match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	PRK13702	85	28	60.0	16	[                          --------               ]	PRK13702	replication protein; Provisional
2	pfam13384	50	34	56.7	3.9	[ --------                                        ]	HTH_23	Homeodomain-like domain.
3	pfam01527	75	21	54.4	11	[                            -----                ]	HTH_Tnp_1	Transposase. 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.
4	pfam13936	44	31	48.2	6.8	[  --------                                       ]	HTH_38	Helix-turn-helix domain. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
5	pfam03786	350	17	37.6	15	[                          ----                   ]	UxuA	D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
6	PRK03906	385	17	35.6	19	[                          ----                   ]	PRK03906	mannonate dehydratase; Provisional
7	pfam06777	146	52	34.5	68	[               -------------                     ]	DUF1227	Protein of unknown function (DUF1227). This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
8	pfam04867	114	51	33.4	46	[               -------------                     ]	DUF643	Protein of unknown function (DUF643). Protein of unknown function found in Borrelia burgdorferi, the Lyme disease spirochete.
9	TIGR01565	58	25	32.9	30	[                           ------                ]	homeo_ZF_HD	homeobox 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.
10	pfam10650	23	11	32.8	14	[                    ---                          ]	zf-C3H1	Putative 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.
11	cd11803	55	49	32.2	16	[                                   ------------- ]	SH3_Endophilin_A	Src 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.
12	pfam10723	85	21	28.8	1.1E+02	[                          ------                 ]	RepB-RCR_reg	Replication 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.
13	COG1312	362	17	26.5	31	[                          ----                   ]	UxuA	D-mannonate dehydratase
14	cd15903	104	43	24.8	2.1E+02	[                       -----------               ]	Dicer_PBD	Partner-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.
15	COG0277	459	49	23.8	2.1E+02	[                        -------------            ]	GlcD	FAD/FMN-containing dehydrogenase
16	COG4650	531	29	23.6	73	[                               ---------         ]	RtcR	Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain
17	cd01109	113	22	23.5	21	[    -----                                        ]	HTH_YyaN	Helix-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.
18	pfam08281	54	36	23.2	27	[---------                                        ]	Sigma70_r4_2	Sigma-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.
19	COG2137	174	54	23.1	2.9E+02	[                 -----------------               ]	RecX	SOS response regulatory protein OraA/RecX, interacts with RecA
20	cd00569	42	29	22.7	85	[                         -------                 ]	HTH_Hin_like	Helix-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.
21	pfam02796	45	31	22.5	1.3E+02	[                         -------                 ]	HTH_7	Helix-turn-helix domain of resolvase.
22	pfam13309	64	23	22.0	56	[                          ------                 ]	HTH_22	HTH domain. This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.
23	pfam08100	50	22	21.3	77	[        ------                                   ]	Dimerization	Dimerization 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.