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Domain-based rules for classifying signal transduction proteins

The rule system is hierarchical and each rule is processed sequentially. Proteins are classified accoring to the first matching rule. Asterisks (*) match all proteins. Marker domains indicate those domains that implicate a proteins as participating in signal transduction. Unless otherwise indicated, all domains are from Pfam. Chemotaxis classification rules are based on the work performed by Wuichet and colleagues (2007).

Rule Classification
Pfam or Agfam marker domain
Chemotaxis domain
HK_CA:Che (Agfam) or CheW + transmitter domain Chemotaxis, CheA
CheW + receiver Chemotaxis, CheV
CheW Chemotaxis, CheW
CheB_methylest Chemotaxis, CheB
CheR or CheR_N Chemotaxis, CheR
CheD Chemotaxis, CheD
CheZ Chemotaxis, CheZ
CheC and not SpoA Chemotaxis, CheCX
MCPsignal Chemotaxis, MCP
* Chemotaxis, other
Transmitter or receiver domain
HATPase_c signaling domain + receiver
HATPase_c before receiver Two-component, hybrid histidine kinase (HHK)
N-terminal receiver Two-component, hybrid response regulator (HRR)
* Two-component, other
HATPase_c signaling domain Two-component, histidine kinase (HK)
Receiver domain Two-component, response regulator
* Two-component, other
Output domain One-component
* Other
ECF domain ECF

View signaling domain table

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