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Conserved domains on  [gi|1473448676|ref|WP_117908021|]
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DnaB-like helicase C-terminal domain-containing protein [Bacteroides stercoris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 245-316 2.75e-07

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


:

Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 48.89  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 245 RLIVTEGERDVLTLREA---GYQYVISVpNGAASDLSKG-----FEAFRPWLDRVQELVICGDSDLPGRTLVKHLADYFG 316
Cdd:pfam01751   1 ELIIVEGPSDAIALEKAlggGFQAVVAV-LGHLLSLEKGpkkkaLKALKELALKAKEVILATDPDREGEAIALKLLELKE 79
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 410-608 9.64e-07

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19483:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 231  Bit Score: 50.26  E-value: 9.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 410 GKTDFLNDLTCRLMAKTGRNVCYLSFEVPDKnKHMANLIRLMLGKVNTAAY-----TREQLQPIVS--FMDRHMVHLDlH 482
Cdd:cd19483    10 GKSTIVRELAYHLITEHGEKVGIISLEESVE-ETAKGLAGKHLGKPEPLELprddiTEEEEDDAFDneLGSGRFFLYD-H 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 483 EVSPTPANIIERAERVKRTMPLKYLIIDPyLFMEMETGRYNTETQAIKGMLTQMQAWGRNNGVWVIIVAHprsLKKLNGK 562
Cdd:cd19483    88 FGSLDWDNLKEKIRYMVKVLGCKVIVLDH-LTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSH---LRRPGGG 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1473448676 563 NELEE---IDMYTISGSANWANLADFIFSISRIEEPDRRY----TRLDMLKVR 608
Cdd:cd19483   164 KGHEEggeVSESDLRGSSAIAQLSDYVIGLERNKQADDPVerntTRVRVLKNR 216
PLN02712 super family cl33553
arogenate dehydrogenase
 574-648 3.03e-03

arogenate dehydrogenase


The actual alignment was detected with superfamily member PLN02712:

Pssm-ID: 215382 [Multi-domain]  Cd Length: 667  Bit Score: 40.73  E-value: 3.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473448676 574 SGSANWANLAdFIFSISRIEEPDRRYTRLD-MLKVRDQDLCRtgsvlFVRQPCGRYDERESEEQIMTEMQGKVLDK 648
Cdd:PLN02712  491 SGKNGWNNLA-FVFDKVRIGSDDRRVSRCDsFLDIFAREGCR-----MVEMSCAEHDWHAAGSQFITHTMGRLLEK 560
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 245-316 2.75e-07

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 48.89  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 245 RLIVTEGERDVLTLREA---GYQYVISVpNGAASDLSKG-----FEAFRPWLDRVQELVICGDSDLPGRTLVKHLADYFG 316
Cdd:pfam01751   1 ELIIVEGPSDAIALEKAlggGFQAVVAV-LGHLLSLEKGpkkkaLKALKELALKAKEVILATDPDREGEAIALKLLELKE 79
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 244-305 3.27e-07

TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.


Pssm-ID: 173779 [Multi-domain]  Cd Length: 79  Bit Score: 48.04  E-value: 3.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473448676 244 PRLIVTEGERDVLTLREAGYQYVISVPNGAASDlskgfEAFRPWLDRVQELVICGDSDLPGR 305
Cdd:cd01029     1 DEVIIVEGYMDVLALHQAGIKNVVAALGTANTE-----EQLRLLKRFARTVILAFDNDEAGK 57
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 410-608 9.64e-07

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 50.26  E-value: 9.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 410 GKTDFLNDLTCRLMAKTGRNVCYLSFEVPDKnKHMANLIRLMLGKVNTAAY-----TREQLQPIVS--FMDRHMVHLDlH 482
Cdd:cd19483    10 GKSTIVRELAYHLITEHGEKVGIISLEESVE-ETAKGLAGKHLGKPEPLELprddiTEEEEDDAFDneLGSGRFFLYD-H 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 483 EVSPTPANIIERAERVKRTMPLKYLIIDPyLFMEMETGRYNTETQAIKGMLTQMQAWGRNNGVWVIIVAHprsLKKLNGK 562
Cdd:cd19483    88 FGSLDWDNLKEKIRYMVKVLGCKVIVLDH-LTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSH---LRRPGGG 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1473448676 563 NELEE---IDMYTISGSANWANLADFIFSISRIEEPDRRY----TRLDMLKVR 608
Cdd:cd19483   164 KGHEEggeVSESDLRGSSAIAQLSDYVIGLERNKQADDPVerntTRVRVLKNR 216
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
245-316 1.15e-06

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 46.49  E-value: 1.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1473448676  245 RLIVTEGERDVLTLREAG-YQYVISVPNGAASDLSKGFEAFRPWLDrvQELVICGDSDLPGRTLVKHLADYFG 316
Cdd:smart00493   2 VLIIVEGPADAIALEKAGgKRGNVVALGGHLLSKEQIKLLKKLAKK--AEVILATDPDREGEAIAWELAELLK 72
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 398-554 2.98e-05

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 45.45  E-value: 2.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 398 GGLIIATGKPNSGKTDFLNDLTCRLM----------AKTGRNVCYLSFEvpDKNKHMANLIRLMLgkvntAAYTREQLQP 467
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAVAtgkpwlggprVPEQGKVLYVSAE--GPADELRRRLRAAG-----ADLDLPARLL 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 468 IVS-FMDRHMVHLDLHEVSPTPAnIIERAERVKRTMPLKYLIIDPYLFMemeTGRYNTETQAIKGMLTQMQAWGRNNGVW 546
Cdd:pfam13481 106 FLSlVESLPLFFLDRGGPLLDAD-VDALEAALEEVEDPDLVVIDPLARA---LGGDENSNSDVGRLVKALDRLARRTGAT 181


                  ....*...
gi 1473448676 547 VIIVAHPR 554
Cdd:pfam13481 182 VLLVHHVG 189
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
356-529 2.39e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 43.91  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 356 SDIIT-VSERADEIMNvlNGNYDHGYDVGYGPLtDRV---FHPTDqggLIIATGKPNSGKTDFLNDLTCRLMAKTGRNVC 431
Cdd:COG0305   151 SDILKeALERIEELYK--NGGGITGVPTGFTDL-DKLtggLQPGD---LIILAARPSMGKTAFALNIARNAAIKEGKPVA 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 432 YLSFEVPDK---NKHMANLIRLMLGKVNTAAYTREQLQPIVSFMDRhMVHLDLH---EVSPTPANIIERAERVKRTMPLK 505
Cdd:COG0305   225 IFSLEMSAEqlvMRLLSSEARIDSSKLRTGKLSDEDWERLSSAAGE-LSEAPIYiddTPGLTIAEIRAKARRLKREHGLG 303

                         170       180
                  ....*....|....*....|....*
gi 1473448676 506 YLIIDpYL-FMEMeTGRYNTETQAI 529
Cdd:COG0305   304 LIVID-YLqLMSG-SGRSENRQQEI 326
PRK08840 PRK08840
replicative DNA helicase; Provisional
 379-596 4.98e-04

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 43.05  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 379 GYDVGYGPLTDRVfhPTDQGG-LIIATGKPNSGKTDFLNDLTCRLMAKTGRNVCYLSFEVPDKN---KHMANLIRLMLGK 454
Cdd:PRK08840  199 GVDTGFTDLNKKT--AGLQGSdLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQlmmRMLASLSRVDQTK 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 455 VNTAAYTREQLQPIVS----FMDRHMVHLDlHEVSPTPANIIERAERVKRTMPLKYLIIDPYLFMEMETGRYNTETQAIK 530
Cdd:PRK08840  277 IRTGQLDDEDWARISStmgiLMEKKNMYID-DSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPALSDNRTLEIA 355

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1473448676 531 GMLTQMQAWGRNNGVWVIIVAH-PRSLKKLNGK----NELEEidmytiSGSANwaNLADFIFSISRIE--EPD 596
Cdd:PRK08840  356 EISRSLKALAKELNVPVVALSQlNRSLEQRADKrpvnSDLRE------SGSIE--QDADLIMFIYRDEvyNPD 420
PLN02712 PLN02712
arogenate dehydrogenase
 574-648 3.03e-03

arogenate dehydrogenase


Pssm-ID: 215382 [Multi-domain]  Cd Length: 667  Bit Score: 40.73  E-value: 3.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473448676 574 SGSANWANLAdFIFSISRIEEPDRRYTRLD-MLKVRDQDLCRtgsvlFVRQPCGRYDERESEEQIMTEMQGKVLDK 648
Cdd:PLN02712  491 SGKNGWNNLA-FVFDKVRIGSDDRRVSRCDsFLDIFAREGCR-----MVEMSCAEHDWHAAGSQFITHTMGRLLEK 560
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 245-316 2.75e-07

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 48.89  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 245 RLIVTEGERDVLTLREA---GYQYVISVpNGAASDLSKG-----FEAFRPWLDRVQELVICGDSDLPGRTLVKHLADYFG 316
Cdd:pfam01751   1 ELIIVEGPSDAIALEKAlggGFQAVVAV-LGHLLSLEKGpkkkaLKALKELALKAKEVILATDPDREGEAIALKLLELKE 79
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 244-305 3.27e-07

TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.


Pssm-ID: 173779 [Multi-domain]  Cd Length: 79  Bit Score: 48.04  E-value: 3.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473448676 244 PRLIVTEGERDVLTLREAGYQYVISVPNGAASDlskgfEAFRPWLDRVQELVICGDSDLPGR 305
Cdd:cd01029     1 DEVIIVEGYMDVLALHQAGIKNVVAALGTANTE-----EQLRLLKRFARTVILAFDNDEAGK 57
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 245-306 7.78e-07

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 47.28  E-value: 7.78e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1473448676 245 RLIVTEGERDVLTLREAGYQYVISVPNGAASDLSK-GFE-AFRPWLDRVQELVICGDSDLPGRT 306
Cdd:pfam13662   2 EIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDGiGPEdLNIDSLGGIKEVILALDGDVAGEK 65
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 410-608 9.64e-07

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 50.26  E-value: 9.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 410 GKTDFLNDLTCRLMAKTGRNVCYLSFEVPDKnKHMANLIRLMLGKVNTAAY-----TREQLQPIVS--FMDRHMVHLDlH 482
Cdd:cd19483    10 GKSTIVRELAYHLITEHGEKVGIISLEESVE-ETAKGLAGKHLGKPEPLELprddiTEEEEDDAFDneLGSGRFFLYD-H 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 483 EVSPTPANIIERAERVKRTMPLKYLIIDPyLFMEMETGRYNTETQAIKGMLTQMQAWGRNNGVWVIIVAHprsLKKLNGK 562
Cdd:cd19483    88 FGSLDWDNLKEKIRYMVKVLGCKVIVLDH-LTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSH---LRRPGGG 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1473448676 563 NELEE---IDMYTISGSANWANLADFIFSISRIEEPDRRY----TRLDMLKVR 608
Cdd:cd19483   164 KGHEEggeVSESDLRGSSAIAQLSDYVIGLERNKQADDPVerntTRVRVLKNR 216
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
245-316 1.15e-06

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 46.49  E-value: 1.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1473448676  245 RLIVTEGERDVLTLREAG-YQYVISVPNGAASDLSKGFEAFRPWLDrvQELVICGDSDLPGRTLVKHLADYFG 316
Cdd:smart00493   2 VLIIVEGPADAIALEKAGgKRGNVVALGGHLLSKEQIKLLKKLAKK--AEVILATDPDREGEAIAWELAELLK 72
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 245-315 2.30e-06

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 45.88  E-value: 2.30e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473448676 245 RLIVTEGERDVLTLREAG-YQYVISVPNGAASDLSkgFEAFRPWLDRVQELVICGDSDLPGRTLVKHLADYF 315
Cdd:cd00188     2 KLIIVEGPSDALALAQAGgYGGAVVALGGHALNKT--RELLKRLLGEAKEVIIATDADREGEAIALRLLELL 71
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 398-554 2.98e-05

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 45.45  E-value: 2.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 398 GGLIIATGKPNSGKTDFLNDLTCRLM----------AKTGRNVCYLSFEvpDKNKHMANLIRLMLgkvntAAYTREQLQP 467
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAVAtgkpwlggprVPEQGKVLYVSAE--GPADELRRRLRAAG-----ADLDLPARLL 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 468 IVS-FMDRHMVHLDLHEVSPTPAnIIERAERVKRTMPLKYLIIDPYLFMemeTGRYNTETQAIKGMLTQMQAWGRNNGVW 546
Cdd:pfam13481 106 FLSlVESLPLFFLDRGGPLLDAD-VDALEAALEEVEDPDLVVIDPLARA---LGGDENSNSDVGRLVKALDRLARRTGAT 181


                  ....*...
gi 1473448676 547 VIIVAHPR 554
Cdd:pfam13481 182 VLLVHHVG 189
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 392-529 3.37e-05

C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 410864 [Multi-domain]  Cd Length: 256  Bit Score: 45.97  E-value: 3.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 392 FHPTDqggLIIATGKPNSGKTDFLNDLTCRLMAKTGRNVCYLSFEVPDK---NKHMANLIRLMLGKVNTAAYTREQLQPI 468
Cdd:cd00984    16 LQPGD---LIIIAARPSMGKTAFALNIAENIALDEGLPVLFFSLEMSAEqlaERLLSSESGVSLSKLRTGRLDDEDWERL 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473448676 469 VSFMDRhMVHLDLH---EVSPTPANIIERAERVKRTMP-LKYLIIDpYL-FMEMEtGRYNTETQAI 529
Cdd:cd00984    93 TAAMGE-LSELPLYiddTPGLTVDEIRAKARRLKREHGgLGLIVID-YLqLIRGS-KRAENRQQEV 155
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 247-335 1.59e-04

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 41.01  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 247 IVTEGERDVLTLREAGYQYVISV-PNGAAsdLSKgfEAFRPWLDRVQELVICGDSDLPGRTLVKHLADYF---GTRCLFT 322
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIKNVLYVaTLGTA--LTE--AQIKLLKRYPKEVILAFDNDEAGRKAAKRLAELLkeaGVDVKIR 76

                          90
                  ....*....|...
gi 1473448676 323 VLPGGcKDISDVL 335
Cdd:pfam13155  77 LLPDG-KDWNEYL 88
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
356-529 2.39e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 43.91  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 356 SDIIT-VSERADEIMNvlNGNYDHGYDVGYGPLtDRV---FHPTDqggLIIATGKPNSGKTDFLNDLTCRLMAKTGRNVC 431
Cdd:COG0305   151 SDILKeALERIEELYK--NGGGITGVPTGFTDL-DKLtggLQPGD---LIILAARPSMGKTAFALNIARNAAIKEGKPVA 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 432 YLSFEVPDK---NKHMANLIRLMLGKVNTAAYTREQLQPIVSFMDRhMVHLDLH---EVSPTPANIIERAERVKRTMPLK 505
Cdd:COG0305   225 IFSLEMSAEqlvMRLLSSEARIDSSKLRTGKLSDEDWERLSSAAGE-LSEAPIYiddTPGLTIAEIRAKARRLKREHGLG 303

                         170       180
                  ....*....|....*....|....*
gi 1473448676 506 YLIIDpYL-FMEMeTGRYNTETQAI 529
Cdd:COG0305   304 LIVID-YLqLMSG-SGRSENRQQEI 326
PRK08840 PRK08840
replicative DNA helicase; Provisional
 379-596 4.98e-04

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 43.05  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 379 GYDVGYGPLTDRVfhPTDQGG-LIIATGKPNSGKTDFLNDLTCRLMAKTGRNVCYLSFEVPDKN---KHMANLIRLMLGK 454
Cdd:PRK08840  199 GVDTGFTDLNKKT--AGLQGSdLIIVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQlmmRMLASLSRVDQTK 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1473448676 455 VNTAAYTREQLQPIVS----FMDRHMVHLDlHEVSPTPANIIERAERVKRTMPLKYLIIDPYLFMEMETGRYNTETQAIK 530
Cdd:PRK08840  277 IRTGQLDDEDWARISStmgiLMEKKNMYID-DSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPALSDNRTLEIA 355

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1473448676 531 GMLTQMQAWGRNNGVWVIIVAH-PRSLKKLNGK----NELEEidmytiSGSANwaNLADFIFSISRIE--EPD 596
Cdd:PRK08840  356 EISRSLKALAKELNVPVVALSQlNRSLEQRADKrpvnSDLRE------SGSIE--QDADLIMFIYRDEvyNPD 420
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 245-305 2.82e-03

TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.


Pssm-ID: 173784 [Multi-domain]  Cd Length: 79  Bit Score: 37.11  E-value: 2.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1473448676 245 RLIVTEGERDVLTLREAGYQYVISVPnGAAsdLSKgfEAFRpWLDR-VQELVICGDSDLPGR 305
Cdd:cd03364     2 KVILVEGYMDVIALHQAGIKNVVASL-GTA--LTE--EQAE-LLKRlAKEVILAFDGDEAGQ 57
PLN02712 PLN02712
arogenate dehydrogenase
 574-648 3.03e-03

arogenate dehydrogenase


Pssm-ID: 215382 [Multi-domain]  Cd Length: 667  Bit Score: 40.73  E-value: 3.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1473448676 574 SGSANWANLAdFIFSISRIEEPDRRYTRLD-MLKVRDQDLCRtgsvlFVRQPCGRYDERESEEQIMTEMQGKVLDK 648
Cdd:PLN02712  491 SGKNGWNNLA-FVFDKVRIGSDDRRVSRCDsFLDIFAREGCR-----MVEMSCAEHDWHAAGSQFITHTMGRLLEK 560
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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