254780553

254780553

Holliday junction DNA helicase RuvA

GeneID in NCBI database:8209549Locus tag:CLIBASIA_02200
Protein GI in NCBI database:254780553Protein Accession:YP_003064966.1
Gene range:+(727084, 727707)Protein Length:207aa
Gene description:Holliday junction DNA helicase RuvA
COG prediction:[L] Holliday junction resolvasome, DNA-binding subunit
KEGG prediction:ruvA; Holliday junction DNA helicase RuvA; K03550 holliday junction DNA helicase RuvA
SEED prediction:Holliday junction DNA helicase RuvA
Pathway involved in KEGG:Homologous recombination [PATH:las03440]
Subsystem involved in SEED:RuvABC plus a hypothetical;
DNA-replication
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC
cccEEEEEEEEEcccEEEEEEccEEEEEEEccHHHHHccccccEEEEEEEEEEcccHHHHcccccHHHHHHHHHHcccccccHHHHHHHHHcccHHHHHHHHHHccHHHHHHcccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHc
cEEEEEEEEEEEEccEEEEEEccEEEEEEccHHHHHHccccccEEEEEEEEEEEccEEEEEEEccHHHHHHHHHHcccccccHHHHHHHHHcccHHHHHHHHHHccHHHHHccccccHHHHHHHHHHHHHHHHHHcccccccHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHcc
MIGKIKGNIEGLYEDYVLIDVQGVCYIIycpirtlsclgkigDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMscvnkeqahicsmpSFAINAISALVnlgygqdqaTTAVVSVLKKEKNIADDSQIIRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILqnskviaqiPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKkekniaddsqiiRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLS**************************AISALVNLGYGQDQATTAVVSVLK*****ADDSQIIRLALRAIS*
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSV***************CSMPSFAINAISALVNLGYGQDQATTAVVSVLKK***IADDSQIIRLALRAISC
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC
MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAISC

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
315122880208 Holliday junction DNA helicase RuvA [Candidatus Liberib 1 6e-95
222086988204 Holliday junction DNA helicase RuvA [Agrobacterium radi 1 2e-49
163758803205 Holliday junction DNA helicase motor protein [Hoeflea p 1 2e-49
332716453205 Holliday junction ATP-dependent DNA helicase ruvA [Agro 1 5e-49
15891225205 Holliday junction DNA helicase motor protein [Agrobacte 1 2e-48
222149652205 Holliday junction DNA helicase RuvA [Agrobacterium viti 1 3e-47
150397836205 Holliday junction DNA helicase RuvA [Sinorhizobium medi 1 2e-46
227823320205 Holliday junction DNA helicase RuvA [Sinorhizobium fred 1 3e-46
86359072204 Holliday junction DNA helicase motor protein [Rhizobium 1 6e-46
299134170205 Holliday junction DNA helicase RuvA [Afipia sp. 1NLS2] 1 1e-45
>gi|315122880|ref|YP_004063369.1| Holliday junction DNA helicase RuvA [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 208 Back     alignment and organism information
 Score =  350 bits (899), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 167/208 (80%), Positives = 194/208 (93%), Gaps = 1/208 (0%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MIGKIKGNIEGLYEDYVLIDVQG+CYI+YCPIRTLSCLGKIGDFCTLFVETH+RQDQIRL
Sbjct: 1   MIGKIKGNIEGLYEDYVLIDVQGICYIVYCPIRTLSCLGKIGDFCTLFVETHVRQDQIRL 60

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           FGFLSDL+R+WF+LLQSVQGVGARVAMGVLSRIT  ELV+SIILQN+K++AQIPGI  K+
Sbjct: 61  FGFLSDLERKWFVLLQSVQGVGARVAMGVLSRITPVELVDSIILQNNKILAQIPGIGAKV 120

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHIC-SMPSFAINAISALVNLGYGQDQATT 179
           ++RIM ELKGKA+SLSS  ++++SC+N E++++C SM S AI+AISALVNLGYGQDQAT 
Sbjct: 121 SNRIMIELKGKAVSLSSSEKKEISCLNGEKSNVCESMSSSAIDAISALVNLGYGQDQATV 180

Query: 180 AVVSVLKKEKNIADDSQIIRLALRAISC 207
           AVVS+LKKEKNI DDSQIIRLALR ++C
Sbjct: 181 AVVSILKKEKNITDDSQIIRLALREMTC 208


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222086988|ref|YP_002545522.1| Holliday junction DNA helicase RuvA [Agrobacterium radiobacter K84] Length = 204 Back     alignment and organism information
>gi|163758803|ref|ZP_02165890.1| Holliday junction DNA helicase motor protein [Hoeflea phototrophica DFL-43] Length = 205 Back     alignment and organism information
>gi|332716453|ref|YP_004443919.1| Holliday junction ATP-dependent DNA helicase ruvA [Agrobacterium sp. H13-3] Length = 205 Back     alignment and organism information
>gi|15891225|ref|NP_356897.1| Holliday junction DNA helicase motor protein [Agrobacterium tumefaciens str. C58] Length = 205 Back     alignment and organism information
>gi|222149652|ref|YP_002550609.1| Holliday junction DNA helicase RuvA [Agrobacterium vitis S4] Length = 205 Back     alignment and organism information
>gi|150397836|ref|YP_001328303.1| Holliday junction DNA helicase RuvA [Sinorhizobium medicae WSM419] Length = 205 Back     alignment and organism information
>gi|227823320|ref|YP_002827292.1| Holliday junction DNA helicase RuvA [Sinorhizobium fredii NGR234] Length = 205 Back     alignment and organism information
>gi|86359072|ref|YP_470964.1| Holliday junction DNA helicase motor protein [Rhizobium etli CFN 42] Length = 204 Back     alignment and organism information
>gi|299134170|ref|ZP_07027363.1| Holliday junction DNA helicase RuvA [Afipia sp. 1NLS2] Length = 205 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
PRK00116192 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Re 9e-52
PRK14604195 PRK14604, ruvA, Holliday junction DNA helicase RuvA; Pr 1e-27
PRK14602203 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Pr 5e-26
PRK14600186 PRK14600, ruvA, Holliday junction DNA helicase RuvA; Pr 5e-25
PRK14605194 PRK14605, ruvA, Holliday junction DNA helicase RuvA; Pr 2e-23
TIGR00084191 TIGR00084, ruvA, Holliday junction DNA helicase, RuvA s 2e-23
PRK14603197 PRK14603, ruvA, Holliday junction DNA helicase RuvA; Pr 7e-18
PRK14606188 PRK14606, ruvA, Holliday junction DNA helicase RuvA; Pr 3e-16
PRK14601183 PRK14601, ruvA, Holliday junction DNA helicase RuvA; Pr 4e-14
COG0632201 COG0632, RuvA, Holliday junction resolvasome, DNA-bindi 1e-43
PRK13901196 PRK13901, ruvA, Holliday junction DNA helicase RuvA; Pr 1e-12
pfam0133061 pfam01330, RuvA_N, RuvA N terminal domain 2e-11
pfam0749947 pfam07499, RuvA_C, RuvA, C-terminal domain 5e-05
>gnl|CDD|178876 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>gnl|CDD|184760 PRK14604, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|173064 PRK14600, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|184761 PRK14605, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|129193 TIGR00084, ruvA, Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>gnl|CDD|184759 PRK14603, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|184762 PRK14606, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|173065 PRK14601, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|139961 PRK13901, ruvA, Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>gnl|CDD|110340 pfam01330, RuvA_N, RuvA N terminal domain Back     alignment and domain information
>gnl|CDD|148866 pfam07499, RuvA_C, RuvA, C-terminal domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 207 Holliday junction DNA helicase RuvA [Candidatus Liberib
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 100.0
COG0632201 RuvA Holliday junction resolvasome, DNA-binding subunit 100.0
PRK13901196 ruvA Holliday junction DNA helicase motor protein; Prov 100.0
TIGR00084217 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR 100.0
pfam0133061 RuvA_N RuvA N terminal domain. The N terminal domain of 99.66
pfam0749947 RuvA_C RuvA, C-terminal domain. Homologous recombinatio 98.53
PRK13766764 Hef nuclease; Provisional 98.12
PRK00558609 uvrC excinuclease ABC subunit C; Validated 97.22
PRK08609 570 hypothetical protein; Provisional 96.99
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recombinati 96.8
smart00483 334 POLXc DNA polymerase X family. includes vertebrate poly 96.15
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 95.95
PRK08609 570 hypothetical protein; Provisional 95.91
cd00141 307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 95.63
TIGR0042670 TIGR00426 competence protein ComEA helix-hairpin-helix 95.46
KOG2534 353 consensus 94.1
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 93.91
COG1796326 POL4 DNA polymerase IV (family X) [DNA replication, rec 93.76
COG1796 326 POL4 DNA polymerase IV (family X) [DNA replication, rec 93.72
KOG2841254 consensus 92.65
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 92.31
PRK10880 350 adenine DNA glycosylase; Provisional 91.83
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 91.63
COG1555149 ComEA DNA uptake protein and related DNA-binding protei 91.55
COG0322581 UvrC Nuclease subunit of the excinuclease complex [DNA 91.07
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 90.92
PRK10702211 endonuclease III; Provisional 90.71
PRK05797 869 consensus 90.54
pfam00730144 HhH-GPD HhH-GPD superfamily base excision DNA repair pr 90.54
COG4277404 Predicted DNA-binding protein with the Helix-hairpin-he 90.31
TIGR02903 616 spore_lon_C ATP-dependent protease, Lon family; InterPr 90.07
TIGR01448 769 recD_rel helicase, RecD/TraA family; InterPro: IPR00634 97.64
PRK07456 975 consensus 94.77
PRK05755 889 DNA polymerase I; Provisional 94.43
PRK06887 954 consensus 94.19
PRK08835 931 consensus 94.07
PRK07300 880 consensus 93.97
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 93.79
PRK07898 902 consensus 93.74
PRK08076 877 consensus 93.73
PRK08928 861 consensus 93.39
PRK05797 869 consensus 91.94
TIGR00615205 recR recombination protein RecR; InterPro: IPR000093 Th 96.89
PRK00076197 recR recombination protein RecR; Reviewed 96.7
PRK13844200 recombination protein RecR; Provisional 96.68
COG0353198 RecR Recombinational DNA repair protein (RecF pathway) 96.08
COG1555149 ComEA DNA uptake protein and related DNA-binding protei 94.79
smart00475259 53EXOc 5'-3' exonuclease. 94.64
pfam0063330 HHH Helix-hairpin-helix motif. The helix-hairpin-helix 94.62
PRK09482256 xni exonuclease IX; Provisional 93.03
TIGR01083192 nth endonuclease III; InterPro: IPR005759 The spectrum 92.34
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) mo 91.99
PRK07456 975 consensus 91.91
PRK10702211 endonuclease III; Provisional 91.21
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1. 90.84
PRK07945 335 hypothetical protein; Provisional 95.22
PTZ00217394 flap endonuclease-1; Provisional 94.68
PRK03980295 flap endonuclease-1; Provisional 93.55
TIGR03674338 fen_arch flap structure-specific endonuclease. Endonucl 92.89
TIGR00593 1005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 94.75
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain of P 92.31
PRK08786 927 consensus 93.84
PRK07997 928 consensus 93.83
PRK07556 977 consensus 92.06
PRK05929 870 consensus 91.92
smart00475259 53EXOc 5'-3' exonuclease. 90.19
PRK08434 887 consensus 90.03
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain of P 93.28
pfam01367100 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold. 90.66
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) mo 90.25
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction Back     alignment and domain information
>pfam01330 RuvA_N RuvA N terminal domain Back     alignment and domain information
>pfam07499 RuvA_C RuvA, C-terminal domain Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae Back     alignment and domain information
>KOG2534 consensus Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG2841 consensus Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10880 adenine DNA glycosylase; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein Back     alignment and domain information
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only] Back     alignment and domain information
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252 This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria Back     alignment and domain information
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>pfam00633 HHH Helix-hairpin-helix motif Back     alignment and domain information
>PRK09482 xni exonuclease IX; Provisional Back     alignment and domain information
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>PRK07945 hypothetical protein; Provisional Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
1bdx_A203 E. Coli Dna Helicase Ruva With Bound Dna Holliday J 2e-46
1cuk_A203 Escherichia Coli Ruva Protein At Ph 4.9 And Room Te 2e-45
2ztc_A212 Mtruva Form Ii Length = 212 7e-32
2h5x_A196 Ruva From Mycobacterium Tuberculosis Length = 196 8e-32
1bvs_A203 Ruva Complexed To A Holliday Junction. Length = 203 2e-29
1ixr_A191 Ruva-Ruvb Complex Length = 191 2e-27
1d8l_A149 E. Coli Holliday Junction Binding Protein Ruva Nh2 1e-31
1ixs_A62 Structure Of Ruvb Complexed With Ruva Domain Iii Le 4e-04
gi|5107494|pdb|1BDX|A Chain A, E. Coli Dna Helicase Ruva With Bound Dna Holliday Junction, Alpha Carbons And Phosphate Atoms Only Length = 203 Back     alignment and structure
 Score =  189 bits (479), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 57/204 (27%), Positives = 99/204 (48%), Gaps = 3/204 (1%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MIG+++G I       VLI+V GV Y ++ P+     L + G    +F    +R+D   L
Sbjct: 1   MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF +  +R  F  L    GVG ++A+ +LS ++A + V ++  +    + ++PGI  K 
Sbjct: 61  YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTA 180
           A R++ E+K +   L   +    + +        +       A++ALV LGY   +A+  
Sbjct: 121 AERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVAALVALGYKPQEASRM 180

Query: 181 VVSVLKKEKNIADDSQIIRLALRA 204
           V  + +     A    +IR ALRA
Sbjct: 181 VSKIAR---PDASSETLIREALRA 201


>gi|157830735|pdb|1CUK|A Chain A, Escherichia Coli Ruva Protein At Ph 4.9 And Room Temperature Length = 203 Back     alignment and structure
>gi|229597664|pdb|2ZTC|A Chain A, Mtruva Form Ii Length = 212 Back     alignment and structure
gi|114794219|pdb|2H5X|A Chain A, Ruva From Mycobacterium Tuberculosis Length = 196 Back     alignment and structure
>gi|6729740|pdb|1BVS|A Chain A, Ruva Complexed To A Holliday Junction. Length = 203 Back     alignment and structure
gi|24987359|pdb|1IXR|A Chain A, Ruva-Ruvb Complex Length = 191 Back     alignment and structure
>gi|7766817|pdb|1D8L|A Chain A, E. Coli Holliday Junction Binding Protein Ruva Nh2 Region Lacking Domain Iii Length = 149 Back     alignment and structure
>gi|24987362|pdb|1IXS|A Chain A, Structure Of Ruvb Complexed With Ruva Domain Iii Length = 62 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-binding, DN 2e-49
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligomeric c 2e-39
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; reco 7e-31
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 7e-05
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Length = 203 Back     alignment and structure
 Score =  190 bits (484), Expect = 2e-49
 Identities = 56/204 (27%), Positives = 99/204 (48%), Gaps = 3/204 (1%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MIG+++G I       VLI+V GV Y ++ P+     L + G    +F    +R+D   L
Sbjct: 1   MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF +  +R  F  L    GVG ++A+ +LS ++A + V ++  +    + ++PGI  K 
Sbjct: 61  YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTA 180
           A R++ E+K +   L   +    + +        +       A++ LV LGY   +A+  
Sbjct: 121 AERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVARLVALGYKPQEASRM 180

Query: 181 VVSVLKKEKNIADDSQIIRLALRA 204
           V  + + +   A    +IR ALRA
Sbjct: 181 VSKIARPD---ASSETLIREALRA 201


>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Length = 191 Back     alignment and structure
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Length = 212 Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Length = 241 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-binding, DN 100.0
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; reco 100.0
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligomeric c 100.0
1ixs_A62 Holliday junction DNA helicase RUVA; heterodimeric prot 98.62
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 98.03
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 97.92
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 97.72
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 97.37
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 97.35
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 97.25
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 96.48
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse H, h 96.25
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 96.17
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DNA rep 95.98
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, transfera 95.97
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucleotide 95.93
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative splicin 95.7
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 95.64
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 2.36A 94.82
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DNA rep 94.66
2zix_A307 Crossover junction endonuclease MUS81; helix-hairpin-he 94.66
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 94.18
1m3q_A317 8-oxoguanine DNA glycosylase; DNA repair, END product, 93.95
3bz1_U104 Photosystem II 12 kDa extrinsic protein; electron trans 93.88
2duy_A75 Competence protein comea-related protein; helix-hairpin 93.79
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, muta 93.74
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA binding do 93.57
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-m 93.57
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 91.92
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynthesis 91.58
1b22_A114 DNA repair protein RAD51; DNA binding, riken structural 90.36
1vdd_A 228 Recombination protein RECR; helix-hairpin-helix, zinc f 96.66
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 96.32
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA binding do 95.06
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynthesis 93.7
2izo_A346 FEN1, flap structure-specific endonuclease; hydrolase, 92.12
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, 91.21
3bz1_U104 Photosystem II 12 kDa extrinsic protein; electron trans 91.08
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replication, 93.03
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, D 91.02
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
Probab=100.00  E-value=0  Score=416.51  Aligned_cols=202  Identities=28%  Similarity=0.425  Sum_probs=181.2

Q ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf             93258999999609979998588323897086889850247984999999997388418999706779999999850100
Q gi|254780553|r    1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG   80 (207)
Q Consensus         1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G   80 (207)
                      ||+||+|++.+++++++|||||||||+|++|.++++.+++.|++++||||++||||+++||||.+.+||++|++|++|||
T Consensus         1 MI~~l~G~i~~~~~~~vvl~v~GvGY~V~v~~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~lF~~Li~VsG   80 (203)
T 1cuk_A            1 MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNG   80 (203)
T ss_dssp             CCCEEEEEEEEEETTEEEEEETTEEEEEECCHHHHTTCCCTTSEEEEEEEEEEETTEEEEEEESSHHHHHHHHHHHHSSS
T ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEEECHHHHHHHHCCCCEEEEEEEEEEECCCCEEEECCCHHHHHHHHHHHCCCC
T ss_conf             96569999999719989999899889999078999961348984999999996167746886194699999999857688


Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             05101124431578999999985156687510457116799999999742221101133443233333445555653158
Q gi|254780553|r   81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA  160 (207)
Q Consensus        81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (207)
                      ||||+||+|||+++|++|++||.++|.+.|+++||||||||+||++|||||+.++.....................++..
T Consensus        81 IGPK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIilELkdK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
T 1cuk_A           81 VGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAE  160 (203)
T ss_dssp             CCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHHGGGCCSTTTCC-------------CCHHH
T ss_pred             CCHHHHHHHHHCCCHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             57566888861279899999987189988606998779999999999999987630122465422123577776666058


Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf             999999996799989999999999851688889899999999974
Q gi|254780553|r  161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI  205 (207)
Q Consensus       161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~L  205 (207)
                      .|+++||++|||++++|++++.++..   +..++|++||.|||..
T Consensus       161 ~d~~~AL~~LGy~~~ea~~ai~~~~~---~~~~~e~lik~aLk~~  202 (203)
T 1cuk_A          161 QEAVARLVALGYKPQEASRMVSKIAR---PDASSETLIREALRAA  202 (203)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHSCC---SSCCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHC---CCCCHHHHHHHHHHHH
T ss_conf             99999999879999999999998616---8999999999999971



>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>1ixs_A Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus} SCOP: a.5.1.1 Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Back     alignment and structure
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 3ktu_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* ... Back     alignment and structure
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Back     alignment and structure
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Back     alignment and structure
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Back     alignment and structure
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 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
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Back     alignment and structure
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Back     alignment and structure
>1a76_A Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanocaldococcus jannaschii} SCOP: a.60.7.1 c.120.1.2 PDB: 1a77_A Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 207 Holliday junction DNA helicase RuvA [Candidatus Liberib
d1cuka364 b.40.4.2 (A:1-64) DNA helicase RuvA subunit, N-terminal 1e-16
d1bvsa363 b.40.4.2 (A:1-63) DNA helicase RuvA subunit, N-terminal 2e-14
d1ixra262 b.40.4.2 (A:1-62) DNA helicase RuvA subunit, N-terminal 1e-13
d1ixra173 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle d 4e-14
d1cuka278 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle d 4e-13
d1bvsa271 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle d 5e-13
d1cuka148 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-termin 2e-04
>d1cuka3 b.40.4.2 (A:1-64) DNA helicase RuvA subunit, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 64 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA helicase RuvA subunit, N-terminal domain
domain: DNA helicase RuvA subunit, N-terminal domain
species: Escherichia coli [TaxId: 562]
 Score = 80.1 bits (198), Expect = 1e-16
 Identities = 21/63 (33%), Positives = 33/63 (52%)

Query: 1  MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
          MIG+++G I       VLI+V GV Y ++ P+     L + G    +F    +R+D   L
Sbjct: 1  MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60

Query: 61 FGF 63
          +GF
Sbjct: 61 YGF 63


>d1bvsa3 b.40.4.2 (A:1-63) DNA helicase RuvA subunit, N-terminal domain {Mycobacterium leprae [TaxId: 1769]} Length = 63 Back     information, alignment and structure
>d1ixra2 b.40.4.2 (A:1-62) DNA helicase RuvA subunit, N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 62 Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Length = 73 Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Length = 78 Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Length = 71 Back     information, alignment and structure
>d1cuka1 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 48 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
d1cuka278 DNA helicase RuvA subunit, middle domain {Escherichia c 99.89
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobacterium 99.89
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus therm 99.88
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 5 98.13
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus 97.91
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia coli [ 97.81
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archaeon P 97.73
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archaeon M 97.53
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sapiens 97.44
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filiformis 97.05
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) [TaxI 96.85
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Thermosyn 94.77
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker's ye 94.51
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 93.28
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermophilus 93.01
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 92.37
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human (Hom 91.52
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 90.29
d3bzka190 Transcriptional accessory factor Tex {Pseudomonas aerug 90.19
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium ther 90.03
d1cuka364 DNA helicase RuvA subunit, N-terminal domain {Escherich 99.75
d1ixra262 DNA helicase RuvA subunit, N-terminal domain {Thermus t 99.7
d1bvsa363 DNA helicase RuvA subunit, N-terminal domain {Mycobacte 99.69
d1cuka148 DNA helicase RuvA subunit, C-terminal domain {Escherich 98.42
d1ixsa_50 DNA helicase RuvA subunit, C-terminal domain {Thermus t 97.65
d1bvsa156 DNA helicase RuvA subunit, C-terminal domain {Mycobacte 96.33
d1vdda_199 Recombination protein RecR {Deinococcus radiodurans [Ta 96.62
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 95.03
d3bzka190 Transcriptional accessory factor Tex {Pseudomonas aerug 94.05
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapie 92.31
d2p6ra2198 Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} 92.15
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Thermosyn 91.93
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeog 91.29
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeog 95.57
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanoc 95.15
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archaeon M 92.9
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanoc 90.26
d1ul1x1140 Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapie 92.56
d1b43a1120 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococc 91.59
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: DNA helicase RuvA subunit, middle domain
domain: DNA helicase RuvA subunit, middle domain
species: Escherichia coli [TaxId: 562]
Probab=99.89  E-value=5.1e-24  Score=177.74  Aligned_cols=73  Identities=27%  Similarity=0.522  Sum_probs=70.1

Q ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             6779999999850100051011244315789999999851566875104571167999999997422211011
Q gi|254780553|r   65 SDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSS  137 (207)
Q Consensus        65 ~~~Er~~F~~Li~V~GIGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~  137 (207)
                      +++||+||++|++|+|||||+||+|||+++++++++||.++|.+.|+++||||+|||+||++||+||+.++..
T Consensus         1 d~~Er~~F~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~eLk~K~~~~~~   73 (78)
T d1cuka2           1 NKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHG   73 (78)
T ss_dssp             SHHHHHHHHHHHHSSSCCHHHHHHHHHHSCHHHHHHHHHTTCHHHHHTSTTCCHHHHHHHHHHHHHHGGGCCS
T ss_pred             CHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             9889999999876688019999999984899999999980688871229997899999999999999985015



>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d1cuka3 b.40.4.2 (A:1-64) DNA helicase RuvA subunit, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixra2 b.40.4.2 (A:1-62) DNA helicase RuvA subunit, N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bvsa3 b.40.4.2 (A:1-63) DNA helicase RuvA subunit, N-terminal domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1cuka1 a.5.1.1 (A:156-203) DNA helicase RuvA subunit, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixsa_ a.5.1.1 (A:) DNA helicase RuvA subunit, C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bvsa1 a.5.1.1 (A:148-203) DNA helicase RuvA subunit, C-terminal domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1ul1x1 a.60.7.1 (X:218-357) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b43a1 a.60.7.1 (A:220-339) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 207 Holliday junction DNA helicase RuvA [Candidatus Li
1ixr_A_191 (A:) Holliday junction DNA helicase RUVA; heterool 3e-34
1cuk_A_1-6565 (A:1-65) RUVA protein; DNA repair, SOS response, D 4e-17
2ztd_A_1-7979 (A:1-79) Holliday junction ATP-dependent DNA helic 4e-15
1cuk_A_66-14479 (A:66-144) RUVA protein; DNA repair, SOS response, 1e-15
2ztd_A_80-15475 (A:80-154) Holliday junction ATP-dependent DNA hel 2e-15
2ztd_A_155-21258 (A:155-212) Holliday junction ATP-dependent DNA he 2e-06
1ixs_A_62 (A:) Holliday junction DNA helicase RUVA; heterodi 2e-06
1cuk_A_145-20359 (A:145-203) RUVA protein; DNA repair, SOS response 2e-04
>1ixr_A (A:) Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus}Length = 191 Back     alignment and structure
 Score =  139 bits (351), Expect = 3e-34
 Identities = 49/205 (23%), Positives = 94/205 (45%), Gaps = 15/205 (7%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MI  ++G +        ++   GV + +  P   L  L + G    +     ++++ + L
Sbjct: 1   MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQAL-EEGKEVGVHTHLLLKEEGLSL 59

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF  + +   F LL SV GVG +VA+ +LS +    L  +++  +++++    G+  ++
Sbjct: 60  YGFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRL 119

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTA 180
           A RI  ELKGK        ++  S   +E             A+ AL  LG+ + QA   
Sbjct: 120 AERIALELKGKVPPHLLAGEKVESEAAEE-------------AVMALAALGFKEAQARAV 166

Query: 181 VVSVLKKEKNIADDSQIIRLALRAI 205
           V+ +L +    A    +I+ AL+ +
Sbjct: 167 VLDLLAQNPK-ARAQDLIKEALKRL 190


>1cuk_A (A:1-65) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli}Length = 65 Back     alignment and structure
>2ztd_A (A:1-79) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_ALength = 79 Back     alignment and structure
>1cuk_A (A:66-144) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli}Length = 79 Back     alignment and structure
>2ztd_A (A:80-154) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_ALength = 75 Back     alignment and structure
>2ztd_A (A:155-212) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_ALength = 58 Back     alignment and structure
>1ixs_A (A:) Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus}Length = 62 Back     alignment and structure
>1cuk_A (A:145-203) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli}Length = 59 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target207 Holliday junction DNA helicase RuvA [Candidatus Liberib
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 100.0
1cuk_A_66-14479 RUVA protein; DNA repair, SOS response, DNA-bindin 99.89
2ztd_A_80-15475 Holliday junction ATP-dependent DNA helicase RUVA; 99.89
3c1y_A_304-37774 DNA integrity scanning protein DISA; DNA damage, D 97.72
1z00_A_89 DNA excision repair protein ERCC-1; helix-hairpin- 97.52
1pzn_A_1-9595 RAD51, DNA repair and recombination protein RAD51, 97.41
1kft_A_78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 97.38
2w9m_A_1-118118 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 96.67
2fmp_A_1-119119 DNA polymerase beta; nucleotidyl transferase, tran 96.3
2ihm_A_1-129129 POL MU, DNA polymerase MU; helix-turn-helix, trans 96.2
1wcn_A_70 Transcription elongation protein NUSA; RNA-binding 95.93
2nrt_A_157-22064 Uvrabc system protein C; UVRC, endonuclease, RNAse 95.9
2a1j_A_63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 95.24
1z00_B_1-7171 DNA repair endonuclease XPF; helix-hairpin-helix, 95.01
3c65_A_226 Uvrabc system protein C; UVRC, endonuclease, nucle 94.79
1ngn_A_1-129129 Methyl-CPG binding protein MBD4; mismacth repair i 94.37
1b22_A_114 DNA repair protein RAD51; DNA binding, riken struc 94.21
3bz1_U_104 Photosystem II 12 kDa extrinsic protein; electron 92.87
2ziu_A_230-31182 MUS81 protein; helix-hairpin-helix, alternative sp 91.83
3e1s_A_1-149149 Exodeoxyribonuclease V, subunit RECD; alpha and be 91.15
1b43_A_212-28877 Protein (FEN-1); nuclease, DNA repair, DNA replica 90.92
2w9m_A_1-118118 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 90.88
2duy_A_75 Competence protein comea-related protein; helix-ha 90.88
1cuk_A_1-6565 RUVA protein; DNA repair, SOS response, DNA-bindin 99.79
2ztd_A_1-7979 Holliday junction ATP-dependent DNA helicase RUVA; 99.75
1ixs_A_62 Holliday junction DNA helicase RUVA; heterodimeric 98.71
2ztd_A_155-21258 Holliday junction ATP-dependent DNA helicase RUVA; 98.69
1cuk_A_145-20359 RUVA protein; DNA repair, SOS response, DNA-bindin 98.54
1vdd_A_1-6666 Recombination protein RECR; helix-hairpin-helix, z 96.83
1a76_A_210-27465 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 94.94
1rxw_A_221-28868 Flap structure-specific endonuclease; helical clam 93.17
1exn_A_182-26180 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 93.08
1b43_A_212-28877 Protein (FEN-1); nuclease, DNA repair, DNA replica 92.98
3i0w_A_111-127_196-23658 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 92.78
3bzc_A_499-56870 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 92.04
2edu_A_98 Kinesin-like protein KIF22; kinesin-like DNA bindi 92.04
1s5l_U_48-13487 Photosystem II 12 kDa extrinsic protein; photosynt 92.0
2izo_A_219-30082 FEN1, flap structure-specific endonuclease; hydrol 91.86
2duy_A_75 Competence protein comea-related protein; helix-ha 91.81
1m3q_A_123-255133 8-oxoguanine DNA glycosylase; DNA repair, END prod 91.53
3fsp_A_34-143110 A/G-specific adenine glycosylase; protein-DNA comp 91.25
3bz1_U_104 Photosystem II 12 kDa extrinsic protein; electron 91.01
3fhf_A_38-150113 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpi 90.65
1ul1_X_1-14_218-29289 Flap endonuclease-1; protein complex, DNA-binding 90.04
1jms_A_1-154154 Terminal deoxynucleotidyltransferase; polymerase; 95.84
2bcq_A_1-128128 DNA polymerase lambda; misalignment, extrahelical, 94.59
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 92.44
1rxw_A_221-28868 Flap structure-specific endonuclease; helical clam 92.28
1a76_A_210-27465 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclea 91.73
1exn_A_182-26180 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Ent 90.7
>1ixr_A (A:) Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=362.38  Aligned_cols=191  Identities=25%  Similarity=0.394  Sum_probs=176.5

Q ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHHHH
Q ss_conf             93258999999609979998588323897086889850247984999999997388418999706779999999850100
Q gi|254780553|r    1 MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRLFGFLSDLDRQWFMLLQSVQG   80 (207)
Q Consensus         1 MI~~i~G~i~~~~~~~ivi~v~GvGY~i~vs~~~~~~l~~~g~~v~l~~~~~vrEd~~~LyGF~~~~Er~~F~~Li~V~G   80 (207)
                      ||+|++|+|.++++++++++|+|+||+|++|.++...+ +.|+++.||||+++|||++.||||.++.||++|++|++|+|
T Consensus         1 MI~~l~G~v~~~~~~~~ii~~~gvGy~i~~~~~~~~~l-~~~~~~~l~~~~~vred~~~l~GF~~~~er~~F~~L~~V~G   79 (191)
T 1ixr_A            1 MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQAL-EEGKEVGVHTHLLLKEEGLSLYGFPDEENLALFELLLSVSG   79 (191)
T ss_dssp             CCCEEEEEEEEECSSEEEEECSSEEEEEECCHHHHHHC-CTTSEEEEEECCCCCSSCCCEEEESSHHHHHHHHHHHSSSC
T ss_pred             CCCEEEEEEEEEECCEEEEEECCEEEEEECCHHHHHHC-CCCCEEEEEEEEEEEECCCEEECCCCHHHHHHHHHHHCCCC
T ss_conf             95669999999839979999899899999277999746-79986999999999607866771082899999999857588


Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             05101124431578999999985156687510457116799999999742221101133443233333445555653158
Q gi|254780553|r   81 VGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFA  160 (207)
Q Consensus        81 IGpK~AL~iLs~l~~~~l~~aI~~~D~~~L~~vpGIGkKtA~rIi~ELk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (207)
                      ||||+|++|||++++++++++|.++|.+.|+++||||+|||+||++|||+|+.++....             ....++..
T Consensus        80 IGpk~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGIG~KtA~rIi~eLk~k~~~~~~~~-------------~~~~~~~~  146 (191)
T 1ixr_A           80 VGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKVPPHLLAG-------------EKVESEAA  146 (191)
T ss_dssp             CCHHHHHHHHHHSCHHHHHHHHHTTCHHHHTTSTTCCHHHHHHHHHHHTTTSCSCC------------------------
T ss_pred             CCHHHHHHHHHCCCHHHHHHHHHCCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCC-------------CCCCCCCH
T ss_conf             47788999985599999999998289998513888456889999999986425210011-------------23355568


Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC
Q ss_conf             9999999967999899999999998516888898999999999745
Q gi|254780553|r  161 INAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS  206 (207)
Q Consensus       161 ~d~~~AL~~LGy~~~ea~~ai~~i~~~~~~~~~~eelIk~aLk~Ls  206 (207)
                      +|+++||.+|||++++|++++.++..+.++ .++|++||.|||+|.
T Consensus       147 ~e~~~aL~~LGy~~~ea~~ai~~~~~~~~~-~~~e~li~~aLk~l~  191 (191)
T 1ixr_A          147 EEAVMALAALGFKEAQARAVVLDLLAQNPK-ARAQDLIKEALKRLR  191 (191)
T ss_dssp             ----------------------------------------------
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHCC
T ss_conf             999999998699999999999999842999-999999999999639



>1cuk_A (A:66-144) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} Back     alignment and structure
>2ztd_A (A:80-154) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>3c1y_A (A:304-377) DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
>1z00_A (A:) DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1pzn_A (A:1-95) RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} Back     alignment and structure
>1kft_A (A:) UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} Back     alignment and structure
>2w9m_A (A:1-118) Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2fmp_A (A:1-119) DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} Back     alignment and structure
>2ihm_A (A:1-129) POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>1wcn_A (A:) Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>2nrt_A (A:157-220) Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>2a1j_A (A:) DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} Back     alignment and structure
>1z00_B (B:1-71) DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>3c65_A (A:) Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>1ngn_A (A:1-129) Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} Back     alignment and structure
>1b22_A (A:) DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>3bz1_U (U:) Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>2ziu_A (A:230-311) MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Back     alignment and structure
>3e1s_A (A:1-149) Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Back     alignment and structure
>1b43_A (A:212-288) Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} Back     alignment and structure
>2w9m_A (A:1-118) Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2duy_A (A:) Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} Back     alignment and structure
>1cuk_A (A:1-65) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} Back     alignment and structure
>2ztd_A (A:1-79) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1ixs_A (A:) Holliday junction DNA helicase RUVA; heterodimeric protein complex, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.20A {Thermus thermophilus} Back     alignment and structure
>2ztd_A (A:155-212) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1cuk_A (A:145-203) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} Back     alignment and structure
>1vdd_A (A:1-66) Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} Back     alignment and structure
>1a76_A (A:210-274) Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, DNA replication, RTH, RAD27, DNA repair; 2.00A {Methanococcus jannaschii} Back     alignment and structure
>1rxw_A (A:221-288) Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} Back     alignment and structure
>1exn_A (A:182-261) 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} Back     alignment and structure
>1b43_A (A:212-288) Protein (FEN-1); nuclease, DNA repair, DNA replication; 2.00A {Pyrococcus furiosus} Back     alignment and structure
>3i0w_A (A:111-127,A:196-236) 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Back     alignment and structure
>3bzc_A (A:499-568) TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} Back     alignment and structure
>2edu_A (A:) Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1s5l_U (U:48-134) Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>2izo_A (A:219-300) FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>2duy_A (A:) Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} Back     alignment and structure
>1m3q_A (A:123-255) 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} Back     alignment and structure
>3fsp_A (A:34-143) A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Back     alignment and structure
>3bz1_U (U:) Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>3fhf_A (A:38-150) Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>1ul1_X (X:1-14,X:218-292) Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} Back     alignment and structure
>1jms_A (A:1-154) Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} Back     alignment and structure