TABLE 2.

The LafK regulon^a

Geneb	Description of predicted product	Fold change
		S vs S(K−)	S vs L	S vs LD
<VP0649>c	hypothetical, 401 aa	5	7	4
VP0763	conserved hypothetical protein; 39 aa	40	39	48
VP1293-94	small RNA (~400 nucleotides)	80	54	54
<VP1682>	type III secretion protein	4	4	3
<VP1701>	type III secretion regulator; ExsC	5	6	4
<VPA0227>	alkaline serine protease	7	20	10
VPA0260	FlgO, lytic transglycosylase	7	9	12
VPA0261	FlgN, chaperone	25	169	124
VPA0262	FlgM, anti sigma factor	15	52	52
VPA0264	FlgB, proximal rod	735	493	485
VPA0265	FlgC, proximal rod	269	249	345
VPA0266	FlgD, hook assembly	302	292	312
VPA0267	FlgE, hook	239	256	299
VPA0268	FlgF, proximal rod	281	169	261
VPA0269	FlgG, distal rod	216	213	250
VPA0270	FlgH, L ring	45	56	54
VPA0271	FlgI, P ring	66	70	70
VPA0272	FlgJ, peptidoglycan hydrolase	54	64	69
VPA0273	FlgK, hook-associated protein 1	296	235	215
VPA0274	FlgL, hook-associated protein 2	119	318	291
VPA0275	FlgU, unknown but required for swarming	13	70	52
VPA1294	SPOR-domain containing protein involved with peptidoglycan binding	174	134	150
VPA1295	hypothetical protein	312	242	317
VPA1492	methyl-accepting chemotaxis protein	13	22	18
VPA1532	FliJ, flagellar export	14	12	16
VPA1533	FliI, flagellum-specific ATP synthase	75	72	79
VPA1534	FliH, flagellar assembly protein	63	77	82
VPA1535	FliG, motor switch protein	78	59	83
VPA1536	FliF, MS ring	253	196	265
VPA1537	FliE, hook-rod junction	159	111	152
VPA1538	LafK, σ54-dependent regulator	54	90	88
VPA1539	MotY, H+ motor component	17	164	136
VPA1548	LafA, lateral flagellin	984	641	584
VPA1550	FliD, distal cap	276	292	276
VPA1551	FliS, chaperone	374	264	450
VPA1552	FliT, chaperone	519	269	350
VPA1553	FliK, hook-length control	366	359	429
VPA1554	FliL, flagellar protein	342	315	371
VPA1555	FliA, lateral specific sigma 28	219	354	288
VPA1556	MotA, H+ motor component	140	166	161
VPA1557	MotB, H+ motor component	219	187	184
VPA1558	FliU, new potential lateral product	24	23	21
VPA1649	Metalloendoprotease, LytM (M23family)	45	188	201
NT01A1551e	CcmA-domain containing protein	20	35	36

^aGenes differentially expressed (>4-fold and p < 0.05) comparing wild-type swarming strain LM5674 and the lafK mutant strain grown on a plate. For all of the genes above, except those noted by brackets, the false discovery rate for each of the three comparisons is below 1%. Complete data, with p and q values are given in supplementary Table 1.

^bBoxed genes indicate potential operons and bold indicates the first gene in the operon.

^c< > Bracketed genes indicate those that have higher false discovery rates (>1%) and are therefore classified as “Tier 2” genes. VP0260 also had a high false discovery rate, but we suspect this is because it is the last gene in an operon.

^dNT01VPA1551 was annotated by TIGR after the original annotation was performed.