TxSEpp


A systematic prediciton platform for secreted proteins of gram-negative bacteria.  



Secreted proteins and their transport pathways

The secretion machines are multi-protein complex, with different protein components. The protein transport processes were also indicated, with Sec and Tat pathways secreting the proteins from bacterial cytoplasm to periplasm or inner membrane, Lol pathways transporting the protein within the periplasm side of inner membrane into the periplasm side of outer membrane, Bam and Tam systems transporting periplasmic protein into outer membrane, T1SSs transporting proteins from bacterial cytoplasm to extracellular space, T2SSs and T9SSs transporting periplasmic proteins to extracellular space, and T3SSs, T4SSs and T6SSs translocating proteins from cytoplasm to host cellular cytoplasm directly. T5SSs are autotransporters that transport themselves extracellularly. The pili and curli proteins are transported out of bacterial outer membrane through T7SSs and T8SSs, respectively. The protein names or component types were shown for each secretion systems.


T1SEstacker


An integrated prediction pipeline for bacterial type I secreted effectors.

T2SEpre


A prediction tool for bacterial type II secreted effectors.

T3SEpp


An integrated prediction pipeline for bacterial type III secreted effectors.

T4SEpre


A prediction tool for bacterial type IV secreted effectors.

T5SEhmm


Predict type V secreted effectors by using HMM.

T6SEpp


An integrated prediction pipeline for bacterial type VI secreted effectors.

T7SEhmm


Predict bacterial type VII secreted effectors by using HMM.

T8SEhmm


Predict type VIII secreted effectors by using HMM.

T9SEpre


A prediction tool for bacterial type IX secreted effectors.

ncSec


A prediction tool for bacterial non-classical Sec substrates.

TMHpp


An integrated prediction pipeline for transmembrane helix(TMH).

TMBpp


Predict β-strands of bacteria outer membrane proteins.