254780454

254780454

DNA polymerase III subunit beta

GeneID in NCBI database:8209440Locus tag:CLIBASIA_01695
Protein GI in NCBI database:254780454Protein Accession:YP_003064867.1
Gene range:-(370373, 371530)Protein Length:385aa
Gene description:DNA polymerase III subunit beta
COG prediction:[L] DNA polymerase sliding clamp subunit (PCNA homolog)
KEGG prediction:dnaA; DNA polymerase III subunit beta (EC:2.7.7.7); K02338 DNA polymerase III subunit beta [EC:2.7.7.7]
SEED prediction:DNA polymerase III beta subunit (EC 2.7.7.7)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
DNA replication [PATH:las03030]
Mismatch repair [PATH:las03430]
Homologous recombination [PATH:las03440]
Subsystem involved in SEED: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-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-----
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
cEEEEEHHHHHHHHHHHHHHccccccccEEcEEEEEEEccEEEEEEEcccEEEEEEEEEEEccccEEEEEHHHHHHHHHHcccccEEEEEEccccccEEEEEEccEEEEEccccHHHcccccccccccEEEEcHHHHHHHHHHHHEEEEcccccEEEEEEEEEEEccccEEEEEEEcccEEEEEEEEcccccccccEEEEEHHHHHHHHHHHcccccEEEEEEEccEEEEEEccEEEEEEEcccccccccccccccccEEEEEEHHHHHHHHHHHHHHHcccccEEEEEEEccEEEEEEEcccccEEEEEEEEEEccccEEEEEEHHHHHHHHHHcccccccccEEEEEEccccccEEEEEccccccccccccccEEEEEEEEEc
cccEEcHHHHHHHHHHHHHHHccccccccHHcEEEEEccccEEEEEEEEEEEEEEEEEccEEEEEEEEccHHHHHHHHHHcccccEEEEEEEcccccEEEEEEcccccccccccHHHcccccccccEEEEEccHHHHHHHHHHHHHHHHcccHHHHHccEEEEEccccEEEEEEEccccEEEEEEcccEEEEEEEEEEEEEHHHHHHHHHHccccccEEEEEEcccEEEEEEccEEEEEEcEccccccHHHHccccccEEEEEEHHHHHHHHHHHHHHccccccEEEEEEEccEEEEEEEcccccEEEEEEEcEEccccEEEEEEHHHHHHHHHHccccEEcccEEEEEEccccccEEEEcccccccccccccccEEEEEEcccc
MKITVERSDILELLGHACRIierkntipvSCHVLLQANDGLleikasgpeieitgaipasvdvcGSITVSAHLLYDIVRKLQDgaqisffkenelgtevnishgdsnfylqsfpesefpstkeeeYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIakmpsiivprKAVGEILRILSskdssvkvslsesRIHLNIESLSMSVRLidgefpnyqnvipcsndkelRVNCTNLRQAVDRVSIMSSVRIQAVKLSLssdklcmtvdnpdmgKAIESMNVyynecpmdicFNYKYLLEIIDnissdevvddeVVFRldssnssvfirgkdkdsknnkdnkvNAFYVLMPMRI
mkitversDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAqiakmpsiivprKAVGEILRIlsskdssvkvslsesrihlniesLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKlslssdklcmtvdnPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVfrldssnssvfirgkdkdsknnkdnkvnafyvlmpmri
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRIlsskdssvkvslsesRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEiidnissdevvddevvFRLDSSNSSVFIRGkdkdsknnkdnkVNAFYVLMPMRI
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDI****AKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPD*GKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSS*********SESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
*KITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
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MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI
MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPASVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI

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
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
315122098370 DNA polymerase III subunit beta [Candidatus Liberibacte 1 1e-152
209551896372 DNA polymerase III subunit beta [Rhizobium leguminosaru 1 3e-98
86355975372 DNA polymerase III subunit beta [Rhizobium etli CFN 42] 1 5e-98
116250102372 DNA polymerase III subunit beta [Rhizobium leguminosaru 1 6e-98
218509914372 DNA polymerase III subunit beta [Rhizobium etli Brasil 1 1e-97
241207273372 DNA polymerase III subunit beta [Rhizobium leguminosaru 1 1e-97
327192029372 DNA polymerase III subunit beta [Rhizobium etli CNPAF51 1 1e-97
190889986372 DNA polymerase III, beta chain protein [Rhizobium etli 1 1e-97
222084599372 DNA polymerase III, beta subunit [Agrobacterium radioba 1 1e-97
227824176372 DNA polymerase III subunit beta [Sinorhizobium fredii N 1 1e-96
>gi|315122098|ref|YP_004062587.1| DNA polymerase III subunit beta [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 370 Back     alignment and organism information
 Score =  544 bits (1401), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 281/386 (72%), Positives = 321/386 (83%), Gaps = 17/386 (4%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
           M+I VERS+ILE L H CRIIER+ TIPV+CHV LQ  DG L++KASGPEIEIT  IPA 
Sbjct: 1   MEIIVERSNILEPLNHVCRIIERRTTIPVACHVFLQTIDGSLKMKASGPEIEITEVIPAV 60

Query: 61  VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPS 120
           ++V GS TVSAHLLYDIVRK  +G++I F K +  GTEV +  GDS FYLQSF ESEFP+
Sbjct: 61  INVGGSATVSAHLLYDIVRKFPEGSEILFSKSDAQGTEVKVVSGDSQFYLQSFSESEFPN 120

Query: 121 TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHR 180
            KEE+Y YSFEL SSVLK L+ERTHFAMATEEIRYYLNGIFFHINEED  LCAVATDGHR
Sbjct: 121 IKEEDYEYSFELESSVLKILIERTHFAMATEEIRYYLNGIFFHINEEDSTLCAVATDGHR 180

Query: 181 LAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSS-KDSSVKVSLSESRIHLNIESLSMSV 239
           LAVA+V++   IAKMPSIIVPRKAVGEI +I+S+ K  SVK+S+SESRIHLNI  LSMS+
Sbjct: 181 LAVAKVNV--PIAKMPSIIVPRKAVGEIQKIISTVKFLSVKISISESRIHLNIGRLSMSI 238

Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299
           RLIDGEFP+YQNVIP +NDK LRVNC++LRQAVDRVS +SSVR QAVKLSLSS+KLCMTV
Sbjct: 239 RLIDGEFPHYQNVIPHNNDKVLRVNCSSLRQAVDRVSTISSVRNQAVKLSLSSEKLCMTV 298

Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359
           DNP+MGKAIE ++V Y++CPMDICFNYKYLLEII NIS     DD+VVFRLDSS+SS  I
Sbjct: 299 DNPEMGKAIEYLDVNYHDCPMDICFNYKYLLEIIGNIS-----DDDVVFRLDSSSSSALI 353

Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMRI 385
           +G +     NKD    AFYVLMPMRI
Sbjct: 354 QGFE-----NKD----AFYVLMPMRI 370


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|209551896|ref|YP_002283813.1| DNA polymerase III subunit beta [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 372 Back     alignment and organism information
>gi|86355975|ref|YP_467867.1| DNA polymerase III subunit beta [Rhizobium etli CFN 42] Length = 372 Back     alignment and organism information
>gi|116250102|ref|YP_765940.1| DNA polymerase III subunit beta [Rhizobium leguminosarum bv. viciae 3841] Length = 372 Back     alignment and organism information
>gi|218509914|ref|ZP_03507792.1| DNA polymerase III subunit beta [Rhizobium etli Brasil 5] Length = 372 Back     alignment and organism information
>gi|241207273|ref|YP_002978369.1| DNA polymerase III subunit beta [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 372 Back     alignment and organism information
>gi|327192029|gb|EGE59010.1| DNA polymerase III subunit beta [Rhizobium etli CNPAF512] Length = 372 Back     alignment and organism information
>gi|190889986|ref|YP_001976528.1| DNA polymerase III, beta chain protein [Rhizobium etli CIAT 652] Length = 372 Back     alignment and organism information
>gi|222084599|ref|YP_002543128.1| DNA polymerase III, beta subunit [Agrobacterium radiobacter K84] Length = 372 Back     alignment and organism information
>gi|227824176|ref|YP_002828149.1| DNA polymerase III subunit beta [Sinorhizobium fredii NGR234] Length = 372 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
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
PRK05643367 PRK05643, PRK05643, DNA polymerase III subunit beta; Va 1e-103
smart00480345 smart00480, POL3Bc, DNA polymerase III beta subunit 5e-68
COG0592364 COG0592, DnaN, DNA polymerase sliding clamp subunit (PC 2e-65
TIGR00663367 TIGR00663, dnan, DNA polymerase III, beta subunit 6e-64
PRK14943374 PRK14943, PRK14943, DNA polymerase III subunit beta; Pr 3e-49
PRK14940367 PRK14940, PRK14940, DNA polymerase III subunit beta; Pr 8e-44
PRK07761376 PRK07761, PRK07761, DNA polymerase III subunit beta; Va 5e-32
PRK14941374 PRK14941, PRK14941, DNA polymerase III subunit beta; Pr 1e-28
PRK14942373 PRK14942, PRK14942, DNA polymerase III subunit beta; Pr 1e-27
PRK14947384 PRK14947, PRK14947, DNA polymerase III subunit beta; Pr 4e-20
PRK14946366 PRK14946, PRK14946, DNA polymerase III subunit beta; Pr 1e-10
cd00140365 cd00140, beta_clamp, Beta clamp domain 2e-85
PRK14945362 PRK14945, PRK14945, DNA polymerase III subunit beta; Pr 6e-36
PRK06673376 PRK06673, PRK06673, DNA polymerase III subunit beta; Va 1e-24
PRK14944375 PRK14944, PRK14944, DNA polymerase III subunit beta; Pr 3e-14
pfam02767116 pfam02767, DNA_pol3_beta_2, DNA polymerase III beta sub 3e-26
pfam00712120 pfam00712, DNA_pol3_beta, DNA polymerase III beta subun 7e-18
pfam02768121 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta sub 1e-15
>gnl|CDD|180180 PRK05643, PRK05643, DNA polymerase III subunit beta; Validated Back     alignment and domain information
>gnl|CDD|128756 smart00480, POL3Bc, DNA polymerase III beta subunit Back     alignment and domain information
>gnl|CDD|30937 COG0592, DnaN, DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|161984 TIGR00663, dnan, DNA polymerase III, beta subunit Back     alignment and domain information
>gnl|CDD|184907 PRK14943, PRK14943, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|184904 PRK14940, PRK14940, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|181105 PRK07761, PRK07761, DNA polymerase III subunit beta; Validated Back     alignment and domain information
>gnl|CDD|184905 PRK14941, PRK14941, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|184906 PRK14942, PRK14942, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|184911 PRK14947, PRK14947, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|184910 PRK14946, PRK14946, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|29053 cd00140, beta_clamp, Beta clamp domain Back     alignment and domain information
>gnl|CDD|184909 PRK14945, PRK14945, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|135998 PRK06673, PRK06673, DNA polymerase III subunit beta; Validated Back     alignment and domain information
>gnl|CDD|184908 PRK14944, PRK14944, DNA polymerase III subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|111640 pfam02767, DNA_pol3_beta_2, DNA polymerase III beta subunit, central domain Back     alignment and domain information
>gnl|CDD|109756 pfam00712, DNA_pol3_beta, DNA polymerase III beta subunit, N-terminal domain Back     alignment and domain information
>gnl|CDD|111641 pfam02768, DNA_pol3_beta_3, DNA polymerase III beta subunit, C-terminal domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 385 DNA polymerase III subunit beta [Candidatus Liberibacte
PRK05643365 DNA polymerase III subunit beta; Validated 100.0
cd00140365 beta_clamp Beta clamp domain. The beta subunit (process 100.0
PRK07761376 DNA polymerase III subunit beta; Validated 100.0
PRK06673376 DNA polymerase III subunit beta; Validated 100.0
smart00480345 POL3Bc DNA polymerase III beta subunit. 100.0
COG0592364 DnaN DNA polymerase sliding clamp subunit (PCNA homolog 100.0
TIGR00663406 dnan DNA polymerase III, beta subunit; InterPro: IPR001 100.0
pfam02768121 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-term 100.0
pfam02747128 PCNA_C Proliferating cell nuclear antigen, C-terminal d 98.05
pfam02767116 DNA_pol3_beta_2 DNA polymerase III beta subunit, centra 99.97
pfam00712120 DNA_pol3_beta DNA polymerase III beta subunit, N-termin 98.94
pfam00712120 DNA_pol3_beta DNA polymerase III beta subunit, N-termin 99.97
pfam02767116 DNA_pol3_beta_2 DNA polymerase III beta subunit, centra 98.84
pfam02768121 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-term 98.08
cd00140365 beta_clamp Beta clamp domain. The beta subunit (process 99.65
smart00480345 POL3Bc DNA polymerase III beta subunit. 99.58
PRK01115245 DNA polymerase sliding clamp; Validated 98.7
PTZ00113277 proliferating cell nuclear antigen (cyclin); Provisiona 98.4
cd00577248 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain f 98.23
KOG1636260 consensus 96.13
PRK05643 365 DNA polymerase III subunit beta; Validated 99.65
PRK07761 376 DNA polymerase III subunit beta; Validated 99.6
COG0592 364 DnaN DNA polymerase sliding clamp subunit (PCNA homolog 99.32
TIGR00663 406 dnan DNA polymerase III, beta subunit; InterPro: IPR001 98.43
PRK06673376 DNA polymerase III subunit beta; Validated 99.52
PRK01115245 DNA polymerase sliding clamp; Validated 99.27
PTZ00113277 proliferating cell nuclear antigen (cyclin); Provisiona 98.95
cd00577248 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain f 99.03
KOG1636260 consensus 97.56
pfam04139252 Rad9 Rad9. Rad9 is required for transient cell-cycle ar 96.48
pfam00705127 PCNA_N Proliferating cell nuclear antigen, N-terminal d 93.88
>PRK05643 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>cd00140 beta_clamp Beta clamp domain Back     alignment and domain information
>PRK07761 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PRK06673 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>smart00480 POL3Bc DNA polymerase III beta subunit Back     alignment and domain information
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00663 dnan DNA polymerase III, beta subunit; InterPro: IPR001001 Describes the beta chain of DNA polymerase III Back     alignment and domain information
>pfam02768 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-terminal domain Back     alignment and domain information
>pfam02747 PCNA_C Proliferating cell nuclear antigen, C-terminal domain Back     alignment and domain information
>pfam02767 DNA_pol3_beta_2 DNA polymerase III beta subunit, central domain Back     alignment and domain information
>pfam00712 DNA_pol3_beta DNA polymerase III beta subunit, N-terminal domain Back     alignment and domain information
>pfam00712 DNA_pol3_beta DNA polymerase III beta subunit, N-terminal domain Back     alignment and domain information
>pfam02767 DNA_pol3_beta_2 DNA polymerase III beta subunit, central domain Back     alignment and domain information
>pfam02768 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-terminal domain Back     alignment and domain information
>cd00140 beta_clamp Beta clamp domain Back     alignment and domain information
>smart00480 POL3Bc DNA polymerase III beta subunit Back     alignment and domain information
>PRK01115 DNA polymerase sliding clamp; Validated Back     alignment and domain information
>PTZ00113 proliferating cell nuclear antigen (cyclin); Provisional Back     alignment and domain information
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea Back     alignment and domain information
>KOG1636 consensus Back     alignment and domain information
>PRK05643 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PRK07761 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>COG0592 DnaN DNA polymerase sliding clamp subunit (PCNA homolog) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00663 dnan DNA polymerase III, beta subunit; InterPro: IPR001001 Describes the beta chain of DNA polymerase III Back     alignment and domain information
>PRK06673 DNA polymerase III subunit beta; Validated Back     alignment and domain information
>PRK01115 DNA polymerase sliding clamp; Validated Back     alignment and domain information
>PTZ00113 proliferating cell nuclear antigen (cyclin); Provisional Back     alignment and domain information
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea Back     alignment and domain information
>KOG1636 consensus Back     alignment and domain information
>pfam04139 Rad9 Rad9 Back     alignment and domain information
>pfam00705 PCNA_N Proliferating cell nuclear antigen, N-terminal domain 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
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
2pol_A366 Three-Dimensional Structure Of The Beta Subunit Of 8e-73
2xur_B373 The G157c Mutation In The Escherichia Coli Sliding 1e-72
1jql_A366 Mechanism Of Processivity Clamp Opening By The Delt 2e-72
3f1v_A366 E. Coli Beta Sliding Clamp, 148-153 Ala Mutant Leng 1e-71
1vpk_A378 Crystal Structure Of Dna Polymerase Iii, Beta Subun 4e-53
2awa_A390 Crystal Structure Of Dna Polymerase Iii, Beta Chain 6e-47
2avt_A378 Crystal Structure Of The Beta Subunit From Dna Poly 2e-46
gi|494833|pdb|2POL|A Chain A, Three-Dimensional Structure Of The Beta Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme: A Sliding Dna Clamp Length = 366 Back     alignment and structure
 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 130/386 (33%), Positives = 211/386 (54%), Gaps = 21/386 (5%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-A 59
           MK TVER  +L+ L      +  + T+P+  ++LLQ  DG L +  +  E+E+   +   
Sbjct: 1   MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV 60

Query: 60  SVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
                G+ TV A   +DI R L +GA+I+   E E    + +  G S F L + P ++FP
Sbjct: 61  QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGE---RMLVRSGRSRFSLSTLPAADFP 117

Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179
           +  + +    F L  + +K L+E T F+MA +++RYYLNG+ F    E  +L  VATDGH
Sbjct: 118 NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGE--ELRTVATDGH 175

Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV 239
           RLAV  + I  Q     S+IVPRK V E++R+L   D+ ++V +  + I  ++     + 
Sbjct: 176 RLAVCSMPI-GQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS 234

Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299
           +L+DG FP+Y+ V+P + DK L   C  L+QA  R +I+S+ + + V+L +S ++L +T 
Sbjct: 235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITA 294

Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359
           +NP+  +A E ++V Y+   M+I FN  Y+L++++ +       + V   L  S SSV I
Sbjct: 295 NNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQI 349

Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMRI 385
                 S           YV+MPMR+
Sbjct: 350 EDAASQSAA---------YVVMPMRL 366


>gi|15988190|pdb|1JQL|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta Subunit Wrench Of The Clamp Loader Complex Of E. Coli Dna Polymerase Iii: Structure Of Beta-Delta (1-140) Length = 366 Back     alignment and structure
>gi|257097208|pdb|3F1V|A Chain A, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant Length = 366 Back     alignment and structure
>gi|56966599|pdb|1VPK|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Subunit (Tm0262) From Thermotoga Maritima At 2.00 A Resolution Length = 378 Back     alignment and structure
>gi|78101467|pdb|2AWA|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec 2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae Tigr4 At 2.50 A Resolution Length = 390 Back     alignment and structure
>gi|88192167|pdb|2AVT|A Chain A, Crystal Structure Of The Beta Subunit From Dna Polymerase Of Streptococcus Pyogenes Length = 378 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
3d1g_A366 DNA polymerase III subunit beta; chemical probe, DNA sl 8e-57
1vpk_A378 DNA polymerase III, beta subunit; TM0262, structural ge 2e-51
2avt_A378 DNA polymerase III beta subunit; beta clamp, sliding cl 2e-44
3k4x_A 798 PCNA, proliferating cell nuclear antigen; DNA replicati 2e-14
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A* Length = 366 Back     alignment and structure
 Score =  216 bits (550), Expect = 8e-57
 Identities = 128/386 (33%), Positives = 212/386 (54%), Gaps = 21/386 (5%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-A 59
           MK TVER  +L+ L      +  + T+P+  ++LLQ  DG L +  +  E+E+   +   
Sbjct: 1   MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV 60

Query: 60  SVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
                G+ TV A   +DI R L +GA+I+   E E    + +  G S F L + P ++FP
Sbjct: 61  QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGE---RMLVRSGRSRFSLSTLPAADFP 117

Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179
           +  + +    F L  + +K L+E T F+MA +++RYYLNG+ F    E+L+  A  TDGH
Sbjct: 118 NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVA--TDGH 175

Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV 239
           RLAV  + I   +    S+IVPRK V E++R+L   D+ ++V +  + I  ++     + 
Sbjct: 176 RLAVCSMPIGQSL-PSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS 234

Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299
           +L+DG FP+Y+ V+P + DK L   C  L+QA  R +I+S+ + + V+L +S ++L +T 
Sbjct: 235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITA 294

Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359
           +NP+  +A E ++V Y+   M+I FN  Y+L++++ +       + V   L  S SSV I
Sbjct: 295 NNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQI 349

Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMRI 385
                          +A YV+MPMR+
Sbjct: 350 EDAASQ---------SAAYVVMPMRL 366


>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 Length = 378 Back     alignment and structure
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A* Length = 378 Back     alignment and structure
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Length = 798 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
3d1g_A366 DNA polymerase III subunit beta; chemical probe, DNA sl 100.0
1vpk_A378 DNA polymerase III, beta subunit; TM0262, structural ge 100.0
2avt_A378 DNA polymerase III beta subunit; beta clamp, sliding cl 100.0
3k4x_A 798 PCNA, proliferating cell nuclear antigen; DNA replicati 99.59
3g65_A296 Cell cycle checkpoint control protein RAD9A; PCNA, DNA 98.47
3a1j_C263 Cell cycle checkpoint protein RAD1; DNA damage, DNA rep 97.68
3d1g_A 366 DNA polymerase III subunit beta; chemical probe, DNA sl 99.57
1vpk_A 378 DNA polymerase III, beta subunit; TM0262, structural ge 99.54
1rwz_A245 DNA polymerase sliding clamp; torus, processivity facto 99.56
3ifv_A247 PCNA; processivity factor, sliding clamp, halophilic, r 99.04
3fds_C249 DNA polymerase sliding clamp C; protein-protein complex 99.0
1plq_A258 Proliferating cell nuclear antigen (PCNA); DNA-binding, 99.0
2ijx_A244 DNA polymerase sliding clamp A; PCNA3 subunit, protein- 98.99
3fds_D245 DNA polymerase sliding clamp C; protein-protein complex 98.92
1u7b_A261 PCNA, cyclin, proliferating cell nuclear antigen; slidi 98.9
1iz5_A249 Proliferating cell nuclear antigen; DNA, replication, p 98.86
2zvv_A276 PCNA 1, proliferating cellular nuclear antigen 1; prote 98.78
1ud9_A245 DNA polymerase sliding clamp A; DNA-binding, DNA replic 98.58
3k4x_A798 PCNA, proliferating cell nuclear antigen; DNA replicati 99.54
3a1j_A266 Cell cycle checkpoint control protein RAD9A; DNA damage 98.44
2avt_A378 DNA polymerase III beta subunit; beta clamp, sliding cl 99.44
1rwz_A245 DNA polymerase sliding clamp; torus, processivity facto 98.83
3fds_C249 DNA polymerase sliding clamp C; protein-protein complex 98.62
1plq_A258 Proliferating cell nuclear antigen (PCNA); DNA-binding, 98.52
2ijx_A244 DNA polymerase sliding clamp A; PCNA3 subunit, protein- 98.44
3ifv_A247 PCNA; processivity factor, sliding clamp, halophilic, r 98.41
1iz5_A249 Proliferating cell nuclear antigen; DNA, replication, p 98.34
2zvv_A276 PCNA 1, proliferating cellular nuclear antigen 1; prote 98.31
1u7b_A261 PCNA, cyclin, proliferating cell nuclear antigen; slidi 98.26
3fds_D245 DNA polymerase sliding clamp C; protein-protein complex 98.22
1ud9_A245 DNA polymerase sliding clamp A; DNA-binding, DNA replic 97.95
3a1j_A266 Cell cycle checkpoint control protein RAD9A; DNA damage 97.84
3g65_A296 Cell cycle checkpoint control protein RAD9A; PCNA, DNA 97.47
3a1j_C263 Cell cycle checkpoint protein RAD1; DNA damage, DNA rep 95.96
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=607.53  Aligned_cols=365  Identities=35%  Similarity=0.624  Sum_probs=345.3

Q ss_pred             CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHCEEEEEEECCEEEEEEECCEEEEEEEEE-EEECCCCEEEEEHHHHHHHHH
Q ss_conf             9589859999999998750203788861013389999899799999678289999997-775268079994998778874
Q gi|254780454|r    1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-ASVDVCGSITVSAHLLYDIVR   79 (385)
Q Consensus         1 Mk~~i~~~~L~~~l~~v~~~i~~k~~~pil~~ilie~~~~~l~l~atd~~~~i~~~i~-~~i~~~G~~~v~a~~l~~iik   79 (385)
                      |||+|+|++|.++|+++++++++|++.|||+|++|++++++|+++|||++++++++++ +++.++|+++|||+.|.+++|
T Consensus         1 Mk~~i~k~~L~~~l~~v~~~i~~k~~~piL~~ili~a~~~~l~l~atd~e~~i~~~i~~~~v~~~G~~~v~ak~l~~ivr   80 (366)
T 3d1g_A            1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICR   80 (366)
T ss_dssp             CEEEEEHHHHHHHHHHHSTTCSSCCCSGGGGEEEEEEETTEEEEEEECSSEEEEEEEECCSCCBCEEEEEEHHHHHHHHH
T ss_pred             CEEEEEHHHHHHHHHHHHHHCCCCCCHHHHCCEEEEEECCEEEEEEECCCEEEEEEEECCEECCCCEEEEECHHHHHHHH
T ss_conf             98999899999999999756188987388747899998999999998887399999904152357469992356777874


Q ss_pred             CCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCEEEECCCCCCCCCEEE
Q ss_conf             07777730477733675089998678202430366211432123324304505611355420220230024556521011
Q gi|254780454|r   80 KLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNG  159 (385)
Q Consensus        80 ~L~~~~~i~~~~~~~~~~~i~i~~~~~~~~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~t~~a~s~d~~r~~L~G  159 (385)
                      +||++..+.+..+   ++++.|++|+++|+|+++++++||.+|..+....+.++++.|+++|++|.||+|+|++||+|+|
T Consensus        81 ~l~~~~~i~~~~~---~~~l~I~~~~~~f~l~~~~~~~fP~~~~~~~~~~~~i~~~~l~~~i~~v~~a~s~d~~r~~L~G  157 (366)
T 3d1g_A           81 GLPEGAEIAVQLE---GERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNG  157 (366)
T ss_dssp             HSCTTCEEEEEEE---TTEEEEEETTEEEEEECBCGGGSCCCCCCCCSEEEEECHHHHHHHHHHHGGGSCSSCSSGGGSE
T ss_pred             CCCCCCEEEEEEC---CCEEEEEECCEEEEEECCCHHHCCCCCCCCCCCEEEECHHHHHHHHHHEEEECCCCCCCEEEEE
T ss_conf             4799974999961---8889999898899960688110876111366614887699999866547731256567432555


Q ss_pred             EEEEECCCCCEEEEEEECCEEEEEEEEECCCCCCCCCHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEECCEEEEEE
Q ss_conf             66776178734899985341576666435787533100000100012222102776464331334553010025069998
Q gi|254780454|r  160 IFFHINEEDLKLCAVATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV  239 (385)
Q Consensus       160 v~~~~~~~~~~l~~vaTDg~RLa~~~~~~~~~~~~~~~~iiP~k~l~el~k~l~~~~~~v~i~~~~~~i~~~~~~~~~~s  239 (385)
                      |||+++++  ++++|||||||||.++.+++... ...+++||+|.+.++.+++.+.+++++++++++++.|.+++.+++|
T Consensus       158 v~~~~~~~--~l~~vaTDg~RLa~~~~~~~~~~-~~~~~iip~k~l~~~~~~~~~~~~~v~i~~~~~~i~f~~~~~~~~s  234 (366)
T 3d1g_A          158 MLFETEGE--ELRTVATDGHRLAVCSMPIGQSL-PSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS  234 (366)
T ss_dssp             EEEEEEEE--EEEEEEECSSEEEEEEEEEEEEE-EEEEEEEEHHHHHHHHHTCCSSSCCEEEEECSSEEEEEETTEEEEE
T ss_pred             EEEEECCC--EEEEEECCCCEEEEEEECCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCEEEEEECCEEEEE
T ss_conf             99996499--99999906843899983046777-6323101523699987664045514787427855999989999999


Q ss_pred             EECCCCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEEECCCC
Q ss_conf             51266553221013555661799848998888988741012355530256517659999807873268999998962884
Q gi|254780454|r  240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECP  319 (385)
Q Consensus       240 rLi~g~yPdy~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~~  319 (385)
                      |||+|+||||+++||+.++.+++++|++|+++++|++++++++++.|.+.++++.+++++.++|.|+++|+++++|+|++
T Consensus       235 rlieg~yP~y~~vip~~~~~~~~v~~~~l~~al~r~~~~~~~~~~~v~l~~~~~~l~l~~~~~d~g~~~e~i~~~~~G~~  314 (366)
T 3d1g_A          235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAE  314 (366)
T ss_dssp             ECCSSCCCCHHHHSCSCCCEEEEEEHHHHHHHHHHHHHTSCTTTCEEEEEEETTEEEEEEECTTCCEEEEEEECBCCSCC
T ss_pred             EEECCCCCCCCEECCCCCCCEEEECHHHHHHHHHHHHHCCCCCCCCEEEEECCCEEEEEECCCCCCEEEEEEEEEECCCC
T ss_conf             95056776410305787762257503565666654301014677723799629959999727876515699976852897


Q ss_pred             EEEEECHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             399963889988987357533466338999658987589943776544455566763799832129
Q gi|254780454|r  320 MDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI  385 (385)
Q Consensus       320 ~~i~fN~~yl~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMPvri  385 (385)
                      ++|+||++||+|+|+++++     ++|.|++.++.+|++|++.++         ++|+||||||||
T Consensus       315 ~~i~fN~~yL~d~L~~~~~-----~~V~i~~~~~~~p~~i~~~~~---------~~~~~liMPvrl  366 (366)
T 3d1g_A          315 MEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQIEDAAS---------QSAAYVVMPMRL  366 (366)
T ss_dssp             EEEEEEHHHHHHHHHHCCS-----SEEEEEECCTTSCEEEEETTE---------EEEEEEECCBCC
T ss_pred             EEEEECHHHHHHHHHCCCC-----CEEEEEECCCCCCEEEECCCC---------CCEEEEEEEEEC
T ss_conf             7999889999999854899-----879999838998589977999---------854899952109



>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 Back     alignment and structure
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A* Back     alignment and structure
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Back     alignment and structure
>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens} Back     alignment and structure
>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C Back     alignment and structure
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A* 1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A* 1jqj_A* 3f1v_A* Back     alignment and structure
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 Back     alignment and structure
>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A* Back     alignment and structure
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A Back     alignment and structure
>3fds_C DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C* Back     alignment and structure
>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity factor; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3l0x_B Back     alignment and structure
>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotrimer, DNA binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C* Back     alignment and structure
>3fds_D DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B* Back     alignment and structure
>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A* Back     alignment and structure
>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A Back     alignment and structure
>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A Back     alignment and structure
>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2 Back     alignment and structure
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae} Back     alignment and structure
>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A Back     alignment and structure
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A* Back     alignment and structure
>1rwz_A DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus} SCOP: d.131.1.2 d.131.1.2 PDB: 1rxm_A* 1rxz_A* Back     alignment and structure
>3fds_C DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2io4_A* 2nti_D* 2hii_A 2hik_A 2ix2_A* 2izo_C* Back     alignment and structure
>1plq_A Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity factor; 2.30A {Saccharomyces cerevisiae} SCOP: d.131.1.2 d.131.1.2 PDB: 1plr_A 2od8_A* 1sxj_F* 3f1w_A 3gpn_A 3gpm_A 3l0w_A 3l0x_A 3l10_A 3l0x_B Back     alignment and structure
>2ijx_A DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotrimer, DNA binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C* Back     alignment and structure
>3ifv_A PCNA; processivity factor, sliding clamp, halophilic, replication; 2.00A {Haloferax volcanii} PDB: 3hi8_A Back     alignment and structure
>1iz5_A Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus} SCOP: d.131.1.2 d.131.1.2 PDB: 3a2f_B* 1iz4_A 1ge8_A 1isq_A Back     alignment and structure
>2zvv_A PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_A Back     alignment and structure
>1u7b_A PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens} SCOP: d.131.1.2 d.131.1.2 PDB: 1u76_A 1axc_A 1ul1_A 1vyj_A 1vym_A 1w60_A 2zvk_A* 2zvl_A* 2zvm_A* Back     alignment and structure
>3fds_D DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B* Back     alignment and structure
>1ud9_A DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii} SCOP: d.131.1.2 d.131.1.2 Back     alignment and structure
>3a1j_A Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_A Back     alignment and structure
>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens} Back     alignment and structure
>3a1j_C Cell cycle checkpoint protein RAD1; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3g65_B 3ggr_C 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 385 DNA polymerase III subunit beta [Candidatus Liberibacte
d1ok7a3122 d.131.1.1 (A:245-366) DNA polymerase III, beta subunit 6e-21
d1vpka3123 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit 7e-20
d1ok7a1122 d.131.1.1 (A:1-122) DNA polymerase III, beta subunit {E 2e-20
d1vpka1120 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {T 8e-16
d1ok7a2122 d.131.1.1 (A:123-244) DNA polymerase III, beta subunit 5e-19
d1vpka2123 d.131.1.1 (A:121-243) DNA polymerase III, beta subunit 9e-19
>d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Length = 123 Back     information, alignment and structure
>d1vpka1 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Length = 120 Back     information, alignment and structure
>d1vpka2 d.131.1.1 (A:121-243) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Length = 123 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
d1vpka3123 DNA polymerase III, beta subunit {Thermotoga maritima [ 99.97
d1ok7a3122 DNA polymerase III, beta subunit {Escherichia coli [Tax 99.97
d1rwza2122 Proliferating cell nuclear antigen (PCNA) {Archaeon Arc 97.99
d1plqa2132 Proliferating cell nuclear antigen (PCNA) {Baker's yeas 97.97
d1iz5a2121 Proliferating cell nuclear antigen (PCNA) {Archaeon Pyr 97.95
d1u7ba2129 Proliferating cell nuclear antigen (PCNA) {Human (Homo 97.93
d1ud9a2119 Proliferating cell nuclear antigen (PCNA) {Archaeon Sul 97.59
d1vpka2123 DNA polymerase III, beta subunit {Thermotoga maritima [ 99.97
d1ok7a2122 DNA polymerase III, beta subunit {Escherichia coli [Tax 99.97
d1vpka1120 DNA polymerase III, beta subunit {Thermotoga maritima [ 99.31
d1ok7a1122 DNA polymerase III, beta subunit {Escherichia coli [Tax 99.15
d1ok7a1122 DNA polymerase III, beta subunit {Escherichia coli [Tax 99.97
d1vpka1120 DNA polymerase III, beta subunit {Thermotoga maritima [ 99.95
d1vpka2123 DNA polymerase III, beta subunit {Thermotoga maritima [ 99.32
d1ok7a2122 DNA polymerase III, beta subunit {Escherichia coli [Tax 99.14
d1vpka3123 DNA polymerase III, beta subunit {Thermotoga maritima [ 98.17
d1ok7a3122 DNA polymerase III, beta subunit {Escherichia coli [Tax 98.03
d1rwza1122 Proliferating cell nuclear antigen (PCNA) {Archaeon Arc 97.47
d1iz5a1119 Proliferating cell nuclear antigen (PCNA) {Archaeon Pyr 95.92
d1plqa1126 Proliferating cell nuclear antigen (PCNA) {Baker's yeas 94.69
d1u7ba1126 Proliferating cell nuclear antigen (PCNA) {Human (Homo 92.3
d1ud9a1119 Proliferating cell nuclear antigen (PCNA) {Archaeon Sul 94.7
>d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNA clamp
superfamily: DNA clamp
family: DNA polymerase III, beta subunit
domain: DNA polymerase III, beta subunit
species: Thermotoga maritima [TaxId: 2336]
Probab=99.97  E-value=3.7e-31  Score=205.28  Aligned_cols=122  Identities=24%  Similarity=0.467  Sum_probs=116.2

Q ss_pred             CCCCCCCCCCEEEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCEEEEEECCCCCEEEEEEEEEEECCCCEEEEECHHHH
Q ss_conf             10135556617998489988889887410123555302565176599998078732689999989628843999638899
Q gi|254780454|r  250 QNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYL  329 (385)
Q Consensus       250 ~~vip~~~~~~~~v~r~~l~~al~Rv~i~~~~~~~~i~l~~~~~~l~i~~~~~e~g~~~e~i~~~~~G~~~~i~fN~~yl  329 (385)
                      ++|||++++++++++|.+|++||+|+++++++++++|+|+|+++++++++.++|.|++.|+++++|+|++++|+||++||
T Consensus         1 ~~viP~~~~~~v~v~r~~l~~al~Rv~~~s~~~~~~V~l~~~~~~l~l~s~~~e~g~~~e~i~~~~~Ge~~~i~fN~~yL   80 (123)
T d1vpka3           1 KRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPDYGEVVDEVEVQKEGEDLVIAFNPKFI   80 (123)
T ss_dssp             GGGSCSCCSEEEEEEHHHHHHHHHHHHHHHTTTTCCEEEEECSSEEEEEEEETTTEEEEEEEECEEEECCEEEEECHHHH
T ss_pred             CCCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEEECCCCCHHCCCCCCCCCCCCCEEEEECHHHH
T ss_conf             95069999879999999999999999988437776358996388148886266520004110100257776999889999


Q ss_pred             HHHHHHCCCCCCCCCEEEEEECCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             88987357533466338999658987589943776544455566763799832129
Q gi|254780454|r  330 LEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI  385 (385)
Q Consensus       330 ~d~L~~~~~~~~~~e~i~l~~~~~~~p~~i~~~~~~~~~~~~~~~~~~~liMPvri  385 (385)
                      +|+|+++++     ++|.|+|.++.+|++|++.++         .+|+||||||||
T Consensus        81 ~d~L~~~~~-----~~V~l~~~~~~~p~~i~~~~~---------~~~~~liMP~ri  122 (123)
T d1vpka3          81 EDVLKHIET-----EEIEMNFVDSTSPCQINPLDI---------SGYLYIVMPIRL  122 (123)
T ss_dssp             HHHHHHCCS-----SEEEEEESCTTSCEEEEETTC---------CSEEEEECCBCC
T ss_pred             HHHHHHCCC-----CEEEEEECCCCCCEEEECCCC---------CCEEEEEEEEEC
T ss_conf             999954789-----879999868999889963899---------953899984881



>d1rwza2 d.131.1.2 (A:123-244) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1plqa2 d.131.1.2 (A:127-258) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1iz5a2 d.131.1.2 (A:126-246) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1u7ba2 d.131.1.2 (A:127-255) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ud9a2 d.131.1.2 (A:127-245) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]} Back     information, alignment and structure
>d1vpka2 d.131.1.1 (A:121-243) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1vpka1 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1vpka1 d.131.1.1 (A:1-120) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1vpka2 d.131.1.1 (A:121-243) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1rwza1 d.131.1.2 (A:1-122) Proliferating cell nuclear antigen (PCNA) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1iz5a1 d.131.1.2 (A:2-120) Proliferating cell nuclear antigen (PCNA) {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1plqa1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1u7ba1 d.131.1.2 (A:1-126) Proliferating cell nuclear antigen (PCNA) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ud9a1 d.131.1.2 (A:1-119) Proliferating cell nuclear antigen (PCNA) {Archaeon Sulfolobus tokodaii [TaxId: 111955]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 385 DNA polymerase III subunit beta [Candidatus Liberi
3k4x_A_798 (A:) PCNA, proliferating cell nuclear antigen; DNA 2e-40
3k4x_A_ 798 (A:) PCNA, proliferating cell nuclear antigen; DNA 7e-26
3k4x_A_ 798 (A:) PCNA, proliferating cell nuclear antigen; DNA 9e-10
1vpk_A_144-207_256-378187 (A:144-207,A:256-378) DNA polymerase III, beta sub 8e-39
2avt_A_140-204_253-378191 (A:140-204,A:253-378) DNA polymerase III beta subu 5e-36
1rwz_A_245 (A:) DNA polymerase sliding clamp; torus, processi 3e-35
2zvv_A_276 (A:) PCNA 1, proliferating cellular nuclear antige 8e-35
1plq_A_258 (A:) Proliferating cell nuclear antigen (PCNA); DN 6e-34
3fds_D_245 (D:) DNA polymerase sliding clamp C; protein-prote 1e-33
3a1j_A_266 (A:) Cell cycle checkpoint control protein RAD9A; 1e-32
1ud9_A_245 (A:) DNA polymerase sliding clamp A; DNA-binding, 1e-31
1iz5_A_249 (A:) Proliferating cell nuclear antigen; DNA, repl 1e-31
2ijx_A_244 (A:) DNA polymerase sliding clamp A; PCNA3 subunit 8e-31
1u7b_A_261 (A:) PCNA, cyclin, proliferating cell nuclear anti 8e-30
3g65_A_296 (A:) Cell cycle checkpoint control protein RAD9A; 2e-20
1vpk_A_1-143_208-255191 (A:1-143,A:208-255) DNA polymerase III, beta subun 1e-24
3d1g_A_1-131_198-244178 (A:1-131,A:198-244) DNA polymerase III subunit bet 3e-24
2avt_A_1-139_205-252187 (A:1-139,A:205-252) DNA polymerase III beta subuni 1e-22
3d1g_A_1-131_198-244178 (A:1-131,A:198-244) DNA polymerase III subunit bet 6e-08
2avt_A_1-139_205-252187 (A:1-139,A:205-252) DNA polymerase III beta subuni 2e-05
3d1g_A_132-197_245-260_333-366116 (A:132-197,A:245-260,A:333-366) DNA polymerase III 4e-16
3d1g_A_132-197_245-260_333-366116 (A:132-197,A:245-260,A:333-366) DNA polymerase III 4e-04
3d1g_A_261-33272 (A:261-332) DNA polymerase III subunit beta; chemi 4e-13
>3k4x_A (A:) PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}Length = 798 Back     alignment and structure
 Score =  160 bits (405), Expect = 2e-40
 Identities = 52/409 (12%), Positives = 128/409 (31%), Gaps = 45/409 (11%)

Query: 1   MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
             +++  S+  +++    ++ +  N +     +   A+  +                  S
Sbjct: 408 STLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETS 467

Query: 61  VDVC----GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPES 116
           + +       +T  A  L DI++      ++     +E       +    +         
Sbjct: 468 IKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSE-----APALFQFDLKSGFLQFF 522

Query: 117 EFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVAT 176
             P   +E        + ++     E + F    +  +  +  + F   E+ +     A 
Sbjct: 523 LAPKFNDEGSNSQASNSGALEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAV 580

Query: 177 DGHRLAVAEVDIVA------QIAKMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIH 229
           D  R+ +  ++I        +     ++ +   ++ +ILR  ++ D+ ++    +   I 
Sbjct: 581 DDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSII 640

Query: 230 LNIESLSM------SVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRI 283
           L  E          S++L+D +    + +     D  L +  +   + V  +S +S    
Sbjct: 641 LLFEDTKKDRIAEYSLKLMDIDADFLK-IEELQYDSTLSLPSSEFSKIVRDLSQLSDSIN 699

Query: 284 QAV-------KLSLSSDKLCMTVDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNI 336
             +                 + +      +  E+      + P+D+ F  KYLL+II   
Sbjct: 700 IMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGS 759

Query: 337 SSDEVVDDEVVFRLDSSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
           S       + V    SS +    +   K             + L P   
Sbjct: 760 SL-----SDRVGIRLSSEAPALFQFDLKSG--------FLQFFLAPKFN 795


>3k4x_A (A:) PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}Length = 798 Back     alignment and structure
>3k4x_A (A:) PCNA, proliferating cell nuclear antigen; DNA replication, DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}Length = 798 Back     alignment and structure
>1vpk_A (A:144-207,A:256-378) DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8}Length = 187 Back     alignment and structure
>2avt_A (A:140-204,A:253-378) DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*Length = 191 Back     alignment and structure
>1rwz_A (A:) DNA polymerase sliding clamp; torus, processivity factor, replication; HET: DNA; 1.80A {Archaeoglobus fulgidus}Length = 245 Back     alignment and structure
>2zvv_A (A:) PCNA 1, proliferating cellular nuclear antigen 1; protein-peptide complex, DNA replication, DNA-binding, nucleus, DNA binding protein; 2.00A {Arabidopsis thaliana} PDB: 2zvw_ALength = 276 Back     alignment and structure
>1plq_A (A:) Proliferating cell nuclear antigen (PCNA); DNA-binding, nuclear protein, DNA replication, processivity factor; 2.30A {Saccharomyces cerevisiae}Length = 258 Back     alignment and structure
>3fds_D (D:) DNA polymerase sliding clamp C; protein-protein complex, cytoplasm, DNA damage, DNA repair, DNA replication, DNA-binding; HET: DNA 1PE PGE; 2.05A {Sulfolobus solfataricus} PDB: 2nti_E* 2io4_B* 2ix2_B* 2hik_B 2hii_B* 2izo_B*Length = 245 Back     alignment and structure
>3a1j_A (A:) Cell cycle checkpoint control protein RAD9A; DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein, polymorphism, cytoplasm; HET: SUC; 2.50A {Homo sapiens} PDB: 3ggr_ALength = 266 Back     alignment and structure
>1ud9_A (A:) DNA polymerase sliding clamp A; DNA-binding, DNA replication, DNA binding protein; HET: DNA; 1.68A {Sulfolobus tokodaii}Length = 245 Back     alignment and structure
>1iz5_A (A:) Proliferating cell nuclear antigen; DNA, replication, processivity, sliding clamp, DNA binding protein; 1.80A {Pyrococcus furiosus}Length = 249 Back     alignment and structure
>2ijx_A (A:) DNA polymerase sliding clamp A; PCNA3 subunit, protein-protein interaction, PCNA123 heterotrimer, DNA binding protein; HET: DNA; 1.90A {Sulfolobus solfataricus P2} PDB: 2nti_F* 2hii_C 2hik_C 2ix2_C*Length = 244 Back     alignment and structure
>1u7b_A (A:) PCNA, cyclin, proliferating cell nuclear antigen; sliding clamp, DNA processing, FEN1, PIP- BOX, replication; 1.88A {Homo sapiens}Length = 261 Back     alignment and structure
>3g65_A (A:) Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding clamp, DNA damage, DNA repair, exonuclease, hydrolase, nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}Length = 296 Back     alignment and structure
>1vpk_A (A:1-143,A:208-255) DNA polymerase III, beta subunit; TM0262, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8}Length = 191 Back     alignment and structure
>3d1g_A (A:1-131,A:198-244) DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli}Length = 178 Back     alignment and structure
>2avt_A (A:1-139,A:205-252) DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*Length = 187 Back     alignment and structure
>3d1g_A (A:1-131,A:198-244) DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli}Length = 178 Back     alignment and structure
>2avt_A (A:1-139,A:205-252) DNA polymerase III beta subunit; beta clamp, sliding clamp, replication, transferase; HET: DNA; 2.00A {Streptococcus pyogenes} PDB: 2awa_A*Length = 187 Back     alignment and structure
>3d1g_A (A:132-197,A:245-260,A:333-366) DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli}Length = 116 Back     alignment and structure
>3d1g_A (A:132-197,A:245-260,A:333-366) DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli}Length = 116 Back     alignment and structure
>3d1g_A (A:261-332) DNA polymerase III subunit beta; chemical probe, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, transferase; HET: DNA 322; 1.64A {Escherichia coli}Length = 72 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target385 DNA polymerase III subunit beta [Candidatus Liberibacte
3k4x_A_798 PCNA, proliferating cell nuclear antigen; DNA repl 100.0
3k4x_A_ 798 PCNA, proliferating cell nuclear antigen; DNA repl 100.0
1vpk_A_144-207_256-378187 DNA polymerase III, beta subunit; TM0262, structur 100.0
2avt_A_140-204_253-378191 DNA polymerase III beta subunit; beta clamp, slidi 100.0
2zvv_A_276 PCNA 1, proliferating cellular nuclear antigen 1; 100.0
1rwz_A_245 DNA polymerase sliding clamp; torus, processivity 100.0
1iz5_A_249 Proliferating cell nuclear antigen; DNA, replicati 100.0
1plq_A_258 Proliferating cell nuclear antigen (PCNA); DNA-bin 100.0
3fds_D_245 DNA polymerase sliding clamp C; protein-protein co 100.0
1ud9_A_245 DNA polymerase sliding clamp A; DNA-binding, DNA r 100.0
2ijx_A_244 DNA polymerase sliding clamp A; PCNA3 subunit, pro 100.0
3a1j_A_266 Cell cycle checkpoint control protein RAD9A; DNA d 100.0
1u7b_A_261 PCNA, cyclin, proliferating cell nuclear antigen; 99.98
3g65_A_296 Cell cycle checkpoint control protein RAD9A; PCNA, 99.8
3fds_C_249 DNA polymerase sliding clamp C; protein-protein co 99.24
3a1j_C_263 Cell cycle checkpoint protein RAD1; DNA damage, DN 97.91
3a1j_B_281 HHUS1, checkpoint protein HUS1; DNA damage, DNA re 97.73
3d1g_A_1-131_198-244178 DNA polymerase III subunit beta; chemical probe, D 100.0
2avt_A_1-139_205-252187 DNA polymerase III beta subunit; beta clamp, slidi 100.0
1vpk_A_1-143_208-255191 DNA polymerase III, beta subunit; TM0262, structur 100.0
1rwz_A_245 DNA polymerase sliding clamp; torus, processivity 99.58
1plq_A_258 Proliferating cell nuclear antigen (PCNA); DNA-bin 99.15
3fds_D_245 DNA polymerase sliding clamp C; protein-protein co 99.11
1ud9_A_245 DNA polymerase sliding clamp A; DNA-binding, DNA r 99.04
2zvv_A_276 PCNA 1, proliferating cellular nuclear antigen 1; 99.03
1iz5_A_249 Proliferating cell nuclear antigen; DNA, replicati 99.0
2ijx_A_<