Citrus Sinensis ID: 026799

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230---
Protein Sequence
MSKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHcccEEEEcccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHccccHHHHHHHHHHHHcccccEEHHHHHHHHcccccHHHHHHHHHHHHHcccEEEEEEccccccEEEEEEccccccccccccccccccHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccEEEccHHHHHHHHHHHHEcccEEEEEccccccEcccccccEEEEEcccccccccccccccccccccccccEccccccccccccccHHHHHHHcc
Coil and Loop (DISEMBL)
mskrkrpdsnapsdsltdhERLIYDVIRSkqdmgiwtRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVefepskeisggawysegsldTEFIKVVKSQCLKQIIKLKVATLEGIsdsikrsgafkvdlTKQQIEEIVRALVLDNQImevksngsgeftnipvgkvcyknvskgggggepktgslasipcgvcpqinickpdgvispktcvyytkwldf
Flexible Loop (DISEMBL)
mskrkrpdsnapsdsltdherliYDVIrskqdmgiwtRDMKRelrvnlpdnivtksikslqnksliKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVatlegisdsikrsgafkvdlTKQQIEEIVRALVLDNQIMEVKsngsgeftnipvGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQInickpdgvispKTCVYYTKWLDF
Low Complexity Region (SEG)
MSKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKgggggEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Disordered region (IsUnstruct)
********************RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYK****************ASIPCGVCPQINICKPDGVISPKTCVYYTKWL**
Disordered Region (DISOPRED)
*********************LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY**************GSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Disordered Region (DISEMBL)
***************LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Disordered Region (DISPRO)
*SKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	233	2.2.26 [Sep-21-2011]
Q2T9S3	316	DNA-directed RNA polymera	yes	no	0.896	0.661	0.316	4e-28
Q9H1D9	316	DNA-directed RNA polymera	yes	no	0.896	0.661	0.311	1e-27
Q921X6	316	DNA-directed RNA polymera	yes	no	0.896	0.661	0.307	3e-27
Q9VD25	293	Probable DNA-directed RNA	yes	no	0.888	0.706	0.286	9e-23
Q86JM3	293	DNA-directed RNA polymera	yes	no	0.892	0.709	0.292	8e-22
O94553	301	Probable DNA-directed RNA	yes	no	0.896	0.694	0.251	3e-18
P91529	296	Probable DNA-directed RNA	yes	no	0.824	0.648	0.251	2e-15
P32910	317	DNA-directed RNA polymera	yes	no	0.390	0.287	0.344	1e-10

>sp|Q2T9S3|RPC6_BOVIN DNA-directed RNA polymerase III subunit RPC6 OS=Bos taurus GN=POLR3F PE=2 SV=1

 Score =  124 bits (312), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 124/234 (52%), Gaps = 25/234 (10%)

Query: 18  DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
           + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct: 90  NQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 147

Query: 78  KHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII-KLKVATLEGISDSIKRS 136
           K  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K + A     +  I+R+
Sbjct: 148 KVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQNKAETARESKQNPMIQRN 207

Query: 137 GAF----------------KVDLTKQQIEEIVRALVLDNQI-MEVKSNGSGEFTNIPVGK 179
            +F                KV+L+ + IE I+  L+ D ++ M + +   G   ++    
Sbjct: 208 SSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGHM 267

Query: 180 VCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
             Y+ VS       P TG L   PCG+CP  + C   G ISP  C+Y T+WL+F
Sbjct: 268 KLYRAVSPII----PPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMTEWLEF 316

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Bos taurus (taxid: 9913)

>sp|Q9H1D9|RPC6_HUMAN DNA-directed RNA polymerase III subunit RPC6 OS=Homo sapiens GN=POLR3F PE=1 SV=1

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 124/234 (52%), Gaps = 25/234 (10%)

Query: 18  DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
           + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct: 90  NQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 147

Query: 78  KHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKLKVATLEGISDSIKRS 136
           K  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K + A     +  I+R+
Sbjct: 148 KVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKAETARESKQNPMIQRN 207

Query: 137 GAF----------------KVDLTKQQIEEIVRALVLDNQI-MEVKSNGSGEFTNIPVGK 179
            +F                KV+L+ + IE I+  L+ D ++ M + +   G   ++    
Sbjct: 208 SSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGHM 267

Query: 180 VCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
             Y+ V+       P TG L   PCG+CP  + C   G ISP  C+Y T+WL+F
Sbjct: 268 KLYRAVNPII----PPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMTEWLEF 316

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Homo sapiens (taxid: 9606)

>sp|Q921X6|RPC6_MOUSE DNA-directed RNA polymerase III subunit RPC6 OS=Mus musculus GN=Polr3f PE=1 SV=1

 Score =  121 bits (304), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 124/234 (52%), Gaps = 25/234 (10%)

Query: 18  DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
           + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct: 90  NQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 147

Query: 78  KHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKLKVATLEGISDSIKRS 136
           K  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K + A     +  I+R+
Sbjct: 148 KVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKAETARESKQNPVIQRN 207

Query: 137 GAF----------------KVDLTKQQIEEIVRALVLDNQI-MEVKSNGSGEFTNIPVGK 179
            +F                KV+L+ + IE I+  L+ D ++ M + +   G   ++    
Sbjct: 208 SSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGHM 267

Query: 180 VCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
             Y+ V+       P TG + + PCG+CP    C   G ISP  C+Y T+WL+F
Sbjct: 268 KLYRAVNPIL----PPTGVVRA-PCGLCPVFEDCHEGGEISPSNCIYMTEWLEF 316

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Mus musculus (taxid: 10090)

>sp|Q9VD25|RPC6_DROME Probable DNA-directed RNA polymerase III subunit RPC6 OS=Drosophila melanogaster GN=CG5380 PE=2 SV=1

 Score =  107 bits (266), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 113/241 (46%), Gaps = 34/241 (14%)

Query: 9   SNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE 68
           S  P D+  + E+++Y ++    + GIW RD++ +  +N+    + K +K+L+ K LIK 
Sbjct: 70  SALPKDA-DNEEKVVYGIVEEGGNKGIWIRDIRMKSNLNMIQ--LNKILKNLETKKLIKA 126

Query: 69  VVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLK------------ 116
           V ++++  KK  M    EP   I+GGAWY +   + EF+ V+  QCL+            
Sbjct: 127 VKSVNASKKKVYMLYNLEPDLSITGGAWYQDQDFEVEFVDVLNQQCLRFLQMKRDSAEKK 186

Query: 117 -----QIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGE 171
                   ++   T+  +   I   G  KV+L +  +E I++ +V D         G+ E
Sbjct: 187 REGPLAFKQMSCCTVNEVQKFISDLGISKVNLAEADLETILKTVVYD---------GNAE 237

Query: 172 FTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWL 231
                 G   Y+ V+       P TG L  +PCG+CP I  C   G ++  TC Y   WL
Sbjct: 238 RVRQQDGSFVYRAVN----APLPPTG-LVQMPCGICPVIKNCSNCGDVTAITCEYMRDWL 292

Query: 232 D 232
           D
Sbjct: 293 D 293

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Drosophila melanogaster (taxid: 7227)

>sp|Q86JM3|RPC6_DICDI DNA-directed RNA polymerase III subunit rpc6 OS=Dictyostelium discoideum GN=polr3f PE=3 SV=1

 Score =  103 bits (258), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 116/246 (47%), Gaps = 38/246 (15%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           K   P+  A    L   + LIY +I +  + G WTR++K           +TK +K+L++
Sbjct: 62  KEVNPEDQAKFRGLGVEDFLIYQLIEASSNTGAWTRELKNS--SGYQQVQITKILKTLES 119

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           + LIK V +I S  KK  M    EPS+EI+GG  YS+ S D ++I+++K   +K  +  K
Sbjct: 120 RKLIKSVKSIQSGRKKVYMLYNMEPSREITGGQLYSDQSYDHQYIQIMKMH-IKTFVDNK 178

Query: 123 VAT-LEGISDSIKRSG--AFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEF------- 172
            A  L  I   +++    A    L  + I+ +V  ++ D  I E++    G         
Sbjct: 179 GAVDLADIITYLRKVAEEATSQSLGPEDIQALVNTVIYDGDIEEMRDTRMGAMLGRRSGI 238

Query: 173 ------TNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVY 226
                 T IPV   C                   ++PCG CP  +IC  +G++SPK CVY
Sbjct: 239 LYKPTKTPIPVNNFC-------------------NMPCGNCPVFDICSDNGLVSPKRCVY 279

Query: 227 YTKWLD 232
           + ++L+
Sbjct: 280 FKQYLE 285

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex.

Dictyostelium discoideum (taxid: 44689)

>sp|O94553|RPC6_SCHPO Probable DNA-directed RNA polymerase III subunit rpc6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc6 PE=2 SV=1

 Score = 92.0 bits (227), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 116/247 (46%), Gaps = 38/247 (15%)

Query: 6   RPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL 65
           R D      ++   E+++Y  I++  + GIW + +   LR NL  ++V + +KSL++K+L
Sbjct: 73  RLDEAKTVSTMEGDEQIVYSFIKNSGNEGIWRKTLT--LRTNLHVSVVDRCLKSLESKNL 130

Query: 66  IKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVA- 124
           +K + ++ +  +K  M  +  PS E++GG W+++  LD EFI+ +K    + +       
Sbjct: 131 VKSIKSVKNPTRKIYMLYDLVPSTELTGGPWFTDQELDVEFIENLKKVIYRYVHSKSFPP 190

Query: 125 -------------------TLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK 165
                              T   I + ++ +   KVDL+   +  +V  L+ D ++ E +
Sbjct: 191 KKAAMGPDLVWGPEYNGYPTALQIHNWLRSTNITKVDLSLANVISLVDVLIYDGKV-EKR 249

Query: 166 SNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCV 225
           S+G+            Y+ +       +  T S    PCG CP  +IC  +  ++P TC 
Sbjct: 250 SDGAS-----------YRAIRVNNENIDAFTES----PCGNCPVSDICDANSRVNPITCE 294

Query: 226 YYTKWLD 232
           Y  KWL+
Sbjct: 295 YLDKWLN 301

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P91529|RPC6_CAEEL Probable DNA-directed RNA polymerase III subunit RPC6 OS=Caenorhabditis elegans GN=W09C3.4 PE=3 SV=1

 Score = 82.8 bits (203), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 104/235 (44%), Gaps = 43/235 (18%)

Query: 17  TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG 76
           T+ E++IY +I   +  GIW ++++    +N     + K++KSL+ K LIK +  + +  
Sbjct: 82  TEEEQVIYSLIEESKTRGIWIKELREGSGLNQLQ--LRKTLKSLETKKLIKTIKAVGTTR 139

Query: 77  KKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC------------------LKQI 118
           K +++    EP   ++GG +YS+  LD+E I  + S C                  ++  
Sbjct: 140 KCYIL-FSIEPDMSLTGGTFYSDQQLDSELINTLISVCGSYAASRRKHAIDENPNNIQMQ 198

Query: 119 IKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVG 178
            +      + I+  I       V L+ + +E I+   VLD  I   +    G+    P  
Sbjct: 199 REASYIRPQEIAQFITEKRVLNVPLSLEDLERILEVAVLDGTI---ERRADGKIRACP-- 253

Query: 179 KVCYKNVSKGGGGGEPKTG--SLASIPCGVCPQINICKPDGVISPKTCVYYTKWL 231
                          P++    L S+PC +CP +  C+P  VISP++C Y   WL
Sbjct: 254 ---------------PRSSISPLVSVPCAICPVVEDCRPGYVISPQSCDYMKNWL 293

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Caenorhabditis elegans (taxid: 6239)

>sp|P32910|RPC6_YEAST DNA-directed RNA polymerase III subunit RPC6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC34 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 56/93 (60%), Gaps = 2/93 (2%)

Query: 15  SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS 74
           +++  E L+Y  I +    GIW++ +K   R NL  ++V K +KSL+++  +K V ++  
Sbjct: 85  TMSAEEALVYSYIEASGREGIWSKTIKA--RTNLHQHVVLKCLKSLESQRYVKSVKSVKF 142

Query: 75  KGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFI 107
             +K  M    +PS +I+GG W+++G LD EFI
Sbjct: 143 PTRKIYMLYSLQPSVDITGGPWFTDGELDIEFI 175

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Involved in recruitment of Pol III to the preinitiation complex. Involved in the configuration of an initiation-competent form of RNA polymerase.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	233
255536881	236	DNA-directed RNA polymerase III subunit	0.982	0.970	0.714	6e-95
224142730	239	predicted protein [Populus trichocarpa]	0.982	0.958	0.714	2e-93
224052869	239	predicted protein [Populus trichocarpa]	0.982	0.958	0.705	5e-93
317106726	235	JHL06P13.1 [Jatropha curcas]	0.978	0.970	0.670	1e-87
225442989	239	PREDICTED: DNA-directed RNA polymerase I	0.982	0.958	0.681	1e-87
359497031	239	PREDICTED: DNA-directed RNA polymerase I	0.982	0.958	0.676	3e-87
359497533	239	PREDICTED: DNA-directed RNA polymerase I	0.982	0.958	0.676	3e-87
296087021	300	unnamed protein product [Vitis vinifera]	0.982	0.763	0.676	3e-87
356567166	239	PREDICTED: DNA-directed RNA polymerase I	0.982	0.958	0.627	3e-82
297743442	493	unnamed protein product [Vitis vinifera]	0.957	0.452	0.672	6e-82

>gi|255536881|ref|XP_002509507.1| DNA-directed RNA polymerase III subunit F, putative [Ricinus communis] gi|223549406|gb|EEF50894.1| DNA-directed RNA polymerase III subunit F, putative [Ricinus communis]

 Score =  352 bits (904), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 165/231 (71%), Positives = 199/231 (86%), Gaps = 2/231 (0%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRK+P+S++P+ SLT+HE  +Y+VI SKQDMGIWTRDMKRE   NLPDN+V KS+K LQ 
Sbjct: 8   KRKQPESSSPAQSLTEHECTLYNVIWSKQDMGIWTRDMKRE--TNLPDNVVNKSLKVLQA 65

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K+LIKEVVNI +KG+KH MA EFEPSKEI+GGAWY EG+LDTEFIK++K  C KQ++KLK
Sbjct: 66  KNLIKEVVNIQNKGRKHYMATEFEPSKEITGGAWYVEGNLDTEFIKLLKEVCTKQVLKLK 125

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VATLEGI+DSIKRSG F  +LTKQQIEEIV+ALVLDN ++EVKSNG  EF+ IP+GKVCY
Sbjct: 126 VATLEGITDSIKRSGIFNTELTKQQIEEIVKALVLDNALIEVKSNGMLEFSFIPIGKVCY 185

Query: 183 KNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           K V KG   GEP+ G++ASIPCGVCP+I+ C PDG+ISP+TCVYY+KWLDF
Sbjct: 186 KCVGKGSTAGEPRIGAMASIPCGVCPRISQCTPDGIISPQTCVYYSKWLDF 236

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142730|ref|XP_002324707.1| predicted protein [Populus trichocarpa] gi|222866141|gb|EEF03272.1| predicted protein [Populus trichocarpa]

 Score =  347 bits (891), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 165/231 (71%), Positives = 194/231 (83%), Gaps = 2/231 (0%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRP+ N+P+ SLT+HERL+YDVIRSKQD+GIWTRDMK+E +  LPDN+V KS+K+LQ 
Sbjct: 11  KRKRPEVNSPAQSLTEHERLLYDVIRSKQDIGIWTRDMKKEAK--LPDNVVNKSLKALQV 68

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI +KG+KH MA EFEPSKEISGGAWY EGSLDTEFI+ +K  C +QI +  
Sbjct: 69  KKLIKEVVNIQNKGRKHFMATEFEPSKEISGGAWYLEGSLDTEFIESLKQLCKRQIERRG 128

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VATLE ++DSI    AF VD+TKQQIEEI+R L+LDN IMEVKSNG GEF +IP G+VCY
Sbjct: 129 VATLEEVTDSINSYPAFNVDVTKQQIEEILRTLILDNVIMEVKSNGMGEFASIPFGEVCY 188

Query: 183 KNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           K +SK G GGEPK G+LASIPCGVCP+I+ C PDG+ISPKTCVYY KWLDF
Sbjct: 189 KYISKVGLGGEPKAGALASIPCGVCPRISQCTPDGIISPKTCVYYQKWLDF 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224052869|ref|XP_002297621.1| predicted protein [Populus trichocarpa] gi|222844879|gb|EEE82426.1| predicted protein [Populus trichocarpa]

 Score =  346 bits (887), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 163/231 (70%), Positives = 194/231 (83%), Gaps = 2/231 (0%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRP+ N+P  SLT+HER++YDVIRSKQD+GIWTRDMK+E +  LPDN+V KS+K+L+ 
Sbjct: 11  KRKRPELNSPVQSLTEHERILYDVIRSKQDIGIWTRDMKKEAK--LPDNVVNKSLKALRV 68

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K+LIKEVVNI +KG+KH MA EFEPSKEISGGAWY EGSLDTEFI+ ++  C +QI K  
Sbjct: 69  KNLIKEVVNIQNKGRKHFMATEFEPSKEISGGAWYLEGSLDTEFIESLRQLCKRQIEKKG 128

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VATLE ++DSI    AF VD+TKQQIEEI+R L+LDN IMEVKSNG GEF +IP GKVCY
Sbjct: 129 VATLEEVTDSINSYPAFNVDVTKQQIEEILRTLILDNAIMEVKSNGMGEFASIPFGKVCY 188

Query: 183 KNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           + +SKG  GGEPK G+LASIPCGVCP+I+ C PDG+ISPKTCVYY KWLDF
Sbjct: 189 RYISKGALGGEPKAGALASIPCGVCPRISHCTPDGIISPKTCVYYQKWLDF 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106726|dbj|BAJ53222.1| JHL06P13.1 [Jatropha curcas]

 Score =  328 bits (841), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 155/231 (67%), Positives = 191/231 (82%), Gaps = 3/231 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRK+P+SN+ + SLT+HE+ +Y+ IRSKQDMGIWTRDMKRE   NLPD +V KS+K LQ 
Sbjct: 8   KRKQPESNSSAQSLTEHEQALYNAIRSKQDMGIWTRDMKRE--TNLPDTVVNKSLKVLQA 65

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K+LIKEVVNI +KG+K+ MA EFEPSKEI+GG WY EG+LDT FI V+K QC KQI KLK
Sbjct: 66  KNLIKEVVNIQNKGRKYYMATEFEPSKEITGGTWYVEGNLDTMFIGVLKDQCKKQIEKLK 125

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT+E ++D I R+G   V LTKQQIEEI++ALVLDN++ EVKSNG GEF +IPVGKVCY
Sbjct: 126 VATVEAVTDFINRTGVSTVHLTKQQIEEILKALVLDNKVTEVKSNGMGEFASIPVGKVCY 185

Query: 183 KNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           K++ K G  G+PK G++ASIPCGVCP+I  C P+G+ISP+TCVYY KWL+F
Sbjct: 186 KSIGK-GSSGDPKIGAMASIPCGVCPRIKHCTPNGIISPQTCVYYGKWLEF 235

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442989|ref|XP_002266428.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Vitis vinifera]

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 158/232 (68%), Positives = 194/232 (83%), Gaps = 3/232 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRPD+NA S  L D ER++YD+IRSK+DMGIWTRDMKRE   NLPDN+VTKS+K+LQ 
Sbjct: 10  KRKRPDTNAASQPLLDAERVLYDLIRSKEDMGIWTRDMKRE--TNLPDNVVTKSLKALQV 67

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI SKG+KH MAVEFEPSKE++GGAWY EG+LDTE+IK++K  C+K + KLK
Sbjct: 68  KKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKETCVKVLSKLK 127

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT EGIS+SI ++G    + + QQI EI+RALVLDN+IMEV+S+GSGEF++IP+G VCY
Sbjct: 128 VATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEFSSIPIGAVCY 187

Query: 183 KNVSK-GGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           +  +K G GGG PK G++ASIPCGVCP+I  C PDG+ISPK+C YY KWLDF
Sbjct: 188 RCTNKGGLGGGGPKIGAMASIPCGVCPRITQCTPDGIISPKSCAYYAKWLDF 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497031|ref|XP_003635403.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Vitis vinifera]

 Score =  327 bits (837), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 157/232 (67%), Positives = 193/232 (83%), Gaps = 3/232 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRPD+N  S  L D ER++YD+IRSK+DMGIWTRDMKRE   NLPDN+VTKS+K+LQ 
Sbjct: 10  KRKRPDTNTASQPLLDAERVLYDLIRSKEDMGIWTRDMKRE--TNLPDNVVTKSLKALQV 67

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI SKG+KH MAVEFEPSKE++GGAWY EG+LDTE+IK++K  C++ + KLK
Sbjct: 68  KKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKETCVRVLSKLK 127

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT EGIS+SI ++G    + + QQI EI+RALVLDN+IMEV+S+GSGEF++IP+G VCY
Sbjct: 128 VATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEFSSIPIGAVCY 187

Query: 183 KNVSK-GGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           +  +K G GGG P  G++ASIPCGVCP+I  C PDG+ISPKTC YYTKWLDF
Sbjct: 188 RCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKWLDF 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359497533|ref|XP_003635557.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Vitis vinifera]

 Score =  327 bits (837), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 157/232 (67%), Positives = 193/232 (83%), Gaps = 3/232 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRPD+N  S  L D ER++YD+IRSK+DMGIWTRDMKRE   NLPDN+VTKS+K+LQ 
Sbjct: 10  KRKRPDTNTASQPLLDAERVLYDLIRSKEDMGIWTRDMKRE--TNLPDNVVTKSLKALQV 67

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI SKG+KH MAVEFEPSKE++GGAWY EG+LDTE+IK++K  C++ + KLK
Sbjct: 68  KKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKKTCVRVLSKLK 127

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT EGIS+SI ++G    + + QQI EI+RALVLDN+IMEV+S+GSGEF++IP+G VCY
Sbjct: 128 VATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEFSSIPIGAVCY 187

Query: 183 KNVSK-GGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           +  +K G GGG P  G++ASIPCGVCP+I  C PDG+ISPKTC YYTKWLDF
Sbjct: 188 RCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKWLDF 239

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087021|emb|CBI33284.3| unnamed protein product [Vitis vinifera]

 Score =  327 bits (837), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 157/232 (67%), Positives = 193/232 (83%), Gaps = 3/232 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRPD+N  S  L D ER++YD+IRSK+DMGIWTRDMKRE   NLPDN+VTKS+K+LQ 
Sbjct: 71  KRKRPDTNTASQPLLDAERVLYDLIRSKEDMGIWTRDMKRE--TNLPDNVVTKSLKALQV 128

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI SKG+KH MAVEFEPSKE++GGAWY EG+LDTE+IK++K  C++ + KLK
Sbjct: 129 KKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKKTCVRVLSKLK 188

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT EGIS+SI ++G    + + QQI EI+RALVLDN+IMEV+S+GSGEF++IP+G VCY
Sbjct: 189 VATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEFSSIPIGAVCY 248

Query: 183 KNVSK-GGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           +  +K G GGG P  G++ASIPCGVCP+I  C PDG+ISPKTC YYTKWLDF
Sbjct: 249 RCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKWLDF 300

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567166|ref|XP_003551792.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Glycine max]

 Score =  310 bits (794), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 145/231 (62%), Positives = 187/231 (80%), Gaps = 2/231 (0%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKR D    + SLTD ER++Y++I SK+DMGIWT DMKRE   NLPD+IV KS+K LQ+
Sbjct: 11  KRKRQDLALVTGSLTDGERVLYNLIHSKKDMGIWTGDMKRE--TNLPDSIVKKSLKLLQS 68

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K+LIKEVVNI +KG+KH MA EFEPSKEI+GG WY++G LDT+FI +VK  CLK I + K
Sbjct: 69  KNLIKEVVNIQNKGRKHYMAAEFEPSKEITGGVWYNQGRLDTDFINLVKDVCLKYIFRQK 128

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT +G+ +  ++SG F V++T QQI+EI+R LVLD++I+EVKS G G+F+++PVG++CY
Sbjct: 129 VATRDGVMEWSRKSGVFNVEVTTQQIDEILRTLVLDDEIVEVKSTGFGDFSSVPVGRICY 188

Query: 183 KNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
           +  SKGG  GE K G++ASIPCGVCP+IN C PDG+ISP+TCVYY KWLDF
Sbjct: 189 RCKSKGGNRGEQKPGAMASIPCGVCPRINFCTPDGIISPRTCVYYQKWLDF 239

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743442|emb|CBI36309.3| unnamed protein product [Vitis vinifera]

 Score =  309 bits (791), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 152/226 (67%), Positives = 189/226 (83%), Gaps = 3/226 (1%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           KRKRPD+NA S  L D ER++YD+IRSK+DMGIWTRDMKRE   NLPDN+VTKS+K+LQ 
Sbjct: 100 KRKRPDTNAASQPLLDAERVLYDLIRSKEDMGIWTRDMKRE--TNLPDNVVTKSLKALQV 157

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K LIKEVVNI SKG+KH MAVEFEPSKE++GGAWY EG+LDTE+IK++K  C+K + KLK
Sbjct: 158 KKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKETCVKVLSKLK 217

Query: 123 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCY 182
           VAT EGIS+SI ++G    + + QQI EI+RALVLDN+IMEV+S+GSGEF++IP+G VCY
Sbjct: 218 VATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEFSSIPIGAVCY 277

Query: 183 KNVSK-GGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYY 227
           +  +K G GGG PK G++ASIPCGVCP+I  C PDG+ISPK+ V+Y
Sbjct: 278 RCTNKGGLGGGGPKIGAMASIPCGVCPRITQCTPDGIISPKSSVHY 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	233
TAIR|locus:2171671	230	AT5G23710 [Arabidopsis thalian	0.974	0.986	0.478	7e-54
UNIPROTKB|F1MYX7	316	POLR3F "DNA-directed RNA polym	0.974	0.718	0.314	1.5e-26
UNIPROTKB|E2RG78	316	POLR3F "Uncharacterized protei	0.974	0.718	0.314	1.9e-26
UNIPROTKB|Q2T9S3	316	POLR3F "DNA-directed RNA polym	0.974	0.718	0.314	2.5e-26
UNIPROTKB|Q9H1D9	316	POLR3F "DNA-directed RNA polym	0.974	0.718	0.314	2.5e-26
UNIPROTKB|J9P638	323	POLR3F "Uncharacterized protei	0.914	0.659	0.317	3.2e-26
RGD|1306428	371	Polr3f "polymerase (RNA) III (	0.974	0.611	0.310	6.6e-26
MGI|MGI:1924086	316	Polr3f "polymerase (RNA) III (	0.974	0.718	0.310	8.4e-26
UNIPROTKB|E1BU41	314	POLR3F "Uncharacterized protei	0.974	0.722	0.310	1.1e-25
UNIPROTKB|F1SBH4	316	POLR3F "Uncharacterized protei	0.974	0.718	0.310	1.4e-25

TAIR|locus:2171671 AT5G23710 [Arabidopsis thaliana (taxid:3702)]

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 113/236 (47%), Positives = 154/236 (65%)

Query:     1 MSKRKRPDSNAPSDSLTD-HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS 59
             MSKRKRPD  +    L + HE+ + D+IR  Q  G    ++KRE  +  P  IVT+ I S
Sbjct:     1 MSKRKRPDPKSSGGDLNEPHEKKLLDLIRINQGRGATMFELKREKTI--PATIVTRLIAS 58

Query:    60 LQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII 119
             L+ K+LIKEV N+++KG KH +A+EFEP  E++GG WY++G+LD   I+ +K++C+  + 
Sbjct:    59 LRKKNLIKEVANMNNKGVKHYLAMEFEPCSELTGGEWYTDGALDLSKIEDLKAKCVMILE 118

Query:   120 K--LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPV 177
             +   +V TLE +     +     VD TK    EI++ L+LDN IMEVKSNG  EF +  +
Sbjct:   119 RHRQRVVTLEVLCGYFVKEEKLSVDQTK----EILKNLILDNLIMEVKSNGMNEFASTRI 174

Query:   178 GKVCYKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
             G+VCY+   K     EP+ G+ ASIPCGVCP I IC PDGVISP TCVY+ KWLDF
Sbjct:   175 GEVCYRLTGKKFGNGEPRAGAFASIPCGVCPHIAICSPDGVISPTTCVYFQKWLDF 230

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0009507 "chloroplast" evidence=IDA

UNIPROTKB|F1MYX7 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Bos taurus (taxid:9913)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 77/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQTKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVSPIIPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0045089 "positive regulation of innate immune response" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2RG78 POLR3F "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 77/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQTKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVNPIIPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q2T9S3 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Bos taurus (taxid:9913)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 77/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII-KL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQNKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVSPIIPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0003677 "DNA binding" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=ISS

GO:0032728 "positive regulation of interferon-beta production" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|Q9H1D9 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Homo sapiens (taxid:9606)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 77/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVNPIIPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0003677 "DNA binding" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=NAS

GO:0006359 "regulation of transcription from RNA polymerase III promoter" evidence=NAS

GO:0032728 "positive regulation of interferon-beta production" evidence=IMP

GO:0045089 "positive regulation of innate immune response" evidence=IMP

GO:0003899 "DNA-directed RNA polymerase activity" evidence=NAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|J9P638 POLR3F "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 73/230 (31%), Positives = 120/230 (52%)

Query:    18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
             + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct:    97 NQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 154

Query:    78 KHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKLKVATLEGISDSIKRS 136
             K  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K + A     +  I+R+
Sbjct:   155 KVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQTKAETARESKQNPMIQRN 214

Query:   137 GAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTNIP-----VGKVC-YK 183
              +F    ++ K   E  +  + L  + +E   N     G  E T I      VG V  + 
Sbjct:   215 SSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGHM 274

Query:   184 NVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLDF 233
              + +      P TG L   PCG+CP  + C   G ISP  C+Y T+WL+F
Sbjct:   275 KLYRAVNPIIPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMTEWLEF 323

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

RGD|1306428 Polr3f "polymerase (RNA) III (DNA directed) polypeptide F" [Rattus norvegicus (taxid:10116)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 76/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:   130 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 187

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   188 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKA 247

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  + T 
Sbjct:   248 ETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVDMTI 307

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   308 IAAKEGTVGSVDGHMKLYRAVNPILPPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 366

Query:   229 KWLDF 233
             +WL+F
Sbjct:   367 EWLEF 371

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=ISO

GO:0045089 "positive regulation of innate immune response" evidence=ISO

MGI|MGI:1924086 Polr3f "polymerase (RNA) III (DNA directed) polypeptide F" [Mus musculus (taxid:10090)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 76/245 (31%), Positives = 126/245 (51%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IP-----VGKVC-YKNVSKXXXXXEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I      VG V  +  + +      P TG + + PCG+CP    C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVNPILPPTGVVRA-PCGLCPVFEDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=ISO

GO:0045087 "innate immune response" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=ISO

GO:0051607 "defense response to virus" evidence=IEA

UNIPROTKB|E1BU41 POLR3F "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 76/245 (31%), Positives = 124/245 (50%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    73 RIKESQNASKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 130

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   131 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQSKA 190

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   191 EAARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 250

Query:   175 IPVGKVCYKNVS---KXXXXXEP---KTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I   +    +V    K      P    TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   251 IAAKEGTVGSVDGQMKLYRAVSPLIQPTG-LVRTPCGLCPVFDDCHEGGEISPSNCIYMT 309

Query:   229 KWLDF 233
             +WL+F
Sbjct:   310 EWLEF 314

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=IEA

UNIPROTKB|F1SBH4 POLR3F "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 76/245 (31%), Positives = 124/245 (50%)

Query:     4 RKRPDSNAPSDSLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
             R +   NA     +D+ E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct:    75 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIR--YKSNLPLTEINKILKNLES 132

Query:    63 KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKL 121
             K LIK V ++ +  KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K 
Sbjct:   133 KKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQTKA 192

Query:   122 KVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRALVLDNQIMEVKSN-----GSGEFTN 174
             + A     +  I+R+ +F    ++ K   E  +  + L  + +E   N     G  E T 
Sbjct:   193 ETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTI 252

Query:   175 IPVGKVCYKNVS---KXXXXXEP---KTGSLASIPCGVCPQINICKPDGVISPKTCVYYT 228
             I   +    +V    K      P    TG L   PCG+CP  + C   G ISP  C+Y T
Sbjct:   253 IAAKEGTVGSVDGHMKLYRAVNPIISPTG-LVRAPCGLCPVFDDCHEGGEISPSNCIYMT 311

Query:   229 KWLDF 233
             +WL+F
Sbjct:   312 EWLEF 316

GO:0045089 "positive regulation of innate immune response" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	233
pfam05158	312	pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 sub	1e-51
COG5111	301	COG5111, RPC34, DNA-directed RNA polymerase III, s	7e-26

>gnl|CDD|218472 pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 subunit

 Score =  169 bits (430), Expect = 1e-51
 Identities = 70/238 (29%), Positives = 117/238 (49%), Gaps = 26/238 (10%)

Query: 15  SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS 74
           +L+D E L+Y +I    + GIWTR +K   R NL  +++ K +KSL++K  IK V ++ +
Sbjct: 81  TLSDEESLVYSIIEESGNEGIWTRTIKN--RTNLHQSVLKKCLKSLESKKYIKSVKSVKA 138

Query: 75  KGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLK-----------------Q 117
             +K  M    EPS+E++GG WY++G LD EFI  ++    +                  
Sbjct: 139 PTRKMYMLYNLEPSEEVTGGPWYTDGELDVEFINTLRRVIFRFVSQKTYVNGFGGEKKAL 198

Query: 118 IIKLKVA---TLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTN 174
                     T+E I+  I   G   V L+++ I+++V  LV D ++ +VK         
Sbjct: 199 PYPAGYKSYPTVEEIATFINELGITNVRLSEEDIQQLVETLVYDGKLEKVKPGAGYRLQR 258

Query: 175 IPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCVYYTKWLD 232
           + + +V   +  +          +    PCG CP  ++C   GV+SPK CVY+ +WL+
Sbjct: 259 VTLQEVLQMSQKRRPLPANGLVEA----PCGNCPVFDLCSEGGVVSPKNCVYFKEWLE 312

Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment. Length = 312

>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34 [Transcription]

 Score =  101 bits (254), Expect = 7e-26
 Identities = 61/254 (24%), Positives = 107/254 (42%), Gaps = 48/254 (18%)

Query: 3   KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
           K       +P +++ D+E  +Y +I      GIW + +K   R NL  N+V K +KSL++
Sbjct: 70  KGVLESEASPINTMDDYELTVYSLISQSGGEGIWLKTIK--DRTNLHHNVVGKCLKSLES 127

Query: 63  KSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLK 122
           K ++K V ++ +  +K  M  +  PS+EI+GG W+++  LD EFI       L +II+  
Sbjct: 128 KRIVKSVKSVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFI-----ARLLEIIERF 182

Query: 123 V-------------------------ATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVL 157
           +                          TLE I + ++      V L    +E +   LV 
Sbjct: 183 LEKNLFPRKNFEEGPNVFYAPKYEDYPTLEDIMNYVRNVNILSVPLRLDNLESLADVLVY 242

Query: 158 DNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDG 217
           D ++ ++ S     +         +K  +K  G GE         P G     +  +   
Sbjct: 243 DGKVEKLHSGPIYRYR-------AFKPYAKNQGEGE---------PAGNKALEDEEEFSF 286

Query: 218 VISPKTCVYYTKWL 231
            + P + VY+ +W 
Sbjct: 287 KMFPASVVYFDEWT 300

Length = 301

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	233
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	100.0
KOG3233	297	consensus RNA polymerase III, subunit C34 [Transcr	100.0
COG5111	301	RPC34 DNA-directed RNA polymerase III, subunit C34	100.0
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	98.49
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	98.35
COG2512	258	Predicted membrane-associated trancriptional regul	98.31
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	98.21
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	98.18
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	98.17
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	98.16
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	98.12
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	97.96
PRK10870	176	transcriptional repressor MprA; Provisional	97.92
COG1846	126	MarR Transcriptional regulators [Transcription]	97.91
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.86
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.85
PF13730	55	HTH_36: Helix-turn-helix domain	97.83
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	97.79
PRK03573	144	transcriptional regulator SlyA; Provisional	97.77
PRK13777	185	transcriptional regulator Hpr; Provisional	97.73
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	97.56
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	97.51
COG3355	126	Predicted transcriptional regulator [Transcription	97.41
COG1522	154	Lrp Transcriptional regulators [Transcription]	97.22
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	97.22
PHA02943	165	hypothetical protein; Provisional	97.18
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	97.13
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	97.11
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	97.02
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	97.02
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.95
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.91
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.86
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	96.75
PRK00215	205	LexA repressor; Validated	96.74
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.62
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.62
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	96.52
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	96.46
COG3888	321	Predicted transcriptional regulator [Transcription	96.4
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.36
PRK11169	164	leucine-responsive transcriptional regulator; Prov	96.36
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.33
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	96.27
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.21
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	96.18
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.11
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	96.03
COG1378	247	Predicted transcriptional regulators [Transcriptio	95.96
PRK06474	178	hypothetical protein; Provisional	95.91
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	95.9
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.87
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	95.87
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	95.87
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.82
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	95.8
PRK14165	217	winged helix-turn-helix domain-containing protein/	95.76
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.59
PRK09334	86	30S ribosomal protein S25e; Provisional	95.56
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.5
PRK12423	202	LexA repressor; Provisional	95.43
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	95.39
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	95.36
COG1733	120	Predicted transcriptional regulators [Transcriptio	95.33
PF06224	327	HTH_42: Winged helix DNA-binding domain; InterPro:	95.23
COG3398	240	Uncharacterized protein conserved in archaea [Func	95.18
PRK09954	362	putative kinase; Provisional	95.16
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.09
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.09
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	95.04
COG1725	125	Predicted transcriptional regulators [Transcriptio	95.04
KOG2165	765	consensus Anaphase-promoting complex (APC), subuni	94.89
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.86
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	94.86
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	94.83
PRK03902	142	manganese transport transcriptional regulator; Pro	94.72
smart00351	125	PAX Paired Box domain.	94.62
cd00131	128	PAX Paired Box domain	94.6
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	94.59
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	94.51
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	94.47
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	94.45
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	94.42
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	94.41
PRK13509	251	transcriptional repressor UlaR; Provisional	94.4
PRK11050	152	manganese transport regulator MntR; Provisional	94.24
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	94.21
PRK06266	178	transcription initiation factor E subunit alpha; V	94.18
COG3432	95	Predicted transcriptional regulator [Transcription	94.07
PF03551	75	PadR: Transcriptional regulator PadR-like family;	93.95
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.95
PRK09462	148	fur ferric uptake regulator; Provisional	93.9
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	93.87
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	93.85
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	93.84
PRK09391	230	fixK transcriptional regulator FixK; Provisional	93.77
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	93.75
PRK11014	141	transcriptional repressor NsrR; Provisional	93.69
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.61
PHA00738	108	putative HTH transcription regulator	93.58
PF08672	60	APC2: Anaphase promoting complex (APC) subunit 2;	93.43
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	93.35
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	93.17
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	93.05
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	93.04
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	93.04
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.01
PRK05638	442	threonine synthase; Validated	93.01
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	92.86
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	92.74
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	92.62
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.58
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	92.57
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	92.53
COG1654	79	BirA Biotin operon repressor [Transcription]	92.34
COG2345	218	Predicted transcriptional regulator [Transcription	92.06
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.97
COG1693	325	Repressor of nif and glnA expression [Transcriptio	91.79
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	91.3
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	91.25
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	91.25
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	91.01
PRK10046	225	dpiA two-component response regulator DpiA; Provis	90.93
COG1414	246	IclR Transcriptional regulator [Transcription]	90.92
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	90.73
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	90.7
PRK09416	135	lstR lineage-specific thermal regulator protein; P	90.67
PF13551	112	HTH_29: Winged helix-turn helix	90.63
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	90.6
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	90.33
PRK00135	188	scpB segregation and condensation protein B; Revie	90.3
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	90.2
PRK11569	274	transcriptional repressor IclR; Provisional	90.19
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	90.14
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	90.12
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	90.12
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	89.97
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	89.84
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	89.6
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	89.47
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	89.4
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	89.21
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	89.11
COG1959	150	Predicted transcriptional regulator [Transcription	89.07
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	88.87
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	88.81
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	88.49
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	88.33
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	88.19
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	88.04
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	87.94
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	87.33
COG3682	123	Predicted transcriptional regulator [Transcription	87.32
COG4189	308	Predicted transcriptional regulator [Transcription	87.3
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	87.19
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	87.19
PRK09483	217	response regulator; Provisional	87.09
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	87.09
COG5625	113	Predicted transcription regulator containing HTH d	87.07
PRK15431	78	ferrous iron transport protein FeoC; Provisional	86.95
PF00538	77	Linker_histone: linker histone H1 and H5 family; I	86.67
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	86.63
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	86.46
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	86.35
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	86.29
PRK09462	148	fur ferric uptake regulator; Provisional	86.2
PRK10840	216	transcriptional regulator RcsB; Provisional	86.03
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	85.56
COG1777	217	Predicted transcriptional regulators [Transcriptio	85.42
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	85.24
PRK00411	394	cdc6 cell division control protein 6; Reviewed	84.48
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	84.26
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	84.01
COG5340	269	Predicted transcriptional regulator [Transcription	83.98
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	83.73
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	83.59
PRK11639	169	zinc uptake transcriptional repressor; Provisional	83.32
COG1695	138	Predicted transcriptional regulators [Transcriptio	83.05
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	82.91
PRK00135	188	scpB segregation and condensation protein B; Revie	82.46
PHA02943	165	hypothetical protein; Provisional	82.43
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	82.38
smart00531	147	TFIIE Transcription initiation factor IIE.	82.26
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	82.25
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	82.09
COG0640	110	ArsR Predicted transcriptional regulators [Transcr	81.82
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	81.81
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	81.48
PRK11083	228	DNA-binding response regulator CreB; Provisional	81.48
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	81.29
COG2188	236	PhnF Transcriptional regulators [Transcription]	81.28
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	81.15
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	81.07
PRK10651	216	transcriptional regulator NarL; Provisional	81.04
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	81.04
COG5647	773	Cullin, a subunit of E3 ubiquitin ligase [Posttran	80.74
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	80.4
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	80.31
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	80.28
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	80.12
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	80.08

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=100.00  E-value=8.7e-78  Score=552.31  Aligned_cols=221  Identities=43%  Similarity=0.812  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799            5 KRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus         5 ~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +.++.++++++|+++|++||++|++|||+|||++|||++|  |||+++|+|+||+||+|+|||+||||++++||+|||||
T Consensus        71 ~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t--~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~  148 (327)
T PF05158_consen   71 VSEEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKT--NLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYD  148 (327)
T ss_dssp             --SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHC--T--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESS
T ss_pred             eCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEcc
Confidence            5678899999999999999999999999999999999999  99999999999999999999999999999999999999


Q ss_pred             cccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCC-----------------------------CCHHHHHHHHHH
Q 026799           85 FEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKV-----------------------------ATLEGISDSIKR  135 (233)
Q Consensus        85 lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~-----------------------------~T~~~I~~~I~~  135 (233)
                      ||||+|||||+||+||+||+|||+.|+++|++||++++.                             ||+++|++||++
T Consensus       149 l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~  228 (327)
T PF05158_consen  149 LEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINK  228 (327)
T ss_dssp             S-------------------------------------------------------------------------------
T ss_pred             CCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999999986544                             999999999999


Q ss_pred             hCCcccccCHHHHHHHHHHHhcCCeEEEEeeCCCCCcccccCccee-------eecccCCCCCCCCCCCCCCCCCCCCCC
Q 026799          136 SGAFKVDLTKQQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVC-------YKNVSKGGGGGEPKTGSLASIPCGVCP  208 (233)
Q Consensus       136 ~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~-------Yr~~~~~~~~~~p~~~~l~~vPCg~CP  208 (233)
                      +||++++||++||++||++|||||+||++.+++.+++.....+..+       ||.+     .+.+..++++++|||+||
T Consensus       229 sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~PCg~CP  303 (327)
T PF05158_consen  229 SGISNVELSEEDIESLLDTLVYDGKIEEVRSGDGYEYYRAPGQSVLYCSKRRYYRAV-----GPEPSASGLTEVPCGVCP  303 (327)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCCCceecCHHHHHHHHHHHhhCceeEEEeccCCceeeeeecccceeeecccccccc-----ccccCCCCccCCCCCCCC
Confidence            9999999999999999999999999999987643333322222222       3322     133457789999999999


Q ss_pred             ccccCCCCCccCcccccchHhhhc
Q 026799          209 QINICKPDGVISPKTCVYYTKWLD  232 (233)
Q Consensus       209 v~~~C~~~G~IsP~~C~Y~~~WL~  232 (233)
                      ||+.|.+||+|||++|+||++||+
T Consensus       304 Vf~~C~~~G~IsP~~C~Yf~~WL~  327 (327)
T PF05158_consen  304 VFDQCSPGGPISPKTCVYFDEWLD  327 (327)
T ss_dssp             ------------------------
T ss_pred             ccceeCCCCCCCchhchHHHHhhC
Confidence            999999999999999999999996

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]

Probab=100.00  E-value=1.2e-72  Score=500.85  Aligned_cols=211  Identities=37%  Similarity=0.776  Sum_probs=198.3

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799            3 KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus         3 ~~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ++|+|+.|...+.++++|++||++|+++||+|||.++||.++  |||+++|+|+||+||+|+|||+||||++++||+|||
T Consensus        69 r~~d~~~a~~~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ks--nLp~~~v~K~LkSLEsKkLIKsVKsv~n~~~KvYmL  146 (297)
T KOG3233|consen   69 RAKDPKSASKGKGMENEEKLVYSLIEESGNEGIWSKEIKRKS--NLPQTVVNKILKSLESKKLIKSVKSVKNSRKKVYML  146 (297)
T ss_pred             eccCchhhcccccCChHHHHHHHHHHHcCCCceeeehhhhcc--CCCHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEE
Confidence            467888888999999999999999999999999999999999  999999999999999999999999999999999999


Q ss_pred             eccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhh-----------------CCCCCHHHHHHHHHHhCCcccccCH
Q 026799           83 VEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIK-----------------LKVATLEGISDSIKRSGAFKVDLTK  145 (233)
Q Consensus        83 ~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~-----------------~~~~T~~~I~~~I~~~~i~~~~Ls~  145 (233)
                      |+|+||.|+|||+||+||+||.|||+.|.++|++|+++                 .+++|++||++||++.+|++|.|+.
T Consensus       147 y~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~ei~~~i~~l~I~nV~Lsl  226 (297)
T KOG3233|consen  147 YDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQEIKEFIRNLNILNVELSL  226 (297)
T ss_pred             ecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHHHHHHHHHcCcccccccH
Confidence            99999999999999999999999999999999999973                 4789999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCeEEEEeeCCCCCcccccCcceeeecccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCccccc
Q 026799          146 QQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCV  225 (233)
Q Consensus       146 ~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~Yr~~~~~~~~~~p~~~~l~~vPCg~CPv~~~C~~~G~IsP~~C~  225 (233)
                      +|++.|+++|||||+||... +|           .+||++..    +.|..+.+.++|||.|||++.|+++|.|||.||+
T Consensus       227 ~dleti~~vlvyDGkvE~r~-dG-----------~~yra~~~----~~~~~~~~~~~Pcg~cPv~~dC~~~g~isP~tC~  290 (297)
T KOG3233|consen  227 EDLETILDVLVYDGKVEKRH-DG-----------PRYRAFGP----NIPRAGLVAGIPCGICPVIDDCSPGGVISPITCV  290 (297)
T ss_pred             HHHHHHhHHheecceeeeee-cC-----------ceeeecCC----CCCCcCccCCCcccCCcchhccCCCCccCchhhH
Confidence            99999999999999999843 32           27998653    3567788889999999999999999999999999


Q ss_pred             chHhhh
Q 026799          226 YYTKWL  231 (233)
Q Consensus       226 Y~~~WL  231 (233)
                      ||++||
T Consensus       291 Ym~~WL  296 (297)
T KOG3233|consen  291 YMDKWL  296 (297)
T ss_pred             HHHhhc
Confidence            999999

>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]

Probab=100.00  E-value=4.7e-60  Score=412.45  Aligned_cols=209  Identities=25%  Similarity=0.426  Sum_probs=191.7

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799            6 RPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus         6 ~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      +.++|+..+.|+++|..||++|+.+|++|||.+.|+.+|  |||.+.|-||||+||+|++||+||||++|+||+||||+|
T Consensus        73 ~~~ea~~~~tm~~~E~~vYs~i~~SG~EGiW~Ktik~rT--Nlh~~vV~kcLkSlESkr~vKSvKsvKnptRKiYmLYdl  150 (301)
T COG5111          73 LESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRT--NLHHNVVGKCLKSLESKRIVKSVKSVKNPTRKIYMLYDL  150 (301)
T ss_pred             ecccCCcccccchHHHHHHHHHHhcCCCceehhhhhhhc--cCcHHHHHHHHHHHHHHHHHHHhhhhcCCCceEEEEecc
Confidence            346788889999999999999999999999999999999  999999999999999999999999999999999999999


Q ss_pred             ccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhh--------------------CCCCCHHHHHHHHHHhCCcccccCH
Q 026799           86 EPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIK--------------------LKVATLEGISDSIKRSGAFKVDLTK  145 (233)
Q Consensus        86 ePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~--------------------~~~~T~~~I~~~I~~~~i~~~~Ls~  145 (233)
                      .||+||||||||||||+|.|||+.|..++++||.+                    .+|||++||++||+..+|.+|+|+.
T Consensus       151 vPS~eiTGGpWFtD~elDvEfi~~ll~ii~rf~~~n~fp~kn~~~gpnv~~~P~y~~ypT~~~I~n~vr~~ni~~v~L~l  230 (301)
T COG5111         151 VPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFYAPKYEDYPTLEDIMNYVRNVNILSVPLRL  230 (301)
T ss_pred             cccccccCCCccccCcccHHHHHHHHHHHHHHHHhccCCccchhcCCccccCCccCCCccHHHHHHHHHhceeeeccccH
Confidence            99999999999999999999999999999999974                    3699999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCeEEEEeeCCCCCcccccCcceeeecccCCCCCCCCCCCCCCCCCCCCCCccccCCCCCccCccccc
Q 026799          146 QQIEEIVRALVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSLASIPCGVCPQINICKPDGVISPKTCV  225 (233)
Q Consensus       146 ~di~~il~~Lv~Dg~ie~v~~~~~g~f~~~~~g~~~Yr~~~~~~~~~~p~~~~l~~vPCg~CPv~~~C~~~G~IsP~~C~  225 (233)
                      ++++++.++|||||++|++.++            ..||...-...    ..+..++-|||.||+-|+|...-.++|.+|+
T Consensus       231 ~n~~sL~dvLvyDgKvEK~~~g------------~~yR~~~~~~~----~~nq~~~ep~gn~~led~~e~s~km~p~s~~  294 (301)
T COG5111         231 DNLESLADVLVYDGKVEKLHSG------------PIYRYRAFKPY----AKNQGEGEPAGNKALEDEEEFSFKMFPASVV  294 (301)
T ss_pred             HHHHHHhHheeecCeeeeeccC------------cceeeeecChh----hhcccCCCCCCCCcccchHhhhcccCceeEE
Confidence            9999999999999999998643            23665332111    2457789999999999999999999999999


Q ss_pred             chHhhhc
Q 026799          226 YYTKWLD  232 (233)
Q Consensus       226 Y~~~WL~  232 (233)
                      ||++|+.
T Consensus       295 y~dew~~  301 (301)
T COG5111         295 YFDEWTI  301 (301)
T ss_pred             eehhhcC
Confidence            9999973

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=98.49  E-value=5.9e-07  Score=66.26  Aligned_cols=65  Identities=25%  Similarity=0.306  Sum_probs=56.7

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc---cCCCeeeEEee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI---HSKGKKHLMAV   83 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV---~~~~rK~Yml~   83 (233)
                      |+.+..|++.|-.++..|||+.||.+.+  +++++.+.+.+|.|+++|||.....+   ..++...++++
T Consensus         1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~--~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~   68 (75)
T PF04182_consen    1 TDIQYCLLERIARSRYNGITQSDLSKLL--GIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLH   68 (75)
T ss_pred             CchHHHHHHHHHhcCCCCEehhHHHHHh--CCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEE
Confidence            5678999999999999999999999999  99999999999999999999986662   33566666654

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=98.35  E-value=2.8e-06  Score=58.97  Aligned_cols=59  Identities=14%  Similarity=0.249  Sum_probs=53.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      +|++.|..|+..|...+..++...+|...+  ++++..++++++.||++|||...++-+++
T Consensus         2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l--~~~~~~vs~~v~~L~~~Glv~r~~~~~D~   60 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPGEELTQSELAERL--GISKSTVSRIVKRLEKKGLVERERDPGDR   60 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTTSGEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred             ccCHHHHHHHHHHHHCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence            689999999999999999999999999999  99999999999999999999998887754

...

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=98.31  E-value=1.8e-06  Score=77.88  Aligned_cols=55  Identities=25%  Similarity=0.477  Sum_probs=51.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .+|+++|+.|..+|.+.|+. |.|+||++++  |+|.+++.|+|+.||++|||+..|.
T Consensus       191 ~~L~~~e~~il~~i~~~GGr-i~Q~eL~r~l--glsktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         191 YDLNEDEKEILDLIRERGGR-ITQAELRRAL--GLSKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             CCCCHHHHHHHHHHHHhCCE-EeHHHHHHhh--CCChHHHHHHHHHHHhCCceEEEEe
Confidence            58999999999999998874 9999999999  9999999999999999999999885

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=98.21  E-value=3.7e-06  Score=60.14  Aligned_cols=62  Identities=23%  Similarity=0.339  Sum_probs=53.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +|++.|..||..+-..|.  +..++|.+.+  +++.+++.++|+.|+++|||.....    +.++|...+
T Consensus         5 gLs~~E~~vy~~Ll~~~~--~t~~eIa~~l--~i~~~~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~   66 (68)
T PF01978_consen    5 GLSENEAKVYLALLKNGP--ATAEEIAEEL--GISRSTVYRALKSLEEKGLVEREEG----RPKVYRAVP   66 (68)
T ss_dssp             CHHHHHHHHHHHHHHHCH--EEHHHHHHHH--TSSHHHHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred             CcCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence            688999999999986665  9999999999  9999999999999999999988772    256776554

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=98.18  E-value=8.6e-06  Score=57.41  Aligned_cols=65  Identities=22%  Similarity=0.322  Sum_probs=52.1

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      ||..|..|+..|. ..+.++..++|...+  +++...++++|++|+++|||....+-++++.++|-|.
T Consensus         1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~--~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT   65 (68)
T PF13463_consen    1 LTRPQWQVLRALA-HSDGPMTQSDLAERL--GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLT   65 (68)
T ss_dssp             --HHHHHHHHHHT---TS-BEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-
T ss_pred             CCHHHHHHHHHHH-ccCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeC
Confidence            5788999999998 556679999999999  9999999999999999999999999988777777654

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=98.17  E-value=9.7e-06  Score=63.29  Aligned_cols=64  Identities=17%  Similarity=0.229  Sum_probs=57.2

Q ss_pred             CCChHHHHHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|.  .+.+.|+.+++|...+  +++...|+++++.||++|+|++.++-.++++...
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l--~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i   87 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEI--LIKQSALVKIIKKLSKKGYLSKERSEDDERKVII   87 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEE
Confidence            78999999999998  6666789999999999  9999999999999999999999999997544433

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=98.16  E-value=7.4e-06  Score=54.77  Aligned_cols=48  Identities=25%  Similarity=0.497  Sum_probs=41.4

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      |++.++.|+.+|.+.+.  +.+++|.+++  |++..++++.|+.|+++|+|+
T Consensus         1 l~~~~~~Il~~l~~~~~--~t~~ela~~~--~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    1 LDETQRKILNYLRENPR--ITQKELAEKL--GISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             --HHHHHHHHHHHHCTT--S-HHHHHHHH--TS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHh--CCCHHHHHHHHHHHHHCcCcC
Confidence            67889999999999655  9999999999  999999999999999999996

...

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=98.12  E-value=1.5e-05  Score=54.99  Aligned_cols=57  Identities=23%  Similarity=0.330  Sum_probs=51.9

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG   76 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~   76 (233)
                      ||..|..++..|.+.|.  +...+|.+.+  +++...++++++.|+++|+|.+..+-++.+
T Consensus         1 lt~~q~~iL~~l~~~~~--~~~~~la~~~--~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R   57 (59)
T PF01047_consen    1 LTPSQFRILRILYENGG--ITQSELAEKL--GISRSTVTRIIKRLEKKGLIERERDPDDRR   57 (59)
T ss_dssp             STHHHHHHHHHHHHHSS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence            67889999999999888  9999999999  999999999999999999999999887644

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=97.96  E-value=4.2e-05  Score=60.01  Aligned_cols=66  Identities=9%  Similarity=0.164  Sum_probs=58.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      .+|+..+..|+..|...|  |+.+++|.+.+  ++...++++.|+.||++|||.+.++-.+++++.|-|.
T Consensus        24 ~~lt~~q~~iL~~l~~~~--~~t~~ela~~~--~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT   89 (118)
T TIGR02337        24 HGLTEQQWRILRILAEQG--SMEFTQLANQA--CILRPSLTGILARLERDGLVTRLKASNDQRRVYISLT   89 (118)
T ss_pred             cCCCHHHHHHHHHHHHcC--CcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEEC
Confidence            478999999999998755  69999999999  9999999999999999999999999988777766543

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=97.92  E-value=4.7e-05  Score=64.49  Aligned_cols=66  Identities=12%  Similarity=0.176  Sum_probs=59.4

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      --+|+..+..|+..|...++.++.+++|...+  +++..+++++++.||++|||.+.++-.+++.+..
T Consensus        50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l--~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v  115 (176)
T PRK10870         50 AQGINETLFMALITLESQENHSIQPSELSCAL--GSSRTNATRIADELEKRGWIERRESDNDRRCLHL  115 (176)
T ss_pred             HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEE
Confidence            34789999999999998888999999999999  9999999999999999999999999887555444

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=97.91  E-value=5.2e-05  Score=57.70  Aligned_cols=63  Identities=17%  Similarity=0.283  Sum_probs=56.7

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      |+..|..|+..|...+..+.  ++|.+.+  +++...+++.|+.||++|||++.++-.+++++++.|
T Consensus        20 lt~~q~~~L~~l~~~~~~~~--~~la~~l--~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l   82 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITV--KELAERL--GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL   82 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcH--HHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence            89999999999999998776  9999999  999999999999999999999999998855555544

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=97.86  E-value=5.3e-05  Score=54.85  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=46.5

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ++.+..|+.++..+|.+|+..++|.+++  +|+.+.|+|+|..|+++|+|..
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--gl~~~~v~r~L~~L~~~G~V~~   54 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNL--GLPKKEVNRVLYSLEKKGKVCK   54 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence            3467799999999999999999999999  9999999999999999999955

Helix-turn-helix-containing domain. Also known as Zab.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.85  E-value=8.1e-05  Score=60.43  Aligned_cols=63  Identities=17%  Similarity=0.164  Sum_probs=55.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+|+..|..|+..|..  +.|+.+++|...+  +++..+++++|+.||++|||.+.++-.+++.+..
T Consensus        36 ~glt~~q~~vL~~l~~--~~~~t~~eLa~~l--~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l   98 (144)
T PRK11512         36 LDITAAQFKVLCSIRC--AACITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLV   98 (144)
T ss_pred             cCCCHHHHHHHHHHHH--cCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEe
Confidence            4799999999999965  4579999999999  9999999999999999999999999887555444

>PF13730 HTH_36: Helix-turn-helix domain

Probab=97.83  E-value=8.4e-05  Score=50.74  Aligned_cols=51  Identities=25%  Similarity=0.493  Sum_probs=44.6

Q ss_pred             CCCChHHHHHHHHHHhhC--CCccc--HHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           14 DSLTDHERLIYDVIRSKQ--DMGIW--TRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG--~~GIw--~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      ++|++.+++||-.|...-  +.|.|  +++|.+.+  ++..++|.|+|+.||++|+|
T Consensus         1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~--g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen    1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDL--GVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCcCC
Confidence            479999999999998653  44444  79999999  99999999999999999997

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=97.79  E-value=0.00014  Score=53.76  Aligned_cols=64  Identities=16%  Similarity=0.290  Sum_probs=53.7

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      --+|+..+..|+.+|...|  ++..++|...+  +++...++++|+.|+++|+|...+.-..+..+.|
T Consensus         5 ~~~l~~~~~~il~~l~~~~--~~~~~~la~~~--~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~   68 (101)
T smart00347        5 PLGLTPTQFLVLRILYEEG--PLSVSELAKRL--GVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLV   68 (101)
T ss_pred             ccCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEE
Confidence            3478999999999999877  59999999999  9999999999999999999988766443333333

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=97.77  E-value=0.00013  Score=58.84  Aligned_cols=66  Identities=12%  Similarity=0.167  Sum_probs=57.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      -+|+..+..|+..|...+ .|+.+++|...+  ++...+|+++++.||++|||.+.++-.+++.+..-|
T Consensus        27 ~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l--~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~L   92 (144)
T PRK03573         27 LELTQTHWVTLHNIHQLP-PEQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKL   92 (144)
T ss_pred             cCCCHHHHHHHHHHHHcC-CCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEE
Confidence            479999999999997653 468999999999  999999999999999999999999988765555543

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=97.73  E-value=0.00014  Score=62.64  Aligned_cols=60  Identities=12%  Similarity=0.022  Sum_probs=53.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      -+|+..|..|+.+|...+  |+.+++|.+.+  +++.++++++|+.||++|||.+.++-.+++.
T Consensus        41 ~gLt~~q~~iL~~L~~~~--~itq~eLa~~l--~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~  100 (185)
T PRK13777         41 YDLNINEHHILWIAYHLK--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLTFSKKEDDKRN  100 (185)
T ss_pred             CCCCHHHHHHHHHHHhCC--CcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCCCCe
Confidence            479999999999997754  79999999999  9999999999999999999999988876433

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=97.56  E-value=0.0023  Score=50.32  Aligned_cols=111  Identities=14%  Similarity=0.195  Sum_probs=73.4

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      |++-|..|.++|=+.|.  +..+||...++.  +++.++|...|+.|++||+|...+.   .+..+|-     |..+   
T Consensus         1 Ls~~E~~IM~~lW~~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~---gr~~~Y~-----p~is---   67 (115)
T PF03965_consen    1 LSDLELEIMEILWESGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI---GRAYVYS-----PLIS---   67 (115)
T ss_dssp             --HHHHHHHHHHHHHSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEE-----ESSS---
T ss_pred             CCHHHHHHHHHHHhCCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec---CCceEEE-----eCCc---
Confidence            68899999999999999  999999999833  6889999999999999999988654   2333441     1111   


Q ss_pred             CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                               -.   +.+...+.+++.+.-.-+...+..++-+..    .||.+|++.|-+.|
T Consensus        68 ---------~~---e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~----~ls~~el~~L~~li  113 (115)
T PF03965_consen   68 ---------RE---EYLAQELRQFLDRLFDGSIPQLVAALVESE----ELSPEELEELRKLI  113 (115)
T ss_dssp             ---------HH---HHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-----S-HHHHHHHHHHH
T ss_pred             ---------HH---HHHHHHHHHHHHHHhCCCHHHHHHHHHhcC----CCCHHHHHHHHHHH
Confidence                     11   233444444444432335666666665554    69999999987765

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=97.51  E-value=0.00033  Score=50.59  Aligned_cols=57  Identities=23%  Similarity=0.387  Sum_probs=43.1

Q ss_pred             CCCCChHHHHHHHHHHhhCC-Cc--ccHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCceeeec
Q 026799           13 SDSLTDHERLIYDVIRSKQD-MG--IWTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~-~G--Iw~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      |+.||+-|+.||.+|.+--. .|  =..+||.+.+  |+. .+.|.+.|+.||+||+|+..+.
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~--g~~S~~tv~~~L~~Le~kG~I~r~~~   61 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEAL--GLKSTSTVQRHLKALERKGYIRRDPG   61 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHH--TSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCcCccCCCC
Confidence            57899999999999986322 23  4679999999  998 8999999999999999988654

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=97.41  E-value=0.0008  Score=54.84  Aligned_cols=70  Identities=13%  Similarity=0.140  Sum_probs=56.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS   88 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs   88 (233)
                      +|++.+..||..+-+ .|.+...-+|...+  |+..++++|+|++|.+.|||.+.+---..|+..| +|.--|.
T Consensus        24 GLs~~Dv~v~~~LL~-~~~~~tvdelae~l--nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~y-iY~~i~~   93 (126)
T COG3355          24 GLSELDVEVYKALLE-ENGPLTVDELAEIL--NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYY-LYKPIDP   93 (126)
T ss_pred             CCcHHHHHHHHHHHh-hcCCcCHHHHHHHH--CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeE-EEecCCH
Confidence            799999999999996 45569999999999  9999999999999999999999885444455444 4443333

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=97.22  E-value=0.0016  Score=52.65  Aligned_cols=71  Identities=21%  Similarity=0.353  Sum_probs=61.2

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC---Cee--eEEeecccc
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK---GKK--HLMAVEFEP   87 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~---~rK--~Yml~~leP   87 (233)
                      +..|++-++.+++++...+.  +..++|.+++  |++..++.+.+|+|++.|+|+....+-++   +..  +++....+|
T Consensus         3 ~~~lD~~D~~IL~~L~~d~r--~~~~eia~~l--glS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~   78 (154)
T COG1522           3 MMKLDDIDRRILRLLQEDAR--ISNAELAERV--GLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLER   78 (154)
T ss_pred             cccccHHHHHHHHHHHHhCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecC
Confidence            45789999999999999999  9999999999  99999999999999999999999987665   433  555555555

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=97.22  E-value=0.0098  Score=48.19  Aligned_cols=112  Identities=19%  Similarity=0.224  Sum_probs=71.6

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .|++.|..|.++|=..|.  +..++|...++  .++..++|...|+.|++||+|...+.   .+..+|-     |-.+  
T Consensus         1 ~Lt~~E~~VM~vlW~~~~--~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~---gr~~~Y~-----p~vs--   68 (130)
T TIGR02698         1 SISDAEWEVMRVVWTLGE--TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE---GRKFIYT-----ALVS--   68 (130)
T ss_pred             CCCHHHHHHHHHHHcCCC--CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecC---CCcEEEE-----ecCC--
Confidence            478999999999987764  78999777762  27899999999999999999977532   2233331     2111  


Q ss_pred             cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                                -.++.....+.+.+.+.  +.....-+..|+..     ..||.+|++.|-+.|
T Consensus        69 ----------~ee~~~~~~~~~~~~~f--~gs~~~ll~~l~~~-----~~ls~eele~L~~li  114 (130)
T TIGR02698        69 ----------EDEAVENAAQELFSRIC--SRKVGAVIADLIEE-----SPLSQTDIEKLEKLL  114 (130)
T ss_pred             ----------HHHHHHHHHHHHHHHHH--CCCHHHHHHHHHhc-----CCCCHHHHHHHHHHH
Confidence                      12333333333332222  22223445555553     369999999998754

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>PHA02943 hypothetical protein; Provisional

Probab=97.18  E-value=0.0072  Score=50.93  Aligned_cols=112  Identities=13%  Similarity=0.217  Sum_probs=82.0

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG  100 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~  100 (233)
                      ..|+.+| ..|-  ..+++|.+.+  +++..++..+|+.||..|.|++|+    .|+..|               |+-+.
T Consensus        14 ~eILE~L-k~G~--~TtseIAkaL--GlS~~qa~~~LyvLErEG~VkrV~----~G~~ty---------------w~l~~   69 (165)
T PHA02943         14 IKTLRLL-ADGC--KTTSRIANKL--GVSHSMARNALYQLAKEGMVLKVE----IGRAAI---------------WCLDE   69 (165)
T ss_pred             HHHHHHH-hcCC--ccHHHHHHHH--CCCHHHHHHHHHHHHHcCceEEEe----ecceEE---------------EEECh
Confidence            4577788 4443  6799999999  999999999999999999999866    355555               34322


Q ss_pred             CCCHHHHHHHHHHHHHHhhh--CCCCCHHHHHHHHHHh--------CCcccccCHHHHHHHHHHHh
Q 026799          101 SLDTEFIKVVKSQCLKQIIK--LKVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRALV  156 (233)
Q Consensus       101 e~D~efI~~l~~~~~~~i~~--~~~~T~~~I~~~I~~~--------~i~~~~Ls~~di~~il~~Lv  156 (233)
                      +==...|+.+.+-+..+|.+  ..++|+..+++.|.+-        .+..|.-+-..|-+.|+-+.
T Consensus        70 day~~~v~~~~Relwrlv~s~~~kfi~p~~l~~li~kd~~a~~~~ak~v~v~~r~a~il~fln~~l  135 (165)
T PHA02943         70 DAYTNLVFEIKRELWRLVCNSRLKFITPSRLLRLIAKDTEAHNIFAKYVPVNSRHAHILSFLNSAL  135 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccccccChHHHHHHHHhCHHHHHHHHHhcCcccchHHHHHHHHHHH
Confidence            11122377777788888864  5799999999999864        24456777788877777543

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=97.13  E-value=0.0016  Score=48.58  Aligned_cols=54  Identities=17%  Similarity=0.292  Sum_probs=40.9

Q ss_pred             HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      |+.++..  +..++-++|++.+  ++++..+++.|+.||+.|+|+.-|....++.++|
T Consensus         5 Il~~L~~--~~~~~f~~L~~~l--~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~   58 (80)
T PF13601_consen    5 ILALLYA--NEEATFSELKEEL--GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTW   58 (80)
T ss_dssp             HHHHHHH--HSEEEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEE
T ss_pred             HHHHHhh--cCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEE
Confidence            4555555  4459999999999  9999999999999999999999998876544433

>TIGR00498 lexA SOS regulatory protein LexA

Probab=97.11  E-value=0.0015  Score=55.73  Aligned_cols=56  Identities=21%  Similarity=0.335  Sum_probs=49.9

Q ss_pred             CCCCChHHHHHHHHHHhh---CCCcccHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCceeee
Q 026799           13 SDSLTDHERLIYDVIRSK---QDMGIWTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~a---G~~GIw~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      |++||+.|..||..|.+.   +..+...++|.+.+  +++ .+++.+.|++||++|+|+...
T Consensus         1 ~~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~--~~~s~~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498         1 MKPLTARQQEVLDLIRAHIESTGYPPSIREIARAV--GLRSPSAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             CCccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh--CCCChHHHHHHHHHHHHCCCEecCC
Confidence            457999999999999954   55668899999999  999 999999999999999998764

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=97.02  E-value=0.0031  Score=54.26  Aligned_cols=55  Identities=13%  Similarity=0.309  Sum_probs=49.8

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ..+|++.+..|+.+|...|  ++..++|.+.+  ++++.++++.|+.|+++|+|...+.
T Consensus       138 ~~~ls~~~~~IL~~l~~~g--~~s~~eia~~l--~is~stv~r~L~~Le~~GlI~r~~~  192 (203)
T TIGR01884       138 LAGLSREELKVLEVLKAEG--EKSVKNIAKKL--GKSLSTISRHLRELEKKGLVEQKGR  192 (203)
T ss_pred             hcCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            4578999999999998765  49999999999  9999999999999999999998863

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=97.02  E-value=0.0025  Score=54.81  Aligned_cols=129  Identities=11%  Similarity=0.159  Sum_probs=76.9

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      ...|+.+|...|.  +..++|...+  +++..+|++.|+.|+++|||...+.....+|.. .+|.|+|.-.    .-|.+
T Consensus         3 r~~IL~~L~~~~~--~t~~eLA~~l--gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~-~~y~LT~~G~----~~~~~   73 (203)
T TIGR02702         3 KEDILSYLLKQGQ--ATAAALAEAL--AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQ-YHYQLSRQGR----EQFPQ   73 (203)
T ss_pred             HHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCc-eEEEECcchh----hhccc
Confidence            3578888887765  9999999999  999999999999999999999876544344443 3445555422    11111


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcc-----cc---cC-HHHHHHHHHHHhcCCeEEEEe
Q 026799          100 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK-----VD---LT-KQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       100 ~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~-----~~---Ls-~~di~~il~~Lv~Dg~ie~v~  165 (233)
                       .+ ..+...+.+.+..-      .+.+++.+++....-..     ..   .+ .+-++.|.+.|--+|-.-++.
T Consensus        74 -~~-~~~~~~ll~~l~~~------l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Gy~~~~~  140 (203)
T TIGR02702        74 -RH-GRFAVSLLDSLAET------LGPEQFEAVLQKQWQRKAEAYRRQLGQGSLAERLAQLVALRQQEGFMAEVH  140 (203)
T ss_pred             -cH-HHHHHHHHHHHHHH------cCHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence             11 12222222222211      34555555554432000     01   11 456788888888777765554

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=96.95  E-value=0.0035  Score=43.89  Aligned_cols=49  Identities=16%  Similarity=0.244  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +.-..||.+|  +.+.++...+|...+  +++++++++.|+.|++.|||+..+
T Consensus        10 p~R~~Il~~L--~~~~~~t~~ela~~l--~~~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   10 PTRLRILRLL--ASNGPMTVSELAEEL--GISQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHHHH--HHCSTBEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHH--hcCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEec
Confidence            4556788888  566779999999999  999999999999999999998865

...

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=96.91  E-value=0.0076  Score=41.49  Aligned_cols=58  Identities=12%  Similarity=0.181  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      ..+..|+..|...+   +..++|.+.+  +++.+++++.|+.|+++|+|....+-   +++.|.+.
T Consensus         7 ~~~~~il~~l~~~~---~~~~ei~~~~--~i~~~~i~~~l~~L~~~g~i~~~~~~---~~~~~~~~   64 (78)
T cd00090           7 PTRLRILRLLLEGP---LTVSELAERL--GLSQSTVSRHLKKLEEAGLVESRREG---RRVYYSLT   64 (78)
T ss_pred             hHHHHHHHHHHHCC---cCHHHHHHHH--CcCHhHHHHHHHHHHHCCCeEEEEec---cEEEEEeC
Confidence            46778888887754   9999999999  99999999999999999999876543   45556443

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.86  E-value=0.0024  Score=48.91  Aligned_cols=54  Identities=19%  Similarity=0.364  Sum_probs=47.9

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      |++.++.|+.++...|.  +..++|.+++  |++..++++.|+.|+++|+|+.+..+-
T Consensus         1 ld~~D~~il~~L~~~~~--~~~~~la~~l--~~s~~tv~~~l~~L~~~g~i~~~~~~~   54 (108)
T smart00344        1 LDEIDRKILEELQKDAR--ISLAELAKKV--GLSPSTVHNRVKRLEEEGVIKGYTAVI   54 (108)
T ss_pred             CCHHHHHHHHHHHHhCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeceEEEe
Confidence            57788999999998765  9999999999  999999999999999999998655443

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=96.75  E-value=0.0057  Score=46.88  Aligned_cols=56  Identities=20%  Similarity=0.210  Sum_probs=46.8

Q ss_pred             CCCCCChHHHHHHHHHHh-h-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           12 PSDSLTDHERLIYDVIRS-K-----QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~-a-----G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ...+++..+..++-.|.. .     ...++.+++|...+  +++..+|+|+|+.||++|+|+..
T Consensus        19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~--g~sr~tVsr~L~~Le~~GlI~r~   80 (95)
T TIGR01610        19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELT--GLSRTHVSDAIKSLARRRIIFRQ   80 (95)
T ss_pred             HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeee
Confidence            355778877777776643 1     47889999999999  99999999999999999999854

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PRK00215 LexA repressor; Validated

Probab=96.74  E-value=0.0043  Score=53.09  Aligned_cols=53  Identities=26%  Similarity=0.391  Sum_probs=48.0

Q ss_pred             CChHHHHHHHHHHh---hCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCceeee
Q 026799           16 LTDHERLIYDVIRS---KQDMGIWTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        16 L~~~e~lVy~~I~~---aG~~GIw~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ||+.|..||..|.+   .++.++..+||.+.+  ++ +.+++++.|+.|+++|+|....
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~--~~~~~~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADAL--GLRSPSAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEeCC
Confidence            78899999999984   467788999999999  99 9999999999999999997755

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.62  E-value=0.01  Score=38.95  Aligned_cols=47  Identities=11%  Similarity=0.326  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +..|+.+|.+.  .++...+|...+  +++.+++++.|+.|+++|+|....
T Consensus         2 ~~~il~~l~~~--~~~s~~~l~~~l--~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        2 QQQILELLAQQ--GKVSVEELAELL--GVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHHHc--CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEee
Confidence            34678888764  469999999999  999999999999999999997644

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=96.62  E-value=0.012  Score=43.68  Aligned_cols=63  Identities=16%  Similarity=0.245  Sum_probs=46.4

Q ss_pred             HHHHHHHhhCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           22 LIYDVIRSKQDMG-IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        22 lVy~~I~~aG~~G-Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .++-++...++.+ +..++|.+++  +++.+.+.++|+.|++.|+|++.+-.+    -=|.|..  |.++||
T Consensus        12 ~~l~~la~~~~~~~~s~~eiA~~~--~i~~~~l~kil~~L~~~Gli~s~~G~~----GGy~L~~--~~~~It   75 (83)
T PF02082_consen   12 RILLYLARHPDGKPVSSKEIAERL--GISPSYLRKILQKLKKAGLIESSRGRG----GGYRLAR--PPEEIT   75 (83)
T ss_dssp             HHHHHHHCTTTSC-BEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEETSTT----SEEEESS---CCGSB
T ss_pred             HHHHHHHhCCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHhhCCeeEecCCCC----CceeecC--CHHHCC
Confidence            3444555666666 9999999999  999999999999999999997765332    4566654  555554

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=96.52  E-value=0.0063  Score=46.72  Aligned_cols=51  Identities=20%  Similarity=0.408  Sum_probs=44.1

Q ss_pred             CCChHHHHHHHHHHh--hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026799           15 SLTDHERLIYDVIRS--KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~--aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      +|++-++.||++|++  ..+.||-..+|.+++  +|+...|+++|..|...|+|=
T Consensus        44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IY   96 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMSENEVRKALDFLSNEGHIY   96 (102)
T ss_dssp             -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEe
Confidence            799999999999997  568899999999999  999999999999999999983

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=96.46  E-value=0.013  Score=41.52  Aligned_cols=45  Identities=24%  Similarity=0.411  Sum_probs=38.5

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +.||.+-+  ++..+..++|.+.+  ++.+.+++..||+|+++|||...
T Consensus        11 ~~Iy~l~~--~~~~v~~~~iA~~L--~vs~~tvt~ml~~L~~~GlV~~~   55 (60)
T PF01325_consen   11 KAIYELSE--EGGPVRTKDIAERL--GVSPPTVTEMLKRLAEKGLVEYE   55 (60)
T ss_dssp             HHHHHHHH--CTSSBBHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHc--CCCCccHHHHHHHH--CCChHHHHHHHHHHHHCCCEEec
Confidence            45676665  67779999999999  99999999999999999999754

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=96.40  E-value=0.0092  Score=54.46  Aligned_cols=58  Identities=16%  Similarity=0.340  Sum_probs=51.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+...++.||..||.|-+|-+=+  ||...+|+-+|+.||.+|.||+ +-|..+.+++|+.
T Consensus         8 klir~Lk~a~~~GI~Q~eIeel~--GlSKStvSEaLs~LE~~giv~R-rkvsGKs~rVwLa   65 (321)
T COG3888           8 KLIRELKRAGPEGIDQTEIEELM--GLSKSTVSEALSELEKQGIVKR-RKVSGKSKRVWLA   65 (321)
T ss_pred             HHHHHHHhcCCCCccHHHHHHHh--CcchhHHHHHHHHHHhcCeeee-eeecCcceEEeec
Confidence            56678999999999999999999  9999999999999999999999 5566678888853

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.36  E-value=0.0065  Score=38.24  Aligned_cols=30  Identities=27%  Similarity=0.450  Sum_probs=26.2

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      +.+.||..-+  |+...+|+|+|+.|+++|+|
T Consensus         3 mtr~diA~~l--G~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYL--GLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHH--TS-HHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHh--CCcHHHHHHHHHHHHHcCCC
Confidence            6788999999  99999999999999999997

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=96.36  E-value=0.0065  Score=50.66  Aligned_cols=59  Identities=12%  Similarity=0.265  Sum_probs=52.8

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      ...|++-++.|+.++...|.  +..++|.+++  |++.+++.+-+++|++.|.|+....+-++
T Consensus         9 ~~~lD~~D~~IL~~Lq~d~R--~s~~eiA~~l--glS~~tv~~Ri~rL~~~GvI~~~~~~v~p   67 (164)
T PRK11169          9 GKDLDRIDRNILNELQKDGR--ISNVELSKRV--GLSPTPCLERVRRLERQGFIQGYTALLNP   67 (164)
T ss_pred             hhhHHHHHHHHHHHhccCCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence            55689999999999999999  8889999999  99999999999999999999976654443

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.33  E-value=0.023  Score=38.07  Aligned_cols=43  Identities=16%  Similarity=0.324  Sum_probs=36.2

Q ss_pred             HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      |+.+|.   +..+...+|...+  +++.++++++|+.|+++|+|....
T Consensus         2 il~~l~---~~~~~~~~i~~~l--~is~~~v~~~l~~L~~~g~i~~~~   44 (66)
T smart00418        2 ILKLLA---EGELCVCELAEIL--GLSQSTVSHHLKKLREAGLVESRR   44 (66)
T ss_pred             HHHHhh---cCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeee
Confidence            345554   4568999999999  999999999999999999997543

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=96.27  E-value=0.062  Score=50.11  Aligned_cols=127  Identities=22%  Similarity=0.243  Sum_probs=82.3

Q ss_pred             CCChHHHHHHHHHHhh-CCCcccHHHHHHH-hhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           15 SLTDHERLIYDVIRSK-QDMGIWTRDMKRE-LRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a-G~~GIw~~dik~~-t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      +|.+-+..||+++.++ +.+|+.++||... .  +++..++-.+|..|.++|+|+-++   ..+.-.|-+.+-+=...+.
T Consensus         6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~--~~~~~~~~~~in~Ll~~~~~~~~~---~~~~l~~~~~~~~~a~k~~   80 (327)
T PF05158_consen    6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIP--GLDLQELVKAINELLSSGLLKLLK---KGGGLSYKAVSEEEAKKLK   80 (327)
T ss_dssp             -HHHHHHHHHHHHHH---SS-EEHHHHHHH-T--TS-HHHHHHHHHHHHHHTSEEEEE----SSSEEEEE--SSS-----
T ss_pred             hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcC--CCCHHHHHHHHHHHHhCCCEEEEE---cCCEEEEEEeCHHHHhhhc
Confidence            5777899999999999 9999999999999 5  899999999999999999999888   3455566554433333333


Q ss_pred             cCCcccCCCCCHHHHHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799           93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus        93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~--~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      |=+             .-.+.+|..|+..+  .....+|.        .+..|....|..+|++|+=.+.|-+|++.
T Consensus        81 ~l~-------------~~e~lvy~~I~~ag~~GIw~~~i~--------~~t~l~~~~~~k~lk~Le~k~lIK~vksv  136 (327)
T PF05158_consen   81 GLS-------------DEERLVYQLIEEAGNKGIWTKDIK--------KKTNLHQTQLTKILKSLESKKLIKSVKSV  136 (327)
T ss_dssp             SSS-------------CCHHHHHHHHHHHTTT-EEHHHHH--------HHCT--HHHHHHHHHHHHHTTSEEEE--S
T ss_pred             CCC-------------HHHHHHHHHHHHhCCCCCcHHHHH--------HHcCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence            321             11235666666432  23222222        23468899999999999999999999864

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=96.21  E-value=0.011  Score=40.22  Aligned_cols=44  Identities=16%  Similarity=0.364  Sum_probs=36.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++.+++. |+..+||.+++  ++|..++.|.|+.|++.|+|.+
T Consensus         7 ~iL~~l~~~~~-~~t~~eia~~~--gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    7 RILEALAESGG-PLTLSEIARAL--GLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHCHHCTBS-CEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHcCCC-CCCHHHHHHHH--CcCHHHHHHHHHHHHHCcCeec
Confidence            45566666544 58999999999  9999999999999999999976

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=96.18  E-value=0.018  Score=56.10  Aligned_cols=52  Identities=19%  Similarity=0.328  Sum_probs=47.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .+|++.|..|+..|...|  ++.+.+|..++  +++..+|+++++.|+++|||...
T Consensus         2 ~~Lt~~e~~vL~~L~~~~--~~s~~eLA~~l--~l~~~tVt~~i~~Le~kGlV~~~   53 (489)
T PRK04172          2 MELHPNEKKVLKALKELK--EATLEELAEKL--GLPPEAVMRAAEWLEEKGLVKVE   53 (489)
T ss_pred             CCCCHHHHHHHHHHHhCC--CCCHHHHHHHh--CcCHHHHHHHHHHHHhCCCEEEE
Confidence            379999999999997665  69999999999  99999999999999999999875

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=96.11  E-value=0.023  Score=37.85  Aligned_cols=43  Identities=19%  Similarity=0.377  Sum_probs=36.1

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..|+.+|.+ |.  ....+|.+.+  ++++.++++.|+.|++.|+|++
T Consensus         5 ~~Il~~L~~-~~--~~~~el~~~l--~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    5 LRILKLLSE-GP--LTVSELAEEL--GLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHTT-SS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHh-CC--CchhhHHHhc--cccchHHHHHHHHHHHCcCeeC
Confidence            456666666 55  8899999999  9999999999999999999974

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=96.03  E-value=0.0087  Score=44.14  Aligned_cols=55  Identities=24%  Similarity=0.360  Sum_probs=41.0

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      .+|+++++.-.+.|.-..+|...+  ||+...+.+.|+.|+++|||+.       ....|.+.+
T Consensus         6 ~Ii~~IL~~l~~~~~~~t~i~~~~--~L~~~~~~~yL~~L~~~gLI~~-------~~~~Y~lTe   60 (77)
T PF14947_consen    6 EIIFDILKILSKGGAKKTEIMYKA--NLNYSTLKKYLKELEEKGLIKK-------KDGKYRLTE   60 (77)
T ss_dssp             HHHHHHHHHH-TT-B-HHHHHTTS--T--HHHHHHHHHHHHHTTSEEE-------ETTEEEE-H
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCcCeeC-------CCCEEEECc
Confidence            377888887778889999999999  9999999999999999999933       345666543

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=95.96  E-value=0.024  Score=50.85  Aligned_cols=63  Identities=21%  Similarity=0.287  Sum_probs=55.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      =+||+.|-.||-.+-..|.  ...++|...+  |+|++.|-.+|++||.||+|...    ..+.+.|-..+
T Consensus        12 lGlt~yEa~vY~aLl~~g~--~tA~eis~~s--gvP~~kvY~vl~sLe~kG~v~~~----~g~P~~y~av~   74 (247)
T COG1378          12 LGLTEYEAKVYLALLCLGE--ATAKEISEAS--GVPRPKVYDVLRSLEKKGLVEVI----EGRPKKYRAVP   74 (247)
T ss_pred             cCCCHHHHHHHHHHHHhCC--ccHHHHHHHc--CCCchhHHHHHHHHHHCCCEEee----CCCCceEEeCC
Confidence            3799999999999999999  9999999999  99999999999999999999764    34556775544

>PRK06474 hypothetical protein; Provisional

Probab=95.91  E-value=0.1  Score=44.49  Aligned_cols=130  Identities=14%  Similarity=0.230  Sum_probs=80.9

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeeccccCCCcccCC
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVEFEPSKEISGGA   95 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~lePs~eiTGG~   95 (233)
                      +.=..|++++...+. ++...+|...++ ++++.+|.+.|+.|++.|||..++.=  .....|+|-+..-  ...+.+..
T Consensus        11 p~R~~Il~~L~~~~~-~~ta~el~~~l~-~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~--~~~~~~~~   86 (178)
T PRK06474         11 PVRMKICQVLMRNKE-GLTPLELVKILK-DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE--DAKIEGSE   86 (178)
T ss_pred             HHHHHHHHHHHhCCC-CCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc--eeeeCHHH
Confidence            345578888877654 499999998872 59999999999999999999987653  3334577754431  11223333


Q ss_pred             cccC---C--CCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHh
Q 026799           96 WYSE---G--SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALV  156 (233)
Q Consensus        96 wy~d---~--e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv  156 (233)
                      |..+   +  .+-+.|...+.+...+|+.+.+-.     -.+-...+.+  ...||+++.+++.+-|.
T Consensus        87 ~~~~~~e~~~~~~~~~~~~~~~~~~~yl~~~~~~-----~~~~d~~~~s~~~L~Lt~ee~~el~~el~  149 (178)
T PRK06474         87 WTGLSDDEKLNYISYYQLSLLQQYQSYLKSLEEQ-----NSKEDKATFSVVELKLDEEEFEEFQSELN  149 (178)
T ss_pred             HHHhCHHHHHHHHHHHHHHHHHHHHHHHHhCccc-----chhccccceeeeeEecCHHHHHHHHHHHH
Confidence            3321   1  122345555556666677653211     1122333433  36799999888877664

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=95.90  E-value=0.022  Score=46.94  Aligned_cols=55  Identities=5%  Similarity=0.156  Sum_probs=50.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      ..|++.++.|+.++...|.  +..++|.+++  |++..+|.+-+++|++.|+|+....+
T Consensus         5 ~~lD~~D~~Il~~Lq~d~R--~s~~eiA~~l--glS~~tV~~Ri~rL~~~GvI~~~~~~   59 (153)
T PRK11179          5 YQIDNLDRGILEALMENAR--TPYAELAKQF--GVSPGTIHVRVEKMKQAGIITGTRVD   59 (153)
T ss_pred             cccCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEE
Confidence            3488999999999999999  9999999999  99999999999999999999876543

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=95.87  E-value=0.035  Score=38.68  Aligned_cols=46  Identities=15%  Similarity=0.441  Sum_probs=42.4

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..|+++|.+.|.  +..++|...+  +.+..+++|=|..|+++|+|+++.
T Consensus         3 ~~Il~~l~~~~~--~s~~ela~~~--~VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    3 QQILELLKEKGK--VSVKELAEEF--GVSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHHcCC--EEHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEc
Confidence            578999999888  9999999999  999999999999999999997753

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=95.87  E-value=0.039  Score=39.96  Aligned_cols=51  Identities=16%  Similarity=0.181  Sum_probs=45.1

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .+.|..|++++.+.|..++....+...+  +.+...|+++|=.|+++|.|...
T Consensus         3 ~~~ee~Il~~L~~~g~~~a~~ia~~~~L--~~~kk~VN~~LY~L~k~g~v~k~   53 (66)
T PF02295_consen    3 QDLEEKILDFLKELGGSTATAIAKALGL--SVPKKEVNRVLYRLEKQGKVCKE   53 (66)
T ss_dssp             HHHHHHHHHHHHHHTSSEEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             hhHHHHHHHHHHhcCCccHHHHHHHhCc--chhHHHHHHHHHHHHHCCCEeeC
Confidence            3568899999999998899999988888  99999999999999999999653

5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=95.87  E-value=0.029  Score=40.31  Aligned_cols=49  Identities=14%  Similarity=0.176  Sum_probs=40.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .|+++|.+. +.++.++||...+  +|+..++++.|..||+.|.|+.++.=+
T Consensus         4 ~Il~~i~~~-~~p~~T~eiA~~~--gls~~~aR~yL~~Le~eG~V~~~~~~r   52 (62)
T PF04703_consen    4 KILEYIKEQ-NGPLKTREIADAL--GLSIYQARYYLEKLEKEGKVERSPVRR   52 (62)
T ss_dssp             CHHHHHHHH-TS-EEHHHHHHHH--TS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            477888886 5679999999999  999999999999999999998865433

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure

Probab=95.82  E-value=0.04  Score=41.51  Aligned_cols=58  Identities=14%  Similarity=0.253  Sum_probs=44.3

Q ss_pred             HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      |+..|.. |  -.-..||++.+ ++++++++++.||.|++.|||.+...-..+.+..|.|.+
T Consensus        10 IL~~l~~-g--~~rf~el~~~l-~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~   67 (90)
T PF01638_consen   10 ILRALFQ-G--PMRFSELQRRL-PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE   67 (90)
T ss_dssp             HHHHHTT-S--SEEHHHHHHHS-TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred             HHHHHHh-C--CCcHHHHHHhc-chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence            4444444 4  47889999887 479999999999999999999888766667777787764

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=95.80  E-value=0.028  Score=43.28  Aligned_cols=66  Identities=9%  Similarity=0.123  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHh-h--cCCChHHHHHHHHHHHhCCCceee--ecccCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKREL-R--VNLPDNIVTKSIKSLQNKSLIKEV--VNIHSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t-~--~~l~~~~v~k~LK~Le~k~lIK~v--ksV~~~~rK~Yml~~   84 (233)
                      -+..|+.++......|-...+.-.+. +  ..+++.+|..+|+.||++|+|.+.  .+-..+.||+|-+.+
T Consensus         5 l~~~iL~~L~~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~   75 (100)
T TIGR03433         5 LDLLILKTLSLGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTA   75 (100)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECH
Confidence            46688888876666665544433332 1  168999999999999999999994  555667788886543

Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=95.76  E-value=0.036  Score=49.03  Aligned_cols=129  Identities=12%  Similarity=0.188  Sum_probs=75.7

Q ss_pred             hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHH
Q 026799           30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKV  109 (233)
Q Consensus        30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~  109 (233)
                      .++.+|.+++|.+.+  ++++.++++.|+.||++|||.+..+=  .++.+++    ++.           |   .++++.
T Consensus        17 ~~~~~IS~~eLA~~L--~iS~~Tvsr~Lk~LEe~GlI~R~~~~--r~~~v~L----Tek-----------G---~~ll~~   74 (217)
T PRK14165         17 NNTVKISSSEFANHT--GTSSKTAARILKQLEDEGYITRTIVP--RGQLITI----TEK-----------G---LDVLYN   74 (217)
T ss_pred             CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEcC--CceEEEE----CHH-----------H---HHHHHH
Confidence            344479999999999  99999999999999999999886552  2222221    111           1   111111


Q ss_pred             HHHHHHHHhh-----------------hCCCCCHHHHH-HHHHHhCCc------ccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          110 VKSQCLKQII-----------------KLKVATLEGIS-DSIKRSGAF------KVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       110 l~~~~~~~i~-----------------~~~~~T~~~I~-~~I~~~~i~------~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +-....+.+.                 -+.|+|.+--. +|-+..|+.      ++.|..+.++...+..-+++...+=-
T Consensus        75 ~~~d~~~if~~~~ei~l~G~v~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypGTLNv~l~~~~~~~~~~~~~~~~i~i~g~  154 (217)
T PRK14165         75 EYADYSRIFSIKDNLELEGNVVKGLGEGKYYINIKGYKIQFEEKLGFIPYPGTLNVKLDNSSSPLLRKLRESPGIRIEGF  154 (217)
T ss_pred             HHHHHHHHhcccccceehhhhhhccCCccEEEeCHHHHHHHHHHhCCcCCCCcEEEEecchhHHHHHHHhcCCCEecCCC
Confidence            1111111111                 12466665443 455566764      47787777666666667777543211


Q ss_pred             eCCCCCcccccCcceeeec
Q 026799          166 SNGSGEFTNIPVGKVCYKN  184 (233)
Q Consensus       166 ~~~~g~f~~~~~g~~~Yr~  184 (233)
                      .++...|.++    .||++
T Consensus       155 ~~~~r~~g~~----~~~~~  169 (217)
T PRK14165        155 TDGERTFGGV----KCYPV  169 (217)
T ss_pred             cCCCceeEEE----EEEEE
Confidence            1344456554    67875

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=95.59  E-value=0.041  Score=38.11  Aligned_cols=36  Identities=19%  Similarity=0.399  Sum_probs=33.0

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +..+..++|...+  +++..+++++|+.|+++|+|...
T Consensus        23 ~~~~s~~ela~~~--g~s~~tv~r~l~~L~~~g~i~~~   58 (67)
T cd00092          23 QLPLTRQEIADYL--GLTRETVSRTLKELEEEGLISRR   58 (67)
T ss_pred             cCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence            3458999999999  99999999999999999999764

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=95.56  E-value=0.031  Score=42.78  Aligned_cols=57  Identities=5%  Similarity=0.136  Sum_probs=45.9

Q ss_pred             HHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           22 LIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        22 lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      -.|+-|.  -..-+=|+...|..++  ++.-+.-+++|+.|+++|+||.|  +++.+..+|..
T Consensus        27 ~t~dkl~kEV~~~K~ITps~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~~~~~q~IYt~   85 (86)
T PRK09334         27 ELLKRVAKEVKKEKIVTPYTLASKY--GIKISVAKKVLRELEKRGVLVLY--SKNRRTPIYVP   85 (86)
T ss_pred             HHHHHHHHHhccCcEEcHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEecc
Confidence            3444443  2335568999999999  99999999999999999999998  56678889853

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=95.50  E-value=0.036  Score=39.78  Aligned_cols=47  Identities=11%  Similarity=0.214  Sum_probs=37.1

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      ..+.+||+.++.+|++||++.+        .++.+.|+.+|+.|+--|+|+++..
T Consensus         3 ~~i~~~l~~~~~~S~~eLa~~~--------~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    3 QEIRDYLRERGRVSLAELAREF--------GISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHHHHS-SEEHHHHHHHT--------T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHHHHcCCcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEEecC
Confidence            4567788888888888888765        4889999999999999999998763

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PRK12423 LexA repressor; Provisional

Probab=95.43  E-value=0.057  Score=46.52  Aligned_cols=56  Identities=23%  Similarity=0.399  Sum_probs=47.0

Q ss_pred             CCCChHHHHHHHHHHhh-CCCcc--cHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCceeeec
Q 026799           14 DSLTDHERLIYDVIRSK-QDMGI--WTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~a-G~~GI--w~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +.||+-++.||+.|.+. ...|+  ..++|.+.+  ++ ..+.++++|+.|+++|+|...+.
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~--g~~s~~~v~~~l~~L~~~G~l~~~~~   61 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAF--GFASRSVARKHVQALAEAGLIEVVPN   61 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEecCC
Confidence            45899999999999975 22334  899999999  96 78899999999999999987554

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=95.39  E-value=0.047  Score=43.47  Aligned_cols=51  Identities=16%  Similarity=0.233  Sum_probs=43.4

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ++.--.++.++..+++..+..++|..++  +++.+.|.++|+.|++.|+|.+.
T Consensus         8 ~~yal~~l~~la~~~~~~~s~~eia~~l--~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944         8 TDYATLVLTTLAQNDSQPYSAAEIAEQT--GLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             HhHHHHHHHHHHhCCCCCccHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEec
Confidence            3445566677777777789999999999  99999999999999999999764

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=95.36  E-value=0.069  Score=41.32  Aligned_cols=72  Identities=21%  Similarity=0.433  Sum_probs=55.0

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeeccccCCCccc
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~lePs~eiTG   93 (233)
                      +++.+..|+.++..+|.+  .-+-|.+.+  +++...|..+|+.||+.|||.++.+  ++...+      .+.|+.|+-.
T Consensus         5 ~~~l~~~IL~hl~~~~~D--y~k~ia~~l--~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~------k~K~~~e~~~   74 (92)
T PF10007_consen    5 LDPLDLKILQHLKKAGPD--YAKSIARRL--KIPLEEVREALEKLEEMGLLERVEGKTIKRSEA------KFKPKKEVHK   74 (92)
T ss_pred             cChhHHHHHHHHHHHCCC--cHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEecCcccchhhh------hcccchhhhc
Confidence            577889999999999995  455688889  9999999999999999999999874  333222      3456666543


Q ss_pred             -CCcc
Q 026799           94 -GAWY   97 (233)
Q Consensus        94 -G~wy   97 (233)
                       +++|
T Consensus        75 hHtYY   79 (92)
T PF10007_consen   75 HHTYY   79 (92)
T ss_pred             CCcee
Confidence             3444

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=95.33  E-value=0.069  Score=42.91  Aligned_cols=49  Identities=14%  Similarity=0.306  Sum_probs=43.0

Q ss_pred             ccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799           35 IWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus        35 Iw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      .-..+|++.+  + +++++|++.||.||+.|+|.+..-=..|-|.-|-|.++
T Consensus        37 ~RF~eL~r~i--~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~   86 (120)
T COG1733          37 KRFNELRRSI--GGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEK   86 (120)
T ss_pred             CcHHHHHHHc--cccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhh
Confidence            4788999999  7 99999999999999999999887766788888877665

>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function

Probab=95.23  E-value=0.61  Score=42.33  Aligned_cols=124  Identities=16%  Similarity=0.142  Sum_probs=95.3

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcC------CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccc-cCCCcc
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVN------LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFE-PSKEIS   92 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~------l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~le-Ps~eiT   92 (233)
                      ...|+..|...|-  +..+||...++..      .+.+....+|..|...|.|-....-. ..+++|-+.+-- |...  
T Consensus        87 ~~~v~~~L~~~gp--lt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~-g~~~~y~l~~~~lP~~~--  161 (327)
T PF06224_consen   87 AEAVLDALRADGP--LTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPR-GRWRTYDLTERWLPAPD--  161 (327)
T ss_pred             HHHHHHHHHhcCC--CCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCC-CceEEEechHHhCCCCc--
Confidence            4567777766665  9999999987333      45679999999999999997665332 345888776643 3222  


Q ss_pred             cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799           93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus        93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                               .|  -=+.+.+.+.+|+..++.+|++|+..|.   |     |+..+++..++.|+-.|.|+++...
T Consensus       162 ---------~~--~~ea~~~Lv~Ryl~~~GPat~~d~a~w~---g-----l~~~~~r~~l~~l~~~~~L~~v~~~  217 (327)
T PF06224_consen  162 ---------DD--REEALAELVRRYLRAYGPATLADFAWWS---G-----LPKTQARRALAQLVEEGELVEVEVE  217 (327)
T ss_pred             ---------CC--HHHHHHHHHHHHHHHcCCccHHHHHHHh---c-----cCHHHHHHHHHhhccCCcEEEEEEc
Confidence                     11  3356788899999999999999999994   3     8889999999999999999988754

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=95.18  E-value=0.23  Score=44.29  Aligned_cols=122  Identities=15%  Similarity=0.184  Sum_probs=88.0

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY   97 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy   97 (233)
                      .--..+|+.|..++.  ....++++..  +++..+++..|+.||+.++|++   ....++-.|..+++.          |
T Consensus       101 s~R~~Iy~~i~~nPG--~~lsEl~~nl--~i~R~TlRyhlriLe~~~li~a---~~~~g~~~yfpa~~t----------~  163 (240)
T COG3398         101 SKRDGIYNYIKPNPG--FSLSELRANL--YINRSTLRYHLRILESNPLIEA---GRVGGALRYFPADMT----------Y  163 (240)
T ss_pred             hhHHHHHHHhccCCC--ccHHHHHHhc--CCChHHHHHHHHHHHhCcchhh---hccCCceEEccCCCC----------c
Confidence            344578999987765  9999999999  9999999999999999999966   334466667555442          1


Q ss_pred             cCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799           98 SEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus        98 ~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      .+.| =.++=+..++.+..+|++.+-.|.-+|+.-+.        ||.+-|.==+..|.-=|.|.+-+
T Consensus       164 ~~~e-~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~--------ls~aTV~~~lk~l~~~Gii~~~~  222 (240)
T COG3398         164 GEAE-VLSLKNETSKAIIYEIQENKCNTNLLIAYELN--------LSVATVAYHLKKLEELGIIPEDR  222 (240)
T ss_pred             ccch-HHHhhchhHHHHHHHHhcCCcchHHHHHHHcC--------ccHHHHHHHHHHHHHcCCCcccc
Confidence            1222 13445566777888888887777777776543        66666666677777777776643

>PRK09954 putative kinase; Provisional

Probab=95.16  E-value=0.069  Score=49.27  Aligned_cols=52  Identities=21%  Similarity=0.264  Sum_probs=46.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      |++-++.|+.+|.+.+.  |.+++|.+++  +++.+++.+.|++|+++|+|+...-
T Consensus         1 ~~~~~~~il~~l~~~~~--~s~~~la~~l--~~s~~~v~~~i~~L~~~g~i~~~~~   52 (362)
T PRK09954          1 MNNREKEILAILRRNPL--IQQNEIADIL--QISRSRVAAHIMDLMRKGRIKGKGY   52 (362)
T ss_pred             CChHHHHHHHHHHHCCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCcCCcEE
Confidence            56778889999999887  9999999999  9999999999999999999965443

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.09  E-value=0.076  Score=39.05  Aligned_cols=45  Identities=11%  Similarity=0.271  Sum_probs=38.7

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..|+.+|...+ .++...+|.+.+  +++.+++++.|+.|++.|+|..
T Consensus         8 ~~Il~~l~~~~-~~~t~~~ia~~l--~i~~~tv~r~l~~L~~~g~l~~   52 (91)
T smart00346        8 LAVLRALAEEP-GGLTLAELAERL--GLSKSTAHRLLNTLQELGYVEQ   52 (91)
T ss_pred             HHHHHHHHhCC-CCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeee
Confidence            35667776552 379999999999  9999999999999999999976

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=95.09  E-value=0.074  Score=38.18  Aligned_cols=48  Identities=21%  Similarity=0.309  Sum_probs=40.3

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .|.++|++.|.  +...+|..++  ++++.+|.-.|..|+.+|.|+++..-.
T Consensus         4 ~i~~~l~~~~~--~S~~eLa~~~--~~s~~~ve~mL~~l~~kG~I~~~~~~~   51 (69)
T PF09012_consen    4 EIRDYLRERGR--VSLAELAREF--GISPEAVEAMLEQLIRKGYIRKVDMSS   51 (69)
T ss_dssp             HHHHHHHHS-S--EEHHHHHHHT--T--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred             HHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            57888999998  9999999999  999999999999999999999876543

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=95.04  E-value=0.38  Score=35.77  Aligned_cols=33  Identities=24%  Similarity=0.362  Sum_probs=29.7

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           37 TRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        37 ~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .++|.+.+  ++++++++++|+.|+++|||...++
T Consensus         2 ~~ela~~l--~is~stvs~~l~~L~~~glI~r~~~   34 (96)
T smart00529        2 TSEIAERL--NVSPPTVTQMLKKLEKDGLVEYEPY   34 (96)
T ss_pred             HHHHHHHh--CCChHHHHHHHHHHHHCCCEEEcCC
Confidence            46889999  9999999999999999999988553

iron dependent repressor

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=95.04  E-value=0.17  Score=41.20  Aligned_cols=83  Identities=19%  Similarity=0.249  Sum_probs=56.3

Q ss_pred             hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC---CCCHHH
Q 026799           30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG---SLDTEF  106 (233)
Q Consensus        30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~---e~D~ef  106 (233)
                      -|.+==..|+|...+  ++++++++|+.+.||+.|+|....     ++-+|+                +++   .+|...
T Consensus        31 pGdkLPSvRelA~~~--~VNpnTv~raY~eLE~eG~i~t~r-----g~G~fV----------------~~~~~~~~~~~~   87 (125)
T COG1725          31 PGDKLPSVRELAKDL--GVNPNTVQRAYQELEREGIVETKR-----GKGTFV----------------TEDAKEILDQLK   87 (125)
T ss_pred             CCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec-----CeeEEE----------------cCCchhhHHHHH
Confidence            455555789999999  999999999999999999997642     444443                333   444444


Q ss_pred             HHHHHHHHHHHhhh--CCCCCHHHHHHHHHH
Q 026799          107 IKVVKSQCLKQIIK--LKVATLEGISDSIKR  135 (233)
Q Consensus       107 I~~l~~~~~~~i~~--~~~~T~~~I~~~I~~  135 (233)
                      -..+.+.+-.||..  .-..|.++|++++++
T Consensus        88 ~~~~~~~l~~~I~~~~~~G~s~eei~~~~~~  118 (125)
T COG1725          88 RELAEEELEEFIEEAKALGLSLEEILELLKE  118 (125)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            45555555555542  234567777777663

>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=94.89  E-value=0.19  Score=51.10  Aligned_cols=144  Identities=14%  Similarity=0.201  Sum_probs=96.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCc-cc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEI-SG   93 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~ei-TG   93 (233)
                      ..|+++-.|..+-.+...  -...++...+  |+|...++|.|+-..++|+|.+.+.+.++  -+|-+-+-+-+..- -|
T Consensus       599 tVsp~qA~iI~~Fqek~t--wt~eelse~l--~ip~~~lrrrL~fWi~~GvL~e~~~~s~t--gt~T~iEse~d~~q~~~  672 (765)
T KOG2165|consen  599 TVSPEQAAIINLFQEKNT--WTLEELSESL--GIPVPALRRRLSFWIQKGVLREEPIISDT--GTLTVIESEMDFDQAEG  672 (765)
T ss_pred             eeCHHHHHHHHHhcCccc--ccHHHHHHHh--CCCHHHHHHHHHHHHHcCeeecCCCCCCC--ceeeeccccccccccCC
Confidence            346777777766666555  6678999999  99999999999999999999998866433  33433332222211 11


Q ss_pred             CCccc-CCCC----CHHHHHHHHH-------HHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHhcCC
Q 026799           94 GAWYS-EGSL----DTEFIKVVKS-------QCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALVLDN  159 (233)
Q Consensus        94 G~wy~-d~e~----D~efI~~l~~-------~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv~Dg  159 (233)
                      -+--. |.+-    ...-++.++.       .|...+.+.+...++-||++++=-+..  ....|.++++.-|+.+|-+|
T Consensus       673 ~~~~e~eee~~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~  752 (765)
T KOG2165|consen  673 TVLLEAEEENYESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREG  752 (765)
T ss_pred             CcccccccccchhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhcc
Confidence            11111 1111    1123344333       233334467889999999999855543  36899999999999999999


Q ss_pred             eEEEE
Q 026799          160 QIMEV  164 (233)
Q Consensus       160 ~ie~v  164 (233)
                      +++-+
T Consensus       753 kL~f~  757 (765)
T KOG2165|consen  753 KLEFI  757 (765)
T ss_pred             ceEEe
Confidence            99875

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.86  E-value=0.11  Score=34.73  Aligned_cols=34  Identities=15%  Similarity=0.370  Sum_probs=31.3

Q ss_pred             cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           34 GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        34 GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      -+ ..++|....  +++..+|+++|+.|++.|+|..+
T Consensus        19 ~l~s~~~la~~~--~vs~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345       19 KLPSERELAAQL--GVSRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             cCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence            46 799999999  99999999999999999999764

>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.86  E-value=0.069  Score=42.26  Aligned_cols=57  Identities=19%  Similarity=0.278  Sum_probs=46.2

Q ss_pred             HHHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           21 RLIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        21 ~lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .-.|+-|.  --+-+=|+...|..++  ++.-+.-+++|+.|+++|+|+.|  +++.+..+|-
T Consensus        44 ~~~~~kl~kEV~~~K~ITp~~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~k~~~~~IYt  102 (105)
T PF03297_consen   44 KETYDKLLKEVPKMKLITPSVLSERL--KINGSLARKALRELESKGLIKPV--SKHHRQRIYT  102 (105)
T ss_dssp             CHHHHHHHHHCTTSSCECHHHHHHHH--CCSCHHHHHHHHHHHHCCSSEEE--ECCTTCEEEE
T ss_pred             HHHHHHHHHHhccCcEeeHHHHHHhH--hhHHHHHHHHHHHHHHCCCEEEE--eccCCeEEEe
Confidence            34555554  2344569999999999  99999999999999999999998  5666888884

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=94.83  E-value=0.17  Score=39.08  Aligned_cols=59  Identities=19%  Similarity=0.263  Sum_probs=47.2

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +.|++++.++ +.-+...+|..+++   ++++..+|.|+|+.|++.|+|+++..-.  +...|.+
T Consensus         4 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~   65 (116)
T cd07153           4 LAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD--GKARYEL   65 (116)
T ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC--CceEEEe
Confidence            5789999887 56799999998883   3689999999999999999999976554  3455543

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=94.72  E-value=0.086  Score=42.71  Aligned_cols=47  Identities=21%  Similarity=0.222  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      --..||.++...|.  +..++|...+  ++++.+|++.|+.|+++|||...
T Consensus         9 yL~~I~~l~~~~~~--~~~~ela~~l--~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902          9 YIEQIYLLIEEKGY--ARVSDIAEAL--SVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             HHHHHHHHHhcCCC--cCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEEe
Confidence            34567777766654  7899999999  99999999999999999999754

>smart00351 PAX Paired Box domain

Probab=94.62  E-value=0.62  Score=37.32  Aligned_cols=93  Identities=19%  Similarity=0.171  Sum_probs=64.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      .++.+++.  .+|.... .|...++|.+++  +++..+|.|.++...+.|.++..+.                     ||
T Consensus        17 ~~s~~~R~--riv~~~~-~G~s~~~iA~~~--gvs~~tV~kwi~r~~~~G~~~pk~~---------------------gg   70 (125)
T smart00351       17 PLPDEERQ--RIVELAQ-NGVRPCDISRQL--CVSHGCVSKILGRYYETGSIRPGAI---------------------GG   70 (125)
T ss_pred             CCCHHHHH--HHHHHHH-cCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCcCC---------------------CC
Confidence            36776654  2333332 578999999999  9999999999999999997654221                     22


Q ss_pred             CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc
Q 026799           95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF  139 (233)
Q Consensus        95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~  139 (233)
                      ..-  ...    .+.....+..++..++..|+.||.+.+.+.||.
T Consensus        71 ~rp--~~~----~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~  109 (125)
T smart00351       71 SKP--KVA----TPKVVKKIADYKQENPGIFAWEIRDRLLSEGVC  109 (125)
T ss_pred             CCC--Ccc----CHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCC
Confidence            111  011    123344566678889999999999999987753

>cd00131 PAX Paired Box domain

Probab=94.60  E-value=1.2  Score=35.90  Aligned_cols=109  Identities=18%  Similarity=0.166  Sum_probs=73.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      +-|+.+.+.  .+|... ..|+..++|.+++  +++.++|.+.++...+.|-++..+.                     |
T Consensus        16 ~~lS~d~R~--rIv~~~-~~G~s~~~iA~~~--~Vs~~tV~r~i~r~~e~G~v~pk~~---------------------g   69 (128)
T cd00131          16 RPLPDSIRQ--RIVELA-QSGIRPCDISRQL--RVSHGCVSKILNRYYETGSIRPGAI---------------------G   69 (128)
T ss_pred             CcCCHHHHH--HHHHHH-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCCCC---------------------C
Confidence            456665543  233333 3689999999999  9999999999999999996644221                     1


Q ss_pred             CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHH
Q 026799           94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRA  154 (233)
Q Consensus        94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~  154 (233)
                      |  ..-...-    +.....+..++..++..|+.|+.+.+...|+.  .+..|..-|-.+|+.
T Consensus        70 g--~rpr~~~----~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          70 G--SKPRVAT----PEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             C--CCCCcCC----HHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence            1  0000011    12223445567889999999999998777764  356788888777654

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=94.59  E-value=0.24  Score=40.81  Aligned_cols=58  Identities=14%  Similarity=0.210  Sum_probs=51.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+|+.-..|++++.++++. ....+|=.++   ++++...+|-|+|+.|++.|+|.++..-.
T Consensus        18 r~T~qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~   78 (145)
T COG0735          18 RLTPQRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG   78 (145)
T ss_pred             CcCHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence            5799999999999999887 9999998887   35799999999999999999998876655

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=94.51  E-value=0.085  Score=34.06  Aligned_cols=33  Identities=21%  Similarity=0.419  Sum_probs=30.4

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..++|...+  +++..+++++|+.|+++|+|..
T Consensus         8 ~~s~~~la~~l--~~s~~tv~~~l~~L~~~g~l~~   40 (48)
T smart00419        8 PLTRQEIAELL--GLTRETVSRTLKRLEKEGLISR   40 (48)
T ss_pred             ccCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            36789999999  9999999999999999999964

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=94.47  E-value=0.19  Score=39.37  Aligned_cols=92  Identities=13%  Similarity=0.194  Sum_probs=63.3

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      +|..-..|+++|.++.. -+...+|.+.++   +++...+|-|+|+.|++.|+|.++..-  .+...|-+..     .-.
T Consensus         6 ~T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~--~~~~~Y~~~~-----~~~   77 (120)
T PF01475_consen    6 LTPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG--DGESRYELST-----CHH   77 (120)
T ss_dssp             HHHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET--TSEEEEEESS-----SSS
T ss_pred             CCHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC--CCcceEeecC-----CCc
Confidence            46777899999999988 899999999883   478889999999999999999998655  3556664444     111


Q ss_pred             cCCcccCC-----CCCHHHHHHHHHHHH
Q 026799           93 GGAWYSEG-----SLDTEFIKVVKSQCL  115 (233)
Q Consensus        93 GG~wy~d~-----e~D~efI~~l~~~~~  115 (233)
                      ..-++-..     +|+.+.++.+.+.+.
T Consensus        78 h~h~iC~~Cg~v~~~~~~~~~~~~~~~~  105 (120)
T PF01475_consen   78 HHHFICTQCGKVIDLDDPELEEILREIA  105 (120)
T ss_dssp             CEEEEETTTS-EEEE-GHHHHHHHHHHH
T ss_pred             ceEEEECCCCCEEEecchhHHHHHHHHH
Confidence            22233321     566666665555443

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=94.45  E-value=0.16  Score=43.73  Aligned_cols=60  Identities=10%  Similarity=0.075  Sum_probs=46.2

Q ss_pred             CCChHHHHHHHHHHhhCCC--cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDM--GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~--GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .++.++++..-++..+...  ...+.+|...+  |++..+|+|+|++|+++|+|+.      .+++++++
T Consensus       148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~l--G~sretvsR~L~~L~~~G~I~~------~~~~i~I~  209 (226)
T PRK10402        148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYL--GVSYRHLLYVLAQFIQDGYLKK------SKRGYLIK  209 (226)
T ss_pred             cChHHHHHHHHHHhcccCCcccchHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEe------eCCEEEEe
Confidence            3466888877776544322  25789999999  9999999999999999999976      34566654

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=94.42  E-value=0.15  Score=42.01  Aligned_cols=51  Identities=16%  Similarity=0.182  Sum_probs=39.5

Q ss_pred             CChHHHHHHHHHH---hhC---CCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIR---SKQ---DMG------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~---~aG---~~G------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.++++..-++.   ..|   +.|      +.+.+|..-+  |++..+|+|+|++|+++|+|+.
T Consensus       113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~  175 (193)
T TIGR03697       113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAI--GSTRVTITRLLGDLRKKKLISI  175 (193)
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence            4556666654443   222   233      6899999999  9999999999999999999976

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=94.41  E-value=0.2  Score=40.21  Aligned_cols=57  Identities=16%  Similarity=0.236  Sum_probs=45.8

Q ss_pred             CCCCCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           11 APSDSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        11 ~~~~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ..++-|.++-+ .|+.+|...|.  ....+|...+  ++++.+|++.|+.|++.|||...+.
T Consensus         8 ~~fkaLadptRl~IL~~L~~~~~--~~v~ela~~l--~lsqstvS~HL~~L~~AGLV~~~r~   65 (117)
T PRK10141          8 QLFKILSDETRLGIVLLLRESGE--LCVCDLCTAL--DQSQPKISRHLALLRESGLLLDRKQ   65 (117)
T ss_pred             HHHHHhCCHHHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEEE
Confidence            34556666544 78888876554  8889999999  9999999999999999999976554

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=94.40  E-value=0.42  Score=42.55  Aligned_cols=112  Identities=6%  Similarity=-0.022  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC--CCcccCCc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS--KEISGGAW   96 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs--~eiTGG~w   96 (233)
                      -...|+.+|.+.|.  +..++|.+.+  +.+..+++|=|+.||++|+|+++..--   ..+      +++  .+.   ++
T Consensus         6 R~~~Il~~l~~~~~--~~~~ela~~l--~vS~~TirRdL~~Le~~g~i~r~~gga---~~~------~~~~~~~~---~~   69 (251)
T PRK13509          6 RHQILLELLAQLGF--VTVEKVIERL--GISPATARRDINKLDESGKLKKVRNGA---EAI------TQQRPRWT---PM   69 (251)
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecCCc---ccc------CCCcccCC---CH
Confidence            45678999998777  9999999999  999999999999999999997733211   110      111  011   12


Q ss_pred             ccCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhCCcccccCHH
Q 026799           97 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQ  146 (233)
Q Consensus        97 y~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~i~~~~Ls~~  146 (233)
                      ..-...+.+.-..|-+.+..+|...      +..|+-.++++|...+++=+.=+..
T Consensus        70 ~~r~~~~~~~K~~IA~~Aa~~I~~g~~Ifld~GsT~~~la~~L~~~~ltVvTnsl~  125 (251)
T PRK13509         70 NIHQAQNHDEKVRIAKAASQLCNPGESVVINCGSTAFLLGRELCGKPVQIITNYLP  125 (251)
T ss_pred             HHHHHhCHHHHHHHHHHHHHhCCCCCEEEECCcHHHHHHHHHhCCCCeEEEeCCHH
Confidence            2233456667777888888888753      5688889999997656544444443

>PRK11050 manganese transport regulator MntR; Provisional

Probab=94.24  E-value=1  Score=37.22  Aligned_cols=43  Identities=26%  Similarity=0.319  Sum_probs=37.1

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|+.+|...  .++..++|...+  +++++.|++.|+.||++|+|..
T Consensus        41 ~I~~~l~~~--~~~t~~eLA~~l--~is~stVsr~l~~Le~~GlI~r   83 (152)
T PRK11050         41 LIADLIAEV--GEARQVDIAARL--GVSQPTVAKMLKRLARDGLVEM   83 (152)
T ss_pred             HHHHHHHhc--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            555666553  469999999999  9999999999999999999975

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=94.21  E-value=0.2  Score=33.82  Aligned_cols=41  Identities=17%  Similarity=0.374  Sum_probs=34.6

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS   64 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~   64 (233)
                      ..|+.++.+++.. +...+|..++  +++.++|.+-|+.|++.+
T Consensus         3 ~~il~~L~~~~~~-it~~eLa~~l--~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESKEP-ITAKELAEEL--GVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTTTS-BEHHHHHHHC--TS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCC-cCHHHHHHHh--CCCHHHHHHHHHHHHHCC
Confidence            4567777666555 9999999999  999999999999999988

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=94.18  E-value=0.2  Score=42.91  Aligned_cols=50  Identities=12%  Similarity=0.131  Sum_probs=43.9

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ++....|+.++...|.  +.-.+|...+  +++.+.|+|+|..|++.|||...+
T Consensus        21 ~~~~~~Vl~~L~~~g~--~tdeeLA~~L--gi~~~~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         21 DEEGFEVLKALIKKGE--VTDEEIAEQT--GIKLNTVRKILYKLYDARLADYKR   70 (178)
T ss_pred             CccHhHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEee
Confidence            4456778888888886  9999999999  999999999999999999998533

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=94.07  E-value=0.035  Score=43.24  Aligned_cols=60  Identities=23%  Similarity=0.258  Sum_probs=48.5

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      .+|++++...-+.|+-...|-...  ||+-....+.++.|+++|+|+.   -++++|+.|++.+.
T Consensus        18 eIi~dIL~~~~~~~~~~Tri~y~a--Nlny~~~~~yi~~L~~~Gli~~---~~~~~~~~y~lT~K   77 (95)
T COG3432          18 EIIFDILKAISEGGIGITRIIYGA--NLNYKRAQKYIEMLVEKGLIIK---QDNGRRKVYELTEK   77 (95)
T ss_pred             HHHHHHHHHhcCCCCCceeeeeec--CcCHHHHHHHHHHHHhCCCEEe---ccCCccceEEEChh
Confidence            388999986666677777788888  9999999999999999998754   34566779988753

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles

Probab=93.95  E-value=0.12  Score=37.39  Aligned_cols=38  Identities=16%  Similarity=0.237  Sum_probs=33.1

Q ss_pred             CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           47 NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        47 ~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      +++..+|-.+|++||++|+|......  ..+.||+|-+.+
T Consensus        28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~   67 (75)
T PF03551_consen   28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITE   67 (75)
T ss_dssp             ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESH
T ss_pred             ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECH
Confidence            68899999999999999999998876  677899997754

In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.95  E-value=0.68  Score=41.05  Aligned_cols=121  Identities=12%  Similarity=0.146  Sum_probs=81.5

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY   97 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy   97 (233)
                      +-+..|+++|.+.+  .+..+||.+.+  ++...+++|-|+.|+++++|++.   +  +.-+|.... .+..+   -+|.
T Consensus         4 ~R~~~Il~~l~~~~--~~~~~eLa~~l--~VS~~TiRRdL~~L~~~~~l~r~---~--Gga~~~~~~-~~~~~---~~~~   70 (240)
T PRK10411          4 ARQQAIVDLLLNHT--SLTTEALAEQL--NVSKETIRRDLNELQTQGKILRN---H--GRAKYIHRQ-NQDSG---DPFH   70 (240)
T ss_pred             HHHHHHHHHHHHcC--CCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe---c--CeEEEecCC-CcccC---CCHH
Confidence            34667899999766  49999999999  99999999999999999999762   2  343443211 11111   1222


Q ss_pred             cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhCCcccccCHHHHHHH
Q 026799           98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEI  151 (233)
Q Consensus        98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~i~~~~Ls~~di~~i  151 (233)
                      .-...+.+.=..|-+.+..+|+..      +..|+.++.++|...+++-+.=+..-.+.+
T Consensus        71 ~r~~~~~~~K~~IA~~Aa~lI~~gd~Ifld~GtT~~~l~~~L~~~~ltVvTNs~~ia~~l  130 (240)
T PRK10411         71 IRLKSHYAHKADIAREALAWIEEGMVIALDASSTCWYLARQLPDINIQVFTNSHPICQEL  130 (240)
T ss_pred             HHHHhHHHHHHHHHHHHHHhCCCCCEEEEcCcHHHHHHHHhhCCCCeEEEeCCHHHHHHH
Confidence            223345566677777788888753      568899999999765555444444444333

>PRK09462 fur ferric uptake regulator; Provisional

Probab=93.90  E-value=0.44  Score=38.93  Aligned_cols=64  Identities=13%  Similarity=0.181  Sum_probs=53.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+.-..||++|.++.+.-+...+|-.++   ++++...+|-|.|+.|++.|+|.++..-.  ++..|
T Consensus        14 r~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~--~~~~y   80 (148)
T PRK09462         14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG--GKSVF   80 (148)
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CcEEE
Confidence            478899999999998877789999998887   33688999999999999999998876333  44455

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=93.87  E-value=0.14  Score=42.78  Aligned_cols=110  Identities=16%  Similarity=0.192  Sum_probs=72.9

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc-
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS-   98 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~-   98 (233)
                      =..||.+++..|-  +-++||...+  +..+.+|++.|++|+++|||.-++.                     ||.+-| 
T Consensus        12 L~~Iy~l~~~~~~--~~~~diA~~L--~Vsp~sVt~ml~rL~~~GlV~~~~y---------------------~gi~LT~   66 (154)
T COG1321          12 LETIYELLEEKGF--ARTKDIAERL--KVSPPSVTEMLKRLERLGLVEYEPY---------------------GGVTLTE   66 (154)
T ss_pred             HHHHHHHHhccCc--ccHHHHHHHh--CCCcHHHHHHHHHHHHCCCeEEecC---------------------CCeEECh
Confidence            3467777774443  9999999999  9999999999999999999966432                     233333 


Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhc
Q 026799           99 EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVL  157 (233)
Q Consensus        99 d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~  157 (233)
                      .|+==...+=...+.+..|+.+.-....+++++--....   -.+|.+-++.|-+.|-+
T Consensus        67 ~G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~le---h~~s~~~~~rl~~~l~~  122 (154)
T COG1321          67 KGREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLE---HALSDETAERLDELLGF  122 (154)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh---hcCCHHHHHHHHHHhCC
Confidence            222112222223334566776544556777775544333   34888888888888765

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=93.85  E-value=0.22  Score=41.45  Aligned_cols=52  Identities=13%  Similarity=0.161  Sum_probs=40.5

Q ss_pred             CCChHHHHHHHHHHhhCC------------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           15 SLTDHERLIYDVIRSKQD------------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~------------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..+..+++..-+++-+..            -=+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~  181 (202)
T PRK13918        118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAV--GSVRETVTKVIGELSREGYIRS  181 (202)
T ss_pred             hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHh--CccHHHHHHHHHHHHHCCCEEc
Confidence            345677777766543321            125799999999  9999999999999999999963

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=93.84  E-value=0.17  Score=43.29  Aligned_cols=52  Identities=13%  Similarity=0.167  Sum_probs=40.5

Q ss_pred             CCChHHHHHHHHHHhh---CC---C------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           15 SLTDHERLIYDVIRSK---QD---M------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a---G~---~------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..+.++|+..-+.+.+   |.   .      -+.+++|..-+  |++..+|+|+|++|+++|+|+-
T Consensus       153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~l--G~sr~tvsR~l~~l~~~g~I~~  216 (235)
T PRK11161        153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYL--GLTVETISRLLGRFQKSGMLAV  216 (235)
T ss_pred             CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence            3466777666555432   21   1      27899999999  9999999999999999999975

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=93.77  E-value=0.16  Score=44.01  Aligned_cols=53  Identities=23%  Similarity=0.270  Sum_probs=41.7

Q ss_pred             CCCChHHHHHHHHHHhh---CCC-----cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           14 DSLTDHERLIYDVIRSK---QDM-----GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~a---G~~-----GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ...+.++|++.-+++.+   |..     -+.+++|..-+  |++..+|+|+||+|+++|+|+.
T Consensus       151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~l--GisretlsR~L~~L~~~GlI~~  211 (230)
T PRK09391        151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYL--GLTIETVSRALSQLQDRGLIGL  211 (230)
T ss_pred             cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEe
Confidence            34577888876666543   322     25789999999  9999999999999999999964

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=93.75  E-value=0.12  Score=43.69  Aligned_cols=46  Identities=17%  Similarity=0.426  Sum_probs=36.1

Q ss_pred             HHHHHHHhhCCCc---ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSKQDMG---IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~aG~~G---Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +++-+|+.....+   +.+++|..++  +++.++|+|++|.|+++++|+++
T Consensus        60 Vl~~il~~~d~~N~v~~t~~~ia~~l--~iS~~Tv~r~ik~L~e~~iI~k~  108 (165)
T PF05732_consen   60 VLMYILENMDKDNAVVATQKEIAEKL--GISKPTVSRAIKELEEKNIIKKI  108 (165)
T ss_pred             HHHHHHHhcCCCCeEEeeHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEc
Confidence            3333444444444   3688999999  99999999999999999999875

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=93.69  E-value=0.27  Score=39.85  Aligned_cols=53  Identities=11%  Similarity=0.058  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhhCC---CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           19 HERLIYDVIRSKQD---MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        19 ~e~lVy~~I~~aG~---~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+.-+..+|..+..   .=+..++|..+.  +++.+.|.|+|+.|++.|||++.+...
T Consensus         7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~--~is~~~vrk~l~~L~~~Glv~s~~G~~   62 (141)
T PRK11014          7 TDYGLRALIYMASLPEGRMTSISEVTEVY--GVSRNHMVKIINQLSRAGYVTAVRGKN   62 (141)
T ss_pred             HhHHHHHHHHHhcCCCCCccCHHHHHHHH--CcCHHHHHHHHHHHHhCCEEEEecCCC
Confidence            45556666665532   236779999999  999999999999999999998876553

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.61  E-value=0.2  Score=41.41  Aligned_cols=66  Identities=11%  Similarity=0.143  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      -+..|+.+|....-.|=.....-...+. .+.+.+|..+|++||+.|+|.+....  ..+.||+|-|.+
T Consensus        25 l~~~IL~~L~~~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe   93 (138)
T TIGR02719        25 LVPFLLLCLKDWNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTD   93 (138)
T ss_pred             HHHHHHHHHccCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECH
Confidence            3567777776655555444333333322 68899999999999999999875433  346689997654

Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).

>PHA00738 putative HTH transcription regulator

Probab=93.58  E-value=0.3  Score=38.92  Aligned_cols=50  Identities=18%  Similarity=0.151  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +-=+.|+.+|.+.+  +....+|...+  +|.+..|++.||.|++.|||.+-+.
T Consensus        12 ptRr~IL~lL~~~e--~~~V~eLae~l--~lSQptVS~HLKvLreAGLV~srK~   61 (108)
T PHA00738         12 ILRRKILELIAENY--ILSASLISHTL--LLSYTTVLRHLKILNEQGYIELYKE   61 (108)
T ss_pred             HHHHHHHHHHHHcC--CccHHHHHHhh--CCCHHHHHHHHHHHHHCCceEEEEE
Confidence            34456777776533  38899999999  9999999999999999999977553

>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase

Probab=93.43  E-value=0.12  Score=36.79  Aligned_cols=51  Identities=16%  Similarity=0.210  Sum_probs=37.5

Q ss_pred             HHHHhhhCCCCCHHHHHHHHHHh--CCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          114 CLKQIIKLKVATLEGISDSIKRS--GAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       114 ~~~~i~~~~~~T~~~I~~~I~~~--~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      |...|.+.+..+++.||..++=.  +-...+.|.+++++.|+.||-||+++..
T Consensus         2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~   54 (60)
T PF08672_consen    2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS   54 (60)
T ss_dssp             HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--
T ss_pred             HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec
Confidence            34556677888999999999977  3234689999999999999999999875

The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=93.35  E-value=0.15  Score=39.26  Aligned_cols=50  Identities=20%  Similarity=0.254  Sum_probs=38.6

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .++...|+.+|-..|.  +.-.||.+.+  +|+.+.++++|-.|.+.|||+..+
T Consensus        12 g~~~~~Il~~L~~~~~--l~de~la~~~--~l~~~~vRkiL~~L~~~~lv~~~~   61 (105)
T PF02002_consen   12 GEEAVRILDALLRKGE--LTDEDLAKKL--GLKPKEVRKILYKLYEDGLVSYRR   61 (105)
T ss_dssp             -STTHHHHHHHHHH----B-HHHHHHTT---S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred             CchHHHHHHHHHHcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeEEEE
Confidence            3567788999988775  9999999999  999999999999999999996654

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=93.17  E-value=0.85  Score=40.74  Aligned_cols=111  Identities=8%  Similarity=0.088  Sum_probs=78.3

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS   98 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~   98 (233)
                      -...|+++|.+.|.  +..+||.+.+  +.+..+++|=|+.||++|+|+++.-    +- ++  .  .++.+.   ++..
T Consensus         6 R~~~Il~~L~~~~~--v~v~eLa~~l--~VS~~TIRRDL~~Le~~g~l~r~~G----ga-~~--~--~~~~~~---~~~~   69 (256)
T PRK10434          6 RQAAILEYLQKQGK--TSVEELAQYF--DTTGTTIRKDLVILEHAGTVIRTYG----GV-VL--N--KEESDP---PIDH   69 (256)
T ss_pred             HHHHHHHHHHHcCC--EEHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEC----CE-Ec--C--CCCCCC---CHHH
Confidence            45689999999888  9999999999  9999999999999999999987641    11 11  0  011111   2222


Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCH
Q 026799           99 EGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTK  145 (233)
Q Consensus        99 d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~  145 (233)
                      -...+.+.=+.|-+....+|...      +..|+-.++++|... +++=+.=|.
T Consensus        70 r~~~~~~~K~~IA~~Aa~~I~~g~tIfld~GtT~~~la~~L~~~~~ltVvTnsl  123 (256)
T PRK10434         70 KTLINTHKKELIAEAAVSLIHDGDSIILDAGSTVLQMVPLLSRFNNITVMTNSL  123 (256)
T ss_pred             HHHhhHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhccCCCeEEEECCH
Confidence            33456666677777788888753      568889999999764 444344333

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=93.05  E-value=0.55  Score=35.36  Aligned_cols=55  Identities=15%  Similarity=0.246  Sum_probs=43.9

Q ss_pred             CChHHHHHHHHHH---hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           16 LTDHERLIYDVIR---SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        16 L~~~e~lVy~~I~---~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      ||+-++.|+..|-   ...+.=|-.++|.+++  +.++.+|+..+..||+.|||.+++.-
T Consensus         2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l--~~s~aTIRN~M~~Le~lGlve~~p~~   59 (78)
T PF03444_consen    2 LTERQREILKALVELYIETGEPVGSKTIAEEL--GRSPATIRNEMADLEELGLVESQPHP   59 (78)
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHH--CCChHHHHHHHHHHHHCCCccCCCCC
Confidence            6776776666554   2334559999999999  99999999999999999999766543

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=93.04  E-value=0.43  Score=39.93  Aligned_cols=32  Identities=22%  Similarity=0.403  Sum_probs=30.1

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.+++|...+  |++..+|+|+|++|++.|+|+.
T Consensus       169 ~t~~~lA~~l--G~tr~tvsR~l~~l~~~gii~~  200 (211)
T PRK11753        169 ITRQEIGRIV--GCSREMVGRVLKMLEDQGLISA  200 (211)
T ss_pred             CCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            5689999999  9999999999999999999975

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=93.04  E-value=0.44  Score=31.10  Aligned_cols=43  Identities=19%  Similarity=0.413  Sum_probs=36.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      ..|++.|+.++.++.    .|...++|...+  +++..+|.+.++.+.+
T Consensus         2 ~~l~~~e~~i~~~~~----~g~s~~eia~~l--~is~~tv~~~~~~~~~   44 (58)
T smart00421        2 ASLTPREREVLRLLA----EGLTNKEIAERL--GISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            468898888887753    578999999999  9999999999988754

lux regulon (activates the bioluminescence operon

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=93.01  E-value=0.32  Score=34.58  Aligned_cols=33  Identities=15%  Similarity=0.347  Sum_probs=30.9

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.+.+|..-+  |++..+++|+|+.|+++|+|..
T Consensus        28 ~lt~~~iA~~~--g~sr~tv~r~l~~l~~~g~I~~   60 (76)
T PF13545_consen   28 PLTQEEIADML--GVSRETVSRILKRLKDEGIIEV   60 (76)
T ss_dssp             ESSHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            56799999999  9999999999999999999973

...

>PRK05638 threonine synthase; Validated

Probab=93.01  E-value=0.32  Score=46.70  Aligned_cols=61  Identities=16%  Similarity=0.246  Sum_probs=47.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcC--CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVN--LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~--l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +.+....|+.+|.+.   -+.-.+|.+.+  +  +++.+|+++||.||+.|||.+..  +..++++|-|.
T Consensus       369 ~~~~r~~IL~~L~~~---~~~~~el~~~l--~~~~s~~~v~~hL~~Le~~GLV~~~~--~~g~~~~Y~Lt  431 (442)
T PRK05638        369 IGGTKLEILKILSER---EMYGYEIWKAL--GKPLKYQAVYQHIKELEELGLIEEAY--RKGRRVYYKLT  431 (442)
T ss_pred             ccchHHHHHHHHhhC---CccHHHHHHHH--cccCCcchHHHHHHHHHHCCCEEEee--cCCCcEEEEEC
Confidence            455678888888743   38899999999  7  89999999999999999997642  22456666554

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=92.86  E-value=0.19  Score=34.24  Aligned_cols=32  Identities=19%  Similarity=0.433  Sum_probs=29.5

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..++|...+  +++..+|+++|+.|+++|+|...
T Consensus        27 ~~~~la~~~--~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377          27 SERELAEEL--GVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence            489999999  99999999999999999999653

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=92.74  E-value=0.32  Score=38.41  Aligned_cols=38  Identities=11%  Similarity=0.302  Sum_probs=34.0

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +...+..++|...+  ++|.+.|.++|..|++.|+|.+..
T Consensus        22 ~~~~~s~~eia~~~--~i~~~~v~~il~~L~~~gli~~~~   59 (132)
T TIGR00738        22 DEGPVSVKEIAERQ--GISRSYLEKILRTLRRAGLVESVR   59 (132)
T ss_pred             CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecc
Confidence            34479999999999  999999999999999999997643

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=92.62  E-value=0.22  Score=32.94  Aligned_cols=42  Identities=21%  Similarity=0.369  Sum_probs=22.8

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKS   59 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~   59 (233)
                      .+.||++|+.......   +.|+..++|.+.+  |.+.++|.+-||.
T Consensus         2 ~~~Lt~~eR~~I~~l~---~~G~s~~~IA~~l--g~s~sTV~relkR   43 (44)
T PF13936_consen    2 YKHLTPEERNQIEALL---EQGMSIREIAKRL--GRSRSTVSRELKR   43 (44)
T ss_dssp             ----------HHHHHH---CS---HHHHHHHT--T--HHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHH---HcCCCHHHHHHHH--CcCcHHHHHHHhc
Confidence            3568999988765554   5789999999999  9999999999984

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=92.58  E-value=0.52  Score=31.03  Aligned_cols=42  Identities=21%  Similarity=0.397  Sum_probs=34.9

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ   61 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le   61 (233)
                      |++-++.|++.+...|.  +..++|..++  |++..+|.+-++.||
T Consensus         1 lD~~D~~Il~~Lq~d~r--~s~~~la~~l--glS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    1 LDELDRKILRLLQEDGR--RSYAELAEEL--GLSESTVRRRIRRLE   42 (42)
T ss_dssp             --HHHHHHHHHHHH-TT--S-HHHHHHHH--TS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCC--ccHHHHHHHH--CcCHHHHHHHHHHhC
Confidence            56778999999999988  9999999999  999999999999996

...

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=92.57  E-value=0.51  Score=40.56  Aligned_cols=64  Identities=17%  Similarity=0.187  Sum_probs=52.1

Q ss_pred             CCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc-eeeecccCCCeeeE
Q 026799           14 DSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI-KEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI-K~vksV~~~~rK~Y   80 (233)
                      ..|++.|. .+..+|...-+.|...++|..++  ++..++|++.+..|.+.|+. ++++..+. +|..|
T Consensus       157 ~~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~-~~~~~  222 (239)
T PRK10430        157 KGLTPQTLRTLCQWIDAHQDYEFSTDELANAV--NISRVSCRKYLIWLVNCHILFTSIHYGVT-GRPVY  222 (239)
T ss_pred             CCCCHHHHHHHHHHHHhCCCCCcCHHHHHHHh--CchHHHHHHHHHHHHhCCEEEEEeeccCC-CCCCe
Confidence            35888774 56688888888999999999999  99999999999999999999 56666543 44433

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=92.53  E-value=0.37  Score=38.80  Aligned_cols=41  Identities=12%  Similarity=0.140  Sum_probs=35.5

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      ++.-+..++|..++  ++|.+.+.|+|..|.+.|||.+.+...
T Consensus        22 ~~~~~s~~~ia~~~--~ip~~~l~kil~~L~~~glv~s~~G~~   62 (135)
T TIGR02010        22 ETGPVTLADISERQ--GISLSYLEQLFAKLRKAGLVKSVRGPG   62 (135)
T ss_pred             CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence            33458999999999  999999999999999999998765543

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=92.34  E-value=0.49  Score=35.59  Aligned_cols=71  Identities=14%  Similarity=0.211  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      ....++.+...+++.=+.-.+|..++  ++....|.|++++|++.|+  .|.++++++.++=.+-++=|...+..
T Consensus         4 ~~~~~~~ll~~~~~~~~SGe~La~~L--giSRtaVwK~Iq~Lr~~G~--~I~s~~~kGY~L~~~~~ll~~~~i~~   74 (79)
T COG1654           4 TSQMLLLLLLLLTGNFVSGEKLAEEL--GISRTAVWKHIQQLREEGV--DIESVRGKGYLLPQLPDLLPQEIIQA   74 (79)
T ss_pred             hHHHHHHHHHHcCCCcccHHHHHHHH--CccHHHHHHHHHHHHHhCC--ceEecCCCceeccCccccCcHHHHHh
Confidence            34567777788888889999999999  9999999999999999998  46778877776666555555444443

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=92.06  E-value=3.6  Score=36.53  Aligned_cols=87  Identities=14%  Similarity=0.252  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe--eeEEeeccccCCCcccCCc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK--KHLMAVEFEPSKEISGGAW   96 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r--K~Yml~~lePs~eiTGG~w   96 (233)
                      -...|+.++...|.  +...||.+++  +++...+++.|..||.+|||...-.=...+|  ++|-|.  +++.+.-+   
T Consensus        12 tr~~il~lL~~~g~--~sa~elA~~L--gis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt--~~g~~~f~---   82 (218)
T COG2345          12 TRERILELLKKSGP--VSADELAEEL--GISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLT--EKGREQFP---   82 (218)
T ss_pred             HHHHHHHHHhccCC--ccHHHHHHHh--CCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeec--ccchhhcc---
Confidence            34566667777776  9999999999  9999999999999999999987622221233  455444  33333111   


Q ss_pred             ccCCCCCHHHHHHHHHHH
Q 026799           97 YSEGSLDTEFIKVVKSQC  114 (233)
Q Consensus        97 y~d~e~D~efI~~l~~~~  114 (233)
                      +..++|=..+++.|.+..
T Consensus        83 ~~y~~l~~~~l~~l~~~~  100 (218)
T COG2345          83 KRYGELALALLDALEETG  100 (218)
T ss_pred             hhhHHHHHHHHHHHHHhc
Confidence            123455566666666554

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=91.97  E-value=0.55  Score=31.21  Aligned_cols=43  Identities=19%  Similarity=0.253  Sum_probs=35.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSL   60 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~L   60 (233)
                      +..||+.|+.|+.+..   -.|...++|...+  |++..+|++.++.-
T Consensus         2 l~~L~~~er~vi~~~y---~~~~t~~eIa~~l--g~s~~~V~~~~~~a   44 (50)
T PF04545_consen    2 LDQLPPREREVIRLRY---FEGLTLEEIAERL--GISRSTVRRILKRA   44 (50)
T ss_dssp             HCTS-HHHHHHHHHHH---TST-SHHHHHHHH--TSCHHHHHHHHHHH
T ss_pred             hhhCCHHHHHHHHHHh---cCCCCHHHHHHHH--CCcHHHHHHHHHHH
Confidence            4689999999988888   7789999999999  99999888776653

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>COG1693 Repressor of nif and glnA expression [Transcription]

Probab=91.79  E-value=0.19  Score=46.38  Aligned_cols=55  Identities=16%  Similarity=0.283  Sum_probs=43.5

Q ss_pred             CCChHHHHHHHHHHhhC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           15 SLTDHERLIYDVIRSKQ---DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG---~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +|+.-+..|+.++.+++   ..++-..+|+++ |-|+..+.|++.||.|+++||++++-
T Consensus         3 ~~~rk~ieIl~il~esd~plgak~Ia~el~kR-Gy~igeRavRYhlk~lderglt~kvg   60 (325)
T COG1693           3 NLNRKLIEILRILAESDEPLGAKIIALELRKR-GYNIGERAVRYHLKKLDERGLTRKVG   60 (325)
T ss_pred             hHHHHHHHHHHHHHhcCCccchHHHHHHHHhc-ccchhHHHHHHHHHHHhhccchhhcc
Confidence            45666778999999998   334445555555 55999999999999999999998876

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=91.30  E-value=0.72  Score=38.64  Aligned_cols=49  Identities=18%  Similarity=0.180  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ++...|+..+-..|.  +.-.||...+  +|+.+.|+|+|..|.++|||...+
T Consensus        14 ~~~v~Vl~aL~~~~~--~tdEeLa~~L--gi~~~~VRk~L~~L~e~~Lv~~~r   62 (158)
T TIGR00373        14 EEVGLVLFSLGIKGE--FTDEEISLEL--GIKLNEVRKALYALYDAGLADYKR   62 (158)
T ss_pred             hhHHHHHHHHhccCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceeee
Confidence            355678888777775  9999999999  999999999999999999996443

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.

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=91.25  E-value=0.38  Score=34.56  Aligned_cols=48  Identities=17%  Similarity=0.151  Sum_probs=37.7

Q ss_pred             HHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          111 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       111 ~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      ++.++.||.. ++.+|..||++-+        .+|.-.++.+|+.|+-+|+|+.+..
T Consensus         2 ke~Il~~i~~~~~p~~T~eiA~~~--------gls~~~aR~yL~~Le~eG~V~~~~~   50 (62)
T PF04703_consen    2 KEKILEYIKEQNGPLKTREIADAL--------GLSIYQARYYLEKLEKEGKVERSPV   50 (62)
T ss_dssp             HHCHHHHHHHHTS-EEHHHHHHHH--------TS-HHHHHHHHHHHHHCTSEEEES-
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecC
Confidence            5677888877 7778888888754        4888999999999999999998753

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=91.25  E-value=0.69  Score=38.36  Aligned_cols=46  Identities=11%  Similarity=0.148  Sum_probs=38.3

Q ss_pred             HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           26 VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        26 ~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      ++......-+..++|..+.  ++|.+-|.|+|..|...|||++++-.+
T Consensus        16 ~LA~~~~~~~s~~eIA~~~--~is~~~L~kIl~~L~~aGlv~S~rG~~   61 (153)
T PRK11920         16 YCAANDGKLSRIPEIARAY--GVSELFLFKILQPLVEAGLVETVRGRN   61 (153)
T ss_pred             HHHhCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCCC
Confidence            3433344457899999999  999999999999999999998887654

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=91.01  E-value=0.6  Score=41.70  Aligned_cols=115  Identities=13%  Similarity=0.176  Sum_probs=77.7

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcc
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWY   97 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy   97 (233)
                      +-...|+.++.+.|.  +...||...+  +++..+++|=|+.||++|+|+++   + .+- +  +.  .+..+   -++.
T Consensus         5 ~R~~~Il~~l~~~~~--~~~~ela~~l--~vS~~TiRRdL~~Le~~g~l~r~---~-GGa-~--~~--~~~~~---~~~~   68 (252)
T PRK10906          5 QRHDAIIELVKQQGY--VSTEELVEHF--SVSPQTIRRDLNDLAEQNKILRH---H-GGA-A--LP--SSSVN---TPWH   68 (252)
T ss_pred             HHHHHHHHHHHHcCC--EeHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe---c-CCE-E--ec--CCCCC---CCHH
Confidence            345678999988887  9999999999  99999999999999999999763   2 121 1  11  11111   1232


Q ss_pred             cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCHHHH
Q 026799           98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQI  148 (233)
Q Consensus        98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~~di  148 (233)
                      .-...+.+.=..|-+....+|...      +..|+.+++++|... +++=+.=|..=+
T Consensus        69 ~r~~~~~~~K~~IA~~Aa~~I~~g~tIflD~GtT~~~la~~L~~~~~ltVvTNsl~ia  126 (252)
T PRK10906         69 DRKATQTEEKERIARKVASQIPNGATLFIDIGTTPEAVAHALLNHSNLRIVTNNLNVA  126 (252)
T ss_pred             HHhhhcHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhcCCCCcEEEECcHHHH
Confidence            223445555566777777788753      568899999999653 454444444333

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=90.93  E-value=1.6  Score=37.27  Aligned_cols=57  Identities=11%  Similarity=0.174  Sum_probs=46.7

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      ||.  +.|+++|. .|..|...++|.+++  ++..++|++.+..|+..|++...-.-...+|
T Consensus       162 Lt~--r~Vl~~~~-~g~~g~s~~eIa~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~gr  218 (225)
T PRK10046        162 LTL--NAVRKLFK-EPGVQHTAETVAQAL--TISRTTARRYLEYCASRHLIIAEIVHGKVGR  218 (225)
T ss_pred             HHH--HHHHHHHH-cCCCCcCHHHHHHHh--CccHHHHHHHHHHHHhCCeEEEEeecCCCCC
Confidence            444  57888886 566789999999999  9999999999999999999987655443344

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=90.92  E-value=0.57  Score=41.65  Aligned_cols=44  Identities=18%  Similarity=0.385  Sum_probs=40.0

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++.+ +..|+...+|.+++  |||.+++.|.|..|++.|++..
T Consensus         8 ~iL~~l~~-~~~~l~l~ela~~~--glpksT~~RlL~tL~~~G~v~~   51 (246)
T COG1414           8 AILDLLAE-GPGGLSLAELAERL--GLPKSTVHRLLQTLVELGYVEQ   51 (246)
T ss_pred             HHHHHHHh-CCCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEE
Confidence            57778887 77778899999999  9999999999999999999976

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=90.73  E-value=0.64  Score=39.16  Aligned_cols=42  Identities=10%  Similarity=0.110  Sum_probs=36.6

Q ss_pred             hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+...+..++|..++  ++|.+.|.|+|..|.+.|||.+.+..+
T Consensus        21 ~~~~~vs~~eIA~~~--~ip~~~l~kIl~~L~~aGLv~s~rG~~   62 (164)
T PRK10857         21 SEAGPVPLADISERQ--GISLSYLEQLFSRLRKNGLVSSVRGPG   62 (164)
T ss_pred             CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeCCCCC
Confidence            344568999999999  999999999999999999998865554

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=90.70  E-value=2.3  Score=36.10  Aligned_cols=124  Identities=15%  Similarity=0.199  Sum_probs=77.0

Q ss_pred             CCCCCCChHHHHHH---------HHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           11 APSDSLTDHERLIY---------DVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        11 ~~~~~L~~~e~lVy---------~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+++.|+.++...|         .++.-.+..+ .-..|.++++++++..+++++|..|++-||||.-.+      -.|.
T Consensus         8 ~~~~~l~~~~~~~~~~W~~~~ir~l~~l~~~~~-d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~------g~y~   80 (171)
T PF14394_consen    8 NKVRVLDEDEFEYYSSWYHPAIRELLPLMPFAP-DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD------GKYV   80 (171)
T ss_pred             cceeeccHHHHHHHhhhHHHHHHHHhhcCCCCC-CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC------CcEE
Confidence            34666777665543         4444444443 778999999999999999999999999999998554      2343


Q ss_pred             eeccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHh
Q 026799           82 AVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALV  156 (233)
Q Consensus        82 l~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv  156 (233)
                      ..    +..+||     ..+.-.+.|-.+..+++..-...    ++.+-  ..+..++  ...++.+++++|.+.|.
T Consensus        81 ~t----~~~l~~-----~~~~~~~avr~~h~q~~~lA~~a----l~~~p--~~~R~~s~~T~~vs~~~~~ki~~~i~  142 (171)
T PF14394_consen   81 QT----DKSLTT-----SSEIPSEAVRSYHKQMLELAQEA----LDRVP--PEERDFSGLTMSVSREDYEKIKKEIR  142 (171)
T ss_pred             Ee----cceeeC-----CCCCcHHHHHHHHHHHHHHHHHH----HHhCC--ccccceeeeEEEeCHHHHHHHHHHHH
Confidence            22    223333     34666777777777766554321    00000  0111233  35678888888877653

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=90.67  E-value=0.81  Score=37.81  Aligned_cols=68  Identities=10%  Similarity=0.129  Sum_probs=48.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHH-HHHh-hc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDM-KREL-RV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~di-k~~t-~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      ..+++-...|+.++... .-|-..... ...+ +. .++..+|-.+|+.||++|+|.+...  .++||+|-+.+
T Consensus        39 ~~~~~~~l~IL~lL~~~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~--~~~RK~Y~ITe  109 (135)
T PRK09416         39 EKEEDILLAILQLLMNE-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWD--HEGAKYYQLTD  109 (135)
T ss_pred             cccccHHHHHHHHHhCC-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeec--CCCceEEEECH
Confidence            35667778888888766 666655443 3333 11 4678999999999999999987543  46789986543

>PF13551 HTH_29: Winged helix-turn helix

Probab=90.63  E-value=4  Score=30.57  Aligned_cols=99  Identities=16%  Similarity=0.214  Sum_probs=65.3

Q ss_pred             Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHH
Q 026799           33 MGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVK  111 (233)
Q Consensus        33 ~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~  111 (233)
                      +|. ..+++.+.+  +++.++|.+.++..++.|+-. +.+-..                 .||....-  ++.+-.+.|.
T Consensus        10 ~g~~~~~~ia~~l--g~s~~Tv~r~~~~~~~~G~~~-l~~~~~-----------------~~g~~~~~--l~~~~~~~l~   67 (112)
T PF13551_consen   10 EGVSTIAEIARRL--GISRRTVYRWLKRYREGGIEG-LLPRKP-----------------RGGRPRKR--LSEEQRAQLI   67 (112)
T ss_pred             cCCCcHHHHHHHH--CcCHHHHHHHHHHHHcccHHH-HHhccc-----------------cCCCCCCC--CCHHHHHHHH
Confidence            466 499999999  999999999999999999322 121110                 12222211  6666666555


Q ss_pred             HHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHH
Q 026799          112 SQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRA  154 (233)
Q Consensus       112 ~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~  154 (233)
                      +.+...-.. ....|+++|.+++.+.. ..+.+|..-|..+|.-
T Consensus        68 ~~~~~~p~~g~~~~t~~~l~~~l~~~~-~~~~~s~~ti~r~L~~  110 (112)
T PF13551_consen   68 ELLRENPPEGRSRWTLEELAEWLIEEE-FGIDVSPSTIRRILKR  110 (112)
T ss_pred             HHHHHCCCCCCCcccHHHHHHHHHHhc-cCccCCHHHHHHHHHH
Confidence            555432222 12689999999983333 3468999999998864

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=90.60  E-value=1.5  Score=33.08  Aligned_cols=58  Identities=16%  Similarity=0.101  Sum_probs=42.3

Q ss_pred             CCCCChHHHHHHHHHHhhC--CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           13 SDSLTDHERLIYDVIRSKQ--DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG--~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      ++.|++++-.|+..||..-  -+=+....|.+.+  +|+...+.++|+.|-..+||.. ....
T Consensus         1 ~r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s--~l~~~~~~~~L~~L~~~kLv~~-~~~~   60 (82)
T PF09202_consen    1 LRYLSKEDFRVLRAIEMGMKNHEWVPLELIEKIS--GLSEGEVEKRLKRLVKLKLVSR-RNKP   60 (82)
T ss_dssp             --T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-E-SS
T ss_pred             CCcCCHHHHHHHHHHHHcccCCccCCHHHHHHHh--CcCHHHHHHHHHHHHhcCCccc-cCCC
Confidence            4679999999999999542  2235578899999  9999999999999999999988 4433

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=90.33  E-value=0.72  Score=39.93  Aligned_cols=49  Identities=16%  Similarity=0.280  Sum_probs=44.8

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +-+++|+.++...|.+ +...+|.+++  ||..+.|+|.|=+|...+.|..+
T Consensus         4 ~~~~~i~~~l~~~~~~-~~a~~i~k~l--~i~k~~vNr~LY~L~~~~~v~~~   52 (183)
T PHA02701          4 DCASLILTLLSSSGDK-LPAKRIAKEL--GISKHEANRCLYRLLESDAVSCE   52 (183)
T ss_pred             hHHHHHHHHHHhcCCC-CcHHHHHHHh--CccHHHHHHHHHHHhhcCcEecC
Confidence            3578999999999966 9999999999  99999999999999999999655

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=90.30  E-value=1.4  Score=38.16  Aligned_cols=52  Identities=25%  Similarity=0.270  Sum_probs=46.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      ..||.....++.+|...+.  |.+.+|.+..  |...   +.+|+.|.++|||++...-
T Consensus        86 ~~LS~aaLEtLaiIay~qP--iTr~eI~~ir--Gv~~---~~ii~~L~~~gLI~e~gr~  137 (188)
T PRK00135         86 QSLSQAALEVLAIIAYKQP--ITRIEIDEIR--GVNS---DGALQTLLAKGLIKEVGRK  137 (188)
T ss_pred             CCCCHHHHHHHHHHHHcCC--cCHHHHHHHH--CCCH---HHHHHHHHHCCCeEEcCcC
Confidence            4799999999999988875  9999999999  8886   8999999999999986433

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=90.20  E-value=0.64  Score=41.63  Aligned_cols=44  Identities=18%  Similarity=0.247  Sum_probs=37.8

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++... +.++..+||.+.+  +||.+++.|.|+.|++.|++..
T Consensus        29 ~IL~~~~~~-~~~~tl~eIa~~l--glpkStv~RlL~tL~~~G~l~~   72 (271)
T PRK10163         29 AILQYLEKS-GGSSSVSDISLNL--DLPLSTTFRLLKVLQAADFVYQ   72 (271)
T ss_pred             HHHHHHHhC-CCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            466666554 3578899999999  9999999999999999999955

>PRK11569 transcriptional repressor IclR; Provisional

Probab=90.19  E-value=0.89  Score=40.74  Aligned_cols=44  Identities=9%  Similarity=0.347  Sum_probs=37.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++.+ .+.++..+||.+.+  +||..++.|.|..|++.|++..
T Consensus        32 ~IL~~l~~-~~~~~~lseia~~l--glpksTv~RlL~tL~~~G~l~~   75 (274)
T PRK11569         32 KLLEWIAE-SNGSVALTELAQQA--GLPNSTTHRLLTTMQQQGFVRQ   75 (274)
T ss_pred             HHHHHHHh-CCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            34555544 46779999999999  9999999999999999999964

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=90.14  E-value=3.4  Score=36.88  Aligned_cols=118  Identities=9%  Similarity=0.151  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCccc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYS   98 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~   98 (233)
                      -.+.|++++.+.|.  +...||...+  +.+..+++|=|..||++|+++++----..       .+ .+..+    ++-.
T Consensus         6 R~~~Il~~l~~~g~--v~v~eLa~~~--~VS~~TIRRDL~~Le~~g~l~R~hGGa~~-------~~-~~~~~----~~~~   69 (253)
T COG1349           6 RHQKILELLKEKGK--VSVEELAELF--GVSEMTIRRDLNELEEQGLLLRVHGGAVL-------PD-SESEY----PFSE   69 (253)
T ss_pred             HHHHHHHHHHHcCc--EEHHHHHHHh--CCCHHHHHHhHHHHHHCCcEEEEeCCEec-------CC-Ccccc----cHHH
Confidence            45689999999999  9999999999  99999999999999999999764311100       00 00000    3333


Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHhC-CcccccCHHHHHHHH
Q 026799           99 EGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSG-AFKVDLTKQQIEEIV  152 (233)
Q Consensus        99 d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~~-i~~~~Ls~~di~~il  152 (233)
                      ......+-=..+-+....+|...      ...|..++.++|.... ++=+.-+..-+..+.
T Consensus        70 r~~~~~~eK~~IA~~Aa~lI~~g~~ifld~GTT~~~la~~L~~~~~ltviTNsl~ia~~l~  130 (253)
T COG1349          70 RKALNTEEKRAIAKAAATLIEDGDTIFLDAGTTTLALARALPDDNNLTVITNSLNIAAALL  130 (253)
T ss_pred             HHHhhHHHHHHHHHHHHhhCCCCCEEEECCCcHHHHHHHHhCcCCCeEEEeCCHHHHHHHH
Confidence            44555555555666666677642      5789999999999665 554555555444443

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=90.12  E-value=3.5  Score=37.13  Aligned_cols=119  Identities=12%  Similarity=0.150  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc-ccCCCcccCCcc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF-EPSKEISGGAWY   97 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l-ePs~eiTGG~wy   97 (233)
                      -...|+++|.+.|.  +...||.+.+  +.+..+++|=|..||+.|+++++.    .+. +  +.+. .|..+.   ++.
T Consensus        18 R~~~Il~~L~~~~~--vtv~eLa~~l--~VS~~TIRRDL~~Le~~G~l~r~~----GGa-~--~~~~~~~~~~~---~~~   83 (269)
T PRK09802         18 RREQIIQRLRQQGS--VQVNDLSALY--GVSTVTIRNDLAFLEKQGIAVRAY----GGA-L--ICDSTTPSVEP---SVE   83 (269)
T ss_pred             HHHHHHHHHHHcCC--EeHHHHHHHH--CCCHHHHHHHHHHHHhCCCeEEEe----CCE-E--ecCcCCCccCC---CHH
Confidence            45678889999888  9999999999  999999999999999999998543    121 1  1110 011111   122


Q ss_pred             cCCCCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHh-CCcccccCHHHHHHH
Q 026799           98 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQIEEI  151 (233)
Q Consensus        98 ~d~e~D~efI~~l~~~~~~~i~~~------~~~T~~~I~~~I~~~-~i~~~~Ls~~di~~i  151 (233)
                      .-...+.+.-..|-+.+..||...      +..|+-+++++|... +++=+.=+..-+..+
T Consensus        84 ~r~~~~~~~K~~IA~~Aa~~I~dgd~Ifld~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l  144 (269)
T PRK09802         84 DKSALNTAMKRSVAKAAVELIQPGHRVILDSGTTTFEIARLMRKHTDVIAMTNGMNVANAL  144 (269)
T ss_pred             HHHHhCHHHHHHHHHHHHhhCCCCCEEEECCchHHHHHHHhcCcCCCeEEEeCCHHHHHHH
Confidence            122345566677777788888753      578899999999654 454445454444433

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=90.12  E-value=1.2  Score=29.21  Aligned_cols=41  Identities=17%  Similarity=0.368  Sum_probs=34.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      |++.|+.++.++.    .|+..++|.+.+  +++.+++.+.++.+.+
T Consensus         1 l~~~e~~i~~~~~----~~~s~~eia~~l--~~s~~tv~~~~~~~~~   41 (57)
T cd06170           1 LTPREREVLRLLA----EGKTNKEIADIL--GISEKTVKTHLRNIMR   41 (57)
T ss_pred             CCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            5777888887763    579999999999  9999999999988754

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=89.97  E-value=1.2  Score=34.85  Aligned_cols=54  Identities=19%  Similarity=0.193  Sum_probs=44.0

Q ss_pred             CCCCChHHHHHHHHHHh------hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           13 SDSLTDHERLIYDVIRS------KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~------aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..+|+.-|..||-.|-.      ...+-|....|...|  +++.+.|+++++.|+++|+|..
T Consensus        27 ~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~t--g~~~~~V~~al~~Li~~~vI~~   86 (100)
T PF04492_consen   27 RADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMT--GLSRDHVSKALNELIRRGVIIR   86 (100)
T ss_pred             hccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence            35788877777666652      345569999999999  9999999999999999999954

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=89.84  E-value=0.67  Score=40.67  Aligned_cols=44  Identities=7%  Similarity=0.124  Sum_probs=37.4

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++.+ .+.++..+||.+++  +||.+++.|.|+.|++.|++..
T Consensus        13 ~IL~~l~~-~~~~~~l~eia~~l--glpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        13 AVIEAFGA-ERPRLTLTDVAEAT--GLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             HHHHHHhc-CCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence            35555544 35789999999999  9999999999999999999964

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=89.60  E-value=0.9  Score=40.34  Aligned_cols=54  Identities=11%  Similarity=0.109  Sum_probs=44.8

Q ss_pred             CCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799            4 RKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus         4 ~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      |+-+...+....||+-|+.|+.+|.+    |...++|.+++  ++..++|.+.++.+-+|
T Consensus       132 ~~~~~~~~~~~~LS~RE~eVL~Lia~----G~SnkEIA~~L--~IS~~TVk~hvs~I~~K  185 (217)
T PRK13719        132 RGLSTNLEAKNKVTKYQNDVFILYSF----GFSHEYIAQLL--NITVGSSKNKISEILKF  185 (217)
T ss_pred             hcccchhhccCCCCHHHHHHHHHHHC----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence            34444456667899999999999976    79999999999  99999999888877654

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=89.47  E-value=2.7  Score=31.19  Aligned_cols=51  Identities=10%  Similarity=0.233  Sum_probs=39.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .|+..|.++ ..+  |++ .+...+|-.+|  +++.+++...|..|.++|+|.+--.
T Consensus         3 klt~~~~IL-~~l--s~~-c~TLeeL~ekT--gi~k~~LlV~LsrL~k~GiI~Rkw~   53 (72)
T PF05584_consen    3 KLTVTQKIL-IIL--SKR-CCTLEELEEKT--GISKNTLLVYLSRLAKRGIIERKWR   53 (72)
T ss_pred             hhhHHHHHH-HHH--Hhc-cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeeeE
Confidence            455555332 222  333 89999999999  9999999999999999999988543

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=89.40  E-value=1.5  Score=31.49  Aligned_cols=49  Identities=10%  Similarity=0.211  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          108 KVVKSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       108 ~~l~~~~~~~i~~~~~--~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      +...+.++.+|..++.  .|+.||++-+        .++...|.++|.+|.-+|.|+..
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~   55 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQ   55 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEec
Confidence            3567889999998877  8999988755        37778999999999999999874

Helix-turn-helix-containing domain. Also known as Zab.

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=89.21  E-value=2.2  Score=32.75  Aligned_cols=54  Identities=13%  Similarity=0.215  Sum_probs=46.1

Q ss_pred             HHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          111 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       111 ~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      |..++++|.. ...+|++||++.+++.+.   .++..-|-..|+.|+=.|.|.++...
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~---~i~~~TVYR~L~~L~~~Gli~~~~~~   57 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRKKGP---SISLATVYRTLELLEEAGLVREIELG   57 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhcCC---CCCHHHHHHHHHHHHhCCCEEEEEeC
Confidence            5678888876 457999999999998862   58889999999999999999998754

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=89.11  E-value=1.4  Score=31.30  Aligned_cols=44  Identities=20%  Similarity=0.288  Sum_probs=37.0

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..|+..+-..|.  ...++|.+.+  +|+.++|.++|-.|.+.+++.=
T Consensus        16 ~~V~~~Ll~~G~--ltl~~i~~~t--~l~~~~Vk~~L~~LiQh~~v~y   59 (62)
T PF08221_consen   16 AKVGEVLLSRGR--LTLREIVRRT--GLSPKQVKKALVVLIQHNLVQY   59 (62)
T ss_dssp             HHHHHHHHHC-S--EEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHHcCCeee
Confidence            468888888887  8999999999  9999999999999999999853

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=89.07  E-value=1.3  Score=36.75  Aligned_cols=52  Identities=12%  Similarity=0.165  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhh--CCC-cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           20 ERLIYDVIRSK--QDM-GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        20 e~lVy~~I~~a--G~~-GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      +..|--++.=|  +.. -+..++|..+.  |+++.-|.|+|..|.+.|||++++-.+
T Consensus         8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~--~is~~~L~kil~~L~kaGlV~S~rG~~   62 (150)
T COG1959           8 EYALRALLYLALLPGGGPVSSAEIAERQ--GISPSYLEKILSKLRKAGLVKSVRGKG   62 (150)
T ss_pred             hHHHHHHHHHHhCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHHcCCEEeecCCC
Confidence            33444444433  333 36799999999  999999999999999999999988755

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=88.87  E-value=0.4  Score=35.63  Aligned_cols=53  Identities=11%  Similarity=0.125  Sum_probs=45.3

Q ss_pred             CCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           10 NAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        10 ~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      ++.+..|++..+.+|.+-+.  .+|+..++|...+  +++.++|...++.+++.|..
T Consensus        10 ~~~l~~l~~~~r~af~L~R~--~eGlS~kEIAe~L--GIS~~TVk~~l~~~~~~~~~   62 (73)
T TIGR03879        10 AERLTWVDSLAEAAAALARE--EAGKTASEIAEEL--GRTEQTVRNHLKGETKAGGL   62 (73)
T ss_pred             HHHHhcCCHHHHHHHHHHHH--HcCCCHHHHHHHH--CcCHHHHHHHHhcCcccchH
Confidence            45677899999999988743  4679999999999  99999999999999887754

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=88.81  E-value=1.1  Score=39.77  Aligned_cols=46  Identities=13%  Similarity=0.222  Sum_probs=38.2

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .|+.++.+. ..++..+||.+++  +++..++.|.|+.|++.|+|....
T Consensus        15 ~iL~~l~~~-~~~ls~~eia~~l--gl~kstv~RlL~tL~~~g~v~~~~   60 (263)
T PRK09834         15 MVLRALNRL-DGGATVGLLAELT--GLHRTTVRRLLETLQEEGYVRRSA   60 (263)
T ss_pred             HHHHHHHhc-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEec
Confidence            455566543 4469999999999  999999999999999999997643

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=88.49  E-value=0.96  Score=34.53  Aligned_cols=49  Identities=12%  Similarity=0.311  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026799          107 IKVVKSQCLKQIIK----LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME  163 (233)
Q Consensus       107 I~~l~~~~~~~i~~----~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~  163 (233)
                      ...+++.|+.||+.    ...+++++|++-+   +     +++++|+..|+.|+-+|.|..
T Consensus        45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l---~-----~~~~~v~~al~~L~~eG~IYs   97 (102)
T PF08784_consen   45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL---G-----MSENEVRKALDFLSNEGHIYS   97 (102)
T ss_dssp             S-HHHHHHHHHHHC----TTTEEHHHHHHHS---T-----S-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh---C-----cCHHHHHHHHHHHHhCCeEec
Confidence            57889999999987    3468899998766   3     789999999999999999975

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=88.33  E-value=2.9  Score=26.89  Aligned_cols=46  Identities=13%  Similarity=0.219  Sum_probs=38.5

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      ..+++++.+.+.+|..+|++.+        .++..-+...|+.|+-+|.|+...
T Consensus         3 ~~il~~l~~~~~~s~~~l~~~l--------~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        3 QQILELLAQQGKVSVEELAELL--------GVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEee
Confidence            3466777777889999999987        478889999999999999998754

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=88.19  E-value=2.7  Score=32.76  Aligned_cols=57  Identities=14%  Similarity=0.160  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          108 KVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       108 ~~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      ..-|.+++++|.+. ..+|++||++.+++.+   ..++..=|-..|+.|+=.|.|.++...
T Consensus         7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~~   64 (120)
T PF01475_consen    7 TPQRLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEFG   64 (120)
T ss_dssp             HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence            35678899999864 5899999999999877   357889999999999999999998754

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=88.04  E-value=1  Score=39.80  Aligned_cols=43  Identities=7%  Similarity=0.217  Sum_probs=36.8

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++++.+  ..++..+||.+++  +||.+++.|.|+.|++.|++..
T Consensus        18 ~IL~~l~~--~~~l~l~eia~~l--gl~kstv~Rll~tL~~~G~l~~   60 (257)
T PRK15090         18 GILQALGE--EREIGITELSQRV--MMSKSTVYRFLQTMKTLGYVAQ   60 (257)
T ss_pred             HHHHHhhc--CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            45666644  3478999999999  9999999999999999999966

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=87.94  E-value=1.5  Score=27.74  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=36.9

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      +..|++.++.++.+...   .|...++|..++  |++.++|.+.++....
T Consensus         8 ~~~l~~~~~~~~~~~~~---~~~~~~~ia~~~--~~s~~~i~~~~~~~~~   52 (55)
T cd06171           8 LDKLPEREREVILLRFG---EGLSYEEIAEIL--GISRSTVRQRLHRALK   52 (55)
T ss_pred             HHhCCHHHHHHHHHHHh---cCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence            45688988888766643   678999999999  9999999999887643

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=87.33  E-value=2.4  Score=36.31  Aligned_cols=50  Identities=14%  Similarity=0.207  Sum_probs=39.2

Q ss_pred             CCChHHHHHHHHHHhhCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           15 SLTDHERLIYDVIRSKQDMG--------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~G--------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      ..+..+++..-+++.+...|        +.+++|..-+  |++..+|+|+|+.|+++|++
T Consensus       146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~l--G~tretvsR~l~~L~~~gl~  203 (236)
T PRK09392        146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYL--GMTPENLSRAFAALASHGVH  203 (236)
T ss_pred             cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHh--CCChhHHHHHHHHHHhCCeE
Confidence            45677877776665544333        4478999999  99999999999999999963

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=87.32  E-value=14  Score=30.02  Aligned_cols=112  Identities=16%  Similarity=0.221  Sum_probs=73.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .+++-|..|.++|=+.|.  ...+||-..++  .....++|+-.|..|.+||+|.+.|.   .++=.|     .|     
T Consensus         3 ~Is~aE~eVM~ilW~~~~--~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd---gr~~~y-----~p-----   67 (123)
T COG3682           3 SISAAEWEVMEILWSRGP--ATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD---GRAFRY-----SP-----   67 (123)
T ss_pred             cccHHHHHHHHHHHHcCC--ccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc---CCeeee-----ec-----
Confidence            578889999999999997  88888888872  26889999999999999999976553   222222     00     


Q ss_pred             cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                         -++    -.+.++...+-+++-+...+.  ..=|..|+.+..     |+.+||++|-+.|
T Consensus        68 ---L~~----~~~~~~~~~~~~l~k~~d~~~--~~lv~~F~~~~~-----l~~~eie~L~~il  116 (123)
T COG3682          68 ---LLT----RDQYVAGESQDLLDKICDGGL--ASLVAHFAEKEK-----LTADEIEALKAIL  116 (123)
T ss_pred             ---ccC----HHHHHHHHHHHHHHHHHcccc--hHHHHHHHHhcc-----CCHHHHHHHHHHH
Confidence               111    123333344334433333333  455788888655     6777777665554

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=87.30  E-value=1.9  Score=39.14  Aligned_cols=55  Identities=20%  Similarity=0.363  Sum_probs=43.2

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc--CCCeeeE
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH--SKGKKHL   80 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~--~~~rK~Y   80 (233)
                      ..|++++..+|.  +-..+|...+  +|||++++--+|.||+.|||.. +.++  ...+|+-
T Consensus        26 v~Il~lL~~k~p--lNvneiAe~l--gLpqst~s~~ik~Le~aGlirT-~t~karkG~QKiC   82 (308)
T COG4189          26 VAILQLLHRKGP--LNVNEIAEAL--GLPQSTMSANIKVLEKAGLIRT-ETVKARKGSQKIC   82 (308)
T ss_pred             HHHHHHHHHhCC--CCHHHHHHHh--CCchhhhhhhHHHHHhcCceee-eeeccccCceeEe
Confidence            356777777775  7789999999  9999999999999999999975 3333  2345554

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=87.19  E-value=1.3  Score=30.97  Aligned_cols=35  Identities=14%  Similarity=0.333  Sum_probs=30.1

Q ss_pred             cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           34 GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        34 GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      =+ ..++|.++.  +.+.+++.++|+.|++.|+|...+
T Consensus        23 ~lps~~~la~~~--~vsr~tvr~al~~L~~~g~i~~~~   58 (64)
T PF00392_consen   23 RLPSERELAERY--GVSRTTVREALRRLEAEGLIERRP   58 (64)
T ss_dssp             BE--HHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             EeCCHHHHHHHh--ccCCcHHHHHHHHHHHCCcEEEEC
Confidence            46 789999999  999999999999999999997754

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=87.19  E-value=7.9  Score=30.50  Aligned_cols=70  Identities=14%  Similarity=0.262  Sum_probs=49.7

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC  114 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~  114 (233)
                      ++++++.+.+  |++.++|    ..-|++||+.+... . .|.+.|                      |.+-|+.|+  .
T Consensus         1 m~IgevA~~~--gvs~~tl----RyYe~~GLl~p~~~-~-~gyR~Y----------------------~~~~l~~l~--~   48 (120)
T cd04781           1 LDIAEVARQS--GLPASTL----RYYEEKGLIASIGR-R-GLRRQY----------------------DPQVLDRLA--L   48 (120)
T ss_pred             CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcC-C-CCceec----------------------CHHHHHHHH--H
Confidence            4678899999  9998876    45788999977553 2 244443                      556666775  3


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHhC
Q 026799          115 LKQIIKLKVATLEGISDSIKRSG  137 (233)
Q Consensus       115 ~~~i~~~~~~T~~~I~~~I~~~~  137 (233)
                      ..+++..++ |+++|.+++...+
T Consensus        49 I~~lr~~G~-~L~eI~~~l~~~~   70 (120)
T cd04781          49 IALGRAAGF-SLDEIQAMLSHDG   70 (120)
T ss_pred             HHHHHHcCC-CHHHHHHHHhccC
Confidence            466666654 6999999998764

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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 two 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, an

>PRK09483 response regulator; Provisional

Probab=87.09  E-value=2.1  Score=34.98  Aligned_cols=46  Identities=26%  Similarity=0.302  Sum_probs=40.7

Q ss_pred             CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ....||+-|+.|+.++.    +|...++|..++  ++..++|+..++++-.|
T Consensus       145 ~~~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l--~is~~TV~~~~~~i~~K  190 (217)
T PRK09483        145 PFASLSERELQIMLMIT----KGQKVNEISEQL--NLSPKTVNSYRYRMFSK  190 (217)
T ss_pred             cccccCHHHHHHHHHHH----CCCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence            45679999999999884    779999999999  99999999999888765

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=87.09  E-value=11  Score=28.83  Aligned_cols=72  Identities=6%  Similarity=0.096  Sum_probs=47.6

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC  114 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~  114 (233)
                      +...++.+.+  |++.++|    +..|++|||.+..                   .-.+|-|+    ||.+-|+.|+.+ 
T Consensus         1 m~I~eva~~~--gvs~~tl----R~Ye~~GLl~p~~-------------------r~~~g~r~----Y~~~dv~~l~~I-   50 (95)
T cd04780           1 MRMSELSKRS--GVSVATI----KYYLREGLLPEGR-------------------RLAPNQAE----YSEAHVERLRLI-   50 (95)
T ss_pred             CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCc-------------------CCCCCCee----cCHHHHHHHHHH-
Confidence            3578899999  9998765    5688899995422                   22233232    666667766654 


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHhC
Q 026799          115 LKQIIKLKVATLEGISDSIKRSG  137 (233)
Q Consensus       115 ~~~i~~~~~~T~~~I~~~I~~~~  137 (233)
                       .++++.-..++++|.+.+...|
T Consensus        51 -~~L~~~~G~~l~~I~~~l~~~~   72 (95)
T cd04780          51 -RALQQEGGLPISQIKEVLDAIA   72 (95)
T ss_pred             -HHHHHHcCCCHHHHHHHHHhcC
Confidence             4444433577999999998733

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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 two 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.

>COG5625 Predicted transcription regulator containing HTH domain [Transcription]

Probab=87.07  E-value=0.85  Score=36.14  Aligned_cols=70  Identities=23%  Similarity=0.389  Sum_probs=57.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS   88 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs   88 (233)
                      -+|-..|.+||+++-+.|. ||-.++|..++  ++..+++.-+++.|-.+||+++ .-|+ ++=-=|+++.-.|.
T Consensus        17 ~glk~~eI~IY~lLve~~~-~mri~ei~rEl--~is~rtvr~~v~~l~rrGll~r-elvq-kgWvGYiya~~~P~   86 (113)
T COG5625          17 IGLKKNEIRIYSLLVEKGR-GMRIREIQREL--GISERTVRAAVAVLLRRGLLAR-ELVQ-KGWVGYIYATTPPP   86 (113)
T ss_pred             cCCCcchhhhhhHHHHhcC-CchHHHHHHHH--hHHHHHHHHHHHHHHHhhHHHH-HHHh-ccceeeEecCCCCc
Confidence            3567788999999988765 89999999999  9999999999999999999985 3444 45556776665554

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=86.95  E-value=4.4  Score=30.55  Aligned_cols=45  Identities=11%  Similarity=0.142  Sum_probs=34.8

Q ss_pred             HHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          113 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       113 ~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      ++.+||..++.+++.+|...+        ..+..=|+..|+.|+-=|+||++.
T Consensus         6 qlRd~l~~~gr~s~~~Ls~~~--------~~p~~~VeaMLe~l~~kGkverv~   50 (78)
T PRK15431          6 QVRDLLALRGRMEAAQISQTL--------NTPQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_pred             HHHHHHHHcCcccHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEeec
Confidence            455666666666666666554        467888999999999999999985

>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication)

Probab=86.67  E-value=3.4  Score=30.14  Aligned_cols=55  Identities=15%  Similarity=0.268  Sum_probs=45.0

Q ss_pred             ChHHHHHHHHHHhhCC-CcccHHHHHHHhhc----CCCh----HHHHHHHHHHHhCCCceeeec
Q 026799           17 TDHERLIYDVIRSKQD-MGIWTRDMKRELRV----NLPD----NIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~-~GIw~~dik~~t~~----~l~~----~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ++-..+|...|.+.+. +|.....|++-...    +++.    ..|.++||.+.++|.+..++.
T Consensus         3 P~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg   66 (77)
T PF00538_consen    3 PPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKG   66 (77)
T ss_dssp             SCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSC
T ss_pred             CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecc
Confidence            4567899999998666 89999999987622    3444    689999999999999998884

Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=86.63  E-value=8.9  Score=31.94  Aligned_cols=108  Identities=21%  Similarity=0.182  Sum_probs=70.8

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      +..|++++.. .|+--...||-..++..++.+.|.|+|..|.++|.|.. |.  ....+||..-.-.. ...+..   ..
T Consensus         3 e~~Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~-K~--~GKqkiY~~~Q~~~-~~~s~e---el   74 (169)
T PF07106_consen    3 EDAILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE-KE--YGKQKIYFANQDEL-EVPSPE---EL   74 (169)
T ss_pred             HHHHHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee-ee--ecceEEEeeCcccc-CCCCch---hH
Confidence            4578888765 47778889999888667999999999999999999977 33  34668885432221 112211   02


Q ss_pred             CCCCHHHHHHHHHHHHHHhh-----------hCCCCCHHHHHHHHHHh
Q 026799          100 GSLDTEFIKVVKSQCLKQII-----------KLKVATLEGISDSIKRS  136 (233)
Q Consensus       100 ~e~D~efI~~l~~~~~~~i~-----------~~~~~T~~~I~~~I~~~  136 (233)
                      .++|.+ |..|+..+-..=.           -.+.||.+++..-|.+.
T Consensus        75 ~~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l  121 (169)
T PF07106_consen   75 AELDAE-IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEEL  121 (169)
T ss_pred             HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            345555 6666665432111           13678888888777655

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators

Probab=86.46  E-value=12  Score=29.97  Aligned_cols=70  Identities=9%  Similarity=0.171  Sum_probs=46.0

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC  114 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~  114 (233)
                      +...++.+.+  |++.++|    +.-|+.|||++.+.-. .+.+.                      ||.+-|+.|+.  
T Consensus         1 m~IgE~A~~~--gvs~~TL----RyYE~~GLl~p~r~~~-~gyR~----------------------Y~~~~~~~l~~--   49 (133)
T cd04787           1 MKVKELANAA--GVTPDTV----RFYTRIGLLRPTRDPV-NGYRL----------------------YSEKDLSRLRF--   49 (133)
T ss_pred             CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcCCC-CCeee----------------------CCHHHHHHHHH--
Confidence            4678899999  9999877    4569999997642211 23333                      35555555533  


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHh
Q 026799          115 LKQIIKLKVATLEGISDSIKRS  136 (233)
Q Consensus       115 ~~~i~~~~~~T~~~I~~~I~~~  136 (233)
                      ..++++. ..|++||.+++...
T Consensus        50 I~~lr~~-G~sL~eI~~~l~~~   70 (133)
T cd04787          50 ILSARQL-GFSLKDIKEILSHA   70 (133)
T ss_pred             HHHHHHc-CCCHHHHHHHHhhh
Confidence            3334455 46799999999854

Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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 two 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. This subgroup lacks one of the c

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=86.35  E-value=1.6  Score=40.75  Aligned_cols=51  Identities=14%  Similarity=0.353  Sum_probs=44.4

Q ss_pred             CCCChHHHHHHH-----HHHhhCCCcccHHHHHHH--hhcCCChHHHHHHHHHHHhCCCcee
Q 026799           14 DSLTDHERLIYD-----VIRSKQDMGIWTRDMKRE--LRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        14 ~~L~~~e~lVy~-----~I~~aG~~GIw~~dik~~--t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.|++-++.|+.     +|..++.  +-.++|.++  .  ++++.++++-++.||+.|+|+.
T Consensus         2 ~~l~~R~~~Il~~IV~~yi~~~~p--v~s~~l~~~~~l--~~S~aTIR~dm~~Le~~G~l~~   59 (339)
T PRK00082          2 SMLDERQREILRAIVEDYIATGEP--VGSKTLSKRYGL--GVSSATIRNDMADLEELGLLEK   59 (339)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCC--cCHHHHHHHhCC--CCChHHHHHHHHHHHhCCCcCC
Confidence            467887777876     7888777  999999987  7  9999999999999999999975

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=86.29  E-value=2.1  Score=30.74  Aligned_cols=46  Identities=13%  Similarity=0.394  Sum_probs=36.6

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|+.++.+++. -+-.+.|.+.+   |.++...+|.+.|+.||..|+++.
T Consensus         2 ~IL~~L~~~~~-P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~   50 (66)
T PF08461_consen    2 FILRILAESDK-PLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRK   50 (66)
T ss_pred             HHHHHHHHcCC-CCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccc
Confidence            46778877653 58888888887   336677999999999999998874

>PRK09462 fur ferric uptake regulator; Provisional

Probab=86.20  E-value=3.8  Score=33.37  Aligned_cols=55  Identities=5%  Similarity=0.088  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          109 VVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       109 ~l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      .-|..++++|.+.  ..+|++||++.+++.+.   .++..-|-..|+.|+=.|.|.++..
T Consensus        17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~---~i~~aTVYR~L~~L~e~Gli~~~~~   73 (148)
T PRK09462         17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHNF   73 (148)
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            3467789999853  58999999999998883   5788999999999999999999864

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=86.03  E-value=2  Score=36.01  Aligned_cols=45  Identities=18%  Similarity=0.258  Sum_probs=40.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ...||+-|+.|+.++.    +|...++|.+++  +++.++|+..++.+-.|
T Consensus       148 ~~~Lt~rE~evl~~~~----~G~s~~eIA~~l--~iS~~TV~~h~~~i~~K  192 (216)
T PRK10840        148 DKRLSPKESEVLRLFA----EGFLVTEIAKKL--NRSIKTISSQKKSAMMK  192 (216)
T ss_pred             cccCCHHHHHHHHHHH----CCCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            3569999999999996    789999999999  99999999988887765

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=85.56  E-value=3.9  Score=26.72  Aligned_cols=47  Identities=9%  Similarity=0.180  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEE
Q 026799          108 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIM  162 (233)
Q Consensus       108 ~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie  162 (233)
                      +..+..++.+|...+..|..||++-+        .+|..-|...|+-|+=+|.|+
T Consensus         2 ~~~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    2 DETQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             -HHHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence            45677889999999999999998865        378889999999999999875

...

>COG1777 Predicted transcriptional regulators [Transcription]

Probab=85.42  E-value=1.2  Score=39.38  Aligned_cols=48  Identities=21%  Similarity=0.419  Sum_probs=38.5

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee-eeccc-CCCeeeEEeec
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE-VVNIH-SKGKKHLMAVE   84 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~-vksV~-~~~rK~Yml~~   84 (233)
                      =...+|...+  |+.|..|-++|+.||..|||-+ +--+. .+.||+|+...
T Consensus        29 ~yvsEiS~~l--gvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~   78 (217)
T COG1777          29 CYVSEISREL--GVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR   78 (217)
T ss_pred             hHHHHHHhhc--CcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence            4567788888  9999999999999999999987 33332 46789997754

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=85.24  E-value=2.1  Score=35.00  Aligned_cols=42  Identities=14%  Similarity=0.247  Sum_probs=37.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      .|..++++.|.  ++.+++...|  +++-+++.+.++.|++.|-|-
T Consensus        16 rIvElVRe~GR--iTi~ql~~~T--GasR~Tvk~~lreLVa~G~l~   57 (127)
T PF06163_consen   16 RIVELVREHGR--ITIKQLVAKT--GASRNTVKRYLRELVARGDLY   57 (127)
T ss_pred             HHHHHHHHcCC--ccHHHHHHHH--CCCHHHHHHHHHHHHHcCCeE
Confidence            46667778888  9999999999  999999999999999999873

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=84.48  E-value=3.7  Score=37.96  Aligned_cols=58  Identities=19%  Similarity=0.165  Sum_probs=47.2

Q ss_pred             CCCCCChHHHHHHHHHHhhCC---CcccHHHHHHH-------hhcCCCh---HHHHHHHHHHHhCCCceeeec
Q 026799           12 PSDSLTDHERLIYDVIRSKQD---MGIWTRDMKRE-------LRVNLPD---NIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~aG~---~GIw~~dik~~-------t~~~l~~---~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .+.+||..|++++..|...+.   ..+...++-++       .  ++.+   +.+...|..|+..|||....+
T Consensus       290 ~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~--~~~~~~~~~~~~~l~~L~~~glI~~~~~  360 (394)
T PRK00411        290 VLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEEL--GYEPRTHTRFYEYINKLDMLGIINTRYS  360 (394)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHc--CCCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence            467899999999998876653   56888888855       5  6654   999999999999999987654

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=84.26  E-value=0.74  Score=39.34  Aligned_cols=72  Identities=8%  Similarity=0.106  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC----------CeeeEEeeccccC
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK----------GKKHLMAVEFEPS   88 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~----------~rK~Yml~~lePs   88 (233)
                      -+..|+.++...|-  +...+|...+  +.+..+++|=|..|++.|++.+..++..+          +-.+=-+-+++|.
T Consensus         8 R~~~Il~~l~~~~~--~~~~~La~~~--~vS~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~~~vD~i~eie~g   83 (185)
T PRK04424          8 RQKALQELIEENPF--ITDEELAEKF--GVSIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEEEVVGELIDLELG   83 (185)
T ss_pred             HHHHHHHHHHHCCC--EEHHHHHHHH--CcCHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCcccceeeEEEecCC
Confidence            56789999999888  9999999999  99999999999999999999887664321          1222245566666


Q ss_pred             CCcccC
Q 026799           89 KEISGG   94 (233)
Q Consensus        89 ~eiTGG   94 (233)
                      ..++|=
T Consensus        84 ~~a~~~   89 (185)
T PRK04424         84 RSAISI   89 (185)
T ss_pred             cEEEEE
Confidence            555543

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=84.01  E-value=4.1  Score=28.58  Aligned_cols=50  Identities=12%  Similarity=0.204  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          109 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       109 ~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      .....++.+|-..+..|++||++.+        .++...|..+|+.|+-.|.|+....
T Consensus         8 ~~E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~   57 (68)
T PF01978_consen    8 ENEAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEG   57 (68)
T ss_dssp             HHHHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            3445677888788899999998865        3888999999999999999998763

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>COG5340 Predicted transcriptional regulator [Transcription]

Probab=83.98  E-value=1.1  Score=40.41  Aligned_cols=55  Identities=18%  Similarity=0.236  Sum_probs=47.9

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .-.|...|+++...++.++-  |.++|...-.  ++.++++.+++..||+||++-+++.
T Consensus        11 ~~~m~~~e~l~~laae~hki--iTirdvae~~--ev~~n~lr~lasrLekkG~LeRi~r   65 (269)
T COG5340          11 GLSMRESELLSHLAAEGHKI--ITIRDVAETL--EVAPNTLRELASRLEKKGWLERILR   65 (269)
T ss_pred             hhhHHHHHHHHHHHHHhCce--EEeHHhhhhc--cCCHHHHHHHHhhhhhcchhhhhcC
Confidence            34567778888888887777  9999999999  9999999999999999999988753

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=83.73  E-value=5.2  Score=27.79  Aligned_cols=46  Identities=22%  Similarity=0.316  Sum_probs=40.1

Q ss_pred             CChHHHHHHHHHHhhC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           16 LTDHERLIYDVIRSKQ----DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG----~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ||+.|+.++..--+.|    .+++...||.+++  |++..+++..|+.-|+|
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~l--gis~st~~~~LRrae~k   50 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEEL--GISKSTVSEHLRRAERK   50 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence            6888888888887777    7889999999999  99999999999887754

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=83.59  E-value=2.8  Score=28.59  Aligned_cols=44  Identities=20%  Similarity=0.414  Sum_probs=36.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ..||+.|..|+.++..    |...++|....  +++.++|...++.+-.|
T Consensus         2 ~~LT~~E~~vl~~l~~----G~~~~eIA~~l--~is~~tV~~~~~~i~~K   45 (58)
T PF00196_consen    2 PSLTERELEVLRLLAQ----GMSNKEIAEEL--GISEKTVKSHRRRIMKK   45 (58)
T ss_dssp             GSS-HHHHHHHHHHHT----TS-HHHHHHHH--TSHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHh----cCCcchhHHhc--CcchhhHHHHHHHHHHH
Confidence            5799999999999875    47799999999  99999999999888754

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=83.32  E-value=4.5  Score=34.02  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=47.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .+|+.=..|++++.+. ..-+...+|-.++   ++++...+|-|.|+.|++.|||.++..
T Consensus        23 R~T~qR~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~   81 (169)
T PRK11639         23 RLTPQRLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVES   81 (169)
T ss_pred             CCCHHHHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEec
Confidence            4688888999999987 4579999998887   337889999999999999999988753

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=83.05  E-value=3.8  Score=32.65  Aligned_cols=67  Identities=19%  Similarity=0.155  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhc---CCChHHHHHHHHHHHhCCCceeeecccC--CCeeeEEeec
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRV---NLPDNIVTKSIKSLQNKSLIKEVVNIHS--KGKKHLMAVE   84 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~---~l~~~~v~k~LK~Le~k~lIK~vksV~~--~~rK~Yml~~   84 (233)
                      .-+..|+.++...-..|-....--.....   ..+..+|-.+|+.||+.|||....-...  +.||+|-+.+
T Consensus         9 ~l~~~iL~~L~~~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe   80 (138)
T COG1695           9 SLELLILSLLSEKPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTE   80 (138)
T ss_pred             hHHHHHHHHHhcCCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECH
Confidence            35677888887776666544333333211   3678899999999999999988654432  4589996654

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=82.91  E-value=4.7  Score=39.91  Aligned_cols=60  Identities=18%  Similarity=0.185  Sum_probs=47.5

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      ...|..|+..+.+.+ ..+...+|.+++  +++...|..+++.|+++|+|+......    ..|.|.
T Consensus         5 ~~~e~~iL~~l~~~~-~~~~~~~la~~~--~~~~~~v~~~~~~L~~kg~v~~~~~~~----~~~~LT   64 (494)
T PTZ00326          5 ELEENTILSKLESEN-EIVNSLALAESL--NIDHQKVVGAIKSLESANYITTEMKKS----NTWTLT   64 (494)
T ss_pred             hHHHHHHHHHHHhcC-CCCCHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEEEEEE----EEEEEC
Confidence            456888888888743 348889999999  999999999999999999997655443    455554

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=82.46  E-value=22  Score=30.71  Aligned_cols=126  Identities=17%  Similarity=0.115  Sum_probs=76.3

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC----CCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK----SLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k----~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      -...|-.+|..+|.-|+..++|.+-+  ++....|..+|..|..+    +--=++..+.. +=+++.-.++.+-..--.+
T Consensus         5 ~~~~iEA~LF~sg~pgls~~~La~~l--~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~-~y~l~tk~e~~~~v~~~~~   81 (188)
T PRK00135          5 YKSIIEALLFVSGEEGLSLEQLAEIL--ELEPTEVQQLLEELQEKYEGDDRGLKLIEFND-VYKLVTKEENADYLQKLVK   81 (188)
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHhhCCCCEEEEEECC-EEEEEEcHHHHHHHHHHhc
Confidence            45678888899999999999999999  99999999999999643    22222333321 2222222222222111111


Q ss_pred             CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799           95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus        95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      .. ...+|....+++|.     .|..++.+|-.||.+--   |++.        ..+|+.|+-.|.|++.
T Consensus        82 ~~-~~~~LS~aaLEtLa-----iIay~qPiTr~eI~~ir---Gv~~--------~~ii~~L~~~gLI~e~  134 (188)
T PRK00135         82 TP-IKQSLSQAALEVLA-----IIAYKQPITRIEIDEIR---GVNS--------DGALQTLLAKGLIKEV  134 (188)
T ss_pred             cc-ccCCCCHHHHHHHH-----HHHHcCCcCHHHHHHHH---CCCH--------HHHHHHHHHCCCeEEc
Confidence            00 01244555554443     33346778888776533   4332        6789999999999875

>PHA02943 hypothetical protein; Provisional

Probab=82.43  E-value=6.5  Score=33.42  Aligned_cols=51  Identities=10%  Similarity=0.190  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          107 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       107 I~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      |-.=...++.|| +.|..|..||++.+        .+|..+++-+|.+|.=+|+|++|+-
T Consensus         9 v~~R~~eILE~L-k~G~~TtseIAkaL--------GlS~~qa~~~LyvLErEG~VkrV~~   59 (165)
T PHA02943          9 VHTRMIKTLRLL-ADGCKTTSRIANKL--------GVSHSMARNALYQLAKEGMVLKVEI   59 (165)
T ss_pred             HHHHHHHHHHHH-hcCCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCceEEEee
Confidence            333345677788 77888898988765        3889999999999999999999873

>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators

Probab=82.38  E-value=17  Score=27.05  Aligned_cols=72  Identities=14%  Similarity=0.163  Sum_probs=46.1

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHH
Q 026799           34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQ  113 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~  113 (233)
                      +...+++.+.+  +++.++|.    ..|++|+|.+...-. .+.+.|                      +.+=|..|+.+
T Consensus         1 ~~ti~evA~~~--gvs~~tLR----~ye~~Gll~p~r~~~-~g~R~Y----------------------s~~dv~~l~~I   51 (88)
T cd01105           1 VIGIGEVSKLT--GVSPRQLR----YWEEKGLIKSIRSDG-GGQRKY----------------------SLADVDRLLVI   51 (88)
T ss_pred             CcCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCccCC-CCceec----------------------CHHHHHHHHHH
Confidence            35678899999  99998876    469999996432222 144444                      33334444433


Q ss_pred             HHHHhhhCCCCCHHHHHHHHHHhC
Q 026799          114 CLKQIIKLKVATLEGISDSIKRSG  137 (233)
Q Consensus       114 ~~~~i~~~~~~T~~~I~~~I~~~~  137 (233)
                        ..+++. ..|+++|.+.+...+
T Consensus        52 --~~Lr~~-G~sl~~i~~~l~~~~   72 (88)
T cd01105          52 --KELLDE-GFTLAAAVEKLRRRR   72 (88)
T ss_pred             --HHHHHC-CCCHHHHHHHHHHcc
Confidence              334454 567999999998655

Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=82.26  E-value=1.3  Score=36.43  Aligned_cols=79  Identities=20%  Similarity=0.254  Sum_probs=53.6

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec-ccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN-IHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks-V~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      ..|+..+-..|-  +.-.||...+  +|+.+.|+|+|-.|.+.++|+..-- ..+            |    -+|+||+-
T Consensus         4 ~~v~d~L~~~~~--~~dedLa~~l--~i~~n~vRkiL~~L~ed~~~~~~~~~e~~------------~----~~~~~~~~   63 (147)
T smart00531        4 FLVLDALMRNGC--VTEEDLAELL--GIKQKQLRKILYLLYDEKLIKIDYKREKD------------P----ETKTWYRY   63 (147)
T ss_pred             EeehHHHHhcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHhhhcchhheeeeeC------------C----CCceEEEE
Confidence            456666666664  8999999999  9999999999999999888754321 111            1    12445543


Q ss_pred             C-CCC-HHHHHHHHHHHHHHhh
Q 026799          100 G-SLD-TEFIKVVKSQCLKQII  119 (233)
Q Consensus       100 ~-e~D-~efI~~l~~~~~~~i~  119 (233)
                      - -+| ..+++.|+-.+....+
T Consensus        64 yw~i~y~~~~~vik~r~~~~~~   85 (147)
T smart00531       64 YWYINYDTLLDVVKYKLDKMRK   85 (147)
T ss_pred             EEEecHHHHHHHHHHHHHHHHH
Confidence            2 455 5677777777665543

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=82.25  E-value=3.7  Score=37.50  Aligned_cols=46  Identities=17%  Similarity=0.161  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCC-ceee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL-IKEV   69 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l-IK~v   69 (233)
                      ++.|+.+|.+  +..+...+|..++  +++.++|.++|+.|++.|+ |.+.
T Consensus         6 ~~~il~~L~~--~~~~s~~~LA~~l--gvsr~tV~~~l~~L~~~G~~i~~~   52 (319)
T PRK11886          6 MLQLLSLLAD--GDFHSGEQLGEEL--GISRAAIWKHIQTLEEWGLDIFSV   52 (319)
T ss_pred             HHHHHHHHHc--CCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceEEe
Confidence            4567777765  4668888999999  9999999999999999999 7554

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=82.09  E-value=2.9  Score=36.38  Aligned_cols=54  Identities=13%  Similarity=0.286  Sum_probs=43.6

Q ss_pred             HHHHHHHHhhCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           21 RLIYDVIRSKQDMGIWT--------RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~--------~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      ..|++.|.+.=..|.|.        ++|..+.  |....+|+++|+.|++.|||.+.     .++=+|+
T Consensus        12 ~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~-----~G~GTfV   73 (241)
T PRK11402         12 ATVRQRLLDDIAQGVYQAGQQIPTENELCTQY--NVSRITIRKAISDLVADGVLIRW-----QGKGTFV   73 (241)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCceeEE
Confidence            35677777766666664        7999999  99999999999999999999875     3555565

>COG0640 ArsR Predicted transcriptional regulators [Transcription]

Probab=81.82  E-value=8.4  Score=27.14  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=35.8

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .++..+...  ......+|...+  +++++++++.|+.|++.|+|..
T Consensus        29 ~il~~l~~~--~~~~~~~l~~~~--~~~~~~v~~hL~~L~~~glv~~   71 (110)
T COG0640          29 EILSLLAEG--GELTVGELAEAL--GLSQSTVSHHLKVLREAGLVEL   71 (110)
T ss_pred             HHHHHHHhc--CCccHHHHHHHH--CCChhHHHHHHHHHHHCCCeEE
Confidence            445555544  456789999999  9999999999999999999988

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=81.81  E-value=4.1  Score=28.74  Aligned_cols=43  Identities=12%  Similarity=0.150  Sum_probs=34.8

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..++.++.++   -+..++|..++  ++..++|.+.|+.|++.|+.-.
T Consensus         3 ~~il~~L~~~---~~~~~eLa~~l--~vS~~tv~~~l~~L~~~g~~i~   45 (69)
T TIGR00122         3 LRLLALLADN---PFSGEKLGEAL--GMSRTAVNKHIQTLREWGVDVL   45 (69)
T ss_pred             HHHHHHHHcC---CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEE
Confidence            3455665533   26699999999  9999999999999999999644

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins

Probab=81.48  E-value=6.2  Score=28.28  Aligned_cols=38  Identities=11%  Similarity=0.373  Sum_probs=28.4

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG   76 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~   76 (233)
                      ....|..+.  +++.+++-.+|++||+.|+|.+ .|.--++
T Consensus         6 vas~iAd~~--GiTRSvIVNALRKleSaGvIes-rSlGmKG   43 (61)
T PF08222_consen    6 VASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGMKG   43 (61)
T ss_dssp             -HHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-EETTSS-
T ss_pred             hHHHHHHHh--CccHHHHHHHHHHHHhcCceee-cccCCCc
Confidence            456788899  9999999999999999999986 4544333

CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=81.48  E-value=4.7  Score=32.94  Aligned_cols=47  Identities=13%  Similarity=0.018  Sum_probs=37.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCC-----hH----HHHHHHHHHHh
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLP-----DN----IVTKSIKSLQN   62 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~-----~~----~v~k~LK~Le~   62 (233)
                      ..||+-|..|+.++.+..++|...++|.+.+  ...     .+    .++++.++|..
T Consensus       153 ~~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        153 LTLTRYEFLLLKTLLLSPGRVFSRQQLMDIV--WEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             eecCHHHHHHHHHHHhCCCceECHHHHHHHh--cCCCCCCCccCHHHHHHHHHHHhcc
Confidence            4699999999999999999999999999999  664     33    45556666653

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=81.29  E-value=24  Score=27.60  Aligned_cols=71  Identities=10%  Similarity=0.155  Sum_probs=45.2

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHH
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQC  114 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~  114 (233)
                      +.+.++.+.+  |++.++|+    .-|++|||.+...                  +-+|--+|++     +-|..|+.  
T Consensus         1 ~~I~eva~~~--gvs~~tLR----yYe~~GLl~p~~r------------------~~~gyR~Y~~-----~~i~~l~~--   49 (123)
T cd04770           1 MKIGELAKAA--GVSPDTIR----YYERIGLLPPPQR------------------SENGYRLYGE-----ADLARLRF--   49 (123)
T ss_pred             CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCCC------------------CCCCCccCCH-----HHHHHHHH--
Confidence            3578899999  99998874    4999999964221                  1122234443     44445533  


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHhC
Q 026799          115 LKQIIKLKVATLEGISDSIKRSG  137 (233)
Q Consensus       115 ~~~i~~~~~~T~~~I~~~I~~~~  137 (233)
                      ..++++. ..|++||.+++....
T Consensus        50 I~~lr~~-G~sl~eI~~~l~~~~   71 (123)
T cd04770          50 IRRAQAL-GFSLAEIRELLSLRD   71 (123)
T ss_pred             HHHHHHC-CCCHHHHHHHHHhhh
Confidence            3334555 467999999997543

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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 two 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.

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=81.28  E-value=3.2  Score=36.46  Aligned_cols=56  Identities=23%  Similarity=0.357  Sum_probs=45.9

Q ss_pred             HHHHHHHhhCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWT--------RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~--------~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      .|++.|++.=..|.|.        ++|.++.  |...-+|+|+|+.|++.|+|.+..     |+=+|+...
T Consensus        11 qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f--~VSR~TvRkAL~~L~~eGli~r~~-----G~GtfV~~~   74 (236)
T COG2188          11 QIAEDIRQRIESGELPPGDKLPSERELAEQF--GVSRMTVRKALDELVEEGLIVRRQ-----GKGTFVASP   74 (236)
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHH--CCcHHHHHHHHHHHHHCCcEEEEe-----cCeeEEcCc
Confidence            6777788777777775        6899999  999999999999999999998753     555666554

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=81.15  E-value=3.4  Score=37.45  Aligned_cols=57  Identities=7%  Similarity=0.206  Sum_probs=41.0

Q ss_pred             CCCCCChHHH-HHHHHHHhhCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           12 PSDSLTDHER-LIYDVIRSKQD--MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        12 ~~~~L~~~e~-lVy~~I~~aG~--~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +++.|+=.|. .|=.+++.-..  --+..++|..+.  |+..+.+..++++||+.|+|+..+
T Consensus       173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerl--GVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecc
Confidence            3456665433 23333333222  248899999999  999999999999999999998744

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=81.07  E-value=4.2  Score=33.08  Aligned_cols=55  Identities=16%  Similarity=0.262  Sum_probs=44.3

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC-----CChHHHHHHHHHHHhC---CCceeeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN-----LPDNIVTKSIKSLQNK---SLIKEVVN   71 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~-----l~~~~v~k~LK~Le~k---~lIK~vks   71 (233)
                      .||+-|..|+.++....+++...++|..++  .     ...++|...++.|-+|   .+|+.+..
T Consensus       149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~lr~Kl~~~~i~t~~g  211 (219)
T PRK10336        149 TLKPKEFALLELLMRNAGRVLPRKLIEEKL--YTWDEEVTSNAVEVHVHHLRRKLGSDFIRTVHG  211 (219)
T ss_pred             ecCHHHHHHHHHHHhCCCccCcHHHHHHHh--cCCCCCCCccCHHHHHHHHHHhcCCCcEEEecC
Confidence            499999999999999999999999999998  5     7877777777666654   34544443

>PRK10651 transcriptional regulator NarL; Provisional

Probab=81.04  E-value=4.8  Score=32.42  Aligned_cols=46  Identities=26%  Similarity=0.408  Sum_probs=40.0

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS   64 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~   64 (233)
                      ...||+.|+.|+.++.    +|...++|..++  +++.++|...++.|-.|=
T Consensus       153 ~~~Lt~rE~~vl~~l~----~g~~~~~ia~~l--~is~~tV~~~~~~l~~Kl  198 (216)
T PRK10651        153 VNQLTPRERDILKLIA----QGLPNKMIARRL--DITESTVKVHVKHMLKKM  198 (216)
T ss_pred             cccCCHHHHHHHHHHH----cCCCHHHHHHHc--CCCHHHHHHHHHHHHHHc
Confidence            4469999999999986    568899999999  999999999999987653

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=81.04  E-value=2.8  Score=27.51  Aligned_cols=30  Identities=23%  Similarity=0.401  Sum_probs=19.8

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026799           34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL   65 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l   65 (233)
                      |...++|.+.+  |++.++|.+.+|...+.|+
T Consensus        17 G~s~~~ia~~l--gvs~~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen   17 GWSIREIAKRL--GVSRSTVYRWIKRYREEGL   46 (50)
T ss_dssp             T--HHHHHHHH--TS-HHHHHHHHT-------
T ss_pred             CCCHHHHHHHH--CcCHHHHHHHHHHcccccc
Confidence            89999999999  9999999999999988774

>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=80.74  E-value=13  Score=38.51  Aligned_cols=140  Identities=8%  Similarity=0.101  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeecc-----------
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVEF-----------   85 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~l-----------   85 (233)
                      -+.+|+.+  -.+++++.-.+|.+.|  +|+...++++|..|-.-+++.-++.  .-+|+-|-|.=.++           
T Consensus       609 ~q~~vfll--~n~~e~lt~eei~e~T--~l~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~  684 (773)
T COG5647         609 YQLLVFLL--FNDHEELTFEEILELT--KLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERIKINY  684 (773)
T ss_pred             HHHHHHHH--hcCccceeHHHHHhhc--CCChhhHHHHHHHHHhhheeeeccccccCCCCceEEEccccccccceeeecc
Confidence            34444433  4567889999999999  9999999999999999999988876  12234444432222           


Q ss_pred             --ccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026799           86 --EPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME  163 (233)
Q Consensus        86 --ePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~  163 (233)
                        +|-..- +| -=+-..+|.+=.-.|+..|.+-+..++...-.++.+.+-+.-=++...++.+|.+-+++|+=-|-||+
T Consensus       685 ~~~~~~~q-~~-~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR  762 (773)
T COG5647         685 IAESECMQ-DN-LDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLER  762 (773)
T ss_pred             cccchhhc-cc-hhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHh
Confidence              111111 11 11113456666667777788888888888888888777665557789999999999999998888887


Q ss_pred             E
Q 026799          164 V  164 (233)
Q Consensus       164 v  164 (233)
                      .
T Consensus       763 ~  763 (773)
T COG5647         763 Q  763 (773)
T ss_pred             c
Confidence            4

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=80.40  E-value=2.6  Score=36.33  Aligned_cols=55  Identities=20%  Similarity=0.339  Sum_probs=41.4

Q ss_pred             HHHHHHHHhhCCCcc--------cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           21 RLIYDVIRSKQDMGI--------WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        21 ~lVy~~I~~aG~~GI--------w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ..|++.|.+.=..|.        .-++|.++.  |....+|+++|+.|++.|||.+..     ++=+|..
T Consensus        11 ~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~~-----G~GtfV~   73 (238)
T TIGR02325        11 RQIADKIEQEIAAGHLRAGDYLPAEMQLAERF--GVNRHTVRRAIAALVERGLLRAEQ-----GRGTFVA   73 (238)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CCEEEEC
Confidence            355666665433343        457999999  999999999999999999998753     4555653

All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=80.31  E-value=14  Score=25.46  Aligned_cols=67  Identities=15%  Similarity=0.269  Sum_probs=42.6

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHHHHHH
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCL  115 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~  115 (233)
                      .++|+.+.+  |++.++|.    ..+++|++...+  ...+++.|                      +.+=|+.|..  .
T Consensus         2 ti~eva~~~--gvs~~tlr----~y~~~gll~~~~--~~~g~r~y----------------------~~~dv~~l~~--i   49 (69)
T PF13411_consen    2 TIKEVAKLL--GVSPSTLR----YYEREGLLPPPR--DENGYRYY----------------------SEEDVERLRE--I   49 (69)
T ss_dssp             EHHHHHHHT--TTTHHHHH----HHHHTTSSTTBE--STTSSEEE-----------------------HHHHHHHHH--H
T ss_pred             cHHHHHHHH--CcCHHHHH----HHHHhcCccccc--ccCceeec----------------------cHHHHHHHHH--H
Confidence            578999999  99998875    578899986655  23344444                      4455555543  3


Q ss_pred             HHhhhCCCCCHHHHHHHHHH
Q 026799          116 KQIIKLKVATLEGISDSIKR  135 (233)
Q Consensus       116 ~~i~~~~~~T~~~I~~~I~~  135 (233)
                      ..+.+ ...|+++|.+.+++
T Consensus        50 ~~l~~-~G~sl~~I~~~l~~   68 (69)
T PF13411_consen   50 KELRK-QGMSLEEIKKLLKQ   68 (69)
T ss_dssp             HHHHH-TTTHHHHHHHHH--
T ss_pred             HHHHH-CcCCHHHHHHHHcc
Confidence            34445 45678888888764

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=80.28  E-value=3.4  Score=37.64  Aligned_cols=47  Identities=11%  Similarity=0.227  Sum_probs=39.4

Q ss_pred             cccHHHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           34 GIWTRDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        34 GIw~~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      -||.++|-.-... ++..+.|.-+|..|+++|+|.+..   ..+|+.|-|.
T Consensus        17 ~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~---~grr~~Y~LT   64 (280)
T TIGR02277        17 AIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQSER---KGRRSFYSLT   64 (280)
T ss_pred             ceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEEeee---cCCCCEEEEC
Confidence            5999999888744 999999999999999999998853   3567888653

This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=80.12  E-value=4.1  Score=33.65  Aligned_cols=43  Identities=14%  Similarity=0.384  Sum_probs=35.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHH----HHHHHHHh
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVT----KSIKSLQN   62 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~----k~LK~Le~   62 (233)
                      .-||+.|+.|+.+.    .+|..+++|..++  +++..+|+    +++++|..
T Consensus         5 ~~Lte~qr~VL~Lr----~~GlTq~EIAe~L--giS~stV~~~e~ra~kkLr~   51 (137)
T TIGR00721         5 TFLTERQIKVLELR----EKGLSQKEIAKEL--KTTRANVSAIEKRAMENIEK   51 (137)
T ss_pred             CCCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHhHHHHHHH
Confidence            46899999999994    3789999999999  99999888    55555653

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []

Probab=80.08  E-value=5.9  Score=28.67  Aligned_cols=54  Identities=11%  Similarity=0.179  Sum_probs=39.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+.+++.+.+.  +.+.-|.+++  .+.-+.-.+++..||+.|+|.+-...  +.|++++
T Consensus        10 ~a~~~V~~~~~--~S~S~lQR~~--rIGynrAariid~LE~~GiVs~~~~~--~~R~Vl~   63 (65)
T PF09397_consen   10 EAVEFVIEEGK--ASISLLQRKF--RIGYNRAARIIDQLEEEGIVSPANGS--KPREVLV   63 (65)
T ss_dssp             HHHHHHHHCTC--ECHHHHHHHH--T--HHHHHHHHHHHHHCTSBE---TT--SEEEB-S
T ss_pred             HHHHHHHHcCC--ccHHHHHHHh--CCCHHHHHHHHHHHHHCCCCCCCCCC--CCCeecc
Confidence            35566777776  9999999999  99999999999999999999876544  4566654

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	233
2dk5_A	91	Solution Structure Of Winged-Helix Domain In Rna Po		4e-05
2yu3_A	95	Solution Structure Of The Domain Swapped Wingedheli		5e-04

>pdb|2DK5|A Chain A, Solution Structure Of Winged-Helix Domain In Rna Polymerase Iii 39kda Polypeptide Length = 91

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK 77
          + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +  K
Sbjct: 20 NQEKLVYQIIEDAGNKGIWSRDVR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASKK 77
Query: 78 KHLM 81
          K  M
Sbjct: 78 KVYM 81

>pdb|2YU3|A Chain A, Solution Structure Of The Domain Swapped Wingedhelix In Dna- Directed Rna Polymerase Iii 39 Kda Polypeptide Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV 69
          + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V
Sbjct: 37 NQEKLVYQIIEDAGNKGIWSRDVR--YKSNLPLTEINKILKNLESKKLIKAV 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	233
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	2e-22
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	3e-16

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85 Length = 91

 Score = 86.4 bits (214), Expect = 2e-22
 Identities = 23/86 (26%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 3  KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
                +        + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct: 5  SSGDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRY--KSNLPLTEINKILKNLES 62

Query: 63 KSLIKEVVNIHSKGKKHLMAVEFEPS 88
          K LIK V ++ +  KK  M       
Sbjct: 63 KKLIKAVKSVAASKKKVYMLYNLSGP 88

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 70.6 bits (173), Expect = 3e-16
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 3  KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN 62
          + K   +        + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++
Sbjct: 22 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRY--KSNLPLTEINKILKNLES 79

Query: 63 KSLIKEVVNIHSK 75
          K LIK V ++   
Sbjct: 80 KKLIKAVKSVSGP 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	233
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	99.93
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	99.88
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	98.57
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	98.27
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	98.23
1okr_A	123	MECI, methicillin resistance regulatory protein ME	98.19
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	98.13
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	98.07
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	98.05
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	98.04
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	98.01
1p6r_A	82	Penicillinase repressor; transcription regulation,	98.0
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	98.0
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	98.0
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.99
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.99
2nnn_A	140	Probable transcriptional regulator; structural gen	97.98
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.98
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.98
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.97
2vn2_A	128	DNAD, chromosome replication initiation protein; D	97.97
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.97
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.96
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.96
3r0a_A	123	Putative transcriptional regulator; structural gen	97.96
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.95
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.95
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.95
3bja_A	139	Transcriptional regulator, MARR family, putative;	97.92
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.91
3nqo_A	189	MARR-family transcriptional regulator; structural	97.91
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	97.91
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.9
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	97.89
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.88
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	97.88
1z91_A	147	Organic hydroperoxide resistance transcriptional;	97.88
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.88
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.87
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	97.87
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.87
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	97.86
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	97.86
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.86
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.85
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.84
3f3x_A	144	Transcriptional regulator, MARR family, putative;	97.83
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.82
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.82
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.8
2pex_A	153	Transcriptional regulator OHRR; transcription regu	97.79
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.79
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	97.75
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.7
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.7
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.7
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	97.69
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	97.68
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	97.66
2fxa_A	207	Protease production regulatory protein HPR; protea	97.65
1ku9_A	152	Hypothetical protein MJ223; putative transcription	97.65
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	97.65
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.65
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.64
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	97.63
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	97.63
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	97.61
1hsj_A	487	Fusion protein consisting of staphylococcus access	97.61
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	97.58
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	97.56
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	97.52
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.47
2w25_A	150	Probable transcriptional regulatory protein; trans	97.44
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.43
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	97.36
4fx0_A	148	Probable transcriptional repressor protein; helix-	97.34
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	97.32
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	97.26
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	97.25
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	97.25
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	97.19
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.19
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	97.18
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.18
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	97.15
2obp_A	96	Putative DNA-binding protein; structural genomics,	97.1
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	97.02
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	97.02
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.02
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.99
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	96.97
2pg4_A	95	Uncharacterized protein; structural genomics, join	96.97
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.96
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.94
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	96.94
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.9
3jth_A	98	Transcription activator HLYU; transcription factor	96.89
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	96.89
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	96.89
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	96.88
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.86
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	96.86
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	96.85
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.76
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.72
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	96.66
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.64
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.56
2kko_A	108	Possible transcriptional regulatory protein (possi	96.55
1xma_A	145	Predicted transcriptional regulator; southea colla	96.54
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	96.54
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.49
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	96.43
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.41
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	96.39
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.36
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.36
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.36
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.3
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.3
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	96.28
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.25
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.24
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.23
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	96.23
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.16
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	96.16
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	96.1
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	96.04
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.02
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.99
2co5_A	99	Viral protein F93; viral protein-winged helix comp	95.96
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	95.96
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	95.88
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	95.85
4g6q_A	182	Putative uncharacterized protein; structural genom	95.84
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	95.66
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.66
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	95.62
3cta_A	230	Riboflavin kinase; structural genomics, transferas	95.61
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	95.48
4esf_A	117	PADR-like transcriptional regulator; PADR family,	95.47
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.43
3elk_A	117	Putative transcriptional regulator TA0346; structu	95.41
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	95.4
2dql_A	115	PEX protein; circadian clock associated protein, c	95.39
1bja_A	95	Transcription regulatory protein MOTA; activation	95.37
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.37
1z05_A	429	Transcriptional regulator, ROK family; structural	95.27
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	95.2
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	95.18
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	95.15
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	95.1
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	95.08
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	94.99
3b02_A	195	Transcriptional regulator, CRP family; structural	94.99
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	94.97
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	94.95
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	94.82
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	94.81
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	94.78
1ft9_A	222	Carbon monoxide oxidation system transcription reg	94.74
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	94.74
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	94.61
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	94.51
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	94.4
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	94.38
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.24
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	94.15
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	94.07
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	93.91
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	93.9
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	93.82
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	93.79
2w57_A	150	Ferric uptake regulation protein; gene regulation,	93.68
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	93.63
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	93.61
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	93.56
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	93.51
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	93.48
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.48
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	93.44
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	93.44
2k27_A	159	Paired box protein PAX-8; paired domain, solution	93.41
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	93.32
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	93.29
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	93.21
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	93.19
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	93.02
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	92.98
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	92.93
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	92.82
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	92.76
1bm9_A	122	RTP, TER, replication terminator protein; DNA-bind	92.74
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	92.73
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	92.61
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	92.6
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	92.46
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	92.4
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	92.4
1ylf_A	149	RRF2 family protein; structural genomics, transcri	92.39
4ets_A	162	Ferric uptake regulation protein; metal binding pr	91.92
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	91.88
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	91.87
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	91.65
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	91.65
1lva_A	258	Selenocysteine-specific elongation factor; winged-	91.65
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	91.56
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	91.55
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	91.5
1xd7_A	145	YWNA; structural genomics, protein structure initi	91.49
2v9v_A	135	Selenocysteine-specific elongation factor; transcr	91.46
2z99_A	219	Putative uncharacterized protein; winged helix dom	91.39
3c57_A	95	Two component transcriptional regulatory protein;	91.38
3k69_A	162	Putative transcription regulator; putative transcr	91.25
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	91.17
2o0m_A	345	Transcriptional regulator, SORC family; structural	90.51
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	90.33
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	90.2
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	90.05
3nw0_A	238	Non-structural maintenance of chromosomes element	89.97
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	89.96
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	89.78
2g7u_A	257	Transcriptional regulator; ICLR family, structural	89.78
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	89.71
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	89.7
3qph_A	342	TRMB, A global transcription regulator; transcript	89.62
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	89.47
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	89.31
3by6_A	126	Predicted transcriptional regulator; structural ge	89.25
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	89.15
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	88.83
1t6s_A	162	Conserved hypothetical protein; A winged helix-tur	88.82
1lva_A	258	Selenocysteine-specific elongation factor; winged-	88.54
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	88.51
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	88.38
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	88.36
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	88.3
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	88.3
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	88.26
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	87.66
3u0k_A	440	Rcamp; fluorescent protein, calcium binding, EF-ha	87.27
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	86.98
2ovk_B	153	RLC, myosin regulatory light chain LC-2, mantle mu	86.91
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	86.37
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	86.19
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	85.96
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	85.3
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	85.27
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	85.27
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	85.16
3eqx_A	373	FIC domain containing transcriptional regulator; F	84.55
2xub_A	534	DNA-directed RNA polymerase III subunit RPC3; tran	84.53
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	84.5
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	84.49
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	83.75
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	83.47
3dpl_C	382	Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus int	83.43
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	83.41
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	83.4
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	83.15
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	83.12
1p6r_A	82	Penicillinase repressor; transcription regulation,	83.02
4asn_A	101	TUBR; transcription, tubulin, FTSZ, segregation, p	82.93
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	82.75
3dtp_E	196	RLC, myosin regulatory light chain; muscle protein	82.7
1ldd_A	74	APC2WHB, anaphase promoting complex; ubiquitin, li	82.59
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	82.58
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	81.95
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	81.39
3eet_A	272	Putative GNTR-family transcriptional regulator; st	80.75

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=99.93  E-value=1.3e-25  Score=170.88  Aligned_cols=84  Identities=27%  Similarity=0.492  Sum_probs=82.3

Q ss_pred             CCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799            5 KRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus         5 ~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      |+|+++.+..+|+++|.+||++|+++|++|||+++|++++  +|++++|+++||.||++||||+++++++++||+||||+
T Consensus         7 ~~~~~~~k~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~--~l~~~tvt~iLk~LE~kglIkr~~~~~~~~rKvy~Ly~   84 (91)
T 2dk5_A            7 GDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVAASKKKVYMLYN   84 (91)
T ss_dssp             CCCCCCCCCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEESS
T ss_pred             cCHHHHhhhcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCCCCcEEEEEec
Confidence            5789999999999999999999999999999999999999  99999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 026799           85 FEPSKE   90 (233)
Q Consensus        85 lePs~e   90 (233)
                      |+||+|
T Consensus        85 l~Ps~e   90 (91)
T 2dk5_A           85 LSGPSS   90 (91)
T ss_dssp             SCCCCC
T ss_pred             cCcCCC
Confidence            999987

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=5e-23  Score=158.17  Aligned_cols=73  Identities=29%  Similarity=0.551  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799            3 KRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus         3 ~~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      +.++++.+.++++|+++|++||++|++|||+|||++||++++  |||+++|+|+||.||+++|||+|++|++++|
T Consensus        22 ~~~~~~~a~k~~~Lt~~E~lVy~~I~~aGn~GIw~kdL~~~t--nL~~~~vtkiLK~LE~k~lIK~Vksv~~~~~   94 (95)
T 2yu3_A           22 RIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVSGPSS   94 (95)
T ss_dssp             EECCSSSCCCCCSCSHHHHHHHHHHHHHTTSCEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEECCSCSSSC
T ss_pred             EEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhCCCEEEecCccCCCC
Confidence            567899999999999999999999999999999999999999  9999999999999999999999999999876

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=98.57  E-value=1.4e-06  Score=66.69  Aligned_cols=114  Identities=16%  Similarity=0.227  Sum_probs=77.0

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE   90 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e   90 (233)
                      ..+||+.|..|+.+|-+.|  |+.+++|...++.  ++..++|++.|+.||+||||.+.++   .++++|.+.       
T Consensus         5 ~~~Lt~~q~~vL~~L~~~~--~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~---~r~~~~~~~-------   72 (126)
T 1sd4_A            5 QVEISMAEWDVMNIIWDKK--SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS---ENIYFYSSN-------   72 (126)
T ss_dssp             CCCCCHHHHHHHHHHHHSS--SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEEEC-------
T ss_pred             CCCCCHHHHHHHHHHHhcC--CCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC---CCeEEEEEe-------
Confidence            4579999999999999865  6999999999922  2689999999999999999999885   345555431       


Q ss_pred             cccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           91 ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        91 iTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                      +|.|             +.+.......+.+.-.-....+...+-+.    ..||.+|++++.+.|
T Consensus        73 ~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~ls~ee~~~l~~~L  120 (126)
T 1sd4_A           73 IKED-------------DIKMKTAKTFLNKLYGGDMKSLVLNFAKN----EELNNKEIEELRDIL  120 (126)
T ss_dssp             SCHH-------------HHHHHHHHHHHHHHHTTCHHHHHHHHHHT----TCSCHHHHHHHHHHH
T ss_pred             cCHH-------------HHHHHHHHHHHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHH
Confidence            1222             22333333333322122344444444332    258899998888776

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=98.27  E-value=3.7e-06  Score=64.79  Aligned_cols=66  Identities=18%  Similarity=0.293  Sum_probs=58.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..|..|+.+|...|..|+..++|...+  +++..+++++|+.||++|||...++-.+++.+.+-
T Consensus        27 ~~lt~~~~~vL~~l~~~~~~~~t~~ela~~l--~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~   92 (139)
T 3eco_A           27 FDITNEQGHTLGYLYAHQQDGLTQNDIAKAL--QRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIG   92 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSTTTCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEEE
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHh--CCCcccHHHHHHHHHHCCCEeecCCCCCCCeeeeE
Confidence            4799999999999999988899999999999  99999999999999999999999888765554443

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=98.23  E-value=5.9e-06  Score=63.50  Aligned_cols=65  Identities=20%  Similarity=0.299  Sum_probs=57.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+|+..|..|+.+|...++.|+..++|.+.+  +++..+++++|+.||++|||...++-.+++.+.+
T Consensus        30 ~~lt~~~~~iL~~l~~~~~~~~~~~ela~~l--~~~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i   94 (141)
T 3bro_A           30 YDLTGTQMTIIDYLSRNKNKEVLQRDLESEF--SIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCL   94 (141)
T ss_dssp             TTCCHHHHHHHHHHHHTTTSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEE
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHH--CCCcchHHHHHHHHHHCCCEEeeCCCcCCCeeee
Confidence            4699999999999999987799999999999  9999999999999999999999888776544443

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=98.19  E-value=3.2e-05  Score=58.82  Aligned_cols=61  Identities=13%  Similarity=0.154  Sum_probs=53.5

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC----CChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN----LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~----l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +.+|++.|..|+.+|...  .++.+++|...+  +    ++.++|++.|+.|+++|||.+.++   .++.+|
T Consensus         5 ~~~lt~~~~~vL~~l~~~--~~~t~~ela~~l--~~~~~~s~~tv~~~l~~L~~~Glv~r~~~---~rr~~~   69 (123)
T 1okr_A            5 TYEISSAEWEVMNIIWMK--KYASANNIIEEI--QMQKDWSPKTIRTLITRLYKKGFIDRKKD---NKIFQY   69 (123)
T ss_dssp             CCCCCHHHHHHHHHHHHH--SSEEHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHTSEEEEEE---TTEEEE
T ss_pred             cccCCHHHHHHHHHHHhC--CCcCHHHHHHHH--hccCCCcHhhHHHHHHHHHHCCCeEEEec---CCeEEE
Confidence            678999999999999884  469999999999  6    889999999999999999999886   355555

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=98.13  E-value=2.6e-05  Score=61.47  Aligned_cols=62  Identities=21%  Similarity=0.282  Sum_probs=52.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC----CChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN----LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~----l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +.+||+.|..|+.+|-.. +.++.+++|...+  +    ++.++|++.|+.||++|||.+.++   .++.+|
T Consensus         4 ~~~lt~~e~~vL~~L~~~-~~~~t~~el~~~l--~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~---~r~~~~   69 (138)
T 2g9w_A            4 LTRLGDLERAVMDHLWSR-TEPQTVRQVHEAL--SARRDLAYTTVMAVLQRLAKKNLVLQIRD---DRAHRY   69 (138)
T ss_dssp             GGGCCHHHHHHHHHHHTC-SSCEEHHHHHHHH--TTTCCCCHHHHHHHHHHHHHTTSEEEEC------CCEE
T ss_pred             cccCCHHHHHHHHHHHhc-CCCCCHHHHHHHH--hccCCCCHHHHHHHHHHHHHCCCEEEEec---CCeEEE
Confidence            568999999999999885 2479999999999  6    899999999999999999999874   344455

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=98.07  E-value=8.1e-06  Score=63.22  Aligned_cols=65  Identities=18%  Similarity=0.241  Sum_probs=57.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+|+..|..|+.+|...+..|+.+++|...+  +++..+++++|+.||++|||.+.++-.+++.+.+
T Consensus        33 ~~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i   97 (127)
T 2frh_A           33 FSISFEEFAVLTYISENKEKEYYLKDIINHL--NYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLI   97 (127)
T ss_dssp             TCCCHHHHHHHHHHHHTCCSEEEHHHHHHHS--SSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEE
T ss_pred             cCCCHHHHHHHHHHHhccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEE
Confidence            4799999999999998766789999999999  9999999999999999999999888776444433

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=98.05  E-value=1.5e-05  Score=63.41  Aligned_cols=65  Identities=8%  Similarity=0.063  Sum_probs=57.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      -+|+..|..|+.+|...|  |+.+++|...+  +++..+|+++|+.||++|||...++-.+++.+.+.|
T Consensus        42 ~glt~~q~~iL~~l~~~~--~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~L  106 (162)
T 3k0l_A           42 LEISLPQFTALSVLAAKP--NLSNAKLAERS--FIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTV  106 (162)
T ss_dssp             TTCCHHHHHHHHHHHHCT--TCCHHHHHHHH--TSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEE
Confidence            479999999999998876  69999999999  999999999999999999999999988766555543

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=98.04  E-value=7.6e-06  Score=65.50  Aligned_cols=62  Identities=16%  Similarity=0.175  Sum_probs=54.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      -+|+..|..|+.+|...|+.|+..++|...+  +++..+|+++|+.||++|||....+-.+++.
T Consensus        42 ~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~  103 (168)
T 3u2r_A           42 FELSAQQYNTLRLLRSVHPEGMATLQIADRL--ISRAPDITRLIDRLDDRGLVLRTRKPENRRV  103 (168)
T ss_dssp             TTCCHHHHHHHHHHHHHTTSCEEHHHHHHHC-----CTHHHHHHHHHHHTTSEEEEEETTEEEE
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEeecCCCCCCCe
Confidence            4799999999999999988999999999999  9999999999999999999999888776433

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=98.01  E-value=2.8e-05  Score=59.54  Aligned_cols=64  Identities=13%  Similarity=0.163  Sum_probs=56.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +|+..+..|+..|...|  ++..++|.+.+  ++++.+|++.|+.||++|+|...++-.+++.+.|.|
T Consensus        28 ~l~~~~~~iL~~l~~~~--~~~~~ela~~l--~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~l   91 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDA--PLHQLALQERL--QIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWP   91 (142)
T ss_dssp             SSCHHHHHHHHHHHHHC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEE
T ss_pred             CCCHHHHHHHHHHHhCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence            68999999999998876  59999999999  999999999999999999999988877666655543

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=98.00  E-value=3.2e-05  Score=55.50  Aligned_cols=57  Identities=18%  Similarity=0.210  Sum_probs=50.0

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeec
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +.+||+.|..|+.+|.+  +.++..++|...++.  +++.++|++.|+.|+++|+|...++
T Consensus         4 ~~~lt~~e~~vL~~L~~--~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A            4 IPQISDAELEVMKVIWK--HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCHHHHHHHHHHHT--SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCCCCHHHHHHHHHHHc--CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec
Confidence            56899999999999988  447999999999922  3789999999999999999998764

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=98.00  E-value=3e-05  Score=59.39  Aligned_cols=63  Identities=17%  Similarity=0.167  Sum_probs=55.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+..|...|  |+..++|...+  ++++.+++++|+.||++|||....+-.+++.+.+
T Consensus        30 ~~lt~~~~~iL~~l~~~~--~~~~~~la~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~   92 (138)
T 1jgs_A           30 LDITAAQFKVLCSIRCAA--CITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLV   92 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEE
T ss_pred             cCCCHHHHHHHHHHHhcC--CCCHHHHHHHH--CCChHHHHHHHHHHHHCCCEEecCCcccCceeEe
Confidence            479999999999998765  69999999999  9999999999999999999999887776544444

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=98.00  E-value=2.3e-05  Score=60.41  Aligned_cols=64  Identities=19%  Similarity=0.242  Sum_probs=56.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..+..|+..|...|  |+..++|...+  ++++.+|+++|+.||++|+|...++-.+++.+.|-
T Consensus        25 ~~lt~~~~~iL~~l~~~~--~~t~~~la~~l--~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~   88 (144)
T 1lj9_A           25 LSLTRGQYLYLVRVCENP--GIIQEKIAELI--KVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIY   88 (144)
T ss_dssp             GTCTTTHHHHHHHHHHST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEE
T ss_pred             cCCCHHHHHHHHHHHHCc--CcCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeecCCCCCceeeeE
Confidence            368999999999998865  79999999999  99999999999999999999998887765555443

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=97.99  E-value=2.5e-05  Score=60.81  Aligned_cols=65  Identities=14%  Similarity=0.229  Sum_probs=56.5

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+..|..|+.+|...|  |+..++|.+.+  +++..+++++|+.||++|||....+-..++.+.+-|
T Consensus        36 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~l  100 (152)
T 3bj6_A           36 EGVTVGQRAILEGLSLTP--GATAPQLGAAL--QMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWL  100 (152)
T ss_dssp             TTCCHHHHHHHHHHHHST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEE
T ss_pred             cCCCHHHHHHHHHHHhCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCcccccceeeEE
Confidence            368999999999998866  79999999999  999999999999999999999988877655554433

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=97.99  E-value=4e-05  Score=56.07  Aligned_cols=54  Identities=20%  Similarity=0.432  Sum_probs=49.6

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      +|++.+..|+.+|...|  ++..++|.+.+  +++..+|+++|+.|+++|+|...+..
T Consensus        17 ~l~~~~~~il~~l~~~~--~~s~~ela~~l--~is~~tv~~~l~~L~~~glv~~~~~~   70 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLERG--GMRVSEIAREL--DLSARFVRDRLKVLLKRGFVRREIVE   70 (109)
T ss_dssp             CCCHHHHHHHHHHHHHC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEeec
Confidence            68899999999998765  49999999999  99999999999999999999998776

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=97.98  E-value=2e-05  Score=60.30  Aligned_cols=62  Identities=10%  Similarity=0.102  Sum_probs=54.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|...|  |+..++|...+  +++..++++.|+.||++|+|....+-.+++.+.|
T Consensus        35 ~l~~~~~~iL~~l~~~~--~~t~~ela~~l--~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~   96 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETG--PCPQNQLGRLT--AMDAATIKGVVERLDKRGLIQRSADPDDGRRLLV   96 (140)
T ss_dssp             CCCHHHHHHHHHHHHHS--SBCHHHHHHHT--TCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeee
Confidence            89999999999998877  79999999999  9999999999999999999999877665444333

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=97.98  E-value=1.1e-05  Score=62.64  Aligned_cols=63  Identities=19%  Similarity=0.359  Sum_probs=46.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+|+..|..|+.+|...|  |+..++|...+  ++++.++++.|+.||++|||...++-.+++.+.+
T Consensus        33 ~~lt~~~~~vL~~l~~~~--~~t~~eLa~~l--~~~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~   95 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDEQR--GLNLQDLGRQM--CRDKALITRKIRELEGRNLVRRERNPSDQRSFQL   95 (142)
T ss_dssp             CCCCHHHHHHHHHHHHTT--TCCHHHHHHHH--C---CHHHHHHHHHHHTTSEEC----------CC
T ss_pred             CCCCHHHHHHHHHHHhCC--CcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEeeccCCCCCCeeee
Confidence            479999999999999876  69999999999  9999999999999999999999888776544443

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=97.98  E-value=2.8e-05  Score=60.37  Aligned_cols=63  Identities=10%  Similarity=0.186  Sum_probs=53.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|...|  ++..++|.+.+  +++..+|+++|+.||++|||...++-.+++.+.|
T Consensus        38 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~  100 (150)
T 2rdp_A           38 YPITPPQFVALQWLLEEG--DLTVGELSNKM--YLACSTTTDLVDRMERNGLVARVRDEHDRRVVRI  100 (150)
T ss_dssp             SSSCHHHHHHHHHHHHHC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCC---CEEE
T ss_pred             CCCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCchhHHHHHHHHHHCCCeeecCCCCCcceeEe
Confidence            479999999999999876  69999999999  9999999999999999999999887765444433

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=97.97  E-value=2.5e-05  Score=60.46  Aligned_cols=64  Identities=14%  Similarity=0.151  Sum_probs=53.5

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..|..|+.+|...|  |+..++|...+  +++..++++.|+.||++|||...++-.+++.+.+-
T Consensus        33 ~~lt~~~~~iL~~l~~~~--~~t~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~   96 (143)
T 3oop_A           33 YDVTPEQWSVLEGIEANE--PISQKEIALWT--KKDTPTVNRIVDVLLRKELIVREISTEDRRISLLS   96 (143)
T ss_dssp             SSSCHHHHHHHHHHHHHS--SEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEE
T ss_pred             CCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCeeccCCCccCceeeee
Confidence            479999999999998874  69999999999  99999999999999999999999888765555553

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=97.97  E-value=1.1e-05  Score=63.43  Aligned_cols=70  Identities=11%  Similarity=0.101  Sum_probs=54.0

Q ss_pred             CCChHHHHHHHHHHhh---CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           15 SLTDHERLIYDVIRSK---QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a---G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      +|++.|..||-.|...   |+.++...+|.+++  +++.++|+++|+.|+++|+|....+-... .++.-.|+|.|
T Consensus        29 gLt~~e~~vll~L~~~~~~~~~~ps~~~LA~~l--~~s~~~V~~~l~~Le~kGlI~~~~~~~~~-g~~~~~Ydl~p  101 (128)
T 2vn2_A           29 GLGEGELVLLLHMQSFFEEGVLFPTPAELAERM--TVSAAECMEMVRRLLQKGMIAIEEHTDEQ-GIRNEKYTLEP  101 (128)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCSSCCHHHHHHTS--SSCHHHHHHHHHHHHHTTSSEECC-----------CEECHH
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEeEECCC-CcEEEEEehHH
Confidence            7999999999999865   66779999999999  99999999999999999999987775543 44556677755

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=97.97  E-value=1.7e-05  Score=61.61  Aligned_cols=63  Identities=19%  Similarity=0.205  Sum_probs=50.1

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+..|...|  |+..++|...+  ++++.++++.|+.||++|||...++-.+++.+.+-
T Consensus        37 ~l~~~~~~iL~~l~~~~--~~t~~ela~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~   99 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSAS--DCSVQKISDIL--GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAIN   99 (148)
T ss_dssp             TCCHHHHHHHHHHHHSS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC---------CCBE
T ss_pred             CCCHHHHHHHHHHHcCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeE
Confidence            79999999999999887  79999999999  99999999999999999999998887765555443

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=97.96  E-value=2.1e-05  Score=62.47  Aligned_cols=63  Identities=6%  Similarity=0.134  Sum_probs=53.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+.+|...|  |+.+++|...+  +++..++++.|+.||++|||...++-.+++.+.+-
T Consensus        50 glt~~q~~vL~~l~~~~--~~t~~eLa~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~  112 (161)
T 3e6m_A           50 KLPTPKLRLLSSLSAYG--ELTVGQLATLG--VMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVV  112 (161)
T ss_dssp             TCCHHHHHHHHHHHHHS--EEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECC---CCCSCEEE
T ss_pred             CCCHHHHHHHHHHHhCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEee
Confidence            68999999999999877  79999999999  99999999999999999999998888765555443

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=97.96  E-value=1.2e-05  Score=62.46  Aligned_cols=65  Identities=12%  Similarity=0.146  Sum_probs=51.5

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      -+|+..|..|+.+|...  .|+..++|.+.+  +++..+++++|+.||++|||...++-.+++.+.+.|
T Consensus        32 ~glt~~q~~vL~~l~~~--~~~t~~eLa~~l--~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~L   96 (140)
T 3hsr_A           32 YDLTYTGYIVLMAIEND--EKLNIKKLGERV--FLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISL   96 (140)
T ss_dssp             GTCCHHHHHHHHHSCTT--CEEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC-------CEEEE
T ss_pred             cCCCHHHHHHHHHHHHc--CCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeE
Confidence            37999999999999764  479999999999  999999999999999999999999888755555543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=97.96  E-value=3.5e-05  Score=59.97  Aligned_cols=71  Identities=18%  Similarity=0.184  Sum_probs=57.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      -+|++.|..||.+|.+++...+...+|.+++  +++.++|.|+|+.|+++|+|.+.+....++...| .|...|
T Consensus        22 ~gLt~~e~~il~~L~~~~~~~~t~~eLa~~l--~~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~~~~-~y~~~~   92 (123)
T 3r0a_A           22 LNLTKADLNVMKSFLNEPDRWIDTDALSKSL--KLDVSTVQRSVKKLHEKEILQRSQQNLDGGGYVY-IYKIYS   92 (123)
T ss_dssp             HTCCHHHHHHHHHHHHSTTCCEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEE-EEEECC
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeeCCccCCCcceE-EEecCC
Confidence            3789999999999988765449999999999  9999999999999999999999876665444333 344444

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=97.95  E-value=6.1e-06  Score=64.49  Aligned_cols=64  Identities=17%  Similarity=0.269  Sum_probs=46.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeee
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKH   79 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~   79 (233)
                      -+|+..|..|+.+|...++.|+.+++|...+  +++..+++++|+.||++|||...++-.+++.+.
T Consensus        37 ~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~  100 (148)
T 3jw4_A           37 LGLNSQQGRMIGYIYENQESGIIQKDLAQFF--GRRGASITSMLQGLEKKGYIERRIPENNARQKN  100 (148)
T ss_dssp             TTCCHHHHHHHHHHHHHTTTCCCHHHHHHC--------CHHHHHHHHHHTTSBCCC--------CC
T ss_pred             CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeeCCCCCchhhe
Confidence            3799999999999999987899999999999  999999999999999999999988877644433

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=97.95  E-value=2.4e-05  Score=60.72  Aligned_cols=65  Identities=15%  Similarity=0.181  Sum_probs=57.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+..|..|+.+|...|.  +..++|...+  +++..++++.|+.||++|||....+-.+++.+.+-|
T Consensus        27 ~~lt~~q~~iL~~l~~~~~--~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~L   91 (145)
T 3g3z_A           27 QDLNYNLFAVLYTLATEGS--RTQKHIGEKW--SLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSL   91 (145)
T ss_dssp             TTCCHHHHHHHHHHHHHCS--BCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEE
T ss_pred             cCCCHHHHHHHHHHHHCCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeE
Confidence            4799999999999988874  9999999999  999999999999999999999988877655555533

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=97.95  E-value=3.3e-05  Score=61.00  Aligned_cols=64  Identities=11%  Similarity=0.222  Sum_probs=54.3

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +|+..|..|+.+|...|  |+..++|...+  +++..+|+++|+.||++|||...++-..++.+.|-|
T Consensus        49 ~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~l  112 (162)
T 3cjn_A           49 GLSTAKMRALAILSAKD--GLPIGTLGIFA--VVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYL  112 (162)
T ss_dssp             TCCHHHHHHHHHHHHSC--SEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEE
T ss_pred             CCCHHHHHHHHHHHHCC--CCCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence            68999999999998765  69999999999  999999999999999999999988877655554443

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=97.92  E-value=2.6e-05  Score=59.55  Aligned_cols=64  Identities=6%  Similarity=0.070  Sum_probs=55.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..|..|+.+|...|  ++..++|.+.+  ++++.+++++|+.||++|+|...++-.+++.+.|-
T Consensus        29 ~~l~~~~~~iL~~l~~~~--~~~~~ela~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~   92 (139)
T 3bja_A           29 YDISYVQFGVIQVLAKSG--KVSMSKLIENM--GCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVY   92 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSC--SEEHHHHHHHC--SSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEE
T ss_pred             cCCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CCChhHHHHHHHHHHHCCCeeeccCCCCCceeEEE
Confidence            369999999999998755  69999999999  99999999999999999999998887765555443

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=97.91  E-value=2.9e-05  Score=61.04  Aligned_cols=63  Identities=11%  Similarity=0.143  Sum_probs=55.6

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+.+|...|  ++..++|.+.+  ++++.+++++|+.||++|||...++-.+++.+.|-
T Consensus        41 ~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~  103 (154)
T 2eth_A           41 DMKTTELYAFLYVALFG--PKKMKEIAEFL--STTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVV  103 (154)
T ss_dssp             HSBHHHHHHHHHHHHHC--CBCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEE
Confidence            68899999999998877  69999999999  99999999999999999999998887765554443

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=97.91  E-value=3.1e-05  Score=63.68  Aligned_cols=65  Identities=11%  Similarity=0.173  Sum_probs=58.1

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+||..|..|+.+|....+.|+..++|...+  +++..+++++|+.||++|||...++-.+++.+.+
T Consensus        37 ~~lt~~q~~vL~~L~~~~~~~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l  101 (189)
T 3nqo_A           37 GILTSRQYMTILSILHLPEEETTLNNIARKM--GTSKQNINRLVANLEKNGYVDVIPSPHDKRAINV  101 (189)
T ss_dssp             CSSCHHHHHHHHHHHHSCGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEE
T ss_pred             ccCCHHHHHHHHHHHhccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEE
Confidence            3699999999999998777889999999999  9999999999999999999999988886554444

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=97.91  E-value=3e-05  Score=61.39  Aligned_cols=66  Identities=12%  Similarity=0.031  Sum_probs=55.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+||..|..|+.+|..+.+.++.+++|...+  +++..+++++|+.||++|||.+.++-.+++.+...
T Consensus        31 ~gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l--~~~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~   96 (147)
T 4b8x_A           31 YGLTFARYEALVLLTFSKSGELPMSKIGERL--MVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLAT   96 (147)
T ss_dssp             GTCCHHHHHHHHHHHTSGGGEEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECC----CEEEE
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHhCCCEEEeecCCcCceeEEE
Confidence            3799999999999988877789999999999  99999999999999999999999998875554443

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=97.90  E-value=2.7e-05  Score=61.02  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=49.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..|..|+.+|...  .|+.+++|...+  +++..+|+++|+.||++|||...++-.+++.+.+.
T Consensus        37 ~~lt~~q~~iL~~l~~~--~~~~~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~  100 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWEE--NPQTLNSIGRHL--DLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLIIT  100 (149)
T ss_dssp             TTCCHHHHHHHHHHHHS--SSEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEC---------CEEE
T ss_pred             cCCCHHHHHHHHHHHHC--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeeee
Confidence            46899999999999876  469999999999  99999999999999999999999888765555443

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.89  E-value=3.2e-05  Score=59.22  Aligned_cols=62  Identities=8%  Similarity=0.185  Sum_probs=54.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+..|...|  |+..++|...+  +++..+|+++|+.||++|+|....+-.+++.+.|
T Consensus        33 ~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~   94 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQQG--EMESYQLANQA--CILRPSMTGVLARLERDGIVRRWKAPKDQRRVYV   94 (142)
T ss_dssp             TCCHHHHHHHHHHHHHC--SEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEE
Confidence            68999999999998876  59999999999  9999999999999999999999887665433333

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=97.88  E-value=5e-05  Score=58.55  Aligned_cols=62  Identities=15%  Similarity=0.134  Sum_probs=54.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|.   +.|+..++|...+  +++..+|+++|+.||++|||...++-.+++.+.|
T Consensus        33 ~~l~~~~~~iL~~l~---~~~~~~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~   94 (146)
T 2gxg_A           33 LNLSYLDFLVLRATS---DGPKTMAYLANRY--FVTQSAITASVDKLEEMGLVVRVRDREDRRKILI   94 (146)
T ss_dssp             TTCCHHHHHHHHHHT---TSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             cCCCHHHHHHHHHHh---cCCcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeecCCCCCceEEE
Confidence            368999999999997   5679999999999  9999999999999999999999888776555444

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=97.88  E-value=3.6e-05  Score=59.37  Aligned_cols=63  Identities=17%  Similarity=0.236  Sum_probs=54.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+.+|...|  ++..++|...+  +++..+|+++|+.||++|||...++-..++.+.|-
T Consensus        34 ~l~~~~~~iL~~l~~~~--~~~~~ela~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~   96 (142)
T 2bv6_A           34 NLTYPQFLVLTILWDES--PVNVKKVVTEL--ALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIH   96 (142)
T ss_dssp             TCCHHHHHHHHHHHHSS--EEEHHHHHHHT--TCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeecCCCCcceEEEE
Confidence            68999999999998866  59999999999  99999999999999999999998876655444443

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=97.88  E-value=2.8e-05  Score=60.14  Aligned_cols=64  Identities=14%  Similarity=0.174  Sum_probs=56.1

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..|..|+..|...|  ++..++|...+  ++++.+|+++|+.||++|||...++-.+++.+.+.
T Consensus        36 ~~l~~~~~~iL~~l~~~~--~~~~~~la~~l--~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~   99 (147)
T 1z91_A           36 LNITYPQYLALLLLWEHE--TLTVKKMGEQL--YLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLIS   99 (147)
T ss_dssp             TCCCHHHHHHHHHHHHHS--EEEHHHHHHTT--TCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHH--CCCcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEE
Confidence            479999999999999877  79999999999  99999999999999999999998877665555444

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=97.88  E-value=3.9e-05  Score=60.66  Aligned_cols=64  Identities=8%  Similarity=0.116  Sum_probs=53.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..|..|+.+|...  .|+..++|...+  +++..+++++|+.||++|||...++-.+++.+.+-
T Consensus        46 ~~lt~~q~~vL~~l~~~--~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~  109 (159)
T 3s2w_A           46 YGIGSGQFPFLMRLYRE--DGINQESLSDYL--KIDKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVF  109 (159)
T ss_dssp             GTCCTTTHHHHHHHHHS--CSEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECC---CCEEEE
T ss_pred             cCCCHHHHHHHHHHHHC--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEE
Confidence            37899999999999876  569999999999  99999999999999999999999888875555443

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=97.87  E-value=5.4e-05  Score=60.70  Aligned_cols=62  Identities=11%  Similarity=0.085  Sum_probs=55.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|...|  |+..++|...+  +++..+++++|+.||++|||...++-.+++.+.+
T Consensus        42 ~lt~~~~~iL~~L~~~~--~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~  103 (168)
T 2nyx_A           42 NITIPQFRTLVILSNHG--PINLATLATLL--GVQPSATGRMVDRLVGAELIDRLPHPTSRRELLA  103 (168)
T ss_dssp             SCCHHHHHHHHHHHHHC--SEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEE
Confidence            79999999999998876  69999999999  9999999999999999999999888776444443

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=97.87  E-value=4.3e-05  Score=58.84  Aligned_cols=62  Identities=15%  Similarity=0.123  Sum_probs=53.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|...|  |+..++|.+.+  +++..+++++|+.||++|+|...++-.+++.+.|
T Consensus        30 ~l~~~~~~iL~~l~~~~--~~~~~~la~~l--~~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~   91 (145)
T 2a61_A           30 GITPAQFDILQKIYFEG--PKRPGELSVLL--GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFL   91 (145)
T ss_dssp             TCCHHHHHHHHHHHHHC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCchhHHHHHHHHHHCCCeeecCCCCCCceEEE
Confidence            68999999999998865  69999999999  9999999999999999999999887665433333

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=97.87  E-value=7.1e-05  Score=59.69  Aligned_cols=64  Identities=13%  Similarity=0.193  Sum_probs=55.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+||..|..|+..|...|. |+.+++|...+  +++..+++++|+.||++|||.+.++-.+++.+..
T Consensus        27 ~gLt~~q~~vL~~L~~~~~-~~~~~eLa~~l--~~~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l   90 (151)
T 4aik_A           27 LELTQTHWVTLYNINRLPP-EQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLITRHTSANDRRAKRI   90 (151)
T ss_dssp             GCCCHHHHHHHHHHHHSCT-TSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             cCCCHHHHHHHHHHHHcCC-CCcHHHHHHHH--CcCHHHHHHHHHHHHhCCCeEeecCCCCCcchhh
Confidence            3799999999999987654 78899999999  9999999999999999999999999887555444

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=97.86  E-value=5.7e-05  Score=58.92  Aligned_cols=63  Identities=14%  Similarity=0.250  Sum_probs=55.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|...|  |+..++|.+.+  +++..+|+++|+.||++|||....+-.+++.+.|
T Consensus        33 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~   95 (155)
T 1s3j_A           33 QGVTPAQLFVLASLKKHG--SLKVSEIAERM--EVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDL   95 (155)
T ss_dssp             TTCCHHHHHHHHHHHHHS--EEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEE
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeecCCCCCCceEEE
Confidence            478999999999998865  69999999999  9999999999999999999999887766554444

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=97.86  E-value=4.5e-05  Score=58.23  Aligned_cols=58  Identities=14%  Similarity=0.245  Sum_probs=52.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      .+|++.|..|+.+|...  .|+..++|.+.+  +++..+++++|+.||++|+|...++-.++
T Consensus        25 ~~l~~~~~~iL~~l~~~--~~~~~~ela~~l--~~s~~tvs~~l~~L~~~glv~~~~~~~d~   82 (138)
T 3bpv_A           25 LNLTDAQVACLLRIHRE--PGIKQDELATFF--HVDKGTIARTLRRLEESGFIEREQDPENR   82 (138)
T ss_dssp             GTCCHHHHHHHHHHHHS--TTCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTEE
T ss_pred             cCCCHHHHHHHHHHHHc--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeecCCCCc
Confidence            37899999999999885  469999999999  99999999999999999999998876653

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=97.86  E-value=4.9e-05  Score=59.36  Aligned_cols=63  Identities=19%  Similarity=0.213  Sum_probs=53.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee--eecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE--VVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~--vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+.+|...|  |+..++|.+.+  ++++.+++++|+.||++|||..  .++-..++.+.+-
T Consensus        38 ~lt~~~~~iL~~l~~~~--~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~  102 (154)
T 2qww_A           38 GLTIQQLAMINVIYSTP--GISVADLTKRL--IITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLK  102 (154)
T ss_dssp             TCCHHHHHHHHHHHHST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEE
T ss_pred             CCCHHHHHHHHHHHHCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeE
Confidence            68999999999998865  59999999999  9999999999999999999999  8777765554443

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.85  E-value=5.4e-05  Score=58.23  Aligned_cols=64  Identities=11%  Similarity=0.253  Sum_probs=53.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|.. .+.++..++|...+  ++++.+++++|+.||++|||...++-.+++.+.+
T Consensus        33 ~~l~~~~~~iL~~l~~-~~~~~t~~~la~~l--~~s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~   96 (146)
T 2fbh_A           33 LGLSQARWLVLLHLAR-HRDSPTQRELAQSV--GVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHI   96 (146)
T ss_dssp             GCCTTTHHHHHHHHHH-CSSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEE
T ss_pred             CCCCHHHHHHHHHHHH-cCCCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCeeecCCCcccCeeee
Confidence            3689999999999932 34479999999999  9999999999999999999999887765444444

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=97.84  E-value=5.3e-05  Score=58.50  Aligned_cols=65  Identities=20%  Similarity=0.289  Sum_probs=49.2

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      --+|++.|..|+.+|...|   +..++|...+  +++..+|+++|+.||++|||...++-.+++.+.|-|
T Consensus        33 ~~~lt~~~~~iL~~l~~~~---~t~~eLa~~l--~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~l   97 (146)
T 3tgn_A           33 EVALTNTQEHILMLLSEES---LTNSELARRL--NVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQL   97 (146)
T ss_dssp             SSCCCHHHHHHHHHHTTCC---CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC----------CCEE
T ss_pred             ccCCCHHHHHHHHHHHhCC---CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEE
Confidence            3478999999999997765   9999999999  999999999999999999999988877655554433

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=97.83  E-value=4.3e-05  Score=59.18  Aligned_cols=62  Identities=10%  Similarity=0.138  Sum_probs=54.1

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +|+..|..|+..|...+.   ..++|...+  ++++.++++.|+.||++|||...++-.+++.+.+-
T Consensus        34 ~lt~~~~~iL~~l~~~~~---~~~~la~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~   95 (144)
T 3f3x_A           34 NLSYLDFSILKATSEEPR---SMVYLANRY--FVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVE   95 (144)
T ss_dssp             SCCHHHHHHHHHHHHSCE---EHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHCCC---CHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCCCceEEEE
Confidence            789999999999987664   999999999  99999999999999999999998887764444443

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=97.82  E-value=3.4e-05  Score=60.45  Aligned_cols=64  Identities=9%  Similarity=0.207  Sum_probs=51.1

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..|..|+.+|...|  |+..++|...+  +++..+++++|+.||++|||....+-.+++.+.|-
T Consensus        39 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~  102 (155)
T 3cdh_A           39 QGLRVPEWRVLACLVDND--AMMITRLAKLS--LMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVR  102 (155)
T ss_dssp             TTCCHHHHHHHHHHSSCS--CBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECC------CCCEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeE
Confidence            368999999999997654  69999999999  99999999999999999999998777665444443

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=97.82  E-value=4.3e-05  Score=60.19  Aligned_cols=62  Identities=10%  Similarity=0.195  Sum_probs=48.4

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|...|  |+..++|...+  +++..+|+++|+.||++|||...++-..++.+.|
T Consensus        46 ~lt~~~~~iL~~l~~~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~  107 (162)
T 2fa5_A           46 GMAIPEWRVITILALYP--GSSASEVSDRT--AMDKVAVSRAVARLLERGFIRRETHGDDRRRSML  107 (162)
T ss_dssp             CCCHHHHHHHHHHHHST--TCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC---------CCC
T ss_pred             CCCHHHHHHHHHHHhCC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEE
Confidence            68999999999998854  79999999999  9999999999999999999998887766544444

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=97.80  E-value=3.3e-05  Score=67.48  Aligned_cols=149  Identities=13%  Similarity=0.069  Sum_probs=99.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE-eec--------
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM-AVE--------   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym-l~~--------   84 (233)
                      -+||..|..|+..|.+.++.|+.+++|..++  ++.+.+++++|+.||++|||.+..+-++. |.+++ |.+        
T Consensus        30 ~~lt~~q~~vL~~L~~~~~~~~~~~el~~~l--~~~~~t~t~~l~rLe~~G~i~R~~~~~Dr-R~~~i~LT~~G~~~~~~  106 (250)
T 1p4x_A           30 VDMTIKEFILLTYLFHQQENTLPFKKIVSDL--CYKQSDLVQHIKVLVKHSYISKVRSKIDE-RNTYISISEEQREKIAE  106 (250)
T ss_dssp             CSSCHHHHHHHHHHHSCSCSEEEHHHHHHHS--SSCGGGTHHHHHHHHHTTSCEEEECSSST-TSEEEECCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCCC-CeEEEEECHHHHHHHHH
Confidence            3799999999999999888899999999999  99999999999999999999999999864 33432 221        


Q ss_pred             cccCCCcccCCcccCCCCC---------HHHH---HHHHHHHHHHhhhCCCCCHHH--HHHHHHHhC---Ccc------c
Q 026799           85 FEPSKEISGGAWYSEGSLD---------TEFI---KVVKSQCLKQIIKLKVATLEG--ISDSIKRSG---AFK------V  141 (233)
Q Consensus        85 lePs~eiTGG~wy~d~e~D---------~efI---~~l~~~~~~~i~~~~~~T~~~--I~~~I~~~~---i~~------~  141 (233)
                      +.|..+-.=..|+.+ +||         ..|.   ..+.+..-.++... ..|..+  |+.+|...+   ++.      .
T Consensus       107 ~~~~~~~~~eq~s~E-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l  184 (250)
T 1p4x_A          107 RVTLFDQIIKQFNLA-DQSESQMIPKDSKEFLNLMMYTMYFKNIIKKHL-TLSFVEFTILAIITSQNKNIVLLKDLIETI  184 (250)
T ss_dssp             HHHHHHHHHHHHHHH-TTCCSSCSCCSHHHHHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHTTTTCCEEHHHHHHHS
T ss_pred             HHHHHHHHHHHHhcc-cccccccchHHHHHHHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhCCCCCcCHHHHHHHH
Confidence            111110000223333 333         1111   11122222222223 355554  566776553   222      3


Q ss_pred             ccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          142 DLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       142 ~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      .++..-|-.+|+.|+=.|.|++.++.
T Consensus       185 ~i~~~tvt~~v~rLe~~GlV~R~~~~  210 (250)
T 1p4x_A          185 HHKYPQTVRALNNLKKQGYLIKERST  210 (250)
T ss_dssp             SSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCChhhHHHHHHHHHHCCCEEeeCCC
Confidence            57889999999999999999998743

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=97.79  E-value=7.1e-05  Score=58.50  Aligned_cols=64  Identities=17%  Similarity=0.158  Sum_probs=50.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..|..|+.+|...|  ++..++|.+.+  +++..+|+++|+.||++|||...++-.+++.+.+.
T Consensus        43 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~  106 (153)
T 2pex_A           43 LDLTYPQYLVMLVLWETD--ERSVSEIGERL--YLDSATLTPLLKRLQAAGLVTRTRAASDERQVIIA  106 (153)
T ss_dssp             TTCCHHHHHHHHHHHHSC--SEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC-------CEEE
T ss_pred             CCCCHHHHHHHHHHHhCC--CcCHHHHHHHh--CCCcccHHHHHHHHHHCCCEeecCCcccCCeeEee
Confidence            478999999999998754  69999999999  99999999999999999999998876654444443

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=97.79  E-value=4.3e-05  Score=59.66  Aligned_cols=64  Identities=11%  Similarity=0.212  Sum_probs=47.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|...+ .++.+++|...+  +++..++++.|+.||++|||.+.++-.+++.+.+
T Consensus        35 ~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l--~i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~   98 (150)
T 3fm5_A           35 TGLRVRSYSVLVLACEQA-EGVNQRGVAATM--GLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLI   98 (150)
T ss_dssp             GTCCHHHHHHHHHHHHST-TCCCSHHHHHHH--TCCHHHHHHHHHHHHTTTSEEC-----------C
T ss_pred             cCCCHHHHHHHHHHHhCC-CCcCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeeCCccccchhee
Confidence            368999999999997654 359999999999  9999999999999999999999888776554444

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=97.75  E-value=8.4e-05  Score=59.76  Aligned_cols=66  Identities=12%  Similarity=0.178  Sum_probs=51.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+..|..|+.+|...+ .|+..++|...+  +++..+|++.|+.||++|||.+.++-.+++.+.+.|
T Consensus        49 ~glt~~q~~vL~~L~~~~-~~~t~~eLa~~l--~i~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~L  114 (166)
T 3deu_A           49 LELTQTHWVTLHNIHQLP-PDQSQIQLAKAI--GIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKL  114 (166)
T ss_dssp             TTCCHHHHHHHHHHHHSC-SSEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CEEEE
T ss_pred             cCCCHHHHHHHHHHHHcC-CCCCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEE
Confidence            479999999999998743 469999999999  999999999999999999999998887655555544

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=97.70  E-value=0.00015  Score=52.66  Aligned_cols=62  Identities=13%  Similarity=0.136  Sum_probs=50.0

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ++....|+.++...|  ++..++|.+.+  ++++.+|++.|+.||++|+|...+....++++.|-|
T Consensus        15 ~~~~~~iL~~L~~~~--~~~~~ela~~l--~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~l   76 (100)
T 1ub9_A           15 NPVRLGIMIFLLPRR--KAPFSQIQKVL--DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             SHHHHHHHHHHHHHS--EEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             ChHHHHHHHHHHhcC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEE
Confidence            345667888887655  59999999999  999999999999999999999877665545555543

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=97.70  E-value=6.8e-05  Score=54.45  Aligned_cols=50  Identities=16%  Similarity=0.271  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .++.|+.++.+.| .+++..++|.+++  +++.++|++.|++||++|+|+.+-
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~L--gvs~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHH--CCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecC
Confidence            4688999999999 7789999999999  999999999999999999998864

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.70  E-value=5.8e-05  Score=58.34  Aligned_cols=64  Identities=8%  Similarity=0.143  Sum_probs=50.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..+..|+..|..+ +.|+..++|...+  ++++.+|+++|+.||++|||....+-.+++.+.+
T Consensus        31 ~~l~~~~~~iL~~l~~~-~~~~~~~~la~~l--~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~   94 (147)
T 2hr3_A           31 DPVQFSQLVVLGAIDRL-GGDVTPSELAAAE--RMRSSNLAALLRELERGGLIVRHADPQDGRRTRV   94 (147)
T ss_dssp             CHHHHHHHHHHHHHHHT-TSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEC------CCEE
T ss_pred             cCCCHHHHHHHHHHHHc-CCCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeCCCCCCCCceee
Confidence            46788999999999873 3469999999999  9999999999999999999999887776544444

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=97.69  E-value=0.00018  Score=61.28  Aligned_cols=118  Identities=11%  Similarity=0.166  Sum_probs=83.0

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccH--HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWT--RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE   90 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~--~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e   90 (233)
                      |++|++.+..++.+|...+..|+.+  ++|.+.+  +++..+++++|+.||++|||...++     +.++          
T Consensus         1 m~~lt~~~e~~L~~L~~l~~~~~~~~~~~La~~l--~vs~~tvs~~l~~Le~~GlV~r~~~-----~~v~----------   63 (230)
T 1fx7_A            1 MNELVDTTEMYLRTIYDLEEEGVTPLRARIAERL--DQSGPTVSQTVSRMERDGLLRVAGD-----RHLE----------   63 (230)
T ss_dssp             CCTTSSHHHHHHHHHHHHHHHTSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECTT-----SCEE----------
T ss_pred             CCCCCHHHHHHHHHHHHHhhcCCCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCC-----ccEE----------
Confidence            3578888888888887665568888  9999999  9999999999999999999988653     2122          


Q ss_pred             cccCCcccC-CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHh
Q 026799           91 ISGGAWYSE-GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALV  156 (233)
Q Consensus        91 iTGG~wy~d-~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv  156 (233)
                            .|+ |.=-.+-+....+....|+...-..+.+++++......   -.+|.+++++|.+.|-
T Consensus        64 ------LT~~G~~~~~~~~~~~~~~e~~l~~~lg~~~~~~~~~a~~le---~~ls~e~~~~L~~~L~  121 (230)
T 1fx7_A           64 ------LTEKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWE---HVMSEDVERRLVKVLN  121 (230)
T ss_dssp             ------ECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHT---TTCCHHHHHHHHHHTT
T ss_pred             ------ECHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH---hcCCHHHHHHHHHHhC
Confidence                  232 11111222233344566776665677888887755432   1489999999998874

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=97.68  E-value=4.9e-05  Score=59.43  Aligned_cols=59  Identities=14%  Similarity=0.212  Sum_probs=46.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee--cccCCCee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV--NIHSKGKK   78 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk--sV~~~~rK   78 (233)
                      +|+..|..|+.+| .  +.|+..++|...+  ++++.+++++|+.||++|||...+  +-.+++.+
T Consensus        35 ~lt~~q~~iL~~l-~--~~~~t~~eLa~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~   95 (151)
T 3kp7_A           35 GISAEQSHVLNML-S--IEALTVGQITEKQ--GVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLK   95 (151)
T ss_dssp             TCCHHHHHHHHHH-H--HSCBCHHHHHHHH--CSCSSHHHHHHHHHHHTTSEEC-----------C
T ss_pred             CCCHHHHHHHHHH-H--cCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCCCCCCee
Confidence            6899999999999 4  4569999999999  999999999999999999999855  66654333

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=97.66  E-value=6.4e-05  Score=73.15  Aligned_cols=127  Identities=9%  Similarity=0.063  Sum_probs=52.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh-----CCCceeeecccCCCeeeEEeec----
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN-----KSLIKEVVNIHSKGKKHLMAVE----   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~-----k~lIK~vksV~~~~rK~Yml~~----   84 (233)
                      ..++..+.+|+.+|.+.+.  |..++|...+  +++.+++++.|++|.+     +|||....       ..|+|..    
T Consensus       426 ~~~~~~~~~iL~~l~~~~~--it~~~la~~l--~~s~~~~~~~L~~L~~~~~~~~glie~~g-------~~y~L~~~~~~  494 (583)
T 3lmm_A          426 RQDDYRIAIVLYLLFQRPF--ITIDVVARGL--QSGKEAARNALEAARQTTVAGAPLIIAHD-------GVWLLGNACRE  494 (583)
T ss_dssp             GTTCHHHHHHHHHHHHSSS--BCHHHHHHHH--TSCHHHHHHHHHHHHTCEETTEESEEEET-------TEEEECHHHHH
T ss_pred             cccchhHHHHHHHHHHCCC--cCHHHHHHHh--CcCHHHHHHHHHHHHhhhccccceEEEeC-------CEEEECHHHHH
Confidence            3466788999999999887  9999999999  9999999999999999     88998863       3577754    


Q ss_pred             -cccCCCcccC-CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEE
Q 026799           85 -FEPSKEISGG-AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIM  162 (233)
Q Consensus        85 -lePs~eiTGG-~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie  162 (233)
                       +.+..+...- .+|..  +|.   +.+.+.+++||+.++.+|..||.+.+.        ||..++..+|+.|+-+|+|+
T Consensus       495 ~~~~~~~~~~~~~~~~~--~~~---~~~~~~I~~~l~~~g~it~~di~~l~~--------ls~~qa~~~L~~Lv~~G~l~  561 (583)
T 3lmm_A          495 ILRKVEPSPFSPVRYLS--TDQ---AELTNAAMLWLSEVGDLATSDLMAMCG--------VSRGTAKACVDGLVDEERVV  561 (583)
T ss_dssp             HHTSCC--------------------------------------------------------------------------
T ss_pred             Hhccccccccccccccc--CCh---hHHHHHHHHHHHHcCCcCHHHHHHHHC--------CCHHHHHHHHHHHHHCCcEE
Confidence             1111110000 12321  222   356678899999988888888887544        78888999999999999997


Q ss_pred             EE
Q 026799          163 EV  164 (233)
Q Consensus       163 ~v  164 (233)
                      .+
T Consensus       562 ~~  563 (583)
T 3lmm_A          562 AV  563 (583)
T ss_dssp             --
T ss_pred             Ee
Confidence            75

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=97.65  E-value=0.0001  Score=61.94  Aligned_cols=63  Identities=11%  Similarity=0.062  Sum_probs=52.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|...|  |+.+++|...+  +++..+++++|+.||++|||.+.++-.+++.+.+
T Consensus        44 ~gLt~~q~~iL~~L~~~~--~~t~~eLa~~l--~i~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l  106 (207)
T 2fxa_A           44 YDLNINEHHILWIAYQLN--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYV  106 (207)
T ss_dssp             GTCCHHHHHHHHHHHHHT--SEEHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEECC------CEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCCCceEEE
Confidence            479999999999998876  69999999999  9999999999999999999999988776444433

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=97.65  E-value=0.00019  Score=55.01  Aligned_cols=64  Identities=19%  Similarity=0.259  Sum_probs=52.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|++.+..|+.+|..+ +.++..++|.+.+  +++.+++++.|+.|+++|+|...++-.. +|.+|+
T Consensus        22 ~gl~~~~~~il~~L~~~-~~~~t~~ela~~l--~~~~stvs~~l~~L~~~G~v~r~~~~~d-~r~~~~   85 (152)
T 1ku9_A           22 HGLNKSVGAVYAILYLS-DKPLTISDIMEEL--KISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYE   85 (152)
T ss_dssp             TTCCHHHHHHHHHHHHC-SSCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEE
T ss_pred             cCCChhHHHHHHHHHHc-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEecCCC-ceEEEe
Confidence            36899999999999533 3579999999999  9999999999999999999998776553 344444

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=97.65  E-value=5.6e-05  Score=59.39  Aligned_cols=63  Identities=8%  Similarity=0.104  Sum_probs=48.4

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|... +.|+..++|.+.+  +++..++++.|+.||++|||...++-.+++.+.+
T Consensus        44 ~l~~~~~~iL~~L~~~-~~~~~~~ela~~l--~i~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~  106 (160)
T 3boq_A           44 GLSLAKFDAMAQLARN-PDGLSMGKLSGAL--KVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSA  106 (160)
T ss_dssp             SCCHHHHHHHHHHHHC-TTCEEHHHHHHHC--SSCCSCHHHHHHHHHHHTSEEEC--------CEE
T ss_pred             CCCHHHHHHHHHHHHc-CCCCCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeecCCCCCCeEEE
Confidence            6899999999999432 3479999999999  9999999999999999999999887775444443

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=97.65  E-value=0.00012  Score=64.01  Aligned_cols=62  Identities=13%  Similarity=0.157  Sum_probs=56.9

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      -+|+..|..|+..|..+++.++.+++|...+  ++++.+++++|+.||++|||.+..+-..++.
T Consensus       154 ~gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l--~i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~  215 (250)
T 1p4x_A          154 LTLSFVEFTILAIITSQNKNIVLLKDLIETI--HHKYPQTVRALNNLKKQGYLIKERSTEDERK  215 (250)
T ss_dssp             CSSCHHHHHHHHHHHTTTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEEECSSSTTC
T ss_pred             CCCCHHHHHHHHHHHhCCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeeCCCCCCCe
Confidence            3799999999999998887789999999999  9999999999999999999999999886433

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=97.64  E-value=9.1e-05  Score=54.56  Aligned_cols=55  Identities=18%  Similarity=0.219  Sum_probs=48.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHH----HHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDM----KRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~di----k~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      .+|+..|..|+..|...  .|+..++|    ...+  ++++.+|++.|+.||++|||.+..+-
T Consensus         4 ~~lt~~q~~iL~~l~~~--~~~~~~el~~~la~~l--~is~~tvs~~l~~Le~~gli~r~~~~   62 (99)
T 1tbx_A            4 TPFFYPEAIVLAYLYDN--EGIATYDLYKKVNAEF--PMSTATFYDAKKFLIQEGFVKERQER   62 (99)
T ss_dssp             CSSBCHHHHHHHHHTTC--TTCBHHHHHHHHHTTS--CCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCHHHHHHHHHHHHc--CCcCHHHHHHHHHHHc--CCCHHHHHHHHHHHHHCCCEEEEecC
Confidence            36889999999999764  46999999    8888  99999999999999999999887653

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=97.63  E-value=0.00047  Score=50.34  Aligned_cols=58  Identities=16%  Similarity=0.166  Sum_probs=46.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS   74 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~   74 (233)
                      .+|++.+..++..+... +.++...+|.+.+  +++..+|+++|+.|+++|+|.....-..
T Consensus        17 ~~l~~~~~~~l~~l~~~-~~~~t~~ela~~l--~is~~tv~~~l~~L~~~g~v~~~~~~~~   74 (109)
T 2d1h_A           17 YKITDTDVAVLLKMVEI-EKPITSEELADIF--KLSKTTVENSLKKLIELGLVVRTKTEGK   74 (109)
T ss_dssp             HTCCHHHHHHHHHHHHH-CSCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC---
T ss_pred             hcCCHHHHHHHHHHHHc-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeeccccC
Confidence            46888877776655542 4579999999999  9999999999999999999999876443

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=97.63  E-value=7.9e-05  Score=56.70  Aligned_cols=63  Identities=13%  Similarity=0.099  Sum_probs=51.6

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      ..+|++.|..|+.+|-+.|  ++.++||.++++.  ++..++|++.|+.||+||||++.++   .+..+|
T Consensus        30 ~~~LT~~e~~VL~~L~~~~--~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~---gR~~~Y   94 (99)
T 2k4b_A           30 EFNVSNAELIVMRVIWSLG--EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKE---GRKFVY   94 (99)
T ss_dssp             -CCCCCSCSHHHHHHHHHS--CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEE---TTEEEE
T ss_pred             CCCCCHHHHHHHHHHHhCC--CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeC---CCEEEE
Confidence            3469999999999999855  7999999999922  3678999999999999999999764   344455

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=97.61  E-value=0.0001  Score=58.96  Aligned_cols=70  Identities=10%  Similarity=0.112  Sum_probs=57.6

Q ss_pred             CCChHHHHHHHHHHh---hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           15 SLTDHERLIYDVIRS---KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~---aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      +||+.|.+|+-.|..   .|+.+....+|.+++  +++.++|.++|..|++||+|........ +-+..-.|+|+|
T Consensus        29 gLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~--~~s~~~v~~~L~~L~~KGlI~i~~~~d~-~g~~~~~ydL~p  101 (135)
T 2v79_A           29 GLNETELILLLKIKMHLEKGSYFPTPNQLQEGM--SISVEECTNRLRMFIQKGFLFIEECEDQ-NGIKFEKYSLQP  101 (135)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTS--SSCHHHHHHHHHHHHHHTSCEEEEEECT-TCCEEEEEECHH
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEeEecC-CCceEEEeeHHH
Confidence            689999998888876   477889999999999  9999999999999999999987544333 244556677766

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=97.61  E-value=9.5e-05  Score=68.32  Aligned_cols=64  Identities=14%  Similarity=0.225  Sum_probs=57.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      -+||..|..|+.+|.+....|+.+++|.+++  ++...+|+++|++||++|||.+.++-+. +|.++
T Consensus       400 ~~lt~~q~~vl~~l~~~~~~~~~~~~l~~~~--~~~~~~~t~~~~~le~~g~v~r~~~~~D-~R~~~  463 (487)
T 1hsj_A          400 FNLNYEEIYILNHILRSESNEISSKEIAKCS--EFKPYYLTKALQKLKDLKLLSKKRSLQD-ERTVI  463 (487)
T ss_dssp             CCCCHHHHHHHHHHHTCSCSEEEHHHHHHSS--CCCHHHHHHHHHHHHTTTTSCCEECCSS-SSCCE
T ss_pred             cCCCHHHHHHHHHHHhCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeecCCCCC-CCeEE
Confidence            4799999999999988766789999999999  9999999999999999999999999886 44444

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=97.58  E-value=4.5e-05  Score=61.86  Aligned_cols=65  Identities=11%  Similarity=0.131  Sum_probs=52.3

Q ss_pred             CCCChHHHHHHHHHHhhCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQD-MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~-~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+.+|...|. .|+..++|...+  +++..+|++.|+.||++|||...++-..++.+.+
T Consensus        65 ~glt~~~~~iL~~L~~~~~~~~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~  130 (181)
T 2fbk_A           65 SGLNAAGWDLLLTLYRSAPPEGLRPTELSALA--AISGPSTSNRIVRLLEKGLIERREDERDRRSASI  130 (181)
T ss_dssp             TTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHC--SCCSGGGSSHHHHHHHHTSEECCC-------CCB
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEE
Confidence            3699999999999998875 489999999999  9999999999999999999999877665444433

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=97.56  E-value=0.00014  Score=53.58  Aligned_cols=64  Identities=13%  Similarity=0.118  Sum_probs=48.2

Q ss_pred             CCChHHHHHHHHHHhh--CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           15 SLTDHERLIYDVIRSK--QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a--G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      .|+..+..|+..|...  ++.++.+++|...+  +++..+++++|+.||++|||   .+-.+++.+.|-|.
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l--~i~~~tvs~~l~~Le~~Glv---~~~~d~R~~~v~LT   74 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKV--NSPHSYVWLIIKKFEEAKMV---ECELEGRTKIIRLT   74 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHTTSE---EEEEETTEEEEEEC
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCcCc---cCCCCCCeEEEEEC
Confidence            5777777776666443  33349999999999  99999999999999999999   33444455555443

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=97.52  E-value=0.0009  Score=51.67  Aligned_cols=113  Identities=14%  Similarity=0.160  Sum_probs=71.6

Q ss_pred             CCCCChHHHHHHHHHHh--hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC
Q 026799           13 SDSLTDHERLIYDVIRS--KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE   90 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~--aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e   90 (233)
                      +.+|++.+..++..|..  ..+.++..++|.+++  +++..+|+++|+.||++|||...+      + .|.|   .|.  
T Consensus         8 ~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l--~is~~tv~~~l~~Le~~Gli~r~~------~-~~~L---t~~--   73 (139)
T 2x4h_A            8 MSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDL--KIAPSSVFEEVSHLEEKGLVKKKE------D-GVWI---TNN--   73 (139)
T ss_dssp             ---CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEET------T-EEEE---CHH--
T ss_pred             HhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHh--CCChHHHHHHHHHHHHCCCEEecC------C-eEEE---Chh--
Confidence            45788877777777764  235679999999999  999999999999999999998754      2 2222   221  


Q ss_pred             cccCCcccCCCCCHHHHHHHH---HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           91 ISGGAWYSEGSLDTEFIKVVK---SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        91 iTGG~wy~d~e~D~efI~~l~---~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                        |          .++...+.   +....++.. ...+.+++..+.....   -.++.+.++.|.+.|
T Consensus        74 --g----------~~~~~~~~~~~~~~~~~~~~-~~~~~~e~~~~~~~l~---~~~~~~~~~~L~~~l  125 (139)
T 2x4h_A           74 --G----------TRSINYLIKAHRVIEILLVN-IGIDKQTACEYSKQFD---YLIPEEIIDKLYNYL  125 (139)
T ss_dssp             --H----------HHHHHHHHHHHHHHHHHHHH-HTCCHHHHHHHHHHHG---GGSCHHHHHHHHHHT
T ss_pred             --H----------HHHHHHHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHH---hcCCHHHHHHHHHHh
Confidence              1          11222222   233444444 2356777766655433   236777777776665

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=97.47  E-value=0.00036  Score=51.33  Aligned_cols=61  Identities=15%  Similarity=0.194  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           18 DHERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        18 ~~e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +-++.|+.+|.+.| .+++..++|.+++  +++.++|++.|++|++.|+|+.+.    .++-.|.+..
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~L--gvsr~tV~~~L~~Le~~G~I~~~g----~~~~~W~i~~   71 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQKEA----GTPPLWKIAV   71 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEES----SSSCEEEEC-
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecC----CCCCeeEEeC
Confidence            35788999999888 6779999999999  999999999999999999998763    2234555543

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=97.44  E-value=0.00061  Score=53.93  Aligned_cols=58  Identities=10%  Similarity=0.213  Sum_probs=51.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG   76 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~   76 (233)
                      .|++.+..|+.++...|.  +..++|.+++  +++..++++.|+.|+++|+|+.....-++.
T Consensus         4 ~ld~~~~~iL~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~~   61 (150)
T 2w25_A            4 ALDDIDRILVRELAADGR--ATLSELATRA--GLSVSAVQSRVRRLESRGVVQGYSARINPE   61 (150)
T ss_dssp             CCCHHHHHHHHHHHHCTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECTG
T ss_pred             ccCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEeccChh
Confidence            488989999999987664  9999999999  999999999999999999999888766544

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=97.43  E-value=0.00069  Score=49.11  Aligned_cols=58  Identities=12%  Similarity=0.200  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +.+..|+.+|.+  +.++..++|.+.+  ++++.++++.|+.|++.|+|...+.   .+++.|-+
T Consensus        24 ~~~~~il~~l~~--~~~~s~~ela~~l--~is~~tvs~~l~~L~~~glv~~~~~---~r~~~y~l   81 (99)
T 3cuo_A           24 PKRLLILCMLSG--SPGTSAGELTRIT--GLSASATSQHLARMRDEGLIDSQRD---AQRILYSI   81 (99)
T ss_dssp             HHHHHHHHHHTT--CCSEEHHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEEEC---SSCEEEEE
T ss_pred             hHHHHHHHHHHh--CCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEec---CCEEEEEE
Confidence            456678888854  3469999999999  9999999999999999999988762   34445543

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=97.36  E-value=0.00078  Score=53.12  Aligned_cols=57  Identities=18%  Similarity=0.296  Sum_probs=50.3

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      .|++-++.|+.++.+.|.  +..++|.+++  |++..++++.|+.|+++|+|+.....-++
T Consensus         2 ~ld~~d~~il~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   58 (144)
T 2cfx_A            2 KLDQIDLNIIEELKKDSR--LSMRELGRKI--KLSPPSVTERVRQLESFGIIKQYTLEVDQ   58 (144)
T ss_dssp             CCCHHHHHHHHHHHHCSC--CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEECT
T ss_pred             CCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEecccCh
Confidence            388889999999987765  9999999999  99999999999999999999987655443

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=97.34  E-value=0.0003  Score=55.78  Aligned_cols=58  Identities=12%  Similarity=0.264  Sum_probs=43.2

Q ss_pred             CCCChHHHHHHHHHHhhC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026799           14 DSLTDHERLIYDVIRSKQ---DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS   74 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG---~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~   74 (233)
                      -+||..|..|+.+|...+   +.++.+++|.+.+  +++..++++.|+.||++||| +..+-.+
T Consensus        29 ~gLt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l--~~~~~tvsr~v~~Le~~glV-r~~~~~D   89 (148)
T 4fx0_A           29 SGLTNTQFSTLAVISLSEGSAGIDLTMSELAARI--GVERTTLTRNLEVMRRDGLV-RVMAGAD   89 (148)
T ss_dssp             GTCCHHHHHHHHHHHC---------CHHHHHHHH--TCCHHHHHHHHHHHHHTTSB-C------
T ss_pred             cCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCE-EeeCCCC
Confidence            379999999999998654   3569999999999  99999999999999999999 5566443

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=97.32  E-value=0.00094  Score=54.70  Aligned_cols=72  Identities=19%  Similarity=0.314  Sum_probs=56.9

Q ss_pred             CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe----eeEEeecccc
Q 026799           12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK----KHLMAVEFEP   87 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r----K~Yml~~leP   87 (233)
                      ....|++.++.|+.++...|.  +..++|.+++  +++..++++.|+.|+++|+|+.+..+-++.+    ..|+...++|
T Consensus        11 ~~~~ld~~d~~IL~~L~~~~~--~s~~eLA~~l--glS~~tv~~~l~~L~~~G~I~~~~~~~d~~~lG~~~a~v~v~~~~   86 (171)
T 2ia0_A           11 SEIHLDDLDRNILRLLKKDAR--LTISELSEQL--KKPESTIHFRIKKLQERGVIERYTIILGEQLKPKHLALIVLEVGK   86 (171)
T ss_dssp             ---CCCHHHHHHHHHHHHCTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECTTTSCSEEEEEEEEESC
T ss_pred             CcCCCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecccCCHHHhhcceEEEEEEECC
Confidence            455689999999999988764  9999999999  9999999999999999999998776554432    3455445554

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=97.26  E-value=0.00088  Score=50.37  Aligned_cols=59  Identities=20%  Similarity=0.208  Sum_probs=48.6

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      .|+..+.   +.++...+|.+.+  + +++.+|++.|+.||++|||.+...-..+.+..|-|.+.
T Consensus        29 ~IL~~L~---~~~~~~~eL~~~l--~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~   88 (107)
T 2fsw_A           29 LIIFQIN---RRIIRYGELKRAI--PGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPL   88 (107)
T ss_dssp             HHHHHHT---TSCEEHHHHHHHS--TTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHH
T ss_pred             HHHHHHH---hCCcCHHHHHHHc--ccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECcc
Confidence            3555553   4469999999999  8 99999999999999999999988877777777766653

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=97.25  E-value=0.0014  Score=52.52  Aligned_cols=59  Identities=12%  Similarity=0.267  Sum_probs=52.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      +..|++-++.|+.++...|.  +..++|.+++  |++..++++.|+.|+++|+|+....+-++
T Consensus         5 ~~~ld~~~~~il~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   63 (162)
T 2p5v_A            5 QLTLDKTDIKILQVLQENGR--LTNVELSERV--ALSPSPCLRRLKQLEDAGIVRQYAALLSP   63 (162)
T ss_dssp             CCCCCHHHHHHHHHHHHCTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECT
T ss_pred             ccCCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEeeecccCCh
Confidence            34589999999999988776  8999999999  99999999999999999999987765544

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=97.25  E-value=0.00083  Score=57.18  Aligned_cols=118  Identities=9%  Similarity=0.135  Sum_probs=79.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccH--HHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWT--RDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEI   91 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~--~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~ei   91 (233)
                      .+||+.+..++..|...+..|+.+  ++|.+.+  ++.+.+++++|+.||++|||...++                    
T Consensus         2 ~~lt~~~e~yL~~i~~l~~~~~~~~~~~la~~l--~vs~~tvs~~l~~Le~~GlV~r~~~--------------------   59 (226)
T 2qq9_A            2 KDLVATTEMYLRTIYELEEEGVTPLRARIAERL--EQSGPTVSQTVARMERDGLVVVASD--------------------   59 (226)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHTCCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECTT--------------------
T ss_pred             CCCCHHHHHHHHHHHHHhhcCCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeCC--------------------
Confidence            467887777777777665567777  9999999  9999999999999999999987543                    


Q ss_pred             ccCCcccC-CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhc
Q 026799           92 SGGAWYSE-GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVL  157 (233)
Q Consensus        92 TGG~wy~d-~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~  157 (233)
                       ++..-|+ |.--.+-+....+....|+...-..+.+++++......   -.+|.+-++.|.+.|-+
T Consensus        60 -~~v~LT~~G~~~~~~~~~~~~~~e~~l~~~lgl~~ee~~~~a~~le---h~~s~~~~~~l~~~l~~  122 (226)
T 2qq9_A           60 -RSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWE---HVMSDEVERRLVKVLKD  122 (226)
T ss_dssp             -SBEEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHT---TTCCHHHHHHHHHHSSC
T ss_pred             -CCeEECHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH---hhCCHHHHHHHHHHhCC
Confidence             1222232 21112222223345556665533577888888777655   13677777777776643

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=97.19  E-value=0.00072  Score=53.48  Aligned_cols=58  Identities=14%  Similarity=0.250  Sum_probs=50.5

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      ..|++-++.|+.++...|.  +..++|.+++  |++..++++.|+.|+++|+|+.+..+-++
T Consensus         5 ~~ld~~d~~il~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~~~   62 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSENSR--LTYRELADIL--NTTRQRIARRIDKLKKLGIIRKFTIIPDI   62 (151)
T ss_dssp             -CCCHHHHHHHHHHHHCTT--CCHHHHHHHT--TSCHHHHHHHHHHHHHHTSEEEEEEEECT
T ss_pred             hhCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEecCCh
Confidence            3589989999999987765  9999999999  99999999999999999999987665443

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=97.19  E-value=0.0014  Score=46.94  Aligned_cols=71  Identities=10%  Similarity=0.071  Sum_probs=50.8

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      ..|+.+|.+.|  ++..++|.+.+  +++.++|++.|+.|++.|+|..... .......|.+.   +.....=.++|+.
T Consensus         3 ~~Il~~L~~~~--~~s~~eLa~~l--gvs~~tv~r~L~~L~~~GlI~~~~~-~~gr~~~y~l~---~~~~~~~~~~~~~   73 (81)
T 2htj_A            3 NEILEFLNRHN--GGKTAEIAEAL--AVTDYQARYYLLLLEKAGMVQRSPL-RRGMATYWFLK---GEKQAGQSCSSTT   73 (81)
T ss_dssp             HHHHHHHHHSC--CCCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEECC-SSSSSCEEEES---SCSSSSCGGGGCS
T ss_pred             HHHHHHHHHcC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecc-CCCCcEEEEEC---hhhhccHHHHHhH
Confidence            46788887765  49999999999  9999999999999999999986543 22233344443   2222223567764

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=97.18  E-value=0.00096  Score=53.27  Aligned_cols=59  Identities=14%  Similarity=0.170  Sum_probs=48.4

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      ..+|+..+.   +.++...+|.+.+  ++++++|++.|+.||++|||.+...-..+ +..|-|.+
T Consensus        26 ~l~IL~~L~---~g~~~~~eLa~~l--gis~~tls~~L~~Le~~GlI~r~~~~~d~-~~~y~LT~   84 (146)
T 2f2e_A           26 SMLIVRDAF---EGLTRFGEFQKSL--GLAKNILAARLRNLVEHGVMVAVPAESGS-HQEYRLTD   84 (146)
T ss_dssp             HHHHHHHHH---TTCCSHHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEEECSSSS-CEEEEECH
T ss_pred             HHHHHHHHH---hCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEEecCCCC-eEEEEECc
Confidence            344555664   3359999999999  99999999999999999999998887777 77776654

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=97.18  E-value=0.0017  Score=48.46  Aligned_cols=49  Identities=14%  Similarity=0.226  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +-...|+.+| ..|  ++..++|.+.+  ++++.+|++.|+.|+++|+|...+.
T Consensus        21 ~~r~~IL~~L-~~~--~~~~~ela~~l--~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           21 ETRWEILTEL-GRA--DQSASSLATRL--PVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             HHHHHHHHHH-HHS--CBCHHHHHHHS--SSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             hHHHHHHHHH-HcC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeEEec
Confidence            3456688888 444  49999999999  9999999999999999999988664

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=97.15  E-value=0.001  Score=46.21  Aligned_cols=45  Identities=24%  Similarity=0.299  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      |..||++|+++|. =+..++..++.  +.+...|-++|++|++||||+
T Consensus        12 e~~lL~yIr~sGG-ildI~~~a~ky--gV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           12 ERELLDYIVNNGG-FLDIEHFSKVY--GVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHHTTS-EEEHHHHHHHH--CCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCC-EEeHHHHHHHh--CCCHHHHHHHHHHHHHCCCee
Confidence            5689999998876 36789999999  999999999999999999997

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=97.10  E-value=0.0032  Score=47.82  Aligned_cols=61  Identities=16%  Similarity=0.229  Sum_probs=52.2

Q ss_pred             CCCChHHHHHHHHHHhh----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCee
Q 026799           14 DSLTDHERLIYDVIRSK----QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKK   78 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~a----G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK   78 (233)
                      .+|++-+..||..+..+    ....+...+|.+.+  .|++.+++|.|+.||.+|||...++ .. +|.
T Consensus        12 ~gl~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l--~l~~stLsR~l~rLe~~GLV~r~~~-~D-~R~   76 (96)
T 2obp_A           12 DGIDPAIVEVLLVLREAGIENGATPWSLPKIAKRA--QLPMSVLRRVLTQLQAAGLADVSVE-AD-GRG   76 (96)
T ss_dssp             -CCCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC-TT-SCE
T ss_pred             cCCCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHh--CCchhhHHHHHHHHHHCCCEEeecC-CC-Cce
Confidence            46999999999988766    44558999999999  9999999999999999999998777 54 454

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=97.02  E-value=0.001  Score=52.45  Aligned_cols=56  Identities=16%  Similarity=0.302  Sum_probs=48.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      |++-+..|+.++...|  ++..++|.+++  |+++.++++.|+.|+++|+|+....+-++
T Consensus         1 ld~~~~~il~~L~~~~--~~~~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   56 (150)
T 2pn6_A            1 MDEIDLRILKILQYNA--KYSLDEIAREI--RIPKATLSYRIKKLEKDGVIKGYYAYINP   56 (150)
T ss_dssp             CCHHHHHHHHHHTTCT--TSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSSCCCCCCCCG
T ss_pred             CChHHHHHHHHHHHcC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEEEeecCH
Confidence            5677888999997766  49999999999  99999999999999999999987665443

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=97.02  E-value=0.0025  Score=50.42  Aligned_cols=56  Identities=7%  Similarity=0.167  Sum_probs=49.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS   74 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~   74 (233)
                      .|++-++.|+.++.+.|.  +..++|.+++  |++..++.+.|+.|+++|+|+....+-+
T Consensus         5 ~ld~~d~~il~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~~   60 (152)
T 2cg4_A            5 LIDNLDRGILEALMGNAR--TAYAELAKQF--GVSPETIHVRVEKMKQAGIITGARIDVS   60 (152)
T ss_dssp             CCCHHHHHHHHHHHHCTT--SCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEEEEEEC
T ss_pred             ccCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcceEEEecC
Confidence            488888999999988765  9999999999  9999999999999999999998775433

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=97.02  E-value=0.001  Score=48.84  Aligned_cols=59  Identities=7%  Similarity=0.101  Sum_probs=49.7

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChH-HHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDN-IVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~-~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +-...|+.++...|.  ...++|.+.+  +++.. .|++.|..||+.|||...    ..+|.+|-|++
T Consensus        11 ~~~~~IL~~Lk~~g~--~ta~eiA~~L--git~~~aVr~hL~~Le~eGlV~~~----~~gRP~w~LT~   70 (79)
T 1xmk_A           11 EIKEKICDYLFNVSD--SSALNLAKNI--GLTKARDINAVLIDMERQGDVYRQ----GTTPPIWHLTD   70 (79)
T ss_dssp             HHHHHHHHHHHHTCC--EEHHHHHHHH--CGGGHHHHHHHHHHHHHTTSEEEE----CSSSCEEEECH
T ss_pred             hHHHHHHHHHHHcCC--cCHHHHHHHc--CCCcHHHHHHHHHHHHHCCCEEec----CCCCCCeEeCH
Confidence            456788999999995  9999999999  99999 999999999999999853    24556776653

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.99  E-value=0.0033  Score=45.77  Aligned_cols=51  Identities=16%  Similarity=0.202  Sum_probs=44.6

Q ss_pred             HHHHHHHHHhh-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           20 ERLIYDVIRSK-----QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        20 e~lVy~~I~~a-----G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+.|+++|.+.     |. -+..+||...+  ++...+|.+-|+.||++|+|+....-.
T Consensus         6 ~~~IL~~I~~~i~~~~g~-~psv~EIa~~l--gvS~~TVrr~L~~Le~kG~I~R~~ggr   61 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGA-PVKTRDIADAA--GLSIYQVRLYLEQLHDVGVLEKVNAGK   61 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTS-CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEESCSS
T ss_pred             HHHHHHHHHHHHhhccCC-CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEecCCCC
Confidence            56789999887     33 39999999999  999999999999999999999987544

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=96.97  E-value=0.0013  Score=52.08  Aligned_cols=57  Identities=16%  Similarity=0.345  Sum_probs=50.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      .|++.++.|+.++...|.  +..++|.+++  |++..++++.|+.|+++|+|+.+..+-++
T Consensus         4 ~ld~~~~~il~~L~~~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   60 (151)
T 2cyy_A            4 PLDEIDKKIIKILQNDGK--APLREISKIT--GLAESTIHERIRKLRESGVIKKFTAIIDP   60 (151)
T ss_dssp             CCCHHHHHHHHHHHHCTT--CCHHHHHHHH--CSCHHHHHHHHHHHHHHTSSCCCCCCCCG
T ss_pred             CcCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEECH
Confidence            488989999999988764  9999999999  99999999999999999999987655433

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=96.97  E-value=0.0014  Score=47.89  Aligned_cols=54  Identities=13%  Similarity=0.025  Sum_probs=41.4

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHH-HHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNI-VTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~-v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .++.+|...| .|+..++|.+.+  ++++.+ +++.|+.||++|||.  .+-.+++.+.+
T Consensus        19 ~~L~~l~~~~-~~~t~~eLa~~l--~is~~t~vs~~l~~Le~~Glv~--~~~~drR~~~~   73 (95)
T 2pg4_A           19 PTLLEFEKKG-YEPSLAEIVKAS--GVSEKTFFMGLKDRLIRAGLVK--EETLSYRVKTL   73 (95)
T ss_dssp             HHHHHHHHTT-CCCCHHHHHHHH--CCCHHHHHTTHHHHHHHTTSEE--EEEEETTEEEE
T ss_pred             HHHHHHHhcC-CCCCHHHHHHHH--CCCchHHHHHHHHHHHHCCCee--cCCCCCCeEEE
Confidence            3444555543 369999999999  999999 999999999999999  44444444444

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.96  E-value=0.0024  Score=44.65  Aligned_cols=51  Identities=10%  Similarity=0.195  Sum_probs=43.1

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|++-...|+.++.+.+ ..+...+|.+++  +++..+|.|.|+.|++.|+|.+
T Consensus         7 ~m~~~~~~IL~~L~~~~-~~~s~~eLA~~l--glsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A            7 TGDNLEQKILQVLSDDG-GPVAIFQLVKKC--QVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             --CHHHHHHHHHHHHHC-SCEEHHHHHHHH--CSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cccHHHHHHHHHHHHcC-CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEec
Confidence            46666678999998754 459999999999  9999999999999999999854

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=96.94  E-value=0.0033  Score=47.21  Aligned_cols=59  Identities=19%  Similarity=0.286  Sum_probs=47.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      .|+..+.   +.++...+|.+.+ .++++.+|++.|+.||++|||.+...-..+.+..|-|.+
T Consensus        18 ~IL~~L~---~~~~~~~eLa~~l-~~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~   76 (107)
T 2hzt_A           18 VILXHLT---HGKKRTSELKRLM-PNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSE   76 (107)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHC-TTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             HHHHHHH---hCCCCHHHHHHHh-cCCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECc
Confidence            4555553   3459999999884 289999999999999999999998887777777776654

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=96.94  E-value=0.0024  Score=55.58  Aligned_cols=51  Identities=12%  Similarity=0.279  Sum_probs=47.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +|++.+..|+..|.+.|  |+..++|.+++  +++.++++|.|+.|+++|+|...
T Consensus       149 ~L~~~~~~IL~~L~~~~--~~s~~eLA~~l--glsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          149 DYSREEMKLLNVLYETK--GTGITELAKML--DKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             CCCHHHHHHHHHHHHHT--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            78999999999997665  69999999999  99999999999999999999886

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=96.90  E-value=0.0034  Score=47.54  Aligned_cols=61  Identities=8%  Similarity=0.135  Sum_probs=50.1

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      ...|+..|.. |  ++...+|.+.+ +++++.+|++.|+.||++|||.+..+-..++++.|-|.+
T Consensus        24 ~~~IL~~L~~-~--~~~~~eLa~~l-~~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~   84 (112)
T 1z7u_A           24 KLSLMDELFQ-G--TKRNGELMRAL-DGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTP   84 (112)
T ss_dssp             HHHHHHHHHH-S--CBCHHHHHHHS-TTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECH
T ss_pred             HHHHHHHHHh-C--CCCHHHHHHHh-ccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECH
Confidence            4467777763 4  59999999886 379999999999999999999999888877777776654

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.89  E-value=0.0029  Score=46.28  Aligned_cols=47  Identities=11%  Similarity=0.199  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ....|+.++.+   .++...+|.+.+  ++++++|++.|+.|++.|||...+
T Consensus        24 ~r~~Il~~L~~---~~~~~~ela~~l--~is~~tvs~~L~~L~~~Glv~~~~   70 (98)
T 3jth_A           24 RRLQILCMLHN---QELSVGELCAKL--QLSQSALSQHLAWLRRDGLVTTRK   70 (98)
T ss_dssp             HHHHHHHHTTT---SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34456666654   469999999999  999999999999999999998753

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=96.89  E-value=0.0033  Score=50.67  Aligned_cols=56  Identities=13%  Similarity=0.321  Sum_probs=50.0

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      |++-++.|+.++.+.|.  +..++|.+++  |++..++.+.|+.|++.|+|+.+..+-++
T Consensus         1 lD~~d~~il~~L~~~~~--~s~~~la~~l--g~s~~tv~~rl~~L~~~g~i~~~~a~~~~   56 (162)
T 3i4p_A            1 MDRLDRKILRILQEDST--LAVADLAKKV--GLSTTPCWRRIQKMEEDGVIRRRVALLDP   56 (162)
T ss_dssp             CCHHHHHHHHHHTTCSC--SCHHHHHHHH--TCCHHHHHHHHHHHHHTTSSCCCCCCCCT
T ss_pred             CCHHHHHHHHHHHHCCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeceeeeCH
Confidence            57788899999998877  8999999999  99999999999999999999987665444

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=96.89  E-value=0.0019  Score=53.58  Aligned_cols=53  Identities=17%  Similarity=0.224  Sum_probs=47.2

Q ss_pred             CCChHHHHHHHHHHhh---CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           15 SLTDHERLIYDVIRSK---QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a---G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +||+-|+.||.+|.+.   .......++|.+.+  +|++.++.+.|+.||++|+|..-
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~l--gl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRF--RITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEECC
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHc--CCCcHHHHHHHHHHHHCCCEEec
Confidence            6899999999999764   33468999999999  99999999999999999999765

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=96.88  E-value=0.0017  Score=47.77  Aligned_cols=62  Identities=10%  Similarity=0.135  Sum_probs=52.5

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      ++.+..|++.+.+||. =+-..+|.+++  +++...|+|+|+.|.+.+.|-+      |.|=.|-+.+-.|
T Consensus        18 ~d~eekVLe~LkeaG~-PlkageIae~~--GvdKKeVdKaik~LKkEgkI~S------PkRCyw~~~~~~~   79 (80)
T 2lnb_A           18 GHLEQRILQVLTEAGS-PVKLAQLVKEC--QAPKRELNQVLYRMKKELKVSL------TSPATWCLGGTDP   79 (80)
T ss_dssp             HHHHHHHHHHHHHHTS-CEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE------EETTEEEESSSSC
T ss_pred             chHHHHHHHHHHHcCC-CCCHHHHHHHH--CCCHHHHHHHHHHHHHcCCccC------CCCceeeCCCCCC
Confidence            4458899999999987 79999999999  9999999999999999999866      5666776654333

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=96.86  E-value=0.0041  Score=46.49  Aligned_cols=47  Identities=19%  Similarity=0.258  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ....|+.+|. .  .++...+|.+.+  ++++++|++.|+.|++.|+|...+
T Consensus        27 ~r~~IL~~L~-~--~~~~~~ela~~l--~is~stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           27 NRIRIMELLS-V--SEASVGHISHQL--NLSQSNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HHHHHHHHHH-H--CCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHH-h--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            4556777776 3  458999999999  999999999999999999998876

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=96.85  E-value=0.0016  Score=50.62  Aligned_cols=58  Identities=16%  Similarity=0.365  Sum_probs=49.0

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      |++.+..|+..+...|.  +..++|.+++  +++.+++++.|+.|++.|+|+.....-++.+
T Consensus         2 ld~~~~~il~~L~~~~~--~~~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~   59 (141)
T 1i1g_A            2 IDERDKIILEILEKDAR--TPFTEIAKKL--GISETAVRKRVKALEEKGIIEGYTIKINPKK   59 (141)
T ss_dssp             CCSHHHHHHHHHHHCTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHHTSSCCCCCCCCSGG
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEeccccccChHH
Confidence            67778889999887654  8999999999  9999999999999999999987765444443

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=96.76  E-value=0.0031  Score=49.56  Aligned_cols=50  Identities=12%  Similarity=0.230  Sum_probs=43.7

Q ss_pred             CCcccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           32 DMGIWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        32 ~~GIw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +.++...+|.+.+  . +++.+|++.|+.||++|||.+...-..+.++.|-|.
T Consensus        46 ~g~~~~~eLa~~l--~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT   96 (131)
T 1yyv_A           46 DGTHRFSDLRRXM--GGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLT   96 (131)
T ss_dssp             GCCEEHHHHHHHS--TTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEEC
T ss_pred             cCCCCHHHHHHHh--ccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEEC
Confidence            4469999999998  7 999999999999999999999888777777777665

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=96.72  E-value=0.0065  Score=44.80  Aligned_cols=47  Identities=2%  Similarity=0.163  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      --..|+.++.. |  .+...+|...+  ++++.+|++.|+.|++.|||...+
T Consensus        24 ~r~~Il~~L~~-~--~~~~~ela~~l--~is~~tvs~~L~~L~~~Glv~~~~   70 (102)
T 3pqk_A           24 VRLMLVCTLVE-G--EFSVGELEQQI--GIGQPTLSQQLGVLRESGIVETRR   70 (102)
T ss_dssp             HHHHHHHHHHT-C--CBCHHHHHHHH--TCCTTHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHh-C--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34557777743 4  38999999999  999999999999999999998755

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=96.66  E-value=0.0075  Score=45.51  Aligned_cols=49  Identities=16%  Similarity=0.274  Sum_probs=42.1

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ++.+..|+.+|.+ |  ++...+|.+.+  ++++.+|++.|+.||+.|+|...+
T Consensus        31 ~~~~~~il~~L~~-~--~~s~~ela~~l--~is~stvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           31 TPSRLMILTQLRN-G--PLPVTDLAEAI--GMEQSAVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             CHHHHHHHHHHHH-C--CCCHHHHHHHH--SSCHHHHHHHHHHHHHHCSEEEEE
T ss_pred             CHHHHHHHHHHHH-C--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            3456677888876 3  58999999999  999999999999999999998765

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=96.64  E-value=0.0061  Score=46.86  Aligned_cols=47  Identities=9%  Similarity=0.107  Sum_probs=39.6

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ...|+.++...|  ++...+|...+  ++++.+|++.|+.|++.|+|...+
T Consensus        44 rl~IL~~L~~~~--~~s~~eLa~~l--~is~stvs~~L~~L~~~Glv~~~~   90 (122)
T 1u2w_A           44 RAKITYALCQDE--ELCVCDIANIL--GVTIANASHHLRTLYKQGVVNFRK   90 (122)
T ss_dssp             HHHHHHHHHHSS--CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHHHCC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            445777776544  58999999999  999999999999999999998753

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=96.56  E-value=0.008  Score=43.98  Aligned_cols=47  Identities=19%  Similarity=0.255  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      +....|+.+|  .|  ++...+|.+.+  ++++.+|++.|+.|++.|+|...+
T Consensus        31 ~~r~~Il~~L--~~--~~~~~eLa~~l--~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           31 PVRRKILRML--DK--GRSEEEIMQTL--SLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHHHH--HT--TCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHH--cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEC
Confidence            3455677777  33  49999999999  999999999999999999998765

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.55  E-value=0.0063  Score=45.80  Aligned_cols=46  Identities=9%  Similarity=0.115  Sum_probs=39.3

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ...|+.+|..   .++..++|.+.+  ++++++|++.|+.|++.|||...+
T Consensus        27 r~~IL~~L~~---~~~s~~eLa~~l--gis~stvs~~L~~L~~~GlV~~~~   72 (108)
T 2kko_A           27 RLQILDLLAQ---GERAVEAIATAT--GMNLTTASANLQALKSGGLVEARR   72 (108)
T ss_dssp             THHHHHHHTT---CCEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            3456666653   468999999999  999999999999999999998765

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=96.54  E-value=0.0049  Score=49.45  Aligned_cols=63  Identities=11%  Similarity=0.238  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh------cCCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR------VNLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~------~~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      -+..|+.+|.+ |.  +.-.+|.+.++      .++...+|+.+|+.||++|||.+....  ..+.|++|-|.+
T Consensus        42 ~~~~IL~~L~~-~~--~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~  112 (145)
T 1xma_A           42 VDTIILSLLIE-GD--SYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITP  112 (145)
T ss_dssp             HHHHHHHHHHH-CC--EEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECH
T ss_pred             HHHHHHHHHHh-CC--CCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECH
Confidence            57788888864 33  77777777762      159999999999999999999988764  456788885554

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=96.54  E-value=0.004  Score=53.94  Aligned_cols=47  Identities=9%  Similarity=0.216  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +....|+.+|.. |  .+...+|...+  ++++.+|++.|+.|++.|||...
T Consensus        12 ~~R~~IL~~L~~-g--~~s~~ELa~~l--glS~stVs~hL~~Le~aGLV~~~   58 (232)
T 2qlz_A           12 KVRRDLLSHLTC-M--ECYFSLLSSKV--SVSSTAVAKHLKIMEREGVLQSY   58 (232)
T ss_dssp             HHHHHHHHHHTT-T--TTCSSSSCTTC--CCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHh-C--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            345668888863 4  48889999999  99999999999999999999884

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=96.49  E-value=0.01  Score=46.58  Aligned_cols=42  Identities=29%  Similarity=0.361  Sum_probs=36.2

Q ss_pred             HHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           25 DVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        25 ~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .+|...|  ++..++|...+  ++++.+|+++|+.||++|||...+
T Consensus        47 ~~l~~~~--~~~~~~la~~l--~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           47 DLIREVG--EARQVDMAARL--GVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             HHHHHHS--CCCHHHHHHHH--TSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             HHHHhCC--CcCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEec
Confidence            3555554  48999999999  999999999999999999997754

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=96.43  E-value=0.006  Score=46.79  Aligned_cols=63  Identities=8%  Similarity=0.075  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhc----C--CCh-HHHHHHHHHHHhCCCceeeecc-cCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRV----N--LPD-NIVTKSIKSLQNKSLIKEVVNI-HSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~----~--l~~-~~v~k~LK~Le~k~lIK~vksV-~~~~rK~Yml~~   84 (233)
                      -+..|+.+|.. +.  +.-.+|.+.+..    .  +++ .+|+.+|+.||++|||.+.... ..+.|++|-|.+
T Consensus        14 ~~~~IL~~L~~-~~--~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~   84 (118)
T 2esh_A           14 LASTILLLVAE-KP--SHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITP   84 (118)
T ss_dssp             HHHHHHHHHHH-SC--BCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECH
T ss_pred             HHHHHHHHHHc-CC--CCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEECh
Confidence            56778888865 33  777888888721    2  889 9999999999999999988754 446788886554

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=96.41  E-value=0.012  Score=41.82  Aligned_cols=59  Identities=10%  Similarity=0.133  Sum_probs=49.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+++....|+.++.+.+...+...+|...++   ++++..+|.|.|+.|+++|+|.++..-.
T Consensus        14 ~~t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~   75 (83)
T 2fu4_A           14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG   75 (83)
T ss_dssp             CCCHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGG
T ss_pred             CcCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCC
Confidence            4788889999999876435799999999983   3799999999999999999999876543

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=96.39  E-value=0.021  Score=43.99  Aligned_cols=109  Identities=11%  Similarity=0.193  Sum_probs=82.0

Q ss_pred             CChHHHHHHHHHHhh-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           16 LTDHERLIYDVIRSK-QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        16 L~~~e~lVy~~I~~a-G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      +++++..+.+-|..+ +..|.|.+|+...+  +++...+.+.|+.|...|.|.++..                       
T Consensus         1 ~~~~~~~l~~~i~~~~~~~p~~~~~la~~~--~~~~~~~~~~l~~l~~~G~l~~i~~-----------------------   55 (121)
T 2pjp_A            1 FSEEQQAIWQKAEPLFGDEPWWVRDLAKET--GTDEQAMRLTLRQAAQQGIITAIVK-----------------------   55 (121)
T ss_dssp             CCHHHHHHHHHHGGGCSSSCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEET-----------------------
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecC-----------------------
Confidence            355555555555443 34889999999999  9999999999999999999977541                       


Q ss_pred             CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeE
Q 026799           95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQI  161 (233)
Q Consensus        95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~i  161 (233)
                          |.-|..+.++.+.+.+..++..++..|+.+..+.+   |     +|-.=.-.||+-|=-.|..
T Consensus        56 ----~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~l---g-----~sRK~ai~lLE~~Dr~g~T  110 (121)
T 2pjp_A           56 ----DRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRL---G-----VGRKLAIQILEYFDRIGFT  110 (121)
T ss_dssp             ----TEEEEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHH---T-----SCHHHHHHHHHHHHHHTSE
T ss_pred             ----CceECHHHHHHHHHHHHHHHHHCCCccHHHHHHHH---C-----CcHHHHHHHHHHHhhcCCe
Confidence                22356788999999999999999999999998887   4     4444444566665444443

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.36  E-value=0.0096  Score=45.32  Aligned_cols=56  Identities=9%  Similarity=0.101  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .-..|+.++.   +.++...+|...+  ++++.+|++.|+.|++.|||...+.   .+.++|-|
T Consensus        19 ~R~~Il~~L~---~~~~~~~eLa~~l--~is~~tvs~hL~~L~~~GlV~~~~~---gr~~~y~l   74 (118)
T 3f6o_A           19 TRRAVLGRLS---RGPATVSELAKPF--DMALPSFMKHIHFLEDSGWIRTHKQ---GRVRTCAI   74 (118)
T ss_dssp             HHHHHHHHHH---TCCEEHHHHHTTC--CSCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEEE
T ss_pred             HHHHHHHHHH---hCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCeEEEec---CCEEEEEE
Confidence            4456777776   2458999999999  9999999999999999999988665   34455543

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=96.36  E-value=0.0074  Score=45.84  Aligned_cols=58  Identities=17%  Similarity=0.260  Sum_probs=43.0

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      ..|+..+. .|...+...+|.+.+ +++++++|++.|+.||+.|||.+...    .+..|-|.+
T Consensus        30 l~IL~~L~-~g~~~~~~~eL~~~l-~gis~~~ls~~L~~Le~~GlV~r~~~----r~~~y~LT~   87 (111)
T 3df8_A           30 MLIISVLG-NGSTRQNFNDIRSSI-PGISSTILSRRIKDLIDSGLVERRSG----QITTYALTE   87 (111)
T ss_dssp             HHHHHHHT-SSSSCBCHHHHHHTS-TTCCHHHHHHHHHHHHHTTSEEEEES----SSEEEEECH
T ss_pred             HHHHHHHh-cCCCCCCHHHHHHHc-cCCCHHHHHHHHHHHHHCCCEEEeec----CcEEEEECc
Confidence            34565664 455434499999988 24999999999999999999998766    455665443

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=96.36  E-value=0.008  Score=44.90  Aligned_cols=51  Identities=16%  Similarity=0.218  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +....|+..+...|.. +...+|...+  |++.++|+++|+.|++.|+|...+.
T Consensus        18 ~~~l~Il~~l~~~g~~-~s~~eLa~~l--gvs~~tV~~~L~~L~~~GlV~~~~~   68 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTE-MTDEEIANQL--NIKVNDVRKKLNLLEEQGFVSYRKT   68 (110)
T ss_dssp             STTHHHHHHHHHHCSC-BCHHHHHHTT--TSCHHHHHHHHHHHHHHTSCEEEEE
T ss_pred             hHHHHHHHHHHHcCCC-CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEec
Confidence            3445566666566643 9999999999  9999999999999999999987643

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.30  E-value=0.0084  Score=44.69  Aligned_cols=46  Identities=7%  Similarity=0.237  Sum_probs=43.0

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..|+++|.+.|.  +..+||.+.+  +++..+|++-|..||++|+|+++.
T Consensus         5 ~~Il~~L~~~g~--vsv~eLA~~l--~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLALQGR--MEAKQLSARL--QTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHHSCS--EEHHHHHHHT--TCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHHcCC--CcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            368889999888  9999999999  999999999999999999999985

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.30  E-value=0.0082  Score=43.69  Aligned_cols=45  Identities=11%  Similarity=0.267  Sum_probs=42.3

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..|+++|.+.|.  +..+||.+.+  +++..+|++-|..||++|+|+++
T Consensus         5 ~~Il~~L~~~g~--vsv~eLa~~l--~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            5 IQVRDLLALRGR--MEAAQISQTL--NTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHHSCS--BCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHcCC--CcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            368889999888  9999999999  99999999999999999999987

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=96.28  E-value=0.01  Score=44.84  Aligned_cols=62  Identities=15%  Similarity=0.314  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeeccc-CCCeeeEEee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIH-SKGKKHLMAV   83 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~-~~~rK~Yml~   83 (233)
                      -+..|+.++.. |.  ..--+|.+.+.  .+++..+|..+|+.||++|||.+..... .+.|++|-|.
T Consensus        10 l~~~IL~~L~~-~~--~~gyel~~~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT   74 (108)
T 3l7w_A           10 IEYLILAIVSK-HD--SYGYDISQTIKLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLT   74 (108)
T ss_dssp             HHHHHHHHHHH-SC--EEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEEC
T ss_pred             HHHHHHHHHHc-CC--CcHHHHHHHHHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEEC
Confidence            46678888876 33  55566666631  1899999999999999999999887643 3446677544

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=96.25  E-value=0.0088  Score=46.24  Aligned_cols=36  Identities=17%  Similarity=0.123  Sum_probs=33.4

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           33 MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        33 ~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .++..++|.+.+  +++..+|+++|+.|+++|||...+
T Consensus        21 ~~~~~~ela~~l--~vs~~tvs~~l~~Le~~Glv~r~~   56 (142)
T 1on2_A           21 GYARVSDIAEAL--AVHPSSVTKMVQKLDKDEYLIYEK   56 (142)
T ss_dssp             SSCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEee
Confidence            469999999999  999999999999999999998753

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=96.24  E-value=0.016  Score=45.89  Aligned_cols=52  Identities=13%  Similarity=0.180  Sum_probs=43.5

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      ...+...+|.+.+ +++++++|++.|+.||+.|||.+...-..+.+..|-|.+
T Consensus        37 ~g~~rf~eL~~~l-~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~   88 (131)
T 4a5n_A           37 DGKKRFNEFRRIC-PSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTE   88 (131)
T ss_dssp             TSCBCHHHHHHHC-TTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             cCCcCHHHHHHHh-cccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECH
Confidence            3458999999886 379999999999999999999998877777777776654

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=96.23  E-value=0.014  Score=42.47  Aligned_cols=51  Identities=14%  Similarity=0.145  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHhhCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           19 HERLIYDVIRSKQDMG-IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~G-Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ...+|.++|..-+..+ +...+|.+++  |++.+.|+|+|=.|+++|+|..+.+
T Consensus        13 ~~~~v~~~i~~L~~~~~~Ta~~IAkkL--g~sK~~vNr~LY~L~kkG~V~~~~~   64 (75)
T 1sfu_A           13 IFSLVKKEVLSLNTNDYTTAISLSNRL--KINKKKINQQLYKLQKEDTVKMVPS   64 (75)
T ss_dssp             HHHHHHHHHHTSCTTCEECHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHhCCCCcchHHHHHHHHH--CCCHHHHHHHHHHHHHCCCEecCCC
Confidence            3457777788888887 9999999999  9999999999999999999988765

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=96.16  E-value=0.0098  Score=46.02  Aligned_cols=52  Identities=13%  Similarity=0.338  Sum_probs=46.3

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      |++-++.|+.++.+.|.  +..++|...++.+++...|++.|+.|++.|||...
T Consensus        11 md~~d~~IL~~L~~~g~--~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           11 MTIWDDRILEIIHEEGN--GSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CCHHHHHHHHHHHHHSC--BCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCHHHHHHHHHHHHcCC--CCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            78888999999998885  99999999884467999999999999999999874

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=96.16  E-value=0.01  Score=49.67  Aligned_cols=51  Identities=18%  Similarity=0.293  Sum_probs=44.8

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +++.+..|+.++. .|  ++..++|..++  ++++.++++.|+.|++.|+|+...+
T Consensus        18 ~d~~~~~IL~~L~-~~--~~s~~eLA~~l--glS~stv~~~l~~Le~~GlI~~~~~   68 (192)
T 1uly_A           18 LEDTRRKILKLLR-NK--EMTISQLSEIL--GKTPQTIYHHIEKLKEAGLVEVKRT   68 (192)
T ss_dssp             HSHHHHHHHHHHT-TC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEec
Confidence            3667778898887 34  59999999999  9999999999999999999999843

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=96.10  E-value=0.022  Score=48.01  Aligned_cols=60  Identities=22%  Similarity=0.372  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEe
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMA   82 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml   82 (233)
                      +....|+.++. .|  ++...+|.+.+  ++++.+|++.|+.|++.|||...+.-  ..+.+++|-+
T Consensus        15 ~~rl~IL~~L~-~~--~~s~~eLa~~l--~is~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~L   76 (202)
T 2p4w_A           15 ETRRRILFLLT-KR--PYFVSELSREL--GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMI   76 (202)
T ss_dssp             HHHHHHHHHHH-HS--CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEE
T ss_pred             HHHHHHHHHHH-hC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEE
Confidence            45667888884 33  59999999999  99999999999999999999987653  2245555544

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=96.04  E-value=0.015  Score=43.37  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=41.5

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..||.+++.-.+ |+..++|...+  ||+.+.+++.|..|+++|||...
T Consensus         8 eIi~~IL~~i~~-~~~~t~La~~~--~ls~~~~~~~l~~L~~~GLI~~~   53 (95)
T 1r7j_A            8 EIIQAILEACKS-GSPKTRIMYGA--NLSYALTGRYIKMLMDLEIIRQE   53 (95)
T ss_dssp             HHHHHHHHHHTT-CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc-CCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCeEEE
Confidence            378888887764 49999999999  99999999999999999999875

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=96.02  E-value=0.025  Score=43.64  Aligned_cols=44  Identities=14%  Similarity=0.315  Sum_probs=37.2

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .|+.++.   +.++...+|.+.+  ++++.+|++.|+.|++.|+|...+
T Consensus        50 ~IL~~L~---~~~~s~~ela~~l--gis~stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           50 RLLSLLA---RSELCVGDLAQAI--GVSESAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHH---cCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            3555553   3468999999999  999999999999999999998765

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.99  E-value=0.0067  Score=44.88  Aligned_cols=45  Identities=20%  Similarity=0.243  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      -+.|+.++..   .|+..++|.+++  +++...|++.|+.||+.|+|...
T Consensus        19 ~~~IL~lL~~---~g~sa~eLAk~L--giSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           19 VCEAIKTIGI---EGATAAQLTRQL--NMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHHSS---STEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHH---cCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeC
Confidence            3455566664   459999999999  99999999999999999999874

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=95.96  E-value=0.024  Score=42.84  Aligned_cols=68  Identities=15%  Similarity=0.236  Sum_probs=50.0

Q ss_pred             CCCChHHHHHHHHHHhhCC--Cc-ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           14 DSLTDHERLIYDVIRSKQD--MG-IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~--~G-Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +-|+.....|+.++...+.  .| =..++|.++.+.++...+|..+|+.||++|+|.+..   .+.||+|-+.+
T Consensus         5 ~~~~~~~~~IL~lL~~~~~~~~g~~i~~ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~---~~~rk~Y~iT~   75 (99)
T 2co5_A            5 KYMRINYYIILKVLVINGSRLEKKRLRSEILKRFDIDISDGVLYPLIDSLIDDKILREEE---APDGKVLFLTE   75 (99)
T ss_dssp             CCCHHHHHHHHHHHHHTTTEEEGGGHHHHHHHHHCCBCCHHHHHHHHHHHHHTTSEEEEC---CTTSCEEEECH
T ss_pred             HhhcccHHHHHHHHHhcCCCCcHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHCCCEEEee---CCCcEEEEECH
Confidence            3466678889998865421  22 233566666633699999999999999999999876   67899996654

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=95.96  E-value=0.054  Score=45.57  Aligned_cols=109  Identities=13%  Similarity=0.124  Sum_probs=72.4

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC-
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE-   99 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d-   99 (233)
                      +.||.+.+  .+.++.+++|.+.+  ++++.+|+++|++||++|||...++                     ++..-|+ 
T Consensus         9 ~~I~~l~~--~~~~~~~~~lA~~l--~vs~~tvs~~l~~Le~~GlV~r~~~---------------------~~i~LT~~   63 (214)
T 3hrs_A            9 KCLYELGT--RHNKITNKEIAQLM--QVSPPAVTEMMKKLLAEELLIKDKK---------------------AGYLLTDL   63 (214)
T ss_dssp             HHHHHTTS--SCSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEETT---------------------TEEEECHH
T ss_pred             HHHHHHHh--cCCCcCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEEecC---------------------CCeEECHH
Confidence            45565544  35579999999999  9999999999999999999987653                     1222232 


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhc
Q 026799          100 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVL  157 (233)
Q Consensus       100 ~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~  157 (233)
                      |.=-.+.+-...+....|+...-..+.+++++.-....   -.+|++-++.|-..|-+
T Consensus        64 G~~~~~~~~~~h~~~e~~l~~~lg~~~~e~~~~a~~lE---h~~s~~~~~~l~~~l~~  118 (214)
T 3hrs_A           64 GLKLVSDLYRKHRLIEVFLVHHLGYTTEEIHEEAEVLE---HTVSDHFVERLDQLLDY  118 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHH---TTSCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh---ccCCHHHHHHHHHHhCC
Confidence            22112222233346667776544566777777666444   24788888888777654

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=95.88  E-value=0.011  Score=53.65  Aligned_cols=50  Identities=18%  Similarity=0.260  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      .++.|+++|...|.  +.+++|.+++  +|+..+|+++++.|++.|+|++....
T Consensus        17 n~~~il~~l~~~~~--~sr~~la~~~--~ls~~tv~~~v~~L~~~g~i~~~~~~   66 (406)
T 1z6r_A           17 NAGAVYRLIDQLGP--VSRIDLSRLA--QLAPASITKIVHEMLEAHLVQELEIK   66 (406)
T ss_dssp             HHHHHHHHHHSSCS--CCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEC---
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEeeccc
Confidence            56789999998876  9999999999  99999999999999999999996543

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=95.85  E-value=0.021  Score=43.83  Aligned_cols=63  Identities=13%  Similarity=0.242  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh---c-CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR---V-NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~---~-~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      -+.+|+.+|.. +.  ..--+|.+.+.   . ++++.+|..+|+.||++|||.+....  ..+.||+|-|.+
T Consensus        10 l~~~IL~~L~~-~~--~~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~   78 (115)
T 4esb_A           10 LEGCILYIISQ-EE--VYGYELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITD   78 (115)
T ss_dssp             HHHHHHHHHHH-SC--EEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECH
T ss_pred             HHHHHHHHHHc-CC--CCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECH
Confidence            46788888874 33  56667777762   1 58999999999999999999987643  346788886543

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=95.84  E-value=0.063  Score=44.19  Aligned_cols=115  Identities=10%  Similarity=0.135  Sum_probs=69.4

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeeccccCCCcccCCccc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVEFEPSKEISGGAWYS   98 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~lePs~eiTGG~wy~   98 (233)
                      .|+.++.   ..+....+|...+  + +++.+|++.|+.|++-|||+.++-  +.....|.|-+..-        +.+..
T Consensus        27 ~il~~L~---~~~~~~~~l~~~l--~~~~~~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~--------~~~~~   93 (182)
T 4g6q_A           27 RITQLLI---GRSLTTRELAELL--PDVATTTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQ--------AGDAD   93 (182)
T ss_dssp             HHHHHTT---TSCEEHHHHHHHC--TTBCHHHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTT--------TTTSS
T ss_pred             HHHHHHH---hCCCCHHHHHHHh--cCCCHHHHHHHHHHHHHCCCeEEEEeecccCcceeEEEeccc--------cccCC
Confidence            4555553   4568999999998  8 999999999999999999987764  44445678865431        12222


Q ss_pred             CCCCCHH--------HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHH
Q 026799           99 EGSLDTE--------FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAL  155 (233)
Q Consensus        99 d~e~D~e--------fI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~L  155 (233)
                      ...++.+        |...+.+....|+.+.. ...     +-...+++  .+.||.++..++.+.|
T Consensus        94 ~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~-~~~-----~~~~~~~s~~~l~Lt~ee~~el~~el  154 (182)
T 4g6q_A           94 HDGVDADRLRTMFTVFVAGVGGHLDQYLEREQ-IDP-----LADGIAFRQTALNLSDEELAEFLTAF  154 (182)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHHHHHHHHTTSSS-CCH-----HHHTCCCCCCCCCCCHHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHHHHHHHHHHHHhhcc-cch-----hhhhhcceeeeEECCHHHHHHHHHHH
Confidence            3334433        22233333334443322 111     11223333  3678999988876655

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=95.66  E-value=0.086  Score=43.33  Aligned_cols=113  Identities=12%  Similarity=0.079  Sum_probs=86.0

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      -+.|+.++. .|-  ..+..|.+++  ||+-.++..+|+.||..|+|++|+.   .++.+++|.+-         .|-. 
T Consensus        13 k~~ILE~Lk-~G~--~~t~~Iak~L--GlShg~aq~~Ly~LeREG~V~~Vk~---GK~ayw~L~~s---------~y~~-   74 (165)
T 2vxz_A           13 LRDILALLA-DGC--KTTSLIQQRL--GLSHGRAKALIYVLEKEGRVTRVAF---GNVALVCLSMD---------QYRQ-   74 (165)
T ss_dssp             HHHHHHHHT-TCC--EEHHHHHHHH--TCCHHHHHHHHHHHHHTTSCEEEEE---TTEEEEESCHH---------HHHH-
T ss_pred             HHHHHHHHH-hCC--ccHHHHHHHh--CCcHHHHHHHHHHHHhcCceEEEEE---ccEEEEEecHH---------HHHH-
Confidence            356888888 777  9999999999  9999999999999999999988764   34566676221         2221 


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHh--------CCcccccCHHHHHHHHHHHh
Q 026799          100 GSLDTEFIKVVKSQCLKQIIKL--KVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRALV  156 (233)
Q Consensus       100 ~e~D~efI~~l~~~~~~~i~~~--~~~T~~~I~~~I~~~--------~i~~~~Ls~~di~~il~~Lv  156 (233)
                            .|+.+.+-+..+|...  .++|+.++++.|.+-        .+..+..+-..+-..|+-+.
T Consensus        75 ------kV~dilrel~~~l~s~gvk~i~p~~l~~li~~d~~~~~~~a~~v~v~~~~~~~l~fl~~~l  135 (165)
T 2vxz_A           75 ------LVDGMIREVERLVTTNKLKFISPPRLHDLIIKDPQARKFFSSIIPIAHRTAIILSFLNHLL  135 (165)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSHHHHHHHHTTSCCSSCCHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHHHcCCeeeCcHHHHHHHHhCHHHHHHHHHhcCcccchhHHHHHHHHHH
Confidence                  6777777777777754  689999999998864        45567777777777776543

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=95.66  E-value=0.016  Score=46.57  Aligned_cols=56  Identities=5%  Similarity=0.099  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      --..|+.+|.   +.++...+|...+  ++++.+|++.|+.|++.|||...+   ..+.++|-|
T Consensus        59 ~R~~IL~~L~---~~~~t~~eLa~~l--gls~stvs~hL~~L~~aGlV~~~~---~Gr~~~y~l  114 (151)
T 3f6v_A           59 TRRRLVQLLT---SGEQTVNNLAAHF--PASRSAISQHLRVLTEAGLVTPRK---DGRFRYYRL  114 (151)
T ss_dssp             HHHHHHHHGG---GCCEEHHHHHTTS--SSCHHHHHHHHHHHHHTTSEEEEE---ETTEEEEEE
T ss_pred             HHHHHHHHHH---hCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe---cCCEEEEEE
Confidence            3456677775   3459999999999  999999999999999999998865   334455543

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=95.62  E-value=0.05  Score=40.11  Aligned_cols=47  Identities=15%  Similarity=0.261  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ....|+..+...|  +....+|.+.+  ++++.++++.|+.|++. +|...+
T Consensus        28 ~Rl~IL~~l~~~~--~~~~~ela~~l--~is~stvs~hL~~L~~~-lv~~~~   74 (99)
T 2zkz_A           28 MRLKIVNELYKHK--ALNVTQIIQIL--KLPQSTVSQHLCKMRGK-VLKRNR   74 (99)
T ss_dssp             HHHHHHHHHHHHS--CEEHHHHHHHH--TCCHHHHHHHHHHHBTT-TBEEEE
T ss_pred             HHHHHHHHHHHCC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHH-hhhheE
Confidence            3445665555555  48999999999  99999999999999999 998765

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=95.61  E-value=0.032  Score=47.06  Aligned_cols=54  Identities=13%  Similarity=0.182  Sum_probs=45.7

Q ss_pred             CChHHHHHHHHHHhhCC----CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           16 LTDHERLIYDVIRSKQD----MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~----~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +.+.+..++..|...|+    .|+...++.+++  ++++..|++.|+.||+++||.+.++
T Consensus         5 ~~~~~l~~l~~l~~~~~l~~~~~~s~s~aA~~L--~isq~avSr~I~~LE~~~L~~R~~~   62 (230)
T 3cta_A            5 TDDQYYRAIKKIKEAAEASNRAYLTSSKLADML--GISQQSASRIIIDLEKNGYITRTVT   62 (230)
T ss_dssp             --CHHHHHHHHHHHHTTTSSEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cHHHHHHHHHHHHHhcccccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            34577788888877665    678899999999  9999999999999999999988754

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=95.48  E-value=0.01  Score=53.78  Aligned_cols=48  Identities=21%  Similarity=0.230  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .++.|+++|. .|.  +.+.||.++|  +|+..+|+++++.|++.|+|++...
T Consensus        21 ~~~~il~~l~-~~~--~sr~~la~~~--gls~~tv~~~v~~L~~~gli~~~~~   68 (380)
T 2hoe_A           21 NISRILKRIM-KSP--VSRVELAEEL--GLTKTTVGEIAKIFLEKGIVVEEKD   68 (380)
T ss_dssp             -CCCSHHHHH-HSC--BCHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHH-cCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecC
Confidence            4557999999 766  9999999999  9999999999999999999999764

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=95.47  E-value=0.046  Score=42.12  Aligned_cols=62  Identities=16%  Similarity=0.256  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHh---hc-CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKREL---RV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t---~~-~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      +.+|+.+|....   ..--+|.+.+   +. +++..+|..+|+.||++|||.+....  ..+.||+|-|.+
T Consensus        13 ~~~IL~lL~~~p---~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~   80 (117)
T 4esf_A           13 EGCVLEIISRRE---TYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNE   80 (117)
T ss_dssp             HHHHHHHHHHSC---BCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECH
T ss_pred             HHHHHHHHHcCC---CCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECH
Confidence            567888887533   4445555554   22 68999999999999999999987643  346788886544

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=95.43  E-value=0.058  Score=39.10  Aligned_cols=46  Identities=11%  Similarity=0.126  Sum_probs=36.7

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +.++++|+.++.+|++|+++.+        .+|+.-|+.-|+.|+-.|+|++++
T Consensus         5 ~~Il~~L~~~g~vsv~eLa~~l--------~VS~~TIRrdL~~Le~~G~l~R~~   50 (78)
T 1xn7_A            5 IQVRDLLALRGRMEAAQISQTL--------NTPQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_dssp             HHHHHHHHHSCSBCHHHHHHHT--------TCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHcCCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEec
Confidence            4566777777777777777654        378899999999999999999874

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=95.41  E-value=0.03  Score=43.20  Aligned_cols=62  Identities=6%  Similarity=0.132  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh----cCCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR----VNLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAV   83 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~----~~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~   83 (233)
                      -+..|+.++.. |.  ..--+|.+.+.    ..+++.+|..+|+.||+.|||.+...  -..+.||+|-|.
T Consensus        15 l~~~IL~lL~~-~p--~~gyel~~~l~~~~~~~i~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT   82 (117)
T 3elk_A           15 ITLYILKELVK-RP--MHGYELQKSMFETTGQALPQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHIT   82 (117)
T ss_dssp             HHHHHHHHHHH-SC--EEHHHHHHHHHHHHSCCCCTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEEC
T ss_pred             HHHHHHHHHHc-CC--CCHHHHHHHHHHHhCCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEEC
Confidence            35678888865 33  55556666651    13899999999999999999998764  244678888544

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=95.40  E-value=0.05  Score=43.63  Aligned_cols=51  Identities=14%  Similarity=0.130  Sum_probs=42.5

Q ss_pred             CChHHHHHHHHHHhhCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQDMG-----------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~G-----------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.++++..-+++-+...|           +.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       117 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          117 QRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAV--GSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             CCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCcEEccCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            4667877776766554443           6899999999  9999999999999999999974

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=95.39  E-value=0.03  Score=42.96  Aligned_cols=63  Identities=16%  Similarity=0.222  Sum_probs=44.0

Q ss_pred             HHHHHHHhhCCCcccH-HHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecc---cCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWT-RDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNI---HSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~-~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV---~~~~rK~Yml~~   84 (233)
                      +|+.+|.+....|-.. +.|...++. +++..+|..+|+.||++|||.+....   ..+.||+|-|.+
T Consensus        26 ~IL~lL~~~~~~Gyei~~~l~~~~~~~~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~   93 (115)
T 2dql_A           26 YILYVLLQGESYGTELIQQLETEHPTYRLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSP   93 (115)
T ss_dssp             HHHHHHTTSCBCHHHHHHHHHHHCTTEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECG
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHcCCCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECH
Confidence            3788887644444432 334433322 69999999999999999999987654   256788887654

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=95.37  E-value=0.031  Score=42.34  Aligned_cols=50  Identities=24%  Similarity=0.330  Sum_probs=47.1

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHH-HhhcCCChHHHHHHHHHHHhCCCce
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKR-ELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~-~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      .+|+.-|.-++-.|...+  .+..++|.. ..  .|..++|+|.|+.|+++|||.
T Consensus        12 ~~L~~~QfsiL~~L~~~~--~~t~~~Lae~~l--~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           12 DVLNEKTATILITIAKKD--FITAAEVREVHP--DLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             TSSCHHHHHHHHHHHHST--TBCHHHHHHTCT--TSCHHHHHHHHHHHHTTTSEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHh--cccHHHHHHHHHHHHHCCCee
Confidence            579999999999998887  799999999 88  999999999999999999997

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=95.37  E-value=0.047  Score=41.83  Aligned_cols=63  Identities=11%  Similarity=0.232  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh-----c-CCChHHHHHHHHHHHhCCCceeeec--ccCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR-----V-NLPDNIVTKSIKSLQNKSLIKEVVN--IHSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~-----~-~l~~~~v~k~LK~Le~k~lIK~vks--V~~~~rK~Yml~~   84 (233)
                      -+..|+.+|.+.-   ..--+|.+.+.     . ++++.+|..+|+.||++|||.+...  ...+.||+|-|.+
T Consensus        13 l~~~IL~~L~~~~---~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~   83 (116)
T 3f8b_A           13 TNVILLNVLKQGD---NYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTE   83 (116)
T ss_dssp             HHHHHHHHHHHCC---BCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEECH
T ss_pred             HHHHHHHHHHhCC---CCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECH
Confidence            3567888887633   34445555441     1 7999999999999999999998763  3557888886543

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=95.27  E-value=0.032  Score=51.24  Aligned_cols=48  Identities=27%  Similarity=0.377  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .++.|+++|...|.  +.+.+|.+.+  +|+..+|+++++.|++.|+|++..
T Consensus        40 n~~~il~~l~~~~~--~sr~ela~~~--gls~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           40 NAGRVYKLIDQKGP--ISRIDLSKES--ELAPASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHHHCS--BCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecc
Confidence            56789999999886  9999999999  999999999999999999999975

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=95.20  E-value=0.07  Score=42.62  Aligned_cols=51  Identities=16%  Similarity=0.252  Sum_probs=41.3

Q ss_pred             CChHHHHHHHHHHhhCCC-----------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQDM-----------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~-----------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++-+...           -+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       138 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~l--g~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          138 LDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIV--GCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             SCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEe
Confidence            456777776666654332           25789999999  9999999999999999999975

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=95.18  E-value=0.07  Score=43.25  Aligned_cols=51  Identities=14%  Similarity=0.292  Sum_probs=41.5

Q ss_pred             CChHHHHHHHHHHhhCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQDMG-----------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~G-----------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++-+...|           +.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       158 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~  219 (230)
T 3iwz_A          158 LDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLV--GCSREMAGRVLKKLQADGLLHA  219 (230)
T ss_dssp             CCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEE
Confidence            4567777666666544322           6899999999  9999999999999999999975

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=95.15  E-value=0.051  Score=44.32  Aligned_cols=62  Identities=15%  Similarity=0.280  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhc------CCChHHHHHHHHHHHhCCCceeeeccc--CCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRV------NLPDNIVTKSIKSLQNKSLIKEVVNIH--SKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~------~l~~~~v~k~LK~Le~k~lIK~vksV~--~~~rK~Yml~~   84 (233)
                      +..|+.++.. |.  +.--+|++....      +++..+|.++|+.||++|||.+.....  .+.||+|-|.+
T Consensus         4 ~~~iL~lL~~-~~--~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~   73 (179)
T 1yg2_A            4 PHVILTVLST-RD--ATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQ   73 (179)
T ss_dssp             HHHHHHHHHH-CC--BCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECH
T ss_pred             HHHHHHHHhc-CC--CCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeCh
Confidence            4578888875 43  777888887721      589999999999999999999866543  35789996554

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=95.10  E-value=0.025  Score=45.12  Aligned_cols=69  Identities=12%  Similarity=0.200  Sum_probs=46.7

Q ss_pred             CChHHHHHHHHHHhhCCCcccH-HHHHHHhhc-CCChHHHHHHHHHHHhCCCceeeecc---cCCCeeeEEeec
Q 026799           16 LTDHERLIYDVIRSKQDMGIWT-RDMKRELRV-NLPDNIVTKSIKSLQNKSLIKEVVNI---HSKGKKHLMAVE   84 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~-~dik~~t~~-~l~~~~v~k~LK~Le~k~lIK~vksV---~~~~rK~Yml~~   84 (233)
                      ++..+.+|+.+|.+....|-.. +.|...++. +++..+|..+|+.||++|||.+....   ..+.||+|-|.+
T Consensus        32 ~~~~~~~IL~lL~~~~~~Gyei~k~l~~~~~~~~is~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT~  105 (138)
T 2e1n_A           32 KELAVCYVLAVLRHEDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQ  105 (138)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHHHHHSTTEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEESC
T ss_pred             chHHHHHHHHHHHhCCCcHHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEECH
Confidence            4456667888887533333322 234433312 69999999999999999999987654   356788886544

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=95.08  E-value=0.045  Score=44.31  Aligned_cols=60  Identities=8%  Similarity=0.192  Sum_probs=48.2

Q ss_pred             HHHHHHHHH-hhCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           20 ERLIYDVIR-SKQD--MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        20 e~lVy~~I~-~aG~--~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +.-.|+-|. +--+  +=|+...|..++  ++.-+.-+++|+.|+++|+|+.|  ++|.+..||.-.
T Consensus        46 Dk~tydKL~KEVpk~gKlITpsvlseRl--kI~gSLARkaLreL~~kGlIk~V--~kh~~q~IYTra  108 (143)
T 2xzm_8           46 EKKNVESIINNPSKVGKVLTVSTVVEKL--KVNGSLARQLMRTMADRKLVEKV--AKNGNQWVYSVI  108 (143)
T ss_dssp             CHHHHHHHHTCCTTSCSEECHHHHHHHH--CBCHHHHHHHHHHHHHTTSEEEE--EEETTEEEEEET
T ss_pred             cHHHHHHHHHHhcccceeecHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEEecC
Confidence            345566555 3333  469999999999  99999999999999999999998  356688999544

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=94.99  E-value=0.072  Score=43.83  Aligned_cols=54  Identities=19%  Similarity=0.229  Sum_probs=44.4

Q ss_pred             CCCCChHHHHHHHHHHhhCCCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           13 SDSLTDHERLIYDVIRSKQDMG------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~G------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +...+.++++..-+++-+...|      +.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       159 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~l--G~sr~tvsR~l~~l~~~glI~~  218 (232)
T 1zyb_A          159 EPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCL--DDTRLNISKTLNELQDNGLIEL  218 (232)
T ss_dssp             CCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSCEE
T ss_pred             HhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEe
Confidence            4456778887776666554433      7899999999  9999999999999999999974

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=94.99  E-value=0.055  Score=43.21  Aligned_cols=53  Identities=11%  Similarity=0.074  Sum_probs=43.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           14 DSLTDHERLIYDVIRSKQDMG-----------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~G-----------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ...+.++++..-+++-+...|           +.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       108 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          108 QTGELRARIARYLLFLADTPLSARDRQGIYVTVSHEEIADAT--ASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             TSSCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHTT--TSCHHHHHHHHHHHHHHTSEEE
T ss_pred             hcCCHHHHHHHHHHHHHHHcCCCCCCCeeeccCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            345678877776666443333           6899999999  9999999999999999999975

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=94.97  E-value=0.089  Score=41.88  Aligned_cols=51  Identities=20%  Similarity=0.272  Sum_probs=39.6

Q ss_pred             CChHHHHHHHHHHhhCC-------C----cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQD-------M----GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~-------~----GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++-+..       .    -+.+++|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       135 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  196 (207)
T 2oz6_A          135 LDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIV--GCSREMVGRVLKSLEEQGLVHV  196 (207)
T ss_dssp             CCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            45677765545443321       1    26899999999  9999999999999999999975

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=94.95  E-value=0.055  Score=41.63  Aligned_cols=63  Identities=13%  Similarity=0.204  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhh---c-CCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELR---V-NLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~---~-~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml~~   84 (233)
                      -+.+|+.+|.+.-   ..--+|.+.+.   . ++++.+|..+|+.||++|||.+....  ..+.||+|-|.+
T Consensus        14 l~~~IL~lL~~~p---~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~   82 (116)
T 3hhh_A           14 LEGLVLAIIQRKE---TYGYEITKILNDQGFTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTS   82 (116)
T ss_dssp             HHHHHHHHHHHSC---BCHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECH
T ss_pred             HHHHHHHHHhcCC---CCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECH
Confidence            3667888887533   44456666652   2 68999999999999999999987642  346788886543

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=94.81  E-value=0.15  Score=41.60  Aligned_cols=51  Identities=6%  Similarity=0.075  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCceeeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ....|+.++......-....+|....  . |.+.+|.+.|+.|++.|||+.+..
T Consensus        30 tR~~IL~~Ll~~p~~~~ta~eL~~~l--~~lS~aTVyrhL~~L~eaGLV~~~~~   81 (151)
T 3u1d_A           30 TRLDVLHQILAQPDGVLSVEELLYRN--PDETEANLRYHVDELVDRGIVEKIPV   81 (151)
T ss_dssp             HHHHHHHHHHHSTTSCBCHHHHHHHC--TTSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHhc--CCCCHHHHHHHHHHHHHCCCeEEeec
Confidence            45567888877754447889999888  7 999999999999999999998753

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=94.78  E-value=0.05  Score=43.19  Aligned_cols=65  Identities=23%  Similarity=0.245  Sum_probs=47.7

Q ss_pred             HHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           20 ERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        20 e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .-.++-+|.... +.-+..++|..+.  +++.+.|.|+|..|.+.|||++++..+    -=|.|.  .|.++||
T Consensus        13 Al~~L~~La~~~~~~~~s~~~IA~~~--~i~~~~l~kil~~L~~aGlv~s~rG~~----GGy~La--r~p~~It   78 (143)
T 3t8r_A           13 GLTLMISLAKKEGQGCISLKSIAEEN--NLSDLYLEQLVGPLRNAGLIRSVRGAK----GGYQLR--VPAEEIS   78 (143)
T ss_dssp             HHHHHHHHHTTTTSCCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECSSSS----SEEEES--SCGGGCB
T ss_pred             HHHHHHHHHhCCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCEEEecCCCC----CCeeec--CCcccCC
Confidence            334444555443 3459999999999  999999999999999999998765443    147665  4666666

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=94.74  E-value=0.055  Score=44.03  Aligned_cols=62  Identities=13%  Similarity=0.212  Sum_probs=46.2

Q ss_pred             CChHHHHHHHHHHhhCCCc------------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           16 LTDHERLIYDVIRSKQDMG------------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~G------------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      .+..+++..-+++-+...|            +.+.+|..-+  |++..+|+|+|+.|++.|+|+.      .+++++.+-
T Consensus       133 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~~t~~~lA~~l--G~sr~tvsR~l~~L~~~g~I~~------~~~~i~~i~  204 (222)
T 1ft9_A          133 HDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLI--GSSRQTTSTALNSLIKEGYISR------QGRGHYTIP  204 (222)
T ss_dssp             HHHHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHH--CSCHHHHHHHHHHHHHTTSSEE------CSTTCEECS
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEE------cCCceEEEc
Confidence            3456766666666553333            7899999999  9999999999999999999975      344545444


Q ss_pred             cc
Q 026799           84 EF   85 (233)
Q Consensus        84 ~l   85 (233)
                      |.
T Consensus       205 d~  206 (222)
T 1ft9_A          205 NL  206 (222)
T ss_dssp             SH
T ss_pred             CH
Confidence            43

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=94.74  E-value=0.11  Score=43.71  Aligned_cols=59  Identities=17%  Similarity=0.264  Sum_probs=44.9

Q ss_pred             CChHHHHHHHHHHhhCCC-----------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           16 LTDHERLIYDVIRSKQDM-----------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~-----------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+..+++..-+++-+...           -+.+.+|..-+  |++..+|+|+|+.|+++|+|+.      .++++.++
T Consensus       188 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~l~lt~~~lA~~l--G~sr~tvsR~l~~L~~~GlI~~------~~~~i~I~  257 (260)
T 3kcc_A          188 LLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIV--GCSRETVGRILKMLEDQNLISA------HGKTIVVY  257 (260)
T ss_dssp             CCHHHHHHHHHHHHHTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------CSSEEEEC
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCCceeecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEE------cCCEEEEE
Confidence            456777766666544332           25789999999  9999999999999999999975      34566553

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=94.61  E-value=0.051  Score=44.64  Aligned_cols=55  Identities=24%  Similarity=0.457  Sum_probs=47.6

Q ss_pred             CCCCChHHHHHHHHHHhh-CCCcc--cHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCceee
Q 026799           13 SDSLTDHERLIYDVIRSK-QDMGI--WTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~a-G~~GI--w~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~v   69 (233)
                      |+.||+.|+.+++.|.++ ...|+  .+++|.+++  |+. ++++++.++.|+++++|..-
T Consensus         1 m~~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~l--giss~~tv~~~~~~l~~~~~l~~~   59 (202)
T 1jhf_A            1 MKALTARQQEVFDLIRDHISQTGMPPTRAEIAQRL--GFRSPNAAEEHLKALARKGVIEIV   59 (202)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHT--TCSSHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHh--CCCChHHHHHHHHHHHHCCCceeC
Confidence            357999999999999876 45588  999999999  999 89999999999999988753

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=94.51  E-value=0.095  Score=38.90  Aligned_cols=46  Identities=4%  Similarity=0.114  Sum_probs=35.3

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +.++++|++++.+|++|+++.+        .+|+.-|+..|+.|+-.|+|.+++
T Consensus         5 ~~Il~~L~~~g~vsv~eLA~~l--------~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLALQGRMEAKQLSARL--------QTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHT--------TCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            3456666666666666666544        478899999999999999999986

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=94.40  E-value=0.15  Score=39.80  Aligned_cols=66  Identities=12%  Similarity=0.091  Sum_probs=52.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+.-..|++++.+++..-+...+|-..++   ++++..+|.|.|+.|++.|+|.++..-.  +...|-+
T Consensus        15 r~T~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~   83 (136)
T 1mzb_A           15 KVTLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDG--GHAVFEL   83 (136)
T ss_dssp             CCCHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSS--SSCEEEE
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCC--CceEEEe
Confidence            5788999999999976535689999988873   4799999999999999999999876544  3445644

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=94.38  E-value=0.16  Score=41.25  Aligned_cols=61  Identities=18%  Similarity=0.286  Sum_probs=46.1

Q ss_pred             HHHHhh-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           25 DVIRSK-QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        25 ~~I~~a-G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      -.|... ++.-+..++|..+.  +++.+.|.|+|..|.+.|||.+++-.+-    =|.|+  .|.++||=
T Consensus        34 ~~LA~~~~~~~~s~~eIA~~~--~i~~~~l~kil~~L~~aGlv~s~rG~~G----Gy~La--r~p~eItL   95 (159)
T 3lwf_A           34 LELAKRIGDGPISLRSIAQDK--NLSEHYLEQLIGPLRNAGIVKSIRGAHG----GYVLN--GDPEKITA   95 (159)
T ss_dssp             HHHHHTTTSCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECSTTC----EEEEC--SCTTTCBH
T ss_pred             HHHHhcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCeEEEecCCCC----ceEec--CCHHHCCH
Confidence            334433 34458999999999  9999999999999999999988755432    37665  46667663

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=94.24  E-value=1.4  Score=33.88  Aligned_cols=108  Identities=17%  Similarity=0.204  Sum_probs=70.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      +.++.+++.  .++... ..|...++|.+.+  +++.++|.+-++..++.|....                 .|    .+
T Consensus        31 ~~~s~e~r~--~iv~~~-~~G~s~~~iA~~l--gis~~TV~rw~~~~~~~G~~~~-----------------~~----r~   84 (149)
T 1k78_A           31 RPLPDVVRQ--RIVELA-HQGVRPCDISRQL--RVSHGCVSKILGRYYETGSIKP-----------------GV----IG   84 (149)
T ss_dssp             SCCCHHHHH--HHHHHH-HTTCCHHHHHHHH--TCCHHHHHHHHHHHHHHSCCCC-----------------CC----CC
T ss_pred             CCCCHHHHH--HHHHHH-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCCCc-----------------cC----CC
Confidence            457777653  233333 2578999999999  9999999999999988775321                 00    11


Q ss_pred             CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHH
Q 026799           94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVR  153 (233)
Q Consensus        94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~  153 (233)
                      |.  ....++.++.+.|.    .++......|+.+|...+...++.  .+.+|..-|..+|.
T Consensus        85 gr--~~~~~~~~~~~~I~----~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~  140 (149)
T 1k78_A           85 GS--KPKVATPKVVEKIA----EYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIR  140 (149)
T ss_dssp             CC--CCSSSCHHHHHHHH----HHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHH
T ss_pred             CC--CCCCCCHHHHHHHH----HHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHH
Confidence            20  12245666555544    444555678899999999776421  23578888877775

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=94.15  E-value=0.11  Score=39.84  Aligned_cols=63  Identities=14%  Similarity=0.174  Sum_probs=44.6

Q ss_pred             HHHHHHHhh-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           22 LIYDVIRSK-QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        22 lVy~~I~~a-G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .|+.+|..+ ++..+..++|..++  +++.+.|.|+|+.|++.|+|.+.+..    ..-|.|.  .|..+||
T Consensus        13 ~iL~~la~~~~~~~~s~~ela~~~--~i~~~~v~~il~~L~~~Glv~~~~g~----~ggy~L~--~~~~~it   76 (129)
T 2y75_A           13 TIMIELAKKHGEGPTSLKSIAQTN--NLSEHYLEQLVSPLRNAGLVKSIRGA----YGGYVLG--SEPDAIT   76 (129)
T ss_dssp             HHHHHHHHTTTSCCBCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEC--------CCEEES--SCGGGCB
T ss_pred             HHHHHHHhCCCCCcCCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEecCCC----CCceEeC--CCHHHCc
Confidence            445555554 35669999999999  99999999999999999999765421    1346654  2445555

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=94.07  E-value=0.058  Score=43.56  Aligned_cols=60  Identities=13%  Similarity=0.300  Sum_probs=42.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHh----hc-CCChHHHHHHHHHHHhCCCceeeeccc---CCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWTRDMKREL----RV-NLPDNIVTKSIKSLQNKSLIKEVVNIH---SKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t----~~-~l~~~~v~k~LK~Le~k~lIK~vksV~---~~~rK~Yml~~   84 (233)
                      +|+.+|.+..   ..--+|.+.+    +. +++..+|..+|++||++|||.+.....   .+.||+|-|.+
T Consensus        48 ~IL~lL~~~p---~~GYeI~k~l~~~~~~~~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~  115 (148)
T 2zfw_A           48 YVLAVLRHED---SYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQ  115 (148)
T ss_dssp             HHHHHHTTCC---EEHHHHHHHHHHHCTTEECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESS
T ss_pred             HHHHHHHhCC---CcHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECH
Confidence            4788886533   4434444443    11 699999999999999999999876542   46788886654

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=93.91  E-value=0.098  Score=42.04  Aligned_cols=51  Identities=14%  Similarity=0.199  Sum_probs=40.4

Q ss_pred             CChHHHHHHHHHHhhCC-----CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQD-----MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~-----~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++.+..     --+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       146 ~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          146 KSLDKRVASFLLEETSIEGTNELKITHETIANHL--GSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             SCHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhhhhcCCceecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            45566666655554432     248999999999  9999999999999999999964

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=93.90  E-value=0.26  Score=38.81  Aligned_cols=64  Identities=14%  Similarity=0.203  Sum_probs=52.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+.-..|++++.++ +.-+...+|-..++   ++++..+|.|.|+.|++.|||.++..-.  +...|-
T Consensus        19 r~T~qR~~Il~~L~~~-~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~   85 (145)
T 2fe3_A           19 RITPQRHAILEYLVNS-MAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGD--ASSRFD   85 (145)
T ss_dssp             CCCHHHHHHHHHHHHC-SSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTT--SCCEEE
T ss_pred             CCCHHHHHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCC--CceEEE
Confidence            5788999999999875 44699999999883   3799999999999999999999887644  344564

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=93.82  E-value=0.13  Score=42.55  Aligned_cols=60  Identities=12%  Similarity=0.198  Sum_probs=45.8

Q ss_pred             CCChHHHHHHHHHHh---hC---------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRS---KQ---------DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~---aG---------~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ..+.++++..-+++-   .|         .--+.+.+|..-+  |++..+|+|+|+.|+++|+|+.      .++++.++
T Consensus       146 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~iA~~l--G~sr~tvsR~l~~L~~~g~I~~------~~~~i~i~  217 (250)
T 3e6c_C          146 TYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEIT--GVHHVTVSRVLASLKRENILDK------KKNKIIVY  217 (250)
T ss_dssp             TSCHHHHHHHHHHHHHHHHCEEETTEEEEECCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------CSSEEEES
T ss_pred             cCCHHHHHHHHHHHHHHHhCCCCCCCcEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCeEe------CCCEEEEe
Confidence            456677766555543   33         1246899999999  9999999999999999999976      35666665

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=93.79  E-value=0.094  Score=42.57  Aligned_cols=51  Identities=8%  Similarity=0.150  Sum_probs=39.6

Q ss_pred             CChHHHHHHHHHHhh---CC---C------cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSK---QD---M------GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~a---G~---~------GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++-+   |.   .      -+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       147 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          147 TDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLV--GASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             SCHHHHHHHHHHHHHHHHEEEETTEEEEECCCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHHhCCcCCCceEEcCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence            456676655454432   21   1      26899999999  9999999999999999999975

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=93.68  E-value=0.27  Score=39.08  Aligned_cols=66  Identities=12%  Similarity=0.130  Sum_probs=53.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+.-..|+.+|.+++..-+...+|-..++   +++...+|.|.|+.|++.|+|.++..-.  +...|-+
T Consensus        14 r~T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~   82 (150)
T 2w57_A           14 KVTLPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEG--GKSVFEL   82 (150)
T ss_dssp             CCCHHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGG--GCEEEEE
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCC--CceEEEe
Confidence            5788999999999877535689999998873   4899999999999999999999886544  3445643

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=93.63  E-value=0.11  Score=43.10  Aligned_cols=51  Identities=14%  Similarity=0.151  Sum_probs=40.2

Q ss_pred             CChHHHHHHHHHHhhC------C------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQ------D------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG------~------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.++++..-+++-+.      .      --+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       163 ~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~l--G~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          163 RDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAI--GSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             SSHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEE
Confidence            4567776655554332      1      236899999999  9999999999999999999975

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=93.61  E-value=0.1  Score=42.19  Aligned_cols=50  Identities=12%  Similarity=0.209  Sum_probs=39.3

Q ss_pred             ChHHHHHHHHHHhh---CC---------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           17 TDHERLIYDVIRSK---QD---------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        17 ~~~e~lVy~~I~~a---G~---------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.++++..-+++.+   |.         -.+.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       138 ~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          138 DARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALML--GTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEE
Confidence            45666655554433   21         247899999999  9999999999999999999975

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=93.56  E-value=0.074  Score=41.23  Aligned_cols=74  Identities=15%  Similarity=0.167  Sum_probs=48.8

Q ss_pred             CCCCCCCCCCCCCCCChHHHHHHHHHH--hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeee
Q 026799            2 SKRKRPDSNAPSDSLTDHERLIYDVIR--SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKH   79 (233)
Q Consensus         2 ~~~~~~~~~~~~~~L~~~e~lVy~~I~--~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~   79 (233)
                      ||-|..|...-.--++   .-.|+-|.  --..+=|+...|..++  ++.-+.-+++|+.|+++|+|+.|.  +|.+..+
T Consensus        28 sKgk~kdK~nn~VlfD---k~t~dkl~KEVpk~KlITpsvlseRl--kI~gSLAR~aLreL~~kGlIk~V~--kh~~q~I  100 (108)
T 3u5c_Z           28 SKKSMKDRAQHAVILD---QEKYDRILKEVPTYRYVSVSVLVDRL--KIGGSLARIALRHLEKEGIIKPIS--KHSKQAI  100 (108)
T ss_dssp             --------CCSCSSCT---THHHHHHHHHCSSCSSBSHHHHHHTT--CCCTTHHHHHHHHHSSSSSCEEEE--CCSSCCE
T ss_pred             ccccHHHHhhcceeeC---HHHHHHHHHHccCCeEEeHHHhhhhh--hhhHHHHHHHHHHHHHCCCEEEEe--cCCCEEE
Confidence            3444444433333333   34454443  2334569999999999  999999999999999999999984  6678889


Q ss_pred             EEe
Q 026799           80 LMA   82 (233)
Q Consensus        80 Yml   82 (233)
                      |--
T Consensus       101 YTr  103 (108)
T 3u5c_Z          101 YTR  103 (108)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            953

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=93.51  E-value=0.98  Score=34.84  Aligned_cols=53  Identities=25%  Similarity=0.365  Sum_probs=40.2

Q ss_pred             HHHHHHHhhCC-------Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           22 LIYDVIRSKQD-------MGI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        22 lVy~~I~~aG~-------~GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .||+.|...=.       .=+ ..++|..+.  ++..++|+++|+.|+..|||...     +++-+|+
T Consensus        18 QI~~~i~~~I~~G~l~pG~~LPser~La~~~--gVSr~tVReAl~~L~~eGlv~~~-----~g~G~~V   78 (134)
T 4ham_A           18 QIVQKIKEQVVKGVLQEGEKILSIREFASRI--GVNPNTVSKAYQELERQEVIITV-----KGKGTFI   78 (134)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEE
T ss_pred             HHHHHHHHHHHcCCCCCCCCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE-----cCcEEEE
Confidence            56777765311       124 678999999  99999999999999999999764     3455555

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=93.48  E-value=0.22  Score=40.49  Aligned_cols=51  Identities=6%  Similarity=0.081  Sum_probs=40.5

Q ss_pred             CChHHHHHHHHHH---hhC--------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIR---SKQ--------DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~---~aG--------~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+..+++..-+++   ..|        .--+.+++|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       151 ~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          151 KHVRGRLAETLLILKENFGFENDGATLSIYLSREELATLS--NMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             SCHHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHHHHcCCCCCCcEEEcccCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEee
Confidence            4567776655544   333        1347899999999  9999999999999999999975

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=93.48  E-value=0.15  Score=43.36  Aligned_cols=45  Identities=16%  Similarity=0.200  Sum_probs=38.6

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .|+.++.+.+ .++...||.+++  +|+.+++.|.|+.|++.|+|...
T Consensus        12 ~iL~~l~~~~-~~~~~~ela~~~--gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           12 EILDFIVKNP-GDVSVSEIAEKF--NMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHHCS-SCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHhCC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEC
Confidence            4666666543 479999999999  99999999999999999999764

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=93.44  E-value=0.038  Score=42.89  Aligned_cols=46  Identities=15%  Similarity=0.206  Sum_probs=41.0

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           33 MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        33 ~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +=|+...|..++  ++.-+.-+++|+.|+++|+|+.|  ++|.+..+|--
T Consensus        59 KlITpsvlseRl--kI~gSLAR~aLreL~~kGlIk~V--~kh~~q~IYTr  104 (108)
T 3iz6_V           59 KQITPSVLSERL--RINGSLARQAIKDLESRGAIRVV--SVHSSQLIYTR  104 (108)
T ss_dssp             SSEEEHHHHHHH--HTCCHHHHHHHHHHHHHHTSCEE--CCCTTSCCEEE
T ss_pred             eEEeHHHHHhhh--cccHHHHHHHHHHHHHCCCEEEE--ecCCCEEEEec
Confidence            458999999999  99999999999999999999998  46778889953

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=93.44  E-value=0.15  Score=43.38  Aligned_cols=45  Identities=20%  Similarity=0.360  Sum_probs=38.2

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .|+.++.+.+ .++...+|.+++  +|+.+++.|.|+.|++.|+|...
T Consensus        10 ~iL~~l~~~~-~~~s~~ela~~~--gl~~stv~r~l~~L~~~G~v~~~   54 (241)
T 2xrn_A           10 SIMRALGSHP-HGLSLAAIAQLV--GLPRSTVQRIINALEEEFLVEAL   54 (241)
T ss_dssp             HHHHHHHTCT-TCEEHHHHHHHT--TSCHHHHHHHHHHHHTTTSEEEC
T ss_pred             HHHHHHHhCC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            3556665443 479999999999  99999999999999999999774

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=93.41  E-value=0.84  Score=35.74  Aligned_cols=113  Identities=16%  Similarity=0.191  Sum_probs=72.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCccc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISG   93 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTG   93 (233)
                      +.++.+++.-  ++... ..|...++|.+.+  +++.++|.+-++..++.|....                 .|    .+
T Consensus        24 ~~~s~e~r~~--ii~l~-~~G~s~~~IA~~l--gis~~TV~rwl~r~~~~G~~~~-----------------~~----r~   77 (159)
T 2k27_A           24 RPLPEVVRQR--IVDLA-HQGVRPCDISRQL--RVSHGCVSKILGRYYETGSIRP-----------------GV----IG   77 (159)
T ss_dssp             CSSCHHHHHH--HHHHH-HHTCCHHHHHHHH--TCCSHHHHHHHCCSSTTSCCCC-----------------CC----CC
T ss_pred             CCCCHHHHHH--HHHHH-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHhcCCccC-----------------CC----CC
Confidence            3567766532  22222 2578999999999  9999999999998776665321                 00    02


Q ss_pred             CCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHHHHhcC
Q 026799           94 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRALVLD  158 (233)
Q Consensus        94 G~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~~Lv~D  158 (233)
                      |.  ....++.++.+.|    ..++......|+.+|.+.+.+.++.  .+.+|..-|..+|....-.
T Consensus        78 gr--~~~~~~~~~~~~I----~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~  138 (159)
T 2k27_A           78 GS--KPKVATPKVVEKI----GDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQ  138 (159)
T ss_dssp             CC--CCCCCCTTHHHHH----HHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCC
T ss_pred             CC--CCCCCCHHHHHHH----HHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCC
Confidence            20  0123344444443    3444556678999999999877642  2468999999999876543

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=93.32  E-value=0.3  Score=38.77  Aligned_cols=64  Identities=9%  Similarity=0.151  Sum_probs=51.9

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+.-..|++++.+++. -+...+|-..++   ++++..+|-|.|+.|++.|+|.++..-.  +...|-
T Consensus        24 r~T~qR~~IL~~l~~~~~-~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~   90 (150)
T 2xig_A           24 KNSKQREEVVSVLYRSGT-HLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSK--SGRRYE   90 (150)
T ss_dssp             -CHHHHHHHHHHHHHCSS-CBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETT--TEEEEE
T ss_pred             CCCHHHHHHHHHHHhCCC-CCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCC--CceEEE
Confidence            467888899999988743 789999988873   4899999999999999999999887655  445564

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=93.29  E-value=0.25  Score=39.09  Aligned_cols=64  Identities=17%  Similarity=0.244  Sum_probs=52.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -.+|+.-+.|++++.+++  -+...+|-.+++   +++...+|-|.|+.|++.|+|.++..-.  +...|-
T Consensus        15 ~r~T~qR~~Il~~l~~~~--h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~--~~~~Y~   81 (145)
T 3eyy_A           15 YRLTPQRQLVLEAVDTLE--HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGH--GAPTYH   81 (145)
T ss_dssp             CCCCHHHHHHHHHHHHHS--SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGG--GCEEEE
T ss_pred             CCcCHHHHHHHHHHHhcC--CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCC--CceEEE
Confidence            357888899999999886  699999988773   3789999999999999999999987644  334453

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=93.21  E-value=0.16  Score=40.71  Aligned_cols=50  Identities=10%  Similarity=0.254  Sum_probs=38.4

Q ss_pred             ChHHHHHHHHHHhh--C---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           17 TDHERLIYDVIRSK--Q---DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        17 ~~~e~lVy~~I~~a--G---~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +..+++..-+++-+  |   .--+.+++|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       141 ~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          141 EARNRVAYALLKLLRQGLGPLFQIRHHELAALA--GTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHHhhcCCccCCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            34555555554432  2   2336899999999  9999999999999999999974

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=93.19  E-value=0.13  Score=41.77  Aligned_cols=32  Identities=16%  Similarity=0.319  Sum_probs=30.5

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.+++|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       176 ~t~~~iA~~l--g~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          176 LGTQDIMART--SSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEe
Confidence            6899999999  9999999999999999999975

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=93.02  E-value=1.2  Score=32.44  Aligned_cols=107  Identities=19%  Similarity=0.200  Sum_probs=67.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      .++.+++.-  ++... ..|...++|.+.+  +++.++|.+.++...+.|....-                 |    .+|
T Consensus        17 ~~s~~~r~~--i~~~~-~~g~s~~~ia~~l--gis~~Tv~~w~~~~~~~g~~~~~-----------------~----~~g   70 (128)
T 1pdn_C           17 PLPNNIRLK--IVEMA-ADGIRPCVISRQL--RVSHGCVSKILNRYQETGSIRPG-----------------V----IGG   70 (128)
T ss_dssp             CCCHHHHHH--HHHHH-HTTCCHHHHHHHH--TCCHHHHHHHHHHHHHHCCSSCC-----------------C----CSC
T ss_pred             cCCHHHHHH--HHHHH-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHhhCCcccc-----------------c----CCC
Confidence            577766532  23322 2578999999999  99999999999999887753210                 0    011


Q ss_pred             CcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCc--ccccCHHHHHHHHH
Q 026799           95 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVR  153 (233)
Q Consensus        95 ~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~--~~~Ls~~di~~il~  153 (233)
                      .  ....++.++.+    .+..++...+..|+.+|...+.+.|+.  ....|..-|..+|.
T Consensus        71 ~--~~~~l~~~~~~----~i~~~~~~~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~  125 (128)
T 1pdn_C           71 S--KPRIATPEIEN----RIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVR  125 (128)
T ss_dssp             C--CCCSSCSTHHH----HHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC-
T ss_pred             C--CCCcCCHHHHH----HHHHHHHhCcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHH
Confidence            0  01233433333    344555566678999999999877752  11467777776664

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=92.98  E-value=0.22  Score=36.45  Aligned_cols=47  Identities=28%  Similarity=0.388  Sum_probs=38.9

Q ss_pred             CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      .....||+.|+.|+.++.    .|...++|...+  +++.++|...++.+-.|
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L--~iS~~TV~~~~~~i~~K   71 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE----KGFTNQEIADAL--HLSKRSIEYSLTSIFNK   71 (90)
T ss_dssp             ----CCCHHHHHHHHHHH----TTCCHHHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence            356789999999999986    689999999999  99999999999887653

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=92.93  E-value=0.19  Score=42.68  Aligned_cols=52  Identities=13%  Similarity=0.130  Sum_probs=39.4

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ++....-.+.+|... +..+-+++|.+++  ++..++|+..||.|+++|||..-+
T Consensus        13 ls~s~EdYLk~I~~L-~~~V~~~~LA~~L--gvS~~SV~~~lkkL~e~GLV~~~~   64 (200)
T 2p8t_A           13 PEYTVEDVLAVIFLL-KEPLGRKQISERL--ELGEGSVRTLLRKLSHLDIIRSKQ   64 (200)
T ss_dssp             -CCCHHHHHHHHHHT-TSCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCCCHHHHHHHHHHH-cCCccHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence            444333344445544 4679999999999  999999999999999999996633

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=92.82  E-value=0.18  Score=44.45  Aligned_cols=49  Identities=14%  Similarity=0.293  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce-ee
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK-EV   69 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK-~v   69 (233)
                      +++++..+..-.-..|+.+++|.+++  +++..+|+|-|+.|+++|+|+ ++
T Consensus         6 ~~~~~~~ia~l~~~~~~~~~ela~~l--~vS~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A            6 DIRLIVKIAQLYYEQDMTQAQIAREL--GIYRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEEe
Confidence            56677777776777889999999999  999999999999999999997 55

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=92.76  E-value=0.33  Score=32.85  Aligned_cols=46  Identities=20%  Similarity=0.323  Sum_probs=39.3

Q ss_pred             CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      .....||+.|+.|+.++    ..|...++|...+  |++.++|.+.++.+..
T Consensus         7 ~~~~~L~~~e~~il~~~----~~g~s~~eIA~~l--~is~~tV~~~~~~~~~   52 (74)
T 1fse_A            7 QSKPLLTKREREVFELL----VQDKTTKEIASEL--FISEKTVRNHISNAMQ   52 (74)
T ss_dssp             -CCCCCCHHHHHHHHHH----TTTCCHHHHHHHH--TSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH----HcCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            35778999999999886    3578999999999  9999999999988664

>1bm9_A RTP, TER, replication terminator protein; DNA-binding protein, contrahelicase; 2.00A {Bacillus subtilis} SCOP: a.4.5.7 PDB: 1f4k_A 1j0r_A 2dpd_A 2dpu_A 2efw_A* 2dqr_A

Probab=92.74  E-value=0.55  Score=36.96  Aligned_cols=84  Identities=11%  Similarity=0.105  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHH-HHHH-h--hcCCChHHHHHHHHHHHhCCCceeeecc-cCC
Q 026799            1 MSKRKRPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRD-MKRE-L--RVNLPDNIVTKSIKSLQNKSLIKEVVNI-HSK   75 (233)
Q Consensus         1 ~~~~~~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~d-ik~~-t--~~~l~~~~v~k~LK~Le~k~lIK~vksV-~~~   75 (233)
                      |-++||...+=-++.+.=-...|+.++.+.---|-|..+ |+.+ +  +-.+++.+|-.+|..||++|++++.... ..+
T Consensus         1 ~~~~~~~~~~~~~~~~~fl~l~IL~ll~~~p~YGYeI~~~L~e~~~~~~~~is~gtlYp~L~rLe~~Gll~~~~~~~~g~   80 (122)
T 1bm9_A            1 MKEEKRSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGA   80 (122)
T ss_dssp             --CCSCCCCSSSCCHHHHHHHHHHHHHHTTCCBSTTHHHHHHHHHTTTTCCCCHHHHHHHHHHHHHTTSEEEEEEECTTS
T ss_pred             CcccccCCchhHHHHHHHHHHHHHHHHccCCchHHHHHHHHHHhhccCcccCCcccHHHHHHHHHHCCCeEEEEeecCCC
Confidence            445666666655555555678899999988888888765 4443 2  3389999999999999999999998874 233


Q ss_pred             Ce---eeEEeec
Q 026799           76 GK---KHLMAVE   84 (233)
Q Consensus        76 ~r---K~Yml~~   84 (233)
                      .+   |+|-+.+
T Consensus        81 ~r~~rkyY~lT~   92 (122)
T 1bm9_A           81 KLQEVVLYQFKD   92 (122)
T ss_dssp             TTCEEEEEEESC
T ss_pred             CCCceeEEEECh
Confidence            33   7776554

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=92.73  E-value=0.21  Score=40.25  Aligned_cols=50  Identities=8%  Similarity=0.201  Sum_probs=39.0

Q ss_pred             ChHHHHHHHHHHhhCC---------CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           17 TDHERLIYDVIRSKQD---------MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~---------~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +..+++..-+++.+..         --+.+++|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       152 ~~~~Rl~~~L~~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  210 (227)
T 3dkw_A          152 NATHRVVRYLLTLAAHAPGENCRVEIPVAKQLVAGHL--SIQPETFSRIMHRLGDEGIIHL  210 (227)
T ss_dssp             HHHHHHHHHHHHHHCSSSSSCCCCCCCSCTHHHHHHT--TSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CHHHHHHHHHHHhhhhcCCCCeEEEecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCcEEe
Confidence            3456665555554432         246789999999  9999999999999999999975

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=92.61  E-value=0.23  Score=44.62  Aligned_cols=48  Identities=15%  Similarity=0.212  Sum_probs=42.3

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL   65 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l   65 (233)
                      |++-.+.|++++.++.+.-+.-.+|..++  +++.+.|.|.++.|++.|+
T Consensus         1 M~~~~~~iL~~L~~~~g~~~Sg~eLa~~l--gvSr~aV~k~i~~L~~~G~   48 (323)
T 3rkx_A            1 MSKYSQDVLQLLYKNKPNYISGQSIAESL--NISRTAVKKVIDQLKLEGC   48 (323)
T ss_dssp             --CHHHHHHHHHHHHTTSCBCHHHHHHHH--TSCHHHHHHHHHHHHHTTC
T ss_pred             CchHHHHHHHHHHhCCCCccCHHHHHHHH--CCCHHHHHHHHHHHHhcCC
Confidence            44566789999988777779999999999  9999999999999999999

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=92.60  E-value=0.059  Score=46.45  Aligned_cols=46  Identities=11%  Similarity=0.204  Sum_probs=38.5

Q ss_pred             HHHHHHHhh--CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSK--QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~a--G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..+.+++.-  .+.++...||.+++  +|+..++.|.|+.|++.|+|...
T Consensus        24 r~l~iL~~l~~~~~~~~~~eia~~~--gl~kstv~r~l~tL~~~G~v~~~   71 (260)
T 2o0y_A           24 RVIDLLELFDAAHPTRSLKELVEGT--KLPKTTVVRLVATMCARSVLTSR   71 (260)
T ss_dssp             HHHHHHTTCBTTBSSBCHHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhhCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEC
Confidence            455565542  34689999999999  99999999999999999999763

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=92.46  E-value=0.19  Score=30.79  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=34.6

Q ss_pred             CCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCC
Q 026799           14 DSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKS   64 (233)
Q Consensus        14 ~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~   64 (233)
                      ..|+++++ .|+.+.    ..|+..++|.+.+  +++.++|.+.++..++.|
T Consensus         4 ~~l~~~~~~~i~~~~----~~g~s~~~IA~~l--gis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C            4 SALSDTERAQLDVMK----LLNVSLHEMSRKI--SRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             CCCCHHHHHHHHHHH----HTTCCHHHHHHHH--TCCHHHHHHHHHCSTTTT
T ss_pred             CCCCHHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHhhHHhcC
Confidence            35777776 444443    3578999999999  999999999998776554

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=92.40  E-value=0.31  Score=38.28  Aligned_cols=65  Identities=9%  Similarity=0.125  Sum_probs=52.3

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .+|+.-+.|++++.+++. -+...+|-..++   +++...+|-|.|+.|++.|+|.++..-.  +...|-+
T Consensus        11 r~T~qR~~Il~~L~~~~~-h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--g~~~Y~~   78 (139)
T 3mwm_A           11 RATRQRAAVSAALQEVEE-FRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAE--GESVYRR   78 (139)
T ss_dssp             HHHHHHHHHHHHHTTCSS-CEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTT--SCEEEEC
T ss_pred             ccCHHHHHHHHHHHhCCC-CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CceEEEE
Confidence            467788899999988754 799999988873   4799999999999999999999887633  4455643

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=92.40  E-value=0.28  Score=37.95  Aligned_cols=57  Identities=18%  Similarity=0.214  Sum_probs=48.2

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      +|+.-..|++++.++ +.-+...+|-..++   ++++..+|-|.|+.|++.|+|.++..-.
T Consensus         9 ~T~qR~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~   68 (131)
T 2o03_A            9 STRQRAAISTLLETL-DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDT   68 (131)
T ss_dssp             HHHHHHHHHHHHHHC-CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTT
T ss_pred             CCHHHHHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCC
Confidence            567778899999875 44689999988873   4899999999999999999999887654

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=92.39  E-value=0.23  Score=39.26  Aligned_cols=63  Identities=11%  Similarity=0.062  Sum_probs=45.3

Q ss_pred             HHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           23 IYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        23 Vy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      ++-+|...++.-+..++|..++  +++.+.|.|+|..|.+.|||.+++- +    --|.|.  .|.++||=|
T Consensus        19 ~L~~La~~~~~~~~~~~iA~~~--~i~~~~l~kil~~L~~~Glv~s~rG-~----GGy~L~--~~p~~Itl~   81 (149)
T 1ylf_A           19 ILSILKNNPSSLCTSDYMAESV--NTNPVVIRKIMSYLKQAGFVYVNRG-P----GGAGLL--KDLHEITLL   81 (149)
T ss_dssp             HHHHHHHSCGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CCEEES--SCGGGCBHH
T ss_pred             HHHHHHhCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEccC-C----CceEeC--CChhhCcHH
Confidence            3334444344458999999999  9999999999999999999987665 2    246664  456677744

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=91.92  E-value=0.52  Score=38.04  Aligned_cols=56  Identities=9%  Similarity=0.191  Sum_probs=47.6

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHh-----hcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKREL-----RVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t-----~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .+|+.-+.|++++.+++ .-+...+|-..+     ++++...+|-|.|+.|++.|+|.++..
T Consensus        30 r~T~qR~~IL~~L~~~~-~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~   90 (162)
T 4ets_A           30 KYTKQREVLLKTLYHSD-THYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISF   90 (162)
T ss_dssp             CCCHHHHHHHHHHHSCC-SCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC-
T ss_pred             CCCHHHHHHHHHHHhCC-CCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEe
Confidence            57888899999999875 578899887765     347999999999999999999988754

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=91.88  E-value=0.3  Score=34.72  Aligned_cols=50  Identities=24%  Similarity=0.395  Sum_probs=40.2

Q ss_pred             CCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799            8 DSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus         8 ~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      .....+..||+.|+.|+.++    -.|...++|...+  +++.++|.+.++.+.+|
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l~----~~g~s~~eIA~~l--~is~~tV~~~l~r~~~k   63 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKLI----AQGLPNKMIARRL--DITESTVKVHVKHMLKK   63 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHHH----TTTCCHHHHHHHH--TSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence            34456778999999999885    3679999999999  99999999888876543

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=91.87  E-value=0.3  Score=44.14  Aligned_cols=51  Identities=16%  Similarity=0.286  Sum_probs=45.5

Q ss_pred             CChHHHHHHH-----HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYD-----VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~-----~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      |++-++.|++     +|+.++.  +-.++|.++.+.++++.+|++-|+.||++|+|++
T Consensus        15 l~eR~~~IL~~i~~~yl~~~~p--V~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r   70 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIENKKP--VSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ   70 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSC--BCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHHHHHHHHHHcCCC--ccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            7888889999     7888888  9999999987447789999999999999999976

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=91.65  E-value=0.42  Score=38.85  Aligned_cols=51  Identities=8%  Similarity=0.026  Sum_probs=40.3

Q ss_pred             CCCCChHHHHHHHHHHhhCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMG--------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSL   65 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~G--------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~l   65 (233)
                      +...+..+++..-+++-+...|        +.+++|..-+  |++..+|+|+|+.|++.|+
T Consensus       149 l~~~~~~~Rl~~~L~~~~~~~~~~~~~~l~~t~~~iA~~l--g~sr~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          149 LKAQTGAQRVAEFLLELCDCDTGACEVTLPYDKMLIAGRL--GMKPESLSRAFSRLKAAGV  207 (237)
T ss_dssp             CCCCCHHHHHHHHHHHHCCC-----EEECCSCTHHHHHHT--TCCHHHHHHHHHHHGGGTE
T ss_pred             HhcCCHHHHHHHHHHHHhhhcCCCeEEEecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCe
Confidence            3456778888777776554332        5589999999  9999999999999999994

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=91.65  E-value=0.56  Score=32.84  Aligned_cols=53  Identities=6%  Similarity=0.091  Sum_probs=45.2

Q ss_pred             HHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          111 KSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       111 ~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      +..++.+|...  +.+|++||++.+++.+.   .++..=|...|+.|+-.|.|.++..
T Consensus        19 r~~IL~~l~~~~~~~~s~~el~~~l~~~~~---~is~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             HHHHHHHHTSGGGSSBCHHHHHHHHHHTTC---CCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHhCC---CCCHhhHHHHHHHHHHCCCeEEEee
Confidence            45688888765  68999999999988762   5889999999999999999998863

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=91.65  E-value=1.4  Score=38.00  Aligned_cols=105  Identities=12%  Similarity=0.232  Sum_probs=75.5

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCCCCCHHHHHHHH
Q 026799           32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEGSLDTEFIKVVK  111 (233)
Q Consensus        32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~e~D~efI~~l~  111 (233)
                      ..||...+|+.+....++...+...|..|++.|.|+....       .+-+.+.+             -.|+.+. +.+.
T Consensus        85 ~~G~~~~~L~~~~~~~~~~~l~~~ll~~l~~~g~l~~~~~-------~v~l~~h~-------------~~~~~~~-~~~~  143 (258)
T 1lva_A           85 RPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAAN-------TVALAGFT-------------PSFSETQ-KKLL  143 (258)
T ss_dssp             SSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEETT-------EEEETTCC-------------CCCCHHH-HHHH
T ss_pred             ccCCCHHHHHHhccccCCHHHHHHHHHHHHHCCCEEecCC-------EEeCCCCc-------------cCCCHHH-HHHH
Confidence            4789999999998435899999999999999999865322       11111111             2455544 5666


Q ss_pred             HHHHHHhhhCC--CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          112 SQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       112 ~~~~~~i~~~~--~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +.+...+.+.+  .|++.|+.+-   .     .+..++++.+|+.|+-.|.|.++.
T Consensus       144 ~~i~~~~~~~g~~pp~~~dl~~~---l-----~~~~~~~~~~l~~l~~~g~lv~l~  191 (258)
T 1lva_A          144 KDLEDKYRVSRWQPPSFKEVAGS---F-----NLDPSELEELLHYLVREGVLVKIN  191 (258)
T ss_dssp             HHHHHHHHHHTTSCCBHHHHHHH---T-----TCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             HHHHHHHHHCCCCCCCHHHHHhH---h-----CCCHHHHHHHHHHHHHCCCEEEec
Confidence            67777676655  5677776643   2     378899999999999999998875

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=91.56  E-value=0.036  Score=45.06  Aligned_cols=51  Identities=14%  Similarity=0.263  Sum_probs=0.4

Q ss_pred             CChHHHHHHHHHHhhCCCc-----ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQDMG-----IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~G-----Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.++++..-+++.+...|     +.+.+|..-+  |++..+|+|+|+.|+++|+|+.
T Consensus       141 ~~~~~Rl~~~L~~~~~~~g~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~G~I~~  196 (213)
T 1o5l_A          141 KTLREKLMNFLVRHMNEKRELTLPVTLEELSRLF--GCARPALSRVFQELEREGYIEK  196 (213)
T ss_dssp             C---------------------------------------------------------
T ss_pred             CCHHHHHHHHHHHHhccCCcccCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCeEEE
Confidence            4556666665555554433     7899999999  9999999999999999999965

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A

Probab=91.55  E-value=0.57  Score=33.60  Aligned_cols=61  Identities=11%  Similarity=0.237  Sum_probs=48.6

Q ss_pred             CCChH-HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHH-HHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           15 SLTDH-ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNI-VTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        15 ~L~~~-e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~-v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      .|++. |..||++++++|.  -..-.|.+.+  ||-... |+..|=.|++++|+.-     +.+.++|.+|.
T Consensus         6 qls~~~ee~I~~fL~~~Gp--~~AL~IAK~L--GlktAK~VNp~LY~m~~~~lL~~-----Dek~~~W~iy~   68 (72)
T 3eyi_A            6 QFSQQREEDIYRFLKDNGP--QRALVIAQAL--GMRTAKDVNRDLYRMKSRHLLDM-----DEQSKAWTIYR   68 (72)
T ss_dssp             CCSSHHHHHHHHHHHHHCS--EEHHHHHHHT--TCCSGGGTHHHHHHHHHTTSEEE-----CTTTCEEEEC-
T ss_pred             hhhhhhHHHHHHHHHHcCC--chHHHHHHHh--CcchhhhcCHHHHHHHHccCcCC-----CCCCCceeEEE
Confidence            46664 7899999999998  6677899999  998775 9999999999999932     34566777664

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=91.50  E-value=0.69  Score=31.29  Aligned_cols=48  Identities=6%  Similarity=0.042  Sum_probs=38.9

Q ss_pred             CCCCCChHHHHHHHHHH-hhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026799           12 PSDSLTDHERLIYDVIR-SKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ   61 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~-~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le   61 (233)
                      .+..||+.|+.|+.+.. -.|-.|...++|...+  |++..+|.+.+...-
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~l--gis~~tV~~~~~ra~   50 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQF--DVTRERIRQIEAKAL   50 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHH--TCCHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHH
Confidence            36789999999988776 3445799999999999  999998887666543

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=91.49  E-value=0.33  Score=38.17  Aligned_cols=62  Identities=13%  Similarity=0.095  Sum_probs=46.1

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      .++-+|....+ + ..++|..+.  ++|.+.|.|+|..|.+.|||.+++- + .   =|.|+  .|.++||=|
T Consensus        13 ~~L~~La~~~~-~-s~~~IA~~~--~i~~~~l~kIl~~L~~aGlv~s~rG-~-G---Gy~La--r~p~~Itl~   74 (145)
T 1xd7_A           13 HILSLISMDEK-T-SSEIIADSV--NTNPVVVRRMISLLKKADILTSRAG-V-P---GASLK--KDPADISLL   74 (145)
T ss_dssp             HHHHHHHTCSC-C-CHHHHHHHH--TSCHHHHHHHHHHHHHTTSEECCSS-S-S---SCEES--SCGGGCBHH
T ss_pred             HHHHHHHhCCC-C-CHHHHHHHH--CcCHHHHHHHHHHHHHCCceEeecC-C-C---Cceec--CCHHHCCHH
Confidence            34444554444 5 999999999  9999999999999999999988765 3 2   36664  456666633

>2v9v_A Selenocysteine-specific elongation factor; transcription, protein conformational change, transcription elongation factor SELB; 1.10A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35

Probab=91.46  E-value=3.6  Score=31.11  Aligned_cols=111  Identities=8%  Similarity=0.073  Sum_probs=82.5

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccC
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSE   99 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d   99 (233)
                      +..|-.++..++.. +...+|...+  +++..++...|..|...+-|..+..   .....|                   
T Consensus         4 ~~~l~~~L~~~~~~-~~~~~l~~~~--~l~~~~l~~~l~~l~~~~~~~~~~~---~~~~~~-------------------   58 (135)
T 2v9v_A            4 EKILAQIIQEHREG-LDWQEAATRA--SLSLEETRKLLQSMAAAGQVTLLRV---ENDLYA-------------------   58 (135)
T ss_dssp             HHHHHHHHHHCSSC-EEHHHHHHHH--TCCHHHHHHHHHHHHHTTCEEEEEE---TTEEEE-------------------
T ss_pred             HHHHHHHHHHcCcC-CCHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEEec---CCCeEE-------------------
Confidence            34567778777765 5559999999  9999999999999998777655432   011112                   


Q ss_pred             CCCCHHHHHHHHHHHHHHhhh-------CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026799          100 GSLDTEFIKVVKSQCLKQIIK-------LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME  163 (233)
Q Consensus       100 ~e~D~efI~~l~~~~~~~i~~-------~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~  163 (233)
                        +..+..+.+++.+...|..       +..+.-+++...+-      -.+...-+..+|+.|+-+|.|..
T Consensus        59 --~~~~~~~~l~~~l~~~L~~yH~~~P~~~G~~keeLr~~~~------~~~~~~~~~~ll~~l~~~g~l~~  121 (135)
T 2v9v_A           59 --ISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYF------SRLPARVYQALLEEWSREGRLQL  121 (135)
T ss_dssp             --EEHHHHHHHHHHHHHHHHHHHHHCTTSSCEEHHHHHHHHC------TTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             --ecHHHHHHHHHHHHHHHHHHHHhCCCccCCCHHHHHHHhc------ccCCHHHHHHHHHHHHHCCCEEe
Confidence              4567888888888888873       34666888776652      13588889999999999999865

>2z99_A Putative uncharacterized protein; winged helix domain, cell cycle, cell division, chromosome partition, cytoplasm; 2.30A {Mycobacterium tuberculosis}

Probab=91.39  E-value=0.73  Score=39.65  Aligned_cols=60  Identities=17%  Similarity=0.153  Sum_probs=49.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      ..|+.-...+|.+|...+.  |.+.+|.+..  |+..   +++++.|.++|||+++..-..++..+|
T Consensus        96 ~~Ls~aaLEtLaiIAy~QP--ITR~eI~~ir--Gv~~---~~~v~~Lle~gLI~e~Gr~~~~Gp~ly  155 (219)
T 2z99_A           96 TKLTRAALETLAVVAYRQP--VTRARVSAVR--GVNV---DAVMRTLLARGLITEVGTDADTGAVTF  155 (219)
T ss_dssp             CCCCHHHHHHHHHHHHHCS--EEHHHHHHHH--TSCC---HHHHHHHHHTTSEEEEEECTTTCCEEE
T ss_pred             CccCHHHHHHHHHHHHcCC--cCHHHHHHHH--CCCH---HHHHHHHHHCCCEEEccccCCCCCeEE
Confidence            4588888889999999876  9999999999  8776   789999999999999865444444444

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=91.38  E-value=0.34  Score=35.43  Aligned_cols=46  Identities=22%  Similarity=0.422  Sum_probs=36.0

Q ss_pred             CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      ..+..||+.|+.|+.++    -.|...++|...+  +++.++|.+.++.+.+
T Consensus        23 ~~l~~Lt~~e~~vl~l~----~~g~s~~eIA~~l--~is~~tV~~~l~r~~~   68 (95)
T 3c57_A           23 DPLSGLTDQERTLLGLL----SEGLTNKQIADRM--FLAEKTVKNYVSRLLA   68 (95)
T ss_dssp             ----CCCHHHHHHHHHH----HTTCCHHHHHHHH--TCCHHHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence            45778999999999996    4679999999999  9999988877766554

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=91.25  E-value=0.29  Score=39.59  Aligned_cols=49  Identities=12%  Similarity=0.229  Sum_probs=39.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      .++-++....+.-+..++|..+.  +++.+.|.|+|+.|.+.|||.+++..
T Consensus        16 r~l~~La~~~~~~~s~~~IA~~~--~is~~~l~kil~~L~~aGlv~s~rG~   64 (162)
T 3k69_A           16 HSILYLDAHRDSKVASRELAQSL--HLNPVMIRNILSVLHKHGYLTGTVGK   64 (162)
T ss_dssp             HHHHHHHTTTTSCBCHHHHHHHH--TSCGGGTHHHHHHHHHTTSSEEECST
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCC
Confidence            34444554444558999999999  99999999999999999999876554

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=91.17  E-value=0.88  Score=31.17  Aligned_cols=50  Identities=6%  Similarity=0.176  Sum_probs=40.9

Q ss_pred             CCCCCCCChHHHHHHHHHH-hhCCCcccHHHHHHHhhcCCChHHHHH----HHHHHH
Q 026799           10 NAPSDSLTDHERLIYDVIR-SKQDMGIWTRDMKRELRVNLPDNIVTK----SIKSLQ   61 (233)
Q Consensus        10 ~~~~~~L~~~e~lVy~~I~-~aG~~GIw~~dik~~t~~~l~~~~v~k----~LK~Le   61 (233)
                      ...+..||+.|+.|+.+.. -.|..|...++|...+  |++.++|.+    ++++|.
T Consensus         5 ~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l--~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            5 EKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYF--GVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             SSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHH--TCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHH
Confidence            3457889999999998877 3566899999999999  999888766    566665

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=90.51  E-value=0.049  Score=48.94  Aligned_cols=49  Identities=16%  Similarity=0.229  Sum_probs=0.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCce
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIK   67 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK   67 (233)
                      .+++.+..|+..|...+  |+.+++|.+++  +++..+|+|.|+.||++|+|+
T Consensus        17 ~~~~r~~~iL~~l~~~~--~~t~~eLa~~l--~vs~~Tv~r~l~~Le~~Glv~   65 (345)
T 2o0m_A           17 DVLQERFQILRNIYWMQ--PIGRRSLSETM--GITERVLRTETDVLKQLNLIE   65 (345)
T ss_dssp             -----------------------------------------------------
T ss_pred             HhhHHHHHHHHHHHHcC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEE
Confidence            46667778888887754  69999999999  999999999999999999997

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=90.33  E-value=0.052  Score=52.69  Aligned_cols=62  Identities=13%  Similarity=0.117  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      -+.+|++++++.|.  |.++||..-+  +++..+++++|+.|+++|+|+.+   -..+--.|.+.+||-
T Consensus       517 ~~~~I~~~l~~~g~--it~~di~~l~--~ls~~qa~~~L~~Lv~~G~l~~~---G~gr~t~Y~~~~~~~  578 (583)
T 3lmm_A          517 LTNAAMLWLSEVGD--LATSDLMAMC--GVSRGTAKACVDGLVDEERVVAV---GGGRSRRYRLVELEH  578 (583)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEe---CCCCceEEEEeeccc
Confidence            45789999999988  9999999999  99999999999999999999664   334556788888764

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=90.20  E-value=0.31  Score=42.37  Aligned_cols=45  Identities=16%  Similarity=0.287  Sum_probs=36.6

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .|+.++.+++ .++...||.+++  +||.+++.|.|+.|++.|++..-
T Consensus        34 ~IL~~l~~~~-~~ltl~eia~~l--gl~ksTv~RlL~tL~~~G~v~~~   78 (275)
T 3mq0_A           34 RILDLVAGSP-RDLTAAELTRFL--DLPKSSAHGLLAVMTELDLLARS   78 (275)
T ss_dssp             HHHHHHHHCS-SCEEHHHHHHHH--TCC--CHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHhhCC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEC
Confidence            3566666554 589999999999  99999999999999999999763

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=90.05  E-value=0.41  Score=35.87  Aligned_cols=33  Identities=6%  Similarity=0.312  Sum_probs=30.9

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..++|.++.  ++...+|+++|+.|++.|+|...+
T Consensus        45 s~~eLa~~l--gVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           45 VASKIADRV--GITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             CHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            899999999  999999999999999999997754

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=89.97  E-value=1.6  Score=37.54  Aligned_cols=139  Identities=14%  Similarity=0.181  Sum_probs=91.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhc-------CCC----hHHHHHHHHHHHhCCC-ceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRV-------NLP----DNIVTKSIKSLQNKSL-IKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~-------~l~----~~~v~k~LK~Le~k~l-IK~vksV~~~~rK~Yml   82 (233)
                      .+++..|..++.|-+.|-  +.-.++++-...       ...    ...|+.+=++|..-++ |+.+++ +..++.+|.+
T Consensus         2 ~y~d~hR~fLQa~msrg~--l~~~~~~~l~~~~~~~~~~~~~~~~l~~~I~~IN~~L~~l~~~Ir~~~~-q~~g~~~y~l   78 (238)
T 3nw0_A            2 VMTDVHRRFLQLLMTHGV--LEEWDVKRLQTHCYKVHDRNATVDKLEDFINNINSVLESLYIEIKRGVT-EDDGRPIYAL   78 (238)
T ss_dssp             CCCHHHHHHHHHHHHSSE--EEHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHHHHHGGGTEEEEEEEC-TTTCCEEEEE
T ss_pred             CcchHHHHHHHHHHcCCC--CCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHhhhcCcEEEEeec-CCCCCEEEEE
Confidence            467888999999998877  777776655411       111    2244444455555444 444443 3468999999


Q ss_pred             eccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeE
Q 026799           83 VEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQI  161 (233)
Q Consensus        83 ~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~i  161 (233)
                      .++.+++..-=++     .|..+-|+-++..+-..+.. .+..+.-++.+-..  .+....|+..+.+++|+.||-||=+
T Consensus        79 VN~~~d~~~klaT-----~yt~~Ei~~fk~lle~i~~s~~~~~s~~~~lnl~~--~~~~k~l~~~eae~lL~~lv~~gWl  151 (238)
T 3nw0_A           79 VNLATTSISKMAT-----DFAENELDLFRKALELIIDSETGFASSTNILNLVD--QLKGKKMRKKEAEQVLQKFVQNKWL  151 (238)
T ss_dssp             EESSSCTTHHHHT-----TSCHHHHHHHHHHHHHHHHSSSSCEEHHHHHGGGT--TCSSSCCCHHHHHHHHHHHHHTTSE
T ss_pred             EeCCCCHHHhhcc-----CCCHHHHHHHHHHHHHHHhCCCCceeHHHHHHHHh--hcccCCCCHHHHHHHHHHHHHhcch
Confidence            9999988766544     55566666666666666653 34555545443322  2233579999999999999999999


Q ss_pred             EE
Q 026799          162 ME  163 (233)
Q Consensus       162 e~  163 (233)
                      +.
T Consensus       152 ~~  153 (238)
T 3nw0_A          152 IE  153 (238)
T ss_dssp             EE
T ss_pred             hh
Confidence            86

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=89.96  E-value=0.83  Score=35.01  Aligned_cols=48  Identities=21%  Similarity=0.279  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           20 ERLIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        20 e~lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      -..||+.|...=..|       + ..++|..+.  +++.++|+++|+.|+..|+|...
T Consensus        15 ~~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~--~vSr~tvr~Al~~L~~~G~i~~~   70 (125)
T 3neu_A           15 YSQISDWMKKQMITGEWKGEDKLPSVREMGVKL--AVNPNTVSRAYQELERAGYIYAK   70 (125)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCeEEEe
Confidence            345677776543222       3 489999999  99999999999999999999764

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=89.78  E-value=0.69  Score=34.79  Aligned_cols=47  Identities=21%  Similarity=0.197  Sum_probs=36.6

Q ss_pred             HHHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           21 RLIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        21 ~lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..||+.|...=..       -+ ..++|..+.  +++.++|+++|+.|++.|+|...
T Consensus        12 ~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~--~vSr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           12 QQLRDKIVEAIIDGSYVEGEMIPSIRKISTEY--QINPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            4566666543222       23 688999999  99999999999999999999664

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=89.78  E-value=0.25  Score=42.26  Aligned_cols=46  Identities=15%  Similarity=0.114  Sum_probs=38.1

Q ss_pred             HHHHHHHhh--CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSK--QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~a--G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..+.+++.-  .+.++..+||.+++  +|+..++.|.|+.|++.|+|..-
T Consensus        15 r~l~iL~~l~~~~~~~~~~eia~~~--gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           15 RGFAVLLAFDAQRPNPTLAELATEA--GLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             HHHHHHHTCSSSCSSCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeC
Confidence            344555532  34689999999999  99999999999999999999763

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=89.71  E-value=0.78  Score=34.16  Aligned_cols=44  Identities=16%  Similarity=0.240  Sum_probs=38.0

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN   62 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~   62 (233)
                      ...||+.|+.|+.++.    .|...++|...+  +++.++|...++.+.+
T Consensus        32 ~~~Lt~re~~Vl~l~~----~G~s~~EIA~~L--~iS~~TV~~~l~ri~~   75 (99)
T 1p4w_A           32 DKRLSPKESEVLRLFA----EGFLVTEIAKKL--NRSIKTISSQKKSAMM   75 (99)
T ss_dssp             SSSCCHHHHHHHHHHH----HTCCHHHHHHHH--TSCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence            5779999999998874    589999999999  9999998888777654

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=89.70  E-value=0.35  Score=35.48  Aligned_cols=48  Identities=13%  Similarity=0.268  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           20 ERLIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        20 e~lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ...||+.|...=-.|       + ..++|..++  +++..+|+++|+.|++.|+|...
T Consensus        13 ~~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~--~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           13 YADVATHFRTLIKSGELAPGDTLPSVADIRAQF--GVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             HHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHS--SSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            345666665433222       3 689999999  99999999999999999999764

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=89.62  E-value=0.0067  Score=55.07  Aligned_cols=61  Identities=21%  Similarity=0.232  Sum_probs=51.1

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +|++.|..||..+-..|.  ....+|.+.+  ++|++.|..+|+.|+++|||....    .+.+.|...
T Consensus        15 Gls~~ea~vY~~Ll~~g~--~t~~eia~~~--gv~~~~Vy~~L~~L~~~GlV~~~~----g~p~~y~av   75 (342)
T 3qph_A           15 GFTKYEILTYWTLLVYGP--STAKEISTKS--GIPYNRVYDTISSLKLRGFVTEIE----GTPKVYAAY   75 (342)
T ss_dssp             HHHHHTTSCSHHHHHHHH--HHHSCCSSST--TSSSCSCCHHHHHHHHHTSEEEEC----CTTCEEEEC
T ss_pred             CCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEc----CceeEEEEc
Confidence            578888899999988876  7889999999  999999999999999999998763    234556543

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=89.47  E-value=0.57  Score=34.01  Aligned_cols=49  Identities=12%  Similarity=0.226  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHH-HHHHHHHHHhcCCeEEEE
Q 026799          108 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQ-QIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       108 ~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~-di~~il~~Lv~Dg~ie~v  164 (233)
                      ...++.++.||.+++..|+.+|++.+.        +|.. .|.+.|..|.-||.|+..
T Consensus        10 ~~~~~~IL~~Lk~~g~~ta~eiA~~Lg--------it~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           10 AEIKEKICDYLFNVSDSSALNLAKNIG--------LTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHHHHHHTCCEEHHHHHHHHC--------GGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hhHHHHHHHHHHHcCCcCHHHHHHHcC--------CCcHHHHHHHHHHHHHCCCEEec
Confidence            477899999999999999999998763        7778 999999999999999954

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=89.31  E-value=0.96  Score=39.00  Aligned_cols=70  Identities=14%  Similarity=0.156  Sum_probs=45.8

Q ss_pred             CCCCChHHHHHHHHHHh---hCCCcccH-------HHHHHHhhcCCCh---HHHHHHHHHHHhCCCceeeecccCCCeee
Q 026799           13 SDSLTDHERLIYDVIRS---KQDMGIWT-------RDMKRELRVNLPD---NIVTKSIKSLQNKSLIKEVVNIHSKGKKH   79 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~---aG~~GIw~-------~dik~~t~~~l~~---~~v~k~LK~Le~k~lIK~vksV~~~~rK~   79 (233)
                      +.+|++.++.++..|..   .|+..+..       ++|...+  +..+   +.+..+|+.|+..|+|..... ...++..
T Consensus       281 ~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~--g~~~~~~~~~~~~l~~L~~~gli~~~~~-~~~~~g~  357 (386)
T 2qby_A          281 ILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKL--GVEAVTQRRVSDIINELDMVGILTAKVV-NRGRYGK  357 (386)
T ss_dssp             HHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHH--TCCCCCHHHHHHHHHHHHHHTSEEEEEC-CCTTSCC
T ss_pred             HHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHHHhCCCEEEEee-cCCCCCC
Confidence            35788999999988875   45554556       5556667  5544   999999999999999987543 2123334


Q ss_pred             EEeecc
Q 026799           80 LMAVEF   85 (233)
Q Consensus        80 Yml~~l   85 (233)
                      |.++.|
T Consensus       358 y~~~~l  363 (386)
T 2qby_A          358 TKEIGL  363 (386)
T ss_dssp             CEEEEE
T ss_pred             eEEEEe
Confidence            544444

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=89.25  E-value=0.65  Score=35.78  Aligned_cols=48  Identities=19%  Similarity=0.291  Sum_probs=38.4

Q ss_pred             HHHHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           20 ERLIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        20 e~lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      -..||..|...=..|       + ..++|..+.  +++.++|+++|+.|+..|+|...
T Consensus        13 ~~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~   68 (126)
T 3by6_A           13 YLQLVDRIKNEVATDVLSANDQLPSVRETALQE--KINPNTVAKAYKELEAQKVIRTI   68 (126)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTCEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            345777776543333       3 689999999  99999999999999999999664

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=89.15  E-value=0.36  Score=34.76  Aligned_cols=48  Identities=17%  Similarity=0.212  Sum_probs=39.8

Q ss_pred             CCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           10 NAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        10 ~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ...+..||+.|+.|+.++    -.|...++|...+  +++.++|.+.++.+.+|
T Consensus        24 ~~~l~~Lt~~e~~vl~l~----~~g~s~~eIA~~l--~is~~tV~~~l~r~~~k   71 (91)
T 2rnj_A           24 AELYEMLTEREMEILLLI----AKGYSNQEIASAS--HITIKTVKTHVSNILSK   71 (91)
T ss_dssp             -CTGGGCCSHHHHHHHHH----HTTCCTTHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence            345678999999999886    3689999999999  99999998888776543

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=88.83  E-value=0.68  Score=35.93  Aligned_cols=46  Identities=11%  Similarity=0.122  Sum_probs=36.3

Q ss_pred             HHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           22 LIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        22 lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .||+.|...=..|       + ..++|..+.  +++.++|+++|+.|+..|+|...
T Consensus         8 ~i~~~i~~~I~~g~l~~G~~LPse~~La~~~--gvSr~tVr~Al~~L~~~Gli~~~   61 (129)
T 2ek5_A            8 QIASLIEDSIVDGTLSIDQRVPSTNELAAFH--RINPATARNGLTLLVEAGILYKK   61 (129)
T ss_dssp             HHHHHHHHHHHTTSSCTTSCBCCHHHHHHHT--TCCHHHHHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEe
Confidence            5666665432222       3 688999999  99999999999999999999764

>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60

Probab=88.82  E-value=0.35  Score=39.73  Aligned_cols=55  Identities=18%  Similarity=0.173  Sum_probs=46.9

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCe
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGK   77 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~r   77 (233)
                      ||.-...+|.+|...+.  |.+.+|.+..  |+.   ++.+++.|.++|||+++..-..++|
T Consensus        92 LS~aaLEtLaiIay~qP--iTR~eI~~ir--Gv~---~~~~v~~L~e~glI~e~g~~~~~GR  146 (162)
T 1t6s_A           92 LSRSMLEVLAVVAWHQP--VTKGEIQQIR--GAS---PDYSIDRLLARGLIEVRGRADSPGR  146 (162)
T ss_dssp             HHHHHHHHHHHHHHHCS--EEHHHHHHHH--TCC---CCSHHHHHHHTTSEEEEEECSSTTC
T ss_pred             cCHHHHHHHHHHHHcCC--cCHHHHHHHH--CCC---HHHHHHHHHHCCCEEEccccCCCCC
Confidence            55555669999999876  9999999999  887   8889999999999999876665676

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=88.54  E-value=3.1  Score=35.69  Aligned_cols=111  Identities=8%  Similarity=0.090  Sum_probs=81.3

Q ss_pred             CCChHHHHHHH----HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC
Q 026799           15 SLTDHERLIYD----VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE   90 (233)
Q Consensus        15 ~L~~~e~lVy~----~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e   90 (233)
                      .+++++..+.+    .+.++|=.--|.+||-..+  +++...+..+|+.|...|.|-++.      .-+|          
T Consensus       134 ~~~~~~~~~~~~i~~~~~~~g~~pp~~~dl~~~l--~~~~~~~~~~l~~l~~~g~lv~l~------~~~~----------  195 (258)
T 1lva_A          134 SFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSF--NLDPSELEELLHYLVREGVLVKIN------DEFY----------  195 (258)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEESS------SSBE----------
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHhHh--CCCHHHHHHHHHHHHHCCCEEEec------CCeE----------
Confidence            46665544443    3445554446999999999  999999999999999999886643      1233          


Q ss_pred             cccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEE
Q 026799           91 ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIME  163 (233)
Q Consensus        91 iTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~  163 (233)
                                 |+.+.++.+.+.+..++ .++..|+.+..+-+   |     +|=.=.-.||+-|=-.|...+
T Consensus       196 -----------~~~~~~~~~~~~l~~~~-~~~~it~a~~Rd~l---g-----~SRK~aIplLE~~Dr~g~TrR  248 (258)
T 1lva_A          196 -----------WHRQALGEAREVIKNLA-STGPFGLAEARDAL---G-----SSRKYVLPLLEYLDQVKFTRR  248 (258)
T ss_dssp             -----------EEHHHHHHHHHHHHHHH-TTSCBCHHHHHHHH---T-----CCHHHHHHHHHHHHHTTSEEE
T ss_pred             -----------EcHHHHHHHHHHHHHHH-hcCCcCHHHHHHHh---C-----CcHHHHHHHHHHHhhcCceee
Confidence                       46788999999999999 99999999988776   3     333444566776655565544

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=88.51  E-value=0.47  Score=38.94  Aligned_cols=33  Identities=12%  Similarity=0.246  Sum_probs=30.8

Q ss_pred             cccHHHHHHHhhcCCCh-HHHHHHHHHHHhCCCcee
Q 026799           34 GIWTRDMKRELRVNLPD-NIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~-~~v~k~LK~Le~k~lIK~   68 (233)
                      -+.+.+|..-+  |++. .+|+|+|+.|+++|+|+.
T Consensus       169 ~~t~~~lA~~l--G~sr~etvsR~l~~l~~~glI~~  202 (238)
T 2bgc_A          169 NLTMQELGYSS--GIAHSSAVSRIISKLKQEKVIVY  202 (238)
T ss_dssp             CCCHHHHHHHT--TCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHh--CCChHHHHHHHHHHHHHCCCEEe
Confidence            57899999999  9999 599999999999999976

>2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, RNA_POL_RPC34 domain, RNA polymerase III C39 subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85

Probab=88.38  E-value=1.8  Score=31.72  Aligned_cols=66  Identities=15%  Similarity=0.136  Sum_probs=54.3

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS   88 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs   88 (233)
                      +-|..|+.+++..- +||...+|...+ ++|+..+.-.+|..|-+.|-|.-.+   .++.-+|-+.+-.||
T Consensus        14 ~ie~~IL~l~~~~P-~GItd~~L~~~~-p~~~~~~r~~aIN~LL~~gkiel~K---~~~~liYr~k~~~~~   79 (81)
T 2dk8_A           14 EIENRIIELCHQFP-HGITDQVIQNEM-PHIEAQQRAVAINRLLSMGQLDLLR---SNTGLLYRIKDSGPS   79 (81)
T ss_dssp             HHHHHHHHHHHHCS-SCEEHHHHHHHC-TTSCHHHHHHHHHHHHHHTSEEEEE---CSSSEEEEECCCCCC
T ss_pred             HHHHHHHHHHHhCC-CCCCHHHHHHHC-CCCCHHHHHHHHHHHHHcCCeEEEe---cCCeEEEEecccccC
Confidence            34677999998874 899999999998 5789999999999999999997554   456778888775544

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=88.36  E-value=0.89  Score=37.03  Aligned_cols=46  Identities=13%  Similarity=0.250  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCC-cee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL-IKE   68 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l-IK~   68 (233)
                      ...|+.++.+.+ ..+..++|.+++  +++.++|.+-|+.|++.|+ |..
T Consensus        23 ~~~Il~~L~~~~-~~~s~~eLa~~l--~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           23 LKSIVRILERSK-EPVSGAQLAEEL--SVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHHCS-SCBCHHHHHHHH--TSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHcC-CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEE
Confidence            456777777543 359999999999  9999999999999999999 865

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=88.30  E-value=0.26  Score=42.40  Aligned_cols=35  Identities=17%  Similarity=0.287  Sum_probs=33.1

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           32 DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        32 ~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.++..+||.+++  +|+.+++.|.|+.|++.|+|..
T Consensus        19 ~~~lsl~eia~~l--gl~ksT~~RlL~tL~~~G~v~~   53 (260)
T 3r4k_A           19 RLEIGLSDLTRLS--GMNKATVYRLMSELQEAGFVEQ   53 (260)
T ss_dssp             BSEEEHHHHHHHH--CSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            4789999999999  9999999999999999999965

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A

Probab=88.30  E-value=0.09  Score=46.05  Aligned_cols=52  Identities=19%  Similarity=0.341  Sum_probs=0.0

Q ss_pred             CCChHHHHHHHHHHhh-CCCcccHHHHHHHhhcC-CChHHHHHHHHHHHhCCCcee
Q 026799           15 SLTDHERLIYDVIRSK-QDMGIWTRDMKRELRVN-LPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~a-G~~GIw~~dik~~t~~~-l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +|++-++.||++|++. .++||-..+|.+++  + ++..+|+++|..|.+.|+|=+
T Consensus       204 ~~~~~~~~Vl~~i~~~~~~~Gi~~~~I~~~l--~~~~~~~v~~al~~L~~eG~IYs  257 (270)
T 2pi2_A          204 GLTVAQNQVLNLIKACPRPEGLNFQDLKNQL--KHMSVSSIKQAVDFLSNEGHIYS  257 (270)
T ss_dssp             --------------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHhCCCccCCCHHHHHHHh--cCCCHHHHHHHHHHHHhCCEEec
Confidence            5777889999999985 56899999999998  5 999999999999999999943

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=88.26  E-value=1.6  Score=28.87  Aligned_cols=46  Identities=13%  Similarity=0.118  Sum_probs=37.2

Q ss_pred             CCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 026799           11 APSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQ   61 (233)
Q Consensus        11 ~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le   61 (233)
                      ..+..||+.++.|+.+..   -.|...++|...+  |++.++|.+.++...
T Consensus        11 ~~l~~L~~~~r~il~l~~---~~g~s~~eIA~~l--gis~~tv~~~~~ra~   56 (70)
T 2o8x_A           11 TMIADLTTDQREALLLTQ---LLGLSYADAAAVC--GCPVGTIRSRVARAR   56 (70)
T ss_dssp             TTTTSSCHHHHHHHHHHH---TSCCCHHHHHHHH--TSCHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHHHHH
Confidence            357789999999987765   3568999999999  999998877766543

>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger, ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A 1ldk_A 1ldk_B 3rtr_A

Probab=87.66  E-value=0.86  Score=45.33  Aligned_cols=144  Identities=8%  Similarity=0.096  Sum_probs=92.3

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee--------cccCCCeeeEEeeccc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV--------NIHSKGKKHLMAVEFE   86 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk--------sV~~~~rK~Yml~~le   86 (233)
                      .+|.-|..|+-+..+.  ..+...+|...|  +|+...+.++|..|...|++...+        .|. ++-...+=.++.
T Consensus       586 ~vs~~Qa~iLllFn~~--~~~t~~ei~~~t--~i~~~~l~r~L~~l~k~~iL~~~~~~~~~~~~~~~-~~~~f~lN~~F~  660 (760)
T 1ldj_A          586 QASTFQMAILLQYNTE--DAYTVQQLTDST--QIKMDILAQVLQILLKSKLLVLEDENANVDEVELK-PDTLIKLYLGYK  660 (760)
T ss_dssp             ECCHHHHHHHHGGGSS--SEEEHHHHHHHT--CCCHHHHHHHHHHHHHTTTEECSCTTCCTTTCCCC-TTCEEEECSSCC
T ss_pred             EEcHHHHHHHHHhcCC--CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcceeCCCccccccCCCC-CCCEEEeecccc
Confidence            4677888888666654  458899999999  999999999999999999886321        011 111111111111


Q ss_pred             cCC---CcccCCccc---------CCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH-hCCcccccCHHHHHHHHH
Q 026799           87 PSK---EISGGAWYS---------EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKR-SGAFKVDLTKQQIEEIVR  153 (233)
Q Consensus        87 Ps~---eiTGG~wy~---------d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~-~~i~~~~Ls~~di~~il~  153 (233)
                      ...   .|.. +.=.         ..+.+.+=...|..+|.+.++.+...+-+++..-+.+ .. .+...++.+|+.-|+
T Consensus       661 ~k~~ri~i~~-~~~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~-~rF~p~~~~IKk~Ie  738 (760)
T 1ldj_A          661 NKKLRVNINV-PMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLS-SRFKPRVPVIKKCID  738 (760)
T ss_dssp             CSSSSBCCCC-CCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHHT-TTCCCCHHHHHHHHH
T ss_pred             CCceEEEecC-ccccccchhhhhHHHHHHHHHHhHheeeehhhhhccCCCcHHHHHHHHHHHHh-ccCCCCHHHHHHHHH
Confidence            100   0000 0000         0111222223677778888888888888888775543 32 345689999999999


Q ss_pred             HHhcCCeEEEEe
Q 026799          154 ALVLDNQIMEVK  165 (233)
Q Consensus       154 ~Lv~Dg~ie~v~  165 (233)
                      .|+=-+-|++..
T Consensus       739 ~LIereYl~R~~  750 (760)
T 1ldj_A          739 ILIEKEYLERVD  750 (760)
T ss_dssp             HHHHTTSEEECS
T ss_pred             HHhhccceeeCC
Confidence            999999999853

>3u0k_A Rcamp; fluorescent protein, calcium binding, EF-hand, genetically E calcium indicator; HET: NFA CRK; 2.10A {Entacmaea quadricolor}

Probab=87.27  E-value=2.1  Score=40.35  Aligned_cols=120  Identities=13%  Similarity=0.244  Sum_probs=74.3

Q ss_pred             CCCCChHH----HHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhC--CCceeeecccCCCeeeEEee
Q 026799           13 SDSLTDHE----RLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNK--SLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        13 ~~~L~~~e----~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k--~lIK~vksV~~~~rK~Yml~   83 (233)
                      ...|+++|    +.+++.++..|+-=|...||+.-+   +.+++...+.+.++.+-..  |.|-- .-.-      -++.
T Consensus       293 ~E~Lt~EEI~ELREaF~~fDkDgdG~IS~eELk~aLrsLG~~~TeeEI~~Lf~~~D~DgDG~IdF-eEFl------~lms  365 (440)
T 3u0k_A          293 RDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDF-PEFL------IMMA  365 (440)
T ss_dssp             CBCCCHHHHHHHHHHHHHHCTTCSSEECHHHHHHHHHHTTCCCCHHHHHHHHHHHCSSCSSSEEH-HHHH------HHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHcCCCCCEECHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCCCCcCcH-HHHH------HHHH
Confidence            56788876    456777777888889999998765   4467788888888877432  22210 0000      0000


Q ss_pred             ccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhh--hCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcC
Q 026799           84 EFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII--KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLD  158 (233)
Q Consensus        84 ~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~--~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~D  158 (233)
                      .           ...+..-+    +.|++ +++.+.  ..+++|.+|+.+.+++.|.   .|+.++++.+++.+=.|
T Consensus       366 ~-----------~lk~~d~e----eeLre-AFk~fDkDgdG~IS~eELr~vL~~lGe---~LSdeEIdeLfke~D~D  423 (440)
T 3u0k_A          366 R-----------KMKDTDSE----EEIRE-AFRVFDKDGNGYISAAELRHVMTNLGE---KLTDEEVDEMIREADID  423 (440)
T ss_dssp             T-----------C------C----HHHHH-HHHHHCTTCSSEECHHHHHHHHHHHTC---CCCHHHHHHHHHHHCTT
T ss_pred             H-----------HhcCCChH----HHHHH-HHHHHCCCCcCcCCHHHHHHHHHHhCC---CCCHHHHHHHHHHhCCC
Confidence            0           00000011    22333 234443  4689999999999999884   69999999999987544

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=86.98  E-value=1.4  Score=31.36  Aligned_cols=46  Identities=7%  Similarity=0.042  Sum_probs=37.8

Q ss_pred             CCCCCChHHHHHHHHHHh-hCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 026799           12 PSDSLTDHERLIYDVIRS-KQDMGIWTRDMKRELRVNLPDNIVTKSIKS   59 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~-aG~~GIw~~dik~~t~~~l~~~~v~k~LK~   59 (233)
                      .+..||+.|+.|+.+..- .++.|...++|...+  |++..+|.+.+..
T Consensus        15 ~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~l--gis~~tV~~~~~r   61 (87)
T 1tty_A           15 VLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYF--NVTRERIRQIEVK   61 (87)
T ss_dssp             HHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHH--TCCHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHH--CCCHHHHHHHHHH
Confidence            456899999999988763 677899999999999  9998887665543

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=86.37  E-value=1  Score=38.61  Aligned_cols=45  Identities=16%  Similarity=0.127  Sum_probs=38.2

Q ss_pred             HHHHHHHhh--CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSK--QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~a--G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ..+.+++.-  ...++..+||.+++  +|+.+++.|.|+.|++.|+|..
T Consensus        22 r~l~iL~~l~~~~~~~~~~eia~~~--gl~~stv~r~l~tL~~~G~v~~   68 (265)
T 2ia2_A           22 RGLAVIRCFDHRNQRRTLSDVARAT--DLTRATARRFLLTLVELGYVAT   68 (265)
T ss_dssp             HHHHHHHTCCSSCSSEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence            455566542  34789999999999  9999999999999999999976

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=86.19  E-value=2.1  Score=33.33  Aligned_cols=55  Identities=7%  Similarity=0.163  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          109 VVKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       109 ~l~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      .-|..++++|.. .+.+|++||++.+++.+-   .++..-|...|+.|+-.|.|.++..
T Consensus        14 ~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~---~is~aTVYR~L~~L~e~Glv~~~~~   69 (139)
T 3mwm_A           14 RQRAAVSAALQEVEEFRSAQELHDMLKHKGD---AVGLTTVYRTLQSLADAGEVDVLRT   69 (139)
T ss_dssp             HHHHHHHHHHTTCSSCEEHHHHHHHHHHTTC---CCCHHHHHHHHHHHHHTTSSEEEEC
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCC---CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            457788998876 468999999999998762   5899999999999999999999875

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=85.96  E-value=1.3  Score=34.91  Aligned_cols=54  Identities=11%  Similarity=0.151  Sum_probs=46.5

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      -|..++++|...+.+|++||++.+++.+-   .++..-|...|+.|+=.|.|.++..
T Consensus        20 qR~~Il~~l~~~~h~ta~ei~~~l~~~~~---~is~~TVYR~L~~L~e~Glv~~i~~   73 (145)
T 3eyy_A           20 QRQLVLEAVDTLEHATPDDILGEVRKTAS---GINISTVYRTLELLEELGLVSHAHL   73 (145)
T ss_dssp             HHHHHHHHHHHHSSBCHHHHHHHHHTTCT---TCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHhhCC---CCCHhHHHHHHHHHHHCCcEEEEEe
Confidence            35678888876668999999999998763   5889999999999999999999874

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=85.30  E-value=3  Score=32.90  Aligned_cols=56  Identities=14%  Similarity=0.209  Sum_probs=47.3

Q ss_pred             HHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          109 VVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       109 ~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      .-|..++.+|... ..+|++||++.+++.+-   .++..=|-..|+.|+-.|.|.++...
T Consensus        27 ~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~---~is~aTVYR~L~~L~e~Glv~~~~~~   83 (150)
T 2xig_A           27 KQREEVVSVLYRSGTHLSPEEITHSIRQKDK---NTSISSVYRILNFLEKENFISVLETS   83 (150)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHHHHST---TCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCC---CCCHhhHHHHHHHHHHCCcEEEEEeC
Confidence            4566788888754 68999999999998763   57899999999999999999998754

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=85.27  E-value=2.5  Score=32.38  Aligned_cols=57  Identities=7%  Similarity=0.222  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          108 KVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       108 ~~l~~~~~~~i~~~-~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      ..-|..++++|.+. +.+|++||++.+++.+-   .++..=|-..|+.|+-.|.|.++...
T Consensus        10 T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~---~is~~TVYR~L~~L~e~Glv~~~~~~   67 (131)
T 2o03_A           10 TRQRAAISTLLETLDDFRSAQELHDELRRRGE---NIGLTTVYRTLQSMASSGLVDTLHTD   67 (131)
T ss_dssp             HHHHHHHHHHHHHCCSCEEHHHHHHHHHHTTC---CCCHHHHHHHHHHHHTTTSEEEEECT
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCC---CCCHhhHHHHHHHHHHCCCEEEEEeC
Confidence            34567788888754 57999999999998762   58899999999999999999998753

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=85.27  E-value=1.7  Score=34.68  Aligned_cols=47  Identities=13%  Similarity=0.119  Sum_probs=41.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcC---CChHHHHHHHHHHHh
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVN---LPDNIVTKSIKSLQN   62 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~---l~~~~v~k~LK~Le~   62 (233)
                      ..||+-|..|+.++.+..++++..++|..++  +   +..++|...++.|-+
T Consensus       144 ~~Lt~rE~~vl~~l~~~~~~~~s~~~Ia~~l--~~~~~s~~tv~~~i~~l~~  193 (220)
T 1p2f_A          144 IHLPKKEFEILLFLAENAGKVVTREKLLETF--WEDPVSPRVVDTVIKRIRK  193 (220)
T ss_dssp             CCCCHHHHHHHHHHHHTTTSCEEHHHHHHHH--CSSCCCTHHHHHHHHHHHH
T ss_pred             EecCHHHHHHHHHHHHCCCceEcHHHHHHHH--hCCCCCcchHHHHHHHHHH
Confidence            4699999999999999999999999999999  8   999988877776654

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=85.16  E-value=1.4  Score=30.12  Aligned_cols=45  Identities=16%  Similarity=0.310  Sum_probs=37.6

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      +..||+.|+.|+.++    -.|...++|...+  +++.++|.+.++...++
T Consensus        14 l~~L~~~e~~vl~l~----~~g~s~~eIA~~l--~is~~tV~~~~~r~~~k   58 (79)
T 1x3u_A           14 LQTLSERERQVLSAV----VAGLPNKSIAYDL--DISPRTVEVHRANVMAK   58 (79)
T ss_dssp             HHHHCHHHHHHHHHH----TTTCCHHHHHHHT--TSCHHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHH----HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence            346899999999885    3689999999999  99999999888776543

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=84.55  E-value=1.1  Score=40.94  Aligned_cols=55  Identities=13%  Similarity=0.109  Sum_probs=42.9

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ..+++++.+.+-  +..+++.+.+  +.+.+++++.|+.|+++|+|++++.   .+.++|+.
T Consensus       300 ~~ll~~l~~~p~--~t~~~~~~~~--~~S~~TA~r~L~~L~e~GiL~~~~~---gR~~~y~~  354 (373)
T 3eqx_A          300 HELVQVIFEQPY--CRIQNLVESG--LAKRQTASVYLKQLCDIGVLEEVQS---GKEKLFVH  354 (373)
T ss_dssp             HHHHHHHHHCSE--EEHHHHHHTS--SSCHHHHHHHHHHHHHTTSCEEC-----CCSCEEEC
T ss_pred             HHHHHHHHHCCC--ccHHHHHHHh--CcCHHHHHHHHHHHHHCCcEEEeCC---CCceEeeh
Confidence            356667766554  7889999999  9999999999999999999998764   34567754

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S

Probab=84.53  E-value=16  Score=34.69  Aligned_cols=124  Identities=11%  Similarity=0.053  Sum_probs=84.9

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCCcccCC
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGAWYSEG  100 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~wy~d~  100 (233)
                      ..|+.++-..|.  ..-++|...|  +|+.++|..+|-.|.+.++|.-...               +    +|-+.|.-.
T Consensus        22 ~~V~~~Ll~~G~--ltL~~I~~~t--~L~~~~Vk~~L~vLIQh~lV~~~~~---------------~----~~~~~Y~~~   78 (534)
T 2xub_A           22 EKIGVHLIRTGS--QPLRVIAHDT--GTSLDQVKKALCVLVQHNLVSYQVH---------------K----RGVVEYEAQ   78 (534)
T ss_dssp             HHHHHHHHHHCS--EEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEE---------------T----TTEEEEEEC
T ss_pred             HHHHHHHHhcCC--cCHHHHHHHh--CCCHHHHHHHHHHHHhcCCeeEEeC---------------C----CCcEEEEEC
Confidence            467777888888  9999999999  9999999999999999999942211               1    123444311


Q ss_pred             C-------CCHHHHHHHH-------HHHHHHhhhCCCCCHHHHHHHHHHhC----CcccccCHHHHHHHHHHHhcCCeEE
Q 026799          101 S-------LDTEFIKVVK-------SQCLKQIIKLKVATLEGISDSIKRSG----AFKVDLTKQQIEEIVRALVLDNQIM  162 (233)
Q Consensus       101 e-------~D~efI~~l~-------~~~~~~i~~~~~~T~~~I~~~I~~~~----i~~~~Ls~~di~~il~~Lv~Dg~ie  162 (233)
                      .       .=.-|+..++       ..++..|-.+|..|++++..-+....    -....-+.++++..+..|+-+|-|+
T Consensus        79 ~~~il~~lR~pk~l~~i~~~~G~~a~~I~~~ll~~G~~t~~~ll~~~~~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fI~  158 (534)
T 2xub_A           79 CSRVLRMLRYPRYIYTTKTLYSDTGELIVEELLLNGKLTMSAVVKKVADRLTETMEDGKTMDYAEVSNTFVRLADTHFVQ  158 (534)
T ss_dssp             HHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCBCHHHHHHHHHHHHHHTSSSSCCCCHHHHHHHHHHHHHTTSEE
T ss_pred             hhhHHHHHhhHHHHHHHHHHhcHHHHHHHHHHHHcCCccHHHHHHHHHhhcccccccccccCHHHHHHHHHHHHhCCCEE
Confidence            0       0011222222       23444445678999999987776431    0112247899999999999999999


Q ss_pred             EEeeC
Q 026799          163 EVKSN  167 (233)
Q Consensus       163 ~v~~~  167 (233)
                      ++.+.
T Consensus       159 rv~~~  163 (534)
T 2xub_A          159 RCPSV  163 (534)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            98753

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=84.50  E-value=0.86  Score=38.36  Aligned_cols=62  Identities=13%  Similarity=0.228  Sum_probs=44.6

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhh-----c-CCChHHHHHHHHHHHhCCCceeeeccc--CCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELR-----V-NLPDNIVTKSIKSLQNKSLIKEVVNIH--SKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~-----~-~l~~~~v~k~LK~Le~k~lIK~vksV~--~~~rK~Yml~~   84 (233)
                      ...|+.++.+ |.  ..--+|++...     . +++..+|..+|++||+.|||.......  .+.||+|-+.+
T Consensus        38 r~~IL~lL~~-~p--~~GYeL~~~l~~~~~~~~~~s~g~lY~~L~rLe~~GlI~~~~~~~~~~p~rk~Y~iT~  107 (204)
T 3l9f_A           38 KDIILGILSK-KE--RSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQDGRPNKNIYAITE  107 (204)
T ss_dssp             HHHHHHHTSS-CC--EEHHHHHHHHHHTSTTTEECCTTCHHHHHHHHHHTTSEEEEEECCTTSCCEEEEEECH
T ss_pred             HHHHHHHHHc-CC--CCHHHHHHHHHHHhCCccCCCcchHHHHHHHHHHCCCeEEEeeccCCCCCceEEEECh
Confidence            4578888853 32  55556666651     1 589999999999999999998865432  35689997654

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=84.49  E-value=1.6  Score=36.98  Aligned_cols=50  Identities=8%  Similarity=0.097  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           18 DHERLIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      +--..||+.|.+.=..       -+ ..++|..+.  +.+..+|+++|+.|++.|+|...
T Consensus         9 ~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~--~vSr~tvr~Al~~L~~~G~i~~~   66 (236)
T 3edp_A            9 PLFEVIASKIKDSINRDEYKTGMLMPNETALQEIY--SSSRTTIRRAVDLLVEEGLVVRK   66 (236)
T ss_dssp             CHHHHHHHHHHHHHHTTSSCCCC--CCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEE
Confidence            3334566666543222       24 588999999  99999999999999999999774

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=83.75  E-value=2  Score=29.98  Aligned_cols=47  Identities=13%  Similarity=0.121  Sum_probs=39.9

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          111 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       111 ~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +..++.+|...+.+|..||++.+   |     +|..-|...|+.|+-+|.|+...
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~l---g-----vs~~tv~r~L~~L~~~GlI~~~~   48 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEAL---A-----VTDYQARYYLLLLEKAGMVQRSP   48 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHH---T-----SCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHH---C-----cCHHHHHHHHHHHHHCCCEEEec
Confidence            56788888888889999999876   3     67888999999999999998653

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=83.47  E-value=1.8  Score=36.16  Aligned_cols=68  Identities=13%  Similarity=0.217  Sum_probs=51.4

Q ss_pred             ccc-CCCCCHHHHHHHHHHHHHHhhh-------CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799           96 WYS-EGSLDTEFIKVVKSQCLKQIIK-------LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus        96 wy~-d~e~D~efI~~l~~~~~~~i~~-------~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      ||- ++-+  ..++.|+..|++-+-+       ..-.++++|+.-++-+|.  -.++++|+|.||-.|++||.|.-..+.
T Consensus       108 ~f~~~~~~--lll~rlr~~v~r~l~rkv~~~~~~~rI~l~~i~~~l~~~~~--~~~~~~evE~ila~lI~~G~Ikg~I~~  183 (203)
T 3t5x_A          108 FFIRCGIF--LILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQV--EDVDIDEVQCILANLIYMGHVKGYISH  183 (203)
T ss_dssp             HHHHHTCH--HHHHTHHHHHHHHHHHHHHHHHCCSEEEHHHHHHHHHHTTC--TTCCHHHHHHHHHHHHHHTSSCEEEET
T ss_pred             HHHHCChH--HHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC--CCCCHHHHHHHHHHHHHcCceEEEEcc
Confidence            554 4544  4578888877766543       456789999999987763  357999999999999999999876543

>3dpl_C Cullin-5; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} PDB: 3dqv_C

Probab=83.43  E-value=12  Score=34.02  Aligned_cols=144  Identities=13%  Similarity=0.079  Sum_probs=89.6

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh----C-CCceeeec------ccCCCeeeEEeec
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN----K-SLIKEVVN------IHSKGKKHLMAVE   84 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~----k-~lIK~vks------V~~~~rK~Yml~~   84 (233)
                      .|..|..|+-+..+.++..+.-.+|...|  +|+...|.++|..|..    | +++...+.      |. ++-...+=.+
T Consensus       197 vs~~Qa~ILllFn~~~~~~lt~~ei~~~t--~i~~~~L~r~L~sL~~~~k~k~~iL~~~~~~~~~~~~~-~~d~f~~N~~  273 (382)
T 3dpl_C          197 VTTFQLAVLFAWNQRPREKISFENLKLAT--ELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSPKDFT-EGTLFSVNQE  273 (382)
T ss_dssp             EEHHHHHHHGGGTTCTTCCEEHHHHHHHH--CCCHHHHHHHHHHHHCCTTCSSCSEEESSCCSSGGGCC-TTCEEEECTT
T ss_pred             EcHHHHHHHHHhccCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHhcccchhcceeeecCCccccCcCC-CCCEEEEcCC
Confidence            46677777766666555789999999999  9999999999999964    2 34432111      11 0111111111


Q ss_pred             cc----------------cCCCcccCCcccC-----CCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCccccc
Q 026799           85 FE----------------PSKEISGGAWYSE-----GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDL  143 (233)
Q Consensus        85 le----------------Ps~eiTGG~wy~d-----~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~L  143 (233)
                      +.                +...+.  + ..+     .+.+.+=-..|..+|.+.+..+...+-+++..-+.+.=-.+...
T Consensus       274 F~~~k~~k~~~r~ki~~~~~~q~~--~-~~e~~~~~~~v~edR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p  350 (382)
T 3dpl_C          274 FSLIKNAKVQKRGKINLIGRLQLT--T-ERMREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLP  350 (382)
T ss_dssp             CCEESSSSEESEEEEECCTTTTSC--C-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEECHHHHHHHHHHHTTTTCCC
T ss_pred             CcCCcccccceeEEEecccccccc--c-chhhhhhHHHHHHHhhheeeEEEehhhhccCcccHHHHHHHHHHHHHhcCCC
Confidence            11                100000  0 001     11222223345566777787788888888777766542235678


Q ss_pred             CHHHHHHHHHHHhcCCeEEEEe
Q 026799          144 TKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       144 s~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      +..+|..-|+.|+=-+-||+..
T Consensus       351 ~~~~IKk~Ie~LIereYleR~~  372 (382)
T 3dpl_C          351 QKKMIKEQIEWLIEHKYIRRDE  372 (382)
T ss_dssp             CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHHHHHhhhhhccCC
Confidence            8999999999999999999853

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=83.41  E-value=1.7  Score=31.18  Aligned_cols=47  Identities=15%  Similarity=0.157  Sum_probs=36.7

Q ss_pred             HHHHHHHhhhC------CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEe
Q 026799          111 KSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVK  165 (233)
Q Consensus       111 ~~~~~~~i~~~------~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~  165 (233)
                      .+.|+.||+..      ..||+.||++.+   |     +|..-|+.-|+.|+=.|.|....
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~l---g-----vS~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAA---G-----LSIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHH---T-----CCHHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHH---C-----CCHHHHHHHHHHHHHCCcEEecC
Confidence            34556666554      778999999876   3     46677999999999999999875

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=83.40  E-value=3.6  Score=32.13  Aligned_cols=56  Identities=9%  Similarity=0.161  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          109 VVKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       109 ~l~~~~~~~i~~-~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      .-|..++.+|.. ...+|++||++.+++.+-   .++..=|-..|+.|+-.|.|.++...
T Consensus        22 ~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~---~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           22 PQRHAILEYLVNSMAHPTADDIYKALEGKFP---NMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             HHHHHHHHHHHHCSSCCCHHHHHHHHGGGCT---TCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCC---CCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            346678888875 467999999999998762   58899999999999999999998643

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=83.15  E-value=0.72  Score=33.85  Aligned_cols=49  Identities=12%  Similarity=0.171  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          107 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       107 I~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      +..+.+.++.+|++.+ .|+.||++-+        .+|...|++.|..|+-+|.|...
T Consensus        15 ~~~~~~~IL~lL~~~g-~sa~eLAk~L--------giSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           15 NAEIVCEAIKTIGIEG-ATAAQLTRQL--------NMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             SHHHHHHHHHHHSSST-EEHHHHHHHS--------SSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             hHHHHHHHHHHHHHcC-CCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeC
Confidence            3577888889998776 8899988754        38889999999999999999875

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=83.12  E-value=2.7  Score=30.26  Aligned_cols=50  Identities=16%  Similarity=0.246  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHhhhCC---CCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          107 IKVVKSQCLKQIIKLK---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       107 I~~l~~~~~~~i~~~~---~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      -+.+.+.++.+|...+   ..|+.+|++-+.        ++...|+..|..|.=+|.|+.+
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lg--------vsr~tV~~~L~~Le~~G~I~~~   60 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLG--------TPKKEINRVLYSLAKKGKLQKE   60 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHT--------CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEec
Confidence            3567788999999888   899999998764        6677899999999999999876

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=83.02  E-value=3.8  Score=28.34  Aligned_cols=53  Identities=11%  Similarity=0.209  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          110 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       110 l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      .+..++.+|...+.+|..||++.+....    .++..-|..+|+.|+-.|.|+..+.
T Consensus        10 ~e~~vL~~L~~~~~~t~~ei~~~l~~~~----~~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A           10 AELEVMKVIWKHSSINTNEVIKELSKTS----TWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             HHHHHHHHHHTSSSEEHHHHHHHHHHHS----CCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHhhcC----CccHHHHHHHHHHHHHCCCeEEEec
Confidence            4566788888888899999999998642    4788999999999999999998764

>4asn_A TUBR; transcription, tubulin, FTSZ, segregation, partition; 3.50A {Bacillus megaterium}

Probab=82.93  E-value=2.8  Score=31.09  Aligned_cols=65  Identities=17%  Similarity=0.162  Sum_probs=55.2

Q ss_pred             CCCCChHHHHHHHHHHhhCC----CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           13 SDSLTDHERLIYDVIRSKQD----MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~----~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      +++|+-++.-|+..+.+.|.    +.|...+|+..+  ......++|.|-+||.-.+||-|..-+  .-|+|+
T Consensus         9 ~~~L~~~D~SIL~~L~~~~A~~~~KAI~K~~I~D~i--E~~TA~~RKsL~rLEAi~FI~~V~G~r--~HK~~L   77 (101)
T 4asn_A            9 MRKLTIEDVSILGWLFQNEANAVFKAIKKSSIADEL--EYSTANFRKTLNKLEAIHFIGTVTGGK--EHKLYL   77 (101)
T ss_dssp             HHTCCHHHHHHHHHHHHTTCCSGGGCEEHHHHHTTS--CCCSHHHHHHHHHHHHTTCEEEECSSS--SCEEEE
T ss_pred             HHhCChhHHHHHHHHHhcCccceeeeecHhhHHHHH--HHhHHHHHHHHHHHHHHHHhhhcccCc--cceeeh
Confidence            46788899999999998776    468889999999  999999999999999999999887655  356764

>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}

Probab=82.75  E-value=1.8  Score=40.10  Aligned_cols=52  Identities=12%  Similarity=0.097  Sum_probs=46.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..|+++|..||+.+.   ...+..-+|..++  +|+...|..+|-.||=+|+|+++.
T Consensus       324 ~~l~~~~~~vl~~l~---~~~~~~D~l~~~~--gl~~~~v~~~L~~LEl~G~v~~~~  375 (382)
T 3maj_A          324 EPDTGDRTRILALLG---PSPVGIDDLIRLS--GISPAVVRTILLELELAGRLERHG  375 (382)
T ss_dssp             CCCTTHHHHHHHHCC---SSCEEHHHHHHHH--CCCHHHHHHHHHHHHHTTCCEECT
T ss_pred             CCCChHHHHHHHhhC---CCCCCHHHHHHHH--CcCHHHHHHHHHHHHhCCcEEeCC
Confidence            358889999999884   3568999999999  999999999999999999998753

>3dtp_E RLC, myosin regulatory light chain; muscle protein, smooth muscle, myosin subfragment 2, heavy meromyosin, essential light chain; 20.00A {Avicularia avicularia}

Probab=82.70  E-value=9.7  Score=30.00  Aligned_cols=112  Identities=11%  Similarity=0.169  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCCCCChHHH----HHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026799            4 RKRPDSNAPSDSLTDHER----LIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG   76 (233)
Q Consensus         4 ~~~~~~~~~~~~L~~~e~----lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~   76 (233)
                      |...........|++++.    .++..+...|+--|...+++.-++   .+++...+...+..+                
T Consensus        39 r~~~~~~~~~~~ls~~~~~~l~~~F~~~D~d~~G~i~~~el~~~l~~lg~~~~~~~~~~l~~~~----------------  102 (196)
T 3dtp_E           39 RAQRSGSNVFAMFTQHQVQEFKEAFQLIDQDKDGFISKNDIRATFDSLGRLCTEQELDSMVAEA----------------  102 (196)
T ss_dssp             GCCCCCCCSSCSSCTTTHHHHHHHHHHHCCSCSSBCCHHHHHHHHHTTSCCCCHHHHHHHHTTS----------------
T ss_pred             cccccchhhhhhCCHHHHHHHHHHHHHHCCCCCCcCCHHHHHHHHHHhCCCCCHHHHHHHHHHc----------------
Confidence            444444556677887543    455556666666688888887652   245555555544432                


Q ss_pred             eeeEEeeccccCCCcccCCcccCCCCC-HHHHHHHHH------------HHHHHhh--hCCCCCHHHHHHHHHHhCCccc
Q 026799           77 KKHLMAVEFEPSKEISGGAWYSEGSLD-TEFIKVVKS------------QCLKQII--KLKVATLEGISDSIKRSGAFKV  141 (233)
Q Consensus        77 rK~Yml~~lePs~eiTGG~wy~d~e~D-~efI~~l~~------------~~~~~i~--~~~~~T~~~I~~~I~~~~i~~~  141 (233)
                                            +|.+| .||+..+..            .+++.+.  ..+++|.+++..++ ..|.   
T Consensus       103 ----------------------~g~i~~~eF~~~~~~~~~~~~~~~~l~~~F~~~D~d~~G~Is~~El~~~l-~~g~---  156 (196)
T 3dtp_E          103 ----------------------PGPINFTMFLTIFGDRIAGTDEEDVIVNAFNLFDEGDGKCKEETLKRSLT-TWGE---  156 (196)
T ss_dssp             ----------------------SSCCBHHHHHHHHHHCCCSSCCHHHHHHHHHTTCSSSSCCBHHHHHHHHH-HSSS---
T ss_pred             ----------------------cCCCcHHHHHHHHHHHhcCCCcHHHHHHHHHHHCCCCCCcCcHHHHHHHH-HcCC---
Confidence                                  22233 345554432            1222222  35899999999999 8873   


Q ss_pred             ccCHHHHHHHHHHHhc
Q 026799          142 DLTKQQIEEIVRALVL  157 (233)
Q Consensus       142 ~Ls~~di~~il~~Lv~  157 (233)
                      .++.++++.+++.+-.
T Consensus       157 ~~~~~~~~~l~~~~D~  172 (196)
T 3dtp_E          157 KFSQDEVDQALSEAPI  172 (196)
T ss_dssp             CCCHHHHHHHHHSSCE
T ss_pred             CCCHHHHHHHHHHcCC
Confidence            6999999999887643

>1ldd_A APC2WHB, anaphase promoting complex; ubiquitin, ligase, ubiquitination, ring finger, winged-helix; 2.00A {Saccharomyces cerevisiae} SCOP: a.4.5.34

Probab=82.59  E-value=3.5  Score=29.57  Aligned_cols=54  Identities=17%  Similarity=0.122  Sum_probs=40.8

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCcc---cccCHHHHHHHHHHHhcCCeEEEE
Q 026799          111 KSQCLKQIIKLKVATLEGISDSIKRSGAFK---VDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       111 ~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~---~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      -..|.-.|.+.+...++.||..++=--...   ...|.+++++.|+.||-|++++.+
T Consensus        10 w~yI~GMLtN~~slpl~RIh~mLkmf~~~~~~~~~it~~eL~~fL~~~v~e~kL~~~   66 (74)
T 1ldd_A           10 LPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYI   66 (74)
T ss_dssp             HHHHHHHHHHHCSEEHHHHHHHHHHHSCGGGCCTTCCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCCCCcCCHHHHHHHHHHHHhCCeEEEe
Confidence            334444455788888999999999554222   235889999999999999999854

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=82.58  E-value=3  Score=32.17  Aligned_cols=55  Identities=7%  Similarity=0.170  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEee
Q 026799          109 VVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKS  166 (233)
Q Consensus       109 ~l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~  166 (233)
                      .-|..++++|...  ..+|++||.+.+++.+-   .++..-|-..|+.|+-.|.|.++..
T Consensus        18 ~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~---~is~aTVYR~L~~L~e~Glv~~~~~   74 (136)
T 1mzb_A           18 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGE---DVGLATVYRVLTQFEAAGLVVRHNF   74 (136)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTC---CCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            3467788888754  58999999999998763   5889999999999999999999864

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=81.39  E-value=2.2  Score=35.82  Aligned_cols=45  Identities=18%  Similarity=0.116  Sum_probs=40.2

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ...||+.|+.|+.++.    .|...++|..++  +++.++|+..++.+-+|
T Consensus       173 ~~~Lt~re~~vl~~~~----~G~s~~eIa~~l--~is~~tV~~~~~~~~~k  217 (237)
T 3szt_A          173 NVRLTARETEMLKWTA----VGKTYGEIGLIL--SIDQRTVKFHIVNAMRK  217 (237)
T ss_dssp             GCCCCHHHHHHHHHHH----TTCCHHHHHHHH--TSCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            4679999999999983    679999999999  99999999999988764

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=80.75  E-value=2.5  Score=36.56  Aligned_cols=47  Identities=15%  Similarity=0.188  Sum_probs=36.9

Q ss_pred             HHHHHHHhhCCC-------cc-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRSKQDM-------GI-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~aG~~-------GI-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .||+.|.+.=..       -+ ..++|.++.  ++...+|+++|..|++.|+|...+
T Consensus        33 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~--~vSr~tvr~Al~~L~~~G~i~~~~   87 (272)
T 3eet_A           33 RVAGDLRKKIVDGSLPPHTRLPSQARIREEY--GVSDTVALEARKVLMAEGLVEGRS   87 (272)
T ss_dssp             HHHHHHHHHHHHTSSCTTSBCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             HHHHHHHHHHHcCCCCCcCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec
Confidence            566666543222       24 689999999  999999999999999999997653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	233
d2dk5a1	78	a.4.5.85 (A:8-85) DNA-directed RNA polymerase III	9e-22

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.2 bits (206), Expect = 9e-22
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 2/67 (2%)

Query: 15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS 74
             + E+L+Y +I    + GIW+RD++   + NLP   + K +K+L++K LIK V ++ +
Sbjct: 10 GSDNQEKLVYQIIEDAGNKGIWSRDVRY--KSNLPLTEINKILKNLESKKLIKAVKSVAA 67

Query: 75 KGKKHLM 81
            KK  M
Sbjct: 68 SKKKVYM 74

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	233
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	99.97
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	98.25
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	98.11
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	98.1
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	98.08
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	98.04
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	98.04
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	98.04
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.99
d1okra_	120	Methicillin resistance regulatory protein MecI {St	97.98
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	97.94
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	97.94
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.94
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.94
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.9
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	97.9
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.89
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.88
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	97.85
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.85
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.82
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.81
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	97.63
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	97.59
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	97.57
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	97.5
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	97.46
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	97.41
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	97.4
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	97.4
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	97.33
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.3
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	97.22
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	97.07
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.94
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	96.59
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	96.57
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.23
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.98
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	95.96
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	95.83
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.78
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	95.77
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	95.72
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	95.69
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	95.69
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	95.68
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	95.65
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	95.58
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	95.55
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	95.4
d1zyba1	73	Probable transcription regulator BT4300, C-termina	95.36
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.33
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	95.33
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	95.23
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.14
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.03
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	94.88
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	94.82
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	94.65
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	94.6
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	94.49
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	94.2
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	94.05
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	94.04
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	93.53
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	93.23
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	91.94
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	91.84
d1fnna1	112	CDC6, C-terminal domain {Archaeon Pyrobaculum aero	91.81
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	91.6
d1w5sa1	110	CDC6-like protein APE0152, C-terminal domain {Aero	91.48
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	91.42
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	91.24
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	91.04
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	90.88
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	90.64
d2v9va2	73	C-terminal fragment of elongation factor SelB {Moo	90.3
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	90.24
d1ldda_	74	Anaphase promoting complex (APC) {Baker's yeast (S	89.84
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	89.81
d1exra_	146	Calmodulin {Ciliate (Paramecium tetraurelia) [TaxI	88.08
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	88.06
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	87.74
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	86.87
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	86.84
d1dtla_	156	Troponin C {Chicken (Gallus gallus) [TaxId: 9031]}	85.87
d1hlva1	66	DNA-binding domain of centromere binding protein B	85.35
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	85.13
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	85.03
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	84.28
d1oyia_	62	dsRNA-binding protein E3 (E3L) {Vaccinia virus [Ta	83.25
d2esna1	89	Probable LysR-type transcriptional regulator PA047	81.61
d2mysc_	145	Myosin Regulatory Chain {Chicken (Gallus gallus) [	81.01
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	80.81
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	80.32

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=3.6e-31  Score=194.68  Aligned_cols=78  Identities=29%  Similarity=0.537  Sum_probs=76.4

Q ss_pred             CCCCCCCCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799            6 RPDSNAPSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus         6 ~~~~~~~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      |+++|.++++|+++|++||++|++|||+|||++||+.++  |||+++|+|+||+||+++|||+|+||++++||+||||+|
T Consensus         1 d~~~a~k~~~l~~~E~lVY~~I~~ag~~GIW~~dir~kt--nL~~~~l~K~LK~Lesk~lIK~VksV~~~~rK~YmL~~L   78 (78)
T d2dk5a1           1 DSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVAASKKKVYMLYNL   78 (78)
T ss_dssp             CCCCCCCCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEESSS
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHccccceeHHHHHHHc--CCCHHHHHHHHHHHHhcCCceeecccCCCCeEEEEeccC
Confidence            578999999999999999999999999999999999999  999999999999999999999999999999999999997

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=98.25  E-value=2.3e-06  Score=65.02  Aligned_cols=69  Identities=19%  Similarity=0.276  Sum_probs=62.6

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      -+|+..|..|+.+|...++.++..+||.+.+  ++...+++++|++|+++|||....+-.+++.+.+-|.+
T Consensus        25 ~glt~~q~~vL~~l~~~~~~~it~~ela~~~--~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~   93 (135)
T d3broa1          25 YDLTGTQMTIIDYLSRNKNKEVLQRDLESEF--SIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTK   93 (135)
T ss_dssp             TTCCHHHHHHHHHHHHTTTSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECH
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCCHHHHHHHH--CcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccH
Confidence            3799999999999999988899999999999  99999999999999999999999999887776665543

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.11  E-value=4e-06  Score=64.17  Aligned_cols=88  Identities=11%  Similarity=0.177  Sum_probs=70.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      +||..|..|+.+|..+++.|+..++|.+.+  +++..+++++++.||++|||.+..+-.++ |++++-  |+|.      
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l--~~~~~~vs~~v~~L~~~glV~r~~~~~D~-R~v~i~--LT~~------   98 (125)
T d1p4xa2          30 TLSFVEFTILAIITSQNKNIVLLKDLIETI--HHKYPQTVRALNNLKKQGYLIKERSTEDE-RKILIH--MDDA------   98 (125)
T ss_dssp             SSCHHHHHHHHHHHTTTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEEECSSST-TCEEEE--CCHH------
T ss_pred             CCCHHHHHHHHHHHHccCCCccHHHHHHHH--CCCcchHHHHHHHHHhccCEeeeecCCCC-CeEEEE--ECHH------
Confidence            799999999999999999999999999999  99999999999999999999999999874 445431  1111      


Q ss_pred             CcccCCCCCHHHHHHHHHHHHHHhhhC
Q 026799           95 AWYSEGSLDTEFIKVVKSQCLKQIIKL  121 (233)
Q Consensus        95 ~wy~d~e~D~efI~~l~~~~~~~i~~~  121 (233)
                           |   .++++.+...+-..|..+
T Consensus        99 -----G---~~~~~~l~~~~~~~i~~k  117 (125)
T d1p4xa2          99 -----Q---QDHAEQLLAQVNQLLADK  117 (125)
T ss_dssp             -----H---HHHHHHHHHHHHHHTSSS
T ss_pred             -----H---HHHHHHHHHHHHHHHhcc
Confidence                 1   356666666666665543

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.10  E-value=3.2e-06  Score=63.65  Aligned_cols=65  Identities=14%  Similarity=0.232  Sum_probs=59.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      --+||..|..|+.+|..+.+.|+..++|.+.+  +++..+++++|+.||++|||.+..+-+++ |.+|
T Consensus        27 ~~~Lt~~q~~vL~~l~~~~~~~~t~~ela~~l--~~~~~~vs~~i~~Le~~gli~r~~~~~D~-R~~~   91 (115)
T d1hsja1          27 KFNLNYEEIYILNHILRSESNEISSKEIAKCS--EFKPYYLTKALQKLKDLKLLSKKRSLQDE-RTVI   91 (115)
T ss_dssp             SCCCCHHHHHHHHHHHTCSCSEEEHHHHHHSS--CCCHHHHHHHHHHHHTTTTSCCEECCSSS-SCCE
T ss_pred             hcCCCHHHHHHHHHHHccCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHcCCeEEEeecCCC-ceEE
Confidence            34899999999999998888899999999999  99999999999999999999999998874 4444

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.08  E-value=3.6e-06  Score=63.21  Aligned_cols=64  Identities=19%  Similarity=0.268  Sum_probs=58.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|....+.++..++|.+.+  +++..+++++++.||++|||...++-++++++..
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~t~~~la~~l--~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i   93 (115)
T d2frha1          30 SISFEEFAVLTYISENKEKEYYLKDIINHL--NYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLI   93 (115)
T ss_dssp             CCCHHHHHHHHHHHHTCCSEEEHHHHHHHS--SSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEE
T ss_pred             CCCHHHHHHHHHHHcCCCCCCCHHHHHHHH--CCCHhHHHHHHHHHHhhhhheeeecccCCceEEE
Confidence            799999999999999988889999999999  9999999999999999999999999997555444

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.04  E-value=4.4e-06  Score=63.62  Aligned_cols=66  Identities=15%  Similarity=0.172  Sum_probs=59.6

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .-+||..|..|+.+|...++.++..++|...+  ++...+++++|+.|+++|||...++-.+ +|.+|+
T Consensus        29 ~~~Lt~~q~~iL~~l~~~~~~~~t~~eia~~~--~~~~~~vs~~l~~L~~~g~v~r~~~~~D-~R~~~i   94 (125)
T d1p4xa1          29 EVDMTIKEFILLTYLFHQQENTLPFKKIVSDL--CYKQSDLVQHIKVLVKHSYISKVRSKID-ERNTYI   94 (125)
T ss_dssp             TCSSCHHHHHHHHHHHSCSCSEEEHHHHHHHS--SSCGGGTHHHHHHHHHTTSCEEEECSSS-TTSEEE
T ss_pred             HcCCCHHHHHHHHHHHHhccCCcCHHHHHHHh--CCCcchHHHHHHHHHHCCCceeecccCC-CCeEEE
Confidence            35799999999999999888899999999999  9999999999999999999999999876 455554

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.04  E-value=9.7e-06  Score=60.22  Aligned_cols=56  Identities=18%  Similarity=0.358  Sum_probs=51.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      -+|++.|..||..+.+.|.  +..++|.+.+  +++.++|+++|+.|+++|||.+...-+
T Consensus        16 lGlt~~e~~v~~~L~~~g~--~t~~eia~~~--~i~~~~v~~~l~~L~~~GlV~r~~~~~   71 (109)
T d1sfxa_          16 LSFKPSDVRIYSLLLERGG--MRVSEIAREL--DLSARFVRDRLKVLLKRGFVRREIVEK   71 (109)
T ss_dssp             TCCCHHHHHHHHHHHHHCC--BCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEES
T ss_pred             cCCCHHHHHHHHHHHhcCC--CCHHHHHHHh--CCCcchHHHHHHHHHhCCCEEEEeccC
Confidence            3789999999999998886  9999999999  999999999999999999998766543

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=98.04  E-value=6.3e-06  Score=62.98  Aligned_cols=65  Identities=14%  Similarity=0.121  Sum_probs=58.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +|+..+..|+..|...|  |+..++|...+  +++..+|+++|+.|+++|||...++-++++.+.+-|.
T Consensus        27 glt~~q~~iL~~i~~~~--~~t~~~la~~l--~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT   91 (139)
T d2a61a1          27 GITPAQFDILQKIYFEG--PKRPGELSVLL--GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVIT   91 (139)
T ss_dssp             TCCHHHHHHHHHHHHHC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEEC
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHh--CCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEEC
Confidence            69999999999998877  59999999999  9999999999999999999999999998766666543

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.99  E-value=1.3e-05  Score=61.55  Aligned_cols=66  Identities=18%  Similarity=0.325  Sum_probs=58.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      -+||..|..|+..|..  +.|+..++|...+  ++....|+++|+.|+++|||...++-++++.+.+.|.
T Consensus        32 ~~lt~~q~~vL~~l~~--~~~~t~~~la~~l--~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT   97 (141)
T d1lnwa_          32 LDLTPPDVHVLKLIDE--QRGLNLQDLGRQM--CRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLT   97 (141)
T ss_dssp             CCCCHHHHHHHHHHHS--STTCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEEC
T ss_pred             CCCCHHHHHHHHHHHH--CCCCCHHHHHHHH--CccHhHHHHHHHHHHHhhceeeeccCCCCcchhhccC
Confidence            3699999999999965  5579999999999  9999999999999999999999999998766655443

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.98  E-value=0.0001  Score=55.13  Aligned_cols=114  Identities=14%  Similarity=0.186  Sum_probs=79.4

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhh--cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELR--VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKE   90 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~--~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~e   90 (233)
                      .-+||+.|..|+.+|=+.|  ++..++|...+.  .++..++|...|+.|++||+|++.++   .+..+|...  .+-  
T Consensus         2 ~~~lt~~E~~VM~~lW~~~--~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~---gr~~~Y~~~--~~~--   72 (120)
T d1okra_           2 TYEISSAEWEVMNIIWMKK--YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD---NKIFQYYSL--VEE--   72 (120)
T ss_dssp             CCCCCHHHHHHHHHHHHHS--SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE---TTEEEEEES--SCH--
T ss_pred             CCCCCHHHHHHHHHHHcCC--CCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEec---CCceEEeec--CCH--
Confidence            3579999999999999987  599999888872  27999999999999999999998664   345566321  111  


Q ss_pred             cccCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           91 ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        91 iTGG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                                   .   +.+......++.+.-.-+...+..++-+..    .||.+|+++|-+.|
T Consensus        73 -------------~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~ls~~el~~L~~lL  117 (120)
T d1okra_          73 -------------S---DIKYKTSKNFINKVYKGGFNSLVLNFVEKE----DLSQDEIEELRNIL  117 (120)
T ss_dssp             -------------H---HHHHHHHHHHHHHHSTTCHHHHHHHHHHHS----CCCHHHHHHHHHHH
T ss_pred             -------------H---HHHHHHHHHHHHHHHcccHHHHHHHHHHcc----CCCHHHHHHHHHHH
Confidence                         1   233444444444432234555444444332    69999999988876

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.94  E-value=1.6e-05  Score=60.36  Aligned_cols=65  Identities=12%  Similarity=0.303  Sum_probs=57.2

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..|..|+..|...++ |+.+++|...+  ++++.+++++++.|+++|||...++-.+++.++..
T Consensus        24 ~glt~~q~~iL~~l~~~~~-~~t~~~la~~~--~~~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~   88 (137)
T d2fbha1          24 LGLSQARWLVLLHLARHRD-SPTQRELAQSV--GVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIV   88 (137)
T ss_dssp             GCCTTTHHHHHHHHHHCSS-CCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEE
T ss_pred             cCCCHHHHHHHHHHHHcCC-CCcHHHHHHHH--CCCHHHHHHHHHHHHHcCCccccCCCCCCCchhhh
Confidence            3689999999999987655 89999999999  99999999999999999999999998876555543

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=97.94  E-value=8.6e-06  Score=62.18  Aligned_cols=64  Identities=14%  Similarity=0.174  Sum_probs=57.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+||..|..|+..|...+  |+..++|.+.+  ++++..++++++.||++|||...++-++++.++.-
T Consensus        29 ~gLt~~q~~vL~~l~~~~--~~t~~~La~~~--~i~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~   92 (137)
T d1z91a1          29 LNITYPQYLALLLLWEHE--TLTVKKMGEQL--YLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLIS   92 (137)
T ss_dssp             TCCCHHHHHHHHHHHHHS--EEEHHHHHHTT--TCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEE
T ss_pred             cCcCHHHHHHHHHHHcCC--CCCHHHHHHHH--CcCHHHHHHHHHHHhhccceEEeecCCCCCeEEEE
Confidence            479999999999998865  79999999999  99999999999999999999999999876655543

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=97.94  E-value=1.6e-05  Score=60.82  Aligned_cols=64  Identities=14%  Similarity=0.239  Sum_probs=57.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      .+|+..|..|+..|...|  |+...+|.+.+  +++...+++.++.||++|||.+.++-++++.+...
T Consensus        31 ~glt~~q~~iL~~l~~~~--~~t~~~la~~~--~i~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~   94 (143)
T d1s3ja_          31 QGVTPAQLFVLASLKKHG--SLKVSEIAERM--EVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLS   94 (143)
T ss_dssp             TTCCHHHHHHHHHHHHHS--EEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHhhhheeeeecCCCCceEEE
Confidence            469999999999999876  69999999999  99999999999999999999999998876554443

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.94  E-value=1.6e-05  Score=57.71  Aligned_cols=62  Identities=13%  Similarity=0.145  Sum_probs=54.2

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ++-+..|+.+|...|.  +..+||.+.+  ++++..++++|+.||++|||...++-..+++++|-|
T Consensus        15 ~p~r~~IL~~L~~~~~--~~~~eLa~~l--~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~L   76 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRK--APFSQIQKVL--DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             SHHHHHHHHHHHHHSE--EEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             CHHHHHHHHHhccCCC--eeHHHHHHHH--hhccccccHHHHHHhhhceeEEEEcCcCCccccccC
Confidence            5668889999988876  9999999999  999999999999999999999988877666666644

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.90  E-value=1.4e-05  Score=60.75  Aligned_cols=64  Identities=8%  Similarity=0.162  Sum_probs=57.1

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +|+..|..|+.+|...|  |+..++|...+  +++...++++|+.|+++|||...++-++++.+...|
T Consensus        27 glt~~q~~vL~~l~~~~--~~t~~~la~~~--~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~l   90 (136)
T d2fbia1          27 GLTEQQWRVIRILRQQG--EMESYQLANQA--CILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNL   90 (136)
T ss_dssp             TCCHHHHHHHHHHHHHC--SEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeecCccCchhhhcc
Confidence            69999999999999876  59999999999  999999999999999999999999999755554433

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.90  E-value=1.5e-05  Score=60.75  Aligned_cols=65  Identities=17%  Similarity=0.223  Sum_probs=58.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEee
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAV   83 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~   83 (233)
                      +||..|..|+.+|...+  |+.+++|...+  +++..+++++++.|+++|||.+.++-++++.+..-|.
T Consensus        31 glt~~q~~vL~~i~~~~--~~t~~~la~~l--~~~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT   95 (136)
T d2bv6a1          31 NLTYPQFLVLTILWDES--PVNVKKVVTEL--ALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLT   95 (136)
T ss_dssp             TCCHHHHHHHHHHHHSS--EEEHHHHHHHT--TCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEEC
T ss_pred             CCCHHHHHHHHHHHcCC--CCCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEEeecCCcccchhhccC
Confidence            79999999999999875  79999999999  9999999999999999999999999987665555443

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=97.89  E-value=2.6e-05  Score=59.53  Aligned_cols=65  Identities=17%  Similarity=0.148  Sum_probs=58.0

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      -+|+..|..|+.+|...|  |+.+++|...+  +++...++++++.||++|||.+.++-.+++.+.+-|
T Consensus        30 ~~Lt~~q~~vL~~l~~~~--~~t~~ela~~~--~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~l   94 (138)
T d1jgsa_          30 LDITAAQFKVLCSIRCAA--CITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKL   94 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEE
T ss_pred             cCCCHHHHHHHHhHHhCc--CCCHHHHHHHH--CCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEE
Confidence            479999999999998877  69999999999  999999999999999999999999888766555543

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=97.88  E-value=2.2e-05  Score=57.90  Aligned_cols=63  Identities=16%  Similarity=0.180  Sum_probs=50.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC-eeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG-KKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~-rK~Y   80 (233)
                      +|++.+..||..|-.+++ ++...+|.+.+  +++..+|++.|+.|+++|||.+.++-.+++ +.+|
T Consensus        18 gLs~~~~~iL~~L~~~~~-~~t~~eLa~~~--~i~~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~   81 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIEK-PITSEELADIF--KLSKTTVENSLKKLIELGLVVRTKTEGKKIGRPKY   81 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCS-CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC-------CCE
T ss_pred             CcCHHHHHHHHHHHHcCC-CCCHHHHHHHH--CccHhHHHHHHHHHHHCCCEEEeecCCCCCceeEE
Confidence            799999999988865533 59999999999  999999999999999999999888766543 4444

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.85  E-value=2.3e-05  Score=59.58  Aligned_cols=68  Identities=13%  Similarity=0.190  Sum_probs=53.3

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      -+||..+..|+..|.+.+ .|+..++|....  +++...++++|+.|+++|||...++-.+++.+.+.|.+
T Consensus        27 ~glt~~~~~~L~~l~~~~-~~~t~~~la~~l--~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~   94 (140)
T d3deua1          27 LELTQTHWVTLHNIHQLP-PDQSQIQLAKAI--GIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTE   94 (140)
T ss_dssp             TTCCHHHHHHHHHHHHSC-SSEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CEEEECG
T ss_pred             cCCCHHHHHHHHHHHHcC-CCccHHHHHHHH--CCCHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECH
Confidence            479999999999998753 589999999999  99999999999999999999999999987777765544

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.85  E-value=2.6e-05  Score=60.01  Aligned_cols=62  Identities=19%  Similarity=0.260  Sum_probs=55.0

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +||..|..|+..|...  .|+.+++|...+  ++....|+++|+.|+++|||....+-++++.+..
T Consensus        26 ~lt~~q~~iL~~i~~~--~~~t~~~la~~l--~i~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l   87 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCEN--PGIIQEKIAELI--KVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRI   87 (144)
T ss_dssp             TCTTTHHHHHHHHHHS--TTEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             CCCHHHHHHHHHHHhC--CCCCHHHHHHHH--CccHhhHHHHHHHHHhhhcccccCCCCCCCcccc
Confidence            6899999999999875  479999999999  9999999999999999999999999887544333

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.82  E-value=6.1e-05  Score=57.54  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=56.4

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      -+|+..+-.||.++-.++ +++...+|.+++  |++...++++|+.|+++|||+..++-.. +|+.|+
T Consensus        22 ~Gl~~~~~~i~~~L~~~~-~plt~~ela~~l--~vsk~~vs~~l~~L~~~GlV~r~~~~~d-rr~~~~   85 (151)
T d1ku9a_          22 HGLNKSVGAVYAILYLSD-KPLTISDIMEEL--KISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYE   85 (151)
T ss_dssp             TTCCHHHHHHHHHHHHCS-SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEE
T ss_pred             cCCCHHHHHHHHHHHhCC-CCcCHHHHHHHh--CCCcchHHHHHHHHHHCCCEEEEEcCCC-CceeEE
Confidence            478999999999998776 469999999999  9999999999999999999999888775 455554

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=97.81  E-value=2.6e-05  Score=59.35  Aligned_cols=66  Identities=11%  Similarity=0.129  Sum_probs=58.4

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      ..+||..|..|+..|...|+  +..++|...+  +++..+++++++.|+++|||.+.++-.+++.+..-|
T Consensus        27 ~~~lt~~q~~iL~~l~~~~~--~t~~~La~~l--~i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~l   92 (140)
T d2etha1          27 ISDMKTTELYAFLYVALFGP--KKMKEIAEFL--STTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVL   92 (140)
T ss_dssp             HHHSBHHHHHHHHHHHHHCC--BCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEE
T ss_pred             hcCCCHHHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhc
Confidence            34789999999999988875  9999999999  999999999999999999999999998766555543

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=97.63  E-value=5.9e-05  Score=59.84  Aligned_cols=62  Identities=11%  Similarity=0.078  Sum_probs=51.6

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      +|+..|..|+.+|...|  |+..++|.+.+  +++..++++++++|+++|||.+..+-.+++.+..
T Consensus        38 ~Lt~~q~~vL~~l~~~~--~~t~~~la~~~--~l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l   99 (162)
T d2fxaa1          38 DLNINEHHILWIAYQLN--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYV   99 (162)
T ss_dssp             TCCHHHHHHHHHHHHHT--SEEHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEECC------CEE
T ss_pred             CCCHHHHHHHhhhccCC--CcCHHHHHHHH--cCCchhhHHHHHHHHHCCCceeecccccCeeeee
Confidence            79999999999998877  59999999999  9999999999999999999999888776544443

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.59  E-value=4.5e-05  Score=58.42  Aligned_cols=66  Identities=8%  Similarity=0.150  Sum_probs=52.6

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEE
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLM   81 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Ym   81 (233)
                      ..+||..+..|+..|..++. ++..++|.+.+  +++...++++|+.|+++|||...++-.+++.+++-
T Consensus        29 ~~glt~~q~~vL~~L~~~~g-~~t~~~La~~~--~~~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~   94 (145)
T d2hr3a1          29 ADPVQFSQLVVLGAIDRLGG-DVTPSELAAAE--RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVS   94 (145)
T ss_dssp             CCHHHHHHHHHHHHHHHTTS-CBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEC------CCEEE
T ss_pred             hcCCCHHHHHHHHHHHHcCC-CCCHHHHHHHH--CCCHHHHHHHHHHHHHcCCeEeeeCccchhHHHhc
Confidence            45788999999999976643 69999999999  99999999999999999999998888875555543

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.57  E-value=2.3e-05  Score=62.37  Aligned_cols=65  Identities=11%  Similarity=0.131  Sum_probs=52.5

Q ss_pred             CCCChHHHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           14 DSLTDHERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      .+|+..|..|+..|..+| +.|+..++|.+.+  ++...+++++|+.||++|||...++-.+++.+..
T Consensus        58 ~gLt~~q~~vL~~L~~~~~~~~lt~~eLa~~l--~i~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i  123 (172)
T d2fbka1          58 SGLNAAGWDLLLTLYRSAPPEGLRPTELSALA--AISGPSTSNRIVRLLEKGLIERREDERDRRSASI  123 (172)
T ss_dssp             TTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHC--SCCSGGGSSHHHHHHHHTSEECCC-------CCB
T ss_pred             cCCCHHHHHHHHHHHhhCCCCCcCHHHHHHHH--CcCHhHHHHHHHHHHhCCCeeeeccccchhhHHh
Confidence            479999999999998776 5689999999999  9999999999999999999999998886544433

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=97.50  E-value=0.00014  Score=49.04  Aligned_cols=57  Identities=7%  Similarity=0.166  Sum_probs=51.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKG   76 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~   76 (233)
                      |++-++.|++++...+.  +..++|.+++  |++..+|.+.+++|+++|+|+.+..+-++.
T Consensus         3 lD~~D~~IL~~L~~~~r--~s~~eiA~~l--~ls~~~v~~Ri~rL~~~GiI~~~~~~id~~   59 (63)
T d2cg4a1           3 IDNLDRGILEALMGNAR--TAYAELAKQF--GVSPETIHVRVEKMKQAGIITGARIDVSPK   59 (63)
T ss_dssp             CCHHHHHHHHHHHHCTT--SCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEEEEEECTT
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEECHH
Confidence            67889999999999988  8999999999  999999999999999999999877655443

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=97.46  E-value=0.00021  Score=48.30  Aligned_cols=56  Identities=18%  Similarity=0.293  Sum_probs=50.7

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHS   74 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~   74 (233)
                      .|++-++.|+.++.+.+.  +..++|.+++  |++..+|.+.+++|++.|+|+....+-+
T Consensus         2 klD~~D~~IL~~L~~n~r--~s~~~iA~~l--gis~~tv~~Ri~~L~~~giI~~~~~~id   57 (63)
T d2cfxa1           2 KLDQIDLNIIEELKKDSR--LSMRELGRKI--KLSPPSVTERVRQLESFGIIKQYTLEVD   57 (63)
T ss_dssp             CCCHHHHHHHHHHHHCSC--CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEEC
T ss_pred             CCCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEEEC
Confidence            488889999999999888  8999999999  9999999999999999999998765443

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.41  E-value=0.00016  Score=48.34  Aligned_cols=56  Identities=16%  Similarity=0.349  Sum_probs=50.2

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      |++-++.++.++...+.  +..++|.+++  +++..+|.+.+++|++.|+|+.+..+-++
T Consensus         1 lD~~D~~Il~~L~~n~r--~s~~eiA~~l--~ls~~~v~~Ri~~L~~~giI~~~~~~id~   56 (60)
T d2cyya1           1 LDEIDKKIIKILQNDGK--APLREISKIT--GLAESTIHERIRKLRESGVIKKFTAIIDP   56 (60)
T ss_dssp             CCHHHHHHHHHHHHCTT--CCHHHHHHHH--CSCHHHHHHHHHHHHHHTSSCCCCCCCCG
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEECH
Confidence            57788999999999888  8999999999  99999999999999999999987765543

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.40  E-value=0.00016  Score=48.40  Aligned_cols=56  Identities=14%  Similarity=0.366  Sum_probs=50.1

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSK   75 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~   75 (233)
                      |++-++.|+.++.+.+.  +..++|.+++  +++..+|.+.+++|++.|+|+....+-++
T Consensus         1 lD~~D~kIl~~L~~n~r--~s~~~lA~~~--gls~~~v~~Ri~~L~~~giI~~~~~~id~   56 (60)
T d1i1ga1           1 IDERDKIILEILEKDAR--TPFTEIAKKL--GISETAVRKRVKALEEKGIIEGYTIKINP   56 (60)
T ss_dssp             CCSHHHHHHHHHHHCTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHHTSSCCCCCCCCS
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEECH
Confidence            57788999999999888  8999999999  99999999999999999999877665443

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.40  E-value=0.00017  Score=50.16  Aligned_cols=54  Identities=19%  Similarity=0.347  Sum_probs=48.5

Q ss_pred             CCCChHHHHHHHHHHh-hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           14 DSLTDHERLIYDVIRS-KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~-aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ++|++-++.||++|.+ .++.||...+|++++ .+|+..+|++++..|.+.|+|=+
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l-~~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQL-KHMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHS-TTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHc-cCCCHHHHHHHHHHHHhCCceec
Confidence            5899999999999984 468899999999997 25999999999999999999953

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=97.33  E-value=0.00032  Score=48.53  Aligned_cols=56  Identities=23%  Similarity=0.394  Sum_probs=47.7

Q ss_pred             CCCChHHHHHHHHHHhhC---CCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhCCCceeeec
Q 026799           14 DSLTDHERLIYDVIRSKQ---DMGIWTRDMKRELRVNL-PDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG---~~GIw~~dik~~t~~~l-~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +.||+-|+.||++|.+.-   +---..+||.+..  |+ .++++.+.|+.||++|+|+..+.
T Consensus         1 ~~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~--g~~S~stv~~~l~~Le~kG~I~r~~~   60 (71)
T d1jhfa1           1 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRL--GFRSPNAAEEHLKALARKGVIEIVSG   60 (71)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHT--TCSSHHHHHHHHHHHHHTTSEEECSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHc--CCCCHHHHHHHHHHHHHCcCeecCCC
Confidence            469999999999998543   2347899999999  99 67899999999999999988654

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=97.30  E-value=0.00033  Score=47.90  Aligned_cols=50  Identities=26%  Similarity=0.335  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      ....||++|...|.  +...||.+.+  +|+..+|+++|+.|++.|+|.+....
T Consensus         7 N~~~Il~~l~~~g~--~sr~eLa~~~--glS~~Tv~~~l~~L~~~Glv~e~~~~   56 (71)
T d1z05a1           7 NAGRVYKLIDQKGP--ISRIDLSKES--ELAPASITKITRELIDAHLIHETTVQ   56 (71)
T ss_dssp             HHHHHHHHHHHHCS--BCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECHH
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCc
Confidence            45689999999886  9999999999  99999999999999999999876543

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.22  E-value=0.0029  Score=47.47  Aligned_cols=112  Identities=15%  Similarity=0.251  Sum_probs=74.2

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .||+-|..|.++|=+.|  ++..+||...++.  +++.++|...|+.|++||+|+.-+.   .+..+|-     |...  
T Consensus         3 ~ls~~E~~VM~~lW~~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~---gr~~~Y~-----~~v~--   70 (122)
T d1sd4a_           3 EISMAEWDVMNIIWDKK--SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS---ENIYFYS-----SNIK--   70 (122)
T ss_dssp             CCCHHHHHHHHHHHHSS--SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEE-----ECSC--
T ss_pred             CCCHHHHHHHHHHHcCC--CCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeecc---CCeEEEe-----ecCC--
Confidence            58999999999999987  4999999999843  8999999999999999999986443   2233442     1111  


Q ss_pred             cCCcccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHH
Q 026799           93 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAL  155 (233)
Q Consensus        93 GG~wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~L  155 (233)
                                -.+   .+.....+++.+.-.-+...+..++-+..    .||.+|+++|-+.|
T Consensus        71 ----------~~~---~~~~~~~~~~~~~~~gs~~~lv~~~~~~~----~ls~~el~eL~~~l  116 (122)
T d1sd4a_          71 ----------EDD---IKMKTAKTFLNKLYGGDMKSLVLNFAKNE----ELNNKEIEELRDIL  116 (122)
T ss_dssp             ----------HHH---HHHHHHHHHHHHHHTTCHHHHHHHHHHTT----CSCHHHHHHHHHHH
T ss_pred             ----------HHH---HHHHHHHHHHHHHhCCCHHHHHHHHHhCC----CCCHHHHHHHHHHH
Confidence                      112   33333444444321113444444444333    68999998877665

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=97.07  E-value=0.00061  Score=48.43  Aligned_cols=37  Identities=11%  Similarity=0.195  Sum_probs=34.2

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           31 QDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        31 G~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      .+.+|..++|.+++  ++++..++++|+.||++|||++-
T Consensus        18 ~~~~lt~~eLa~~l--~i~~~~vs~~l~~Le~~GlV~r~   54 (85)
T d3ctaa1          18 NRAYLTSSKLADML--GISQQSASRIIIDLEKNGYITRT   54 (85)
T ss_dssp             SEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeee
Confidence            34579999999999  99999999999999999999983

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.94  E-value=0.00073  Score=46.23  Aligned_cols=49  Identities=18%  Similarity=0.280  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ....|+++|...|.  +...||.+.+  +|+..+|++++..|++.|+|.+...
T Consensus         6 N~~~Il~~i~~~g~--~sr~eLa~~~--gLS~~Tvs~iv~~L~~~glv~e~g~   54 (70)
T d1z6ra1           6 NAGAVYRLIDQLGP--VSRIDLSRLA--QLAPASITKIVHEMLEAHLVQELEI   54 (70)
T ss_dssp             HHHHHHHHHHSSCS--CCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEC--
T ss_pred             HHHHHHHHHHHcCC--cCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeeCC
Confidence            45789999998877  9999999999  9999999999999999999988643

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.59  E-value=0.0025  Score=42.76  Aligned_cols=45  Identities=22%  Similarity=0.260  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      =+.||.+.++.|.  +..+||.+.+  |+.+..|+..+|+|+++|||..
T Consensus         9 Lk~I~~l~~~~~~--v~~~~iA~~L--~vs~~SVs~mikrL~~~GlV~~   53 (61)
T d2ev0a1           9 IEQIYMLIEEKGY--ARVSDIAEAL--AVHPSSVTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             HHHHHHHHHHHSS--CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHhcCCC--ccHHHHHHHh--CCCchhHHHHHHHHHHCCCEEE
Confidence            3578888887764  9999999999  9999999999999999999965

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.57  E-value=0.0025  Score=43.11  Aligned_cols=44  Identities=16%  Similarity=0.330  Sum_probs=39.1

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.||.+.++.|.  +...||.+.+  +..+.+|++.+|+|+++|||.-
T Consensus        12 ~~I~~L~~~~~~--v~~~~iA~~L--~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          12 RTIYDLEEEGVT--PLRARIAERL--DQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             HHHHHHHHTTCC--CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhcCCC--CcHHHHHHHh--CCCchhHHHHHHHHHHCCCEEE
Confidence            568877766654  9999999999  9999999999999999999965

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=96.23  E-value=0.0037  Score=41.81  Aligned_cols=47  Identities=19%  Similarity=0.198  Sum_probs=41.3

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .|+++|.+ |  .|...||.+.+  +|+..+|+++++.|++.|+|.+.....
T Consensus         3 ~Il~~i~~-~--pisr~eLa~~~--gls~~TVs~~v~~L~~~GlV~e~~~~~   49 (62)
T d2hoea1           3 RILKRIMK-S--PVSRVELAEEL--GLTKTTVGEIAKIFLEKGIVVEEKDSP   49 (62)
T ss_dssp             CSHHHHHH-S--CBCHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEECCC
T ss_pred             HHHHHHHH-C--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEECCCCC
Confidence            36788874 4  49999999999  999999999999999999999987554

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=95.98  E-value=0.013  Score=43.62  Aligned_cols=56  Identities=13%  Similarity=0.119  Sum_probs=44.7

Q ss_pred             HhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           28 RSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        28 ~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      .-|.+..+..++|.+.+  ++++..|.|+|+.|.+.|||++++-.. .+   | |.  .|.++||
T Consensus        12 ~la~~~~~ss~~IA~~~--~~~~~~v~kIl~~L~~aglV~s~rG~~-GG---y-La--r~p~~It   67 (127)
T d1xd7a_          12 LISMDEKTSSEIIADSV--NTNPVVVRRMISLLKKADILTSRAGVP-GA---S-LK--KDPADIS   67 (127)
T ss_dssp             HHHTCSCCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEECCSSSS-SC---E-ES--SCGGGCB
T ss_pred             HHhcCCCCCHHHHHHHh--CcCHHHHHHHHHHHHHhCcccccCCCC-Cc---c-cc--CCHHhCc
Confidence            33456779999999999  999999999999999999998877743 33   5 54  3555655

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.96  E-value=0.0096  Score=46.04  Aligned_cols=57  Identities=16%  Similarity=0.218  Sum_probs=44.5

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +|+..+. .|.  .--.||++.+  ++++++|++.||.|++.|||.++.+ +.+.+..|.|.+
T Consensus        24 ~Il~~l~-~G~--~rf~el~~~l--gis~~vLs~rL~~L~~~gLv~r~~~-~~p~r~~Y~LT~   80 (142)
T d2f2ea1          24 LIVRDAF-EGL--TRFGEFQKSL--GLAKNILAARLRNLVEHGVMVAVPA-ESGSHQEYRLTD   80 (142)
T ss_dssp             HHHHHHH-TTC--CSHHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEEEC-SSSSCEEEEECH
T ss_pred             HHHHHHH-cCC--CCHHHHHHHh--hccHHHHHHHHHHHHHhcceeeecC-CCCCeeEEecCc
Confidence            3444443 355  6689999999  9999999999999999999998654 556777787653

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=95.83  E-value=0.038  Score=39.65  Aligned_cols=44  Identities=14%  Similarity=0.315  Sum_probs=36.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .|+.++.   +......+|...+  ++++.++++.|+.|++.|||+.-+
T Consensus        27 ~Il~~L~---~~~~~v~ela~~l--~is~stvS~HL~~L~~aglV~~~r   70 (98)
T d1r1ta_          27 RLLSLLA---RSELCVGDLAQAI--GVSESAVSHQLRSLRNLRLVSYRK   70 (98)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEE
Confidence            3444552   3458999999999  999999999999999999998764

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.78  E-value=0.033  Score=43.58  Aligned_cols=58  Identities=14%  Similarity=0.150  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc--cCCCeeeEEe
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI--HSKGKKHLMA   82 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV--~~~~rK~Yml   82 (233)
                      =+.|+.++. .|  .....+|...+  ++++.+++++|+.|++.|||...+.-  ....+|+|-+
T Consensus        21 R~~Il~~L~-~~--~~s~~ela~~l--g~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~   80 (190)
T d1ulya_          21 RRKILKLLR-NK--EMTISQLSEIL--GKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGR   80 (190)
T ss_dssp             HHHHHHHHT-TC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEE
T ss_pred             HHHHHHHHH-hC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEE
Confidence            345788774 34  48999999999  99999999999999999999876532  2233577744

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.77  E-value=0.021  Score=38.15  Aligned_cols=32  Identities=19%  Similarity=0.335  Sum_probs=30.8

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.+.||..-+  |++..+|+|+|+.|++.|+|+.
T Consensus        30 lt~~~lA~~~--G~sRetvsr~L~~l~~~glI~~   61 (69)
T d1i5za1          30 ITRQEIGQIV--GCSRETVGRILKMLEDQNLISA   61 (69)
T ss_dssp             CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            8999999999  9999999999999999999975

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.72  E-value=0.012  Score=42.23  Aligned_cols=45  Identities=18%  Similarity=0.250  Sum_probs=40.1

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+|+++++.. ..|+-...|..+.  ||+...+.+.|+.|+++|||+.
T Consensus         6 eIi~DIL~~~-~~g~~kT~i~~~a--NLs~~~~~kyl~~L~~~GLI~~   50 (90)
T d1r7ja_           6 EIIQAILEAC-KSGSPKTRIMYGA--NLSYALTGRYIKMLMDLEIIRQ   50 (90)
T ss_dssp             HHHHHHHHHH-TTCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHH-hCCCCccHHHHHc--CCCHHHHHHHHHHHHHCCCeee
Confidence            4788888877 4688899999999  9999999999999999999975

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.69  E-value=0.018  Score=38.30  Aligned_cols=47  Identities=17%  Similarity=0.292  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           20 ERLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        20 e~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      |..|+..+++-| .+-+..++|..++  ++|.+.|+|+|=+|+++|....
T Consensus         1 Eq~vl~~l~~lg~~~~~tA~~LA~kl--~vpKk~iNr~LYsL~~kgkl~k   48 (59)
T d2gxba1           1 EQRILKFLEELGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQK   48 (59)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ChHHHHHHHhcCCccchhHHHHHHHh--CCcHHHHHHHHHHHHHccchhh
Confidence            567889999866 7889999999999  9999999999999999998765

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.69  E-value=0.013  Score=43.67  Aligned_cols=59  Identities=22%  Similarity=0.298  Sum_probs=50.5

Q ss_pred             CCCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhCCCceeeec
Q 026799           12 PSDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRV--NLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~--~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      ++..|++-|..|+++|=+.| .++..+||...++.  ++..++|...|+.|++||+|+..+.
T Consensus         1 k~~~L~~~E~~IM~~lW~~g-~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~   61 (122)
T d2g9wa1           1 KLTRLGDLERAVMDHLWSRT-EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD   61 (122)
T ss_dssp             CGGGCCHHHHHHHHHHHTCS-SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             CCCCCCHHHHHHHHHHHcCC-CCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeec
Confidence            35679999999999999876 45899999999843  6889999999999999999987653

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=95.68  E-value=0.025  Score=39.55  Aligned_cols=57  Identities=18%  Similarity=0.224  Sum_probs=49.2

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHh--hcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKREL--RVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t--~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      +..|++.|..|.++|=+.|  .+..+||...+  +.+.+.++|...|..|++||+|..-+.
T Consensus         4 ~~~Ls~~E~~IM~~lW~~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~   62 (82)
T d1p6ra_           4 IPQISDAELEVMKVIWKHS--SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCHHHHHHHHHHHTSS--SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHhCC--CCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEec
Confidence            5579999999999999866  48999998887  338899999999999999999987544

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=95.65  E-value=0.023  Score=40.73  Aligned_cols=59  Identities=19%  Similarity=0.299  Sum_probs=45.4

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +|+..| ..|.  .--.+|++.. ++++++++++.||.||+.|||.+...=..|.+..|.|.+
T Consensus        15 ~Il~~L-~~g~--~rF~el~~~l-~gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~   73 (95)
T d2hzta1          15 VILCHL-THGK--KRTSELKRLM-PNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSE   73 (95)
T ss_dssp             HHHHHH-TTCC--BCHHHHHHHC-TTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             HHHHHH-HcCC--CCHHHHHHHh-hcCChhHHHHHHHHHHHhHHHhheeccccccchhhhhhh
Confidence            344445 3455  5689999883 289999999999999999999987665667777787754

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=95.58  E-value=0.017  Score=39.51  Aligned_cols=44  Identities=2%  Similarity=0.033  Sum_probs=36.3

Q ss_pred             HHHHHHhhCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           23 IYDVIRSKQDMG--------IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        23 Vy~~I~~aG~~G--------Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ++.+.+..|..+        +.+.||..-+  |++..+|+|+|+.|++.|+|..
T Consensus        10 Ll~l~~~~g~~~~~~~i~~~lt~~eLA~~~--G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          10 LLILKENFGFENDGATLSIYLSREELATLS--NMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             HHHHHHHHCBCTTSSBBSCCCCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhCCCCCCCEEeecCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence            455555555443        6899999999  9999999999999999999964

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.55  E-value=0.016  Score=41.40  Aligned_cols=57  Identities=12%  Similarity=0.209  Sum_probs=44.5

Q ss_pred             CCChHHHHHHHHHHh---hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecc
Q 026799           15 SLTDHERLIYDVIRS---KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNI   72 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~---aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV   72 (233)
                      .||+-++.|+..|.+   .-..-+..++|.+..+.++.+.+|+..|+.||++|+|+. ...
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~-~h~   60 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ-PHT   60 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC-CSS
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC-CCC
Confidence            378888888886653   234569999999998224569999999999999999977 444

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=95.40  E-value=0.026  Score=41.05  Aligned_cols=50  Identities=18%  Similarity=0.205  Sum_probs=41.0

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           34 GIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        34 GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      -.--.+|++.. ++++++++++.||.||+.|+|.+...=..|.+..|-|.+
T Consensus        33 ~~rF~el~~~l-~gIs~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~   82 (102)
T d2fswa1          33 IIRYGELKRAI-PGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTP   82 (102)
T ss_dssp             CEEHHHHHHHS-TTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECH
T ss_pred             CCCHHHHHhhC-cccchhHHHHHHHHHHHCCceeecccCCCCCeehhhhhH
Confidence            37789999984 289999999999999999999886655556677787765

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=95.36  E-value=0.028  Score=38.29  Aligned_cols=51  Identities=20%  Similarity=0.238  Sum_probs=39.9

Q ss_pred             CChHHHHHHHHHHhhCC---Cc---ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQD---MG---IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~---~G---Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      ++-+++++.-++..+..   .+   +.+.||..-+  |++..+|+|+|+.|+++|+|..
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~l--g~sr~tvsr~l~~l~~~g~I~~   59 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCL--DDTRLNISKTLNELQDNGLIEL   59 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSCEE
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence            34466666655554332   22   7999999999  9999999999999999999964

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.33  E-value=0.018  Score=39.42  Aligned_cols=44  Identities=16%  Similarity=0.213  Sum_probs=37.7

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      .|+++|..+ ..++..+||.+++  ++|..++.|.|+.|++.|++.+
T Consensus         9 ~IL~~~a~~-~~~~s~~eia~~~--~~~~st~~rll~tL~~~g~l~~   52 (75)
T d1mkma1           9 EILDFIVKN-PGDVSVSEIAEKF--NMSVSNAYKYMVVLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            345555544 4689999999999  9999999999999999999976

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=95.33  E-value=0.019  Score=43.13  Aligned_cols=60  Identities=12%  Similarity=0.136  Sum_probs=44.8

Q ss_pred             HHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcc
Q 026799           24 YDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEIS   92 (233)
Q Consensus        24 y~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiT   92 (233)
                      +-++....++-+..++|..++  ++|+..|.|+|+.|.+.|||++.+- + .|   |.|.  .|.++||
T Consensus        13 L~~la~~~~~~vss~~IA~~~--~i~~~~l~kil~~L~~aGlv~S~rG-~-GG---~~L~--~~p~~It   72 (138)
T d1ylfa1          13 LSILKNNPSSLCTSDYMAESV--NTNPVVIRKIMSYLKQAGFVYVNRG-P-GG---AGLL--KDLHEIT   72 (138)
T ss_dssp             HHHHHHSCGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC-----CC---EEES--SCGGGCB
T ss_pred             HHHHHhCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeecC-C-CC---ceec--CCHhhcC
Confidence            334443445569999999999  9999999999999999999988766 4 33   6675  4666666

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.23  E-value=0.012  Score=40.86  Aligned_cols=49  Identities=8%  Similarity=0.189  Sum_probs=44.5

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCCh-HHHHHHHHHHHhCCCcee
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPD-NIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~-~~v~k~LK~Le~k~lIK~   68 (233)
                      |++.|..||+++++.|.  ....+|.+++  ||+. +.|+++|=.|+.+|.+..
T Consensus         3 ~~d~eekI~~~L~~~g~--~~Al~iak~l--Gl~kakeVN~~LY~L~k~g~v~k   52 (73)
T d1xmka1           3 MAEIKEKICDYLFNVSD--SSALNLAKNI--GLTKARDINAVLIDMERQGDVYR   52 (73)
T ss_dssp             HHHHHHHHHHHHHHTCC--EEHHHHHHHH--CGGGHHHHHHHHHHHHHTTSEEE
T ss_pred             hHHHHHHHHHHHHHcCC--chHHHHHHHh--CCCcHHHHhHHHHHHHHCCCeec
Confidence            45678899999999996  8899999999  9999 589999999999999976

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.14  E-value=0.032  Score=36.97  Aligned_cols=46  Identities=9%  Similarity=0.092  Sum_probs=38.9

Q ss_pred             ChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           17 TDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        17 ~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      ++-...|+.++.+  +.-+...+|.+++  |++.++|.+-|+.|++.|++
T Consensus         4 ~~~~~~iL~~L~~--~~~~s~~eLa~~l--~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           4 NTVPLKLIALLAN--GEFHSGEQLGETL--GMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             CHHHHHHHHHHTT--SSCBCHHHHHHHH--TSCHHHHHHHHHHHHHTTCC
T ss_pred             cHHHHHHHHHHHH--CCcCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCc
Confidence            4455678888854  4459999999999  99999999999999999984

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.03  E-value=0.044  Score=43.33  Aligned_cols=60  Identities=20%  Similarity=0.315  Sum_probs=47.3

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee--cccCCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV--NIHSKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk--sV~~~~rK~Yml~~   84 (233)
                      =..|+.++.. |  .....+|..++  ++++..|++.|+.|++.|||...+  +...+.+++|.+.+
T Consensus        17 R~~Il~~L~~-~--~~~~~ela~~l--~~s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~   78 (194)
T d2p4wa1          17 RRRILFLLTK-R--PYFVSELSREL--GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKK   78 (194)
T ss_dssp             HHHHHHHHHH-S--CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECT
T ss_pred             HHHHHHHHHh-C--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEecc
Confidence            3457777753 4  48999999999  999999999999999999998654  33345577887654

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.88  E-value=0.031  Score=41.40  Aligned_cols=50  Identities=10%  Similarity=0.230  Sum_probs=42.0

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecc
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEF   85 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~l   85 (233)
                      .--.+|++.+ +++++++|++.||.||+.|||.+...=..|.+..|.|.+.
T Consensus        38 ~RF~el~~~l-~gis~~~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~   87 (114)
T d1yyva1          38 HRFSDLRRKM-GGVSEKMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPL   87 (114)
T ss_dssp             EEHHHHHHHS-TTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHH
T ss_pred             CCHHHHHHHc-cccchhHHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHh
Confidence            5688999987 3699999999999999999998877666678888887653

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=94.82  E-value=0.043  Score=37.72  Aligned_cols=49  Identities=14%  Similarity=0.173  Sum_probs=42.0

Q ss_pred             HHHHHHHHhhC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeec
Q 026799           21 RLIYDVIRSKQ-DMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVN   71 (233)
Q Consensus        21 ~lVy~~I~~aG-~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vks   71 (233)
                      .+|-+.+.+-| ++++...+|.+++  +++.+.|+|+|=+|+++|.+..+..
T Consensus        10 ~lvk~~l~~L~~~~~~tA~~LAk~L--g~~Kk~VNr~LY~L~~~G~v~~~~~   59 (70)
T d1sfua_          10 SLVKKEVLSLNTNDYTTAISLSNRL--KINKKKINQQLYKLQKEDTVKMVPS   59 (70)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHhcCCCCCchHHHHHHHh--CCCHHHHHHHHHHHHHCCCeecCCC
Confidence            45666666555 7899999999999  9999999999999999999987654

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=94.65  E-value=0.047  Score=37.26  Aligned_cols=32  Identities=9%  Similarity=0.200  Sum_probs=30.3

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.+.||..-+  |++..+|+|+|+.|+++|+|+.
T Consensus        31 ~t~~eiA~~l--G~sretvsr~l~~l~~~g~I~~   62 (80)
T d1ft9a1          31 FTVEEIANLI--GSSRQTTSTALNSLIKEGYISR   62 (80)
T ss_dssp             CCHHHHHHHH--CSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            5799999999  9999999999999999999975

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=94.60  E-value=0.032  Score=40.31  Aligned_cols=66  Identities=9%  Similarity=0.176  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHhhCCCcccHHH-HHHHh-hc-CCChHHHHHHHHHHHhCCCceee--ecccCCCeeeEEeec
Q 026799           19 HERLIYDVIRSKQDMGIWTRD-MKREL-RV-NLPDNIVTKSIKSLQNKSLIKEV--VNIHSKGKKHLMAVE   84 (233)
Q Consensus        19 ~e~lVy~~I~~aG~~GIw~~d-ik~~t-~~-~l~~~~v~k~LK~Le~k~lIK~v--ksV~~~~rK~Yml~~   84 (233)
                      -+.+|+.+|.+.-..|-..+. |...+ +. +++..+|-.+|++||++|+|.+-  .+-..+.||+|.+.+
T Consensus         8 l~~~IL~lL~~~~~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~   78 (103)
T d1xmaa_           8 VDTIILSLLIEGDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITP   78 (103)
T ss_dssp             HHHHHHHHHHHCCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECH
T ss_pred             HHHHHHHHHhhCCccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECH
Confidence            467888888774444443322 23233 11 69999999999999999999863  344556789997765

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=94.49  E-value=0.064  Score=39.28  Aligned_cols=59  Identities=8%  Similarity=0.159  Sum_probs=44.4

Q ss_pred             HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           22 LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        22 lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      +|+..|. .|.  .--.||++.. +++++++|++.||.||+.|||.+...=..|.+..|-|.+
T Consensus        23 ~Il~~L~-~g~--~RF~el~~~l-~gIS~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~   81 (108)
T d1z7ua1          23 SLMDELF-QGT--KRNGELMRAL-DGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTP   81 (108)
T ss_dssp             HHHHHHH-HSC--BCHHHHHHHS-TTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECH
T ss_pred             HHHHHHH-cCC--CCHHHHHHHC-cCCChhHHHHHHHHHHHCCcceeeccCCCcceehhhhch
Confidence            4455554 365  4689999995 279999999999999999999875554556676776654

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=94.20  E-value=0.09  Score=34.90  Aligned_cols=53  Identities=8%  Similarity=0.144  Sum_probs=44.2

Q ss_pred             CChHHHHHHH----HHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           16 LTDHERLIYD----VIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        16 L~~~e~lVy~----~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      |+++|+.+.+    +..++|-.=-|.+||-..+  |++...+...|+.|...|.+-+|+
T Consensus         1 ls~~q~~l~~~I~~~~~~~g~~PP~vrdl~~~l--~~~e~~~~~lL~~l~~~G~lvkI~   57 (64)
T d1lvaa3           1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSF--NLDPSELEELLHYLVREGVLVKIN   57 (64)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec
Confidence            4566665554    4458898999999999999  999999999999999999886653

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.05  E-value=0.066  Score=38.09  Aligned_cols=61  Identities=20%  Similarity=0.260  Sum_probs=45.5

Q ss_pred             CCCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           14 DSLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        14 ~~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      +.|.+.-| .|+.++.. |.  ....+|...+  ++++.++++.|+.|+..|||+.-+   ..+...|-|
T Consensus        13 kaL~d~~Rl~Il~~L~~-~~--~~v~el~~~l--~~s~~~vS~HL~~L~~~glv~~~r---~G~~~~Y~l   74 (94)
T d1r1ua_          13 KALGDYNRIRIMELLSV-SE--ASVGHISHQL--NLSQSNVSHQLKLLKSVHLVKAKR---QGQSMIYSL   74 (94)
T ss_dssp             HHTCSHHHHHHHHHHHH-CC--BCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE---ETTEEEEEE
T ss_pred             HHhCCHHHHHHHHHHHc-CC--ccHHHHHHHH--CCCHHHHHHHHHHHHHCCceEEEE---ECCEEEEEE
Confidence            34555433 46666653 54  7789999999  999999999999999999998764   334455544

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.04  E-value=0.089  Score=38.28  Aligned_cols=46  Identities=9%  Similarity=0.106  Sum_probs=38.1

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..|+..+...|  +....+|...+  ++++.++++.|+.|++.|||+.-+
T Consensus        34 l~Il~~L~~~~--~~~v~ela~~l--~~s~s~vS~HL~~L~~aGlv~~~r   79 (108)
T d1u2wa1          34 AKITYALCQDE--ELCVCDIANIL--GVTIANASHHLRTLYKQGVVNFRK   79 (108)
T ss_dssp             HHHHHHHHHSS--CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHhCC--CccHHHHHHHH--ccChhHHHHHHHHHHHCCeeEEEE
Confidence            35666665444  48899999999  999999999999999999998754

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=93.53  E-value=0.1  Score=34.80  Aligned_cols=46  Identities=15%  Similarity=0.265  Sum_probs=37.9

Q ss_pred             HHHHHHHh--------hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRS--------KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~--------aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .||+.|++        .|.. +..++|.++.  ++...+|+++|+.|+..|+|...+
T Consensus         6 qi~~~l~~~I~~g~~~~G~~-l~~~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~~   59 (69)
T d2hs5a1           6 RVAGILRDAIIDGTFRPGAR-LSEPDICAAL--DVSRNTVREAFQILIEDRLVAHEL   59 (69)
T ss_dssp             HHHHHHHHHHHHTSSCTTCE-ECHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHcCCCCCcCc-cCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEEc
Confidence            46666653        3444 6789999999  999999999999999999997753

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=93.23  E-value=0.071  Score=36.22  Aligned_cols=32  Identities=9%  Similarity=0.268  Sum_probs=30.0

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhCCCcee
Q 026799           35 IWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        35 Iw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~   68 (233)
                      +.+.||..-+  |++..+|+|+|+.|++.|+|+.
T Consensus        31 lt~~elA~~~--g~sretvsr~l~~l~~~glI~~   62 (80)
T d3e5ua1          31 LSQKSIGEIT--GVHHVTVSRVLASLKRENILDK   62 (80)
T ss_dssp             CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEe
Confidence            6789999999  9999999999999999999963

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=91.94  E-value=0.32  Score=35.95  Aligned_cols=104  Identities=17%  Similarity=0.159  Sum_probs=72.6

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccCC
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGGA   95 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG~   95 (233)
                      |+.+.+.  .+|+.. ..|+..++|.+++  +.+..+|.|.++...+.|.+..-+.=..+.+.                 
T Consensus        17 Ls~dlR~--rIv~~~-~~G~s~r~iA~~~--~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~-----------------   74 (123)
T d1pdnc_          17 LPNNIRL--KIVEMA-ADGIRPCVISRQL--RVSHGCVSKILNRYQETGSIRPGVIGGSKPRI-----------------   74 (123)
T ss_dssp             CCHHHHH--HHHHHH-HTTCCHHHHHHHH--TCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCS-----------------
T ss_pred             CCHHHHH--HHHHHH-HhcCCHHHHHHHH--CcCHHHHHHHHHHHHccCCcCcCCCCCCCCCC-----------------
Confidence            5554332  233333 3589999999999  99999999999999999998654321111110                 


Q ss_pred             cccCCCCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCcc--cccCHHHHHHH
Q 026799           96 WYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK--VDLTKQQIEEI  151 (233)
Q Consensus        96 wy~d~e~D~efI~~l~~~~~~~i~~~~~~T~~~I~~~I~~~~i~~--~~Ls~~di~~i  151 (233)
                            .    .+.....+..++..++..|+.||.+.+...|+..  ...|+.-|..+
T Consensus        75 ------~----t~~~~~~I~~~~~~~P~~t~~El~~~L~~egv~~~~~~pSvStI~Ri  122 (123)
T d1pdnc_          75 ------A----TPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRL  122 (123)
T ss_dssp             ------S----CSTHHHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHH
T ss_pred             ------C----CHHHHHHHHHHHHhCCCccHHHHHHHHHHcCCCCCCCCCChhhHhhc
Confidence                  0    1234566777788899999999999999999753  35666666554

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=91.84  E-value=0.15  Score=33.64  Aligned_cols=45  Identities=27%  Similarity=0.437  Sum_probs=40.2

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      +..||+-|..|+.++.+    |...++|..++  +++.++|...++.+-.|
T Consensus         4 l~~LT~rE~~vl~ll~~----G~s~~eIA~~l--~iS~~TV~~~~~~i~~K   48 (67)
T d1a04a1           4 VNQLTPRERDILKLIAQ----GLPNKMIARRL--DITESTVKVHVKHMLKK   48 (67)
T ss_dssp             GGGSCHHHHHHHHHHHT----TCCHHHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHh----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            56799999999999985    78999999999  99999999999887653

>d1fnna1 a.4.5.11 (A:277-388) CDC6, C-terminal domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6, C-terminal domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=91.81  E-value=0.14  Score=37.43  Aligned_cols=59  Identities=17%  Similarity=0.105  Sum_probs=46.5

Q ss_pred             CCCCCChHHHHHHHHH----HhhCCCcccHHHHHH-------Hhhc-CCChHHHHHHHHHHHhCCCceeee
Q 026799           12 PSDSLTDHERLIYDVI----RSKQDMGIWTRDMKR-------ELRV-NLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I----~~aG~~GIw~~dik~-------~t~~-~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .+++||.++++|+..|    +..++..|.+.++-.       +.+. .+.++.+...|+.|+..|+|....
T Consensus         5 ~i~~Lp~h~klvL~ai~~~~~~~~~~~ittgevy~~Y~~lc~~~~~~pls~rr~~~~l~~Le~lGiI~~r~   75 (112)
T d1fnna1           5 VLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQ   75 (112)
T ss_dssp             HHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHhCCCeeeee
Confidence            3568999999998766    345777788877744       3434 678999999999999999998755

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein TM0937
species: Thermotoga maritima [TaxId: 2336]

Probab=91.60  E-value=0.13  Score=37.48  Aligned_cols=65  Identities=9%  Similarity=0.020  Sum_probs=41.6

Q ss_pred             HHHHHHHHHhhCCCcccH-HHHHHHh-hc--CCChHHHHHHHHHHHhCCCceeeecc-cCCCeeeEEeec
Q 026799           20 ERLIYDVIRSKQDMGIWT-RDMKREL-RV--NLPDNIVTKSIKSLQNKSLIKEVVNI-HSKGKKHLMAVE   84 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~-~dik~~t-~~--~l~~~~v~k~LK~Le~k~lIK~vksV-~~~~rK~Yml~~   84 (233)
                      +..|+.+|.+.-..|--. +.|.... +.  .++..+|-.+|+.||++|+|++.... ..+.||+|-+.+
T Consensus        12 ~~~iL~lL~~~~~~GYei~~~i~~~~~~~~~~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~   81 (114)
T d2esha1          12 ASTILLLVAEKPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITP   81 (114)
T ss_dssp             HHHHHHHHHHSCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECH
T ss_pred             HHHHHHHHhcCCccHHHHHHHHHHhcCCCcccCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECH
Confidence            456777776654444433 2233221 11  45678999999999999999875432 335588886643

>d1w5sa1 a.4.5.11 (A:300-409) CDC6-like protein APE0152, C-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6-like protein APE0152, C-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=91.48  E-value=0.27  Score=36.11  Aligned_cols=60  Identities=17%  Similarity=0.096  Sum_probs=48.6

Q ss_pred             CCCCCCChHHHHHHHHHHhh---CCCcccHHHHHHHh--------hc-CCChHHHHHHHHHHHhCCCceeee
Q 026799           11 APSDSLTDHERLIYDVIRSK---QDMGIWTRDMKREL--------RV-NLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        11 ~~~~~L~~~e~lVy~~I~~a---G~~GIw~~dik~~t--------~~-~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .++++||.+|++|+..|..+   |..-|.+.+|.+.-        +. .+..+++.+.|+.|+..|+|....
T Consensus         2 ~~l~~L~~H~~lvL~~I~~~~~~~~~~~~tGei~~~Y~ev~c~~~~~~P~~~t~~~~~l~~Le~lGiI~~r~   73 (110)
T d1w5sa1           2 HELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKP   73 (110)
T ss_dssp             CSSSSSCHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             chhhccCHhHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHcCCeEEEe
Confidence            46889999999999988754   77888899887653        11 367889999999999999998654

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.24  E-value=0.5  Score=34.72  Aligned_cols=68  Identities=12%  Similarity=0.102  Sum_probs=53.5

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeec
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELR---VNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVE   84 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~---~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~   84 (233)
                      .+|+.=+.|+++|.+++++=....+|-..++   +.+...+|-|.|+.|++.|+|.++..-.  +...|-+.+
T Consensus        13 R~T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~~~--~~~~y~~~~   83 (134)
T d1mzba_          13 KVTLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDG--GHAVFELAD   83 (134)
T ss_dssp             CCCHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSS--SSCEEEESS
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEeecC--CceEEEecC
Confidence            4688888999999998777788899988762   4688899999999999999999866544  345565544

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.04  E-value=0.3  Score=31.97  Aligned_cols=45  Identities=13%  Similarity=0.269  Sum_probs=37.8

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCC-cee
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSL-IKE   68 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~l-IK~   68 (233)
                      ..|++++.++ +..+...+|..++  +.+.++|.|-|+.|++.|+ |.+
T Consensus        10 ~~Il~~L~~~-~~~vs~~~La~~l--~VS~~TI~rdi~~L~~~G~~I~~   55 (65)
T d1j5ya1          10 KSIVRILERS-KEPVSGAQLAEEL--SVSRQVIVQDIAYLRSLGYNIVA   55 (65)
T ss_dssp             HHHHHHHHHC-SSCBCHHHHHHHH--TSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHc-CCCCcHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEE
Confidence            3577777664 4569999999999  9999999999999999997 543

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.88  E-value=0.15  Score=34.60  Aligned_cols=32  Identities=6%  Similarity=0.187  Sum_probs=30.4

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceee
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEV   69 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~v   69 (233)
                      ..++|.++.  ++...+|+++|+.|+..|+|...
T Consensus        29 s~~eLa~~~--~vSr~tvr~Al~~L~~~G~i~~~   60 (74)
T d1hw1a1          29 AERELSELI--GVTRTTLREVLQRLARDGWLTIQ   60 (74)
T ss_dssp             CHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE
Confidence            689999999  99999999999999999999875

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=90.64  E-value=0.16  Score=36.56  Aligned_cols=33  Identities=12%  Similarity=0.247  Sum_probs=29.9

Q ss_pred             cccHHHHHHHhhcCCC-hHHHHHHHHHHHhCCCcee
Q 026799           34 GIWTRDMKRELRVNLP-DNIVTKSIKSLQNKSLIKE   68 (233)
Q Consensus        34 GIw~~dik~~t~~~l~-~~~v~k~LK~Le~k~lIK~   68 (233)
                      .+.+.||..-+  |+. ..+|+|+|+.|++.|+|+.
T Consensus        31 ~lTqeeLA~~l--G~s~ReTVsR~L~~L~~~GlI~~   64 (100)
T d2bgca1          31 NLTMQELGYSS--GIAHSSAVSRIISKLKQEKVIVY   64 (100)
T ss_dssp             CCCHHHHHHHT--TCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHh--CCchHHHHHHHHHHHHHCCCEEE
Confidence            47899999999  996 5789999999999999975

>d2v9va2 a.4.5.35 (A:438-510) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=90.30  E-value=0.29  Score=32.67  Aligned_cols=52  Identities=12%  Similarity=0.246  Sum_probs=43.4

Q ss_pred             hCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccC
Q 026799           30 KQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPS   88 (233)
Q Consensus        30 aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs   88 (233)
                      --..||-..+|+.+..++++.+....+|..|.+.|.|+.       ...++-|.++.||
T Consensus        22 P~~~G~~keeLr~~l~~~~~~~~f~~lL~~l~~~g~l~~-------~g~~v~L~~f~ps   73 (73)
T d2v9va2          22 PLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQL-------AANTVALAGFTPS   73 (73)
T ss_dssp             TTSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEE-------CSSEEEETTCCCC
T ss_pred             ccccCCCHHHHHHHhcccCCHHHHHHHHHHHHHCCChhe-------eCCEEECCCCCCC
Confidence            345799999999999789999999999999999999976       3345556777775

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=90.24  E-value=0.15  Score=34.52  Aligned_cols=33  Identities=21%  Similarity=0.309  Sum_probs=30.8

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           36 WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        36 w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      ..++|..+.  +.+.++|+++|+.|+..|+|...+
T Consensus        24 se~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          24 VLETLMAQF--EVSKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEEc
Confidence            689999999  999999999999999999998763

>d1ldda_ a.4.5.34 (A:) Anaphase promoting complex (APC) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.84  E-value=0.31  Score=33.51  Aligned_cols=53  Identities=17%  Similarity=0.106  Sum_probs=41.4

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHh---CCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRS---GAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~---~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      ..|.-.|.+.+...++.||..++=-   |-.-...|.++++..|+.+|-+|+++.+
T Consensus        11 ~yI~gMLtN~~slpleRIh~mLkmfv~~~~~~~~~t~~eL~~FL~~~V~e~kL~~v   66 (74)
T d1ldda_          11 PFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYI   66 (74)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHHHHHSCGGGCCTTCCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHcCCCCCCCCcCHHHHHHHHHHHHhcCceEEe
Confidence            3445555678888899999999944   2122468999999999999999999865

>d1yg2a_ a.4.5.61 (A:) Hypothetical protein AphA {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein AphA
species: Vibrio cholerae [TaxId: 666]

Probab=89.81  E-value=0.22  Score=38.35  Aligned_cols=61  Identities=15%  Similarity=0.287  Sum_probs=36.2

Q ss_pred             HHHHHHHHhhCCCcccHHHHHHHh----hc--CCChHHHHHHHHHHHhCCCceee--ecccCCCeeeEEeec
Q 026799           21 RLIYDVIRSKQDMGIWTRDMKREL----RV--NLPDNIVTKSIKSLQNKSLIKEV--VNIHSKGKKHLMAVE   84 (233)
Q Consensus        21 ~lVy~~I~~aG~~GIw~~dik~~t----~~--~l~~~~v~k~LK~Le~k~lIK~v--ksV~~~~rK~Yml~~   84 (233)
                      ..|+.++.+.-..|   =+|++..    +.  +++..+|-.+|++||++|+|...  .....|.||+|-+.+
T Consensus         4 ~~iLg~L~~~~~~G---Yei~~~~~~~~~~~w~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~   72 (178)
T d1yg2a_           4 HVILTVLSTRDATG---YDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQ   72 (178)
T ss_dssp             HHHHHHHHHCCBCH---HHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECH
T ss_pred             HHHHHHHhhCCCCH---HHHHHHHHHHhCCccCCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECH
Confidence            45666666533333   3444443    11  68999999999999999999863  334556889997654

>d1exra_ a.39.1.5 (A:) Calmodulin {Ciliate (Paramecium tetraurelia) [TaxId: 5888]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Calmodulin
species: Ciliate (Paramecium tetraurelia) [TaxId: 5888]

Probab=88.08  E-value=3.2  Score=29.31  Aligned_cols=108  Identities=16%  Similarity=0.310  Sum_probs=72.0

Q ss_pred             CCChHH----HHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeecccc
Q 026799           15 SLTDHE----RLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEP   87 (233)
Q Consensus        15 ~L~~~e----~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~leP   87 (233)
                      +||++|    +.++..++..|+-=|...+++.-+   +..++...+...++.+..          ...++-.|       
T Consensus         2 ~lt~~e~~~l~~~F~~~D~~~~G~Is~~e~~~~l~~~~~~~~~~~~~~~~~~~d~----------~~~g~i~~-------   64 (146)
T d1exra_           2 QLTEEQIAEFKEAFALFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDA----------DGNGTIDF-------   64 (146)
T ss_dssp             CCCHHHHHHHHHHHHHHCTTCSSEECHHHHHHHHHHHTCCCCHHHHHHHHHHHCT----------TCSSSEEH-------
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCeECHHHHHHHHHhcCCCCCHHHHHHHHHhcCC----------CCCCcccH-------
Confidence            577766    345778888888888888887665   336666777777776532          11122111       


Q ss_pred             CCCcccCCcccCCCCCHHHHHHHHHHH------------HHHh--hhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHH
Q 026799           88 SKEISGGAWYSEGSLDTEFIKVVKSQC------------LKQI--IKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVR  153 (233)
Q Consensus        88 s~eiTGG~wy~d~e~D~efI~~l~~~~------------~~~i--~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~  153 (233)
                                      .+|+..+....            ++.+  .+.++.+.+|+..++...|.   .++.++++.|++
T Consensus        65 ----------------~ef~~~~~~~~~~~~~~~~~~~~F~~~D~d~~G~i~~~e~~~~l~~~~~---~~~~~~~~~i~~  125 (146)
T d1exra_          65 ----------------PEFLSLMARKMKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGE---KLTDDEVDEMIR  125 (146)
T ss_dssp             ----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHSTTCSSCBCHHHHHHHHHHTTC---CCCHHHHHHHHH
T ss_pred             ----------------HHHHHHHHHHhhccChHHHHHHHHHHhCCCCCCcCCHHHHHHHHHHHhh---cCCHHHHHHHHH
Confidence                            25555553332            2222  24689999999999999884   689999999998


Q ss_pred             HHhcC
Q 026799          154 ALVLD  158 (233)
Q Consensus       154 ~Lv~D  158 (233)
                      .+=.|
T Consensus       126 ~~D~d  130 (146)
T d1exra_         126 EADID  130 (146)
T ss_dssp             HHCSS
T ss_pred             HhCCC
Confidence            76443

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=88.06  E-value=0.51  Score=30.73  Aligned_cols=44  Identities=14%  Similarity=0.084  Sum_probs=38.7

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ..||+-|..|+.++.+    |...++|..++  +++.++|...++.+-.|
T Consensus         3 ~~Lt~rE~~vl~l~~~----G~s~~eIA~~l--~iS~~TV~~~~~~i~~K   46 (65)
T d1l3la1           3 AWLDPKEATYLRWIAV----GKTMEEIADVE--GVKYNSVRVKLREAMKR   46 (65)
T ss_dssp             CCCCHHHHHHHHHHTT----TCCHHHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHh----cCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            4699999999999865    78999999999  99999999998887654

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=87.74  E-value=0.49  Score=30.90  Aligned_cols=43  Identities=23%  Similarity=0.380  Sum_probs=37.8

Q ss_pred             CCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           15 SLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        15 ~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      -||+-|..|+.++.    +|...++|..++  +++.++|...++.+-.|
T Consensus         4 ~LT~rE~~vl~l~~----~G~s~~eIA~~L--~is~~TV~~~~~~i~~K   46 (67)
T d1fsea_           4 LLTKREREVFELLV----QDKTTKEIASEL--FISEKTVRNHISNAMQK   46 (67)
T ss_dssp             CCCHHHHHHHHHHT----TTCCHHHHHHHH--TSCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH----ccCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            39999999999886    578999999999  99999999998887654

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.87  E-value=0.82  Score=33.44  Aligned_cols=55  Identities=7%  Similarity=0.172  Sum_probs=46.7

Q ss_pred             HHHHHHHHhhhC--CCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEEeeC
Q 026799          110 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEVKSN  167 (233)
Q Consensus       110 l~~~~~~~i~~~--~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v~~~  167 (233)
                      -|.+++++|.+.  ..+|++||++.+++.+.   .++..=|-..|+.|+=.|.|.++...
T Consensus        17 qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~---~i~~aTVYR~L~~l~e~gli~~~~~~   73 (134)
T d1mzba_          17 PRVKILQMLDSAEQRHMSAEDVYKALMEAGE---DVGLATVYRVLTQFEAAGLVVRHNFD   73 (134)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTC---CCCHHHHHHHHHHHHHHTSEEEECSS
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCC---CccHHHHHHHHHHHHhccEEEEEeec
Confidence            467889999754  37999999999999884   47888999999999999999998643

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.84  E-value=0.51  Score=33.45  Aligned_cols=59  Identities=10%  Similarity=0.050  Sum_probs=48.1

Q ss_pred             CCCCCChHHHHHHHHHHhhCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeeccc
Q 026799           12 PSDSLTDHERLIYDVIRSKQD--MGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIH   73 (233)
Q Consensus        12 ~~~~L~~~e~lVy~~I~~aG~--~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~   73 (233)
                      .+..|+++|..|+..||..=.  +=+-...|.+.+  +|+...+.++|+.|...+||.. ..+.
T Consensus         5 ~~~~L~~~dfRvL~aiE~gmrnhE~VP~~lI~~~a--~l~~~~~~~~L~~L~k~kLv~~-~~~~   65 (89)
T d1zara1           5 LYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHA--RIGEEKARNILKYLSDLRVVQN-RQKD   65 (89)
T ss_dssp             HHHTCCHHHHHHHHHHHTTTTTCSSEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE-ECSS
T ss_pred             HHHHcCHHHHHHHHHHHhccccCccccHHHHHHHH--CCCHHHHHHHHHHHHHcCCeec-cCCC
Confidence            356799999999999995422  224568899999  9999999999999999999976 4443

>d1dtla_ a.39.1.5 (A:) Troponin C {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Troponin C
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=85.87  E-value=1.1  Score=32.41  Aligned_cols=127  Identities=13%  Similarity=0.174  Sum_probs=70.8

Q ss_pred             CCCCCCChHHH----HHHHHHHhhCCCc-ccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEe
Q 026799           11 APSDSLTDHER----LIYDVIRSKQDMG-IWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMA   82 (233)
Q Consensus        11 ~~~~~L~~~e~----lVy~~I~~aG~~G-Iw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml   82 (233)
                      .++..||++|.    .+|+.+...|+.| |...+++.-+   |.+++...+...+..+-..+--.    +....-..++.
T Consensus         3 ~~~~~Lt~~~~~~l~~~F~~~D~d~~dG~I~~~e~~~~l~~lg~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~   78 (156)
T d1dtla_           3 AAVEQLTEEQKNEFKAAFDIFVLGAEDGSISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGT----VDFDEFLVMMV   78 (156)
T ss_dssp             TGGGGSCHHHHHHHHHHHHHHTTTCGGGSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHCTTSSSS----BCHHHHHHHHH
T ss_pred             HHHHHCCHHHHHHHHHHHHHHcCCCCCCeECHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCCCc----cchhhhhhhhh
Confidence            34678999773    3577777776555 8888887543   44677777777777664332100    00000000000


Q ss_pred             eccccCCCcccCCcccCCCCCHHHHHHHHHHHHHHhh--hCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcC
Q 026799           83 VEFEPSKEISGGAWYSEGSLDTEFIKVVKSQCLKQII--KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLD  158 (233)
Q Consensus        83 ~~lePs~eiTGG~wy~d~e~D~efI~~l~~~~~~~i~--~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~D  158 (233)
                      .           ..+.....+  ..+.|+.+ ++...  ..++.|.+|+.+.+...|.   .||.++++.|++.+=.|
T Consensus        79 ~-----------~~~~~~~~~--~~~~l~~~-F~~~D~d~~G~I~~~e~~~~~~~~~~---~ls~~e~~~i~~~~D~d  139 (156)
T d1dtla_          79 R-----------SMKDDSKGK--SEEELSDL-FRMFDKNADGYIDLEELKIMLQATGE---TITEDDIEELMKDGDKN  139 (156)
T ss_dssp             H-----------HHC-----C--HHHHHHHH-HHHHCTTCSSEEEHHHHGGGGTTC-----CCCHHHHHHHHHHHCTT
T ss_pred             h-----------ccccccccc--HHHHHHHH-HHHhCcCCCCcCcHHHHHHHHhhcCC---CCCHHHHHHHHHHhCCC
Confidence            0           000000111  11334333 33332  4589999999999887773   69999999999987555

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.35  E-value=0.73  Score=30.82  Aligned_cols=42  Identities=21%  Similarity=0.403  Sum_probs=34.0

Q ss_pred             CCChHHH-HHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 026799           15 SLTDHER-LIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSL   60 (233)
Q Consensus        15 ~L~~~e~-lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~L   60 (233)
                      .||.+|+ .|.+.+++.+.  +.+.||.+..  |++.++|+++||.=
T Consensus         7 ~LT~~eK~~ii~~~e~g~k--~sq~eIA~~f--Gv~~STvs~IlKnK   49 (66)
T d1hlva1           7 QLTFREKSRIIQEVEENPD--LRKGEIARRF--NIPPSTLSTILKNK   49 (66)
T ss_dssp             CCCHHHHHHHHHHHHHCTT--SCHHHHHHHH--TCCHHHHHHHHHTH
T ss_pred             cCCHHHHHHHHHHHHcCCc--chHHHHHHHh--CCChhHHHHHHHHH
Confidence            3777655 57777777655  6799999999  99999999999863

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=85.13  E-value=0.34  Score=34.40  Aligned_cols=47  Identities=13%  Similarity=0.273  Sum_probs=38.4

Q ss_pred             HHHHHHHhhCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           22 LIYDVIRSKQDMG-------I-WTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        22 lVy~~I~~aG~~G-------I-w~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      .||+.|+..=..|       + ..++|..+.  +++.++|+++|+.|++.|||....
T Consensus        13 qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~--~vSr~tvr~Al~~L~~~Gli~~~~   67 (100)
T d1v4ra1          13 DVATHFRTLIKSGELAPGDTLPSVADIRAQF--GVAAKTVSRALAVLKSEGLVSSRG   67 (100)
T ss_dssp             HHHHHHHHHTTTTSCCTTSBCCCHHHHHHHS--SSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHHcCCCCCcCCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEec
Confidence            4777777543333       4 579999999  999999999999999999997753

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=85.03  E-value=0.85  Score=30.10  Aligned_cols=44  Identities=20%  Similarity=0.346  Sum_probs=38.8

Q ss_pred             CCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhC
Q 026799           14 DSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNK   63 (233)
Q Consensus        14 ~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k   63 (233)
                      ..||+-|..|+.++.    .|...++|..++  +++.++|...++.+-.|
T Consensus        11 ~~LT~rE~~vl~~l~----~G~s~~eIA~~l--~iS~~TV~~~~~~i~~K   54 (70)
T d1yioa1          11 SSLTGREQQVLQLTI----RGLMNKQIAGEL--GIAEVTVKVHRHNIMQK   54 (70)
T ss_dssp             HTSCHHHHHHHHHHT----TTCCHHHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence            479999999999986    468999999999  99999999999887654

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=84.28  E-value=1  Score=29.51  Aligned_cols=45  Identities=22%  Similarity=0.218  Sum_probs=39.4

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHHHhcCCeEEEE
Q 026799          112 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRALVLDNQIMEV  164 (233)
Q Consensus       112 ~~~~~~i~~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~Lv~Dg~ie~v  164 (233)
                      ..++.+|..++.+|..||++.+        .||..=|..+|+.|+-+|.|++.
T Consensus         9 ~~Il~~l~~~g~~sr~eLa~~~--------glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           9 GRVYKLIDQKGPISRIDLSKES--------ELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHH--------TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEe
Confidence            4688899999999999998865        38888999999999999999875

>d1oyia_ a.4.5.19 (A:) dsRNA-binding protein E3 (E3L) {Vaccinia virus [TaxId: 10245]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: dsRNA-binding protein E3 (E3L)
species: Vaccinia virus [TaxId: 10245]

Probab=83.25  E-value=1.2  Score=28.58  Aligned_cols=45  Identities=20%  Similarity=0.387  Sum_probs=41.0

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCc
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLI   66 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lI   66 (233)
                      ..+|...|..-|-+|....+|.+++  ||..+.|+|+|-.|..--++
T Consensus         4 a~ivceaik~ig~egata~qltrql--nmekrevnkalydlqrsamv   48 (62)
T d1oyia_           4 AEIVCEAIKTIGIEGATAAQLTRQL--NMEKREVNKALYDLQRSAMV   48 (62)
T ss_dssp             HHHHHHHHHHHSSSTEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHhccccchHHHHHHHHH--hHHHHHHHHHHHHHHHhhhe
Confidence            3588999999999999999999999  99999999999999876655

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=81.61  E-value=1.9  Score=29.38  Aligned_cols=50  Identities=14%  Similarity=0.280  Sum_probs=39.1

Q ss_pred             CCCCChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---CCCcee
Q 026799           13 SDSLTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQN---KSLIKE   68 (233)
Q Consensus        13 ~~~L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~---k~lIK~   68 (233)
                      +++|+=....++..|-+.|+  +  ..-.+++  ++++..|++.|+.||+   ..|..+
T Consensus         3 l~~ldl~~L~~f~~v~~~gs--~--t~AA~~l--~isq~avs~~l~~lE~~~g~~Lf~R   55 (89)
T d2esna1           3 LRRLDLNLLLVFDALYRHRN--V--GTAASEL--AISASAFSHALGRLRQGLDDELFLR   55 (89)
T ss_dssp             TTTSCTTHHHHHHHHHHHSS--H--HHHHHHH--TCCHHHHHHHHHHHHHHHTSCCEEE
T ss_pred             cccCCHHHHHHHHHHHHhCC--H--HHHHHHH--CCCCcHhhHHHHHHHhcCCceeEEE
Confidence            56777778888999999987  3  3335667  9999999999999996   445543

>d2mysc_ a.39.1.5 (C:) Myosin Regulatory Chain {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Myosin Regulatory Chain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=81.01  E-value=6.8  Score=27.58  Aligned_cols=102  Identities=12%  Similarity=0.202  Sum_probs=62.7

Q ss_pred             hHHHHHHHHHHhhCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeEEeeccccCCCcccC
Q 026799           18 DHERLIYDVIRSKQDMGIWTRDMKREL---RVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHLMAVEFEPSKEISGG   94 (233)
Q Consensus        18 ~~e~lVy~~I~~aG~~GIw~~dik~~t---~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Yml~~lePs~eiTGG   94 (233)
                      ++=+.+++.++..|+--|...+++.-+   |.+++...+.+.+......                         ..  | 
T Consensus         4 eelke~F~~~D~d~~G~I~~~el~~~l~~lg~~~~~~e~~~~~~~~~~d-------------------------~~--~-   55 (145)
T d2mysc_           4 DDFKEAFLLFDRTGDAKITASQVGDIARALGQNPTNAEINKILGNPSKE-------------------------EM--N-   55 (145)
T ss_pred             HHHHHHHHHHcCCCCCeECHHHHHHHHHHhhhcchhhhhHHHHHHHhhc-------------------------cc--c-
Confidence            345678999999888778888887654   2244555555555443211                         00  0 


Q ss_pred             CcccCCCCC-HHHHHHHHHHH--------------HHHhh--hCCCCCHHHHHHHHHHhCCcccccCHHHHHHHHHH
Q 026799           95 AWYSEGSLD-TEFIKVVKSQC--------------LKQII--KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRA  154 (233)
Q Consensus        95 ~wy~d~e~D-~efI~~l~~~~--------------~~~i~--~~~~~T~~~I~~~I~~~~i~~~~Ls~~di~~il~~  154 (233)
                          ++.+| .+|+..+....              ++.+.  +.|++|.+|+.+.++..|.   .++.++++.+++.
T Consensus        56 ----~g~i~~~eF~~~~~~~~~~~~~~~~~~l~~aF~~~D~d~~G~I~~~el~~~l~~~g~---~~~~~e~~~l~~~  125 (145)
T d2mysc_          56 ----AAAITFEEFLPMLQAAANNKDQGTFEDFVEGLRVFDKEGNGTVMGAELRHVLATLGE---KMTEEEVEELMKG  125 (145)
T ss_pred             ----cCccchhHHHHHHhhhhhccccchHHHHHHHHHHhhcCCCCEEcHHHHHHHHHHhCC---CCCHHHHHHHHhh
Confidence                11222 23444333221              22221  4689999999999998884   6899999998863

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.81  E-value=1.1  Score=30.04  Aligned_cols=59  Identities=10%  Similarity=0.061  Sum_probs=47.6

Q ss_pred             CChHHHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeeecccCCCeeeE
Q 026799           16 LTDHERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVVNIHSKGKKHL   80 (233)
Q Consensus        16 L~~~e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vksV~~~~rK~Y   80 (233)
                      |+.++..||++.+..|-  +..+.|+.++  +-.......+|..|...||.=-  .-++.+...|
T Consensus         1 Ls~Dqt~vLe~a~~~G~--Vt~s~l~~~l--gW~~~Ra~~aLd~lv~eGl~Wv--D~Q~~~e~~Y   59 (68)
T d1u5ta2           1 LTSDQTKILEICSILGY--SSISLLKANL--GWEAVRSKSALDEMVANGLLWI--DYQGGAEALY   59 (68)
T ss_dssp             CCTTHHHHHHTTTTTSC--CBHHHHHHHH--CCCSHHHHHHHHHHHHTTSSEE--ECSSSSSCEE
T ss_pred             CCchHHHHHHHHHHcCc--eeHHHHHHHh--CCCHHHHHHHHHHHHhcCcEEE--ecCCCCCcee
Confidence            67788999999988775  8999999999  9999999999999999998722  2243444455

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=80.32  E-value=2.2  Score=28.93  Aligned_cols=46  Identities=13%  Similarity=0.107  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhhCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhCCCceeee
Q 026799           20 ERLIYDVIRSKQDMGIWTRDMKRELRVNLPDNIVTKSIKSLQNKSLIKEVV   70 (233)
Q Consensus        20 e~lVy~~I~~aG~~GIw~~dik~~t~~~l~~~~v~k~LK~Le~k~lIK~vk   70 (233)
                      |.-|+++|. .|  .+...+|..++  +++...+.+.|+.|...|++.+..
T Consensus        23 ~L~ifd~l~-~g--p~s~~eLA~~~--g~~~~~l~rlLr~l~a~gl~~e~~   68 (85)
T d1tw3a1          23 TLRLVDHIL-AG--ARTVKALAART--DTRPEALLRLIRHLVAIGLLEEDA   68 (85)
T ss_dssp             HTTHHHHHH-TT--CCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HcCcHHHhc-cC--CCCHHHHHHHh--CcChhHHHHHHHHHHHCCCeEecC
Confidence            445777884 33  59999999999  999999999999999999998743