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
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
Involved in the biosynthesis of lipopolysaccharides (LPSs). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate
K03270,K21749
-
2.7.7.43,2.7.7.92,3.1.3.45
0.000000000000000000000000000000000000299
146.0
MMD2_k127_1242378_2
Macrocin-O-methyltransferase (TylF)
-
-
-
0.00000000005891
63.0
MMD2_k127_1272078_0
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
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
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
K01872
-
6.1.1.7
0.0000000000000000000002633
97.0
MMD2_k127_1540369_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
K00525
-
1.17.4.1
7.499e-255
807.0
MMD2_k127_1540369_1
DEAD DEAH box helicase domain protein
K06877
-
-
0.000000000000000000000000000000000000188
147.0
MMD2_k127_1540369_2
PFAM ATP corrinoid adenosyltransferase BtuR CobO CobP
This protein specifically catalyzes the removal of signal peptides from prolipoproteins
K03101
-
3.4.23.36
0.00000001478
63.0
MMD2_k127_1670827_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
PemK-like, MazF-like toxin of type II toxin-antitoxin system
K07171
-
-
0.00000000000000000002181
95.0
MMD2_k127_1697876_4
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
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
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)
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
0.00000000002549
68.0
MMD2_k127_1989020_0
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
Nucleotidyl transferase AbiEii toxin, Type IV TA system
-
-
-
0.00000000000000000000000000000001987
134.0
MMD2_k127_2035449_1
DNA polymerase beta domain protein region
K07075
-
-
0.0000000000000000000000002271
108.0
MMD2_k127_2035449_2
Concanavalin A-like lectin/glucanases superfamily
-
-
-
0.0000000000000000000000004961
114.0
MMD2_k127_2036870_0
-O-antigen
-
-
-
0.00000000000000000000005392
115.0
MMD2_k127_2036870_1
-O-antigen
-
-
-
0.0000000000000000003759
103.0
MMD2_k127_2036870_2
-O-antigen
-
-
-
0.000000000000000001139
100.0
MMD2_k127_2036870_3
domain, Protein
-
-
-
0.00001899
56.0
MMD2_k127_205019_0
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 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 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)
K01866
-
6.1.1.1
0.000000000000000000002624
96.0
MMD2_k127_2073514_0
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
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)
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
6.705e-263
825.0
MMD2_k127_233026_1
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
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
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
K02109
-
-
0.0000000000000000002145
94.0
MMD2_k127_2694865_6
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
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
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
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
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
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
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
Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism
K03111
-
-
0.0000000000000000000000000000000000007177
144.0
MMD2_k127_2876160_3
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
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
9.07e-271
865.0
MMD2_k127_2888332_1
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
K03550
-
3.6.4.12
0.00000000000000000000000000009062
123.0
MMD2_k127_2906099_0
Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions
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
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
K02343
-
2.7.7.7
0.00000000000000000000008991
99.0
MMD2_k127_3291268_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 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)
K01881
-
6.1.1.15
0.0000000000000000000000000000000000002932
148.0
MMD2_k127_3311118_4
Protein of unknown function (DUF1653)
-
-
-
0.000000000000000006038
85.0
MMD2_k127_3311118_5
Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions
K03530
-
-
0.000000000000009557
81.0
MMD2_k127_3311118_6
GNAT family
-
-
-
0.000000000002722
73.0
MMD2_k127_3331984_0
This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis
-
-
-
0.00000000000000000000002217
104.0
MMD2_k127_3331984_1
Protein of unknown function (DUF4012)
-
-
-
0.00000000000000001553
95.0
MMD2_k127_3331984_2
Acetyltransferase (GNAT) domain
-
-
-
0.000000000003484
67.0
MMD2_k127_3331984_3
Conserved repeat domain
-
-
-
0.00000000004486
76.0
MMD2_k127_340943_0
Peptidoglycan polymerase that is essential for cell wall elongation
K05837
-
-
0.00000000000000000000000000000000000002034
153.0
MMD2_k127_3460370_0
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
COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain
K07657,K07662
-
-
0.00000000000000006554
87.0
MMD2_k127_3492302_8
Belongs to the ompA family
K20276
-
-
0.000003719
60.0
MMD2_k127_3492302_9
Domain of unknown function (DUF333)
K14475
-
-
0.00002441
53.0
MMD2_k127_3519711_0
Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate
K11175
-
2.1.2.2
0.0000000000000000000000000000001893
132.0
MMD2_k127_3519711_1
Helix-turn-helix XRE-family like proteins
K07729
-
-
0.0000000000000000000001775
97.0
MMD2_k127_3519711_2
mRNA binding
K07339
-
-
0.000000000001428
70.0
MMD2_k127_3519711_3
Mazg nucleotide pyrophosphohydrolase
-
-
-
0.00000001412
60.0
MMD2_k127_3519711_5
PFAM Uncharacterised protein family UPF0150
-
-
-
0.00001262
49.0
MMD2_k127_3519711_6
Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
K01775
-
5.1.1.1
0.0003345
45.0
MMD2_k127_3519937_0
Phenylacetic acid degradation operon negative regulatory protein PaaX
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
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
-
-
0.000000000000000000000000000000000003046
143.0
MMD2_k127_3623639_1
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
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
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
K05946
-
2.4.1.187
0.00000000006455
65.0
MMD2_k127_3690306_0
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
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
Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
K01874
-
6.1.1.10
0.000000000000000000000000002688
115.0
MMD2_k127_3692663_2
Required for the insertion and or proper folding and or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins
K03217
-
-
0.00000001803
64.0
MMD2_k127_3692663_3
SPFH Band 7 PHB domain protein
-
-
-
0.000001101
58.0
MMD2_k127_3720425_0
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 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)
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
-
-
0.0000000002575
71.0
MMD2_k127_3797695_11
Involved in formation and maintenance of cell shape
Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA RNA and avoiding chromosomal lesions
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
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein
K00997
-
2.7.8.7
0.000000000000000004259
89.0
MMD2_k127_3884439_2
-
-
-
-
0.00000000000000001615
91.0
MMD2_k127_388752_0
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
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)
COG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
K00059
-
1.1.1.100
0.00000000000000000000000001531
119.0
MMD2_k127_4098561_3
Belongs to the peptidase S41A family
K03797
-
3.4.21.102
0.0000000000000000000000000647
119.0
MMD2_k127_4098561_4
Belongs to the peptidase S11 family
K07262
-
-
0.000000000005352
77.0
MMD2_k127_4098561_5
-
-
-
-
0.00000001873
62.0
MMD2_k127_411599_0
Belongs to the arginase family
K01480
-
3.5.3.11
0.000000000000000000000000000000000001102
151.0
MMD2_k127_411599_1
Negative regulator of class I heat shock genes (grpE- dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
K03705
-
-
0.00000000000000000000000352
110.0
MMD2_k127_411599_2
Deoxyhypusine synthase
K00809
-
2.5.1.46
0.00000000000000000001453
94.0
MMD2_k127_411599_3
PFAM Heat shock protein Hsp20
K13993
-
-
0.0000000000000000004816
92.0
MMD2_k127_411599_4
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
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
K10563
-
3.2.2.23,4.2.99.18
0.0000000000000000000000000000001487
130.0
MMD2_k127_4148437_0
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
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
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP
Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
K03086,K03087
-
-
0.000000000000001667
89.0
MMD2_k127_4272951_0
Protein of unknown function (DUF541)
K09807
-
-
0.000000000000000000000000000000002492
139.0
MMD2_k127_4272951_1
Belongs to the phosphoglycerate kinase family
K00927
-
2.7.2.3
0.000000000000000000000003256
107.0
MMD2_k127_4287049_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
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
-
-
0.000000000000000000000000000000000004029
141.0
MMD2_k127_4287049_4
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
-
-
0.0000000000000000000000008377
106.0
MMD2_k127_4287049_5
Belongs to the bacterial ribosomal protein bL36 family
K02919
-
-
0.00000000006224
63.0
MMD2_k127_4287049_6
-
-
-
-
0.00000001459
62.0
MMD2_k127_4298915_0
chaperone-mediated protein folding
-
-
-
0.000000000000000000000000000006894
136.0
MMD2_k127_4298915_1
4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family
-
-
-
0.000002294
56.0
MMD2_k127_4336478_0
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)
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
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
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
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
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
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
-
-
4.596e-311
976.0
MMD2_k127_5042584_1
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
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
-
-
0.0000000000000000000000000000000000000002474
156.0
MMD2_k127_5070192_2
DNA polymerase III, delta subunit
K02341
-
2.7.7.7
0.00000000000000000000000000000227
132.0
MMD2_k127_5070192_3
K COG5665 CCR4-NOT transcriptional regulation complex, NOT5 subunit
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)
ADP-L-glycero-beta-D-manno-heptose biosynthetic process
K00980
-
2.7.7.39
0.000000000000000000000000000000000001341
152.0
MMD2_k127_511648_2
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
Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine
-
-
-
0.00000000000000000000000000000000000000000001783
167.0
MMD2_k127_5209294_1
Acid phosphatase homologues
K19302
-
3.6.1.27
0.0000000000000000000001012
104.0
MMD2_k127_5209294_2
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
K10563
-
3.2.2.23,4.2.99.18
0.000000000000000000000116
100.0
MMD2_k127_5235933_0
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 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
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
Part of the ABC transporter FtsEX involved in cellular division
K09811
-
-
0.000000000000000000000000009288
121.0
MMD2_k127_524075_4
Belongs to the sigma-70 factor family. ECF subfamily
K03088
-
-
0.00000000005596
66.0
MMD2_k127_524075_5
PFAM Septum formation initiator
K05589
-
-
0.00002225
51.0
MMD2_k127_524075_6
PFAM membrane-flanked domain
-
-
-
0.0008296
49.0
MMD2_k127_5301257_0
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
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
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
Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair
Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
K00969
-
2.7.7.18
0.00006543
49.0
MMD2_k127_5372075_0
-
-
-
-
0.00000000000000000000000001505
118.0
MMD2_k127_5372075_1
by glimmer
-
-
-
0.000000009122
60.0
MMD2_k127_5372075_2
domain protein
-
-
-
0.00000004898
61.0
MMD2_k127_5372075_3
PFAM C-5 cytosine-specific DNA methylase
K00558
-
2.1.1.37
0.00001533
55.0
MMD2_k127_5378359_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
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
-
-
0.0000000000000000000000004908
107.0
MMD2_k127_5412934_0
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction
Catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen. Regulates intracellular CTP levels through interactions with the four ribonucleotide triphosphates
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
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
-
-
0.0000000000000000000000000001873
121.0
MMD2_k127_5681200_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
K05896
-
-
0.000000000000000000000000002008
121.0
MMD2_k127_5681200_4
Aminoacyl-tRNA editing domain
K19055
-
-
0.000000000001044
76.0
MMD2_k127_5731660_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 protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase
Copper binding proteins, plastocyanin/azurin family
-
-
-
0.0000000002944
65.0
MMD2_k127_5845230_4
PFAM Rubredoxin-type Fe(Cys)4 protein
-
-
-
0.000000004797
58.0
MMD2_k127_5889645_0
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)
Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue
K02654
-
3.4.23.43
0.000000000000000000000000000000000000001067
158.0
MMD2_k127_5913447_1
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
K01972
-
6.5.1.2
0.0000000000000000000000009532
105.0
MMD2_k127_5913447_2
Type IV pilus assembly protein PilM;
K02662
-
-
0.0000000000000000001673
97.0
MMD2_k127_5913447_3
Prokaryotic N-terminal methylation motif
K02650
-
-
0.00000000007154
69.0
MMD2_k127_5930199_0
GtrA-like protein
-
-
-
0.000000000000000000003674
99.0
MMD2_k127_5930199_1
glycosyl transferase family 2
-
-
-
0.000000000000006193
77.0
MMD2_k127_5930199_2
4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family
-
-
-
0.00000000003419
72.0
MMD2_k127_6002656_0
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
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
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)
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
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
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 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
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
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
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
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
K00939
-
2.7.4.3
0.0000000000000000000000059
104.0
MMD2_k127_959907_3
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
