| 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
|
