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Protein

Primosomal protein N'

Gene

priA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.UniRule annotation10 Publications

Enzyme regulationi

ATPase activity is stimulated by binding to DNA. Helicase activity is stimulated by SSB.3 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi224 – 2318ATPUniRule annotation
Zinc fingeri436 – 44813C4-typeUniRule annotationAdd
BLAST
Zinc fingeri463 – 47917C4-typeUniRule annotationAdd
BLAST

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • ATP-dependent 3'-5' DNA helicase activity Source: EcoCyc
  • DNA binding Source: UniProtKB-HAMAP
  • helicase activity Source: EcoCyc
  • zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • DNA-dependent DNA replication Source: EcoliWiki
  • DNA recombination Source: EcoliWiki
  • DNA replication Source: EcoCyc
  • DNA replication, synthesis of RNA primer Source: UniProtKB-KW
  • DNA replication initiation Source: EcoCyc
  • DNA unwinding involved in DNA replication Source: EcoCyc
  • double-strand break repair Source: EcoliWiki
  • plasmid maintenance Source: EcoCyc
  • response to antibiotic Source: EcoliWiki
  • response to gamma radiation Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10763-MONOMER.
ECOL316407:JW3906-MONOMER.
MetaCyc:EG10763-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Primosomal protein N'UniRule annotation (EC:3.6.4.-UniRule annotation)
Alternative name(s):
ATP-dependent helicase PriAUniRule annotation
Replication factor Y
Gene namesi
Name:priAUniRule annotation
Ordered Locus Names:b3935, JW3906
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10763. priA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Primosome

Pathology & Biotechi

Disruption phenotypei

Mutants show delayed replication restart after exposition to UV.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi226 – 2261T → V: Strong decrease in ATPase and helicase activities. Does not affect DNA binding. 1 Publication
Mutagenesisi230 – 2301K → D: Lack of ATPase activity and strong decrease in helicase activity. Does not affect DNA binding. 2 Publications
Mutagenesisi230 – 2301K → R: Lack of helicase activity. Decreases Mu DNA replication. 2 Publications
Mutagenesisi320 – 3201D → A: Strong decrease in ATPase and helicase activities. Decreases DNA binding. 1 Publication
Mutagenesisi584 – 5841R → A: Does not affect DNA binding, but impairs ATPase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 732732Primosomal protein N'PRO_0000102123Add
BLAST

Proteomic databases

PaxDbiP17888.

Expressioni

Inductioni

Induced by hydroxyurea.1 Publication

Interactioni

Subunit structurei

Component of the primosome, which is composed of PriA, PriB, PriC, DnaB, DnaC, DnaG and DnaT. Binds ssDNA as a monomer. Interacts with SSB and PriB.UniRule annotation4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
priBP070133EBI-552050,EBI-1125223
ssbP0AGE02EBI-552050,EBI-1118620

Protein-protein interaction databases

BioGridi4262651. 62 interactions.
DIPiDIP-10562N.
IntActiP17888. 16 interactions.
MINTiMINT-1274231.
STRINGi511145.b3935.

Structurei

Secondary structure

1
732
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75Combined sources
Beta strandi16 – 194Combined sources
Beta strandi31 – 366Combined sources
Turni37 – 393Combined sources
Beta strandi40 – 5112Combined sources
Helixi57 – 593Combined sources
Beta strandi60 – 623Combined sources
Helixi75 – 8713Combined sources
Helixi92 – 10413Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D7EX-ray2.50A/B/C/D1-105[»]
2D7GX-ray3.30A/B/C/D1-105[»]
2D7HX-ray3.00A/B/C/D1-105[»]
2DWLX-ray3.20A/B/C/D1-105[»]
2DWMX-ray3.15A/B/C/D1-105[»]
2DWNX-ray3.35A/B/C/D1-105[»]
ProteinModelPortaliP17888.
SMRiP17888. Positions 1-732.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17888.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini211 – 377167Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini447 – 638192Helicase C-terminalUniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi320 – 3234DEAH box

Domaini

Contains an N-terminal DNA-binding domain and a C-terminal helicase domain. The helicase domain plays an important role in high affinity and stable binding of PriA to forked DNAs.2 Publications

Sequence similaritiesi

Belongs to the helicase family. PriA subfamily.UniRule annotation
Contains 1 helicase ATP-binding domain.UniRule annotation
Contains 1 helicase C-terminal domain.UniRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri436 – 44813C4-typeUniRule annotationAdd
BLAST
Zinc fingeri463 – 47917C4-typeUniRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C25. Bacteria.
COG1198. LUCA.
HOGENOMiHOG000037413.
InParanoidiP17888.
KOiK04066.
OMAiQRFNAPV.
OrthoDBiEOG6KT2K4.
PhylomeDBiP17888.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00983. PriA.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR005259. PriA.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00595. priA. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P17888-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPVAHVALPV PLPRTFDYLL PEGMTVKAGC RVRVPFGKQQ ERIGIVVSVS
60 70 80 90 100
DASELPLNEL KAVVEVLDSE PVFTHSVWRL LLWAADYYHH PIGDVLFHAL
110 120 130 140 150
PILLRQGRPA ANAPMWYWFA TEQGQAVDLN SLKRSPKQQQ ALAALRQGKI
160 170 180 190 200
WRDQVATLEF NDAALQALRK KGLCDLASET PEFSDWRTNY AVSGERLRLN
210 220 230 240 250
TEQATAVGAI HSAADTFSAW LLAGVTGSGK TEVYLSVLEN VLAQGKQALV
260 270 280 290 300
MVPEIGLTPQ TIARFRERFN APVEVLHSGL NDSERLSAWL KAKNGEAAIV
310 320 330 340 350
IGTRSALFTP FKNLGVIVID EEHDSSYKQQ EGWRYHARDL AVYRAHSEQI
360 370 380 390 400
PIILGSATPA LETLCNVQQK KYRLLRLTRR AGNARPAIQH VLDLKGQKVQ
410 420 430 440 450
AGLAPALITR MRQHLQADNQ VILFLNRRGF APALLCHDCG WIAECPRCDH
460 470 480 490 500
YYTLHQAQHH LRCHHCDSQR PVPRQCPSCG STHLVPVGLG TEQLEQTLAP
510 520 530 540 550
LFPGVPISRI DRDTTSRKGA LEQQLAEVHR GGARILIGTQ MLAKGHHFPD
560 570 580 590 600
VTLVALLDVD GALFSADFRS AERFAQLYTQ VAGRAGRAGK QGEVVLQTHH
610 620 630 640 650
PEHPLLQTLL YKGYDAFAEQ ALAERRMMQL PPWTSHVIVR AEDHNNQHAP
660 670 680 690 700
LFLQQLRNLI LSSPLADEKL WVLGPVPALA PKRGGRWRWQ ILLQHPSRVR
710 720 730
LQHIINGTLA LINTIPDSRK VKWVLDVDPI EG
Length:732
Mass (Da):81,655
Last modified:July 19, 2003 - v2
Checksum:iAB6C90F43042A363
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti156 – 1561A → R in AAA24416 (PubMed:2162050).Curated
Sequence conflicti621 – 6211A → R in AAA24416 (PubMed:2162050).Curated
Sequence conflicti649 – 6491A → V in BAA00491 (PubMed:2162049).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33293 Genomic DNA. Translation: AAA24416.1.
D00616 Genomic DNA. Translation: BAA00491.1.
L19201 Genomic DNA. Translation: AAB03067.1.
U00096 Genomic DNA. Translation: AAC76917.1.
AP009048 Genomic DNA. Translation: BAE77375.1.
PIRiS40878. A35505.
RefSeqiNP_418370.1. NC_000913.3.
WP_001301269.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76917; AAC76917; b3935.
BAE77375; BAE77375; BAE77375.
GeneIDi948426.
KEGGiecj:JW3906.
eco:b3935.
PATRICi32123387. VBIEscCol129921_4054.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33293 Genomic DNA. Translation: AAA24416.1.
D00616 Genomic DNA. Translation: BAA00491.1.
L19201 Genomic DNA. Translation: AAB03067.1.
U00096 Genomic DNA. Translation: AAC76917.1.
AP009048 Genomic DNA. Translation: BAE77375.1.
PIRiS40878. A35505.
RefSeqiNP_418370.1. NC_000913.3.
WP_001301269.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D7EX-ray2.50A/B/C/D1-105[»]
2D7GX-ray3.30A/B/C/D1-105[»]
2D7HX-ray3.00A/B/C/D1-105[»]
2DWLX-ray3.20A/B/C/D1-105[»]
2DWMX-ray3.15A/B/C/D1-105[»]
2DWNX-ray3.35A/B/C/D1-105[»]
ProteinModelPortaliP17888.
SMRiP17888. Positions 1-732.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262651. 62 interactions.
DIPiDIP-10562N.
IntActiP17888. 16 interactions.
MINTiMINT-1274231.
STRINGi511145.b3935.

Proteomic databases

PaxDbiP17888.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76917; AAC76917; b3935.
BAE77375; BAE77375; BAE77375.
GeneIDi948426.
KEGGiecj:JW3906.
eco:b3935.
PATRICi32123387. VBIEscCol129921_4054.

Organism-specific databases

EchoBASEiEB0756.
EcoGeneiEG10763. priA.

Phylogenomic databases

eggNOGiENOG4105C25. Bacteria.
COG1198. LUCA.
HOGENOMiHOG000037413.
InParanoidiP17888.
KOiK04066.
OMAiQRFNAPV.
OrthoDBiEOG6KT2K4.
PhylomeDBiP17888.

Enzyme and pathway databases

BioCyciEcoCyc:EG10763-MONOMER.
ECOL316407:JW3906-MONOMER.
MetaCyc:EG10763-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP17888.
PROiP17888.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_00983. PriA.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR005259. PriA.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00595. priA. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The priA gene encoding the primosomal replicative n' protein of Escherichia coli."
    Lee E.H., Masai H., Allen G.C. Jr., Kornberg A.
    Proc. Natl. Acad. Sci. U.S.A. 87:4620-4624(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-21.
  2. "Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y."
    Nurse P., Digate R., Zavitz K., Marians K.
    Proc. Natl. Acad. Sci. U.S.A. 87:4615-4619(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 3-16.
  3. "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes."
    Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 21:3391-3398(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase."
    Lee M.S., Marians K.J.
    Proc. Natl. Acad. Sci. U.S.A. 84:8345-8349(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family."
    Ouzounis C.A., Blencowe B.J.
    Nucleic Acids Res. 19:6953-6953(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO DEAD-BOX HELICASES.
  8. "Assembly of the primosome of DNA replication in Escherichia coli."
    Allen G.C. Jr., Kornberg A.
    J. Biol. Chem. 268:19204-19209(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, SUBUNIT.
  9. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  10. "Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate."
    Jones J.M., Nakai H.
    J. Mol. Biol. 289:503-516(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN BACTERIOPHAGE MU DNA REPLICATION, DNA-BINDING, MUTAGENESIS OF LYS-230.
  11. "Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA."
    Jezewska M.J., Bujalowski W.
    Biochemistry 39:10454-10467(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, SUBUNIT.
  12. "Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins."
    Rangarajan S., Woodgate R., Goodman M.F.
    Mol. Microbiol. 43:617-628(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  13. "ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination-dependent DNA replication."
    Tanaka T., Taniyama C., Arai K., Masai H.
    Genes Cells 8:251-261(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, ENZYME REGULATION, DOMAIN, MUTAGENESIS OF THR-226; LYS-230; ASP-320 AND ARG-584.
  14. "A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks."
    Mizukoshi T., Tanaka T., Arai K., Kohda D., Masai H.
    J. Biol. Chem. 278:42234-42239(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING.
  15. "PriA helicase and SSB interact physically and functionally."
    Cadman C.J., McGlynn P.
    Nucleic Acids Res. 32:6378-6387(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, INTERACTION WITH SSB.
  16. "Escherichia coli PriA protein, two modes of DNA binding and activation of ATP hydrolysis."
    Tanaka T., Mizukoshi T., Sasaki K., Kohda D., Masai H.
    J. Biol. Chem. 282:19917-19927(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, ENZYME REGULATION, DOMAIN.
  17. "A hand-off mechanism for primosome assembly in replication restart."
    Lopper M., Boonsombat R., Sandler S.J., Keck J.L.
    Mol. Cell 26:781-793(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, INTERACTION WITH PRIB.
  18. "Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli."
    Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J., Walker G.C.
    Mol. Cell 36:845-860(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY HYDROXYUREA.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  19. "The PriA replication restart protein blocks replicase access prior to helicase assembly and directs template specificity through its ATPase activity."
    Manhart C.M., McHenry C.S.
    J. Biol. Chem. 288:3989-3999(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  20. "Structural basis for the specific recognition of the 3' terminal nucleotide of DNA by the PriA protein from E.coli."
    Sasaki K., Ose T., Okamoto N., Tanaka T., Maenaka K., Masai H., Kohda D.
    Submitted (NOV-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-105 IN COMPLEXES WITH DAMP AND DCMP.
  21. "Insights into base nonselective recognition of 3'-terminus of DNA in stalled replication forks by the PriA protein."
    Sasaki K., Ose T., Okamoto N., Tanaka T., Maenaka K., Shirai T., Masai H., Kohda D.
    Submitted (AUG-2006) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS) OF 1-105.

Entry informationi

Entry nameiPRIA_ECOLI
AccessioniPrimary (citable) accession number: P17888
Secondary accession number(s): Q2M8N1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: July 19, 2003
Last modified: April 13, 2016
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.