Table 3. The result of computational screening for sRNA candidates in S. pyogenes.

SSRCa	Up ORF number	Up ORF name	up ORFb	Down ORF number	Down ORF name	down ORFb	Method#	Remark and reference
SSRC 1	SPyM3_0029	hypothetical protein	>>>	SPyM3_0030	adenylosuccinate lyase	>>>	Q, Z
SSRC 2	SPyM3_0054	30S ribosomal protein S8	>>>	SPyM3_0055	50S ribosomal protein L6	>>>	Q, Z
SSRC 3	SPyM3_0156	glucose-6-phosphate isomerase	>>>	SPyM3_0157	putative regulatory protein RofA related	<<<	Q, Z	RivX [15]
SSRC 4	SPyM3_0174	putative response regulator	>>>	SPyM3_0175	ribonuclease P	>>>	Q, Z	FasX [12]
SSRC 5	SPyM3_0199	30S ribosomal protein S7	>>>	SPyM3_0200	elongation factor G	>>>	Q, Z
SSRC 6	SPyM3_0201	glyceraldehyde-3-phosphate dehydrogenase	>>>	SPyM3_0202	putative amino acid ABC transporter ATP-binding protein	<<<	Q, Z
SSRC 7	SPyM3_0219	putative oligopeptide ABC transporter	>>>	rRNA	rRNA	>>>	Q, P
SSRC 8*	SPyM3_0298	putative cell envelope proteinase	>>>	SPyM3_0299	hypothetical protein	>>>	Q, Z, P
SSRC 9	SPyM3_0300	methionyl-tRNA synthetase	>>>	SPyM3_0301	ribonucleotide-diphosphate reductase subunit beta	>>>	Q, Z
SSRC10	SPyM3_0439	hypothetical protein	>>>	SPyM3_0440	putative calcium transporter	>>>	Q, P
SSRC11	SPyM3_0455	putative cell-division protein	>>>	SPyM3_0457	putative metallo-beta-lactamase superfamily protein	<<<	Q, Z
SSRC12*	SPyM3_0480	streptolysin S associated protein	>>>	SPyM3_0481	streptolysin S associated protein	>>>	Q, Z, P	Pel [13], [14]
SSRC13	SPyM3_0505	putative DNA-entry nuclease	>>>	SPyM3_0506	phenylalanyl-tRNA synthetase subunit alpha	>>>	Q, Z
SSRC14	SPyM3_0557	putative ribosomal large subunit pseudouridine synthase	>>>	SPyM3_0558	bifunctional pyrimidine regulatory protein	>>>	Q, P
SSRC15*	SPyM3_0582	putative peptidoglycan hydrolase	>>>	SPyM3_0583	hypothetical protein	<<<	Q, Z, P
SSRC16	SPyM3_0588	putative ABC transporter ATP-binding protein	>>>	SPyM3_0589	hypothetical protein	>>>	Q, Z
SSRC17	SPyM3_0611	purine nucleoside phosphorylase	>>>	SPyM3_0612	putative purine nucleoside phosphorylase	>>>	Q, Z
SSRC18	SPyM3_0663	branched-chain alpha-keto acid dehydrogenase subunit E2	>>>	SPyM3_0664	putative dihydrolipoamide dehydrogenase component E3	>>>	Q, Z
SSRC19	SPyM3_0664	putative dihydrolipoamide dehydrogenase component E3	>>>	SPyM3_0665	extracellular hyaluronate lyase	<<<	Q, Z
SSRC20	SPyM3_0762	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	>>>	SPyM3_0763	UDP-N-acetylenolpyruvoylglucosamine reductase	>>>	Q, P
SSRC21	SPyM3_0851	putative anaerobic ribonucleotide reductase	<<<	SPyM3_0852	putative cardiolipin synthetase	<<<	Q, P	[20], [42]
SSRC22	SPyM3_0918	hypothetical protein	<<<	SPyM3_0919	hypothetical protein	<<<	Q, Z
SSRC23	SPyM3_0983	putative maltose/maltodextrin-binding protein	>>>	SPyM3_0984	putative maltose/maltodextrin ABC transport system (permease)	>>>	Q, Z
SSRC24	SPyM3_0989	hypothetical protein	<<<	SPyM3_0990	putative esterase	<<<	Q, Z
SSRC25	SPyM3_1093	putative heavy metal/cadmium-transporting ATPase	<<<	SPyM3_1094	hypothetical protein	<<<	Q, Z
SSRC26	SPyM3_1166	isoleucyl-tRNA synthetase	<<<	SPyM3_1167	putative cell-division initiation protein	<<<	Q, Z
SSRC27	SPyM3_1176	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase	<<<	SPyM3_1177	hypothetical protein	<<<	Q, P
SSRC28	SPyM3_1190	asparagine synthetase AsnA	<<<	SPyM3_1191	carbamate kinase	<<<	Q, Z
SSRC29	SPyM3_1276	hypothetical protein	<<<	SPyM3_1277	hypothetical protein	<<<	Q, P	[20], [42]
SSRC30*	SPyM3_1280	3-dehydroquinate synthase	>>>	SPyM3_1281	putative acetate kinase	<<<	Q, Z, P
SSRC31	SPyM3_1356	hypothetical protein	>>>	SPyM3_1357	hypothetical protein	>>>	Q, Z
SSRC32*	SPyM3_1386	putative N6-adenine-specific DNA methylase	<<<	SPyM3_1387	hypothetical protein	<<<	Q, Z, P	[20], [42]
SSRC33*	SPyM3_1391	putative aminopeptidase C	<<<	SPyM3_1392	NAD synthetase	<<<	Q, Z, P
SSRC34	SPyM3_1510	hypothetical protein	>>>	SPyM3_1511	putative mannose-specific phosphotransferase system component IIAB	>>>	Q, Z
SSRC35	SPyM3_1533	heat-inducible transcription repressor	<<<	SPyM3_1534	N-acetylmuramoyl-L-alanine amidase	<<<	Q, Z
SSRC36	SPyM3_1644	putative deoxyribonuclease hsdM modification subunit	>>>	SPyM3_1645	putative response regulator of salavaricin regulon	<<<	Q, Z
SSRC37	SPyM3_1673	hypothetical protein	<<<	SPyM3_1674	putative serine acetyltransferase	<<<	Q, Z
SSRC38	SPyM3_1725	laminin-binding protein	<<<	SPyM3_1726	C5A peptidase precursor	<<<	Q, Z
SSRC39	SPyM3_1726	C5A peptidase precursor	<<<	SPyM3_1727	antiphagocytic M protein, type 3	<<<	Q, Z	[40]
SSRC40	SPyM3_1766	co-chaperonin GroES	<<<	SPyM3_1767	putative endopeptidase Clp ATP-binding chain C	<<<	Q, P
SSRC41	SPyM3_1798	hypothetical protein	<<<	SPyM3_1799	transcriptional regulator Spx	<<<	Q, Z
SSRC42	SPyM3_1817	50S ribosomal protein L33	>>>	SPyM3_1818	putative cadmium resistance protein	>>>	Q, Z	[40]
SSRC43	SPyM3_1822	hypothetical protein	>>>	SPyM3_1823	hypothetical protein	<<<	Q, Z
SSRC44	SPyM3_1836	hypothetical protein	<<<	SPyM3_1838	tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA	<<<	Q, Z
SSRC45	SPyM3_1843	hypothetical protein	<<<	SPyM3_1844	putative ABC transporter membrane-spanning permease	<<<	Q, Z

^aSSRC: S. pyogenes Small RNA Candidate. The nucleotide coordinates of SSRC predicted by each computational algorithm are listed in Table S5.

^bGenes present on the strand given in the S. pyogenes MGAS315 genome databases are indicated by >>> and those on the complementary strand by <<<.

^#Algorithms that identify each sRNA candidate: Q, eQRNA; Z, RNAz; P, sRNAPredict.

^*sRNA candidates predicted by all the three algorithms, eQRNA, RNAz, and sRNAPredict.