BISON: bio-interface for the semi-global analysis of network patterns

Table 1 Functional categories of proteins whose genes are regulated by FlhD/FlhC

Regulator gene¹	HMM of the regulator²	Regulated genes³	HMM of regulated proteins⁴
Flagellar proteins
flhD	flhd	flgB, flgC, flgE, fleF, flgG	flg_bb_rod
flhD	flhd	tar, tsr, tap, trg, aer	mcpsignal
Anaerobic metabolism
flhD	flhd	dmsA, ynfE, ynfF, napA, narG, narZ	molydopterin_oxidoreductase, molydop_binding, molybdopterin
Transport proteins
flhD	flhd	nagE, frvB, treB, murP, mngA, chbC, malX, fruA, ptsG	pts_eiic
flhD	flhd	rbsA, oppD, nikD, fepC, proV, nikE, btuD, uup, metN, thiQ, phnK, msbA, fhuC, mglA, ybhF, dppD	abc_trans
Transcriptional regulators
flhD	flhd	cynR, dsdC, xapR, tdcA, ydcI, ybbS, nhaR, argP, yeeV	lysr_substrate, hth_1

¹The gene 'flhD'.
²HMM for FlhD.
³Genes that are regulated by FlhD/FlhC are taken from the 'Gene 1' column in BISON that is associated with a selection of the property combinations in the 'Descriptors' column.
⁴HMMs for the regulated proteins are taken from the 'Descriptors' column in BISON.

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