Protein: RL4
Large ribosomal subunit protein uL4 (50S ribosomal protein L4)

Gene: RL4, rplD
Organism: Escherichia coli K-12
Interactions: 243
UniProt ID: P60723

Gene Ontology (top 5):
GO:0001070 - RNA-binding transcription regulator activity
GO:0002181 - cytoplasmic translation
GO:0003677 - DNA binding
GO:0003735 - structural constituent of ribosome
GO:0005737 - cytoplasm

Download interactions: TXT   MITAB-2.5

Interaction Interactor Experiments Homologs Category Interaction
Score
Confidence

496306

CSPE
Cold shock-like protein CspE

3

8

High-throughput

0.657

High

497439

CSPC
Cold shock-like protein CspC

3

8

High-throughput

0.657

High

950950

RL2
Large ribosomal subunit protein uL2

3

3

High-throughput

0.657

High

365841

RPOD
RNA polymerase sigma factor RpoD

3

0

High-throughput

0.629

High

639468

LPXD
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase

3

0

High-throughput

0.629

High

953317

RL22
Large ribosomal subunit protein uL22

1

2

High-throughput

0.625

High

491513

IF3
Translation initiation factor IF-3 [Cleaved into: Translation initiation factor IF-3, N-terminally processed; Translation initiation factor IF-3S]

3

0

High-throughput

0.616

High

494334

RS5
Small ribosomal subunit protein uS5

2

1

High-throughput

0.612

High

785877

CBPA
Curved DNA-binding protein

2

1

High-throughput

0.612

High

790848

RLUB
Ribosomal large subunit pseudouridine synthase B

2

3

High-throughput

0.612

High

953337

DCYD
D-cysteine desulfhydrase

2

2

High-throughput

0.601

High

421129

PNP
Polyribonucleotide nucleotidyltransferase

2

1

High-throughput

0.588

High

492788

RL1
Large ribosomal subunit protein uL1

2

2

High-throughput

0.588

High

493278

RS10
Small ribosomal subunit protein uS10

2

1

High-throughput

0.588

High

493434

RS13
Small ribosomal subunit protein uS13

2

1

High-throughput

0.588

High

493976

RS3
Small ribosomal subunit protein uS3

2

2

High-throughput

0.588

High

497529

RL13
Large ribosomal subunit protein uL13

2

2

High-throughput

0.588

High

498022

IOJAP
Ribosomal silencing factor RsfS

2

1

High-throughput

0.588

High

499878

RL14
Large ribosomal subunit protein uL14

2

2

High-throughput

0.588

High

501298

RL6
Large ribosomal subunit protein uL6

2

1

High-throughput

0.588

High

569575

SELB
Selenocysteine-specific elongation factor

2

4

High-throughput

0.588

High

953319

RL5
Large ribosomal subunit protein uL5

2

1

High-throughput

0.588

High

501542

SSB
Single-stranded DNA-binding protein

2

1

High-throughput

0.584

High

492083

IPYR
Inorganic pyrophosphatase

2

0

High-throughput

0.576

High

499956

RL23
Large ribosomal subunit protein uL23

2

0

High-throughput

0.576

High

500735

NUSG
Transcription termination/antitermination protein NusG

2

0

High-throughput

0.576

High

811769

RSGA
Small ribosomal subunit biogenesis GTPase RsgA

2

0

High-throughput

0.576

High

953331

RLMI
Ribosomal RNA large subunit methyltransferase I

2

0

High-throughput

0.569

High

368968

SYGA
Glycine--tRNA ligase alpha subunit

2

0

High-throughput

0.563

High

395092

DNAA
Chromosomal replication initiator protein DnaA

2

0

High-throughput

0.563

High

460406

SYL
Leucine--tRNA ligase

2

0

High-throughput

0.563

High

490910

HFQ
RNA-binding protein Hfq

2

0

High-throughput

0.563

High

494182

RS4
Small ribosomal subunit protein uS4

2

0

High-throughput

0.563

High

494899

TGT
Queuine tRNA-ribosyltransferase

2

0

High-throughput

0.563

High

495937

RPOB
DNA-directed RNA polymerase subunit beta

2

0

High-throughput

0.563

High

498004

YBCJ
Putative RNA-binding protein YbcJ

2

0

High-throughput

0.563

High

501040

SSPB
Stringent starvation protein B

2

0

High-throughput

0.563

High

501654

YHBY
RNA-binding protein YhbY

2

0

High-throughput

0.563

High

578338

HELD
DNA helicase IV

2

0

High-throughput

0.563

High

628111

PARE
DNA topoisomerase 4 subunit B

2

0

High-throughput

0.563

High

705895

HOLC
DNA polymerase III subunit chi

2

0

High-throughput

0.563

High

953326

NFI
Endonuclease V

2

0

High-throughput

0.563

High

432421

T1SK
Type I restriction enzyme EcoKI specificity subunit

2

0

High-throughput

0.547

High

494992

TIG
Trigger factor

2

0

Small-scale

0.545

High

895858

END8
Endonuclease 8

2

1

High-throughput

0.537

High

480643

RHAS
HTH-type transcriptional activator RhaS

1

1

High-throughput

0.536

High

492336

RF1
Peptide chain release factor RF1

1

4

High-throughput

0.536

High

492453

RL11
Large ribosomal subunit protein uL11

1

2

High-throughput

0.536

High

496321

CSPG
Cold shock-like protein CspG

1

8

High-throughput

0.536

High

496329

CSPI
Cold shock-like protein CspI

1

8

High-throughput

0.536

High

498439

CYSK
Cysteine synthase A

1

1

High-throughput

0.536

High

499087

DBHA
DNA-binding protein HU-alpha

1

1

High-throughput

0.536

High

663291

FMT
Methionyl-tRNA formyltransferase

1

1

High-throughput

0.536

High

664202

RECG
ATP-dependent DNA helicase RecG

1

1

High-throughput

0.536

High

683077

RHLE
ATP-dependent RNA helicase RhlE

1

2

High-throughput

0.536

High

788393

CSPB
Cold shock-like protein CspB

1

8

High-throughput

0.536

High

827670

ARFB
Peptidyl-tRNA hydrolase ArfB

1

2

High-throughput

0.536

High

953325

GRCA
Autonomous glycyl radical cofactor

1

1

High-throughput

0.536

High

408532

3MG2
DNA-3-methyladenine glycosylase 2

1

0

High-throughput

0.513

High

416323

SYE
Glutamate--tRNA ligase

1

0

High-throughput

0.513

High

445433

AGAL
Alpha-galactosidase

1

0

High-throughput

0.513

High

450153

SDIA
Regulatory protein SdiA

1

0

High-throughput

0.513

High

457023

CHER
Chemotaxis protein methyltransferase

1

0

High-throughput

0.513

High

489383

END4
Endonuclease 4

1

0

High-throughput

0.513

High

490375

COAD
Phosphopantetheine adenylyltransferase

1

0

High-throughput

0.513

High

490433

DEF
Peptide deformylase

1

0

High-throughput

0.513

High

493050

RL29
Large ribosomal subunit protein uL29

1

0

High-throughput

0.513

High

493517

RS16
Small ribosomal subunit protein bS16

1

0

High-throughput

0.513

High

496621

MUG
G/U mismatch-specific DNA glycosylase

1

0

High-throughput

0.513

High

496823

SLYD
FKBP-type peptidyl-prolyl cis-trans isomerase SlyD

1

0

High-throughput

0.513

High

498163

KBL
2-amino-3-ketobutyrate coenzyme A ligase

1

0

High-throughput

0.513

High

499210

HSLR
Heat shock protein 15

1

0

High-throughput

0.513

High

499504

YEBG
Uncharacterized protein YebG

1

0

High-throughput

0.513

High

499678

SUHB
Nus factor SuhB

1

0

High-throughput

0.513

High

499792

RLMM
Ribosomal RNA large subunit methyltransferase M

1

0

High-throughput

0.513

High

500260

MIAB
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase

1

0

High-throughput

0.513

High

500972

GLRR
Transcriptional regulatory protein GlrR

1

0

High-throughput

0.513

High

501577

THIO2
Thioredoxin 2

1

0

High-throughput

0.513

High

501880

ISCX
Protein IscX

1

0

High-throughput

0.513

High

664120

YFFB
Protein YffB

1

0

High-throughput

0.513

High

664182

INTD
Prophage integrase IntD

1

0

High-throughput

0.513

High

664191

ACPS
Holo-[acyl-carrier-protein] synthase

1

0

High-throughput

0.513

High

687556

FLIS
Flagellar secretion chaperone FliS

1

0

High-throughput

0.513

High

705888

TREC
Trehalose-6-phosphate hydrolase

1

0

High-throughput

0.513

High

728736

TRMN6
tRNA1(Val)

1

0

High-throughput

0.513

High

732766

YIIS
UPF0381 protein YiiS

1

0

High-throughput

0.513

High

749436

SFGH2
S-formylglutathione hydrolase YeiG

1

0

High-throughput

0.513

High

749441

RIHB
Pyrimidine-specific ribonucleoside hydrolase RihB

1

0

High-throughput

0.513

High

787525

RSMB
Ribosomal RNA small subunit methyltransferase B

1

0

High-throughput

0.513

High

790771

RLMJ
Ribosomal RNA large subunit methyltransferase J

1

0

High-throughput

0.513

High

790778

YHJB
Putative HTH-type transcriptional regulator YhjB

1

0

High-throughput

0.513

High

811838

RSMC
Ribosomal RNA small subunit methyltransferase C

1

0

High-throughput

0.513

High

840166

YHAK
Pirin-like protein YhaK

1

0

High-throughput

0.513

High

847966

LPXH
UDP-2,3-diacylglucosamine hydrolase

1

0

High-throughput

0.513

High

953345

CSE2
CRISPR system Cascade subunit CasB

1

0

High-throughput

0.513

High

953347

MURR
HTH-type transcriptional regulator MurR

1

0

High-throughput

0.513

High

953351

XDHB
Putative xanthine dehydrogenase FAD-binding subunit XdhB

1

0

High-throughput

0.513

High

953352

NORV
Anaerobic nitric oxide reductase flavorubredoxin

1

0

High-throughput

0.513

High

421080

APPY
HTH-type transcriptional regulator AppY

1

1

High-throughput

0.489

High

501088

RELA
GTP pyrophosphokinase

1

1

High-throughput

0.489

High

365884

DPO1
DNA polymerase I

1

1

High-throughput

0.484

High

382744

RS7
Small ribosomal subunit protein uS7

1

1

High-throughput

0.484

High

480616

PFLB
Formate acetyltransferase 1

1

1

High-throughput

0.484

High

490274

CLPP
ATP-dependent Clp protease proteolytic subunit

1

1

High-throughput

0.484

High

490533

EFG
Elongation factor G

1

2

High-throughput

0.484

High

490564

DER
GTPase Der

1

5

High-throughput

0.484

High

490972

IHFB
Integration host factor subunit beta

1

1

High-throughput

0.484

High

491237

DNAK
Chaperone protein DnaK

1

3

High-throughput

0.484

High

493315

RS11
Small ribosomal subunit protein uS11

1

1

High-throughput

0.484

High

493818

RS2
Small ribosomal subunit protein uS2

1

1

High-throughput

0.484

High

497118

DEAD
ATP-dependent RNA helicase DeaD

1

2

High-throughput

0.484

High

497279

ULAR
HTH-type transcriptional regulator UlaR

1

1

High-throughput

0.484

High

497391

CSPA
Cold shock protein CspA

1

8

High-throughput

0.484

High

497648

RLUC
Ribosomal large subunit pseudouridine synthase C

1

3

High-throughput

0.484

High

501109

SPOT
Bifunctional

1

1

High-throughput

0.484

High

501204

RL17
Large ribosomal subunit protein bL17

1

3

High-throughput

0.484

High

578598

SRLR
Glucitol operon repressor

1

1

High-throughput

0.484

High

638614

SRMB
ATP-dependent RNA helicase SrmB

1

3

High-throughput

0.484

High

676567

MNME
tRNA modification GTPase MnmE

1

4

High-throughput

0.484

High

951024

RL3
Large ribosomal subunit protein uL3

1

3

High-throughput

0.484

High

952517

RL24
Large ribosomal subunit protein uL24

1

1

High-throughput

0.484

High

953316

LEPA
Elongation factor 4

1

6

High-throughput

0.484

High

497295

ETTA
Energy-dependent translational throttle protein EttA

1

0

High-throughput

0.479

High

559589

FDHE
Protein FdhE

1

0

High-throughput

0.479

High

499782

YGAM
Uncharacterized protein YgaM

1

1

High-throughput

0.479

High

501617

YFIF
Uncharacterized tRNA/rRNA methyltransferase YfiF

1

2

High-throughput

0.479

High

361756

PHSM
Maltodextrin phosphorylase

1

0

High-throughput

0.464

High

420153

KDSB
3-deoxy-manno-octulosonate cytidylyltransferase

1

0

High-throughput

0.464

High

480557

GRPE
Protein GrpE

1

0

High-throughput

0.464

High

490356

HSLU
ATP-dependent protease ATPase subunit HslU

1

0

High-throughput

0.464

High

490684

FABZ
3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ

1

0

High-throughput

0.464

High

490710

FIS
DNA-binding protein Fis

1

0

High-throughput

0.464

High

490832

GREA
Transcription elongation factor GreA

1

0

High-throughput

0.464

High

491559

KDSA
2-dehydro-3-deoxyphosphooctonate aldolase

1

0

High-throughput

0.464

High

491823

MURA
UDP-N-acetylglucosamine 1-carboxyvinyltransferase

1

0

High-throughput

0.464

High

491953

RPPH
RNA pyrophosphohydrolase

1

0

High-throughput

0.464

High

492144

HSLV
ATP-dependent protease subunit HslV

1

0

High-throughput

0.464

High

492171

PTH
Peptidyl-tRNA hydrolase

1

0

High-throughput

0.464

High

492255

PYRH
Uridylate kinase

1

0

High-throughput

0.464

High

492406

RL10
Large ribosomal subunit protein uL10

1

0

High-throughput

0.464

High

494648

RPOA
DNA-directed RNA polymerase subunit alpha

1

0

High-throughput

0.464

High

495369

UVRC
UvrABC system protein C

1

0

High-throughput

0.464

High

495412

YIHI
Der GTPase-activating protein YihI

1

0

High-throughput

0.464

High

495857

RPOC
DNA-directed RNA polymerase subunit beta'

1

0

High-throughput

0.464

High

496738

PHOL
PhoH-like protein

1

0

High-throughput

0.464

High

496869

PPIC
Peptidyl-prolyl cis-trans isomerase C

1

0

High-throughput

0.464

High

498401

CLPA
ATP-dependent Clp protease ATP-binding subunit ClpA

1

0

High-throughput

0.464

High

498604

DPS
DNA protection during starvation protein

1

0

High-throughput

0.464

High

498960

DNAB
Replicative DNA helicase DnaB

1

0

High-throughput

0.464

High

500030

MAP1
Methionine aminopeptidase

1

0

High-throughput

0.464

High

500712

NUSA
Transcription termination/antitermination protein NusA

1

0

High-throughput

0.464

High

501142

RHO
Transcription termination factor Rho

1

0

High-throughput

0.464

High

501516

SRP54
Signal recognition particle protein

1

0

High-throughput

0.464

High

501888

RLME
Ribosomal RNA large subunit methyltransferase E

1

0

High-throughput

0.464

High

516001

RCSA
Transcriptional regulatory protein RcsA

1

0

High-throughput

0.464

High

521494

SECA
Protein translocase subunit SecA

1

0

High-throughput

0.464

High

522223

DPO3A
DNA polymerase III subunit alpha

1

0

High-throughput

0.464

High

597641

ICLR
Transcriptional repressor IclR

1

0

High-throughput

0.464

High

638583

RNR
Ribonuclease R

1

0

High-throughput

0.464

High

638633

RNE
Ribonuclease E

1

0

High-throughput

0.464

High

649701

MUKB
Chromosome partition protein MukB

1

0

High-throughput

0.464

High

788376

RLMN
Dual-specificity RNA methyltransferase RlmN

1

0

High-throughput

0.464

High

789063

DCTR
HTH-type transcriptional regulator DctR

1

0

High-throughput

0.464

High

953318

RISB
6,7-dimethyl-8-ribityllumazine synthase

1

0

High-throughput

0.464

High

953320

ISPH
4-hydroxy-3-methylbut-2-enyl diphosphate reductase

1

0

High-throughput

0.464

High

953329

GNGF
Putative gluconeogenesis factor

1

0

High-throughput

0.464

High

495590

TMAR
Pole-localizer protein TmaR

1

0

High-throughput

0.458

High

495999

DARP
Dual-action ribosomal maturation protein DarP

1

0

High-throughput

0.458

High

498315

PCNB
Poly(A) polymerase I

1

0

High-throughput

0.458

High

499608

KPYK1
Pyruvate kinase I

1

0

High-throughput

0.458

High

953321

GMHBB
D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase

1

0

High-throughput

0.458

High

953327

YTFE
Iron-sulfur cluster repair protein YtfE

1

0

High-throughput

0.458

High

953328

CSRA
Carbon storage regulator

1

0

High-throughput

0.458

High

953334

YNCE
Uncharacterized protein YncE

1

0

High-throughput

0.458

High

953350

MENI
1,4-dihydroxy-2-naphthoyl-CoA hydrolase

1

0

High-throughput

0.458

High

506295

EFTU1
Elongation factor Tu 1

1

3

High-throughput

0.445

High

506348

EFTU2
Elongation factor Tu 2

1

3

High-throughput

0.445

High

680562

YIDC
Membrane protein insertase YidC

1

1

Small-scale

0.437

High

953324

YQJD
Uncharacterized protein YqjD

1

1

High-throughput

0.437

High

491686

KPRS
Ribose-phosphate pyrophosphokinase

1

0

High-throughput

0.426

High

497308

ZNUC
Zinc import ATP-binding protein ZnuC

2

0

High-throughput

0.319

High

791931

USPF
Universal stress protein F

2

0

High-throughput

0.318

High

641742

RECJ
Single-stranded-DNA-specific exonuclease RecJ

2

0

High-throughput

0.313

High

497834

FTSH
ATP-dependent zinc metalloprotease FtsH

2

0

High-throughput

0.307

High

571334

TOP3
DNA topoisomerase 3

2

0

High-throughput

0.307

High

953330

YBJX
Uncharacterized protein YbjX

2

0

High-throughput

0.307

High

367455

TRPE
Anthranilate synthase component 1

1

0

High-throughput

0.279

Low

393953

RBSB
Ribose import binding protein RbsB

1

0

High-throughput

0.279

Low

469387

YCIH
Uncharacterized protein YciH

1

0

High-throughput

0.279

Low

498077

TUSE
Sulfurtransferase TusE

1

0

High-throughput

0.279

Low

498732

FLIG
Flagellar motor switch protein FliG

1

0

High-throughput

0.279

Low

499535

YECA
Uncharacterized protein YecA

1

0

High-throughput

0.279

Low

499822

YGIC
Putative acid--amine ligase YgiC

1

0

High-throughput

0.279

Low

500194

DMA
DNA adenine methylase

1

0

High-throughput

0.279

Low

500690

NUOE
NADH-quinone oxidoreductase subunit E

1

0

High-throughput

0.279

Low

500914

ATL
DNA base-flipping protein

1

0

High-throughput

0.279

Low

501155

RIBF
Bifunctional riboflavin kinase/FMN adenylyltransferase

1

0

High-throughput

0.279

Low

547518

DAMX
Cell division protein DamX

1

0

High-throughput

0.279

Low

659730

GLXK1
Glycerate 2-kinase

1

0

High-throughput

0.279

Low

744427

YJBM
Uncharacterized protein YjbM

1

0

High-throughput

0.279

Low

744432

YJCF
Uncharacterized protein YjcF

1

0

High-throughput

0.279

Low

750357

YEBE
Inner membrane protein YebE

1

0

High-throughput

0.279

Low

751937

YEHZ
Glycine betaine-binding protein YehZ

1

0

High-throughput

0.279

Low

751946

YOHF
Uncharacterized oxidoreductase YohF

1

0

High-throughput

0.279

Low

784848

AMIA
N-acetylmuramoyl-L-alanine amidase AmiA

1

0

High-throughput

0.279

Low

788482

YCHJ
UPF0225 protein YchJ

1

0

High-throughput

0.279

Low

852333

YHBQ
UPF0213 protein YhbQ

1

0

High-throughput

0.279

Low

861428

AAAT
L-amino acid N-acetyltransferase AaaT

1

0

High-throughput

0.279

Low

909918

RATB
UPF0125 protein RatB

1

0

High-throughput

0.279

Low

953322

EUTS
Bacterial microcompartment shell protein EutS

1

0

High-throughput

0.279

Low

953332

YMGA
Probable two-component-system connector protein YmgA

1

0

High-throughput

0.279

Low

953335

YNEG
Uncharacterized protein YneG

1

0

High-throughput

0.279

Low

953336

YOBB
Uncharacterized protein YobB

1

0

High-throughput

0.279

Low

953339

YEGL
Uncharacterized protein YegL

1

0

High-throughput

0.279

Low

953340

YFDS
Uncharacterized protein YfdS

1

0

High-throughput

0.279

Low

953341

YFEZ
Inner membrane protein YfeZ

1

0

High-throughput

0.279

Low

953342

EUTK
Bacterial microcompartment shell protein EutK

1

0

High-throughput

0.279

Low

953343

EUTQ
Acetate kinase EutQ

1

0

High-throughput

0.279

Low

953344

EUTP
Probable acetate kinase EutP

1

0

High-throughput

0.279

Low

953354

TCDA
tRNA threonylcarbamoyladenosine dehydratase

1

0

High-throughput

0.279

Low

498655

EXBB
Biopolymer transport protein ExbB

1

0

High-throughput

0.261

Low

499461

LAPA
Lipopolysaccharide assembly protein A

1

0

High-throughput

0.261

Low

499814

YGGE
Uncharacterized protein YggE

1

0

High-throughput

0.261

Low

492049

PLSB
Glycerol-3-phosphate acyltransferase

1

0

High-throughput

0.253

Low

494580

RNPA
Ribonuclease P protein component

1

0

High-throughput

0.253

Low

495289

YACL
UPF0231 protein YacL

1

0

High-throughput

0.253

Low

495450

TRMB
tRNA

1

0

High-throughput

0.253

Low

505917

GATZ
D-tagatose-1,6-bisphosphate aldolase subunit GatZ

1

0

High-throughput

0.253

Low

664228

RP54
RNA polymerase sigma-54 factor

1

0

High-throughput

0.253

Low

676592

RIBD
Riboflavin biosynthesis protein RibD [Includes: Diaminohydroxyphosphoribosylaminopyrimidine deaminase

1

0

High-throughput

0.253

Low

722845

3PASE
Inorganic triphosphatase

1

0

High-throughput

0.253

Low

953353

YGCP
Uncharacterized protein YgcP

1

0

High-throughput

0.253

Low

496040

YBGC
Acyl-CoA thioester hydrolase YbgC

1

0

High-throughput

0.249

Low

499632

NLPD
Murein hydrolase activator NlpD

1

0

High-throughput

0.249

Low

786972

YADG
Uncharacterized ABC transporter ATP-binding protein YadG

1

0

High-throughput

0.249

Low

811843

YJJU
Uncharacterized protein YjjU

1

0

High-throughput

0.249

Low

852329

YRAR

1

0

High-throughput

0.249

Low

953323

YODD
Uncharacterized protein YodD

1

0

High-throughput

0.249

Low

953333

RLHA
23S rRNA 5-hydroxycytidine C2501 synthase

1

0

High-throughput

0.249

Low

953338

YEGH
UPF0053 protein YegH

1

0

High-throughput

0.249

Low

953348

GTRB
Prophage bactoprenol glucosyl transferase homolog

1

0

High-throughput

0.249

Low

953349

YBAY
Uncharacterized lipoprotein YbaY

1

0

High-throughput

0.249

Low

953346

YFCU
Putative outer membrane usher protein YfcU

1

0

High-throughput

0.232

Low


Service provided by Combinatics, Japan

Last updated: 11Aug2025