254780804

254780804

DNA polymerase III subunit delta

GeneID in NCBI database:8209810Locus tag:CLIBASIA_03475
Protein GI in NCBI database:254780804Protein Accession:YP_003065217.1
Gene range:-(451620, 452678)Protein Length:352aa
Gene description:DNA polymerase III subunit delta
COG prediction:[L] DNA polymerase III, delta subunit
KEGG prediction:holA; DNA polymerase III subunit delta; K02340 DNA polymerase III subunit delta [EC:2.7.7.7]
SEED prediction:DNA polymerase III delta 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
TOPPREDnone TM-Helix
HMMTOP1 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--
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
cccHHHHHHHHHHHHHHHHHccEEEEEcccHHHHHHHHHHHHHHHcccccccccEEEEEHHHHHccHHHHHHHHHccccccccEEEEEEccccccHHHHHHHHHHHcccccEEEEEEccccccccHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccccc
ccHHccHHHHHHHHccccccccEEEEEcccHHHHHHHHHHHHHHHcccccccccEEEEcHHHHcccHHHHHHHHHcccccccccEEEEEcccccccHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccc
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNisityhdpfsLVVLNALEIQKNISTFWneinstslfskkkIILIENLSTEKKVLDCLEEIIIKNICNHIIIIksneikknNTLRKIAEKFTSVLAiscypdnkiHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFlaskmpshaLLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACknnnfykrt
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHiiiiksneikknntLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLeeiiiknicnhiiiiksneikknnTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
***********KSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKI*****************TEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIA*************
********FIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
*****SHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNN******
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT
MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIAQTACKNNNFYKRT

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
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
222087924345 DNA polymerase III, delta subunit [Agrobacterium radiob 1 1e-46
190893974346 DNA polymerase III protein, delta subunit [Rhizobium et 1 1e-45
241206935346 DNA polymerase III subunit delta [Rhizobium leguminosar 1 3e-45
86359696346 DNA polymerase III subunit delta [Rhizobium etli CFN 42 1 5e-45
227823851343 DNA polymerase III subunit delta [Sinorhizobium fredii 1 6e-45
209551497346 DNA polymerase III subunit delta [Rhizobium leguminosar 1 5e-44
150398392343 DNA polymerase III subunit delta [Sinorhizobium medicae 1 8e-44
15889999345 DNA polymerase III subunit delta [Agrobacterium tumefac 1 5e-43
116254458346 DNA polymerase III subunit delta [Rhizobium leguminosar 1 7e-43
325294120345 DNA polymerase III, delta subunit [Agrobacterium sp. H1 1 3e-42
>gi|222087924|ref|YP_002546462.1| DNA polymerase III, delta subunit [Agrobacterium radiobacter K84] Length = 345 Back     alignment and organism information
 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 112/357 (31%), Positives = 193/357 (54%), Gaps = 24/357 (6%)

Query: 1   MATIESHKF---IQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVV 57
           M+ I+SH+F   +Q + +N    + +F+ YG D+GL+ E   Q      +   DPFSL+ 
Sbjct: 1   MSEIKSHEFDGFLQNAARN----YRLFVIYGPDRGLVSERAGQVAGKTGVDLKDPFSLIK 56

Query: 58  LNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICN-HIIII 116
           L+  ++Q +     +E+N+  LF  +K++ I   + EK ++D L+ II  N  N   +II
Sbjct: 57  LDVGDLQNDAGRLLDEVNAIGLFGGEKLVWIRGAANEKALIDSLQ-IIADNPPNASFVII 115

Query: 117 KSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLAN 176
           ++ ++KK + LRK+AE    +  + CY D+   L  LI+  L      IS  A+Q+LL  
Sbjct: 116 EAGDLKKGSGLRKVAEASRKIATVPCYADDGRALNSLIDTELASENLRISPAARQMLLEL 175

Query: 177 LGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIML 236
           LGGDRIASRNE++KL+ YC  +  I E HV DII D   +  ++ ++A ++G        
Sbjct: 176 LGGDRIASRNEVRKLALYCRGEGTIEEGHVADIIGDASAISADDAVDAILKGD------- 228

Query: 237 ADFFL-------ASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPM 289
           +D FL       ASK     +L G L++FQLL+ +    +   +   +++Q   +++   
Sbjct: 229 SDAFLHAMQKIAASKTSMFLVLQGCLRQFQLLDVMRTEMDEKRVPPAQVMQTLGRHLHFR 288

Query: 290 KRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLEKNIIFQTILYIA-QTACKN 345
           ++ I++++LR W    +   ++++   I   R++  LE  I  QT+L    Q+A K+
Sbjct: 289 RKPIIEQALRSWTAPAIAREMNRLQSAILQTRQRASLEDTIATQTLLATTLQSARKS 345


Species: Agrobacterium tumefaciens
Genus: Agrobacterium
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|190893974|ref|YP_001980516.1| DNA polymerase III protein, delta subunit [Rhizobium etli CIAT 652] Length = 346 Back     alignment and organism information
>gi|241206935|ref|YP_002978031.1| DNA polymerase III subunit delta [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 346 Back     alignment and organism information
>gi|86359696|ref|YP_471588.1| DNA polymerase III subunit delta [Rhizobium etli CFN 42] Length = 346 Back     alignment and organism information
>gi|227823851|ref|YP_002827824.1| DNA polymerase III subunit delta [Sinorhizobium fredii NGR234] Length = 343 Back     alignment and organism information
>gi|209551497|ref|YP_002283414.1| DNA polymerase III subunit delta [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 346 Back     alignment and organism information
>gi|150398392|ref|YP_001328859.1| DNA polymerase III subunit delta [Sinorhizobium medicae WSM419] Length = 343 Back     alignment and organism information
>gi|15889999|ref|NP_355680.1| DNA polymerase III subunit delta [Agrobacterium tumefaciens str. C58] Length = 345 Back     alignment and organism information
>gi|116254458|ref|YP_770296.1| DNA polymerase III subunit delta [Rhizobium leguminosarum bv. viciae 3841] Length = 346 Back     alignment and organism information
>gi|325294120|ref|YP_004279984.1| DNA polymerase III, delta subunit [Agrobacterium sp. H13-3] Length = 345 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
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
PRK06585343 PRK06585, holA, DNA polymerase III subunit delta; Revie 3e-42
COG1466334 COG1466, HolA, DNA polymerase III, delta subunit [DNA r 5e-23
TIGR01128302 TIGR01128, holA, DNA polymerase III, delta subunit 9e-13
PRK05574340 PRK05574, holA, DNA polymerase III subunit delta; Revie 2e-07
>gnl|CDD|180631 PRK06585, holA, DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>gnl|CDD|31655 COG1466, HolA, DNA polymerase III, delta subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|162213 TIGR01128, holA, DNA polymerase III, delta subunit Back     alignment and domain information
>gnl|CDD|180139 PRK05574, holA, DNA polymerase III subunit delta; Reviewed Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 352 DNA polymerase III subunit delta [Candidatus Liberibact
PRK06585343 holA DNA polymerase III subunit delta; Reviewed 100.0
PRK07452326 DNA polymerase III subunit delta; Validated 100.0
PRK05574336 holA DNA polymerase III subunit delta; Reviewed 100.0
PRK05629331 hypothetical protein; Validated 100.0
COG1466334 HolA DNA polymerase III, delta subunit [DNA replication 100.0
PRK07914320 hypothetical protein; Reviewed 100.0
PRK08487328 DNA polymerase III subunit delta; Validated 100.0
) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex sub-assembly of DNA polymerase III holoenzyme, which couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. Both delta and delta prime are monomeric in their native state, and they bind each other tightly to form a 1:1 complex. Neither delta nor delta prime alone binds tightly to the gamma subunit . ; GO: 0003677 DNA binding, 0003891 delta DNA polymerase activity, 0006260 DNA replication, 0043625 delta DNA polymerase complex." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR01128">TIGR01128331 holA DNA polymerase III, delta subunit; InterPro: IPR00 100.0
PRK05563 541 DNA polymerase III subunits gamma and tau; Validated 99.93
PRK06647 560 DNA polymerase III subunits gamma and tau; Validated 99.92
PRK06305 462 DNA polymerase III subunits gamma and tau; Validated 99.92
TIGR02397363 dnaX_nterm DNA polymerase III, subunits gamma and tau; 99.91
PRK06674 563 DNA polymerase III subunits gamma and tau; Validated 99.91
PRK07270 557 DNA polymerase III subunits gamma and tau; Validated 99.9
PRK05907311 hypothetical protein; Provisional 99.89
PRK07764 775 DNA polymerase III subunits gamma and tau; Validated 99.84
PRK09111 600 DNA polymerase III subunits gamma and tau; Validated 99.84
PRK06645 507 DNA polymerase III subunits gamma and tau; Validated 99.83
COG2812 515 DnaX DNA polymerase III, gamma/tau subunits [DNA replic 99.81
PRK00440318 rfc replication factor C small subunit; Reviewed 99.73
PRK12323 721 DNA polymerase III subunits gamma and tau; Provisional 99.73
PRK07133 718 DNA polymerase III subunits gamma and tau; Validated 99.73
PRK12402337 replication factor C small subunit 2; Reviewed 99.72
PRK08691 704 DNA polymerase III subunits gamma and tau; Validated 99.7
PRK07003 816 DNA polymerase III subunits gamma and tau; Validated 99.67
PRK05648 705 DNA polymerase III subunits gamma and tau; Reviewed 99.67
PRK07994 643 DNA polymerase III subunits gamma and tau; Validated 99.66
PRK08853 717 DNA polymerase III subunits gamma and tau; Validated 99.66
PRK06872 696 DNA polymerase III subunits gamma and tau; Provisional 99.62
PRK05564313 DNA polymerase III subunit delta'; Validated 99.61
PRK08770 663 DNA polymerase III subunits gamma and tau; Validated 99.6
KOG0989346 consensus 99.53
PRK08058329 DNA polymerase III subunit delta'; Validated 99.4
PRK07940395 DNA polymerase III subunit delta'; Validated 99.36
PRK05707328 DNA polymerase III subunit delta'; Validated 99.31
PRK06871324 DNA polymerase III subunit delta'; Validated 99.1
PRK07993334 DNA polymerase III subunit delta'; Validated 99.07
PRK08699325 DNA polymerase III subunit delta'; Validated 99.03
PRK06964342 DNA polymerase III subunit delta'; Validated 98.95
PRK07471363 DNA polymerase III subunit delta'; Validated 98.94
PRK07399314 DNA polymerase III subunit delta'; Validated 98.73
PRK05917290 DNA polymerase III subunit delta'; Validated 98.71
PRK06090319 DNA polymerase III subunit delta'; Validated 98.44
pfam06144172 DNA_pol3_delta DNA polymerase III, delta subunit. DNA p 99.96
PRK08769319 DNA polymerase III subunit delta'; Validated 98.59
TIGR03420226 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members 98.57
PRK06893229 DNA replication initiation factor; Validated 98.57
TIGR00678216 holB DNA polymerase III, delta' subunit; InterPro: IPR0 98.49
PRK05642234 DNA replication initiation factor; Validated 98.49
PRK08084235 DNA replication initiation factor; Provisional 98.42
PRK07276290 DNA polymerase III subunit delta'; Validated 98.42
PRK08727233 hypothetical protein; Validated 98.27
pfam00308219 Bac_DnaA Bacterial dnaA protein. 98.27
PRK08903227 hypothetical protein; Validated 98.22
COG0470325 HolB ATPase involved in DNA replication [DNA replicatio 98.16
PRK07132303 DNA polymerase III subunit delta'; Validated 98.05
PRK09087226 hypothetical protein; Validated 97.88
PRK06620214 hypothetical protein; Validated 97.75
pfam05496234 RuvB_N Holliday junction DNA helicase ruvB N-terminus. 97.58
pfam05673248 DUF815 Protein of unknown function (DUF815). This famil 96.89
TIGR02903616 spore_lon_C ATP-dependent protease, Lon family; InterPr 96.4
pfam03215490 Rad17 Rad17 cell cycle checkpoint protein. 95.31
pfam01637223 Arch_ATPase Archaeal ATPase. This family contain a cons 94.79
COG2607287 Predicted ATPase (AAA+ superfamily) [General function p 94.57
PTZ00112650 origin recognition complex 1 protein; Provisional 94.55
PRK08451 523 DNA polymerase III subunits gamma and tau; Validated 99.79
PRK05896 613 DNA polymerase III subunits gamma and tau; Validated 99.77
PRK04195403 replication factor C large subunit; Provisional 99.43
COG2256436 MGS1 ATPase related to the helicase subunit of the Holl 98.78
PRK09112352 DNA polymerase III subunit delta'; Validated 98.76
KOG0991333 consensus 98.55
KOG2028554 consensus 97.87
KOG0990360 consensus 97.4
KOG2035351 consensus 97.09
KOG1970 634 consensus 94.25
PRK13342417 recombination factor protein RarA; Reviewed 99.44
PRK13341 726 recombination factor protein RarA/unknown domain fusion 99.07
PRK11361457 acetoacetate metabolism regulatory protein AtoC; Provis 92.62
pfam12169143 DNA_pol3_gamma3 DNA polymerase III subunits gamma and t 99.17
PRK04132863 replication factor C small subunit; Provisional 98.77
PRK05818262 DNA polymerase III subunit delta'; Validated 98.37
COG0593408 DnaA ATPase involved in DNA replication initiation [DNA 98.36
PRK00149447 dnaA chromosomal replication initiation protein; Review 98.35
PRK12422455 chromosomal replication initiation protein; Provisional 98.08
KOG1969 877 consensus 96.94
PRK00411394 cdc6 cell division control protein 6; Reviewed 96.39
PRK06581263 DNA polymerase III subunit delta'; Validated 96.87
TIGR03015269 pepcterm_ATPase putative secretion ATPase, PEP-CTERM lo 94.92
pfam1221372 Dpoe2NT DNA polymerases epsilon N terminal. This domain 90.62
>PRK06585 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>PRK07452 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>PRK05574 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>PRK05629 hypothetical protein; Validated Back     alignment and domain information
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07914 hypothetical protein; Reviewed Back     alignment and domain information
>PRK08487 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>TIGR01128 holA DNA polymerase III, delta subunit; InterPro: IPR005790 DNA polymerase III delta (holA, Back     alignment and domain information
>PRK05563 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK06647 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK06305 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763 This entry represents the well-conserved first N-terminal domain of DnaX, approx Back     alignment and domain information
>PRK06674 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK07270 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK05907 hypothetical protein; Provisional Back     alignment and domain information
>PRK07764 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK09111 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK06645 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00440 rfc replication factor C small subunit; Reviewed Back     alignment and domain information
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional Back     alignment and domain information
>PRK07133 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK12402 replication factor C small subunit 2; Reviewed Back     alignment and domain information
>PRK08691 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK07003 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed Back     alignment and domain information
>PRK07994 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK08853 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional Back     alignment and domain information
>PRK05564 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK08770 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>KOG0989 consensus Back     alignment and domain information
>PRK08058 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK07940 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK05707 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK06871 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK07993 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK08699 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK06964 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK07471 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK07399 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK05917 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK06090 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>pfam06144 DNA_pol3_delta DNA polymerase III, delta subunit Back     alignment and domain information
>PRK08769 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda Back     alignment and domain information
>PRK06893 DNA replication initiation factor; Validated Back     alignment and domain information
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2 Back     alignment and domain information
>PRK05642 DNA replication initiation factor; Validated Back     alignment and domain information
>PRK08084 DNA replication initiation factor; Provisional Back     alignment and domain information
>PRK07276 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK08727 hypothetical protein; Validated Back     alignment and domain information
>pfam00308 Bac_DnaA Bacterial dnaA protein Back     alignment and domain information
>PRK08903 hypothetical protein; Validated Back     alignment and domain information
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07132 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>PRK09087 hypothetical protein; Validated Back     alignment and domain information
>PRK06620 hypothetical protein; Validated Back     alignment and domain information
>pfam05496 RuvB_N Holliday junction DNA helicase ruvB N-terminus Back     alignment and domain information
>pfam05673 DUF815 Protein of unknown function (DUF815) 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
>pfam03215 Rad17 Rad17 cell cycle checkpoint protein Back     alignment and domain information
>pfam01637 Arch_ATPase Archaeal ATPase Back     alignment and domain information
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only] Back     alignment and domain information
>PTZ00112 origin recognition complex 1 protein; Provisional Back     alignment and domain information
>PRK08451 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK05896 DNA polymerase III subunits gamma and tau; Validated Back     alignment and domain information
>PRK04195 replication factor C large subunit; Provisional Back     alignment and domain information
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09112 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>KOG0991 consensus Back     alignment and domain information
>KOG2028 consensus Back     alignment and domain information
>KOG0990 consensus Back     alignment and domain information
>KOG2035 consensus Back     alignment and domain information
>KOG1970 consensus Back     alignment and domain information
>PRK13342 recombination factor protein RarA; Reviewed Back     alignment and domain information
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed Back     alignment and domain information
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional Back     alignment and domain information
>pfam12169 DNA_pol3_gamma3 DNA polymerase III subunits gamma and tau domain III Back     alignment and domain information
>PRK04132 replication factor C small subunit; Provisional Back     alignment and domain information
>PRK05818 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed Back     alignment and domain information
>PRK12422 chromosomal replication initiation protein; Provisional Back     alignment and domain information
>KOG1969 consensus Back     alignment and domain information
>PRK00411 cdc6 cell division control protein 6; Reviewed Back     alignment and domain information
>PRK06581 DNA polymerase III subunit delta'; Validated Back     alignment and domain information
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily Back     alignment and domain information
>pfam12213 Dpoe2NT DNA polymerases epsilon N terminal 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
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
1jr3_D343 Crystal Structure Of The Processivity Clamp Loader 2e-08
1xxh_A343 Atpgs Bound E. Coli Clamp Loader Complex Length = 3 5e-08
gi|15988195|pdb|1JR3|D Chain D, Crystal Structure Of The Processivity Clamp Loader Gamma Complex Of E. Coli Dna Polymerase Iii Length = 343 Back     alignment and structure
 Score = 65.1 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 37/296 (12%), Positives = 106/296 (35%), Gaps = 14/296 (4%)

Query: 35  FELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKK--IILIENLS 92
            + + Q         H  FS+      +   + +  ++   + SLF+ ++  ++L+    
Sbjct: 35  QDAVRQVAAAQGFEEHHTFSI------DPNTDWNAIFSLCQAMSLFASRQTLLLLLPENG 88

Query: 93  TEKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKFTSV-LAISCYPDNKIHLM 151
               + + L  +      + ++I++ N++ K            +  + ++C    +  L 
Sbjct: 89  PNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLP 148

Query: 152 DLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIIC 211
             +          +   A Q+L     G+ +A    L++LS    +   +T   V+  + 
Sbjct: 149 RWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGK-LTLPRVEQAVN 207

Query: 212 DTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLHGFLQKFQLLEKIHIIKECS 271
           D         ++A + GK   A+ +             LL    ++   L  +++ ++ +
Sbjct: 208 DAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQREL--LLLVNLKRQSA 265

Query: 272 NISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRIHLARKKKYLE 327
           +     +  K    +   +R ++ E+L   ++  +R+ +  +       ++     
Sbjct: 266 HTPLRALFDKHR--VWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQS 319


>gi|61679660|pdb|1XXH|A Chain A, Atpgs Bound E. Coli Clamp Loader Complex Length = 343 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
1jr3_D343 DNA polymerase III, delta subunit; processivity, proces 4e-15
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A* Length = 343 Back     alignment and structure
 Score = 77.6 bits (190), Expect = 4e-15
 Identities = 41/316 (12%), Positives = 110/316 (34%), Gaps = 14/316 (4%)

Query: 1   MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60
           M  +   +   +  + L      ++  G+D  L+ E  +  ++  +      F      +
Sbjct: 1   MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54

Query: 61  LEIQKNISTFWNEINSTSLFSKKKIILIENLSTEK--KVLDCLEEIIIKNICNHIIIIKS 118
           ++   + +  ++   + SLF+ ++              + + L  +      + ++I++ 
Sbjct: 55  IDPNTDWNAIFSLCQAMSLFASRQTXXXXXPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114

Query: 119 NEIKKNNTLRKIAEKFTSV-LAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANL 177
           N++ K            +  + ++C    +  L   +          +   A Q+L    
Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCY 174

Query: 178 GGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLA 237
            G+ +A    L++LS     D  +T   V+  + D         ++A + GK   A+ + 
Sbjct: 175 EGNLLALAQALERLSLLW-PDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHIL 233

Query: 238 DFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQES 297
                       LL    ++  LL  +       +     +  K    +   +R ++ E+
Sbjct: 234 QQLRLEGSEPVILLRTLQRELLLLVNLKRQSA--HTPLRALFDKH--RVWQNRRGMMGEA 289

Query: 298 LRIWNKNLVRETLHKI 313
           L   ++  +R+ +  +
Sbjct: 290 LNRLSQTQLRQAVQLL 305


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
1jr3_D343 DNA polymerase III, delta subunit; processivity, proces 100.0
1jr3_A373 DNA polymerase III subunit gamma; processivity, process 99.85
1sxj_D353 Activator 1 41 kDa subunit; clamp loader, processivity 99.73
1sxj_C340 Activator 1 40 kDa subunit; clamp loader, processivity 99.49
2chq_A319 Replication factor C small subunit; DNA-binding protein 99.41
1iqp_A327 RFCS; clamp loader, extended AAA-ATPase domain, complex 99.39
1sxj_B323 Activator 1 37 kDa subunit; clamp loader, processivity 99.33
1a5t_A334 Delta prime, HOLB; zinc finger, DNA replication; 2.20A 99.32
1sxj_E354 Activator 1 40 kDa subunit; clamp loader, processivity 99.01
1jql_B140 DNA polymerase III, delta subunit; processivity clamp, 99.79
2gno_A305 DNA polymerase III, gamma subunit-related protein; TM07 98.29
1njg_A250 DNA polymerase III subunit gamma; rossman-like fold, AA 99.34
2chg_A226 Replication factor C small subunit; DNA-binding protein 98.96
1sxj_A516 Activator 1 95 kDa subunit; clamp loader, processivity 98.69
2z4s_A440 Chromosomal replication initiator protein DNAA; AAA+ AT 98.56
3bos_A242 Putative DNA replication factor; YP_927791.1, putative 98.48
1l8q_A324 Chromosomal replication initiator protein DNAA; AAA+, h 97.91
2qby_B384 CDC6 homolog 3, cell division control protein 6 homolog 96.98
1w5s_A412 ORC2; CDC6, DNA replication initiation, DNA binding pro 96.96
2bjv_A265 PSP operon transcriptional activator; AAA, transcriptio 92.99
3b9p_A297 CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleoti 91.53
1fnn_A389 CDC6P, cell division control protein 6; ORC1, AAA prote 90.4
3pfi_A338 Holliday junction ATP-dependent DNA helicase RUVB; prob 98.12
1in4_A334 RUVB, holliday junction DNA helicase RUVB; AAA+-class A 98.1
2c9o_A456 RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-bindi 93.95
1qvr_A 854 CLPB protein; coiled coil, AAA ATPase, chaperone; HET: 93.81
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=353.35  Aligned_cols=333  Identities=12%  Similarity=0.165  Sum_probs=295.9

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEHHHHHCCHHHHHHHHHCCCCC
Q ss_conf             97633378875321001013847999569965899999999997335666773077620889641899999987178888
Q gi|254780804|r    1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLF   80 (352)
Q Consensus         1 ~~~i~~~~~~~~~~~~~~~~~~iyLi~G~d~~l~~~~~~~l~k~~~~~~~~~~~~~~~~~~e~~~d~~~l~~~~~t~slF   80 (352)
                      |+.|++.++.+.+++++   +++||+||+|+|+++++++.+.+.+..++.+++++...++.   .|++.+.+++.|+|||
T Consensus         1 m~~i~~~~l~~~l~k~~---~~vyll~G~e~~l~~~~~~~i~~~~~~~~~~e~~~~~~~~~---~~~~~l~~~~~t~slF   74 (343)
T 1jr3_D            1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPN---TDWNAIFSLCQAMSLF   74 (343)
T ss_dssp             CEEECTTTHHHHHHHCC---CSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCTT---CCHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHCCC---CCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC---CCHHHHHHHHCCCCCC
T ss_conf             99789999999984679---97799973949999999999999976089742045525676---8999999986068977


Q ss_pred             CCCEEEEEECCCC--HHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHH-HHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf             8823999847741--04578988988510565607999852654311356676543-11210146644200135889887
Q gi|254780804|r   81 SKKKIILIENLST--EKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEKF-TSVLAISCYPDNKIHLMDLIEES  157 (352)
Q Consensus        81 ~~~klIii~~~~~--~k~~~~~l~~~~~~~~~~~~li~~a~~l~k~~kl~k~~e~~-~~~~~v~~~~~~~~~l~~~i~~~  157 (352)
                      |++|+|++++...  .++..+.+..++..|++++++++..+..++.++.++.+... +.+.+++|++++.+++..|++++
T Consensus        75 ~~kr~viv~~~~~~~~~~~~~~l~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~l~~~i~~~  154 (343)
T 1jr3_D           75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAAR  154 (343)
T ss_dssp             CSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHHHHHHHH
T ss_pred             CCCEEECCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             77610022043323341599999998707999869999847752045789999972066699607899889999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             54302566756799999620012355689999997510344434888887753101221114678887641023699999
Q gi|254780804|r  158 LLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLA  237 (352)
Q Consensus       158 ~~~~g~~i~~~a~~~L~~~~g~d~~~l~~EleKL~ly~~~~~~It~~dI~~~v~~~~~~~if~L~dai~~~~~~~a~~~l  237 (352)
                      +++.|++|+++|+++|++.+|+|+..+.||++||++|+++ ++||.++|..+++...+.++|+|+||++.||..+|++.+
T Consensus       155 ~~~~g~~i~~~a~~~L~~~~~~d~~~l~~EleKL~l~~~~-~~it~~~i~~~~~~~~~~~~f~L~dal~~~~~~~a~~~l  233 (343)
T 1jr3_D          155 AKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPD-GKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHIL  233 (343)
T ss_dssp             HHHTTCEECHHHHHHHHHSSTTCHHHHHHHHHHHHHHCTT-CEECHHHHHHHHHHHCCCCHHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             9985898889999999998435789999999999973667-652046799884230020399999999755879999999


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             99853110001458999999999999999830256898999986089999768999999986499899999999999999
Q gi|254780804|r  238 DFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRI  317 (352)
Q Consensus       238 ~~l~~~g~~~~~il~~L~~~f~~L~~~~~~~~~~g~~~~~~~~~~~~p~~~~~k~~~~~q~~~~s~~~l~~~l~~L~~~d  317 (352)
                      ..+..+|++|+.+++++.++|+.|+.++..  .++.+..++.+..+  +||++++.+.+++++|+.+++.+++..|.++|
T Consensus       234 ~~l~~~g~~~~~il~~l~~~~~~l~~i~~~--~~~~~~~~~~~~~~--i~~~~~~~~~~~~~~~s~~~l~~~l~~L~~~D  309 (343)
T 1jr3_D          234 QQLRLEGSEPVILLRTLQRELLLLVNLKRQ--SAHTPLRALFDKHR--VWQNRRGMMGEALNRLSQTQLRQAVQLLTRTE  309 (343)
T ss_dssp             TSSTTTTCCHHHHHHHHHHHHHHHHHHHTC--SSSSCHHHHHHHHT--CCSSHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH--HCCCCHHHHHHHCC--CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             999877998599999999999999999987--35899999998859--99999999999997399999999999999999


Q ss_pred             HHHHCCC-CCHHHHHHHHHHHHHHHHHC
Q ss_conf             9953289-99899999999999996310
Q gi|254780804|r  318 HLARKKK-YLEKNIIFQTILYIAQTACK  344 (352)
Q Consensus       318 ~~~K~~~-~~~~~il~~~ll~l~~~a~~  344 (352)
                      +.+|++. .+++..++.+++.+|..+--
T Consensus       310 ~~iK~~~~~~~~~~le~l~l~l~~~~~~  337 (343)
T 1jr3_D          310 LTLKQDYGQSVWAELEGLSLLLCHKPLA  337 (343)
T ss_dssp             HHHHHSSCSCHHHHHHHHHHHTTSCCCC
T ss_pred             HHHCCCCCCCHHHHHHHHHHHHHCHHHH
T ss_conf             9970799999999999999999681757



>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B* Back     alignment and structure
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Back     alignment and structure
>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E* Back     alignment and structure
>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp loader, DNA replication, AAA+ ATPase, transferase; HET: DNA; 2.50A {Escherichia coli} SCOP: c.37.1.20 Back     alignment and structure
>2gno_A DNA polymerase III, gamma subunit-related protein; TM0771, structural genomics, PSI, protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima MSB8} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A* Back     alignment and structure
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Back     alignment and structure
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A* Back     alignment and structure
>3bos_A Putative DNA replication factor; YP_927791.1, putative DNA replication regulator HDA, structural genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis SB2B} Back     alignment and structure
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, replication initiation; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 2hcb_A* Back     alignment and structure
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Back     alignment and structure
>1w5s_A ORC2; CDC6, DNA replication initiation, DNA binding protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A* Back     alignment and structure
>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A* Back     alignment and structure
>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Back     alignment and structure
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Back     alignment and structure
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} Back     alignment and structure
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A* Back     alignment and structure
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} Back     alignment and structure
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 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

No hit with e-value below 0.005

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

IdentityAlignment graphLength Definition Probability
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
d1jqlb_140 delta subunit of DNA polymerase III, N-domain {Escheric 99.8
d2gnoa2198 gamma subunit of DNA polymerase III, N-domain {Thermoto 98.02
d1jr3d1127 delta subunit {Escherichia coli [TaxId: 562]} 99.71
d1jr3a1126 gamma subunit {Escherichia coli [TaxId: 562]} 98.5
d1njfa_239 delta prime subunit of DNA polymerase III, N-domain {Es 99.38
d1sxjc2227 Replication factor C3 {Baker's yeast (Saccharomyces cer 99.11
d1sxjb2224 Replication factor C4 {Baker's yeast (Saccharomyces cer 98.9
d1sxjd2237 Replication factor C2 {Baker's yeast (Saccharomyces cer 98.86
d1iqpa2231 Replication factor C {Archaeon Pyrococcus furiosus [Tax 98.65
d1a5ta2207 delta prime subunit of DNA polymerase III, N-domain {Es 98.61
d1sxja2253 Replication factor C1 {Baker's yeast (Saccharomyces cer 98.27
d1l8qa2213 Chromosomal replication initiation factor DnaA {Aquifex 97.9
d1ixsb2239 Holliday junction helicase RuvB {Thermus thermophilus [ 97.83
d1in4a2238 Holliday junction helicase RuvB {Thermotoga maritima [T 97.52
d1fnna2276 CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 96.21
d1ny5a2247 Transcriptional activator sigm54 (NtrC1), C-terminal do 93.72
d1ixza_247 AAA domain of cell division protein FtsH {Thermus therm 93.36
d1sxje2252 Replication factor C5 {Baker's yeast (Saccharomyces cer 98.03
d1w5sa2287 CDC6-like protein APE0152, N-terminal domain {Aeropyrum 91.98
>d1jqlb_ c.37.1.20 (B:) delta subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]
Probab=99.80  E-value=2.4e-19  Score=144.12  Aligned_cols=137  Identities=11%  Similarity=0.193  Sum_probs=111.4

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEHHHHHCCHHHHHHHHHCCCCC
Q ss_conf             97633378875321001013847999569965899999999997335666773077620889641899999987178888
Q gi|254780804|r    1 MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLF   80 (352)
Q Consensus         1 ~~~i~~~~~~~~~~~~~~~~~~iyLi~G~d~~l~~~~~~~l~k~~~~~~~~~~~~~~~~~~e~~~d~~~l~~~~~t~slF   80 (352)
                      |..|++.++.+.+++++   .+||++||+|.||+++..+.+.+.+..++.++++...++ .+  .+++.+++++.|+|||
T Consensus         1 Mm~i~~~~L~~~l~k~l---~~vyll~G~E~~L~~~~~~~i~~~~~~~~~~~~~~~~~~-~~--~~~~~l~~~~~t~slF   74 (140)
T d1jqlb_           1 MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSID-PN--TDWNAIFSLCQAMSLF   74 (140)
T ss_dssp             CEECCGGGHHHHHHHCC---CSEEEEESSCHHHHHHHHHHHHHHHHHTTCCEEECCCCS-TT--CCHHHHHHHHHCCCTT
T ss_pred             CCCCCHHHHHHHHHCCC---CCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEECCC-CC--CCHHHHHHHHCCCCCC
T ss_conf             98479999999985279---848999848299999999999999885896204665036-66--8999999997079865


Q ss_pred             CCCEEEEEECCCC--HHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHH-HHHHHHCCCC
Q ss_conf             8823999847741--0457898898851056560799985265431135667654-3112101466
Q gi|254780804|r   81 SKKKIILIENLST--EKKVLDCLEEIIIKNICNHIIIIKSNEIKKNNTLRKIAEK-FTSVLAISCY  143 (352)
Q Consensus        81 ~~~klIii~~~~~--~k~~~~~l~~~~~~~~~~~~li~~a~~l~k~~kl~k~~e~-~~~~~~v~~~  143 (352)
                      |++|+|+|++...  .++..+.|.+|+.+|++++++|+.++++++.++-.|++.. .+.+..|+|.
T Consensus        75 ~~krli~i~~~~~~~~k~~~~~L~~~~~~~~~~~~lii~~~~~~k~~~~~k~~K~l~k~g~vI~Cq  140 (140)
T d1jqlb_          75 ASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQ  140 (140)
T ss_dssp             CCCEEEEEECCTTCSCTTHHHHHHHHHHHCCSSCCEEEECSSCCTTGGGSHHHHHHGGGCEEEECC
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCEEEECC
T ss_conf             686799998378798477899999998279998799998278771456519999998397489588



>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1jr3d1 a.80.1.1 (D:212-338) delta subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jr3a1 a.80.1.1 (A:243-368) gamma subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Back     information, alignment and structure
>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 352 DNA polymerase III subunit delta [Candidatus Liber
1jr3_D_1-144144 (D:1-144) DNA polymerase III, delta subunit; proce 7e-10
1jql_B_140 (B:) DNA polymerase III, delta subunit; processivi 4e-08
1jr3_D_145-21167 (D:145-211) DNA polymerase III, delta subunit; pro 9e-07
>1jr3_D (D:1-144) DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli}Length = 144 Back     alignment and structure
 Score = 59.2 bits (143), Expect = 7e-10
 Identities = 16/150 (10%), Positives = 56/150 (37%), Gaps = 9/150 (6%)

Query: 1   MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60
           M  +   +   +  + L      ++  G+D  L+ E  +  ++  +      F      +
Sbjct: 1   MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54

Query: 61  LEIQKNISTFWNEINSTSLFSKKKIILIENLS--TEKKVLDCLEEIIIKNICNHIIIIKS 118
           ++   + +  ++   + SLF+ ++ +L+          + + L  +      + ++I++ 
Sbjct: 55  IDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114

Query: 119 NEIKKNNTLRKIAEKFTSV-LAISCYPDNK 147
           N++ K            +  + ++C    +
Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTCQTPEQ 144


>1jql_B (B:) DNA polymerase III, delta subunit; processivity clamp, clamp loader, DNA replication, AAA+ ATPase, transferase; HET: DNA; 2.50A {Escherichia coli}Length = 140 Back     alignment and structure
>1jr3_D (D:145-211) DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli}Length = 67 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target352 DNA polymerase III subunit delta [Candidatus Liberibact
1jr3_D_1-144144 DNA polymerase III, delta subunit; processivity, p 99.8
1jql_B_140 DNA polymerase III, delta subunit; processivity cl 99.78
1sxj_B_1-166166 Activator 1 37 kDa subunit; clamp loader, processi 96.37
2gno_A_1-140140 DNA polymerase III, gamma subunit-related protein; 96.07
1njg_A_1-185185 DNA polymerase III subunit gamma; rossman-like fol 95.74
1jr3_A_1-177177 DNA polymerase III subunit gamma; processivity, pr 94.17
1sxj_E_1-192192 Activator 1 40 kDa subunit; clamp loader, processi 93.58
1sxj_C_1-168168 Activator 1 40 kDa subunit; clamp loader, processi 93.52
1a5t_A_1-166166 Delta prime, HOLB; zinc finger, DNA replication; 2 90.92
1iqp_A_1-168168 RFCS; clamp loader, extended AAA-ATPase domain, co 90.6
1jr3_D_212-343132 DNA polymerase III, delta subunit; processivity, p 99.61
1jr3_A_244-373130 DNA polymerase III subunit gamma; processivity, pr 99.02
1sxj_D_256-35398 Activator 1 41 kDa subunit; clamp loader, processi 91.41
1jr3_D_145-21167 DNA polymerase III, delta subunit; processivity, p 99.21
1jr3_A_178-24366 DNA polymerase III subunit gamma; processivity, pr 97.43
1njg_A_186-25065 DNA polymerase III subunit gamma; rossman-like fol 97.38
2chq_A_161-22565 Replication factor C small subunit; DNA-binding pr 97.25
1sxj_C_169-23870 Activator 1 40 kDa subunit; clamp loader, processi 97.19