. 2018 Feb 2;19:117. doi: 10.1186/s12864-018-4501-8

Table 3.

Summary of variable genes across M. synoviae strains MS-H, MS53 and WVU-1853

Gene product	ORF (locus tag^a)
Gene product	MS-H	MS53	WVU-1853
N-acetylneuraminate lyase variant	MSH_00300	–	–
Transcriptional regulator	MSH_00310^b MSH_00330^b	MS53_0024	VY93_00145
Translation elongation factor G	MSH_00500	MS53_0039^b	VY93_00220^b
Multiple sugar ABC transporter, ATP-binding protein	MSH_01200^c	MS53_0102	VY93_00560
Hypothetical protein	MSH_01840^c	–	VY93_00865
Hypothetical protein	MSH_01960	–	VY93_00910
Hypothetical protein	MSH_01930 MSH_01970	–	VY93_00915
Type II restriction enzyme MjaIII	MSH_02140	–	VY93_01010 VY93_02580
Methyl-directed repair DNA adenine methylase	MSH_02150	–	VY93_01015 VY93_02585
3′-to-5′ oligoribonuclease A	MSH_02940^b MSH_02950^b MSH_02960^b	MS53_0278^b MS53_0279^b	VY93_01505^b VY93_01510^b
Aspartate-ammonia ligase	MSH_02990	MS53_0281^b	VY93_01515
Hypothetical protein	MSH_03480^b MSH_03490^b	MS53_0293	VY93_01595^b
Asparaginyl-tRNA synthetase-related protein	MSH_03500	MS53_0291^b MS53_0700^b	VY93_01590^b
Deoxyribose-phosphate aldolase	MSH_03520	–	–
Oligopeptide transport ATP-binding protein OppF	MSH_03740^b MSH_03750^b	MS53_0345	VY93_01875
Lipoprotein	MSH_03790	MS53_0349	VY93_01895^b VY93_01900^b
Hypothetical protein	MSH_04620	MS53_0430^b	VY93_02305
Hypothetical protein	MSH_04790^b	MS53_0442
Hypothetical protein	MSH_04880		VY93_02420
Hypothetical protein	MSH_04960	MS53_0458^b MS53_0459^b	VY93_02465
Hypothetical protein	MSH_05850^b MSH_05860^b	MS53_0713^b MS53_0540^b	VY93_02935^b
CRISPR-associated protein, Csn1	MSH_06430^b MSH_06440^b	MS53_0582	VY93_03200^b VY93_03205^b
IS30 family transposase	MSH_07180 MSH_07210	–	VY93_00200 VY93_00900 VY93_01540 VY93_02375
ATP-dependent DNA helicase	MSH_07190	–	–
Hypothetical protein	MSH_07360^b	MS53_0668	VY93_03635
Hypothetical protein	MSH_07370^b	MS53_0669^b	VY93_03640
ABC transporter ATP-binding and permease protein	MSH_07380	MS53_0670^b	VY93_03645^b
Hypothetical protein	MSH_07610^c	MS53_0680	VY93_03760^b
PTS system enzyme IIB component	MSH_07640^b	MS53_0682	VY93_03770
Ascorbate-specific PTS system, EIIC component	MSH_07650^b MSH_07660^b MSH_07670^b MSH_07680^b	MS53_0683	VY93_03775^b
Type III restriction-modification system methylation subunit	MSH_07490^b MSH_07500^b	–	VY93_03700^b VY93_03705^b
Hypothetical protein	MSH_07510	–	VY93_03710^b
Hypothetical protein	MSH_07520	–	VY93_03720^b
Hypothetical protein	MSH_07530	–	VY93_03725^b
Hypothetical protein	MSH_07540 ^b	–	VY93_03730
Integrase	MSH_07560	–	VY93_03735
Type I restriction-modification system, specificity subunit S	MSH_07570^b MSH_07580^b	–	VY93_03740^b VY93_03745^b
Type I restriction-modification system, restriction subunit R	MSH_07590	–	VY93_03750
Type I restriction-modification system, DNA-methyltransferase subunit M	MSH_07600	–	VY93_03755

^aPseudogenes that have lost more than 30% of their full length; nucleotide positions corresponding to the locus tags of MS-H are listed in Additional file 1: Table S1. IS elements and the vlhA locus were not included in pseudogenisation analysis. ^bPseudogenes that result from a frameshift mutation. ^c Pseudogenes that result from acquisition of an internal stop codon. “−” indicates the absence of the gene in a strain. Genes without a specified locus tag are not indicated in this table