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date Thu, 22 Dec 2016 04:45:31 -0500
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Proteins with PFAM domains:
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<center><b>PROKKA_00001</b><br>
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<pre> 
MENNLENLTIGVFAKAAGVNVETIRFYQRKGLLREPDKPYGSIRRYGEADVVRVKFVKSAQ<br>RLGFSLDEIAELLRLDDGTHCEEASSLAEHKLKDVREKMADLARMETVLSELVCACHARK<br>GNVSCPLIASLQGEAGLARSAMP*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00376> PF00376</a>merR; <br>MerR family regulatory protein Prosite & Pfam-B_3021 (Release 7.5) 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<a href=http://pfam.xfam.org/family/PF09278> PF09278</a>MerR, DNA binding<br>Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold  . 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<center><b>PROKKA_00002</b><br>
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MSEPQNGRGALFAGGLAAILASTCCLGPLVLVALGFSGAWIGNLTVLEPYRPLFIGAALVA<br>LFFAWKRIYRPVQACKPGEVCAIPQVRATYKLIFWIVAVLVLVALGFPYVVPFFY*
 </pre>
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<a href=http://pfam.xfam.org/family/PF02411> PF02411</a>MerT mercuric transport protein<br>MerT mercuric transport protein MerT is an mercuric transport integral membrane protein and  is responsible for transport of the Hg2+ iron from periplasmic  MerP (also part of the transport system) to mercuric reductase (MerE). 

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<center><b>PROKKA_00003</b><br>
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MKKLFASLALAAAVAPVWAATQTVTLAVPGMTCAACPITVKKALSKVEGVSKVDVGFEKRE<br>AVVTFDDTKASVQKLTKATADAGYPSSVKQ*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00403> PF00403</a>Heavy-metal-associated domain<br>

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<center><b>PROKKA_00004</b><br>
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MGLMTRIADKTGALGSVVSAMGCAACFPALASFGAAIGLGFLSQYEGLFISRLLPLFAALA<br>FLANALGWFSHRQWLRSLLGMIGPAIVFAATVWLLGNWWTANLMYVGLALMIGVSIWDFV<br>SPAHRRCGPDGCELPAKRL*
 </pre>
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<a href=http://pfam.xfam.org/family/PF03203> PF03203</a>MerC mercury resistance protein<br>MerC mercury resistance protein 

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<center><b>PROKKA_00005</b><br>
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MSTLKITGMTCDSCAVHVKDALEKVPGVQSADVSYAKGSAKLAIEVGTSPDALTAAVAGLG<br>YRATLADAPSVSTPGGLLDKMRDLLGRNDKTGSSGALHIAVIGSGGAAMAAALKAVEQGA<br>RVTLIERGTIGGTCVNVGCVPSKIMIRAAHIAHLRRESPFDGGIAATTPTIQRTALLAQQ<br>QARVDELRHAKYEGILEGNPAITVLHGSARFKDNRNLIVQLNDGGERVVAFDRCLIATGA<br>SPAVPPIPGLKDTPYWTSTEALVSETIPKRLAVIGSSVVALELAQAFARLGAKVTILARS<br>TLFFREDPAIGEAVTAAFRMEGIEVREHTQASQVAYINGEGDGEFVLTTAHGELRADKLL<br>VATGRAPNTRKLALDATGVTLTPQGAIVIDPGMRTSVEHIYAAGDCTDQPQFVYVAAAAG<br>TRAAINMTGGDAALNLTAMPAVVFTDPQVATVGYSEAEAHHDGIKTDSRTLTLDNVPRAL<br>ANFDTRGFIKLVVEEGSGRLIGVQAVAPEAGELIQTAALAIRNRMTVQELADQLFPYLTM<br>VEGLKLAAQTFNKDVKQLSCCAG*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00403> PF00403</a>Heavy-metal-associated domain<br>

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<a href=http://pfam.xfam.org/family/PF07992> PF07992</a>Pyridine nucleotide-disulphide oxidoreductase<br>Pyridine nucleotide-disulphide oxidoreductase This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.  This domain is actually  a small NADH binding domain within a larger FAD binding domain. 

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<a href=http://pfam.xfam.org/clan/CL0063> CL0063</a> FAD/NAD(P)-binding Rossmann fold Superfamily A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme.  The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction.  Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site  .  In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD. 

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<a href=http://pfam.xfam.org/family/PF00070> PF00070</a>pyr_redox; <br>Pyridine nucleotide-disulphide oxidoreductase Sonnhammer ELL, Griffiths-Jones SR This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.  This domain is actually  a small NADH binding domain within a larger FAD binding domain. 

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<a href=http://pfam.xfam.org/clan/CL0063> CL0063</a> FAD/NAD(P)-binding Rossmann fold Superfamily A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme.  The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction.  Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site  .  In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD. 

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<a href=http://pfam.xfam.org/family/PF02852> PF02852</a>pyr_redox_dim; <br>Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. 

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<center><b>PROKKA_00006</b><br>
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MSAYTVSQLAHNAGVSVHIVRDYLVRGLLRPVACTTGGYGVFDDAALQRLCFVRAAFEAGI<br>GLDALARLCRALDAADGAQAAAQLAVLRQLVERRRAALAHLDAQLASMPAERAHEEALP*<br>
 </pre>
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<a href=http://pfam.xfam.org/family/PF13411> PF13411</a>MerR HTH family regulatory protein<br>MerR HTH family regulatory protein 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<center><b>PROKKA_00007</b><br>
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VNAPDKLPPETRQPVSGYLWGALAVLTCPCHLPILAAVLAGTTAGAFLGEHWGVAALALTG<br>LFVLAVTRLLRAFRGGS*
 </pre>
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<a href=http://pfam.xfam.org/family/PF05052> PF05052</a>MerE protein<br>The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon. The protein is thought not to have any direct role in conferring mercury resistance to the organism but may be a mercury resistance transposon [1,2].  

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<center><b>PROKKA_00008</b><br>
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MTSSQPAGWTAAELAQAAARGQLDLHYQPLVDLRDHRIAGAEALMRWRHPRLGLLPPGQFL<br>PLAESFGLMPEIGAWVLGEACRQMHKWQGPAWQPFRLAINVSASQVGPTFDDEVKRVLAD<br>MALPAELLEIELTESVAFGNPALFASFDALRAIGVRFAADDFGTGYSCLQHLKCCPITTL<br>KIDQSFVARLPDDARDQTIVRAVIQLAHGLGMDVIFRRRLHQLIGRNGCCAASS*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00563> PF00563</a>DUF2; <br>Alignment kindly provided by SMART This domain is found in diverse bacterial signaling proteins.  It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function  . The domain contains many conserved acidic residues  that could participate in metal binding and might form the phosphodiesterase active site  . 

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<center><b>PROKKA_00009</b><br>
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MATDTPRIPEQGVATLPDEAWERARRRAEIISPLAQSETVGHEAADMAAQALGLSRRQVYV<br>LIRRARQGSGLVTDLVPGQSGGGKGKGRLPEPVERVIHELLQKRFLTKQKRSLAAFHREV<br>TQVCKAQKLRVPARNTVALRIASLDPRKVIRRREGQDAARDLQGVGGEPPAVTAPLEQVQ<br>IDHTVIDLIVVDDRDRQPIGRPYLTLAIDVFTRCVLGMVVTLEAPSAVSVGLCLVHVACD<br>KRPWLEGLNVEMDWQMSGKPLLLYLDNAAEFKSEALRRGCEQHGIRLDYRPLGQPHYGGI<br>VERIIGTAMQMIHDELPGTTFSNPDQRGDYDSENKAALTLRELERWLTLAVGTYHGSVHN<br>GLLQPPAARWAEAVARVGVPAVVTRATSFLVDFLPILRRTLTRTGFVIDHIHYYADGHCC<br>K*
 </pre>
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<a href=http://pfam.xfam.org/family/PF13518> PF13518</a>Helix-turn-helix domain<br>This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding. 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<a href=http://pfam.xfam.org/family/PF00665> PF00665</a>Integrase core domain<br>Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  The amino-terminal domain is a zinc binding domain Pfam:PF02022.  This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site  . 

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<a href=http://pfam.xfam.org/clan/CL0219> CL0219</a> Ribonuclease H-like superfamily This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H. 

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<center><b>PROKKA_00010</b><br>
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MNPFKGRHFQRDIILWAVRWYCKYGISYRELQEMLAERGVNVDHSTIYRWVQRYAPEMEKR<br>LRWYWRNPSDLCPWHMDETYVKVNGRWAYLYRAVDSRGRTVDFYLSSRRNSKAAYRFLGK<br>ILNNVKKWQIPRFINTDKAPAYGRALALLKREGRCPSDVEHRQIKYRNNVIECDHGKLKR<br>IIGATLGFKSMKTAYATIKGIEVMRALRKGQASAFYYGDPLGEMRLVSRVFEM*
 </pre>
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<a href=http://pfam.xfam.org/family/PF13610> PF13610</a>DDE domain<br>This DDE domain is found in a wide variety of transposases including those found in IS240, IS26, IS6100 and IS26. 

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<a href=http://pfam.xfam.org/clan/CL0219> CL0219</a> Ribonuclease H-like superfamily This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H. 

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<center><b>PROKKA_00011</b><br>
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MKLRHLDIFYAVMTCGSLTRAAEVLHISQPAASKALKHAEH*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00126> PF00126</a>Bacterial regulatory helix-turn-helix protein, lysR family<br>Bacterial regulatory helix-turn-helix protein, lysR family 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<center><b>PROKKA_00013</b><br>
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MILDASYTLLVACIALLIGMFVVKFTPFLQKNHIPEAVVGGFIVAIVLLIIDKTSGYSFTF<br>DASLQSLLMLTFFSSIGLSSDFSRLIKGGKPLVLLTIAVTILIAIQNTVGMSMAVMMNES<br>PFIGLIAGSITLTGGHGNAGAWGPILADKYGVTGAVELAMACATLGLVLGGLVGGPVARH<br>LLKKVSIPKTTEQERDTIVEAFEQPSVKRKINANNVIETISMLIICIVVGGYISALFKDT<br>FLQLPTFVWCLFVGIIIRNTLTHVFKHEVFEPTVDVLGSVALSLFLAMALMSLKFGQLAS<br>MAGPVLIIIAVQTVVMVLFACFVTFKMMGKDYDAVVISAGHCGFGMGATPTAIANMQTVT<br>KAFGPSHKAFLVVPMVGAFIVDISNSILIKIFIEIGTYFT*
 </pre>
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<a href=http://pfam.xfam.org/family/PF03616> PF03616</a>Sodium/glutamate symporter<br>

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<a href=http://pfam.xfam.org/clan/CL0064> CL0064</a> CPA/AT transporter superfamily This Clan contains transporter proteins that belong to the CPA superfamily and AT superfamily according to TCDB  . 

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<center><b>PROKKA_00014</b><br>
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MIAVIFEVQIQPDQQTRYLTLAEELRPLLSHVAGFISIERFQSLATEGKMLSLSWWENEYA<br>VLQWKNHVLHAKAQQEGRESIFDFYKISIAHITREYSFKKDKDNV*
 </pre>
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<a href=http://pfam.xfam.org/family/PF03992> PF03992</a>Antibiotic biosynthesis monooxygenase<br>Antibiotic biosynthesis monooxygenase This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 (Swiss:Q9X9W3) is  suggestive that the other proteins function as  multimers. There is also a conserved histidine which is likely to be an active site residue. 

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<a href=http://pfam.xfam.org/clan/CL0032> CL0032</a> Dimeric alpha/beta barrel superfamily This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel.  The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases. 

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<center><b>PROKKA_00015</b><br>
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<pre> 
MFDVHVVLDNQIGQLALLGKTLGNKGIGLEGGGIFTVGDECHAHFLVEQGKEAKIALEQAG<br>LLVLAIRTPLIRKLKQEKPGELGEIARVLAENNINILVQYSDHANQLILITDNDSMAASV<br>TLPWAIK*
 </pre>
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<a href=http://pfam.xfam.org/family/PF01842> PF01842</a>ACT domain<br>This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme.  The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine  . Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585 

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<a href=http://pfam.xfam.org/clan/CL0070> CL0070</a> These domains are involved in binding to amino-acids and causing allosteric regulation of linked enzyme domains  . The relationship between these two families was first noticed in  . 

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<center><b>PROKKA_00016</b><br>
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MSDISRVKILSALMDGRAWTATELSSVANISASTASSHLSKLLDCQLITVVAQGKHRYFRL<br>AGKDIAELMESMMGISLNHGVHARVSTPVHLRKARTCYDHLAGEVAVKIYDSLCQQQWIT<br>ENGSMITLSGIQYFHEMGIDVPSKHSRKICCACLDWSERRFHLGGYVGAALFSLYESKGW<br>LTRHLGYREVTITEKGYAAFKTHFHI*
 </pre>
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<a href=http://pfam.xfam.org/family/PF12840> PF12840</a>Helix-turn-helix domain<br>This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins. 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

</p>
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<center><b>PROKKA_00017</b><br>
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<pre> 
MSRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLD<br>RHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLC<br>QQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQG<br>AEPAFLFGLELIICGLEKQLKCESGS*
 </pre>
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<a href=http://pfam.xfam.org/family/PF00440> PF00440</a>tetR; <br>Bacterial regulatory proteins, tetR family 

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<a href=http://pfam.xfam.org/clan/CL0123> CL0123</a> This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif. 

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<a href=http://pfam.xfam.org/family/PF02909> PF02909</a>tetR_C; <br>Tetracyclin repressor, C-terminal all-alpha domain 

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<a href=http://pfam.xfam.org/clan/CL0174> CL0174</a> TetR protein, C-terminal domain-like This clan features families of transcriptional regulators for multidrug efflux pumps, which belong to the TetR superfamily. They are induced by the presence of a variety of factors, such as antibiotics or organic solvents. The C-terminal region featured in these families is thought to contain the inducer-binding site; the divergent sequences in this region allow for the binding of a variety of different inducers [1-4]. 

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