TABLE 7.

Protein-coding genes in the hypothetical minimal actinobacterial cells

ORF designationaProminent features
BL0053Mrp; COG family, ATPases involved in chromosome partitioning; PFAM_ID, DUF59; PFAM_ID, fer4_NifH
BL0065Involved in peptide bond synthesis; alters affinity of the ribosome for aminoacyl-tRNA
BL0067Composed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate
BL0068CarB
BL0070Gmp kinase; COG family, guanylate kinase; PFAM_ID, Guanylate_kin
BL0097Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-d-xylulose-5-phosphate (DXP) to 2-C-methyl-d-erythritol 4-phosphate
BL0100Involved in DNA repair and recF pathway recombination
BL0118GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA interact with and regulate FtsZ function
BL0193COG family, Mg-dependent DNase; PFAM_ID, TatD_DNase
BL0291Pantetheine-phosphate adenylyltransferase; PpaT; dephospho-CoA pyrophosphorylase; CoaD; COG family, phosphopantetheine adenylyltransferase; PFAM_ID, Cytidylyltransf
BL0295RNase III; RncS; COG family, double-stranded-RNA-specific RNase; PFAM_ID, Ribonuclease_3; PFAM_ID, dsrm
BL0305RpsP; COG family, ribosomal protein S16; PFAM_ID, Ribosomal_S16
BL0327M1g-methyltransferase; tRNA [GM37] methyltransferase; TrmD; COG family, tRNA-(guanine-N1)-methyltransferase; PFAM_ID, tRNA_m1G_MT
BL0328COG family, N6-adenine-specific methylase
BL0358AtpG; COG family, F0F1-type ATP synthase gamma subunit; PFAM_ID, ATP-synt
BL0395Catalyzes formation of valyl-tRNA(Val) from valine and tRNA(Val)
BL0402Allows 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
BL0413RplI; COG family, ribosomal protein L9; PFAM_ID, Ribosomal_L9
BL0431DnaB; COG family, replicative DNA helicase; PFAM_ID, DnaB
BL0499COG family, recombinational DNA repair protein; PFAM_ID, RecR; PFAM_ID, Toprim
BL0500Plays a role in assembling DnaB onto the primer template and interacts with the core polymerase
BL0519Hsp-70 cofactor; GrpE; COG family, molecular chaperone GrpE (heat shock protein); PFAM_ID, GrpE
BL0549Catalyzes formation of N6-(1,2,-dicarboxyethyl)-AMP from l-aspartate, IMP, and GTP in AMP biosynthesis
BL0637COG family, recombinational DNA repair ATPase
BL0640DnaA; COG family, ATPase involved in DNA replication initiation; PFAM_ID, AAA; PFAM_ID, bac_DNAA
BL0648ParB; COG family, predicted transcriptional regulators; PFAM_ID, ParBc
BL0703UvrC; COG family, nuclease subunit of the excinuclease complex; PFAM_ID, Exci_endo_N; PFAM_ID, UVR; PFAM_ID, HHH
BL0706COG family, uncharacterized Bcr; PFAM_ID, DUF199
BL0707Catalyzes formation of 3-phospho-d-glyceroyl phosphate from 3-phospho-d-glycerate
BL0726COG family, uncharacterized Acr; PFAM_ID, DUF28
BL0727Cleaves the cruciform structure in supercoiled DNA by nicking strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms
BL0728COG family, Holliday junction resolvasome DNA-binding subunit; PFAM_ID, RuvA; PFAM_ID, RuvA_II
BL0729COG family, Holliday junction resolvasome helicase subunit; PFAM_ID, AAA
BL0735Involved in de novo purine biosynthesis
BL0848Binds to the ribosome on the universally conserved alpha-sarcin loop
BL0849RpsT; COG family, ribosomal protein S20; PFAM_ID, Ribosomal_S20p
BL0859Bex; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds cell membrane through apparent C-terminal domain
BL0861COG family, predicted metal-dependent hydrolase; PFAM_ID, UPF0054
BL0870COG family, iron-regulated ABC transporter ATPase subunit SufC; PFAM_ID, ABC_tran
BL0878Catalyzes formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
BL0881COG family, predicted endonuclease involved in recombination (possible Holliday junction resolvase in mycoplasmas and B. subtilis)
BL0926COG family, predicted GTPase
BL0943Binds and unfolds substrates as part of the ClpXP protease
BL0947Tig; RopA; peptidyl-prolyl cis/trans-isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
BL0960Contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
BL0964N-Acetylglucosamine-1-phosphate uridyltransferase; Tms protein; GlmU; COG family, N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains); PFAM_ID, NTP_transferase
BL0990UvrABC repair system catalyzes recognition and processing of DNA lesions; beta-hairpin of the UvrB subunit is inserted between the strands, where it probes for the presence of a lesion
BL0992Binds mRNA to the ribosomes and plays a role in delivering transfer mRNA to stalled ribosomes
BL1032Transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD), which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
BL1043Recombination protein N; COG family, ATPases involved in DNA repair
BL1051Tyrosine-tRNA ligase; TyrRS; TyrS; COG family, tyrosyl-tRNA synthetase; PFAM_ID, tRNA-synt_1b; PFAM_ID, S4
BL1066Phenylalanine-tRNA ligase beta chain; PheRS; PheT; COG family, emap domain
BL1067Catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesiusm
BL1099One of the primary rRNA-binding proteins; 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
BL1100Important for translational accuracy; 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
BL1108PurL
BL1121Glutamine phosphoribosylpyrophosphate amidotransferase; PurF; COG family, glutamine phosphoribosylpyrophosphate amidotransferase; PFAM_ID, GATase_2; PFAM_ID, Pribosyltran
BL1122Catalyzes formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1- (5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
BL1123GarS; glycinamide ribonucleotide synthetase; phosphoribosylglycinamide synthetase; PurD; COG family, phosphoribosylamine-glycine ligase; PFAM_ID, GARS_N; PFAM_ID, GARS_B; PFAM_ID, GARS; PFAM_ID, GARS_C
BL1130Air carboxylase; AirC; PurE; COG family, phosphoribosylcarboxyaminoimidazole (ncair) mutase; PFAM_ID, AIRC
BL1180Binds to ssrA RNA and is required for its successful binding to ribosomes
BL1182FtsX; COG family, cell division protein; PFAM_ID, DUF214
BL1187MrsA; COG family, phosphomannomutase; PFAM_ID, PGM_PMM_I; PFAM_ID, PGM_PMM_II; PFAM_ID, PGM_PMM_III; PFAM_ID, PGM_PMM
BL1192COG family, predicted hydrolase of the metallo-beta-lactamase superfamily; PFAM_ID, lactamase_B; PFAM_ID, UPF0036
BL1204DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
BL1275HK; ThrB; COG family, homoserine kinase; PFAM_ID, GHMP_kinases
BL1282RplU; COG family, ribosomal protein L21; PFAM_ID, Ribosomal_L21p
BL1283Function of this ribosomal subunit is unknown
BL1284Obg; COG family, predicted GTPase; PFAM_ID, GTP1_OBG
BL1288NusG; COG family, transcription antiterminator; PFAM_ID, NusG
BL1312COG family, predicted transcriptional regulator; consists of a Zn-ribbon and ATP-cone domains; PFAM_ID, DUF193
BL1316COG family, predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis; PFAM_ID, Methyltransf_5
BL1320Catalyzes binding of UDP-N-acetylmuramoyl(pentapeptide) to bactoprenol to produce lipid I in peptidoglycan synthesis
BL1321UDP-N-acetylmuramoyl-l-alanyl-d-glutamate synthetase; d-glutamic acid-adding enzyme; MurD; COG family, UDP-N-acetylmuramoylalanine-d-glutamate ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase_C
BL1323UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane associated; last step of peptidoglycan synthesis
BL1324UDP-N-acetylmuramoyl-l-alanine synthetase; MurC; COG family, UDP-N-acetylmuramate-alanine ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase; PFAM_ID, Mur_ligase_C
BL1366InfC; COG family, translation initiation factor If3; PFAM_ID, IF3
BL1366aRpmI; COG family, ribosomal protein L35; PFAM_ID, Ribosomal_L35p
BL1367Protein binds directly to 23S rRNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit
BL1415Catalyzes hydrolysis of ATP in the presence of single-stranded DNA, ATP-dependent uptake of single-stranded DNA by duplex DNA, and ATP-dependent hybridization of homologous single-stranded DNAs
BL1438dUTPase; dUTP pyrophosphatase; DutP; COG family, dUTPase; PFAM_ID, dUTPase
BL1450Leucine-tRNA ligase; LeuRS; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA
BL1503Essential for binding of S1 to the small ribosomal subunit
BL1504EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP, resulting in regeneration of the active form of EF-Tu
BL1505UK; UMP kinase; UMP kinase; PyrH; COG family, uridylate kinase; PFAM_ID, aakinase
BL1506Ribosome-releasing factor; Frr; COG family, ribosome-recycling factor; PFAM_ID, RRF
BL1507CDP-diglyceride synthetase; CDP-diglyceride pyrophosphorylase; CDP-diacylglycerol synthase; CdsA; COG family, CDP-diglyceride synthetase; PFAM_ID, Cytidylyltrans
BL1545aRpsO; COG family, ribosomal protein S15p/S13e; PFAM_ID, Ribosomal_S15
BL1546Polynucleotide phosphorylase; Pnpase; COG family, polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase); PFAM_ID, RNase_PH; PFAM_ID, RNase_PH; PFAM_ID, KH-domain; PFAM_ID, S1
BL1549Binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
BL1550RplL; COG family, ribosomal protein L7/L12; PFAM_ID, Ribosomal_L12
BL1558GroES; COG family, cochaperonin GroES (Hsp10); PFAM_ID, cpn10
BL1571L13 is associated with the antitermination complex
BL1572RpsI; COG family, ribosomal protein S9; PFAM_ID, Ribosomal_S9
BL1577Involved in the binding of tRNA to the ribosomes
BL1578RplC; COG family, ribosomal protein L3; PFAM_ID, Ribosomal_L3
BL1579Subunit important during the early stages of 50S assembly, initially binding near the 5′ end of the 23S rRNA
BL1580Binds signal recognition particle and trigger factor at the peptide exit area on the 50S ribosome
BL1581One of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding, and for peptide bond formation
BL1582RpsS; COG family, ribosomal protein S19; PFAM_ID, Ribosomal_S19
BL1583RplV; COG family, ribosomal protein L22; PFAM_ID, Ribosomal_L22
BL1584Forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation
BL1586Located in the peptidyl transferase center and may be involved in peptidyl transferase activity
BL1588RpmC; COG family, ribosomal protein L29; PFAM_ID, Ribosomal_L29
BL1589RpsQ; COG family, ribosomal protein S17; PFAM_ID, Ribosomal_S17
BL1590RplN; COG family, ribosomal protein L14; PFAM_ID, Ribosomal_L14
BL1591RplX; COG family, ribosomal protein L24; PFAM_ID, Ribosomal_L24
BL1592Mediates attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
BL1594Binds directly to 16S rRNA central domain, where it helps coordinate assembly of the platform of the 30S subunit
BL1595RplF; COG family, ribosomal protein L6; PFAM_ID, Ribosomal_L6
BL1596RplR; COG family, ribosomal protein L18; PFAM_ID, Ribosomal_L18p
BL1597Located at the back of the 30S subunit body, where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy
BL1599Associates with 23S rRNA and is involved in 50S ribosome assembly
BL1600With SecE and SecG forms a protein conduction channel in the inner membrane
BL1604Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA
BL1604.1Located 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
BL1607RplQ; COG family, ribosomal protein L17; PFAM_ID, Ribosomal_L17
BL1615Binds to RNA polymerase and RNA; stimulates rho-independent termination by promoting hairpin formation; also interacts with N protein and prevents hairpin formation, thereby preventing termination
BL1616Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis; also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
BL1618tRNA pseudouridine 55 synthase; Psi55 synthase; pseudouridylate synthase; uracil hydrolyase; TruB; COG family, pseudouridine synthase; PFAM_ID, TruB_N
BL1619Fad pyrophosphorylase; Fad synthetase; RibF; COG family, FAD synthase; PFAM_ID, FAD_Synth
BL1777Catalyzes formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile)
BL0642RpmH; COG family, ribosomal protein L34; PFAM_ID, Ribosomal_L34
  • a The ORF designations refer to those of B. longum biotype longum NCC2705 (384).