Agfam

The Agfam database is a focused collection of signal transduction-specific protein families, each of which is represented by hidden Markov models (HMMs). Although the primary focus of Agfam is Chemotaxis signal transduction, it is also useful for one and two-component signal transduction studies.

Usage

These HMM models are intended for use with the HMMER3 package. To search for matches using HMMER3, first "hmmpress" agfam.hmm.

Release 2.0

This release includes all HMMs from version 1 and the following models. CheA and MCP classes are retrieved from [Kristen and Zhulin 2010] 1 and [Alexander and Zhulin 2007] 2 respectively.

• chea-F1 F1 system-specific CheA
• chea-F2 F2 system-specific CheA
• chea-F3 F3 system-specific CheA
• chea-F4 F4 system-specific CheA
• chea-F5 F5 system-specific CheA
• chea-F6 F6 system-specific CheA
• chea-F7 F7 system-specific CheA
• chea-F8 F8 system-specific CheA
• chea-F9 F9 system-specific CheA
• chea-F10 F10 system-specific CheA
• chea-F11 F11 system-specific CheA
• chea-F12 F12 system-specific CheA
• chea-F13 F13 system-specific CheA
• chea-F14 F14 system-specific CheA
• chea-F15 F15 system-specific CheA
• chea-F16 F16 system-specific CheA
• chea-F17 F17 system-specific CheA
• chea-ACF ACF system-specific CheA
• chea-Tfp TFP system-specific CheA
• chea-Uncat Uncategorized CheA
• MCP-24H 24-heptad MCPsignal
• MCP-28H 28-heptad MCPsignal
• MCP-34H 34-heptad MCPsignal
• MCP-36H 36-heptad MCPsignal
• MCP-38H 38-heptad MCPsignal
• MCP-40H 40-heptad MCPsignal
• MCP-42H 42-heptad MCPsignal
• MCP-44H 44-heptad MCPsignal
• MCP-48H 48-heptad MCPsignal
• MCP-52H 52-heptad MCPsignal
• MCP-58H 58-heptad MCPsignal
• MCP-64H 64-heptad MCPsignal

Release 1.0

• 4HB_MCP The Methyl-accepting protein version of Four helix bundle
• HK_CA Histidine kinase type I general class
• HK_CA:1 Histidine kinase type I evolutionary distinct group
• HK_CA:2 Histidine kinase type I evolutionary distinct group
• HK_CA:3 Histidine kinase type I evolutionary distinct group
• HK_CA:5 Histidine kinase type I evolutionary distinct group
• HK_CA:6 Histidine kinase type I evolutionary distinct group
• HK_CA:7 Histidine kinase type I evolutionary distinct group
• HK_CA:8 Histidine kinase type I evolutionary distinct group
• HK_CA:9 Histidine kinase type I evolutionary distinct group
• HK_CA:10 Histidine kinase type I evolutionary distinct group
• HK_CA:11 Histidine kinase type I evolutionary distinct group
• HK_CA:12 Histidine kinase type I evolutionary distinct group
• HK_CA:13 Histidine kinase type I evolutionary distinct group
• HK_CA:14 Histidine kinase type I evolutionary distinct group
• HK_CA:15 Histidine kinase type I evolutionary distinct group
• HK_CA:16 Histidine kinase type I evolutionary distinct group
• HK_CA:17 Histidine kinase type I evolutionary distinct group
• HK_CA:18 Histidine kinase type I evolutionary distinct group
• HK_CA:19 Histidine kinase type I evolutionary distinct group
• HK_CA:20 Histidine kinase type I evolutionary distinct group
• HK_CA:21 Histidine kinase type I evolutionary distinct group
• HK_CA:22 Histidine kinase type I evolutionary distinct group
• HK_CA:23 Histidine kinase type I evolutionary distinct group
• HK_CA:Che Histidine kinase type II - CheA
• RR Response regulator

References

• Alexander, Roger P., and Igor B. Zhulin. "Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors." Proceedings of the National Academy of Sciences 104.8 (2007): 2885-2890.
• Wuichet, Kristin, and Igor B. Zhulin. "Origins and diversification of a complex signal transduction system in prokaryotes." Science Signaling 3.128 (2010): ra50.