match idtarget lengthalignment lengthprobabilityE-valuecoveragematch description
1COG067536424099.94.6E-22[       ------------------------------------------]InsQTransposase
2pfam07282696199.87.3E-20[                                        ---------]OrfB_Zn_ribbonPutative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesise this domain is DNA-binding.
3pfam0138522616199.34.3E-11[       ---------------------------               ]OrfB_IS605Probable transposase. This family includes IS891, IS1136 and IS1341. DUF1225, pfam06774, has now been merged into this family.
4TIGR01766825799.13.7E-10[                                   ---------     ]tspaseT_teng_Ctransposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins.
5COG2888614194.20.018[                                          ------ ]COG2888Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family
6PRK12286573293.60.035[                                            -----]rpmF50S ribosomal protein L32; Reviewed
7pfam095381043792.60.055[                                           ------]FYDLN_acidProtein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif
8pfam10571262491.90.05[                                            ---- ]UPF0547Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif.
9PRK00432502791.30.072[                                            ---- ]PRK0043230S ribosomal protein S27ae; Validated
10TIGR04165503090.70.12[                                            ---- ]methano_modCysCys-rich peptide, TIGR04165 family. Members of this small peptide family occur strictly in a subset of archaeal methanogens. Members have four invariant Cys residues in two Cys-Xaa-Xaa-Cys-Gly motifs and may have other Cys residues as well. At least two members occur next to family TIGR04083 radical SAM enzymes predicted to act in peptide or protein modification.
11COG16451313590.40.14[                                         ------- ]COG1645Uncharacterized Zn-finger containing protein, UPF0148 family
12cd00656453190.30.14[                                            ---- ]Zn-ribbonC-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit. The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.
13COG1998512890.30.11[                                            ---- ]RPS27AERibosomal protein S27AE
14cd10511473189.50.15[                                            ---- ]Zn-ribbon_TFSC-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS). TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains.
15PRK14890592688.40.2[                                            ---- ]PRK14890putative Zn-ribbon RNA-binding protein; Provisional
16pfam07754181187.60.22[                                               - ]DUF1610Domain of unknown function (DUF1610). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
17PRK14890594186.10.46[                                          ------ ]PRK14890putative Zn-ribbon RNA-binding protein; Provisional
18pfam13240232186.00.28[                                            ---- ]zinc_ribbon_2zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773.
19TIGR04330128612485.72.4[                          --------------------   ]cas_Cpf1CRISPR-associated protein Cpf1, subtype PREFRAN. This family is the long protein of a novel CRISPR subtype, PREFRAN, which is most common in Prevotella and Francisella, although widely distributed. The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the helicase Cas3 and endonuclease Cas3-HD.
20pfam09297322985.10.55[                                            ---- ]zf-NADH-PPaseNADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
21COG2888612684.80.49[                                            ---- ]COG2888Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family
22PRK081738628084.80.86[                                   ------------- ]PRK08173DNA topoisomerase III; Validated
23COG1996493084.30.54[                                            ---- ]RPC10DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger
24COG3357974483.90.72[                                         --------]COG3357Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon
25pfam08274302783.50.67[                                            -----]PhnA_Zn_RibbonPhnA Zinc-Ribbon.
26COG10961882983.40.52[                                            -----]Csl4Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains
27PRK004201123882.60.76[                                         ------- ]PRK00420hypothetical protein; Validated
28TIGR01031553082.00.75[                                            -----]rpmF_bactribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
29PRK04179623380.60.63[                                            -----]rpl37e50S ribosomal protein L37e; Reviewed
30pfam13248262479.50.77[                                            ---- ]zf-ribbon_3zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773.
31pfam09151362778.91.1[                                            ---- ]DUF1936Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold.
32COG2126613578.50.91[                                            -----]RPL37ARibosomal protein L37E
33PRK14892991378.01.2[                                              -- ]PRK14892putative transcription elongation factor Elf1; Provisional
34COG28162793477.61[                                           ----- ]NPY1NADH pyrophosphatase NudC, Nudix superfamily
35pfam13453412576.91.2[                                            ---- ]zf-TFIIBTranscription factor zinc-finger.
36pfam01783563076.71.2[                                            -----]Ribosomal_L32pRibosomal L32p protein family.
37COG0333573176.31.5[                                            -----]RpmFRibosomal protein L32
38PRK095211893076.11.4[                                            -----]PRK09521exosome complex RNA-binding protein Csl4; Provisional
39COG15792393075.314[                                            -----]COG1579Predicted nucleic acid-binding protein, contains Zn-ribbon domain
40PRK0940111764175.11.1[                                          -------]PRK09401reverse gyrase; Reviewed
41cd13946542775.01.7[                                            ---- ]LysWLysine biosynthesis protein LysW. LysW functions as a carrier protein in the biosynthesis pathway of lysine. The C-terminal glutamate sidechain of LysW attaches to the amino group of alpha-aminoadipate (AAA); this peptide bond formation is catalyzed by the ligase LysX. AAA remains associated with LysW throughout its biosynthetic conversion to lysine. LysW also acts to protect the amino group of glutamate in arginine biosynthesis.
42PRK14892993874.81.2[                                           ------]PRK14892putative transcription elongation factor Elf1; Provisional
43pfam12760463274.81.8[                                           ----- ]Zn_Tnp_IS1595Transposase zinc-ribbon domain. This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA.
44cd00729342674.61.1[                                            -----]rubredoxin_SMRubredoxin, Small Modular nonheme iron binding domain containing a
45COG48881044274.31.6[                                           ------]Elf1Transcription elongation factor Elf1, contains Zn-ribbon domain
46pfam02150352974.31.8[                                            -----]RNA_POL_M_15KDRNA polymerases M/15 Kd subunit.
47pfam08271412973.71.8[                                            -----]TF_Zn_RibbonTFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
48COG15921662273.52.3[                                            ---- ]YotDRubrerythrin
49pfam03604322573.31.9[                                            ---- ]DNA_RNApol_7kDDNA directed RNA polymerase, 7 kDa subunit.
50pfam14803342672.71.6[                                            ---- ]Nudix_N_2Nudix N-terminal. Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases.
51pfam038338525572.41.4[          ---------                              ]PolC_DP2DNA polymerase II large subunit DP2.
52COG45301293472.41.5[                                            -----]COG4530Uncharacterized protein
53PRK03976902771.81.7[                                            ---- ]rpl37ae50S ribosomal protein L37Ae; Reviewed
54TIGR004675154671.74.4[                                          -------]lysS_archlysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
55COG15714213571.11.6[                                           ------]TiaStRNA(Ile2) C34 agmatinyltransferase TiaS
56COG1997892669.92.2[                                            ---- ]RPL43ARibosomal protein L37AE/L43A
57TIGR04104942969.91.4[                                            -----]cxxc_20_cxxccxxc_20_cxxc protein. This small, uncommon, poorly conserved protein is found primarily in the Firmicutes. It features are pair of CxxC motifs separated by about 20 amino acids, followed by a highly hydrophobic region of about 45 amino acids. It has no conserved gene neighborhood, and its function is unknown.
58pfam135975433869.73.1[                                         ------- ]NRDDAnaerobic ribonucleoside-triphosphate reductase.
59pfam13719372969.22.4[                                            ---- ]zinc_ribbon_5zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773.
60cd033611703068.32.1[                                           ----- ]TOPRIM_TopoIA_RevGyrTopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
61pfam06677413267.92.3[                                          ------ ]Auto_anti-p27Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis.
62PRK00398462767.52[                                            ---- ]rpoPDNA-directed RNA polymerase subunit P; Provisional
63pfam10058513666.74.3[                                           ----- ]DUF2296Predicted integral membrane metal-binding protein (DUF2296). This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function.
64cd00350332464.92.6[                                            ---- ]rubredoxin_likeRubredoxin_like; nonheme iron binding domain containing a
65TIGR005152852762.22.7[                                            ---- ]accDacetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
66TIGR00280922562.24.1[                                            ---- ]eL43_euk_archribosomal protein eL43. This model finds eukaryotic ribosomal protein eL43 (previously L37a) and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
67PRK002412563562.23.7[                                           ----- ]nudCNADH pyrophosphatase; Reviewed
68PRK056542922861.92.2[                                            ---- ]PRK05654acetyl-CoA carboxylase subunit beta; Validated
69TIGR01206542961.84.1[                                            ---- ]lysWlysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
70TIGR02098382961.14.4[                                            ---- ]MJ0042_CXXCMJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
71pfam13717362960.44.5[                                            ---- ]zinc_ribbon_4zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773.
72pfam072951484360.33.3[                                         ------- ]DUF1451Protein of unknown function (DUF1451). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
73cd096806502758.649[                                            ---- ]Cas10_IIICRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family
74COG15941133257.85.1[                                            -----]RPB9DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS
75pfam12773452757.86.6[                                            -----]DZRDouble zinc ribbon. This family consists of a pair of zinc ribbon domains.
76cd10509463157.25.3[                                            ---- ]Zn-ribbon_RPC11C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III. The C-terminal zinc ribbon domain (C_ribbon) of subunit C11 (C-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 have strong homology to RPB9 of Pol II and RPA12 of Pol I. C-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker.
77COG111011873257.24.1[                                           ------]TopG2Reverse gyrase
78PRK082706564156.44.6[                                         --------]PRK08270anaerobic ribonucleoside triphosphate reductase; Provisional
79TIGR013841043556.35.6[                                           ----- ]TFS_archtranscription factor S, archaeal. This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
80pfam13824542355.65.1[                                            ---- ]zf-Mss51Zinc-finger of mitochondrial splicing suppressor 51. Mss51 regulates the expression of cytochrome oxidase, so this domain is probably DNA-binding.
81TIGR023001293154.75.4[                                           ----- ]FYDLN_acidTIGR02300 family protein. Members of this family are bacterial proteins with a conserved motif
82COG29563896654.46.3[                                    ------------ ]YciMLipopolysaccharide biosynthesis regulator YciM, contains six TPR domains and a predicted metal-binding C-terminal domain
83pfam09723433053.54.8[                                            -----]Zn-ribbon_8Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
84PRK0110327410153.35.2[                                ---------------- ]PRK01103formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
85pfam14446553451.710[                                           ------]Prok-RING_1Prokaryotic RING finger family 1. RING finger family found sporadically in bacteria and archaea, and associated in gene neighborhoods with other components of the ubiquitin-based signaling and degradation system, including ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase. The bacterial versions contain transmembrane helices.
86COG13794033450.75.4[                                           ------]YqxKPHP family phosphoesterase with a Zn ribbon
87PRK123362013049.86.4[                                            ---- ]PRK12336translation initiation factor IF-2 subunit beta; Provisional
88pfam02591562849.46.2[                                            ---- ]DUF164Putative zinc ribbon domain. Structural modelling suggests this domain may bind nucleic acids.
89PRK1471413378948.78.1[             ---------------                     ]PRK14714DNA polymerase II large subunit; Provisional
90cd044761662948.39.5[                                            ---- ]RPA1_DBD_CRPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.
91cd10507473147.79.9[                                            ---- ]Zn-ribbon_RPA12C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I. The C-terminal zinc ribbon domain (C_ribbon) of subunit A12 (C-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.
92PRK039881383247.57[                                            -----]PRK03988translation initiation factor IF-2 subunit beta; Validated
93PRK1471516272147.39.6[                                            ---- ]PRK14715DNA polymerase II large subunit; Provisional
94COG02662732847.17.3[                                            ---- ]NeiFormamidopyrimidine-DNA glycosylase
95COG15451402647.18.1[                                            ---- ]COG1545Uncharacterized OB-fold protein, contains Zn-ribbon domain
96PRK072256053147.18.2[                                            -----]PRK07225DNA-directed RNA polymerase subunit B'; Validated
97COG07772942746.75.1[                                            ---- ]AccDAcetyl-CoA carboxylase beta subunit
98pfam06827302646.18.3[                                            ---- ]zf-FPG_IleRSZinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:
99PRK039541211645.85.8[                                            --   ]PRK03954ribonuclease P protein component 4; Validated
100PRK092637112945.78.3[                                            ---- ]PRK09263anaerobic ribonucleoside triphosphate reductase; Provisional
101COG2093642545.610[                                            ---- ]Spt4RNA polymerase subunit RPABC4/transcription elongation factor Spt4
102TIGR024875794445.416[                                        -------- ]NrdDanaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
103TIGR0035410952645.19.4[                                            -----]polCDNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
104PRK124952266345.130[                                    -------------]PRK12495hypothetical protein; Provisional
105COG13287004044.818[                                         ------- ]NrdDAnaerobic ribonucleoside-triphosphate reductase
106TIGR02605523144.79[                                            -----]CxxC_CxxC_SSSSputative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
107PRK040114113244.18.5[                                            -----]PRK04011peptide chain release factor 1; Provisional
108PRK085796252643.99.5[                                            ---- ]PRK08579anaerobic ribonucleoside triphosphate reductase; Provisional
109PRK074186162543.69.4[                                            ---- ]PRK07418acetolactate synthase 3 catalytic subunit; Reviewed
110pfam14354563143.511[                                            ---- ]Lar_restr_allevRestriction alleviation protein Lar. This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli. This protein modulates the activity of the Escherichia coli restriction and modification system.
111PRK142823693042.912[                                           ----- ]PRK14282chaperone protein DnaJ; Provisional
112PRK1471413374342.510[                                          -------]PRK14714DNA polymerase II large subunit; Provisional
113COG03751152742.410[                                            -----]HybFHydrogenase maturation metallochaperone HypA/HybF, involved in Ni insertion
114PRK132088003742.111[                                           ------]valSvalyl-tRNA synthetase; Reviewed
115PRK123666373241.911[                                            -----]PRK12366replication factor A; Reviewed
116cd025828611541.98.3[                                              ---]RNAP_archeal_A'A' subunit of archaeal RNA polymerase (RNAP). A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
117pfam01907543441.711[                                            -----]Ribosomal_L37eRibosomal protein L37e. This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc.
118COG16561653041.112[                                            ---- ]COG1656Uncharacterized conserved protein, contains PIN domain
119TIGR036705993040.912[                                            -----]rpoB_archDNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
120cd016755554540.311[                                        -------- ]RNR_IIIClass III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.
121PRK122685561339.821[                                 -               ]PRK12268methionyl-tRNA synthetase; Reviewed
122PRK065569532439.813[                                            ---- ]PRK06556vitamin B12-dependent ribonucleotide reductase; Validated
123pfam01096392839.415[                                            ---- ]TFIIS_CTranscription factor S-II (TFIIS).
124TIGR036764033139.112[                                            ---- ]aRF1/eRF1peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
125pfam145772356438.818[                       ----------                ]SEO_CSieve element occlusion C-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the C-terminus of SEO proteins.
126pfam01780902737.715[                                            ---- ]Ribosomal_L37aeRibosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.
127COG11987302837.414[                                         -----   ]PriAPrimosomal protein N' (replication factor Y) - superfamily II helicase
128COG13845214237.415[                                          -------]LysSLysyl-tRNA synthetase, class I
129PRK142783782037.312[                                            ---- ]PRK14278chaperone protein DnaJ; Provisional
130PRK04136482837.118[                                            -----]rpl40e50S ribosomal protein L40e; Provisional
131pfam058765573237.018[                                            -----]Terminase_GpAPhage terminase large subunit (GpA). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities.
132COG28704675836.812[                               ------------      ]RfaEADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase
133COG52041122936.513[                                            ---- ]SPT4Transcription elongation factor SPT4
134COG51799684236.455[                                         ------- ]TAF1Transcription initiation factor TFIID, subunit TAF1
135pfam09855641336.017[                                            --   ]DUF2082Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082). This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function.
136TIGR0057727210535.913[                               ----------------- ]fpgDNA-formamidopyrimidine glycosylase. All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
137cd07157862935.78.8[                                            -----]2DBD_NR_DBD1The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
138PRK04023112110335.517[          ------------------                     ]PRK04023DNA polymerase II large subunit; Validated
139pfam05129743535.325[                                            -----]Elf1Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. ELF1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae.
140PRK085668821534.813[                                              ---]PRK08566DNA-directed RNA polymerase subunit A'; Validated
141PRK110321603334.718[                                           ----- ]PRK11032hypothetical protein; Provisional
142PRK055806794834.716[                                         ------- ]PRK05580primosome assembly protein PriA; Validated
143PRK003908051734.614[                                               --]leuSleucyl-tRNA synthetase; Validated
144pfam08209331134.323[                                               - ]Sgf11Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation.
145pfam05810582834.36.1[                                            -----]NinFNinF protein. This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
146PRK055826504234.046[                                       -------   ]PRK05582DNA topoisomerase I; Validated
147TIGR03655533033.727[                                            -----]anti_R_Larrestriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
148pfam08273393133.127[                                            -----]Prim_Zn_RibbonZinc-binding domain of primase-helicase.
149pfam05265603432.613[                                           ----- ]DUF723Protein of unknown function (DUF723). This family contains several uncharacterized proteins from Neisseria meningitidis. These proteins may have a role in DNA-binding.
150TIGR003731582732.29.5[                                            ---- ]TIGR00373transcription factor E. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
151COG36771295032.134[                                        ---------]InsATransposase
152pfam019213553831.618[                                           ------]tRNA-synt_1ftRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes.
153pfam13465261331.623[                                              -- ]zf-H2C2_2Zinc-finger double domain.
154PRK082716235031.231[                                       --------- ]PRK08271anaerobic ribonucleoside triphosphate reductase; Provisional
155TIGR0105411713330.818[                                           ------]rgyreverse gyrase. This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
156TIGR023908681530.714[                                              ---]RNA_pol_rpoA1DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
157pfam011551133230.421[                                           ------]HypAHydrogenase expression/synthesis hypA family. Four conserved cysteines lie either side of the least conserved region.
158COG3809882630.223[                                            ---- ]COG3809Predicted nucleic acid-binding protein, contains Zn-finger domain
159cd07167932229.916[                                            ---- ]NR_DBD_Lrh-1_likeThe DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as monomers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
160pfam04606472629.724[                                            ---- ]Ogr_DeltaOgr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
161pfam146203605929.416[                  ---------                      ]YPEBYpeB sporulation. YPEB is a protein that is necessary for the functioning of SleB during spore-cortex hydrolysis.
162pfam13005461529.329[                                            --   ]zf-IS66zinc-finger binding domain of transposase IS66. This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase.
163cd15728633029.222[                                           ----- ]FYVE_ANFY1FYVE domain found in ankyrin repeat and FYVE domain-containing protein 1 (ANFY1) and similar proteins. ANFY1, also termed ankyrin repeats hooked to a zinc finger motif (Ankhzn), is a novel cytoplasmic protein that belongs to a new group of double zinc finger proteins involved in vesicle or protein transport. It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, ankyrin repeats in the middle, and a C-terminal FYVE domain.
164COG16011513129.210[                                            ---- ]GCD7Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain
165PRK086657522728.428[                                            ---- ]PRK08665ribonucleotide-diphosphate reductase subunit alpha; Validated
166COG53491262828.316[                                            ---- ]COG5349Uncharacterized conserved protein, DUF983 family
167PRK147249875127.962[                                       --------  ]PRK14724DNA topoisomerase III; Provisional
168PRK142833783027.527[                                            ---- ]PRK14283chaperone protein DnaJ; Provisional
169cd006743533927.431[                                           ------]LysRS_core_class_Icatalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
170PRK139452823427.324[                                           ----- ]PRK13945formamidopyrimidine-DNA glycosylase; Provisional
171pfam06093772327.226[                                            ---- ]Spt4Spt4/RpoE2 zinc finger. This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.
172PRK132641773227.119[                      -----                      ]PRK132643-hydroxyanthranilate 3,4-dioxygenase; Provisional
173PRK122685561226.922[                                            -    ]PRK12268methionyl-tRNA synthetase; Reviewed
174COG2176144417426.831[                   ------------------------------]PolCDNA polymerase III, alpha subunit (gram-positive type)
175pfam018731252926.725[                                            ---- ]eIF-5_eIF-2BDomain found in IF2B/IF5. This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger.
176PRK077266585426.547[                                       --------- ]PRK07726DNA topoisomerase III; Provisional
177TIGR032695202526.127[                                            ---- ]met_CoM_red_A2methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.
178COG11987303026.131[                                           ----- ]PriAPrimosomal protein N' (replication factor Y) - superfamily II helicase
179COG36734239326.12.1E+02[                          ---------------        ]COG3673Uncharacterized protein, PA2063/DUF2235 family
180PRK0856511032825.929[                                            -----]PRK08565DNA-directed RNA polymerase subunit B; Provisional
181pfam12172372425.927[                                            ---- ]DUF35_NRubredoxin-like zinc ribbon domain (DUF35_N). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Rv3521. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.
182pfam005082015125.41.2E+02[                                    --------     ]PPV_E2_NE2 (early) protein, N terminal.
183pfam143531281325.235[                                               - ]CpXCCpXC protein. This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs.
184PRK040004113924.939[                                          ------ ]PRK04000translation initiation factor IF-2 subunit gamma; Validated
185TIGR028894358624.932[             --------------                      ]spore_YpeBgermination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function.
186COG351310883524.83.1E+02[                                      -----      ]Cas9CRISPR/Cas system Type II associated protein, contains McrA/HNH and RuvC-like nuclease domains
187pfam00301472724.433[                                            ---- ]RubredoxinRubredoxin.
188pfam103331806124.492[                  ---------                      ]Pga1GPI-Mannosyltransferase II co-activator. Pga1 is found only in yeasts and not in mammals. It localizes in the ER as a glycosylated integral membrane protein. It binds to the GPI-mannosyltransferase II subunit of the GPI and it is responsible for the second mannose addition to GPI precursors. The GPI-anchoring complex is a glycolipid that functions as a membrane anchor for many cell-surface proteins.
189COG16751762924.417[                                            ---- ]TFA1Transcription initiation factor IIE, alpha subunit
190PRK142983774223.942[                                         ------- ]PRK14298chaperone protein DnaJ; Provisional
191pfam07503342423.830[                                            ---- ]zf-HYPFHypF finger. The HypF family of proteins are involved in the maturation and regulation of hydrogenase. In the N-terminus they appear to have two Zinc finger domains, as modelled by this family.
192PRK004812423523.532[                                            -----]PRK00481NAD-dependent deacetylase; Provisional
193TIGR028275955223.365[                                       --------- ]RNR_anaer_Bdellanaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
194PRK08351611723.235[                                            ---  ]PRK08351DNA-directed RNA polymerase subunit E''; Validated
195PRK055806793122.641[                                           ----- ]PRK05580primosome assembly protein PriA; Validated
196pfam01485632822.650[                                            ---- ]IBRIBR domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.
197pfam019271464322.584[                                         ------- ]Mut7-CMut7-C RNAse domain. RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.
198pfam12738634821.770[                                 ----------      ]PTCB-BRCTtwin BRCT domain. This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair.
199PRK148112693021.435[                                            ---- ]PRK14811formamidopyrimidine-DNA glycosylase; Provisional
200PRK071117354021.340[                                         ------- ]PRK07111anaerobic ribonucleoside triphosphate reductase; Provisional
201PRK1470116383621.230[                                           ------]PRK14701reverse gyrase; Provisional
202pfam093343884721.118[                                        -------- ]tRNA-synt_1gtRNA synthetases class I (M). This family includes methionyl tRNA synthetases.
203COG1552502821.033[                                            -----]RPL40ARibosomal protein L40E
204pfam08234746220.82.7E+02[                       ----------                ]Spindle_Spc25Chromosome segregation protein Spc25. This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex, and in vertebrates it forms part of the Ndc80 complex.
205cd09394551920.661[                                              ---]LIM1_RgaThe first LIM domain of Rga GTPase-Activating Proteins. The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.
206PRK007505104020.546[                                           ------]lysKlysyl-tRNA synthetase; Reviewed
207PRK059781482820.524[                                            ---- ]PRK05978hypothetical protein; Provisional
208cd07169902620.435[                                            ---- ]NR_DBD_GCNF_likeDNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
209pfam145772351720.435[                                           ---   ]SEO_CSieve element occlusion C-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the C-terminus of SEO proteins.
210COG4049651320.440[                                              -- ]COG4049Uncharacterized protein, contains archaeal-type C2H2 Zn-finger
211PRK104452632720.351[                                            ---- ]PRK10445endonuclease VIII; Provisional
212COG35772159720.258[                     -------------------         ]COG3577Predicted aspartyl protease