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 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)
Catalyzes the phosphorylation of (R)-mevalonate (MVA) to (R)-mevalonate 5-phosphate (MVAP). Functions in the mevalonate (MVA) pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoid compounds such as archaeal membrane lipids
Catalyzes the phosphorylation of (R)-mevalonate (MVA) to (R)-mevalonate 5-phosphate (MVAP). Functions in the mevalonate (MVA) pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoid compounds such as archaeal membrane lipids
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
The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis
Participates in transcription elongation, termination and antitermination
K02601
-
-
0.000000000000000000000000000000000004443
139.0
YHH1_k127_10668745_3
Belongs to the bacterial ribosomal protein bL33 family
K02913
-
-
0.00000000000003256
73.0
YHH1_k127_10668745_4
Essential subunit of the Sec protein translocation channel SecYEG. Clamps together the 2 halves of SecY. May contact the channel plug during translocation
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
K01928,K15792
-
6.3.2.10,6.3.2.13
0.0000000000000000000000001287
110.0
YHH1_k127_1095535_0
permease
-
-
-
0.000000000000000000000000000000000009102
150.0
YHH1_k127_1095535_1
PFAM PKD domain containing protein
-
-
-
0.00000000003672
77.0
YHH1_k127_1095535_2
Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide
K02020
-
-
0.000007481
56.0
YHH1_k127_1095535_3
-
-
-
-
0.0008175
45.0
YHH1_k127_1096839_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)
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
-
-
0.00000000000000000000000000000000000000002808
158.0
YHH1_k127_1096839_2
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
-
-
0.000000000000000000000000000003241
123.0
YHH1_k127_1096839_3
Belongs to the bacterial ribosomal protein bL35 family
K02916
-
-
0.000001483
52.0
YHH1_k127_10977529_0
RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication
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
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
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)
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
Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene
K03664
-
-
0.0000001271
55.0
YHH1_k127_1441461_0
domain, Protein
K01729,K03561,K09942,K12287,K20276
-
4.2.2.3
0.0000000000000000000000000000000000001117
162.0
YHH1_k127_1441461_1
P22 coat protein - gene protein 5
-
-
-
0.000000000000000001482
96.0
YHH1_k127_1475272_0
Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
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, this protein initially binds near the 5'-end of the 23S rRNA. 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
K02926
-
-
0.00000000000000000000000000000000000000000000342
172.0
YHH1_k127_1633992_3
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
K02892
-
-
0.0002845
49.0
YHH1_k127_1650203_0
TIGRFAM cell shape determining protein, MreB Mrl family
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
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
An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control
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
-
-
0.000000000000000000001821
99.0
YHH1_k127_2386051_0
Psort location CytoplasmicMembrane, score
-
-
-
0.000000000000101
84.0
YHH1_k127_2386051_1
Transmembrane protein 260
-
-
-
0.0000546
55.0
YHH1_k127_2583130_0
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)
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)
K01876
-
6.1.1.12
0.00000000000000000000000000000000000000000008449
163.0
YHH1_k127_2864040_0
LAGLIDADG endonuclease
-
-
-
0.00000000000000000000000000000004593
131.0
YHH1_k127_2864040_1
the current gene model (or a revised gene model) may contain a premature stop
-
-
-
0.0000000000000000005202
90.0
YHH1_k127_2864040_2
LAGLIDADG DNA endonuclease family
-
-
-
0.00000000211
66.0
YHH1_k127_2864040_3
-
-
-
-
0.00006198
49.0
YHH1_k127_2867318_0
Involved in peptidoglycan biosynthesis. Transports lipid-linked peptidoglycan precursors from the inner to the outer leaflet of the cytoplasmic membrane
Catalyzes the reversible conversion of 2- phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis
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 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
-
-
1.4e-282
885.0
YHH1_k127_3808394_2
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
K03043
-
2.7.7.6
2.519e-275
866.0
YHH1_k127_3808394_3
This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
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
K02992
-
-
0.0000000000000000000000000000000000000000003435
163.0
YHH1_k127_3851103_0
Catalyzes the decarboxylative condensation of pimeloyl- acyl-carrier protein and L-alanine to produce 8-amino-7- oxononanoate (AON), acyl-carrier protein , and carbon dioxide
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
Alpha/beta hydrolase of unknown function (DUF1100)
-
-
-
0.00000000000000002174
88.0
YHH1_k127_3851103_5
Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
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)
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
Metal dependent phosphohydrolases with conserved 'HD' motif.
K06951
-
-
0.00000000000000000000000000000000000000001651
160.0
YHH1_k127_3939906_4
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
K02428
-
3.6.1.66
0.00000000000000000000000000000002863
133.0
YHH1_k127_3939906_5
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
-
-
0.0000000000000000000000000000006229
126.0
YHH1_k127_3939906_6
Spermine/spermidine synthase domain
K00797
-
2.5.1.16
0.0000000000000005606
87.0
YHH1_k127_3953556_0
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate
Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family
K00384
-
1.8.1.9
0.0000001789
52.0
YHH1_k127_4080739_5
COG NOG38524 non supervised orthologous group
-
-
-
0.0000004698
52.0
YHH1_k127_4165512_0
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
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
-
-
0.00000000000000000000002607
101.0
YHH1_k127_4165512_3
Belongs to the universal ribosomal protein uS9 family
K02996
-
-
0.0000000000000000001766
91.0
YHH1_k127_4165512_4
Modulates RecA activity
K03565
-
-
0.0000000000000005143
84.0
YHH1_k127_43005_0
Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
K00943
-
2.7.4.9
0.00000000000000000000000004785
111.0
YHH1_k127_43005_3
Deoxynucleoside kinase
K15518
-
2.7.1.113
0.0000000000000000000000001359
114.0
YHH1_k127_43005_4
HAD-hyrolase-like
K07025,K08723
-
3.1.3.5
0.0000000002054
70.0
YHH1_k127_4329661_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
K03701
-
-
0.0
1111.0
YHH1_k127_4329661_1
damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage
PemK-like, MazF-like toxin of type II toxin-antitoxin system
K07171
-
-
0.000000000000000000000001988
103.0
YHH1_k127_4400817_4
Isoprenylcysteine carboxyl methyltransferase (ICMT) family
-
-
-
0.000000000002735
73.0
YHH1_k127_4400817_5
Toxic component of a toxin-antitoxin (TA) module
K07171
-
-
0.00000000001309
66.0
YHH1_k127_4400817_6
Reversible hydration of carbon dioxide
K01673
-
4.2.1.1
0.00000006323
55.0
YHH1_k127_4486264_0
Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
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
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
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
Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction
K00962
-
2.7.7.8
7.843e-207
666.0
YHH1_k127_4952928_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
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
K12574
-
-
0.00000000000000000000000000000000000001782
149.0
YHH1_k127_4952928_3
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
K02519
-
-
0.000000000000000000000000000000000002051
148.0
YHH1_k127_4952928_4
Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
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
K03703
-
-
0.000000000000000000000000000000009603
136.0
YHH1_k127_5050243_2
Bacterial extracellular solute-binding proteins, family 5 Middle
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
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
K03596
-
-
7.499e-197
631.0
YHH1_k127_5321273_10
Methionine biosynthesis protein MetW
-
-
-
0.000000000000000000000003101
110.0
YHH1_k127_5321273_11
ComEA protein
K02237
-
-
0.00000000000000000005197
99.0
YHH1_k127_5321273_2
PFAM natural resistance-associated macrophage protein
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)
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)
ABC-type transport system involved in Fe-S cluster assembly, ATPase component
K09013
-
-
0.000000000000000000000009048
102.0
YHH1_k127_574439_7
nitrite reductase [NAD(P)H] activity
K05710
-
-
0.000000000000001298
80.0
YHH1_k127_574439_8
4Fe-4S single cluster domain of Ferredoxin I
-
-
-
0.000000001675
63.0
YHH1_k127_5763736_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
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
Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site
K02954
-
-
0.00000000000001271
73.0
YHH1_k127_5865936_2
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
Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
K02988
-
-
0.00000000000000000000000000000000000001007
150.0
YHH1_k127_5865936_5
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
-
-
0.00000000000000000000000000000000002762
139.0
YHH1_k127_5865936_6
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
0.000000000000000000000000000000003573
136.0
YHH1_k127_5865936_7
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
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
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
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
K01159
-
3.1.22.4
0.000000000000000000000000000000000000000001022
161.0
YHH1_k127_5966841_5
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
0.00000000000000000000000000000241
126.0
YHH1_k127_5966841_6
Part of the ABC transporter FtsEX involved in asymmetric cellular division facilitating the initiation of sporulation
K09811
-
-
0.0000000000000000000000000085
121.0
YHH1_k127_5966841_7
DSBA oxidoreductase
-
-
-
0.000000389
53.0
YHH1_k127_6264580_0
Phosphotransfer between the C1 and C5 carbon atoms of pentose
Could be involved in insertion of integral membrane proteins into the membrane
K08998
-
-
0.000000000000000000000003176
103.0
YHH1_k127_6264580_3
Jag protein
K06346
-
-
0.000000000000000000003223
101.0
YHH1_k127_6264580_4
Belongs to the bacterial ribosomal protein bL34 family
K02914
-
-
0.00000001201
57.0
YHH1_k127_6337254_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
K01338
-
3.4.21.53
2.376e-221
707.0
YHH1_k127_6337254_1
Beta-lactamase enzyme family
K17836
-
3.5.2.6
0.00000000000000000003524
96.0
YHH1_k127_6364250_0
COG0365 Acyl-coenzyme A synthetases AMP-(fatty) acid ligases
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
Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP)
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
ATPases associated with a variety of cellular activities
K09013
-
-
0.00000000000000000000000000000000000000000002655
167.0
YHH1_k127_7008465_2
GlcNAc-PI de-N-acetylase
K22135
-
-
0.00000000000003628
81.0
YHH1_k127_7008465_3
Belongs to the cytochrome b5 family
-
-
-
0.00000000000006797
76.0
YHH1_k127_7008465_4
Alpha beta-Hydrolases superfamily protein
K02946,K06889
-
-
0.00005935
52.0
YHH1_k127_7008465_5
cellulase activity
-
-
-
0.0003154
51.0
YHH1_k127_7032088_0
Catalyzes the addition of an amino acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
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
-
-
0.0000000000000000000000000000000007627
136.0
YHH1_k127_7060228_1
competence protein
-
-
-
0.000000000000000000000000000000003797
138.0
YHH1_k127_7060228_2
Bacterial PH domain
-
-
-
0.00002097
54.0
YHH1_k127_7060228_3
protein serine/threonine phosphatase activity
-
-
-
0.00002482
57.0
YHH1_k127_706505_0
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
K06168
-
2.8.4.3
0.000000000000000000000000000000000000000001381
164.0
YHH1_k127_706505_1
Cof-like hydrolase
-
-
-
0.000000000000000000009115
101.0
YHH1_k127_706505_2
TIGRFAM cell envelope-related function transcriptional attenuator, LytR CpsA family
-
-
-
0.00000009226
61.0
YHH1_k127_7067654_0
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
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
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
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
K03076
-
-
6.077e-224
700.0
YHH1_k127_751022_1
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
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
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
Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
K17758,K17759
-
4.2.1.136,5.1.99.6
0.00000000000000000000000000000000003958
144.0
YHH1_k127_7655130_5
Catalyzes the reversible phosphorylation of UMP to UDP
K09903
-
2.7.4.22
0.00000000000000009386
89.0
YHH1_k127_773160_0
ATPase related to the helicase subunit of the Holliday junction resolvase
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
Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII
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
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
DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N- glycosidic bond, leaving an AP (apurinic apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
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
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
Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides
-
-
-
0.0000000000000000000000224
107.0
YHH1_k127_7892434_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)
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
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
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 gluconeogenesis. Catalyzes stereospecifically the conversion of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde-3-phosphate (G3P)
K01803
-
5.3.1.1
0.000000000000000000000000000000000000000001984
163.0
YHH1_k127_8019218_8
TRANSCRIPTIONal
-
-
-
0.00000000000000000000000000000000000884
149.0
YHH1_k127_8019218_9
PFAM Glycosyl transferase family 2
-
-
-
0.000000000000000000000000000000001281
139.0
YHH1_k127_8046223_0
Heat shock 70 kDa protein
K04043
-
-
3.206e-238
752.0
YHH1_k127_8046223_1
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
K03686
-
-
0.000000000000000000000000000000000000003536
151.0
YHH1_k127_8046223_2
Negative regulator of class I heat shock genes (grpE- dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
K03705
-
-
0.00000000000000000000000000000001576
136.0
YHH1_k127_8046223_3
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
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
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
-
2.1.2.9
0.000000000000000000000000000000000000000003778
164.0
YHH1_k127_8592106_1
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
0.00000000000000000000000001778
115.0
YHH1_k127_8592106_2
O-Antigen ligase
-
-
-
0.0000004508
61.0
YHH1_k127_8814356_0
Belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family
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)
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 reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis
COG1807 4-amino-4-deoxy-L-arabinose transferase and related
-
-
-
0.0000000000000000000000007083
117.0
YHH1_k127_9108390_4
Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in the regulation of osmotic pressure changes within the cell
Q COG2931 RTX toxins and related Ca2 -binding proteins
K01406
-
3.4.24.40
0.000102
53.0
YHH1_k127_9146977_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
2.253e-210
674.0
YHH1_k127_9146977_1
XFP C-terminal domain
K01621
-
4.1.2.22,4.1.2.9
0.0000000000000000000000000000000002241
132.0
YHH1_k127_9146977_2
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
K07738
-
-
0.00000000000000004548
82.0
YHH1_k127_9146977_3
Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
K07738
-
-
0.000000009691
56.0
YHH1_k127_9197834_0
Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release
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
-
-
0.00000000000000000000000000000001405
132.0
YHH1_k127_9223257_2
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
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
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
0.00000000000002415
78.0
YHH1_k127_9357350_4
-
-
-
-
0.000005509
50.0
YHH1_k127_9357350_5
Belongs to the bacterial ribosomal protein bS21 family
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 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
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
Belongs to the bacterial ribosomal protein bL36 family
K02919
-
-
0.0000000000002875
71.0
YHH1_k127_9722811_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)
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
