SII-SWORD/CoKE huggingface dataset:
Guanine deaminase (Guanine_deaminase)
Type: Family

This entry describes guanine deaminase, which hydrolyses guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. Xanthine can then be converted to urate by xanthine dehydrogenase. This reaction also removes the guanine base from the pool and therefore can play a role in the regulation of cellular GTP and the guanylate nucleotide pool . In some bacteria, the guanine deaminase gene is found near the xdhABC genes for xanthine dehydrogenase. Non-homologous forms of guanine deaminase also exist, as well as more distantly related homologues which are not included in this entry.
Succinate dehydrogenase, hydrophobic membrane anchor (Succ_DH_anchor)
Type: Family

In Escherichia coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase (a TCA cycle enzyme) are SdhC and SdhD . This entry is the SdhD, the hydrophobic membrane anchor protein. SdhC is apocytochrome b558, which also plays a role in anchoring the complex.
Aldehyde oxidase (Aldehyde_oxidase)
Type: Family

Aldehyde oxidase catalyses the reaction:
aldehyde + H2O + O2 = a carboxylic acid + H2O2

It contains molybdenum, [2Fe-2S] centres and FAD. It also oxidizes quinoline and pyridine derivatives. It is probably identical to retinal oxidase (

) .

Aldehyde oxidase oxidises various aliphatic and aromatic aldehydes using oxygen as an electron acceptor. It has a molecular mass of 132kDa and consists of three non-identical subunits with molecular masses of 88, 39, and 18kDa. It belongs to the xanthine oxidase family. This enzyme shows high thermostability .
Succinate dehydrogenase, cytochrome b556 subunit (Succ_DH_cytb556)
Type: Family

In Escherichia coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase (a TCA cycle enzyme) are SdhC and SdhD. This entry represents SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see

) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex . In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see

).
ABC transporter, membrane fusion protein, DevB type (ABC_heterocyst_DevB)
Type: Family

Members of this protein are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. (strain PCC 7120) is partially characterised as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter required for heterocyst formation . Most Cyanobacteria have one member only, but some have as many as 7 members Nostoc punctiforme (strain ATCC 29133/PCC 73102) which has seven members.
Trimethylamine N-oxide reductase system, TorE (TMAO_TorE)
Type: Family

Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Transcription activator PspF (Transcription_activator_PspF)
Type: Family

Members of this protein are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, found in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol and filamentous phage infection.
Phage shock protein, PspG (Phageshock_PspG)
Type: Family

This protein previously was designated yjbO in Escherichia coli, and it is also known as envelope stress response protein PspG. It is found only in genomes that have the phage shock operon (psp), but it is only rarely encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins and heat shock .
Phage shock protein, PspA (Phageshock_PspA)
Type: Family

This entry represents the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, represented in

. PspA is required for membrane integrity, as it maintains the proton motive force under stress conditions that include over expression of certain phage secretins, heat shock, ethanol and protein export defects . PspA also negatively regulates expression of the pspABCDE promoter and of pspG through negative regulation of the psp-specific transcriptional activator PspF .
Phage shock protein, PspC (Phageshock_PspC)
Type: Family

All members of this protein are the phage shock protein PspC . The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor; PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin over expression, ethanol, heat shock and protein export defects.
Phage shock protein, PspD (Phageshock_PspD)
Type: Family

Members of this entry are phage shock protein PspD, they are found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.
RNA polymerase sigma-B/F/G type (RNA_pol_sigma-B/F/G)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:

and SigG:

as well as SigB:

), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Thiosulfate sulfurtransferase PspE (PspE)
Type: Family

Members of this very narrowly defined protein are active as rhodanese (

) and are found in extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species . Note that the designation phage shock protein PspE has been applied, incorrectly, because in many instances the genome lacks the phage shock regulon entirely.
ABC transporter ATP-binding subunit, DevA type (ABC_heterocyst_DevA)
Type: Family

This entry represents the ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation.
RNA polymerase sigma-E factor, actinobacteria (RNA_pol_sigma-E_actinobac)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
RNA polymerase sigma-70 factor, Planctomycetaceae (RNA_pol_sigma-70_Plancto)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This group of sigma factors contain the sigma-70 family-like domain (

) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.
RNA polymerase sigma-70, Bacteroidetes type (RNA_pol_sigma70_bacteroid)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Tannerella forsythensis ATCC 43037 (Bacteroides forsythus ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis (strain ATCC 25285/NCTC 9343) contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Restriction endonuclease, type II, Alw26I/Eco31I/Esp3I (Restrct_endonuc_II_Alw26I)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family , whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
M6 adenine DNA methyltransferase, Alw26I (M6_adenine_DNA_mtrans_Alw26I)
Type: Family

Members of this entry are the m6-adenine DNA methyltransferase protein, or a fusion protein that also carries m5 cytosine methyltransferase activity of type II restriction systems of the Alw26I/Eco31I/Esp3I family.

A type II restriction endonuclease always accompanies a methyltransferase of this type from Alw26I/Eco31I/Esp3I(

) and by an adenine-specific modification methyltransferase. Members of this are unusual in that the regions of similarity to homologues outside this family are circularly permuted.
RNA-binding S4-related,YaaA (RNA-bd_S4-rel_YaaA)
Type: Family

YaaA has a single S4 domain (

). It may be a ribosome maturation protein that its overexpression can restore both the growth and the sporulation defects caused by mutation of rplB, encoding ribosomal protein L2 .

The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
RNA polymerase sigma-70 ECF-like, Rhodopirellula baltica (RNA_pol_sigma70_ECF_RHOBA)
Type: Family

The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.

With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors .

The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors .

This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.
Ectoine utilization protein EutA (Ectoine_EutA)
Type: Family

Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include include Rhizobium loti (Mesorhizobium loti), Silicibacter pomeroyi and Sinorhizobium meliloti 1021, where it is known to be induced by ectoine. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.

,
Ectoine utilization protein EutB (Ectoine_EutB)
Type: Family

Members of this entry are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Rhizobium loti (Mesorhizobium loti), Silicibacter pomeroyi, Agrobacterium tumefaciens, Pseudomonas putida and Sinorhizobium meliloti 1021, where it is known to be induced by ectoine. Members resemble threonine dehydratases.
Ectoine utilization protein EutC (Ectoine_EutC)
Type: Family

Members of this protein family are EutC, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine) , Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. This family belongs to the ornithine cyclodeaminase/mu-crystallin family (

).
Ectoine utilization protein EutD (Ectoine_EutD)
Type: Family

EutD is known as DoeA in Halomonas elongata. DoeA is involved in the ectoine degradation pathway where it hydrolyses ectoine to alpha-N-acetyl diaminobutyric acid .
N-alpha-acetyl diaminobutyrate deacetylase DoeB (DoeB)
Type: Family

N-alpha-acetyl diaminobutyrate deacetylase DoeB (also known as EutE) is involved in the ectoine degradation pathway in Halomonas elongata. Ectoine is hydrolysed by DoeA to alpha-N-acetyl diaminobutyric acid which is then deacetylated to diaminobutyric acid by DoeB .
Ectoine/Hydroxyectoine ABC transporter, substrate-binding protein EhuB (Ectoine_EhuB)
Type: Family

This family represents the periplasmic substrate-binding proteins (PBPs) of ABC transport systems that are involved in the uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings . This family are an example of type 2 periplasmic binding fold proteins, which are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap .

This entry is named for one of the constituent proteins from Rhizobium meliloti (Sinorhizobium meliloti), involved in ectoine and 5-hydroxyectoine uptake, both for osmoprotection and for catabolism. The crystal structure of EhuB was solved in complex with either ectoine or 5-hydroxyectoine .