SII-SWORD/CoKE huggingface dataset:
Replication factor A protein-like (RFA2-like)
Type: Family

This entry contains proteins with a winged helix DNA-binding domain, including replication factor A protein 2 (RFA2) and CST complex subunit STN1.

Rfa2 (also known as RPA32) is a component of the replication protein A (RPA) complex, which binds to and removes secondary structure from ssDNA. The RPA complex is involved in DNA replication, repair, and recombination .

Stn1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required to protect telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity by themselves. In addition to telomere protection, the CST complex has probably a more general role in DNA metabolism at non-telomeric sites .
Protein FAM240 (FAM240)
Type: Family

This family of uncharacterised proteins includes FAM240A, FAM240B and FAM240C from vertebrates.
Uncharacterized protein At4g38062-like (At4g38062-like)
Type: Family

This family of plant proteins has not been characterised.
PWWP domain-containing DNA repair factor 3A/3B/4 (PWP3A_3B_4)
Type: Family

This entry includes MUM1 (also known as PWWP3A or EXPAND1), MUM1-like protein 1 (MUM1L1 or PWWP3B) and PWWP domain-containing DNA repair factor 4 from animals.

PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage . MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organization of chromatin structure .
Uncharacterized protein T15H9.4-like (T15H9.4-like)
Type: Family

This entry represents a group of uncharacterised proteins from Nematoda, including T15H9.4 from C. elegans.
Protein CHUP1/IPGA1-like (CHUP1/IPGA1-like)
Type: Family

This entry represents a group of plant proteins, including CHUP1 and At4g04980 from Arabidopsis. CHUP1 (CHLOROPLAST UNUSUAL POSITIONING1) interacts with actin and profilin . It mediates actin-based light-induced chloroplast avoidance movement . The function of At4g04980 is not clear.

This entry also includes Protein INCREASED PETAL GROWTH ANISOTROPY 1, a microtubule-associated protein involved in the regulation of anisotropic petal and cotyledons growth and shape by affecting cortical microtubule organization . It cooperatively functions with ANGUSTIFOLIA (AN), and negatively regulates cortical microtubules (CMTs) organization in response to mechanical stress and modulates pavement cells morphogenesis leading to puzzle shape, probably in an AAA1/KTN1-dependent manner .
TMF-regulated nuclear protein 1 (TRNP1)
Type: Family

TRNP1 is a nuclear regulator of radial glial cell fate. In mammals, it regulates expansion and folding of the cerebral cortex .
F-box protein EID1-like (EID1-like)
Type: Family

This entry includes a group of plant F-box proteins, including EID1 and EDL1/2/3 from Arabidopsis. EID1 is part of the SCF (ASK-cullin-F-box) E3 ubiquitin ligase complex . It functions as a negative regulator in far-red light signaling downstream of the phyA in Arabidopsis . The allelic variation of the tomato homologue of the Arabidopsis EID1 has been linked to slower circadian rhythms . EID1-like protein 3 (EDL3) is involved in the regulation of abscisic acid signalling .
Armadillo-like helical domain-containing protein 2 (ARMH2)
Type: Family

The function of this Armadillo-like helical domain-containing protein is not known.
VAN3-binding protein (VAB)
Type: Family

This entry represents a group of plant proteins, including VAN3-binding protein (VAB, also known as FORKED1 or AT3G63300) from Arabidopsis. FORKED1 is a PH domain protein required for PIN1 localization in developing leaf veins . It interacts with SCARFACE/VAN3 (SFC), an ADP ribosylation factor GTPase-activating protein (ARF-GAP) important for vein patterning .
Uncharacterized protein T19C3.2-like (T19C3.2-like)
Type: Family

This family of uncharacterised proteins is found in Nematoda.
PAMP-induced secreted peptide 1 (PIP1)
Type: Family

PIP1 is a secreted peptide that acts as a positive regulator of the defense response in plants .
CLAVATA3/ESR (CLE)-related protein 27/43 (CLE27/CLE43)
Type: Family

The CLAVATA3/ESR-related (CLE) gene family has 31 CLE members in the Arabidopsis genome . CLE sequences share a short conserved region of 14 amino acids and are thought to function in plant morphogenesis as intercellular signaling molecules .

This entry includes CLE27 and CLE43. CLE27 may have redundant roles with CLE16 and CLE17 in the Arabidopsis shoot apical meristem .
F-box domain containing protein At5g39450-like (At5g39450-like)
Type: Family

This entry represents a group of plant F-box domain containing proteins, including At5g39450. Their function is not clear.
Uncharacterized protein At4g26450-like (At4g26450-like)
Type: Family

This family of uncharacterised proteins from plants includes At4g26450 from Arabidopsis thaliana.
Uncharacterized protein Os04g0629400-like (Os04g0629400-like)
Type: Family

This uncharacterised family of proteins from plants includes Os04g0629400 from Oryza sativa (rice).
UPF0426 protein (UPF0426)
Type: Family

The UPF0426 family is found in plants and Cyanobacteria. Its function is not known.
Protein FAM163B (FAM163B)
Type: Family

The function of FAM163B is not clear.
Protein FAM163A (FAM163A)
Type: Family

The function of FAM163A is not clear.
Abnormal cell migration protein 18-like (Mig-18-like)
Type: Family

MIG-18 functions together with MIG-17 in the regulation of directional migration of gonadal distal tip cells (DTCs) during gonadogenesis in Caenorhabditis elegans . This entry also includes other uncharacterised proteins from C. elegans.
Transmembrane protein DDB_G0292058-like (DDB_G0292058-like)
Type: Family

This entry represents a group of transmembrane proteins, including G0292058 from Dictyostelium discoideum. Their function is not known.
Prolyl-tRNA editing protein ProX/PRXD1 (ProX/PRXD1)
Type: Family

This entry includes prolyl-tRNA editing protein ProX from Acetoanaerobium sticklandii and uncharacterised eukaryotic proteins known as prolyl-tRNA synthetase associated domain-containing proteins. ProX functions in trans to edit the amino acid moiety from incorrectly charged Ala-tRNA(Pro) .
CRM domain-containing protein At3g25440-like (At3g25440-like)
Type: Family

This entry represents a group of plant proteins, including At3g25440. Their function is not clear.
Repulsive guidance molecule (RGM)
Type: Family

This entry represents the repulsive guidance molecule (RGM) family, which consists of bone morphogenetic protein (BMP) coreceptors RGMA, DRAGON (RGMB), and hemojuvelin (RGMC) .

RGM is a GPI-linked axon guidance molecule of the retinotectal system, and controls cell motility, adhesion, immune cell regulation and systemic iron metabolism . RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons can receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM will likely provide positional information for temporal axons invading the optic tectum in the stratum opticum .
PX domain-containing protein 1 (PXDC1)
Type: Family

This entry represents a group of PX domain-containing proteins from vertebrates, including PXDC1. Their function is not clear.
Microtubule binding protein 2C (MBP2C)
Type: Family

MPB2C proteins are involved in regulating cell-to-cell trafficking of homeodomain proteins in plants. MPB2C negatively regulates KNOTTED1 (KN1) association to plasmodesmata and, consequently, KN1 cell-to-cell transport . MPB2C has also been linked to roles in organization of cortical microtubules, stomata patterning, and tobamovirus infectivity .
Protein E6-like (Prot_E6-like)
Type: Family

E6 is one of the predominant fibre-specific mRNAs present during early fibre development. However, E6 seems not to be critical for the normal development or structural integrity of cotton fibres. The distinguishing feature of E6 protein is the presence of a motif where a dimer, Ser-Gly, is repeated several times .
Uncharacterized transmembrane protein DDB_G0287341-like (DDB_G0287341-like)
Type: Family

This family of uncharacterised proteins is found mainly in Acytosteliales and Dictyosteliales.
Uncharacterized protein C2orf78-like (C2orf78-like)
Type: Family

This entry represents a group of vertebrate proteins, including C2orf78 from humans. Their function is not clear.
Nodulin-related protein 1/2 (Nodulin-rel_1/2)
Type: Family

Nodulin-related protein 1 (NRP1) may play a role in the negative-feedback regulation of the abscisic acid (ABA) synthesis pathway. Overexpression of NRP1 enhanced susceptibility to heat stress and was accompanied of decreased accumulation of ABA after heat treatment . The function of NRP2 is not clear.
Photosystem II 5kDa protein, chloroplastic (PSBT)
Type: Family

PsbT encodes photosystem II 5kDa subunit PSII-T. It is part of the psbB-psbT-psbH-petB-petD operon .
Multivesicular body subunit 12B (MVB12B)
Type: Family

MVB12B is a subunit of the ESCRT-I complex, which mediates the sorting of ubiquitinated cargo protein from the plasma membrane to the endosomal vesicle .
Protein FERTILITY RESTORER RF2-like (RF2K-like)
Type: Family

This family of uncharacterised proteins from plants includes protein FERTILITY RESTORER RF2 (RF2) and protein YELLOW LEAF 1 (YL1) from Oryza sativa. RF2 is a mitochondrial glycine-rich protein that can restore fertility in rice varieties with LD-type cytoplasmic male sterility (CMS) . YL1 is required for photosynthetic protein complex assembly in chloroplast thylakoid membranes during leaf development .
Uncharacterized protein At3g49055-like (At3g49055-like)
Type: Family

This family of uncharacterised proteins from plants includes At3g49055 from Arabidopsis thaliana.
Secretoglobin 3A (Secretoglobin_3A)
Type: Family

This family consists of secretoglobin family 3A member 1 (SCGB3A1) and member 2 (SCGB3A2) . They are a small secreted proteins expressed in airway epithelial cells. SCGB3A2, also known as UGRP1, has an important anti-inflammatory activity and is involved in asthma . SCGB3A2 mediates its anti-inflammatory action through inhibition of ERK and JNK activation . It is also involved in lung development .
ATG8-interacting protein 1/2 (ATG8-IP-1/2)
Type: Family

Atg8-interacting proteins (ATI1 and ATI2) are unique to plants. Under conditions of carbon starvation, ATI1 and ATI2 become associated with spherical compartments that dynamically move along the ER network . ATI1 is also located on bodies associating with plastids, and it seems to be involved in autophagic plastid-to-vacuole trafficking through its ability to interact with both plastid proteins and ATG8 .
At1g75730-like (At1g75730-like)
Type: Family

This entry represents a group of plant proteins, including At1g75730 (

). Their function is not clear.
Os02g0753200-like (Os02g0753200-like)
Type: Family

This entry represents a group of proteins of unknown function from plants and protists, including Os02g0753200 from rice.
Large ribosomal subunit protein cL37 (Ribosomal_cL37)
Type: Family

Large ribosomal subunit protein cL37 (also known as PSRP5) is a component of the plastid ribosomal protein (PRP) complex. Plastid-specific 50S ribosomal proteins (PSRPs) may have evolved to perform functions unique to plastid translation and its regulation .
HUWE1-associated protein modifying stress responses (HAPR1)
Type: Family

This entry represents the HUWE1-associated protein modifying stress responses (HAPR1, also known as TAPR1, telomere attrition and p53 response 1 protein) from animals, including HAPSTR1 (also known as C16orf72/TAPR1) from human, which functions as a negative regulator of TP53/P53 in the cellular response to telomere erosion and probably also DNA damage. It may attenuate p53/TP53 activation through the E3 ubiquitin ligase HUWE1 . HAPSTR2 plays a central regulatory role in the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding together with HAPSTR1 by stabilizing HAPSTR1, but also independently of HAPSTR1.
H/ACA ribonucleoprotein complex non-core subunit Naf1 (Naf1)
Type: Family

Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex and being replaced by Gar1 to yield mature H/ACA snoRNPs complex. The core domain of Naf1 is homologous to the core domain of Gar1, suggesting that they share a common Cbf5 binding surface .
DDB_G0292248 (DDB_G0292248)
Type: Family

This entry includes a group of proteins from Dictyosteliales and Acytosteliales, including DDB_G0292248 from Dictyostelium discoideum. Their function is not clear.
Coiled-coil domain-containing protein 3 (CCDC3)
Type: Family

This entry represents a group of animal proteins, including CCDC3 from humans. CCDC3 is a secretory protein that represses tumour necrosis factor-alpha/nuclear factor kappaB-induced endothelial inflammation .
FLYWCH-type zinc finger-containing protein 1/2 (FWCH1/FWCH2)
Type: Family

This entry represents a group of animal FLYWCH-type zinc finger-containing proteins, including FLYWCH1 and FLYWCH2. FLYWCH1 is a transcription modulator that suppresses the transcriptional activity of Wnt/beta-catenin signaling. It may function as a tumor suppressor in colorectal cancer .
Keratin-associated protein 6 (KAP6)
Type: Family

This entry represents a group of animal keratin-associated proteins, including KAP6.1/6.2/6.3 from humans. Hair keratin-associated proteins (KAP) are a major component of the hair fibre and play crucial roles in forming a strong hair shaft through a cross-linked network with keratin intermediate filaments (KIF) .
Protein DOP1 (DOP1)
Type: Family

Dop1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans) . Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation . In Saccharomyces cerevisiae, Dop1 is essential for viability and, affects cellular morphogenesis . Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2, a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus .
WD repeat-containing protein WDR46/Utp7 (WDR46/Utp7)
Type: Family

This entry contains proteins with a BING4-like, C-terminal domain. WD repeat-containing protein 46 (WDR46) is a component of the nuclear scaffold, which is an insoluble structure that contributes to the inner nuclear organization. WDR46 is a fundamental scaffold component of the nucleolar structure, binding nucleolin and DDX21 . Also in this family is U3 small nucleolar RNA-associated protein 7 (UTP7) from baker's yeast, which is involved in nucleolar processing of pre-18S ribosomal RNA .
Integrator complex subunit 5 (INTS5)
Type: Family

INTS5 is part of the integrator complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing .
LSD1-like (LSD1-like)
Type: Family

This entry represents a group of zinc finger containing proteins from plants and green algae, including LSD and LOL proteins. LSD (LESION SIMULATING DISEASE1) functions as a negative programmed cell death regulator that integrates various signaling pathways in response to both biotic and abiotic stresses . It regulates crosstalk between light acclimation and immunity in Arabidopsis . LSD1 and LOL1 have antagonistic effects on CSD1 and CSD2 accumulation to regulate oxidative stress-induced cell death . The rice LOL2 is involved in rice growth and disease resistance .
Uncharacterized protein At4g37920-like (At4g37920-like)
Type: Family

This entry represents a group of Viridiplantae proteins, including At4g37920. Their function is not clear.
Coiled-coil domain-containing protein SCD2-like (SCD2-like)
Type: Family

This entry represents a group of plant proteins, including SCD2 from Arabidopsis. SCD2 (STOMATAL CYTOKINESIS DEFECTIVE 2) functions in clathrin-mediated membrane transport. In Arabidopsis, loss of SCD2 function disrupts cytokinesis and cell expansion and impairs fertility .
RNA-binding protein RO60 (TROVE2)
Type: Family

Proteins in this family contain a TROVE (Telomerase, Ro and Vault) domain and include RNA-binding protein RO60 (TROVE2), an RNA-binding protein that binds to misfolded non-coding RNAs, pre-5S rRNA, and several small cytoplasmic RNA molecules known as Y RNAs .
EARP and GARP complex-interacting protein 1 (EIPR1)
Type: Family

Proteins in this entry contain WD40 repeats. This entry includes mammalian EARP and GARP complex-interacting protein 1 (EIPR1 or TSSC1), which is a component of the endosomal retrieval machinery, binding to both the tethering complexes GARP and EARP. GARP participates in SNARE-dependent fusion of endosome-derived carriers with the trans-Golgi network, wheras EARP does the same for recycling endosomes . Also included in this family is the EARP-interacting protein 1 from the nematode Caenorhabditis elegans, which trafficks cargo to the dense-core vesicle, a secretory organelle that mediates the regulated release of peptide hormones, growth factors, and biogenic amines and which originates from the trans-Golgi of neurons and neuroendocrine cells . The WD repeat-containing protein DWA2 from Arabidopsis thaliana is also a member of this family. DWA2 is a component of an E3 ubiquitin-protein ligase complex that acts as negative regulator in abscisic acid signaling .
WD repeat-containing protein WDR44/Dgr2 (WDR44/Dgr2)
Type: Family

Proteins in this entry contain WD40 repeats. Besides a number of uncharacterised proteins, the family includes the following:

WD repeat-containing protein 44 (WDR44; also known as Rabphilin-11), found in vertebrates, which binds the small G protein Rab11 and is implicated in vesicle recycling .

2-deoxy-glucose resistant protein 2 (Dgr2) from yeast, which increases cellular tolerance to 2-deoxy-glucose .
RIMS-binding protein 1/2/3 (RIMBP1/2/3)
Type: Family

Proteins in this family contain SH3 and fibronectin type III (FN3) domains, with the FN3 domains inserted within the SH3 domains. Members include peripheral-type benzodiazepine receptor-associated protein 1 (PRAX-1, TSPOAP1 or RIMBP1, also known as RIMS-binding protein 1 or TSPO-associated protein 1) and RIMS-binding protein 2 (RIMBP2). PRAX-1 interacts with the peripheral benzodiazepine receptor . RIMBP2 interacts with subunits of the voltage-gated Ca(2+) channels .

RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2 . RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3 . RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery . RIM-BPs contain three SH3 domains (

) and two to three fibronectin III repeats (

). Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3 . RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis . The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits .
HAP2/GCS1 (HAP2/GCS1)
Type: Family

The gene encoding Arabidopsis HAP2 is allelic with GCS1 (Generative cell-specific protein 1). HAP2 is expressed only in the haploid sperm and is required for efficient guidance of the pollen tube to the ovules. In Arabidopsis the protein is a predicted membrane protein with an N-terminal secretion signal, a single transmembrane domain and a C-terminal histidine-rich domain . HAP2-GCS1 is found from plants to lower eukaryotes and is necessary for the fusion of the gametes in fertilisation. It is involved in a novel mechanism for gamete fusion where a first species-specific protein binds male and female gamete membranes together after which a second, broadly conserved protein, either directly or indirectly, causes fusion of the two membranes together. The broadly conserved protein is represented by this HAP2-GCS1 domain, conserved from plants to lower eukaryotes . In Plasmodium berghei the protein is expressed only in male gametocytes and gametes, having a male-specific function during the interaction with female gametes, and being indispensable for parasite fertilisation. The gene in plants and eukaryotes might well have originated from acquisition of plastids from red algae .
TLC domain-containing protein At5g14285-like (At5g14285-like)
Type: Family

This entry represents a group of plant proteins, including At5g14285. Their function is not clear.
Uncharacterized protein DDB_G0279899-like (DDB_G0279899-like)
Type: Family

This entry represents a group of proteins from Dictyosteliales, including DDB_G0279899 from Dictyostelium discoideum. Their function is not known.
Chemokine-like protein TAFA-5 (TAFA-5)
Type: Family

This entry represents a group of animal proteins, including TAFA-5 from mammals. TAFA-5 is a secreted protein distantly related to the CC-chemokine family. It has been shown to inhibit postinjury neointima formation via sphingosine-1-phosphate receptor 2-G12/13-RhoA signaling . Together with its target receptor FPR2 can negatively regulate osteoclast formation .
LYR motif-containing protein 1 (LYRM1)
Type: Family

Proteins in this family contain a highly conserved tripeptide motif LYR close to the N terminus. Human LYR motif-containing protein 1 (LYRM1) is highly expressed in omental adipose tissue of obese subjects, promotes preadipocyte proliferation, and inhibits apoptosis of preadipocytes .