match idtarget lengthalignment lengthprobabilityE-valuecoveragematch description
1PRK13702852860.016[                          --------               ]PRK13702replication protein; Provisional
2pfam13384503456.73.9[ --------                                        ]HTH_23Homeodomain-like domain.
3pfam01527752154.411[                            -----                ]HTH_Tnp_1Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
4pfam13936443148.26.8[  --------                                       ]HTH_38Helix-turn-helix domain. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
5pfam037863501737.615[                          ----                   ]UxuAD-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
6PRK039063851735.619[                          ----                   ]PRK03906mannonate dehydratase; Provisional
7pfam067771465234.568[               -------------                     ]DUF1227Protein of unknown function (DUF1227). This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
8pfam048671145133.446[               -------------                     ]DUF643Protein of unknown function (DUF643). Protein of unknown function found in Borrelia burgdorferi, the Lyme disease spirochete.
9TIGR01565582532.930[                           ------                ]homeo_ZF_HDhomeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam00046. It is found in both C4 and C3 plants.
10pfam10650231132.814[                    ---                          ]zf-C3H1Putative zinc-finger domain. This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
11cd11803554932.216[                                   ------------- ]SH3_Endophilin_ASrc homology 3 domain of Endophilin-A. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms (A1, A2, and A3). Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. They tubulate membranes and regulate calcium influx into neurons to trigger the activation of the endocytic machinery. They are also involved in the sorting of plasma membrane proteins, actin filament assembly, and the uncoating of clathrin-coated vesicles for fusion with endosomes. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies.
12pfam10723852128.81.1E+02[                          ------                 ]RepB-RCR_regReplication regulatory protein RepB. This is a family of proteins which regulate replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of replication of RCR plasmids occurs mainly at initiation of leading strand synthesis at the dso, such that Rep protein concentration controls plasmid replication.
13COG13123621726.531[                          ----                   ]UxuAD-mannonate dehydratase
14cd159031044324.82.1E+02[                       -----------               ]Dicer_PBDPartner-binding domain of the endoribonuclease Dicer. The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases.
15COG02774594923.82.1E+02[                        -------------            ]GlcDFAD/FMN-containing dehydrogenase
16COG46505312923.673[                               ---------         ]RtcRSigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain
17cd011091132223.521[    -----                                        ]HTH_YyaNHelix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
18pfam08281543623.227[---------                                        ]Sigma70_r4_2Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
19COG21371745423.12.9E+02[                 -----------------               ]RecXSOS response regulatory protein OraA/RecX, interacts with RecA
20cd00569422922.785[                         -------                 ]HTH_Hin_likeHelix-turn-helix domain of Hin and related proteins. This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.
21pfam02796453122.51.3E+02[                         -------                 ]HTH_7Helix-turn-helix domain of resolvase.
22pfam13309642322.056[                          ------                 ]HTH_22HTH domain. This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.
23pfam08100502221.377[        ------                                   ]DimerizationDimerization domain. This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerization of these proteins.