A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
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
Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons
K03625
-
-
0.000000000000000000000000006942
116.0
MMD1_k127_103039_5
ASCH
-
-
-
0.00000000000000000006642
93.0
MMD1_k127_103039_6
Belongs to the bacterial ribosomal protein bL32 family
K02911
GO:0003674,GO:0003735,GO:0005198
-
0.00001965
48.0
MMD1_k127_1219372_0
DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
ATP binding to DnaK triggers the release of the substrate protein, thus completing the reaction cycle. Several rounds of ATP-dependent interactions between DnaJ, DnaK and GrpE are required for fully efficient folding. Also involved, together with DnaK and GrpE, in the DNA replication of plasmids through activation of initiation proteins
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision
Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS
Master enzyme that delivers sulfur to a number of partners involved in Fe-S cluster assembly, tRNA modification or cofactor biosynthesis. Catalyzes the removal of elemental sulfur atoms from cysteine to produce alanine. Functions as a sulfur delivery protein for Fe-S cluster synthesis onto IscU, an Fe-S scaffold assembly protein, as well as other S acceptor proteins
Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase
Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate
K02233
-
2.7.8.26
0.000000000000000000000000000000000000007205
154.0
MMD1_k127_1410972_4
BFD domain protein 2Fe-2S -binding domain protein
K04488
-
-
0.00000000000000000000000000000000000009164
147.0
MMD1_k127_1410972_5
Transcriptional regulator
-
-
-
0.0000000000000000000518
94.0
MMD1_k127_1410972_6
electron transfer activity
K05337
-
-
0.000000000000005759
76.0
MMD1_k127_1410972_7
Probably plays a role in a hydrogenase nickel cofactor insertion step
K04651
-
-
0.00007283
48.0
MMD1_k127_1414253_0
histidyl-tRNA aminoacylation
K01892
-
6.1.1.21
0.000000000000000000000000000000000002299
143.0
MMD1_k127_1414253_1
Domain of unknown function (DUF4215)
-
-
-
0.000000000000000000000000000000000002853
162.0
MMD1_k127_1414253_2
carbon-nitrogen ligase activity, with glutamine as amido-N-donor
K09117
-
-
0.00000000000000000001592
96.0
MMD1_k127_1414253_3
Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA
K01489,K07042
-
3.5.4.5
0.000000000000002885
81.0
MMD1_k127_1414253_4
chlorophyll binding
-
-
-
0.00000000000002267
82.0
MMD1_k127_1414253_5
Protein of unknown function (DUF3494)
-
-
-
0.00000000003285
76.0
MMD1_k127_1414253_6
C-terminal domain of CHU protein family
-
-
-
0.000064
54.0
MMD1_k127_1414253_7
Belongs to the 1-acyl-sn-glycerol-3-phosphate acyltransferase family
K00655
-
2.3.1.51
0.0002169
53.0
MMD1_k127_1453212_0
Belongs to the class-I aminoacyl-tRNA synthetase family
K01869
-
6.1.1.4
5.382e-304
955.0
MMD1_k127_1453212_1
Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family
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
Negative regulator of class I heat shock genes (grpE- dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
K03705
-
-
0.0000000000000000000001358
106.0
MMD1_k127_1564458_2
Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ
K03687
-
-
0.000000000000000003286
90.0
MMD1_k127_1564458_3
Methyltransferase domain
-
-
-
0.0000000000007074
76.0
MMD1_k127_15772_0
magnesium-translocating P-type ATPase
K01531
-
3.6.3.2
1.462e-285
900.0
MMD1_k127_15772_1
Transglycosylase
-
-
-
5.102e-230
745.0
MMD1_k127_15772_10
L,D-transpeptidase catalytic domain
-
-
-
0.0000000000000000000000000000000000000000001666
168.0
MMD1_k127_15772_11
Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
K00764
-
2.4.2.14
0.000000000000000000000000000000003837
142.0
MMD1_k127_15772_13
PFAM RNP-1 like RNA-binding protein
-
-
-
0.00000000000000000000000000427
113.0
MMD1_k127_15772_14
Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
K02005
-
-
0.00000000000000000001214
106.0
MMD1_k127_15772_15
-
-
-
-
0.00000000000000000002416
93.0
MMD1_k127_15772_16
COG NOG14552 non supervised orthologous group
-
-
-
0.000000000000000001951
87.0
MMD1_k127_15772_18
-
-
-
-
0.00000000000000006248
82.0
MMD1_k127_15772_19
Belongs to the bacterial ribosomal protein bS16 family
K02959
-
-
0.000000000000002389
79.0
MMD1_k127_15772_2
ATPase, P-type (transporting), HAD superfamily, subfamily IC
Hydrolyzes the pyrophosphate bond of UDP-2,3- diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Non-canonical ABC transporter that contains transmembrane domains (TMD), which form a pore in the membrane, and an ATP-binding domain (NBD), which is responsible for energy generation. Confers resistance against macrolides
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
K02838
-
-
0.0000000000000000000000000000000000000007125
155.0
MMD1_k127_162181_6
Glycosyl transferase family 2
-
-
-
0.000000000000000000000000000000008603
138.0
MMD1_k127_162181_7
TIGRFAM DNA polymerase III, delta prime subunit
K02341
-
2.7.7.7
0.00000000000000000000000002675
119.0
MMD1_k127_162181_8
cellulose binding
-
-
-
0.000000000000000000001921
107.0
MMD1_k127_162181_9
Pfam:DUF955
-
-
-
0.00000000000000000155
92.0
MMD1_k127_1667228_0
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth
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
The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
ADP-L-glycero-beta-D-manno-heptose biosynthetic process
K00980
-
2.7.7.39
0.0000000000000000000000000000000000000005919
153.0
MMD1_k127_233022_5
Peptidyl-prolyl cis-trans
K01802,K03772
-
5.2.1.8
0.0000000000000000000000000000000001087
139.0
MMD1_k127_233022_7
-
K01278,K03561,K12287
-
3.4.14.5
0.0000000000002163
83.0
MMD1_k127_233022_8
helicase activity
K06915,K19172
-
-
0.0000009178
61.0
MMD1_k127_233022_9
23S rRNA-intervening sequence protein
-
-
-
0.0002925
52.0
MMD1_k127_2349918_0
Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA)
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
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
K02355
-
-
1.961e-315
979.0
MMD1_k127_2481923_1
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
K02358
-
-
9.915e-199
625.0
MMD1_k127_2481923_2
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
Belongs to the bacterial ribosomal protein bL28 family
K02902
GO:0003674,GO:0003735,GO:0005198
-
0.0005303
44.0
MMD1_k127_2482236_0
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)
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)
Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NADPH and FADH(2) as the reductant
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
Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A)
Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
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
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
K01462
-
3.5.1.88
0.00000000000000000000000000004541
121.0
MMD1_k127_2547067_2
Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA
K04066
-
-
0.00000009213
59.0
MMD1_k127_2572898_0
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
K03043
-
2.7.7.6
0.0
1305.0
MMD1_k127_2572898_1
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate- limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth
Catalyzes the base-exchange of a guanine (G) residue with the queuine precursor 7-aminomethyl-7-deazaguanine (PreQ1) at position 34 (anticodon wobble position) in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). Catalysis occurs through a double-displacement mechanism. The nucleophile active site attacks the C1' of nucleotide 34 to detach the guanine base from the RNA, forming a covalent enzyme-RNA intermediate. The proton acceptor active site deprotonates the incoming PreQ1, allowing a nucleophilic attack on the C1' of the ribose to form the product. After dissociation, two additional enzymatic reactions on the tRNA convert PreQ1 to queuine (Q), resulting in the hypermodified nucleoside queuosine (7-(((4,5-cis-dihydroxy-2- cyclopenten-1-yl)amino)methyl)-7-deazaguanosine)
DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria
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
K03536
-
3.1.26.5
0.0000000000004392
73.0
MMD1_k127_274286_6
Belongs to the bacterial ribosomal protein bL34 family
Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP- GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5- monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
K00762
-
2.4.2.10
0.0000000000000000000000000000000000000000007456
166.0
MMD1_k127_3291116_5
COG NOG14600 non supervised orthologous group
-
-
-
0.0000000000000000000000311
101.0
MMD1_k127_3291116_6
LAGLIDADG endonuclease
-
-
-
0.000000000000000003969
90.0
MMD1_k127_3291116_7
COG NOG15344 non supervised orthologous group
-
-
-
0.000000000000000203
82.0
MMD1_k127_3291116_8
COG NOG15344 non supervised orthologous group
-
-
-
0.0000000000000859
74.0
MMD1_k127_3291116_9
extracellular nuclease
K07004
-
-
0.0000000000001211
85.0
MMD1_k127_3396358_0
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)
Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates
Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins
Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions
Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme
Belongs to the small heat shock protein (HSP20) family
-
-
-
0.0000000000000000002709
92.0
MMD1_k127_3685433_0
Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
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
K02357
-
-
0.000000000000000000000000000000008676
129.0
MMD1_k127_3755884_4
Protein of unknown function (DUF541)
K09807
-
-
0.00000000000000000000000000000004303
135.0
MMD1_k127_3808383_0
Membrane protein insertase, YidC Oxa1 family
K03217
-
-
0.0000000000000000000000000000008164
131.0
MMD1_k127_3808383_1
nucleotidyltransferase activity
-
-
-
0.00000000000000000000000004686
119.0
MMD1_k127_3816030_0
Fibronectin type 3 domain
-
-
-
0.0000000000000005031
92.0
MMD1_k127_3818452_0
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)
K01870
-
6.1.1.5
5.347e-273
870.0
MMD1_k127_3818452_1
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
K01873
-
6.1.1.9
1.519e-209
682.0
MMD1_k127_3818452_10
pfkB family carbohydrate kinase
-
-
-
0.0000000000000000000000000000000005042
143.0
MMD1_k127_3818452_11
Methicillin resistance protein
-
-
-
0.000000000000000000000000000000002565
139.0
MMD1_k127_3818452_12
The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB
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)
The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by UvrB, the UvrA molecules dissociate
K03701
-
-
4.48e-320
1005.0
MMD1_k127_3879269_1
DNA methylase
K00590
-
2.1.1.113
1.74e-223
704.0
MMD1_k127_3879269_10
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
K02884
-
-
0.000000000000000000000001032
107.0
MMD1_k127_3879269_11
L-ascorbic acid binding
-
-
-
0.0000000001177
70.0
MMD1_k127_3879269_12
P-P-bond-hydrolysis-driven protein transmembrane transporter activity
An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay
DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA
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)
Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue
K02654
-
3.4.23.43
0.000000000000000000000000000000000000000002675
166.0
MMD1_k127_3886837_4
Transposase IS200 like
-
-
-
0.0000000000000000000000471
108.0
MMD1_k127_3886837_5
Type IV pilus assembly protein PilM;
K02662
-
-
0.0000000000001062
82.0
MMD1_k127_3886837_6
Prokaryotic N-terminal methylation motif
K02650
-
-
0.0000000000241
70.0
MMD1_k127_3886837_7
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)
K02435
-
6.3.5.6,6.3.5.7
0.000006764
51.0
MMD1_k127_4046788_0
COGs COG1748 Saccharopine dehydrogenase and related protein
K19064
-
1.4.1.18
0.00003995
50.0
MMD1_k127_4134398_0
Protein of unknown function (DUF2723)
-
-
-
0.000000000000000000000000000000001854
148.0
MMD1_k127_4134398_1
Signal peptidase (SPase) II
K03101
-
3.4.23.36
0.000001322
53.0
MMD1_k127_414095_0
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
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
K02948
-
-
0.000000000000000000000000000000000000000007694
157.0
MMD1_k127_414095_12
Polysaccharide deacetylase
-
-
-
0.00000000000000000000000000000000000000001027
167.0
MMD1_k127_414095_13
Diacylglycerol kinase catalytic domain
-
-
-
0.0000000000000000000000000000000000005701
153.0
MMD1_k127_414095_14
Ribosomal protein S9/S16
K02996
-
-
0.0000000000000000000000000000002338
130.0
MMD1_k127_414095_15
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
K02952
-
-
0.0000000000000000000000000000002688
125.0
MMD1_k127_414095_16
Ribosomal protein L17
K02879
-
-
0.0000000000000000000000000000005321
125.0
MMD1_k127_414095_17
PFAM Glycosyl transferase family 2
-
-
-
0.000000000000000000000000000001967
129.0
MMD1_k127_414095_18
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
K02518
-
-
0.000000000000000000000001032
105.0
MMD1_k127_414095_19
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
Membrane protein involved in the export of O-antigen and teichoic acid
-
-
-
0.000000000000008111
87.0
MMD1_k127_414095_21
Belongs to the bacterial ribosomal protein bL36 family
K02919
-
-
0.00000000002966
64.0
MMD1_k127_414095_23
prohibitin homologues
-
-
-
0.00000005499
62.0
MMD1_k127_414095_24
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth
K03086
-
-
0.0000004232
51.0
MMD1_k127_414095_25
Membrane protein insertase, YidC Oxa1 family
K03217
-
-
0.0000008759
59.0
MMD1_k127_414095_26
-
-
-
-
0.00003358
55.0
MMD1_k127_414095_3
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
K05808
-
-
0.0004438
47.0
MMD1_k127_4196572_0
Glycosyltransferase Family 4
-
-
-
0.0000000000000000000000000000000000000001713
163.0
MMD1_k127_4196572_1
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
K02520
-
-
0.00000000000000000000000000000000000006462
148.0
MMD1_k127_4196572_2
the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide , a short internal open reading frame. During trans-translation Ala- aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA
K03664
-
-
0.0000000000000000000000000000000006293
136.0
MMD1_k127_4196572_3
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
K02887
-
-
0.00000000000000000000005592
102.0
MMD1_k127_4196572_4
Belongs to the bacterial ribosomal protein bL35 family
Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
-
-
-
0.0000000000000000000000000000000013
132.0
MMD1_k127_4422600_0
Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins
Belongs to the small heat shock protein (HSP20) family
K13993
-
-
0.0000000000000000004295
93.0
MMD1_k127_4422600_6
NUDIX domain
-
-
-
0.000000001273
65.0
MMD1_k127_4422600_7
Saccharopine dehydrogenase C-terminal domain
K00290
-
1.5.1.7
0.00000002411
63.0
MMD1_k127_4446786_0
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
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
K00604,K11175
-
2.1.2.2,2.1.2.9
0.00000000000000000000000000000006441
135.0
MMD1_k127_4582350_7
4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family
Belongs to the bacterial ribosomal protein bL33 family
K02913
-
-
0.000000000001357
68.0
MMD1_k127_4720767_6
Tetratricopeptide repeat
-
-
-
0.0000003423
61.0
MMD1_k127_4720767_8
Involved in the tonB-independent uptake of proteins
-
-
-
0.00003361
54.0
MMD1_k127_4886018_0
Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and or for immediate growth after restoration of oxygen
6-O-methylguanine DNA methyltransferase, DNA binding domain
K00567,K10778
-
2.1.1.63
0.00000000000000000009783
91.0
MMD1_k127_49902_6
PFAM Glycosyl transferase, group 1
-
-
-
0.00004461
47.0
MMD1_k127_5019522_0
DNA polymerase III alpha subunit
K02337
-
2.7.7.7
3.694e-313
996.0
MMD1_k127_5019522_1
ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance
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)
Integral membrane protein CcmA involved in cell shape determination
-
-
-
0.0000000000000001152
85.0
MMD1_k127_5230417_3
lipid kinase, YegS Rv2252 BmrU family
-
-
-
0.00000002863
65.0
MMD1_k127_5230417_4
LAGLIDADG-like domain
-
-
-
0.0000001804
60.0
MMD1_k127_5264331_0
Proton pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for proton movement across the membrane. Generates a proton motive force
K15987
-
3.6.1.1
2.21e-264
829.0
MMD1_k127_5264331_1
In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase
Part of a stress-induced multi-chaperone system, it is involved in the recovery of the cell from heat-induced damage, in cooperation with DnaK, DnaJ and GrpE
K03695
-
-
2.934e-320
1002.0
MMD1_k127_5363664_1
Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits
K02112
-
3.6.3.14
1.459e-221
694.0
MMD1_k127_5363664_10
Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex
Catalyzes the conversion of GlcNAc-PP-undecaprenol into ManNAc-GlcNAc-PP-undecaprenol, the first committed lipid intermediate in the de novo synthesis of teichoic acid
Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
-
-
-
0.00000000000000000000000000000000000000000002011
171.0
MMD1_k127_5363664_19
Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus. GreA releases sequences of 2 to 3 nucleotides
K03624
-
-
0.0000000000000000000000000000000000005436
144.0
MMD1_k127_5363664_2
Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
PFAM ATP corrinoid adenosyltransferase BtuR CobO CobP
K19221
-
2.5.1.17
0.0000000000000000000000001232
113.0
MMD1_k127_5363664_24
Acid phosphatase homologues
K19302
-
3.6.1.27
0.0000000000000000000000002984
111.0
MMD1_k127_5363664_25
Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA
K04066
-
-
0.00000000000000000000002076
112.0
MMD1_k127_5363664_26
Produces ATP from ADP in the presence of a proton gradient across the membrane
Involved in formation and maintenance of cell shape
K03570
-
-
0.0000000000000004045
88.0
MMD1_k127_5363664_28
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
K03805,K12228
-
-
0.00000000000145
78.0
MMD1_k127_5363664_3
Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and or for immediate growth after restoration of oxygen
Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
K02109
-
-
0.00000000000882
72.0
MMD1_k127_5363664_31
hydrolase, family 25
-
-
-
0.00000000001374
77.0
MMD1_k127_5363664_32
alpha beta
-
-
-
0.0000000001453
70.0
MMD1_k127_5363664_33
Thioredoxin
-
-
-
0.0000000002136
71.0
MMD1_k127_5363664_34
reversible hydration of carbon dioxide
K01673
-
4.2.1.1
0.000000001376
64.0
MMD1_k127_5363664_35
Catalyzes the conversion of dihydroorotate to orotate
K17828
-
1.3.1.14
0.000000222
62.0
MMD1_k127_5363664_36
F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
K02113
-
-
0.0000003009
57.0
MMD1_k127_5363664_39
Cell division protein FtsQ
K03589
-
-
0.0004951
51.0
MMD1_k127_5363664_4
Belongs to the class-II aminoacyl-tRNA synthetase family
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)
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)
Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr)
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)
Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves
K06024
-
-
0.000000000000000000000000000000465
128.0
MMD1_k127_5497079_3
Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves
-
-
-
0.00000000000000000000000000004781
125.0
MMD1_k127_5497079_4
Involved in DNA repair and RecF pathway recombination
Required for accurate and efficient protein synthesis under certain stress conditions. May act as a fidelity factor of the translation reaction, by catalyzing a one-codon backward translocation of tRNAs on improperly translocated ribosomes. Back- translocation proceeds from a post-translocation (POST) complex to a pre-translocation (PRE) complex, thus giving elongation factor G a second chance to translocate the tRNAs correctly. Binds to ribosomes in a GTP-dependent manner
Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
This protein binds to 23S rRNA in the presence of protein L20
K02888
-
-
0.0000000000000000000000002728
108.0
MMD1_k127_737256_6
Metal dependent phosphohydrolases with conserved 'HD' motif.
K06885
-
-
0.00000000000000000008403
103.0
MMD1_k127_737256_7
amino acid
K03834
-
-
0.0000000609
64.0
MMD1_k127_737256_8
Uncharacterized ACR, COG1430
K09005
-
-
0.0000004287
53.0
MMD1_k127_745483_0
A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
K02867
-
-
0.00000000000000004671
82.0
MMD1_k127_745483_11
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
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
The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently
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
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
K02994
-
-
0.000000000000000000000000000000000000339
143.0
MMD1_k127_771411_12
Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
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
its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity)
One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
K02895
-
-
0.0000000000000000000000000965
109.0
MMD1_k127_771411_18
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
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
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism
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
Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins
Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity
Destroys radicals which are normally produced within the cells and which are toxic to biological systems
K04564
-
1.15.1.1
0.000000001835
58.0
MMD1_k127_96335_0
Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone
