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Copyright ©2014 Baishideng Publishing Group Co.
World J Gastroenterol. Feb 14, 2014; 20(6): 1402-1423
Published online Feb 14, 2014. doi: 10.3748/wjg.v20.i6.1402
Table 1 Proteins that have been experimentally identified as secreted in one of the reported papers or predicted based on a secretion signal
LabelName and/or functionRef.PDB codeUniProtKB
Outer membrane proteins (Omps)
HP0009Outer membrane protein (Omp1), HopZyQ7X2J7
HP0025Outer membrane protein (Omp2)b’, yO24870
HP0078/79Outer membrane protein (Omp3)yO24907/O24908
HP0127Outer membrane protein (omp4), HorBb’, y, zO24941
HP0227Outer membrane protein (Omp5)b’, yO34523
HP0229Outer membrane protein (Omp6)b’, y, zO25015
HP0232UPF0323 lipoprotein HP_0232bO25018
HP0252Outer membrane protein (Omp7), HopFb’, yO25034
HP0253Outer membrane protein (Omp8)yO25035
HP0317Outer membrane protein (Omp9)b’, yO25086
HP0324Outer membrane protein (Omp10)yO25091
HP0410Putative neuraminyllactose-binding hemagglutininzO25166
HP0472Outer membrane protein (Omp11)b’, y, zO25218
HP0477Outer membrane protein (Omp12)yO25222
HP0486Putative outer membrane protein, HofCb’, yO25230
HP0487Putative outer membrane protein, HofDb’O25231
HP0638Outer membrane protein (Omp13)yO25355
HP0671Outer membrane protein (Omp14)b’, yO25382
HP0694Putative outer membrane proteinb’, yO25401
HP0706Outer membrane protein (Omp15)b’, zO25410
HP0710Outer membrane protein (HomA)zO25414
HP0722Outer membrane protein (Omp16)y
HP0725Outer membrane protein (Omp17)yQ7X2J9
HP0797Neuraminyllactose-binding hemagglutinin, HpaAb, y3BGHP55969
HP0896Outer membrane protein (Omp19). BabBb’, yO25556
HP0912Outer membrane protein (omp20), AlpAq, u, b’, y, zO25570
HP0913Outer membrane protein (omp21)q, u, b’, yO25571
HP0923Outer membrane protein (Omp22)yO25580
HP1107Outer membrane protein (Omp23)b’, yO25735
HP1125Outer membrane protein (Omp18), peptidoglycan-associated lipoprotein, PALs, yO25625
HP1156Outer membrane protein (Omp25)yO25771
HP1157Outer membrane protein (Omp26)yO25772
HP1177Outer membrane protein (Omp27), HopOb’, yO25791
HP1243Outer membrane protein (Omp28) BabAb’, yO25840
HP1342Outer membrane protein (Omp29)b’, yO34523
HP1395Outer membrane protein (Omp30)y, zO25945
HP1456Lpp20 lipoproteinb, y, zP0A0V0
HP1469Outer membrane protein (Omp31)b’, yO26005
HP1501Outer membrane protein, HopWy, zO26031
HP1512Iron regulated outer membrane proteinyO26042
HP1564Outer membrane protein, lipoproteinu, yO26084
HP1571RlpA-like lipoproteinb, yO26091
HP0284Mechanosensitive ion channel membrane proteinb’O25059
Cag proteins
HP0528CagX, Cag8b’O25263
HP0529CagW, Cag9b’O25264
HP0532CagT, Cag12bP97245
HP0537CagM, Cag16b’O25270
HP0540CagI, Cag19b’O25273
HP0545CagDz3CWX, 3CWYO25277
HP0546Cag25b’O25278
HP0547CagA, Cag26b’, y4G0H, 4DVY, 4DVZ, 3IECP55980
Flagellar components
HP0115Flagellin B, FlaByQ07911
HP0126Flagellar P-ring protein, FlgLbO25028
HP0295Flagellar hook-associated protein 3, HAP3yO25068
HP0325Flagellar L-ring proteinbO25092
HP0601Flagellin A, FlaAv, yP0A0S1
HP0752Flagellar hook-associated protein 2, HAP2zP96786
HP0870Flagellar hook protein FlgEa, yP50610
HP0907Hook flagella assembly protein FlgDa, qO25565
HP1119Flagellar hook-associated protein 1, HAP1yO25744
HP1462Secreted protein involved in flagellar motilityyO25998
HP1557Flagellar hook-basal body protein FliEaP67708
Binding or transport proteins
HP0243Neutophil-activating protein, HP-NAPy, z1JI4, 4EVB, 4EVC, 4EVD, 4EVE, 3T9J, 3TA8P43313
HP0298Periplasmic dipeptide-binding protein, DppAzO25069
HP0508Plasminogen-binding protein pgbAb’O25249
HP0888/Iron (III) dicitrate ABC transporter, ATP-binding proteinvO05732
HP0889
HP0970Nickel-cobalt-cadmium import protein (NccB)b’O25623
HP1073Copper-binding protein, CopPz1YG0Q48271
HP1252Oligopeptide ABC transporter periplasmic oligopeptide-binding protein (OppA)b’O25845
HP1286YceI-like acidic stress response, lipocalina, e, l, u, b’, z3HPEO25873
HP1561/ABC transporter periplasmic binding protein (CeuE)b’O26083/
HP1562O26082
VacA and other toxins
HP0289VacA-like protein, ImaAdO25063
HP0609/HP0610VacA-like protein, FaaAdO25330/
O25531
HP0887Vacuolating cytotoxin VacAa, b, g, u, z2QV3P55981
HP0922VacA-like protein, VlpCdO25579
HP0596Tumor necrosis factor α-inducing protein, Tip-αf, m, n3VNC, 3GUQ, 3GIO, 2WCQ, 2WCRO25318
Enzymes
Redox systems and the electron transport chain
HP0224Peptide methionine sulfoxide reductase MsrA/MsrBb’O25011
HP0231Disulphide interchange protein (DsbG, or DscB or HpDsbA)a, q, u3TDGO25017
HP0330Ketol-acid reductoisomerase, IlvCzO25097
HP0377Thiol-disulfide interchange protein DsbCa, b’4FYB, 4FYCO25140
HP0389Superoxide dismutase, SODx3CEIP43312
HP0390Adhesin-thiol peroxidase, TagDyO25151
HP0485Catalase-like proteinb’O25229
HP0824Thioredoxin TrxAa, wP66928
HP0825Thioredoxin reductase, trxBb’3ISH, 2Q0K, 2Q0LP56431
HP0875Catalase, katAx, b’,z2IQF, 2A9E, 1QWL, 1QWMP77872
HP1136ATP synthase subunit bb’P56086
HP1161Flavodoxin FldAa2W5U, 2BMV, 1FUEO25776
HP1212ATP synthase subunit cb’P56087
HP1227Cytochrome c-553bO25825
HP1266NADH-ubiquinone oxidoreductase, NQO3 subunitzO25856
HP1458Thioredoxin TrxCa, u, zO25996
HP1461Cytochrome c551 peroxidaseb’O25997
Putative solenoid proteins
HP0160Beta-lactamase HcpDb, o, pO24968
HP0211Beta-lactamase HcpA, Cysteine-rich 28 kDa proteinb, o, p, b’O25001
HP0235Beta-lactamase HcpEb, o, p, b’O25021
HP0336Beta-lactamase HcpBo1KLXO25103
HP1098Beta-lactamase, Cysteine-rich protein C HcpCa, b, o, q, t, b’, z1OUVO25728
HP0519Hypothetical Sel1-like proteinpQ7X5D6
HP0628Hypothetical Sel1-like proteinpO25345
HP1117Hypothetical Sel1-like protein, Cys-rich protein XpO25742
HP1124Tetratricopeptide-like repeat proteinb’O25749
Proteases
HP0570Aminopeptidase, PepAzO25294
HP0657Processing protease (YmxG)b’, zO25371
HP1012Putative Zinc proteasezO25656
HP1018/HP1019Serine protease (HtrA)a, f, q, r, zO25663
HP1037Amino peptidaseb’O25681
HP1350Carboxyl-terminal proteasezO25905
Other enzymes
HP0026Citrate synthasezP56062
HP0072Urease B (UreB)a, q, v, y1E9Y, 1E9ZP69996
HP0073Urease A (UreA)y1E9Y, 1E9ZP14916
HP0154Enolase, phosphopyruvate hydratase, enozP48285
HP0194Triosephosphate isomerase, tpiAb’2JGQP56076
HP0275ATP-dependent nuclease (addB)b’, zO25025
HP0294Aliphatic amidase, AimEzO25067
HP0310Polysaccharide deacetylasez3QBU, 4LY4O25080
HP0323Membrane-bound endonuclease (nuc)b’, yO25090
HP0380Glutamate dehydrogenasezP55990
HP0392Histidine kinase, CheAb’O25153
HP0672Member of the PLP-dependent aminotransferase superfamily clan, AspBz3EZSO25383
HP1118γ-Glutamyltranspetptidasea, q, b’, z3FNM, 2QM6, 2QMC, 2NQOO25743
HP1178Purine nucleoside phosphorylase DeoD-typeb’P56463
HP1186Carbonic anhydrasea, q, zO25798
HP1375UDP-N-acetylglucosamine acyltransferase, LpxAz1J2ZO25927
Others
HP0010GroEL, HSP60cP42383
HP0011GroESzP0A0R3
HP0166Response regulator, ArsSzO24973
HP0305Putative human regulator of G protein signaling 12u, bO25076
HP0743Rod shape-determining proteinyP56098
HP1000PARA proteinb’O25646
HP1126Protein TolBbO25751
HP0827ssDNA-binding 12RNP2 precursoru2KI2O25501
HP0835Histone-like DNA-binding protein HUuO25506
HP1v1Ribosomal protein L1uP56029
HP1202Ribosomal protein L11uP66052
Hypothetical proteins
HP0122Hypothetical uncharacterized proteinbP64653, O24940
HP0129Hypothetical uncharacterized proteinuO24943
HP0130Hypothetical uncharacterized proteinb’O24944
HP0135Hypothetical uncharacterized proteinbP64655, O24948
HP0149Hypothetical uncharacterized proteinb’O24960
HP0169Hypothetical secreted colagenasebP56113
HP0204Hypothetical uncharacterized proteinb’O24996
HP0367Hypothetical uncharacterized proteinaO25131
HP0555Hypothetical uncharacterized proteinb’O25382
HP0583Hypothetical uncharacterized proteinb’O25305
HP0659SurA N-terminal domain protein, SurA chaperone of outer membrane proteinsb’O25373
HP0719Hypothetical uncharacterized proteinb’O25421
HP0720Hypothetical uncharacterized proteinuK4NCD4
HP0721Sialic acid-specific adhesion, metal homeostasisi, u2XRHO25423
HP0781Hypothetical uncharacterized proteinb’O25470
HP0783Hypothetical uncharacterized proteinb’O25742
HP0902Hypothetical uncharacterized proteinuO25562
HP0953Hypothetical uncharacterized proteinb’, zO25607
HP0973Hypothetical uncharacterized proteinu, b’O26525
HP1023Hypothetical uncharacterized proteinb’O25270
HP1055Hypothetical uncharacterized proteinb’O25695
HP1056Hypothetical uncharacterized proteinb’O25696
HP1057Hypothetical uncharacterized proteinb’O25697
HP1173Hypothetical uncharacterized proteina, b, zO25787
HP1285lipoprotein, e(P4) familyb’, zO25872
HP1454Hypothetical uncharacterized proteina, zO25993
HP1527Hypothetical uncharacterized proteinb’O26055
HP1580Hypothetical uncharacterized proteinb’O26100
The first column refers to the symbol for strain ACT 700392/26695, the third to the reference, the forth to the PDB ID code if the X-ray structure has been determined, and the fifth to the UniProtKB code. The proteins are grouped according to their function, as explained in the text. a[20], b’[23]; (b refers to proteins having a signal peptide as reported in Supplementary Table mmc4 of reference[23]), c[142], d[84], e[72], f[151], g[152], h[153], i[148], l[74], m[154], n[88], o[112], p[116], q[123], r[119], s[155], t[156], u[21], v[75], w[91], x[102], y[17], z[22].
Table 2 Outer membrane biogenesis complex components[153]
LabelProtein symbolName and/or functionRef.
HP0785lolAPeriplasmic chaperoneb', b
HP0787lolC (lolE)Integral membrane protein
HP1568lptAPeriplasmic chaperone
HP0715lptBInner membrane (IM) ATP-binding-cassette transporter domain
HP1569lptCIM associated lipoprotein
HP1216lptDOuter membranes (OM) lipopolysaccharide (LPS) transport protein
HP1546lptEOM-associated lipoprotein
HP0362lptFIntegral membrane protein
HP1498lptGIntegral membrane protein
HP1082msbAIM LPS flippase
HP0655bamAOM β-barrel assembly componentb', b
HP1378bamDOM-associated lipoproteinb'
HP0786secAPreprotein translocase subunit
HP1300secYPreprotein translocase subunit
HP1203secEPreprotein translocase subunit
HP1255secGPreprotein translocase subunit
HP1550secDPreprotein translocase subunit
HP1549secFPreprotein translocase subunit
HP1551yajCPreprotein translocase subunit
HP1540yidCIM protein translocase component
HP1152ffhSignal recognition particle (SRP)
HP0763tfsYSRP receptor
HP0320tatASec-independent translocase
HP1060tatBSec-independent translocase
HP1061tatCSec-independent translocase
HP0175surAPeptidyl-prolyl cis-trans isomerasea, b', q, u, z
HP1019degPSerine protease
a[20], b’[23]; (b refers to proteins having a signal peptide as reported in Supplementary Table mmc4 of reference[23]), q[123] u[21], z[22].
Table 3 Flagella components
Protein symbolSymbolName or proposed functionUniProtKB codeProtein Data Bank code or homology model
FlaBHP0115Flagellin subunitQ07911
FliRHP0173Export componentO24978
FlgJHP0245Rod capping protein; muramidaseP64657
FlgIHP0246P-ring protein; part of bushing; internal disulfide bridgeO25028
FliJHP0256General chaperoneO25037
FlgLHP0295Hook-associated protein 3; second hook-filament junction proteinModel
FlgHHP0325L-ring protein; part of bushing; lipoproteinO25092
FliFHP0351MS-ring protein; mounting flange for rotor/ switch and rod; housing for export apparatusO25118Model
FliGHP0352Rotor/switch protein; torque generation; strong interaction with MS ringO251194FQ0, 3USY, 343
FliHHP0353Negative regulator of FliIO25120Model
FliOHP0583Export componentO25305
FliNHP0584C ring; rotor/switch proteinO25306Model
FlaAHP0601Flagellin subunit. Polymerizes with FlaB
FliPHP0685Export componentO25394
FlgRHP0703Transcriptional activator of flagellar proteinsO25408Model
FliDHP0752HAP2; filament-capping protein; flagellin folding chaperoneP96786
FliSHP0753FliC-specific chaperoneO254483IQC
FliTHP0754FliD-specific chaperoneO25449
FlhBHP0770Export component; substrate specificity switch; target for soluble export complexP56416Model
MotAHP0815Stator protein; exerts torque against rotor/switchP65410
MotBHP0816Stator protein; converts proton energy into torqueP564273S02, 3S03, 3S06, 3S0H, 3S0W, 3S0Y, 3CYP, 3CYQ
FlgEHP0870Hook proteinP50610
FliKHP0906Hook-length-control proteinQ4FEW5
FlgDHP0907Hook-capping proteinO25565Model
FliMHP1031C ring; rotor/switch protein; target for CheY-P binding4GC8
ylxHHP1034Flagellum site-determining protein YlxHO25678Model
FlhFHP1035Flagellar biosynthesis proteinO25679Model
FlhAHP1041Export component; target for soluble export complexO067583MYD
FliS-chaperonHP10763K1H, 3K1I
FlgG_1HP1092O25724Model
FlgKHP1119HAP1; first hook-filament junction proteinO25744Model
FliW1HP1154Flagellar assembly factor FliW1O25769Model
pFlAHP1274Paralysed flagella proteinO25864
FliW2HP1377Flagellar assembly factor FliW2O25929Model
FliQHP1419Export componentPOAO53
FliIHP1420ATPase; drives type III flagellar exportO07025Model
FliCHP1450Filament protein; flagellin
FlgNHP1457FlgK-, FlgL-specific chaperoneO25995
FlgAHP1477Chaperone for P-ring proteinO26012Model
FliEHP1557MS-ring rod junction protein; export gateP67708
FlgCHP1558Rod protein; transmission shaftO26080
FlgBHP1559Rod protein; transmission shaftO26081
FlgGHP1585Distal rod protein; transmission shaftO26104
FlgFHP1585?Rod protein; transmission shaft
The first column refers to the protein symbol, the second to the symbol used for strain ACT 700392/26695, the third to the protein name, the fourth to the UniProtKB code, and the fifth to the Protein Data Bank code, if a three-dimensional structure exists, or to the model if it is possible to build an homology-based molecular model.