SII-SWORD/CoKE huggingface dataset:
Pfam PF00140: Sigma-70 factor, region 1.2 (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 .
Wikipedia: A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).
Pfam PF12276: Protein of unknown function (DUF3617) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09138: Urm1 (Ubiquitin related modifier) (domain)
Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily.
Wikipedia: Ubiquitin-related modifier-1 (URM1) is a ubiquitin-like protein that modifies proteins in the yeast ubiquitin-like urmylation pathway. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily.
Pfam PF10307: HAD domain family 1 in Swiss Army Knife RNA repair proteins (domain)
Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation.There are two characteristic sequence motifs, GGWW and TGR.
Pfam PF14731: Staphopain proregion (domain)
This domain is the proregion of the cysteine protease staphopain. Like many papain type peptidases, staphopain is synthesised as an inactive precursor and cleavage of the proregion is required for activation. This proregion has a half-barrel or barrel-sandwich hybrid fold. The proregion blocks the active site cleft of the mature enzyme on one side of the nucleophilic cysteine
Pfam PF05940: NnrS protein (family)
This family consists of several bacterial NnrS like proteins. NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family. Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase. NnrS contributes to nitrosative-stress tolerance in V. cholerae and protects the cellular iron pool from the formation of dinitrosyl iron complexes (DNICs), thus protecting critical metabolic pathways from inhibition.
Pfam PF17090: YtcA family (family)
This is a family of bacterial transmembrane proteins. The function is unknown.
Pfam PF22543: Soluble Rieske-type ferredoxin (domain)
This entry represents soluble Rieske-type ferredoxins from animals , referred to as MRF and HRF for the mouse and human proteins, respectively, whose function is not yet known.
Pfam PF17893: CRISPR-associated endonuclease Cas9 beta-hairpin domain (domain)
This is beta-hairpin domain found in Cas9 proteins from Actinobacteria. The beta-hairpin domain is not conserved in all type II-C Cas9 proteins. The beta-hairpin in Cas 9 from Streptococcus pyogenes blocks the HNH domain active site.
Pfam PF07613: Protein of unknown function (DUF1576) (family)
This small family is found in several undescribed proteins. The alignment is distinguished by the frequent occurrence of conserved glycine and aromatic residues.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19037: Second Longin domain of FUZ, MON1 and HPS1 (domain)
This entry represents a longin-like domain found in Fuz and related proteins. This entry is specific to the second Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia.
Pfam PF15172: Prolactin-releasing peptide (family)
Prolactin-releasing peptide (PrRP) stimulates prolactin (PRL) release and regulates the expression of prolactin through its receptor GPR10. It may stimulate lactotrophs directly to secrete PRL .
Wikipedia: Prolactin-releasing peptide (PrRP) is a peptide hormone that in humans is encoded by the PRLH gene. PrRP stimulates prolactin (PRL) release and regulates the expression of prolactin through binding to the prolactin-releasing peptide receptor (GPR10).
Pfam PF00562: RNA polymerase Rpb2, domain 6 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain.  The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex.  This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion.  This domain is also involved in binding to Rpb1 and Rpb3.  Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pfam PF20671: Conserved oligomeric Golgi complex subunit 3, C-terminal (repeat)
This entry includes the Conserved oligomeric Golgi complex subunit 3 (COG3, also known as Sec34) which is a component of the peripheral membrane COG complex, involved in intra-Golgi protein trafficking.. COG is a member of the complexes associated with tethering containing helical rods (CATCHR) family which also includes the exocyst, GARP and DSL1 complexes, which are evolutionarily related and share structural features consisting of alpha-helical bundles towards the C-terminal and an N-terminal coiled-coil region. This entry represents the alpha-helical bundles of COG3.
Pfam PF21451: Salmon anemia virus nucleoprotein N-terminal domain (domain)
This entry represents the N-terminal domain of the Salmon anemia virus nucleoprotein which has an alpha/beta fold consisting of three anti-parallel beta-strands and two alpha helices in an extended shape and interacts with the rest of the structure. This domain may regulate the dynamics of the NP RNA binding.
Pfam PF19370: Family of unknown function (DUF5945) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13586: Transposase DDE domain (domain)
Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.
Pfam PF03314: Protein of unknown function, DUF273 (family)
This is a family of proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23419: E3 ubiquitin-protein ligase RFWD3 WD40 domain (repeat)
This entry represents the WD40-repeat (WDR) of the E3 ubiquitin-protein ligase RFWD3, a protein required for the repair of DNA interstrand cross-links (ICL) in response to DNA damage. This domain is responsible for the functional interactions that allow RFWD3 o maintain genomic stability.
Pfam PF13034: Protein of unknown function (DUF3895) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two completely conserved residues (Y and L) that may be functionally important.
Pfam PF01434: Peptidase family M41 (domain)
This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.

The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
Pfam PF07077: Protein of unknown function (DUF1345) (family)
This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09947: Uncharacterized protein conserved in archaea (DUF2180) (family)
This domain, found in various hypothetical archaeal proteins, has no known function. A few of the family members contain a zinc finger domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22380: Chromo domain-containing protein 1-like, SPOC domain (domain)
This entry represents the SPOC domain of Chromo domain-containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation.
Pfam PF13564: DoxX-like family (family)
This family of uncharacterised proteins are related to DoxX [pfam:PF07681].
Pfam PF07263: Dentin matrix protein 1 (DMP1) (disordered)
This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralised dentin.  DMP1 is primarily localised in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralised matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown.
Pfam PF22505: Ribonuclease J, beta-CASP domain (domain)
This domain is found in Ribonuclease J from Thermus thermophilus (RNaseJ) and similar bacterial proteins. RNaseJ is an RNase that has endonuclease and possibly 5'-3' exonuclease activity. It is probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. This protein shows three globular domains: the beta lactamase core (formed by two separate regions, [pfam:PF12706] and [pfam:PF07521]), the beta-CASP (this entry) and the C-terminal domain (Pfam: PF17770). This domain consists of a central five-stranded parallel beta-sheet that is surrounded by five alpha-helices.
Pfam PF03886: ABC-type transport auxiliary lipoprotein component (family)
ABC_trans_aux is a family of bacterial proteins that act as auxiliarires to the ABC-transporter in the gamma-hexachlorocyclohexane uptake permease system in Sphingobium japonicum. Gamma-hexachlorocyclohexane, or Lindane, can be used as the sole source of carbon in S.japonicum in aerobic conditions. Lindane is an insecticide.
Pfam PF13630: SdpI/YfhL protein family (family)
This family of proteins includes the SdpI and YfhL proteins from B. subtilis. The SdpI protein is a multipass integral membrane protein that protects toxin-producing cells from being killed. Killing is mediated by the exported toxic protein SdpC an extracellular protein that induces the synthesis of an immunity protein.
Pfam PF16158: Ig-like domain from next to BRCA1 gene (domain)
Domain present between positions 365-485 in the human next to BRCA1 gene 1 protein Q14596 (NBR1_HUMAN) Distant homology and fold prediction analysis suggests this domain has an immunoglobulin like fold and is distantly homologous to domains involved in cell adhesion such as CARDB (PF07705). JCSG construct was crystalized confirming the domain boundaries
Pfam PF12251: snRNA-activating protein complex (SNAPc), subunit 3 (family)
This entry represents the C-terminal part of the SNAPC3 protein found in eukaryotes.  This protein is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.
Pfam PF13125: Protein of unknown function (DUF3958) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are two conserved sequence motifs: RLF and TWH.
Pfam PF23839: Family of unknown function (DUF7209) (family)
This entry represents a protein that is a component of the virion particle in several bacteriophages infecting hosts such as Bacillus, Staphylococcus, Listeria, Enterococcus and Lactobacillus. The exact function is unknown but it is likely to play a structural role.  The protein is typically between 65-80 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14031: Putative serine dehydratase domain (domain)
This domain is found at the C-terminus of yeast D-serine dehydratase. Structures have been solved for two bacterial members of this family. The yeast protein has been shown to be a zinc dependant enzyme.
Pfam PF16016: VAD1 Analog of StAR-related lipid transfer domain (domain)
The VASt (VAD1 Analog of StAR-related lipid transfer) domain is conserved across eukaryotes and is structurally related to Bet v1-like domains, including START lipid-binding domains. The 190-amino acid VASt domain is predominantly associated with lipid binding domains such as GRAM [pfam:PF02893], C2 and PH domains. The VASt domain is likely to have a function in binding large hydrophobic ligands and may be specific for sterol. The predicted structure of the VASt domain is a two-layer sandwich alpha beta fold, also called 'helix grip fold', containing three alpha helices (alpha1 to 3), six beta-sheets (beta1 to 6) and two loops (omega1 and 2) numbered from N to C terminus. Some proteins known to contain a VASt domain are : Plant vascular associated death1 (VAD1), a regulator of programmed cell death (PCD) harboring a GRAM putative lipid-binding domain. Yeast SNF1 Interacting Protein 3 (SIP3), may be involved in sterol transfer between intracellular membranes. Yeast Suicide Protein 1 (YSP1), a mitochondrial protein specifically required for the mitochondrial thread-grain transition, de-energization, and the cell death. May be involved in sterol transfer between intracellular membranes. Yeast Suicide Protein 2 (YSP2), a mitochondrial membrane protein involved in mitochondrial fragmentation and may be involved in sterol transfer between intracellular membranes.It is also found in human GramD1a-c.
Wikipedia: VAD1 analog of StAR-related lipid transfer (VASt) is a steroidogenic acute regulatory protein‐related lipid transfer (StART)-like lipid-binding domain first identified in the vad1 protein in Arabidopsis thaliana. Proteins containing these domains are found in eukaryotes and usually contain another lipid-binding domain, typically the GRAM domain and sometimes the C2 domain in plants and the integral peroxisomal membrane peroxin Pex24p domain in oomycetes.
Pfam PF11247: Bacteriophage T7, gene 5.5 (family)
This family of phage proteins include Bacteriophage T7 gene 5.5 (also known as Protein suppressor of silencing) which plays a role in the inhibition of gene silencing by the host nucleoid-associated protein H-NS/hns. It disrupts higher-order H-NS-DNA complexes.
Pfam PF05226: CHASE2 domain (domain)
CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE2 domains are found in histidine kinases, adenylate cyclases, serine/threonine kinases and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE2 domains are not known at this time.
Pfam PF21471: Reelin subrepeat B (repeat)
Reelin is an extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. It regulates microtubule function in neurons and neuronal migration. It binds to the extracellular domains of lipoprotein receptors VLDLR and LRP8/APOER2 which induces tyrosine phosphorylation of DAB1 and modulation of TAU phosphorylation. Reelin consists of a signal sequence, an F-spondin-like region and nine sequentially concatenated repeat units. Each complete reelin repeat contains a central epidermal growth factor (EGF) module flanked by two subrepeats of 150-190 amino acids (subrepeats A and B). This entry represents subrepeat B (also referred to R3B) which adopts a beta jelly-roll fold similar to bacterial xylanase. They contain the signature Asp-box motif.