA 470

Query: 359 NEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDHSKFIKYLKKINKNFESIIVKIQ 418
           +E++   +   +  + +  +M  +LI   H      + +   ++L++  ++FES+I +I 
Sbjct: 471 SELDDAALDAVAHFAPDRAEMLARLITASHAMGEQANFATLAEHLREGGEDFESLIAEIA 530

Query: 419 DNFEYSIEIAKKTLLDAIYK 438
              E   E A+  L  AI +
Sbjct: 531 AESESETEAARLELAGAIRQ 550

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria
>gi|399017720|ref|ZP_10719909.1| DNA primase, catalytic core [Herbaspirillum sp. CF444] gi|398102487|gb|EJL92667.1| DNA primase, catalytic core [Herbaspirillum sp. CF444] Back     alignment and taxonomy information
>gi|300310202|ref|YP_003774294.1| DNA primase [Herbaspirillum seropedicae SmR1] gi|300072987|gb|ADJ62386.1| DNA primase protein [Herbaspirillum seropedicae SmR1] Back     alignment and taxonomy information
>gi|409404649|ref|ZP_11253128.1| DNA primase [Herbaspirillum sp. GW103] gi|386436168|gb|EIJ48991.1| DNA primase [Herbaspirillum sp. GW103] Back     alignment and taxonomy information
>gi|152979908|ref|YP_001352182.1| DNA primase [Janthinobacterium sp. Marseille] gi|151279985|gb|ABR88395.1| DNA primase [Janthinobacterium sp. Marseille] Back     alignment and taxonomy information
>gi|398836333|ref|ZP_10593670.1| DNA primase, catalytic core [Herbaspirillum sp. YR522] gi|398211967|gb|EJM98578.1| DNA primase, catalytic core [Herbaspirillum sp. YR522] Back     alignment and taxonomy information
>gi|134093712|ref|YP_001098787.1| DNA primase [Herminiimonas arsenicoxydans] gi|133737615|emb|CAL60658.1| DNA primase [Herminiimonas arsenicoxydans] Back     alignment and taxonomy information
>gi|445499115|ref|ZP_21465970.1| DNA primase DnaG [Janthinobacterium sp. HH01] gi|444789110|gb|ELX10658.1| DNA primase DnaG [Janthinobacterium sp. HH01] Back     alignment and taxonomy information
>gi|427400731|ref|ZP_18891969.1| DNA primase [Massilia timonae CCUG 45783] gi|425720244|gb|EKU83167.1| DNA primase [Massilia timonae CCUG 45783] Back     alignment and taxonomy information
>gi|395763825|ref|ZP_10444494.1| DNA primase [Janthinobacterium lividum PAMC 25724] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query444
UNIPROTKB|P0ABS5581 dnaG [Escherichia coli K-12 (t 0.576 0.440 0.383 2e-47
TIGR_CMR|CBU_1595572 CBU_1595 "DNA primase" [Coxiel 0.610 0.473 0.403 1.1e-46
TIGR_CMR|SO_1286574 SO_1286 "DNA primase" [Shewane 0.572 0.442 0.382 4.4e-45
TIGR_CMR|CPS_4335585 CPS_4335 "DNA primase" [Colwel 0.783 0.594 0.309 2.2e-43
TIGR_CMR|BA_4516598 BA_4516 "DNA primase" [Bacillu 0.560 0.416 0.334 1e-39
TIGR_CMR|CHY_0454575 CHY_0454 "DNA primase" [Carbox 0.878 0.678 0.293 6.2e-33
TIGR_CMR|GSU_3090587 GSU_3090 "DNA primase" [Geobac 0.585 0.442 0.313 1.6e-30
TIGR_CMR|SPO_1749649 SPO_1749 "DNA primase" [Rueger 0.551 0.377 0.324 8.3e-30
TIGR_CMR|ECH_0761588 ECH_0761 "DNA primase" [Ehrlic 0.572 0.431 0.314 1.9e-29
TIGR_CMR|DET_0552590 DET_0552 "DNA primase" [Dehalo 0.556 0.418 0.337 5.6e-29
UNIPROTKB|P0ABS5 dnaG [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
 Score = 496 (179.7 bits), Expect = 2.0e-47, P = 2.0e-47
 Identities = 104/271 (38%), Positives = 163/271 (60%)

Query:     7 FYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEW-NALNKVFLDYNNINTLASS 63
             FY+  L+   +  A  +L+KRGL+ E+I RF +G+AP  W N L +   +  N  +L  +
Sbjct:   126 FYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDA 185

Query:    64 GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
             G++V             ++ + YDRFR R+MFPI++  G++IGFGGR++  ++  KY+NS
Sbjct:   186 GMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVL-GNDTPKYLNS 233

Query:   124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
             PET +FHK  +LYGL+EA+    +   +L+ EGYMDV+ L+Q+G    VA LGT+ T+ H
Sbjct:   234 PETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADH 293

Query:   184 IKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
             I+ +   TN++I  +DGD+         LE  L Y TD + ++F+FLPD  DPD+ +RK 
Sbjct:   294 IQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKE 353

Query:   244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKT 274
             G + F  ++ +AM L  F    ++   +L T
Sbjct:   354 GKEAFEARMEQAMPLSAFLFNSLMPQVDLST 384
GO:0008270 "zinc ion binding" evidence=IEA;IDA
GO:0006269 "DNA replication, synthesis of RNA primer" evidence=IEA;IDA
GO:0005737 "cytoplasm" evidence=IDA
GO:0003896 "DNA primase activity" evidence=IEA;IDA
GO:0046872 "metal ion binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
GO:0005658 "alpha DNA polymerase:primase complex" evidence=IEA
TIGR_CMR|CBU_1595 CBU_1595 "DNA primase" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
TIGR_CMR|SO_1286 SO_1286 "DNA primase" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_4335 CPS_4335 "DNA primase" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|BA_4516 BA_4516 "DNA primase" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_0454 CHY_0454 "DNA primase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_3090 GSU_3090 "DNA primase" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_1749 SPO_1749 "DNA primase" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|ECH_0761 ECH_0761 "DNA primase" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0552 DET_0552 "DNA primase" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9CLI9PRIM_PASMU2, ., 7, ., 7, ., -0.32030.89630.6838yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer2.7.7LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query444
PRK05667580 PRK05667, dnaG, DNA primase; Validated 1e-115
TIGR01391415 TIGR01391, dnaG, DNA primase, catalytic core 8e-88
COG0358568 COG0358, DnaG, DNA primase (bacterial type) [DNA r 5e-72
pfam08275128 pfam08275, Toprim_N, DNA primase catalytic core, N 3e-44
cd0336479 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primase 4e-24
cd0102979 cd01029, TOPRIM_primases, TOPRIM_primases: The top 1e-20
pfam1315590 pfam13155, Toprim_2, Toprim-like 3e-13
pfam1366281 pfam13662, Toprim_4, Toprim domain 5e-13
smart0049375 smart00493, TOPRIM, topoisomerases, DnaG-type prim 4e-08
cd0018883 cd00188, TOPRIM, Topoisomerase-primase domain 3e-07
pfam0175186 pfam01751, Toprim, Toprim domain 4e-07
PHA02031266 PHA02031, PHA02031, putative DnaG-like primase 0.001
PRK08624373 PRK08624, PRK08624, hypothetical protein; Provisio 0.003
>gnl|CDD|235551 PRK05667, dnaG, DNA primase; Validated Back     alignment and domain information 
 Score =  350 bits (900), Expect = e-115
 Identities = 136/366 (37%), Positives = 194/366 (53%), Gaps = 30/366 (8%)

Query: 4   ASDFYKIQL--KNSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NINTL 60
           A+ FY+ QL      EA  +L KRGL+EE I RF +GYAP+ W+AL K       +   L
Sbjct: 117 AAKFYQQQLRTPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSEKEL 176

Query: 61  ASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKY 120
             +GL++             +    YDRFR RIMFPI++  G++IGFGGR++ D  + KY
Sbjct: 177 EEAGLLIKNE----------DGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDD-KPKY 225

Query: 121 INSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACT 180
           +NSPETPLFHK   LYGL EA+ AI K   V++ EGYMDVI L Q G    VA LGTA T
Sbjct: 226 LNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVASLGTALT 285

Query: 181 STHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 240
             H+K +   T+ +I  FDGD+AGR+AA RALE+ L    D + ++  FLPD  DPD  +
Sbjct: 286 EEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDPDDLV 345

Query: 241 RKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPL-----S 295
           RK G + F   + +A+ L +F +  +I   +L T +           L +  PL      
Sbjct: 346 RKEGPEAFRALLEQAIPLSEFLIRRLIPGKDLDTPEG------RAALLERAAPLIAKIPD 399

Query: 296 SSLRFKIISSLSKIIKVSFNEINNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYP 355
            +LR      L++ + +  +             +      K  +P   E +++ LL+ +P
Sbjct: 400 PTLRDSYRRKLAERLGILDDAQLEQLVPKAQEPQ-----LKAERPRTAERELLALLLQHP 454

Query: 356 SLINEI 361
            L  E+
Sbjct: 455 ELAEEV 460

Length = 580
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core Back     alignment and domain information
>gnl|CDD|223435 COG0358, DnaG, DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|219773 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain Back     alignment and domain information
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>gnl|CDD|221942 pfam13155, Toprim_2, Toprim-like Back     alignment and domain information
>gnl|CDD|222298 pfam13662, Toprim_4, Toprim domain Back     alignment and domain information
>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain Back     alignment and domain information
>gnl|CDD|216679 pfam01751, Toprim, Toprim domain Back     alignment and domain information
>gnl|CDD|222844 PHA02031, PHA02031, putative DnaG-like primase Back     alignment and domain information
>gnl|CDD|236314 PRK08624, PRK08624, hypothetical protein; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 444
PRK05667580 dnaG DNA primase; Validated 100.0
TIGR01391415 dnaG DNA primase, catalytic core. This protein con 100.0
COG0358568 DnaG DNA primase (bacterial type) [DNA replication 100.0
TIGR00646218 MG010 DNA primase-related protein. The DNA primase 100.0
PHA02540337 61 DNA primase; Provisional 100.0
PHA02031266 putative DnaG-like primase 100.0
PRK08624373 hypothetical protein; Provisional 100.0
PF08275128 Toprim_N: DNA primase catalytic core, N-terminal d 100.0
TIGR027601960 TraI_TIGR conjugative transfer relaxase protein Tr 99.83
PHA02415 930 DNA primase domain-containing protein 99.74
PRK04031408 DNA primase; Provisional 99.73
cd0336479 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The top 99.69
PF1315596 Toprim_2: Toprim-like 99.64
PF1366281 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 99.58
cd0102781 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The to 99.54
cd0102979 TOPRIM_primases TOPRIM_primases: The topoisomerase 99.51
PF1336296 Toprim_3: Toprim domain 99.29
smart0049376 TOPRIM topoisomerases, DnaG-type primases, OLD fam 99.28
PRK07078 759 hypothetical protein; Validated 99.09
PF12965130 DUF3854: Domain of unknown function (DUF3854); Int 99.02
PF1041059 DnaB_bind: DnaB-helicase binding domain of primase 98.99
cd0018883 TOPRIM Topoisomerase-primase domain. This is a nuc 98.69
PF01751100 Toprim: Toprim domain; InterPro: IPR006171 This is 97.98
PRK04017132 hypothetical protein; Provisional 97.9
PF08278127 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; In 97.79
COG1658127 Small primase-like proteins (Toprim domain) [DNA r 97.66
TIGR00334174 5S_RNA_mat_M5 ribonuclease M5. This family of orth 97.52
smart00766125 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG 97.5
COG4643366 Uncharacterized protein conserved in bacteria [Fun 97.06
PRK14719360 bifunctional RNAse/5-amino-6-(5-phosphoribosylamin 96.15
KOG2373|consensus 514 95.07
PF00772103 DnaB: DnaB-like helicase N terminal domain; InterP 94.46
PF1315477 DUF3991: Protein of unknown function (DUF3991) 94.27
COG3593581 Predicted ATP-dependent endonuclease of the OLD fa 93.86
COG4026290 Uncharacterized protein containing TOPRIM domain, 93.49
cd0102697 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPR 91.84
PRK00076196 recR recombination protein RecR; Reviewed 90.08
cd01025112 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TO 90.01
TIGR00615195 recR recombination protein RecR. This family is ba 87.21
COG0353198 RecR Recombinational DNA repair protein (RecF path 87.12
PRK13844200 recombination protein RecR; Provisional 82.07
>PRK05667 dnaG DNA primase; Validated Back     alignment and domain information 
Probab=100.00  E-value=2.1e-77  Score=641.56  Aligned_cols=417  Identities=36%  Similarity=0.554  Sum_probs=353.4

Q ss_pred             CHHHHHHHHHHhc--CCHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCC
Q psy15222          1 MICASDFYKIQLK--NSKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQ   76 (444)
Q Consensus         1 ~~~a~~~y~~~L~--~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~   76 (444)
                      |+.|++||+.+|.  .++.|++||++||||++||++|+|||+|.+|+.|.++|.+  ++. +.|.++||+..++++    
T Consensus       114 ~~~a~~~y~~~L~~~~~~~a~~YL~~RGls~~~i~~f~lGyap~~~~~L~~~l~~~~~~~-~~l~~~GL~~~~~~~----  188 (580)
T PRK05667        114 MELAAKFYQQQLRTPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSE-KELEEAGLLIKNEDG----  188 (580)
T ss_pred             HHHHHHHHHHHHcCccchHHHHHHHHcCCCHHHHHHhCCccCCChHHHHHHHHHhcCCCH-HHHHHCCceEecCCC----
Confidence            4689999999995  4578999999999999999999999999999999999975  666 889999999876541    


Q ss_pred             CcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecC
Q psy15222         77 SPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEG  156 (444)
Q Consensus        77 g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG  156 (444)
                      |      .+||+|++||||||+|.+|+||||+||.+ +++.|||+|||||++|+|++.|||+|.|++++++.++||||||
T Consensus       189 ~------~~yd~Fr~RimfPI~d~~G~vigF~GR~l-~~~~pKYlNSpet~iF~K~~~LYgl~~a~~~i~~~~~viivEG  261 (580)
T PRK05667        189 G------GPYDRFRNRIMFPIRDLRGRVIGFGGRVL-GDDKPKYLNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEG  261 (580)
T ss_pred             C------CcchhcCCeEEEEEECCCCcEEEEEeeec-CCCCCeeeCCCCCCCccCCccccCccHHHHhcccCCeEEEEee
Confidence            4      58999999999999999999999999999 4678999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCc
Q psy15222        157 YMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDP  236 (444)
Q Consensus       157 ~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDp  236 (444)
                      |||||+++|+|++||||++||++|.+|+++|++++++||+|||||.||++||+|+++.++++...|+.|+++.+|+|+||
T Consensus       262 ~~Dvisl~q~Gi~naVA~lGtalt~~~~~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~gkDp  341 (580)
T PRK05667        262 YMDVIALHQAGITNAVASLGTALTEEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDP  341 (580)
T ss_pred             HHHHHHHHHcCCCcEEEeCCCCCCHHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCCCCCh
Confidence            99999999999999999999999999999999999999999999999999999999997777778999999999999999


Q ss_pred             chhhhhhcHHHHHHHHHhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHH
Q psy15222        237 DSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNE  316 (444)
Q Consensus       237 dd~l~~~G~~~~~~~l~~a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~  316 (444)
                      |||++++|.++|.++++++.|+++|+++++.+++|++++++|.++++++.++|+.+++ |++|+.|++++|+++|++.+.
T Consensus       342 dd~l~~~G~~~~~~~i~~a~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~-~~~~~~~~~~l~~~~~~~~~~  420 (580)
T PRK05667        342 DDLVRKEGPEAFRALLEQAIPLSEFLIRRLIPGKDLDTPEGRAALLERAAPLIAKIPD-PTLRDSYRRKLAERLGILDDA  420 (580)
T ss_pred             HHHHHHhCHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHHCcCHHH
Confidence            9999999999999999999999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             HHHHHhhcccccccccccccCCChhHHHHHHHHHHhcCcchhhhcchhhhhhhhccCccHHHHHHHHHHHHHhhCCCCCH
Q psy15222        317 INNLFKINTSSIKHKTIEKKNIQPICIEYQIMKLLISYPSLINEINSEDMIIFSKCSQNYVKMFFQLIDTIHIFKNDIDH  396 (444)
Q Consensus       317 i~~~~~~~~~~~~~~~~~~~~~~~~~~E~~ll~~ll~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  396 (444)
                      +.+.+.....  +   +..+......+|+.+|++|+++|++...+... +... .|  +....+..++..+...+...+.
T Consensus       421 l~~~~~~~~~--~---~~~~~~~~~~~~~~ll~~ll~~p~~~~~~~~~-~~~~-~~--~~~~~~~~l~~~~~~~~~~~~~  491 (580)
T PRK05667        421 QLEQLVPKAQ--E---PQLKAERPRTAERELLALLLQHPELAEEVRDA-LDEE-DF--EGLPLFRALLEAILAQPGLTTG  491 (580)
T ss_pred             HHHHHhhccc--c---ccccccccchHHHHHHHHHHhCHHHHHHHHHh-cccc-cc--cCcHHHHHHHHHHHhcCCCCcH
Confidence            9887653111  1   11122345678999999999999999888653 2111 12  1344455555555553556677


Q ss_pred             HHHHHHHHhh-hHHHHHHHHHHhcCCCCCH-HHH--HHHHHHHHHhh
Q psy15222        397 SKFIKYLKKI-NKNFESIIVKIQDNFEYSI-EIA--KKTLLDAIYKD  439 (444)
Q Consensus       397 ~~l~~~l~~~-~~~~~~~~~~~~~~~e~~~-e~~--~~~~~~~~~~~  439 (444)
                      ..|++.+.+. ...+...+..+....+... +..  .+.+.|++...
T Consensus       492 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~d~~~~l  538 (580)
T PRK05667        492 SQLLEHLRDAGLEELAALLESLAVWEEISEEDIAALEKELKDALEKL  538 (580)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHhccccccchhhhHHHHHHHHHHHHH
Confidence            7999999976 2223333344443344332 222  47777776654

>TIGR01391 dnaG DNA primase, catalytic core Back     alignment and domain information
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00646 MG010 DNA primase-related protein Back     alignment and domain information
>PHA02540 61 DNA primase; Provisional Back     alignment and domain information
>PHA02031 putative DnaG-like primase Back     alignment and domain information
>PRK08624 hypothetical protein; Provisional Back     alignment and domain information
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>PHA02415 DNA primase domain-containing protein Back     alignment and domain information
>PRK04031 DNA primase; Provisional Back     alignment and domain information
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>PF13155 Toprim_2: Toprim-like Back     alignment and domain information
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A Back     alignment and domain information
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea Back     alignment and domain information
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>PF13362 Toprim_3: Toprim domain Back     alignment and domain information
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>PRK07078 hypothetical protein; Validated Back     alignment and domain information
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [] Back     alignment and domain information
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase [] Back     alignment and domain information
>cd00188 TOPRIM Topoisomerase-primase domain Back     alignment and domain information
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase Back     alignment and domain information
>PRK04017 hypothetical protein; Provisional Back     alignment and domain information
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome Back     alignment and domain information
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5 Back     alignment and domain information
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding Back     alignment and domain information
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional Back     alignment and domain information
>KOG2373|consensus Back     alignment and domain information
>PF00772 DnaB: DnaB-like helicase N terminal domain; InterPro: IPR007693 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork Back     alignment and domain information
>PF13154 DUF3991: Protein of unknown function (DUF3991) Back     alignment and domain information
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair] Back     alignment and domain information
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only] Back     alignment and domain information
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR Back     alignment and domain information
>TIGR00615 recR recombination protein RecR Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query444
1dd9_A338 Structure Of The Dnag Catalytic Core Length = 338 2e-54
3b39_A322 Structure Of The Dnag Primase Catalytic Domain Boun 3e-54
1eqn_A321 E.Coli Primase Catalytic Core Length = 321 1e-50
2au3_A407 Crystal Structure Of The Aquifex Aeolicus Primase ( 1e-33
4e2k_A329 The Structure Of The S. Aureus Dnag Rna Polymerase 6e-30
>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core Length = 338 Back     alignment and structure 
Iteration: 1

 Score =  209 bits (532), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 163/271 (60%), Gaps = 15/271 (5%)
Query: 7   FYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEW-NALNKVFLDYNNINTLASS 63
           FY+  L+   +  A  +L+KRGL+ E+I RF +G+AP  W N L +   +  N  +L  +
Sbjct: 31  FYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDA 90
Query: 64  GLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINS 123
           G++V             ++ + YDRFR R+MFPI++  G++IGFGGR++ + +  KY+NS
Sbjct: 91  GMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 138
Query: 124 PETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTSTH 183
           PET +FHK  +LYGL+EA+    +   +L+ EGYMDV+ L+Q+G    VA LGT+ T+ H
Sbjct: 139 PETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADH 198
Query: 184 IKKILFYTNSIIFSFDGDQXXXXXXXXXLEVCLLYATDDKIIKFLFLPDKYDPDSYIRKF 243
           I+ +   TN++I  +DGD+         LE  L Y TD + ++F+FLPD  DPD+ +RK 
Sbjct: 199 IQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKE 258
Query: 244 GYKIFSKKVLEAMSLLQFFLEEIILNYNLKT 274
           G + F  ++ +AM L  F    ++   +L T
Sbjct: 259 GKEAFEARMEQAMPLSAFLFNSLMPQVDLST 289
>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To Ssdna Length = 322 Back     alignment and structure
>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core Length = 321 Back     alignment and structure
>pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc Binding And Rna Polymerase Domains) Length = 407 Back     alignment and structure
>pdb|4E2K|A Chain A, The Structure Of The S. Aureus Dnag Rna Polymerase Domain Length = 329 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query444
1dd9_A338 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 1e-121
2au3_A407 DNA primase; zinc ribbon, toprim, RNA polymerase, 1e-119
4edg_A329 DNA primase; catalytic domain, nucleoside triphosp 1e-114
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-05
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Length = 338 Back     alignment and structure
 Score =  356 bits (915), Expect = e-121
 Identities = 117/320 (36%), Positives = 183/320 (57%), Gaps = 16/320 (5%)

Query: 1   MICASDFYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYN-NI 57
           M   + FY+  L+   +  A  +L+KRGL+ E+I RF +G+AP  W+ + K F     N 
Sbjct: 25  MDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENR 84

Query: 58  NTLASSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNE 117
            +L  +G++V             ++ + YDRFR R+MFPI++  G++IGFGGR++ +   
Sbjct: 85  QSLIDAGMLVTN-----------DQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGND-T 132

Query: 118 AKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGT 177
            KY+NSPET +FHK  +LYGL+EA+    +   +L+ EGYMDV+ L+Q+G    VA LGT
Sbjct: 133 PKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGT 192

Query: 178 ACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPD 237
           + T+ HI+ +   TN++I  +DGD+AGR AA RALE  L Y TD + ++F+FLPD  DPD
Sbjct: 193 STTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPD 252

Query: 238 SYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSS 297
           + +RK G + F  ++ +AM L  F    ++   +L T     +       L   +P   +
Sbjct: 253 TLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP-GET 311

Query: 298 LRFKIISSLSKIIKVSFNEI 317
           LR  +   L   + +  +  
Sbjct: 312 LRIYLRQELGNKLGILDDSQ 331
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transf; HET: DNA; 2.00A {Aquifex aeolicus} Length = 407 Back     alignment and structure
>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside polyph protein-ligand complex, transferase; HET: DNA ATP; 2.00A {Staphylococcus aureus} PDB: 4edk_A* 4edr_A* 4edt_A* 4edv_A* 4ee1_A* Length = 329 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query444
4edg_A329 DNA primase; catalytic domain, nucleoside triphosp 100.0
1dd9_A338 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 100.0
2au3_A407 DNA primase; zinc ribbon, toprim, RNA polymerase, 100.0
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim f 100.0
1q57_A 503 DNA primase/helicase; dntpase, DNA replication, tr 100.0
1t6t_1118 Putative protein; structural genomics, PSI, protei 99.48
2fcj_A119 Small toprim domain protein; structural genomics, 98.38
1t3w_A148 DNA primase; DNAG, DNA-directed RNA polymerase, E. 97.4
2r6a_C143 DNAG primase, helicase binding domain, replicative 93.81
1b79_A119 DNAB helicase; hexamer, DNA replication, hydrolase 90.58
3gxv_A123 Replicative DNA helicase; hexameric helicase, prim 88.04
3vdp_A212 Recombination protein RECR; zinc finger, DNA repai 87.32
1vdd_A228 Recombination protein RECR; helix-hairpin-helix, z 85.72
2r5u_A200 Replicative DNA helicase; DNAB, primase, replicati 85.5
>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside polyph protein-ligand complex, transferase; HET: DNA ATP; 2.00A {Staphylococcus aureus} PDB: 4e2k_A* 4edk_A* 4edr_A* 4edt_A* 4edv_A* 4ee1_A* Back     alignment and structure
Probab=100.00  E-value=2.1e-76  Score=593.83  Aligned_cols=302  Identities=30%  Similarity=0.510  Sum_probs=281.6

Q ss_pred             CHHHHHHHHHHhcC---CHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhc--cCCchhHHHHcCCceeccccccC
Q psy15222          1 MICASDFYKIQLKN---SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFL--DYNNINTLASSGLVVDKIINKVN   75 (444)
Q Consensus         1 ~~~a~~~y~~~L~~---~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~--~~~~~~~l~~~GL~~~~~~~~~~   75 (444)
                      |+.|++|||++|.+   +..|++||++||||+++|++|+|||+|++|+.|.++|.  +|+. +.|.++||+..+++    
T Consensus        12 ~~~a~~~y~~~L~~~~~g~~a~~YL~~Rgl~~e~i~~f~lGyap~~~~~l~~~l~~~g~~~-~~l~~~GL~~~~~~----   86 (329)
T 4edg_A           12 HELIQEFYYYALTKTVEGEQALTYLQERGFTDALIKERGIGFAPDSSHFCHDFLQKKGYDI-ELAYEAGLLSRNEE----   86 (329)
T ss_dssp             HHHHHHHHHHHHHHSSTTHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHHHTTCCH-HHHHHTTSEEEETT----
T ss_pred             HHHHHHHHHHHHccCcccHHHHHHHHHcCCCHHHHHhCCeeeccCcHHHHHHHHHHCCCCH-HHHHHCCCeEECCC----
Confidence            57899999999964   35799999999999999999999999999999999987  4777 99999999997765    


Q ss_pred             CCcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEec
Q psy15222         76 QSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITE  155 (444)
Q Consensus        76 ~g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvE  155 (444)
                       |     .++||+|++||||||+|.+|+||||+||.+ +++.|||+|||||++|+|++.|||+|.|+++|++.+.+||||
T Consensus        87 -g-----~~~yd~Fr~Ri~fPI~d~~G~vigF~gR~l-~~~~pKYlNspet~~f~K~~~Lygl~~a~~~i~~~~~vivvE  159 (329)
T 4edg_A           87 -N-----FSYYDRFRNRIMFPLKNAQGRIVGYSGRTY-TGQEPKYLNSPETPIFQKRKLLYNLDKARKSIRKLDEIVLLE  159 (329)
T ss_dssp             -T-----TEEEESCCSEEEEEEECTTSCEEEEEEECS-SSCSSSEEECCCCSSCCTTTCCBTHHHHHHHHHHHTCEEEES
T ss_pred             -C-----CccccccCCEEEEEEECCCCCEEEEEeEEC-CCCCCeEeCCCCcccccccchhccHHHHHHHhccCCcEEEEe
Confidence             3     158999999999999999999999999999 556899999999999999999999999999999999999999


Q ss_pred             ChhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCC
Q psy15222        156 GYMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYD  235 (444)
Q Consensus       156 G~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkD  235 (444)
                      ||||||+++|+|++||||++||++|++|+++|++++++||+|||||.||++|++|+++.+.+   .|+.++++.+|+|||
T Consensus       160 G~~Dvial~q~Gi~naVA~lGTalt~~~~~~L~r~~~~Vil~~D~D~AG~~Aa~r~~~~l~~---~g~~v~v~~lP~gkD  236 (329)
T 4edg_A          160 GFMDVIKSDTAGLKNVVATMGTQLSDEHITFIRKLTSNITLMFDGDFAGSEATLKTGQHLLQ---QGLNVFVIQLPSGMD  236 (329)
T ss_dssp             CHHHHHHHHHHTCCSEEECSSSCCCHHHHHHHHHHCSEEEECCCSSHHHHHHHHHHHHHHHH---TTCEEEECCCCTTCC
T ss_pred             cHHHHHHHHHcCCCeEEECCccCCCHHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHh---cCCeEEEEECCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999998764   689999999999999


Q ss_pred             cchhhhhhcHHHHHHHH-HhcCCHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhC
Q psy15222        236 PDSYIRKFGYKIFSKKV-LEAMSLLQFFLEEIILN---YNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIK  311 (444)
Q Consensus       236 pdd~l~~~G~~~~~~~l-~~a~~~~~f~~~~~~~~---~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~g  311 (444)
                      ||||++++|.++|.++| +++.|+++|+++.+.++   +|++++    ++++++.+.|+.+++ +++|+.|++++|+.+|
T Consensus       237 pdd~l~~~G~~~~~~~i~~~~~~~~~f~~~~~~~~~~~~~l~~~----~~~~~~~~~i~~i~~-~~~r~~y~~~la~~~~  311 (329)
T 4edg_A          237 PDEYIGKYGNDAFTTFVKNDKKSFAHYKVSILKDEIAHNDLSYE----RYLKELSHDISLMKS-SILQQKAINDVAPFFN  311 (329)
T ss_dssp             HHHHHHHHCHHHHHHHHHHCCEEHHHHHHHHTHHHHHHCHHHHH----HHHHHHHHHHHHCCC-HHHHHHHHHHHGGGGT
T ss_pred             HHHHHHHhCHHHHHHHHHhcCCCHHHHHHHHHHhhccCCCCcHH----HHHHHHHHHHHhCCC-HHHHHHHHHHHHHHHC
Confidence            99999999999999985 78999999999999888   776655    899999999999999 9999999999999999


Q ss_pred             CCHHHHHHHHh
Q psy15222        312 VSFNEINNLFK  322 (444)
Q Consensus       312 i~~~~i~~~~~  322 (444)
                      ++++.|.+.+.
T Consensus       312 i~~~~l~~~~~  322 (329)
T 4edg_A          312 VSPEQLANEIQ  322 (329)
T ss_dssp             CCHHHHHHHC-
T ss_pred             cCHHHHHHHHH
Confidence            99999988764
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Back     alignment and structure
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transf; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Back     alignment and structure
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Back     alignment and structure
>1t6t_1 Putative protein; structural genomics, PSI, protein structur initiative, midwest center for structural genomics, MCSG, U function; 1.80A {Aquifex aeolicus} SCOP: c.136.1.1 Back     alignment and structure
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Back     alignment and structure
>1t3w_A DNA primase; DNAG, DNA-directed RNA polymerase, E. coli, DNA replication, replication; HET: DNA MSE; 2.80A {Escherichia coli} SCOP: a.236.1.1 PDB: 2haj_A* Back     alignment and structure
>2r6a_C DNAG primase, helicase binding domain, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_G 1z8s_A* Back     alignment and structure
>1b79_A DNAB helicase; hexamer, DNA replication, hydrolase; 2.30A {Escherichia coli} SCOP: a.81.1.1 PDB: 1jwe_A Back     alignment and structure
>3gxv_A Replicative DNA helicase; hexameric helicase, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication; 2.20A {Helicobacter pylori} PDB: 3gxv_D 3gxv_C Back     alignment and structure
>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D Back     alignment and structure
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Back     alignment and structure
>2r5u_A Replicative DNA helicase; DNAB, primase, replication, ATP-binding, autocatal cleavage, DNA replication, DNA-binding, endonuclease; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 444
d1dd9a_314 e.13.1.1 (A:) DNA primase DnaG catalytic core {Esc 1e-45
d1t6t1_108 c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquif 5e-16
d1nuia1192 e.13.1.2 (A:64-255) Primase fragment of primase-he 3e-14
d2fcja1114 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 3e-12
>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]} Length = 314 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]

 Score =  158 bits (401), Expect = 1e-45
 Identities = 112/312 (35%), Positives = 176/312 (56%), Gaps = 14/312 (4%)

Query: 4   ASDFYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLDYNNINTLA 61
            + FY+  L+   +  A  +L+KRGL+ E+I RF +G+AP  W+ + K F          
Sbjct: 9   LNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNP------ 62

Query: 62  SSGLVVDKIINKVNQSPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYI 121
                  + +         ++ + YDRFR R+MFPI++  G++IGFGGR++ + +  KY+
Sbjct: 63  ----ENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYL 117

Query: 122 NSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEGYMDVIGLSQFGFLQTVAILGTACTS 181
           NSPET +FHK  +LYGL+EA+    +   +L+ EGYMDV+ L+Q+G    VA LGT+ T+
Sbjct: 118 NSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTA 177

Query: 182 THIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIR 241
            HI+ +   TN++I  +DGD+AGR AA RALE  L Y TD + ++F+FLPD  DPD+ +R
Sbjct: 178 DHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVR 237

Query: 242 KFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFK 301
           K G + F  ++ +AM L  F    ++   +L T     +       L   +P   +LR  
Sbjct: 238 KEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP-GETLRIY 296

Query: 302 IISSLSKIIKVS 313
           +   L   + + 
Sbjct: 297 LRQELGNKLGIL 308
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Length = 108 Back     information, alignment and structure
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Length = 192 Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Length = 114 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query444
d1dd9a_314 DNA primase DnaG catalytic core {Escherichia coli 100.0
d1nuia1192 Primase fragment of primase-helicase protein {Bact 99.95
d1t6t1_108 Hypothetical protein aq_2086 {Aquifex aeolicus [Ta 99.86
d2fcja1114 Hypothetical protein RBSTP2199 {Bacillus stearothe 99.6
d1t3wa_134 DNA primase DnaG, C-terminal domain {Escherichia c 97.7
d1b79a_102 N-terminal domain of DnaB helicase {Escherichia co 93.42
d1vdda_199 Recombination protein RecR {Deinococcus radioduran 82.45
>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.3e-76  Score=591.26  Aligned_cols=303  Identities=39%  Similarity=0.691  Sum_probs=286.5

Q ss_pred             CHHHHHHHHHHhcC--CHHHHHHHHHcCCCHHHHHHccceeecCCchHHHHHhcc--CCchhHHHHcCCceeccccccCC
Q psy15222          1 MICASDFYKIQLKN--SKEAINFLKKRGLNEEIILRFNLGYAPNEWNALNKVFLD--YNNINTLASSGLVVDKIINKVNQ   76 (444)
Q Consensus         1 ~~~a~~~y~~~L~~--~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~L~~~l~~--~~~~~~l~~~GL~~~~~~~~~~~   76 (444)
                      |+.|++|||++|.+  +++|++||++||||+++|++|+|||||.+|+.|.+++.+  ++. +.|..+||+..+++     
T Consensus         6 ~~~a~~~y~~~L~~~~~~~a~~YL~~Rgl~~~~i~~f~lGyap~~~~~l~~~l~~~~~~~-~~l~~~gl~~~~~~-----   79 (314)
T d1dd9a_           6 MDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENR-QSLIDAGMLVTNDQ-----   79 (314)
T ss_dssp             HHHHHHHHHHHHTSGGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHCSSHHHH-HHHHHTTSEEEC-------
T ss_pred             HHHHHHHHHHHhCCCchHHHHHHHHHCCCCHHHHHHcccccCcccHHHHHHHHhhCCCch-hhhhhhhheeeccc-----
Confidence            47899999999986  478999999999999999999999999999999999975  555 89999999998876     


Q ss_pred             CcccccccccccCCceEEEEEecCCCCEEEEEeeecCCCCCcccccCCCCCccccCCcccCcHHHHHHhhccCcEEEecC
Q psy15222         77 SPVIEKYKRYDRFRGRIMFPIKNTDGQIIGFGGRLIKDSNEAKYINSPETPLFHKSNELYGLFEAKNAIEKSGYVLITEG  156 (444)
Q Consensus        77 g~~~~~~~~yd~F~~RiifPI~d~~G~vvgf~gR~l~~~~~pKYlNspet~~F~K~~~Lygl~~a~~~i~~~~~viIvEG  156 (444)
                      |      .+||+|++||||||+|.+|+||||+||.+ ++..|||+|||||++|+|++.|||++.|++.+++.++||||||
T Consensus        80 g------~~~d~F~~ri~fPI~d~~g~~i~f~gR~~-~~~~~KY~ns~et~~f~k~~~ly~~~~a~~~~~~~~~~iivEG  152 (314)
T d1dd9a_          80 G------RSYDRFRERVMFPIRDKRGRVIGFGGRVL-GNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEG  152 (314)
T ss_dssp             -------CEEESCCSEEEEEEECTTSCEEEEEEEES-SSCSCSEEECCCCSSCCTTTCCBTHHHHHHTCSSCSCEEEESS
T ss_pred             c------ccchhccceeEEEEecccceEEEEeeeec-ccccccccCCCccccccchhhcccHHHHHhhhccccceEEEec
Confidence            5      68999999999999999999999999999 6678999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHcCCCeEEEcCCccCCHHHHHHHhccCCeEEEEeCCChhHHHHHHHHHHHHHhhcCCCcEEEEEeCCCCCCc
Q psy15222        157 YMDVIGLSQFGFLQTVAILGTACTSTHIKKILFYTNSIIFSFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDP  236 (444)
Q Consensus       157 ~~Dvlsl~q~Gi~naVA~lGtalt~~q~~~L~r~~~~Vil~~D~D~AG~~aa~r~~~~l~~~~~~g~~v~v~~lP~gkDp  236 (444)
                      |||||+++|+|++||||+|||++|++|++.|++++++|++|||||.||++|+.|+++.++++...|+.|+++.+|+|+||
T Consensus       153 ~~Dvi~l~q~Gi~n~Va~~Gta~t~~~~~~l~~~~~~i~l~~D~D~AG~~A~~r~~~~~~~~~~~g~~v~v~~lp~g~DP  232 (314)
T d1dd9a_         153 YMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDP  232 (314)
T ss_dssp             HHHHHHHHHTTCCCEEECCC-CCCHHHHHHHHHHCSEEEEEEESSHHHHHHHHHHHHHHGGGCCTTCEEEEEEECTTCCH
T ss_pred             hHHHHHHHHcccccchhHHhhhhhhHHHHHHHhcCCceEEEeecCcchhhHHHhHHHHhhHHhcCCCeEEEEeccCcCCH
Confidence            99999999999999999999999999999999999999999999999999999999998887778999999999999999


Q ss_pred             chhhhhhcHHHHHHHHHhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhCCCHHH
Q psy15222        237 DSYIRKFGYKIFSKKVLEAMSLLQFFLEEIILNYNLKTIKDIEKSKYNIEYLFKIIPLSSSLRFKIISSLSKIIKVSFNE  316 (444)
Q Consensus       237 dd~l~~~G~~~~~~~l~~a~~~~~f~~~~~~~~~~~~~~~~k~~~~~~~~~~l~~i~~~~~~r~~~~~~la~~~gi~~~~  316 (444)
                      |||++++|.++|.++++++.|+++|+++.+.+++|++++++|.++++++.++++.+++ +++|+.|++++|+++|+++++
T Consensus       233 De~l~k~G~e~~~~ll~~a~~~~eFli~~~~~~~d~~s~e~k~~~~~~l~~~i~~i~d-~~~r~~y~~~la~~lgise~a  311 (314)
T d1dd9a_         233 DTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPG-ETLRIYLRQELGNKLGILDDS  311 (314)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEHHHHHHHHHGGGCCTTSHHHHHHHHHHHHHHHTTCCC-HHHHHHHHHHHHHHHTCSCGG
T ss_pred             HHHHHhcCHHHHHHHHhcCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHcCCChHH
Confidence            9999999999999999999999999999999999999999999999999999999999 999999999999999999765


Q ss_pred             H
Q psy15222        317 I  317 (444)
Q Consensus       317 i  317 (444)
                      +
T Consensus       312 ~  312 (314)
T d1dd9a_         312 Q  312 (314)
T ss_dssp             G
T ss_pred             h
Confidence            3
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1t3wa_ a.236.1.1 (A:) DNA primase DnaG, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1b79a_ a.81.1.1 (A:) N-terminal domain of DnaB helicase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure