Genomic Tools

OG ID	OG function	Label	Gene	Product	COG	PFAM short name	KO
3NK51	Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr)	ACIAD0013	tyrS	tyrosyl-tRNA synthetase	COG0162	tRNA-synt_1b	K01866
3NIHR	amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile)	ACIAD0022	ileS	isoleucyl-tRNA synthetase	COG0060	Anticodon_1, tRNA-synt_1, zf-FPG_IleRS	K01870
3NNMM	May reduce aminoacrylate peracid to aminoacrylate. Required to remove a toxic intermediate produce by the pyrimidine nitrogen degradation	ACIAD0029	rutC	putative 3-aminoacrylate deaminase RutC (Pyrimidine utilization protein C)	COG0251	Ribonuc_L-PSP	K09021
3NJQV	Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates	ACIAD0050	rph	ribonuclease PH (RNase PH), tRNA nucleotidyltransferase	COG0689	RNase_PH, RNase_PH_C	K00989
3NNHV	Endoribonuclease L-PSP	ACIAD0117		conserved hypothetical protein; putative endoribonuclease L-PSP		Ribonuc_L-PSP
3NK37	Arginyl-tRNA synthetase	ACIAD0164	argS	arginyl-tRNA synthetase	COG0018	Arg_tRNA_synt_N, DALR_1, tRNA-synt_1d	K01887
3NSRJ	MafB19-like deaminase	ACIAD0204		putative cytidine and deoxycytidylate deaminase zinc-binding like protein		dCMP_cyt_deam_1
3NKGI	Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-) CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate	ACIAD0208		putative ribosome maturation factor (dsRNA-binding protein) (RimN)	COG0009	Sua5_yciO_yrdC	K07566
3NKDT	Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions	ACIAD0211	def	peptide deformylase 1 (N-formylmethionylaminoacyl-tRNA deformylase, binds Zn(II))	COG0242	Pep_deformylase	K01462
3NNI5	Endoribonuclease L-PSP	ACIAD0222		putative RidA family protein		Ribonuc_L-PSP
3NK6Q	Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5- dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon	ACIAD0272		putative glutamyl t-RNA synthetase		tRNA-synt_1c	K01894
3NIQ7	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis	ACIAD0299	tufB	protein chain elongation factor EF-Tu, possible GTP-binding factor (duplicate of tufA)		GTP_EFTU, GTP_EFTU_D2, GTP_EFTU_D3
3NJ44	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors	ACIAD0302	rplK	50S ribosomal protein L11		Ribosomal_L11, Ribosomal_L11_N
3NIPW	Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release	ACIAD0304	rplA	50S ribosomal protein L1	COG0081	Ribosomal_L1	K02863
3NIS4	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors	ACIAD0305	rplJ	50S ribosomal protein L10	COG0244	Ribosomal_L10	K02864
3NNIS	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation	ACIAD0306	rplL	50S ribosomal protein L7/L12	COG0222	Ribosomal_L12, Ribosomal_L12_N	K02935
3NKH2	Specifically methylates the ribose of guanosine 2251 in 23S rRNA	ACIAD0357		putative tRNA/rRNA methyltransferase	COG0566	SpoU_methylase, SpoU_sub_bind	K03218
3NKI1	One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex	ACIAD0369	infB	protein chain initiation factor IF-2	COG0532	GTP_EFTU, IF-2, IF2_N, IF2_assoc	K02519
3NN3B	One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA	ACIAD0370	rbfA	ribosome-binding factor A	COG0858	RBFA	K02834
3NNXP	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome	ACIAD0401	rpsO	30S ribosomal protein S15	COG0184	Ribosomal_S15	K02956
3NIGW	Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction	ACIAD0402	pnp	polyribonucleotide nucleotidyltransferase (Polynucleotide phosphorylase) (PNPase)	COG1185	KH_1, PNPase, RNase_PH, RNase_PH_C, S1	K00962
3NPDX	Ribosomal protein L31	ACIAD0425	rpmE2	50S ribosomal protein L31 type B	COG0254	Ribosomal_L31	K02909
3NJRE	Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs	ACIAD0438	rne	ribonuclease E (RNase E): endoribonuclease for rRNA processing and mRNA degradation	COG1530	RNase_E_G, S1	K08300
3NJU3	Responsible for synthesis of pseudouridine from uracil	ACIAD0442	rluC	23S rRNA pseudouridylate synthase	COG0564	PseudoU_synth_2, S4	K06179
3NPBC	One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex	ACIAD0472	infA	protein chain initiation factor IF-1	COG0361	eIF-1a	K02518
3NJS9	Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs	ACIAD0474	truA	tRNA-pseudouridine synthase I	COG0101	PseudoU_synth_1	K06173
3NJPT	Asparaginase	ACIAD0476		putative L-asparaginase I (AnsA)	COG0252	Asparaginase	K01424
3NPRW	Belongs to the bacterial ribosomal protein bL33 family	ACIAD0501	rpmG	50S ribosomal protein L33		Ribosomal_L33
3NNZ1	Belongs to the bacterial ribosomal protein bL28 family	ACIAD0502	rpmB	50S ribosomal protein L28		Ribosomal_L28
3NJI9	Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs	ACIAD0557	rlmN	23S rRNA adenosine methyltransferase	COG0820	Radical_SAM	K06941
3NKTF	histidyl-tRNA synthetase	ACIAD0562	hisS	histidyl-tRNA synthetase	COG0124	HGTP_anticodon, tRNA-synt_His	K01892
3NKA4	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)	ACIAD0591	queA	S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein )	COG0809	Queuosine_synth	K07568
3NMGU	Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus	ACIAD0603		conserved hypothetical protein
3NJ1X	Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn)	ACIAD0609	aspS	aspartyl-tRNA synthetase	COG0173	GAD, tRNA-synt_2, tRNA_anti-codon	K01876
3NNGT	Sigma 54 modulation protein / S30EA ribosomal protein	ACIAD0658		putative sigma(54) modulation protein RpoX	COG1544	Ribosomal_S30AE	K05808
3NJ9H	Specifically methylates the guanosine in position 1516 of 16S rRNA	ACIAD0679		conserved hypothetical protein; putative methyltransferase	COG0500	SAM_MT	K15984
3NIIK	Specifically methylates the guanine in position 1207 of 16S rRNA in the 30S particle	ACIAD0701	rsmC	ribosomal RNA small subunit methyltransferase C (rRNA (guanine-N(2)-)-methyltransferase) (16S rRNA m2G1207 methyltransferase)	COG2813	MTS, MTS_N	K00564
3NIT3	Responsible for synthesis of pseudouridine from uracil	ACIAD0715		putative dual specificity pseudouridine synthase for 23S rRNA and tRNAphe modification (RluA-like)	COG0564	PseudoU_synth_2	K06177
3NIRS	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation	ACIAD0768	metG	methionyl-tRNA synthetase	COG0143	tRNA-synt_1g, tRNA_bind	K01874
3NJJ4	Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction proline is first activated by ATP to form Pro- AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS	ACIAD0782	proS	prolyl-tRNA synthetase	COG0442	HGTP_anticodon, tRNA-synt_2b, tRNA_edit	K01881
3NIRM	Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)	ACIAD0822	gatB	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B	COG0064	GatB_N, GatB_Yqey	K02434
3NIMZ	Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln)	ACIAD0823	gatA	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A	COG0154	Amidase	K02433
3NJ6P	Ribonuclease E/G family	ACIAD0830	cafA	ribonuclease G, endoribonuclease G (cytoplasmic axial filament protein )	COG1530	RNase_E_G, S1	K08301
3NJKN	Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U16 in tRNAs	ACIAD0837	dusC	tRNA-dihydrouridine synthase C	COG0042	Dus	K05541
3NIUW	Belongs to the pseudouridine synthase RsuA family	ACIAD0861		putative ribosomal large subunit pseudouridine synthase B (Pseudouridylate synthase) (Uracil hydrolyase)	COG1187	PseudoU_synth_2, S4	K06178
3NM1N	Acetyltransferases including N-acetylases of ribosomal proteins	ACIAD0864		putative acetyltransferase		Acetyltransf_3
3NJAG	Belongs to the SUA5 family	ACIAD0865		putative translation factor		Sua5_yciO_yrdC
3NPDH	Belongs to the bacterial ribosomal protein bL32 family	ACIAD0869	rpmF	50S ribosomal protein L32		Ribosomal_L32p
3NN2Z	Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit	ACIAD0881	rpsL	30S ribosomal protein S12		Ribosom_S12_S23
3NM4A	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA	ACIAD0883	rpsG	30S ribosomal protein S7		Ribosomal_S7
3NIEG	Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome	ACIAD0884	fusA	protein chain elongation factor EF-G, GTP-binding	COG0480	EFG_C, EFG_II, EFG_IV, GTP_EFTU, GTP_EFTU_D2	K02355
3NIQ7	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis	ACIAD0885	tufA	protein chain elongation factor EF-Tu (duplicate of tufB)	COG0050	GTP_EFTU, GTP_EFTU_D2, GTP_EFTU_D3	K02358
3NSQ3	Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions	ACIAD1039	def2	peptide deformylase 2	COG0242	Pep_deformylase	K01462
3NJ38	Belongs to the class-II aminoacyl-tRNA synthetase family	ACIAD1069	lysS	lysyl-tRNA synthetase	COG1190	tRNA-synt_2, tRNA_anti-codon	K04567
3NK7T	Specifically methylates the guanine in position 966 of 16S rRNA in the assembled 30S particle	ACIAD1100		putative methyltransferase	COG0742	Cons_hypoth95	K08316
3NJF6	Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA	ACIAD1113	rlmH	Ribosomal RNA large subunit methyltransferase H	COG1576	SPOUT_MTase	K00783
3NJ80	Pseudouridine synthase	ACIAD1203	rluA	dual specificity pseudouridine synthase for 23S rRNA and tRNAphe modification	COG0564	PseudoU_synth_2	K06177
3NJVQ	Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34	ACIAD1221	trmU	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase	COG0482	tRNA_Me_trans	K00566
3NIN9	Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain	ACIAD1253	alaS	alanyl-tRNA synthetase	COG0013	DHHA1, tRNA-synt_2c, tRNA_SAD	K01872
3NKZ8	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA	ACIAD1268		putative N-6 Adenine-specific DNA methylase	COG1092, COG0116	Methyltrans_SAM, THUMP, UPF0020	K12297
1RS1C	GNAT family acetyltransferase	ACIAD1279	cphA	Cyanophycin synthetase	COG1181	Mur_ligase_C, Mur_ligase_M, RimK	K03802
3NJ1J	Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA	ACIAD1302	trmB	tRNA(guanine-7)methyltransferase	COG0220	Methyltransf_4	K03439
3NIY4	DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA	ACIAD1314	rhlB	ATP-dependent RNA helicase (DEAD box)	COG0513	DEAD, Helicase_C	K03732
3NPA3	Belongs to the bacterial ribosomal protein bS21 family	ACIAD1331	rpsU	30S ribosomal protein S21		Ribosomal_S21
3NIP5	Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12	ACIAD1371	rimO	Ribosomal protein S12 methylthiotransferases	COG0621	Radical_SAM, UPF0004	K14441
3NK5V	Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another	ACIAD1373	frr	ribosome releasing factor	COG0233	RRF	K02838
3NN87	Belongs to the HSP15 family	ACIAD1386	hslR	heat shock protein 15	COG1188	S4	K04762
3NNXB	Binds directly to 16S ribosomal RNA	ACIAD1389	rpsT	30S ribosomal protein S20	COG0268	Ribosomal_S20p	K02968
3NKQW	Belongs to the class-I aminoacyl-tRNA synthetase family	ACIAD1481	cysS	cysteinyl-tRNA synthetase	COG0215	DALR_2, tRNA-synt_1e	K01883
3NKR8	Nodulation protein S (NodS)	ACIAD1557		putative methyltransferase		NodS
3NQQ9	Amidase	ACIAD1618	amdA	amidase	COG0154	Amidase	K01426
3NJW0	Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA)	ACIAD1645	trmA	tRNA (uracil-5-)-methyltransferase	COG2265	tRNA_U5-meth_tr	K00557
3NK4U	tRNA synthetases class I (E and Q), anti-codon binding domain	ACIAD1920	glnS	glutaminyl-tRNA synthetase	COG0008	tRNA-synt_1c, tRNA-synt_1c_C	K01886
3NM3S	PELOTA RNA binding domain	ACIAD1960	stiP	Cysteine protease StiP		PELOTA_1, PRTase_1
3NMYH	ATP-grasp in the biosynthetic pathway with Ter operon	ACIAD1963		conserved hypothetical protein		ATPgrasp_Ter
3NIW2	Specifically methylates the 50S ribosomal protein L3 on a specific glutamine residue	ACIAD2029		putative adenine-specific methylase	COG2890	MTS	K07320
3NJ4G	ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner	ACIAD2071		putative GTP-binding protein	COG0012	MMR_HSR1, YchF-GTPase_C	K06942
3NKAE	Asparaginase	ACIAD2088	aspQ	glutaminase-asparaginase	COG0252	Asparaginase	K05597
3NJAD	Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA	ACIAD2090	TrmJ	tRNA (cytidine/uridine-2'-O-)-methyltransferase	COG0565	SpoU_methylase	K15396
3NSP0	Siderophore biosynthesis protein domain	ACIAD2117		putative siderophore biosynthese protein (bfnL)		Acetyltransf_8
3NJZR	Involved in peptide bond synthesis. Alleviates ribosome stalling that occurs when 3 or more consecutive Pro residues or the sequence PPG is present in a protein, possibly by augmenting the peptidyl transferase activity of the ribosome. Modification of Lys-34 is required for alleviation	ACIAD2206	efp	elongation factor P	COG0231	EFP, EFP_N, Elong-fact-P_C	K02356
3NPGX	Binds the 23S rRNA	ACIAD2210	rpmE	50S ribosomal protein L31	COG0254	Ribosomal_L31	K02909
3NJR4	Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome	ACIAD2268	tsf	protein chain elongation factor EF-Ts	COG0264	EF_TS	K02357
3NIVD	Belongs to the universal ribosomal protein uS2 family	ACIAD2269	rpsB	30S ribosomal protein S2	COG0052	Ribosomal_S2	K02967
3NIW8	Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit	ACIAD2284		putative ribosomal RNA small subunit methyltransferase E (rsmE)	COG1385	Methyltrans_RNA	K09761
3NK6J	Catalyzes the addition and repair of the essential 3'- terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate	ACIAD2288	cca	Multifunctional protein [Includes: CCA-adding enzyme ; 2'-nucleotidase ; 2',3'-cyclic phosphodiesterase ; Phosphatase]	COG0617	PolyA_pol, PolyA_pol_RNAbd	K00974
3NJ9N	HRDC domain	ACIAD2310	rnd	ribonuclease D, processes tRNA	COG0349	DNA_pol_A_exo1, HRDC	K03684
3NM5D	thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence	ACIAD2347	rpsA	30S ribosomal protein S1	COG0539	S1	K02945
3NN6N	Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2)	ACIAD2350		putative deaminase		MafB19-deam
3NJAY	Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	ACIAD2368	gidB	glucose-inhibited division protein B (methyltransferase)	COG0357	GidB	K03501
3NJ0U	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits (eIF-2Bgamma eIF-2Bepsilon)	ACIAD2369		putative nucleotidyl transferase	COG1208	NTP_transferase	K00992
3NK0S	RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs	ACIAD2373	hfq	host factor I for bacteriophage Q beta replication, a growth-related protein	COG1923	Hfq	K03666
3NK7C	RNA pseudouridylate synthase	ACIAD2377		putative pseudouridylate synthase	COG0564	PseudoU_synth_2	K06177
3NJ1F	Belongs to the pseudouridine synthase RsuA family	ACIAD2380	rsuA	16S rRNA pseudouridylate 516 synthase	COG1187	PseudoU_synth_2, S4	K06183
3NKB7	Methylates the class 1 translation termination release factors RF1 PrfA and RF2 PrfB on the glutamine residue of the universally conserved GGQ motif	ACIAD2417	hemK	methyl transferase	COG2890	Methyltransf_31	K02493
3NJCS	Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA	ACIAD2418	prfA	peptide chain release factor 1	COG0216	PCRF, RF-1	K02835
3NN4A	Binds together with S18 to 16S ribosomal RNA	ACIAD2430	rpsF	30S ribosomal protein S6	COG0360	Ribosomal_S6	K02990
3NPB6	Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit	ACIAD2431	rpsR	30S ribosomal protein S18	COG0238	Ribosomal_S18	K02963
3NKTG	Binds to the 23S rRNA	ACIAD2432	rplI	50S ribosomal protein L9	COG0359	Ribosomal_L9_C, Ribosomal_L9_N	K02939
3NIXE	Methylates ribosomal protein L11	ACIAD2443	prmA	methylation of 50S ribosomal subunit protein L11 (ribosomal protein L11 methyltransferase)	COG2264	PrmA	K02687
3NIZ0	Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines	ACIAD2557	dusB	tRNA-dihydrouridine synthase B	COG0042	Dus	K05540
3NJAF	tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)	ACIAD2576		conserved hypothetical protein; putative tRNA hydroxylase	COG4445	MiaE	K06169
3NJNF	Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre- crRNA and tracrRNA of type II CRISPR loci if present in the organism	ACIAD2581	rnc	ribonuclease III, ds RNA	COG0571	Ribonucleas_3_3, dsrm	K03685
3NSMG	SpoU rRNA Methylase family	ACIAD2626		putative tRNA/rRNA methyltransferase	COG0566	SpoU_methylase	K03437
3NJ3Z	tRNA synthetases class II (D, K and N)	ACIAD2666		putative lysyl-tRNA synthetase (Lysine--tRNA ligase)(PoxA)	COG2269	tRNA-synt_2	K04568
3NJJX	Siderophore biosynthesis protein domain	ACIAD2767	fbsK	putative siderophore biosynthesis protein; putative acetyltransferase		Acetyltransf_8
3NJ2H	Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit	ACIAD2854	ftsJ	cell division protein (filamentous temperature sensitivity, 23S rRNA U2552 ribose 2'-O-methyltransferase, SAM-dependent)	COG0293	FtsJ	K02427
3NT6Q	CRS1_YhbY	ACIAD2855		putative RNA-binding protein	COG1534	CRS1_YhbY	K07574
3NIKH	Belongs to the class-I aminoacyl-tRNA synthetase family	ACIAD2871	trpS	tryptophanyl-tRNA synthetase	COG0180	tRNA-synt_1b	K01867
3NJP8	Responsible for synthesis of pseudouridine from uracil	ACIAD2897	rluD	ribosomal large subunit pseudouridine synthase D (Pseudouridylate synthase) (Uracil hydrolyase)	COG0564	PseudoU_synth_2, S4	K06180
3NNWM	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance	ACIAD2908	rplY	50S ribosomal protein L25	COG1825	Ribosomal_L25p	K02897
3NIT4	The natural substrate for this enzyme may be peptidyl- tRNAs which drop off the ribosome during protein synthesis	ACIAD2909	pth	peptidyl-tRNA hydrolase	COG0193	Pept_tRNA_hydro	K01056
3NJB1	Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide	ACIAD2933		putative tRNA/rRNA methyltransferase	COG0219	SpoU_methylase	K03216
3NJIM	Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)	ACIAD2935	serS	seryl-tRNA synthetase ; also charges selenocystein tRNA with serine	COG0172	Seryl_tRNA_N, tRNA-synt_2b	K01875
3NNY1	Belongs to the bacterial ribosomal protein bL27 family	ACIAD2938	rpmA	50S ribosomal protein L27	COG0211	Ribosomal_L27	K02899
3NNGD	This protein binds to 23S rRNA in the presence of protein L20	ACIAD2939	rplU	50S ribosomal protein L21	COG0261	Ribosomal_L21p	K02888
3NISD	amino acids such as threonine, to avoid such errors, it has a posttransfer editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner	ACIAD2950	valS	valyl-tRNA synthetase	COG0525	Anticodon_1, Val_tRNA-synt_C, tRNA-synt_1	K01873
3NJCM	Methyltransferase domain	ACIAD2995		putative methyltransferase		Methyltransf_32
3NPVS	ribosome binding	ACIAD2999		conserved hypothetical protein
3NK8E	Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits	ACIAD3009	ksgA	S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase, kasugamycin resistance	COG0030	RrnaAD	K02528
3NJCQ	This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly	ACIAD3012	rplM	50S ribosomal protein L13		Ribosomal_L13
3NN52	Belongs to the universal ribosomal protein uS9 family	ACIAD3013	rpsI	30S ribosomal protein S9	COG0103	Ribosomal_S9	K02996
3NK31	Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily	ACIAD3041	pheT	phenylalanyl-tRNA synthetase, beta subunit	COG0072	B3_4, B5, FDX-ACB, tRNA_bind	K01890
3NJCI	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily	ACIAD3042	pheS	phenylalanyl-tRNA synthetase, alpha-subunit	COG0016	Phe_tRNA-synt_N, tRNA-synt_2d	K01889
3NNG8	Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit	ACIAD3046	rplT	50S ribosomal protein L20, also posttranslational autoregulator	COG0292	Ribosomal_L20	K02887
3NPCF	Belongs to the bacterial ribosomal protein bL35 family	ACIAD3047	rpmI	50S ribosomal protein L35		Ribosomal_L35p
3NISA	IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins	ACIAD3054	infC	protein chain initiation factor IF-3	COG0290	IF3_C, IF3_N	K02520
3NIJ5	Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr)	ACIAD3055	thrS	threonyl-tRNA synthetase	COG0441	HGTP_anticodon, TGS, tRNA-synt_2b, tRNA_SAD	K01868
3NJ8X	Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control	ACIAD3063	pcnB	poly(A) polymerase I (PAP)	COG0617	PolyA_pol, PolyA_pol_RNAbd, PolyA_pol_arg_C	K00970
3NJ5F	Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA	ACIAD3069	rumA	23S rRNA (Uracil-5-)-methyltransferase(23S rRNA(M- 5-U1939)-methyltransferase)	COG2265	TRAM, tRNA_U5-meth_tr	K03215
3NN48	Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation	ACIAD3076		conserved hypothetical protein	COG0799	RsfS	K09710
3NTA6	Endoribonuclease L-PSP	ACIAD3083		conserved hypothetical protein		Ribonuc_L-PSP
3NKCC	Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs	ACIAD3085	dusA	tRNA-dihydrouridine synthase A	COG0042	Dus	K05539
3NR9Y	YjgF/chorismate_mutase-like, putative endoribonuclease	ACIAD3089	ridA	imine deaminase		YjgF_endoribonc
3NJ7Y	Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP	ACIAD3095	prfC	peptide chain release factor 3	COG0480	GTP_EFTU, GTP_EFTU_D2, RF3_C	K02837
3NJJI	Belongs to the class-I aminoacyl-tRNA synthetase family	ACIAD3106	leuS	leucyl-tRNA synthetase	COG0495	Anticodon_1, tRNA-synt_1, tRNA-synt_1_2	K01869
3NJNV	Belongs to the RNase T2 family	ACIAD3156		conserved hypothetical protein		Ribonuclease_T2	K01166
3NK7G	Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine	ACIAD3158		putative tRNA-i(6)A37 modification enzyme (MiaB)	COG0621	Radical_SAM, TRAM, UPF0004	K06168
3NMDH	Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA	ACIAD3160		putative metalloprotease ybeY-like	COG0319	UPF0054	K07042
3NJ9W	3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs	ACIAD3179	rnr	exoribonuclease R	COG0557	OB_RNB, RNB, S1	K12573
3NN8W	Ribosomal protein L17	ACIAD3193	rplQ	50S ribosomal protein L17	COG0203	Ribosomal_L17	K02879
3NJVB	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit	ACIAD3195	rpsD	30S ribosomal protein S4	COG0522	Ribosomal_S4, S4	K02986
3NN3C	Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome	ACIAD3196	rpsK	30S ribosomal protein S11		Ribosomal_S11
3NNKC	Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits	ACIAD3197	rpsM	30S ribosomal protein S13	COG0099	Ribosomal_S13	K02952
3NQ70	Belongs to the bacterial ribosomal protein bL36 family	ACIAD3198	rpmJ	50S ribosomal protein L36		Ribosomal_L36
3NN66	binds to the 23S rRNA	ACIAD3200	rplO	50S ribosomal protein L15	COG0200	Ribosomal_L27A	K02876
3NPR9	Ribosomal protein L30	ACIAD3201	rpmD	50S ribosomal protein L30	COG1841	Ribosomal_L30	K02907
3NJBV	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body	ACIAD3202	rpsE	30S ribosomal protein S5		Ribosomal_S5, Ribosomal_S5_C
3NNGJ	This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance	ACIAD3203	rplR	50S ribosomal protein L18	COG0256	Ribosomal_L18p	K02881
3NIFW	This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center	ACIAD3204	rplF	50S ribosomal protein L6	COG0097	Ribosomal_L6	K02933
3NN47	One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit	ACIAD3205	rpsH	30S ribosomal protein S8	COG0096	Ribosomal_S8	K02994
3NNIJ	Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site	ACIAD3206	rpsN	30S ribosomal protein S14	COG0199	Ribosomal_S14	K02954
3NIKY	This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits	ACIAD3207	rplE	50S ribosomal protein L5	COG0094	Ribosomal_L5, Ribosomal_L5_C	K02931
3NP82	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit	ACIAD3208	rplX	50S ribosomal protein L24	COG0198	KOW, ribosomal_L24	K02895
3NN4P	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome	ACIAD3209	rplN	50S ribosomal protein L14	COG0093	Ribosomal_L14	K02874
3NNW9	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA	ACIAD3210	rpsQ	30S ribosomal protein S17	COG0186	Ribosomal_S17	K02961
3NPA8	Belongs to the universal ribosomal protein uL29 family	ACIAD3211	rpmC	50S ribosomal protein L29	COG0255	Ribosomal_L29	K02904
3NN5W	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs	ACIAD3212	rplP	50S ribosomal protein L16	COG0197	Ribosomal_L16	K02878
3NK5Y	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation	ACIAD3213	rpsC	30S ribosomal protein S3	COG0092	KH_2, Ribosomal_S3_C	K02982
3NNGH	The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome	ACIAD3214	rplV	50S ribosomal protein L22	COG0091	Ribosomal_L22	K02890
3NNXA	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA	ACIAD3215	rpsS	30S ribosomal protein S19		Ribosomal_S19
3NK9Q	One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity	ACIAD3216	rplB	50S ribosomal protein L2	COG0090	Ribosomal_L2, Ribosomal_L2_C	K02886
3NNHP	One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome	ACIAD3217	rplW	50S ribosomal protein L23	COG0089	Ribosomal_L23	K02892
3NK1G	Forms part of the polypeptide exit tunnel	ACIAD3218	rplD	50S ribosomal protein L4, regulates expression of S10 operon	COG0088	Ribosomal_L4	K02926
3NJ2J	One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit	ACIAD3219	rplC	50S ribosomal protein L3	COG0087	Ribosomal_L3	K02906
3NNK0	Involved in the binding of tRNA to the ribosomes	ACIAD3220	rpsJ	30S ribosomal protein S10	COG0051	Ribosomal_S10	K02946
3NIRE	glycyl-tRNA synthetase, alpha subunit	ACIAD3268	glyQ	glycyl-tRNA synthetase, alpha chain	COG0752	tRNA-synt_2e	K01878
3NIHP	Glycyl-tRNA synthetase beta subunit	ACIAD3269	glyS	glycyl-tRNA synthetase, beta chain	COG0751	DALR_1, tRNA_synt_2f	K01879
3NJN4	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs	ACIAD3307	truB	tRNA pseudouridine 55 synthase	COG0130	TruB-C_2, TruB_C_2, TruB_N	K03177
3NN51	This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site	ACIAD3310	rplS	50S ribosomal protein L19	COG0335	Ribosomal_L19	K02884
3NJ5E	Belongs to the RNA methyltransferase TrmD family	ACIAD3311	trmD	tRNA (guanine-1-)-methyltransferase.	COG0336	tRNA_m1G_MT	K00554
3NJ2R	An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes	ACIAD3312	rimM	16S rRNA processing protein	COG0806	PRC, RimM	K02860
3NNWP	Belongs to the bacterial ribosomal protein bS16 family	ACIAD3313	rpsP	30S ribosomal protein S16	COG0228	Ribosomal_S16	K02959
3NN5J	Endoribonuclease L-PSP	ACIAD3327		putative 2-iminobutanoate/2-iminopropanoate deaminase (RidA like)		Ribonuc_L-PSP
3NIS5	Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA	ACIAD3368	mraW	Ribosomal RNA small subunit methyltransferase H	COG0275	Methyltransf_5	K03438
3NKI0	Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu)	ACIAD3371	gltX	glutamyl-tRNA synthetase	COG0008	tRNA-synt_1c	K01885
3NJIX	Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit	ACIAD3478		conserved hypothetical protein		Methyltrans_RNA
3NN62	Endoribonuclease L-PSP	ACIAD3493		conserved hypothetical protein		Ribonuc_L-PSP
3NIHM	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA	ACIAD3498	prfB	peptide chain release factor 2	COG1186	PCRF, RF-1	K02836
3NNXE	Sigma 54 modulation protein / S30EA ribosomal protein	ACIAD3535		conserved hypothetical protein		Ribosomal_S30AE
3NN49	rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality	ACIAD3563	dtd	D-tyrosyl tRNA(tyr) deacylase	COG1490	Tyr_Deacylase	K07560
3NJJR	Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus	ACIAD3637	fmt	methionyl-tRNA formyltransferase	COG0223	Formyl_trans_C, Formyl_trans_N	K00604
3NJ2I	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA	ACIAD3638	sun	16S rRNA m5C967 SAM-dependent methyltransferase	COG0144	Methyltr_RsmB-F, NusB	K03500
3NJ32	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34	ACIAD3680	trmE	GTPase involved in tRNA modification and in thiophene and furan oxidation	COG0486	MMR_HSR1, MnmE_helical, TrmE_N	K03650
3NN9R	RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme	ACIAD3683	rnpA	RNase P, protein C5 component, processes tRNA, 4.5S RNA	COG0594	Ribonuclease_P	K03536
3NPR1	Belongs to the bacterial ribosomal protein bL34 family	ACIAD3684	rpmH	50S ribosomal protein L34		Ribosomal_L34

3NK51

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr)

ACIAD0013

tyrS

tyrosyl-tRNA synthetase

COG0162

tRNA-synt_1b

K01866

3NIHR

amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile)

ACIAD0022

ileS

isoleucyl-tRNA synthetase

COG0060

Anticodon_1, tRNA-synt_1, zf-FPG_IleRS

K01870

3NNMM

May reduce aminoacrylate peracid to aminoacrylate. Required to remove a toxic intermediate produce by the pyrimidine nitrogen degradation

ACIAD0029

rutC

putative 3-aminoacrylate deaminase RutC (Pyrimidine utilization protein C)

COG0251

Ribonuc_L-PSP

K09021

3NJQV

Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates

ACIAD0050

rph

ribonuclease PH (RNase PH), tRNA nucleotidyltransferase

COG0689

RNase_PH, RNase_PH_C

K00989

3NNHV

Endoribonuclease L-PSP

ACIAD0117

conserved hypothetical protein; putative endoribonuclease L-PSP

Ribonuc_L-PSP

3NK37

Arginyl-tRNA synthetase

ACIAD0164

argS

arginyl-tRNA synthetase

COG0018

Arg_tRNA_synt_N, DALR_1, tRNA-synt_1d

K01887

3NSRJ

MafB19-like deaminase

ACIAD0204

putative cytidine and deoxycytidylate deaminase zinc-binding like protein

dCMP_cyt_deam_1

3NKGI

Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, HCO(3)(-) CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of diphosphate

ACIAD0208

putative ribosome maturation factor (dsRNA-binding protein) (RimN)

COG0009

Sua5_yciO_yrdC

K07566

3NKDT

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions

ACIAD0211

def

peptide deformylase 1 (N-formylmethionylaminoacyl-tRNA deformylase, binds Zn(II))

COG0242

Pep_deformylase

K01462

3NNI5

Endoribonuclease L-PSP

ACIAD0222

putative RidA family protein

Ribonuc_L-PSP

3NK6Q

Catalyzes the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto a tRNA(Asp). Glutamate is transferred on the 2-amino-5-(4,5- dihydroxy-2-cyclopenten-1-yl) moiety of the queuosine in the wobble position of the QUC anticodon

ACIAD0272

putative glutamyl t-RNA synthetase

tRNA-synt_1c

K01894

3NIQ7

This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis

ACIAD0299

tufB

protein chain elongation factor EF-Tu, possible GTP-binding factor (duplicate of tufA)

GTP_EFTU, GTP_EFTU_D2, GTP_EFTU_D3

3NJ44

Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors

ACIAD0302

rplK

50S ribosomal protein L11

Ribosomal_L11, Ribosomal_L11_N

3NIPW

Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release

ACIAD0304

rplA

50S ribosomal protein L1

COG0081

Ribosomal_L1

K02863

3NIS4

Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors

ACIAD0305

rplJ

50S ribosomal protein L10

COG0244

Ribosomal_L10

K02864

3NNIS

Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation

ACIAD0306

rplL

50S ribosomal protein L7/L12

COG0222

Ribosomal_L12, Ribosomal_L12_N

K02935

3NKH2

Specifically methylates the ribose of guanosine 2251 in 23S rRNA

ACIAD0357

putative tRNA/rRNA methyltransferase

COG0566

SpoU_methylase, SpoU_sub_bind

K03218

3NKI1

One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex

ACIAD0369

infB

protein chain initiation factor IF-2

COG0532

GTP_EFTU, IF-2, IF2_N, IF2_assoc

K02519

3NN3B

One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA

ACIAD0370

rbfA

ribosome-binding factor A

COG0858

RBFA

K02834

3NNXP

Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome

ACIAD0401

rpsO

30S ribosomal protein S15

COG0184

Ribosomal_S15

K02956

3NIGW

Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction

ACIAD0402

pnp

polyribonucleotide nucleotidyltransferase (Polynucleotide phosphorylase) (PNPase)

COG1185

KH_1, PNPase, RNase_PH, RNase_PH_C, S1

K00962

3NPDX

Ribosomal protein L31

ACIAD0425

rpmE2

50S ribosomal protein L31 type B

COG0254

Ribosomal_L31

K02909

3NJRE

Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs

ACIAD0438

rne

ribonuclease E (RNase E): endoribonuclease for rRNA processing and mRNA degradation

COG1530

RNase_E_G, S1

K08300

3NJU3

Responsible for synthesis of pseudouridine from uracil

ACIAD0442

rluC

23S rRNA pseudouridylate synthase

COG0564

PseudoU_synth_2, S4

K06179

3NPBC

One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex

ACIAD0472

infA

protein chain initiation factor IF-1

COG0361

eIF-1a

K02518

3NJS9

Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs

ACIAD0474

truA

tRNA-pseudouridine synthase I

PseudoU_synth_1

Asparaginase

putative L-asparaginase I (AnsA)

COG0252

Asparaginase

K01424

3NPRW

Belongs to the bacterial ribosomal protein bL33 family

ACIAD0501

rpmG

50S ribosomal protein L33

Ribosomal_L33

3NNZ1

Belongs to the bacterial ribosomal protein bL28 family

ACIAD0502

rpmB

50S ribosomal protein L28

Ribosomal_L28

3NJI9

Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs

ACIAD0557

rlmN

23S rRNA adenosine methyltransferase

COG0820

Radical_SAM

K06941

3NKTF

histidyl-tRNA synthetase

ACIAD0562

hisS

histidyl-tRNA synthetase

COG0124

HGTP_anticodon, tRNA-synt_His

K01892

3NKA4

Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)

ACIAD0591

queA

S-adenosylmethionine:tRNA ribosyltransferase-isomerase (Queuosine biosynthesis protein )

COG0809

Queuosine_synth

K07568

3NMGU

Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus

ACIAD0603

conserved hypothetical protein

3NJ1X

Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn)

ACIAD0609

aspS

aspartyl-tRNA synthetase

COG0173

GAD, tRNA-synt_2, tRNA_anti-codon

K01876

3NNGT

Sigma 54 modulation protein / S30EA ribosomal protein

ACIAD0658

putative sigma(54) modulation protein RpoX

COG1544

Ribosomal_S30AE

K05808

3NJ9H

Specifically methylates the guanosine in position 1516 of 16S rRNA

ACIAD0679

conserved hypothetical protein; putative methyltransferase

COG0500

SAM_MT

K15984

3NIIK

Specifically methylates the guanine in position 1207 of 16S rRNA in the 30S particle

ACIAD0701

rsmC

ribosomal RNA small subunit methyltransferase C (rRNA (guanine-N(2)-)-methyltransferase) (16S rRNA m2G1207 methyltransferase)

COG2813

MTS, MTS_N

K00564

3NIT3

Responsible for synthesis of pseudouridine from uracil

ACIAD0715

putative dual specificity pseudouridine synthase for 23S rRNA and tRNAphe modification (RluA-like)

COG0564

PseudoU_synth_2

K06177

3NIRS

Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation

ACIAD0768

metG

methionyl-tRNA synthetase

COG0143

tRNA-synt_1g, tRNA_bind

K01874

3NJJ4

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction proline is first activated by ATP to form Pro- AMP and then transferred to the acceptor end of tRNA(Pro). As ProRS can inadvertently accommodate and process non-cognate amino acids such as alanine and cysteine, to avoid such errors it has two additional distinct editing activities against alanine. One activity is designated as 'pretransfer' editing and involves the tRNA(Pro)-independent hydrolysis of activated Ala-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Ala-tRNA(Pro). The misacylated Cys- tRNA(Pro) is not edited by ProRS

ACIAD0782

proS

prolyl-tRNA synthetase

COG0442

HGTP_anticodon, tRNA-synt_2b, tRNA_edit

K01881

3NIRM

Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)

ACIAD0822

gatB

aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

COG0064

GatB_N, GatB_Yqey

K02434

3NIMZ

Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln)

ACIAD0823

gatA

aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A

COG0154

Amidase

K02433

3NJ6P

Ribonuclease E/G family

ACIAD0830

cafA

ribonuclease G, endoribonuclease G (cytoplasmic axial filament protein )

COG1530

RNase_E_G, S1

K08301

3NJKN

Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U16 in tRNAs

ACIAD0837

dusC

tRNA-dihydrouridine synthase C

COG0042

Dus

K05541

3NIUW

Belongs to the pseudouridine synthase RsuA family

ACIAD0861

putative ribosomal large subunit pseudouridine synthase B (Pseudouridylate synthase) (Uracil hydrolyase)

COG1187

PseudoU_synth_2, S4

K06178

3NM1N

Acetyltransferases including N-acetylases of ribosomal proteins

ACIAD0864

putative acetyltransferase

Acetyltransf_3

3NJAG

Belongs to the SUA5 family

ACIAD0865

putative translation factor

Sua5_yciO_yrdC

3NPDH

Belongs to the bacterial ribosomal protein bL32 family

ACIAD0869

rpmF

50S ribosomal protein L32

Ribosomal_L32p

3NN2Z

Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit

ACIAD0881

rpsL

30S ribosomal protein S12

Ribosom_S12_S23

3NM4A

One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA

ACIAD0883

rpsG

30S ribosomal protein S7

Ribosomal_S7

3NIEG

Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome

ACIAD0884

fusA

protein chain elongation factor EF-G, GTP-binding

COG0480

EFG_C, EFG_II, EFG_IV, GTP_EFTU, GTP_EFTU_D2

K02355

3NIQ7

This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis

ACIAD0885

tufA

protein chain elongation factor EF-Tu (duplicate of tufB)

COG0050

GTP_EFTU, GTP_EFTU_D2, GTP_EFTU_D3

K02358

3NSQ3

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions

ACIAD1039

def2

peptide deformylase 2

COG0242

Pep_deformylase

K01462

3NJ38

Belongs to the class-II aminoacyl-tRNA synthetase family

ACIAD1069

lysS

lysyl-tRNA synthetase

COG1190

tRNA-synt_2, tRNA_anti-codon

K04567

3NK7T

Specifically methylates the guanine in position 966 of 16S rRNA in the assembled 30S particle

ACIAD1100

putative methyltransferase

COG0742

Cons_hypoth95

K08316

3NJF6

Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA

ACIAD1113

rlmH

Ribosomal RNA large subunit methyltransferase H

COG1576

SPOUT_MTase

K00783

3NJ80

Pseudouridine synthase

ACIAD1203

rluA

dual specificity pseudouridine synthase for 23S rRNA and tRNAphe modification

COG0564

PseudoU_synth_2

K06177

3NJVQ

Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34

ACIAD1221

trmU

tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase

COG0482

tRNA_Me_trans

K00566

3NIN9

Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain

ACIAD1253

alaS

alanyl-tRNA synthetase

COG0013

DHHA1, tRNA-synt_2c, tRNA_SAD

K01872

3NKZ8

Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA

ACIAD1268

putative N-6 Adenine-specific DNA methylase

COG1092, COG0116

Methyltrans_SAM, THUMP, UPF0020

K12297

1RS1C

GNAT family acetyltransferase

ACIAD1279

cphA

Cyanophycin synthetase

COG1181

Mur_ligase_C, Mur_ligase_M, RimK

K03802

3NJ1J

Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA

ACIAD1302

trmB

tRNA(guanine-7)methyltransferase

COG0220

Methyltransf_4

K03439

3NIY4

DEAD-box RNA helicase involved in RNA degradation. Has RNA-dependent ATPase activity and unwinds double-stranded RNA

ACIAD1314

rhlB

ATP-dependent RNA helicase (DEAD box)

COG0513

DEAD, Helicase_C

K03732

3NPA3

Belongs to the bacterial ribosomal protein bS21 family

ACIAD1331

rpsU

30S ribosomal protein S21

Ribosomal_S21

3NIP5

Catalyzes the methylthiolation of an aspartic acid residue of ribosomal protein S12

ACIAD1371

rimO

Ribosomal protein S12 methylthiotransferases

COG0621

Radical_SAM, UPF0004

K14441

3NK5V

Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another

ACIAD1373

frr

ribosome releasing factor

COG0233

RRF

K02838

3NN87

Belongs to the HSP15 family

ACIAD1386

hslR

heat shock protein 15

COG1188

S4

K04762

3NNXB

Binds directly to 16S ribosomal RNA

ACIAD1389

rpsT

30S ribosomal protein S20

COG0268

Ribosomal_S20p

K02968

3NKQW

Belongs to the class-I aminoacyl-tRNA synthetase family

ACIAD1481

cysS

cysteinyl-tRNA synthetase

COG0215

DALR_2, tRNA-synt_1e

K01883

3NKR8

Nodulation protein S (NodS)

ACIAD1557

putative methyltransferase

NodS

3NQQ9

Amidase

ACIAD1618

amdA

amidase

COG0154

Amidase

K01426

3NJW0

Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA)

ACIAD1645

trmA

tRNA (uracil-5-)-methyltransferase

COG2265

tRNA_U5-meth_tr

K00557

3NK4U

tRNA synthetases class I (E and Q), anti-codon binding domain

ACIAD1920

glnS

glutaminyl-tRNA synthetase

COG0008

tRNA-synt_1c, tRNA-synt_1c_C

K01886

3NM3S

PELOTA RNA binding domain

ACIAD1960

stiP

Cysteine protease StiP

PELOTA_1, PRTase_1

3NMYH

ATP-grasp in the biosynthetic pathway with Ter operon

ACIAD1963

conserved hypothetical protein

ATPgrasp_Ter

3NIW2

Specifically methylates the 50S ribosomal protein L3 on a specific glutamine residue

ACIAD2029

putative adenine-specific methylase

COG2890

MTS

K07320

3NJ4G

ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner

ACIAD2071

putative GTP-binding protein

COG0012

MMR_HSR1, YchF-GTPase_C

K06942

3NKAE

Asparaginase

ACIAD2088

aspQ

glutaminase-asparaginase

COG0252

Asparaginase

K05597

3NJAD

Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA

ACIAD2090

TrmJ

tRNA (cytidine/uridine-2'-O-)-methyltransferase

COG0565

SpoU_methylase

K15396

3NSP0

Siderophore biosynthesis protein domain

ACIAD2117

putative siderophore biosynthese protein (bfnL)

Acetyltransf_8

3NJZR

Involved in peptide bond synthesis. Alleviates ribosome stalling that occurs when 3 or more consecutive Pro residues or the sequence PPG is present in a protein, possibly by augmenting the peptidyl transferase activity of the ribosome. Modification of Lys-34 is required for alleviation

ACIAD2206

efp

elongation factor P

COG0231

EFP, EFP_N, Elong-fact-P_C

K02356

3NPGX

Binds the 23S rRNA

ACIAD2210

rpmE

50S ribosomal protein L31

COG0254

Ribosomal_L31

K02909

3NJR4

Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome

ACIAD2268

tsf

protein chain elongation factor EF-Ts

COG0264

EF_TS

K02357

3NIVD

Belongs to the universal ribosomal protein uS2 family

ACIAD2269

rpsB

30S ribosomal protein S2

COG0052

Ribosomal_S2

K02967

3NIW8

Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit

ACIAD2284

putative ribosomal RNA small subunit methyltransferase E (rsmE)

COG1385

Methyltrans_RNA

K09761

3NK6J

Catalyzes the addition and repair of the essential 3'- terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate

ACIAD2288

cca

Multifunctional protein [Includes: CCA-adding enzyme ; 2'-nucleotidase ; 2',3'-cyclic phosphodiesterase ; Phosphatase]

COG0617

PolyA_pol, PolyA_pol_RNAbd

K00974

3NJ9N

HRDC domain

ACIAD2310

rnd

ribonuclease D, processes tRNA

COG0349

DNA_pol_A_exo1, HRDC

K03684

3NM5D

thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence

ACIAD2347

rpsA

30S ribosomal protein S1

COG0539

S1

K02945

3NN6N

Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2)

ACIAD2350

putative deaminase

MafB19-deam

3NJAY

Specifically methylates the N7 position of guanine in position 527 of 16S rRNA

ACIAD2368

gidB

glucose-inhibited division protein B (methyltransferase)

COG0357

GidB

K03501

3NJ0U

COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits (eIF-2Bgamma eIF-2Bepsilon)

ACIAD2369

putative nucleotidyl transferase

COG1208

NTP_transferase

K00992

3NK0S

RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Also binds with high specificity to tRNAs

ACIAD2373

hfq

host factor I for bacteriophage Q beta replication, a growth-related protein

COG1923

Hfq

K03666

3NK7C

RNA pseudouridylate synthase

ACIAD2377

putative pseudouridylate synthase

COG0564

PseudoU_synth_2

K06177

3NJ1F

Belongs to the pseudouridine synthase RsuA family

ACIAD2380

rsuA

16S rRNA pseudouridylate 516 synthase

COG1187

PseudoU_synth_2, S4

K06183

3NKB7

Methylates the class 1 translation termination release factors RF1 PrfA and RF2 PrfB on the glutamine residue of the universally conserved GGQ motif

ACIAD2417

hemK

methyl transferase

COG2890

Methyltransf_31

K02493

3NJCS

Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA

ACIAD2418

prfA

peptide chain release factor 1

COG0216

PCRF, RF-1

K02835

3NN4A

Binds together with S18 to 16S ribosomal RNA

ACIAD2430

rpsF

30S ribosomal protein S6

COG0360

Ribosomal_S6

K02990

3NPB6

Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit

ACIAD2431

rpsR

30S ribosomal protein S18

COG0238

Ribosomal_S18

K02963

3NKTG

Binds to the 23S rRNA

ACIAD2432

rplI

50S ribosomal protein L9

COG0359

Ribosomal_L9_C, Ribosomal_L9_N

K02939

3NIXE

Methylates ribosomal protein L11

ACIAD2443

prmA

methylation of 50S ribosomal subunit protein L11 (ribosomal protein L11 methyltransferase)

COG2264

PrmA

K02687

3NIZ0

Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines

ACIAD2557

dusB

tRNA-dihydrouridine synthase B

COG0042

Dus

K05540

3NJAF

tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)

ACIAD2576

conserved hypothetical protein; putative tRNA hydroxylase

COG4445

MiaE

K06169

3NJNF

Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre- crRNA and tracrRNA of type II CRISPR loci if present in the organism

ACIAD2581

rnc

ribonuclease III, ds RNA

COG0571

Ribonucleas_3_3, dsrm

K03685

3NSMG

SpoU rRNA Methylase family

ACIAD2626

putative tRNA/rRNA methyltransferase

COG0566

SpoU_methylase

K03437

3NJ3Z

tRNA synthetases class II (D, K and N)

ACIAD2666

putative lysyl-tRNA synthetase (Lysine--tRNA ligase)(PoxA)

COG2269

tRNA-synt_2

K04568

3NJJX

Siderophore biosynthesis protein domain

ACIAD2767

fbsK

putative siderophore biosynthesis protein; putative acetyltransferase

Acetyltransf_8

3NJ2H

Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit

ACIAD2854

ftsJ

cell division protein (filamentous temperature sensitivity, 23S rRNA U2552 ribose 2'-O-methyltransferase, SAM-dependent)

FtsJ

CRS1_YhbY

putative RNA-binding protein

COG1534

CRS1_YhbY

K07574

3NIKH

Belongs to the class-I aminoacyl-tRNA synthetase family

ACIAD2871

trpS

tryptophanyl-tRNA synthetase

COG0180

tRNA-synt_1b

K01867

3NJP8

Responsible for synthesis of pseudouridine from uracil

ACIAD2897

rluD

ribosomal large subunit pseudouridine synthase D (Pseudouridylate synthase) (Uracil hydrolyase)

COG0564

PseudoU_synth_2, S4

K06180

3NNWM

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance

ACIAD2908

rplY

50S ribosomal protein L25

COG1825

Ribosomal_L25p

K02897

3NIT4

The natural substrate for this enzyme may be peptidyl- tRNAs which drop off the ribosome during protein synthesis

ACIAD2909

pth

peptidyl-tRNA hydrolase

COG0193

Pept_tRNA_hydro

K01056

3NJB1

Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide

ACIAD2933

putative tRNA/rRNA methyltransferase

COG0219

SpoU_methylase

K03216

3NJIM

Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)

ACIAD2935

serS

seryl-tRNA synthetase ; also charges selenocystein tRNA with serine

COG0172

Seryl_tRNA_N, tRNA-synt_2b

K01875

3NNY1

Belongs to the bacterial ribosomal protein bL27 family

ACIAD2938

rpmA

50S ribosomal protein L27

COG0211

Ribosomal_L27

K02899

3NNGD

This protein binds to 23S rRNA in the presence of protein L20

ACIAD2939

rplU

50S ribosomal protein L21

COG0261

Ribosomal_L21p

K02888

3NISD

amino acids such as threonine, to avoid such errors, it has a posttransfer editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner

ACIAD2950

valS

valyl-tRNA synthetase

COG0525

Anticodon_1, Val_tRNA-synt_C, tRNA-synt_1

K01873

3NJCM

Methyltransferase domain

ACIAD2995

putative methyltransferase

Methyltransf_32

3NPVS

ribosome binding

ACIAD2999

conserved hypothetical protein

3NK8E

Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits

ACIAD3009

ksgA

S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase, kasugamycin resistance

COG0030

RrnaAD

K02528

3NJCQ

This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly

ACIAD3012

rplM

50S ribosomal protein L13

Ribosomal_L13

3NN52

Belongs to the universal ribosomal protein uS9 family

ACIAD3013

rpsI

30S ribosomal protein S9

COG0103

Ribosomal_S9

K02996

3NK31

Belongs to the phenylalanyl-tRNA synthetase beta subunit family. Type 1 subfamily

ACIAD3041

pheT

phenylalanyl-tRNA synthetase, beta subunit

COG0072

B3_4, B5, FDX-ACB, tRNA_bind

K01890

3NJCI

Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily

ACIAD3042

pheS

phenylalanyl-tRNA synthetase, alpha-subunit

COG0016

Phe_tRNA-synt_N, tRNA-synt_2d

K01889

3NNG8

Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit

ACIAD3046

rplT

50S ribosomal protein L20, also posttranslational autoregulator

COG0292

Ribosomal_L20

K02887

3NPCF

Belongs to the bacterial ribosomal protein bL35 family

ACIAD3047

rpmI

50S ribosomal protein L35

Ribosomal_L35p

3NISA

IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins

ACIAD3054

infC

protein chain initiation factor IF-3

COG0290

IF3_C, IF3_N

K02520

3NIJ5

Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr)

ACIAD3055

thrS

threonyl-tRNA synthetase

COG0441

HGTP_anticodon, TGS, tRNA-synt_2b, tRNA_SAD

K01868

3NJ8X

Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control

ACIAD3063

pcnB

poly(A) polymerase I (PAP)

COG0617

PolyA_pol, PolyA_pol_RNAbd, PolyA_pol_arg_C

K00970

3NJ5F

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA

ACIAD3069

rumA

23S rRNA (Uracil-5-)-methyltransferase(23S rRNA(M- 5-U1939)-methyltransferase)

COG2265

TRAM, tRNA_U5-meth_tr

K03215

3NN48

Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation

ACIAD3076

conserved hypothetical protein

COG0799

RsfS

K09710

3NTA6

Endoribonuclease L-PSP

ACIAD3083

conserved hypothetical protein

Ribonuc_L-PSP

3NKCC

Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs

ACIAD3085

dusA

tRNA-dihydrouridine synthase A

COG0042

Dus

K05539

3NR9Y

YjgF/chorismate_mutase-like, putative endoribonuclease

ACIAD3089

ridA

imine deaminase

YjgF_endoribonc

3NJ7Y

Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP

ACIAD3095

prfC

peptide chain release factor 3

COG0480

GTP_EFTU, GTP_EFTU_D2, RF3_C

K02837

3NJJI

Belongs to the class-I aminoacyl-tRNA synthetase family

ACIAD3106

leuS

leucyl-tRNA synthetase

COG0495

Anticodon_1, tRNA-synt_1, tRNA-synt_1_2

K01869

3NJNV

Belongs to the RNase T2 family

ACIAD3156

conserved hypothetical protein

Ribonuclease_T2

K01166

3NK7G

Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine

ACIAD3158

putative tRNA-i(6)A37 modification enzyme (MiaB)

COG0621

Radical_SAM, TRAM, UPF0004

K06168

3NMDH

Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA

ACIAD3160

putative metalloprotease ybeY-like

COG0319

UPF0054

K07042

3NJ9W

3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs

ACIAD3179

rnr

exoribonuclease R

COG0557

OB_RNB, RNB, S1

K12573

3NN8W

Ribosomal protein L17

ACIAD3193

rplQ

50S ribosomal protein L17

COG0203

Ribosomal_L17

K02879

3NJVB

One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit

ACIAD3195

rpsD

30S ribosomal protein S4

COG0522

Ribosomal_S4, S4

K02986

3NN3C

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome

ACIAD3196

rpsK

30S ribosomal protein S11

Ribosomal_S11

3NNKC

Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits

ACIAD3197

rpsM

30S ribosomal protein S13

COG0099

Ribosomal_S13

K02952

3NQ70

Belongs to the bacterial ribosomal protein bL36 family

ACIAD3198

rpmJ

50S ribosomal protein L36

Ribosomal_L36

3NN66

binds to the 23S rRNA

ACIAD3200

rplO

50S ribosomal protein L15

COG0200

Ribosomal_L27A

K02876

3NPR9

Ribosomal protein L30

ACIAD3201

rpmD

50S ribosomal protein L30

COG1841

Ribosomal_L30

K02907

3NJBV

Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body

ACIAD3202

rpsE

30S ribosomal protein S5

Ribosomal_S5, Ribosomal_S5_C

3NNGJ

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance

ACIAD3203

rplR

50S ribosomal protein L18

COG0256

Ribosomal_L18p

K02881

3NIFW

This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center

ACIAD3204

rplF

50S ribosomal protein L6

COG0097

Ribosomal_L6

K02933

3NN47

One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit

ACIAD3205

rpsH

30S ribosomal protein S8

COG0096

Ribosomal_S8

K02994

3NNIJ

Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site

ACIAD3206

rpsN

30S ribosomal protein S14

COG0199

Ribosomal_S14

K02954

3NIKY

This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits

ACIAD3207

rplE

50S ribosomal protein L5

COG0094

Ribosomal_L5, Ribosomal_L5_C

K02931

3NP82

One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit

ACIAD3208

rplX

50S ribosomal protein L24

COG0198

KOW, ribosomal_L24

K02895

3NN4P

Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome

ACIAD3209

rplN

50S ribosomal protein L14

COG0093

Ribosomal_L14

K02874

3NNW9

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA

ACIAD3210

rpsQ

30S ribosomal protein S17

COG0186

Ribosomal_S17

K02961

3NPA8

Belongs to the universal ribosomal protein uL29 family

ACIAD3211

rpmC

50S ribosomal protein L29

COG0255

Ribosomal_L29

K02904

3NN5W

Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs

ACIAD3212

rplP

50S ribosomal protein L16

COG0197

Ribosomal_L16

K02878

3NK5Y

Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation

ACIAD3213

rpsC

30S ribosomal protein S3

COG0092

KH_2, Ribosomal_S3_C

K02982

3NNGH

The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome

ACIAD3214

rplV

50S ribosomal protein L22

COG0091

Ribosomal_L22

K02890

3NNXA

Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA

ACIAD3215

rpsS

30S ribosomal protein S19

Ribosomal_S19

3NK9Q

One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity

ACIAD3216

rplB

50S ribosomal protein L2

COG0090

Ribosomal_L2, Ribosomal_L2_C

K02886

3NNHP

One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome

ACIAD3217

rplW

50S ribosomal protein L23

COG0089

Ribosomal_L23

K02892

3NK1G

Forms part of the polypeptide exit tunnel

ACIAD3218

rplD

50S ribosomal protein L4, regulates expression of S10 operon

COG0088

Ribosomal_L4

K02926

3NJ2J

One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit

ACIAD3219

rplC

50S ribosomal protein L3

COG0087

Ribosomal_L3

K02906

3NNK0

Involved in the binding of tRNA to the ribosomes

ACIAD3220

rpsJ

30S ribosomal protein S10

COG0051

Ribosomal_S10

K02946

3NIRE

glycyl-tRNA synthetase, alpha subunit

ACIAD3268

glyQ

glycyl-tRNA synthetase, alpha chain

COG0752

tRNA-synt_2e

K01878

3NIHP

Glycyl-tRNA synthetase beta subunit

ACIAD3269

glyS

glycyl-tRNA synthetase, beta chain

COG0751

DALR_1, tRNA_synt_2f

K01879

3NJN4

Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs

ACIAD3307

truB

tRNA pseudouridine 55 synthase

COG0130

TruB-C_2, TruB_C_2, TruB_N

K03177

3NN51

This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site

ACIAD3310

rplS

50S ribosomal protein L19

COG0335

Ribosomal_L19

K02884

3NJ5E

Belongs to the RNA methyltransferase TrmD family

ACIAD3311

trmD

tRNA (guanine-1-)-methyltransferase.

COG0336

tRNA_m1G_MT

K00554

3NJ2R

An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes

ACIAD3312

rimM

16S rRNA processing protein

COG0806

PRC, RimM

K02860

3NNWP

Belongs to the bacterial ribosomal protein bS16 family

ACIAD3313

rpsP

30S ribosomal protein S16

COG0228

Ribosomal_S16

K02959

3NN5J

Endoribonuclease L-PSP

ACIAD3327

putative 2-iminobutanoate/2-iminopropanoate deaminase (RidA like)

Ribonuc_L-PSP

3NIS5

Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA

ACIAD3368

mraW

Ribosomal RNA small subunit methyltransferase H

COG0275

Methyltransf_5

K03438

3NKI0

Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu)

ACIAD3371

gltX

glutamyl-tRNA synthetase

COG0008

tRNA-synt_1c

K01885

3NJIX

Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit

ACIAD3478

conserved hypothetical protein

Methyltrans_RNA

3NN62

Endoribonuclease L-PSP

ACIAD3493

conserved hypothetical protein

Ribonuc_L-PSP

3NIHM

Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA

ACIAD3498

prfB

peptide chain release factor 2

COG1186

PCRF, RF-1

K02836

3NNXE

Sigma 54 modulation protein / S30EA ribosomal protein

ACIAD3535

conserved hypothetical protein

Ribosomal_S30AE

3NN49

rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality

ACIAD3563

dtd

D-tyrosyl tRNA(tyr) deacylase

COG1490

Tyr_Deacylase

K07560

3NJJR

Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus

ACIAD3637

fmt

methionyl-tRNA formyltransferase

COG0223

Formyl_trans_C, Formyl_trans_N

K00604

3NJ2I

Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA

ACIAD3638

sun

16S rRNA m5C967 SAM-dependent methyltransferase

COG0144

Methyltr_RsmB-F, NusB

K03500

3NJ32

Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34

ACIAD3680

trmE

GTPase involved in tRNA modification and in thiophene and furan oxidation

COG0486

MMR_HSR1, MnmE_helical, TrmE_N

K03650

3NN9R

RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme

ACIAD3683

rnpA

RNase P, protein C5 component, processes tRNA, 4.5S RNA

COG0594

Ribonuclease_P

K03536

3NPR1

Belongs to the bacterial ribosomal protein bL34 family

ACIAD3684

rpmH

50S ribosomal protein L34

Ribosomal_L34

CDSs classified by EGGNOG in COG category J