| Evidence_63715 |
TIGR02487 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| GenProp0291 |
class III (anaerobic) ribonucleotide reductase~Ribonucleotide reductases (RNRs) are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. The class III RNRs consist of two components, the catalytic enzyme (NrdD) and a radical-SAM domain enzyme (NrdG) which activates the catalytic enzyme by the generation of a protein-centered radical. |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51160 |
aerobic RNR, alpha (large) chain |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63721 |
TIGR02495 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63724 |
TIGR00333 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Component_51163 |
redoxin, ribonucleotide-reductase related |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63716 |
TIGR02491 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51602 |
transcriptional regulator NrdR |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Component_51162 |
Unknown function |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63741 |
GenProp0290 GENPROP |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_72410 |
TIGR02827 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51164 |
B12-dependent ribonucleotide reductase |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63740 |
TIGR02194 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51145 |
class I (aerobic) ribonucleotide reductase: GenProp0289 |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| GenProp0287 |
ribonucleotide reduction~The reduction of the ribose sugar of ribonucleotide triphosphates to deoxyribose is one of the essential steps in the biosynthesis of DNA. This chemically challenging step is carried out be a number of distinctly different enzyme systems [1]. Each of these systems utilizes a different mechanism for the generation of a transient cysteine-thiyl radical which initiates the reduction of the substrate. Class I enzymes utilize a diferric non-heme iron cluster to generate a stable tyrosine radical [2]. Note that earlier reports of a manganese-based class IV system related to class I in high GC gram positive species was proved to be spurious [3]. Class II enzymes utilize adenosylcobalamin (vitamin B12) [4]. Class III enzymes utilize radical-SAM domain proteins to generate stable glycine radicals [5]. A very small number of genomes appear to be devoid of ribonucleotide reductase sequences, Mycoplasma arthritidis 158L3-1, Mycoplasma bovis Donetta PG45, Ureaplasma urealyticum parvum biovar serovar 3, Borrelia burgdorferi B31 and Borrelia garinii PBi. Each of these is a reduced genome with a limited metabolic portfolio, however other mycoplasma species do contain RNRs. Three possibilities are likely, 1) these genomes harbor a non-orthologous RNR, 2) these genes are located on plasmids or small chromosomes which were lost prior to genomic sequencing (Borrelia, in particular has a number of small chromosomes and plasmids which were sequenced) or 3) these species strictly rely on import of deoxyribonucleic acid from the host environment. |
None - {{∅}} |
None - {{∅},{t}} |
Unexplained |
|
| Evidence_63739 |
GenProp0289 GENPROP |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_72411 |
TIGR02826 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51149 |
class II (B12-dependent) ribonucleotide reductase: GenProp0290 |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51165 |
class III (anaerobic) ribonucleotide reductase: GenProp0291 |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_72406 |
TIGR00244 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Component_51166 |
anaerobic ribonucleoside-triphosphate reductase |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51167 |
activating protein for anaerobic ribonucleotide triphosphate reductase |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Component_51161 |
aerobic RNR, beta (small) chain |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63736 |
TIGR02504 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| GenProp0290 |
class II (B12-dependent) ribonucleotide reductase~Ribonucleotide reductases (RNRs) are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. The class II RNRs consist of a single subunit and generate the required radical via an adenosylcobalamin (B12) cofactor. The most common gene symbols for this gene is NrdJ, although the gene in mycobacterium is called NrdZ. The first characterized NrdJ gene, from Lactobacillus leichmannii, acted specifically on nucleoside triphosphates like the class III enzymes (1.17.4.2) and unlike the class I enzymes which act on the diphosphates (1.17.4.1). However, as further B12-dependent RNRs were characterized, it became clear that this is the exception rather than the rule. This property captures both types. |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63727 |
TIGR02505 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63738 |
TIGR02510 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| Evidence_63722 |
TIGR02506 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63742 |
GenProp0291 GENPROP |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
| GenProp0289 |
class I (aerobic) ribonucleotide reductase~Ribonucleotide reductases (RNRs) are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. The class I RNRs [1] consist of two subunits, alpha and beta (also known as the large and small subunbits, respectively). Class I RNRs generate the required radical (on tyrosine) via a non-heme iron cofactor which resides in the beta subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The most common gene symbols for these genes are NrdE (alpha) and NrdF (beta), althought the first characterized complex from E.coli (NrdAB) turns out to be one of a pair in gammaproteobacteria and the more divergent one at that. Where multiple class I enzymes exist in a single organism they are presumed to be under differential regulation. Note that earlier reports of a manganese-based class IV system related to class I in high GC gram positive species was proved to be spurious [2]. Electrons for this reduction are supplied by glutaredoxin-like (NrdH, in some species [3]), or flavodoxins specific to this system which are in turn reduced by oxygen via thioredoxin reductase. Detection of this component is not required to set the YES state because of incomplete knowledge of the various homologs involved. Certain class I RNRs are associated with a gene of unknown function (NrdI). NrdI shows up more frequently, but not exclusively in species with more than one class I RNR, so it may be involved in regulation in some way. |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63725 |
PF00268 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
| Evidence_63744 |
TIGR01754 HMM |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|