Citrus Sinensis ID: 025493

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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-------240-------250--
Protein Sequence
MKYSFTDLYLLGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
Secondary Structure (PSIPRED)
ccccHHHHHHHHHcccccEEEEEccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHccccHHHHHHHHHHHHHcccEEEEcccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEEEEEcccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHccccEEEEEccHHHHHHccccHHHHHHHHHHHHHcccccEEHHHHHHHHcccccHHHHHHHHHHHHHcccEEEEcEccccccEEEEEEEcccccccccccccccccHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccEEEccHHHHHHHHHHHHccccEEEEEccccccEcccccccEEEEEccccccccccccccccccccccccccccccccccccccccHHHHHHHcc
Coil and Loop (DISEMBL)
mkysftdlYLLGlakgsgmskrkrpdsnapsdsltdheRLIYDVIRSNKQDMGIWTRDMKRELKvnlpdnivtKSIKSLQNKSLIKEVVNIHNKGKKHLMAVefepskdisggawysegsldTEFIKVVKSQCLKQIIKLKVATLEGIsdsikrsgafkvdlTKQQIEEIVRAVVLDNQImevksngsgeftnipvgkvcyknvskgggggepktgssasvpcgvcpqinfctpdgvispktcvyytkwldf
Flexible Loop (DISEMBL)
mkysftdlYLLGLakgsgmskrkrpdsnapsdsltdherLIYDVIrsnkqdmgiwTRDMKRELKvnlpdnivtksikslqnkslIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVatlegisdsikrsgafkvdltkQQIEEIVRAVVLDNQIMEVksngsgeftnipvGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINfctpdgvispkTCVYYTKWLDF
Low Complexity Region (SEG)
MKYSFTDLYLLGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKgggggEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
Disordered region (IsUnstruct)
****FTDLYLLGL*************************RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYK******************VPCGVCPQINFCTPDGVISPKTCVYYTKWL**
Disordered Region (DISOPRED)
****FTDLYLLGLAKGSGM*******************RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK****GEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
Disordered Region (DISEMBL)
MKYSFTDLYLLGLAKG*****************LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK**************VPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
Disordered Region (DISPRO)
*KYSFTDLYLLGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKYSFTDLYLLGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF
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	252	2.2.26 [Sep-21-2011]
Q2T9S3	316	DNA-directed RNA polymera	yes	no	0.920	0.734	0.305	7e-26
Q9H1D9	316	DNA-directed RNA polymera	yes	no	0.920	0.734	0.301	2e-25
Q921X6	316	DNA-directed RNA polymera	yes	no	0.920	0.734	0.301	2e-25
Q9VD25	293	Probable DNA-directed RNA	yes	no	0.876	0.754	0.297	2e-21
Q86JM3	293	DNA-directed RNA polymera	yes	no	0.825	0.709	0.283	1e-19
O94553	301	Probable DNA-directed RNA	yes	no	0.873	0.730	0.242	2e-16
P91529	296	Probable DNA-directed RNA	yes	no	0.761	0.648	0.258	1e-14
P32910	317	DNA-directed RNA polymera	yes	no	0.361	0.287	0.340	3e-10

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

 Score =  117 bits (293), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 79/259 (30%), Positives = 132/259 (50%), Gaps = 27/259 (10%)

Query: 13  LAKGSGMSKRKRPDSNAPSDSLTD-HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
           L   +G+  R +   NA     +D  E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct: 66  LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query: 72  VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
           + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct: 123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query: 132 QCLKQII-KLKVATLEGISDSIKRSGAF----------------KVDLTKQQIEEIVRAV 174
           QC K +  K + A     +  I+R+ +F                KV+L+ + IE I+  +
Sbjct: 183 QCFKFLQNKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query: 175 VLDNQI-MEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCT 233
           + D ++ M + +   G   ++      Y+ VS       P TG     PCG+CP  + C 
Sbjct: 243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVSPII----PPTG-LVRAPCGLCPVFDDCH 297

Query: 234 PDGVISPKTCVYYTKWLDF 252
             G ISP  C+Y T+WL+F
Sbjct: 298 EGGEISPSNCIYMTEWLEF 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 =  116 bits (290), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/259 (30%), Positives = 132/259 (50%), Gaps = 27/259 (10%)

Query: 13  LAKGSGMSKRKRPDSNAPSDSLTD-HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
           L   +G+  R +   NA     +D  E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct: 66  LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query: 72  VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
           + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct: 123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query: 132 QCLKQI-IKLKVATLEGISDSIKRSGAF----------------KVDLTKQQIEEIVRAV 174
           QC K +  K + A     +  I+R+ +F                KV+L+ + IE I+  +
Sbjct: 183 QCFKFLQSKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query: 175 VLDNQI-MEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCT 233
           + D ++ M + +   G   ++      Y+ V+       P TG     PCG+CP  + C 
Sbjct: 243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPII----PPTG-LVRAPCGLCPVFDDCH 297

Query: 234 PDGVISPKTCVYYTKWLDF 252
             G ISP  C+Y T+WL+F
Sbjct: 298 EGGEISPSNCIYMTEWLEF 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 =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/259 (30%), Positives = 131/259 (50%), Gaps = 27/259 (10%)

Query: 13  LAKGSGMSKRKRPDSNAPSDSLTD-HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
           L   +G+  R +   NA     +D  E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct: 66  LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query: 72  VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
           + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct: 123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query: 132 QCLKQI-IKLKVATLEGISDSIKRSGAF----------------KVDLTKQQIEEIVRAV 174
           QC K +  K + A     +  I+R+ +F                KV+L+ + IE I+  +
Sbjct: 183 QCFKFLQSKAETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query: 175 VLDNQI-MEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCT 233
           + D ++ M + +   G   ++      Y+ V+       P TG     PCG+CP    C 
Sbjct: 243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPIL----PPTG-VVRAPCGLCPVFEDCH 297

Query: 234 PDGVISPKTCVYYTKWLDF 252
             G ISP  C+Y T+WL+F
Sbjct: 298 EGGEISPSNCIYMTEWLEF 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 =  102 bits (255), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/259 (29%), Positives = 120/259 (46%), Gaps = 38/259 (14%)

Query: 13  LAKGSGMSKR-KRPD--SNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPD 69
           L KG  +  R K P+  S  P D+  + E+++Y ++     + GIW RD++  +K NL  
Sbjct: 53  LKKGEKLVYRAKDPEKKSALPKDA-DNEEKVVYGIVEEGG-NKGIWIRDIR--MKSNLNM 108

Query: 70  NIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVV 129
             + K +K+L+ K LIK V +++   KK  M    EP   I+GGAWY +   + EF+ V+
Sbjct: 109 IQLNKILKNLETKKLIKAVKSVNASKKKVYMLYNLEPDLSITGGAWYQDQDFEVEFVDVL 168

Query: 130 KSQCLK-----------------QIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVR 172
             QCL+                    ++   T+  +   I   G  KV+L +  +E I++
Sbjct: 169 NQQCLRFLQMKRDSAEKKREGPLAFKQMSCCTVNEVQKFISDLGISKVNLAEADLETILK 228

Query: 173 AVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFC 232
            VV D         G+ E      G   Y+ V+       P TG    +PCG+CP I  C
Sbjct: 229 TVVYD---------GNAERVRQQDGSFVYRAVN----APLPPTG-LVQMPCGICPVIKNC 274

Query: 233 TPDGVISPKTCVYYTKWLD 251
           +  G ++  TC Y   WLD
Sbjct: 275 SNCGDVTAITCEYMRDWLD 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 = 96.7 bits (239), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 117/247 (47%), Gaps = 39/247 (15%)

Query: 21  KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
           K   P+  A    L   + LIY +I ++  + G WTR++K           +TK +K+L+
Sbjct: 62  KEVNPEDQAKFRGLGVEDFLIYQLIEASS-NTGAWTRELKNSSGYQQVQ--ITKILKTLE 118

Query: 81  NKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL 140
           ++ LIK V +I +  KK  M    EPS++I+GG  YS+ S D ++I+++K   +K  +  
Sbjct: 119 SRKLIKSVKSIQSGRKKVYMLYNMEPSREITGGQLYSDQSYDHQYIQIMKMH-IKTFVDN 177

Query: 141 KVAT-LEGISDSIKRSG--AFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEF------ 191
           K A  L  I   +++    A    L  + I+ +V  V+ D  I E++    G        
Sbjct: 178 KGAVDLADIITYLRKVAEEATSQSLGPEDIQALVNTVIYDGDIEEMRDTRMGAMLGRRSG 237

Query: 192 -------TNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCV 244
                  T IPV   C                   ++PCG CP  + C+ +G++SPK CV
Sbjct: 238 ILYKPTKTPIPVNNFC-------------------NMPCGNCPVFDICSDNGLVSPKRCV 278

Query: 245 YYTKWLD 251
           Y+ ++L+
Sbjct: 279 YFKQYLE 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 = 85.9 bits (211), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/260 (24%), Positives = 121/260 (46%), Gaps = 40/260 (15%)

Query: 13  LAKGSGMSKRK-RPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
           L +G+ +  R  R D      ++   E+++Y  I+ N  + GIW + +   L+ NL  ++
Sbjct: 61  LRQGNVLVYRAVRLDEAKTVSTMEGDEQIVYSFIK-NSGNEGIWRKTLT--LRTNLHVSV 117

Query: 72  VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
           V + +KSL++K+L+K + ++ N  +K  M  +  PS +++GG W+++  LD EFI+ +K 
Sbjct: 118 VDRCLKSLESKNLVKSIKSVKNPTRKIYMLYDLVPSTELTGGPWFTDQELDVEFIENLKK 177

Query: 132 QCLKQIIKLKVA--------------------TLEGISDSIKRSGAFKVDLTKQQIEEIV 171
              + +                          T   I + ++ +   KVDL+   +  +V
Sbjct: 178 VIYRYVHSKSFPPKKAAMGPDLVWGPEYNGYPTALQIHNWLRSTNITKVDLSLANVISLV 237

Query: 172 RAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINF 231
             ++ D ++ E +S+G+            Y+ +       +  T S    PCG CP  + 
Sbjct: 238 DVLIYDGKV-EKRSDGAS-----------YRAIRVNNENIDAFTES----PCGNCPVSDI 281

Query: 232 CTPDGVISPKTCVYYTKWLD 251
           C  +  ++P TC Y  KWL+
Sbjct: 282 CDANSRVNPITCEYLDKWLN 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 = 80.1 bits (196), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 103/236 (43%), Gaps = 44/236 (18%)

Query: 35  TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK 94
           T+ E++IY +I  +K   GIW ++++    +N     + K++KSL+ K LIK +  +   
Sbjct: 82  TEEEQVIYSLIEESK-TRGIWIKELREGSGLNQLQ--LRKTLKSLETKKLIKTIKAVGTT 138

Query: 95  GKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC------------------LKQ 136
            K +++    EP   ++GG +YS+  LD+E I  + S C                  ++ 
Sbjct: 139 RKCYIL-FSIEPDMSLTGGTFYSDQQLDSELINTLISVCGSYAASRRKHAIDENPNNIQM 197

Query: 137 IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPV 196
             +      + I+  I       V L+ + +E I+   VLD  I   +    G+    P 
Sbjct: 198 QREASYIRPQEIAQFITEKRVLNVPLSLEDLERILEVAVLDGTI---ERRADGKIRACP- 253

Query: 197 GKVCYKNVSKGGGGGEPKTGSS--ASVPCGVCPQINFCTPDGVISPKTCVYYTKWL 250
                           P++  S   SVPC +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 = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 59/94 (62%), Gaps = 3/94 (3%)

Query: 33  SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH 92
           +++  E L+Y  I ++ ++ GIW++ +K   + NL  ++V K +KSL+++  +K V ++ 
Sbjct: 85  TMSAEEALVYSYIEASGRE-GIWSKTIKA--RTNLHQHVVLKCLKSLESQRYVKSVKSVK 141

Query: 93  NKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFI 126
              +K  M    +PS DI+GG W+++G LD EFI
Sbjct: 142 FPTRKIYMLYSLQPSVDITGGPWFTDGELDIEFI 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	252
255536881	236	DNA-directed RNA polymerase III subunit	0.908	0.970	0.706	2e-93
224142730	239	predicted protein [Populus trichocarpa]	0.932	0.983	0.693	2e-92
224052869	239	predicted protein [Populus trichocarpa]	0.932	0.983	0.684	4e-92
317106726	235	JHL06P13.1 [Jatropha curcas]	0.904	0.970	0.663	2e-86
225442989	239	PREDICTED: DNA-directed RNA polymerase I	0.940	0.991	0.648	7e-86
296087021	300	unnamed protein product [Vitis vinifera]	0.944	0.793	0.646	1e-85
359497031	239	PREDICTED: DNA-directed RNA polymerase I	0.944	0.995	0.641	3e-85
359497533	239	PREDICTED: DNA-directed RNA polymerase I	0.944	0.995	0.641	3e-85
356567166	239	PREDICTED: DNA-directed RNA polymerase I	0.932	0.983	0.617	5e-82
297743442	493	unnamed protein product [Vitis vinifera]	0.936	0.478	0.634	1e-81

>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 =  348 bits (892), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 164/232 (70%), Positives = 199/232 (85%), Gaps = 3/232 (1%)

Query: 21  KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
           KRK+P+S++P+ SLT+HE  +Y+VI S KQDMGIWTRDMKRE   NLPDN+V KS+K LQ
Sbjct: 8   KRKQPESSSPAQSLTEHECTLYNVIWS-KQDMGIWTRDMKRE--TNLPDNVVNKSLKVLQ 64

Query: 81  NKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL 140
            K+LIKEVVNI NKG+KH MA EFEPSK+I+GGAWY EG+LDTEFIK++K  C KQ++KL
Sbjct: 65  AKNLIKEVVNIQNKGRKHYMATEFEPSKEITGGAWYVEGNLDTEFIKLLKEVCTKQVLKL 124

Query: 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVC 200
           KVATLEGI+DSIKRSG F  +LTKQQIEEIV+A+VLDN ++EVKSNG  EF+ IP+GKVC
Sbjct: 125 KVATLEGITDSIKRSGIFNTELTKQQIEEIVKALVLDNALIEVKSNGMLEFSFIPIGKVC 184

Query: 201 YKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
           YK V KG   GEP+ G+ AS+PCGVCP+I+ CTPDG+ISP+TCVYY+KWLDF
Sbjct: 185 YKCVGKGSTAGEPRIGAMASIPCGVCPRISQCTPDGIISPQTCVYYSKWLDF 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 =  344 bits (882), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 165/238 (69%), Positives = 196/238 (82%), Gaps = 3/238 (1%)

Query: 15  KGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTK 74
           +G    KRKRP+ N+P+ SLT+HERL+YDVIRS KQD+GIWTRDMK+E K  LPDN+V K
Sbjct: 5   QGPSSLKRKRPEVNSPAQSLTEHERLLYDVIRS-KQDIGIWTRDMKKEAK--LPDNVVNK 61

Query: 75  SIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134
           S+K+LQ K LIKEVVNI NKG+KH MA EFEPSK+ISGGAWY EGSLDTEFI+ +K  C 
Sbjct: 62  SLKALQVKKLIKEVVNIQNKGRKHFMATEFEPSKEISGGAWYLEGSLDTEFIESLKQLCK 121

Query: 135 KQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNI 194
           +QI +  VATLE ++DSI    AF VD+TKQQIEEI+R ++LDN IMEVKSNG GEF +I
Sbjct: 122 RQIERRGVATLEEVTDSINSYPAFNVDVTKQQIEEILRTLILDNVIMEVKSNGMGEFASI 181

Query: 195 PVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
           P G+VCYK +SK G GGEPK G+ AS+PCGVCP+I+ CTPDG+ISPKTCVYY KWLDF
Sbjct: 182 PFGEVCYKYISKVGLGGEPKAGALASIPCGVCPRISQCTPDGIISPKTCVYYQKWLDF 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 =  343 bits (880), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 163/238 (68%), Positives = 196/238 (82%), Gaps = 3/238 (1%)

Query: 15  KGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTK 74
           +G    KRKRP+ N+P  SLT+HER++YDVIRS KQD+GIWTRDMK+E K  LPDN+V K
Sbjct: 5   QGPSSLKRKRPELNSPVQSLTEHERILYDVIRS-KQDIGIWTRDMKKEAK--LPDNVVNK 61

Query: 75  SIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134
           S+K+L+ K+LIKEVVNI NKG+KH MA EFEPSK+ISGGAWY EGSLDTEFI+ ++  C 
Sbjct: 62  SLKALRVKNLIKEVVNIQNKGRKHFMATEFEPSKEISGGAWYLEGSLDTEFIESLRQLCK 121

Query: 135 KQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNI 194
           +QI K  VATLE ++DSI    AF VD+TKQQIEEI+R ++LDN IMEVKSNG GEF +I
Sbjct: 122 RQIEKKGVATLEEVTDSINSYPAFNVDVTKQQIEEILRTLILDNAIMEVKSNGMGEFASI 181

Query: 195 PVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
           P GKVCY+ +SKG  GGEPK G+ AS+PCGVCP+I+ CTPDG+ISPKTCVYY KWLDF
Sbjct: 182 PFGKVCYRYISKGALGGEPKAGALASIPCGVCPRISHCTPDGIISPKTCVYYQKWLDF 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 =  324 bits (830), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 154/232 (66%), Positives = 191/232 (82%), Gaps = 4/232 (1%)

Query: 21  KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
           KRK+P+SN+ + SLT+HE+ +Y+ IRS KQDMGIWTRDMKRE   NLPD +V KS+K LQ
Sbjct: 8   KRKQPESNSSAQSLTEHEQALYNAIRS-KQDMGIWTRDMKRE--TNLPDTVVNKSLKVLQ 64

Query: 81  NKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL 140
            K+LIKEVVNI NKG+K+ MA EFEPSK+I+GG WY EG+LDT FI V+K QC KQI KL
Sbjct: 65  AKNLIKEVVNIQNKGRKYYMATEFEPSKEITGGTWYVEGNLDTMFIGVLKDQCKKQIEKL 124

Query: 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVC 200
           KVAT+E ++D I R+G   V LTKQQIEEI++A+VLDN++ EVKSNG GEF +IPVGKVC
Sbjct: 125 KVATVEAVTDFINRTGVSTVHLTKQQIEEILKALVLDNKVTEVKSNGMGEFASIPVGKVC 184

Query: 201 YKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
           YK++ K G  G+PK G+ AS+PCGVCP+I  CTP+G+ISP+TCVYY KWL+F
Sbjct: 185 YKSIGK-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 =  322 bits (826), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 157/242 (64%), Positives = 200/242 (82%), Gaps = 5/242 (2%)

Query: 13  LAKGSGMS-KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
           +++  G+S KRKRPD+NA S  L D ER++YD+IRS K+DMGIWTRDMKRE   NLPDN+
Sbjct: 1   MSRSQGLSLKRKRPDTNAASQPLLDAERVLYDLIRS-KEDMGIWTRDMKRE--TNLPDNV 57

Query: 72  VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
           VTKS+K+LQ K LIKEVVNI +KG+KH MAVEFEPSK+++GGAWY EG+LDTE+IK++K 
Sbjct: 58  VTKSLKALQVKKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILKE 117

Query: 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEF 191
            C+K + KLKVAT EGIS+SI ++G    + + QQI EI+RA+VLDN+IMEV+S+GSGEF
Sbjct: 118 TCVKVLSKLKVATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGEF 177

Query: 192 TNIPVGKVCYKNVSK-GGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWL 250
           ++IP+G VCY+  +K G GGG PK G+ AS+PCGVCP+I  CTPDG+ISPK+C YY KWL
Sbjct: 178 SSIPIGAVCYRCTNKGGLGGGGPKIGAMASIPCGVCPRITQCTPDGIISPKSCAYYAKWL 237

Query: 251 DF 252
           DF
Sbjct: 238 DF 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 =  322 bits (824), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 157/243 (64%), Positives = 199/243 (81%), Gaps = 5/243 (2%)

Query: 12  GLAKGSGMS-KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDN 70
           G+++  G S KRKRPD+N  S  L D ER++YD+IRS K+DMGIWTRDMKRE   NLPDN
Sbjct: 61  GMSRSQGSSLKRKRPDTNTASQPLLDAERVLYDLIRS-KEDMGIWTRDMKRE--TNLPDN 117

Query: 71  IVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVK 130
           +VTKS+K+LQ K LIKEVVNI +KG+KH MAVEFEPSK+++GGAWY EG+LDTE+IK++K
Sbjct: 118 VVTKSLKALQVKKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILK 177

Query: 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGE 190
             C++ + KLKVAT EGIS+SI ++G    + + QQI EI+RA+VLDN+IMEV+S+GSGE
Sbjct: 178 KTCVRVLSKLKVATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGE 237

Query: 191 FTNIPVGKVCYKNVSK-GGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKW 249
           F++IP+G VCY+  +K G GGG P  G+ AS+PCGVCP+I  CTPDG+ISPKTC YYTKW
Sbjct: 238 FSSIPIGAVCYRCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKW 297

Query: 250 LDF 252
           LDF
Sbjct: 298 LDF 300

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 =  320 bits (820), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 156/243 (64%), Positives = 199/243 (81%), Gaps = 5/243 (2%)

Query: 11  LGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDN 70
           +  ++GS + KRKRPD+N  S  L D ER++YD+IRS K+DMGIWTRDMKRE   NLPDN
Sbjct: 1   MSRSQGSSL-KRKRPDTNTASQPLLDAERVLYDLIRS-KEDMGIWTRDMKRE--TNLPDN 56

Query: 71  IVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVK 130
           +VTKS+K+LQ K LIKEVVNI +KG+KH MAVEFEPSK+++GGAWY EG+LDTE+IK++K
Sbjct: 57  VVTKSLKALQVKKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILK 116

Query: 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGE 190
             C++ + KLKVAT EGIS+SI ++G    + + QQI EI+RA+VLDN+IMEV+S+GSGE
Sbjct: 117 ETCVRVLSKLKVATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGE 176

Query: 191 FTNIPVGKVCYKNVSK-GGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKW 249
           F++IP+G VCY+  +K G GGG P  G+ AS+PCGVCP+I  CTPDG+ISPKTC YYTKW
Sbjct: 177 FSSIPIGAVCYRCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKW 236

Query: 250 LDF 252
           LDF
Sbjct: 237 LDF 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 =  320 bits (820), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 156/243 (64%), Positives = 199/243 (81%), Gaps = 5/243 (2%)

Query: 11  LGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDN 70
           +  ++GS + KRKRPD+N  S  L D ER++YD+IRS K+DMGIWTRDMKRE   NLPDN
Sbjct: 1   MSRSQGSSL-KRKRPDTNTASQPLLDAERVLYDLIRS-KEDMGIWTRDMKRE--TNLPDN 56

Query: 71  IVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVK 130
           +VTKS+K+LQ K LIKEVVNI +KG+KH MAVEFEPSK+++GGAWY EG+LDTE+IK++K
Sbjct: 57  VVTKSLKALQVKKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYIKILK 116

Query: 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGE 190
             C++ + KLKVAT EGIS+SI ++G    + + QQI EI+RA+VLDN+IMEV+S+GSGE
Sbjct: 117 KTCVRVLSKLKVATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSSGSGE 176

Query: 191 FTNIPVGKVCYKNVSK-GGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKW 249
           F++IP+G VCY+  +K G GGG P  G+ AS+PCGVCP+I  CTPDG+ISPKTC YYTKW
Sbjct: 177 FSSIPIGAVCYRCTNKGGLGGGGPTIGAMASIPCGVCPRITQCTPDGIISPKTCAYYTKW 236

Query: 250 LDF 252
           LDF
Sbjct: 237 LDF 239

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 (793), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 147/238 (61%), Positives = 191/238 (80%), Gaps = 3/238 (1%)

Query: 15  KGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTK 74
           +GS   KRKR D    + SLTD ER++Y++I S K+DMGIWT DMKRE   NLPD+IV K
Sbjct: 5   QGSSSLKRKRQDLALVTGSLTDGERVLYNLIHS-KKDMGIWTGDMKRE--TNLPDSIVKK 61

Query: 75  SIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134
           S+K LQ+K+LIKEVVNI NKG+KH MA EFEPSK+I+GG WY++G LDT+FI +VK  CL
Sbjct: 62  SLKLLQSKNLIKEVVNIQNKGRKHYMAAEFEPSKEITGGVWYNQGRLDTDFINLVKDVCL 121

Query: 135 KQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNI 194
           K I + KVAT +G+ +  ++SG F V++T QQI+EI+R +VLD++I+EVKS G G+F+++
Sbjct: 122 KYIFRQKVATRDGVMEWSRKSGVFNVEVTTQQIDEILRTLVLDDEIVEVKSTGFGDFSSV 181

Query: 195 PVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
           PVG++CY+  SKGG  GE K G+ AS+PCGVCP+INFCTPDG+ISP+TCVYY KWLDF
Sbjct: 182 PVGRICYRCKSKGGNRGEQKPGAMASIPCGVCPRINFCTPDGIISPRTCVYYQKWLDF 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 =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 153/241 (63%), Positives = 199/241 (82%), Gaps = 5/241 (2%)

Query: 8   LYLLGLAKGSGMS-KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN 66
           + +LG+++  G+S KRKRPD+NA S  L D ER++YD+IRS K+DMGIWTRDMKRE   N
Sbjct: 86  ILILGMSRSQGLSLKRKRPDTNAASQPLLDAERVLYDLIRS-KEDMGIWTRDMKRE--TN 142

Query: 67  LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFI 126
           LPDN+VTKS+K+LQ K LIKEVVNI +KG+KH MAVEFEPSK+++GGAWY EG+LDTE+I
Sbjct: 143 LPDNVVTKSLKALQVKKLIKEVVNIQSKGRKHYMAVEFEPSKELTGGAWYVEGNLDTEYI 202

Query: 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186
           K++K  C+K + KLKVAT EGIS+SI ++G    + + QQI EI+RA+VLDN+IMEV+S+
Sbjct: 203 KILKETCVKVLSKLKVATAEGISESINKTGLCATECSTQQIAEILRALVLDNEIMEVRSS 262

Query: 187 GSGEFTNIPVGKVCYKNVSK-GGGGGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVY 245
           GSGEF++IP+G VCY+  +K G GGG PK G+ AS+PCGVCP+I  CTPDG+ISPK+ V+
Sbjct: 263 GSGEFSSIPIGAVCYRCTNKGGLGGGGPKIGAMASIPCGVCPRITQCTPDGIISPKSSVH 322

Query: 246 Y 246
           Y
Sbjct: 323 Y 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	252
TAIR|locus:2171671	230	AT5G23710 [Arabidopsis thalian	0.900	0.986	0.468	8e-53
UNIPROTKB|J9P638	323	POLR3F "Uncharacterized protei	0.829	0.647	0.306	1.2e-26
UNIPROTKB|F1MYX7	316	POLR3F "DNA-directed RNA polym	0.936	0.746	0.313	3.2e-26
UNIPROTKB|E2RG78	316	POLR3F "Uncharacterized protei	0.936	0.746	0.313	4e-26
UNIPROTKB|Q2T9S3	316	POLR3F "DNA-directed RNA polym	0.936	0.746	0.313	5.2e-26
UNIPROTKB|Q9H1D9	316	POLR3F "DNA-directed RNA polym	0.936	0.746	0.313	5.2e-26
MGI|MGI:1924086	316	Polr3f "polymerase (RNA) III (	0.936	0.746	0.313	8.4e-26
RGD|1306428	371	Polr3f "polymerase (RNA) III (	0.936	0.636	0.309	1.4e-25
UNIPROTKB|E1BU41	314	POLR3F "Uncharacterized protei	0.940	0.754	0.307	1.8e-25
UNIPROTKB|F1SBH4	316	POLR3F "Uncharacterized protei	0.940	0.75	0.307	1.8e-25

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

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 111/237 (46%), Positives = 155/237 (65%)

Query:    19 MSKRKRPDSNAPSDSLTD-HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK 77
             MSKRKRPD  +    L + HE+ + D+IR N Q  G    ++KRE  +  P  IVT+ I 
Sbjct:     1 MSKRKRPDPKSSGGDLNEPHEKKLLDLIRIN-QGRGATMFELKREKTI--PATIVTRLIA 57

Query:    78 SLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQI 137
             SL+ K+LIKEV N++NKG KH +A+EFEP  +++GG WY++G+LD   I+ +K++C+  +
Sbjct:    58 SLRKKNLIKEVANMNNKGVKHYLAMEFEPCSELTGGEWYTDGALDLSKIEDLKAKCVMIL 117

Query:   138 IK--LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIP 195
              +   +V TLE +     +     VD TK    EI++ ++LDN IMEVKSNG  EF +  
Sbjct:   118 ERHRQRVVTLEVLCGYFVKEEKLSVDQTK----EILKNLILDNLIMEVKSNGMNEFASTR 173

Query:   196 VGKVCYKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
             +G+VCY+   K     EP+ G+ AS+PCGVCP I  C+PDGVISP TCVY+ KWLDF
Sbjct:   174 IGEVCYRLTGKKFGNGEPRAGAFASIPCGVCPHIAICSPDGVISPTTCVYFQKWLDF 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|J9P638 POLR3F "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 72/235 (30%), Positives = 123/235 (52%)

Query:    36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95
             + E+L+Y +I  +  + GIW+RD++   K NLP   + K +K+L++K LIK V ++    
Sbjct:    97 NQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTEINKILKNLESKKLIKAVKSVAASK 153

Query:    96 KKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQI-IKLKVATLEGISDSIKR 154
             KK  M    +P + ++GGAWYS+   ++EF++V+  QC K +  K + A     +  I+R
Sbjct:   154 KKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQQCFKFLQTKAETARESKQNPMIQR 213

Query:   155 SGAF----------------KVDLTKQQIEEIVRAVVLDNQI-MEVKSNGSGEFTNIPVG 197
             + +F                KV+L+ + IE I+  ++ D ++ M + +   G   ++   
Sbjct:   214 NSSFASSHEVWKYICELGISKVELSMEDIETILNTLIYDGKVEMTIIAAKEGTVGSVDGH 273

Query:   198 KVCYKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLDF 252
                Y+ V+       P TG     PCG+CP  + C   G ISP  C+Y T+WL+F
Sbjct:   274 MKLYRAVNPII----PPTGL-VRAPCGLCPVFDDCHEGGEISPSNCIYMTEWLEF 323

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

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

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 80/255 (31%), Positives = 129/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQTKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  E T I      VG V  +  + +      P TG     PCG+CP  + C   G 
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVSPIIPPTGL-VRAPCGLCPVFDDCHEGGE 301

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   302 ISPSNCIYMTEWLEF 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 = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 80/255 (31%), Positives = 129/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQTKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  E T I      VG V  +  + +      P TG     PCG+CP  + C   G 
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPIIPPTGL-VRAPCGLCPVFDDCHEGGE 301

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   302 ISPSNCIYMTEWLEF 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 = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 80/255 (31%), Positives = 129/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQII-KLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQNKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  E T I      VG V  +  + +      P TG     PCG+CP  + C   G 
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVSPIIPPTGL-VRAPCGLCPVFDDCHEGGE 301

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   302 ISPSNCIYMTEWLEF 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 = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 80/255 (31%), Positives = 129/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQSKAETARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  E T I      VG V  +  + +      P TG     PCG+CP  + C   G 
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPIIPPTGL-VRAPCGLCPVFDDCHEGGE 301

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   302 ISPSNCIYMTEWLEF 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

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 = 80/255 (31%), Positives = 128/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQSKAETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  E T I      VG V  +  + +      P TG     PCG+CP    C   G 
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPILPPTGV-VRAPCGLCPVFEDCHEGGE 301

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   302 ISPSNCIYMTEWLEF 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

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

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 79/255 (30%), Positives = 129/255 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:   121 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 177

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   178 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 237

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   238 QCFKFLQSKAETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 297

Query:   187 ---GSGEFTNIP-----VGKVC-YKNVSKXXXXXEPKTGSSASVPCGVCPQINFCTPDGV 237
                G  + T I      VG V  +  + +      P TG     PCG+CP  + C   G 
Sbjct:   298 IYDGKVDMTIIAAKEGTVGSVDGHMKLYRAVNPILPPTGL-VRAPCGLCPVFDDCHEGGE 356

Query:   238 ISPKTCVYYTKWLDF 252
             ISP  C+Y T+WL+F
Sbjct:   357 ISPSNCIYMTEWLEF 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

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

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 78/254 (30%), Positives = 127/254 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    64 LRSNAGLLYRIKESQNASKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 120

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   121 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 180

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   181 QCFKFLQSKAEAARESKQNPMIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 240

Query:   187 ---GSGEFTNIPVGKVCYKNVS---KXXXXXEPKTGSSASV--PCGVCPQINFCTPDGVI 238
                G  E T I   +    +V    K      P    +  V  PCG+CP  + C   G I
Sbjct:   241 IYDGKVEMTIIAAKEGTVGSVDGQMKLYRAVSPLIQPTGLVRTPCGLCPVFDDCHEGGEI 300

Query:   239 SPKTCVYYTKWLDF 252
             SP  C+Y T+WL+F
Sbjct:   301 SPSNCIYMTEWLEF 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 = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 78/254 (30%), Positives = 127/254 (50%)

Query:    13 LAKGSGMSKRKRPDSNAPSDSLTDH-ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI 71
             L   +G+  R +   NA     +D+ E+L+Y +I  +  + GIW+RD++   K NLP   
Sbjct:    66 LRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDIR--YKSNLPLTE 122

Query:    72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKS 131
             + K +K+L++K LIK V ++    KK  M    +P + ++GGAWYS+   ++EF++V+  
Sbjct:   123 INKILKNLESKKLIKAVKSVAASKKKVYMLYNLQPDRSVTGGAWYSDQDFESEFVEVLNQ 182

Query:   132 QCLKQI-IKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVRAVVLDNQIMEVKSN-- 186
             QC K +  K + A     +  I+R+ +F    ++ K   E  +  V L  + +E   N  
Sbjct:   183 QCFKFLQTKAETARESKQNPVIQRNSSFASSHEVWKYICELGISKVELSMEDIETILNTL 242

Query:   187 ---GSGEFTNIPVGKVCYKNVS---KXXXXXEPKTGSSASV--PCGVCPQINFCTPDGVI 238
                G  E T I   +    +V    K      P    +  V  PCG+CP  + C   G I
Sbjct:   243 IYDGKVEMTIIAAKEGTVGSVDGHMKLYRAVNPIISPTGLVRAPCGLCPVFDDCHEGGEI 302

Query:   239 SPKTCVYYTKWLDF 252
             SP  C+Y T+WL+F
Sbjct:   303 SPSNCIYMTEWLEF 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	252
pfam05158	312	pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 sub	2e-50
COG5111	301	COG5111, RPC34, DNA-directed RNA polymerase III, s	4e-24

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

 Score =  167 bits (424), Expect = 2e-50
 Identities = 71/263 (26%), Positives = 125/263 (47%), Gaps = 28/263 (10%)

Query: 10  LLGLAKGSGMS-KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLP 68
           L+ L +  G+  K    +      +L+D E L+Y +I  +  + GIWTR +K   + NL 
Sbjct: 57  LVLLKQNDGLVYKAVTREEAKKKATLSDEESLVYSIIEESGNE-GIWTRTIKN--RTNLH 113

Query: 69  DNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV 128
            +++ K +KSL++K  IK V ++    +K  M    EPS++++GG WY++G LD EFI  
Sbjct: 114 QSVLKKCLKSLESKKYIKSVKSVKAPTRKMYMLYNLEPSEEVTGGPWYTDGELDVEFINT 173

Query: 129 VKSQCLK-----------------QIIKLKVA---TLEGISDSIKRSGAFKVDLTKQQIE 168
           ++    +                            T+E I+  I   G   V L+++ I+
Sbjct: 174 LRRVIFRFVSQKTYVNGFGGEKKALPYPAGYKSYPTVEEIATFINELGITNVRLSEEDIQ 233

Query: 169 EIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQ 228
           ++V  +V D ++ +VK         + + +V   +  +          +    PCG CP 
Sbjct: 234 QLVETLVYDGKLEKVKPGAGYRLQRVTLQEVLQMSQKRRPLPANGLVEA----PCGNCPV 289

Query: 229 INFCTPDGVISPKTCVYYTKWLD 251
            + C+  GV+SPK CVY+ +WL+
Sbjct: 290 FDLCSEGGVVSPKNCVYFKEWLE 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 = 97.7 bits (243), Expect = 4e-24
 Identities = 60/255 (23%), Positives = 107/255 (41%), Gaps = 49/255 (19%)

Query: 21  KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
           K       +P +++ D+E  +Y +I S     GIW + +K   + NL  N+V K +KSL+
Sbjct: 70  KGVLESEASPINTMDDYELTVYSLI-SQSGGEGIWLKTIK--DRTNLHHNVVGKCLKSLE 126

Query: 81  NKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL 140
           +K ++K V ++ N  +K  M  +  PS++I+GG W+++  LD EFI       L +II+ 
Sbjct: 127 SKRIVKSVKSVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFI-----ARLLEIIER 181

Query: 141 KV-------------------------ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVV 175
            +                          TLE I + ++      V L    +E +   +V
Sbjct: 182 FLEKNLFPRKNFEEGPNVFYAPKYEDYPTLEDIMNYVRNVNILSVPLRLDNLESLADVLV 241

Query: 176 LDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQINFCTPD 235
            D ++ ++ S     +         +K  +K  G GE         P G     +     
Sbjct: 242 YDGKVEKLHSGPIYRYR-------AFKPYAKNQGEGE---------PAGNKALEDEEEFS 285

Query: 236 GVISPKTCVYYTKWL 250
             + P + VY+ +W 
Sbjct: 286 FKMFPASVVYFDEWT 300

Length = 301

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	252
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;	98.33
COG2512	258	Predicted membrane-associated trancriptional regul	98.0
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	97.92
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	97.91
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.81
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.8
PF13730	55	HTH_36: Helix-turn-helix domain	97.78
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	97.59
PRK03573	144	transcriptional regulator SlyA; Provisional	97.59
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.53
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.49
COG1846	126	MarR Transcriptional regulators [Transcription]	97.46
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	97.45
PRK10870	176	transcriptional repressor MprA; Provisional	97.42
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	97.41
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	97.36
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.22
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	97.08
PRK13777	185	transcriptional regulator Hpr; Provisional	97.07
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.92
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	96.83
COG1522	154	Lrp Transcriptional regulators [Transcription]	96.45
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.34
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	96.33
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	96.33
COG3355	126	Predicted transcriptional regulator [Transcription	96.29
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	96.23
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.2
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.12
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.92
PRK00215	205	LexA repressor; Validated	95.9
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	95.9
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	95.76
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	95.48
COG3888	321	Predicted transcriptional regulator [Transcription	95.47
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	95.46
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.45
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.23
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.95
COG1725	125	Predicted transcriptional regulators [Transcriptio	94.87
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	94.74
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.67
PRK06474	178	hypothetical protein; Provisional	94.41
PHA02943	165	hypothetical protein; Provisional	94.31
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	94.23
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.18
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	94.11
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	94.1
PRK14165	217	winged helix-turn-helix domain-containing protein/	94.04
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	93.99
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	93.95
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.82
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	93.7
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	93.68
COG3398	240	Uncharacterized protein conserved in archaea [Func	93.67
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	93.6
PF08672	60	APC2: Anaphase promoting complex (APC) subunit 2;	93.59
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	93.47
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	93.26
PRK11169	164	leucine-responsive transcriptional regulator; Prov	93.22
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	92.91
PRK09334	86	30S ribosomal protein S25e; Provisional	92.84
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	92.73
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	92.38
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	92.31
COG1378	247	Predicted transcriptional regulators [Transcriptio	92.27
KOG2165	765	consensus Anaphase-promoting complex (APC), subuni	92.21
PRK12423	202	LexA repressor; Provisional	92.14
COG1733	120	Predicted transcriptional regulators [Transcriptio	92.14
PRK11014	141	transcriptional repressor NsrR; Provisional	92.1
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	92.09
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	91.88
PF06224	327	HTH_42: Winged helix DNA-binding domain; InterPro:	91.62
cd00131	128	PAX Paired Box domain	91.61
PF03551	75	PadR: Transcriptional regulator PadR-like family;	91.57
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	91.49
PRK09462	148	fur ferric uptake regulator; Provisional	91.09
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	91.02
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	90.94
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	90.93
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	90.76
PRK06266	178	transcription initiation factor E subunit alpha; V	90.65
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.5
PRK03902	142	manganese transport transcriptional regulator; Pro	90.43
PHA00738	108	putative HTH transcription regulator	90.32
smart00351	125	PAX Paired Box domain.	90.16
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	90.09
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	90.05
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	89.85
PRK09954	362	putative kinase; Provisional	89.82
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.72
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.45
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	89.39
PRK09391	230	fixK transcriptional regulator FixK; Provisional	89.06
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	88.95
PRK11050	152	manganese transport regulator MntR; Provisional	88.94
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	88.94
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	88.79
COG1654	79	BirA Biotin operon repressor [Transcription]	88.66
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	88.61
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	88.48
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	88.36
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	88.35
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	88.34
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	87.31
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	87.23
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.22
COG3432	95	Predicted transcriptional regulator [Transcription	87.15
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	87.13
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	86.93
PRK09462	148	fur ferric uptake regulator; Provisional	86.75
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	86.73
PRK15431	78	ferrous iron transport protein FeoC; Provisional	86.59
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	86.42
PF13034	78	DUF3895: Protein of unknown function (DUF3895)	86.34
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	86.12
PRK05638	442	threonine synthase; Validated	85.58
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	85.54
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	85.47
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	85.2
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	85.05
PHA02943	165	hypothetical protein; Provisional	84.83
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	84.71
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	84.5
PRK13509	251	transcriptional repressor UlaR; Provisional	84.27
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.08
COG1777	217	Predicted transcriptional regulators [Transcriptio	83.98
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	83.87
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	83.81
COG1959	150	Predicted transcriptional regulator [Transcription	83.71
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	83.64
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	83.64
PRK09416	135	lstR lineage-specific thermal regulator protein; P	83.45
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	83.45
PF13551	112	HTH_29: Winged helix-turn helix	82.81
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	82.66
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	82.39
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	81.74
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	81.72
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	81.49
COG3682	123	Predicted transcriptional regulator [Transcription	80.95
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	80.73
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	80.44
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	80.44
PRK11569	274	transcriptional repressor IclR; Provisional	80.13
PRK11639	169	zinc uptake transcriptional repressor; Provisional	80.06

>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=3.3e-78  Score=562.33  Aligned_cols=236  Identities=42%  Similarity=0.771  Sum_probs=69.4

Q ss_pred             hHHHhhccCCC-cccc-cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493            8 LYLLGLAKGSG-MSKR-KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI   85 (252)
Q Consensus         8 ~~~~~~~~~~~-~~~~-~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI   85 (252)
                      ..++.+.++++ ..++ +.++.++++++|+++|++||++|++ |||+|||++|||++|  |||+++|+|+||+||+|+||
T Consensus        54 ~~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~-ag~~GIw~~~i~~~t--~l~~~~~~k~lk~Le~k~lI  130 (327)
T PF05158_consen   54 SGLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEE-AGNKGIWTKDIKKKT--NLHQTQLTKILKSLESKKLI  130 (327)
T ss_dssp             HTSEEEEE-SSSEEEEE--SSS-----SSSCCHHHHHHHHHH-HTTT-EEHHHHHHHC--T--HHHHHHHHHHHHHTTSE
T ss_pred             CCCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHH-hCCCCCcHHHHHHHc--CCCHHHHHHHHHHHHhCCCE
Confidence            34444444433 3444 6678889999999999999999999 999999999999999  99999999999999999999


Q ss_pred             eeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCC-----------------------
Q 025493           86 KEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKV-----------------------  142 (252)
Q Consensus        86 K~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~-----------------------  142 (252)
                      |+||||++++|||||||||+||+|||||+||+|||||+|||+.|+++|++||++++.                       
T Consensus       131 K~vksv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  210 (327)
T PF05158_consen  131 KSVKSVKNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYP  210 (327)
T ss_dssp             EEE--SS-SS--EEEESSS-------------------------------------------------------------
T ss_pred             EEecCcCCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccc
Confidence            999999999999999999999999999999999999999999999999999986544                       


Q ss_pred             ------CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCccee-------ecccCCCC
Q 025493          143 ------ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCY-------KNVSKGGG  209 (252)
Q Consensus       143 ------~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~Y-------R~~~~~~~  209 (252)
                            ||++||++||+++||++++|+++||++||++|||||+||++.+++..++...+....++       |....   
T Consensus       211 ~~~~~~~T~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  287 (327)
T PF05158_consen  211 AGYASYPTLEEIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSGDGYEYYRAPGQSVLYCSKRRYYRAVGP---  287 (327)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccCCCCCHHHHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEeccCCceeeeeecccceeeecccccccccc---
Confidence                  99999999999999999999999999999999999999999977444443333333332       22222   


Q ss_pred             CCCCCCCCcccCCCCCCCccccCCCCCccCcccccchHhhhc
Q 025493          210 GGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLD  251 (252)
Q Consensus       210 ~~~~~~~~l~~vPCg~CPv~~~C~~gG~IsP~tC~Y~~eWL~  251 (252)
                        .+..++++++|||+||||+.|.+||+|||++|+||++||+
T Consensus       288 --~~~~~~~~~~PCg~CPVf~~C~~~G~IsP~~C~Yf~~WL~  327 (327)
T PF05158_consen  288 --EPSASGLTEVPCGVCPVFDQCSPGGPISPKTCVYFDEWLD  327 (327)
T ss_dssp             ------------------------------------------
T ss_pred             --ccCCCCccCCCCCCCCccceeCCCCCCCchhchHHHHhhC
Confidence              2446789999999999999999999999999999999996

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-73  Score=513.71  Aligned_cols=224  Identities=36%  Similarity=0.744  Sum_probs=205.3

Q ss_pred             hHHHhhccCC-C-cccccCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493            8 LYLLGLAKGS-G-MSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI   85 (252)
Q Consensus         8 ~~~~~~~~~~-~-~~~~~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI   85 (252)
                      ..+|++.+.+ + .+++++++.+...+++++||++||++|++ +||+|||.++||.++  |||+++|+|+||+||+|+||
T Consensus        54 ~~~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe~-sg~~GIW~k~ik~ks--nLp~~~v~K~LkSLEsKkLI  130 (297)
T KOG3233|consen   54 RGLLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSLIEE-SGNEGIWSKEIKRKS--NLPQTVVNKILKSLESKKLI  130 (297)
T ss_pred             cCcchhhccCCcceEeccCchhhcccccCChHHHHHHHHHHH-cCCCceeeehhhhcc--CCCHHHHHHHHHHHHHHHHH
Confidence            4567777666 3 34457888888899999999999999999 999999999999999  99999999999999999999


Q ss_pred             eeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhh-----------------CCCCCHHHH
Q 025493           86 KEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIK-----------------LKVATLEGI  148 (252)
Q Consensus        86 K~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~-----------------~~~~T~~~I  148 (252)
                      |+||||++++||+||||+|+||.|+|||+||+||+||.|||+.|.++|++|+++                 .+++|++||
T Consensus       131 KsVKsv~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~ei  210 (297)
T KOG3233|consen  131 KSVKSVKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQEI  210 (297)
T ss_pred             HHHHhhcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHHH
Confidence            999999999999999999999999999999999999999999999999999973                 479999999


Q ss_pred             HHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCCCCCCCCCCcccCCCCCCCc
Q 025493          149 SDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQ  228 (252)
Q Consensus       149 ~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~~~~~~~~~l~~vPCg~CPv  228 (252)
                      ++||++.+|++|.|+.+|++.|+++|||||+||+.. +|           .+||+.....    |..+.+.++|||.|||
T Consensus       211 ~~~i~~l~I~nV~Lsl~dleti~~vlvyDGkvE~r~-dG-----------~~yra~~~~~----~~~~~~~~~Pcg~cPv  274 (297)
T KOG3233|consen  211 KEFIRNLNILNVELSLEDLETILDVLVYDGKVEKRH-DG-----------PRYRAFGPNI----PRAGLVAGIPCGICPV  274 (297)
T ss_pred             HHHHHHcCcccccccHHHHHHHhHHheecceeeeee-cC-----------ceeeecCCCC----CCcCccCCCcccCCcc
Confidence            999999999999999999999999999999999833 33           3799887764    3456778899999999


Q ss_pred             cccCCCCCccCcccccchHhhh
Q 025493          229 INFCTPDGVISPKTCVYYTKWL  250 (252)
Q Consensus       229 ~~~C~~gG~IsP~tC~Y~~eWL  250 (252)
                      ++.|+|||.|||.||+||++||
T Consensus       275 ~~dC~~~g~isP~tC~Ym~~WL  296 (297)
T KOG3233|consen  275 IDDCSPGGVISPITCVYMDKWL  296 (297)
T ss_pred             hhccCCCCccCchhhHHHHhhc
Confidence            9999999999999999999999

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

Probab=100.00  E-value=4.2e-63  Score=436.83  Aligned_cols=226  Identities=24%  Similarity=0.411  Sum_probs=208.7

Q ss_pred             hhHHHhhccCCCcccc--cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493            7 DLYLLGLAKGSGMSKR--KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL   84 (252)
Q Consensus         7 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l   84 (252)
                      +.+||+|.+++++.+.  +..+++...+.|+++|.+||++|++ +|++|||.+.|+.+|  |||++.+-||||+||+|++
T Consensus        54 ~r~li~l~rq~~vL~y~~v~~~ea~~~~tm~~~E~~vYs~i~~-SG~EGiW~Ktik~rT--Nlh~~vV~kcLkSlESkr~  130 (301)
T COG5111          54 KRQLISLFRQKGVLYYKGVLESEASPINTMDDYELTVYSLISQ-SGGEGIWLKTIKDRT--NLHHNVVGKCLKSLESKRI  130 (301)
T ss_pred             HHhhhhHHhcCCEEEEeeeecccCCcccccchHHHHHHHHHHh-cCCCceehhhhhhhc--cCcHHHHHHHHHHHHHHHH
Confidence            4689999999999886  5778888899999999999999999 999999999999999  9999999999999999999


Q ss_pred             eeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhh--------------------CCCCC
Q 025493           85 IKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIK--------------------LKVAT  144 (252)
Q Consensus        85 IK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~--------------------~~~~T  144 (252)
                      ||+||||++|+||+||||+|.||+||||||||||||+|.|||+.|.+++.+||..                    .+|||
T Consensus       131 vKSvKsvKnptRKiYmLYdlvPS~eiTGGpWFtD~elDvEfi~~ll~ii~rf~~~n~fp~kn~~~gpnv~~~P~y~~ypT  210 (301)
T COG5111         131 VKSVKSVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFYAPKYEDYPT  210 (301)
T ss_pred             HHHhhhhcCCCceEEEEecccccccccCCCccccCcccHHHHHHHHHHHHHHHHhccCCccchhcCCccccCCccCCCcc
Confidence            9999999999999999999999999999999999999999999999999999983                    37999


Q ss_pred             HHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCCCCCCCCCCcccCCCC
Q 025493          145 LEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCG  224 (252)
Q Consensus       145 ~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~~~~~~~~~l~~vPCg  224 (252)
                      ++||++||++.+|.+|+|+.++++++.++|||||++|++.++.            .||...-..    -..+..++-|||
T Consensus       211 ~~~I~n~vr~~ni~~v~L~l~n~~sL~dvLvyDgKvEK~~~g~------------~yR~~~~~~----~~~nq~~~ep~g  274 (301)
T COG5111         211 LEDIMNYVRNVNILSVPLRLDNLESLADVLVYDGKVEKLHSGP------------IYRYRAFKP----YAKNQGEGEPAG  274 (301)
T ss_pred             HHHHHHHHHhceeeeccccHHHHHHHhHheeecCeeeeeccCc------------ceeeeecCh----hhhcccCCCCCC
Confidence            9999999999999999999999999999999999999987542            366544332    125778999999


Q ss_pred             CCCccccCCCCCccCcccccchHhhhc
Q 025493          225 VCPQINFCTPDGVISPKTCVYYTKWLD  251 (252)
Q Consensus       225 ~CPv~~~C~~gG~IsP~tC~Y~~eWL~  251 (252)
                      .||+-+.|.....+.|.+|+||++|+.
T Consensus       275 n~~led~~e~s~km~p~s~~y~dew~~  301 (301)
T COG5111         275 NKALEDEEEFSFKMFPASVVYFDEWTI  301 (301)
T ss_pred             CCcccchHhhhcccCceeEEeehhhcC
Confidence            999999999999999999999999973

>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=98.33  E-value=2.5e-06  Score=63.75  Aligned_cols=65  Identities=23%  Similarity=0.299  Sum_probs=56.7

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc---ccCCeeeEEec
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI---HNKGKKHLMAV  102 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv---~~~~rK~YmL~  102 (252)
                      |+.+..|+..|-. |+..|||+.||.+.+  ++.++.+...+|.|+.+|||.....+   ..++...++|+
T Consensus         1 t~~~~~~Le~I~r-sR~~Gi~q~~L~~~~--~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~   68 (75)
T PF04182_consen    1 TDIQYCLLERIAR-SRYNGITQSDLSKLL--GIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLH   68 (75)
T ss_pred             CchHHHHHHHHHh-cCCCCEehhHHHHHh--CCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEE
Confidence            5678999999999 999999999999999  99999999999999999999996552   34456666664

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.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=98.00  E-value=2e-05  Score=72.00  Aligned_cols=56  Identities=25%  Similarity=0.470  Sum_probs=51.1

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      .-.|+++|+.|..+|.+ .|+. |-|+||++++  |++.+.+.|+|+.||++|+|+..|.
T Consensus       190 ~~~L~~~e~~il~~i~~-~GGr-i~Q~eL~r~l--glsktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         190 EYDLNEDEKEILDLIRE-RGGR-ITQAELRRAL--GLSKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             cCCCCHHHHHHHHHHHH-hCCE-EeHHHHHHhh--CCChHHHHHHHHHHHhCCceEEEEe
Confidence            35899999999999999 5532 9999999999  9999999999999999999999875

>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=97.92  E-value=7.2e-05  Score=52.45  Aligned_cols=58  Identities=14%  Similarity=0.248  Sum_probs=52.6

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+..|.. .+..++-..+|...+  ++++..++++++.||++|||...++-+.
T Consensus         2 glt~~q~~vL~~l~~-~~~~~~t~~~la~~l--~~~~~~vs~~v~~L~~~Glv~r~~~~~D   59 (62)
T PF12802_consen    2 GLTPSQFRVLMALAR-HPGEELTQSELAERL--GISKSTVSRIVKRLEKKGLVERERDPGD   59 (62)
T ss_dssp             TSTHHHHHHHHHHHH-STTSGEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred             ccCHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence            689999999999999 999999999999999  9999999999999999999999876553

...

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=97.91  E-value=0.00014  Score=57.56  Aligned_cols=85  Identities=16%  Similarity=0.234  Sum_probs=69.1

Q ss_pred             CCChHHHHHHHHHH--hhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCc
Q 025493           33 SLTDHERLIYDVIR--SNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDI  110 (252)
Q Consensus        33 ~l~~~e~~vy~~I~--~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ei  110 (252)
                      +|+..|..|+..|.  + +.+.|+..++|...+  +++...++++++.||++|+|+.+++.+. .|++|+-  |+|.   
T Consensus        22 ~ls~~q~~vL~~l~~~~-~~~~~~t~~eL~~~l--~~~~stvs~~i~~Le~kg~I~r~~~~~D-~R~~~i~--lT~~---   92 (109)
T TIGR01889        22 NLSLEELLILYYLGKLE-NNEGKLTLKEIIKEI--LIKQSALVKIIKKLSKKGYLSKERSEDD-ERKVIIS--INKE---   92 (109)
T ss_pred             CCCHHHHHHHHHHHhhh-ccCCcCcHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeccCCccc-CCeEEEE--ECHH---
Confidence            79999999999998  6 667889999999999  9999999999999999999999999887 4444432  3333   


Q ss_pred             cCCccccCCcCCHHHHHHHHHHHHHHh
Q 025493          111 SGGAWYSEGSLDTEFIKVVKSQCLKQI  137 (252)
Q Consensus       111 TGG~wy~d~e~D~efV~~l~~~~~~~i  137 (252)
                                 -.+.++.+...+.+++
T Consensus        93 -----------G~~~~~~~~~~~~~~~  108 (109)
T TIGR01889        93 -----------QRSKIESLISEIEQII  108 (109)
T ss_pred             -----------HHHHHHHHHHHHHHHh
Confidence                       2456677777766664

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.

>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=97.81  E-value=5e-05  Score=54.99  Aligned_cols=62  Identities=23%  Similarity=0.328  Sum_probs=52.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      +|++.|..||..+-+   +.+.-.++|...+  +++.+.+.++|+.|+.+|+|...+.    +.++|-..+
T Consensus         5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l--~i~~~~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~   66 (68)
T PF01978_consen    5 GLSENEAKVYLALLK---NGPATAEEIAEEL--GISRSTVYRALKSLEEKGLVEREEG----RPKVYRAVP   66 (68)
T ss_dssp             CHHHHHHHHHHHHHH---HCHEEHHHHHHHH--TSSHHHHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence            688999999999876   4678899999999  9999999999999999999999762    266776643

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.

>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=97.80  E-value=8.9e-05  Score=50.13  Aligned_cols=48  Identities=25%  Similarity=0.487  Sum_probs=41.1

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK   86 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK   86 (252)
                      ||+.++.|+.+|.+   +.++.+++|..++  |++...+++.|+.|+++|+|+
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~--~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKL--GISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHH--TS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCcCcC
Confidence            67889999999999   4459999999999  999999999999999999996

...

>PF13730 HTH_36: Helix-turn-helix domain

Probab=97.78  E-value=0.00011  Score=50.93  Aligned_cols=52  Identities=25%  Similarity=0.489  Sum_probs=45.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCc-cc--HHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMG-IW--TRDMKRELKVNLPDNIVTKSIKSLQNKSLI   85 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~G-Iw--~~dik~~~~~~l~~~~l~k~lK~Le~k~lI   85 (252)
                      ++|++.|++||-.|...+++.| .|  .+.|.+.+  ++..++|.|+|+.||++|+|
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            3799999999999998664444 44  79999999  99999999999999999997

>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=97.59  E-value=0.00035  Score=48.71  Aligned_cols=55  Identities=24%  Similarity=0.342  Sum_probs=49.4

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      ||..|..++..|.+ .|+  +-..+|...+  +++...++++++.||++|+|....+-+.
T Consensus         1 lt~~q~~iL~~l~~-~~~--~~~~~la~~~--~~~~~~~t~~i~~L~~~g~I~r~~~~~D   55 (59)
T PF01047_consen    1 LTPSQFRILRILYE-NGG--ITQSELAEKL--GISRSTVTRIIKRLEKKGLIERERDPDD   55 (59)
T ss_dssp             STHHHHHHHHHHHH-HSS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCHHHHHHHHHHHH-cCC--CCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCC
Confidence            57789999999999 665  9999999999  9999999999999999999999888765

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 ....

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=97.59  E-value=0.0015  Score=53.41  Aligned_cols=66  Identities=12%  Similarity=0.175  Sum_probs=55.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+|+..+..|+..|.+ .+ .|+.+++|...+  ++..+.++++++.||++|||...++-+.+..+..-|
T Consensus        27 ~glt~~q~~vL~~l~~-~~-~~~t~~eLa~~l--~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~L   92 (144)
T PRK03573         27 LELTQTHWVTLHNIHQ-LP-PEQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKL   92 (144)
T ss_pred             cCCCHHHHHHHHHHHH-cC-CCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEE
Confidence            4799999999999987 53 468899999999  999999999999999999999999887644444333

>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=97.53  E-value=0.00051  Score=48.88  Aligned_cols=64  Identities=22%  Similarity=0.335  Sum_probs=49.8

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ||..|..|+..|.  ..+..+-.++|...+  ++++..++++|++|+.+|||....+-+.+..+.|-|
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~--~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~L   64 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERL--GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRL   64 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEe
Confidence            5778888888887  246778889999999  999999999999999999999999888755566655

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

Probab=97.49  E-value=0.00041  Score=50.88  Aligned_cols=51  Identities=20%  Similarity=0.284  Sum_probs=47.2

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ++.+..|+.++.+ +|.+|+-.++|.+++  +|+...++|+|.+|+++|+|...
T Consensus         5 ~~~~~~IL~~L~~-~g~~~~ta~eLa~~l--gl~~~~v~r~L~~L~~~G~V~~~   55 (68)
T smart00550        5 DSLEEKILEFLEN-SGDETSTALQLAKNL--GLPKKEVNRVLYSLEKKGKVCKQ   55 (68)
T ss_pred             hHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence            4567899999999 999999999999999  99999999999999999999763

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

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=97.46  E-value=0.00061  Score=52.43  Aligned_cols=63  Identities=17%  Similarity=0.292  Sum_probs=55.8

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      |+..|..|+..|.. .+..+.  .+|..++  +++...+++.|+.||.+|||+..++-..+.++++.|
T Consensus        20 lt~~q~~~L~~l~~-~~~~~~--~~la~~l--~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l   82 (126)
T COG1846          20 LTPPQYQVLLALYE-AGGITV--KELAERL--GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL   82 (126)
T ss_pred             CCHHHHHHHHHHHH-hCCCcH--HHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence            89999999999999 888777  9999999  999999999999999999999999887744444444

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=97.45  E-value=0.00069  Score=53.77  Aligned_cols=65  Identities=9%  Similarity=0.175  Sum_probs=57.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..+..|+..|.. .|  |+-.++|.+.+  ++..+.+++.|+.||++|||...++-..+.++.|-|
T Consensus        24 ~~lt~~q~~iL~~l~~-~~--~~t~~ela~~~--~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~L   88 (118)
T TIGR02337        24 HGLTEQQWRILRILAE-QG--SMEFTQLANQA--CILRPSLTGILARLERDGLVTRLKASNDQRRVYISL   88 (118)
T ss_pred             cCCCHHHHHHHHHHHH-cC--CcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEE
Confidence            4789999999999987 54  78899999999  999999999999999999999998888766666555

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=97.42  E-value=0.00071  Score=58.05  Aligned_cols=61  Identities=10%  Similarity=0.177  Sum_probs=56.7

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .-+|+..+..|+..|.+ .++.++-.++|...+  +++...++++++.||++|||...++-..+
T Consensus        50 ~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l--~l~~~tvsr~v~rLe~kGlV~R~~~~~Dr  110 (176)
T PRK10870         50 AQGINETLFMALITLES-QENHSIQPSELSCAL--GSSRTNATRIADELEKRGWIERRESDNDR  110 (176)
T ss_pred             HCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCC
Confidence            35799999999999998 999999999999999  99999999999999999999999887763

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=97.41  E-value=0.0063  Score=49.99  Aligned_cols=53  Identities=21%  Similarity=0.272  Sum_probs=44.2

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|++-|..|.++|=+ .|  ++..++|....+.  ++..+++...|+.|+.||+|...
T Consensus         1 ~Lt~~E~~VM~vlW~-~~--~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~   55 (130)
T TIGR02698         1 SISDAEWEVMRVVWT-LG--ETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE   55 (130)
T ss_pred             CCCHHHHHHHHHHHc-CC--CCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence            378899999999988 76  4678996665421  78999999999999999999875

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.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=97.36  E-value=0.0012  Score=49.33  Aligned_cols=57  Identities=18%  Similarity=0.332  Sum_probs=50.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      -+|+..|..|+.+|.. .|  ++-.++|...+  ++++..+++.|+.|+++|+|...+.-..
T Consensus         6 ~~l~~~~~~il~~l~~-~~--~~~~~~la~~~--~~s~~~i~~~l~~L~~~g~v~~~~~~~~   62 (101)
T smart00347        6 LGLTPTQFLVLRILYE-EG--PLSVSELAKRL--GVSPSTVTRVLDRLEKKGLIRRLPSPED   62 (101)
T ss_pred             cCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CCCchhHHHHHHHHHHCCCeEecCCCCC
Confidence            4789999999999998 66  68899999999  9999999999999999999998766433

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.22  E-value=0.0018  Score=53.18  Aligned_cols=59  Identities=19%  Similarity=0.201  Sum_probs=53.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG   95 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~   95 (252)
                      .+|+..|..|+..|.. .  .|+-+++|...+  ++....++++|+.||++|||....+-+.+.
T Consensus        36 ~glt~~q~~vL~~l~~-~--~~~t~~eLa~~l--~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR   94 (144)
T PRK11512         36 LDITAAQFKVLCSIRC-A--ACITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKR   94 (144)
T ss_pred             cCCCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence            4899999999999976 4  579999999999  999999999999999999999998887633

>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=97.08  E-value=0.014  Score=46.39  Aligned_cols=111  Identities=13%  Similarity=0.187  Sum_probs=71.3

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      |++-|..|.++|=+ .|.  +..++|....+-  +++.+++...|+.|+.||+|..-+.   .+..+|-.  +.+-    
T Consensus         1 Ls~~E~~IM~~lW~-~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~---gr~~~Y~p--~is~----   68 (115)
T PF03965_consen    1 LSDLELEIMEILWE-SGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI---GRAYVYSP--LISR----   68 (115)
T ss_dssp             --HHHHHHHHHHHH-HSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEEE--SSSH----
T ss_pred             CCHHHHHHHHHHHh-CCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec---CCceEEEe--CCcH----
Confidence            67889999999999 888  999999998743  5789999999999999999999654   22333421  1111    


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV  174 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL  174 (252)
                                 .   +.+...+.+++.+--.-+...+..++-+..    .||.+|+++|-+.|
T Consensus        69 -----------~---e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~----~ls~~el~~L~~li  113 (115)
T PF03965_consen   69 -----------E---EYLAQELRQFLDRLFDGSIPQLVAALVESE----ELSPEELEELRKLI  113 (115)
T ss_dssp             -----------H---HHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-----S-HHHHHHHHHHH
T ss_pred             -----------H---HHHHHHHHHHHHHHhCCCHHHHHHHHHhcC----CCCHHHHHHHHHHH
Confidence                       1   233334444444332335555555555444    68899998887765

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 ....

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=97.07  E-value=0.0027  Score=55.41  Aligned_cols=57  Identities=11%  Similarity=-0.001  Sum_probs=52.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      -+|+..|..|+..|.. .  .|+.+++|.+.+  +++.++++++|+.||++|||...++-..
T Consensus        41 ~gLt~~q~~iL~~L~~-~--~~itq~eLa~~l--~l~~sTvtr~l~rLE~kGlI~R~~~~~D   97 (185)
T PRK13777         41 YDLNINEHHILWIAYH-L--KGASISEIAKFG--VMHVSTAFNFSKKLEERGYLTFSKKEDD   97 (185)
T ss_pred             CCCCHHHHHHHHHHHh-C--CCcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCC
Confidence            5899999999999887 4  489999999999  9999999999999999999999888665

>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=96.92  E-value=0.0015  Score=47.77  Aligned_cols=58  Identities=22%  Similarity=0.404  Sum_probs=45.9

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ++.||+-|+.||..|.+.--..|.  ..++|....  |+. .+.+.+.|+.||.||+|+..+.
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            357999999999999885555666  468999999  998 8999999999999999998654

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.

>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=96.83  E-value=0.018  Score=54.41  Aligned_cols=133  Identities=21%  Similarity=0.291  Sum_probs=85.1

Q ss_pred             CCChHHHHHHHHHHhhc-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           33 SLTDHERLIYDVIRSNK-QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~a-g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      .+.+-|..||+++.+ + +.+|+..+||....+ +++...+-.+|..|.++++|+-++   ..++-+|-+-+-+=...+.
T Consensus         6 ~~~~~~~~l~~~~~~-~~~~~~~~~~~L~~~~~-~~~~~~~~~~in~Ll~~~~~~~~~---~~~~l~~~~~~~~~a~k~~   80 (327)
T PF05158_consen    6 KLSELEKKLLELCRE-NPSPKGFSQEDLQQLIP-GLDLQELVKAINELLSSGLLKLLK---KGGGLSYKAVSEEEAKKLK   80 (327)
T ss_dssp             -HHHHHHHHHHHHHH----SS-EEHHHHHHH-T-TS-HHHHHHHHHHHHHHTSEEEEE----SSSEEEEE--SSS-----
T ss_pred             hHHHHHHHHHHHHHH-hcCCCCcCHHHHHhhcC-CCCHHHHHHHHHHHHhCCCEEEEE---cCCEEEEEEeCHHHHhhhc
Confidence            567789999999999 6 999999999999942 899999999999999999999998   4456566654333222222


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---Cc------ceecCHHHHHHHHHHHhhcCeeEE
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSG---AF------KVDLTKQQIEEIVRAVVLDNQIME  182 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~---i~------~~~Ls~~di~~IL~tLVyDgkIE~  182 (252)
                      |=                            ...-.-|.+.|.++|   |-      +..|....|..+|++|+-.+.|-+
T Consensus        81 ~l----------------------------~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~  132 (327)
T PF05158_consen   81 GL----------------------------SDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS  132 (327)
T ss_dssp             SS----------------------------SCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred             CC----------------------------CHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence            22                            122233444444443   21      356888999999999999999999


Q ss_pred             EeeCCCCCcccccCCcceeeccc
Q 025493          183 VKSNGSGEFTNIPVGKVCYKNVS  205 (252)
Q Consensus       183 v~~~g~~~f~~~~~g~~~YR~~~  205 (252)
                      |++...       .+++.|-+..
T Consensus       133 vksv~~-------~~rK~Yml~~  148 (327)
T PF05158_consen  133 VKSVKN-------PNRKVYMLYD  148 (327)
T ss_dssp             E--SS--------SS--EEEESS
T ss_pred             ecCcCC-------CCeEEEEEcc
Confidence            987542       3567776653

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.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=96.45  E-value=0.015  Score=47.67  Aligned_cols=71  Identities=21%  Similarity=0.361  Sum_probs=59.5

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC---Cee--eEEecccc
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK---GKK--HLMAVEFE  105 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~---~rK--~YmL~~le  105 (252)
                      ...|++-++.|++++++ -|.  +..++|.++.  |++.+.+.+.+|.||..|+|+....+-++   +..  +++....+
T Consensus         3 ~~~lD~~D~~IL~~L~~-d~r--~~~~eia~~l--glS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~   77 (154)
T COG1522           3 MMKLDDIDRRILRLLQE-DAR--ISNAELAERV--GLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLE   77 (154)
T ss_pred             cccccHHHHHHHHHHHH-hCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEec
Confidence            34689999999999999 444  9999999999  99999999999999999999999987665   444  55555555


Q ss_pred             c
Q 025493          106 P  106 (252)
Q Consensus       106 P  106 (252)
                      |
T Consensus        78 ~   78 (154)
T COG1522          78 R   78 (154)
T ss_pred             C
Confidence            5

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.34  E-value=0.014  Score=50.93  Aligned_cols=64  Identities=13%  Similarity=0.232  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      ...|+..+.. .|.  +..++|...+  +++.+.+++.|+.||++|||.........+|.. .+|.|+|.
T Consensus         3 r~~IL~~L~~-~~~--~t~~eLA~~l--gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~-~~y~LT~~   66 (203)
T TIGR02702         3 KEDILSYLLK-QGQ--ATAAALAEAL--AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQ-YHYQLSRQ   66 (203)
T ss_pred             HHHHHHHHHH-cCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCc-eEEEECcc
Confidence            3567888887 654  9999999999  999999999999999999999876543344443 34455655

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.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=96.33  E-value=0.018  Score=50.11  Aligned_cols=55  Identities=13%  Similarity=0.309  Sum_probs=49.8

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ..++++.+..|+..|.+ .|  ++-.++|.+.+  +++++.+++.|+.||++|+|...+.
T Consensus       138 ~~~ls~~~~~IL~~l~~-~g--~~s~~eia~~l--~is~stv~r~L~~Le~~GlI~r~~~  192 (203)
T TIGR01884       138 LAGLSREELKVLEVLKA-EG--EKSVKNIAKKL--GKSLSTISRHLRELEKKGLVEQKGR  192 (203)
T ss_pred             hcCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            45789999999999988 54  68999999999  9999999999999999999999863

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.

>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=96.33  E-value=0.01  Score=46.18  Aligned_cols=53  Identities=19%  Similarity=0.388  Sum_probs=44.9

Q ss_pred             CCChHHHHHHHHHHh-hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRS-NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~-~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +|++-.+.||++|++ ...+.||-..+|.+++  +|+..+|.++|..|...|+|=+
T Consensus        44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYs   97 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMSENEVRKALDFLSNEGHIYS   97 (102)
T ss_dssp             -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEec
Confidence            799999999999999 7899999999999999  9999999999999999999843

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=96.29  E-value=0.023  Score=46.97  Aligned_cols=71  Identities=13%  Similarity=0.128  Sum_probs=57.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      -+|++.|.-||.++-+  -|.+...-+|..++  |+..++++|+|++|...|||.+.|----.++-.| +|.--|.
T Consensus        23 ~GLs~~Dv~v~~~LL~--~~~~~tvdelae~l--nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~y-iY~~i~~   93 (126)
T COG3355          23 YGLSELDVEVYKALLE--ENGPLTVDELAEIL--NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYY-LYKPIDP   93 (126)
T ss_pred             hCCcHHHHHHHHHHHh--hcCCcCHHHHHHHH--CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeE-EEecCCH
Confidence            4799999999999985  36788899999999  9999999999999999999999885444455444 4443333

>TIGR00498 lexA SOS regulatory protein LexA

Probab=96.23  E-value=0.014  Score=50.35  Aligned_cols=56  Identities=21%  Similarity=0.347  Sum_probs=49.5

Q ss_pred             CCCChHHHHHHHHHHhh--cCCCcccHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeeee
Q 025493           32 DSLTDHERLIYDVIRSN--KQDMGIWTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~--ag~~GIw~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++||+.|..|+..|.++  .+..+...++|...+  ++. .+.+.+.|++||++|+|+...
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~--~~~s~~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAV--GLRSPSAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh--CCCChHHHHHHHHHHHHCCCEecCC
Confidence            56999999999999962  356667889999999  999 999999999999999999864

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.

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

Probab=96.20  E-value=0.041  Score=38.22  Aligned_cols=58  Identities=12%  Similarity=0.181  Sum_probs=48.1

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +..+..|+..|.. .+   +-.++|...+  +++.+.+.+.|+.|+++++|....+-   .++.|.+
T Consensus         6 ~~~~~~il~~l~~-~~---~~~~ei~~~~--~i~~~~i~~~l~~L~~~g~i~~~~~~---~~~~~~~   63 (78)
T cd00090           6 DPTRLRILRLLLE-GP---LTVSELAERL--GLSQSTVSRHLKKLEEAGLVESRREG---RRVYYSL   63 (78)
T ss_pred             ChHHHHHHHHHHH-CC---cCHHHHHHHH--CcCHhHHHHHHHHHHHCCCeEEEEec---cEEEEEe
Confidence            3567788888887 54   8899999999  99999999999999999999986543   4566655

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.

>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=96.12  E-value=0.034  Score=41.73  Aligned_cols=62  Identities=15%  Similarity=0.256  Sum_probs=45.1

Q ss_pred             HHHHHHhhcCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           41 IYDVIRSNKQDMG-IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        41 vy~~I~~~ag~~G-Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      +.-.+.. .++.+ +..++|..++  +++...+.|+++.|++.|+|++.+..+    -=|.|..  |.++||
T Consensus        13 ~l~~la~-~~~~~~~s~~eiA~~~--~i~~~~l~kil~~L~~~Gli~s~~G~~----GGy~L~~--~~~~It   75 (83)
T PF02082_consen   13 ILLYLAR-HPDGKPVSSKEIAERL--GISPSYLRKILQKLKKAGLIESSRGRG----GGYRLAR--PPEEIT   75 (83)
T ss_dssp             HHHHHHC-TTTSC-BEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEETSTT----SEEEESS---CCGSB
T ss_pred             HHHHHHh-CCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHhhCCeeEecCCCC----CceeecC--CHHHCC
Confidence            3344555 55555 9999999999  999999999999999999998875332    3566643  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.

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

Probab=95.92  E-value=0.019  Score=41.87  Aligned_cols=47  Identities=9%  Similarity=0.198  Sum_probs=37.1

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      ..+.+||+.++.+|+.||+..+        .++.+.|+.+|+.|+--|+|+++..
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            4577788888888888888765        4789999999999999999998864

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

>PRK00215 LexA repressor; Validated

Probab=95.90  E-value=0.023  Score=49.28  Aligned_cols=54  Identities=26%  Similarity=0.391  Sum_probs=48.2

Q ss_pred             CChHHHHHHHHHHhh--cCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeee
Q 025493           34 LTDHERLIYDVIRSN--KQDMGIWTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        34 l~~~e~~vy~~I~~~--ag~~GIw~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ||+.|..|+..|.+.  .++.++..++|.+.+  ++ +.+.+++.|++||++|+|....
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            688999999999841  467788999999999  99 9999999999999999998864

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=95.90  E-value=0.022  Score=44.20  Aligned_cols=53  Identities=19%  Similarity=0.380  Sum_probs=47.1

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      |++.++.|+.++.+ .|  .+..++|..++  |++...+.+.++.|+++|+|+.+..+
T Consensus         1 ld~~D~~il~~L~~-~~--~~~~~~la~~l--~~s~~tv~~~l~~L~~~g~i~~~~~~   53 (108)
T smart00344        1 LDEIDRKILEELQK-DA--RISLAELAKKV--GLSPSTVHNRVKRLEEEGVIKGYTAV   53 (108)
T ss_pred             CCHHHHHHHHHHHH-hC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeceEEE
Confidence            57788999999999 54  58899999999  99999999999999999999965544

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

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

Probab=95.76  E-value=0.015  Score=43.95  Aligned_cols=43  Identities=19%  Similarity=0.299  Sum_probs=35.9

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493           51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG   95 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~   95 (252)
                      +..+.-++|+..+  ++++..+++.|+.||+.|+|+.-|....+.
T Consensus        12 ~~~~~f~~L~~~l--~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~   54 (80)
T PF13601_consen   12 NEEATFSELKEEL--GLTDGNLSKHLKKLEEAGYVEVEKEFEGRR   54 (80)
T ss_dssp             HSEEEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEE-SSS-
T ss_pred             cCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEEEeccCCC
Confidence            5679999999999  999999999999999999999988876543

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

Probab=95.48  E-value=0.058  Score=41.83  Aligned_cols=58  Identities=19%  Similarity=0.166  Sum_probs=47.5

Q ss_pred             CCCCCChHHHHHHHHHHhhc-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           30 PSDSLTDHERLIYDVIRSNK-----QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        30 ~~~~l~~~e~~vy~~I~~~a-----g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ...+++..+..++-.|....     ...+|.+++|-..+  ++....++|+|+.||++|+|+...
T Consensus        19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~--g~sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELT--GLSRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeec
Confidence            35678888877777554201     47899999999999  999999999999999999999643

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

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=95.47  E-value=0.042  Score=50.93  Aligned_cols=62  Identities=16%  Similarity=0.327  Sum_probs=53.9

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.-| .+...+++ ||..||.|-+|-.=+  |+...+++-+|+.||.+|.||+ +-|..+++.||+.
T Consensus         4 ~~re-klir~Lk~-a~~~GI~Q~eIeel~--GlSKStvSEaLs~LE~~giv~R-rkvsGKs~rVwLa   65 (321)
T COG3888           4 SLRE-KLIRELKR-AGPEGIDQTEIEELM--GLSKSTVSEALSELEKQGIVKR-RKVSGKSKRVWLA   65 (321)
T ss_pred             cHHH-HHHHHHHh-cCCCCccHHHHHHHh--CcchhHHHHHHHHHHhcCeeee-eeecCcceEEeec
Confidence            3344 45567888 999999999999999  9999999999999999999999 6677788999865

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

Probab=95.46  E-value=0.037  Score=40.61  Aligned_cols=51  Identities=16%  Similarity=0.181  Sum_probs=45.6

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ++.|..|++++++ +|..++....+....  +.+...||++|=.|+.+|.|...
T Consensus         3 ~~~ee~Il~~L~~-~g~~~a~~ia~~~~L--~~~kk~VN~~LY~L~k~g~v~k~   53 (66)
T PF02295_consen    3 QDLEEKILDFLKE-LGGSTATAIAKALGL--SVPKKEVNRVLYRLEKQGKVCKE   53 (66)
T ss_dssp             HHHHHHHHHHHHH-HTSSEEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             hhHHHHHHHHHHh-cCCccHHHHHHHhCc--chhHHHHHHHHHHHHHCCCEeeC
Confidence            4568899999999 999999999999999  89999999999999999999764

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 ....

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.45  E-value=0.079  Score=35.04  Aligned_cols=46  Identities=11%  Similarity=0.321  Sum_probs=40.2

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ..|++.+.+ .  .++-..+|....  +++.+.+.+.|+.|+.+|+|....
T Consensus         3 ~~il~~l~~-~--~~~s~~~l~~~l--~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        3 QQILELLAQ-Q--GKVSVEELAELL--GVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHH-c--CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEee
Confidence            457888877 4  369999999999  999999999999999999998754

>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=95.23  E-value=0.12  Score=36.41  Aligned_cols=50  Identities=16%  Similarity=0.245  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +.=..|+.++   +++.+....+|...+  +++++.+.+.|+.|+..|||+.++.
T Consensus        10 p~R~~Il~~L---~~~~~~t~~ela~~l--~~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   10 PTRLRILRLL---ASNGPMTVSELAEEL--GISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHHHH---HHCSTBEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHH---hcCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEecc
Confidence            3445677777   347899999999999  9999999999999999999998753

...

>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=94.95  E-value=0.055  Score=37.12  Aligned_cols=43  Identities=16%  Similarity=0.370  Sum_probs=35.3

Q ss_pred             HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      |++++.+ + ..++-..+|-+++  ++|.+.+.|.|++|+..|+|..
T Consensus         8 iL~~l~~-~-~~~~t~~eia~~~--gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    8 ILEALAE-S-GGPLTLSEIARAL--GLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHCHHC-T-BSCEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHc-C-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCcCeec
Confidence            4555555 3 3447999999999  9999999999999999999986

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=94.87  E-value=0.2  Score=41.34  Aligned_cols=86  Identities=17%  Similarity=0.237  Sum_probs=58.7

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHH
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV  128 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~  128 (252)
                      -|.+==..|+|...+  +++.++++|+.+.||..|+|...     +++-+|+-.+-.+             .+|...-..
T Consensus        31 pGdkLPSvRelA~~~--~VNpnTv~raY~eLE~eG~i~t~-----rg~G~fV~~~~~~-------------~~~~~~~~~   90 (125)
T COG1725          31 PGDKLPSVRELAKDL--GVNPNTVQRAYQELEREGIVETK-----RGKGTFVTEDAKE-------------ILDQLKREL   90 (125)
T ss_pred             CCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe-----cCeeEEEcCCchh-------------hHHHHHHHH
Confidence            466666789999999  99999999999999999999986     3454554422100             455555555


Q ss_pred             HHHHHHHHhhh--CCCCCHHHHHHHHHH
Q 025493          129 VKSQCLKQIIK--LKVATLEGISDSIKR  154 (252)
Q Consensus       129 l~~~~~~~i~~--~~~~T~~~I~~~i~~  154 (252)
                      +.+.+..||..  .-..|.++|+++++.
T Consensus        91 ~~~~l~~~I~~~~~~G~s~eei~~~~~~  118 (125)
T COG1725          91 AEEELEEFIEEAKALGLSLEEILELLKE  118 (125)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            55556666653  345666666666653

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

Probab=94.74  E-value=0.046  Score=40.82  Aligned_cols=55  Identities=24%  Similarity=0.360  Sum_probs=41.6

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .+|+++++. ..+.|.-..+|-.++  ||+...+.+.|+.|+++|||+.       ....|.+.+
T Consensus         6 ~Ii~~IL~~-l~~~~~~~t~i~~~~--~L~~~~~~~yL~~L~~~gLI~~-------~~~~Y~lTe   60 (77)
T PF14947_consen    6 EIIFDILKI-LSKGGAKKTEIMYKA--NLNYSTLKKYLKELEEKGLIKK-------KDGKYRLTE   60 (77)
T ss_dssp             HHHHHHHHH-H-TT-B-HHHHHTTS--T--HHHHHHHHHHHHHTTSEEE-------ETTEEEE-H
T ss_pred             HHHHHHHHH-HHcCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCcCeeC-------CCCEEEECc
Confidence            378888888 658888899999999  9999999999999999999943       456777643

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

Probab=94.67  E-value=0.064  Score=34.22  Aligned_cols=30  Identities=27%  Similarity=0.450  Sum_probs=25.8

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI   85 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI   85 (252)
                      +...||-.-+  |+...+++|+|+.|+++|+|
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            4578999999  99999999999999999998

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 ....

>PRK06474 hypothetical protein; Provisional

Probab=94.41  E-value=0.54  Score=40.55  Aligned_cols=130  Identities=13%  Similarity=0.219  Sum_probs=80.4

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEecccccCCCccCC
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAVEFEPSKDISGG  113 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~~lePs~eiTGG  113 (252)
                      +.=..|++.+.. .+. +....+|-..++ ++++.+|.+.|+.|+..|||..++.=  +....|.|-+-.-  .-.+.+.
T Consensus        11 p~R~~Il~~L~~-~~~-~~ta~el~~~l~-~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~--~~~~~~~   85 (178)
T PRK06474         11 PVRMKICQVLMR-NKE-GLTPLELVKILK-DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE--DAKIEGS   85 (178)
T ss_pred             HHHHHHHHHHHh-CCC-CCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc--eeeeCHH
Confidence            344578888877 654 499999998884 79999999999999999999998753  3333466755331  1123333


Q ss_pred             ccccCC-----cCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHHHh
Q 025493          114 AWYSEG-----SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAVV  175 (252)
Q Consensus       114 ~wy~d~-----e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~tLV  175 (252)
                      .|..+.     .+-+.|...+.+...+|+.+.+.     .-.+-...+.+  ...||+++.+++.+-|.
T Consensus        86 ~~~~~~~e~~~~~~~~~~~~~~~~~~~yl~~~~~-----~~~~~d~~~~s~~~L~Lt~ee~~el~~el~  149 (178)
T PRK06474         86 EWTGLSDDEKLNYISYYQLSLLQQYQSYLKSLEE-----QNSKEDKATFSVVELKLDEEEFEEFQSELN  149 (178)
T ss_pred             HHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhCcc-----cchhccccceeeeeEecCHHHHHHHHHHHH
Confidence            333211     12234555566666677765321     11122333333  46799999888765543

>PHA02943 hypothetical protein; Provisional

Probab=94.31  E-value=0.29  Score=41.96  Aligned_cols=113  Identities=12%  Similarity=0.131  Sum_probs=82.0

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCC
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEG  119 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~  119 (252)
                      .|+.+| . .|  +-.+.+|-+.+  ++...++.=+|+.||+.|.|++|+   -...-+|++-+               .
T Consensus        15 eILE~L-k-~G--~~TtseIAkaL--GlS~~qa~~~LyvLErEG~VkrV~---~G~~tyw~l~~---------------d   70 (165)
T PHA02943         15 KTLRLL-A-DG--CKTTSRIANKL--GVSHSMARNALYQLAKEGMVLKVE---IGRAAIWCLDE---------------D   70 (165)
T ss_pred             HHHHHH-h-cC--CccHHHHHHHH--CCCHHHHHHHHHHHHHcCceEEEe---ecceEEEEECh---------------H
Confidence            466666 3 23  35689999999  999999999999999999999976   32344555522               1


Q ss_pred             cCCHHHHHHHHHHHHHHhhh--CCCCCHHHHHHHHHHc--------CCcceecCHHHHHHHHHHHhhc
Q 025493          120 SLDTEFIKVVKSQCLKQIIK--LKVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRAVVLD  177 (252)
Q Consensus       120 e~D~efV~~l~~~~~~~i~~--~~~~T~~~I~~~i~~~--------~i~~~~Ls~~di~~IL~tLVyD  177 (252)
                      .+ ...|+.+.+-+..++.+  ..++|+..+++.|.+-        .+..|.-....|-+.|+-+.-+
T Consensus        71 ay-~~~v~~~~Relwrlv~s~~~kfi~p~~l~~li~kd~~a~~~~ak~v~v~~r~a~il~fln~~l~~  137 (165)
T PHA02943         71 AY-TNLVFEIKRELWRLVCNSRLKFITPSRLLRLIAKDTEAHNIFAKYVPVNSRHAHILSFLNSALEM  137 (165)
T ss_pred             HH-HHHHHHHHHHHHHHHHhccccccChHHHHHHHHhCHHHHHHHHHhcCcccchHHHHHHHHHHHHH
Confidence            11 12377778888888874  5799999999999864        2345677777888887766544

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=94.23  E-value=0.18  Score=49.83  Aligned_cols=62  Identities=18%  Similarity=0.289  Sum_probs=51.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      +|+..|..|+..|.+ .|  ++-+.+|..++  ++....|+++++.||++|||.....    .++.|-|.+
T Consensus         3 ~Lt~~e~~vL~~L~~-~~--~~s~~eLA~~l--~l~~~tVt~~i~~Le~kGlV~~~~~----~~~~i~LTe   64 (489)
T PRK04172          3 ELHPNEKKVLKALKE-LK--EATLEELAEKL--GLPPEAVMRAAEWLEEKGLVKVEER----VEEVYVLTE   64 (489)
T ss_pred             CCCHHHHHHHHHHHh-CC--CCCHHHHHHHh--CcCHHHHHHHHHHHHhCCCEEEEee----eEEEEEECH
Confidence            689999999999977 55  78999999999  9999999999999999999998532    234555543

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

Probab=94.18  E-value=0.28  Score=35.69  Aligned_cols=49  Identities=14%  Similarity=0.176  Sum_probs=40.8

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      .|++.|.+ . +.++-++||...+  +|...++.+.|..||+.|.|+.++.=+
T Consensus         4 ~Il~~i~~-~-~~p~~T~eiA~~~--gls~~~aR~yL~~Le~eG~V~~~~~~r   52 (62)
T PF04703_consen    4 KILEYIKE-Q-NGPLKTREIADAL--GLSIYQARYYLEKLEKEGKVERSPVRR   52 (62)
T ss_dssp             CHHHHHHH-H-TS-EEHHHHHHHH--TS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred             HHHHHHHH-c-CCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            47778888 5 7889999999999  999999999999999999999865433

>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=94.11  E-value=0.15  Score=38.78  Aligned_cols=53  Identities=13%  Similarity=0.228  Sum_probs=41.2

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      ...-.=-.+|+++++ +++++.|++.||.||..|||.....-..|.+.-|.|.+
T Consensus        15 ~~g~~rf~el~~~l~-~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~   67 (90)
T PF01638_consen   15 FQGPMRFSELQRRLP-GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE   67 (90)
T ss_dssp             TTSSEEHHHHHHHST-TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred             HhCCCcHHHHHHhcc-hhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence            334455678988885 89999999999999999999887765667777787744

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.

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

Probab=94.10  E-value=0.55  Score=35.35  Aligned_cols=33  Identities=24%  Similarity=0.362  Sum_probs=29.6

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      .++|...+  +++++.++++|+.||++|||...++
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            46788999  9999999999999999999999653

iron dependent repressor

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

Probab=94.04  E-value=0.2  Score=44.85  Aligned_cols=130  Identities=11%  Similarity=0.163  Sum_probs=76.5

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHH
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV  128 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~  128 (252)
                      .++.+|.+++|.+.+  ++.+..++|.|+.||++|||....+=  .++.++    |++.            .  .++.+.
T Consensus        17 ~~~~~IS~~eLA~~L--~iS~~Tvsr~Lk~LEe~GlI~R~~~~--r~~~v~----LTek------------G--~~ll~~   74 (217)
T PRK14165         17 NNTVKISSSEFANHT--GTSSKTAARILKQLEDEGYITRTIVP--RGQLIT----ITEK------------G--LDVLYN   74 (217)
T ss_pred             CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEcC--CceEEE----ECHH------------H--HHHHHH
Confidence            445579999999999  99999999999999999999886541  222222    2222            0  111122


Q ss_pred             HHHHHHHHhh-----------------hCCCCCHHHHH-HHHHHcCCc------ceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          129 VKSQCLKQII-----------------KLKVATLEGIS-DSIKRSGAF------KVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       129 l~~~~~~~i~-----------------~~~~~T~~~I~-~~i~~~~i~------~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      +-....+.+.                 -+-|.+.+--. +|-+..|+.      ++.|..+.++...+..-+++....=-
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            2211122111                 12366765544 455566765      47787776666666666676443211


Q ss_pred             eCCCCCcccccCCcceeecc
Q 025493          185 SNGSGEFTNIPVGKVCYKNV  204 (252)
Q Consensus       185 ~~g~~~f~~~~~g~~~YR~~  204 (252)
                      .++...|..+    .||++.
T Consensus       155 ~~~~r~~g~~----~~~~~~  170 (217)
T PRK14165        155 TDGERTFGGV----KCYPVK  170 (217)
T ss_pred             cCCCceeEEE----EEEEEE
Confidence            2334455555    677654

>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=93.99  E-value=0.27  Score=35.19  Aligned_cols=45  Identities=24%  Similarity=0.411  Sum_probs=37.9

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      +.||.+-+   ++..+-.++|..++  |+.+..++..||.|+.+|||.-.
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            34565554   57889999999999  99999999999999999999864

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 ....

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=93.95  E-value=0.19  Score=39.14  Aligned_cols=63  Identities=11%  Similarity=0.109  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHH-HHhh--cCCChHHHHHHHHHHHhcCCeeee--eccccCCeeeEEe
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMK-RELK--VNLPDNIVTKSIKSLQNKSLIKEV--VNIHNKGKKHLMA  101 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik-~~~~--~~l~~~~l~k~lK~Le~k~lIK~v--ksv~~~~rK~YmL  101 (252)
                      +.+|+.++.+ ....|-+..+.= ..++  ..+.+.+|..+|+.||++|+|.+.  .+-..+.||+|-+
T Consensus         6 ~~~iL~~L~~-~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~i   73 (100)
T TIGR03433         6 DLLILKTLSL-GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRL   73 (100)
T ss_pred             HHHHHHHHhc-CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEE
Confidence            4566666665 555555544332 2221  168899999999999999999994  5556667888876

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

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.82  E-value=0.19  Score=40.44  Aligned_cols=52  Identities=15%  Similarity=0.216  Sum_probs=43.9

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++.--.+..++.. +++..+..++|..++  +++.+.+.|+|+.|++.|+|.+.+
T Consensus         8 ~~yal~~l~~la~-~~~~~~s~~eia~~l--~is~~~v~~~l~~L~~~Gli~~~~   59 (130)
T TIGR02944         8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQT--GLNAPTVSKILKQLSLAGIVTSKR   59 (130)
T ss_pred             HhHHHHHHHHHHh-CCCCCccHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecC
Confidence            3344456667777 777889999999999  999999999999999999998754

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.

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

Probab=93.70  E-value=0.38  Score=38.12  Aligned_cols=57  Identities=12%  Similarity=0.147  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          127 KVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       127 ~~l~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      ..-|.+++++|... ..+|++||.+.+++.+   ..++..-|-+.|+.|+-.|.|.++...
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            34678899999864 5999999999999876   467889999999999999999998765

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 ....

>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=93.68  E-value=0.2  Score=35.05  Aligned_cols=36  Identities=19%  Similarity=0.399  Sum_probs=33.1

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      +..+..++|...+  +++...++|+|+.|+++|+|...
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            4568899999999  99999999999999999999875

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=93.67  E-value=0.94  Score=41.09  Aligned_cols=124  Identities=15%  Similarity=0.206  Sum_probs=93.7

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGG  113 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG  113 (252)
                      +++--..||+.|..   |-|....++++..  +++-.+++=.|+.||+.++|++.   ...++-.|.-+++.        
T Consensus        99 ~ns~R~~Iy~~i~~---nPG~~lsEl~~nl--~i~R~TlRyhlriLe~~~li~a~---~~~g~~~yfpa~~t--------  162 (240)
T COG3398          99 LNSKRDGIYNYIKP---NPGFSLSELRANL--YINRSTLRYHLRILESNPLIEAG---RVGGALRYFPADMT--------  162 (240)
T ss_pred             hhhhHHHHHHHhcc---CCCccHHHHHHhc--CCChHHHHHHHHHHHhCcchhhh---ccCCceEEccCCCC--------
Confidence            34445679999988   6789999999999  99999999999999999999985   33456667655542        


Q ss_pred             ccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          114 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       114 ~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                        |.+.| =.++-+..++.+..+|+..+..|.-+|+.-+        .+|.+-|.==+..|.-=|.|.+-+
T Consensus       163 --~~~~e-~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l--------~ls~aTV~~~lk~l~~~Gii~~~~  222 (240)
T COG3398         163 --YGEAE-VLSLKNETSKAIIYEIQENKCNTNLLIAYEL--------NLSVATVAYHLKKLEELGIIPEDR  222 (240)
T ss_pred             --cccch-HHHhhchhHHHHHHHHhcCCcchHHHHHHHc--------CccHHHHHHHHHHHHHcCCCcccc
Confidence              22222 1456667778888888888888888887654        366777777788888888887654

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

Probab=93.60  E-value=0.23  Score=38.95  Aligned_cols=72  Identities=19%  Similarity=0.363  Sum_probs=55.7

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEecccccCCCcc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~~lePs~eiT  111 (252)
                      +++.+..|+..+.. +|.+=.|.  |.+.+  +++...+..+|+.||+.|||..+.+  ++...+      .+.|+.|+-
T Consensus         5 ~~~l~~~IL~hl~~-~~~Dy~k~--ia~~l--~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~------k~K~~~e~~   73 (92)
T PF10007_consen    5 LDPLDLKILQHLKK-AGPDYAKS--IARRL--KIPLEEVREALEKLEEMGLLERVEGKTIKRSEA------KFKPKKEVH   73 (92)
T ss_pred             cChhHHHHHHHHHH-HCCCcHHH--HHHHH--CCCHHHHHHHHHHHHHCCCeEEecCcccchhhh------hcccchhhh
Confidence            57788999999999 99987664  66788  9999999999999999999999985  444322      346666643


Q ss_pred             C-Cccc
Q 025493          112 G-GAWY  116 (252)
Q Consensus       112 G-G~wy  116 (252)
                      . ++.|
T Consensus        74 ~hHtYY   79 (92)
T PF10007_consen   74 KHHTYY   79 (92)
T ss_pred             cCCcee
Confidence            3 3444

>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=93.59  E-value=0.13  Score=37.13  Aligned_cols=51  Identities=14%  Similarity=0.195  Sum_probs=38.1

Q ss_pred             HHHHhhhCCCCCHHHHHHHHHHc--CCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          133 CLKQIIKLKVATLEGISDSIKRS--GAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       133 ~~~~i~~~~~~T~~~I~~~i~~~--~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      |.-.|.+.+..+++.||..++--  +-...+.|.+++++.|+.||-||+++..
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            44566788889999999999977  3344689999999999999999999975

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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=93.47  E-value=0.33  Score=32.67  Aligned_cols=37  Identities=16%  Similarity=0.300  Sum_probs=33.1

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +..+-..+|...+  +++.+.++++|+.|+++|+|....
T Consensus         8 ~~~~~~~~i~~~l--~is~~~v~~~l~~L~~~g~i~~~~   44 (66)
T smart00418        8 EGELCVCELAEIL--GLSQSTVSHHLKKLREAGLVESRR   44 (66)
T ss_pred             cCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeee
Confidence            4567889999999  999999999999999999998653

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=93.26  E-value=1.1  Score=35.89  Aligned_cols=39  Identities=10%  Similarity=0.290  Sum_probs=35.2

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .|...+..++|...+  ++|.+.+.++|..|+..|+|.+..
T Consensus        21 ~~~~~~s~~eia~~~--~i~~~~v~~il~~L~~~gli~~~~   59 (132)
T TIGR00738        21 PDEGPVSVKEIAERQ--GISRSYLEKILRTLRRAGLVESVR   59 (132)
T ss_pred             CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecc
Confidence            455689999999999  999999999999999999998754

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=93.22  E-value=0.19  Score=42.45  Aligned_cols=58  Identities=14%  Similarity=0.285  Sum_probs=49.3

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      ...|++-++.|+.++.+ -|  -+..++|.+++  |+..+.+.+-++.||+.|.|+....+-+
T Consensus         9 ~~~lD~~D~~IL~~Lq~-d~--R~s~~eiA~~l--glS~~tv~~Ri~rL~~~GvI~~~~~~v~   66 (164)
T PRK11169          9 GKDLDRIDRNILNELQK-DG--RISNVELSKRV--GLSPTPCLERVRRLERQGFIQGYTALLN   66 (164)
T ss_pred             hhhHHHHHHHHHHHhcc-CC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEEC
Confidence            45689999999999888 44  45569999999  9999999999999999999998665443

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

Probab=92.91  E-value=0.2  Score=36.47  Aligned_cols=49  Identities=14%  Similarity=0.144  Sum_probs=38.8

Q ss_pred             HHHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          129 VKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       129 l~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      +++.|+.||.. ++.+|..||++-+        .+|.-.++.+|+.|+-+|+|++++.
T Consensus         1 ~ke~Il~~i~~~~~p~~T~eiA~~~--------gls~~~aR~yL~~Le~eG~V~~~~~   50 (62)
T PF04703_consen    1 MKEKILEYIKEQNGPLKTREIADAL--------GLSIYQARYYLEKLEKEGKVERSPV   50 (62)
T ss_dssp             -HHCHHHHHHHHTS-EEHHHHHHHH--------TS-HHHHHHHHHHHHHCTSEEEES-
T ss_pred             CcHHHHHHHHHcCCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecC
Confidence            35678888887 7888888988764        4788999999999999999998764

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=92.84  E-value=0.28  Score=38.06  Aligned_cols=57  Identities=7%  Similarity=0.145  Sum_probs=46.0

Q ss_pred             HHHHHHH-hhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           40 LIYDVIR-SNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        40 ~vy~~I~-~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..|+-|. +...-+=|....|..+.  ++.-+.-.++|+.||++|+||.|  +++....+|.
T Consensus        27 ~t~dkl~kEV~~~K~ITps~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~~~~~q~IYt   84 (86)
T PRK09334         27 ELLKRVAKEVKKEKIVTPYTLASKY--GIKISVAKKVLRELEKRGVLVLY--SKNRRTPIYV   84 (86)
T ss_pred             HHHHHHHHHhccCcEEcHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEec
Confidence            4455443 53556778888999999  99999999999999999999999  5666778884

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=92.73  E-value=0.42  Score=35.53  Aligned_cols=46  Identities=11%  Similarity=0.244  Sum_probs=39.0

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ..|+.+|.+ .+ .++-..+|-..+  +++.+.+.+.|+.|++.|+|...
T Consensus         8 ~~Il~~l~~-~~-~~~t~~~ia~~l--~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346        8 LAVLRALAE-EP-GGLTLAELAERL--GLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             HHHHHHHHh-CC-CCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeeec
Confidence            346666766 42 379999999999  99999999999999999999873

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=92.38  E-value=0.58  Score=31.57  Aligned_cols=34  Identities=15%  Similarity=0.370  Sum_probs=31.3

Q ss_pred             cc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           53 GI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        53 GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      -+ ..++|....  +++...+.++|+.|++.|+|..+
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 699999999  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=92.31  E-value=0.5  Score=31.73  Aligned_cols=34  Identities=21%  Similarity=0.397  Sum_probs=30.2

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .-.-..+|...+  ++++..+++.|+.|++.|+|++
T Consensus        14 ~~~~~~el~~~l--~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen   14 GPLTVSELAEEL--GLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             SSEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCCchhhHHHhc--cccchHHHHHHHHHHHCcCeeC
Confidence            457788999999  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 ....

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=92.27  E-value=0.49  Score=43.05  Aligned_cols=62  Identities=21%  Similarity=0.298  Sum_probs=52.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      -+||+.|..||-.+-. -|.  .-.++|...+  |+|++.|-.+|++||.||+|...    ....+.|-..
T Consensus        12 lGlt~yEa~vY~aLl~-~g~--~tA~eis~~s--gvP~~kvY~vl~sLe~kG~v~~~----~g~P~~y~av   73 (247)
T COG1378          12 LGLTEYEAKVYLALLC-LGE--ATAKEISEAS--GVPRPKVYDVLRSLEKKGLVEVI----EGRPKKYRAV   73 (247)
T ss_pred             cCCCHHHHHHHHHHHH-hCC--ccHHHHHHHc--CCCchhHHHHHHHHHHCCCEEee----CCCCceEEeC
Confidence            3799999999999988 665  4678999999  99999999999999999999986    3355667663

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

Probab=92.21  E-value=1.7  Score=45.13  Aligned_cols=142  Identities=16%  Similarity=0.227  Sum_probs=95.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc-------
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF-------  104 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l-------  104 (252)
                      ...++++..|..+-.+ -..  -...++...+  |+|...++|.|+-..++|+|-+...+..++  +|-+-+=       
T Consensus       598 ~tVsp~qA~iI~~Fqe-k~t--wt~eelse~l--~ip~~~lrrrL~fWi~~GvL~e~~~~s~tg--t~T~iEse~d~~q~  670 (765)
T KOG2165|consen  598 LTVSPEQAAIINLFQE-KNT--WTLEELSESL--GIPVPALRRRLSFWIQKGVLREEPIISDTG--TLTVIESEMDFDQA  670 (765)
T ss_pred             EeeCHHHHHHHHHhcC-ccc--ccHHHHHHHh--CCCHHHHHHHHHHHHHcCeeecCCCCCCCc--eeeecccccccccc
Confidence            3567788777777666 332  4457899999  999999999999999999999987553322  3333221       


Q ss_pred             ------ccCCC--ccCCccccCC-cCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcc--eecCHHHHHHHHHH
Q 025493          105 ------EPSKD--ISGGAWYSEG-SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK--VDLTKQQIEEIVRA  173 (252)
Q Consensus       105 ------ePs~e--iTGG~wy~d~-e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~--~~Ls~~di~~IL~t  173 (252)
                            |-.+|  =++.+|+.|+ +.  |+. .-+..|...+.+.+...++-||++++=-....  ...+.++++.-|+.
T Consensus       671 ~~~~~~e~eee~~e~~~as~vdqle~--el~-~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~  747 (765)
T KOG2165|consen  671 EGTVLLEAEEENYESHNASEVDQLEE--ELT-LFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQR  747 (765)
T ss_pred             CCCcccccccccchhhhhhHHHHHHH--HHH-HHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHH
Confidence                  11111  2344444333 11  110 11123334444679999999999998655443  68999999999999


Q ss_pred             HhhcCeeEEE
Q 025493          174 VVLDNQIMEV  183 (252)
Q Consensus       174 LVyDgkIE~v  183 (252)
                      +|-+|+++-+
T Consensus       748 kV~e~kL~f~  757 (765)
T KOG2165|consen  748 KVREGKLEFI  757 (765)
T ss_pred             HhhccceEEe
Confidence            9999999865

>PRK12423 LexA repressor; Provisional

Probab=92.14  E-value=0.4  Score=41.86  Aligned_cols=56  Identities=21%  Similarity=0.345  Sum_probs=47.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeeec
Q 025493           33 SLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      .||+-++.||+.|.+.-...|+  ..++|....  ++ ..+.+.+.|+.|+++|+|..-+.
T Consensus         3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~--g~~s~~~v~~~l~~L~~~G~l~~~~~   61 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAF--GFASRSVARKHVQALAEAGLIEVVPN   61 (202)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEecCC
Confidence            4899999999999983344455  899999999  96 78899999999999999987544

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=92.14  E-value=0.36  Score=39.28  Aligned_cols=48  Identities=15%  Similarity=0.335  Sum_probs=41.0

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493           56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF  104 (252)
Q Consensus        56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l  104 (252)
                      -.+|++.++ ++++++|++.||.||+.|+|....-=..|-|--|=|.++
T Consensus        39 F~eL~r~i~-~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~   86 (120)
T COG1733          39 FNELRRSIG-GISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEK   86 (120)
T ss_pred             HHHHHHHcc-ccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhh
Confidence            478899983 599999999999999999999987666688888888665

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=92.10  E-value=0.48  Score=38.89  Aligned_cols=52  Identities=12%  Similarity=0.077  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHhhcC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           37 HERLIYDVIRSNKQ---DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        37 ~e~~vy~~I~~~ag---~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .+..|..+|.. |-   +.=+..++|..+.  |++.+.|.|+|+.|++.|||++.+..
T Consensus         7 ~~YAl~~~i~l-a~~~~g~~~s~~~ia~~~--~is~~~vrk~l~~L~~~Glv~s~~G~   61 (141)
T PRK11014          7 TDYGLRALIYM-ASLPEGRMTSISEVTEVY--GVSRNHMVKIINQLSRAGYVTAVRGK   61 (141)
T ss_pred             HhHHHHHHHHH-hcCCCCCccCHHHHHHHH--CcCHHHHHHHHHHHHhCCEEEEecCC
Confidence            35556666655 42   2236779999999  99999999999999999999998654

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

Probab=92.09  E-value=0.39  Score=38.56  Aligned_cols=57  Identities=19%  Similarity=0.293  Sum_probs=46.6

Q ss_pred             HHHHHH-HhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           40 LIYDVI-RSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        40 ~vy~~I-~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      -.|+-| .+.-+-+=|....|..+.  ++.-+.-.++|+.|+++|+|+.|  +++....+|-
T Consensus        45 ~~~~kl~kEV~~~K~ITp~~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~k~~~~~IYt  102 (105)
T PF03297_consen   45 ETYDKLLKEVPKMKLITPSVLSERL--KINGSLARKALRELESKGLIKPV--SKHHRQRIYT  102 (105)
T ss_dssp             HHHHHHHHHCTTSSCECHHHHHHHH--CCSCHHHHHHHHHHHHCCSSEEE--ECCTTCEEEE
T ss_pred             HHHHHHHHHhccCcEeeHHHHHHhH--hhHHHHHHHHHHHHHHCCCEEEE--eccCCeEEEe
Confidence            445544 453566778999999999  99999999999999999999999  5666777884

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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=91.88  E-value=0.39  Score=31.31  Aligned_cols=32  Identities=22%  Similarity=0.449  Sum_probs=29.7

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +..++|...+  +++...+++.|+.|+++|+|..
T Consensus         9 ~s~~~la~~l--~~s~~tv~~~l~~L~~~g~l~~   40 (48)
T smart00419        9 LTRQEIAELL--GLTRETVSRTLKRLEKEGLISR   40 (48)
T ss_pred             cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence            5678999999  9999999999999999999975

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

Probab=91.62  E-value=6.1  Score=36.29  Aligned_cols=124  Identities=16%  Similarity=0.124  Sum_probs=93.1

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcC------CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccc-cCCCc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVN------LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFE-PSKDI  110 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~------l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~le-Ps~ei  110 (252)
                      ...|...|+.   ...+..++|.......      .+.+....+|..|...|.|-...... ...+.|-+.+-- |... 
T Consensus        87 ~~~v~~~L~~---~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~-g~~~~y~l~~~~lP~~~-  161 (327)
T PF06224_consen   87 AEAVLDALRA---DGPLTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPR-GRWRTYDLTERWLPAPD-  161 (327)
T ss_pred             HHHHHHHHHh---cCCCCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCC-CceEEEechHHhCCCCc-
Confidence            3445555544   5578899999876322      45568999999999999998876442 245888876632 3311 


Q ss_pred             cCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          111 SGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       111 TGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                                .|  --+.+.+.+.+|++.++.+|++++..|..        |+..+++..++.|+-.|.++++...
T Consensus       162 ----------~~--~~ea~~~Lv~Ryl~~~GPat~~d~a~w~g--------l~~~~~r~~l~~l~~~~~L~~v~~~  217 (327)
T PF06224_consen  162 ----------DD--REEALAELVRRYLRAYGPATLADFAWWSG--------LPKTQARRALAQLVEEGELVEVEVE  217 (327)
T ss_pred             ----------CC--HHHHHHHHHHHHHHHcCCccHHHHHHHhc--------cCHHHHHHHHHhhccCCcEEEEEEc
Confidence                      11  44568888999999999999999999954        7788999999999999999988765

>cd00131 PAX Paired Box domain

Probab=91.61  E-value=5.2  Score=32.68  Aligned_cols=109  Identities=18%  Similarity=0.167  Sum_probs=74.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      +.||.+++.  .+|.. + ..|...++|.+++  ++..+.|.|.++...+.|-++..+.=   ++        .|+    
T Consensus        16 ~~lS~d~R~--rIv~~-~-~~G~s~~~iA~~~--~Vs~~tV~r~i~r~~e~G~v~pk~~g---g~--------rpr----   74 (128)
T cd00131          16 RPLPDSIRQ--RIVEL-A-QSGIRPCDISRQL--RVSHGCVSKILNRYYETGSIRPGAIG---GS--------KPR----   74 (128)
T ss_pred             CcCCHHHHH--HHHHH-H-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCCCCC---CC--------CCC----
Confidence            456766543  23333 3 3699999999999  99999999999999998865542211   11        011    


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHH
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRA  173 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~t  173 (252)
                              ..    .+.....+..++..++..|+.|+.+.+...|+.  .+.+|..-|-.+|+.
T Consensus        75 --------~~----~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          75 --------VA----TPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             --------cC----CHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence                    00    012233445578889999999999998777764  367788888887764

>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=91.57  E-value=0.3  Score=35.74  Aligned_cols=38  Identities=16%  Similarity=0.237  Sum_probs=33.2

Q ss_pred             CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEecc
Q 025493           66 NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAVE  103 (252)
Q Consensus        66 ~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~~  103 (252)
                      ++....|-.+|+.||.+|+|.+....  +.+.||+|-+.+
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  677899998743

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 ....

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

Probab=91.49  E-value=1  Score=35.11  Aligned_cols=55  Identities=11%  Similarity=0.186  Sum_probs=46.8

Q ss_pred             HHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493          130 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG  187 (252)
Q Consensus       130 ~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g  187 (252)
                      |..++++|.. ...+|++||++.+++.+   -.++..-|.+.|+.|+-.|.|.++...+
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~   58 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGD   58 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCC
Confidence            5678888876 46899999999999886   3578899999999999999999987543

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.

>PRK09462 fur ferric uptake regulator; Provisional

Probab=91.09  E-value=1.7  Score=35.99  Aligned_cols=55  Identities=5%  Similarity=0.059  Sum_probs=47.4

Q ss_pred             HHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          129 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       129 l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      -|..|+++|...  ..+|++||++.+++.+   ..++..-|-+.|+.|+-.|.|.++...
T Consensus        18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~~~   74 (148)
T PRK09462         18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNFE   74 (148)
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEEcC
Confidence            467889999863  5999999999999888   357889999999999999999998743

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=91.02  E-value=0.75  Score=37.54  Aligned_cols=48  Identities=13%  Similarity=0.105  Sum_probs=38.6

Q ss_pred             HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .-.+..+.++.-+..++|..++  ++|.+.+.|+|..|.+.|||.+++..
T Consensus        14 l~~La~~~~~~~~s~~~ia~~~--~ip~~~l~kil~~L~~~glv~s~~G~   61 (135)
T TIGR02010        14 MLDLALNAETGPVTLADISERQ--GISLSYLEQLFAKLRKAGLVKSVRGP   61 (135)
T ss_pred             HHHHHhCCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeCC
Confidence            3344431455568889999999  99999999999999999999986554

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

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=90.94  E-value=0.66  Score=39.63  Aligned_cols=48  Identities=8%  Similarity=0.078  Sum_probs=40.7

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      .+...+..++|..+.  ++|.+.+.|+|..|.+.|||.+.+..+-    =|.|.
T Consensus        21 ~~~~~vs~~eIA~~~--~ip~~~l~kIl~~L~~aGLv~s~rG~~G----Gy~La   68 (164)
T PRK10857         21 SEAGPVPLADISERQ--GISLSYLEQLFSRLRKNGLVSSVRGPGG----GYLLG   68 (164)
T ss_pred             CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeCCCCCC----Ceecc
Confidence            455678999999999  9999999999999999999998665543    37774

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=90.93  E-value=1  Score=39.21  Aligned_cols=60  Identities=10%  Similarity=0.052  Sum_probs=47.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCc--ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMG--IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~G--Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .++.++|+..-+... ++...  .-+.+|...+  |++...|+|+|++|+++|+|+.-      ++++.++
T Consensus       148 ~~~~~~Rla~~L~~~-~~~~~~~~t~~~lA~~l--G~sretvsR~L~~L~~~G~I~~~------~~~i~I~  209 (226)
T PRK10402        148 SFPLENRLAAFILLT-QEGDLYHEKHTQAAEYL--GVSYRHLLYVLAQFIQDGYLKKS------KRGYLIK  209 (226)
T ss_pred             cChHHHHHHHHHHhc-ccCCcccchHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEee------CCEEEEe
Confidence            457788888877765 54332  4679999999  99999999999999999999873      4667765

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=90.76  E-value=0.76  Score=38.24  Aligned_cols=54  Identities=6%  Similarity=0.169  Sum_probs=47.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .|++.++.|+.++.. -  --+..++|.+++  |++...+.+-++.|+..|.|+....+
T Consensus         6 ~lD~~D~~Il~~Lq~-d--~R~s~~eiA~~l--glS~~tV~~Ri~rL~~~GvI~~~~~~   59 (153)
T PRK11179          6 QIDNLDRGILEALME-N--ARTPYAELAKQF--GVSPGTIHVRVEKMKQAGIITGTRVD   59 (153)
T ss_pred             ccCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEE
Confidence            589999999999998 3  457899999999  99999999999999999999976543

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=90.65  E-value=2.6  Score=36.55  Aligned_cols=50  Identities=12%  Similarity=0.131  Sum_probs=42.2

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++....|..++.. .|.  +...+|...+  +|+.+.|.|+|..|+..|||...+
T Consensus        21 ~~~~~~Vl~~L~~-~g~--~tdeeLA~~L--gi~~~~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         21 DEEGFEVLKALIK-KGE--VTDEEIAEQT--GIKLNTVRKILYKLYDARLADYKR   70 (178)
T ss_pred             CccHhHHHHHHHH-cCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEee
Confidence            4445677787777 663  8899999999  999999999999999999999644

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

Probab=90.50  E-value=1.7  Score=33.83  Aligned_cols=59  Identities=17%  Similarity=0.251  Sum_probs=45.4

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..|++++.+ + +.-+...+|-.+++   +++...+|-|+|+.|++.|+|+++..-.  ++..|.+
T Consensus         4 ~~Il~~l~~-~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~   65 (116)
T cd07153           4 LAILEVLLE-S-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD--GKARYEL   65 (116)
T ss_pred             HHHHHHHHh-C-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC--CceEEEe
Confidence            468888888 6 56678888877663   2689999999999999999999986554  2455544

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=90.43  E-value=0.84  Score=37.39  Aligned_cols=47  Identities=21%  Similarity=0.213  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .=..||.+++. .|  .+-.++|...+  ++.+..+++.|+.|+.+|+|...
T Consensus         9 yL~~I~~l~~~-~~--~~~~~ela~~l--~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902          9 YIEQIYLLIEE-KG--YARVSDIAEAL--SVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             HHHHHHHHHhc-CC--CcCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEEe
Confidence            33467777766 43  55789999999  99999999999999999999854

>PHA00738 putative HTH transcription regulator

Probab=90.32  E-value=1.1  Score=36.31  Aligned_cols=50  Identities=18%  Similarity=0.145  Sum_probs=40.3

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++-=+.|+..+.+ .+  +.-..+|...+  +|.+..|++.||.|+.-|||.+-+
T Consensus        11 dptRr~IL~lL~~-~e--~~~V~eLae~l--~lSQptVS~HLKvLreAGLV~srK   60 (108)
T PHA00738         11 KILRRKILELIAE-NY--ILSASLISHTL--LLSYTTVLRHLKILNEQGYIELYK   60 (108)
T ss_pred             CHHHHHHHHHHHH-cC--CccHHHHHHhh--CCCHHHHHHHHHHHHHCCceEEEE
Confidence            3344566666655 32  47888999999  999999999999999999999854

>smart00351 PAX Paired Box domain

Probab=90.16  E-value=4.5  Score=32.75  Aligned_cols=93  Identities=19%  Similarity=0.167  Sum_probs=64.2

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG  112 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG  112 (252)
                      .++.+++.  .+|.. .. .|...++|.+++  ++....|.|.++...+.|.++..+.                     |
T Consensus        17 ~~s~~~R~--riv~~-~~-~G~s~~~iA~~~--gvs~~tV~kwi~r~~~~G~~~pk~~---------------------g   69 (125)
T smart00351       17 PLPDEERQ--RIVEL-AQ-NGVRPCDISRQL--CVSHGCVSKILGRYYETGSIRPGAI---------------------G   69 (125)
T ss_pred             CCCHHHHH--HHHHH-HH-cCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCcCC---------------------C
Confidence            36776654  23443 32 588999999999  9999999999999998887554221                     1


Q ss_pred             CccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc
Q 025493          113 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF  158 (252)
Q Consensus       113 G~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~  158 (252)
                      |..-  ..    ..+.....+..++..+...|+.||.+.+.+.||.
T Consensus        70 g~rp--~~----~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~  109 (125)
T smart00351       70 GSKP--KV----ATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVC  109 (125)
T ss_pred             CCCC--Cc----cCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCC
Confidence            1111  00    1123344566678889999999999999887753

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

Probab=90.09  E-value=0.59  Score=40.06  Aligned_cols=60  Identities=20%  Similarity=0.311  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhhcCCCcc---cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCC
Q 025493           38 ERLIYDVIRSNKQDMGI---WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSK  108 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GI---w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~  108 (252)
                      ...|+..|-++....+.   .+++|..++  ++..+++.|++|.|+.+++|+.++      ..+||+   -|..
T Consensus        57 ~~~Vl~~il~~~d~~N~v~~t~~~ia~~l--~iS~~Tv~r~ik~L~e~~iI~k~~------~G~Y~i---NP~~  119 (165)
T PF05732_consen   57 AFRVLMYILENMDKDNAVVATQKEIAEKL--GISKPTVSRAIKELEEKNIIKKIR------NGAYMI---NPNF  119 (165)
T ss_pred             HHHHHHHHHHhcCCCCeEEeeHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEcc------CCeEEE---CcHH
Confidence            34444444443666653   578899999  999999999999999999999862      347887   6663

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

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

Probab=90.05  E-value=1.2  Score=32.37  Aligned_cols=50  Identities=8%  Similarity=0.185  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHhhhCCC--CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          127 KVVKSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       127 ~~l~~~~~~~i~~~~~--~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      +...+.++.+|..++.  .|+.||++-+        .++...|.++|.+|.-+|.|++..
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecC
Confidence            3567889999998877  8999998755        467789999999999999998753

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

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=89.85  E-value=1.1  Score=37.61  Aligned_cols=64  Identities=11%  Similarity=0.143  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      +..|+.++.+ .---|=.....-.+.+. .+.+.+|..+|+.||+.|+|.+....  ..|.||+|-|.
T Consensus        26 ~~~IL~~L~~-~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LT   92 (138)
T TIGR02719        26 VPFLLLCLKD-WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLT   92 (138)
T ss_pred             HHHHHHHHcc-CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEEC
Confidence            4455555544 43344333222222211 68889999999999999999975433  34668999873

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).

>PRK09954 putative kinase; Provisional

Probab=89.82  E-value=1.2  Score=41.62  Aligned_cols=50  Identities=22%  Similarity=0.303  Sum_probs=44.4

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      |++-++.|+.++.+ .+  =|..++|.+++  ++..+.+.+.|++|+++|+|+.-
T Consensus         1 ~~~~~~~il~~l~~-~~--~~s~~~la~~l--~~s~~~v~~~i~~L~~~g~i~~~   50 (362)
T PRK09954          1 MNNREKEILAILRR-NP--LIQQNEIADIL--QISRSRVAAHIMDLMRKGRIKGK   50 (362)
T ss_pred             CChHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCcCCc
Confidence            56778889999999 44  59999999999  99999999999999999999643

>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=89.72  E-value=1.7  Score=29.61  Aligned_cols=41  Identities=17%  Similarity=0.374  Sum_probs=34.2

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcC
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKS   83 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~   83 (252)
                      ..|..++.+ +++. +...+|..++  ++..++|.+-|+.|+..+
T Consensus         3 ~~il~~L~~-~~~~-it~~eLa~~l--~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLE-SKEP-ITAKELAEEL--GVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHH-TTTS-BEHHHHHHHC--TS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHH-cCCC-cCHHHHHHHh--CCCHHHHHHHHHHHHHCC
Confidence            456667766 5555 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 ....

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=89.45  E-value=2.2  Score=27.81  Aligned_cols=46  Identities=11%  Similarity=0.203  Sum_probs=38.9

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      ..+++++.+++.+|..+|++.+        .++..-+...|+.|+-+|.|++..
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        578999999999999999998754

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=89.39  E-value=1.2  Score=37.05  Aligned_cols=61  Identities=16%  Similarity=0.153  Sum_probs=45.0

Q ss_pred             CCCChHHHHHHHHHH---hhcC---CCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIR---SNKQ---DMG------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~---~~ag---~~G------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      ...+.++|+..-++.   . .|   +.|      +.+.+|..-+  |++...|+|+|+.|+++|+|+.-      .+++.
T Consensus       111 ~~~~~~~Rla~~L~~l~~~-~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~~------~~~i~  181 (193)
T TIGR03697       111 AHRDMGSRLVSFLLILCRD-FGVPGQRGVTIDLRLSHQAIAEAI--GSTRVTITRLLGDLRKKKLISIH------KKKIT  181 (193)
T ss_pred             HhCCHHHHHHHHHHHHHHH-hCCCCCCeEEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEec------CCEEE
Confidence            345667776655443   3 33   233      5799999999  99999999999999999999862      45566


Q ss_pred             Ee
Q 025493          100 MA  101 (252)
Q Consensus       100 mL  101 (252)
                      ++
T Consensus       182 I~  183 (193)
T TIGR03697       182 VH  183 (193)
T ss_pred             Ee
Confidence            54

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.

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=89.06  E-value=0.91  Score=39.80  Aligned_cols=55  Identities=24%  Similarity=0.283  Sum_probs=42.1

Q ss_pred             CCCCChHHHHHHHHHHh--hcCCCc-----ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           31 SDSLTDHERLIYDVIRS--NKQDMG-----IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~--~ag~~G-----Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ....+.++|++.-+++.  ..|..+     +-+++|..-+  |++...|+|+||.|+++|+|+.
T Consensus       150 l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~l--GisretlsR~L~~L~~~GlI~~  211 (230)
T PRK09391        150 LGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYL--GLTIETVSRALSQLQDRGLIGL  211 (230)
T ss_pred             HcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEe
Confidence            34567788887666553  033322     4578999999  9999999999999999999974

>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=88.95  E-value=2.2  Score=32.61  Aligned_cols=59  Identities=15%  Similarity=0.128  Sum_probs=43.4

Q ss_pred             CCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +.|+.+|..|+..||....| +=+-...|.+.+  +|....+.++|+.|-..+||.. +....
T Consensus         2 r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s--~l~~~~~~~~L~~L~~~kLv~~-~~~~Y   61 (82)
T PF09202_consen    2 RYLSKEDFRVLRAIEMGMKNHEWVPLELIEKIS--GLSEGEVEKRLKRLVKLKLVSR-RNKPY   61 (82)
T ss_dssp             -T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-E-SSS
T ss_pred             CcCCHHHHHHHHHHHHcccCCccCCHHHHHHHh--CcCHHHHHHHHHHHHhcCCccc-cCCCc
Confidence            57899999999999983222 224567899999  9999999999999999999998 44443

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.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=88.94  E-value=1.2  Score=37.23  Aligned_cols=45  Identities=24%  Similarity=0.293  Sum_probs=37.9

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ..|+.+|.+ -  .++-.++|...+  ++.++.+++.|+.||.+|+|...
T Consensus        40 ~~I~~~l~~-~--~~~t~~eLA~~l--~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         40 ELIADLIAE-V--GEARQVDIAARL--GVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             HHHHHHHHh-c--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence            355666655 3  478899999999  99999999999999999999763

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

Probab=88.94  E-value=0.78  Score=31.52  Aligned_cols=32  Identities=19%  Similarity=0.433  Sum_probs=29.6

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      -.++|....  +++...++++|+.|+.+|+|...
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  99999999999999999999764

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

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

Probab=88.79  E-value=1.5  Score=31.75  Aligned_cols=47  Identities=21%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .|.++|++   +.-+..++|..+.  +++...|.-.|..|+.+|.|+++..-
T Consensus         4 ~i~~~l~~---~~~~S~~eLa~~~--~~s~~~ve~mL~~l~~kG~I~~~~~~   50 (69)
T PF09012_consen    4 EIRDYLRE---RGRVSLAELAREF--GISPEAVEAMLEQLIRKGYIRKVDMS   50 (69)
T ss_dssp             HHHHHHHH---S-SEEHHHHHHHT--T--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred             HHHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEecCC
Confidence            35667777   4568899999999  99999999999999999999987643

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

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=88.66  E-value=1.5  Score=33.35  Aligned_cols=69  Identities=14%  Similarity=0.211  Sum_probs=54.4

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      ...++.+... +++.=+.-.+|..++  ++..+.|.|++++|+..|+  .|.++++++.++=++-++=|...+.
T Consensus         5 ~~~~~~ll~~-~~~~~~SGe~La~~L--giSRtaVwK~Iq~Lr~~G~--~I~s~~~kGY~L~~~~~ll~~~~i~   73 (79)
T COG1654           5 SQMLLLLLLL-LTGNFVSGEKLAEEL--GISRTAVWKHIQQLREEGV--DIESVRGKGYLLPQLPDLLPQEIIQ   73 (79)
T ss_pred             HHHHHHHHHH-cCCCcccHHHHHHHH--CccHHHHHHHHHHHHHhCC--ceEecCCCceeccCccccCcHHHHH
Confidence            3466777777 888889999999999  9999999999999999997  5677777777766665555544443

>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=88.61  E-value=2.2  Score=29.92  Aligned_cols=46  Identities=15%  Similarity=0.411  Sum_probs=40.8

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ..|+++|.+ .  .-+..++|....  +....++.|=|..|+++|+|+.+.
T Consensus         3 ~~Il~~l~~-~--~~~s~~ela~~~--~VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    3 QQILELLKE-K--GKVSVKELAEEF--GVSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHH-c--CCEEHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEc
Confidence            467888888 4  468999999999  999999999999999999998864

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

>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=88.48  E-value=1.4  Score=31.44  Aligned_cols=50  Identities=10%  Similarity=0.189  Sum_probs=42.2

Q ss_pred             HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      .....++.+|-.++..|++||++.+        .++...|..+|+.|+-.|.|++...
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            3456678888888999999999865        4788999999999999999998863

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.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=88.36  E-value=2  Score=28.21  Aligned_cols=43  Identities=19%  Similarity=0.430  Sum_probs=35.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN   81 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~   81 (252)
                      ..|++.|+.++.++.+     |...++|-..+  +++...+.+.++.+..
T Consensus         2 ~~l~~~e~~i~~~~~~-----g~s~~eia~~l--~is~~tv~~~~~~~~~   44 (58)
T smart00421        2 ASLTPREREVLRLLAE-----GLTNKEIAERL--GISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCCCHHHHHHHHHHHc-----CCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            4588999888877643     68999999999  9999999999988743

lux regulon (activates the bioluminescence operon

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=88.35  E-value=1.6  Score=36.81  Aligned_cols=60  Identities=15%  Similarity=0.102  Sum_probs=44.7

Q ss_pred             CCChHHHHHHHHHHhhc---C----CC-----cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           33 SLTDHERLIYDVIRSNK---Q----DM-----GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~a---g----~~-----GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..+.++|+..-+++- +   |    +.     =+.+.+|..-+  |+....|+|+|+.|+++|+|+.      .++++.+
T Consensus       118 ~~~~~~Rla~~Ll~l-~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~------~~~~i~I  188 (202)
T PRK13918        118 GQRLKNRIAAALLEL-SDTPLATQEDSGETMIYATHDELAAAV--GSVRETVTKVIGELSREGYIRS------GYGKIQL  188 (202)
T ss_pred             hCchHHHHHHHHHHH-HHHhCCCCCCCCeEEecCCHHHHHHHh--CccHHHHHHHHHHHHHCCCEEc------CCCEEEE
Confidence            456678887766543 3   2    11     25689999999  9999999999999999999974      2355665


Q ss_pred             e
Q 025493          101 A  101 (252)
Q Consensus       101 L  101 (252)
                      +
T Consensus       189 ~  189 (202)
T PRK13918        189 L  189 (202)
T ss_pred             E
Confidence            4

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=88.34  E-value=1.2  Score=38.55  Aligned_cols=53  Identities=13%  Similarity=0.133  Sum_probs=41.5

Q ss_pred             CCCChHHHHHHHHHHhhc---C---CC------cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           32 DSLTDHERLIYDVIRSNK---Q---DM------GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~a---g---~~------GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ...+.++|+..-+.+- +   |   ..      -+.+++|..-+  |++...|+|+|+.|+++|+|+-
T Consensus       152 ~~~~~~~Rla~~L~~l-~~~~~~~~~~~~~~~~~lt~~~iA~~l--G~sr~tvsR~l~~l~~~g~I~~  216 (235)
T PRK11161        152 SKKNAEERLAAFIYNL-SRRFAQRGFSPREFRLTMTRGDIGNYL--GLTVETISRLLGRFQKSGMLAV  216 (235)
T ss_pred             hCCCHHHHHHHHHHHH-HHHHhhcCCCCceeEccccHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence            3456778776655543 3   2   12      26789999999  9999999999999999999996

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=87.31  E-value=8.8  Score=34.46  Aligned_cols=121  Identities=11%  Similarity=0.132  Sum_probs=81.7

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcc
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAW  115 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~w  115 (252)
                      +-+..|++++.+ .  ..+-.++|...+  ++...++.|-|+.|+.+++|+.+     .+.-+|.... .+..+   -+|
T Consensus         4 ~R~~~Il~~l~~-~--~~~~~~eLa~~l--~VS~~TiRRdL~~L~~~~~l~r~-----~Gga~~~~~~-~~~~~---~~~   69 (240)
T PRK10411          4 ARQQAIVDLLLN-H--TSLTTEALAEQL--NVSKETIRRDLNELQTQGKILRN-----HGRAKYIHRQ-NQDSG---DPF   69 (240)
T ss_pred             HHHHHHHHHHHH-c--CCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe-----cCeEEEecCC-CcccC---CCH
Confidence            345678888887 4  479999999999  99999999999999999999873     2343443211 11101   122


Q ss_pred             ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHcCCcceecCHHHHHHH
Q 025493          116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEI  170 (252)
Q Consensus       116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~~i~~~~Ls~~di~~I  170 (252)
                      ..-...+.+.=..|-+.+..+|+..      +..|+.++.++|...+++=+.=+..-.+.+
T Consensus        70 ~~r~~~~~~~K~~IA~~Aa~lI~~gd~Ifld~GtT~~~l~~~L~~~~ltVvTNs~~ia~~l  130 (240)
T PRK10411         70 HIRLKSHYAHKADIAREALAWIEEGMVIALDASSTCWYLARQLPDINIQVFTNSHPICQEL  130 (240)
T ss_pred             HHHHHhHHHHHHHHHHHHHHhCCCCCEEEEcCcHHHHHHHHhhCCCCeEEEeCCHHHHHHH
Confidence            2223345566677888888888854      578899999999866655555455444443

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

Probab=87.23  E-value=2.1  Score=33.81  Aligned_cols=66  Identities=14%  Similarity=0.259  Sum_probs=50.3

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      +|..-..|+++|.+ ++. -+...+|..+..   +++..++|-|+|+.|++.|+|..+..-  .+...|=+..
T Consensus         6 ~T~~R~~Il~~l~~-~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~--~~~~~Y~~~~   74 (120)
T PF01475_consen    6 LTPQRLAILELLKE-SPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG--DGESRYELST   74 (120)
T ss_dssp             HHHHHHHHHHHHHH-HSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET--TSEEEEEESS
T ss_pred             CCHHHHHHHHHHHc-CCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC--CCcceEeecC
Confidence            46677899999999 777 788888887653   378889999999999999999998655  2455664443

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 ....

>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=87.22  E-value=2.9  Score=27.77  Aligned_cols=47  Identities=6%  Similarity=0.164  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493          127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM  181 (252)
Q Consensus       127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE  181 (252)
                      +..+..++.+|..++.+|..||++-+        .+|..-+.+.|+.|+-+|.|+
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            45677899999999999999999865        478899999999999999885

...

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=87.15  E-value=0.87  Score=35.97  Aligned_cols=60  Identities=25%  Similarity=0.277  Sum_probs=47.8

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF  104 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l  104 (252)
                      .+|+++++. .-+.|+-...|--..  ||+-....+.++.|+.+|+|+.-   +++.|+.|++.+.
T Consensus        18 eIi~dIL~~-~~~~~~~~Tri~y~a--Nlny~~~~~yi~~L~~~Gli~~~---~~~~~~~y~lT~K   77 (95)
T COG3432          18 EIIFDILKA-ISEGGIGITRIIYGA--NLNYKRAQKYIEMLVEKGLIIKQ---DNGRRKVYELTEK   77 (95)
T ss_pred             HHHHHHHHH-hcCCCCCceeeeeec--CcCHHHHHHHHHHHHhCCCEEec---cCCccceEEEChh
Confidence            388889886 556666666777778  99999999999999999977763   4556779999553

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=87.13  E-value=3.4  Score=35.91  Aligned_cols=58  Identities=17%  Similarity=0.159  Sum_probs=49.6

Q ss_pred             CCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe-eeeeccc
Q 025493           32 DSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI-KEVVNIH   92 (252)
Q Consensus        32 ~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI-K~vksv~   92 (252)
                      ..|++.|. .+..+|.+ .-+.|...++|-.++  ++..++|.+.+..|-+.++. +++|..+
T Consensus       157 ~~Lt~re~~~l~~~i~~-~~~~g~s~~eIA~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~  216 (239)
T PRK10430        157 KGLTPQTLRTLCQWIDA-HQDYEFSTDELANAV--NISRVSCRKYLIWLVNCHILFTSIHYGV  216 (239)
T ss_pred             CCCCHHHHHHHHHHHHh-CCCCCcCHHHHHHHh--CchHHHHHHHHHHHHhCCEEEEEeeccC
Confidence            35888774 56678888 688999999999999  99999999999999999999 5666544

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=86.93  E-value=2.3  Score=35.75  Aligned_cols=42  Identities=12%  Similarity=0.172  Sum_probs=36.9

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+.-+..++|..+.  +++.+-|.|+|..|...|+|++++..+-
T Consensus        21 ~~~~~s~~eIA~~~--~is~~~L~kIl~~L~~aGlv~S~rG~~G   62 (153)
T PRK11920         21 DGKLSRIPEIARAY--GVSELFLFKILQPLVEAGLVETVRGRNG   62 (153)
T ss_pred             CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCCCC
Confidence            33457899999999  9999999999999999999999886543

>PRK09462 fur ferric uptake regulator; Provisional

Probab=86.75  E-value=5.3  Score=32.97  Aligned_cols=65  Identities=12%  Similarity=0.162  Sum_probs=52.6

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      .+|..=..|++++.+ +.+.-+...+|-.++.   +++...+|-|+|+.|++.|+|.++..-.  ++..|-
T Consensus        14 r~T~qR~~Il~~l~~-~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~--~~~~y~   81 (148)
T PRK09462         14 KVTLPRLKILEVLQE-PDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG--GKSVFE   81 (148)
T ss_pred             CCCHHHHHHHHHHHh-CCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CcEEEE
Confidence            478899999999999 8778899988877652   3678899999999999999999986433  344553

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=86.73  E-value=4.5  Score=32.85  Aligned_cols=56  Identities=16%  Similarity=0.221  Sum_probs=44.7

Q ss_pred             CCCCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           30 PSDSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        30 ~~~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      .++.|.+.-| .|+.++.+ .|  +.-..+|-..+  +++++.+++.|+.|++-|||...+.
T Consensus         9 ~fkaLadptRl~IL~~L~~-~~--~~~v~ela~~l--~lsqstvS~HL~~L~~AGLV~~~r~   65 (117)
T PRK10141          9 LFKILSDETRLGIVLLLRE-SG--ELCVCDLCTAL--DQSQPKISRHLALLRESGLLLDRKQ   65 (117)
T ss_pred             HHHHhCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEEE
Confidence            3445665544 67777776 54  47788999999  9999999999999999999988643

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=86.59  E-value=4.5  Score=30.89  Aligned_cols=45  Identities=9%  Similarity=0.126  Sum_probs=34.4

Q ss_pred             HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      ++-+||..++-+++.++...+        ..+..=|+..|+.|+--|+||++.
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            455666666666666666544        467888999999999999999986

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=86.42  E-value=2.9  Score=35.37  Aligned_cols=54  Identities=19%  Similarity=0.307  Sum_probs=40.4

Q ss_pred             CCCCChHHHHHHHHH---HhhcCC----Cc----ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           31 SDSLTDHERLIYDVI---RSNKQD----MG----IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I---~~~ag~----~G----Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ....+..+|+..-+.   +. .|.    .|    +.+++|...+  |++...++|+|+.|++.|+|+.
T Consensus       136 ~~~~~~~~Rl~~~L~~l~~~-~~~~~~~~~~~~~~t~~~lA~~l--G~tr~tvsR~l~~l~~~gii~~  200 (211)
T PRK11753        136 LAFLDVTGRIAQTLLDLAKQ-PDAMTHPDGMQIKITRQEIGRIV--GCSREMVGRVLKMLEDQGLISA  200 (211)
T ss_pred             HHhcChhhHHHHHHHHHHHh-cCCcCCCCceecCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            344566777765443   32 221    23    5579999999  9999999999999999999986

>PF13034 DUF3895: Protein of unknown function (DUF3895)

Probab=86.34  E-value=3.7  Score=31.35  Aligned_cols=61  Identities=8%  Similarity=0.104  Sum_probs=50.0

Q ss_pred             HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc-ceecCHH------HHHHHHHHHhhcCeeEEEeeCCC
Q 025493          128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAF-KVDLTKQ------QIEEIVRAVVLDNQIMEVKSNGS  188 (252)
Q Consensus       128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~-~~~Ls~~------di~~IL~tLVyDgkIE~v~~~g~  188 (252)
                      ..++.+..||++..-.|+.|+++|+-+.+-+ +-..+..      +|-..|+-|+..|+|.=+.+.|.
T Consensus         4 ~e~~~i~~yi~n~~~Isa~elcE~LI~~~~~~~~rysTgKpkiY~~Vc~yLe~L~~eg~l~~i~~~~~   71 (78)
T PF13034_consen    4 LEKEFINWYIQNEEEISARELCEYLIENGGSPNKRYSTGKPKIYPYVCNYLEYLVKEGKLSFIENDGT   71 (78)
T ss_pred             HHHHHHHHHHhccccccHHHHHHHHHHcCCCccccccCCCceeHHHHHHHHHHHHHCCeEEEEecCcc
Confidence            3467788899999999999999999988754 4444443      99999999999999998876653

>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=86.12  E-value=18  Score=30.55  Aligned_cols=109  Identities=21%  Similarity=0.178  Sum_probs=74.3

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcccc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYS  117 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~  117 (252)
                      |..|++++.+  .|.--...||-..++..++.+.+.|+|..|..+|.|.. |..  ...|||..-.-.. ...+..   .
T Consensus         3 e~~Il~y~~~--qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~-K~~--GKqkiY~~~Q~~~-~~~s~e---e   73 (169)
T PF07106_consen    3 EDAILEYMKE--QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE-KEY--GKQKIYFANQDEL-EVPSPE---E   73 (169)
T ss_pred             HHHHHHHHHH--cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee-eee--cceEEEeeCcccc-CCCCch---h
Confidence            5678888876  78888999999977546888999999999999999987 433  4568887643221 112211   1


Q ss_pred             CCcCCHHHHHHHHHHHHHHhh-----------hCCCCCHHHHHHHHHHcC
Q 025493          118 EGSLDTEFIKVVKSQCLKQII-----------KLKVATLEGISDSIKRSG  156 (252)
Q Consensus       118 d~e~D~efV~~l~~~~~~~i~-----------~~~~~T~~~I~~~i~~~~  156 (252)
                      ..++|.+ |..|+..+...=.           -.+.||.+++..-|.+..
T Consensus        74 l~~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~  122 (169)
T PF07106_consen   74 LAELDAE-IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELE  122 (169)
T ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            2356666 7777666553311           146888888888776553

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 [].

>PRK05638 threonine synthase; Validated

Probab=85.58  E-value=2.9  Score=40.75  Aligned_cols=61  Identities=16%  Similarity=0.250  Sum_probs=46.8

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC--CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN--LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~--l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +++-...|+.++.+ .   -+--.+|.+++  +  +++..|.++|+.||+.|||.+-.  +...|+.|-|.
T Consensus       369 ~~~~r~~IL~~L~~-~---~~~~~el~~~l--~~~~s~~~v~~hL~~Le~~GLV~~~~--~~g~~~~Y~Lt  431 (442)
T PRK05638        369 IGGTKLEILKILSE-R---EMYGYEIWKAL--GKPLKYQAVYQHIKELEELGLIEEAY--RKGRRVYYKLT  431 (442)
T ss_pred             ccchHHHHHHHHhh-C---CccHHHHHHHH--cccCCcchHHHHHHHHHHCCCEEEee--cCCCcEEEEEC
Confidence            44567888888876 3   37788999999  7  89999999999999999998742  22345556553

>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=85.54  E-value=1.6  Score=33.71  Aligned_cols=50  Identities=8%  Similarity=0.247  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHhhh----CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          126 IKVVKSQCLKQIIK----LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       126 V~~l~~~~~~~i~~----~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      ...+++.|+.||+.    ...+++++|++-+        .+++++|+..|+.|+-+|.|...
T Consensus        45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             S-HHHHHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSEEES
T ss_pred             CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeEecc
Confidence            57889999999987    3578899999776        36799999999999999999753

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.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=85.47  E-value=5.2  Score=33.60  Aligned_cols=37  Identities=14%  Similarity=0.264  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       141 ~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      ..+|.++|++.+        .++..-+++|+..|+-.|.|+..+.
T Consensus        23 ~~~s~~eIA~~~--------~is~~~L~kIl~~L~~aGlv~S~rG   59 (153)
T PRK11920         23 KLSRIPEIARAY--------GVSELFLFKILQPLVEAGLVETVRG   59 (153)
T ss_pred             CcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeecC
Confidence            457888888754        4778999999999999999998873

>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=85.20  E-value=3.6  Score=31.00  Aligned_cols=34  Identities=9%  Similarity=0.206  Sum_probs=32.9

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .+...+|-.+|  |++.+.+...|..|..+|+|.+=
T Consensus        18 c~TLeeL~ekT--gi~k~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen   18 CCTLEELEEKT--GISKNTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeee
Confidence            99999999999  99999999999999999999984

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=85.05  E-value=9.4  Score=34.52  Aligned_cols=112  Identities=9%  Similarity=0.096  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccc
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWY  116 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy  116 (252)
                      -...|++++.+ .|.  +-.+||-..+  +....++.|=|+.||++|+|+++..    +- ++  .  .++.+.   ++.
T Consensus         6 R~~~Il~~L~~-~~~--v~v~eLa~~l--~VS~~TIRRDL~~Le~~g~l~r~~G----ga-~~--~--~~~~~~---~~~   68 (256)
T PRK10434          6 RQAAILEYLQK-QGK--TSVEELAQYF--DTTGTTIRKDLVILEHAGTVIRTYG----GV-VL--N--KEESDP---PID   68 (256)
T ss_pred             HHHHHHHHHHH-cCC--EEHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEC----CE-Ec--C--CCCCCC---CHH
Confidence            35578888888 554  9999999999  9999999999999999999999742    11 11  0  111111   222


Q ss_pred             cCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHc-CCcceecCHH
Q 025493          117 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQ  165 (252)
Q Consensus       117 ~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~-~i~~~~Ls~~  165 (252)
                      .-...+.+.=+.|-+....+|...      +..|+-+++++|... +++=+.=|..
T Consensus        69 ~r~~~~~~~K~~IA~~Aa~~I~~g~tIfld~GtT~~~la~~L~~~~~ltVvTnsl~  124 (256)
T PRK10434         69 HKTLINTHKKELIAEAAVSLIHDGDSIILDAGSTVLQMVPLLSRFNNITVMTNSLH  124 (256)
T ss_pred             HHHHhhHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhccCCCeEEEECCHH
Confidence            233456666777888888888754      578899999999764 4544444443

>PHA02943 hypothetical protein; Provisional

Probab=84.83  E-value=4.4  Score=34.90  Aligned_cols=51  Identities=8%  Similarity=0.176  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      |..=...++.|| +.|..|..||++.+        .+|..+++=+|.+|+-+|+|++|+-
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            333445677777 78888899998765        4789999999999999999999873

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=84.71  E-value=3.5  Score=34.91  Aligned_cols=110  Identities=14%  Similarity=0.143  Sum_probs=69.1

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccC
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSE  118 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d  118 (252)
                      ..||.++++   ..-+-++||...+  +..+..+++.|+.|+++|||.-++      .+-|.|.+              .
T Consensus        13 ~~Iy~l~~~---~~~~~~~diA~~L--~Vsp~sVt~ml~rL~~~GlV~~~~------y~gi~LT~--------------~   67 (154)
T COG1321          13 ETIYELLEE---KGFARTKDIAERL--KVSPPSVTEMLKRLERLGLVEYEP------YGGVTLTE--------------K   67 (154)
T ss_pred             HHHHHHHhc---cCcccHHHHHHHh--CCCcHHHHHHHHHHHHCCCeEEec------CCCeEECh--------------h
Confidence            345655553   3348899999999  999999999999999999998863      22233321              1


Q ss_pred             CcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhh
Q 025493          119 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVL  176 (252)
Q Consensus       119 ~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVy  176 (252)
                      |+==...+=...+.+..|+.+.-....+++++--....   -.++.+.++.|-+.|-+
T Consensus        68 G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~le---h~~s~~~~~rl~~~l~~  122 (154)
T COG1321          68 GREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLE---HALSDETAERLDELLGF  122 (154)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh---hcCCHHHHHHHHHHhCC
Confidence            22112222223334556666655566666664433322   35778888888777765

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=84.50  E-value=2.7  Score=36.98  Aligned_cols=50  Identities=16%  Similarity=0.255  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +-|++|..++.. .|.+ +-..+|.+++  ||..+.++|.|=.|...+.|..+.
T Consensus         4 ~~~~~i~~~l~~-~~~~-~~a~~i~k~l--~i~k~~vNr~LY~L~~~~~v~~~~   53 (183)
T PHA02701          4 DCASLILTLLSS-SGDK-LPAKRIAKEL--GISKHEANRCLYRLLESDAVSCED   53 (183)
T ss_pred             hHHHHHHHHHHh-cCCC-CcHHHHHHHh--CccHHHHHHHHHHHhhcCcEecCC
Confidence            458899999999 9977 9999999999  999999999999999999998763

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=84.27  E-value=12  Score=33.65  Aligned_cols=111  Identities=6%  Similarity=-0.042  Sum_probs=77.2

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC--CCccCCcc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS--KDISGGAW  115 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs--~eiTGG~w  115 (252)
                      ...|+.++++   +.-+-.++|..++  ++...++.|=|+.||++|+|+.+..-.   ..+      +++  .+.   ++
T Consensus         7 ~~~Il~~l~~---~~~~~~~ela~~l--~vS~~TirRdL~~Le~~g~i~r~~gga---~~~------~~~~~~~~---~~   69 (251)
T PRK13509          7 HQILLELLAQ---LGFVTVEKVIERL--GISPATARRDINKLDESGKLKKVRNGA---EAI------TQQRPRWT---PM   69 (251)
T ss_pred             HHHHHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecCCc---ccc------CCCcccCC---CH
Confidence            4567777777   4568899999999  999999999999999999998854321   110      111  011   12


Q ss_pred             ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHcCCcceecCHH
Q 025493          116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQ  165 (252)
Q Consensus       116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~~i~~~~Ls~~  165 (252)
                      ..-...+.+--..|-+.+..+|...      +..|+-+++++|...+++=+.=+..
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            2233456677778888888888754      5788899999997656554554443

>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=84.08  E-value=2.1  Score=30.70  Aligned_cols=33  Identities=15%  Similarity=0.347  Sum_probs=30.6

Q ss_pred             cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .+.+.+|..-+  |++...++|+|+.|+.+|+|..
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            46789999999  9999999999999999999984

...

>COG1777 Predicted transcriptional regulators [Transcription]

Probab=83.98  E-value=1.4  Score=39.50  Aligned_cols=48  Identities=21%  Similarity=0.419  Sum_probs=39.8

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee-eeccc-cCCeeeEEecc
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE-VVNIH-NKGKKHLMAVE  103 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~-vksv~-~~~rK~YmL~~  103 (252)
                      =+..+|....  ++.|..|-++|+.||..|||-+ +--+. .+.||.|+...
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            4556778889  9999999999999999999998 54443 57789999875

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

Probab=83.87  E-value=5.3  Score=33.26  Aligned_cols=55  Identities=7%  Similarity=0.209  Sum_probs=47.7

Q ss_pred             HHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493          130 KSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG  187 (252)
Q Consensus       130 ~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g  187 (252)
                      |..++++|... +.+|+++|++.+++.+   ..+|..-|.+.|+.|+--|.|.++...+
T Consensus        23 R~~vl~~L~~~~~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~   78 (145)
T COG0735          23 RLAVLELLLEADGHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEG   78 (145)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence            56688888854 6799999999999977   5678999999999999999999988654

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=83.81  E-value=11  Score=32.02  Aligned_cols=49  Identities=18%  Similarity=0.156  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++...|..++-. .|  .+.-.+|...+  +|+.+.|.|+|..|...|||...+
T Consensus        14 ~~~v~Vl~aL~~-~~--~~tdEeLa~~L--gi~~~~VRk~L~~L~e~~Lv~~~r   62 (158)
T TIGR00373        14 EEVGLVLFSLGI-KG--EFTDEEISLEL--GIKLNEVRKALYALYDAGLADYKR   62 (158)
T ss_pred             hhHHHHHHHHhc-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceeee
Confidence            345667776665 45  48899999999  999999999999999999996544

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=83.71  E-value=3.4  Score=34.70  Aligned_cols=42  Identities=12%  Similarity=0.188  Sum_probs=36.7

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      ++.-+..++|..+.  |++..-+.|++..|.+.|||++++-.+-
T Consensus        22 ~~~~~s~~~IA~~~--~is~~~L~kil~~L~kaGlV~S~rG~~G   63 (150)
T COG1959          22 GGGPVSSAEIAERQ--GISPSYLEKILSKLRKAGLVKSVRGKGG   63 (150)
T ss_pred             CCCcccHHHHHHHh--CcCHHHHHHHHHHHHHcCCEEeecCCCC
Confidence            33346789999999  9999999999999999999999987654

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

Probab=83.64  E-value=5.5  Score=33.17  Aligned_cols=59  Identities=14%  Similarity=0.205  Sum_probs=49.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      -.+|+.-..|++++.+ +++. +...+|=.+..   +++...+|-|+|+.|+..|+|.++..-.
T Consensus        17 lr~T~qR~~vl~~L~~-~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~   78 (145)
T COG0735          17 LRLTPQRLAVLELLLE-ADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG   78 (145)
T ss_pred             CCcCHHHHHHHHHHHh-cCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence            3579999999999999 8777 88888877653   3788999999999999999999986654

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=83.64  E-value=3.6  Score=37.06  Aligned_cols=45  Identities=13%  Similarity=0.226  Sum_probs=37.8

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|+..+.+ . +.++-.++|-+++  +++.+.+.|+|++|+..|+|...
T Consensus        15 ~iL~~l~~-~-~~~ls~~eia~~l--gl~kstv~RlL~tL~~~g~v~~~   59 (263)
T PRK09834         15 MVLRALNR-L-DGGATVGLLAELT--GLHRTTVRRLLETLQEEGYVRRS   59 (263)
T ss_pred             HHHHHHHh-c-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            34555554 3 3469999999999  99999999999999999999875

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=83.45  E-value=1.5  Score=36.73  Aligned_cols=68  Identities=12%  Similarity=0.134  Sum_probs=49.8

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHH-HHHhh--cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDM-KRELK--VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~di-k~~~~--~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      ...+++-...|+.++.+ . .-|-..... ...+.  ..+...+|-.+|+.||.+|+|.+-..  .++||+|-+.
T Consensus        38 ~~~~~~~~l~IL~lL~~-~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~--~~~RK~Y~IT  108 (135)
T PRK09416         38 SEKEEDILLAILQLLMN-E-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWD--HEGAKYYQLT  108 (135)
T ss_pred             hcccccHHHHHHHHHhC-C-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeec--CCCceEEEEC
Confidence            44677888899998888 6 677665544 33331  14678999999999999999988543  4578998763

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=83.45  E-value=2.7  Score=38.17  Aligned_cols=44  Identities=18%  Similarity=0.239  Sum_probs=37.6

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .|++++.+ .+ .++-..+|-+++  +||.+.+.|.|++|+..|++..
T Consensus        29 ~IL~~~~~-~~-~~~tl~eIa~~l--glpkStv~RlL~tL~~~G~l~~   72 (271)
T PRK10163         29 AILQYLEK-SG-GSSSVSDISLNL--DLPLSTTFRLLKVLQAADFVYQ   72 (271)
T ss_pred             HHHHHHHh-CC-CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            45666655 43 578899999999  9999999999999999999966

>PF13551 HTH_29: Winged helix-turn helix

Probab=82.81  E-value=15  Score=27.68  Aligned_cols=98  Identities=16%  Similarity=0.226  Sum_probs=64.6

Q ss_pred             Cccc-HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHH
Q 025493           52 MGIW-TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVK  130 (252)
Q Consensus        52 ~GIw-~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~  130 (252)
                      +|.. .+++.+.+  +++..++.+.++..++.|+-. +.+-+.                 .||....-  ++.+-.+.|.
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            3665 99999999  999999999999999988322 222110                 02211111  5666666555


Q ss_pred             HHHHHHhhh-CCCCCHHHHHHHH-HHcCCcceecCHHHHHHHHHH
Q 025493          131 SQCLKQIIK-LKVATLEGISDSI-KRSGAFKVDLTKQQIEEIVRA  173 (252)
Q Consensus       131 ~~~~~~i~~-~~~~T~~~I~~~i-~~~~i~~~~Ls~~di~~IL~t  173 (252)
                      +.+...-.. ....|+++|.+++ .+.  ..+.+|..-|..+|..
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            544432222 1368999999998 444  3578899999999874

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

Probab=82.66  E-value=2.8  Score=37.24  Aligned_cols=43  Identities=7%  Similarity=0.136  Sum_probs=36.8

Q ss_pred             HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      |++++.+  .+.++-.+||-+++  +||.+++.|.|++|+..|++..
T Consensus        14 IL~~l~~--~~~~~~l~eia~~l--glpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        14 VIEAFGA--ERPRLTLTDVAEAT--GLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             HHHHHhc--CCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence            4555544  35789999999999  9999999999999999999975

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.

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

Probab=82.39  E-value=2.6  Score=28.13  Aligned_cols=41  Identities=22%  Similarity=0.394  Sum_probs=22.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS   78 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~   78 (252)
                      +-||.+|+.......    +.|...++|.+.+  |.+.++|.+.||.
T Consensus         3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~l--g~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALL----EQGMSIREIAKRL--GRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHH----CS---HHHHHHHT--T--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHH----HcCCCHHHHHHHH--CcCcHHHHHHHhc
Confidence            458888887755444    4789999999999  9999999999874

>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=81.74  E-value=4.4  Score=28.38  Aligned_cols=47  Identities=9%  Similarity=0.156  Sum_probs=40.5

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      ++.++.+|..++.+|.+|+++.+.        .|..-|+.=|+.|+-.|.|.++.
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~--------VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFG--------VSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEEEc
Confidence            357888999999999999998763        57888999999999999999875

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

>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=81.72  E-value=3.2  Score=32.30  Aligned_cols=50  Identities=20%  Similarity=0.230  Sum_probs=37.6

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .++...|..++-. .|  .+--.||...+  +|+.+.+.|+|-.|...+||+..+
T Consensus        12 g~~~~~Il~~L~~-~~--~l~de~la~~~--~l~~~~vRkiL~~L~~~~lv~~~~   61 (105)
T PF02002_consen   12 GEEAVRILDALLR-KG--ELTDEDLAKKL--GLKPKEVRKILYKLYEDGLVSYRR   61 (105)
T ss_dssp             -STTHHHHHHHHH-H----B-HHHHHHTT---S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred             CchHHHHHHHHHH-cC--CcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeEEEE
Confidence            3566788888887 55  58899999999  999999999999999999997654

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.

>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=81.49  E-value=4.8  Score=29.28  Aligned_cols=49  Identities=18%  Similarity=0.267  Sum_probs=41.5

Q ss_pred             HHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          132 QCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       132 ~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      .|+++|..+ .+++..+|.+.+...|   .++|++-|..-|+.|.-||.++++
T Consensus         2 ~IL~~L~~~~~P~g~~~l~~~L~~~g---~~~se~avRrrLr~me~~Glt~~~   51 (66)
T PF08461_consen    2 FILRILAESDKPLGRKQLAEELKLRG---EELSEEAVRRRLRAMERDGLTRKV   51 (66)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhcC---hhhhHHHHHHHHHHHHHCCCcccc
Confidence            467777755 5789999999999887   689999999999999999976653

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=80.95  E-value=4  Score=33.70  Aligned_cols=55  Identities=9%  Similarity=0.165  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      .+-..+.+.|=.++.+|++||+++|.+.    -+++..-|..+|+.|+--|.|-+.+.+
T Consensus         6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~----~ews~sTV~TLl~RL~KKg~l~~~kdg   60 (123)
T COG3682           6 AAEWEVMEILWSRGPATVREIIEELPAD----REWSYSTVKTLLNRLVKKGLLTRKKDG   60 (123)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHhhc----ccccHHHHHHHHHHHHhccchhhhhcC
Confidence            4566788888899999999999999976    479999999999999999999887754

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

Probab=80.73  E-value=6.7  Score=31.04  Aligned_cols=55  Identities=20%  Similarity=0.213  Sum_probs=45.8

Q ss_pred             CCCCChHHHHHHHHHHh-----hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           31 SDSLTDHERLIYDVIRS-----NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~-----~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+|+.-|..|+..|-.     |...+-|....+...|  +++.+.++++++.|+.+++|..
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            35788888888877765     2355678889999999  9999999999999999999954

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

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=80.44  E-value=15  Score=34.04  Aligned_cols=146  Identities=15%  Similarity=0.155  Sum_probs=84.5

Q ss_pred             cchhHHHhhccCCCcccc-----cCCCCCCCCCCCChHHHHHH-----HHHHhhcCC-Cccc-HHHHHHHhhcCCChHHH
Q 025493            5 FTDLYLLGLAKGSGMSKR-----KRPDSNAPSDSLTDHERLIY-----DVIRSNKQD-MGIW-TRDMKRELKVNLPDNIV   72 (252)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~~e~~vy-----~~I~~~ag~-~GIw-~~dik~~~~~~l~~~~l   72 (252)
                      |..++..+.++....++.     .......+.+-|+.++...|     -.|++.+.- .|-| ...|.+++++.++..++
T Consensus        77 F~~lV~f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev  156 (271)
T TIGR02147        77 FEAMVNFGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQV  156 (271)
T ss_pred             HHHHHHHhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHH
Confidence            445555566665544332     11111234456788776643     456663332 2442 44599999445999999


Q ss_pred             HHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhC---CCCCHHHHH
Q 025493           73 TKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL---KVATLEGIS  149 (252)
Q Consensus        73 ~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~---~~~T~~~I~  149 (252)
                      +.+|..|++-||||.-.+-      .|...+    ..+|||     .+.-.+.|-.+..+++.+-...   -.+.     
T Consensus       157 ~~sL~~L~~~glikk~~~g------~y~~t~----~~l~~~-----~~~~~~avr~~h~q~l~lA~~al~~~p~~-----  216 (271)
T TIGR02147       157 KESLDLLERLGLIKKNEDG------FYKQTD----KAVSTG-----DEVIPLAVRQYQKQMIDLAKEALDALPPS-----  216 (271)
T ss_pred             HHHHHHHHHCCCeeECCCC------cEEeec----ceeecC-----CccchHHHHHHHHHHHHHHHHHHHhCCcc-----
Confidence            9999999999999985332      233222    234433     4555677777777777665432   1111     


Q ss_pred             HHHHHcCCcc--eecCHHHHHHHHHHH
Q 025493          150 DSIKRSGAFK--VDLTKQQIEEIVRAV  174 (252)
Q Consensus       150 ~~i~~~~i~~--~~Ls~~di~~IL~tL  174 (252)
                          ...++.  ..++.++.++|.+.|
T Consensus       217 ----eR~~S~lT~~i~~~~~~~i~~~i  239 (271)
T TIGR02147       217 ----ERDVSTVTFGISEEAYKEIVKKI  239 (271)
T ss_pred             ----ccccceeeEecCHHHHHHHHHHH
Confidence                112333  467788888886655

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=80.44  E-value=4.5  Score=36.18  Aligned_cols=45  Identities=4%  Similarity=0.258  Sum_probs=36.5

Q ss_pred             HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .++++..+...++-.++|-+++  +||.+.+.|.|++|+..|++..-
T Consensus        17 l~IL~~l~~~~~l~l~eia~~l--gl~kstv~Rll~tL~~~G~l~~~   61 (257)
T PRK15090         17 FGILQALGEEREIGITELSQRV--MMSKSTVYRFLQTMKTLGYVAQE   61 (257)
T ss_pred             HHHHHHhhcCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEc
Confidence            3344443334578899999999  99999999999999999999773

>PRK11569 transcriptional repressor IclR; Provisional

Probab=80.13  E-value=4.1  Score=36.99  Aligned_cols=43  Identities=9%  Similarity=0.371  Sum_probs=36.9

Q ss_pred             HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      |++++.+  .+.++-.++|-+.+  +||.+++.|.|.+|+..|++..
T Consensus        33 IL~~l~~--~~~~~~lseia~~l--glpksTv~RlL~tL~~~G~l~~   75 (274)
T PRK11569         33 LLEWIAE--SNGSVALTELAQQA--GLPNSTTHRLLTTMQQQGFVRQ   75 (274)
T ss_pred             HHHHHHh--CCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence            4555544  35778999999999  9999999999999999999975

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=80.06  E-value=6.6  Score=33.46  Aligned_cols=53  Identities=8%  Similarity=0.095  Sum_probs=44.5

Q ss_pred             HHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          130 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       130 ~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      |..|+.+|.. .+.+|+++|.+.+++.+   ..++..-|-+.|+.|+-.|.|.++..
T Consensus        28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~---~~is~aTVYRtL~~L~e~Glv~~~~~   81 (169)
T PRK11639         28 RLEVLRLMSLQPGAISAYDLLDLLREAE---PQAKPPTVYRALDFLLEQGFVHKVES   81 (169)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHhhC---CCCCcchHHHHHHHHHHCCCEEEEec
Confidence            5567777764 46899999999999988   35677899999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	252
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	3e-21
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	3e-15

>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 = 84.1 bits (208), Expect = 3e-21
 Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 3/87 (3%)

Query: 21  KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
                 +        + E+L+Y +I  +  + GIW+RD++   K NLP   + K +K+L+
Sbjct: 5   SSGDSQNAGKMKGSDNQEKLVYQIIE-DAGNKGIWSRDVRY--KSNLPLTEINKILKNLE 61

Query: 81  NKSLIKEVVNIHNKGKKHLMAVEFEPS 107
           +K LIK V ++    KK  M       
Sbjct: 62  SKKLIKAVKSVAASKKKVYMLYNLSGP 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 = 68.3 bits (167), Expect = 3e-15
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 21 KRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80
          + K   +        + E+L+Y +I     + GIW+RD++   K NLP   + K +K+L+
Sbjct: 22 RIKDSQNAGKMKGSDNQEKLVYQIIED-AGNKGIWSRDVRY--KSNLPLTEINKILKNLE 78

Query: 81 NKSLIKEVVNIHNK 94
          +K LIK V ++   
Sbjct: 79 SKKLIKAVKSVSGP 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	252
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	99.91
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	99.89
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	98.09
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	98.08
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.9
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	97.83
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	97.81
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.81
2nnn_A	140	Probable transcriptional regulator; structural gen	97.75
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.75
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.75
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.75
1okr_A	123	MECI, methicillin resistance regulatory protein ME	97.74
3bja_A	139	Transcriptional regulator, MARR family, putative;	97.73
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.73
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.72
3r0a_A	123	Putative transcriptional regulator; structural gen	97.72
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.7
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.7
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.7
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.68
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.67
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.67
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.66
2vn2_A	128	DNAD, chromosome replication initiation protein; D	97.64
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.62
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	97.62
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	97.61
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	97.61
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.6
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.58
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.58
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	97.57
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	97.55
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	97.53
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.51
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	97.51
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	97.49
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.48
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.48
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.47
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.47
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	97.44
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	97.41
1p6r_A	82	Penicillinase repressor; transcription regulation,	97.4
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.38
3nqo_A	189	MARR-family transcriptional regulator; structural	97.37
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	97.37
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.35
1z91_A	147	Organic hydroperoxide resistance transcriptional;	97.35
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	97.33
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	97.33
3f3x_A	144	Transcriptional regulator, MARR family, putative;	97.28
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.27
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.27
2pex_A	153	Transcriptional regulator OHRR; transcription regu	97.27
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	97.22
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.19
1ku9_A	152	Hypothetical protein MJ223; putative transcription	97.15
1hsj_A	487	Fusion protein consisting of staphylococcus access	97.13
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.13
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.12
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.11
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	97.09
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.05
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	97.04
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.04
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	96.98
2fxa_A	207	Protease production regulatory protein HPR; protea	96.95
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.88
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.82
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.8
2w25_A	150	Probable transcriptional regulatory protein; trans	96.68
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.64
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.6
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.59
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	96.56
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.53
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	96.5
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	96.4
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.38
4fx0_A	148	Probable transcriptional repressor protein; helix-	96.31
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.29
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.26
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.25
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	96.23
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.2
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.17
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.13
2obp_A	96	Putative DNA-binding protein; structural genomics,	96.12
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	96.1
2pg4_A	95	Uncharacterized protein; structural genomics, join	96.02
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	96.02
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.98
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.97
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	95.94
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.92
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.9
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	95.87
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	95.7
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.54
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	95.51
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.42
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.35
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.28
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	95.26
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.21
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	95.11
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.05
3jth_A	98	Transcription activator HLYU; transcription factor	95.03
2kko_A	108	Possible transcriptional regulatory protein (possi	94.97
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.93
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.9
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.87
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.82
1xma_A	145	Predicted transcriptional regulator; southea colla	94.73
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	94.64
1y0u_A	96	Arsenical resistance operon repressor, putative; s	94.54
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.52
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	94.45
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	94.39
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	94.24
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	94.1
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.1
2co5_A	99	Viral protein F93; viral protein-winged helix comp	94.0
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	93.97
3df8_A	111	Possible HXLR family transcriptional factor; APC89	93.94
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	93.94
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.93
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	93.82
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	93.75
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	93.68
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	93.63
3cta_A	230	Riboflavin kinase; structural genomics, transferas	93.52
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	93.32
2dql_A	115	PEX protein; circadian clock associated protein, c	93.28
2h09_A	155	Transcriptional regulator MNTR; transcription regu	93.28
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	93.21
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	93.09
4esf_A	117	PADR-like transcriptional regulator; PADR family,	93.08
1bja_A	95	Transcription regulatory protein MOTA; activation	93.07
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	93.07
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	92.94
4g6q_A	182	Putative uncharacterized protein; structural genom	92.83
1lva_A	258	Selenocysteine-specific elongation factor; winged-	92.76
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	92.64
1lva_A	258	Selenocysteine-specific elongation factor; winged-	92.54
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	92.5
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	92.46
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	92.41
3elk_A	117	Putative transcriptional regulator TA0346; structu	92.39
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	92.39
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	92.25
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	92.2
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	92.09
1xd7_A	145	YWNA; structural genomics, protein structure initi	92.08
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	92.03
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	92.03
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	91.98
3b02_A	195	Transcriptional regulator, CRP family; structural	91.92
1z05_A	429	Transcriptional regulator, ROK family; structural	91.77
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	91.77
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	91.72
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	91.58
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	91.58
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	91.48
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	91.47
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	91.42
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	91.1
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	91.06
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	91.02
1ylf_A	149	RRF2 family protein; structural genomics, transcri	90.87
1ft9_A	222	Carbon monoxide oxidation system transcription reg	90.71
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	90.66
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	90.65
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	90.37
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	89.96
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	89.82
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	89.79
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	89.79
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	89.78
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	89.33
3k69_A	162	Putative transcription regulator; putative transcr	89.21
1mkm_A	249	ICLR transcriptional regulator; structural genomic	88.91
2v9v_A	135	Selenocysteine-specific elongation factor; transcr	88.8
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.71
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	88.64
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	88.63
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	88.42
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	88.41
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	88.34
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	88.2
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	88.06
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	88.04
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	87.91
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	87.68
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	87.6
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	87.38
1p6r_A	82	Penicillinase repressor; transcription regulation,	87.38
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	87.34
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	87.31
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	86.92
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	86.91
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	86.84
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	86.38
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	86.28
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	86.18
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	86.15
2w57_A	150	Ferric uptake regulation protein; gene regulation,	86.14
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	85.76
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	85.36
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	85.31
2w57_A	150	Ferric uptake regulation protein; gene regulation,	84.97
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	84.54
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	84.4
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	84.38
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	83.68
4ets_A	162	Ferric uptake regulation protein; metal binding pr	83.54
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	83.39
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	83.33
2k27_A	159	Paired box protein PAX-8; paired domain, solution	83.13
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	82.84
4ets_A	162	Ferric uptake regulation protein; metal binding pr	82.84
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	82.66
1ldj_A	760	Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc	82.65
2g7u_A	257	Transcriptional regulator; ICLR family, structural	82.58
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	82.2
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	81.85
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	81.82
2o0m_A	345	Transcriptional regulator, SORC family; structural	81.33
3by6_A	126	Predicted transcriptional regulator; structural ge	81.29
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	80.75
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	80.64
1ldd_A	74	APC2WHB, anaphase promoting complex; ubiquitin, li	80.59
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	80.17
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	80.03

>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=99.91  E-value=7.7e-25  Score=168.81  Aligned_cols=84  Identities=27%  Similarity=0.488  Sum_probs=81.2

Q ss_pred             cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           23 KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        23 ~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      ++++.+.+..+||++|.+||++|++ +|++|||+++|++++  ||++++++++|+.||+|||||+++++++++||+||||
T Consensus         7 ~~~~~~~k~~~Lt~~q~~Vl~~I~~-~g~~gi~qkeLa~~~--~l~~~tvt~iLk~LE~kglIkr~~~~~~~~rKvy~Ly   83 (91)
T 2dk5_A            7 GDSQNAGKMKGSDNQEKLVYQIIED-AGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVAASKKKVYMLY   83 (91)
T ss_dssp             CCCCCCCCCCCSCSSHHHHHHHHHH-HCTTCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEES
T ss_pred             cCHHHHhhhcCCCHHHHHHHHHHHH-cCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCCCCcEEEEEe
Confidence            4678888999999999999999999 999999999999999  9999999999999999999999999999999999999


Q ss_pred             ccccCCC
Q 025493          103 EFEPSKD  109 (252)
Q Consensus       103 ~lePs~e  109 (252)
                      +|+||+|
T Consensus        84 ~l~Ps~e   90 (91)
T 2dk5_A           84 NLSGPSS   90 (91)
T ss_dssp             SSCCCCC
T ss_pred             ccCcCCC
Confidence            9999987

>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=99.89  E-value=1.2e-23  Score=163.64  Aligned_cols=74  Identities=28%  Similarity=0.535  Sum_probs=70.5

Q ss_pred             ccccCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493           20 SKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK   96 (252)
Q Consensus        20 ~~~~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r   96 (252)
                      .++++++.+.+.++||++|++||++|++ |||+|||++||++++  |||+++|+|+||.||+++|||+|+||++|+|
T Consensus        21 ~~~~~~~~a~k~~~Lt~~E~lVy~~I~~-aGn~GIw~kdL~~~t--nL~~~~vtkiLK~LE~k~lIK~Vksv~~~~~   94 (95)
T 2yu3_A           21 YRIKDSQNAGKMKGSDNQEKLVYQIIED-AGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVSGPSS   94 (95)
T ss_dssp             EEECCSSSCCCCCSCSHHHHHHHHHHHH-HTTSCEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEECCSCSSSC
T ss_pred             EEEeCHHHHhhhcCCCHHHHHHHHHHHH-hCCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhCCCEEEecCccCCCC
Confidence            4457888899999999999999999999 999999999999999  9999999999999999999999999999886

>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=98.09  E-value=8.7e-05  Score=57.34  Aligned_cols=65  Identities=15%  Similarity=0.235  Sum_probs=54.0

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+||+.|..|+.+|-+ .|  |+.+++|..+++.  ++..+.++++|+.||+||+|...++   ..+++|.+
T Consensus         5 ~~~Lt~~q~~vL~~L~~-~~--~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~---~r~~~~~~   71 (126)
T 1sd4_A            5 QVEISMAEWDVMNIIWD-KK--SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS---ENIYFYSS   71 (126)
T ss_dssp             CCCCCHHHHHHHHHHHH-SS--SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHh-cC--CCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC---CCeEEEEE
Confidence            45799999999999999 65  7999999999932  2689999999999999999999875   34555543

>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=98.08  E-value=5.7e-05  Score=58.76  Aligned_cols=65  Identities=18%  Similarity=0.325  Sum_probs=56.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+||..|..|+..|.. .|+.|+..++|...+  +++...++++|+.||++|||...++-..+..+.+
T Consensus        27 ~~lt~~~~~vL~~l~~-~~~~~~t~~ela~~l--~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~   91 (139)
T 3eco_A           27 FDITNEQGHTLGYLYA-HQQDGLTQNDIAKAL--QRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNI   91 (139)
T ss_dssp             GTCCHHHHHHHHHHHH-STTTCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEE
T ss_pred             cCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHh--CCCcccHHHHHHHHHHCCCEeecCCCCCCCeeee
Confidence            4799999999999999 998999999999999  9999999999999999999999887765333333

>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=97.90  E-value=6.2e-05  Score=66.66  Aligned_cols=147  Identities=12%  Similarity=0.093  Sum_probs=98.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC----
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS----  107 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs----  107 (252)
                      -+||..|..|+..|.+ .|+.|+.+++|..++  ++....++++|+.||++|||....+-+. .|.+++-  |+|.    
T Consensus        30 ~~lt~~q~~vL~~L~~-~~~~~~~~~el~~~l--~~~~~t~t~~l~rLe~~G~i~R~~~~~D-rR~~~i~--LT~~G~~~  103 (250)
T 1p4x_A           30 VDMTIKEFILLTYLFH-QQENTLPFKKIVSDL--CYKQSDLVQHIKVLVKHSYISKVRSKID-ERNTYIS--ISEEQREK  103 (250)
T ss_dssp             CSSCHHHHHHHHHHHS-CSCSEEEHHHHHHHS--SSCGGGTHHHHHHHHHTTSCEEEECSSS-TTSEEEE--CCHHHHHH
T ss_pred             cCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCC-CCeEEEE--ECHHHHHH
Confidence            3799999999999999 999999999999999  9999999999999999999999998876 3444432  1111    


Q ss_pred             --------CCccCCccccCCcCC---------HHHH---HHHHHHHHHHhhhCCCCCHHH--HHHHHHHcC---Ccc---
Q 025493          108 --------KDISGGAWYSEGSLD---------TEFI---KVVKSQCLKQIIKLKVATLEG--ISDSIKRSG---AFK---  159 (252)
Q Consensus       108 --------~eiTGG~wy~d~e~D---------~efV---~~l~~~~~~~i~~~~~~T~~~--I~~~i~~~~---i~~---  159 (252)
                              .+.- -.|+.+ ++|         ..|.   ..+.+..-.++.. ...|..+  |+.+|...+   ++.   
T Consensus       104 ~~~~~~~~~~~~-eq~s~E-~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~gLt~~q~~vL~~L~~~~~~~~t~~eL  180 (250)
T 1p4x_A          104 IAERVTLFDQII-KQFNLA-DQSESQMIPKDSKEFLNLMMYTMYFKNIIKKH-LTLSFVEFTILAIITSQNKNIVLLKDL  180 (250)
T ss_dssp             HHHHHHHHHHHH-HHHHHH-TTCCSSCSCCSHHHHHHHHHHHHHHHHHHHHH-CSSCHHHHHHHHHHHTTTTCCEEHHHH
T ss_pred             HHHHHHHHHHHH-HHHhcc-cccccccchHHHHHHHHHHHHHHHHHHHHHhh-CCCCHHHHHHHHHHHhCCCCCcCHHHH
Confidence                    0011 222222 332         1111   1111111122222 2345444  566666553   332   


Q ss_pred             ---eecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493          160 ---VDLTKQQIEEIVRAVVLDNQIMEVKSNG  187 (252)
Q Consensus       160 ---~~Ls~~di~~IL~tLVyDgkIE~v~~~g  187 (252)
                         ..++...+-.+|+.|+-.|.|++.+...
T Consensus       181 a~~l~i~~~tvt~~v~rLe~~GlV~R~~~~~  211 (250)
T 1p4x_A          181 IETIHHKYPQTVRALNNLKKQGYLIKERSTE  211 (250)
T ss_dssp             HHHSSSCHHHHHHHHHHHHHHTSSEEEECSS
T ss_pred             HHHHCCChhhHHHHHHHHHHCCCEEeeCCCC
Confidence               4567889999999999999999988543

>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=97.83  E-value=9.7e-05  Score=57.31  Aligned_cols=60  Identities=18%  Similarity=0.298  Sum_probs=55.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .+|+..|..|+..|.. .|+.|+..++|...+  +++...++++|+.||++|||...++-..+
T Consensus        30 ~~lt~~~~~iL~~l~~-~~~~~~~~~ela~~l--~~~~~tvs~~l~~Le~~Gli~r~~~~~d~   89 (141)
T 3bro_A           30 YDLTGTQMTIIDYLSR-NKNKEVLQRDLESEF--SIKSSTATVLLQRMEIKKLLYRKVSGKDS   89 (141)
T ss_dssp             TTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCT
T ss_pred             cCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CCCcchHHHHHHHHHHCCCEEeeCCCcCC
Confidence            3699999999999999 888899999999999  99999999999999999999998776553

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=97.81  E-value=0.00021  Score=56.93  Aligned_cols=56  Identities=23%  Similarity=0.310  Sum_probs=50.2

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC----CChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN----LPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~----l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +.+||..|..|+.+|-+ . +.++..++|...+  +    +..+.|++.|+.||.+|+|...++
T Consensus         4 ~~~lt~~e~~vL~~L~~-~-~~~~t~~el~~~l--~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~   63 (138)
T 2g9w_A            4 LTRLGDLERAVMDHLWS-R-TEPQTVRQVHEAL--SARRDLAYTTVMAVLQRLAKKNLVLQIRD   63 (138)
T ss_dssp             GGGCCHHHHHHHHHHHT-C-SSCEEHHHHHHHH--TTTCCCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             cccCCHHHHHHHHHHHh-c-CCCCCHHHHHHHH--hccCCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            45799999999999988 6 4589999999999  6    899999999999999999999874

>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=97.81  E-value=0.00025  Score=56.89  Aligned_cols=65  Identities=8%  Similarity=0.070  Sum_probs=56.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..|..|+..|.. .|  |+..++|...+  +++...++++|+.||++|||...++-..+..+.+-|
T Consensus        42 ~glt~~q~~iL~~l~~-~~--~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~L  106 (162)
T 3k0l_A           42 LEISLPQFTALSVLAA-KP--NLSNAKLAERS--FIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTV  106 (162)
T ss_dssp             TTCCHHHHHHHHHHHH-CT--TCCHHHHHHHH--TSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEE
Confidence            4799999999999998 66  89999999999  999999999999999999999998877644444433

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=97.75  E-value=0.00027  Score=54.49  Aligned_cols=56  Identities=11%  Similarity=0.132  Sum_probs=51.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+..|.+ .|  ++-.++|...+  ++++..++++|+.||++|+|....+-..
T Consensus        35 ~l~~~~~~iL~~l~~-~~--~~t~~ela~~l--~~~~~tvs~~l~~L~~~glv~r~~~~~d   90 (140)
T 2nnn_A           35 GLTPTQWAALVRLGE-TG--PCPQNQLGRLT--AMDAATIKGVVERLDKRGLIQRSADPDD   90 (140)
T ss_dssp             CCCHHHHHHHHHHHH-HS--SBCHHHHHHHT--TCCHHHHHHHHHHHHHTTCEEEEEETTE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCC
Confidence            899999999999988 66  89999999999  9999999999999999999998776554

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=97.75  E-value=0.00042  Score=55.27  Aligned_cols=65  Identities=11%  Similarity=0.207  Sum_probs=54.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..|..|+..|.+ .|  |+..++|...+  +++...++++|+.||++|+|...++-..+..+.|-|
T Consensus        48 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~l  112 (162)
T 3cjn_A           48 LGLSTAKMRALAILSA-KD--GLPIGTLGIFA--VVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYL  112 (162)
T ss_dssp             HTCCHHHHHHHHHHHH-SC--SEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence            3699999999999988 65  79999999999  999999999999999999999987765544444333

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=97.75  E-value=0.00041  Score=54.39  Aligned_cols=57  Identities=11%  Similarity=0.205  Sum_probs=51.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..|.. .|  ++-.++|...+  ++++..++++|+.||++|||...++-..
T Consensus        38 ~~l~~~~~~iL~~l~~-~~--~~t~~ela~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~d   94 (150)
T 2rdp_A           38 YPITPPQFVALQWLLE-EG--DLTVGELSNKM--YLACSTTTDLVDRMERNGLVARVRDEHD   94 (150)
T ss_dssp             SSSCHHHHHHHHHHHH-HC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCC-
T ss_pred             CCCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCchhHHHHHHHHHHCCCeeecCCCCC
Confidence            4799999999999998 65  79999999999  9999999999999999999999876654

>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=97.75  E-value=0.00039  Score=54.58  Aligned_cols=63  Identities=14%  Similarity=0.255  Sum_probs=54.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.. .|  |+-.++|...+  +++...++++|+.||++|+|...++-..+..+.+
T Consensus        36 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~   98 (152)
T 3bj6_A           36 EGVTVGQRAILEGLSL-TP--GATAPQLGAAL--QMKRQYISRILQEVQRAGLIERRTNPEHARSHRY   98 (152)
T ss_dssp             TTCCHHHHHHHHHHHH-ST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEE
T ss_pred             cCCCHHHHHHHHHHHh-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCcccccceee
Confidence            3699999999999998 66  89999999999  9999999999999999999999877655433333

>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=97.74  E-value=0.00073  Score=51.80  Aligned_cols=62  Identities=13%  Similarity=0.151  Sum_probs=53.4

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC----CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN----LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~----l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..+|+..|..|+.+|.+ .  .++..++|...+  +    ++.+.++++|+.||++|||...++   ..+.+|+
T Consensus         5 ~~~lt~~~~~vL~~l~~-~--~~~t~~ela~~l--~~~~~~s~~tv~~~l~~L~~~Glv~r~~~---~rr~~~~   70 (123)
T 1okr_A            5 TYEISSAEWEVMNIIWM-K--KYASANNIIEEI--QMQKDWSPKTIRTLITRLYKKGFIDRKKD---NKIFQYY   70 (123)
T ss_dssp             CCCCCHHHHHHHHHHHH-H--SSEEHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHTSEEEEEE---TTEEEEE
T ss_pred             cccCCHHHHHHHHHHHh-C--CCcCHHHHHHHH--hccCCCcHhhHHHHHHHHHHCCCeEEEec---CCeEEEE
Confidence            56899999999999988 4  479999999999  6    889999999999999999999876   3455553

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=97.73  E-value=0.00036  Score=53.78  Aligned_cols=63  Identities=6%  Similarity=0.082  Sum_probs=54.4

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.+ .|  ++-.++|...+  ++++..++++|+.||++|+|...++-..+..+.|
T Consensus        29 ~~l~~~~~~iL~~l~~-~~--~~~~~ela~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~   91 (139)
T 3bja_A           29 YDISYVQFGVIQVLAK-SG--KVSMSKLIENM--GCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLV   91 (139)
T ss_dssp             GTCCHHHHHHHHHHHH-SC--SEEHHHHHHHC--SSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             cCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CCChhHHHHHHHHHHHCCCeeeccCCCCCceeEE
Confidence            3699999999999988 55  79999999999  9999999999999999999999877665434333

>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=97.73  E-value=9.3e-05  Score=58.38  Aligned_cols=59  Identities=19%  Similarity=0.283  Sum_probs=45.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..|.. .++.|+..++|...+  +++...++++|+.||++|||...++-..
T Consensus        37 ~glt~~q~~vL~~l~~-~~~~~~t~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~D   95 (148)
T 3jw4_A           37 LGLNSQQGRMIGYIYE-NQESGIIQKDLAQFF--GRRGASITSMLQGLEKKGYIERRIPENN   95 (148)
T ss_dssp             TTCCHHHHHHHHHHHH-HTTTCCCHHHHHHC--------CHHHHHHHHHHTTSBCCC-----
T ss_pred             CCCCHHHHHHHHHHHh-CCCCCCCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeeCCCCC
Confidence            4799999999999999 888899999999999  9999999999999999999999877655

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=97.72  E-value=0.00037  Score=54.42  Aligned_cols=65  Identities=14%  Similarity=0.132  Sum_probs=53.4

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..|..|+..|.. .  .|+..++|...+  +++...++++|+.||++|||...++-..+..+.+-|
T Consensus        33 ~~lt~~~~~iL~~l~~-~--~~~t~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~L   97 (143)
T 3oop_A           33 YDVTPEQWSVLEGIEA-N--EPISQKEIALWT--KKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSL   97 (143)
T ss_dssp             SSSCHHHHHHHHHHHH-H--SSEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEEE
T ss_pred             CCCCHHHHHHHHHHHH-c--CCcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCeeccCCCccCceeeeeE
Confidence            4799999999999998 5  689999999999  999999999999999999999988776644444433

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=97.72  E-value=0.00036  Score=54.90  Aligned_cols=62  Identities=21%  Similarity=0.252  Sum_probs=53.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK   96 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r   96 (252)
                      -+|++.|..||.++.+ .+...+...+|..++  +++.+++.|.|+.|+++|+|...+....++.
T Consensus        22 ~gLt~~e~~il~~L~~-~~~~~~t~~eLa~~l--~~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~   83 (123)
T 3r0a_A           22 LNLTKADLNVMKSFLN-EPDRWIDTDALSKSL--KLDVSTVQRSVKKLHEKEILQRSQQNLDGGG   83 (123)
T ss_dssp             HTCCHHHHHHHHHHHH-STTCCEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEECTTSC
T ss_pred             cCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeeCCccCCCc
Confidence            4799999999999998 765449999999999  9999999999999999999999876554443

>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=97.70  E-value=0.0002  Score=55.99  Aligned_cols=58  Identities=19%  Similarity=0.393  Sum_probs=45.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      -+|+..|..|+..|.. .|  |+..++|...+  +++...++++|+.||++|||...++-..+
T Consensus        33 ~~lt~~~~~vL~~l~~-~~--~~t~~eLa~~l--~~~~~tvs~~l~~L~~~Glv~r~~~~~Dr   90 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDE-QR--GLNLQDLGRQM--CRDKALITRKIRELEGRNLVRRERNPSDQ   90 (142)
T ss_dssp             CCCCHHHHHHHHHHHH-TT--TCCHHHHHHHH--C---CHHHHHHHHHHHTTSEEC-------
T ss_pred             CCCCHHHHHHHHHHHh-CC--CcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEeeccCCCCC
Confidence            4799999999999999 66  89999999999  99999999999999999999998776653

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=97.70  E-value=0.00032  Score=56.23  Aligned_cols=63  Identities=6%  Similarity=0.149  Sum_probs=53.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.. .|  |+..++|...+  +++...++++|+.||++|||...++-..+..+.+
T Consensus        49 ~glt~~q~~vL~~l~~-~~--~~t~~eLa~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~  111 (161)
T 3e6m_A           49 EKLPTPKLRLLSSLSA-YG--ELTVGQLATLG--VMEQSTTSRTVDQLVDEGLAARSISDADQRKRTV  111 (161)
T ss_dssp             HTCCHHHHHHHHHHHH-HS--EEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECC---CCCSCEE
T ss_pred             cCCCHHHHHHHHHHHh-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEe
Confidence            3689999999999998 76  89999999999  9999999999999999999999887665433333

>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=97.70  E-value=0.00034  Score=55.55  Aligned_cols=63  Identities=11%  Similarity=0.146  Sum_probs=54.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.+ .|  ++..++|...+  ++++..++++|+.||++|+|...++-..+..+.|
T Consensus        40 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~  102 (154)
T 2eth_A           40 SDMKTTELYAFLYVAL-FG--PKKMKEIAEFL--STTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRV  102 (154)
T ss_dssp             HHSBHHHHHHHHHHHH-HC--CBCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEE
T ss_pred             cCCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEE
Confidence            3689999999999998 66  79999999999  9999999999999999999999877665434333

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=97.68  E-value=0.00048  Score=55.79  Aligned_cols=57  Identities=11%  Similarity=0.114  Sum_probs=52.1

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      +|+..|..|+..|.+ .|  |+-.++|...+  +++...++++|+.||++|||...++-..+
T Consensus        42 ~lt~~~~~iL~~L~~-~~--~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~Dr   98 (168)
T 2nyx_A           42 NITIPQFRTLVILSN-HG--PINLATLATLL--GVQPSATGRMVDRLVGAELIDRLPHPTSR   98 (168)
T ss_dssp             SCCHHHHHHHHHHHH-HC--SEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCS
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEeccCCCCC
Confidence            799999999999988 65  79999999999  99999999999999999999998776553

>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=97.67  E-value=0.00028  Score=55.28  Aligned_cols=64  Identities=13%  Similarity=0.163  Sum_probs=50.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      .+|+..|..|+..|.+ .  .|+..++|...+  +++...++++|+.||++|||...++-..+..+.+-
T Consensus        32 ~glt~~q~~vL~~l~~-~--~~~t~~eLa~~l--~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~   95 (140)
T 3hsr_A           32 YDLTYTGYIVLMAIEN-D--EKLNIKKLGERV--FLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQIS   95 (140)
T ss_dssp             GTCCHHHHHHHHHSCT-T--CEEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC-------CEEE
T ss_pred             cCCCHHHHHHHHHHHH-c--CCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCeEecCCCCCcceeeee
Confidence            3799999999988876 4  489999999999  99999999999999999999998887664444443

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=97.67  E-value=0.0011  Score=53.42  Aligned_cols=59  Identities=12%  Similarity=0.189  Sum_probs=53.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      -+||..|..|+..|.. +|. |+-+++|...+  ++....++++|+.||++|||...++-..+
T Consensus        27 ~gLt~~q~~vL~~L~~-~~~-~~~~~eLa~~l--~~~~~tvs~~v~~Le~~GlV~R~~~~~Dr   85 (151)
T 4aik_A           27 LELTQTHWVTLYNINR-LPP-EQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLITRHTSANDR   85 (151)
T ss_dssp             GCCCHHHHHHHHHHHH-SCT-TSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCT
T ss_pred             cCCCHHHHHHHHHHHH-cCC-CCcHHHHHHHH--CcCHHHHHHHHHHHHhCCCeEeecCCCCC
Confidence            4799999999999987 654 78889999999  99999999999999999999999887763

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.66  E-value=0.00074  Score=52.39  Aligned_cols=57  Identities=11%  Similarity=0.240  Sum_probs=50.4

Q ss_pred             CCCChHHHHHHHHH-HhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVI-RSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I-~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..| ..   +.++..++|...+  +++++.++++|+.||++|||...++-..
T Consensus        33 ~~l~~~~~~iL~~l~~~---~~~~t~~~la~~l--~~s~~~vs~~l~~L~~~glv~r~~~~~d   90 (146)
T 2fbh_A           33 LGLSQARWLVLLHLARH---RDSPTQRELAQSV--GVEGPTLARLLDGLESQGLVRRLAVAED   90 (146)
T ss_dssp             GCCTTTHHHHHHHHHHC---SSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCBTT
T ss_pred             CCCCHHHHHHHHHHHHc---CCCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCeeecCCCcc
Confidence            36899999999999 44   3579999999999  9999999999999999999999876654

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=97.64  E-value=7.2e-05  Score=59.59  Aligned_cols=72  Identities=11%  Similarity=0.074  Sum_probs=55.3

Q ss_pred             CCCChHHHHHHHHHHhhc---CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           32 DSLTDHERLIYDVIRSNK---QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~a---g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      -+|++.|..||-.|.. .   |+.++...+|..++  ++..++|+++|+.||++|+|....+-... .++.-.|+|.|-
T Consensus        28 lgLt~~e~~vll~L~~-~~~~~~~~ps~~~LA~~l--~~s~~~V~~~l~~Le~kGlI~~~~~~~~~-g~~~~~Ydl~pl  102 (128)
T 2vn2_A           28 LGLGEGELVLLLHMQS-FFEEGVLFPTPAELAERM--TVSAAECMEMVRRLLQKGMIAIEEHTDEQ-GIRNEKYTLEPL  102 (128)
T ss_dssp             TTCCHHHHHHHHHHHH-HHTTTCSSCCHHHHHHTS--SSCHHHHHHHHHHHHHTTSSEECC-----------CEECHHH
T ss_pred             cCCCHHHHHHHHHHHH-HHhcCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEeEECCC-CcEEEEEehHHH
Confidence            3799999999999986 4   67779999999999  99999999999999999999997665543 455567787664

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=97.62  E-value=0.0002  Score=56.73  Aligned_cols=63  Identities=17%  Similarity=0.186  Sum_probs=49.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.. .  .|+..++|...+  +++...++++|+.||++|||...++-..+..+.+
T Consensus        37 ~~lt~~q~~iL~~l~~-~--~~~~~~eLa~~l--~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~   99 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWE-E--NPQTLNSIGRHL--DLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLII   99 (149)
T ss_dssp             TTCCHHHHHHHHHHHH-S--SSEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEC---------CEE
T ss_pred             cCCCHHHHHHHHHHHH-C--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeee
Confidence            4799999999999988 5  689999999999  9999999999999999999999887765433333

>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=97.62  E-value=0.00084  Score=54.54  Aligned_cols=66  Identities=12%  Similarity=0.186  Sum_probs=51.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..|..|+..|.+ ++ .|+..++|...+  +++...++++|+.||++|||...++-..+..+.+-|
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 LELTQTHWVTLHNIHQ-LP-PDQSQIQLAKAI--GIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKL  114 (166)
T ss_dssp             TTCCHHHHHHHHHHHH-SC-SSEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CEEEE
T ss_pred             cCCCHHHHHHHHHHHH-cC-CCCCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEE
Confidence            4799999999999987 54 579999999999  999999999999999999999988776543333333

>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=97.61  E-value=0.00072  Score=53.21  Aligned_cols=61  Identities=13%  Similarity=0.244  Sum_probs=53.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKK   97 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK   97 (252)
                      .+|+..|..|+..|.. .|  |+-.++|...+  ++++..++++|+.||++|||....+-..+..+
T Consensus        33 ~~l~~~~~~iL~~l~~-~~--~~t~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~   93 (155)
T 1s3j_A           33 QGVTPAQLFVLASLKK-HG--SLKVSEIAERM--EVKPSAVTLMADRLEQKNLIARTHNTKDRRVI   93 (155)
T ss_dssp             TTCCHHHHHHHHHHHH-HS--EEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCTTSE
T ss_pred             cCCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeecCCCCCCceE
Confidence            4799999999999988 55  79999999999  99999999999999999999998776553333

>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=97.61  E-value=0.0005  Score=53.43  Aligned_cols=56  Identities=14%  Similarity=0.127  Sum_probs=51.2

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+..|.. .|  |+-.++|...+  +++...++++|+.||++|+|...++-..
T Consensus        30 ~l~~~~~~iL~~l~~-~~--~~~~~~la~~l--~~s~~tvs~~l~~L~~~glv~r~~~~~d   85 (145)
T 2a61_A           30 GITPAQFDILQKIYF-EG--PKRPGELSVLL--GVAKSTVTGLVKRLEADGYLTRTPDPAD   85 (145)
T ss_dssp             TCCHHHHHHHHHHHH-HC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCchhHHHHHHHHHHCCCeeecCCCCC
Confidence            699999999999988 55  79999999999  9999999999999999999999876554

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=97.60  E-value=0.00064  Score=54.24  Aligned_cols=63  Identities=8%  Similarity=0.119  Sum_probs=52.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.. .  .|+..++|...+  +++...++++|+.||++|||...++-..+..+.+
T Consensus        46 ~~lt~~q~~vL~~l~~-~--~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l  108 (159)
T 3s2w_A           46 YGIGSGQFPFLMRLYR-E--DGINQESLSDYL--KIDKGTTARAIQKLVDEGYVFRQRDEKDRRSYRV  108 (159)
T ss_dssp             GTCCTTTHHHHHHHHH-S--CSEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECC---CCEEE
T ss_pred             cCCCHHHHHHHHHHHH-C--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCCCCeeEE
Confidence            4789999999999988 5  579999999999  9999999999999999999999888766433333

>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=97.58  E-value=0.00017  Score=56.44  Aligned_cols=59  Identities=20%  Similarity=0.278  Sum_probs=54.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      -+|+..|..|+..|.. .+..|+-.++|...+  +++...++++|+.||++|||...++-..
T Consensus        33 ~~lt~~q~~vL~~l~~-~~~~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D   91 (127)
T 2frh_A           33 FSISFEEFAVLTYISE-NKEKEYYLKDIINHL--NYKQPQVVKAVKILSQEDYFDKKRNEHD   91 (127)
T ss_dssp             TCCCHHHHHHHHHHHH-TCCSEEEHHHHHHHS--SSHHHHHHHHHHHHHHTTSSCCBCCSSS
T ss_pred             cCCCHHHHHHHHHHHh-ccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCC
Confidence            4799999999999999 877899999999999  9999999999999999999999877665

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=97.58  E-value=0.00053  Score=54.52  Aligned_cols=58  Identities=9%  Similarity=0.177  Sum_probs=47.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      -+|+..|..|+..|.. .|  |+-.++|...+  +++...++++|+.||++|||...++-..+
T Consensus        45 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~is~~tvs~~l~~Le~~glv~r~~~~~d~  102 (162)
T 2fa5_A           45 YGMAIPEWRVITILAL-YP--GSSASEVSDRT--AMDKVAVSRAVARLLERGFIRRETHGDDR  102 (162)
T ss_dssp             HCCCHHHHHHHHHHHH-ST--TCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC-------
T ss_pred             cCCCHHHHHHHHHHHh-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeecCCCCC
Confidence            3699999999999988 54  89999999999  99999999999999999999987765543

>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=97.57  E-value=0.0007  Score=52.64  Aligned_cols=61  Identities=18%  Similarity=0.245  Sum_probs=53.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKH   98 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~   98 (252)
                      +|+..|..|+..|.. .|  ++-.++|...+  +++++.++++|+.||++|+|...++-..+..+.
T Consensus        34 ~l~~~~~~iL~~l~~-~~--~~~~~ela~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~   94 (142)
T 2bv6_A           34 NLTYPQFLVLTILWD-ES--PVNVKKVVTEL--ALDTGTVSPLLKRMEQVDLIKRERSEVDQREVF   94 (142)
T ss_dssp             TCCHHHHHHHHHHHH-SS--EEEHHHHHHHT--TCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEE
T ss_pred             CCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeecCCCCcceEE
Confidence            689999999999988 65  79999999999  999999999999999999999987655433333

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=97.55  E-value=0.00014  Score=58.74  Aligned_cols=59  Identities=19%  Similarity=0.200  Sum_probs=52.4

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+.+|.. .|+.|+..++|...+  ++....++++|+.||++|||....+-..
T Consensus        42 ~glt~~q~~vL~~l~~-~~~~~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D  100 (168)
T 3u2r_A           42 FELSAQQYNTLRLLRS-VHPEGMATLQIADRL--ISRAPDITRLIDRLDDRGLVLRTRKPEN  100 (168)
T ss_dssp             TTCCHHHHHHHHHHHH-HTTSCEEHHHHHHHC-----CTHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             cCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEeecCCCCC
Confidence            4799999999999999 999999999999999  9999999999999999999999877665

>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=97.53  E-value=0.00036  Score=54.30  Aligned_cols=63  Identities=21%  Similarity=0.262  Sum_probs=54.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+..|.. .|  |+..++|...+  +++++.++++|+.||++|+|...++-..+..+.+
T Consensus        25 ~~lt~~~~~iL~~l~~-~~--~~t~~~la~~l--~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~   87 (144)
T 1lj9_A           25 LSLTRGQYLYLVRVCE-NP--GIIQEKIAELI--KVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRI   87 (144)
T ss_dssp             GTCTTTHHHHHHHHHH-ST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             cCCCHHHHHHHHHHHH-Cc--CcCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeecCCCCCceeee
Confidence            3689999999999998 65  89999999999  9999999999999999999999887665444333

>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=97.51  E-value=0.0007  Score=53.35  Aligned_cols=59  Identities=10%  Similarity=0.218  Sum_probs=47.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .+|+..|..|+.+|.. .+ .++..++|...+  +++...++++|+.||++|||...++-..+
T Consensus        35 ~glt~~q~~vL~~l~~-~~-~~~t~~eLa~~l--~i~~~tvs~~l~~Le~~Glv~r~~~~~D~   93 (150)
T 3fm5_A           35 TGLRVRSYSVLVLACE-QA-EGVNQRGVAATM--GLDPSQIVGLVDELEERGLVVRTLDPSDR   93 (150)
T ss_dssp             GTCCHHHHHHHHHHHH-ST-TCCCSHHHHHHH--TCCHHHHHHHHHHHHTTTSEEC-------
T ss_pred             cCCCHHHHHHHHHHHh-CC-CCcCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeeCCcccc
Confidence            4789999999999977 44 459999999999  99999999999999999999998776653

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=97.51  E-value=0.00043  Score=53.49  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=55.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +|+..|..|+..|.+ .|  ++-.++|...+  ++++..+++.|+.||++|+|...++-..+..+.|-|
T Consensus        28 ~l~~~~~~iL~~l~~-~~--~~~~~ela~~l--~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~l   91 (142)
T 3bdd_A           28 GISLTRYSILQTLLK-DA--PLHQLALQERL--QIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWP   91 (142)
T ss_dssp             SSCHHHHHHHHHHHH-HC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEE
T ss_pred             CCCHHHHHHHHHHHh-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence            799999999999988 65  69999999999  999999999999999999999988776554444433

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=97.49  E-value=0.0011  Score=52.86  Aligned_cols=60  Identities=13%  Similarity=0.075  Sum_probs=53.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      -+||..|..|+.+|.. +.+.++-.++|...+  +++...++++|+.||++|||...++-..+
T Consensus        31 ~gLt~~q~~vL~~L~~-~~~~~~t~~eLa~~l--~~~~~tvs~~v~~Le~~Glv~r~~~~~Dr   90 (147)
T 4b8x_A           31 YGLTFARYEALVLLTF-SKSGELPMSKIGERL--MVHPTSVTNTVDRLVRSGLVAKRPNPNDG   90 (147)
T ss_dssp             GTCCHHHHHHHHHHHT-SGGGEEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECC---
T ss_pred             cCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHhCCCEEEeecCCcC
Confidence            4799999999999988 878889999999999  99999999999999999999999887653

>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=97.48  E-value=0.00048  Score=53.20  Aligned_cols=58  Identities=19%  Similarity=0.213  Sum_probs=52.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .+|+..|..|+..|.+ .|  |+-.++|...+  +++++.++++|+.||++|+|....+-..+
T Consensus        30 ~~lt~~~~~iL~~l~~-~~--~~~~~~la~~l--~~~~~tvs~~l~~L~~~gli~r~~~~~d~   87 (138)
T 1jgs_A           30 LDITAAQFKVLCSIRC-AA--CITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDK   87 (138)
T ss_dssp             TTSCHHHHHHHHHHHH-HS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECTTCS
T ss_pred             cCCCHHHHHHHHHHHh-cC--CCCHHHHHHHH--CCChHHHHHHHHHHHHCCCEEecCCcccC
Confidence            4799999999999988 55  78999999999  99999999999999999999998766553

>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=97.48  E-value=0.00064  Score=50.12  Aligned_cols=61  Identities=21%  Similarity=0.414  Sum_probs=52.4

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      +|++.+..|+.+|.. .|  ++-.++|...+  +++...++++|+.|+++|+|...+..  .+|..|.
T Consensus        17 ~l~~~~~~il~~l~~-~~--~~s~~ela~~l--~is~~tv~~~l~~L~~~glv~~~~~~--~~r~~~~   77 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE-RG--GMRVSEIAREL--DLSARFVRDRLKVLLKRGFVRREIVE--KGWVGYI   77 (109)
T ss_dssp             CCCHHHHHHHHHHHH-HC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEE--SSSEEEE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEeec--CCceEEE
Confidence            689999999999987 54  58999999999  99999999999999999999998766  3444443

>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=97.47  E-value=0.0017  Score=50.35  Aligned_cols=61  Identities=15%  Similarity=0.130  Sum_probs=51.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKH   98 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~   98 (252)
                      .+|+..|..|+..|.    +.|+-.++|...+  +++...++++|+.||++|+|...++-..+..+.
T Consensus        33 ~~l~~~~~~iL~~l~----~~~~~~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~   93 (146)
T 2gxg_A           33 LNLSYLDFLVLRATS----DGPKTMAYLANRY--FVTQSAITASVDKLEEMGLVVRVRDREDRRKIL   93 (146)
T ss_dssp             TTCCHHHHHHHHHHT----TSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEE
T ss_pred             cCCCHHHHHHHHHHh----cCCcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeecCCCCCceEE
Confidence            368999988888875    5689999999999  999999999999999999999987765533333

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=97.47  E-value=0.00029  Score=55.28  Aligned_cols=63  Identities=19%  Similarity=0.201  Sum_probs=49.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      -+|+..|..|+..|.. .|  |+..++|...+  ++++..++++|+.||++|||...++-..+..+.+
T Consensus        36 ~~l~~~~~~iL~~l~~-~~--~~t~~ela~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~   98 (148)
T 3nrv_A           36 FGIGMTEWRIISVLSS-AS--DCSVQKISDIL--GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAI   98 (148)
T ss_dssp             GTCCHHHHHHHHHHHH-SS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC---------CCB
T ss_pred             cCCCHHHHHHHHHHHc-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEe
Confidence            3799999999999999 77  99999999999  9999999999999999999999877665434333

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=97.44  E-value=0.00069  Score=53.72  Aligned_cols=57  Identities=9%  Similarity=0.141  Sum_probs=47.4

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+..|.. . +.|+..++|...+  +++...+++.|+.||++|||...++-..
T Consensus        44 ~l~~~~~~iL~~L~~-~-~~~~~~~ela~~l--~i~~~tvs~~l~~Le~~Gli~r~~~~~d  100 (160)
T 3boq_A           44 GLSLAKFDAMAQLAR-N-PDGLSMGKLSGAL--KVTNGNVSGLVNRLIKDGMVVKAMSADD  100 (160)
T ss_dssp             SCCHHHHHHHHHHHH-C-TTCEEHHHHHHHC--SSCCSCHHHHHHHHHHHTSEEEC-----
T ss_pred             CCCHHHHHHHHHHHH-c-CCCCCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeecCCCC
Confidence            689999999999954 3 3489999999999  9999999999999999999999876655

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=97.41  E-value=0.00027  Score=57.32  Aligned_cols=72  Identities=10%  Similarity=0.105  Sum_probs=58.3

Q ss_pred             CCChHHHHHHHHHHh--hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           33 SLTDHERLIYDVIRS--NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~--~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      +||+.|.+|+-.|..  ..|+.++...+|..++  ++..++|.++|.+|++||+|.-...... +-+..-.|+|+|-
T Consensus        29 gLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~--~~s~~~v~~~L~~L~~KGlI~i~~~~d~-~g~~~~~ydL~pL  102 (135)
T 2v79_A           29 GLNETELILLLKIKMHLEKGSYFPTPNQLQEGM--SISVEECTNRLRMFIQKGFLFIEECEDQ-NGIKFEKYSLQPL  102 (135)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTS--SSCHHHHHHHHHHHHHHTSCEEEEEECT-TCCEEEEEECHHH
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEeEecC-CCceEEEeeHHHH
Confidence            699999998877776  1378889999999999  9999999999999999999997443333 3445567788664

>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=97.40  E-value=0.00091  Score=48.39  Aligned_cols=57  Identities=18%  Similarity=0.212  Sum_probs=49.6

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ..+||+.|..|+.+|.+ .  .++..++|...++.  ++..+.+++.|+.||.+|+|...++
T Consensus         4 ~~~lt~~e~~vL~~L~~-~--~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A            4 IPQISDAELEVMKVIWK-H--SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCHHHHHHHHHHHT-S--SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCCCCHHHHHHHHHHHc-C--CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec
Confidence            45799999999999987 4  48999999999832  3789999999999999999999864

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=97.38  E-value=0.00045  Score=54.04  Aligned_cols=65  Identities=15%  Similarity=0.189  Sum_probs=55.4

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+..|..|+..|.. .|  |+..++|...+  +++...++++|+.||++|||....+-..+..+.+-|
T Consensus        27 ~~lt~~q~~iL~~l~~-~~--~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~L   91 (145)
T 3g3z_A           27 QDLNYNLFAVLYTLAT-EG--SRTQKHIGEKW--SLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSL   91 (145)
T ss_dssp             TTCCHHHHHHHHHHHH-HC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeE
Confidence            4799999999999988 66  59999999999  999999999999999999999987766543444433

>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=97.37  E-value=0.00068  Score=56.31  Aligned_cols=60  Identities=12%  Similarity=0.193  Sum_probs=55.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG   95 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~   95 (252)
                      +||..|..|+..|.. ..+.|+-.++|...+  +++...++++|+.||++|||...++-..+.
T Consensus        38 ~lt~~q~~vL~~L~~-~~~~~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~DrR   97 (189)
T 3nqo_A           38 ILTSRQYMTILSILH-LPEEETTLNNIARKM--GTSKQNINRLVANLEKNGYVDVIPSPHDKR   97 (189)
T ss_dssp             SSCHHHHHHHHHHHH-SCGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCSS
T ss_pred             cCCHHHHHHHHHHHh-ccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCCCCCC
Confidence            599999999999999 888899999999999  999999999999999999999988876643

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.37  E-value=0.00052  Score=53.04  Aligned_cols=57  Identities=9%  Similarity=0.207  Sum_probs=51.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..|.. .|  ++-.++|...+  ++++..++++|+.||++|+|....+-..
T Consensus        32 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~~s~~~vs~~l~~Le~~glv~r~~~~~d   88 (142)
T 2fbi_A           32 HGLTEQQWRVIRILRQ-QG--EMESYQLANQA--CILRPSMTGVLARLERDGIVRRWKAPKD   88 (142)
T ss_dssp             HTCCHHHHHHHHHHHH-HC--SEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             cCCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEeecCCCC
Confidence            3689999999999988 65  69999999999  9999999999999999999999876554

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=97.35  E-value=0.00071  Score=53.33  Aligned_cols=62  Identities=19%  Similarity=0.233  Sum_probs=52.1

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee--eeccccCCeeeE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE--VVNIHNKGKKHL   99 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~--vksv~~~~rK~Y   99 (252)
                      +|+..|..|+..|.. .|  |+-.++|...+  ++++..++++|+.||++|||..  .++-..+..+.+
T Consensus        38 ~lt~~~~~iL~~l~~-~~--~~t~~eLa~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~  101 (154)
T 2qww_A           38 GLTIQQLAMINVIYS-TP--GISVADLTKRL--IITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTL  101 (154)
T ss_dssp             TCCHHHHHHHHHHHH-ST--TEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEE
T ss_pred             CCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEe
Confidence            689999999999998 64  69999999999  9999999999999999999998  776655433333

>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=97.35  E-value=0.00042  Score=54.14  Aligned_cols=64  Identities=14%  Similarity=0.183  Sum_probs=55.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      .+|+..|..|+..|.. .|  ++-.++|...+  ++++..++++|+.||++|||...++-..+..+.+.
T Consensus        36 ~~l~~~~~~iL~~l~~-~~--~~~~~~la~~l--~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~   99 (147)
T 1z91_A           36 LNITYPQYLALLLLWE-HE--TLTVKKMGEQL--YLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLIS   99 (147)
T ss_dssp             TCCCHHHHHHHHHHHH-HS--EEEHHHHHHTT--TCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEE
Confidence            4799999999999998 76  89999999999  99999999999999999999998766554344333

>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=97.33  E-value=0.0014  Score=51.68  Aligned_cols=55  Identities=13%  Similarity=0.238  Sum_probs=46.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee--cccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV--NIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk--sv~~   93 (252)
                      +||..|..|+..| . .  .|+..++|...+  ++++..++++|+.||++|||...+  +-..
T Consensus        35 ~lt~~q~~iL~~l-~-~--~~~t~~eLa~~l--~~~~~~vs~~l~~Le~~Glv~r~~~~~~~D   91 (151)
T 3kp7_A           35 GISAEQSHVLNML-S-I--EALTVGQITEKQ--GVNKAAVSRRVKKLLNAELVKLEKPDSNTD   91 (151)
T ss_dssp             TCCHHHHHHHHHH-H-H--SCBCHHHHHHHH--CSCSSHHHHHHHHHHHTTSEEC--------
T ss_pred             CCCHHHHHHHHHH-H-c--CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeeCCCCCCC
Confidence            7899999999999 6 3  579999999999  999999999999999999999865  5444

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=97.33  E-value=0.00078  Score=51.88  Aligned_cols=57  Identities=16%  Similarity=0.251  Sum_probs=51.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..|.. .  .|+..++|...+  +++++.++++|+.||++|+|...++-..
T Consensus        25 ~~l~~~~~~iL~~l~~-~--~~~~~~ela~~l--~~s~~tvs~~l~~L~~~glv~~~~~~~d   81 (138)
T 3bpv_A           25 LNLTDAQVACLLRIHR-E--PGIKQDELATFF--HVDKGTIARTLRRLEESGFIEREQDPEN   81 (138)
T ss_dssp             GTCCHHHHHHHHHHHH-S--TTCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             cCCCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeecCCCC
Confidence            3789999999999988 5  579999999999  9999999999999999999999876554

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=97.28  E-value=0.00071  Score=52.85  Aligned_cols=55  Identities=11%  Similarity=0.193  Sum_probs=50.7

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+..|.. .|.   ..++|...+  ++++..+++.|+.||++|+|...++-..
T Consensus        34 ~lt~~~~~iL~~l~~-~~~---~~~~la~~l--~~~~~tvs~~l~~Le~~Glv~r~~~~~D   88 (144)
T 3f3x_A           34 NLSYLDFSILKATSE-EPR---SMVYLANRY--FVTQSAITAAVDKLEAKGLVRRIRDSKD   88 (144)
T ss_dssp             SCCHHHHHHHHHHHH-SCE---EHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             CCCHHHHHHHHHHHH-CCC---CHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCC
Confidence            689999999999998 664   999999999  9999999999999999999999877665

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=97.27  E-value=0.00054  Score=53.43  Aligned_cols=63  Identities=21%  Similarity=0.319  Sum_probs=48.5

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .-+||..|..|+..|.. .|   +-.++|...+  +++.+.++++|+.||++|||...++-..+..+.|
T Consensus        33 ~~~lt~~~~~iL~~l~~-~~---~t~~eLa~~l--~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~   95 (146)
T 3tgn_A           33 EVALTNTQEHILMLLSE-ES---LTNSELARRL--NVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFY   95 (146)
T ss_dssp             SSCCCHHHHHHHHHHTT-CC---CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC----------CC
T ss_pred             ccCCCHHHHHHHHHHHh-CC---CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEE
Confidence            35799999999999988 65   9999999999  9999999999999999999999877655433333

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=97.27  E-value=0.00055  Score=54.14  Aligned_cols=63  Identities=10%  Similarity=0.228  Sum_probs=50.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      .+|+..|..|+.+|.. .|  |+..++|...+  +++...++++|+.||++|+|....+-..+..+.+
T Consensus        39 ~~lt~~~~~iL~~l~~-~~--~~t~~ela~~l--~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~  101 (155)
T 3cdh_A           39 QGLRVPEWRVLACLVD-ND--AMMITRLAKLS--LMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRV  101 (155)
T ss_dssp             TTCCHHHHHHHHHHSS-CS--CBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECC------CCCE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEe
Confidence            3789999999999977 54  79999999999  9999999999999999999998776655333333

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=97.27  E-value=0.00095  Score=52.63  Aligned_cols=58  Identities=19%  Similarity=0.191  Sum_probs=49.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .+|+..|..|+..|.. .|  ++-.++|...+  +++...++++|+.||++|||...++-..+
T Consensus        43 ~~l~~~~~~iL~~l~~-~~--~~t~~ela~~l--~~s~~tvs~~l~~Le~~glv~r~~~~~d~  100 (153)
T 2pex_A           43 LDLTYPQYLVMLVLWE-TD--ERSVSEIGERL--YLDSATLTPLLKRLQAAGLVTRTRAASDE  100 (153)
T ss_dssp             TTCCHHHHHHHHHHHH-SC--SEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC-----
T ss_pred             CCCCHHHHHHHHHHHh-CC--CcCHHHHHHHh--CCCcccHHHHHHHHHHCCCEeecCCcccC
Confidence            4799999999999988 54  79999999999  99999999999999999999998765543

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=97.22  E-value=0.00048  Score=67.92  Aligned_cols=124  Identities=9%  Similarity=0.078  Sum_probs=51.7

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh-----cCCeeeeeccccCCeeeEEecccccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN-----KSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~-----k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      .++..+.+|+.+|.+ .+  -|..++|+..+  +++..++.+.|+.|.+     +|||....       ..|+|..-  .
T Consensus       427 ~~~~~~~~iL~~l~~-~~--~it~~~la~~l--~~s~~~~~~~L~~L~~~~~~~~glie~~g-------~~y~L~~~--~  492 (583)
T 3lmm_A          427 QDDYRIAIVLYLLFQ-RP--FITIDVVARGL--QSGKEAARNALEAARQTTVAGAPLIIAHD-------GVWLLGNA--C  492 (583)
T ss_dssp             TTCHHHHHHHHHHHH-SS--SBCHHHHHHHH--TSCHHHHHHHHHHHHTCEETTEESEEEET-------TEEEECHH--H
T ss_pred             ccchhHHHHHHHHHH-CC--CcCHHHHHHHh--CcCHHHHHHHHHHHHhhhccccceEEEeC-------CEEEECHH--H
Confidence            456788999999998 44  59999999999  9999999999999988     88999963       35887541  0


Q ss_pred             CCccCC--------ccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCe
Q 025493          108 KDISGG--------AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQ  179 (252)
Q Consensus       108 ~eiTGG--------~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgk  179 (252)
                      .+.+|.        .+|..  +|.   +.+.+.++.||+.++..|..||.+-+.        ++..++..+|+.|+-+|+
T Consensus       493 ~~~~~~~~~~~~~~~~~~~--~~~---~~~~~~I~~~l~~~g~it~~di~~l~~--------ls~~qa~~~L~~Lv~~G~  559 (583)
T 3lmm_A          493 REILRKVEPSPFSPVRYLS--TDQ---AELTNAAMLWLSEVGDLATSDLMAMCG--------VSRGTAKACVDGLVDEER  559 (583)
T ss_dssp             HHHHTSCC------------------------------------------------------------------------
T ss_pred             HHHhccccccccccccccc--CCh---hHHHHHHHHHHHHcCCcCHHHHHHHHC--------CCHHHHHHHHHHHHHCCc
Confidence            111221        12321  221   356678999999998888888887654        678889999999999999


Q ss_pred             eEEE
Q 025493          180 IMEV  183 (252)
Q Consensus       180 IE~v  183 (252)
                      |+++
T Consensus       560 l~~~  563 (583)
T 3lmm_A          560 VVAV  563 (583)
T ss_dssp             ----
T ss_pred             EEEe
Confidence            9875

>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=97.19  E-value=0.00096  Score=48.91  Aligned_cols=60  Identities=15%  Similarity=0.209  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.|+.|+.++.+|+-.+++..++|.+++  +++.+.|++.|+.||++|+|+.+-  .  ++-.|.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~L--gvs~~tV~~~L~~L~~~G~I~~~g--~--~~~~W~i   73 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQKEA--G--TPPLWKI   73 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHH--CCCHHHHHHHHHHHHHHTSEEEEC--S--SSCEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecC--C--CCCceEe
Confidence            3468899999994448899999999999  999999999999999999999874  1  2345655

>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=97.15  E-value=0.0016  Score=50.47  Aligned_cols=63  Identities=19%  Similarity=0.265  Sum_probs=52.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      +++..+..|+.++.. + +.++..++|..++  +++.+.++++|+.||++|+|...++-.. .|.+|+
T Consensus        23 gl~~~~~~il~~L~~-~-~~~~t~~ela~~l--~~~~stvs~~l~~L~~~G~v~r~~~~~d-~r~~~~   85 (152)
T 1ku9_A           23 GLNKSVGAVYAILYL-S-DKPLTISDIMEEL--KISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYE   85 (152)
T ss_dssp             TCCHHHHHHHHHHHH-C-SSCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEE
T ss_pred             CCChhHHHHHHHHHH-c-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEecCCC-ceEEEe
Confidence            689999999999954 3 3689999999999  9999999999999999999998765433 344444

>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=97.13  E-value=0.00067  Score=63.46  Aligned_cols=65  Identities=14%  Similarity=0.239  Sum_probs=58.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      -+||..|..|+..|.+ ....|+.+++|..++  ++....++++|+.||++|||.+.++-+- .|.+++
T Consensus       400 ~~lt~~q~~vl~~l~~-~~~~~~~~~~l~~~~--~~~~~~~t~~~~~le~~g~v~r~~~~~D-~R~~~i  464 (487)
T 1hsj_A          400 FNLNYEEIYILNHILR-SESNEISSKEIAKCS--EFKPYYLTKALQKLKDLKLLSKKRSLQD-ERTVIV  464 (487)
T ss_dssp             CCCCHHHHHHHHHHHT-CSCSEEEHHHHHHSS--CCCHHHHHHHHHHHHTTTTSCCEECCSS-SSCCEE
T ss_pred             cCCCHHHHHHHHHHHh-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeecCCCCC-CCeEEE
Confidence            4799999999999999 766899999999999  9999999999999999999999998776 455544

>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=97.13  E-value=0.0011  Score=58.67  Aligned_cols=65  Identities=14%  Similarity=0.190  Sum_probs=57.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      -+||..|..|+..|.. .++.++.+++|...+  ++.+..++++|+.||++|||....+-.- .|.+++
T Consensus       154 ~gLt~~q~~vL~~L~~-~~~~~~t~~eLa~~l--~i~~~tvt~~v~rLe~~GlV~R~~~~~D-rR~~~i  218 (250)
T 1p4x_A          154 LTLSFVEFTILAIITS-QNKNIVLLKDLIETI--HHKYPQTVRALNNLKKQGYLIKERSTED-ERKILI  218 (250)
T ss_dssp             CSSCHHHHHHHHHHHT-TTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEEECSSS-TTCEEE
T ss_pred             CCCCHHHHHHHHHHHh-CCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCEEeeCCCCC-CCeEEE
Confidence            4799999999999999 887789999999999  9999999999999999999999988775 344443

>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=97.12  E-value=0.00081  Score=52.45  Aligned_cols=61  Identities=8%  Similarity=0.145  Sum_probs=50.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK   96 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r   96 (252)
                      .+|+..|..|+..|.. + +.|+..++|...+  ++++..++++|+.||++|||....+-..+..
T Consensus        31 ~~l~~~~~~iL~~l~~-~-~~~~~~~~la~~l--~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~   91 (147)
T 2hr3_A           31 DPVQFSQLVVLGAIDR-L-GGDVTPSELAAAE--RMRSSNLAALLRELERGGLIVRHADPQDGRR   91 (147)
T ss_dssp             CHHHHHHHHHHHHHHH-T-TSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEC------C
T ss_pred             cCCCHHHHHHHHHHHH-c-CCCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeCCCCCCCCc
Confidence            4789999999999987 5 5689999999999  9999999999999999999999877655333

>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=97.11  E-value=0.002  Score=47.16  Aligned_cols=62  Identities=13%  Similarity=0.145  Sum_probs=48.8

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ++-...|+..+.+ .|  ++...+|...+  ++++..+++.|+.||++|+|...+....+.++.|-|
T Consensus        15 ~~~~~~iL~~L~~-~~--~~~~~ela~~l--~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~l   76 (100)
T 1ub9_A           15 NPVRLGIMIFLLP-RR--KAPFSQIQKVL--DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             SHHHHHHHHHHHH-HS--EEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             ChHHHHHHHHHHh-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEE
Confidence            3456677887866 44  68999999999  999999999999999999999877664434444444

>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=97.09  E-value=0.0041  Score=45.75  Aligned_cols=57  Identities=16%  Similarity=0.169  Sum_probs=46.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      .+|++.+..++..+.. . +.++-..+|...+  +++.+.++++|+.|+++|+|...+.-.
T Consensus        17 ~~l~~~~~~~l~~l~~-~-~~~~t~~ela~~l--~is~~tv~~~l~~L~~~g~v~~~~~~~   73 (109)
T 2d1h_A           17 YKITDTDVAVLLKMVE-I-EKPITSEELADIF--KLSKTTVENSLKKLIELGLVVRTKTEG   73 (109)
T ss_dssp             HTCCHHHHHHHHHHHH-H-CSCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC--
T ss_pred             hcCCHHHHHHHHHHHH-c-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeecccc
Confidence            4688887766655544 3 4579999999999  999999999999999999999987543

>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=97.05  E-value=0.0013  Score=48.82  Aligned_cols=55  Identities=18%  Similarity=0.219  Sum_probs=48.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHH----HHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDM----KRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~di----k~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .+|+..|..|+..|.+ .  .|+..++|    ...+  ++++..++++|+.||++|||....+-
T Consensus         4 ~~lt~~q~~iL~~l~~-~--~~~~~~el~~~la~~l--~is~~tvs~~l~~Le~~gli~r~~~~   62 (99)
T 1tbx_A            4 TPFFYPEAIVLAYLYD-N--EGIATYDLYKKVNAEF--PMSTATFYDAKKFLIQEGFVKERQER   62 (99)
T ss_dssp             CSSBCHHHHHHHHHTT-C--TTCBHHHHHHHHHTTS--CCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCHHHHHHHHHHHH-c--CCcCHHHHHHHHHHHc--CCCHHHHHHHHHHHHHCCCEEEEecC
Confidence            3688899999998876 4  57899999    8889  99999999999999999999987653

>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=97.04  E-value=0.0029  Score=54.44  Aligned_cols=118  Identities=11%  Similarity=0.179  Sum_probs=81.9

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccH--HHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWT--RDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKD  109 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~--~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~e  109 (252)
                      +.||+-+..++..|.. .+..|+..  ++|..++  ++..+.++++|+.||++|||...++     + .+.|   +|.  
T Consensus         2 ~~lt~~~e~~L~~L~~-l~~~~~~~~~~~La~~l--~vs~~tvs~~l~~Le~~GlV~r~~~-----~-~v~L---T~~--   67 (230)
T 1fx7_A            2 NELVDTTEMYLRTIYD-LEEEGVTPLRARIAERL--DQSGPTVSQTVSRMERDGLLRVAGD-----R-HLEL---TEK--   67 (230)
T ss_dssp             CTTSSHHHHHHHHHHH-HHHHTSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECTT-----S-CEEE---CHH--
T ss_pred             CCCCHHHHHHHHHHHH-HhhcCCCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCC-----c-cEEE---CHH--
Confidence            4688877788888877 55568888  9999999  9999999999999999999998653     2 2222   221  


Q ss_pred             ccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHh
Q 025493          110 ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVV  175 (252)
Q Consensus       110 iTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLV  175 (252)
                               |.=-.+-+....+....|+...-..+.+++++......   -.+|++++++|.+.|-
T Consensus        68 ---------G~~~~~~~~~~~~~~e~~l~~~lg~~~~~~~~~a~~le---~~ls~e~~~~L~~~L~  121 (230)
T 1fx7_A           68 ---------GRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWE---HVMSEDVERRLVKVLN  121 (230)
T ss_dssp             ---------HHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHT---TTCCHHHHHHHHHHTT
T ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH---hcCCHHHHHHHHHHhC
Confidence                     11111122233344567777666778888877654322   2478999999988774

>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=97.04  E-value=0.0022  Score=47.70  Aligned_cols=61  Identities=15%  Similarity=0.208  Sum_probs=50.9

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +-++.|+.+|.+|+-.+++-.++|.+++  +++.+.|++.|+.||+.|+|+.+.    .++-.|.+.
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~L--gvsr~tV~~~L~~Le~~G~I~~~g----~~~~~W~i~   70 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQKEA----GTPPLWKIA   70 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEES----SSSCEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecC----CCCCeeEEe
Confidence            4577899999994437899999999999  999999999999999999998873    233567664

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=96.98  E-value=0.0011  Score=51.05  Aligned_cols=57  Identities=12%  Similarity=0.135  Sum_probs=48.8

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ..+|++.|..|+.+|-+ .|  ++..++|..+++.  ++..+.|+++|+.||+||+|+..++
T Consensus        30 ~~~LT~~e~~VL~~L~~-~~--~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~   88 (99)
T 2k4b_A           30 EFNVSNAELIVMRVIWS-LG--EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKE   88 (99)
T ss_dssp             -CCCCCSCSHHHHHHHH-HS--CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEE
T ss_pred             CCCCCHHHHHHHHHHHh-CC--CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeC
Confidence            44799999999999998 65  8999999999822  3678999999999999999999764

>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=96.95  E-value=0.0018  Score=54.93  Aligned_cols=57  Identities=11%  Similarity=0.063  Sum_probs=50.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+.+|.. .|  |+-.++|...+  +++...++++|+.||++|||...++-..
T Consensus        44 ~gLt~~q~~iL~~L~~-~~--~~t~~eLa~~l--~i~~stvs~~l~~Le~~GlV~r~~~~~D  100 (207)
T 2fxa_A           44 YDLNINEHHILWIAYQ-LN--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLRFSKRLND  100 (207)
T ss_dssp             GTCCHHHHHHHHHHHH-HT--SEEHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEECC---
T ss_pred             cCCCHHHHHHHHHHHH-CC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCCCC
Confidence            4799999999999988 65  89999999999  9999999999999999999999887665

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=96.88  E-value=0.00072  Score=55.39  Aligned_cols=59  Identities=12%  Similarity=0.131  Sum_probs=51.1

Q ss_pred             CCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..|.. .|. .|+-.++|...+  ++++..+++.|+.||++|||...++-..
T Consensus        65 ~glt~~~~~iL~~L~~-~~~~~~~t~~eLa~~l--~is~~tvs~~l~~Le~~GlV~r~~~~~D  124 (181)
T 2fbk_A           65 SGLNAAGWDLLLTLYR-SAPPEGLRPTELSALA--AISGPSTSNRIVRLLEKGLIERREDERD  124 (181)
T ss_dssp             TTCCHHHHHHHHHHHH-HCCSSCBCHHHHHHHC--SCCSGGGSSHHHHHHHHTSEECCC----
T ss_pred             cCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCcCEEecCCCCC
Confidence            4799999999999999 765 589999999999  9999999999999999999999776554

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=96.82  E-value=0.026  Score=43.82  Aligned_cols=56  Identities=18%  Similarity=0.265  Sum_probs=45.1

Q ss_pred             CCCChHHHHHHHHHHhhc-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           32 DSLTDHERLIYDVIRSNK-QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~a-g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .+|+..+..++..|...+ .+.++..++|..++  ++++..++++|+.||++|||...+
T Consensus         9 ~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l--~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A            9 SNLSRREFSYLLTIKRYNDSGEGAKINRIAKDL--KIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             --CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             hhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHh--CCChHHHHHHHHHHHHCCCEEecC
Confidence            467887776766665412 35689999999999  999999999999999999999854

>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=96.80  E-value=0.0023  Score=47.58  Aligned_cols=51  Identities=14%  Similarity=0.191  Sum_probs=41.5

Q ss_pred             CCChHHHHHHHHHHh-hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493           33 SLTDHERLIYDVIRS-NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI   85 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~-~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI   85 (252)
                      .|+.-+..|+..|.. ..|+..+..++|...+  +++...++++|+.||++|||
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l--~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKV--NSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHTTSE
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCcCc
Confidence            567767666666644 1234459999999999  99999999999999999999

>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=96.68  E-value=0.0087  Score=47.78  Aligned_cols=58  Identities=12%  Similarity=0.226  Sum_probs=50.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG   95 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~   95 (252)
                      .|++-+..|+.++.+ .|  .+..++|..++  |++...+.+.|+.||++|+|+.+...-.+.
T Consensus         4 ~ld~~~~~iL~~L~~-~~--~~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~~   61 (150)
T 2w25_A            4 ALDDIDRILVRELAA-DG--RATLSELATRA--GLSVSAVQSRVRRLESRGVVQGYSARINPE   61 (150)
T ss_dssp             CCCHHHHHHHHHHHH-CT--TCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECTG
T ss_pred             ccCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEeccChh
Confidence            388889999999988 54  58999999999  999999999999999999999888765543

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=96.64  E-value=0.0074  Score=44.52  Aligned_cols=68  Identities=13%  Similarity=0.232  Sum_probs=50.9

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCCC
Q 025493          131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGG  210 (252)
Q Consensus       131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~~  210 (252)
                      +.|+++|+.++.+|++|+++.+        .+|+.-|+.-|+.|+-.|+|++++..|.                      
T Consensus         5 ~~Il~~L~~~g~vsv~eLa~~l--------~VS~~TIRrdL~~Le~~G~l~R~~~~Gg----------------------   54 (78)
T 1xn7_A            5 IQVRDLLALRGRMEAAQISQTL--------NTPQPMINAMLQQLESMGKAVRIQEEPD----------------------   54 (78)
T ss_dssp             HHHHHHHHHSCSBCHHHHHHHT--------TCCHHHHHHHHHHHHHHTSEEEECCCCC----------------------
T ss_pred             HHHHHHHHHcCCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEecCcCC----------------------
Confidence            4677777777888888877754        4788999999999999999999853221                      


Q ss_pred             CCCCCCCcccCCCCCCCccccCCC
Q 025493          211 GEPKTGSSASVPCGVCPQINFCTP  234 (252)
Q Consensus       211 ~~~~~~~l~~vPCg~CPv~~~C~~  234 (252)
                            +-..-.|+.||--..|.+
T Consensus        55 ------aC~~g~C~~C~~~~~c~~   72 (78)
T 1xn7_A           55 ------GCLSGSCKSCPEGKACLR   72 (78)
T ss_dssp             ------CCCCSSCCCCCCCCCCCC
T ss_pred             ------CCCCCCCCCCCCCCCCCc
Confidence                  111126999999888864

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=96.60  E-value=0.0095  Score=43.48  Aligned_cols=58  Identities=12%  Similarity=0.200  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.+..|+.+|.+   +.++...+|...+  ++++..+++.|+.|++.|+|...+.   ..++.|-+
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            456667777744   3478999999999  9999999999999999999998752   33444544

>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=96.59  E-value=0.01  Score=47.15  Aligned_cols=56  Identities=18%  Similarity=0.299  Sum_probs=49.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .|++-++.|+.++.+ .|  .+..++|..++  |++...+.+.|+.||++|+|+.....-+
T Consensus         2 ~ld~~d~~il~~L~~-~~--~~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d   57 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK-DS--RLSMRELGRKI--KLSPPSVTERVRQLESFGIIKQYTLEVD   57 (144)
T ss_dssp             CCCHHHHHHHHHHHH-CS--CCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEEC
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEecccC
Confidence            388889999999988 44  58999999999  9999999999999999999998765443

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=96.56  E-value=0.0056  Score=43.06  Aligned_cols=45  Identities=24%  Similarity=0.299  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK   86 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK   86 (252)
                      |..||+.|++ +|. =|-.++..++.  +.....|-++|++||+||||+
T Consensus        12 e~~lL~yIr~-sGG-ildI~~~a~ky--gV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           12 ERELLDYIVN-NGG-FLDIEHFSKVY--GVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHH-TTS-EEEHHHHHHHH--CCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHH-cCC-EEeHHHHHHHh--CCCHHHHHHHHHHHHHCCCee
Confidence            5689999999 552 25678888999  999999999999999999997

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.53  E-value=0.016  Score=41.74  Aligned_cols=71  Identities=10%  Similarity=0.070  Sum_probs=50.5

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccC
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSE  118 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d  118 (252)
                      ..|+.++.+ .|  ++..++|...+  +++.+.+.+.|+.|++.|+|..... .......|.+.   +.....=.++|+.
T Consensus         3 ~~Il~~L~~-~~--~~s~~eLa~~l--gvs~~tv~r~L~~L~~~GlI~~~~~-~~gr~~~y~l~---~~~~~~~~~~~~~   73 (81)
T 2htj_A            3 NEILEFLNR-HN--GGKTAEIAEAL--AVTDYQARYYLLLLEKAGMVQRSPL-RRGMATYWFLK---GEKQAGQSCSSTT   73 (81)
T ss_dssp             HHHHHHHHH-SC--CCCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEECC-SSSSSCEEEES---SCSSSSCGGGGCS
T ss_pred             HHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecc-CCCCcEEEEEC---hhhhccHHHHHhH
Confidence            467888888 54  58999999999  9999999999999999999986543 22223344442   2222222566754

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=96.50  E-value=0.012  Score=48.66  Aligned_cols=72  Identities=19%  Similarity=0.311  Sum_probs=56.3

Q ss_pred             CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe----eeEEecccc
Q 025493           30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK----KHLMAVEFE  105 (252)
Q Consensus        30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r----K~YmL~~le  105 (252)
                      ....|++-++.|+.++.+ .|  .+..++|.+++  |++...+.+.|+.||++|+|+.+..+-++.+    ..|+...++
T Consensus        11 ~~~~ld~~d~~IL~~L~~-~~--~~s~~eLA~~l--glS~~tv~~~l~~L~~~G~I~~~~~~~d~~~lG~~~a~v~v~~~   85 (171)
T 2ia0_A           11 SEIHLDDLDRNILRLLKK-DA--RLTISELSEQL--KKPESTIHFRIKKLQERGVIERYTIILGEQLKPKHLALIVLEVG   85 (171)
T ss_dssp             ---CCCHHHHHHHHHHHH-CT--TCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECTTTSCSEEEEEEEEES
T ss_pred             CcCCCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecccCCHHHhhcceEEEEEEEC
Confidence            345689999999999988 54  58999999999  9999999999999999999998776544332    345554554


Q ss_pred             c
Q 025493          106 P  106 (252)
Q Consensus       106 P  106 (252)
                      |
T Consensus        86 ~   86 (171)
T 2ia0_A           86 K   86 (171)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=96.40  E-value=0.096  Score=40.77  Aligned_cols=113  Identities=12%  Similarity=0.170  Sum_probs=89.7

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGG  113 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG  113 (252)
                      ++++|..+.+.|.+.-+..|.|.+|+-...  +++...+.+.|+.|...|.|..+.      .-+|              
T Consensus         1 ~~~~~~~l~~~i~~~~~~~p~~~~~la~~~--~~~~~~~~~~l~~l~~~G~l~~i~------~~~~--------------   58 (121)
T 2pjp_A            1 FSEEQQAIWQKAEPLFGDEPWWVRDLAKET--GTDEQAMRLTLRQAAQQGIITAIV------KDRY--------------   58 (121)
T ss_dssp             CCHHHHHHHHHHGGGCSSSCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEE------TTEE--------------
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec------CCce--------------
Confidence            456666667766663556899999999999  999999999999999999988874      2233              


Q ss_pred             ccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          114 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       114 ~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                             |..+.++.+.+.+..++..++..|+.+..+.+   |     +|-.=.-.||+-|=-.|...++
T Consensus        59 -------~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~l---g-----~sRK~ai~lLE~~Dr~g~TrR~  113 (121)
T 2pjp_A           59 -------YRNDRIVEFANMIRDLDQECGSTCAADFRDRL---G-----VGRKLAIQILEYFDRIGFTRRR  113 (121)
T ss_dssp             -------EEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHH---T-----SCHHHHHHHHHHHHHHTSEEEE
T ss_pred             -------ECHHHHHHHHHHHHHHHHHCCCccHHHHHHHH---C-----CcHHHHHHHHHHHhhcCCeEee
Confidence                   45788999999999999999999999999988   3     5566666777777666655543

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=96.38  E-value=0.019  Score=46.42  Aligned_cols=58  Identities=10%  Similarity=0.263  Sum_probs=50.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      ..|++-++.|+.++.+ .|.  +..++|..++  |++...+.+.|+.||++|+|+....+-++
T Consensus         6 ~~ld~~~~~il~~L~~-~~~--~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   63 (162)
T 2p5v_A            6 LTLDKTDIKILQVLQE-NGR--LTNVELSERV--ALSPSPCLRRLKQLEDAGIVRQYAALLSP   63 (162)
T ss_dssp             CCCCHHHHHHHHHHHH-CTT--CCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEEEECT
T ss_pred             cCCCHHHHHHHHHHHH-cCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEeeecccCCh
Confidence            3589999999999988 554  8999999999  99999999999999999999987765443

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=96.31  E-value=0.0059  Score=48.86  Aligned_cols=70  Identities=11%  Similarity=0.258  Sum_probs=46.7

Q ss_pred             CCCChHHHHHHHHHHhhcC--CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           32 DSLTDHERLIYDVIRSNKQ--DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag--~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      .+||..|..|+..|..+-|  +.++.+++|...+  +++...++++|+.||++||| ...+-.. +| ... ..|+|.
T Consensus        29 ~gLt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l--~~~~~tvsr~v~~Le~~glV-r~~~~~D-rR-~~~-v~LT~~  100 (148)
T 4fx0_A           29 SGLTNTQFSTLAVISLSEGSAGIDLTMSELAARI--GVERTTLTRNLEVMRRDGLV-RVMAGAD-AR-CKR-IELTAK  100 (148)
T ss_dssp             GTCCHHHHHHHHHHHC---------CHHHHHHHH--TCCHHHHHHHHHHHHHTTSB-C--------------CCBCHH
T ss_pred             cCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHCCCE-EeeCCCC-CC-eeE-EEECHH
Confidence            4799999999999987223  3569999999999  99999999999999999999 4455332 33 332 246665

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.29  E-value=0.012  Score=41.67  Aligned_cols=51  Identities=10%  Similarity=0.195  Sum_probs=43.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .|++-+..|+.++.+ .| ..+...+|..++  +++...|.|+|+.|+..|+|.+
T Consensus         7 ~m~~~~~~IL~~L~~-~~-~~~s~~eLA~~l--glsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A            7 TGDNLEQKILQVLSD-DG-GPVAIFQLVKKC--QVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             --CHHHHHHHHHHHH-HC-SCEEHHHHHHHH--CSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cccHHHHHHHHHHHH-cC-CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEec
Confidence            577667789999987 54 459999999999  9999999999999999999865

>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=96.26  E-value=0.013  Score=44.33  Aligned_cols=51  Identities=18%  Similarity=0.183  Sum_probs=42.8

Q ss_pred             CCcccHHHHHHHhhcC-CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           51 DMGIWTRDMKRELKVN-LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~-l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      +.++-..+|...+  + +.+..+++.|+.||++|||.....-..+.+..|-|.+
T Consensus        36 ~~~~~~~eL~~~l--~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~   87 (107)
T 2fsw_A           36 RRIIRYGELKRAI--PGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTP   87 (107)
T ss_dssp             TSCEEHHHHHHHS--TTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECH
T ss_pred             hCCcCHHHHHHHc--ccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECc
Confidence            4568999999999  7 9999999999999999999998776665566666643

>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=96.25  E-value=0.0093  Score=48.10  Aligned_cols=49  Identities=12%  Similarity=0.198  Sum_probs=42.6

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .++-..+|.+.+  ++.++.+++.|+.||++|||.....-..+ +..|-|.+
T Consensus        36 g~~~~~eLa~~l--gis~~tls~~L~~Le~~GlI~r~~~~~d~-~~~y~LT~   84 (146)
T 2f2e_A           36 GLTRFGEFQKSL--GLAKNILAARLRNLVEHGVMVAVPAESGS-HQEYRLTD   84 (146)
T ss_dssp             TCCSHHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEEECSSSS-CEEEEECH
T ss_pred             CCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEEecCCCC-eEEEEECc
Confidence            368899999999  99999999999999999999998877666 77776643

>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=96.23  E-value=0.0094  Score=51.26  Aligned_cols=119  Identities=9%  Similarity=0.166  Sum_probs=76.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccH--HHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCC
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWT--RDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKD  109 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~--~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~e  109 (252)
                      .+||+.+..++..|.. .+..|+..  ++|..++  ++.+..++++|+.||++|||...++     +.++    |++.  
T Consensus         2 ~~lt~~~e~yL~~i~~-l~~~~~~~~~~~la~~l--~vs~~tvs~~l~~Le~~GlV~r~~~-----~~v~----LT~~--   67 (226)
T 2qq9_A            2 KDLVATTEMYLRTIYE-LEEEGVTPLRARIAERL--EQSGPTVSQTVARMERDGLVVVASD-----RSLQ----MTPT--   67 (226)
T ss_dssp             -CHHHHHHHHHHHHHH-HHHHTCCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEECTT-----SBEE----ECHH--
T ss_pred             CCCCHHHHHHHHHHHH-HhhcCCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeCC-----CCeE----ECHH--
Confidence            3567766667777766 55557776  9999999  9999999999999999999988543     1111    2222  


Q ss_pred             ccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhh
Q 025493          110 ISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVL  176 (252)
Q Consensus       110 iTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVy  176 (252)
                               |.--.+-+....+....|+...-..+.+++++......   -.+|.+-+++|.+.|-+
T Consensus        68 ---------G~~~~~~~~~~~~~~e~~l~~~lgl~~ee~~~~a~~le---h~~s~~~~~~l~~~l~~  122 (226)
T 2qq9_A           68 ---------GRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWE---HVMSDEVERRLVKVLKD  122 (226)
T ss_dssp             ---------HHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHT---TTCCHHHHHHHHHHSSC
T ss_pred             ---------HHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH---hhCCHHHHHHHHHHhCC
Confidence                     21111222222345556666544578888887766554   23566667777666643

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=96.20  E-value=0.021  Score=42.89  Aligned_cols=49  Identities=14%  Similarity=0.226  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +-...|+.++ . .|  ++..++|...+  +++++.+++.|+.|+.+|+|...+.
T Consensus        21 ~~r~~IL~~L-~-~~--~~~~~ela~~l--~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           21 ETRWEILTEL-G-RA--DQSASSLATRL--PVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             HHHHHHHHHH-H-HS--CBCHHHHHHHS--SSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             hHHHHHHHHH-H-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeEEec
Confidence            3456677788 5 44  48999999999  9999999999999999999998764

>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=96.17  E-value=0.0083  Score=47.74  Aligned_cols=56  Identities=18%  Similarity=0.319  Sum_probs=47.9

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      |++-+..|+.++.+ .|  ++..++|..++  |++...+.+.|+.||++|+|+.+..+-++
T Consensus         1 ld~~~~~il~~L~~-~~--~~~~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d~   56 (150)
T 2pn6_A            1 MDEIDLRILKILQY-NA--KYSLDEIAREI--RIPKATLSYRIKKLEKDGVIKGYYAYINP   56 (150)
T ss_dssp             CCHHHHHHHHHHTT-CT--TSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSSCCCCCCCCG
T ss_pred             CChHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEEEeecCH
Confidence            56778888888877 44  69999999999  99999999999999999999987655443

>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=96.13  E-value=0.019  Score=43.50  Aligned_cols=51  Identities=18%  Similarity=0.262  Sum_probs=42.2

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +.++-..+|.+.++ ++.+..+++.|+.||++|||.....-..+.+..|-|.
T Consensus        25 ~~~~~~~eLa~~l~-~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT   75 (107)
T 2hzt_A           25 HGKKRTSELKRLMP-NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELS   75 (107)
T ss_dssp             TCCBCHHHHHHHCT-TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEEC
T ss_pred             hCCCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEEC
Confidence            44688999999864 8999999999999999999999877666556666553

>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=96.12  E-value=0.033  Score=42.68  Aligned_cols=67  Identities=16%  Similarity=0.250  Sum_probs=55.0

Q ss_pred             CCCChHHHHHHHHHHhhc----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccccc
Q 025493           32 DSLTDHERLIYDVIRSNK----QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEP  106 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~a----g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~leP  106 (252)
                      .+|+.-+..||..+.+ +    ....+-..+|.+.+  .|++..++|.|+.||.+|||....+  .-+|..   ..|+|
T Consensus        12 ~gl~~~q~~vL~~L~~-~~~~~~g~~~s~~eLa~~l--~l~~stLsR~l~rLe~~GLV~r~~~--~D~R~~---v~LT~   82 (96)
T 2obp_A           12 DGIDPAIVEVLLVLRE-AGIENGATPWSLPKIAKRA--QLPMSVLRRVLTQLQAAGLADVSVE--ADGRGH---ASLTQ   82 (96)
T ss_dssp             -CCCHHHHHHHHHHHH-HTSSTTCCCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC--TTSCEE---EEECH
T ss_pred             cCCCHHHHHHHHHHHH-HHhhCCCCCcCHHHHHHHh--CCchhhHHHHHHHHHHCCCEEeecC--CCCcee---EEECH
Confidence            5799999999997876 5    55668999999999  9999999999999999999998666  345653   25555

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=96.10  E-value=0.015  Score=46.26  Aligned_cols=57  Identities=14%  Similarity=0.253  Sum_probs=49.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      .|++-++.|+.++.+ .  ..+..++|..++  |++...+.+.|+.|+++|+|+.+..+-++
T Consensus         6 ~ld~~d~~il~~L~~-~--~~~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~~~   62 (151)
T 2dbb_A            6 KLDRVDMQLVKILSE-N--SRLTYRELADIL--NTTRQRIARRIDKLKKLGIIRKFTIIPDI   62 (151)
T ss_dssp             CCCHHHHHHHHHHHH-C--TTCCHHHHHHHT--TSCHHHHHHHHHHHHHHTSEEEEEEEECT
T ss_pred             hCCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEecCCh
Confidence            488889999999988 4  459999999999  99999999999999999999987765443

>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=96.02  E-value=0.014  Score=43.03  Aligned_cols=43  Identities=9%  Similarity=0.025  Sum_probs=36.5

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHH-HHHHHHHHHhcCCee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI-VTKSIKSLQNKSLIK   86 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~-l~k~lK~Le~k~lIK   86 (252)
                      .++..+.+ .| .|+-.++|.+.+  ++++.. +++.|+.||++|+|+
T Consensus        19 ~~L~~l~~-~~-~~~t~~eLa~~l--~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           19 PTLLEFEK-KG-YEPSLAEIVKAS--GVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHH-TT-CCCCHHHHHHHH--CCCHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHHh-cC-CCCCHHHHHHHH--CCCchHHHHHHHHHHHHCCCee
Confidence            34445555 43 379999999999  999999 999999999999999

>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=96.02  E-value=0.0067  Score=50.93  Aligned_cols=54  Identities=17%  Similarity=0.215  Sum_probs=47.1

Q ss_pred             CCChHHHHHHHHHHhhcC--CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           33 SLTDHERLIYDVIRSNKQ--DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag--~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .||+-|+.|+..|.+...  ......++|...+  +|++..+.+.|+.||++|+|..-
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            589999999999987322  3458999999999  99999999999999999999875

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=95.98  E-value=0.03  Score=41.12  Aligned_cols=52  Identities=15%  Similarity=0.201  Sum_probs=44.6

Q ss_pred             HHHHHHHHHhhc-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           38 ERLIYDVIRSNK-----QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        38 e~~vy~~I~~~a-----g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      ...|+++|.+ .     |. -+..++|...+  ++....+.+-|+.||++|+|+.+..-..
T Consensus         6 ~~~IL~~I~~-~i~~~~g~-~psv~EIa~~l--gvS~~TVrr~L~~Le~kG~I~R~~ggr~   62 (77)
T 2jt1_A            6 VTKIISIVQE-RQNMDDGA-PVKTRDIADAA--GLSIYQVRLYLEQLHDVGVLEKVNAGKG   62 (77)
T ss_dssp             HHHHHHHHHH-HHHHHTTS-CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEESCSSS
T ss_pred             HHHHHHHHHH-HHhhccCC-CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEecCCCCC
Confidence            4578899988 6     33 48999999999  9999999999999999999999875443

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=95.97  E-value=0.02  Score=50.41  Aligned_cols=51  Identities=12%  Similarity=0.279  Sum_probs=47.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      +|++.+..|+..|.+ .|  |+..++|.+++  ++++++++|.|+.||++|+|...
T Consensus       149 ~L~~~~~~IL~~L~~-~~--~~s~~eLA~~l--glsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          149 DYSREEMKLLNVLYE-TK--GTGITELAKML--DKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             CCCHHHHHHHHHHHH-HT--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            799999999999977 44  69999999999  99999999999999999999986

>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=95.94  E-value=0.027  Score=41.71  Aligned_cols=59  Identities=5%  Similarity=0.075  Sum_probs=48.9

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChH-HHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDN-IVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~-~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      +-...|+.++.. .|  +.-.++|.+.+  ++... .|++.|..||+.|||...    ..+|.+|-|++
T Consensus        11 ~~~~~IL~~Lk~-~g--~~ta~eiA~~L--git~~~aVr~hL~~Le~eGlV~~~----~~gRP~w~LT~   70 (79)
T 1xmk_A           11 EIKEKICDYLFN-VS--DSSALNLAKNI--GLTKARDINAVLIDMERQGDVYRQ----GTTPPIWHLTD   70 (79)
T ss_dssp             HHHHHHHHHHHH-TC--CEEHHHHHHHH--CGGGHHHHHHHHHHHHHTTSEEEE----CSSSCEEEECH
T ss_pred             hHHHHHHHHHHH-cC--CcCHHHHHHHc--CCCcHHHHHHHHHHHHHCCCEEec----CCCCCCeEeCH
Confidence            446688899999 76  68899999999  99999 999999999999999854    23566776653

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=95.92  E-value=0.015  Score=43.93  Aligned_cols=46  Identities=4%  Similarity=0.105  Sum_probs=36.8

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      +.|+++|+.++.+|++|+++.+        .+|+.-|+.-|+.|+-.|+|++++
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            4566677777777777776654        478899999999999999999986

>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=95.90  E-value=0.015  Score=46.44  Aligned_cols=56  Identities=16%  Similarity=0.356  Sum_probs=49.6

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .|++.++.|+.++.+ .|  .+..++|..++  |++...+.+.|+.|+++|+|+.+..+-+
T Consensus         4 ~ld~~~~~il~~L~~-~~--~~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~d   59 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN-DG--KAPLREISKIT--GLAESTIHERIRKLRESGVIKKFTAIID   59 (151)
T ss_dssp             CCCHHHHHHHHHHHH-CT--TCCHHHHHHHH--CSCHHHHHHHHHHHHHHTSSCCCCCCCC
T ss_pred             CcCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEEC
Confidence            588989999999988 54  68999999999  9999999999999999999998765433

>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=95.87  E-value=0.036  Score=44.23  Aligned_cols=55  Identities=5%  Similarity=0.152  Sum_probs=48.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      .|++-++.|+.++.+ .|  .+..++|..++  |++...+.+.|+.||++|+|+....+-
T Consensus         5 ~ld~~d~~il~~L~~-~~--~~s~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~   59 (152)
T 2cg4_A            5 LIDNLDRGILEALMG-NA--RTAYAELAKQF--GVSPETIHVRVEKMKQAGIITGARIDV   59 (152)
T ss_dssp             CCCHHHHHHHHHHHH-CT--TSCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEEEEEE
T ss_pred             ccCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcceEEEec
Confidence            488888999999988 44  68999999999  999999999999999999999877543

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=95.70  E-value=0.041  Score=48.17  Aligned_cols=46  Identities=11%  Similarity=0.255  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      -...|+.+|..    ..+...+|...+  ++++..|+++|+.|+..|||...
T Consensus        13 ~R~~IL~~L~~----g~~s~~ELa~~l--glS~stVs~hL~~Le~aGLV~~~   58 (232)
T 2qlz_A           13 VRRDLLSHLTC----MECYFSLLSSKV--SVSSTAVAKHLKIMEREGVLQSY   58 (232)
T ss_dssp             HHHHHHHHHTT----TTTCSSSSCTTC--CCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            45567777753    357778999999  99999999999999999999984

>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=95.54  E-value=0.022  Score=43.53  Aligned_cols=60  Identities=8%  Similarity=0.140  Sum_probs=47.9

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      ...|+..+.+    .++-..+|...++ ++++..+++.|+.||++|||....+-..+.++.|-|.
T Consensus        24 ~~~IL~~L~~----~~~~~~eLa~~l~-~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT   83 (112)
T 1z7u_A           24 KLSLMDELFQ----GTKRNGELMRALD-GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLT   83 (112)
T ss_dssp             HHHHHHHHHH----SCBCHHHHHHHST-TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEEC
T ss_pred             HHHHHHHHHh----CCCCHHHHHHHhc-cCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEEC
Confidence            3456666654    3688999999884 7999999999999999999999887766666666663

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=95.51  E-value=0.024  Score=42.24  Aligned_cols=61  Identities=8%  Similarity=0.077  Sum_probs=51.6

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .+++-+..|++.+++ ||. =+-..+|-.++  +++...|+|+|+.|-+.+.|-+      |.|=.|-+.+
T Consensus        16 ~~~d~eekVLe~Lke-aG~-PlkageIae~~--GvdKKeVdKaik~LKkEgkI~S------PkRCyw~~~~   76 (80)
T 2lnb_A           16 REGHLEQRILQVLTE-AGS-PVKLAQLVKEC--QAPKRELNQVLYRMKKELKVSL------TSPATWCLGG   76 (80)
T ss_dssp             HHHHHHHHHHHHHHH-HTS-CEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE------EETTEEEESS
T ss_pred             ccchHHHHHHHHHHH-cCC-CCCHHHHHHHH--CCCHHHHHHHHHHHHHcCCccC------CCCceeeCCC
Confidence            345568899999999 987 89999999999  9999999999999999999877      4566665543

>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=95.35  E-value=0.024  Score=44.33  Aligned_cols=57  Identities=16%  Similarity=0.366  Sum_probs=48.0

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG   95 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~   95 (252)
                      |++.+..|+..+.+ .|  .+..++|.+++  +++.+.+.+.|+.||+.|+|+.....-.+.
T Consensus         2 ld~~~~~il~~L~~-~~--~~~~~ela~~l--g~s~~tv~~~l~~L~~~G~i~~~~~~~~~~   58 (141)
T 1i1g_A            2 IDERDKIILEILEK-DA--RTPFTEIAKKL--GISETAVRKRVKALEEKGIIEGYTIKINPK   58 (141)
T ss_dssp             CCSHHHHHHHHHHH-CT--TCCHHHHHHHH--TSCHHHHHHHHHHHHHHTSSCCCCCCCCSG
T ss_pred             CCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEeccccccChH
Confidence            67778888888887 44  57899999999  999999999999999999998776544443

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=95.28  E-value=0.056  Score=43.88  Aligned_cols=69  Identities=12%  Similarity=0.284  Sum_probs=54.4

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe-----eeEEecccccC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK-----KHLMAVEFEPS  107 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r-----K~YmL~~lePs  107 (252)
                      ||+.++.|+.++.+ .|  .+..++|.+++  |+....+.+.|+.||+.|+|+.+..+-++.+     ..|+...+.|.
T Consensus         1 lD~~d~~il~~L~~-~~--~~s~~~la~~l--g~s~~tv~~rl~~L~~~g~i~~~~a~~~~~~lG~~~~a~v~v~v~~~   74 (162)
T 3i4p_A            1 MDRLDRKILRILQE-DS--TLAVADLAKKV--GLSTTPCWRRIQKMEEDGVIRRRVALLDPVKVNTKVTVFVSIRTASH   74 (162)
T ss_dssp             CCHHHHHHHHHHTT-CS--CSCHHHHHHHH--TCCHHHHHHHHHHHHHTTSSCCCCCCCCTTTTTCCEEEEEEEECCSC
T ss_pred             CCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeceeeeCHHHhcCcEEEEEEEEEcCC
Confidence            57788899999888 44  47999999999  9999999999999999999998776544332     34555555543

>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=95.26  E-value=0.065  Score=39.51  Aligned_cols=51  Identities=14%  Similarity=0.145  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHhhcCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           37 HERLIYDVIRSNKQDMG-IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~G-Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ...+|.++|.. -+..+ +-..+|.+++  |++.+.++|+|=+|+++|+|..+.+
T Consensus        13 ~~~~v~~~i~~-L~~~~~~Ta~~IAkkL--g~sK~~vNr~LY~L~kkG~V~~~~~   64 (75)
T 1sfu_A           13 IFSLVKKEVLS-LNTNDYTTAISLSNRL--KINKKKINQQLYKLQKEDTVKMVPS   64 (75)
T ss_dssp             HHHHHHHHHHT-SCTTCEECHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHHh-CCCCcchHHHHHHHHH--CCCHHHHHHHHHHHHHCCCEecCCC
Confidence            34477788888 77777 9999999999  9999999999999999999999865

>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=95.21  E-value=0.11  Score=39.10  Aligned_cols=47  Identities=19%  Similarity=0.263  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      -...|+.++.+    .++-..+|...+  +++++.+++.|+.|+..|+|...+
T Consensus        27 ~r~~IL~~L~~----~~~~~~ela~~l--~is~stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           27 NRIRIMELLSV----SEASVGHISHQL--NLSQSNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HHHHHHHHHHH----CCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34567777654    357899999999  999999999999999999999876

>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=95.11  E-value=0.097  Score=38.80  Aligned_cols=47  Identities=2%  Similarity=0.163  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      --..|+.++.+  |  .....+|...+  +++++.+++.|+.|+..|+|...+
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            34456667643  3  38899999999  999999999999999999999864

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=95.05  E-value=0.05  Score=43.10  Aligned_cols=50  Identities=12%  Similarity=0.223  Sum_probs=42.0

Q ss_pred             CCcccHHHHHHHhhcC-CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           51 DMGIWTRDMKRELKVN-LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~-l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +.++-..+|...+  . +.+..|++.|+.||++|||.....-..+.++.|-|.
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            4568999999998  5 999999999999999999999877655556666553

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=95.03  E-value=0.093  Score=38.55  Aligned_cols=36  Identities=11%  Similarity=0.223  Sum_probs=33.7

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .++-..+|...+  +++++.+++.|+.|+..|+|...+
T Consensus        35 ~~~~~~ela~~l--~is~~tvs~~L~~L~~~Glv~~~~   70 (98)
T 3jth_A           35 QELSVGELCAKL--QLSQSALSQHLAWLRRDGLVTTRK   70 (98)
T ss_dssp             SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            578999999999  999999999999999999998863

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=94.97  E-value=0.07  Score=40.48  Aligned_cols=45  Identities=9%  Similarity=0.115  Sum_probs=38.1

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ..|+.++.+    .++-.++|...+  +++++.+++.|+.|++.|+|...+
T Consensus        28 ~~IL~~L~~----~~~s~~eLa~~l--gis~stvs~~L~~L~~~GlV~~~~   72 (108)
T 2kko_A           28 LQILDLLAQ----GERAVEAIATAT--GMNLTTASANLQALKSGGLVEARR   72 (108)
T ss_dssp             HHHHHHHTT----CCEEHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHc----CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            345555532    468999999999  999999999999999999999875

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=94.93  E-value=0.07  Score=38.18  Aligned_cols=59  Identities=10%  Similarity=0.134  Sum_probs=49.2

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      .+|+....|++++.+ .+...+...+|-..++   ++++..+|.|.|+.|+++|+|..+..-.
T Consensus        14 ~~t~~r~~IL~~l~~-~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~   75 (83)
T 2fu4_A           14 KVTLPRLKILEVLQE-PDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG   75 (83)
T ss_dssp             CCCHHHHHHHHHHTS-GGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGG
T ss_pred             CcCHHHHHHHHHHHh-CCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCC
Confidence            478888999999988 6435789999988773   3799999999999999999999876543

>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=94.90  E-value=0.052  Score=40.89  Aligned_cols=51  Identities=16%  Similarity=0.218  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +....|+..+.. .|.. +...+|...+  |++++.|.++|+.|++.|+|...+.
T Consensus        18 ~~~l~Il~~l~~-~g~~-~s~~eLa~~l--gvs~~tV~~~L~~L~~~GlV~~~~~   68 (110)
T 1q1h_A           18 DDVIDVLRILLD-KGTE-MTDEEIANQL--NIKVNDVRKKLNLLEEQGFVSYRKT   68 (110)
T ss_dssp             STTHHHHHHHHH-HCSC-BCHHHHHHTT--TSCHHHHHHHHHHHHHHTSCEEEEE
T ss_pred             hHHHHHHHHHHH-cCCC-CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEec
Confidence            344556666655 5644 8999999999  9999999999999999999988643

>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=94.87  E-value=0.1  Score=40.41  Aligned_cols=47  Identities=9%  Similarity=0.107  Sum_probs=39.6

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ...|+.++.+ .|  ++-..+|...+  +++++.+++.|+.|+..|+|...+
T Consensus        44 rl~IL~~L~~-~~--~~s~~eLa~~l--~is~stvs~~L~~L~~~Glv~~~~   90 (122)
T 1u2w_A           44 RAKITYALCQ-DE--ELCVCDIANIL--GVTIANASHHLRTLYKQGVVNFRK   90 (122)
T ss_dssp             HHHHHHHHHH-SS--CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHHH-CC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            4457777765 43  58899999999  999999999999999999998854

>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=94.82  E-value=0.053  Score=42.28  Aligned_cols=36  Identities=17%  Similarity=0.123  Sum_probs=33.6

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .++-.++|...+  +++...++++|+.||.+|+|...+
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  999999999999999999998863

>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=94.73  E-value=0.073  Score=43.08  Aligned_cols=62  Identities=8%  Similarity=0.209  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhh------cCCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELK------VNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~------~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      -+..|+.++.+ .   ...-.+|.+++.      .++...+|..+|+.||++|||.+....  ..+.||+|-|.
T Consensus        42 ~~~~IL~~L~~-~---~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT  111 (145)
T 1xma_A           42 VDTIILSLLIE-G---DSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRIT  111 (145)
T ss_dssp             HHHHHHHHHHH-C---CEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEEC
T ss_pred             HHHHHHHHHHh-C---CCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEEC
Confidence            57788888865 3   355556655541      149999999999999999999998764  45678888663

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=94.64  E-value=0.11  Score=41.51  Aligned_cols=51  Identities=12%  Similarity=0.160  Sum_probs=42.0

Q ss_pred             CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +...-..+|.+.++ ++.++.|++.|+.||..|||.....-..+.+..|-|.
T Consensus        37 ~g~~rf~eL~~~l~-gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT   87 (131)
T 4a5n_A           37 DGKKRFNEFRRICP-SITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLT   87 (131)
T ss_dssp             TSCBCHHHHHHHCT-TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEEC
T ss_pred             cCCcCHHHHHHHhc-ccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEEC
Confidence            44678899999985 8999999999999999999998876666556666663

>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=94.54  E-value=0.18  Score=37.02  Aligned_cols=47  Identities=19%  Similarity=0.234  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +-...|+.+| .    .++-..+|..++  ++++..+++.|+.|+..|+|...+
T Consensus        31 ~~r~~Il~~L-~----~~~~~~eLa~~l--~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           31 PVRRKILRML-D----KGRSEEEIMQTL--SLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHHHH-H----TTCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHH-c----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEC
Confidence            3455677777 4    358899999999  999999999999999999999865

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.52  E-value=0.17  Score=38.31  Aligned_cols=49  Identities=16%  Similarity=0.257  Sum_probs=41.6

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +..+..|+..+.+    .++-..+|...+  ++++..+++.|+.||+.|+|...+
T Consensus        31 ~~~~~~il~~L~~----~~~s~~ela~~l--~is~stvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           31 TPSRLMILTQLRN----GPLPVTDLAEAI--GMEQSAVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             CHHHHHHHHHHHH----CCCCHHHHHHHH--SSCHHHHHHHHHHHHHHCSEEEEE
T ss_pred             CHHHHHHHHHHHH----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4456667777765    368899999999  999999999999999999998765

>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=94.45  E-value=0.085  Score=39.73  Aligned_cols=45  Identities=18%  Similarity=0.254  Sum_probs=41.2

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      +||.++.. -.+ |+-.++|...+  ||+.+.+++.|..|+++|||...
T Consensus         9 Ii~~IL~~-i~~-~~~~t~La~~~--~ls~~~~~~~l~~L~~~GLI~~~   53 (95)
T 1r7j_A            9 IIQAILEA-CKS-GSPKTRIMYGA--NLSYALTGRYIKMLMDLEIIRQE   53 (95)
T ss_dssp             HHHHHHHH-HTT-CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHH-HHc-CCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCeEEE
Confidence            78999988 654 49999999999  99999999999999999999986

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=94.39  E-value=0.083  Score=40.82  Aligned_cols=62  Identities=8%  Similarity=0.094  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhc------CCCh-HHHHHHHHHHHhcCCeeeeecc-ccCCeeeEEec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKV------NLPD-NIVTKSIKSLQNKSLIKEVVNI-HNKGKKHLMAV  102 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~------~l~~-~~l~k~lK~Le~k~lIK~vksv-~~~~rK~YmL~  102 (252)
                      -+..|+.++.+ .   ...-.+|.+....      ++.+ .+|..+|+.||++|||.+...- ..+.||+|-|.
T Consensus        14 ~~~~IL~~L~~-~---~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT   83 (118)
T 2esh_A           14 LASTILLLVAE-K---PSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRIT   83 (118)
T ss_dssp             HHHHHHHHHHH-S---CBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEEC
T ss_pred             HHHHHHHHHHc-C---CCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEC
Confidence            45667777755 3   2445566655510      2888 9999999999999999998754 44678888663

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=94.24  E-value=0.053  Score=40.53  Aligned_cols=44  Identities=18%  Similarity=0.230  Sum_probs=37.8

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      +.|+.++.+ .|   +..++|.+++  +++...+++.|+.||..|+|+..
T Consensus        20 ~~IL~lL~~-~g---~sa~eLAk~L--giSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           20 CEAIKTIGI-EG---ATAAQLTRQL--NMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHSS-ST---EEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHH-cC---CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeC
Confidence            345566665 44   9999999999  99999999999999999999985

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=94.10  E-value=0.06  Score=41.04  Aligned_cols=62  Identities=15%  Similarity=0.237  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhhcCCCccc-HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc-cCCeeeEEe
Q 025493           37 HERLIYDVIRSNKQDMGIW-TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH-NKGKKHLMA  101 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw-~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~-~~~rK~YmL  101 (252)
                      -+..|+.++.+ ....|-- .++|....  ++...+|..+|+.||++|||.+..... .+.|++|-|
T Consensus        10 l~~~IL~~L~~-~~~~gyel~~~l~~~~--~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~L   73 (108)
T 3l7w_A           10 IEYLILAIVSK-HDSYGYDISQTIKLIA--SIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHL   73 (108)
T ss_dssp             HHHHHHHHHHH-SCEEHHHHHHHHTTTC--CCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEE
T ss_pred             HHHHHHHHHHc-CCCcHHHHHHHHHHHh--CCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEE
Confidence            35677777766 4333321 12333336  899999999999999999999987543 344677765

>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=94.10  E-value=0.11  Score=43.83  Aligned_cols=50  Identities=18%  Similarity=0.277  Sum_probs=43.7

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +++-+..|+.++.+    .++..++|..++  ++++..+++.|+.||+.|+|+...
T Consensus        18 ~d~~~~~IL~~L~~----~~~s~~eLA~~l--glS~stv~~~l~~Le~~GlI~~~~   67 (192)
T 1uly_A           18 LEDTRRKILKLLRN----KEMTISQLSEIL--GKTPQTIYHHIEKLKEAGLVEVKR   67 (192)
T ss_dssp             HSHHHHHHHHHHTT----CCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHHHHc----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            46667788888863    369999999999  999999999999999999999984

>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=94.00  E-value=0.091  Score=40.11  Aligned_cols=67  Identities=13%  Similarity=0.218  Sum_probs=49.0

Q ss_pred             CCCChHHHHHHHHHHhhcCC--Cc-ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           32 DSLTDHERLIYDVIRSNKQD--MG-IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~--~G-Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      +-|+.-...|+.++.. .+.  .| =-.++|..+.+.++...+|..+|+.||++|+|.+..   .+.||+|-+.
T Consensus         5 ~~~~~~~~~IL~lL~~-~~~~~~g~~i~~ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~---~~~rk~Y~iT   74 (99)
T 2co5_A            5 KYMRINYYIILKVLVI-NGSRLEKKRLRSEILKRFDIDISDGVLYPLIDSLIDDKILREEE---APDGKVLFLT   74 (99)
T ss_dssp             CCCHHHHHHHHHHHHH-TTTEEEGGGHHHHHHHHHCCBCCHHHHHHHHHHHHHTTSEEEEC---CTTSCEEEEC
T ss_pred             HhhcccHHHHHHHHHh-cCCCCcHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHCCCEEEee---CCCcEEEEEC
Confidence            3466667788888865 321  22 234566666633689999999999999999999986   6789998773

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=93.97  E-value=0.17  Score=36.12  Aligned_cols=53  Identities=6%  Similarity=0.067  Sum_probs=45.7

Q ss_pred             HHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          130 KSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       130 ~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      +..|+.+|...  +.+|++||++.+++.+   ..++..-|.+.|+.|+-.|.|.++..
T Consensus        19 r~~IL~~l~~~~~~~~s~~el~~~l~~~~---~~is~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           19 RLKILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             HHHHHHHHTSGGGSSBCHHHHHHHHHHTT---CCCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHhC---CCCCHhhHHHHHHHHHHCCCeEEEee
Confidence            55788888765  6899999999998876   36789999999999999999998864

>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=93.94  E-value=0.13  Score=39.28  Aligned_cols=47  Identities=13%  Similarity=0.217  Sum_probs=37.3

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      |...+-..+|.+.++ ++.++.|++.|+.||+.|||.....    .+..|-|
T Consensus        39 g~~~~~~~eL~~~l~-gis~~~ls~~L~~Le~~GlV~r~~~----r~~~y~L   85 (111)
T 3df8_A           39 GSTRQNFNDIRSSIP-GISSTILSRRIKDLIDSGLVERRSG----QITTYAL   85 (111)
T ss_dssp             SSSCBCHHHHHHTST-TCCHHHHHHHHHHHHHTTSEEEEES----SSEEEEE
T ss_pred             CCCCCCHHHHHHHcc-CCCHHHHHHHHHHHHHCCCEEEeec----CcEEEEE
Confidence            444344899999983 6999999999999999999998765    3455555

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=93.93  E-value=0.45  Score=40.35  Aligned_cols=110  Identities=11%  Similarity=0.075  Sum_probs=70.7

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccC
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSE  118 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d  118 (252)
                      +.||.+.+   .+.++-+++|...+  ++.+..++++|+.||++|||...++     +. +   .|+|.           
T Consensus         9 ~~I~~l~~---~~~~~~~~~lA~~l--~vs~~tvs~~l~~Le~~GlV~r~~~-----~~-i---~LT~~-----------   63 (214)
T 3hrs_A            9 KCLYELGT---RHNKITNKEIAQLM--QVSPPAVTEMMKKLLAEELLIKDKK-----AG-Y---LLTDL-----------   63 (214)
T ss_dssp             HHHHHTTS---SCSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEETT-----TE-E---EECHH-----------
T ss_pred             HHHHHHHh---cCCCcCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEEecC-----CC-e---EECHH-----------
Confidence            34555433   35689999999999  9999999999999999999998653     11 1   12222           


Q ss_pred             CcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhh
Q 025493          119 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVL  176 (252)
Q Consensus       119 ~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVy  176 (252)
                      |.=-.+.+-...+....|+...-..+.+++++.-....   -.+|++-+++|-..|-+
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            21112222233346667776654566777766655443   34677777777776644

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=93.82  E-value=0.2  Score=38.31  Aligned_cols=56  Identities=9%  Similarity=0.102  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      --..|+.++.+    .++-..+|...+  ++++..+++.|+.|+..|||...+.   ..++.|-|
T Consensus        19 ~R~~Il~~L~~----~~~~~~eLa~~l--~is~~tvs~hL~~L~~~GlV~~~~~---gr~~~y~l   74 (118)
T 3f6o_A           19 TRRAVLGRLSR----GPATVSELAKPF--DMALPSFMKHIHFLEDSGWIRTHKQ---GRVRTCAI   74 (118)
T ss_dssp             HHHHHHHHHHT----CCEEHHHHHTTC--CSCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEEE
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCeEEEec---CCEEEEEE
Confidence            34556666653    457899999999  9999999999999999999998665   23444544

>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=93.75  E-value=0.27  Score=41.79  Aligned_cols=61  Identities=20%  Similarity=0.322  Sum_probs=47.5

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      +....|+.++..    .++...+|...+  +++++.|+++|+.|+..|||...+..  ..+.+++|-+.
T Consensus        15 ~~rl~IL~~L~~----~~~s~~eLa~~l--~is~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt   77 (202)
T 2p4w_A           15 ETRRRILFLLTK----RPYFVSELSREL--GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIK   77 (202)
T ss_dssp             HHHHHHHHHHHH----SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEEC
T ss_pred             HHHHHHHHHHHh----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEEC
Confidence            345667777744    358999999999  99999999999999999999997653  22445666553

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=93.68  E-value=0.19  Score=38.86  Aligned_cols=62  Identities=13%  Similarity=0.184  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHh---hc-CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKREL---KV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~---~~-~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      -+.+|+.++.+ .-.   .--+|.++.   +. ++...+|..+|+.||++|||.+....  ..+.||+|-|.
T Consensus        10 l~~~IL~~L~~-~~~---~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT   77 (115)
T 4esb_A           10 LEGCILYIISQ-EEV---YGYELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHIT   77 (115)
T ss_dssp             HHHHHHHHHHH-SCE---EHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEEC
T ss_pred             HHHHHHHHHHc-CCC---CHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEEC
Confidence            35677777766 433   334455544   11 58999999999999999999987643  34678888763

>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=93.63  E-value=0.098  Score=48.04  Aligned_cols=50  Identities=18%  Similarity=0.254  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      .++.|+++|.+ .|  .+.+.+|.+++  +|...+++++++.|++.|+|++....
T Consensus        17 n~~~il~~l~~-~~--~~sr~~la~~~--~ls~~tv~~~v~~L~~~g~i~~~~~~   66 (406)
T 1z6r_A           17 NAGAVYRLIDQ-LG--PVSRIDLSRLA--QLAPASITKIVHEMLEAHLVQELEIK   66 (406)
T ss_dssp             HHHHHHHHHHS-SC--SCCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEC---
T ss_pred             HHHHHHHHHHH-cC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEeeccc
Confidence            46789999998 55  59999999999  99999999999999999999997543

>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=93.52  E-value=0.17  Score=43.18  Aligned_cols=54  Identities=13%  Similarity=0.182  Sum_probs=45.5

Q ss_pred             CChHHHHHHHHHHhhcCC----CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           34 LTDHERLIYDVIRSNKQD----MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~----~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +++.+..++..|.. .|.    .|+...++..++  ++.+..|++.|+.||+++||...++
T Consensus         5 ~~~~~l~~l~~l~~-~~~l~~~~~~s~s~aA~~L--~isq~avSr~I~~LE~~~L~~R~~~   62 (230)
T 3cta_A            5 TDDQYYRAIKKIKE-AAEASNRAYLTSSKLADML--GISQQSASRIIIDLEKNGYITRTVT   62 (230)
T ss_dssp             --CHHHHHHHHHHH-HTTTSSEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cHHHHHHHHHHHHH-hcccccCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            45577788888877 654    788899999999  9999999999999999999998754

>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=93.32  E-value=0.11  Score=40.43  Aligned_cols=62  Identities=15%  Similarity=0.226  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHh---hc-CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKREL---KV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~---~~-~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      -+.+|+.++.+ .-..|-   +|.++.   +. ++...+|..+|+.||++|||.+....  ..|.||+|-|.
T Consensus        14 l~~~IL~lL~~-~p~~Gy---ei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT   81 (116)
T 3hhh_A           14 LEGLVLAIIQR-KETYGY---EITKILNDQGFTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLT   81 (116)
T ss_dssp             HHHHHHHHHHH-SCBCHH---HHHHHHHTTSCSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEEC
T ss_pred             HHHHHHHHHhc-CCCCHH---HHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEEC
Confidence            35667777766 443343   444443   11 68999999999999999999987642  45678888663

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=93.28  E-value=0.16  Score=39.32  Aligned_cols=62  Identities=16%  Similarity=0.227  Sum_probs=44.1

Q ss_pred             HHHHHHhhcCCCcccH-HHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeecc---ccCCeeeEEecc
Q 025493           41 IYDVIRSNKQDMGIWT-RDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNI---HNKGKKHLMAVE  103 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~-~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv---~~~~rK~YmL~~  103 (252)
                      |+.++.+ .-..|--. +.|...++. ++...+|..+|+.||++|+|.+....   ..+.||+|-|.+
T Consensus        27 IL~lL~~-~~~~Gyei~~~l~~~~~~~~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~   93 (115)
T 2dql_A           27 ILYVLLQ-GESYGTELIQQLETEHPTYRLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSP   93 (115)
T ss_dssp             HHHHHTT-SCBCHHHHHHHHHHHCTTEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECG
T ss_pred             HHHHHHh-CCCCHHHHHHHHHHHcCCCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECH
Confidence            7777766 54455443 344443321 69999999999999999999987654   356789987743

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=93.28  E-value=0.16  Score=40.19  Aligned_cols=45  Identities=31%  Similarity=0.382  Sum_probs=37.4

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .|+.+|.. .|  ++..++|...+  ++.+..|+++|+.||.+|||...+
T Consensus        44 ~i~~~l~~-~~--~~~~~~la~~l--~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           44 LISDLIRE-VG--EARQVDMAARL--GVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             HHHHHHHH-HS--CCCHHHHHHHH--TSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             HHHHHHHh-CC--CcCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEec
Confidence            34446666 44  57889999999  999999999999999999998763

>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=93.21  E-value=0.21  Score=36.80  Aligned_cols=49  Identities=12%  Similarity=0.217  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHH-HHHHHHHHHhhcCeeEEE
Q 025493          127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQ-QIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~-di~~IL~tLVyDgkIE~v  183 (252)
                      ...++.|+.||.+++..|+.+|++.+.        ++.. .|.+.|..|.-||.|++.
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            477899999999999999999998764        6777 999999999999999964

>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=93.09  E-value=0.34  Score=37.60  Aligned_cols=36  Identities=17%  Similarity=0.340  Sum_probs=33.4

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .+.-..+|...+  ++++..+++.|+.||+.|+|...+
T Consensus        58 ~~~s~~ela~~l--gis~stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           58 SELCVGDLAQAI--GVSESAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             CCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEE
Confidence            468899999999  999999999999999999999865

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=93.08  E-value=0.32  Score=37.78  Aligned_cols=61  Identities=16%  Similarity=0.268  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHh---hc-CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKREL---KV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV  102 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~---~~-~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~  102 (252)
                      +.+|+.++.+ .-..|-   +|.++.   +. ++...+|..+|+.||++|||.+....  ..+.||+|-|.
T Consensus        13 ~~~IL~lL~~-~p~~Gy---ei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT   79 (117)
T 4esf_A           13 EGCVLEIISR-RETYGY---EITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLN   79 (117)
T ss_dssp             HHHHHHHHHH-SCBCHH---HHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEEC
T ss_pred             HHHHHHHHHc-CCCCHH---HHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEEC
Confidence            4566666665 433343   333332   22 68999999999999999999997642  45678888763

>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=93.07  E-value=0.21  Score=38.28  Aligned_cols=50  Identities=24%  Similarity=0.330  Sum_probs=47.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHH-HhhcCCChHHHHHHHHHHHhcCCee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKR-ELKVNLPDNIVTKSIKSLQNKSLIK   86 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~-~~~~~l~~~~l~k~lK~Le~k~lIK   86 (252)
                      .+|+.-|.-|+-.|.. .|  .+..++|.. ..  .|..+.|+|.|+.|+++|||.
T Consensus        12 ~~L~~~QfsiL~~L~~-~~--~~t~~~Lae~~l--~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           12 DVLNEKTATILITIAK-KD--FITAAEVREVHP--DLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             TSSCHHHHHHHHHHHH-ST--TBCHHHHHHTCT--TSCHHHHHHHHHHHHTTTSEE
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHHh--cccHHHHHHHHHHHHHCCCee
Confidence            5899999999999988 66  999999999 99  999999999999999999998

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=93.07  E-value=0.19  Score=39.21  Aligned_cols=53  Identities=13%  Similarity=0.305  Sum_probs=45.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      -|++-++.|+.++.+ .|  .+...+|...+..+++...|++.|+.|+..|||...
T Consensus        10 ~md~~d~~IL~~L~~-~g--~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           10 WMTIWDDRILEIIHE-EG--NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             TCCHHHHHHHHHHHH-HS--CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             hcCHHHHHHHHHHHH-cC--CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            378888999999988 66  688999999773357999999999999999999984

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=92.94  E-value=0.24  Score=39.72  Aligned_cols=64  Identities=20%  Similarity=0.247  Sum_probs=47.3

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      .++-.+..+.++.-+..++|..+.  +++.+.|.|+|..|.+.|+|++++..+.    =|.|.  .|.++||
T Consensus        15 ~~L~~La~~~~~~~~s~~~IA~~~--~i~~~~l~kil~~L~~aGlv~s~rG~~G----Gy~La--r~p~~It   78 (143)
T 3t8r_A           15 TLMISLAKKEGQGCISLKSIAEEN--NLSDLYLEQLVGPLRNAGLIRSVRGAKG----GYQLR--VPAEEIS   78 (143)
T ss_dssp             HHHHHHHTTTTSCCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEECSSSSS----EEEES--SCGGGCB
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCEEEecCCCCC----Ceeec--CCcccCC
Confidence            344445552344568999999999  9999999999999999999998754432    37774  4555555

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=92.83  E-value=0.45  Score=39.50  Aligned_cols=50  Identities=8%  Similarity=0.147  Sum_probs=41.1

Q ss_pred             CCcccHHHHHHHhhcC-CChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEec
Q 025493           51 DMGIWTRDMKRELKVN-LPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAV  102 (252)
Q Consensus        51 ~~GIw~~dik~~~~~~-l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~  102 (252)
                      +.+....+|...+  + +++..+++.|+.|++-|||+.++-  +.....|.|-+.
T Consensus        34 ~~~~~~~~l~~~l--~~~~~~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~   86 (182)
T 4g6q_A           34 GRSLTTRELAELL--PDVATTTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLN   86 (182)
T ss_dssp             TSCEEHHHHHHHC--TTBCHHHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEEC
T ss_pred             hCCCCHHHHHHHh--cCCCHHHHHHHHHHHHHCCCeEEEEeecccCcceeEEEec
Confidence            4578899999998  6 999999999999999999998874  344346788653

>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=92.76  E-value=2.1  Score=37.36  Aligned_cols=114  Identities=6%  Similarity=0.067  Sum_probs=86.9

Q ss_pred             CCCChHHHHHHHHHHhh---cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCC
Q 025493           32 DSLTDHERLIYDVIRSN---KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSK  108 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~---ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~  108 (252)
                      ..+++++..+.+.|...   +|=.--|.+||-..+  +++...+..+|+.|...|.|-.|.      .-+|         
T Consensus       133 ~~~~~~~~~~~~~i~~~~~~~g~~pp~~~dl~~~l--~~~~~~~~~~l~~l~~~g~lv~l~------~~~~---------  195 (258)
T 1lva_A          133 PSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSF--NLDPSELEELLHYLVREGVLVKIN------DEFY---------  195 (258)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEESS------SSBE---------
T ss_pred             cCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHhHh--CCCHHHHHHHHHHHHHCCCEEEec------CCeE---------
Confidence            35777666655555432   444445999999999  999999999999999999988862      3344         


Q ss_pred             CccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          109 DISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       109 eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                                  |..+.++.+.+.+..++ .++..|+.+..+-+.        +|-.=.-.||+-|=-.|...++
T Consensus       196 ------------~~~~~~~~~~~~l~~~~-~~~~it~a~~Rd~lg--------~SRK~aIplLE~~Dr~g~TrR~  249 (258)
T 1lva_A          196 ------------WHRQALGEAREVIKNLA-STGPFGLAEARDALG--------SSRKYVLPLLEYLDQVKFTRRV  249 (258)
T ss_dssp             ------------EEHHHHHHHHHHHHHHH-TTSCBCHHHHHHHHT--------CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ------------EcHHHHHHHHHHHHHHH-hcCCcCHHHHHHHhC--------CcHHHHHHHHHHHhhcCceeee
Confidence                        34778999999999999 999999999888764        3455566778877777766654

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=92.64  E-value=0.39  Score=38.78  Aligned_cols=60  Identities=13%  Similarity=0.078  Sum_probs=47.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMG-----------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~G-----------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+.++++..-+++- +...|           +.+.+|..-+  |++...|+|+|+.|+++|+|+.-      ++++.++
T Consensus       116 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~~------~~~i~i~  186 (202)
T 2zcw_A          116 TQRLKNRMAAALLEL-SETPLAHEEEGKVVLKATHDELAAAV--GSVRETVTKVIGELAREGYIRSG------YGKIQLL  186 (202)
T ss_dssp             HCCHHHHHHHHHHHH-TTSTTEEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE------TTEEEES
T ss_pred             cCCHHHHHHHHHHHH-HHhcCCCCCCcEEccCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEeC------CCEEEEe
Confidence            457788887777765 65444           6789999999  99999999999999999999852      3556654

>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=92.54  E-value=0.9  Score=39.69  Aligned_cols=106  Identities=12%  Similarity=0.260  Sum_probs=78.1

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHH
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVV  129 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l  129 (252)
                      =..|+-...|+.+..+.++...+..+|..|+..|.|+....       .+-+.+.+|             .|+.+ .+.+
T Consensus        84 ~~~G~~~~~L~~~~~~~~~~~l~~~ll~~l~~~g~l~~~~~-------~v~l~~h~~-------------~~~~~-~~~~  142 (258)
T 1lva_A           84 LRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAAN-------TVALAGFTP-------------SFSET-QKKL  142 (258)
T ss_dssp             TSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEETT-------EEEETTCCC-------------CCCHH-HHHH
T ss_pred             CccCCCHHHHHHhccccCCHHHHHHHHHHHHHCCCEEecCC-------EEeCCCCcc-------------CCCHH-HHHH
Confidence            45899999999997335899999999999999999887432       222322222             34443 4566


Q ss_pred             HHHHHHHhhhCC--CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          130 KSQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       130 ~~~~~~~i~~~~--~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      .+.+...+...+  .|++.|+.+-+        .++.++++++|..|+-.|.|.++.
T Consensus       143 ~~~i~~~~~~~g~~pp~~~dl~~~l--------~~~~~~~~~~l~~l~~~g~lv~l~  191 (258)
T 1lva_A          143 LKDLEDKYRVSRWQPPSFKEVAGSF--------NLDPSELEELLHYLVREGVLVKIN  191 (258)
T ss_dssp             HHHHHHHHHHHTTSCCBHHHHHHHT--------TCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHhHh--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence            677777776655  67888876532        367889999999999999999875

>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=92.50  E-value=0.41  Score=36.94  Aligned_cols=64  Identities=11%  Similarity=0.163  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhhcCCCcccH-HHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEec
Q 025493           38 ERLIYDVIRSNKQDMGIWT-RDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAV  102 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~-~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~  102 (252)
                      +..|+.++.+ .-..|--. +.|...++.  ++...+|..+|+.||++|||.+...  ...+.||+|-|.
T Consensus        14 ~~~IL~~L~~-~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT   82 (116)
T 3f8b_A           14 NVILLNVLKQ-GDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLT   82 (116)
T ss_dssp             HHHHHHHHHH-CCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEEC
T ss_pred             HHHHHHHHHh-CCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEEC
Confidence            5567777766 44444322 223333211  6899999999999999999998753  355778888663

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=92.46  E-value=0.61  Score=38.26  Aligned_cols=60  Identities=18%  Similarity=0.282  Sum_probs=46.0

Q ss_pred             HHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           44 VIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        44 ~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      .+..+.++.-+..++|..+.  +++.+.|.|+|..|.+.|||.+++..+.    =|.|.  .|.++||
T Consensus        35 ~LA~~~~~~~~s~~eIA~~~--~i~~~~l~kil~~L~~aGlv~s~rG~~G----Gy~La--r~p~eIt   94 (159)
T 3lwf_A           35 ELAKRIGDGPISLRSIAQDK--NLSEHYLEQLIGPLRNAGIVKSIRGAHG----GYVLN--GDPEKIT   94 (159)
T ss_dssp             HHHHTTTSCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECSTTC----EEEEC--SCTTTCB
T ss_pred             HHHhcCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCeEEEecCCCC----ceEec--CCHHHCC
Confidence            34442345568999999999  9999999999999999999999865432    37774  4666655

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=92.41  E-value=0.17  Score=40.72  Aligned_cols=69  Identities=13%  Similarity=0.204  Sum_probs=48.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccH-HHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeecc---ccCCeeeEEec
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWT-RDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNI---HNKGKKHLMAV  102 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~-~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv---~~~~rK~YmL~  102 (252)
                      .++..+.+|+.++.+ .-..|-.. +.|...++. ++...+|..+|+.||++|||.+....   ..+.||+|-|.
T Consensus        31 ~~~~~~~~IL~lL~~-~~~~Gyei~k~l~~~~~~~~is~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT  104 (138)
T 2e1n_A           31 SKELAVCYVLAVLRH-EDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLA  104 (138)
T ss_dssp             CHHHHHHHHHHHHTT-SCEEHHHHHHHHHHHSTTEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEES
T ss_pred             cchHHHHHHHHHHHh-CCCcHHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEEC
Confidence            455667778888876 44445443 345543321 69999999999999999999997654   35678888763

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=92.39  E-value=0.3  Score=37.97  Aligned_cols=64  Identities=9%  Similarity=0.095  Sum_probs=41.8

Q ss_pred             HHHHHHHHHhhcCCCcccH-HHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEec
Q 025493           38 ERLIYDVIRSNKQDMGIWT-RDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAV  102 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~-~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~  102 (252)
                      +..|+.++.+ .-..|--. +.|...++..+++.+|..+|+.||..|||.+...  -..+.||+|-|.
T Consensus        16 ~~~IL~lL~~-~p~~gyel~~~l~~~~~~~i~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT   82 (117)
T 3elk_A           16 TLYILKELVK-RPMHGYELQKSMFETTGQALPQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHIT   82 (117)
T ss_dssp             HHHHHHHHHH-SCEEHHHHHHHHHHHHSCCCCTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEEC
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHHHHhCCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEEC
Confidence            4567777765 33333322 2233333113889999999999999999998764  245678888663

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=92.39  E-value=0.3  Score=37.75  Aligned_cols=48  Identities=15%  Similarity=0.228  Sum_probs=38.7

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .|+.++..+.++..+..++|..++  +++.+.+.|+|+.|++.|+|.+.+
T Consensus        13 ~iL~~la~~~~~~~~s~~ela~~~--~i~~~~v~~il~~L~~~Glv~~~~   60 (129)
T 2y75_A           13 TIMIELAKKHGEGPTSLKSIAQTN--NLSEHYLEQLVSPLRNAGLVKSIR   60 (129)
T ss_dssp             HHHHHHHHTTTSCCBCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHhCCCCCcCCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEecC
Confidence            344455551345678999999999  999999999999999999998764

>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=92.25  E-value=0.52  Score=37.91  Aligned_cols=52  Identities=15%  Similarity=0.237  Sum_probs=42.5

Q ss_pred             CCChHHHHHHHHHHhhcCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMG-----------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~G-----------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+.++++..-+++- +...|           +.+.+|..-+  |++...++|+|+.|+++|+|+.
T Consensus       137 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~~t~~~iA~~l--g~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          137 FLDVTGRIAQTLLNL-AKQPDAMTHPDGMQIKITRQEIGQIV--GCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             HSCHHHHHHHHHHHH-TTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCHHHHHHHHHHHH-HHhcCcCCCCCceEeccCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEe
Confidence            356788877766665 54432           5689999999  9999999999999999999986

>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=92.20  E-value=0.52  Score=38.46  Aligned_cols=60  Identities=15%  Similarity=0.279  Sum_probs=46.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMG-----------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~G-----------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+.++++..-+++- +...|           +.+.+|..-+  |++...|+|+|+.|+++|+|+.-      ++++.++
T Consensus       157 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~lt~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~~------~~~i~i~  227 (230)
T 3iwz_A          157 FLDVTDRIVRTLHDL-SKEPEAMSHPQGTQLRVSRQELARLV--GCSREMAGRVLKKLQADGLLHAR------GKTVVLY  227 (230)
T ss_dssp             HCCHHHHHHHHHHHH-TTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE------TTEEEEE
T ss_pred             cCCHHHHHHHHHHHH-HHhhCCCCCCCceecCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEEC------CCEEEEe
Confidence            457788877766665 54433           5789999999  99999999999999999999862      4555554

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=92.09  E-value=0.38  Score=35.20  Aligned_cols=44  Identities=11%  Similarity=0.267  Sum_probs=39.5

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|.++|.+ .  .-+...+|..++  ++...+|.+-|..||++|+|+++
T Consensus         6 ~Il~~L~~-~--g~vsv~eLa~~l--~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLAL-R--GRMEAAQISQTL--NTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHH-S--CSBCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHH-c--CCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            56777777 4  458899999999  99999999999999999999998

>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=92.08  E-value=0.38  Score=38.36  Aligned_cols=58  Identities=14%  Similarity=0.149  Sum_probs=44.3

Q ss_pred             HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      .-.|.. ..+ + ..++|..+.  ++|.+.|.|+|..|.+.|||.+++. +.    =|.|.  .|.++||
T Consensus        15 L~~La~-~~~-~-s~~~IA~~~--~i~~~~l~kIl~~L~~aGlv~s~rG-~G----Gy~La--r~p~~It   72 (145)
T 1xd7_A           15 LSLISM-DEK-T-SSEIIADSV--NTNPVVVRRMISLLKKADILTSRAG-VP----GASLK--KDPADIS   72 (145)
T ss_dssp             HHHHHT-CSC-C-CHHHHHHHH--TSCHHHHHHHHHHHHHTTSEECCSS-SS----SCEES--SCGGGCB
T ss_pred             HHHHHh-CCC-C-CHHHHHHHH--CcCHHHHHHHHHHHHHCCceEeecC-CC----Cceec--CCHHHCC
Confidence            334444 333 4 999999999  9999999999999999999999875 32    36663  4566665

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=92.03  E-value=0.36  Score=36.21  Aligned_cols=45  Identities=7%  Similarity=0.231  Sum_probs=40.5

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .|.++|.+ .  .-+..++|..++  ++...+|.+-|..||++|+|+++.
T Consensus         6 ~Il~~L~~-~--g~vsv~eLA~~l--~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLAL-Q--GRMEAKQLSARL--QTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHH-S--CSEEHHHHHHHT--TCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHH-c--CCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            57778877 4  468999999999  999999999999999999999985

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=92.03  E-value=0.26  Score=39.97  Aligned_cols=46  Identities=7%  Similarity=0.174  Sum_probs=38.4

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      -..|+.++.    +.++...+|...+  ++++..|++.|+.|+..|||...+
T Consensus        60 R~~IL~~L~----~~~~t~~eLa~~l--gls~stvs~hL~~L~~aGlV~~~~  105 (151)
T 3f6v_A           60 RRRLVQLLT----SGEQTVNNLAAHF--PASRSAISQHLRVLTEAGLVTPRK  105 (151)
T ss_dssp             HHHHHHHGG----GCCEEHHHHHTTS--SSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHH----hCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            344555553    3568999999999  999999999999999999999865

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=91.98  E-value=0.84  Score=35.48  Aligned_cols=40  Identities=20%  Similarity=0.337  Sum_probs=34.1

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..++|..+.  ++..+.|.++|+.|+..|+|...     +++-.|+.
T Consensus        39 s~~~La~~~--~vSr~tvr~Al~~L~~~G~i~~~-----~g~G~~V~   78 (125)
T 3neu_A           39 SVREMGVKL--AVNPNTVSRAYQELERAGYIYAK-----RGMGSFVT   78 (125)
T ss_dssp             CHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEEC
T ss_pred             CHHHHHHHH--CcCHHHHHHHHHHHHHCCeEEEe-----cCCEEEEe
Confidence            489999999  99999999999999999999886     34555543

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=91.92  E-value=0.41  Score=38.51  Aligned_cols=61  Identities=10%  Similarity=0.071  Sum_probs=47.7

Q ss_pred             CCCChHHHHHHHHHHhhcCCCc-----------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMG-----------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~G-----------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ...+.++++..-+++- +...|           +.+.+|..-+  |++...|+|+|+.|+++|+|+.-      ++++.+
T Consensus       108 ~~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~~------~~~i~i  178 (195)
T 3b02_A          108 QTGELRARIARYLLFL-ADTPLSARDRQGIYVTVSHEEIADAT--ASIRESVSKVLADLRREGLIATA------YRRVYL  178 (195)
T ss_dssp             TSSCHHHHHHHHHHHH-TTSTTEEEETTEEEEECCHHHHHHTT--TSCHHHHHHHHHHHHHHTSEEEE------TTEEEE
T ss_pred             hcCCHHHHHHHHHHHH-HHHcCCCCCCCeeeccCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEec------CCEEEE
Confidence            4567788887777665 54433           5789999999  99999999999999999999752      355555


Q ss_pred             e
Q 025493          101 A  101 (252)
Q Consensus       101 L  101 (252)
                      +
T Consensus       179 ~  179 (195)
T 3b02_A          179 L  179 (195)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=91.77  E-value=0.28  Score=45.55  Aligned_cols=48  Identities=27%  Similarity=0.371  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .++.|+++|.+ .|  .+.+.+|.+++  +|...+++++++.|++.|+|++..
T Consensus        40 n~~~il~~l~~-~~--~~sr~ela~~~--gls~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           40 NAGRVYKLIDQ-KG--PISRIDLSKES--ELAPASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHH-HC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHH-cC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecc
Confidence            46789999999 55  69999999999  999999999999999999999985

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=91.72  E-value=0.97  Score=37.21  Aligned_cols=63  Identities=5%  Similarity=0.062  Sum_probs=48.5

Q ss_pred             hHHHHHHHHHHhhcCCCcccHHHHHHHhhcC-CChHHHHHHHHHHHhcCCeeeeecc-----ccCCeeeEEe
Q 025493           36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVN-LPDNIVTKSIKSLQNKSLIKEVVNI-----HNKGKKHLMA  101 (252)
Q Consensus        36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~-l~~~~l~k~lK~Le~k~lIK~vksv-----~~~~rK~YmL  101 (252)
                      +....|++.+.. ....-.-..+|....  . |.+..|.+.|+.|+..|||+.+..-     ..+-+|.|.|
T Consensus        29 ~tR~~IL~~Ll~-~p~~~~ta~eL~~~l--~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~L   97 (151)
T 3u1d_A           29 ETRLDVLHQILA-QPDGVLSVEELLYRN--PDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAV   97 (151)
T ss_dssp             HHHHHHHHHHHH-STTSCBCHHHHHHHC--TTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEE
T ss_pred             hHHHHHHHHHHc-CCCCCCCHHHHHHhc--CCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEE
Confidence            355678888888 644447788998888  5 9999999999999999999987532     2334567766

>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=91.58  E-value=0.56  Score=38.89  Aligned_cols=55  Identities=18%  Similarity=0.221  Sum_probs=45.7

Q ss_pred             CCCCCChHHHHHHHHHHhhcCCCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           30 PSDSLTDHERLIYDVIRSNKQDMG------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        30 ~~~~l~~~e~~vy~~I~~~ag~~G------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .....+.++++..-+++- +...|      +.+.+|..-+  |++...|+|+|+.|+++|+|+.
T Consensus       158 ~l~~~~~~~Rl~~~L~~l-~~~~~~~~~~~~t~~~lA~~l--G~sr~tvsR~l~~l~~~glI~~  218 (232)
T 1zyb_A          158 DEPTLDLKSKIIRFFLSH-CEKPQGEKTFKVKMDDLARCL--DDTRLNISKTLNELQDNGLIEL  218 (232)
T ss_dssp             SCCCCSHHHHHHHHHHTT-CSSSSSCEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSCEE
T ss_pred             HHhhcCHHHHHHHHHHHH-HhhcCCeEEecCCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEe
Confidence            355678888888766665 65544      7899999999  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=91.58  E-value=0.69  Score=37.06  Aligned_cols=52  Identities=19%  Similarity=0.249  Sum_probs=40.8

Q ss_pred             CCChHHHHHHHHHHhhcCC-------C----cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQD-------M----GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~-------~----GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+.++++..-+.+- +..       .    -+.+++|..-+  |++...|+|+|+.|+++|+|+.
T Consensus       134 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  196 (207)
T 2oz6_A          134 FLDVTGRVARTLLDL-CQQPDAMTHPDGMQIKITRQEIGRIV--GCSREMVGRVLKSLEEQGLVHV  196 (207)
T ss_dssp             HCCHHHHHHHHHHHH-TTSTTCEEETTEEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHHHHHH-HHhcCCCCCCCceecccCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence            456778776555543 332       2    26789999999  9999999999999999999976

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=91.48  E-value=0.73  Score=34.12  Aligned_cols=47  Identities=15%  Similarity=0.261  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ....|+..+.. .|  +....+|...+  ++++..+++.|+.|++. +|..-+
T Consensus        28 ~Rl~IL~~l~~-~~--~~~~~ela~~l--~is~stvs~hL~~L~~~-lv~~~~   74 (99)
T 2zkz_A           28 MRLKIVNELYK-HK--ALNVTQIIQIL--KLPQSTVSQHLCKMRGK-VLKRNR   74 (99)
T ss_dssp             HHHHHHHHHHH-HS--CEEHHHHHHHH--TCCHHHHHHHHHHHBTT-TBEEEE
T ss_pred             HHHHHHHHHHH-CC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHH-hhhheE
Confidence            34456655555 33  58899999999  99999999999999999 998765

>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=91.47  E-value=2.5  Score=32.92  Aligned_cols=40  Identities=28%  Similarity=0.458  Sum_probs=34.6

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..++|..+.  ++..+.|.++|+.|+..|||...     +++-.|+.
T Consensus        40 ser~La~~~--gVSr~tVReAl~~L~~eGlv~~~-----~g~G~~V~   79 (134)
T 4ham_A           40 SIREFASRI--GVNPNTVSKAYQELERQEVIITV-----KGKGTFIA   79 (134)
T ss_dssp             CHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEEC
T ss_pred             cHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE-----cCcEEEEe
Confidence            678999999  99999999999999999999886     45556653

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=91.42  E-value=0.3  Score=39.89  Aligned_cols=63  Identities=13%  Similarity=0.279  Sum_probs=43.5

Q ss_pred             HHHHHHHhhcCCCcccH-HHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeecc---ccCCeeeEEecc
Q 025493           40 LIYDVIRSNKQDMGIWT-RDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNI---HNKGKKHLMAVE  103 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~-~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv---~~~~rK~YmL~~  103 (252)
                      +|+.++.+ .-..|--. +.|...++. ++...+|..+|+.||++|||.+....   ..+.||+|-|.+
T Consensus        48 ~IL~lL~~-~p~~GYeI~k~l~~~~~~~~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~  115 (148)
T 2zfw_A           48 YVLAVLRH-EDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQ  115 (148)
T ss_dssp             HHHHHHTT-CCEEHHHHHHHHHHHCTTEECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESS
T ss_pred             HHHHHHHh-CCCcHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECH
Confidence            47777765 44444433 344443311 59999999999999999999987643   256789987743

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=91.10  E-value=0.91  Score=35.67  Aligned_cols=54  Identities=7%  Similarity=0.139  Sum_probs=46.8

Q ss_pred             HHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          129 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       129 l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      -|..|+.+|...  ..+|++||.+.+++.+   -.++..-|-+.|+.|+-.|.|.++..
T Consensus        19 qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~---~~is~aTVYR~L~~L~e~Glv~~~~~   74 (136)
T 1mzb_A           19 PRVKILQMLDSAEQRHMSAEDVYKALMEAG---EDVGLATVYRVLTQFEAAGLVVRHNF   74 (136)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTT---CCCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            467888888754  5899999999999876   35789999999999999999999874

>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=91.06  E-value=0.75  Score=39.01  Aligned_cols=60  Identities=17%  Similarity=0.245  Sum_probs=45.8

Q ss_pred             CCChHHHHHHHHHHhhcCCC-----------cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDM-----------GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~-----------GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+.++++..-+++- +...           -+.+.+|..-+  |+....|+|+|+.|+++|+|+.      .++++.++
T Consensus       187 ~~~~~~Rla~~Ll~l-~~~~~~~~~~~~~~l~lt~~~lA~~l--G~sr~tvsR~l~~L~~~GlI~~------~~~~i~I~  257 (260)
T 3kcc_A          187 FLLVTGRIAQTLLNL-AKQPDAMTHPDGMQIKITRQEIGQIV--GCSRETVGRILKMLEDQNLISA------HGKTIVVY  257 (260)
T ss_dssp             HCCHHHHHHHHHHHH-HTSTTCEEETTEEEEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------CSSEEEEC
T ss_pred             cCCHHHHHHHHHHHH-HHhcCCCCCCCceeecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEE------cCCEEEEE
Confidence            356788877666654 4332           24689999999  9999999999999999999985      24566654

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=91.02  E-value=0.32  Score=39.85  Aligned_cols=68  Identities=10%  Similarity=0.169  Sum_probs=51.9

Q ss_pred             CCCCChHHHHHHHHHHhhcCC--CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493           31 SDSLTDHERLIYDVIRSNKQD--MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~--~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~  102 (252)
                      .+++---+.-.|+-|...--+  +=|....|-.++  ++.-+.-.++|+.||++|+||.|  +++....||.-.
T Consensus        39 ~nn~VlfDk~tydKL~KEVpk~gKlITpsvlseRl--kI~gSLARkaLreL~~kGlIk~V--~kh~~q~IYTra  108 (143)
T 2xzm_8           39 VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKL--KVNGSLARQLMRTMADRKLVEKV--AKNGNQWVYSVI  108 (143)
T ss_dssp             CCCBSCCCHHHHHHHHTCCTTSCSEECHHHHHHHH--CBCHHHHHHHHHHHHHTTSEEEE--EEETTEEEEEET
T ss_pred             HhcceeecHHHHHHHHHHhcccceeecHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEEecC
Confidence            344433445667666532444  579999999999  99999999999999999999999  455578888654

>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=90.87  E-value=0.62  Score=37.25  Aligned_cols=61  Identities=8%  Similarity=0.037  Sum_probs=44.7

Q ss_pred             HHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCC
Q 025493           43 DVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGG  113 (252)
Q Consensus        43 ~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG  113 (252)
                      -.+.. .++.-+..++|..+.  +++.+.|.|+|..|.+.|||.+++. +    --|.|.  .|.++||=|
T Consensus        21 ~~La~-~~~~~~~~~~iA~~~--~i~~~~l~kil~~L~~~Glv~s~rG-~----GGy~L~--~~p~~Itl~   81 (149)
T 1ylf_A           21 SILKN-NPSSLCTSDYMAESV--NTNPVVIRKIMSYLKQAGFVYVNRG-P----GGAGLL--KDLHEITLL   81 (149)
T ss_dssp             HHHHH-SCGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CCEEES--SCGGGCBHH
T ss_pred             HHHHh-CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEccC-C----CceEeC--CChhhCcHH
Confidence            33444 344568899999999  9999999999999999999998765 2    247663  555666633

>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=90.71  E-value=0.44  Score=39.07  Aligned_cols=52  Identities=12%  Similarity=0.136  Sum_probs=42.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCc------------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMG------------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~G------------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+.++++..-+.+- +...|            +.+.+|..-+  |++...|+|+|+.|++.|+|+.
T Consensus       132 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~~~~~~t~~~lA~~l--G~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          132 FHDIKQRIAGFFIDH-ANTTGRQTQGGVIVSVDFTVEEIANLI--GSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             THHHHHHHHHHHHHT-CBCCCSCC--CCCCEECCCHHHHHHHH--CSCHHHHHHHHHHHHHTTSSEE
T ss_pred             cCCHHHHHHHHHHHH-HHHhCCCCCCcEEEeccCCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEE
Confidence            345677777666665 64433            6899999999  9999999999999999999976

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=90.66  E-value=0.65  Score=38.15  Aligned_cols=62  Identities=13%  Similarity=0.260  Sum_probs=39.3

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhh----c--CCChHHHHHHHHHHHhcCCeeeeeccc--cCCeeeEEecc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELK----V--NLPDNIVTKSIKSLQNKSLIKEVVNIH--NKGKKHLMAVE  103 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~----~--~l~~~~l~k~lK~Le~k~lIK~vksv~--~~~rK~YmL~~  103 (252)
                      +..|+.++.+ .   ...--+|++...    .  ++...+|.++|+.||++|||.+.....  .+.||+|-|.+
T Consensus         4 ~~~iL~lL~~-~---~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~   73 (179)
T 1yg2_A            4 PHVILTVLST-R---DATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQ   73 (179)
T ss_dssp             HHHHHHHHHH-C---CBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECH
T ss_pred             HHHHHHHHhc-C---CCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeCh
Confidence            3456666655 3   244455555541    1  588999999999999999999865542  36799998765

>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=90.65  E-value=0.3  Score=40.46  Aligned_cols=55  Identities=24%  Similarity=0.456  Sum_probs=48.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ..||+.|..+++.|++.-...|+  .+++|.+++  |+. ++.+++.++.|+++++|..-
T Consensus         2 ~~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~l--giss~~tv~~~~~~l~~~~~l~~~   59 (202)
T 1jhf_A            2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRL--GFRSPNAAEEHLKALARKGVIEIV   59 (202)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHT--TCSSHHHHHHHHHHHHHTTSEEEC
T ss_pred             CccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHh--CCCChHHHHHHHHHHHHCCCceeC
Confidence            36999999999999884466788  999999999  999 89999999999999988753

>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=90.37  E-value=0.5  Score=37.82  Aligned_cols=55  Identities=9%  Similarity=0.125  Sum_probs=47.3

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      -|..|+.+|...+.+|++||++.+++.+   -.++..-|.+.|+.|+-.|.|.++...
T Consensus        20 qR~~Il~~l~~~~h~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Glv~~i~~~   74 (145)
T 3eyy_A           20 QRQLVLEAVDTLEHATPDDILGEVRKTA---SGINISTVYRTLELLEELGLVSHAHLG   74 (145)
T ss_dssp             HHHHHHHHHHHHSSBCHHHHHHHHHTTC---TTCCHHHHHHHHHHHHHHTSEEEEECG
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHhhC---CCCCHhHHHHHHHHHHHCCcEEEEEeC
Confidence            4677888887666999999999999876   357899999999999999999998753

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=89.96  E-value=0.91  Score=35.44  Aligned_cols=56  Identities=7%  Similarity=0.207  Sum_probs=47.7

Q ss_pred             HHHHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          128 VVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       128 ~l~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      .-|..|+.+|... +.+|++||++.+++.+   -.++..-|-+.|+.|+-.|.|.++...
T Consensus        11 ~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Glv~~~~~~   67 (131)
T 2o03_A           11 RQRAAISTLLETLDDFRSAQELHDELRRRG---ENIGLTTVYRTLQSMASSGLVDTLHTD   67 (131)
T ss_dssp             HHHHHHHHHHHHCCSCEEHHHHHHHHHHTT---CCCCHHHHHHHHHHHHTTTSEEEEECT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC---CCCCHhhHHHHHHHHHHCCCEEEEEeC
Confidence            4577888888754 5899999999999876   367899999999999999999998754

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=89.82  E-value=0.9  Score=36.00  Aligned_cols=56  Identities=5%  Similarity=0.130  Sum_probs=48.0

Q ss_pred             HHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          128 VVKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       128 ~l~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      .-|..|+++|.. .+.+|++||++.+++.+   -.++..-|.+.|+.|+-.|.|.++...
T Consensus        14 ~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~---~~is~aTVYR~L~~L~e~Glv~~~~~~   70 (139)
T 3mwm_A           14 RQRAAVSAALQEVEEFRSAQELHDMLKHKG---DAVGLTTVYRTLQSLADAGEVDVLRTA   70 (139)
T ss_dssp             HHHHHHHHHHTTCSSCEEHHHHHHHHHHTT---CCCCHHHHHHHHHHHHHTTSSEEEECT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC---CCCCHHHHHHHHHHHHHCCCEEEEEcC
Confidence            457788998876 46899999999999876   358899999999999999999998753

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=89.79  E-value=1.3  Score=34.75  Aligned_cols=66  Identities=12%  Similarity=0.092  Sum_probs=51.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+.-..|++++.+ ++..-+...+|-.+++   +++...+|-|.|+.|++.|+|.++..-.  +...|-+
T Consensus        15 r~T~qR~~Il~~L~~-~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~   83 (136)
T 1mzb_A           15 KVTLPRVKILQMLDS-AEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDG--GHAVFEL   83 (136)
T ss_dssp             CCCHHHHHHHHHHHC-C-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSS--SSCEEEE
T ss_pred             CCCHHHHHHHHHHHh-CCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCC--CceEEEe
Confidence            578899999999998 7645688888877652   3799999999999999999999986543  3445644

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=89.79  E-value=1.1  Score=37.34  Aligned_cols=113  Identities=11%  Similarity=0.060  Sum_probs=84.7

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCC
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEG  119 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~  119 (252)
                      .|+.++.    .-...+..|-+++  ||.-.++.=+|+.||..|+|++|+.   .++.+++|.+-         .|-.  
T Consensus        15 ~ILE~Lk----~G~~~t~~Iak~L--GlShg~aq~~Ly~LeREG~V~~Vk~---GK~ayw~L~~s---------~y~~--   74 (165)
T 2vxz_A           15 DILALLA----DGCKTTSLIQQRL--GLSHGRAKALIYVLEKEGRVTRVAF---GNVALVCLSMD---------QYRQ--   74 (165)
T ss_dssp             HHHHHHT----TCCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSCEEEEE---TTEEEEESCHH---------HHHH--
T ss_pred             HHHHHHH----hCCccHHHHHHHh--CCcHHHHHHHHHHHHhcCceEEEEE---ccEEEEEecHH---------HHHH--
Confidence            4455544    3457888999999  9999999999999999999999864   35677777211         2211  


Q ss_pred             cCCHHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHc--------CCcceecCHHHHHHHHHHHhhc
Q 025493          120 SLDTEFIKVVKSQCLKQIIKL--KVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRAVVLD  177 (252)
Q Consensus       120 e~D~efV~~l~~~~~~~i~~~--~~~T~~~I~~~i~~~--------~i~~~~Ls~~di~~IL~tLVyD  177 (252)
                           .|+.+.+-+..+|...  .++|+.++++.|.+-        .+..+.-+...+-..|+-+.-|
T Consensus        75 -----kV~dilrel~~~l~s~gvk~i~p~~l~~li~~d~~~~~~~a~~v~v~~~~~~~l~fl~~~l~~  137 (165)
T 2vxz_A           75 -----LVDGMIREVERLVTTNKLKFISPPRLHDLIIKDPQARKFFSSIIPIAHRTAIILSFLNHLLKM  137 (165)
T ss_dssp             -----HHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSHHHHHHHHTTSCCSSCCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHcCCeeeCcHHHHHHHHhCHHHHHHHHHhcCcccchhHHHHHHHHHHHH
Confidence                 6777777777888754  589999999999864        3556777888888888776554

>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=89.78  E-value=0.33  Score=38.08  Aligned_cols=58  Identities=12%  Similarity=0.194  Sum_probs=46.6

Q ss_pred             HHHHHHH-HhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           39 RLIYDVI-RSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        39 ~~vy~~I-~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ...|+-| .+.-.-+=|....|-.++  ++.-+.-.++|+.|+++|+|+.|-  ++....+|-
T Consensus        44 k~t~dkl~KEVpk~KlITpsvlseRl--kI~gSLAR~aLreL~~kGlIk~V~--kh~~q~IYT  102 (108)
T 3u5c_Z           44 QEKYDRILKEVPTYRYVSVSVLVDRL--KIGGSLARIALRHLEKEGIIKPIS--KHSKQAIYT  102 (108)
T ss_dssp             THHHHHHHHHCSSCSSBSHHHHHHTT--CCCTTHHHHHHHHHSSSSSCEEEE--CCSSCCEEE
T ss_pred             HHHHHHHHHHccCCeEEeHHHhhhhh--hhhHHHHHHHHHHHHHCCCEEEEe--cCCCEEEEe
Confidence            4455544 343556778889999999  999999999999999999999993  666778884

>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=89.33  E-value=0.56  Score=40.31  Aligned_cols=45  Identities=20%  Similarity=0.360  Sum_probs=38.3

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|+.++.+ .+ .++...+|-.++  +|+.+.+.|.|++|+..|+|...
T Consensus        10 ~iL~~l~~-~~-~~~s~~ela~~~--gl~~stv~r~l~~L~~~G~v~~~   54 (241)
T 2xrn_A           10 SIMRALGS-HP-HGLSLAAIAQLV--GLPRSTVQRIINALEEEFLVEAL   54 (241)
T ss_dssp             HHHHHHHT-CT-TCEEHHHHHHHT--TSCHHHHHHHHHHHHTTTSEEEC
T ss_pred             HHHHHHHh-CC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence            35556655 43 479999999999  99999999999999999999874

>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=89.21  E-value=0.83  Score=37.37  Aligned_cols=61  Identities=11%  Similarity=0.195  Sum_probs=44.8

Q ss_pred             HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      +-++.. ..+.-+..++|..+.  +++.+.|.|+|+.|.+.|+|.+++..+-    =|.|.  .|.++||
T Consensus        18 l~~La~-~~~~~~s~~~IA~~~--~is~~~l~kil~~L~~aGlv~s~rG~~G----Gy~La--r~p~~It   78 (162)
T 3k69_A           18 ILYLDA-HRDSKVASRELAQSL--HLNPVMIRNILSVLHKHGYLTGTVGKNG----GYQLD--LALADMN   78 (162)
T ss_dssp             HHHHHT-TTTSCBCHHHHHHHH--TSCGGGTHHHHHHHHHTTSSEEECSTTC----EEECC--SCGGGSB
T ss_pred             HHHHHh-CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCCCC----CeEec--CChhhCc
Confidence            334444 444558999999999  9999999999999999999988755432    26664  3444443

>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=88.91  E-value=0.7  Score=39.75  Aligned_cols=45  Identities=16%  Similarity=0.200  Sum_probs=38.8

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|+.++.+ .+ .++...+|-.++  +|+.+.+.|.|++|+..|+|...
T Consensus        12 ~iL~~l~~-~~-~~~~~~ela~~~--gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           12 EILDFIVK-NP-GDVSVSEIAEKF--NMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHH-CS-SCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHh-CC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEC
Confidence            46666766 43 479999999999  99999999999999999999874

>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=88.80  E-value=6.5  Score=30.02  Aligned_cols=112  Identities=8%  Similarity=0.067  Sum_probs=83.1

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcccc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYS  117 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~  117 (252)
                      +..|-.++.. +|.. +-..+|...+  +++..++...|..|...+-|..+..   .+...|                  
T Consensus         4 ~~~l~~~L~~-~~~~-~~~~~l~~~~--~l~~~~l~~~l~~l~~~~~~~~~~~---~~~~~~------------------   58 (135)
T 2v9v_A            4 EKILAQIIQE-HREG-LDWQEAATRA--SLSLEETRKLLQSMAAAGQVTLLRV---ENDLYA------------------   58 (135)
T ss_dssp             HHHHHHHHHH-CSSC-EEHHHHHHHH--TCCHHHHHHHHHHHHHTTCEEEEEE---TTEEEE------------------
T ss_pred             HHHHHHHHHH-cCcC-CCHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEEec---CCCeEE------------------
Confidence            3467777888 7766 4449999999  9999999999999988777666532   111112                  


Q ss_pred             CCcCCHHHHHHHHHHHHHHhhh-------CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          118 EGSLDTEFIKVVKSQCLKQIIK-------LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       118 d~e~D~efV~~l~~~~~~~i~~-------~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                         +..+..+.+++.+...|..       +..+.-+++.+.+-      -.++..-+..+|+.|+-+|.|...
T Consensus        59 ---~~~~~~~~l~~~l~~~L~~yH~~~P~~~G~~keeLr~~~~------~~~~~~~~~~ll~~l~~~g~l~~~  122 (135)
T 2v9v_A           59 ---ISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYF------SRLPARVYQALLEEWSREGRLQLA  122 (135)
T ss_dssp             ---EEHHHHHHHHHHHHHHHHHHHHHCTTSSCEEHHHHHHHHC------TTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             ---ecHHHHHHHHHHHHHHHHHHHHhCCCccCCCHHHHHHHhc------ccCCHHHHHHHHHHHHHCCCEEec
Confidence               4566788888888888873       35677788776652      124688899999999999999753

>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=88.71  E-value=7  Score=30.24  Aligned_cols=109  Identities=17%  Similarity=0.204  Sum_probs=70.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      +.++.+++.  .++.. . ..|...++|.+.+  +++.++|.+.++..+..|....                 .|    .
T Consensus        31 ~~~s~e~r~--~iv~~-~-~~G~s~~~iA~~l--gis~~TV~rw~~~~~~~G~~~~-----------------~~----r   83 (149)
T 1k78_A           31 RPLPDVVRQ--RIVEL-A-HQGVRPCDISRQL--RVSHGCVSKILGRYYETGSIKP-----------------GV----I   83 (149)
T ss_dssp             SCCCHHHHH--HHHHH-H-HTTCCHHHHHHHH--TCCHHHHHHHHHHHHHHSCCCC-----------------CC----C
T ss_pred             CCCCHHHHH--HHHHH-H-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCCCc-----------------cC----C
Confidence            357777653  34444 3 2478899999999  9999999999999987775321                 01    0


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHH
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRA  173 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~t  173 (252)
                      +|.  ....++.++.+.|.    .++......|+.+|+..+...++.  .+.+|..-|..+|..
T Consensus        84 ~gr--~~~~~~~~~~~~I~----~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~  141 (149)
T 1k78_A           84 GGS--KPKVATPKVVEKIA----EYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRT  141 (149)
T ss_dssp             CCC--CCSSSCHHHHHHHH----HHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHC
T ss_pred             CCC--CCCCCCHHHHHHHH----HHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHH
Confidence            110  01235555555444    444555678999999999776421  245777878777753

>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=88.64  E-value=0.23  Score=38.94  Aligned_cols=48  Identities=15%  Similarity=0.198  Sum_probs=40.7

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .-+=|....|-.++  ++.-+.-.++|+.|+++|+|+.|  +++....+|--
T Consensus        57 k~KlITpsvlseRl--kI~gSLAR~aLreL~~kGlIk~V--~kh~~q~IYTr  104 (108)
T 3iz6_V           57 KYKQITPSVLSERL--RINGSLARQAIKDLESRGAIRVV--SVHSSQLIYTR  104 (108)
T ss_dssp             HHSSEEEHHHHHHH--HTCCHHHHHHHHHHHHHHTSCEE--CCCTTSCCEEE
T ss_pred             CCeEEeHHHHHhhh--cccHHHHHHHHHHHHHCCCEEEE--ecCCCEEEEec
Confidence            34677788888999  99999999999999999999999  46667788853

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=88.63  E-value=1.9  Score=30.55  Aligned_cols=47  Identities=11%  Similarity=0.099  Sum_probs=40.4

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      +..++.+|...+.+|..||++.+        .+|..-|.+.|+.|+-.|.|++..
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~l--------gvs~~tv~r~L~~L~~~GlI~~~~   48 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEAL--------AVTDYQARYYLLLLEKAGMVQRSP   48 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHH--------TSCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEec
Confidence            56788889888889999999876        367889999999999999998754

>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=88.42  E-value=1.1  Score=40.78  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=48.5

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC-eeeeeccccCCeeeEEec
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL-IKEVVNIHNKGKKHLMAV  102 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l-IK~vksv~~~~rK~YmL~  102 (252)
                      |++-.+.|++++.+ +.+.-+.-.+|..++  ++..+.|.|.|+.|++.|+ |.++      ..|-|.|.
T Consensus         1 M~~~~~~iL~~L~~-~~g~~~Sg~eLa~~l--gvSr~aV~k~i~~L~~~G~~i~~~------~~~GY~L~   61 (323)
T 3rkx_A            1 MSKYSQDVLQLLYK-NKPNYISGQSIAESL--NISRTAVKKVIDQLKLEGCKIDSV------NHKGHLLQ   61 (323)
T ss_dssp             --CHHHHHHHHHHH-HTTSCBCHHHHHHHH--TSCHHHHHHHHHHHHHTTCEEEEE------TTTEEEEE
T ss_pred             CchHHHHHHHHHHh-CCCCccCHHHHHHHH--CCCHHHHHHHHHHHHhcCCeEEEe------CCCeEEEe
Confidence            45566789999988 877889999999999  9999999999999999999 4444      23467664

>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=88.41  E-value=1.3  Score=36.28  Aligned_cols=52  Identities=6%  Similarity=0.080  Sum_probs=41.6

Q ss_pred             CCChHHHHHHHHHH---hhcC--------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIR---SNKQ--------DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~---~~ag--------~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+.++++..-+++   . .|        .--+.+++|..-+  |++...|+|+|+.|+++|+|+.
T Consensus       150 ~~~~~~Rl~~~L~~l~~~-~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          150 QKHVRGRLAETLLILKEN-FGFENDGATLSIYLSREELATLS--NMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             HSCHHHHHHHHHHHHHHH-HCBCTTSSBBSCCCCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHHHHHHHHH-cCCCCCCcEEEcccCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEee
Confidence            35677877665554   4 33        1346889999999  9999999999999999999976

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=88.34  E-value=1.4  Score=35.34  Aligned_cols=57  Identities=12%  Similarity=0.165  Sum_probs=47.7

Q ss_pred             HHHHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493          128 VVKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG  187 (252)
Q Consensus       128 ~l~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g  187 (252)
                      .-|..|+.+|.. ...+|++||++.+++.+   -.++..-|-+.|+.|+-.|.|.++...+
T Consensus        27 ~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~---~~is~aTVYR~L~~L~e~Glv~~~~~~~   84 (150)
T 2xig_A           27 KQREEVVSVLYRSGTHLSPEEITHSIRQKD---KNTSISSVYRILNFLEKENFISVLETSK   84 (150)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHHHHS---TTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhC---CCCCHhhHHHHHHHHHHCCcEEEEEeCC
Confidence            346678888875 46899999999999876   2578999999999999999999987543

>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=88.20  E-value=0.093  Score=46.61  Aligned_cols=54  Identities=20%  Similarity=0.353  Sum_probs=0.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +|++-+..||++|++++.++||-..+|.++++ +++..+|.++|..|.+.|+|=+
T Consensus       204 ~~~~~~~~Vl~~i~~~~~~~Gi~~~~I~~~l~-~~~~~~v~~al~~L~~eG~IYs  257 (270)
T 2pi2_A          204 GLTVAQNQVLNLIKACPRPEGLNFQDLKNQLK-HMSVSSIKQAVDFLSNEGHIYS  257 (270)
T ss_dssp             -------------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHhCCCccCCCHHHHHHHhc-CCCHHHHHHHHHHHHhCCEEec
Confidence            57788899999999966789999999999983 4999999999999999999854

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=88.06  E-value=0.71  Score=37.37  Aligned_cols=60  Identities=13%  Similarity=0.145  Sum_probs=45.5

Q ss_pred             CCChHHHHHHHHHHhhcCC-----CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQD-----MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~-----~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+.++++..-+.+. +..     --+.+.+|..-+  |++...++|+|+.|+++|+|+.      .++++.++
T Consensus       145 ~~~~~~Rl~~~L~~~-~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~L~~~g~I~~------~~~~i~i~  209 (220)
T 3dv8_A          145 WKSLDKRVASFLLEE-TSIEGTNELKITHETIANHL--GSHREVITRMLRYFQVEGLVKL------SRGKITIL  209 (220)
T ss_dssp             HSCHHHHHHHHHHHH-HHHHTSSEECCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------ETTEEEES
T ss_pred             cCCHHHHHHHHHHHh-hhhcCCceecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe------CCCEEEEe
Confidence            356677776666554 432     257899999999  9999999999999999999975      14556554

>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=88.04  E-value=0.93  Score=37.85  Aligned_cols=62  Identities=11%  Similarity=0.209  Sum_probs=46.8

Q ss_pred             CCCChHHHHHHHHHHh--hcC---------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           32 DSLTDHERLIYDVIRS--NKQ---------DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~--~ag---------~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ...+.++++..-+.+-  ..|         .--+.+.+|..-+  |++...|+|+|+.|+++|+|+.      .++++.+
T Consensus       145 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~iA~~l--G~sr~tvsR~l~~L~~~g~I~~------~~~~i~i  216 (250)
T 3e6c_C          145 NTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEIT--GVHHVTVSRVLASLKRENILDK------KKNKIIV  216 (250)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHCEEETTEEEEECCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------CSSEEEE
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCCCCCCcEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCeEe------CCCEEEE
Confidence            3467788776655543  033         1246899999999  9999999999999999999986      2466766


Q ss_pred             e
Q 025493          101 A  101 (252)
Q Consensus       101 L  101 (252)
                      +
T Consensus       217 ~  217 (250)
T 3e6c_C          217 Y  217 (250)
T ss_dssp             S
T ss_pred             e
Confidence            6

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=87.91  E-value=0.78  Score=33.43  Aligned_cols=47  Identities=11%  Similarity=0.087  Sum_probs=37.4

Q ss_pred             HHHHHHHhhhC------CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          130 KSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       130 ~~~~~~~i~~~------~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      .+.|+.||+..      ..||+.||++.+.        +|..-|+.-|+.|+-.|.|.++.
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~lg--------vS~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAAG--------LSIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHHT--------CCHHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHHC--------CCHHHHHHHHHHHHHCCcEEecC
Confidence            34566666554      7889999998763        46777999999999999999986

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=87.68  E-value=2.7  Score=33.26  Aligned_cols=65  Identities=14%  Similarity=0.202  Sum_probs=51.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|+.-..|++++.+ ++ .-+...+|-..++   +++...+|-|.|+.|++.|||.++..-.  +...|-+
T Consensus        19 r~T~qR~~Il~~L~~-~~-~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~   86 (145)
T 2fe3_A           19 RITPQRHAILEYLVN-SM-AHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGD--ASSRFDF   86 (145)
T ss_dssp             CCCHHHHHHHHHHHH-CS-SCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTT--SCCEEEE
T ss_pred             CCCHHHHHHHHHHHh-CC-CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCC--CceEEEC
Confidence            589999999999998 64 4688888877763   3799999999999999999999987643  3445543

>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=87.60  E-value=0.71  Score=37.74  Aligned_cols=52  Identities=8%  Similarity=0.129  Sum_probs=40.5

Q ss_pred             CCChHHHHHHHHHHhhc---CC---C------cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           33 SLTDHERLIYDVIRSNK---QD---M------GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~a---g~---~------GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..+.++++..-+.+- +   |.   .      -+.+.+|..-+  |++...|+|+|+.|+++|+|+.
T Consensus       146 ~~~~~~Rl~~~L~~l-~~~~~~~~~~~~~i~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          146 FTDVPGRVAKQLLQL-AQRFGTQEGGALRVTHDLTQEEIAQLV--GASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             HSCHHHHHHHHHHHH-HHHHEEEETTEEEEECCCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHHHHHH-HHHhCCcCCCceEEcCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence            456777776555443 3   21   1      26789999999  9999999999999999999976

>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=87.38  E-value=0.74  Score=38.48  Aligned_cols=60  Identities=15%  Similarity=0.131  Sum_probs=45.3

Q ss_pred             CCChHHHHHHHHHHhhcC------C------CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           33 SLTDHERLIYDVIRSNKQ------D------MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag------~------~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..+.++++..-+++- +.      .      --+-+.+|..-+  |+....|+|+|+.|+++|+|+.-      ++++.+
T Consensus       162 ~~~~~~Rla~~L~~l-~~~~g~~~~~~~~i~~~lt~~~lA~~l--G~sr~tvsR~l~~L~~~GlI~~~------~~~i~I  232 (243)
T 3la7_A          162 HRDMGSRLVSFLLIL-CRDFGVPCADGITIDLKLSHQAIAEAI--GSTRVTVTRLLGDLREKKMISIH------KKKITV  232 (243)
T ss_dssp             CSSHHHHHHHHHHHH-HHHHEEECSSSEEECSCCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE------TTEEEE
T ss_pred             cCCHHHHHHHHHHHH-HHHhCCCCCCCeEEeccCCHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEEc------CCEEEE
Confidence            456778776655543 32      2      236789999999  99999999999999999999852      456665


Q ss_pred             e
Q 025493          101 A  101 (252)
Q Consensus       101 L  101 (252)
                      +
T Consensus       233 ~  233 (243)
T 3la7_A          233 H  233 (243)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=87.38  E-value=2.2  Score=30.09  Aligned_cols=53  Identities=9%  Similarity=0.186  Sum_probs=45.0

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      .+..++.+|...+.+|..||++.+...    ..++..-|..+|+.|+-.|.|++.+.
T Consensus        10 ~e~~vL~~L~~~~~~t~~ei~~~l~~~----~~~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A           10 AELEVMKVIWKHSSINTNEVIKELSKT----STWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             HHHHHHHHHHTSSSEEHHHHHHHHHHH----SCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHhhc----CCccHHHHHHHHHHHHHCCCeEEEec
Confidence            356788888888899999999999853    24788999999999999999998864

>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=87.34  E-value=0.73  Score=37.55  Aligned_cols=51  Identities=12%  Similarity=0.191  Sum_probs=40.3

Q ss_pred             CChHHHHHHHHHHhhc---CC---------CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           34 LTDHERLIYDVIRSNK---QD---------MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        34 l~~~e~~vy~~I~~~a---g~---------~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .+.++++..-+.+- +   |.         -.+.+.+|..-+  |++...++|+|+.|+++|+|+.
T Consensus       137 ~~~~~Rl~~~L~~l-~~~~g~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          137 KDARLRLAEFLVQA-AMDTGLKVPQGIKLELGLNTEEIALML--GTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             HHHHHHHHHHHHHH-HHHHCEEETTEEEEECSSCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHH-HHHhCCCCCCcEEEeccCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEE
Confidence            45667766655443 3   32         247899999999  9999999999999999999976

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=87.31  E-value=1.6  Score=34.61  Aligned_cols=55  Identities=9%  Similarity=0.151  Sum_probs=46.7

Q ss_pred             HHHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          129 VKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       129 l~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      -|..|+.+|.. ...+|++||++.+++.+   -.++..-|-+.|+.|+-.|.|.++...
T Consensus        23 qR~~Il~~L~~~~~~~sa~ei~~~l~~~~---~~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           23 QRHAILEYLVNSMAHPTADDIYKALEGKF---PNMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             HHHHHHHHHHHCSSCCCHHHHHHHHGGGC---TTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhC---CCCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            46678888875 46899999999999876   357899999999999999999998754

>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=86.92  E-value=1.6  Score=31.95  Aligned_cols=51  Identities=14%  Similarity=0.224  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHhhhCC---CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          126 IKVVKSQCLKQIIKLK---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       126 V~~l~~~~~~~i~~~~---~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      -+.+.+.++.+|...+   ..|+.+|++-+.        ++...|++.|..|.-+|.|+.+.
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lg--------vsr~tV~~~L~~Le~~G~I~~~g   61 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLG--------TPKKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHT--------CCHHHHHHHHHHHHHTTSEEEES
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEecC
Confidence            3566788999999888   899999998765        66789999999999999998863

>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=86.91  E-value=3.8  Score=30.36  Aligned_cols=67  Identities=13%  Similarity=0.131  Sum_probs=55.7

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      .+-|..|+.++++ . -+||-..+|...++ +|+..+.-.+|..|-+.+-|.-.|   .++.-+|-+-+-.||
T Consensus        13 ~~ie~~IL~l~~~-~-P~GItd~~L~~~~p-~~~~~~r~~aIN~LL~~gkiel~K---~~~~liYr~k~~~~~   79 (81)
T 2dk8_A           13 VEIENRIIELCHQ-F-PHGITDQVIQNEMP-HIEAQQRAVAINRLLSMGQLDLLR---SNTGLLYRIKDSGPS   79 (81)
T ss_dssp             HHHHHHHHHHHHH-C-SSCEEHHHHHHHCT-TSCHHHHHHHHHHHHHHTSEEEEE---CSSSEEEEECCCCCC
T ss_pred             HHHHHHHHHHHHh-C-CCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHcCCeEEEe---cCCeEEEEecccccC
Confidence            3447779999988 6 69999999999995 899999999999999999998664   457778888776554

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=86.84  E-value=1  Score=36.26  Aligned_cols=58  Identities=9%  Similarity=0.164  Sum_probs=43.5

Q ss_pred             ChHHHHHHHHHHhhc--C---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           35 TDHERLIYDVIRSNK--Q---DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        35 ~~~e~~vy~~I~~~a--g---~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.++++..-+.+- +  |   .--+.+++|..-+  |++...|+|+|+.|+++|+|+.-      ++++.++
T Consensus       141 ~~~~Rl~~~L~~~-~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~~------~~~i~i~  203 (216)
T 4ev0_A          141 EARNRVAYALLKL-LRQGLGPLFQIRHHELAALA--GTSRETVSRVLHALAEEGVVRLG------PGTVEVR  203 (216)
T ss_dssp             HHHHHHHHHHHHH-HHTTCCSEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEE------TTEEEES
T ss_pred             CHHHHHHHHHHHH-hhcCCccCCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEec------CCEEEEe
Confidence            4566666655543 3  3   2346799999999  99999999999999999999752      3556554

>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=86.38  E-value=0.9  Score=37.21  Aligned_cols=40  Identities=13%  Similarity=0.252  Sum_probs=34.4

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.+++|..-+  |++...|+|+|+.|+++|+|+.      .++++.++
T Consensus       176 ~t~~~iA~~l--g~sr~tvsR~l~~L~~~g~I~~------~~~~i~i~  215 (231)
T 3e97_A          176 LGTQDIMART--SSSRETVSRVLKRLEAHNILEV------SPRSVTLL  215 (231)
T ss_dssp             CCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE------CSSCEEES
T ss_pred             CCHHHHHHHh--CCcHHHHHHHHHHHHHCCcEEe------cCCEEEEe
Confidence            5789999999  9999999999999999999985      24566654

>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=86.28  E-value=2  Score=35.17  Aligned_cols=61  Identities=10%  Similarity=0.061  Sum_probs=46.1

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMG--------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~G--------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ....+.++++..-+.+- +...|        +.+++|..-+  |++...|+|+|+.|+++| | .+     .++++.++
T Consensus       149 l~~~~~~~Rl~~~L~~~-~~~~~~~~~~~l~~t~~~iA~~l--g~sr~tvsR~l~~L~~~g-i-~~-----~~~~i~I~  217 (237)
T 3fx3_A          149 LKAQTGAQRVAEFLLEL-CDCDTGACEVTLPYDKMLIAGRL--GMKPESLSRAFSRLKAAG-V-TV-----KRNHAEIE  217 (237)
T ss_dssp             CCCCCHHHHHHHHHHHH-CCC-----EEECCSCTHHHHHHT--TCCHHHHHHHHHHHGGGT-E-EC-----CTTEEEES
T ss_pred             HhcCCHHHHHHHHHHHH-hhhcCCCeEEEecCCHHHHHHHh--CCCHHHHHHHHHHHHHCC-e-Ee-----eCCEEEEc
Confidence            35678889888877776 65433        3488999999  999999999999999999 4 22     24667665

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=86.18  E-value=1.4  Score=35.80  Aligned_cols=58  Identities=9%  Similarity=0.220  Sum_probs=43.6

Q ss_pred             ChHHHHHHHHHHhhcCC---------CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           35 TDHERLIYDVIRSNKQD---------MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~---------~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.++++..-+++. +..         --+.+++|..-+  |++...|+|+|+.|+++|+|+.      .++++.++
T Consensus       152 ~~~~Rl~~~L~~~-~~~~~~~~~~~~~~~t~~~lA~~l--g~sr~tvsR~l~~l~~~g~I~~------~~~~i~i~  218 (227)
T 3dkw_A          152 NATHRVVRYLLTL-AAHAPGENCRVEIPVAKQLVAGHL--SIQPETFSRIMHRLGDEGIIHL------DGREISIL  218 (227)
T ss_dssp             HHHHHHHHHHHHH-HCSSSSSCCCCCCCSCTHHHHHHT--TSCHHHHHHHHHHHHHHTSEEE------SSSCEEES
T ss_pred             CHHHHHHHHHHHh-hhhcCCCCeEEEecCCHHHHHHHh--CCCHHHHHHHHHHHHHCCcEEe------cCCEEEEe
Confidence            4567766555554 432         236789999999  9999999999999999999975      24556554

>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=86.15  E-value=0.69  Score=42.13  Aligned_cols=48  Identities=19%  Similarity=0.196  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      .++.|+++|. +   ..+.+.+|.+++  +|...+++++++.|++.|+|++...
T Consensus        21 ~~~~il~~l~-~---~~~sr~~la~~~--gls~~tv~~~v~~L~~~gli~~~~~   68 (380)
T 2hoe_A           21 NISRILKRIM-K---SPVSRVELAEEL--GLTKTTVGEIAKIFLEKGIVVEEKD   68 (380)
T ss_dssp             -CCCSHHHHH-H---SCBCHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHH-c---CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecC
Confidence            3456888887 3   469999999999  9999999999999999999999764

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=86.14  E-value=1.9  Score=34.59  Aligned_cols=66  Identities=12%  Similarity=0.132  Sum_probs=52.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|..-..|++++.+ ++..-+...+|-..+.   +++...+|-|.|+.|++.|+|.++..-.  +...|-+
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 KVTLPRLKILEVLQQ-PECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEG--GKSVFEL   82 (150)
T ss_dssp             CCCHHHHHHHHHHTS-GGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGG--GCEEEEE
T ss_pred             CCCHHHHHHHHHHHh-CCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCC--CceEEEe
Confidence            578898999999988 6535678888877652   3799999999999999999999986543  3445644

>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=85.76  E-value=1.5  Score=26.83  Aligned_cols=45  Identities=16%  Similarity=0.231  Sum_probs=33.9

Q ss_pred             CCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcC
Q 025493           32 DSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKS   83 (252)
Q Consensus        32 ~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~   83 (252)
                      ..|+++++ .|..+. .    .|+..++|.+.+  +++..+|.+.++..+..|
T Consensus         4 ~~l~~~~~~~i~~~~-~----~g~s~~~IA~~l--gis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C            4 SALSDTERAQLDVMK-L----LNVSLHEMSRKI--SRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             CCCCHHHHHHHHHHH-H----TTCCHHHHHHHH--TCCHHHHHHHHHCSTTTT
T ss_pred             CCCCHHHHHHHHHHH-H----cCCCHHHHHHHH--CcCHHHHHHHHhhHHhcC
Confidence            35777776 444443 2    378899999999  999999999998766543

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=85.36  E-value=2  Score=33.39  Aligned_cols=57  Identities=16%  Similarity=0.202  Sum_probs=46.7

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      +|..-..|++++.+ + +.-+...+|-.+++   +++...+|-|.|+.|++.|+|.++..-.
T Consensus         9 ~T~qR~~Il~~l~~-~-~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~   68 (131)
T 2o03_A            9 STRQRAAISTLLET-L-DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDT   68 (131)
T ss_dssp             HHHHHHHHHHHHHH-C-CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTT
T ss_pred             CCHHHHHHHHHHHh-C-CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCC
Confidence            57777889999988 6 34677888877652   3899999999999999999999987654

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=85.31  E-value=0.58  Score=34.84  Aligned_cols=48  Identities=10%  Similarity=0.178  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      ..+++.++.+|+..+ .|+.||++-+        .+|...|.+.|..|+-+|.|...
T Consensus        16 ~~~~~~IL~lL~~~g-~sa~eLAk~L--------giSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEG-ATAAQLTRQL--------NMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHHHHHSSST-EEHHHHHHHS--------SSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHHHHHcC-CCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeC
Confidence            577888889999776 9999998754        47889999999999999999875

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=84.97  E-value=1.6  Score=34.98  Aligned_cols=54  Identities=6%  Similarity=0.047  Sum_probs=46.4

Q ss_pred             HHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          129 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       129 l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      -|..|+.+|...  ..+|++||++.+++.+   -.++..-|.+.|+.|+-.|.|.++..
T Consensus        18 qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~---~~is~aTVYR~L~~L~e~Glv~~~~~   73 (150)
T 2w57_A           18 PRLKILEVLQQPECQHISAEELYKKLIDLG---EEIGLATVYRVLNQFDDAGIVTRHHF   73 (150)
T ss_dssp             HHHHHHHHHTSGGGSSEEHHHHHHHHHHTT---CCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhC---CCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            467788888754  6899999999999876   35789999999999999999999874

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=84.54  E-value=1.5  Score=39.06  Aligned_cols=50  Identities=14%  Similarity=0.273  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee-eee
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK-EVV   89 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK-~vk   89 (252)
                      +++++..+..- --..|+-+++|.+++  ++...+|.|-|+.|+++|+|+ ++.
T Consensus         6 ~~~~~~~ia~l-~~~~~~~~~ela~~l--~vS~~tIrRdL~~l~~~G~v~iri~   56 (315)
T 2w48_A            6 DIRLIVKIAQL-YYEQDMTQAQIAREL--GIYRTTISRLLKRGREQGIVTIAIN   56 (315)
T ss_dssp             HHHHHHHHHHH-HHTSCCCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHH-HHcCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEEec
Confidence            45566555555 667889999999999  999999999999999999998 763

>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=84.40  E-value=3.1  Score=33.04  Aligned_cols=65  Identities=14%  Similarity=0.192  Sum_probs=51.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -.+|..-+.|++++.+ ++  -+...+|-.+..   +++...+|-|.|+.|++.|+|.++..-..  ...|-+
T Consensus        15 ~r~T~qR~~Il~~l~~-~~--h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~--~~~Y~~   82 (145)
T 3eyy_A           15 YRLTPQRQLVLEAVDT-LE--HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHG--APTYHL   82 (145)
T ss_dssp             CCCCHHHHHHHHHHHH-HS--SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGG--CEEEEE
T ss_pred             CCcCHHHHHHHHHHHh-cC--CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCC--ceEEEe
Confidence            3578898999999999 76  688878766542   37899999999999999999999876433  344543

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=84.38  E-value=2.5  Score=33.81  Aligned_cols=65  Identities=8%  Similarity=0.134  Sum_probs=51.1

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|..-..|++++.+ ++. -+...+|-..++   +++...+|-|.|+.|++.|+|.++..-.  +...|-+
T Consensus        24 r~T~qR~~IL~~l~~-~~~-~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~   91 (150)
T 2xig_A           24 KNSKQREEVVSVLYR-SGT-HLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSK--SGRRYEI   91 (150)
T ss_dssp             -CHHHHHHHHHHHHH-CSS-CBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETT--TEEEEEE
T ss_pred             CCCHHHHHHHHHHHh-CCC-CCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCC--CceEEEe
Confidence            578888899999998 743 678888876652   3799999999999999999999987654  3455543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=83.68  E-value=2.6  Score=28.56  Aligned_cols=45  Identities=20%  Similarity=0.346  Sum_probs=38.3

Q ss_pred             CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493           30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN   81 (252)
Q Consensus        30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~   81 (252)
                      ....|++.|+.|+.++ .    .|...++|...+  |++.+.|.+.++.+..
T Consensus         8 ~~~~L~~~e~~il~~~-~----~g~s~~eIA~~l--~is~~tV~~~~~~~~~   52 (74)
T 1fse_A            8 SKPLLTKREREVFELL-V----QDKTTKEIASEL--FISEKTVRNHISNAMQ   52 (74)
T ss_dssp             CCCCCCHHHHHHHHHH-T----TTCCHHHHHHHH--TSCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHH-H----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            4678999999999886 3    367999999999  9999999999888653

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=83.54  E-value=4  Score=33.18  Aligned_cols=58  Identities=9%  Similarity=0.141  Sum_probs=47.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHh-----hcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKREL-----KVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~-----~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      -.+|..-+.|++++.+ ++ .-+...+|-.+.     ++++...+|-|.|+.|++.|+|.++..-
T Consensus        29 ~r~T~qR~~IL~~L~~-~~-~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~~   91 (162)
T 4ets_A           29 LKYTKQREVLLKTLYH-SD-THYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISFG   91 (162)
T ss_dssp             CCCCHHHHHHHHHHHS-CC-SCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             CCCCHHHHHHHHHHHh-CC-CCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEeC
Confidence            3578888999999998 75 678888776543     3489999999999999999999998653

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=83.39  E-value=1.4  Score=38.80  Aligned_cols=45  Identities=16%  Similarity=0.287  Sum_probs=37.2

Q ss_pred             HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .|+.++.+ ++ .++-..+|-.++  +||.+++.|+|++|+..|++...
T Consensus        34 ~IL~~l~~-~~-~~ltl~eia~~l--gl~ksTv~RlL~tL~~~G~v~~~   78 (275)
T 3mq0_A           34 RILDLVAG-SP-RDLTAAELTRFL--DLPKSSAHGLLAVMTELDLLARS   78 (275)
T ss_dssp             HHHHHHHH-CS-SCEEHHHHHHHH--TCC--CHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHhh-CC-CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEC
Confidence            36666666 54 689999999999  99999999999999999999874

>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=83.33  E-value=1.7  Score=31.08  Aligned_cols=52  Identities=21%  Similarity=0.362  Sum_probs=39.4

Q ss_pred             cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493           23 KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN   81 (252)
Q Consensus        23 ~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~   81 (252)
                      ...........|++.|+.|+.++ .    .|...++|..++  ++..++|.+.++.+-+
T Consensus        11 ~~~~~~~~~~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l--~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           11 GSATTERDVNQLTPRERDILKLI-A----QGLPNKMIARRL--DITESTVKVHVKHMLK   62 (82)
T ss_dssp             ------CCGGGSCHHHHHHHHHH-T----TTCCHHHHHHHH--TSCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHH--CcCHHHHHHHHHHHHH
Confidence            34445556788999999999986 3    478999999999  9999999988877644

>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=83.13  E-value=5.1  Score=31.55  Aligned_cols=114  Identities=16%  Similarity=0.182  Sum_probs=72.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      +.++.+++.  .++.. . ..|...++|.+.+  +++.++|.+.++..+..|....                 .|    .
T Consensus        24 ~~~s~e~r~--~ii~l-~-~~G~s~~~IA~~l--gis~~TV~rwl~r~~~~G~~~~-----------------~~----r   76 (159)
T 2k27_A           24 RPLPEVVRQ--RIVDL-A-HQGVRPCDISRQL--RVSHGCVSKILGRYYETGSIRP-----------------GV----I   76 (159)
T ss_dssp             CSSCHHHHH--HHHHH-H-HHTCCHHHHHHHH--TCCSHHHHHHHCCSSTTSCCCC-----------------CC----C
T ss_pred             CCCCHHHHH--HHHHH-H-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHhcCCccC-----------------CC----C
Confidence            357777653  23333 2 2478999999999  9999999999998766554321                 00    0


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHHHhhcC
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAVVLDN  178 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~tLVyDg  178 (252)
                      +|.  ....++.++.+.    +..++......|+.+|.+.+...++.  .+.+|..-|..+|....-.|
T Consensus        77 ~gr--~~~~~~~~~~~~----I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~  139 (159)
T 2k27_A           77 GGS--KPKVATPKVVEK----IGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQP  139 (159)
T ss_dssp             CCC--CCCCCCTTHHHH----HHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCC
T ss_pred             CCC--CCCCCCHHHHHH----HHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCC
Confidence            110  011233334333    33444555678999999999877642  24688899999988765444

>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=82.84  E-value=2.5  Score=36.22  Aligned_cols=52  Identities=13%  Similarity=0.130  Sum_probs=40.3

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ++....-.+.+|.. . +..+-+++|..++  ++....|+..+|.|+++|||..-+
T Consensus        13 ls~s~EdYLk~I~~-L-~~~V~~~~LA~~L--gvS~~SV~~~lkkL~e~GLV~~~~   64 (200)
T 2p8t_A           13 PEYTVEDVLAVIFL-L-KEPLGRKQISERL--ELGEGSVRTLLRKLSHLDIIRSKQ   64 (200)
T ss_dssp             -CCCHHHHHHHHHH-T-TSCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCCCHHHHHHHHHH-H-cCCccHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence            33333334456666 5 4679999999999  999999999999999999997743

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=82.84  E-value=2.4  Score=34.53  Aligned_cols=53  Identities=11%  Similarity=0.122  Sum_probs=44.5

Q ss_pred             HHHHHHHhhhC-CCCCHHHHHHHHHHc--CCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          130 KSQCLKQIIKL-KVATLEGISDSIKRS--GAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       130 ~~~~~~~i~~~-~~~T~~~I~~~i~~~--~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      |..|+++|... ..+|++||++.+++.  +   -.++..-|-+.|+.|+-.|.|.++..
T Consensus        35 R~~IL~~L~~~~~h~sA~eI~~~l~~~~~~---~~is~aTVYRtL~~L~e~Glv~~i~~   90 (162)
T 4ets_A           35 REVLLKTLYHSDTHYTPESLYMEIKQAEPD---LNVGIATVYRTLNLLEEAEMVTSISF   90 (162)
T ss_dssp             HHHHHHHHHSCCSCBCHHHHHHHHHHHCGG---GCCCHHHHHHHHHHHHHTTSEEECC-
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhhcCC---CCCCHHHHHHHHHHHHHCCCEEEEEe
Confidence            56778887654 789999999999987  4   35789999999999999999998864

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=82.66  E-value=2.2  Score=33.70  Aligned_cols=65  Identities=11%  Similarity=0.128  Sum_probs=50.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+|..-+.|++++.+ ++. -+...+|-.+++   +++...+|-|.|+.|++.|+|.++..-.  +...|-+
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 RATRQRAAVSAALQE-VEE-FRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAE--GESVYRR   78 (139)
T ss_dssp             HHHHHHHHHHHHHTT-CSS-CEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTT--SCEEEEC
T ss_pred             ccCHHHHHHHHHHHh-CCC-CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CceEEEE
Confidence            467788889999988 653 788888877653   3799999999999999999999987643  3445644

>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=82.65  E-value=2.4  Score=42.70  Aligned_cols=148  Identities=7%  Similarity=0.076  Sum_probs=95.2

Q ss_pred             CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee--------ccccCCeeeEEe
Q 025493           30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV--------NIHNKGKKHLMA  101 (252)
Q Consensus        30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk--------sv~~~~rK~YmL  101 (252)
                      +.-..|..+..|+-+..+ .  ..+.-.+|...|  +|+...+.++|..|...+++..-+        .|. ++-...+=
T Consensus       583 ~~l~vs~~Qa~iLllFn~-~--~~~t~~ei~~~t--~i~~~~l~r~L~~l~k~~iL~~~~~~~~~~~~~~~-~~~~f~lN  656 (760)
T 1ldj_A          583 YTLQASTFQMAILLQYNT-E--DAYTVQQLTDST--QIKMDILAQVLQILLKSKLLVLEDENANVDEVELK-PDTLIKLY  656 (760)
T ss_dssp             CEEECCHHHHHHHHGGGS-S--SEEEHHHHHHHT--CCCHHHHHHHHHHHHHTTTEECSCTTCCTTTCCCC-TTCEEEEC
T ss_pred             EEEEEcHHHHHHHHHhcC-C--CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcceeCCCccccccCCCC-CCCEEEee
Confidence            344678889888876655 3  567889999999  999999999999999999887321        011 01111111


Q ss_pred             cccccCC---CccCCcccc---------CCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHH
Q 025493          102 VEFEPSK---DISGGAWYS---------EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEE  169 (252)
Q Consensus       102 ~~lePs~---eiTGG~wy~---------d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~  169 (252)
                      .++....   .|.. +-=.         ..+.+.+=...|..+|.+.+..+...+-+++..-+.+.=-.+...+..+|.+
T Consensus       657 ~~F~~k~~ri~i~~-~~~~e~~~e~~~~~~~v~~dR~~~i~AaIVRIMK~rK~l~h~~Lv~ev~~ql~~rF~p~~~~IKk  735 (760)
T 1ldj_A          657 LGYKNKKLRVNINV-PMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKK  735 (760)
T ss_dssp             SSCCCSSSSBCCCC-CCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHHTTTCCCCHHHHHH
T ss_pred             ccccCCceEEEecC-ccccccchhhhhHHHHHHHHHHhHheeeehhhhhccCCCcHHHHHHHHHHHHhccCCCCHHHHHH
Confidence            1111100   0000 0000         0112222223677888888888888888888776554321356789999999


Q ss_pred             HHHHHhhcCeeEEEe
Q 025493          170 IVRAVVLDNQIMEVK  184 (252)
Q Consensus       170 IL~tLVyDgkIE~v~  184 (252)
                      -|+.|+--+-|++..
T Consensus       736 ~Ie~LIereYl~R~~  750 (760)
T 1ldj_A          736 CIDILIEKEYLERVD  750 (760)
T ss_dssp             HHHHHHHTTSEEECS
T ss_pred             HHHHHhhccceeeCC
Confidence            999999999999864

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=82.58  E-value=1.1  Score=38.78  Aligned_cols=47  Identities=15%  Similarity=0.116  Sum_probs=38.6

Q ss_pred             HHHHHHHhhc-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           40 LIYDVIRSNK-QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        40 ~vy~~I~~~a-g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      ..+.+++..+ .+.++-..+|-+++  +++.+.+.|+|++|+..|+|..-
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            3445555523 24689999999999  99999999999999999999873

>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=82.20  E-value=3  Score=30.65  Aligned_cols=47  Identities=28%  Similarity=0.398  Sum_probs=38.5

Q ss_pred             CCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493           29 APSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK   82 (252)
Q Consensus        29 ~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k   82 (252)
                      .....||+.|+.|+.++.+     |...++|...+  ++..++|...++.+-.|
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~~-----G~s~~eIA~~L--~iS~~TV~~~~~~i~~K   71 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVEK-----GFTNQEIADAL--HLSKRSIEYSLTSIFNK   71 (90)
T ss_dssp             ----CCCHHHHHHHHHHHT-----TCCHHHHHHHH--TCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHHHc-----CCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence            3467899999999999865     89999999999  99999999988887443

>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=81.85  E-value=2  Score=32.50  Aligned_cols=33  Identities=6%  Similarity=0.312  Sum_probs=31.1

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ..++|..+.  ++..+.|.++|+.|++.|+|...+
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  999999999999999999998863

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B

Probab=81.82  E-value=15  Score=31.57  Aligned_cols=106  Identities=8%  Similarity=0.050  Sum_probs=72.6

Q ss_pred             HHhhcCCCcccHHHHHHHhhcC-------CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcccc
Q 025493           45 IRSNKQDMGIWTRDMKRELKVN-------LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYS  117 (252)
Q Consensus        45 I~~~ag~~GIw~~dik~~~~~~-------l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~  117 (252)
                      ... +|.. |--.|++...  |       +.+..+.|+++.|+..|+==++..+.  +.++++- . .|           
T Consensus        89 ~~~-~GG~-I~L~dl~~~~--nraRG~~lVSp~Dl~~A~~~l~~Lg~~~~l~~~~--sg~~vvq-s-~~-----------  149 (218)
T 3cuq_B           89 LEE-RGGI-MSLTEVYCLV--NRARGMELLSPEDLVNACKMLEALKLPLRLRVFD--SGVMVIE-L-QS-----------  149 (218)
T ss_dssp             HHH-TTSE-EEHHHHHHHH--HHTCSSSCCCHHHHHHHHHTTTTTTCSEEEEECT--TSBEEEE-E-TT-----------
T ss_pred             HHh-CCCe-EEHHHHHHHH--HHHcCCCCCCHHHHHHHHHHHHHcCCCEEEEEEC--CCcEEEE-c-CC-----------
Confidence            444 4544 7777887766  4       89999999999999988754555554  2333332 1 11           


Q ss_pred             CCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          118 EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       118 d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                       .++     +.....++.+++..+++|+.++.+-+        ..+..=.++.|+.++-+|.+-+=
T Consensus       150 -~~~-----~~~~~~il~~~~~~g~vt~~~la~~l--------~ws~~~a~e~L~~~e~~G~l~~D  201 (218)
T 3cuq_B          150 -HKE-----EEMVASALETVSEKGSLTSEEFAKLV--------GMSVLLAKERLLLAEKMGHLCRD  201 (218)
T ss_dssp             -CCG-----GGGHHHHHHHHHHTSCBCHHHHHHHH--------TCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             -Cch-----HHHHHHHHHHHHHCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHcCCEEEE
Confidence             121     12334455566678999999999766        36677888999999999999764

>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=81.33  E-value=0.3  Score=44.37  Aligned_cols=49  Identities=14%  Similarity=0.193  Sum_probs=0.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK   86 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK   86 (252)
                      .+++.+..|+..|..   +.|+.+++|..++  ++...+|+|.|+.||++|+|+
T Consensus        17 ~~~~r~~~iL~~l~~---~~~~t~~eLa~~l--~vs~~Tv~r~l~~Le~~Glv~   65 (345)
T 2o0m_A           17 DVLQERFQILRNIYW---MQPIGRRSLSETM--GITERVLRTETDVLKQLNLIE   65 (345)
T ss_dssp             ------------------------------------------------------
T ss_pred             HhhHHHHHHHHHHHH---cCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEE
Confidence            355666677777776   3589999999999  999999999999999999997

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=81.29  E-value=3.2  Score=32.25  Aligned_cols=55  Identities=20%  Similarity=0.349  Sum_probs=41.0

Q ss_pred             HHHHHHHHhhcCCCc-------c-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           39 RLIYDVIRSNKQDMG-------I-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        39 ~~vy~~I~~~ag~~G-------I-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..||+.|.+ .=..|       + ..++|..+.  ++..+.|.++|+.|+..|+|...     +++-.|+.
T Consensus        14 ~~i~~~l~~-~I~~g~~~~G~~lPse~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~-----~g~G~~V~   76 (126)
T 3by6_A           14 LQLVDRIKN-EVATDVLSANDQLPSVRETALQE--KINPNTVAKAYKELEAQKVIRTI-----PGKGTFIT   76 (126)
T ss_dssp             HHHHHHHHH-HHHTTSSCTTCEECCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEEC
T ss_pred             HHHHHHHHH-HHHhCCCCCCCcCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe-----cCCeEEEc
Confidence            356666655 32222       3 689999999  99999999999999999999875     34545543

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=80.75  E-value=1.6  Score=36.97  Aligned_cols=68  Identities=13%  Similarity=0.220  Sum_probs=51.5

Q ss_pred             ccc-cCCcCCHHHHHHHHHHHHHHhhh-------CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          114 AWY-SEGSLDTEFIKVVKSQCLKQIIK-------LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       114 ~wy-~d~e~D~efV~~l~~~~~~~i~~-------~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      .|| .++-+  ..++.++..|++-+-+       ..-.++++|+.-++-+|.  -.++.+|+|.||-.|++||.|+-.-+
T Consensus       107 ~~f~~~~~~--lll~rlr~~v~r~l~rkv~~~~~~~rI~l~~i~~~l~~~~~--~~~~~~evE~ila~lI~~G~Ikg~I~  182 (203)
T 3t5x_A          107 AFFIRCGIF--LILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQV--EDVDIDEVQCILANLIYMGHVKGYIS  182 (203)
T ss_dssp             HHHHHHTCH--HHHHTHHHHHHHHHHHHHHHHHCCSEEEHHHHHHHHHHTTC--TTCCHHHHHHHHHHHHHHTSSCEEEE
T ss_pred             HHHHHCChH--HHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC--CCCCHHHHHHHHHHHHHcCceEEEEc
Confidence            355 45554  4578888888766643       456789999999987763  34689999999999999999985443

>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=80.64  E-value=2.4  Score=30.39  Aligned_cols=49  Identities=14%  Similarity=0.228  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhhhCC---CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          128 VVKSQCLKQIIKLK---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       128 ~l~~~~~~~i~~~~---~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      .+.+.++.+|...+   ..|+.||++-+.        ++...|.+.|..|.-+|.|+++.
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lg--------vs~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLG--------TPKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHC--------CCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEecC
Confidence            44678889999888   899999998764        66788999999999999999874

>1ldd_A APC2WHB, anaphase promoting complex; ubiquitin, ligase, ubiquitination, ring finger, winged-helix; 2.00A {Saccharomyces cerevisiae} SCOP: a.4.5.34

Probab=80.59  E-value=4.7  Score=29.34  Aligned_cols=55  Identities=15%  Similarity=0.098  Sum_probs=41.9

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcce---ecCHHHHHHHHHHHhhcCeeEEE
Q 025493          129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKV---DLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~---~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      .-..|.-.|.+.+...++.||..++=--....   ..|.+++++.|+.||-+|+++.+
T Consensus         9 ~w~yI~GMLtN~~slpl~RIh~mLkmf~~~~~~~~~it~~eL~~fL~~~v~e~kL~~~   66 (74)
T 1ldd_A            9 SLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYI   66 (74)
T ss_dssp             HHHHHHHHHHHHCSEEHHHHHHHHHHHSCGGGCCTTCCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCCCCcCCHHHHHHHHHHHHhCCeEEEe
Confidence            33444555568899999999999996543322   35779999999999999999853

>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=80.17  E-value=7.6  Score=26.63  Aligned_cols=51  Identities=6%  Similarity=0.169  Sum_probs=41.0

Q ss_pred             CCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHH----HHHHHH
Q 025493           28 NAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTK----SIKSLQ   80 (252)
Q Consensus        28 ~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k----~lK~Le   80 (252)
                      ...+..|++.|+.|+.+..-..|..|...++|...+  |++...|.+    +++.|.
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            345778999999999888742667899999999999  999888766    555554

>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=80.03  E-value=12  Score=28.52  Aligned_cols=79  Identities=14%  Similarity=0.174  Sum_probs=55.3

Q ss_pred             CCHHHHHH-HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcc
Q 025493          121 LDTEFIKV-VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKV  199 (252)
Q Consensus       121 ~D~efV~~-l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~  199 (252)
                      .+.+|+.- +.-.++..|.. +..+--+|.+.|.+..-....++..-|-.+|+.|+-+|.|+.......     ....++
T Consensus         4 ~~~~~~~g~l~~~IL~~L~~-~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~-----~~~~rk   77 (116)
T 3f8b_A            4 IPKEMLRAQTNVILLNVLKQ-GDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDES-----QGGRRK   77 (116)
T ss_dssp             -CHHHHHHHHHHHHHHHHHH-CCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC---------CCEE
T ss_pred             cHHHHHhchHHHHHHHHHHh-CCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccC-----CCCCce
Confidence            34556544 44456666664 678899999999987655568999999999999999999998653110     012457


Q ss_pred             eeeccc
Q 025493          200 CYKNVS  205 (252)
Q Consensus       200 ~YR~~~  205 (252)
                      .|+++.
T Consensus        78 ~Y~LT~   83 (116)
T 3f8b_A           78 YYRLTE   83 (116)
T ss_dssp             EEEECH
T ss_pred             EEEECH
Confidence            787764

---

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	252
d2dk5a1	78	a.4.5.85 (A:8-85) DNA-directed RNA polymerase III	8e-21

>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 = 81.3 bits (201), Expect = 8e-21
 Identities = 24/68 (35%), Positives = 40/68 (58%), Gaps = 3/68 (4%)

Query: 33  SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH 92
              + E+L+Y +I  +  + GIW+RD++   K NLP   + K +K+L++K LIK V ++ 
Sbjct: 10  GSDNQEKLVYQIIE-DAGNKGIWSRDVRY--KSNLPLTEINKILKNLESKKLIKAVKSVA 66

Query: 93  NKGKKHLM 100
              KK  M
Sbjct: 67  ASKKKVYM 74

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	252
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	99.97
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	98.1
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	97.87
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	97.84
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	97.83
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	97.82
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	97.8
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	97.74
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	97.68
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.65
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	97.6
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.55
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.53
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.48
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.46
d1okra_	120	Methicillin resistance regulatory protein MecI {St	97.46
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.38
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	97.37
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.36
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.36
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	97.32
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.26
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.2
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	96.99
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.89
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	96.89
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	96.74
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	96.64
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.51
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.48
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.33
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.33
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.05
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.03
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	95.64
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	95.47
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	95.15
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	95.08
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.05
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.05
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	94.71
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	94.3
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	94.24
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	94.21
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	94.14
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.04
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	93.95
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	93.89
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	93.68
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	93.6
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	93.42
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	93.35
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	92.8
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.77
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	92.71
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	92.35
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	92.3
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	92.27
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	92.03
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	91.87
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	91.71
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	90.85
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	90.26
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.1
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	89.86
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	88.89
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	88.2
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	87.98
d2v9va2	73	C-terminal fragment of elongation factor SelB {Moo	87.42
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	87.12
d1w5sa1	110	CDC6-like protein APE0152, C-terminal domain {Aero	86.82
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	86.72
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	86.08
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	85.15
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	84.85
d1ldda_	74	Anaphase promoting complex (APC) {Baker's yeast (S	84.72
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	83.7
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	83.64
d1fnna1	112	CDC6, C-terminal domain {Archaeon Pyrobaculum aero	83.52
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	83.24
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	82.68
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	82.37
d1dtla_	156	Troponin C {Chicken (Gallus gallus) [TaxId: 9031]}	81.78
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	81.59
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	80.57
d1exra_	146	Calmodulin {Ciliate (Paramecium tetraurelia) [TaxI	80.36

>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=7.3e-32  Score=200.92  Aligned_cols=77  Identities=30%  Similarity=0.540  Sum_probs=74.7

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493           25 PDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF  104 (252)
Q Consensus        25 ~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l  104 (252)
                      ++.+.++++|+++|++||++|++ |||+|||++|||.++  |||+++|+|+||+||+|+|||+|+||++++||+||||+|
T Consensus         2 ~~~a~k~~~l~~~E~lVY~~I~~-ag~~GIW~~dir~kt--nL~~~~l~K~LK~Lesk~lIK~VksV~~~~rK~YmL~~L   78 (78)
T d2dk5a1           2 SQNAGKMKGSDNQEKLVYQIIED-AGNKGIWSRDVRYKS--NLPLTEINKILKNLESKKLIKAVKSVAASKKKVYMLYNL   78 (78)
T ss_dssp             CCCCCCCCCSCSSHHHHHHHHHH-HCTTCEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEESSS
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHH-ccccceeHHHHHHHc--CCCHHHHHHHHHHHHhcCCceeecccCCCCeEEEEeccC
Confidence            56788899999999999999999 999999999999999  999999999999999999999999999999999999987

>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=98.10  E-value=1.8e-05  Score=60.70  Aligned_cols=66  Identities=20%  Similarity=0.305  Sum_probs=59.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +||..|..|+..|.. .++.+|..++|...+  ++..+.++++|+.||++|+|....+-..+..+.+-|
T Consensus        26 glt~~q~~vL~~l~~-~~~~~it~~ela~~~--~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~l   91 (135)
T d3broa1          26 DLTGTQMTIIDYLSR-NKNKEVLQRDLESEF--SIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKL   91 (135)
T ss_dssp             TCCHHHHHHHHHHHH-TTTSCCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEE
T ss_pred             CCCHHHHHHHHHHHH-cCCCCCCHHHHHHHH--CcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcc
Confidence            799999999999999 888999999999999  999999999999999999999999887755554444

>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=97.87  E-value=3e-05  Score=58.76  Aligned_cols=85  Identities=20%  Similarity=0.278  Sum_probs=70.3

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG  112 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG  112 (252)
                      +||..|..|+..|.+ ..+.++..++|.+.+  ++....++++++.||++|||...++.+. .|++++  .|+|.     
T Consensus        30 ~Ls~~q~~vL~~l~~-~~~~~~t~~~la~~l--~~~~~tvs~~i~~Le~~gli~r~~~~~D-~R~~~i--~LT~~-----   98 (115)
T d2frha1          30 SISFEEFAVLTYISE-NKEKEYYLKDIINHL--NYKQPQVVKAVKILSQEDYFDKKRNEHD-ERTVLI--LVNAQ-----   98 (115)
T ss_dssp             CCCHHHHHHHHHHHH-TCCSEEEHHHHHHHS--SSHHHHHHHHHHHHHHTTSSCCBCCSSS-SCCCEE--ECCSH-----
T ss_pred             CCCHHHHHHHHHHHc-CCCCCCCHHHHHHHH--CCCHhHHHHHHHHHHhhhhheeeecccC-CceEEE--EECHH-----
Confidence            799999999999999 888889999999999  9999999999999999999999999887 454443  24554     


Q ss_pred             CccccCCcCCHHHHHHHHHHHHHHh
Q 025493          113 GAWYSEGSLDTEFIKVVKSQCLKQI  137 (252)
Q Consensus       113 G~wy~d~e~D~efV~~l~~~~~~~i  137 (252)
                               -.++++.+...+.++|
T Consensus        99 ---------G~~~~~~~~~~~~~~i  114 (115)
T d2frha1          99 ---------QRKKIESLLSRVNKRI  114 (115)
T ss_dssp             ---------HHHHHHHHHHHHHHHH
T ss_pred             ---------HHHHHHHHHHHHHhhc
Confidence                     1556666666666655

>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=97.84  E-value=2.2e-05  Score=60.70  Aligned_cols=88  Identities=11%  Similarity=0.175  Sum_probs=72.4

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG  112 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG  112 (252)
                      +||..|..|+..|.. +++.|+-.++|...+  +++.+.++++++.||++|||...++-.. .|++++-  |+|.     
T Consensus        30 ~Ls~~q~~vL~~l~~-~~~~~~~~~~ia~~l--~~~~~~vs~~v~~L~~~glV~r~~~~~D-~R~v~i~--LT~~-----   98 (125)
T d1p4xa2          30 TLSFVEFTILAIITS-QNKNIVLLKDLIETI--HHKYPQTVRALNNLKKQGYLIKERSTED-ERKILIH--MDDA-----   98 (125)
T ss_dssp             SSCHHHHHHHHHHHT-TTTCCEEHHHHHHHS--SSCHHHHHHHHHHHHHHTSSEEEECSSS-TTCEEEE--CCHH-----
T ss_pred             CCCHHHHHHHHHHHH-ccCCCccHHHHHHHH--CCCcchHHHHHHHHHhccCEeeeecCCC-CCeEEEE--ECHH-----
Confidence            799999999999999 999999999999999  9999999999999999999999888877 5666654  4444     


Q ss_pred             CccccCCcCCHHHHHHHHHHHHHHhhhC
Q 025493          113 GAWYSEGSLDTEFIKVVKSQCLKQIIKL  140 (252)
Q Consensus       113 G~wy~d~e~D~efV~~l~~~~~~~i~~~  140 (252)
                      |         .++++.+...+-..|...
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         366666666666655543

>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=97.83  E-value=1.6e-05  Score=61.13  Aligned_cols=66  Identities=15%  Similarity=0.185  Sum_probs=60.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+||..|..|+..|.. .++.++..++|...+  ++..+.++++|+.||.+|+|..+++-.. .|.+|+-
T Consensus        30 ~~Lt~~q~~iL~~l~~-~~~~~~t~~eia~~~--~~~~~~vs~~l~~L~~~g~v~r~~~~~D-~R~~~i~   95 (125)
T d1p4xa1          30 VDMTIKEFILLTYLFH-QQENTLPFKKIVSDL--CYKQSDLVQHIKVLVKHSYISKVRSKID-ERNTYIS   95 (125)
T ss_dssp             CSSCHHHHHHHHHHHS-CSCSEEEHHHHHHHS--SSCGGGTHHHHHHHHHTTSCEEEECSSS-TTSEEEE
T ss_pred             cCCCHHHHHHHHHHHH-hccCCcCHHHHHHHh--CCCcchHHHHHHHHHHCCCceeecccCC-CCeEEEE
Confidence            4799999999999999 888899999999999  9999999999999999999999999765 5666654

>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=97.82  E-value=0.00015  Score=55.41  Aligned_cols=63  Identities=13%  Similarity=0.298  Sum_probs=55.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKH   98 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~   98 (252)
                      -+|+..|..|+..|.. .++ |+-.++|...+  ++.++.++++++.||++|||....+-..+..++
T Consensus        24 ~glt~~q~~iL~~l~~-~~~-~~t~~~la~~~--~~~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~   86 (137)
T d2fbha1          24 LGLSQARWLVLLHLAR-HRD-SPTQRELAQSV--GVEGPTLARLLDGLESQGLVRRLAVAEDRRAKH   86 (137)
T ss_dssp             GCCTTTHHHHHHHHHH-CSS-CCBHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCE
T ss_pred             cCCCHHHHHHHHHHHH-cCC-CCcHHHHHHHH--CCCHHHHHHHHHHHHHcCCccccCCCCCCCchh
Confidence            4799999999999987 655 89999999999  999999999999999999999998887643333

>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=97.80  E-value=2.7e-05  Score=55.08  Aligned_cols=55  Identities=20%  Similarity=0.360  Sum_probs=51.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      .+|++-++.||++|++..++.||-..+|+++++ +|+..+|.+++..|.+.|+|=+
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~-~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLK-HMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHST-TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHcc-CCCHHHHHHHHHHHHhCCceec
Confidence            589999999999999999999999999999984 7999999999999999999964

>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=97.74  E-value=2.9e-05  Score=58.93  Aligned_cols=67  Identities=13%  Similarity=0.221  Sum_probs=60.2

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .-+||..|..|+.+|.. +.+.|+..++|...+  +++.+.++++|+.||++|||....+-+. +|.+++-
T Consensus        27 ~~~Lt~~q~~vL~~l~~-~~~~~~t~~ela~~l--~~~~~~vs~~i~~Le~~gli~r~~~~~D-~R~~~i~   93 (115)
T d1hsja1          27 KFNLNYEEIYILNHILR-SESNEISSKEIAKCS--EFKPYYLTKALQKLKDLKLLSKKRSLQD-ERTVIVY   93 (115)
T ss_dssp             SCCCCHHHHHHHHHHHT-CSCSEEEHHHHHHSS--CCCHHHHHHHHHHHHTTTTSCCEECCSS-SSCCEEE
T ss_pred             hcCCCHHHHHHHHHHHc-cCCCCcCHHHHHHHH--CCChhhHHHHHHHHHHcCCeEEEeecCC-CceEEEE
Confidence            34899999999999998 888999999999999  9999999999999999999999999776 4656543

>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=97.68  E-value=0.0003  Score=53.85  Aligned_cols=66  Identities=12%  Similarity=0.186  Sum_probs=52.4

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+||..+..|+..|.+ .+ .|+-.++|-...  ++.++.++++|+.||++|||...++-..+..+.+.|
T Consensus        27 ~glt~~~~~~L~~l~~-~~-~~~t~~~la~~l--~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~l   92 (140)
T d3deua1          27 LELTQTHWVTLHNIHQ-LP-PDQSQIQLAKAI--GIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKL   92 (140)
T ss_dssp             TTCCHHHHHHHHHHHH-SC-SSEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC--------CEEEE
T ss_pred             cCCCHHHHHHHHHHHH-cC-CCccHHHHHHHH--CCCHhHHHHHHHHHHhCCCEEecccCCCCCceeeEE
Confidence            4899999999999988 64 599999999999  999999999999999999999999988755555554

>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=97.65  E-value=0.0003  Score=54.52  Aligned_cols=57  Identities=21%  Similarity=0.280  Sum_probs=52.6

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      +||..|..|+..|.+ .  .|+-.++|...+  ++..+.++++|+.||++|||....+-+.+
T Consensus        26 ~lt~~q~~iL~~i~~-~--~~~t~~~la~~l--~i~~~tvs~~l~~L~~~glI~r~~~~~D~   82 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCE-N--PGIIQEKIAELI--KVDRTTAARAIKRLEEQGFIYRQEDASNK   82 (144)
T ss_dssp             TCTTTHHHHHHHHHH-S--TTEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECSSCT
T ss_pred             CCCHHHHHHHHHHHh-C--CCCCHHHHHHHH--CccHhhHHHHHHHHHhhhcccccCCCCCC
Confidence            799999999999988 4  489999999999  99999999999999999999998887763

>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=97.60  E-value=0.00034  Score=52.16  Aligned_cols=54  Identities=20%  Similarity=0.424  Sum_probs=49.1

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      -+|++.|..||..+.+ .|  ++..++|.+.+  +++.+.++++|+.||++|||.....
T Consensus        16 lGlt~~e~~v~~~L~~-~g--~~t~~eia~~~--~i~~~~v~~~l~~L~~~GlV~r~~~   69 (109)
T d1sfxa_          16 LSFKPSDVRIYSLLLE-RG--GMRVSEIAREL--DLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             TCCCHHHHHHHHHHHH-HC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCCCHHHHHHHHHHHh-cC--CCCHHHHHHHh--CCCcchHHHHHHHHHhCCCEEEEec
Confidence            4799999999999998 55  77899999999  9999999999999999999987654

>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=97.55  E-value=0.00011  Score=56.58  Aligned_cols=64  Identities=14%  Similarity=0.132  Sum_probs=57.1

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +|+..|..|+..|.. .|  |+-.++|...+  +++.+.++++|+.||.+|||...++-+.+..+.+-|
T Consensus        27 glt~~q~~iL~~i~~-~~--~~t~~~la~~l--~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~L   90 (139)
T d2a61a1          27 GITPAQFDILQKIYF-EG--PKRPGELSVLL--GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVI   90 (139)
T ss_dssp             TCCHHHHHHHHHHHH-HC--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHh--CCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEE
Confidence            799999999999998 76  78899999999  999999999999999999999999888755555544

>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=97.53  E-value=0.00027  Score=54.45  Aligned_cols=65  Identities=18%  Similarity=0.252  Sum_probs=57.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+|+..+-.||.++-. ++ +++...+|..++  |++...++++|+.|+++|||+..++-.. .|+.|+.
T Consensus        22 ~Gl~~~~~~i~~~L~~-~~-~plt~~ela~~l--~vsk~~vs~~l~~L~~~GlV~r~~~~~d-rr~~~~~   86 (151)
T d1ku9a_          22 HGLNKSVGAVYAILYL-SD-KPLTISDIMEEL--KISKGNVSMSLKKLEELGFVRKVWIKGE-RKNYYEA   86 (151)
T ss_dssp             TTCCHHHHHHHHHHHH-CS-SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECCTTC-SSCEEEE
T ss_pred             cCCCHHHHHHHHHHHh-CC-CCcCHHHHHHHh--CCCcchHHHHHHHHHHCCCEEEEEcCCC-CceeEEe
Confidence            4799999999999998 77 469999999999  9999999999999999999999877665 4656655

>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=97.48  E-value=0.00022  Score=55.01  Aligned_cols=65  Identities=18%  Similarity=0.339  Sum_probs=57.0

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+||..|..|+..|.+   +.|+-..+|...+  ++....++++|+.||++|+|...++-+.+..+.+.|
T Consensus        32 ~~lt~~q~~vL~~l~~---~~~~t~~~la~~l--~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~l   96 (141)
T d1lnwa_          32 LDLTPPDVHVLKLIDE---QRGLNLQDLGRQM--CRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFL   96 (141)
T ss_dssp             CCCCHHHHHHHHHHHS---STTCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEE
T ss_pred             CCCCHHHHHHHHHHHH---CCCCCHHHHHHHH--CccHhHHHHHHHHHHHhhceeeeccCCCCcchhhcc
Confidence            4799999999999976   4479999999999  999999999999999999999999988765555544

>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=97.46  E-value=0.00053  Score=52.47  Aligned_cols=66  Identities=11%  Similarity=0.133  Sum_probs=56.7

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      ..+||..|..|+..|.. .|  |+-..+|...+  +++.+.++++++.||++|||...++-..+..+..-|
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 ISDMKTTELYAFLYVAL-FG--PKKMKEIAEFL--STTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVL   92 (140)
T ss_dssp             HHHSBHHHHHHHHHHHH-HC--CBCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEE
T ss_pred             hcCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhc
Confidence            34799999999999998 65  68999999999  999999999999999999999999887744444333

>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=97.46  E-value=0.0017  Score=48.82  Aligned_cols=114  Identities=13%  Similarity=0.186  Sum_probs=77.6

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCC
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSK  108 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~  108 (252)
                      .-+||+-|..|..+|=+ .|  ++..++|...+..  ++..++|...|+.||+||+|+.-++   .++.+|..  +.+. 
T Consensus         2 ~~~lt~~E~~VM~~lW~-~~--~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~---gr~~~Y~~--~~~~-   72 (120)
T d1okra_           2 TYEISSAEWEVMNIIWM-KK--YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD---NKIFQYYS--LVEE-   72 (120)
T ss_dssp             CCCCCHHHHHHHHHHHH-HS--SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE---TTEEEEEE--SSCH-
T ss_pred             CCCCCHHHHHHHHHHHc-CC--CCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEec---CCceEEee--cCCH-
Confidence            34799999999999999 76  7999998776522  7999999999999999999998664   34556633  1111 


Q ss_pred             CccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493          109 DISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV  174 (252)
Q Consensus       109 eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL  174 (252)
                                    .   +.+......++.+.-.-+...+..++-..    ..||.+|+++|-+.|
T Consensus        73 --------------~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~ls~~el~~L~~lL  117 (120)
T d1okra_          73 --------------S---DIKYKTSKNFINKVYKGGFNSLVLNFVEK----EDLSQDEIEELRNIL  117 (120)
T ss_dssp             --------------H---HHHHHHHHHHHHHHSTTCHHHHHHHHHHH----SCCCHHHHHHHHHHH
T ss_pred             --------------H---HHHHHHHHHHHHHHHcccHHHHHHHHHHc----cCCCHHHHHHHHHHH
Confidence                          1   23333444444433233445544444332    258999999988776

>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=97.38  E-value=0.00025  Score=52.64  Aligned_cols=65  Identities=17%  Similarity=0.220  Sum_probs=51.3

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC-CeeeEE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK-GKKHLM  100 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~-~rK~Ym  100 (252)
                      -+|++.|..|+..+-+ +++ ++...+|...+  +++.+.++++|+.||++|||...++-..+ ++++|+
T Consensus        17 ~gLs~~~~~iL~~L~~-~~~-~~t~~eLa~~~--~i~~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~   82 (109)
T d2d1ha1          17 YKITDTDVAVLLKMVE-IEK-PITSEELADIF--KLSKTTVENSLKKLIELGLVVRTKTEGKKIGRPKYY   82 (109)
T ss_dssp             HTCCHHHHHHHHHHHH-HCS-CEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEC-------CCEE
T ss_pred             cCcCHHHHHHHHHHHH-cCC-CCCHHHHHHHH--CccHhHHHHHHHHHHHCCCEEEeecCCCCCceeEEE
Confidence            3799999999988866 533 69999999999  99999999999999999999988765442 344554

>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=97.37  E-value=0.00026  Score=54.23  Aligned_cols=62  Identities=18%  Similarity=0.247  Sum_probs=55.0

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      +||..|..|+..|.. .  .|+..++|...+  +++...++++++.||++|||...++-+.+..+..
T Consensus        31 glt~~q~~vL~~i~~-~--~~~t~~~la~~l--~~~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l   92 (136)
T d2bv6a1          31 NLTYPQFLVLTILWD-E--SPVNVKKVVTEL--ALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFI   92 (136)
T ss_dssp             TCCHHHHHHHHHHHH-S--SEEEHHHHHHHT--TCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEE
T ss_pred             CCCHHHHHHHHHHHc-C--CCCCHHHHHHHH--CCCHhHHHHHHHHHHHCCCEEEeecCCcccchhh
Confidence            799999999999998 5  489999999999  9999999999999999999999888877433333

>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=97.36  E-value=0.00023  Score=54.40  Aligned_cols=62  Identities=8%  Similarity=0.194  Sum_probs=55.2

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      +||..|..|+..|.. .|  |+-.++|...+  +++...++++|+.||++|||...++-+.+..+..
T Consensus        27 glt~~q~~vL~~l~~-~~--~~t~~~la~~~--~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l   88 (136)
T d2fbia1          27 GLTEQQWRVIRILRQ-QG--EMESYQLANQA--CILRPSMTGVLARLERDGIVRRWKAPKDQRRVYV   88 (136)
T ss_dssp             TCCHHHHHHHHHHHH-HC--SEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeecCccCchhhh
Confidence            799999999999998 66  68999999999  9999999999999999999999998887433333

>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=97.36  E-value=0.00031  Score=53.98  Aligned_cols=60  Identities=13%  Similarity=0.260  Sum_probs=54.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK   96 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r   96 (252)
                      .+|+..|..|+..|.. .|  |+...+|.+.+  +++...++++++.||.+|||...++-+.+..
T Consensus        31 ~glt~~q~~iL~~l~~-~~--~~t~~~la~~~--~i~~~~vs~~l~~L~~~glv~r~~~~~D~R~   90 (143)
T d1s3ja_          31 QGVTPAQLFVLASLKK-HG--SLKVSEIAERM--EVKPSAVTLMADRLEQKNLIARTHNTKDRRV   90 (143)
T ss_dssp             TTCCHHHHHHHHHHHH-HS--EEEHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEEECSSCTTS
T ss_pred             cCCCHHHHHHHHHHHH-CC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHhhhheeeeecCCCCc
Confidence            4799999999999998 65  89999999999  9999999999999999999999988876433

>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=97.32  E-value=0.00021  Score=54.83  Aligned_cols=63  Identities=14%  Similarity=0.173  Sum_probs=55.8

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      -+||..|..|+..|.. .  .|+-.++|...+  ++....++++++.||++|||...++-+.+..++.
T Consensus        29 ~gLt~~q~~vL~~l~~-~--~~~t~~~La~~~--~i~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i   91 (137)
T d1z91a1          29 LNITYPQYLALLLLWE-H--ETLTVKKMGEQL--YLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLI   91 (137)
T ss_dssp             TCCCHHHHHHHHHHHH-H--SEEEHHHHHHTT--TCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEE
T ss_pred             cCcCHHHHHHHHHHHc-C--CCCCHHHHHHHH--CcCHHHHHHHHHHHhhccceEEeecCCCCCeEEE
Confidence            4899999999999988 5  489999999999  9999999999999999999999999877444433

>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=97.26  E-value=0.00055  Score=52.51  Aligned_cols=65  Identities=17%  Similarity=0.157  Sum_probs=56.2

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      -+|+..|..|+..|.. .|  |+..++|...+  +++.+.++++++.||++|+|...++-..+..+..-|
T Consensus        30 ~~Lt~~q~~vL~~l~~-~~--~~t~~ela~~~--~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~l   94 (138)
T d1jgsa_          30 LDITAAQFKVLCSIRC-AA--CITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKL   94 (138)
T ss_dssp             TTSCHHHHHHHHHHHH-HS--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEE
T ss_pred             cCCCHHHHHHHHhHHh-Cc--CCCHHHHHHHH--CCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEE
Confidence            4799999999999988 66  79999999999  999999999999999999999988877644444433

>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=97.20  E-value=0.00057  Score=49.75  Aligned_cols=65  Identities=14%  Similarity=0.158  Sum_probs=52.9

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      ++-+..|+.++.+ .|  ++..++|.+.+  ++.+..++++|+.||.+|+|...++-..+.++.|   .|+|.
T Consensus        15 ~p~r~~IL~~L~~-~~--~~~~~eLa~~l--~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~---~LT~~   79 (100)
T d1ub9a_          15 NPVRLGIMIFLLP-RR--KAPFSQIQKVL--DLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVV---EITDF   79 (100)
T ss_dssp             SHHHHHHHHHHHH-HS--EEEHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEE---EECHH
T ss_pred             CHHHHHHHHHhcc-CC--CeeHHHHHHHH--hhccccccHHHHHHhhhceeEEEEcCcCCccccc---cCCHH
Confidence            5567889999988 65  48889999999  9999999999999999999999877665444444   34554

>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=96.99  E-value=0.00027  Score=56.66  Aligned_cols=60  Identities=12%  Similarity=0.131  Sum_probs=51.5

Q ss_pred             CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+|+..|..|+..+..++++.|+...+|...+  ++....++++|+.||++|||...++-..
T Consensus        58 ~gLt~~q~~vL~~L~~~~~~~~lt~~eLa~~l--~i~~~tvsr~l~~Le~~GlV~r~~~~~D  117 (172)
T d2fbka1          58 SGLNAAGWDLLLTLYRSAPPEGLRPTELSALA--AISGPSTSNRIVRLLEKGLIERREDERD  117 (172)
T ss_dssp             TTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHC--SCCSGGGSSHHHHHHHHTSEECCC----
T ss_pred             cCCCHHHHHHHHHHHhhCCCCCcCHHHHHHHH--CcCHhHHHHHHHHHHhCCCeeeeccccc
Confidence            48999999999999882456799999999999  9999999999999999999999988765

>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=96.89  E-value=0.00075  Score=51.96  Aligned_cols=65  Identities=8%  Similarity=0.168  Sum_probs=52.0

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL   99 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y   99 (252)
                      ..+||..+..|+..|.. ++. ++..++|..+.  ++....++++|+.||++|||...++-..+..+++
T Consensus        29 ~~glt~~q~~vL~~L~~-~~g-~~t~~~La~~~--~~~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i   93 (145)
T d2hr3a1          29 ADPVQFSQLVVLGAIDR-LGG-DVTPSELAAAE--RMRSSNLAALLRELERGGLIVRHADPQDGRRTRV   93 (145)
T ss_dssp             CCHHHHHHHHHHHHHHH-TTS-CBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEEC------CCEE
T ss_pred             hcCCCHHHHHHHHHHHH-cCC-CCCHHHHHHHH--CCCHHHHHHHHHHHHHcCCeEeeeCccchhHHHh
Confidence            45899999999999987 653 69999999999  9999999999999999999999887666444333

>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=96.89  E-value=0.0011  Score=52.87  Aligned_cols=56  Identities=11%  Similarity=0.080  Sum_probs=49.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      +|+..|..|+.+|.. .|  |+..++|.+.+  +++...++++++.||++|||....+-..
T Consensus        38 ~Lt~~q~~vL~~l~~-~~--~~t~~~la~~~--~l~~~tvs~~i~rL~~~gli~r~~~~~D   93 (162)
T d2fxaa1          38 DLNINEHHILWIAYQ-LN--GASISEIAKFG--VMHVSTAFNFSKKLEERGYLRFSKRLND   93 (162)
T ss_dssp             TCCHHHHHHHHHHHH-HT--SEEHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEECC---
T ss_pred             CCCHHHHHHHhhhcc-CC--CcCHHHHHHHH--cCCchhhHHHHHHHHHCCCceeeccccc
Confidence            799999999999988 55  78999999999  9999999999999999999999877665

>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=96.74  E-value=0.016  Score=43.86  Aligned_cols=112  Identities=14%  Similarity=0.244  Sum_probs=72.8

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDI  110 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ei  110 (252)
                      .||+-|..|.++|=+ .|  .+..++|...++.  +++.+++...|+.|+.||+|+.-+.   .+.-+|-. -+.+.   
T Consensus         3 ~ls~~E~~VM~~lW~-~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~---gr~~~Y~~-~v~~~---   72 (122)
T d1sd4a_           3 EISMAEWDVMNIIWD-KK--SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS---ENIYFYSS-NIKED---   72 (122)
T ss_dssp             CCCHHHHHHHHHHHH-SS--SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE---TTEEEEEE-CSCHH---
T ss_pred             CCCHHHHHHHHHHHc-CC--CCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeecc---CCeEEEee-cCCHH---
Confidence            589999999999999 77  5999999988643  7899999999999999999986432   12224421 12222   


Q ss_pred             cCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493          111 SGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV  174 (252)
Q Consensus       111 TGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL  174 (252)
                                   +   .+.....+++.+--.-+...+..++-+.    -.||.+|+++|-+.|
T Consensus        73 -------------~---~~~~~~~~~~~~~~~gs~~~lv~~~~~~----~~ls~~el~eL~~~l  116 (122)
T d1sd4a_          73 -------------D---IKMKTAKTFLNKLYGGDMKSLVLNFAKN----EELNNKEIEELRDIL  116 (122)
T ss_dssp             -------------H---HHHHHHHHHHHHHHTTCHHHHHHHHHHT----TCSCHHHHHHHHHHH
T ss_pred             -------------H---HHHHHHHHHHHHHhCCCHHHHHHHHHhC----CCCCHHHHHHHHHHH
Confidence                         2   3333334444432112444444444332    368888888876655

>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=96.64  E-value=0.0014  Score=45.80  Aligned_cols=57  Identities=23%  Similarity=0.415  Sum_probs=48.6

Q ss_pred             CCCChHHHHHHHHHHhhcCCCc--ccHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeeec
Q 025493           32 DSLTDHERLIYDVIRSNKQDMG--IWTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        32 ~~l~~~e~~vy~~I~~~ag~~G--Iw~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +.||+-|+.||+.|.+.--..|  -..++|.+..  |+ ..+.+...|+.||++|+|+..+.
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            3699999999999998444445  6789999999  99 57799999999999999999743

>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=96.51  E-value=0.0046  Score=41.78  Aligned_cols=56  Identities=5%  Similarity=0.161  Sum_probs=49.4

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      |++-++.|.+.+.+ .  --+..++|.+++  |++.+.+.+.++.|++.|.|+.+..+-++
T Consensus         3 lD~~D~~IL~~L~~-~--~r~s~~eiA~~l--~ls~~~v~~Ri~rL~~~GiI~~~~~~id~   58 (63)
T d2cg4a1           3 IDNLDRGILEALMG-N--ARTAYAELAKQF--GVSPETIHVRVEKMKQAGIITGARIDVSP   58 (63)
T ss_dssp             CCHHHHHHHHHHHH-C--TTSCHHHHHHHH--TSCHHHHHHHHHHHHHHTSEEEEEEEECT
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEECH
Confidence            78889999999999 3  456899999999  99999999999999999999988776554

>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=96.48  E-value=0.0033  Score=43.18  Aligned_cols=49  Identities=27%  Similarity=0.327  Sum_probs=44.2

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI   91 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv   91 (252)
                      ...|+++|.+ .|  ++...+|.+.+  +|+...++++++.|++.|+|.+....
T Consensus         8 ~~~Il~~l~~-~g--~~sr~eLa~~~--glS~~Tv~~~l~~L~~~Glv~e~~~~   56 (71)
T d1z05a1           8 AGRVYKLIDQ-KG--PISRIDLSKES--ELAPASITKITRELIDAHLIHETTVQ   56 (71)
T ss_dssp             HHHHHHHHHH-HC--SBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEECHH
T ss_pred             HHHHHHHHHH-cC--CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEecCc
Confidence            5689999999 65  69999999999  99999999999999999999987543

>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=96.33  E-value=0.0046  Score=41.35  Aligned_cols=56  Identities=16%  Similarity=0.335  Sum_probs=48.6

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK   94 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~   94 (252)
                      ||+-++.|.+++.+ -  --+..++|.+++  +++...+.+.++.|++.|.|+....+-++
T Consensus         1 lD~~D~~Il~~L~~-n--~r~s~~eiA~~l--~ls~~~v~~Ri~~L~~~giI~~~~~~id~   56 (60)
T d2cyya1           1 LDEIDKKIIKILQN-D--GKAPLREISKIT--GLAESTIHERIRKLRESGVIKKFTAIIDP   56 (60)
T ss_dssp             CCHHHHHHHHHHHH-C--TTCCHHHHHHHH--CSCHHHHHHHHHHHHHHTSSCCCCCCCCG
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEECH
Confidence            67788999999999 3  445899999999  99999999999999999999987765443

>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=96.33  E-value=0.0087  Score=40.44  Aligned_cols=56  Identities=18%  Similarity=0.299  Sum_probs=48.9

Q ss_pred             CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .||+-++.|..++.+ .|  -+..++|.+++  |++..++.+.++.|++.|+|+....+-+
T Consensus         2 klD~~D~~IL~~L~~-n~--r~s~~~iA~~l--gis~~tv~~Ri~~L~~~giI~~~~~~id   57 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK-DS--RLSMRELGRKI--KLSPPSVTERVRQLESFGIIKQYTLEVD   57 (63)
T ss_dssp             CCCHHHHHHHHHHHH-CS--CCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEEC
T ss_pred             CCCHHHHHHHHHHHH-cC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEEEC
Confidence            488889999999999 44  44799999999  9999999999999999999998765544

>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=96.05  E-value=0.0041  Score=44.49  Aligned_cols=37  Identities=11%  Similarity=0.195  Sum_probs=34.3

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      .+.+|..++|..++  ++.++.++++|+.||.+|||+.-
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            44589999999999  99999999999999999999983

>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=96.03  E-value=0.0078  Score=40.30  Aligned_cols=55  Identities=16%  Similarity=0.386  Sum_probs=47.8

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      ||+-++.|..++.+ -  -=+..++|.+++  |++...+.+.++.|+..|+|+....+-+
T Consensus         1 lD~~D~kIl~~L~~-n--~r~s~~~lA~~~--gls~~~v~~Ri~~L~~~giI~~~~~~id   55 (60)
T d1i1ga1           1 IDERDKIILEILEK-D--ARTPFTEIAKKL--GISETAVRKRVKALEEKGIIEGYTIKIN   55 (60)
T ss_dssp             CCSHHHHHHHHHHH-C--TTCCHHHHHHHH--TSCHHHHHHHHHHHHHHTSSCCCCCCCC
T ss_pred             CCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeEEEEEC
Confidence            57788999999999 3  356899999999  9999999999999999999998766544

>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=95.64  E-value=0.011  Score=40.52  Aligned_cols=49  Identities=18%  Similarity=0.244  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ....|+++|.+   +..+...+|-+.+  ||....|++++..|+..|+|.+...
T Consensus         6 N~~~Il~~i~~---~g~~sr~eLa~~~--gLS~~Tvs~iv~~L~~~glv~e~g~   54 (70)
T d1z6ra1           6 NAGAVYRLIDQ---LGPVSRIDLSRLA--QLAPASITKIVHEMLEAHLVQELEI   54 (70)
T ss_dssp             HHHHHHHHHHS---SCSCCHHHHHHHT--TCCHHHHHHHHHHHHHHTSEEEC--
T ss_pred             HHHHHHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeeCC
Confidence            35679999998   6689999999999  9999999999999999999998643

>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=95.47  E-value=0.086  Score=39.43  Aligned_cols=58  Identities=22%  Similarity=0.308  Sum_probs=49.3

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +..|++-|..|.++|=+ .| .++..++|...++.  ++..++|...|+.|+.||+|+..+.
T Consensus         2 ~~~L~~~E~~IM~~lW~-~g-~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~   61 (122)
T d2g9wa1           2 LTRLGDLERAVMDHLWS-RT-EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD   61 (122)
T ss_dssp             GGGCCHHHHHHHHHHHT-CS-SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             CCCCCHHHHHHHHHHHc-CC-CCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeec
Confidence            35699999999999998 65 56889999998743  5788999999999999999998653

>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=95.15  E-value=0.025  Score=38.42  Aligned_cols=44  Identities=16%  Similarity=0.321  Sum_probs=38.7

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ..||.+.++ .|  .+-+.||...+  ++.+..+++.+|.|+.+|||.-
T Consensus        12 ~~I~~L~~~-~~--~v~~~~iA~~L--~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          12 RTIYDLEEE-GV--TPLRARIAERL--DQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             HHHHHHHHT-TC--CCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhc-CC--CCcHHHHHHHh--CCCchhHHHHHHHHHHCCCEEE
Confidence            568877666 44  48999999999  9999999999999999999985

>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=95.08  E-value=0.023  Score=38.26  Aligned_cols=46  Identities=22%  Similarity=0.232  Sum_probs=40.2

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      =+.||.+.++ .|  .+-+.||...+  |+....+++.+|.|+.+|||..-
T Consensus         9 Lk~I~~l~~~-~~--~v~~~~iA~~L--~vs~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1           9 IEQIYMLIEE-KG--YARVSDIAEAL--AVHPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             HHHHHHHHHH-HS--SCCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHhc-CC--CccHHHHHHHh--CCCchhHHHHHHHHHHCCCEEEc
Confidence            3578988877 55  68999999999  99999999999999999999763

>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=95.05  E-value=0.037  Score=41.53  Aligned_cols=54  Identities=15%  Similarity=0.161  Sum_probs=44.1

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      |.+..+..++|...+  |+++..|.|+|+.|.+.|||++++.. +.+   | |.  .|.++||
T Consensus        14 a~~~~~ss~~IA~~~--~~~~~~v~kIl~~L~~aglV~s~rG~-~GG---y-La--r~p~~It   67 (127)
T d1xd7a_          14 SMDEKTSSEIIADSV--NTNPVVVRRMISLLKKADILTSRAGV-PGA---S-LK--KDPADIS   67 (127)
T ss_dssp             HTCSCCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEECCSSS-SSC---E-ES--SCGGGCB
T ss_pred             hcCCCCCHHHHHHHh--CcCHHHHHHHHHHHHHhCcccccCCC-CCc---c-cc--CCHHhCc
Confidence            556789999999999  99999999999999999999998875 323   5 54  4455554

>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=95.05  E-value=0.02  Score=38.50  Aligned_cols=46  Identities=20%  Similarity=0.217  Sum_probs=40.7

Q ss_pred             HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493           41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH   92 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~   92 (252)
                      |+++|.+ .   .|...+|.+.+  +|+...|+++++.|+..|+|.+.....
T Consensus         4 Il~~i~~-~---pisr~eLa~~~--gls~~TVs~~v~~L~~~GlV~e~~~~~   49 (62)
T d2hoea1           4 ILKRIMK-S---PVSRVELAEEL--GLTKTTVGEIAKIFLEKGIVVEEKDSP   49 (62)
T ss_dssp             SHHHHHH-S---CBCHHHHHHHH--TCCHHHHHHHHHHHHHHTSEEEEECCC
T ss_pred             HHHHHHH-C---CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEECCCCC
Confidence            6778876 3   49999999999  999999999999999999999987554

>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=94.71  E-value=0.035  Score=40.28  Aligned_cols=54  Identities=19%  Similarity=0.244  Sum_probs=44.4

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .+|+++++. + ..|+-...|-.++  ||+...+.+.|+.|+++|||+..       ++.|.+.+
T Consensus         6 eIi~DIL~~-~-~~g~~kT~i~~~a--NLs~~~~~kyl~~L~~~GLI~~~-------~~~Y~iT~   59 (90)
T d1r7ja_           6 EIIQAILEA-C-KSGSPKTRIMYGA--NLSYALTGRYIKMLMDLEIIRQE-------GKQYMLTK   59 (90)
T ss_dssp             HHHHHHHHH-H-TTCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-------TTEEEECH
T ss_pred             HHHHHHHHH-H-hCCCCccHHHHHc--CCCHHHHHHHHHHHHHCCCeeec-------CCEEEECc
Confidence            377888887 6 4578889999999  99999999999999999999753       45677633

>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=94.30  E-value=0.035  Score=43.27  Aligned_cols=45  Identities=13%  Similarity=0.312  Sum_probs=38.4

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      =.||++.+  ++++++|++.||.||..|||.++.+ +.+.+..|.|.+
T Consensus        36 f~el~~~l--gis~~vLs~rL~~L~~~gLv~r~~~-~~p~r~~Y~LT~   80 (142)
T d2f2ea1          36 FGEFQKSL--GLAKNILAARLRNLVEHGVMVAVPA-ESGSHQEYRLTD   80 (142)
T ss_dssp             HHHHHHHH--CCCHHHHHHHHHHHHHTTSEEEEEC-SSSSCEEEEECH
T ss_pred             HHHHHHHh--hccHHHHHHHHHHHHHhcceeeecC-CCCCeeEEecCc
Confidence            68999999  9999999999999999999998744 556777787743

>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=94.24  E-value=0.048  Score=39.54  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=40.8

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .|...  =.+|++..+ ++++++|++.||.||..|||.....=..|.+..|-|.+
T Consensus        22 ~g~~r--F~el~~~l~-gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~   73 (95)
T d2hzta1          22 HGKKR--TSELKRLMP-NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSE   73 (95)
T ss_dssp             TCCBC--HHHHHHHCT-TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             cCCCC--HHHHHHHhh-cCChhHHHHHHHHHHHhHHHhheeccccccchhhhhhh
Confidence            44443  688988854 99999999999999999999986655566677777744

>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=94.21  E-value=0.033  Score=41.86  Aligned_cols=48  Identities=10%  Similarity=0.272  Sum_probs=40.2

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493           56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF  104 (252)
Q Consensus        56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l  104 (252)
                      =.+|++..+ ++++++|++.||.||..|||.....-..|.+..|.|.+.
T Consensus        40 F~el~~~l~-gis~~~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~   87 (114)
T d1yyva1          40 FSDLRRKMG-GVSEKMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPL   87 (114)
T ss_dssp             HHHHHHHST-TCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHH
T ss_pred             HHHHHHHcc-ccchhHHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHh
Confidence            578999885 899999999999999999999876556677888887543

>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=94.14  E-value=0.077  Score=35.64  Aligned_cols=47  Identities=17%  Similarity=0.292  Sum_probs=42.4

Q ss_pred             HHHHHHHHHhhcC-CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           38 ERLIYDVIRSNKQ-DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        38 e~~vy~~I~~~ag-~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      |..|....++ -| .+-+-.++|..++  ++|.+.|||+|=+|+++|....
T Consensus         1 Eq~vl~~l~~-lg~~~~~tA~~LA~kl--~vpKk~iNr~LYsL~~kgkl~k   48 (59)
T d2gxba1           1 EQRILKFLEE-LGEGKATTAHDLSGKL--GTPKKEINRVLYSLAKKGKLQK   48 (59)
T ss_dssp             HHHHHHHHHH-HCTTCCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ChHHHHHHHh-cCCccchhHHHHHHHh--CCcHHHHHHHHHHHHHccchhh
Confidence            4578888888 66 8899999999999  9999999999999999998765

>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=94.04  E-value=0.051  Score=36.63  Aligned_cols=32  Identities=19%  Similarity=0.335  Sum_probs=30.3

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +.+.||..-+  |+....++|+|+.|++.|+|+-
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            7889999999  9999999999999999999975

>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=93.95  E-value=0.094  Score=36.42  Aligned_cols=51  Identities=14%  Similarity=0.136  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493           38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      ..+|-+.+.+...++++...+|.+++  +++.+.|+|.|=+|+++|.|..+..
T Consensus         9 ~~lvk~~l~~L~~~~~~tA~~LAk~L--g~~Kk~VNr~LY~L~~~G~v~~~~~   59 (70)
T d1sfua_           9 FSLVKKEVLSLNTNDYTTAISLSNRL--KINKKKINQQLYKLQKEDTVKMVPS   59 (70)
T ss_dssp             HHHHHHHHHTSCTTCEECHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHh--CCCHHHHHHHHHHHHHCCCeecCCC
Confidence            34777788886679999999999999  9999999999999999999998754

>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=93.89  E-value=0.055  Score=39.76  Aligned_cols=49  Identities=18%  Similarity=0.239  Sum_probs=38.7

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      .==.+|++..+ ++++++|++.||.||..|+|.....=..|.+..|-|.+
T Consensus        34 ~rF~el~~~l~-gIs~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~   82 (102)
T d2fswa1          34 IRYGELKRAIP-GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTP   82 (102)
T ss_dssp             EEHHHHHHHST-TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECH
T ss_pred             CCHHHHHhhCc-ccchhHHHHHHHHHHHCCceeecccCCCCCeehhhhhH
Confidence            44578988864 89999999999999999999886544455666677754

>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=93.68  E-value=0.048  Score=38.28  Aligned_cols=50  Identities=8%  Similarity=0.175  Sum_probs=44.4

Q ss_pred             CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCCh-HHHHHHHHHHHhcCCeeee
Q 025493           34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPD-NIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~-~~l~k~lK~Le~k~lIK~v   88 (252)
                      |++.|..|++++++ .|.  .-..+|.+++  ||+. ..||++|=+||.+|.+...
T Consensus         3 ~~d~eekI~~~L~~-~g~--~~Al~iak~l--Gl~kakeVN~~LY~L~k~g~v~k~   53 (73)
T d1xmka1           3 MAEIKEKICDYLFN-VSD--SSALNLAKNI--GLTKARDINAVLIDMERQGDVYRQ   53 (73)
T ss_dssp             HHHHHHHHHHHHHH-TCC--EEHHHHHHHH--CGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHHHH-cCC--chHHHHHHHh--CCCcHHHHhHHHHHHHHCCCeecC
Confidence            45778899999999 885  6688999999  9999 5899999999999999873

>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=93.60  E-value=0.084  Score=39.94  Aligned_cols=53  Identities=11%  Similarity=0.080  Sum_probs=41.7

Q ss_pred             CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      .++-+..++|..++  ++|+..|.|+|+.|.+.|+|++.+. + .+   |.|.  .|.++||
T Consensus        20 ~~~~vss~~IA~~~--~i~~~~l~kil~~L~~aGlv~S~rG-~-GG---~~L~--~~p~~It   72 (138)
T d1ylfa1          20 PSSLCTSDYMAESV--NTNPVVIRKIMSYLKQAGFVYVNRG-P-GG---AGLL--KDLHEIT   72 (138)
T ss_dssp             CGGGCCHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEEC-----CC---EEES--SCGGGCB
T ss_pred             CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeecC-C-CC---ceec--CCHhhcC
Confidence            44568999999999  9999999999999999999999876 4 33   6774  4555665

>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=93.42  E-value=0.4  Score=37.53  Aligned_cols=57  Identities=16%  Similarity=0.168  Sum_probs=44.2

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEe
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMA  101 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL  101 (252)
                      +.|++++.+  |  ...-.+|...+  ++++..+.++|+.|+..|||...+.-  ....+|+|-+
T Consensus        22 ~~Il~~L~~--~--~~s~~ela~~l--g~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~   80 (190)
T d1ulya_          22 RKILKLLRN--K--EMTISQLSEIL--GKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGR   80 (190)
T ss_dssp             HHHHHHHTT--C--CBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEE
T ss_pred             HHHHHHHHh--C--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEE
Confidence            347777633  3  57899999999  99999999999999999999876543  2333677755

>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=93.35  E-value=0.095  Score=35.99  Aligned_cols=44  Identities=16%  Similarity=0.221  Sum_probs=38.2

Q ss_pred             HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493           41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV   88 (252)
Q Consensus        41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v   88 (252)
                      |.++|.+ + +.++-.++|.+++  ++|.+.+.|+|++|+..|++.+-
T Consensus        10 IL~~~a~-~-~~~~s~~eia~~~--~~~~st~~rll~tL~~~g~l~~~   53 (75)
T d1mkma1          10 ILDFIVK-N-PGDVSVSEIAEKF--NMSVSNAYKYMVVLEEKGFVLRK   53 (75)
T ss_dssp             HHHHHHH-C-SSCBCHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHh-C-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEC
Confidence            4555555 4 4689999999999  99999999999999999999973

>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=92.80  E-value=0.13  Score=35.12  Aligned_cols=32  Identities=3%  Similarity=0.153  Sum_probs=29.9

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +.+.||..-+  |++...++|+|+.|++.|+|..
T Consensus        30 lt~~eLA~~~--G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          30 LSREELATLS--NMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCHHHHHHHT--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence            5789999999  9999999999999999999975

>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=92.77  E-value=0.2  Score=34.20  Aligned_cols=51  Identities=20%  Similarity=0.238  Sum_probs=40.4

Q ss_pred             CChHHHHHHHHHHhhcCC---Cc---ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           34 LTDHERLIYDVIRSNKQD---MG---IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        34 l~~~e~~vy~~I~~~ag~---~G---Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ++-++|++.-++.. +..   .+   +.+.||..-+  |++...|+|+|+.|++.|+|..
T Consensus         3 ~dv~~Rla~~Ll~~-~~~~~~~~~i~lt~~elA~~l--g~sr~tvsr~l~~l~~~g~I~~   59 (73)
T d1zyba1           3 LDLKSKIIRFFLSH-CEKPQGEKTFKVKMDDLARCL--DDTRLNISKTLNELQDNGLIEL   59 (73)
T ss_dssp             CSHHHHHHHHHHTT-CSSSSSCEEEECCHHHHHHHH--TSCHHHHHHHHHHHHHTTSCEE
T ss_pred             CCHHHHHHHHHHHh-hhhhCCCeEeecCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEe
Confidence            45567776666554 432   22   6899999999  9999999999999999999974

>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=92.71  E-value=0.16  Score=38.08  Aligned_cols=55  Identities=7%  Similarity=0.161  Sum_probs=47.0

Q ss_pred             HHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          129 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       129 l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      -|.+++++|.+.  ..+|++||++.+++.+.   .++..-|-+.|+.|+-.|.|.++...
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            367889999754  37999999999999883   57888999999999999999998754

>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=92.35  E-value=0.11  Score=38.47  Aligned_cols=47  Identities=9%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493           56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE  103 (252)
Q Consensus        56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~  103 (252)
                      =.+|++..+ ++++++|++.||.||..|||.....=..|.+-.|-|.+
T Consensus        35 F~el~~~l~-gIS~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~   81 (108)
T d1z7ua1          35 NGELMRALD-GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTP   81 (108)
T ss_dssp             HHHHHHHST-TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECH
T ss_pred             HHHHHHHCc-CCChhHHHHHHHHHHHCCcceeeccCCCcceehhhhch
Confidence            478999863 89999999999999999999875444455566677644

>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=92.30  E-value=0.22  Score=39.56  Aligned_cols=59  Identities=20%  Similarity=0.300  Sum_probs=46.8

Q ss_pred             HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee--ccccCCeeeEEecc
Q 025493           39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV--NIHNKGKKHLMAVE  103 (252)
Q Consensus        39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk--sv~~~~rK~YmL~~  103 (252)
                      +.|++++..    ......+|..++  ++++..+.+.|+.||+.|||...+  +...+.+++|.+.+
T Consensus        18 ~~Il~~L~~----~~~~~~ela~~l--~~s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~   78 (194)
T d2p4wa1          18 RRILFLLTK----RPYFVSELSREL--GVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKK   78 (194)
T ss_dssp             HHHHHHHHH----SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECT
T ss_pred             HHHHHHHHh----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEecc
Confidence            456666654    357889999999  999999999999999999998754  33345578888755

>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=92.27  E-value=0.48  Score=33.95  Aligned_cols=36  Identities=17%  Similarity=0.340  Sum_probs=33.0

Q ss_pred             CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ...-..+|...+  ++++..+++.|+.|+..|+|+.-+
T Consensus        35 ~~~~v~ela~~l--~is~stvS~HL~~L~~aglV~~~r   70 (98)
T d1r1ta_          35 SELCVGDLAQAI--GVSESAVSHQLRSLRNLRLVSYRK   70 (98)
T ss_dssp             CCBCHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEE
Confidence            457889999999  999999999999999999999854

>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=92.03  E-value=0.17  Score=36.72  Aligned_cols=65  Identities=9%  Similarity=0.170  Sum_probs=42.4

Q ss_pred             HHHHHHHHHhhcCCCcccHHH-HHHHhhc--CCChHHHHHHHHHHHhcCCeeee--eccccCCeeeEEecc
Q 025493           38 ERLIYDVIRSNKQDMGIWTRD-MKRELKV--NLPDNIVTKSIKSLQNKSLIKEV--VNIHNKGKKHLMAVE  103 (252)
Q Consensus        38 e~~vy~~I~~~ag~~GIw~~d-ik~~~~~--~l~~~~l~k~lK~Le~k~lIK~v--ksv~~~~rK~YmL~~  103 (252)
                      +.+|+.++.+ .--.|-..+. |...++.  +++...|-.+|+.||.+|+|.+-  .+...|.||+|-+.+
T Consensus         9 ~~~IL~lL~~-~~~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~   78 (103)
T d1xmaa_           9 DTIILSLLIE-GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITP   78 (103)
T ss_dssp             HHHHHHHHHH-CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECH
T ss_pred             HHHHHHHHhh-CCccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECH
Confidence            5566666666 3334433322 3333311  68999999999999999999863  445567799998844

>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=91.87  E-value=0.37  Score=33.62  Aligned_cols=57  Identities=18%  Similarity=0.222  Sum_probs=48.0

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeec
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVN   90 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vks   90 (252)
                      +..|++-|..|.++|=+ .|  .+..++|...+..  +.+.+++...|..|+.||+|..-+.
T Consensus         4 ~~~Ls~~E~~IM~~lW~-~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~   62 (82)
T d1p6ra_           4 IPQISDAELEVMKVIWK-HS--SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCHHHHHHHHHHHT-SS--SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCHHHHHHHHHHHh-CC--CCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEec
Confidence            45799999999999988 66  5889998776533  7899999999999999999997543

>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=91.71  E-value=0.31  Score=32.55  Aligned_cols=53  Identities=8%  Similarity=0.137  Sum_probs=44.6

Q ss_pred             CChHHHHHHHH----HHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           34 LTDHERLIYDV----IRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        34 l~~~e~~vy~~----I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      ||++|+.+.+.    .++ +|-.=-|.+||-..+  |++...+...|+.|...|.+-.|+
T Consensus         1 ls~~q~~l~~~I~~~~~~-~g~~PP~vrdl~~~l--~~~e~~~~~lL~~l~~~G~lvkI~   57 (64)
T d1lvaa3           1 FSETQKKLLKDLEDKYRV-SRWQPPSFKEVAGSF--NLDPSELEELLHYLVREGVLVKIN   57 (64)
T ss_dssp             CCHHHHHHHHHHHHHHHH-HTTSCCBHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             CCHHHHHHHHHHHHHHHH-cCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec
Confidence            46666655554    456 899999999999999  999999999999999999887773

>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=90.85  E-value=0.27  Score=35.09  Aligned_cols=54  Identities=13%  Similarity=0.236  Sum_probs=42.9

Q ss_pred             CChHHHHHHHHHHhh--cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           34 LTDHERLIYDVIRSN--KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        34 l~~~e~~vy~~I~~~--ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      ||+-++.|++.|.+.  .-..-+-.++|....+.++....|...|+.||.+|+|++
T Consensus         2 Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~   57 (87)
T d1stza1           2 LNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ   57 (87)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             cCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC
Confidence            788888888866541  235668899999998224469999999999999999987

>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=90.26  E-value=1  Score=32.72  Aligned_cols=53  Identities=9%  Similarity=0.139  Sum_probs=41.0

Q ss_pred             CCCChHH-HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493           32 DSLTDHE-RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        32 ~~l~~~e-~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +.|.+.- ..|+..+.. .  .+.-..+|...+  ++++..+++.|+.|++-|||+.-+
T Consensus        26 kaLadp~Rl~Il~~L~~-~--~~~~v~ela~~l--~~s~s~vS~HL~~L~~aGlv~~~r   79 (108)
T d1u2wa1          26 KAIADENRAKITYALCQ-D--EELCVCDIANIL--GVTIANASHHLRTLYKQGVVNFRK   79 (108)
T ss_dssp             HHHHSHHHHHHHHHHHH-S--SCEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHhCCHHHHHHHHHHHh-C--CCccHHHHHHHH--ccChhHHHHHHHHHHHCCeeEEEE
Confidence            3454444 356666654 3  347889999999  999999999999999999999854

>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=90.10  E-value=0.49  Score=31.30  Aligned_cols=49  Identities=10%  Similarity=0.133  Sum_probs=39.0

Q ss_pred             ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC-eeee
Q 025493           35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL-IKEV   88 (252)
Q Consensus        35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l-IK~v   88 (252)
                      ++-...|+.++.+   +.-+...+|..++  |+..+.|.|-|+.|++.|+ |.++
T Consensus         4 ~~~~~~iL~~L~~---~~~~s~~eLa~~l--~vS~~ti~r~i~~L~~~G~~I~~~   53 (63)
T d1biaa1           4 NTVPLKLIALLAN---GEFHSGEQLGETL--GMSRAAINKHIQTLRDWGVDVFTV   53 (63)
T ss_dssp             CHHHHHHHHHHTT---SSCBCHHHHHHHH--TSCHHHHHHHHHHHHHTTCCCEEE
T ss_pred             cHHHHHHHHHHHH---CCcCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCcEEEe
Confidence            4445567777744   4568899999999  9999999999999999998 4443

>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=89.86  E-value=0.44  Score=32.47  Aligned_cols=32  Identities=9%  Similarity=0.200  Sum_probs=29.9

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +.+.+|..-+  |++...++|+|+.|++.|+|+-
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            4688999999  9999999999999999999986

>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=88.89  E-value=0.31  Score=35.86  Aligned_cols=37  Identities=5%  Similarity=-0.006  Sum_probs=28.9

Q ss_pred             CCChHHHHHHHHHHHhcCCeeeeec-cccCCeeeEEec
Q 025493           66 NLPDNIVTKSIKSLQNKSLIKEVVN-IHNKGKKHLMAV  102 (252)
Q Consensus        66 ~l~~~~l~k~lK~Le~k~lIK~vks-v~~~~rK~YmL~  102 (252)
                      .++..+|-.+|+.||.+|+|.+-.. -..+.||+|-+.
T Consensus        43 ~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT   80 (114)
T d2esha1          43 IGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRIT   80 (114)
T ss_dssp             CCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEEC
T ss_pred             cCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEEC
Confidence            5677899999999999999987543 234568888773

>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=88.20  E-value=1.2  Score=31.59  Aligned_cols=61  Identities=20%  Similarity=0.263  Sum_probs=44.7

Q ss_pred             CCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           32 DSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        32 ~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      +.|.+.-| .|+.++.+  |.  .-..+|...+  +++++.+++.|+.|+.-|||+.-+   ..+...|-|
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 46666655  33  5678999999  999999999999999999999864   223445544

>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=87.98  E-value=1.4  Score=32.63  Aligned_cols=105  Identities=16%  Similarity=0.149  Sum_probs=73.5

Q ss_pred             CCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493           33 SLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS  111 (252)
Q Consensus        33 ~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT  111 (252)
                      -|+.+.+ .|..+++     .|+-.++|.++.  ++....+.|+++.....|.+..-+. ..+..+.     +.      
T Consensus        16 pLs~dlR~rIv~~~~-----~G~s~r~iA~~~--~VS~~tV~k~l~r~~~~G~~~~~~~-~~~rpr~-----~t------   76 (123)
T d1pdnc_          16 PLPNNIRLKIVEMAA-----DGIRPCVISRQL--RVSHGCVSKILNRYQETGSIRPGVI-GGSKPRI-----AT------   76 (123)
T ss_dssp             CCCHHHHHHHHHHHH-----TTCCHHHHHHHH--TCCHHHHHHHHHHHHHHCCSSCCCC-SCCCCCS-----SC------
T ss_pred             CCCHHHHHHHHHHHH-----hcCCHHHHHHHH--CcCHHHHHHHHHHHHccCCcCcCCC-CCCCCCC-----CC------
Confidence            3555533 3344443     489999999999  9999999999999999998876432 1111111     11      


Q ss_pred             CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcc--eecCHHHHHHHH
Q 025493          112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK--VDLTKQQIEEIV  171 (252)
Q Consensus       112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~--~~Ls~~di~~IL  171 (252)
                                     +.....+..++..+...|+.||.+.+...|+..  ...|..-|.++|
T Consensus        77 ---------------~~~~~~I~~~~~~~P~~t~~El~~~L~~egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          77 ---------------PEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             ---------------STHHHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC
T ss_pred             ---------------HHHHHHHHHHHHhCCCccHHHHHHHHHHcCCCCCCCCCChhhHhhcC
Confidence                           234566777788899999999999999999754  356666665553

>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=87.42  E-value=0.64  Score=31.30  Aligned_cols=53  Identities=11%  Similarity=0.229  Sum_probs=44.3

Q ss_pred             hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493           48 NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS  107 (252)
Q Consensus        48 ~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs  107 (252)
                      |--..||-..+|+++..++++......+|..|...|.|+.-       ...+=|.++.||
T Consensus        21 ~P~~~G~~keeLr~~l~~~~~~~~f~~lL~~l~~~g~l~~~-------g~~v~L~~f~ps   73 (73)
T d2v9va2          21 YPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLA-------ANTVALAGFTPS   73 (73)
T ss_dssp             CTTSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEC-------SSEEEETTCCCC
T ss_pred             CccccCCCHHHHHHHhcccCCHHHHHHHHHHHHHCCChhee-------CCEEECCCCCCC
Confidence            46678999999999997799999999999999999999873       334556666665

>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=87.12  E-value=0.76  Score=30.65  Aligned_cols=44  Identities=14%  Similarity=0.200  Sum_probs=36.8

Q ss_pred             cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      .|.. +-.++|..+.  ++....+.++|+.|+..|+|...     +++-.|+
T Consensus        22 ~G~~-l~~~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~-----~~~G~~V   65 (69)
T d2hs5a1          22 PGAR-LSEPDICAAL--DVSRNTVREAFQILIEDRLVAHE-----LNRGVFV   65 (69)
T ss_dssp             TTCE-ECHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEE
T ss_pred             CcCc-cCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE-----cCCEEEe
Confidence            3555 6789999999  99999999999999999999986     3444554

>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=86.82  E-value=0.98  Score=33.41  Aligned_cols=61  Identities=16%  Similarity=0.079  Sum_probs=48.7

Q ss_pred             CCCCCCChHHHHHHHHHHh--hcCCCcccHHHHHHHhh--------c-CCChHHHHHHHHHHHhcCCeeeee
Q 025493           29 APSDSLTDHERLIYDVIRS--NKQDMGIWTRDMKRELK--------V-NLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        29 ~~~~~l~~~e~~vy~~I~~--~ag~~GIw~~dik~~~~--------~-~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      .++++|+.+|++|+-.|..  -.|..-|-+.+|.+.-.        . .+..+++.+.|+.||..|+|..-.
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            3578999999999988865  14888899998877431        1 367899999999999999998643

>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=86.72  E-value=0.37  Score=32.85  Aligned_cols=32  Identities=9%  Similarity=0.268  Sum_probs=29.7

Q ss_pred             ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493           54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE   87 (252)
Q Consensus        54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~   87 (252)
                      +.+.||..-+  |++...++|+|+.|++.|+|+.
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            5689999999  9999999999999999999974

>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=86.08  E-value=0.27  Score=38.36  Aligned_cols=38  Identities=8%  Similarity=0.114  Sum_probs=26.1

Q ss_pred             CCChHHHHHHHHHHHhcCCeee--eeccccCCeeeEEecc
Q 025493           66 NLPDNIVTKSIKSLQNKSLIKE--VVNIHNKGKKHLMAVE  103 (252)
Q Consensus        66 ~l~~~~l~k~lK~Le~k~lIK~--vksv~~~~rK~YmL~~  103 (252)
                      ++...+|-..|++||.+|+|.+  +.....|.||+|-+.+
T Consensus        33 ~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~   72 (178)
T d1yg2a_          33 KASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQ   72 (178)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEECCC---------CEEECH
T ss_pred             CCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECH
Confidence            6889999999999999999986  3445567899998865

>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=85.15  E-value=0.98  Score=30.66  Aligned_cols=39  Identities=10%  Similarity=0.231  Sum_probs=34.0

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..++|..+.  ++..+.+.++|+.|+..|+|...     +++-.|+
T Consensus        29 s~~eLa~~~--~vSr~tvr~Al~~L~~~G~i~~~-----~g~G~~V   67 (74)
T d1hw1a1          29 AERELSELI--GVTRTTLREVLQRLARDGWLTIQ-----HGKPTKV   67 (74)
T ss_dssp             CHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEEE-----TTEEEEE
T ss_pred             cHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE-----eCceEEE
Confidence            689999999  99999999999999999999986     3454554

>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=84.85  E-value=0.93  Score=30.11  Aligned_cols=45  Identities=20%  Similarity=0.202  Sum_probs=39.8

Q ss_pred             HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      ..++.+|..++.+|..||++.+        .||..-|..+++.|+-+|.|++.
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            4688899999999999999865        48899999999999999999875

>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=84.72  E-value=0.88  Score=31.58  Aligned_cols=55  Identities=15%  Similarity=0.070  Sum_probs=42.7

Q ss_pred             HHHHHHHHhhhCCCCCHHHHHHHHHHc---CCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493          129 VKSQCLKQIIKLKVATLEGISDSIKRS---GAFKVDLTKQQIEEIVRAVVLDNQIMEV  183 (252)
Q Consensus       129 l~~~~~~~i~~~~~~T~~~I~~~i~~~---~i~~~~Ls~~di~~IL~tLVyDgkIE~v  183 (252)
                      --..|.-.|.+.+...++.||..++=-   +-.-...|.++++..|+.+|-+|+++-+
T Consensus         9 ~w~yI~gMLtN~~slpleRIh~mLkmfv~~~~~~~~~t~~eL~~FL~~~V~e~kL~~v   66 (74)
T d1ldda_           9 SLPFIEGMLTNLGAMKLHKIHSFLKITVPKDWGYNRITLQQLEGYLNTLADEGRLKYI   66 (74)
T ss_dssp             HHHHHHHHHHHHCSEEHHHHHHHHHHHSCGGGCCTTCCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHcCCCCCCCCcCHHHHHHHHHHHHhcCceEEe
Confidence            334455566688899999999999944   2222467899999999999999999865

>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=83.70  E-value=2.5  Score=30.12  Aligned_cols=60  Identities=13%  Similarity=0.118  Sum_probs=48.0

Q ss_pred             CCCCChHHHHHHHHHHhhcCCC-cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493           31 SDSLTDHERLIYDVIRSNKQDM-GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN   93 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~-GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~   93 (252)
                      .+.|+++|..|+..||...-|. =+-...|.+.+  +|+...+.++|+.|...+||.. +.+..
T Consensus         6 ~~~L~~~dfRvL~aiE~gmrnhE~VP~~lI~~~a--~l~~~~~~~~L~~L~k~kLv~~-~~~~Y   66 (89)
T d1zara1           6 YGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHA--RIGEEKARNILKYLSDLRVVQN-RQKDY   66 (89)
T ss_dssp             HHTCCHHHHHHHHHHHTTTTTCSSEEHHHHHHHH--TCCHHHHHHHHHHHHHTTSEEE-ECSSS
T ss_pred             HHHcCHHHHHHHHHHHhccccCccccHHHHHHHH--CCCHHHHHHHHHHHHHcCCeec-cCCCc
Confidence            4579999999999999822222 23467888999  9999999999999999999976 55543

>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=83.64  E-value=0.92  Score=29.99  Aligned_cols=44  Identities=25%  Similarity=0.422  Sum_probs=39.8

Q ss_pred             CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493           31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN   81 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~   81 (252)
                      +..||+-|..|+.++.+     |...++|-.++  ++..++|...++.+-.
T Consensus         4 l~~LT~rE~~vl~ll~~-----G~s~~eIA~~l--~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1           4 VNQLTPRERDILKLIAQ-----GLPNKMIARRL--DITESTVKVHVKHMLK   47 (67)
T ss_dssp             GGGSCHHHHHHHHHHHT-----TCCHHHHHHHH--TCCHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHh-----CCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence            45799999999999998     99999999999  9999999999888744

>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=83.52  E-value=1.4  Score=32.19  Aligned_cols=59  Identities=17%  Similarity=0.083  Sum_probs=46.2

Q ss_pred             CCCCChHHHHHHHHHH---hhcCCCcccHHHHHH-------Hhhc-CCChHHHHHHHHHHHhcCCeeeee
Q 025493           31 SDSLTDHERLIYDVIR---SNKQDMGIWTRDMKR-------ELKV-NLPDNIVTKSIKSLQNKSLIKEVV   89 (252)
Q Consensus        31 ~~~l~~~e~~vy~~I~---~~ag~~GIw~~dik~-------~~~~-~l~~~~l~k~lK~Le~k~lIK~vk   89 (252)
                      +++|+.++++|+..|-   ++.++..|-+.++-.       +.+. .+.++.+...|+.||..|+|.+-.
T Consensus         6 i~~Lp~h~klvL~ai~~~~~~~~~~~ittgevy~~Y~~lc~~~~~~pls~rr~~~~l~~Le~lGiI~~r~   75 (112)
T d1fnna1           6 LIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQ   75 (112)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHhCCCeeeee
Confidence            4679999999987763   226777888887754       3433 678999999999999999998754

>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=83.24  E-value=2.1  Score=30.67  Aligned_cols=41  Identities=10%  Similarity=0.178  Sum_probs=33.1

Q ss_pred             cccHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493           53 GIWTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA  101 (252)
Q Consensus        53 GIw~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL  101 (252)
                      .+.+.||..-+  |+. ...|+|+|+.|+..|+|+.-      +++++++
T Consensus        31 ~lTqeeLA~~l--G~s~ReTVsR~L~~L~~~GlI~~~------~~~i~I~   72 (100)
T d2bgca1          31 NLTMQELGYSS--GIAHSSAVSRIISKLKQEKVIVYK------NSCFYVQ   72 (100)
T ss_dssp             CCCHHHHHHHT--TCCCHHHHHHHHHHHHHTTSEEEE------TTEEEES
T ss_pred             ccCHHHHHHHh--CCchHHHHHHHHHHHHHCCCEEEc------CCEEEEe
Confidence            36788999999  996 67899999999999999962      4555544

>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=82.68  E-value=0.74  Score=31.31  Aligned_cols=39  Identities=21%  Similarity=0.361  Sum_probs=33.9

Q ss_pred             cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493           55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM  100 (252)
Q Consensus        55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym  100 (252)
                      ..++|..+.  +...+.|.++|+.|+..|+|.+.     +++-+|+
T Consensus        24 se~~La~~~--~vSr~tvr~Al~~L~~~Gli~~~-----~g~G~~V   62 (78)
T d3bwga1          24 VLETLMAQF--EVSKSTITKSLELLEQKGAIFQV-----RGSGIFV   62 (78)
T ss_dssp             CHHHHHHHT--TCCHHHHHHHHHHHHHTTSEEEE-----TTTEEEE
T ss_pred             CHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEEE-----cCcEEEE
Confidence            678999999  99999999999999999999987     3444554

>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=82.37  E-value=1.3  Score=30.91  Aligned_cols=54  Identities=15%  Similarity=0.192  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493          125 FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN  186 (252)
Q Consensus       125 fV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~  186 (252)
                      +.+-.+-.|+.+|..++..|+.||++.+        .++..-+-..|+.|+-+|.|++.+..
T Consensus        13 l~~p~r~~IL~~L~~~~~~~~~eLa~~l--------~is~~~vs~~l~~L~~~glV~~~~~~   66 (100)
T d1ub9a_          13 LGNPVRLGIMIFLLPRRKAPFSQIQKVL--------DLTPGNLDSHIRVLERNGLVKTYKVI   66 (100)
T ss_dssp             HHSHHHHHHHHHHHHHSEEEHHHHHHHT--------TCCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             cCCHHHHHHHHHhccCCCeeHHHHHHHH--------hhccccccHHHHHHhhhceeEEEEcC
Confidence            3355677888999888889999998754        46788899999999999999987654

>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=81.78  E-value=0.5  Score=34.98  Aligned_cols=124  Identities=14%  Similarity=0.155  Sum_probs=68.5

Q ss_pred             CCCCChHHH----HHHHHHHhhcCCCc-ccHHHHHH---HhhcCCChHHHHHHHHHHHhcCC--eeeeeccccCCeeeEE
Q 025493           31 SDSLTDHER----LIYDVIRSNKQDMG-IWTRDMKR---ELKVNLPDNIVTKSIKSLQNKSL--IKEVVNIHNKGKKHLM  100 (252)
Q Consensus        31 ~~~l~~~e~----~vy~~I~~~ag~~G-Iw~~dik~---~~~~~l~~~~l~k~lK~Le~k~l--IK~vksv~~~~rK~Ym  100 (252)
                      +..||++|.    .+|+.+.. .|+.| |-..+++.   +.|.+++...+...+..+-..+-  |.--...      .++
T Consensus         5 ~~~Lt~~~~~~l~~~F~~~D~-d~~dG~I~~~e~~~~l~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~   77 (156)
T d1dtla_           5 VEQLTEEQKNEFKAAFDIFVL-GAEDGSISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFL------VMM   77 (156)
T ss_dssp             GGGSCHHHHHHHHHHHHHHTT-TCGGGSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHCTTSSSSBCHHHHH------HHH
T ss_pred             HHHCCHHHHHHHHHHHHHHcC-CCCCCeECHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCCCccchhhhh------hhh
Confidence            457888873    36788888 77555 88888774   45446667777777766633221  0000000      000


Q ss_pred             ecccccCCCccCCccccCCcCCHHHHHHHHHHHHHH-hhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhc
Q 025493          101 AVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQ-IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLD  177 (252)
Q Consensus       101 L~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~-i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyD  177 (252)
                      ..-+           +.....  ...+.|+.+.-.| ....|+.|.+|+.+.+...|   ..++.++++.|++.+=.|
T Consensus        78 ~~~~-----------~~~~~~--~~~~~l~~~F~~~D~d~~G~I~~~e~~~~~~~~~---~~ls~~e~~~i~~~~D~d  139 (156)
T d1dtla_          78 VRSM-----------KDDSKG--KSEEELSDLFRMFDKNADGYIDLEELKIMLQATG---ETITEDDIEELMKDGDKN  139 (156)
T ss_dssp             HHHH-----------C-------CHHHHHHHHHHHHCTTCSSEEEHHHHGGGGTTC-----CCCHHHHHHHHHHHCTT
T ss_pred             hhcc-----------cccccc--cHHHHHHHHHHHhCcCCCCcCcHHHHHHHHhhcC---CCCCHHHHHHHHHHhCCC
Confidence            0000           000000  1113333332222 12458999999999988777   479999999999987555

>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=81.59  E-value=1.1  Score=32.89  Aligned_cols=45  Identities=13%  Similarity=0.118  Sum_probs=38.0

Q ss_pred             HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493          132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK  184 (252)
Q Consensus       132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~  184 (252)
                      .++.||..++.+|.++|++.+.        ++..-+++|+..|.--|.|+..+
T Consensus         8 ~~L~~la~~~~~ss~~IA~~~~--------~~~~~v~kIl~~L~~aglV~s~r   52 (127)
T d1xd7a_           8 HILSLISMDEKTSSEIIADSVN--------TNPVVVRRMISLLKKADILTSRA   52 (127)
T ss_dssp             HHHHHHHTCSCCCHHHHHHHHT--------SCHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHHHHHhcCCCCCHHHHHHHhC--------cCHHHHHHHHHHHHHhCcccccC
Confidence            3577888888899999998654        67889999999999999998765

>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=80.57  E-value=1.4  Score=29.10  Aligned_cols=51  Identities=12%  Similarity=0.260  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493          127 KVVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS  185 (252)
Q Consensus       127 ~~l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~  185 (252)
                      +.|.+.+.......  .+|++.||++-+        .+++.+++.+|+.|+-.|.+.+|..
T Consensus         6 ~~l~~~I~~~~~~~g~~PP~vrdl~~~l--------~~~e~~~~~lL~~l~~~G~lvkI~~   58 (64)
T d1lvaa3           6 KKLLKDLEDKYRVSRWQPPSFKEVAGSF--------NLDPSELEELLHYLVREGVLVKIND   58 (64)
T ss_dssp             HHHHHHHHHHHHHHTTSCCBHHHHHHHT--------TCCHHHHHHHHHHHHHTTSEEESSS
T ss_pred             HHHHHHHHHHHHHcCCCCCcHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecc
Confidence            34566666666554  589999998765        3779999999999999999998853

>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=80.36  E-value=7.8  Score=27.46  Aligned_cols=108  Identities=16%  Similarity=0.295  Sum_probs=71.1

Q ss_pred             CCChHH----HHHHHHHHhhcCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccc
Q 025493           33 SLTDHE----RLIYDVIRSNKQDMGIWTRDMKREL---KVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFE  105 (252)
Q Consensus        33 ~l~~~e----~~vy~~I~~~ag~~GIw~~dik~~~---~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~le  105 (252)
                      .||++|    +.+|+.+.. .|+.=|...+++.-.   +..+....+...++.+..          ...++--|      
T Consensus         2 ~lt~~e~~~l~~~F~~~D~-~~~G~Is~~e~~~~l~~~~~~~~~~~~~~~~~~~d~----------~~~g~i~~------   64 (146)
T d1exra_           2 QLTEEQIAEFKEAFALFDK-DGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDA----------DGNGTIDF------   64 (146)
T ss_dssp             CCCHHHHHHHHHHHHHHCT-TCSSEECHHHHHHHHHHHTCCCCHHHHHHHHHHHCT----------TCSSSEEH------
T ss_pred             CCCHHHHHHHHHHHHHHcC-CCCCeECHHHHHHHHHhcCCCCCHHHHHHHHHhcCC----------CCCCcccH------
Confidence            477766    345788888 888888888887643   225666677777766522          11111111      


Q ss_pred             cCCCccCCccccCCcCCHHHHHHHHHHHH------------HHh--hhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHH
Q 025493          106 PSKDISGGAWYSEGSLDTEFIKVVKSQCL------------KQI--IKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIV  171 (252)
Q Consensus       106 Ps~eiTGG~wy~d~e~D~efV~~l~~~~~------------~~i--~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL  171 (252)
                                       .+|+..+.....            +.+  ...++.+.+|+..+++..|   ..++.+++++|+
T Consensus        65 -----------------~ef~~~~~~~~~~~~~~~~~~~~F~~~D~d~~G~i~~~e~~~~l~~~~---~~~~~~~~~~i~  124 (146)
T d1exra_          65 -----------------PEFLSLMARKMKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLG---EKLTDDEVDEMI  124 (146)
T ss_dssp             -----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHSTTCSSCBCHHHHHHHHHHTT---CCCCHHHHHHHH
T ss_pred             -----------------HHHHHHHHHHhhccChHHHHHHHHHHhCCCCCCcCCHHHHHHHHHHHh---hcCCHHHHHHHH
Confidence                             255555433322            222  2468999999999999988   478999999999


Q ss_pred             HHHhhc
Q 025493          172 RAVVLD  177 (252)
Q Consensus       172 ~tLVyD  177 (252)
                      +.+=.|
T Consensus       125 ~~~D~d  130 (146)
T d1exra_         125 READID  130 (146)
T ss_dssp             HHHCSS
T ss_pred             HHhCCC
Confidence            876444