TABLE 3.

Complex relationships between genes of C. acetobutylicum and B. subtilis—nonorthologous and xenologous gene displacement and differences in domain architectures^a

C.a. gene ID	B.s. gene product	Commentb
CAC0039, CAC0408	YukA	DNA segregation ATPase FtsK/SpoIIIE; both contain 3 ATPase domains; C.a. protein in addition contains C-terminal FHA domain
CAC0578	YitJ	Methionine synthase I; same domain organization as in E.c., D.r., Syn., and M.t. but not B.s.
CAC0459, CAC3088	RocR	Arginine degradation positive regulator; AAA-ATPase domain (NtrC family) fused to PAS domains; C.a. proteins contain an unknown domain at the N terminus similar to the N-terminal domain of PrpR E.c.
CAC0538-40, CAC2556	YdhT	Beta-mannanase ManB; C.a. proteins have more complex domain organization
CAC0577	YxiA	Endo-arabinase-related enzyme (family 43, glycosyl hydrolase domain); C.a. contains additional ricin B-like domain
CAP0120	XynD	Xylanase; C.a. contains additional ricin B-like domain
CAC1655	PurQ and PurL	Phosphoribosylformylglycinamidine synthase; C.a. has PurL/PurQ fusion; B.s.—separate proteins
CAC1847	YqfP and YpfD	C.a. has fusion of LytB protein and S1 RNA-binding domain; B.s.—separate proteins
CAC1793	LexA	C.a. has fusion of P-loop ATPase and LexA; B.s. has only a LexA protein and has no ortholog of the ATPase domain
CAC2927	FolA and FolK	Folate biosynthesis enzymes; C.a. has fusion FolA and FolK; B.s.—separate proteins
CAC0404	YbdM	C.a. has fusion Pkn2 protein kinase with TPR repeats; B.s. has only a Pkn2 ortholog without the TPR domain.
CAC3245	8 one-domain proteins	C.a. has fusion of two B. subtilis domains; B.s. has only separate proteins
CAC3195	GlyQ, GlyS	Glycyl-tRNA synthetase; typical bacterial version (two subunits) in B.s.; eukaryotic version (one subunit) in C.a.
CAC0219, CAC2997	Ung	Uracil-DNA glycosylase; typical bacterial version in B.s.; archaeal version in C.a.
CAC1256, CAC1909	Rph	C.a. encodes RNase D and RNAse E/G, whereas B.s. encodes the unrelated RNAse PH; it can be predicted that these RNases complement each other's functions.
CAC0752	YoqV, YoqU	ATP-dependent DNA ligases; B.s. encodes two copies of a typical ATP-dependent ligase strongly similar to archaeal homologs (one fused to a eukaryotic-type DNA primase); in contrast, C.a. has an extremely diverged version with significant similarity only to predicted ligases from D.r.
CAC1041	ArgS	Arginyl-tRNA synthetase; eukaryotic version in C.a.
CAC0935, CAC2740	HisS, HisZ	Histidyl-tRNA synthetase; B.s. encodes two recently diverged copies of the typical bacterial enzyme; C.a. possesses an archaeal-eukaryotic version and a distinct bacterial variant shared with D.r. and Syn
CAC3038	IleS	Isoleucyl-tRNA synthetase; archaeal-eukaryotic version in C.a.
CAC1047	YosO	Ribonucleotide reductase in B.s. contains an intein; there is no ortholog of this in C.a.; instead, C.a. contains a distinct ribonucleotide reductase with an archaeal evolutionary affinity

^aSee the Table 1 a footnote for abbreviations. Additional abbreviations of bacterial species are as follows: D.r., Deinococcus radiodurans; Syn, Synechocystis sp. 

^bThe first 12 comparisons relate to different domain organization; the last 8 relate to nonorthologous and xenologous gene displacement.