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The motifs used in PSORTb v.3.0 and PSORTb v2.0: OMPMotif, Motif, and Profile modules are listed below. For a description of how these motifs were selected, please see the PSORT-B paper (Gardy et al, 2003).

Motifs used in the v.3.0 and v.2.0 OMPMotif module (279): ompmotifs.txt

Gram-negative motifs used in the v.3.0 and v.2.0 motif module: negmotifs.txt

  • PS00538 Cytoplasmic Membrane RTE[EQ]Q.{2}[SA][LIVM].[EQ]TAASMEQLTATV
  • PS00755 Cytoplasmic Membrane [GST][LIVMF][LIVMFCA].[LIVMF][GSA][LIVM].P[LIVMFY]{2}.[AS][GSTQ][LIVMFAT]{3}[EQ][LIVMFA]{2}
  • PS00756 Cytoplasmic Membrane [LIVMFYW]{2}.[DE].[LIVM][STDNQ].{2,3}[GK][LIVMF][GST][NST]G.[GST][LIV][LIVFP]
  • PS00192 Cytoplasmic Membrane [DENQ]...G[FYWMQ].[LIVMF]R..H
  • PS00193 Cytoplasmic Membrane P[DE]W[FY][LFY]{2}
  • PS01303 Cytoplasmic Membrane [GSDN]WT[LIVM].[FY]W.WW
  • PS00449 Cytoplasmic Membrane [STAGN].[STAG][LIVMF]RL.[SAGV]N[LIVMT]
  • PS00713 Cytoplasmic Membrane P.{0,1}G[DE].[LIVMF]{2}.[LIVM]{2}[KREQ][LIVM]{3}.P
  • PS00714 Cytoplasmic Membrane P.G.[STA].[NT][LIVMC]DG[STAN].[LIVM][FY].{2}[LIVM].{2}[LIVM][FY][LI][SA]Q
  • PS00217 Cytoplasmic Membrane [LIVMF].G[LIVMFA]..G.{8}[LIFY]..[EQ].{6}[RK]
  • PS00218 Cytoplasmic Membrane [STAGC]G[PAG].{2,3}[LIVMFYWA]{2}.[LIVMFYW].[LIVMFWSTAGC]{2}[STAGC]...[LIVMFYWT].[LIVMST]...[LIVMCTA][GA]E.{5}[PSAL]
  • PS00943 Cytoplasmic Membrane N...[DEH]..[LIMF]D..[VM].R[ST]..R.{4}G
  • PS00077 Cytoplasmic Membrane [YWG][LIVFYWTA]{2}[VGS]H[LNP].V.{44,47}HH
  • PS00221 Cytoplasmic Membrane [HNQA].NP[STA][LIVMF][ST][LIVMF][GSTAFY]
  • PS00428 Cytoplasmic Membrane [NV].{5}[GTR][LIVMA].P[PTLIVM].G[LIVM]...[LIVMFW][LIVMFW]S[YSA]GG[STN][SA]
  • PS00994 Cytoplasmic Membrane R[LIVM][GSA]EV[GSA]ARF[STAIV]LD[GSA][LM]PGKQM[GSA]ID[GSA][DA]
  • PS00896 Cytoplasmic Membrane G[LIVM]{2}.D[RK]LGL[RK]{2}.[LIVM]{2}W
  • PS00897 Cytoplasmic Membrane P.[LIVMF]{2}NR[LIVM]G.KN[STA][LIVM]{3}
  • PS00942 Cytoplasmic Membrane [QEK][RF]G.{3}[GSA][LIVF][WL][NS].[SA][HM]N[LIV][GA]G
  • PS01307 Cytoplasmic Membrane A[LMF].[GAT]T[LIVMF].G.[LIVMF].{7}P
  • PS00594 Cytoplasmic Membrane IG[GA]GM[LF][SA].P.{3}[SA]G.{2}F
  • PS01039 Periplasmic G[FYIL][DE][LIVMT][DE][LIVMF]...[LIVMA][VAGC]..[LIVMAGN]
  • PS01037 Periplasmic [GAP][LIVMFA][STAVDN]....[GSAV][LIVMFY]{2}Y[ND]...[LIVMF].[KNDE]
  • PS01040 Periplasmic [AG].{6,7}[DNEG]..[STAIVE][LIVMFYWA].[LIVMFY].[LIVM][KR][KRHDE][GDN][LIVMA][KNGSP][FW]
  • PS01157 Periplasmic GSYPSGHT
  • PS00635 Periplasmic [LIVMFY][APN].[DNS][KREQ]E[STR][LIVMAR].[FYWT].[NC][LIVM]..[LIVM]P[PAS]
  • PS00087 Periplasmic [GA][IMFAT]H[LIVF]H.{2}[GP][SDG].[STAGDE]
  • PS00123 Periplasmic [IV].DS[GAS][GASC][GAST][GA]T
  • PS00332 Periplasmic G[GN][SGA]G.R.[SGA]C.{2}[IV]
  • PS00401 Periplasmic K.[NQEK][GT]G[DQ].[LIVM].{3}QS
  • PS00556 Periplasmic [LIVMA]{4}C[LIVMFA]T[LIVMA]{2}.{4}[LIVM].[RG].{2}L[CY]
  • PS00757 Periplasmic NPK[ST]SG.AR
  • PS00968 Periplasmic [LIVFAG].[GASV][LIVFA].[IV]H.{3}[LIVM][GSTAE][STANH].{1,3}[STN]W[LIVMFYW]
  • PS00969 Periplasmic [EQ].{4}H.{5}[GSTA].{3}[FY].{3}[AG].{2}[AV]H.{7}P
  • PS00576 Outer Membrane [LIVMFY]..G..Y.F.K..[SN][STAV][LIVMFYW]V
  • PS00694 Outer Membrane (G[LIVMFY]N[LIVM]KYRYE)
  • PS00695 Outer Membrane ([FYW]..G.GY[KR]F)
  • PS01151 Outer Membrane [VL][PASQ][PAS]G[PAD][FY].[LI][DNQSTAP][DNH][LIVMFY]
  • PS00875 Outer Membrane [GR][DEQKG][STVM][LIVMA]{3}[GA]G[LIVMFY].{11}[LIVM]P[LIVMFYWGS][LIVMF][GSAE].[LIVM]P[LIVMFYW]{2}..[LV]F
  • PS00834, PS00835 Outer Membrane ((WTD.S.HP.T).*(AGYQE[ST]R[FYW]S[FYW][TN]A.GG[ST]Y))|((AGYQE[ST]R[FYW]S[FYW][TN]A.GG[ST]Y).*(WTD.S.HP.T))
  • PS01068 Outer Membrane [LIVMA].[GT].[TA][DA]..[DG][GSTP]..[LFYDE][NQS]..[LI][SG][QE][KRQE]RA..[LV]...[LIVMF].{4,5}[LIVM]....[LIVM]...[SG].G
  • PS00274 Extracellular [KT]..NW..T[DN]T
  • PS00330 Extracellular D.[LI].{4}G.D.[LI].GG.{3}D
  • GGXGXD Extracellular (GG.G.D.*){4}

Gram-positive motifs used in the v.3.0 and v.2.0 motif module: posmotifs.txt

  • PS00369 Cytoplasmic G[LIVM]H[STAV]R[PAS][GSTA][STAMVN]
  • PS00589 Cytoplasmic [GSTADE][KREQSTIV].{EPRK}{VPGL}.[KRDN]S[LIVMF]{2}.{EVPL}[LIVM]{EATN}.[LIVM][GADE]
  • PS00077 Cytoplasmic Membrane [YWG][LIVFYWTA]{2}[VGS]H[LNP].V.{44,47}
  • PS00192 Cytoplasmic Membrane [DENQ]...G[FYWMQ].[LIVMF]R..
  • PS00193 Cytoplasmic Membrane P[DE]W[FY][LFY]{2}
  • PS00216 Cytoplasmic Membrane [LIVMSTAG][LIVMFSAG]..[LIVMSA][DE].[LIVMFYWA]GR[RK].{4,6}[GSTA]
  • PS00217 Cytoplasmic Membrane [LIVMF].G[LIVMFA]{V}.G{KP}.{7}[LIFY]..[EQ].{6}[RK]
  • PS00218 Cytoplasmic Membrane [STAGC]G[PAG].{2,3}[LIVMFYWA]{2}.[LIVMFYW].[LIVMFWSTAGC]{2}[STAGC]...[LIVMFYWT].[LIVMST]...[LIVMCTA][GA]E.{5}[PSAL]
  • PS00449 Cytoplasmic Membrane [STAGN].[STAG][LIVMF]RL.[SAGV]N[LIVMT]
  • PS00713 Cytoplasmic Membrane P.{0,1}G[DE].[LIVMF]{2}.[LIVM]{2}[KREQ][LIVM]{3}.P
  • PS00714 Cytoplasmic Membrane P.G.[STA].[NT][LIVMC]DG[STAN].[LIVM][FY]..[LIVM]..[LIVM][FY][LI][SA]Q
  • PS00872 Cytoplasmic Membrane [DG]...G...[DN].{6,8}[GA][KRHQ][FSA][KR][PT][FYW][LIVMWQ][LIV].[GAFV][GSTA]
  • PS00943 Cytoplasmic Membrane N...[DEH]..[LIMF]D..[VM].R[ST]..R.{4}G
  • PS01022 Cytoplasmic Membrane [GA][GAS][LIVMFYWA][LIVM][GAS]D.[LIVMFYWT][LIVMFYW]G...[TAV][IV]...[GSTAV].[LIVMF]...[GA]
  • PS01023 Cytoplasmic Membrane [FYT]..[LMFY][FYV][LIVMFYWA].[IVG]N[LIVMAG]G[GSA][LIMF]
  • PS01219 Cytoplasmic Membrane D[FYWS]AG[GSC].{2}[IV].{3}[SAG]{2}.{2}[SAG][LIVMF].{3}[LIVMFYWA]{2}.[GK].R
  • PS01303 Cytoplasmic Membrane [GSDN]WT[LIVM].[FY]W.WW
  • PS01327 Cytoplasmic Membrane [KR]GN[LIV]{2}D[LIVM]A[LIVM][GA][LIVM]{3}G
  • PS00755 Cytoplasmic Membrane [GST][LIVMF][LIVMFCA].[LIVMF][GSA][LIVM].P[LIVMFY]{2}.[AS][GSTQ][LIVMFAT]{3}[EQ][LIVMFA]{2}
  • PS00756 Cytoplasmic Membrane [LIVMFYW]{2}.[DE].[LIVM][STDNQ].{2,3}[GK][LIVMF][GST][NST]G.[GST][LIV][LIVFP]
  • PS01072 Cellwall [LVFYT].[DA].{2,5}[DNGSATPHY][FYWPDA].{4}[LIV]..[GTALV].{4,6}[LIVFYC]..G.[PGSTA].{2,3}[MFYA].[PGAV].{3,10}[LIVMA][STKR][RY].[EQ].[STALIVM]
  • PS00274 Extracellular [KT]..NW..T[DN]T
  • PS00277 Extracellular YGG[LIV]T.{4}N
  • PS00278 Extracellular K..[LIVF].{4}[LIVF]D...R..L.{5}[LIV]Y
  • PS00429 Extracellular ARP...K.S.TNAYNVTT..[DN]G...YG

Archaeal motifs used in the v.3.0 motif module: archmotifs.txt (same as Gram-positive motifs, with the following motifs updated)

  • PS00589 Cytoplasmic [GSTADE][KREQSTIV].{EPRK}{VPGL}.[KRDN]S[LIVMF]{2}.{EVPL}[LIVM]{EATN}.[LIVM][GADE]
  • PS00217 Cytoplasmic Membrane [LIVMF].G[LIVMFA]{V}.G{KP}.{7}[LIFY]..[EQ].{6}[RK]
  • PS00216 removed from archaeal motifs

Profiles used in both the Gram-negative and Gram-positive v.3.0 profile modules:

Profiles used in the Gram-positive v.3.0 profile module:

  • LPXTG Cell Wall
  • PS50830 Extracellular

 

 


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