Identification of the type II cytochrome cmaturation pathway in anammox bacteria by comparative genomics

BMC Microbiology

Table 1 CcsA and CcsB homologs identified in four anammox genera

Anammox genus	Homolog	Gene product	Length (aa)	BLAST*	HHPRED**	HMMER**	Motif	His residues	TMHs	Pfam family
*Kuenenia*	CcsA	kustd1760	283	✓	✓	✓	✓	✓	8	PF01578
	CcsB	kustd1761	629	✓	✗	✓	✓	✓	4	PF05140
	CcsA	kuste3100	257	✓	✗	✓	M	✓	8	PF01578
	CcsB	kuste3101	322	✗	✓	✓	T	✓	4	✗
KSU-1	CcsA	GAB62001.1	282	✓	✓	✓	✓	✓	8	PF01578
	CcsB	GAB62000.1	621	✗	✓	✓	✓	✓	4	PF05140
	CcsA	GAB64165.1	255	✓	✓	✓	M	✓	8	PF01578
	CcsB	GAB64166.1	335	✗	✓	✓	T	✓	4	✗
*Scalindua*	CcsA	scal00629c	291	✓	✓	✓	✓	✓	8	PF01578
	CcsB	scal00630c	625	✓	✓	✓	T	✓	3	PF05140
	CcsA	scal00436	258	✓	✓	✓	M	✓	8	PF01578
	CcsB	scal00437	322	✗	✓	✓	✗	✓	4	✗
*Brocadia*	CcsA	BFUL_01704	281	✓	✓	✓	✓	✓	8	PF01578
	CcsB	BFUL_01703	499	✓	✓	✓	✓	✓	2	PF05140
	CcsA	BFUL_02788	255	✓	✓	✓	M	✓	8	PF01578
	CcsB	BFUL_02789	319	✓	✓	✓	T	✓	4	PF05140

Legend: Initial blastP search of whole anammox genomes against a reference database (for details see Additional file 3), comprising UNIPROT entries for CcsA and CcsB, together with intra- and intergenome searches with the significant hits from Kuenenia as queries were performed (Additional file 4). Retrieved results were further analyzed with HHpred and HMMER (Additional file 5), transmembrane helices were predicted with TMHMM, protein family matches were identified via Pfam, and conserved motifs together with critical residues were identified manually. Regarding the motif search, symbol (✓) denotes identification of the canonical motif as known from the literature (CcsA: WAXX(A/δ)WGX(F/Y)WXWDXKEXX and CcsB: VNX_1-4P), letter (M) denotes presence of the CcsA modified heme-binding motif as found in the anammox genera tested (WGXXAWGXYFLWDAK(V/L)(V/L)W), and letter (T) denotes presence of the truncated CcsB motif (VN). TMHs: transmembrane helices; (*): E-value cut off set at 10^-6; (**): E-value cut off set at 10^-3; (✓): significant annotation and/or identification; (✗): absence of significant hits and/or protein matches.

ISSN: 1471-2180