SII-SWORD/CoKE huggingface dataset:
Citrate lyase, beta subunit, bacteria (Citrate_lyase_beta_bac)
Type: Family

This group of sequences represent the beta subunit of the holoenzyme citrate lyase (

) composed of alpha (

), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The group contains an experimentally characterised member from Leuconostoc mesenteroides . The group contains sequences from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only the sequences from gammaproteobacteria are present.
Conserved hypothetical protein CHP01589, plant (CHP01589_pln)
Type: Family

This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Variant antigen yir/bir/cir (Yir_bir_cir)
Type: Family

This group of sequences identifies a large paralogous family of variant antigens from several Plasmodium species (Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi). It is not believed that there are any orthologs of this family in Plasmodium falciparum.
Formate dehydrogenase, alpha subunit (Formate_DH_asu)
Type: Family

This group of sequences describe a subset of formate dehydrogenase alpha chains found mainly in the archaea but also in alpha and gamma proteobacteria and a small number of Gram-positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized) . The alpha subunit of a version of nitrate reductase is closely related.
Holin (Holin)
Type: Family

This entry represents holin proteins from tailed bacteriophages, actinobacteria and firmicutes, including Holin from Bacillus subtilis (XhlB), involved in cell lysis upon induction of PbsX, and

from Bacillus phage SPP1, which accumulates harmlessly in the cytoplasmic membrane until it reaches a critical concentration that triggers the formation of micron-scale pores (holes) causing host cell membrane disruption and endolysin escape into the periplasmic space .

Holins form large oligomeric flexible pores in the cytoplasmic membranes of bacteria to allow the endolysins to gain access to the cell wall, where they exert their actions by cleaving various bonds in the peptidoglycan polymer and inducing cell death. These proteins and its corresponding genes have been identified in a wide variety of Gram-negative and Gram-positive bacteria and their phages .
Bacteriophage holin family (Phage_holin_4_1)
Type: Family

Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile . The 1.E.10 family is represented by Bacillus subtilis phi29 holin ; 1.E.16 represents the Cph1 holin; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis .
Bacteriophage lambda, GpS, holin (Phage_lambda_GpS_holin)
Type: Family

This protein family represent one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
CRISPR-associated protein Cas7, subtype I-B/I-C (Cas7_Csh2/Csh2)
Type: Family

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry represents Cas7 from the I-B (Csh2) and I-C (Csd2) subtypes. The Cascade I-B complex requires Cas5, Cas6, and Cas7 for maintaining a stable crRNA population .
CRISPR-associated Cas3-type, HD domain (CRISPR-assoc_Cas3_HD)
Type: Domain

This entry represents the HD domain, which is found in a number of Cas proteins that tend to be found near CRISPR repeats. These domains can be found either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein. CRISPR loci appear to be mobile elements with a wide host range. The Cas3-type HD domain has nuclease activity against ssDNA and ssRNA .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Plasmodium yoelii subtelomeric PYST-B (PYST_B)
Type: Family

The sequences in this group represent a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes . There are no obvious homologues to these genes in any other organism.
Bacteriophage-like holin (Phage-like_holin)
Type: Family

This family of holins is found in tailed bacteriophages, antinobacteria and firmicutes.

Phage proteins for bacterial lysis typically include a membrane-disrupting protein, or holin, and one or more cell wall degrading enzymes that reach the cell wall because of holin action. Holins are found in a large number of mutually non-homologous families.

Holins form large oligomeric flexible pores in the cytoplasmic membranes of bacteria to allow the endolysins to gain access to the cell wall, where they exert their actions by cleaving various bonds in the peptidoglycan polymer and inducing cell death. These proteins and its corresponding genes have been identified in a wide variety of Gram-negative and Gram-positive bacteria and their phages .
Plasmodium yoelii subtelomeric PYST-A (PYST_A)
Type: Family

A single high-scoring gene was identified in the complete genome of P. falciparum as well as a single gene from Plasmodium chabaudi. There are no obvious homologues to these genes in any non-Plasmodium organism. These observations suggest an expansion of this family in Plasmodium yoelii from a common Plasmodium ancestor gene (present in a single copy in Plasmodium falciparum).
Bacteriophage lambda, Tail tip protein L (Phage_lambda_L)
Type: Family

This entry represents Tail tip protein (L) from Bacteriophage lambda and similar proteins found in tailed bacteriophages (Caudovirales) and prophages mostly from Proteobacteria. L is part of the distal tail tip complex which plays a role in DNA ejection during entry, and in tail assembly initiation during exit. The tail tip complex is assembled successively with three tail tip proteins J, one tail tip protein I, one tail tip protein L and one tail tip protein K. The tail tip complex interacts with tail measure protein to initiate tail tube assembly. The formation of the tail tip complex is completed by the addition of tail tip protein M, which is followed by tail tube polymerisation .
PYST-C1-like, N-terminal (PYST-C1_N)
Type: Domain

This entry represents the N-terminal domain of a paralogous family of Plasmodium yoelii proteins that are preferentially encoded in the subtelomeric regions of the chromosomes. There are no obvious homologues to these proteins in other organisms. The C-terminal portions of the proteins are divergent and some contain other Plasmodium-specific paralogous domains such as PYST-C2 (

).
Plasmodium yoelii repeat of length 46 (PY-rept-46)
Type: Repeat

This repeat is found in the products of 2 genes in Plasmodium yoelii. Closely related repeats are found in other Plasmodium species.
Phage major tail protein, phi13 family (Maj_tail_phi13)
Type: Family

This is a set of proteins that share low levels of sequence similarity but similar lengths and similar patterns of charged, hydrophobic, and Gly/Pro residues. Most members belong to phage of Gram-positive bacteria. Several are identified as phage major tail proteins.
Plasmodium yoelii subtelomeric PYST-C2 (PYST_C2)
Type: Domain

These sequences represent a domain found in a paralogous gene family of Plasmodium yoelii preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologues to these genes in any other organism. The proteins often contain an N-terminal yoelii-specific domain such as PYST-C1 (

).
Plasmodium yoelii subtelomeric PYST-D (PYST_D)
Type: Family

The proteins in this set represent a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. These genes are generally very short (ca. 50 residues). There are no obvious homologues to these genes in any other organism.
Holin, BlyA (Holin_BlyA)
Type: Family

This family is represented by BlyA, a small holin found in Borrelia circular plasmids that prove to be temperate phage . This protein was previously proposed to be a haemolysin. BlyA is small (67 residues) and contains two largely hydrophobic helices and a highly charged C terminus.
Plasmodium subtelomeric PST-A (PST_A)
Type: Family

These proteins represent a paralogous family of genes found in Plasmodium falciparum and Plasmodium yoelii that are closely related to various phospholipases and lysophospholipases of plants as well as generally being related to the α/β-fold superfamily of hydrolases. These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii.
Citrate lyase acyl carrier protein CitD (CitD)
Type: Family

This group of sequences represent the acyl carrier protein (gamma subunit) of the holoenzyme citrate lyase (

) composed of alpha (

), beta (

), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The set contains an experimentally characterised member from Leuconostoc mesenteroides . The sequences come from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only sequences from the gamma proteobacteria are included.
Conserved hypothetical protein CHP01609, Plasmodium spp (CHP01606_Plasmodium_spp)
Type: Family

This entry represents a set of protein sequences found in Plasmodium species. An interesting feature is five perfectly conserved Trp residues.
Bacteriophage lambda, Replication protein O, N-terminal (Phage_lambda_VrpO_N)
Type: Domain

This entry represents the N-terminal domain of Replication protein O from Bacteriophage lambda and similar proteins found in tailed bacteriophages and bacterial prophages. O is necessary for the bidirectional replication of DNA. It interacts with the ori (origin of replication) region of the genome during the initiation of replication .
Tail tube protein (Tail_tube)
Type: Family

These sequences represent the tail tube protein of the contractile tail of phage P2, and homologous proteins from other phage .
Reticulocyte binding protein (Reticulocyte-bd)
Type: Family

These sequences represent a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235kDa family protein and rhoptry protein. Rhoptry protein is localised on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite . These proteins are found in Plasmodium.
Helicase, putative, phage/plasmid, C-terminal domain (Helicase_put_C_phage/plasmid)
Type: Domain

This entry represents the C-terminal domain of the putative helicase 022R from Frog virus and similar sequences found in virus and plasmids from bacteria and archaea. These sequences form a clade within a larger family of proteins from viruses of bacteria and animals.
Pectinesterase inhibitor domain (Pectinesterase_inhib_dom)
Type: Domain

This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex . It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension . It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein . It is also found at the N-termini of PMEs, suggesting that both PMEs and their inhibitor are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly α-helical .
Protein of unknown function PDDEXK-like (PDDEXK-like)
Type: Family

PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as α-β-β-β-α-β. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core β-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding α-helix . The family is not in general fused with any other domains, so its function cannot be predicted .

This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Nitrogenase-associated protein (Nase-assoc)
Type: Family

This set of sequences describe a small family of uncharacterised proteins only found so far in alpha and gamma proteobacteria and in the Cyanobacterium Anabaena sp. (strain PCC 7120). The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal.
Transcriptional regulator Spx/MgsR (Tscrpt_reg_Spx/MgsR)
Type: Family

Characterised members of this family include Spx and MgsR from Bacillus subtilis. Spx is a global transcription regulator that plays a key role in stress response and exerts either positive or negative regulation of genes. Induces the expression of a large number of genes in response to a variety of stress conditions, such as disulfide, heat and cell wall stress. It interacts with RNA polymerase . MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B .
Phage nucleotide-binding protein (Phage_nucleotide-bp)
Type: Family

These sequences represent an uncharacterised family of proteins from a number of phage of Gram-positive bacteria, including Streptococcus phage Sfi11 and Lactobacillus phage JNU_P5. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The function of these proteins is unknown.
Conserved hypothetical protein CHP01619 (CHP01619)
Type: Family

These sequences represent a hypothetical equivalog of gamma proteobacteria, which includes HI0040.
Uncharacterised protein family UPF0283 (UPF0283)
Type: Family

These are putative membrane proteins from alpha and gamma proteobacteria, each making up their own clade. The two clades have less than 25% identity between them.
Pseudouridine synthase, RluA-like (PsdUridine_synth_RluA-like)
Type: Family

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are :

Pseudouridine synthase I, TruA.

Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.

Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.

Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.

Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.

These sequences represent a clade within family 3 pseudouridine synthases, which includes RluA, RluB, RluC, RluD, and RsuA. The sequences in this clade are most closely related to RluA ; only Neisseria does not appear to have an RluA homologue. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Splicing factor, RBM39-like (RBM39_SF)
Type: Family

This entry represents RBM39 (also known as CAPER, CC1, RNPC2) proteins from mammals and a group of putative RNA splicing factors including the Pad1 protein from fungi. All are characterised by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 human paralogs, two) RNA recognition domains. These proteins are closely related to the U2AF splicing factor family (

).
Zinc finger, lateral root primordium type 1 (Znf_LRP1)
Type: Domain

These sequences contain a putative zinc finger domain found predominantly in plants. Arabidopsis thaliana (Mouse-ear cress) has at least 10 distinct members. Proteins containing this domain, including LRP1 (lateral root primordium 1), generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. But are excluded from this family because of their low similarity.

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Short internodes, C-terminal (SHI_C)
Type: Domain

These sequences contain a tightly conserved small domain found in Short internodes (SHI) and related plant proteins. SHI proteins also contain a well-conserved adjacent N-terminal putative zinc finger domain (

). SHI may act as a negative regulator of GA responses through transcriptional control .
YidE/YbjL duplication (YidE_YbjL)
Type: Domain

These sequences contain a domain that is duplicated in HI0035 of Haemophilus influenzae, in YidE and YbjL of Escherichia coli, and in a number of other putative transporters. Member proteins may have 0, 1, or 2 copies of the TrkA-C potassium uptake domain (

) between the duplications. The duplication appears distantly related to both the N- and the C-terminal domains the sodium/hydrogen exchanger family domain (

). The domain contains several apparent transmembrane regions and is proposed here to act in transport.
YtfJ-like family (YtfJ_HI0045)
Type: Family

These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ. It is predicted to adopt Thioredoxin-like fold, particularly similar to Glutathione peroxidase family (

).
IRX15/GXM/AGM (IRX15/GXM/AGM)
Type: Family

This entry includes IRREGULAR XYLEM IRX15/IRX15L, glucuronoxylan 4-O-methyltransferases 1(GXM1), 2(GXM2) and 3(GXM3) from plants. GXMs and IRX15/15L are all expressed in secondary wall-forming cells and they are all involved in xylan biosynthesis. However, they have different functions . GXM1/GXM2/GXM3 are methyltransferases catalysing 4-O-methylation of GlcA side chains on xylan . IRX15/IRX15L are required for xylan biosynthesis and/or xylan deposition, although their precise enzymatic activity is unknown . This entry also includes arabinogalactan O-methyltransferase 1 AGM1 (also known as probable methyltransferase At1g27930) and arabinogalactan O-methyltransferase 2 AGM2 (At1g67330) which are required for 4-O-methylation of glucuronic acid of arabinogalactan proteins, a different plant cell wall component .
Polyadenylate binding protein, human types 1, 2, 3, 4 (PABP_1234)
Type: Family

These eukaryotic proteins recognise the poly-A of mRNA and consist of four tandem RNA recognition domains at the N terminus followed by a PABP-specific domain at the C terminus. The protein is involved in the transport of mRNAs from the nucleus to the cytoplasm . There are four paralogs in Homo sapiens (Human) which are expressed in testis , platelets (

), broadly expressed (

) and of unknown tissue range (

).
Replication-associated protein G2P (G2P)
Type: Family

This entry represents a family of phage and plasmid replication proteins. In bacteriophage IKe and related phage, the full-length protein is designated gene II protein (G2P). A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein (G10P). Members of this family also include plasmid replication proteins.
Phage terminase large subunit-like, C-terminal domain (Phage_terminase_lsu-like_C)
Type: Domain

This entry represents the C-terminal domain of a group of proteins from tailed bacteriophages that are typically about 400-500 amino acids in length, although some members are considerably shorter. Most proteins in this family have an apparent P-loop nucleotide-binding sequence toward the N terminus, consistent with the ATPase activity of phage terminase large subunit (TerL). The assignment as TerL is suggested by gene context in numerous phage as well as by homology to better characterised families of TerL . This domain is also found in bacterial prophages.