Citrus Sinensis ID: 034587

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90
Protein Sequence
MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHccccccccHHHHHcccccccccccccccccHHHHHHHHHHHHHccccccccccccEEcHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccEEEcccccEEEccccHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MSELVTSMARKIYLRQglgvgsfrriyggskrngsrpphfckssGAIARHILQQLQNmniidiepkggrritssgqrdldQVAGRIVVAP
Flexible Loop (DISEMBL)
MSELVTSMARKIylrqglgvgsfRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGgrritssgqrdldqvagrivvap
Low Complexity Region (SEG)
MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Disordered region (IsUnstruct)
********ARKIYLRQGLGVGSFRRIYGG**********FCKSSGAIARHILQQLQNMNIIDI***************************
Disordered Region (DISOPRED)
**ELVTSMARKIYLRQGLGVGSFRRIYGG*************SSGAIARHILQQLQNMNIIDIEP***RRITSSGQRDLDQVAGRIVVAP
Disordered Region (DISEMBL)
MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Disordered Region (DISPRO)
****VTSMARKIYLRQGLGVGSFRRIYGGS*R****P******SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
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	90	2.2.26 [Sep-21-2011]
Q9SGA6	143	40S ribosomal protein S19	yes	no	0.955	0.601	0.825	5e-37
Q9FNP8	143	40S ribosomal protein S19	no	no	0.944	0.594	0.823	9e-37
Q9LF30	143	40S ribosomal protein S19	yes	no	0.933	0.587	0.821	2e-35
P40978	146	40S ribosomal protein S19	yes	no	0.933	0.575	0.761	3e-32
Q9Y0H3	145	40S ribosomal protein S19	N/A	no	0.933	0.579	0.488	2e-20
Q94613	149	40S ribosomal protein S19	N/A	no	0.922	0.557	0.481	3e-20
P17074	145	40S ribosomal protein S19	yes	no	0.944	0.586	0.482	3e-19
Q9CZX8	145	40S ribosomal protein S19	yes	no	0.944	0.586	0.482	3e-19
Q54X51	148	40S ribosomal protein S19	yes	no	0.911	0.554	0.481	1e-18
Q5R8M9	145	40S ribosomal protein S19	yes	no	0.944	0.586	0.470	2e-18

>sp|Q9SGA6|RS191_ARATH 40S ribosomal protein S19-1 OS=Arabidopsis thaliana GN=RPS19A PE=2 SV=1

 Score =  152 bits (385), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 71/86 (82%), Positives = 78/86 (90%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ MNI++++
Sbjct: 58  AASMARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELD 117

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVAP 90
            KGGRRITSSGQRDLDQVAGRI V P
Sbjct: 118 TKGGRRITSSGQRDLDQVAGRIAVEP 143

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FNP8|RS193_ARATH 40S ribosomal protein S19-3 OS=Arabidopsis thaliana GN=RPS19C PE=2 SV=1

 Score =  152 bits (383), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 70/85 (82%), Positives = 77/85 (90%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG +ARHILQQLQ MNI+D++
Sbjct: 58  AASMARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLD 117

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVA 89
            KGGR+ITSSGQRDLDQVAGRI  A
Sbjct: 118 TKGGRKITSSGQRDLDQVAGRIAAA 142

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LF30|RS192_ARATH 40S ribosomal protein S19-2 OS=Arabidopsis thaliana GN=RPS19B PE=2 SV=1

 Score =  147 bits (370), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 69/84 (82%), Positives = 76/84 (90%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARKIYLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ M+I++++
Sbjct: 58  AASMARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELD 117

Query: 65  PKGGRRITSSGQRDLDQVAGRIVV 88
            KGGRRITSSGQRDLDQVAGRI  
Sbjct: 118 TKGGRRITSSGQRDLDQVAGRIAA 141

Arabidopsis thaliana (taxid: 3702)

>sp|P40978|RS19_ORYSJ 40S ribosomal protein S19 OS=Oryza sativa subsp. japonica GN=RPS19A PE=3 SV=1

 Score =  137 bits (344), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 75/84 (89%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            S+ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++P
Sbjct: 61  ASIARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDP 120

Query: 66  KGGRRITSSGQRDLDQVAGRIVVA 89
           KGGR ITS G+RDLDQVAGR+ V 
Sbjct: 121 KGGRLITSQGRRDLDQVAGRVDVT 144

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9Y0H3|RS19_MYXGL 40S ribosomal protein S19 OS=Myxine glutinosa GN=rps19 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 41/84 (48%), Positives = 65/84 (77%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             S+AR +Y+R G+GVG+  +IYGG +RNG+RP H+ + S  +AR +LQ L+ + +++ +
Sbjct: 57  TASVARHLYMRGGVGVGAMTKIYGGRQRNGTRPSHYSRGSRNVARKVLQSLEMLKMVEKD 116

Query: 65  PKGGRRITSSGQRDLDQVAGRIVV 88
           P GGRR+TS GQRD+D++AG++VV
Sbjct: 117 PNGGRRLTSIGQRDMDRIAGQVVV 140

Myxine glutinosa (taxid: 7769)

>sp|Q94613|RS19_MYAAR 40S ribosomal protein S19 OS=Mya arenaria GN=RPS19 PE=2 SV=1

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 62/83 (74%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             S+ R +Y+R   G+GSF +IYGG +R G+ P HFCK++G+I+R +LQ L+ + I++ +
Sbjct: 56  AASICRHLYIRSPAGIGSFEKIYGGRRRRGTAPSHFCKANGSISRRLLQSLEGLKIVEKD 115

Query: 65  PKGGRRITSSGQRDLDQVAGRIV 87
           P GGRR+TS G+RDLD++A +I 
Sbjct: 116 PNGGRRLTSQGRRDLDRIAAQIA 138

Mya arenaria (taxid: 6604)

>sp|P17074|RS19_RAT 40S ribosomal protein S19 OS=Rattus norvegicus GN=Rps19 PE=2 SV=3

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 60/85 (70%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +
Sbjct: 57  AASTARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKD 116

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct: 117 QDGGRKLTPQGQRDLDRIAGQVAAA 141

Required for pre-rRNA processing and maturation of 40S ribosomal subunits.

Rattus norvegicus (taxid: 10116)

>sp|Q9CZX8|RS19_MOUSE 40S ribosomal protein S19 OS=Mus musculus GN=Rps19 PE=1 SV=3

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 41/85 (48%), Positives = 60/85 (70%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +
Sbjct: 57  AASTARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKD 116

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct: 117 QDGGRKLTPQGQRDLDRIAGQVAAA 141

Required for pre-rRNA processing and maturation of 40S ribosomal subunits.

Mus musculus (taxid: 10090)

>sp|Q54X51|RS19_DICDI 40S ribosomal protein S19 OS=Dictyostelium discoideum GN=rps19 PE=3 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 64/83 (77%), Gaps = 1/83 (1%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
           + ++ARK+Y+R G GV ++RR++GG++RNG RP HF   +G   R+ L+QLQN+ +I+ +
Sbjct: 59  IATLARKVYIRGGDGVATYRRVFGGNRRNGVRPNHFADVNGGNIRYCLKQLQNLKVIETD 118

Query: 65  P-KGGRRITSSGQRDLDQVAGRI 86
             KGGR IT++G+RDLD++A +I
Sbjct: 119 AVKGGRTITATGRRDLDRIAKQI 141

Dictyostelium discoideum (taxid: 44689)

>sp|Q5R8M9|RS19_PONAB 40S ribosomal protein S19 OS=Pongo abelii GN=RPS19 PE=2 SV=3

 Score = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/85 (47%), Positives = 59/85 (69%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             S AR +YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +
Sbjct: 57  AASTARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKD 116

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct: 117 QDGGRKLTPQGQRDLDRIAGQVAAA 141

Required for pre-rRNA processing and maturation of 40S ribosomal subunits.

Pongo abelii (taxid: 9601)

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	90
224077760	143	predicted protein [Populus trichocarpa]	0.944	0.594	0.905	6e-39
224141061	143	predicted protein [Populus trichocarpa]	0.944	0.594	0.917	1e-38
255570268	143	40S ribosomal protein S19, putative [Ric	0.955	0.601	0.918	2e-38
255570270	143	40S ribosomal protein S19-3, putative [R	0.944	0.594	0.917	3e-38
449491502	143	PREDICTED: 40S ribosomal protein S19-3-l	0.944	0.594	0.882	6e-38
449447418	143	PREDICTED: 40S ribosomal protein S19-3-l	0.944	0.594	0.882	7e-38
351722318	143	uncharacterized protein LOC100499800 [Gl	0.955	0.601	0.872	6e-37
225423503	146	PREDICTED: 40S ribosomal protein S19-1 [	0.944	0.582	0.882	9e-37
449462326	143	PREDICTED: 40S ribosomal protein S19-3-l	0.944	0.594	0.858	9e-37
255560408	143	40S ribosomal protein S19, putative [Ric	0.944	0.594	0.882	1e-36

>gi|224077760|ref|XP_002305397.1| predicted protein [Populus trichocarpa] gi|222848361|gb|EEE85908.1| predicted protein [Populus trichocarpa]

 Score =  164 bits (415), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 77/85 (90%), Positives = 83/85 (97%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+FRRIYGGS+RNGSRPPHFCKSSG++ARHILQQLQNMNIID++P
Sbjct: 59  ASMARKIYLRGGLGVGAFRRIYGGSQRNGSRPPHFCKSSGSVARHILQQLQNMNIIDVDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITSSGQRDLDQVAGRIVVAP
Sbjct: 119 KGGRRITSSGQRDLDQVAGRIVVAP 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224141061|ref|XP_002323893.1| predicted protein [Populus trichocarpa] gi|118487378|gb|ABK95517.1| unknown [Populus trichocarpa] gi|222866895|gb|EEF04026.1| predicted protein [Populus trichocarpa]

 Score =  163 bits (413), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 78/85 (91%), Positives = 83/85 (97%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIY+R GLGVG+FRRIYGGSKRNGSRPPHFCKSSG+IARHILQQLQN+NIIDI+P
Sbjct: 59  ASMARKIYIRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGSIARHILQQLQNVNIIDIDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITSSGQRDLDQVAGRIVVAP
Sbjct: 119 KGGRRITSSGQRDLDQVAGRIVVAP 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570268|ref|XP_002526094.1| 40S ribosomal protein S19, putative [Ricinus communis] gi|223534591|gb|EEF36288.1| 40S ribosomal protein S19, putative [Ricinus communis]

 Score =  163 bits (412), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 79/86 (91%), Positives = 82/86 (95%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+
Sbjct: 58  AASMARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDID 117

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVAP 90
           PKGGRRITSSGQRDLDQVAGRIVVAP
Sbjct: 118 PKGGRRITSSGQRDLDQVAGRIVVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255570270|ref|XP_002526095.1| 40S ribosomal protein S19-3, putative [Ricinus communis] gi|223534592|gb|EEF36289.1| 40S ribosomal protein S19-3, putative [Ricinus communis]

 Score =  162 bits (410), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 78/85 (91%), Positives = 82/85 (96%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+P
Sbjct: 59  ASMARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGR+ITSSGQRDLDQVAGRIVVAP
Sbjct: 119 KGGRKITSSGQRDLDQVAGRIVVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491502|ref|XP_004158918.1| PREDICTED: 40S ribosomal protein S19-3-like [Cucumis sativus]

 Score =  160 bits (406), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 75/85 (88%), Positives = 82/85 (96%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFC+SSGAIARHILQQLQ MNI+D++P
Sbjct: 59  ASMARKIYLRGGLGVGAFKRIYGGSKRNGSRPPHFCESSGAIARHILQQLQEMNIVDVDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITSSG+RDLDQVAGRIVVAP
Sbjct: 119 KGGRRITSSGRRDLDQVAGRIVVAP 143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447418|ref|XP_004141465.1| PREDICTED: 40S ribosomal protein S19-3-like [Cucumis sativus] gi|449481377|ref|XP_004156165.1| PREDICTED: 40S ribosomal protein S19-3-like [Cucumis sativus]

 Score =  160 bits (406), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 75/85 (88%), Positives = 82/85 (96%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFC+SSGAIARHILQQLQ MNI+D++P
Sbjct: 59  ASMARKIYLRGGLGVGAFKRIYGGSKRNGSRPPHFCESSGAIARHILQQLQEMNIVDVDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITSSG+RDLDQVAGRIVVAP
Sbjct: 119 KGGRRITSSGRRDLDQVAGRIVVAP 143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722318|ref|NP_001236216.1| uncharacterized protein LOC100499800 [Glycine max] gi|255626719|gb|ACU13704.1| unknown [Glycine max]

 Score =  157 bits (398), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 75/86 (87%), Positives = 82/86 (95%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII+++
Sbjct: 58  AASMARKIYLRGGLGVGAFQRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIELD 117

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVAP 90
            KGGR+ITSSG+RDLDQVAGRIVVAP
Sbjct: 118 TKGGRKITSSGRRDLDQVAGRIVVAP 143

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225423503|ref|XP_002269657.1| PREDICTED: 40S ribosomal protein S19-1 [Vitis vinifera] gi|147798403|emb|CAN70140.1| hypothetical protein VITISV_032083 [Vitis vinifera] gi|297738070|emb|CBI27271.3| unnamed protein product [Vitis vinifera]

 Score =  157 bits (396), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 75/85 (88%), Positives = 80/85 (94%)

Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             SMARKIYLRQGLGVG FRRIYGGSKRNGSRPPHFCKSSG+IARHILQQL+ MNII+ +
Sbjct: 61  AASMARKIYLRQGLGVGGFRRIYGGSKRNGSRPPHFCKSSGSIARHILQQLEKMNIIEND 120

Query: 65  PKGGRRITSSGQRDLDQVAGRIVVA 89
           P+GGRRITSSGQRDLDQVAGRIVVA
Sbjct: 121 PRGGRRITSSGQRDLDQVAGRIVVA 145

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462326|ref|XP_004148892.1| PREDICTED: 40S ribosomal protein S19-3-like [Cucumis sativus]

 Score =  157 bits (396), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 73/85 (85%), Positives = 80/85 (94%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+F+RIY GSKRNGSRPPHFC+SSGAI RHILQQLQ MNI+D++P
Sbjct: 59  ASMARKIYLRGGLGVGAFKRIYNGSKRNGSRPPHFCESSGAIVRHILQQLQEMNIVDVDP 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITSSG+RDLDQVAGRIVVAP
Sbjct: 119 KGGRRITSSGRRDLDQVAGRIVVAP 143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255560408|ref|XP_002521219.1| 40S ribosomal protein S19, putative [Ricinus communis] gi|223539584|gb|EEF41171.1| 40S ribosomal protein S19, putative [Ricinus communis]

 Score =  156 bits (395), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 75/85 (88%), Positives = 80/85 (94%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            SMARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+ 
Sbjct: 59  ASMARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDS 118

Query: 66  KGGRRITSSGQRDLDQVAGRIVVAP 90
           KGGRRITS+GQRDLDQVAG I+VAP
Sbjct: 119 KGGRRITSTGQRDLDQVAGHIIVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	90
TAIR|locus:2078633	143	AT3G02080 [Arabidopsis thalian	0.933	0.587	0.845	5.1e-35
TAIR|locus:2159486	143	AT5G61170 [Arabidopsis thalian	0.922	0.580	0.843	1.1e-34
TAIR|locus:2180912	143	AT5G15520 [Arabidopsis thalian	0.888	0.559	0.862	1.5e-33
MGI|MGI:1333780	145	Rps19 "ribosomal protein S19"	0.922	0.572	0.493	1.5e-19
RGD|2321315	145	LOC100360843 "ribosomal protei	0.922	0.572	0.493	1.5e-19
RGD|68440	145	Rps19 "ribosomal protein S19"	0.922	0.572	0.493	1.5e-19
RGD|2318347	145	LOC100362339 "ribosomal protei	0.922	0.572	0.493	2.5e-19
UNIPROTKB|F1M8C7	156	F1M8C7 "Uncharacterized protei	0.977	0.564	0.465	4e-19
RGD|1562153	160	Rps19l1 "ribosomal protein S19	0.922	0.518	0.481	5.1e-19
UNIPROTKB|E1BHA5	145	E1BHA5 "Uncharacterized protei	0.922	0.572	0.481	6.5e-19

TAIR|locus:2078633 AT3G02080 [Arabidopsis thaliana (taxid:3702)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 71/84 (84%), Positives = 78/84 (92%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             SMARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ MNI++++ K
Sbjct:    60 SMARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTK 119

Query:    67 GGRRITSSGQRDLDQVAGRIVVAP 90
             GGRRITSSGQRDLDQVAGRI V P
Sbjct:   120 GGRRITSSGQRDLDQVAGRIAVEP 143

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2159486 AT5G61170 [Arabidopsis thaliana (taxid:3702)]

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 70/83 (84%), Positives = 77/83 (92%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             SMARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG +ARHILQQLQ MNI+D++ K
Sbjct:    60 SMARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTK 119

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR+ITSSGQRDLDQVAGRI  A
Sbjct:   120 GGRKITSSGQRDLDQVAGRIAAA 142

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2180912 AT5G15520 [Arabidopsis thaliana (taxid:3702)]

 Score = 365 (133.5 bits), Expect = 1.5e-33, P = 1.5e-33
 Identities = 69/80 (86%), Positives = 76/80 (95%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             SMARKIYLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ M+I++++ K
Sbjct:    60 SMARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELDTK 119

Query:    67 GGRRITSSGQRDLDQVAGRI 86
             GGRRITSSGQRDLDQVAGRI
Sbjct:   120 GGRRITSSGQRDLDQVAGRI 139

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

MGI|MGI:1333780 Rps19 "ribosomal protein S19" [Mus musculus (taxid:10090)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 41/83 (49%), Positives = 60/83 (72%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  
Sbjct:    59 STARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQD 118

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   119 GGRKLTPQGQRDLDRIAGQVAAA 141

GO:0000028 "ribosomal small subunit assembly" evidence=ISO

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005622 "intracellular" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

GO:0005829 "cytosol" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0006364 "rRNA processing" evidence=ISO

GO:0006412 "translation" evidence=IEA

GO:0017134 "fibroblast growth factor binding" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO

GO:0030218 "erythrocyte differentiation" evidence=ISO

GO:0030490 "maturation of SSU-rRNA" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0031369 "translation initiation factor binding" evidence=ISO

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISO

RGD|2321315 LOC100360843 "ribosomal protein S19-like" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 41/83 (49%), Positives = 60/83 (72%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  
Sbjct:    59 STARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQD 118

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   119 GGRKLTPQGQRDLDRIAGQVAAA 141

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

RGD|68440 Rps19 "ribosomal protein S19" [Rattus norvegicus (taxid:10116)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 41/83 (49%), Positives = 60/83 (72%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  
Sbjct:    59 STARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQD 118

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   119 GGRKLTPQGQRDLDRIAGQVAAA 141

GO:0000028 "ribosomal small subunit assembly" evidence=ISO

GO:0003735 "structural constituent of ribosome" evidence=ISO;ISS;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=ISO;ISS;IDA

GO:0005829 "cytosol" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0006364 "rRNA processing" evidence=ISO

GO:0006412 "translation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0017134 "fibroblast growth factor binding" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO;ISS;IDA

GO:0030218 "erythrocyte differentiation" evidence=ISO;ISS

GO:0030490 "maturation of SSU-rRNA" evidence=ISO

GO:0031369 "translation initiation factor binding" evidence=IPI

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISO

RGD|2318347 LOC100362339 "ribosomal protein S19-like" [Rattus norvegicus (taxid:10116)]

 Score = 231 (86.4 bits), Expect = 2.5e-19, P = 2.5e-19
 Identities = 41/83 (49%), Positives = 60/83 (72%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  
Sbjct:    59 STARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMMEKDQD 118

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   119 GGRKLTPQGQRDLDRIAGQVAAA 141

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|F1M8C7 F1M8C7 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 229 (85.7 bits), Expect = 4.0e-19, P = 4.0e-19
 Identities = 41/88 (46%), Positives = 60/88 (68%)

Query:     2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII 61
             S    S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + ++
Sbjct:    65 STRAASTARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMV 124

Query:    62 DIEPKGGRRITSSGQRDLDQVAGRIVVA 89
             + +  GGR++T  G RDLD++AG++  A
Sbjct:   125 EKDQDGGRKLTPQGHRDLDRIAGQVAAA 152

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

RGD|1562153 Rps19l1 "ribosomal protein S19-like 1" [Rattus norvegicus (taxid:10116)]

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 40/83 (48%), Positives = 59/83 (71%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG RP HF + S ++A  +LQ L+ + +++ +  
Sbjct:    74 STARHLYLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVAHRVLQALEGLKMVEKDQD 133

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   134 GGRKLTPQGQRDLDRIAGQVAAA 156

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|E1BHA5 E1BHA5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 40/83 (48%), Positives = 59/83 (71%)

Query:     7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
             S AR +YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +  
Sbjct:    59 STARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQD 118

Query:    67 GGRRITSSGQRDLDQVAGRIVVA 89
             GGR++T  GQRDLD++AG++  A
Sbjct:   119 GGRKLTPQGQRDLDRIAGQVAAA 141

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0003735 "structural constituent of ribosome" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P40978	RS19_ORYSJ	No assigned EC number	0.7619	0.9333	0.5753	yes	no
Q9LF30	RS192_ARATH	No assigned EC number	0.8214	0.9333	0.5874	yes	no
Q9SGA6	RS191_ARATH	No assigned EC number	0.8255	0.9555	0.6013	yes	no

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	90
pfam01090	140	pfam01090, Ribosomal_S19e, Ribosomal protein S19e	4e-40
COG2238	147	COG2238, RPS19A, Ribosomal protein S19E (S16A) [Tr	2e-26
PRK09333	150	PRK09333, PRK09333, 30S ribosomal protein S19e; Pr	9e-25
PTZ00095	169	PTZ00095, PTZ00095, 40S ribosomal protein S19; Pro	2e-17

>gnl|CDD|144617 pfam01090, Ribosomal_S19e, Ribosomal protein S19e

 Score =  128 bits (325), Expect = 4e-40
 Identities = 42/81 (51%), Positives = 58/81 (71%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+ RK+YLR  +GVG  R+IYGG KR G RP HF K SG+I R  LQQL+   +++ +PK
Sbjct: 56  SILRKLYLRGPVGVGRLRKIYGGRKRRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDPK 115

Query: 67  GGRRITSSGQRDLDQVAGRIV 87
           GGRR+T  G+ DLD++A  ++
Sbjct: 116 GGRRLTPQGRSDLDRIAAEVL 136

Length = 140

>gnl|CDD|225147 COG2238, RPS19A, Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]

 Score = 93.9 bits (234), Expect = 2e-26
 Identities = 35/80 (43%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+ RKIY+   +G+   R  YGG K  GSRP  F K SG+I R +LQQL+   +++  PK
Sbjct: 57  SILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTPK 116

Query: 67  GGRRITSSGQRDLDQVAGRI 86
            GR +T  G+  LD++A  I
Sbjct: 117 -GRVLTPKGRSLLDRIATEI 135

Length = 147

>gnl|CDD|236470 PRK09333, PRK09333, 30S ribosomal protein S19e; Provisional

 Score = 89.9 bits (224), Expect = 9e-25
 Identities = 35/80 (43%), Positives = 47/80 (58%), Gaps = 1/80 (1%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+ RK+Y+   +GV   R  YGG K  G RP HF K SG+I R ILQQL+   +++   K
Sbjct: 57  SILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK 116

Query: 67  GGRRITSSGQRDLDQVAGRI 86
            GR IT  G+  LD +A  +
Sbjct: 117 -GRVITPKGRSLLDNLAAEV 135

Length = 150

>gnl|CDD|140127 PTZ00095, PTZ00095, 40S ribosomal protein S19; Provisional

 Score = 71.7 bits (176), Expect = 2e-17
 Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           ++ R +YLR  +G G  R+ +   KR GS P H  ++SG I R I QQL+ + +++  PK
Sbjct: 81  AVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPK 140

Query: 67  G-GRRITSSGQRDLDQVAGRI 86
             GRR+T  G    +  A ++
Sbjct: 141 KKGRRLTRKGCNFANAFARQV 161

Length = 169

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	90
PF01090	139	Ribosomal_S19e: Ribosomal protein S19e; InterPro:	100.0
PTZ00095	169	40S ribosomal protein S19; Provisional	100.0
KOG3411	143	consensus 40S ribosomal protein S19 [Translation,	100.0
PRK09333	150	30S ribosomal protein S19e; Provisional	100.0
COG2238	147	RPS19A Ribosomal protein S19E (S16A) [Translation,	100.0
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	97.73
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	97.57
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	97.25
COG1420	346	HrcA Transcriptional regulator of heat shock gene	97.15
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	97.13
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.07
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	97.0
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.97
PRK11050	152	manganese transport regulator MntR; Provisional	96.95
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.85
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	96.85
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.83
COG1846	126	MarR Transcriptional regulators [Transcription]	96.8
PRK03911	260	heat-inducible transcription repressor; Provisiona	96.62
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.62
PRK10870	176	transcriptional repressor MprA; Provisional	96.61
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	96.48
PRK03573	144	transcriptional regulator SlyA; Provisional	96.41
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.3
COG3388	101	Predicted transcriptional regulator [Transcription	96.29
PRK13777	185	transcriptional regulator Hpr; Provisional	96.19
PRK03902	142	manganese transport transcriptional regulator; Pro	96.08
PF14338	92	Mrr_N: Mrr N-terminal domain	96.07
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	96.01
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	95.93
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	95.68
PF10711	102	DUF2513: Hypothetical protein (DUF2513); InterPro:	95.68
COG3432	95	Predicted transcriptional regulator [Transcription	95.65
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	95.64
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.58
TIGR03338	212	phnR_burk phosphonate utilization associated trans	95.51
COG1693	325	Repressor of nif and glnA expression [Transcriptio	95.49
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.37
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	95.21
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	95.16
PRK05638	442	threonine synthase; Validated	95.16
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.12
PF03551	75	PadR: Transcriptional regulator PadR-like family;	95.08
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	94.84
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	94.8
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	94.73
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	94.71
PF09114	96	MotA_activ: Transcription factor MotA, activation	94.65
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	94.44
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	94.36
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.33
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	94.24
COG1802	230	GntR Transcriptional regulators [Transcription]	94.22
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	94.18
COG1725	125	Predicted transcriptional regulators [Transcriptio	94.17
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.07
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.07
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	93.91
COG1733	120	Predicted transcriptional regulators [Transcriptio	93.85
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	93.82
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	93.65
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	93.45
PRK11014	141	transcriptional repressor NsrR; Provisional	93.24
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	92.97
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	92.88
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	92.74
PRK09416	135	lstR lineage-specific thermal regulator protein; P	92.53
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	92.51
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.51
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	92.46
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	92.35
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	92.06
PRK04984	239	fatty acid metabolism regulator; Provisional	92.01
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	91.98
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	91.85
PRK03837	241	transcriptional regulator NanR; Provisional	91.76
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	91.75
PRK08599	377	coproporphyrinogen III oxidase; Provisional	91.72
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	91.64
PRK09057	380	coproporphyrinogen III oxidase; Provisional	91.49
COG1414	246	IclR Transcriptional regulator [Transcription]	91.43
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	91.16
PRK14165	217	winged helix-turn-helix domain-containing protein/	91.08
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	91.07
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	91.0
PRK11569	274	transcriptional repressor IclR; Provisional	90.8
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	90.55
COG1695	138	Predicted transcriptional regulators [Transcriptio	90.07
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	89.95
PF09382	106	RQC: RQC domain; InterPro: IPR018982 This entry re	89.29
COG3355	126	Predicted transcriptional regulator [Transcription	89.27
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	88.8
PRK07379	400	coproporphyrinogen III oxidase; Provisional	88.75
PRK05660	378	HemN family oxidoreductase; Provisional	88.65
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	88.58
PRK05628	375	coproporphyrinogen III oxidase; Validated	88.52
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	88.47
PF13814	191	Replic_Relax: Replication-relaxation	88.42
PRK08208	430	coproporphyrinogen III oxidase; Validated	88.31
PRK05799	374	coproporphyrinogen III oxidase; Provisional	87.79
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	87.58
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	87.57
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	87.34
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	87.33
COG2186	241	FadR Transcriptional regulators [Transcription]	87.17
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	87.14
COG2524	294	Predicted transcriptional regulator, contains C-te	87.09
PRK06582	390	coproporphyrinogen III oxidase; Provisional	86.91
PRK06294	370	coproporphyrinogen III oxidase; Provisional	86.88
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	86.65
PRK13347	453	coproporphyrinogen III oxidase; Provisional	86.31
PRK00215	205	LexA repressor; Validated	85.94
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	85.71
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	85.59
PRK09249	453	coproporphyrinogen III oxidase; Provisional	85.16
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	85.09
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	84.99
PRK08898	394	coproporphyrinogen III oxidase; Provisional	84.91
COG1959	150	Predicted transcriptional regulator [Transcription	84.12
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	83.95
PRK06266	178	transcription initiation factor E subunit alpha; V	83.81
PRK08629	433	coproporphyrinogen III oxidase; Provisional	83.75
PRK14999	241	histidine utilization repressor; Provisional	83.74
TIGR00538	455	hemN oxygen-independent coproporphyrinogen III oxi	83.72
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	83.6
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	83.55
PRK13626	552	transcriptional regulator SgrR; Provisional	83.15
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	83.08
PRK09334	86	30S ribosomal protein S25e; Provisional	82.77
PRK10079	241	phosphonate metabolism transcriptional regulator P	82.71
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	82.46
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	81.88
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	81.59
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	81.46
PRK09058	449	coproporphyrinogen III oxidase; Provisional	81.25

>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=2.9e-44  Score=255.21  Aligned_cols=87  Identities=52%  Similarity=0.954  Sum_probs=79.1

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +||||||||||++||+||++|+++|||+||||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+|
T Consensus        52 ~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~i  131 (139)
T PF01090_consen   52 IRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRI  131 (139)
T ss_dssp             HHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHH
T ss_pred             eeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             HHHhhcC
Q 034587           83 AGRIVVA   89 (90)
Q Consensus        83 A~~v~~~   89 (90)
                      |.+|+++
T Consensus       132 A~~v~~~  138 (139)
T PF01090_consen  132 AGQVAKE  138 (139)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHc
Confidence            9999864

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 [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.

>PTZ00095 40S ribosomal protein S19; Provisional

Probab=100.00  E-value=3.9e-43  Score=255.94  Aligned_cols=87  Identities=33%  Similarity=0.604  Sum_probs=84.0

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchHhhHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRDLDQ   81 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~lD~   81 (90)
                      +||||||||||++||+||++|++.|||+||||++|+||++|||+|||+||||||++|||++++ ++||+|||+||+|||+
T Consensus        77 iRaASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~  156 (169)
T PTZ00095         77 IRCAAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANA  156 (169)
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHH
Confidence            699999999999999999999999999999999999999999999999999999999999996 4899999999999999


Q ss_pred             HHHHhhcC
Q 034587           82 VAGRIVVA   89 (90)
Q Consensus        82 iA~~v~~~   89 (90)
                      ||.+|+++
T Consensus       157 iA~~v~~~  164 (169)
T PTZ00095        157 FARQVTIR  164 (169)
T ss_pred             HHHHHHHH
Confidence            99999753

>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.3e-42  Score=246.25  Aligned_cols=88  Identities=56%  Similarity=0.999  Sum_probs=86.0

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      .|||||+||||+++|+||+.|+++|||+||||++|+||+.+||+|+|++||+||++||||++|++||+||++||+|||+|
T Consensus        55 tRaASiaRhiylR~~~gvg~~~KiYGg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrI  134 (143)
T KOG3411|consen   55 TRAASIARHIYLRGPVGVGALTKIYGGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRI  134 (143)
T ss_pred             HHHHHHHHHHHhccccchhHHHHHhcccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHH
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCC
Q 034587           83 AGRIVVAP   90 (90)
Q Consensus        83 A~~v~~~~   90 (90)
                      |++|.+++
T Consensus       135 a~~i~~~~  142 (143)
T KOG3411|consen  135 AGQIREEQ  142 (143)
T ss_pred             HHHHHhcc
Confidence            99998764

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=100.00  E-value=2.3e-41  Score=242.84  Aligned_cols=86  Identities=40%  Similarity=0.663  Sum_probs=83.7

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +||||||||||++||+||++|++.||++||||++|+||++|||+|||++|||||++|||++++ +||+|||+||++||+|
T Consensus        53 ~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~i  131 (150)
T PRK09333         53 VRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNL  131 (150)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHH
Confidence            699999999999999999999999999999999999999999999999999999999999998 8999999999999999


Q ss_pred             HHHhhcC
Q 034587           83 AGRIVVA   89 (90)
Q Consensus        83 A~~v~~~   89 (90)
                      |.+|+++
T Consensus       132 A~~i~~~  138 (150)
T PRK09333        132 AAEVKKE  138 (150)
T ss_pred             HHHHHHH
Confidence            9999753

>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2e-41  Score=241.84  Aligned_cols=86  Identities=40%  Similarity=0.677  Sum_probs=83.9

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +|||||||||||+||+||++|++.|||+||||++|+||.+|||+|+|++|||||++|||++++ +||+|||+||++||+|
T Consensus        53 ~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~  131 (147)
T COG2238          53 VRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRI  131 (147)
T ss_pred             HHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHH
Confidence            699999999999999999999999999999999999999999999999999999999999999 7999999999999999


Q ss_pred             HHHhhcC
Q 034587           83 AGRIVVA   89 (90)
Q Consensus        83 A~~v~~~   89 (90)
                      |.+|+++
T Consensus       132 a~ei~ee  138 (147)
T COG2238         132 ATEIKEE  138 (147)
T ss_pred             HHHHHHH
Confidence            9999764

>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=97.73  E-value=8.5e-05  Score=46.44  Aligned_cols=63  Identities=21%  Similarity=0.221  Sum_probs=50.6

Q ss_pred             HHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587            8 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL   79 (90)
Q Consensus         8 i~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l   79 (90)
                      ||+.|+-. +|+|=..|+....-.   |      ..-|-.-+|.-|.+||+.||+++...+||.||++|...|
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~---g------~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~G~~~L   66 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLR---G------EELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL   66 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhc---C------hhhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence            67777765 689999999877653   2      223446799999999999999988788999999998764

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

Probab=97.57  E-value=6.9e-05  Score=49.15  Aligned_cols=57  Identities=25%  Similarity=0.514  Sum_probs=46.8

Q ss_pred             HHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcchHhhHHH
Q 034587           11 KIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRDLDQ   81 (90)
Q Consensus        11 klYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G~~~lD~   81 (90)
                      ..|++  .|||=..+....+-              |..-||+.++.||++|||++.  +.+||+-|++|-+.+++
T Consensus        15 ~~Y~~~~~PVgSk~ia~~l~~--------------s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~   75 (78)
T PF03444_consen   15 ELYIETGEPVGSKTIAEELGR--------------SPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR   75 (78)
T ss_pred             HHHHhcCCCcCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence            35775  69999999987542              236899999999999999964  46999999999998864

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

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=97.25  E-value=0.0034  Score=41.56  Aligned_cols=67  Identities=13%  Similarity=0.111  Sum_probs=52.9

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..|+..|+-++++.+..|++..|-.+              +-+-.+++.||+.|||+..+  .+.|    .||++|+..+
T Consensus        31 ~~iL~~l~~~~~~t~~ela~~~~~~~--------------~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~   96 (118)
T TIGR02337        31 WRILRILAEQGSMEFTQLANQACILR--------------PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALY   96 (118)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHhCCCc--------------hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHH
Confidence            45777788888899999999877654              35678999999999999654  3444    6999999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +++....
T Consensus        97 ~~~~~~~  103 (118)
T TIGR02337        97 ASLSPQI  103 (118)
T ss_pred             HHhhHHH
Confidence            9886654

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.

>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]

Probab=97.15  E-value=0.0012  Score=52.84  Aligned_cols=65  Identities=26%  Similarity=0.371  Sum_probs=53.2

Q ss_pred             hhhHHHHHHHH---hhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587            2 SELVTSMARKI---YLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~Rkl---Yl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G   75 (90)
                      ..|-..|||-|   |+.  -|||=.+|.+.|+-            .-|..-||+.+++||++|+++|.. -.||+.|++|
T Consensus         5 ~~Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l------------~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~G   72 (346)
T COG1420           5 DERQRLILRAIVEDYLATGEPVGSKTLSEKYNL------------DLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKG   72 (346)
T ss_pred             hHHHHHHHHHHHHHHHhcCCccchHHHHHHhCC------------CCCchhHHHHHHHHHHCCCccCccccCCcCCcHhH
Confidence            45677777764   775  59999999998863            245678999999999999999776 4799999999


Q ss_pred             Hhh
Q 034587           76 QRD   78 (90)
Q Consensus        76 ~~~   78 (90)
                      -+.
T Consensus        73 yr~   75 (346)
T COG1420          73 YRY   75 (346)
T ss_pred             HHH
Confidence            764

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

Probab=97.13  E-value=0.0018  Score=40.99  Aligned_cols=62  Identities=15%  Similarity=0.241  Sum_probs=43.6

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA   83 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA   83 (90)
                      +.||.-+- .++.....+..              .++=+-+.+...|+.|++.|+|++. ++.-.||++|...|+.+-
T Consensus         9 ~~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l~   70 (77)
T PF14947_consen    9 FDILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEELE   70 (77)
T ss_dssp             HHHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHHH
Confidence            44555544 67777766663              3345668999999999999999774 578999999999999874

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.07  E-value=0.0058  Score=41.83  Aligned_cols=66  Identities=14%  Similarity=0.152  Sum_probs=52.1

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..|+..|+-.+++....|+...+-.+              +-+=.+++.||+.|||++.+  .++|    .||++|+..
T Consensus        42 q~~vL~~l~~~~~~t~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~  107 (144)
T PRK11512         42 QFKVLCSIRCAACITPVELKKVLSVDL--------------GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAI  107 (144)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHH
Confidence            356788888888889999999877754              46777899999999999654  4455    589999999


Q ss_pred             HHHHHH
Q 034587           79 LDQVAG   84 (90)
Q Consensus        79 lD~iA~   84 (90)
                      ++++..
T Consensus       108 ~~~~~~  113 (144)
T PRK11512        108 CEQCHQ  113 (144)
T ss_pred             HHHHHH
Confidence            887643

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=97.00  E-value=0.002  Score=46.77  Aligned_cols=61  Identities=15%  Similarity=0.251  Sum_probs=49.9

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCCe-----eeCcchHh
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~GR-----~lT~~G~~   77 (90)
                      -+|+.-|.-.+++.+..|+...|-.              ..-++..|+.||+.|||+..+   ..||     .||++|..
T Consensus         4 ~~IL~~L~~~~~~t~~eLA~~lgis--------------~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~   69 (203)
T TIGR02702         4 EDILSYLLKQGQATAAALAEALAIS--------------PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGRE   69 (203)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhh
Confidence            3577778778999999999988764              258999999999999998762   3578     99999987


Q ss_pred             hHH
Q 034587           78 DLD   80 (90)
Q Consensus        78 ~lD   80 (90)
                      .+.
T Consensus        70 ~~~   72 (203)
T TIGR02702        70 QFP   72 (203)
T ss_pred             hcc
Confidence            553

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.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.97  E-value=0.013  Score=36.20  Aligned_cols=71  Identities=17%  Similarity=0.225  Sum_probs=54.8

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC------CeeeCcch
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~------GR~lT~~G   75 (90)
                      +.-.-.|+..|+..+++.+..+....+-.              ..-+...|+.|++.|||+...++      .-.||++|
T Consensus         9 ~~~~~~il~~l~~~~~~~~~~la~~~~~s--------------~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g   74 (101)
T smart00347        9 TPTQFLVLRILYEEGPLSVSELAKRLGVS--------------PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEG   74 (101)
T ss_pred             CHHHHHHHHHHHHcCCcCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhH
Confidence            34455688888889999999999876532              13478999999999999866532      35699999


Q ss_pred             HhhHHHHHHHh
Q 034587           76 QRDLDQVAGRI   86 (90)
Q Consensus        76 ~~~lD~iA~~v   86 (90)
                      ...++.+...+
T Consensus        75 ~~~~~~~~~~~   85 (101)
T smart00347       75 RELIEELLEAR   85 (101)
T ss_pred             HHHHHHHHHHH
Confidence            99998877654

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.95  E-value=0.0062  Score=42.85  Aligned_cols=63  Identities=16%  Similarity=0.191  Sum_probs=51.7

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG   84 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~   84 (90)
                      |++.++-.+++.+..|+..++-.+              +-+...|++||+.|||...+.+|-.||++|+..+..+..
T Consensus        42 I~~~l~~~~~~t~~eLA~~l~is~--------------stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~  104 (152)
T PRK11050         42 IADLIAEVGEARQVDIAARLGVSQ--------------PTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE  104 (152)
T ss_pred             HHHHHHhcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence            445555668899999999887643              689999999999999998777789999999998776653

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

Probab=96.85  E-value=0.0029  Score=40.08  Aligned_cols=41  Identities=22%  Similarity=0.398  Sum_probs=35.7

Q ss_pred             chhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587           44 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG   84 (90)
Q Consensus        44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~   84 (90)
                      +.+-+..+|+.||+.|||++.++++-.||++|+...+.+..
T Consensus        12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~   52 (96)
T smart00529       12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLR   52 (96)
T ss_pred             ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHH
Confidence            34679999999999999999987799999999998877654

iron dependent repressor

>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=96.85  E-value=0.0043  Score=39.90  Aligned_cols=65  Identities=12%  Similarity=0.178  Sum_probs=50.0

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC------CeeeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~------GR~lT~~G~~~   78 (90)
                      +..|++.|+. ||...+.|.+.-             ...|.+++-.-|..||+.|+|++....      -..||++|+++
T Consensus         7 ~~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l   72 (90)
T PF01638_consen    7 TLLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKEL   72 (90)
T ss_dssp             HHHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHH
T ss_pred             HHHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHH
Confidence            4678888888 888888888744             345678999999999999999876422      37899999998


Q ss_pred             HHHHH
Q 034587           79 LDQVA   83 (90)
Q Consensus        79 lD~iA   83 (90)
                      ++-+.
T Consensus        73 ~~~l~   77 (90)
T PF01638_consen   73 LPVLE   77 (90)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

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.

>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=96.83  E-value=0.003  Score=37.57  Aligned_cols=58  Identities=19%  Similarity=0.284  Sum_probs=41.8

Q ss_pred             hHHHHHHHHh-hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587            4 LVTSMARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG   75 (90)
Q Consensus         4 r~ASi~RklY-l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G   75 (90)
                      .-..||+.|+ -+++.....|+...+-.+              .-+..++++|++.|||++.+  ..+|    .|||+|
T Consensus         4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~--------------~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    4 PQWQVLRALAHSDGPMTQSDLAERLGISK--------------STVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHHHHHT--TS-BEHHHHHHHTT--H--------------HHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHHHHHccCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            4457889999 778999999999887643              46679999999999997654  3455    578877

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=96.80  E-value=0.011  Score=37.35  Aligned_cols=66  Identities=20%  Similarity=0.333  Sum_probs=50.3

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..++..||..++.+...|+...+-.+              +-+=.+++.||+.|||+..+  .++|    .||++|+..
T Consensus        24 q~~~L~~l~~~~~~~~~~la~~l~i~~--------------~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~   89 (126)
T COG1846          24 QYQVLLALYEAGGITVKELAERLGLDR--------------STVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGREL   89 (126)
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHH
Confidence            356777888887776677777666543              56778899999999998555  3455    799999999


Q ss_pred             HHHHHH
Q 034587           79 LDQVAG   84 (90)
Q Consensus        79 lD~iA~   84 (90)
                      +.++..
T Consensus        90 ~~~~~~   95 (126)
T COG1846          90 LEQLLP   95 (126)
T ss_pred             HHHhcc
Confidence            988755

>PRK03911 heat-inducible transcription repressor; Provisional

Probab=96.62  E-value=0.0073  Score=47.26  Aligned_cols=65  Identities=17%  Similarity=0.280  Sum_probs=51.0

Q ss_pred             hhhHHHHHHH---Hhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587            2 SELVTSMARK---IYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~Rk---lYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G   75 (90)
                      ..|--.|++.   -|+.  .|||=..|.+.|+-.            -|.+-||+.++.||++|++++.. ..||+.|.+|
T Consensus         2 ~~R~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l~------------~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~g   69 (260)
T PRK03911          2 LNKKDLLLDSIIQTYLQDNEPIGSNELKSLMNLK------------ISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKA   69 (260)
T ss_pred             chHHHHHHHHHHHHHhccCCccCHHHHHHHcCCC------------CCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHH
Confidence            3455556664   4775  599999999988753            35578999999999999998665 4799999999


Q ss_pred             Hhh
Q 034587           76 QRD   78 (90)
Q Consensus        76 ~~~   78 (90)
                      -+.
T Consensus        70 yr~   72 (260)
T PRK03911         70 MKN   72 (260)
T ss_pred             HHH
Confidence            864

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.62  E-value=0.014  Score=32.91  Aligned_cols=59  Identities=19%  Similarity=0.260  Sum_probs=43.5

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC---CeeeCc-chHhhHHH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS-SGQRDLDQ   81 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~-~G~~~lD~   81 (90)
                      |+..|+ .+++.+..+...+|-              |..-++.+|++|++.|||+...++   .-.+|+ .|...++.
T Consensus         2 il~~l~-~~~~~~~~i~~~l~i--------------s~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~   64 (66)
T smart00418        2 ILKLLA-EGELCVCELAEILGL--------------SQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE   64 (66)
T ss_pred             HHHHhh-cCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence            566777 889999999999973              235799999999999999966532   233666 55555543

>PRK10870 transcriptional repressor MprA; Provisional

Probab=96.61  E-value=0.013  Score=42.01  Aligned_cols=65  Identities=17%  Similarity=0.193  Sum_probs=47.7

Q ss_pred             HHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCee----eCcchHhh
Q 034587            7 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~----lT~~G~~~   78 (90)
                      .||..||-.  +++.+..|+...+-.+              +-+=.+++.||+.|||++.+  +++|.    ||++|+..
T Consensus        59 ~iL~~L~~~~~~~it~~eLa~~l~l~~--------------~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~  124 (176)
T PRK10870         59 MALITLESQENHSIQPSELSCALGSSR--------------TNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEF  124 (176)
T ss_pred             HHHHHHhcCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHH
Confidence            455566542  3566678887776543              46677899999999999654  56777    99999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++++-..
T Consensus       125 ~~~i~~~  131 (176)
T PRK10870        125 LREVLPP  131 (176)
T ss_pred             HHHHHHH
Confidence            9997543

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=96.48  E-value=0.019  Score=37.89  Aligned_cols=68  Identities=10%  Similarity=0.098  Sum_probs=51.4

Q ss_pred             HHHHHHHh----hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCee----eCcch
Q 034587            6 TSMARKIY----LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSG   75 (90)
Q Consensus         6 ASi~RklY----l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~----lT~~G   75 (90)
                      -.||..||    -.+++....|+..-+-.+              +-+=.++..||+.|||++.+  ++.|.    ||++|
T Consensus        28 ~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~--------------stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G   93 (109)
T TIGR01889        28 LLILYYLGKLENNEGKLTLKEIIKEILIKQ--------------SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQ   93 (109)
T ss_pred             HHHHHHHHhhhccCCcCcHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHH
Confidence            34677777    346788888888766543              45667899999999999655  44552    99999


Q ss_pred             HhhHHHHHHHhh
Q 034587           76 QRDLDQVAGRIV   87 (90)
Q Consensus        76 ~~~lD~iA~~v~   87 (90)
                      +..++.+..++-
T Consensus        94 ~~~~~~~~~~~~  105 (109)
T TIGR01889        94 RSKIESLISEIE  105 (109)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887763

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.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.41  E-value=0.036  Score=37.60  Aligned_cols=65  Identities=14%  Similarity=0.139  Sum_probs=47.4

Q ss_pred             HHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            7 SMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         7 Si~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      .+|..|+-. ++..+..|+...|-.+              +-+=.+++.||+.|||++.+  ++.|    .||++|+..+
T Consensus        35 ~vL~~l~~~~~~~t~~eLa~~l~~~~--------------~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~  100 (144)
T PRK03573         35 VTLHNIHQLPPEQSQIQLAKAIGIEQ--------------PSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLI  100 (144)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCh--------------hhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHH
Confidence            456666654 3567778887776643              35668999999999999665  3455    4999999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +.+...
T Consensus       101 ~~~~~~  106 (144)
T PRK03573        101 SEVEAV  106 (144)
T ss_pred             HHHHHH
Confidence            886544

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.30  E-value=0.027  Score=35.08  Aligned_cols=60  Identities=20%  Similarity=0.267  Sum_probs=49.0

Q ss_pred             hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchH
Q 034587            3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~   76 (90)
                      .|+-.|+..|.-. +++++..+....|-.              .+-++..|+.||+.|||+.++ ++...+++...
T Consensus         5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~--------------~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~   66 (91)
T smart00346        5 ERGLAVLRALAEEPGGLTLAELAERLGLS--------------KSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL   66 (91)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence            4778899988887 799999999988653              368999999999999999875 34567877544

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=96.29  E-value=0.009  Score=40.93  Aligned_cols=69  Identities=22%  Similarity=0.268  Sum_probs=56.9

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +|--+|+..+-=.+|+|+..|+..-|-       |+|.       +|+.|.=||+.++|.-.. .|=++|+.+-.+++++
T Consensus        14 ~RHl~Vl~~v~eeqPiGI~klS~~TGm-------p~HK-------VRYSLRVLEq~~iI~PS~-~GAi~td~~~e~ie~i   78 (101)
T COG3388          14 KRHLSVLKVVLEEQPIGIIKLSDETGM-------PEHK-------VRYSLRVLEQENIISPSR-QGAILTDDFPEFIEEI   78 (101)
T ss_pred             HHHHHHHHHHHHhCCceeEeechhcCC-------chhh-------hhhhhhhhhhcCccCccc-cCCccCccHHHHHHHH
Confidence            344566666777899999999998886       6563       799999999999997664 6999999999999988


Q ss_pred             HHHh
Q 034587           83 AGRI   86 (90)
Q Consensus        83 A~~v   86 (90)
                      ..++
T Consensus        79 ~~dl   82 (101)
T COG3388          79 IGDL   82 (101)
T ss_pred             HHHH
Confidence            7664

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=96.19  E-value=0.039  Score=40.62  Aligned_cols=67  Identities=12%  Similarity=0.142  Sum_probs=50.0

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR----~lT~~G~~~l   79 (90)
                      ..||-.||-.+++....|++..+-.+              +-+=.+++.||+.|||+..  +++.|    .||++|+..+
T Consensus        48 ~~iL~~L~~~~~itq~eLa~~l~l~~--------------sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~  113 (185)
T PRK13777         48 HHILWIAYHLKGASISEIAKFGVMHV--------------STAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELL  113 (185)
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHCCCH--------------hhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            35777788888888899988554421              2456699999999999854  44455    3999999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +++...+
T Consensus       114 ~~l~~~~  120 (185)
T PRK13777        114 LETMEEY  120 (185)
T ss_pred             HHHHHHH
Confidence            9876543

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=96.08  E-value=0.039  Score=37.84  Aligned_cols=55  Identities=13%  Similarity=0.107  Sum_probs=42.9

Q ss_pred             hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      -.+++-+..|+...+-.+              .-+...|+.||+.|||+....++=.||++|+.....+
T Consensus        19 ~~~~~~~~ela~~l~vs~--------------~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~   73 (142)
T PRK03902         19 EKGYARVSDIAEALSVHP--------------SSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL   73 (142)
T ss_pred             cCCCcCHHHHHHHhCCCh--------------hHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence            357788888888666532              4677789999999999866667899999998876655

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=96.07  E-value=0.0089  Score=38.64  Aligned_cols=35  Identities=26%  Similarity=0.352  Sum_probs=31.2

Q ss_pred             hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587           46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus        46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      .-++++++-|.++|+|++...|--.||++|++.|.
T Consensus        55 ~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~   89 (92)
T PF14338_consen   55 NRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA   89 (92)
T ss_pred             HhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence            46899999999999999877777999999999874

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=96.01  E-value=0.025  Score=44.77  Aligned_cols=65  Identities=23%  Similarity=0.368  Sum_probs=49.8

Q ss_pred             hhhHHHHHHH---Hhh--cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587            2 SELVTSMARK---IYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~Rk---lYl--~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G   75 (90)
                      +.|--.|+..   .|+  ..|+|...|.+.|+-.            -|..-||+-+..||++|++++.- ..||+.|.+|
T Consensus         5 ~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~------------~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kG   72 (339)
T PRK00082          5 DERQREILRAIVEDYIATGEPVGSKTLSKRYGLG------------VSSATIRNDMADLEELGLLEKPHTSSGRIPTDKG   72 (339)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCC------------CChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHH
Confidence            4555566652   455  5799999999875542            24478999999999999998655 4699999999


Q ss_pred             Hhh
Q 034587           76 QRD   78 (90)
Q Consensus        76 ~~~   78 (90)
                      -+.
T Consensus        73 YR~   75 (339)
T PRK00082         73 YRY   75 (339)
T ss_pred             HHH
Confidence            774

>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.93  E-value=0.0043  Score=40.54  Aligned_cols=58  Identities=21%  Similarity=0.273  Sum_probs=37.0

Q ss_pred             HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587            9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus         9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      +...|-.||||+.+|+..-|-.+             ..|.=.+===|-..|+|++.+ .||++|++|.+.|.
T Consensus        17 l~~~f~ggPvGl~tlA~~l~ed~-------------~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~l~   74 (76)
T PF05491_consen   17 LIENFKGGPVGLDTLAAALGEDK-------------ETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEHLG   74 (76)
T ss_dssp             HHHCSTTS-B-HHHHHHHTTS-H-------------HHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHHTT
T ss_pred             HHHHcCCCCeeHHHHHHHHCCCH-------------hHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHHhC
Confidence            34445578999999998666532             112222222466789999998 59999999987663

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=95.68  E-value=0.023  Score=37.27  Aligned_cols=47  Identities=17%  Similarity=0.225  Sum_probs=35.0

Q ss_pred             cccCchhHHHHHHHHHHhCCccccc--C-CCC-----eeeCcchHhhHHHHHHHh
Q 034587           40 FCKSSGAIARHILQQLQNMNIIDIE--P-KGG-----RRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        40 ~~~asg~iiR~~LqqLE~~glV~k~--~-~~G-----R~lT~~G~~~lD~iA~~v   86 (90)
                      +..-+-+-+=.+|..||+.|||+..  + .++     -.||++|+..++......
T Consensus        34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~   88 (100)
T TIGR03433        34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW   88 (100)
T ss_pred             ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            3344445688899999999999973  2 223     259999999999887654

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

>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known

Probab=95.68  E-value=0.021  Score=37.87  Aligned_cols=47  Identities=23%  Similarity=0.226  Sum_probs=38.0

Q ss_pred             CCCccccCchhHHHHHHHHHHhCCcccccCCCC---------eeeCcchHhhHHHH
Q 034587           36 RPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---------RRITSSGQRDLDQV   82 (90)
Q Consensus        36 ~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---------R~lT~~G~~~lD~i   82 (90)
                      .+..+..-+-..+-+-+++|+++|||+......         ..||.+|..+||.|
T Consensus        25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~I   80 (102)
T PF10711_consen   25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAI   80 (102)
T ss_pred             chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHh
Confidence            455666667779999999999999998665322         48999999999986

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=95.65  E-value=0.02  Score=38.76  Aligned_cols=43  Identities=19%  Similarity=0.232  Sum_probs=34.2

Q ss_pred             ccCchhHHHHHHHHHHhCCcccccCCC---CeeeCcchHhhHHHHH
Q 034587           41 CKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA   83 (90)
Q Consensus        41 ~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~~G~~~lD~iA   83 (90)
                      ++=+=.+.+++++.|++.|++++...+   .-.||++|.+++..+-
T Consensus        41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~   86 (95)
T COG3432          41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS   86 (95)
T ss_pred             cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence            344457999999999999988877643   3579999999987653

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=95.64  E-value=0.044  Score=39.76  Aligned_cols=60  Identities=13%  Similarity=0.142  Sum_probs=47.5

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCcch
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~~G   75 (90)
                      +.+-..|+..|.-++++.+..++...|-.              .+-++..|+.||+.|||+..++  ..-.||++|
T Consensus       142 s~~~~~IL~~l~~~g~~s~~eia~~l~is--------------~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G  203 (203)
T TIGR01884       142 SREELKVLEVLKAEGEKSVKNIAKKLGKS--------------LSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG  203 (203)
T ss_pred             CHHHHHHHHHHHHcCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence            45666788888877899999999988753              3578999999999999998763  234578776

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.

>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=95.58  E-value=0.028  Score=32.72  Aligned_cols=49  Identities=18%  Similarity=0.259  Sum_probs=41.1

Q ss_pred             hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .|+..|+.-|.-.+ ++++..++..-|-.+              +-+..+|+.|++.|||+++|
T Consensus         3 ~ral~iL~~l~~~~~~~t~~eia~~~gl~~--------------stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    3 ERALRILEALAESGGPLTLSEIARALGLPK--------------STVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHHHHHCHHCTBSCEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCcCeecCc
Confidence            57888999888865 479999999888754              68899999999999999875

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.

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=95.51  E-value=0.023  Score=40.57  Aligned_cols=65  Identities=17%  Similarity=0.224  Sum_probs=48.6

Q ss_pred             hHHHHHHHHhhcCC------CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587            4 LVTSMARKIYLRQG------LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~------vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      .++..++.-=+.|.      +.-..|+..||-              |..-+|.+|+.||..|||+..|..|-.+++-...
T Consensus        15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV--------------SRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~   80 (212)
T TIGR03338        15 LVQDEIERAILSGELPPGAKLNESDIAARLGV--------------SRGPVREAFRALEEAGLVRNEKNRGVFVREISLA   80 (212)
T ss_pred             HHHHHHHHHHHcCCCCCCCEecHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence            34444555444442      445678888886              4479999999999999999999889999887777


Q ss_pred             hHHHH
Q 034587           78 DLDQV   82 (90)
Q Consensus        78 ~lD~i   82 (90)
                      ++..+
T Consensus        81 ~~~ei   85 (212)
T TIGR03338        81 EADEI   85 (212)
T ss_pred             HHHHH
Confidence            66554

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>COG1693 Repressor of nif and glnA expression [Transcription]

Probab=95.49  E-value=0.017  Score=46.38  Aligned_cols=65  Identities=20%  Similarity=0.234  Sum_probs=48.1

Q ss_pred             HHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587            8 MARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ   81 (90)
Q Consensus         8 i~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~   81 (90)
                      |||=|.=.+ |+|-...+..---   ||+.      =+---+|+=||-||+.||+.|+--.||.||++|-+.|.+
T Consensus        11 Il~il~esd~plgak~Ia~el~k---RGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~   76 (325)
T COG1693          11 ILRILAESDEPLGAKIIALELRK---RGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR   76 (325)
T ss_pred             HHHHHHhcCCccchHHHHHHHHh---cccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence            445454444 7887766655422   2332      222469999999999999999988999999999999998

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

Probab=95.37  E-value=0.1  Score=30.14  Aligned_cols=40  Identities=18%  Similarity=0.299  Sum_probs=31.6

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT   72 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT   72 (90)
                      .+..|+..||-              |...++.+|+.|++.|||+..+..|-.||
T Consensus        27 ~~~~la~~~~i--------------s~~~v~~~l~~L~~~G~i~~~~~~~~~l~   66 (66)
T cd07377          27 SERELAEELGV--------------SRTTVREALRELEAEGLVERRPGRGTFVA   66 (66)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence            37788887765              34789999999999999987776666654

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

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=95.21  E-value=0.07  Score=42.21  Aligned_cols=63  Identities=22%  Similarity=0.255  Sum_probs=48.7

Q ss_pred             hHHHHHH-----HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcchHh
Q 034587            4 LVTSMAR-----KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQR   77 (90)
Q Consensus         4 r~ASi~R-----klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~   77 (90)
                      |--.|++     .+--.+|+|+..|.+.|+-.            -|..-||.-+.+||+.|++++.-. .||.-|.+|-+
T Consensus         3 R~~~il~aIV~~~l~~~~pv~s~~l~~~~~~~------------vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR   70 (337)
T TIGR00331         3 RQRKILKAIVEEYIKTGQPVGSKTLLEKYNLG------------LSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYR   70 (337)
T ss_pred             HHHHHHHHHHHHHHhcCCCcCHHHHHhhcCCC------------CChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHH
Confidence            4445554     33335899999999986542            345789999999999999987654 59999999987


Q ss_pred             h
Q 034587           78 D   78 (90)
Q Consensus        78 ~   78 (90)
                      .
T Consensus        71 ~   71 (337)
T TIGR00331        71 Y   71 (337)
T ss_pred             H
Confidence            6

In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.

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

Probab=95.16  E-value=0.046  Score=34.94  Aligned_cols=61  Identities=13%  Similarity=0.336  Sum_probs=40.3

Q ss_pred             HhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC-----eeeCcchHhhHHHHHH
Q 034587           12 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG-----RRITSSGQRDLDQVAG   84 (90)
Q Consensus        12 lYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G-----R~lT~~G~~~lD~iA~   84 (90)
                      ||-.+.+-...|+..-|-              +.+-+..-|+.||++|+|+..+  .++     -.||++|++.+++.-.
T Consensus         9 L~~~~~~~f~~L~~~l~l--------------t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~   74 (80)
T PF13601_consen    9 LYANEEATFSELKEELGL--------------TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA   74 (80)
T ss_dssp             HHHHSEEEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred             HhhcCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence            333455555555554433              4467888999999999998554  333     2699999999987665


Q ss_pred             Hh
Q 034587           85 RI   86 (90)
Q Consensus        85 ~v   86 (90)
                      .+
T Consensus        75 ~L   76 (80)
T PF13601_consen   75 AL   76 (80)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>PRK05638 threonine synthase; Validated

Probab=95.16  E-value=0.057  Score=43.62  Aligned_cols=63  Identities=16%  Similarity=0.282  Sum_probs=48.1

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCee----eCcchHhhHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR----ITSSGQRDLDQV   82 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~----lT~~G~~~lD~i   82 (90)
                      .||..|. +++.-+..|.+..+.            .-|...+...|+.||++|||+...+.||+    ||++|+..+..+
T Consensus       375 ~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~  441 (442)
T PRK05638        375 EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL  441 (442)
T ss_pred             HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence            4666665 568889999998874            13667999999999999999854223444    999999998764

>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=95.12  E-value=0.072  Score=31.00  Aligned_cols=50  Identities=16%  Similarity=0.214  Sum_probs=41.9

Q ss_pred             hhhHHHHHHHHhhcCC--CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            2 SELVTSMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~--vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      +.--..||..|+-.++  +.+..|+...+-.+              +-+-.+++.||+.|||++.+
T Consensus         4 t~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~--------------~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    4 TPSQFRVLMALARHPGEELTQSELAERLGISK--------------STVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             THHHHHHHHHHHHSTTSGEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEeC
Confidence            4445789999999998  99999999888754              57888999999999999766

...

>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=95.08  E-value=0.021  Score=35.32  Aligned_cols=42  Identities=29%  Similarity=0.409  Sum_probs=32.2

Q ss_pred             cccCchhHHHHHHHHHHhCCcccccCC---CC-----eeeCcchHhhHHH
Q 034587           40 FCKSSGAIARHILQQLQNMNIIDIEPK---GG-----RRITSSGQRDLDQ   81 (90)
Q Consensus        40 ~~~asg~iiR~~LqqLE~~glV~k~~~---~G-----R~lT~~G~~~lD~   81 (90)
                      +..-+-+-+=.+|+.||+.|||+....   +|     -.||++|+..|.+
T Consensus        26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E   75 (75)
T PF03551_consen   26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE   75 (75)
T ss_dssp             TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred             CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence            345567788999999999999985542   12     4699999998863

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 ....

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=94.84  E-value=0.04  Score=39.18  Aligned_cols=44  Identities=20%  Similarity=0.317  Sum_probs=33.1

Q ss_pred             CchhHHHHHHHHHHhCCccccc---CCCCe-----eeCcchHhhHHHHHHHh
Q 034587           43 SSGAIARHILQQLQNMNIIDIE---PKGGR-----RITSSGQRDLDQVAGRI   86 (90)
Q Consensus        43 asg~iiR~~LqqLE~~glV~k~---~~~GR-----~lT~~G~~~lD~iA~~v   86 (90)
                      .+-+-+=.+|+.||+.|||+..   ..+||     .||+.|+..++....+.
T Consensus        55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w  106 (138)
T TIGR02719        55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF  106 (138)
T ss_pred             CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            3445677899999999999853   22344     49999999888876653

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).

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=94.80  E-value=0.15  Score=38.19  Aligned_cols=62  Identities=18%  Similarity=0.194  Sum_probs=50.7

Q ss_pred             hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchHhh
Q 034587            3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD   78 (90)
Q Consensus         3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~   78 (90)
                      .|+..||+-|.-.+ ++++..|.+..|-.|              +-+..+|+.|++.|||++++ ++...||++....
T Consensus        11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~k--------------stv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l   74 (263)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELTGLHR--------------TTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL   74 (263)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence            47888998887654 599999999997654              68999999999999999886 4567888877543

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=94.73  E-value=0.19  Score=33.83  Aligned_cols=69  Identities=14%  Similarity=0.203  Sum_probs=50.3

Q ss_pred             hHHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcch-Hhh
Q 034587            4 LVTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSG-QRD   78 (90)
Q Consensus         4 r~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G-~~~   78 (90)
                      .|-.++..|.-.  +++.+..|+..+|-.              .+.++++|+.|++.|||+..  +.+|..|.... +-.
T Consensus        10 yal~~l~~la~~~~~~~s~~eia~~l~is--------------~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it   75 (130)
T TIGR02944        10 YATLVLTTLAQNDSQPYSAAEIAEQTGLN--------------APTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDIT   75 (130)
T ss_pred             HHHHHHHHHHhCCCCCccHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccC
Confidence            455566666654  478999999988874              47999999999999999854  35777777655 334


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      +++|...+
T Consensus        76 ~~~v~~~l   83 (130)
T TIGR02944        76 VADIVKAV   83 (130)
T ss_pred             HHHHHHHH
Confidence            66666554

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.

>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=94.71  E-value=0.2  Score=29.24  Aligned_cols=57  Identities=18%  Similarity=0.240  Sum_probs=39.6

Q ss_pred             hhHHHHHHHHhh--------cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587            3 ELVTSMARKIYL--------RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus         3 ~r~ASi~RklYl--------~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      .|.|..+-.++-        .+++....|+...|-              |..-+..+|++|++.|||+..+.+.-.|||
T Consensus         3 ~ria~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~   67 (67)
T cd00092           3 ERLASFLLNLSLRYGAGDLVQLPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP   67 (67)
T ss_pred             hHHHHHHHHHHHHcCCCccccCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence            355555554443        245777777777765              346789999999999999988645566664

>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase

Probab=94.65  E-value=0.29  Score=33.35  Aligned_cols=73  Identities=16%  Similarity=0.130  Sum_probs=55.0

Q ss_pred             ChhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587            1 MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus         1 ~~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      +|+.+|+|+=+||-+.=+..+.++-.-.            ...+-..+-+=++-|-+-|||||.-| |-++|..|+..+-
T Consensus        14 lsE~~~~ilI~v~Kk~Fit~~ev~e~l~------------~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~   80 (96)
T PF09114_consen   14 LSENAANILIQVAKKNFITASEVREALA------------TEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIII   80 (96)
T ss_dssp             S-HHHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHccCCHHHHHHHHH------------HHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHH
Confidence            4678999999999998888888887432            23334566666899999999999975 7999999999999


Q ss_pred             HHHHHh
Q 034587           81 QVAGRI   86 (90)
Q Consensus        81 ~iA~~v   86 (90)
                      ++|.--
T Consensus        81 ~AA~l~   86 (96)
T PF09114_consen   81 QAAELW   86 (96)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988643

Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=94.44  E-value=0.071  Score=38.13  Aligned_cols=61  Identities=18%  Similarity=0.355  Sum_probs=47.2

Q ss_pred             HHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587            7 SMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~   81 (90)
                      .-+..||.    .+++.++.++..-+=      .|        +-+-..|+.|++.|||+..+.+|=.||++|.+.--.
T Consensus        10 dYL~~Iy~l~~~~~~~~~~diA~~L~V------sp--------~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~   74 (154)
T COG1321          10 DYLETIYELLEEKGFARTKDIAERLKV------SP--------PSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKE   74 (154)
T ss_pred             HHHHHHHHHHhccCcccHHHHHHHhCC------Cc--------HHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHH
Confidence            34556662    477888888886543      34        467789999999999999999999999999865443

>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=94.36  E-value=0.11  Score=32.66  Aligned_cols=45  Identities=24%  Similarity=0.346  Sum_probs=35.4

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG   75 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G   75 (90)
                      ++.+..|+..++-.              -..+++++++|++.|+|+..+  .||-.|+..-
T Consensus        25 ~~s~~eiA~~~~i~--------------~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~   71 (83)
T PF02082_consen   25 PVSSKEIAERLGIS--------------PSYLRKILQKLKKAGLIESSRGRGGGYRLARPP   71 (83)
T ss_dssp             -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred             CCCHHHHHHHHCcC--------------HHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence            48899999988874              368999999999999998554  5788887643

(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.

>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=94.33  E-value=0.13  Score=29.89  Aligned_cols=49  Identities=18%  Similarity=0.280  Sum_probs=40.3

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .--..+|..||-.+++.+..|....+-.              .+-+-.++++||+.|||++.+
T Consensus         3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~--------------~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    3 PSQFRILRILYENGGITQSELAEKLGIS--------------RSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEecc
Confidence            3446789999999999999999988774              356778999999999998554

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 ....

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=94.24  E-value=0.08  Score=38.21  Aligned_cols=51  Identities=20%  Similarity=0.279  Sum_probs=41.5

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +-...|+..||-.              ...+|.+|+.||..|||+..|..|-.+++--..++..+
T Consensus        31 L~e~eLae~lgVS--------------RtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei   81 (224)
T PRK11534         31 LRMSLLTSRYALG--------------VGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDI   81 (224)
T ss_pred             CCHHHHHHHHCCC--------------hHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHHH
Confidence            4567889988874              47899999999999999999988888887766665543

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=94.22  E-value=0.3  Score=35.54  Aligned_cols=52  Identities=19%  Similarity=0.348  Sum_probs=46.1

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      ++....|+..||-..              ..||.+|+.|+..|||+..|..|-.+++--.++++.+
T Consensus        39 ~l~e~~La~~~gvSr--------------tPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei   90 (230)
T COG1802          39 RLSEEELAEELGVSR--------------TPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI   90 (230)
T ss_pred             CccHHHHHHHhCCCC--------------ccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence            578899999999853              5799999999999999999999999999888888774

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=94.18  E-value=0.086  Score=38.30  Aligned_cols=42  Identities=14%  Similarity=0.229  Sum_probs=35.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .-..|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-
T Consensus        32 sE~~La~~lgV--------------SRtpVREAL~~Le~eGlV~~~~~~G~~V~~~   73 (235)
T TIGR02812        32 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNNF   73 (235)
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence            56678888876              4589999999999999999999889888873

Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=94.17  E-value=0.083  Score=37.18  Aligned_cols=37  Identities=22%  Similarity=0.343  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           46 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        46 ~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      .-+.++.|.||..|+|++....|..+|++++..+|..
T Consensus        50 nTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~   86 (125)
T COG1725          50 NTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQL   86 (125)
T ss_pred             HHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHH
Confidence            5789999999999999988888999999999877653

>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=94.07  E-value=0.11  Score=30.98  Aligned_cols=46  Identities=17%  Similarity=0.229  Sum_probs=39.2

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      ..|++.|-..+|..++.|....|-.              -+-+.+=|+.||++|||+...
T Consensus        13 ~~Il~~L~~~~~~t~~ela~~l~~~--------------~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   13 LRILRLLASNGPMTVSELAEELGIS--------------QSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEec
Confidence            4688888889999999999999743              367899999999999999775

...

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

Probab=94.07  E-value=0.28  Score=27.98  Aligned_cols=63  Identities=16%  Similarity=0.183  Sum_probs=46.9

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQV   82 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~i   82 (90)
                      .-|+..++-.+ +.+..+.+..|-.              ..-++..|++|++.|||.....   .-..+|+ |...++.+
T Consensus        10 ~~il~~l~~~~-~~~~ei~~~~~i~--------------~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~   73 (78)
T cd00090          10 LRILRLLLEGP-LTVSELAERLGLS--------------QSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALL   73 (78)
T ss_pred             HHHHHHHHHCC-cCHHHHHHHHCcC--------------HhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHH
Confidence            45666666655 8999999877542              3578999999999999986542   2457898 88888876


Q ss_pred             HH
Q 034587           83 AG   84 (90)
Q Consensus        83 A~   84 (90)
                      ..
T Consensus        74 ~~   75 (78)
T cd00090          74 ES   75 (78)
T ss_pred             HH
Confidence            53

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.

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=93.91  E-value=0.076  Score=38.96  Aligned_cols=45  Identities=18%  Similarity=0.129  Sum_probs=37.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      .-..|+..||-              |...+|.+|+.||..|||+..+..|-.+++-...
T Consensus        33 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~   77 (251)
T PRK09990         33 SERRLCEKLGF--------------SRSALREGLTVLRGRGIIETAQGRGSFVARLNRV   77 (251)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence            45688888886              4589999999999999999999888888766544

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=93.85  E-value=0.22  Score=34.21  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=46.9

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC------CCCeeeCcchHhhHHH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRRITSSGQRDLDQ   81 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~------~~GR~lT~~G~~~lD~   81 (90)
                      |++++.- |+.--+.|++.-++             =|.+++=.-|++||+.|+|++..      +-...||+.|+++..-
T Consensus        28 Il~~L~~-g~~RF~eL~r~i~~-------------Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~v   93 (120)
T COG1733          28 ILRDLFD-GPKRFNELRRSIGG-------------ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPV   93 (120)
T ss_pred             HHHHHhc-CCCcHHHHHHHccc-------------cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHH
Confidence            5666665 77777777775554             45578888999999999998765      3478899999998765


Q ss_pred             HH
Q 034587           82 VA   83 (90)
Q Consensus        82 iA   83 (90)
                      +.
T Consensus        94 l~   95 (120)
T COG1733          94 LL   95 (120)
T ss_pred             HH
Confidence            43

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=93.82  E-value=0.095  Score=40.50  Aligned_cols=43  Identities=23%  Similarity=0.283  Sum_probs=37.3

Q ss_pred             hHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHHHHHhhc
Q 034587           46 AIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRIVV   88 (90)
Q Consensus        46 ~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~iA~~v~~   88 (90)
                      ..+|.+|.-|++.|||+....   ....||++|++.++..+..|+.
T Consensus        35 ~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~   80 (280)
T TIGR02277        35 RLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD   80 (280)
T ss_pred             chHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence            579999999999999987653   5778999999999998887764

This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=93.65  E-value=0.11  Score=37.41  Aligned_cols=51  Identities=22%  Similarity=0.311  Sum_probs=39.9

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +-...|+..||-.              ...+|.+|+.||..|||+..+..|-.+++--..++..+
T Consensus        35 L~e~~La~~lgVS--------------RtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei   85 (221)
T PRK11414         35 LITKNLAEQLGMS--------------ITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI   85 (221)
T ss_pred             cCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence            4456788988874              46899999999999999999887877776665555543

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=93.45  E-value=0.095  Score=29.66  Aligned_cols=36  Identities=19%  Similarity=0.310  Sum_probs=28.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG   68 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G   68 (90)
                      .+..|+..||-              |..-+|.+|++|++.|+|+..+.+|
T Consensus        22 s~~~la~~~~v--------------s~~tv~~~l~~L~~~g~i~~~~~~g   57 (60)
T smart00345       22 SERELAAQLGV--------------SRTTVREALSRLEAEGLVQRRPGSG   57 (60)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCe
Confidence            67777887765              4478999999999999998776443

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=93.24  E-value=0.23  Score=34.10  Aligned_cols=43  Identities=21%  Similarity=0.310  Sum_probs=34.6

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCc
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITS   73 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~   73 (90)
                      ++.+..|+..||-.              ...+|++|++|++.|||+..+.  ||-.|+.
T Consensus        25 ~~s~~~ia~~~~is--------------~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~   69 (141)
T PRK11014         25 MTSISEVTEVYGVS--------------RNHMVKIINQLSRAGYVTAVRGKNGGIRLGK   69 (141)
T ss_pred             ccCHHHHHHHHCcC--------------HHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence            57788899888874              4699999999999999997763  4666654

>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term

Probab=92.97  E-value=0.11  Score=35.61  Aligned_cols=39  Identities=26%  Similarity=0.399  Sum_probs=32.6

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      ++.+..|+..+....|              -.|.+|++|++.|||+-.|..||
T Consensus        19 ~vtl~elA~~l~cS~R--------------n~r~lLkkm~~~gWi~W~pg~GR   57 (115)
T PF12793_consen   19 EVTLDELAELLFCSRR--------------NARTLLKKMQEEGWITWQPGRGR   57 (115)
T ss_pred             ceeHHHHHHHhCCCHH--------------HHHHHHHHHHHCCCeeeeCCCCC
Confidence            4788888888777553              58999999999999999997666

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

Probab=92.88  E-value=0.12  Score=30.92  Aligned_cols=37  Identities=24%  Similarity=0.398  Sum_probs=29.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      ....|+..||-              |...+|.+|+.|++.|||+..+..|-
T Consensus        26 s~~~la~~~~v--------------sr~tvr~al~~L~~~g~i~~~~~~G~   62 (64)
T PF00392_consen   26 SERELAERYGV--------------SRTTVREALRRLEAEGLIERRPGRGT   62 (64)
T ss_dssp             -HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             CHHHHHHHhcc--------------CCcHHHHHHHHHHHCCcEEEECCceE
Confidence            77788888876              45799999999999999998886553

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

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=92.74  E-value=0.46  Score=26.06  Aligned_cols=45  Identities=13%  Similarity=0.182  Sum_probs=36.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .|+..+.-++++.+..|+..++-.              -.-++..|+.|++.|||+...
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~s--------------~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGVS--------------EMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEee
Confidence            466666667889999999998542              256899999999999998765

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=92.53  E-value=0.14  Score=36.53  Aligned_cols=43  Identities=14%  Similarity=0.170  Sum_probs=32.8

Q ss_pred             CchhHHHHHHHHHHhCCcccccCC----CCeeeCcchHhhHHHHHHH
Q 034587           43 SSGAIARHILQQLQNMNIIDIEPK----GGRRITSSGQRDLDQVAGR   85 (90)
Q Consensus        43 asg~iiR~~LqqLE~~glV~k~~~----~GR~lT~~G~~~lD~iA~~   85 (90)
                      .+-+-|=-+|+.||+.|||+....    .=..||++|+..|+....+
T Consensus        75 ~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~  121 (135)
T PRK09416         75 GNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN  121 (135)
T ss_pred             CCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence            344567789999999999986432    2346999999999987653

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

Probab=92.51  E-value=0.41  Score=32.02  Aligned_cols=50  Identities=18%  Similarity=0.187  Sum_probs=39.4

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI   71 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l   71 (90)
                      =-|+.|+|--||--...+++..              ...-.-++.+|..||++|||+...  |..|
T Consensus        10 ~~IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~--g~~i   59 (92)
T PF10007_consen   10 LKILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE--GKTI   59 (92)
T ss_pred             HHHHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec--Cccc
Confidence            3588999999988888888765              334468999999999999999875  4444

>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=92.51  E-value=0.62  Score=26.21  Aligned_cols=47  Identities=13%  Similarity=0.167  Sum_probs=37.3

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID   62 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~   62 (90)
                      +..--.|+.-|+-+|++.+..++...|-.              .+-+.+.|++|++.|||+
T Consensus         2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is--------------~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    2 DETQRKILNYLRENPRITQKELAEKLGIS--------------RSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             -HHHHHHHHHHHHCTTS-HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCcCcC
Confidence            34445678888889999999999988864              468999999999999985

...

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

Probab=92.46  E-value=0.54  Score=28.98  Aligned_cols=46  Identities=9%  Similarity=-0.005  Sum_probs=39.0

Q ss_pred             HHHHHHHhhcCC--CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            6 TSMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         6 ASi~RklYl~g~--vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      ..|+..|.-+|+  +....|++.-|=.+              +.++..|..||+.|+|++..
T Consensus         9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~--------------~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550        9 EKILEFLENSGDETSTALQLAKNLGLPK--------------KEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecC
Confidence            357777777877  99999999988754              58999999999999999865

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

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=92.35  E-value=0.14  Score=37.75  Aligned_cols=42  Identities=19%  Similarity=0.135  Sum_probs=35.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .-..|+..||=              |...+|.+|+.||..|||+..+..|-.+++-
T Consensus        28 sE~eLae~~gV--------------SRtpVREAL~~Le~~GlV~~~~~~G~~V~~~   69 (253)
T PRK10421         28 AERQLAMQLGV--------------SRNSLREALAKLVSEGVLLSRRGGGTFIRWR   69 (253)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence            35678888886              4579999999999999999888888888764

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=92.06  E-value=0.15  Score=37.58  Aligned_cols=44  Identities=11%  Similarity=0.186  Sum_probs=36.6

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ   76 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~   76 (90)
                      ....|+..||=              |...+|.+|+.||..|||+..+..|-.+++...
T Consensus        35 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~   78 (257)
T PRK10225         35 PEREIAEMLDV--------------TRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG   78 (257)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence            46689998887              457999999999999999999877888876543

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=92.01  E-value=0.18  Score=36.60  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=34.7

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      .-..|+..||-              |...+|.+|+.||..|||+..+..|-.+++
T Consensus        33 sE~eLae~~gV--------------SRt~VReAL~~L~~eGlv~~~~g~G~~V~~   73 (239)
T PRK04984         33 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN   73 (239)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence            45678888876              558999999999999999999887877765

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=91.98  E-value=0.52  Score=35.02  Aligned_cols=58  Identities=14%  Similarity=0.139  Sum_probs=47.2

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcc
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~   74 (90)
                      .|+-.||.-|.-.+++++..|++.=|-.|              +-+..+|+.|++.|||+.++. +...|+++
T Consensus        14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~k--------------stv~Rll~tL~~~G~l~~~~~~~~Y~lG~~   72 (257)
T PRK15090         14 LKVFGILQALGEEREIGITELSQRVMMSK--------------STVYRFLQTMKTLGYVAQEGESEKYSLTLK   72 (257)
T ss_pred             HHHHHHHHHhhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence            47788898888778899999999888754              688999999999999998763 44556554

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=91.85  E-value=0.18  Score=37.08  Aligned_cols=41  Identities=17%  Similarity=0.225  Sum_probs=33.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      .-..|+..||-              |...+|.+|+.||..|||+..+..|-.+++
T Consensus        36 sE~eLa~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~   76 (254)
T PRK09464         36 PERELAKQFDV--------------SRPSLREAIQRLEAKGLLLRRQGGGTFVQS   76 (254)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence            45668888876              457999999999999999998877866665

>PRK03837 transcriptional regulator NanR; Provisional

Probab=91.76  E-value=0.2  Score=36.30  Aligned_cols=42  Identities=17%  Similarity=0.298  Sum_probs=34.7

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      ....|+..||=              |...+|.+|+.||..|||+..+..|-.+++-
T Consensus        39 ~E~~Lae~~gV--------------SRt~VREAL~~L~~eGlv~~~~~~G~~V~~~   80 (241)
T PRK03837         39 SERELMAFFGV--------------GRPAVREALQALKRKGLVQISHGERARVSRP   80 (241)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence            56678888886              5589999999999999999988767766653

>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=91.75  E-value=0.56  Score=27.95  Aligned_cols=47  Identities=15%  Similarity=0.184  Sum_probs=40.4

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      -..|+..|--++.+.+..|+..||-.              -.-||.=|+.||+.|+|.+.-
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~VS--------------~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGVS--------------EMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEc
Confidence            34677888889999999999999764              368999999999999998875

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

>PRK08599 coproporphyrinogen III oxidase; Provisional

Probab=91.72  E-value=0.63  Score=36.45  Aligned_cols=61  Identities=18%  Similarity=0.317  Sum_probs=46.5

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhcC
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA   89 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~~   89 (90)
                      ..++-...+...||..             -.......+++|++.||++.+. +.=+||++|+-..|.|+..++-+
T Consensus       316 ~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~~~  376 (377)
T PRK08599        316 KSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFLLD  376 (377)
T ss_pred             hCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHhhh
Confidence            4566667777776642             1245677889999999999764 46789999999999999987643

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=91.64  E-value=0.19  Score=37.06  Aligned_cols=42  Identities=12%  Similarity=0.122  Sum_probs=34.7

Q ss_pred             hhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           20 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        20 V~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      -..|+..||=              |...+|.+|+.||..|||+..+..|-.+++.-
T Consensus        35 E~eLae~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~   76 (253)
T PRK11523         35 ERFIADEKNV--------------SRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ   76 (253)
T ss_pred             HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence            4578888876              45799999999999999999987777776643

>PRK09057 coproporphyrinogen III oxidase; Provisional

Probab=91.49  E-value=1  Score=35.60  Aligned_cols=57  Identities=21%  Similarity=0.352  Sum_probs=44.5

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ..++-...+...||-.-                ....|+.|++.||++.+.++.=+||++|+.++|.|+..++
T Consensus       323 ~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~  379 (380)
T PRK09057        323 REGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA  379 (380)
T ss_pred             hCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence            45677789999888531                1247999999999986543246899999999999999875

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=91.43  E-value=0.68  Score=34.81  Aligned_cols=57  Identities=16%  Similarity=0.254  Sum_probs=45.5

Q ss_pred             hhHHHHHHHHhhcCCC--chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC-eeeCcc
Q 034587            3 ELVTSMARKIYLRQGL--GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl~g~v--GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G-R~lT~~   74 (90)
                      .|+..||.-|.- +|.  ++..|.+.-|-.|              +=++.+|+.|++.|||+.+++.| ..|+++
T Consensus         4 ~ral~iL~~l~~-~~~~l~l~ela~~~glpk--------------sT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~   63 (246)
T COG1414           4 ERALAILDLLAE-GPGGLSLAELAERLGLPK--------------STVHRLLQTLVELGYVEQDPEDGRYRLGPR   63 (246)
T ss_pred             HHHHHHHHHHHh-CCCCCCHHHHHHHhCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEeehHH
Confidence            578889988887 454  4999999888754              67899999999999999998654 455543

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

Probab=91.16  E-value=1.1  Score=29.15  Aligned_cols=50  Identities=14%  Similarity=0.038  Sum_probs=36.8

Q ss_pred             hhhHHHHHHHHh--------hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            2 SELVTSMARKIY--------LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         2 ~~r~ASi~RklY--------l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      +.|-|++|-.|.        ...++.-..|+...|-.              ..-+-.+|++||+.|||+...
T Consensus        24 ~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~s--------------r~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        24 SGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLS--------------RTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             CHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeeeec
Confidence            456677766665        45677777777777764              246888999999999998654

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

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

Probab=91.08  E-value=0.36  Score=36.53  Aligned_cols=55  Identities=24%  Similarity=0.170  Sum_probs=41.5

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCeeeCcchHhhHHHHHHHh
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~lD~iA~~v   86 (90)
                      +..+.|++..+-              |..-+-..|+.||+.|||+....   .--.||++|+..+++.....
T Consensus        22 IS~~eLA~~L~i--------------S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~   79 (217)
T PRK14165         22 ISSSEFANHTGT--------------SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADY   79 (217)
T ss_pred             cCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHH
Confidence            446678776654              44678889999999999986642   24579999999998877553

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=91.07  E-value=2  Score=28.45  Aligned_cols=49  Identities=20%  Similarity=0.308  Sum_probs=39.3

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCeeeCcchHhh
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRD   78 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~lT~~G~~~   78 (90)
                      +|+.+..|+..++-.              ...++.+|+.|++.|||...  ..+|-.|+......
T Consensus        24 ~~~s~~eia~~~~i~--------------~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i   74 (132)
T TIGR00738        24 GPVSVKEIAERQGIS--------------RSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI   74 (132)
T ss_pred             CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC
Confidence            388999999988774              47999999999999999854  34678888776544

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.

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=91.00  E-value=0.6  Score=27.76  Aligned_cols=52  Identities=21%  Similarity=0.425  Sum_probs=36.1

Q ss_pred             HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587           11 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ   76 (90)
Q Consensus        11 klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~   76 (90)
                      .+=+..++-+..+...||..             --......|+.|++.|||+.+. +.=++|++|+
T Consensus        14 ~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~   65 (66)
T PF06969_consen   14 GLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR   65 (66)
T ss_dssp             HHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred             HHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence            34445678888888888864             1234578899999999998885 5778999996

This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=90.80  E-value=0.87  Score=34.36  Aligned_cols=58  Identities=10%  Similarity=0.099  Sum_probs=46.3

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcc
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~   74 (90)
                      .|+-.||+-|-- .+|+++..|.+.=|-.|              +-+..+|+.|++.|||+.+++ +...|.+.
T Consensus        28 ~ral~IL~~l~~~~~~~~lseia~~lglpk--------------sTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   87 (274)
T PRK11569         28 TRGLKLLEWIAESNGSVALTELAQQAGLPN--------------STTHRLLTTMQQQGFVRQVGELGHWAIGAH   87 (274)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence            477888888876 46899999999888765              689999999999999998864 33455544

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=90.55  E-value=0.97  Score=34.12  Aligned_cols=58  Identities=12%  Similarity=0.051  Sum_probs=46.6

Q ss_pred             hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC-eeeCcc
Q 034587            3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G-R~lT~~   74 (90)
                      .|+-+||+-|.-. +++++..|++.-|-.|              +-+..+|+.|++.|||+.++..| ..|++.
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpk--------------Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   84 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDLPL--------------STTFRLLKVLQAADFVYQDSQLGWWHIGLG   84 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence            4788999999764 5799999999988865              67899999999999999886433 345543

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=90.07  E-value=0.47  Score=32.08  Aligned_cols=42  Identities=21%  Similarity=0.344  Sum_probs=31.7

Q ss_pred             chhHHHHHHHHHHhCCcccccC--CC------CeeeCcchHhhHHHHHHH
Q 034587           44 SGAIARHILQQLQNMNIIDIEP--KG------GRRITSSGQRDLDQVAGR   85 (90)
Q Consensus        44 sg~iiR~~LqqLE~~glV~k~~--~~------GR~lT~~G~~~lD~iA~~   85 (90)
                      |-+.|=-+|+.||+.|||+...  .+      --.||++|+..|.+...+
T Consensus        43 s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~   92 (138)
T COG1695          43 SPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREE   92 (138)
T ss_pred             CCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHH
Confidence            3345667899999999998642  22      237999999999987654

>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=89.95  E-value=0.43  Score=29.62  Aligned_cols=40  Identities=20%  Similarity=0.216  Sum_probs=30.6

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      |..|..++..+|-             .|-+-+..-|++||+.|+|+.++...|
T Consensus        25 ~Pt~rEIa~~~g~-------------~S~~tv~~~L~~Le~kG~I~r~~~~~R   64 (65)
T PF01726_consen   25 PPTVREIAEALGL-------------KSTSTVQRHLKALERKGYIRRDPGKAR   64 (65)
T ss_dssp             ---HHHHHHHHTS-------------SSHHHHHHHHHHHHHTTSEEEGCCSCC
T ss_pred             CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCcCccCCCCCCC
Confidence            5688888887776             356789999999999999999885443

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.

>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes

Probab=89.29  E-value=2.2  Score=27.41  Aligned_cols=79  Identities=16%  Similarity=0.155  Sum_probs=52.6

Q ss_pred             hhhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCcc------cc---CchhHHHHHHHHHHhCCcccccCC----C
Q 034587            2 SELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHF------CK---SSGAIARHILQQLQNMNIIDIEPK----G   67 (90)
Q Consensus         2 ~~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~------~~---asg~iiR~~LqqLE~~glV~k~~~----~   67 (90)
                      +.-|..|++=|+- .+.+|...+..++-|.++......++      -.   =+..-++.++++|...|+++....    .
T Consensus         3 T~~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~   82 (106)
T PF09382_consen    3 TEEAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYP   82 (106)
T ss_dssp             HHHHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTE
T ss_pred             HHHHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCccccc
Confidence            3445666666665 57899999999999999887544333      11   144589999999999999965542    1


Q ss_pred             CeeeCcchHhhHH
Q 034587           68 GRRITSSGQRDLD   80 (90)
Q Consensus        68 GR~lT~~G~~~lD   80 (90)
                      -=.+|++|++.|.
T Consensus        83 ~l~~~~~~~~~l~   95 (106)
T PF09382_consen   83 YLKLTPKGKELLN   95 (106)
T ss_dssp             EEEE-GGGHHHHC
T ss_pred             EEEECHHHHHHHC
Confidence            3468999998875

RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.27  E-value=1.5  Score=30.96  Aligned_cols=59  Identities=25%  Similarity=0.326  Sum_probs=45.8

Q ss_pred             hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCCe-----------eeCcchHhhH
Q 034587           14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----------RITSSGQRDL   79 (90)
Q Consensus        14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~GR-----------~lT~~G~~~l   79 (90)
                      -+||..|..|+..-+-              +.+-+-++||.|.++|+|++.+   ++||           .++.+..++|
T Consensus        39 ~~~~~tvdelae~lnr--------------~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l  104 (126)
T COG3355          39 ENGPLTVDELAEILNR--------------SRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL  104 (126)
T ss_pred             hcCCcCHHHHHHHHCc--------------cHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence            4899999999987654              3478899999999999998654   3444           2566778888


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      |..+.++
T Consensus       105 ~~w~~~~  111 (126)
T COG3355         105 DEWYDKM  111 (126)
T ss_pred             HHHHHHH
Confidence            8888776

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=88.80  E-value=0.46  Score=37.18  Aligned_cols=61  Identities=11%  Similarity=0.151  Sum_probs=46.7

Q ss_pred             HHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-C-CCeeeCcchHhhHHH
Q 034587            7 SMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-K-GGRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~-~GR~lT~~G~~~lD~   81 (90)
                      .|++.|=- +|-+.-..|+..+|=              |.+.+|.+++.||++|+|+..+ . .|-.+.+....++|.
T Consensus       187 ~IL~~L~~~egrlse~eLAerlGV--------------SRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e  250 (251)
T TIGR02787       187 HIFEELDGNEGLLVASKIADRVGI--------------TRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE  250 (251)
T ss_pred             HHHHHhccccccccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence            35555544 356666777777764              5589999999999999999888 5 488888888888875

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>PRK07379 coproporphyrinogen III oxidase; Provisional

Probab=88.75  E-value=0.59  Score=37.35  Aligned_cols=39  Identities=23%  Similarity=0.296  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhCCcccccCCCCe--eeCc-chHhhHHHHHHHhh
Q 034587           47 IARHILQQLQNMNIIDIEPKGGR--RITS-SGQRDLDQVAGRIV   87 (90)
Q Consensus        47 iiR~~LqqLE~~glV~k~~~~GR--~lT~-~G~~~lD~iA~~v~   87 (90)
                      .....|++|++.||++.+  +++  +||+ +|.-++|.|+.+++
T Consensus       352 ~~~~~l~~l~~~gll~~~--~~~~~~lT~~~G~~~~~~i~~~~~  393 (400)
T PRK07379        352 QILQCLQPYFQQGWVELE--GDRRLRLTDPEGFLFSNTVLASLF  393 (400)
T ss_pred             HHHHHHHHHHHCCCEEEe--CCeEEEECchHHhHHHHHHHHHHH
Confidence            456778999999999865  355  8995 99999999999875

>PRK05660 HemN family oxidoreductase; Provisional

Probab=88.65  E-value=0.76  Score=36.42  Aligned_cols=58  Identities=14%  Similarity=0.123  Sum_probs=42.5

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhcC
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA   89 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~~   89 (90)
                      ++-+..+...||..      +       -. ....++.|++.||++.+. +-=+||++|+-++|.|+..++.+
T Consensus       321 G~~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~~~~~~  378 (378)
T PRK05660        321 AAPRADFEAYTGLP------E-------SV-IRPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLELFLAE  378 (378)
T ss_pred             CCCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHHHHhcC
Confidence            45556666666642      1       11 356889999999998664 34678999999999999988753

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=88.58  E-value=0.56  Score=33.12  Aligned_cols=47  Identities=23%  Similarity=0.329  Sum_probs=37.3

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchH
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ   76 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~   76 (90)
                      .++.+..++..++-.              ...++++||+|.++|||+...  +||-.|+..-.
T Consensus        23 ~~~s~~eIA~~~~is--------------~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~   71 (153)
T PRK11920         23 KLSRIPEIARAYGVS--------------ELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAA   71 (153)
T ss_pred             CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHH
Confidence            357788888877663              479999999999999998655  57989986554

>PRK05628 coproporphyrinogen III oxidase; Validated

Probab=88.52  E-value=0.68  Score=36.33  Aligned_cols=38  Identities=18%  Similarity=0.194  Sum_probs=32.7

Q ss_pred             HHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           49 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        49 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ...|++|++.|++..+. +.=+||++|+-.+|.|+..++
T Consensus       337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~  374 (375)
T PRK05628        337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVRDLL  374 (375)
T ss_pred             HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHHHHh
Confidence            57899999999998764 357899999999999998764

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=88.47  E-value=0.55  Score=33.92  Aligned_cols=43  Identities=12%  Similarity=0.183  Sum_probs=34.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      .-..|+..||-              |..-+|++|+.|++.|+|+.....|-.+++..
T Consensus        34 sE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~~   76 (238)
T TIGR02325        34 AEMQLAERFGV--------------NRHTVRRAIAALVERGLLRAEQGRGTFVAARR   76 (238)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEECCCc
Confidence            44577787776              45799999999999999999887788887553

All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.

>PF13814 Replic_Relax: Replication-relaxation

Probab=88.42  E-value=1.4  Score=30.68  Aligned_cols=62  Identities=23%  Similarity=0.289  Sum_probs=46.4

Q ss_pred             HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-----C-----eeeCcchHhh
Q 034587            9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----G-----RRITSSGQRD   78 (90)
Q Consensus         9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-----G-----R~lT~~G~~~   78 (90)
                      |+-||-...+....|...+....+..           .-++..|++|++.|+|+.....     |     -.||++|.+.
T Consensus         1 L~~L~~~r~lt~~Qi~~l~~~~~~~~-----------~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~   69 (191)
T PF13814_consen    1 LRLLARHRFLTTDQIARLLFPSSKSE-----------RTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARL   69 (191)
T ss_pred             ChhHHHhcCcCHHHHHHHHcCCCcch-----------HHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHH
Confidence            34566677888888888887754321           1789999999999999866531     2     2699999998


Q ss_pred             HHH
Q 034587           79 LDQ   81 (90)
Q Consensus        79 lD~   81 (90)
                      ++.
T Consensus        70 l~~   72 (191)
T PF13814_consen   70 LAD   72 (191)
T ss_pred             HHh
Confidence            874

>PRK08208 coproporphyrinogen III oxidase; Validated

Probab=88.31  E-value=0.45  Score=38.35  Aligned_cols=58  Identities=22%  Similarity=0.351  Sum_probs=43.5

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhhc
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV   88 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~~   88 (90)
                      .++-...+...||..      +       .. .-..|++|++.|||+.+. +.=+||++|+-..|.|+.+++.
T Consensus       360 ~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~  417 (430)
T PRK08208        360 QGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFIS  417 (430)
T ss_pred             CCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcC
Confidence            466667777777742      1       12 335789999999998764 3458999999999999998864

>PRK05799 coproporphyrinogen III oxidase; Provisional

Probab=87.79  E-value=0.88  Score=35.55  Aligned_cols=40  Identities=5%  Similarity=0.200  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           47 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        47 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      .....|+.|++.||++.+. +.=+||++|+-++|.|+.+++
T Consensus       334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~  373 (374)
T PRK05799        334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMSDFL  373 (374)
T ss_pred             HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHHHHh
Confidence            3556689999999998664 346889999999999998864

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=87.58  E-value=0.73  Score=31.45  Aligned_cols=46  Identities=13%  Similarity=0.265  Sum_probs=36.5

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cCCCCeeeCcch
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG   75 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~~~GR~lT~~G   75 (90)
                      +++.+..++..++-              +...++++|++|.++|||+.  .+.||-.|+..-
T Consensus        24 ~~~s~~~ia~~~~i--------------p~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~   71 (135)
T TIGR02010        24 GPVTLADISERQGI--------------SLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA   71 (135)
T ss_pred             CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH
Confidence            47899999987776              34799999999999999974  335788887643

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

>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=87.57  E-value=0.8  Score=27.50  Aligned_cols=48  Identities=10%  Similarity=0.063  Sum_probs=38.8

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .=+.|...|--+|+..+..+++.-|-.              .+-+..+|+.|++.|||+..+
T Consensus         9 ~E~~vy~~Ll~~~~~t~~eIa~~l~i~--------------~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen    9 NEAKVYLALLKNGPATAEEIAEELGIS--------------RSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHHHHCHEEHHHHHHHHTSS--------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEc
Confidence            345566666668999999999877764              368999999999999999876

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.

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=87.34  E-value=0.64  Score=33.78  Aligned_cols=41  Identities=15%  Similarity=0.239  Sum_probs=34.2

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      +-..|+..||-              |..-+|++|+.|++.|+|.+.+..|-.+++
T Consensus        27 sE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~   67 (230)
T TIGR02018        27 SEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAE   67 (230)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEcc
Confidence            56678888886              457999999999999999998877777654

This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=87.33  E-value=0.84  Score=24.85  Aligned_cols=35  Identities=17%  Similarity=0.220  Sum_probs=26.9

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      |+.+..++..+|-.              ..-+..+|++|++.|||+...
T Consensus         8 ~~s~~~la~~l~~s--------------~~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419        8 PLTRQEIAELLGLT--------------RETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             ccCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEeC
Confidence            55666677766653              357899999999999998764

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=87.17  E-value=0.72  Score=34.52  Aligned_cols=41  Identities=17%  Similarity=0.366  Sum_probs=31.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      +-..|+..||=              |..++|-+|+.||..|||+.-+..|=.+++
T Consensus        36 ~EreLae~fgV--------------SR~~vREAl~~L~a~Glve~r~G~Gt~V~~   76 (241)
T COG2186          36 SERELAERFGV--------------SRTVVREALKRLEAKGLVEIRQGSGTFVRP   76 (241)
T ss_pred             CHHHHHHHHCC--------------CcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence            35567777775              457999999999999999987765655554

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=87.14  E-value=1.9  Score=35.61  Aligned_cols=69  Identities=7%  Similarity=0.067  Sum_probs=52.8

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCeeeCcchHhhH
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDL   79 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR~lT~~G~~~l   79 (90)
                      +.--..||..|+-.+++....|+...|-.+              +-+-.++..||+.|||+...+  .--.||++|++.+
T Consensus         5 t~~e~~vL~~L~~~~~~s~~eLA~~l~l~~--------------~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~   70 (489)
T PRK04172          5 HPNEKKVLKALKELKEATLEELAEKLGLPP--------------EAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYA   70 (489)
T ss_pred             CHHHHHHHHHHHhCCCCCHHHHHHHhCcCH--------------HHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHH
Confidence            344567899998889999999998776532              345566889999999986652  3457999999999


Q ss_pred             HHHHH
Q 034587           80 DQVAG   84 (90)
Q Consensus        80 D~iA~   84 (90)
                      +++.-
T Consensus        71 ~~g~p   75 (489)
T PRK04172         71 EEGLP   75 (489)
T ss_pred             HhcCH
Confidence            87543

>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]

Probab=87.09  E-value=0.54  Score=37.49  Aligned_cols=36  Identities=28%  Similarity=0.454  Sum_probs=31.4

Q ss_pred             hHHHHHHHHHHhCCcccccC--CCCeeeCcchHhhHHH
Q 034587           46 AIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ   81 (90)
Q Consensus        46 ~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~lD~   81 (90)
                      +-+|+.+|.|..+||||-.|  +||.+-|.+.-..|+.
T Consensus        40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~i   77 (294)
T COG2524          40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSI   77 (294)
T ss_pred             chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhcc
Confidence            47999999999999999666  7999999998877753

>PRK06582 coproporphyrinogen III oxidase; Provisional

Probab=86.91  E-value=3.6  Score=32.99  Aligned_cols=59  Identities=15%  Similarity=0.284  Sum_probs=43.8

Q ss_pred             hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHH-HHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIA-RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~ii-R~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      +..++-+..+...||-.-             -... ...|++|++.||++. . +.=.||++|+-+.|.|+.+++
T Consensus       330 ~~~Gl~~~~~~~~~g~~~-------------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~~~~  389 (390)
T PRK06582        330 LSKGINISTLEQKLNTKL-------------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVPRLI  389 (390)
T ss_pred             hhCCCCHHHHHHHHCcCH-------------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHHHHh
Confidence            346677778888887421             0111 467889999999987 3 457899999999999998864

>PRK06294 coproporphyrinogen III oxidase; Provisional

Probab=86.88  E-value=0.98  Score=35.69  Aligned_cols=39  Identities=10%  Similarity=0.146  Sum_probs=32.6

Q ss_pred             HHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           48 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        48 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ....+++|++.||++.+. +.=.||++|+-++|.|+.+++
T Consensus       332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~~~~  370 (370)
T PRK06294        332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAEEIM  370 (370)
T ss_pred             HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHhC
Confidence            557789999999998764 356899999999999998753

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=86.65  E-value=2.3  Score=30.56  Aligned_cols=46  Identities=13%  Similarity=0.230  Sum_probs=37.4

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cCCCCeeeCcch
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG   75 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~~~GR~lT~~G   75 (90)
                      +|+.+..++..++-.              ...++++|++|.++|||+.  .++||..|...-
T Consensus        24 ~~vs~~eIA~~~~ip--------------~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p   71 (164)
T PRK10857         24 GPVPLADISERQGIS--------------LSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA   71 (164)
T ss_pred             CcCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH
Confidence            478999999988763              4799999999999999984  456788886553

>PRK13347 coproporphyrinogen III oxidase; Provisional

Probab=86.31  E-value=1.1  Score=36.32  Aligned_cols=66  Identities=18%  Similarity=0.208  Sum_probs=46.1

Q ss_pred             HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHh
Q 034587            9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI   86 (90)
Q Consensus         9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v   86 (90)
                      +-.|-....+-...+...||-.      +..+.     -....|++|++.|||+.+. +.=+||++|+-.+|.|+..+
T Consensus       373 ~~~L~~~~~ld~~~~~~~~g~~------~~~~~-----~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~f  438 (453)
T PRK13347        373 IETLMCNFPVDLAAIAARHGFF------ARYFL-----DELARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAAAF  438 (453)
T ss_pred             HHHHHhhCCcCHHHHHHHHCCC------HHHHH-----HHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHH
Confidence            3334445566777888888743      11110     1245789999999999764 35689999999999999854

>PRK00215 LexA repressor; Validated

Probab=85.94  E-value=3.7  Score=29.38  Aligned_cols=64  Identities=16%  Similarity=0.159  Sum_probs=44.2

Q ss_pred             hhhHHHHHHHHh---hc--CCCchhHHHHHhcC-CCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe--eeCc
Q 034587            2 SELVTSMARKIY---LR--QGLGVGSFRRIYGG-SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR--RITS   73 (90)
Q Consensus         2 ~~r~ASi~RklY---l~--g~vGV~~Lr~~YGg-~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR--~lT~   73 (90)
                      +.+-..|+..|.   .+  .+..+..|+...|- .+              +-+-..|+.||+.|||+..++..|  .|++
T Consensus         3 t~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~--------------~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~   68 (205)
T PRK00215          3 TKRQQEILDFIRDHIEETGYPPSRREIADALGLRSP--------------SAVHEHLKALERKGFIRRDPGRSRAIEVAA   68 (205)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCh--------------HHHHHHHHHHHHCCCEEeCCCCcceEEecc
Confidence            344556666665   22  35789999998886 32              467789999999999998886554  3555


Q ss_pred             chHhhH
Q 034587           74 SGQRDL   79 (90)
Q Consensus        74 ~G~~~l   79 (90)
                      .|+..+
T Consensus        69 ~~~~~~   74 (205)
T PRK00215         69 PAQLEL   74 (205)
T ss_pred             cccccc
Confidence            555443

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

Probab=85.71  E-value=2  Score=26.73  Aligned_cols=37  Identities=22%  Similarity=0.185  Sum_probs=29.3

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      ++|+-...++...|=.              -.-+|+.|++||+.|.|++.|
T Consensus        13 ~~p~~T~eiA~~~gls--------------~~~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen   13 NGPLKTREIADALGLS--------------IYQARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             TS-EEHHHHHHHHTS---------------HHHHHHHHHHHHHCTSEEEES
T ss_pred             CCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEEEec
Confidence            6777777777777653              367999999999999999877

>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

Probab=85.59  E-value=0.77  Score=31.85  Aligned_cols=40  Identities=23%  Similarity=0.384  Sum_probs=30.7

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI   71 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l   71 (90)
                      -|.+..|...||-              +++|.|.+|..||+.|+|.... ++|+.
T Consensus        59 ~VTpy~la~r~gI--------------~~SvAr~vLR~LeeeGvv~lvs-knrR~   98 (107)
T COG4901          59 VVTPYVLASRYGI--------------NGSVARIVLRHLEEEGVVQLVS-KNRRQ   98 (107)
T ss_pred             eecHHHHHHHhcc--------------chHHHHHHHHHHHhCCceeeec-cCccc
Confidence            3566667777765              4789999999999999998775 35554

>PRK09249 coproporphyrinogen III oxidase; Provisional

Probab=85.16  E-value=1.1  Score=36.33  Aligned_cols=62  Identities=15%  Similarity=0.233  Sum_probs=42.2

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ..++-...+...||..         +...-...+ ..|++|++.|||+.+. +.=+||++|+-.+|.|+..+.
T Consensus       378 ~~gl~~~~~~~~fg~~---------~~~~~~~~~-~~l~~l~~~gll~~~~-~~~~lT~~G~~~~d~i~~~f~  439 (453)
T PRK09249        378 NFELDFAAIEAAFGID---------FAEYFAEEL-ERLAPLEADGLVELDE-NGITVTPKGRLLVRNIAMAFD  439 (453)
T ss_pred             cCCcCHHHHHHHHCCC---------HHHHHHHHH-HHHHHHHHCCCEEEEC-CEEEECccchHHHHHHHHHHH
Confidence            3455566777777742         110011111 2478999999999775 457899999999999998653

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=85.09  E-value=1  Score=32.70  Aligned_cols=41  Identities=20%  Similarity=0.221  Sum_probs=33.6

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      .=..|+..||-              |...+|.+|+.|++.|+|+.....|-.+++
T Consensus        26 sE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~G~GTfV~~   66 (233)
T TIGR02404        26 SEHELMDQYGA--------------SRETVRKALNLLTEAGYIQKIQGKGSIVLN   66 (233)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence            34567777776              457999999999999999998877877764

subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=84.99  E-value=1.1  Score=32.91  Aligned_cols=43  Identities=19%  Similarity=0.281  Sum_probs=34.4

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      .-..|+..||-              |..-+|.+|+.|++.|+|.+.+..|-.+++..
T Consensus        31 sE~eL~~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~~   73 (240)
T PRK09764         31 TESALQTEFGV--------------SRVTVRQALRQLVEQQILESIQGSGTYVKEER   73 (240)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEcccc
Confidence            44677777775              45799999999999999998887777776554

>PRK08898 coproporphyrinogen III oxidase; Provisional

Probab=84.91  E-value=1.2  Score=35.45  Aligned_cols=58  Identities=19%  Similarity=0.189  Sum_probs=41.9

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ..++=...+...||-.              ..-+-..|+.|++.|||+.+. +.=+||++|+-++|.|+.+++
T Consensus       336 ~~Gld~~~f~~~~g~~--------------~~~~~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d~i~~~~~  393 (394)
T PRK08898        336 TDGVPAHLFQERTGLP--------------LAAIEPQLAAAEQRGLLERDH-TRIRPTPLGQRFLNDLQELFL  393 (394)
T ss_pred             hCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEEC-CEEEEChhHhHHHHHHHHHHh
Confidence            3455566777666631              012345889999999998664 234799999999999998875

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=84.12  E-value=1.2  Score=31.40  Aligned_cols=45  Identities=18%  Similarity=0.256  Sum_probs=36.3

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG   75 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G   75 (90)
                      ++-+..++..+|-.              -..++++|++|.++|+|+...  +||-+|...-
T Consensus        25 ~~s~~~IA~~~~is--------------~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~   71 (150)
T COG1959          25 PVSSAEIAERQGIS--------------PSYLEKILSKLRKAGLVKSVRGKGGGYRLARPP   71 (150)
T ss_pred             cccHHHHHHHhCcC--------------HHHHHHHHHHHHHcCCEEeecCCCCCccCCCCh
Confidence            57788888877763              379999999999999998554  6899987654

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=83.95  E-value=1.7  Score=33.41  Aligned_cols=53  Identities=17%  Similarity=0.298  Sum_probs=39.9

Q ss_pred             hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHH-HHHhCCcccccCCCCeeeCcchHhhHH
Q 034587           13 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus        13 Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~Lq-qLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      |-.+|+|+..++..-|-...              -+-..+. .|-+.|+|+..+ .||++|++|.+.|.
T Consensus       272 ~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~~~~  325 (328)
T PRK00080        272 FGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTP-RGRVATPKAYEHLG  325 (328)
T ss_pred             cCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCC-chHHHHHHHHHHhC
Confidence            34578999999888776432              2333344 888999998776 69999999998875

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=83.81  E-value=3.1  Score=30.33  Aligned_cols=42  Identities=14%  Similarity=0.170  Sum_probs=36.3

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID   62 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~   62 (90)
                      -|+..|.-+|++..+.|+..-|-+.              .-+|++|+.|++.|||.
T Consensus        26 ~Vl~~L~~~g~~tdeeLA~~Lgi~~--------------~~VRk~L~~L~e~gLv~   67 (178)
T PRK06266         26 EVLKALIKKGEVTDEEIAEQTGIKL--------------NTVRKILYKLYDARLAD   67 (178)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeE
Confidence            4677777789999999999887754              68999999999999998

>PRK08629 coproporphyrinogen III oxidase; Provisional

Probab=83.75  E-value=3.7  Score=33.48  Aligned_cols=58  Identities=17%  Similarity=0.167  Sum_probs=44.3

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      +.+-...+...||..             --......|++|++.||++.+. +-=.||++|+-.+|.|..+++
T Consensus       357 ~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~f~  414 (433)
T PRK08629        357 GRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKEFY  414 (433)
T ss_pred             CCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHHH
Confidence            566667777777742             1234667889999999998764 345899999999999998875

>PRK14999 histidine utilization repressor; Provisional

Probab=83.74  E-value=1.3  Score=32.46  Aligned_cols=42  Identities=14%  Similarity=0.103  Sum_probs=35.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .-..|+..||-              |..-+|++|+.|++.|+|.+.+..|--+++.
T Consensus        38 sE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~GkGTfV~~~   79 (241)
T PRK14999         38 SEAELVAQYGF--------------SRMTINRALRELTDEGWLVRLQGVGTFVAEP   79 (241)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCcEEEECCC
Confidence            56778888886              4579999999999999999888778777654

>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase

Probab=83.72  E-value=1.4  Score=35.68  Aligned_cols=36  Identities=19%  Similarity=0.407  Sum_probs=30.5

Q ss_pred             HHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHh
Q 034587           50 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        50 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v   86 (90)
                      ..|++|++.|||+.+. +.=+||++|+-.+|.|+.++
T Consensus       403 ~~l~~l~~~gll~~~~-~~~~lT~~G~~~~~~i~~~f  438 (455)
T TIGR00538       403 ELLKPLEEDGLLDVDE-KGIEVTPKGRLLIRNIAMVF  438 (455)
T ss_pred             HHHHHHHhCCCEEEEC-CEEEECcCChHHHHHHHHHH
Confidence            3578999999999764 46789999999999999875

This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=83.60  E-value=1.3  Score=32.06  Aligned_cols=32  Identities=22%  Similarity=0.253  Sum_probs=26.1

Q ss_pred             CchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           43 SSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        43 asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      -+-.=+|.+|+-|+++|+|+++.+|.-..|.+
T Consensus        53 is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~   84 (171)
T PF14394_consen   53 ISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDK   84 (171)
T ss_pred             CCHHHHHHHHHHHHHCCCeEECCCCcEEEecc
Confidence            34567999999999999999998766666664

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

Probab=83.55  E-value=3.8  Score=30.15  Aligned_cols=57  Identities=16%  Similarity=0.110  Sum_probs=45.2

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .|+-.||.-|-- .+|+++..|++.-|-.|              +-+..+|+.|++.|||+++. +...|+++
T Consensus         9 ~ral~IL~~l~~~~~~~~l~eia~~lglpk--------------sT~~RlL~tL~~~G~l~~~~-~~Y~lG~~   66 (248)
T TIGR02431         9 ARGLAVIEAFGAERPRLTLTDVAEATGLTR--------------AAARRFLLTLVELGYVTSDG-RLFWLTPR   66 (248)
T ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeCC-CEEEecHH
Confidence            467788887764 57899999999888755              67899999999999999864 44556554

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.

>PRK13626 transcriptional regulator SgrR; Provisional

Probab=83.15  E-value=1.4  Score=36.40  Aligned_cols=39  Identities=18%  Similarity=0.343  Sum_probs=33.1

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      .+.+..|+....+..|              -+|.+|++|++.|||+-.|..||
T Consensus        23 ~~~l~~la~~l~cs~R--------------~~~~~l~~~~~~gwl~w~~~~GR   61 (552)
T PRK13626         23 ETTLNELAELLNCSRR--------------HMRTLLNTMQQRGWLTWQAEAGR   61 (552)
T ss_pred             eeeHHHHHHHhcCChh--------------HHHHHHHHHHHCCCeeeecCCCC
Confidence            5788888888877654              58999999999999999997676

>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=83.08  E-value=3.2  Score=23.43  Aligned_cols=42  Identities=17%  Similarity=0.243  Sum_probs=32.6

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI   63 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k   63 (90)
                      .|+..|.- +|..+..|+...|-.              -+.+.+=|..|+++|+|++
T Consensus         6 ~Il~~L~~-~~~~~~el~~~l~~s--------------~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    6 RILKLLSE-GPLTVSELAEELGLS--------------QSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHTT-SSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHh-CCCchhhHHHhcccc--------------chHHHHHHHHHHHCcCeeC
Confidence            34444443 889999999988874              3788999999999999975

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 ....

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=82.77  E-value=1.5  Score=29.18  Aligned_cols=22  Identities=14%  Similarity=0.373  Sum_probs=18.9

Q ss_pred             chhHHHHHHHHHHhCCcccccC
Q 034587           44 SGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus        44 sg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .+|+.|.+|++||+-|+|.-..
T Consensus        54 ~~SlAr~~Lr~L~~kG~Ik~V~   75 (86)
T PRK09334         54 KISVAKKVLRELEKRGVLVLYS   75 (86)
T ss_pred             hHHHHHHHHHHHHHCCCEEEEe
Confidence            4789999999999999996543

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=82.71  E-value=1.4  Score=32.31  Aligned_cols=42  Identities=12%  Similarity=0.071  Sum_probs=33.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      +=..|+..||-              |..-+|++|++|++.|+|+.....|-.+++.
T Consensus        37 sE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~   78 (241)
T PRK10079         37 AEQQLAARYEV--------------NRHTLRRAIDQLVEKGWVQRRQGVGVLVLMR   78 (241)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEecC
Confidence            34567777765              5579999999999999999888778777543

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=82.46  E-value=4.7  Score=30.96  Aligned_cols=58  Identities=14%  Similarity=0.047  Sum_probs=44.8

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCc-ccccCCCCeeeCcc
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~gl-V~k~~~~GR~lT~~   74 (90)
                      .|...|++-|.-..++....|+..+|-.              .+-++..++.|++.|+ |...+..|-.|.+.
T Consensus         4 ~r~~~il~~L~~~~~~s~~~LA~~lgvs--------------r~tV~~~l~~L~~~G~~i~~~~~~Gy~L~~~   62 (319)
T PRK11886          4 TVMLQLLSLLADGDFHSGEQLGEELGIS--------------RAAIWKHIQTLEEWGLDIFSVKGKGYRLAEP   62 (319)
T ss_pred             cHHHHHHHHHHcCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCceEEecCCeEEecCc
Confidence            4677788888777789999999999874              3689999999999999 44444447776544

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=81.88  E-value=1.7  Score=31.70  Aligned_cols=43  Identities=14%  Similarity=0.063  Sum_probs=34.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      +-..|+..||-              |..-+|.+|+.|++.|||.+....|=-+++..
T Consensus        35 sE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GTfV~~~~   77 (241)
T PRK11402         35 TENELCTQYNV--------------SRITIRKAISDLVADGVLIRWQGKGTFVQSQK   77 (241)
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEECCCc
Confidence            34567777775              45799999999999999998887777776654

>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=81.59  E-value=6.3  Score=23.80  Aligned_cols=52  Identities=19%  Similarity=0.293  Sum_probs=38.0

Q ss_pred             hhHHHHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC
Q 034587            3 ELVTSMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG   68 (90)
Q Consensus         3 ~r~ASi~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G   68 (90)
                      ...---|+-||.    .+++....++...|-++              .-+=..|+.|++.|||+..+.+|
T Consensus         4 ~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~--------------~tvt~ml~~L~~~GlV~~~~y~g   59 (60)
T PF01325_consen    4 ESEEDYLKAIYELSEEGGPVRTKDIAERLGVSP--------------PTVTEMLKRLAEKGLVEYEPYKG   59 (60)
T ss_dssp             CHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEETTTE
T ss_pred             cHHHHHHHHHHHHHcCCCCccHHHHHHHHCCCh--------------HHHHHHHHHHHHCCCEEecCCCC
Confidence            334445566665    36899999999887642              45778899999999999887654

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 ....

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=81.46  E-value=9.1  Score=22.89  Aligned_cols=53  Identities=11%  Similarity=0.125  Sum_probs=38.6

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .|++.+- +++..+..|+..+|-.              ..-|+..++.||+.|+....++.|..+.+.
T Consensus         4 ~il~~L~-~~~~~~~eLa~~l~vS--------------~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~   56 (69)
T TIGR00122         4 RLLALLA-DNPFSGEKLGEALGMS--------------RTAVNKHIQTLREWGVDVLTVGKGYRLPPP   56 (69)
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEecCCceEecCc
Confidence            3455544 6778899999988763              378999999999999964333567777543

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PRK09058 coproporphyrinogen III oxidase; Provisional

Probab=81.25  E-value=2.1  Score=34.83  Aligned_cols=39  Identities=15%  Similarity=0.244  Sum_probs=33.1

Q ss_pred             HHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHhh
Q 034587           48 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        48 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v~   87 (90)
                      ....|++|++.|||+.+. +.=+||++|+-..|.|+..++
T Consensus       398 ~~~~l~~~~~~Gll~~~~-~~l~lT~~G~~~~~~i~~~~~  436 (449)
T PRK09058        398 LAPLLAQWQQAGLVELSS-DCLRLTLAGRFWAVNLTQGLI  436 (449)
T ss_pred             HHHHHHHHHHCCCEEEEC-CEEEECCCcccHHHHHHHHHH
Confidence            445889999999999764 467899999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	90
3iz6_S	146	Localization Of The Small Subunit Ribosomal Protein		2e-33
3jyv_T	141	Structure Of The 40s Rrna And Proteins And PE TRNA		2e-18
3izb_S	144	Localization Of The Small Subunit Ribosomal Protein		2e-18
3j20_U	150	Promiscuous Behavior Of Proteins In Archaeal Riboso		4e-10
2v7f_A	150	Structure Of P. Abyssi Rps19 Protein Length = 150		5e-10
2xzm_T	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-05
3zey_O	167	High-resolution Cryo-electron Microscopy Structure		4e-05

>pdb|3IZ6|S Chain S, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 146

Iteration: 1
 Score =  137 bits (344), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 64/84 (76%), Positives = 75/84 (89%)
Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            S+ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++P
Sbjct: 61  ASIARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDP 120
Query: 66  KGGRRITSSGQRDLDQVAGRIVVA 89
           KGGR ITS G+RDLDQVAGR+ V 
Sbjct: 121 KGGRLITSQGRRDLDQVAGRVDVT 144

>pdb|3JYV|T Chain T, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 141

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 39/82 (47%), Positives = 59/82 (71%)
Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            S+AR IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I P
Sbjct: 56  ASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISP 115
Query: 66  KGGRRITSSGQRDLDQVAGRIV 87
           KGGRRI+ +GQRDLD++A + +
Sbjct: 116 KGGRRISENGQRDLDRIAAQTL 137

>pdb|3IZB|S Chain S, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 144

Iteration: 1
 Score = 87.0 bits (214), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 39/82 (47%), Positives = 59/82 (71%)
Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            S+AR IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I P
Sbjct: 59  ASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISP 118
Query: 66  KGGRRITSSGQRDLDQVAGRIV 87
           KGGRRI+ +GQRDLD++A + +
Sbjct: 119 KGGRRISENGQRDLDRIAAQTL 140

>pdb|3J20|U Chain U, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (30s Ribosomal Subunit) Length = 150

Iteration: 1
 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 45/82 (54%)
Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
           V S+ R++YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  
Sbjct: 55  VASILRRVYLDGPVGIERLRTYYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKV 114
Query: 65  PKGGRRITSSGQRDLDQVAGRI 86
           P  GR IT  G+  LD++A  +
Sbjct: 115 PGKGRVITPKGRSFLDKIATEL 136

>pdb|2V7F|A Chain A, Structure Of P. Abyssi Rps19 Protein Length = 150

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 45/82 (54%)
Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
           V S+ R++YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  
Sbjct: 55  VASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKV 114
Query: 65  PKGGRRITSSGQRDLDQVAGRI 86
           P  GR IT  G+  LD++A  +
Sbjct: 115 PGKGRVITPKGRSFLDKIATEL 136

>pdb|2XZM|T Chain T, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 155

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII----- 61
           ++ARK+YL+   G+ + + I+G +K  G+         G I R  L+ L+++ II     
Sbjct: 63  ALARKVYLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKN 122
Query: 62  DIEPKGGRRITSSGQRDLDQVAGRIVV 88
               K  R IT  G  +L+++A +I +
Sbjct: 123 SATKKFSRVITKEGMTELNRIATQIAI 149

>pdb|3ZEY|O Chain O, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 167

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 41/84 (48%)
Query: 5   VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 64
             ++ R +YLR G+G G   + +   K  GSRP    ++S  +     + L  + +++  
Sbjct: 74  CAAVLRAVYLRPGVGYGGLSKRFSSKKNRGSRPEITTRASKGLLHWCCKSLTKLELLEKC 133
Query: 65  PKGGRRITSSGQRDLDQVAGRIVV 88
              G R+T  G++  D +A +I +
Sbjct: 134 KGAGHRVTKLGRKVADTIAFKIAL 157
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	90
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	4e-34
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	5e-34
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	6e-34
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	1e-30

>3u5c_T 40S ribosomal protein S19-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_S 3o30_M 3o2z_M 3u5g_T 3jyv_T* Length = 144

 Score =  113 bits (283), Expect = 4e-34
 Identities = 39/81 (48%), Positives = 59/81 (72%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+AR IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I PK
Sbjct: 60  SVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPK 119

Query: 67  GGRRITSSGQRDLDQVAGRIV 87
           GGRRI+ +GQRDLD++A + +
Sbjct: 120 GGRRISENGQRDLDRIAAQTL 140

>3iz6_S 40S ribosomal protein S19 (S19E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 146

 Score =  113 bits (283), Expect = 5e-34
 Identities = 63/80 (78%), Positives = 74/80 (92%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++PK
Sbjct: 62  SIARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPK 121

Query: 67  GGRRITSSGQRDLDQVAGRI 86
           GGR ITS G+RDLDQVAGR+
Sbjct: 122 GGRLITSQGRRDLDQVAGRV 141

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84 Length = 150

 Score =  113 bits (283), Expect = 6e-34
 Identities = 30/80 (37%), Positives = 44/80 (55%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 66
           S+ R++YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  P 
Sbjct: 57  SILRRVYLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPG 116

Query: 67  GGRRITSSGQRDLDQVAGRI 86
            GR IT  G+  LD++A  +
Sbjct: 117 KGRVITPKGRSFLDKIATEL 136

>2xzm_T RPS19E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_T Length = 155

 Score =  104 bits (261), Expect = 1e-30
 Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 5/88 (5%)

Query: 7   SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP- 65
           ++ARK+YL+   G+ + + I+G +K  G+         G I R  L+ L+++ II  +  
Sbjct: 63  ALARKVYLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKN 122

Query: 66  ----KGGRRITSSGQRDLDQVAGRIVVA 89
               K  R IT  G  +L+++A +I + 
Sbjct: 123 SATKKFSRVITKEGMTELNRIATQIAIK 150

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	90
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	100.0
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	100.0
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	100.0
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	99.95
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.66
2pg4_A	95	Uncharacterized protein; structural genomics, join	97.57
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.52
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	97.51
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	97.49
2h09_A	155	Transcriptional regulator MNTR; transcription regu	97.49
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.48
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.47
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.46
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.43
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.42
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	97.38
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	97.36
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.36
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.33
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	97.32
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	97.3
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.3
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.3
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.29
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.28
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.28
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.26
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	97.22
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.22
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.21
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.2
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.2
3bja_A	139	Transcriptional regulator, MARR family, putative;	97.19
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.16
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	97.15
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.14
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	97.14
2nnn_A	140	Probable transcriptional regulator; structural gen	97.12
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.1
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.1
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.09
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	97.03
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	97.01
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.0
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.0
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.98
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.97
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.93
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.93
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	96.92
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.92
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.92
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.91
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.9
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.88
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.85
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.82
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.73
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	96.69
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.67
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.65
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.64
2o0m_A	345	Transcriptional regulator, SORC family; structural	96.62
3nqo_A	189	MARR-family transcriptional regulator; structural	96.62
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	96.6
3f3x_A	144	Transcriptional regulator, MARR family, putative;	96.53
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.53
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	96.51
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.5
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.48
2fxa_A	207	Protease production regulatory protein HPR; protea	96.47
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	96.46
1z91_A	147	Organic hydroperoxide resistance transcriptional;	96.44
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.43
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	96.39
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	96.32
1bja_A	95	Transcription regulatory protein MOTA; activation	96.32
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.31
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.24
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	96.19
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	96.18
1okr_A	123	MECI, methicillin resistance regulatory protein ME	96.16
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.11
4fx0_A	148	Probable transcriptional repressor protein; helix-	96.06
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.06
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.02
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	96.0
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	95.91
3jth_A	98	Transcription activator HLYU; transcription factor	95.79
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	95.7
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.68
2obp_A	96	Putative DNA-binding protein; structural genomics,	95.63
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.59
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	95.51
1hsj_A	487	Fusion protein consisting of staphylococcus access	95.49
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.42
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	95.39
2kko_A	108	Possible transcriptional regulatory protein (possi	95.32
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	95.3
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.2
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.2
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	95.13
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	95.12
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	95.08
1xma_A	145	Predicted transcriptional regulator; southea colla	95.01
3by6_A	126	Predicted transcriptional regulator; structural ge	95.0
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	94.98
2co5_A	99	Viral protein F93; viral protein-winged helix comp	94.97
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	94.96
4esf_A	117	PADR-like transcriptional regulator; PADR family,	94.79
1mkm_A	249	ICLR transcriptional regulator; structural genomic	94.77
3c7j_A	237	Transcriptional regulator, GNTR family; structural	94.69
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	94.67
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	94.65
2dql_A	115	PEX protein; circadian clock associated protein, c	94.62
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	94.6
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	94.57
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	94.5
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	94.49
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	94.23
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.23
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	94.16
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	94.16
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.09
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	93.9
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	93.75
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	93.6
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	93.56
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	93.43
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	93.41
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	93.33
3elk_A	117	Putative transcriptional regulator TA0346; structu	93.23
1ylf_A	149	RRF2 family protein; structural genomics, transcri	93.14
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.1
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	93.09
3aaf_A	134	Werner syndrome ATP-dependent helicase; helix-turn	93.09
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	92.9
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	92.85
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	92.68
3cta_A	230	Riboflavin kinase; structural genomics, transferas	92.67
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	92.5
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	92.35
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	92.2
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	92.16
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	91.91
2g7u_A	257	Transcriptional regulator; ICLR family, structural	91.52
3k69_A	162	Putative transcription regulator; putative transcr	91.5
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	91.43
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	91.39
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	91.36
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	91.07
2rkh_A	180	Putative APHA-like transcription factor; ZP_002083	90.66
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	90.61
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	90.56
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	89.87
1p6r_A	82	Penicillinase repressor; transcription regulation,	89.8
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	89.44
3l09_A	266	Putative transcriptional regulator; structural gen	89.33
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	88.96
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	88.88
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	88.59
3eet_A	272	Putative GNTR-family transcriptional regulator; st	88.59
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	88.23
1xd7_A	145	YWNA; structural genomics, protein structure initi	88.12
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	88.01
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	87.7
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	87.51
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	87.09
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	86.93
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	86.41
3kfw_X	247	Uncharacterized protein; structural genomics, PSI-	85.52
1olt_A	457	Oxygen-independent coproporphyrinogen III oxidase;	84.59
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	84.56
2qm3_A	373	Predicted methyltransferase; putative methyltransf	84.1
3r0a_A	123	Putative transcriptional regulator; structural gen	84.06
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	82.08
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	80.58

>3iz6_S 40S ribosomal protein S19 (S19E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=5.1e-45  Score=259.84  Aligned_cols=87  Identities=74%  Similarity=1.223  Sum_probs=84.9

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +||||||||||++||+||++|+++|||+||||++|+||++|||+|||+||||||++||||+++++||+|||+||+|||+|
T Consensus        58 ~RaASi~R~lYlrg~vGV~~lrk~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g~Vek~~~gGR~lT~~G~~~LD~i  137 (146)
T 3iz6_S           58 TRAASIARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQV  137 (146)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHSSSCCCCCCCSSCCCCCCCCHHHHHHHHHHHHHHTSEEEETTTEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCcHHHHHHHHCCCCCCCCCCCcccCCCcHHHHHHHHHHHHCCCeEecCCCCcEECHhHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             HHHhhcC
Q 034587           83 AGRIVVA   89 (90)
Q Consensus        83 A~~v~~~   89 (90)
                      |.+|+++
T Consensus       138 A~~v~~~  144 (146)
T 3iz6_S          138 AGRVDVT  144 (146)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9999753

>3u5c_T 40S ribosomal protein S19-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_S 3o30_M 3o2z_M 3u5g_T 3jyv_T*

Probab=100.00  E-value=3.6e-45  Score=260.12  Aligned_cols=87  Identities=45%  Similarity=0.866  Sum_probs=85.0

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +||||||||||++||+||++|+++|||+||||++|+||++|||+|||+||||||++|||++++++||+|||+||+|||+|
T Consensus        56 ~RaASi~R~lYl~g~vGV~~lrk~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g~vek~~~~GR~lT~~G~~~LD~i  135 (144)
T 3u5c_T           56 KRAASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRI  135 (144)
T ss_dssp             HHHHHHHHHHHTSSBCCHHHHHHHHCCEEEETTEEEEECCCCHHHHHHHHHHHHHTTSEECCSSSSCEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCcHHHHHHHHCCCCCCCCCCccccccCcHHHHHHHHHHHHCCCeeecCCCCcEECHhHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             HHHhhcC
Q 034587           83 AGRIVVA   89 (90)
Q Consensus        83 A~~v~~~   89 (90)
                      |.+|+++
T Consensus       136 A~~v~~~  142 (144)
T 3u5c_T          136 AAQTLEE  142 (144)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9999864

>2xzm_T RPS19E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_T

Probab=100.00  E-value=1.3e-43  Score=254.64  Aligned_cols=86  Identities=28%  Similarity=0.543  Sum_probs=84.0

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-----CeeeCcchHh
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----GRRITSSGQR   77 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-----GR~lT~~G~~   77 (90)
                      +|||||||||||+||+||++|+++|||+||||++|+||++|||+|||+||||||++||||+++++     ||+|||+||+
T Consensus        59 iRaASi~R~lYlrg~vGV~~lrk~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g~Vek~~~g~~~k~GR~lT~~G~~  138 (155)
T 2xzm_T           59 IRTAALARKVYLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMT  138 (155)
T ss_dssp             HHHHHHHHHHHHSTTCCHHHHHHHTCCEECCSSSCCEECCCCHHHHHHHHHHHHHTTSEEECSSCSSSTTCEEECHHHHH
T ss_pred             HHHHHHHHHHhccCCCCHHHHHHHHCCCCCCCCCCCcccCCCcHHHHHHHHHHHHCCCEeecCCCCcCCCCCEECHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999877     9999999999


Q ss_pred             hHHHHHHHhhc
Q 034587           78 DLDQVAGRIVV   88 (90)
Q Consensus        78 ~lD~iA~~v~~   88 (90)
                      |||+||.+|+.
T Consensus       139 ~LDriA~~i~~  149 (155)
T 2xzm_T          139 ELNRIATQIAI  149 (155)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999975

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=99.95  E-value=6.8e-28  Score=170.66  Aligned_cols=87  Identities=36%  Similarity=0.605  Sum_probs=80.2

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ   81 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~   81 (90)
                      ..++|+++|++|++|+.|+..|++.|||+||||++|+||++.|+++||.+||+||++|||++.+++|+.+|+.|+++||+
T Consensus        52 y~ria~~lr~~i~~g~~G~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~~~G~~Vt~~~~~~l~~  131 (150)
T 2v7f_A           52 YYRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDK  131 (150)
T ss_dssp             HHHHHHHHHHHHHHCSBCHHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEeCCCceEECCCCHHHHHH
Confidence            36899999999999999999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHHhhc
Q 034587           82 VAGRIVV   88 (90)
Q Consensus        82 iA~~v~~   88 (90)
                      ||.+|++
T Consensus       132 ia~~i~~  138 (150)
T 2v7f_A          132 IATELKK  138 (150)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999875

>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=97.66  E-value=0.00013  Score=46.93  Aligned_cols=63  Identities=14%  Similarity=0.096  Sum_probs=51.7

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG   84 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~   84 (90)
                      ...||+.++ .+ +|...|+..-|=.              -+.++..+..|++.|||++.. +|-.||++|...|+.+..
T Consensus        10 i~~IL~~i~-~~-~~~t~La~~~~ls--------------~~~~~~~l~~L~~~GLI~~~~-~~~~LT~kG~~~l~~l~~   72 (95)
T 1r7j_A           10 IQAILEACK-SG-SPKTRIMYGANLS--------------YALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDIRK   72 (95)
T ss_dssp             HHHHHHHHT-TC-BCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHhCcC--------------HHHHHHHHHHHHHCCCeEEEC-CeeEEChhHHHHHHHHHH
Confidence            467888887 45 9999998876653              379999999999999999885 689999999987776543

>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=97.57  E-value=0.00015  Score=45.02  Aligned_cols=70  Identities=11%  Similarity=0.066  Sum_probs=54.9

Q ss_pred             hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhH-HHHHHHHHHhCCcccccCCCCe----eeCcchH
Q 034587            3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAI-ARHILQQLQNMNIIDIEPKGGR----RITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~i-iR~~LqqLE~~glV~k~~~~GR----~lT~~G~   76 (90)
                      .|.-.++..++-.+ ++.+..|++..|-.              .+- +-.+++.||+.|||+.++.++|    .||++|+
T Consensus        15 ~~~l~~L~~l~~~~~~~t~~eLa~~l~is--------------~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~   80 (95)
T 2pg4_A           15 IRILPTLLEFEKKGYEPSLAEIVKASGVS--------------EKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGR   80 (95)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHCCC--------------HHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHH
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHCCC--------------chHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHH
Confidence            35566777777777 89999999988753              245 7778999999999996654444    6999999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++.+....
T Consensus        81 ~~~~~~~~~~   90 (95)
T 2pg4_A           81 RLAECLEKCR   90 (95)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999886653

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

Probab=97.52  E-value=0.0004  Score=44.87  Aligned_cols=69  Identities=7%  Similarity=0.080  Sum_probs=55.1

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .++|    .||++|+.
T Consensus        32 ~q~~iL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~   97 (145)
T 3g3z_A           32 NLFAVLYTLATEGSRTQKHIGEKWSLP--------------KQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKA   97 (145)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHH
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHH
Confidence            345788899999999999999988753              256778999999999999754  3444    49999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus        98 ~~~~~~~~~  106 (145)
T 3g3z_A           98 YAAPLTESA  106 (145)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998876543

>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=97.51  E-value=0.00042  Score=45.21  Aligned_cols=68  Identities=15%  Similarity=0.150  Sum_probs=54.7

Q ss_pred             hhHHHHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587            3 ELVTSMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD   78 (90)
Q Consensus         3 ~r~ASi~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~   78 (90)
                      .....+++.||.    .+++.+..|+...|-.              .+-++.+|+.||+.|||+..+.++-.||++|+..
T Consensus         4 ~~~~~~L~~i~~l~~~~~~~~~~ela~~l~vs--------------~~tvs~~l~~Le~~Glv~r~~~~~~~LT~~g~~~   69 (142)
T 1on2_A            4 PSMEMYIEQIYMLIEEKGYARVSDIAEALAVH--------------PSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKI   69 (142)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHhhcCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEEEeeCceEEEchhHHHH
Confidence            344456666663    5899999999998753              3688999999999999998876778999999998


Q ss_pred             HHHHHH
Q 034587           79 LDQVAG   84 (90)
Q Consensus        79 lD~iA~   84 (90)
                      ++.+..
T Consensus        70 ~~~~~~   75 (142)
T 1on2_A           70 GKRLVY   75 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

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

Probab=97.49  E-value=0.00048  Score=44.68  Aligned_cols=68  Identities=15%  Similarity=0.151  Sum_probs=55.1

Q ss_pred             hhhHHHHHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587            2 SELVTSMARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus         2 ~~r~ASi~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      +.....+++.||.    .+++.+..|+...|-.              .+-++.+|+.||+.|||+..+ ++-.||++|+.
T Consensus        12 t~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is--------------~~tv~~~l~~Le~~Gli~r~~-~~~~Lt~~g~~   76 (139)
T 2x4h_A           12 SRREFSYLLTIKRYNDSGEGAKINRIAKDLKIA--------------PSSVFEEVSHLEEKGLVKKKE-DGVWITNNGTR   76 (139)
T ss_dssp             CHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEET-TEEEECHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCC--------------hHHHHHHHHHHHHCCCEEecC-CeEEEChhHHH
Confidence            3445567777765    5789999999998753              368999999999999999887 68899999999


Q ss_pred             hHHHHHH
Q 034587           78 DLDQVAG   84 (90)
Q Consensus        78 ~lD~iA~   84 (90)
                      ..+.+..
T Consensus        77 ~~~~~~~   83 (139)
T 2x4h_A           77 SINYLIK   83 (139)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876654

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=97.49  E-value=0.00035  Score=46.34  Aligned_cols=62  Identities=18%  Similarity=0.190  Sum_probs=51.3

Q ss_pred             HHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587            9 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG   84 (90)
Q Consensus         9 ~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~   84 (90)
                      +..++-.+++.+..|+..+|-.              .+-++.+|+.||+.|||+..+..|-.||+.|+..++.+..
T Consensus        46 ~~~l~~~~~~~~~~la~~l~vs--------------~~tvs~~l~~Le~~Glv~r~~~~~~~lT~~g~~~~~~~~~  107 (155)
T 2h09_A           46 SDLIREVGEARQVDMAARLGVS--------------QPTVAKMLKRLATMGLIEMIPWRGVFLTAEGEKLAQESRE  107 (155)
T ss_dssp             HHHHHHHSCCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTCEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHHHhCCCcCHHHHHHHhCcC--------------HHHHHHHHHHHHHCCCEEEecCCceEEChhHHHHHHHHHH
Confidence            3344556889999999998764              3689999999999999998877788999999998887654

>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=97.48  E-value=0.0006  Score=43.70  Aligned_cols=67  Identities=13%  Similarity=0.093  Sum_probs=53.4

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+ .+++.+..|+...|-              +.+-+..+|+.||+.|||+..+  .++|    .||++|+.
T Consensus        38 ~~~~iL~~l~-~~~~~~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~  102 (146)
T 2gxg_A           38 LDFLVLRATS-DGPKTMAYLANRYFV--------------TQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLE  102 (146)
T ss_dssp             HHHHHHHHHT-TSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHH
T ss_pred             HHHHHHHHHh-cCCcCHHHHHHHhCC--------------CchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHH
Confidence            3456888899 999999999998864              3367888999999999998654  2333    68999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       103 ~~~~~~~~  110 (146)
T 2gxg_A          103 TFNKGIEI  110 (146)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887654

>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=97.47  E-value=0.00076  Score=44.65  Aligned_cols=68  Identities=22%  Similarity=0.207  Sum_probs=54.9

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..||..|+-.+++.+..|+...|-.+              +-+-.+++.||+.|||++.+  ..+|    .||++|+..
T Consensus        48 q~~iL~~l~~~~~~t~~eLa~~l~~~~--------------~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~  113 (162)
T 3k0l_A           48 QFTALSVLAAKPNLSNAKLAERSFIKP--------------QSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDK  113 (162)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCG--------------GGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHH
Confidence            356889999999999999999887543              45778999999999998654  3444    599999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++++...+
T Consensus       114 ~~~~~~~~  121 (162)
T 3k0l_A          114 LNQCNQVV  121 (162)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

>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=97.46  E-value=0.00058  Score=44.08  Aligned_cols=69  Identities=17%  Similarity=0.173  Sum_probs=51.4

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..||..|+-.+++.+..|+...|-.+              +-+-.+++.||+.|||+..++  ++|    .||++|+.
T Consensus        38 ~~~~vL~~l~~~~~~t~~eLa~~l~~~~--------------~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~  103 (142)
T 3ech_A           38 PDVHVLKLIDEQRGLNLQDLGRQMCRDK--------------ALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLA  103 (142)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHC-----------------CHHHHHHHHHHHTTSEEC----------CCEECHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHhCCCH--------------HHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHH
Confidence            3457889999999999999999887543              467789999999999987552  344    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus       104 ~~~~~~~~~  112 (142)
T 3ech_A          104 IHLHAELIM  112 (142)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876543

>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=97.43  E-value=0.00082  Score=42.80  Aligned_cols=69  Identities=12%  Similarity=0.124  Sum_probs=53.5

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  +++|    .||++|+.
T Consensus        35 ~~~~iL~~l~~~~~~~~~~la~~l~~~--------------~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~  100 (138)
T 1jgs_A           35 AQFKVLCSIRCAACITPVELKKVLSVD--------------LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAA  100 (138)
T ss_dssp             HHHHHHHHHHHHSSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHCCC--------------hHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHH
Confidence            345678888888999999999877643              256778999999999998653  3444    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++++...+
T Consensus       101 ~~~~~~~~~  109 (138)
T 1jgs_A          101 ICEQCHQLV  109 (138)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998876543

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

Probab=97.42  E-value=0.00046  Score=44.48  Aligned_cols=68  Identities=13%  Similarity=0.135  Sum_probs=53.8

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+..
T Consensus        39 ~~~iL~~l~~~~~~t~~eLa~~l~~~--------------~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~  104 (143)
T 3oop_A           39 QWSVLEGIEANEPISQKEIALWTKKD--------------TPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKE  104 (143)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHH
Confidence            45688888888999999999988653              356778999999999998655  3454    499999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++.+...+
T Consensus       105 ~~~~~~~~  112 (143)
T 3oop_A          105 TTELRDIV  112 (143)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876553

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=97.38  E-value=0.00026  Score=44.15  Aligned_cols=70  Identities=19%  Similarity=0.275  Sum_probs=53.6

Q ss_pred             hhhHHHHHHHHhhc-CC---CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCc
Q 034587            2 SELVTSMARKIYLR-QG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITS   73 (90)
Q Consensus         2 ~~r~ASi~RklYl~-g~---vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~   73 (90)
                      +.+...|+-.+|-. ++   +.+..|+...|-.              .+-+-.+|+.||+.||| .++..+|    .||+
T Consensus        11 ~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~--------------~~tvs~~l~~Le~~Glv-~~~~d~R~~~v~LT~   75 (95)
T 2qvo_A           11 KEKALEILMTIYYESLGGNDVYIQYIASKVNSP--------------HSYVWLIIKKFEEAKMV-ECELEGRTKIIRLTD   75 (95)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSC--------------HHHHHHHHHHHHHTTSE-EEEEETTEEEEEECH
T ss_pred             chhHHHHHHHHHHccCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCcCc-cCCCCCCeEEEEECh
Confidence            45666777777653 45   8899999987653              25677789999999999 4444566    7999


Q ss_pred             chHhhHHHHHHHh
Q 034587           74 SGQRDLDQVAGRI   86 (90)
Q Consensus        74 ~G~~~lD~iA~~v   86 (90)
                      +|+..++++...+
T Consensus        76 ~G~~~~~~~~~~~   88 (95)
T 2qvo_A           76 KGQKIAQQIKSII   88 (95)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            9999999887654

>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=97.36  E-value=0.00084  Score=42.93  Aligned_cols=69  Identities=17%  Similarity=0.255  Sum_probs=53.5

Q ss_pred             hHHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587            4 LVTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG   75 (90)
Q Consensus         4 r~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G   75 (90)
                      --..|+..|+-.+  ++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .++|    .||++|
T Consensus        32 ~~~~vL~~l~~~~~~~~t~~ela~~l~~~--------------~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G   97 (139)
T 3eco_A           32 EQGHTLGYLYAHQQDGLTQNDIAKALQRT--------------GPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSG   97 (139)
T ss_dssp             HHHHHHHHHHHSTTTCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHhCCC--------------cccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHH
Confidence            3457888899887  99999999988753              256778999999999998654  3455    499999


Q ss_pred             HhhHHHHHHHh
Q 034587           76 QRDLDQVAGRI   86 (90)
Q Consensus        76 ~~~lD~iA~~v   86 (90)
                      +..++.+...+
T Consensus        98 ~~~~~~~~~~~  108 (139)
T 3eco_A           98 IKLVEAFTSIF  108 (139)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999876543

>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=97.36  E-value=0.00055  Score=44.41  Aligned_cols=68  Identities=7%  Similarity=0.084  Sum_probs=53.0

Q ss_pred             HHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe----eeCcchH
Q 034587            5 VTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR----~lT~~G~   76 (90)
                      -..||..||-.  +++.+..|+...|-.              .+-+-.+|+.||+.|||++.  +.++|    .||++|+
T Consensus        39 q~~vL~~l~~~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~  104 (127)
T 2frh_A           39 EFAVLTYISENKEKEYYLKDIINHLNYK--------------QPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQR  104 (127)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSSH--------------HHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHH
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHH
Confidence            34678888887  888999999977743              24667789999999999874  34455    6999999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++++...+
T Consensus       105 ~~~~~~~~~~  114 (127)
T 2frh_A          105 KKIESLLSRV  114 (127)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999876654

>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=97.33  E-value=0.00085  Score=40.85  Aligned_cols=70  Identities=17%  Similarity=0.146  Sum_probs=55.6

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCe----eeCcchHh
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGR----RITSSGQR   77 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR----~lT~~G~~   77 (90)
                      ..-..|+..|+-.+++.+..|+...|-              +.+-+...|+.||+.|||+..+. ++|    .+|+.|+.
T Consensus        20 ~~~~~il~~l~~~~~~s~~ela~~l~i--------------s~~tv~~~l~~L~~~glv~~~~~~~~r~~~~~~t~~g~~   85 (109)
T 1sfx_A           20 PSDVRIYSLLLERGGMRVSEIARELDL--------------SARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEK   85 (109)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEeecCCceEEEEecCcHHH
Confidence            344668888888899999999998864              34689999999999999986543 455    69999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus        86 ~~~~~~~~~   94 (109)
T 1sfx_A           86 VLKEFKSSI   94 (109)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988776543

>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=97.32  E-value=0.0012  Score=42.02  Aligned_cols=68  Identities=9%  Similarity=0.092  Sum_probs=53.1

Q ss_pred             hHHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587            4 LVTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG   75 (90)
Q Consensus         4 r~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G   75 (90)
                      .-..|+..|+-.+  ++.+..|+...|-.              .+-+..+++.||+.|||+..+  +++|    .||++|
T Consensus        35 ~~~~iL~~l~~~~~~~~~~~ela~~l~~~--------------~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G  100 (141)
T 3bro_A           35 TQMTIIDYLSRNKNKEVLQRDLESEFSIK--------------SSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKA  100 (141)
T ss_dssp             HHHHHHHHHHHTTTSCCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHH
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCC--------------cchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHH
Confidence            3456788888887  89999999988753              357888999999999998654  3333    389999


Q ss_pred             HhhHHHHHHH
Q 034587           76 QRDLDQVAGR   85 (90)
Q Consensus        76 ~~~lD~iA~~   85 (90)
                      +..++.+...
T Consensus       101 ~~~~~~~~~~  110 (141)
T 3bro_A          101 NKLETIILSY  110 (141)
T ss_dssp             HTTHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998876554

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

Probab=97.30  E-value=0.0011  Score=42.06  Aligned_cols=69  Identities=13%  Similarity=0.211  Sum_probs=54.5

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      ..-..|+..|+-.+++.+..|+...|-.              .+-+..+++.||+.|||+..+  .++|    .||++|+
T Consensus        29 ~~~~~iL~~l~~~~~~~~~ela~~l~~s--------------~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~   94 (138)
T 3bpv_A           29 DAQVACLLRIHREPGIKQDELATFFHVD--------------KGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGE   94 (138)
T ss_dssp             HHHHHHHHHHHHSTTCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHH
Confidence            3445688888888999999999988642              367888999999999999754  2333    5999999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++.+...
T Consensus        95 ~~~~~~~~~  103 (138)
T 3bpv_A           95 EIIPLILKV  103 (138)
T ss_dssp             HTHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887654

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

Probab=97.30  E-value=0.00087  Score=43.54  Aligned_cols=67  Identities=13%  Similarity=0.220  Sum_probs=52.9

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cC--CCCe----eeCcchH
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EP--KGGR----RITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~--~~GR----~lT~~G~   76 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+.  .+  .++|    .||++|+
T Consensus        43 ~~~iL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~  108 (154)
T 2qww_A           43 QLAMINVIYSTPGISVADLTKRLIIT--------------GSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGE  108 (154)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHH
Confidence            35688888889999999999988642              3567789999999999998  33  3344    5999999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++++...
T Consensus       109 ~~~~~~~~~  117 (154)
T 2qww_A          109 DLSKRSTAN  117 (154)
T ss_dssp             HHHHHHHSC
T ss_pred             HHHHHHHhh
Confidence            998877544

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

Probab=97.30  E-value=0.0013  Score=42.42  Aligned_cols=69  Identities=12%  Similarity=0.163  Sum_probs=52.7

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..+  .++|    .||++|+.
T Consensus        43 ~~~~iL~~l~~~~~~t~~ela~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~  108 (150)
T 2rdp_A           43 PQFVALQWLLEEGDLTVGELSNKMYLA--------------CSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGER  108 (150)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHH
Confidence            345678888888999999999988642              356788999999999998653  3343    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus       109 ~~~~~~~~~  117 (150)
T 2rdp_A          109 IIEEVIEKR  117 (150)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998876543

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

Probab=97.29  E-value=0.00078  Score=44.02  Aligned_cols=68  Identities=18%  Similarity=0.196  Sum_probs=52.2

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..||..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .++|    .||++|+..
T Consensus        43 q~~iL~~l~~~~~~~~~eLa~~l~~~--------------~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~  108 (149)
T 4hbl_A           43 QYLVMLTLWEENPQTLNSIGRHLDLS--------------SNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQ  108 (149)
T ss_dssp             HHHHHHHHHHSSSEEHHHHHHHHTCC--------------HHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHH
Confidence            45688888889999999999988653              357778999999999998654  3455    499999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++.+...+
T Consensus       109 ~~~~~~~~  116 (149)
T 4hbl_A          109 QEAVFEAI  116 (149)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876654

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

Probab=97.28  E-value=0.001  Score=44.52  Aligned_cols=67  Identities=15%  Similarity=0.225  Sum_probs=53.1

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..||..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+..
T Consensus        47 ~~~iL~~L~~~~~~t~~eLa~~l~is--------------~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  112 (168)
T 2nyx_A           47 QFRTLVILSNHGPINLATLATLLGVQ--------------PSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDV  112 (168)
T ss_dssp             HHHHHHHHHHHCSEEHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHH
Confidence            34678888888999999999988653              356777999999999998643  3344    599999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++++...
T Consensus       113 ~~~~~~~  119 (168)
T 2nyx_A          113 VRQVTEH  119 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9886554

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

Probab=97.28  E-value=0.00094  Score=43.95  Aligned_cols=67  Identities=15%  Similarity=0.174  Sum_probs=53.0

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..||..|+-.+++.+..|+...|-.+              +-+-.+++.||+.|||++.+  .++|    .||++|+..+
T Consensus        53 ~~vL~~l~~~~~~t~~eLa~~l~~~~--------------~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  118 (159)
T 3s2w_A           53 FPFLMRLYREDGINQESLSDYLKIDK--------------GTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLE  118 (159)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHH
Confidence            56888888899999999999887542              57788999999999998654  3444    4999999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +.+...+
T Consensus       119 ~~~~~~~  125 (159)
T 3s2w_A          119 PDMKKIA  125 (159)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876553

>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=97.26  E-value=0.00084  Score=41.58  Aligned_cols=69  Identities=12%  Similarity=0.031  Sum_probs=51.6

Q ss_pred             hHHHHHHHHhhcCCCchhHH----HHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC---CeeeCcchH
Q 034587            4 LVTSMARKIYLRQGLGVGSF----RRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQ   76 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~L----r~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~~G~   76 (90)
                      .-..|+..|+-.+++.+..|    +...|-              +.+-+-.+|+.||+.|||++.++.   .-.||++|+
T Consensus         9 ~q~~iL~~l~~~~~~~~~el~~~la~~l~i--------------s~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~   74 (99)
T 1tbx_A            9 PEAIVLAYLYDNEGIATYDLYKKVNAEFPM--------------STATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGK   74 (99)
T ss_dssp             HHHHHHHHHTTCTTCBHHHHHHHHHTTSCC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHHHHcCC--------------CHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHH
Confidence            34567888888889999999    553332              335778899999999999876532   235999999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++.+...+
T Consensus        75 ~~~~~~~~~~   84 (99)
T 1tbx_A           75 LFAISLKTAI   84 (99)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998876543

>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=97.22  E-value=0.00099  Score=42.72  Aligned_cols=68  Identities=9%  Similarity=0.117  Sum_probs=53.1

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.+              +-+..+|+.||+.|||+..++  ++|    .||++|+.
T Consensus        38 ~~~~iL~~l~~~~~~~~~ela~~l~~~~--------------~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~  103 (142)
T 2bv6_A           38 PQFLVLTILWDESPVNVKKVVTELALDT--------------GTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSET  103 (142)
T ss_dssp             HHHHHHHHHHHSSEEEHHHHHHHTTCCT--------------TTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCh--------------hhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHH
Confidence            3456888888889999999999887532              357789999999999986542  344    57999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       104 ~~~~~~~~  111 (142)
T 2bv6_A          104 IRPELSNA  111 (142)
T ss_dssp             HHHHHTTH
T ss_pred             HHHHHHHH
Confidence            99887543

>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=97.22  E-value=0.0013  Score=42.25  Aligned_cols=67  Identities=15%  Similarity=0.149  Sum_probs=52.2

Q ss_pred             HHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            5 VTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      -..|+..|+- .+++.+..|+...|-.              .+-+-.+++.||+.|||+..++  ++|    .||++|+.
T Consensus        37 ~~~iL~~l~~~~~~~~~~~la~~l~i~--------------~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~  102 (147)
T 2hr3_A           37 QLVVLGAIDRLGGDVTPSELAAAERMR--------------SSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRR  102 (147)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCC--------------hhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHH
Confidence            3568888888 8999999999987643              3678889999999999987642  344    59999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       103 ~~~~~~~~  110 (147)
T 2hr3_A          103 NLYGNRAK  110 (147)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887654

>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=97.21  E-value=0.00093  Score=43.38  Aligned_cols=68  Identities=18%  Similarity=0.270  Sum_probs=47.5

Q ss_pred             HHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCee----eCcchH
Q 034587            5 VTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~----lT~~G~   76 (90)
                      -..|+..|+-.  +++.+..|+...|-.+              +-+-.+++.||+.|||++.+  .++|.    ||++|+
T Consensus        43 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~--------------~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~  108 (148)
T 3jw4_A           43 QGRMIGYIYENQESGIIQKDLAQFFGRRG--------------ASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGA  108 (148)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHC--------------------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHH
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCCCh--------------hHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHH
Confidence            35688888887  8999999999776432              35668999999999998664  34553    999999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++.+...+
T Consensus       109 ~~~~~~~~~~  118 (148)
T 3jw4_A          109 ALVEEFNNIF  118 (148)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998876543

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

Probab=97.20  E-value=0.0012  Score=43.71  Aligned_cols=68  Identities=15%  Similarity=0.168  Sum_probs=54.1

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..||..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||++.+  +++|    .||++|+..
T Consensus        55 q~~vL~~l~~~~~~t~~eLa~~l~~~--------------~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~  120 (161)
T 3e6m_A           55 KLRLLSSLSAYGELTVGQLATLGVME--------------QSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKK  120 (161)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHH
Confidence            34688888888999999999987653              257778999999999998665  3344    599999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++++...+
T Consensus       121 ~~~~~~~~  128 (161)
T 3e6m_A          121 LAEISPLI  128 (161)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

>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=97.20  E-value=0.0018  Score=42.35  Aligned_cols=69  Identities=9%  Similarity=0.068  Sum_probs=54.3

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      ..-..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .++|    .||++|+
T Consensus        44 ~~~~~iL~~l~~~~~~t~~ela~~l~is--------------~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~  109 (154)
T 2eth_A           44 TTELYAFLYVALFGPKKMKEIAEFLSTT--------------KSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGK  109 (154)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHTTSC--------------HHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHH
Confidence            3445688889988999999999988642              356778999999999998643  3344    5899999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++.+...
T Consensus       110 ~~~~~~~~~  118 (154)
T 2eth_A          110 EIFGEILSN  118 (154)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887654

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

Probab=97.19  E-value=0.0016  Score=41.18  Aligned_cols=68  Identities=12%  Similarity=0.146  Sum_probs=53.0

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.+              +-+-.+|+.||+.|||+..+  .++|    .||++|+.
T Consensus        34 ~~~~iL~~l~~~~~~~~~ela~~l~~~~--------------~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~   99 (139)
T 3bja_A           34 VQFGVIQVLAKSGKVSMSKLIENMGCVP--------------SNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEE   99 (139)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHCSSCC--------------TTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCh--------------hHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHH
Confidence            3456788888889999999999886532              35677899999999998643  3343    59999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       100 ~~~~~~~~  107 (139)
T 3bja_A          100 TKKQVDVQ  107 (139)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887654

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

Probab=97.16  E-value=0.0025  Score=41.65  Aligned_cols=67  Identities=12%  Similarity=0.086  Sum_probs=51.2

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC----eeeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G----R~lT~~G~~~   78 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..+  .++    -.||++|+..
T Consensus        51 ~~~iL~~l~~~~~~t~~ela~~l~is--------------~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~  116 (162)
T 2fa5_A           51 EWRVITILALYPGSSASEVSDRTAMD--------------KVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQV  116 (162)
T ss_dssp             HHHHHHHHHHSTTCCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHH
Confidence            35688888888999999999988743              257888999999999998754  233    3599999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++.+...
T Consensus       117 ~~~~~~~  123 (162)
T 2fa5_A          117 YETVAPL  123 (162)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876554

>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=97.15  E-value=0.0022  Score=41.69  Aligned_cols=65  Identities=15%  Similarity=0.304  Sum_probs=48.9

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc----cCCCCe----eeCcchHh
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI----EPKGGR----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k----~~~~GR----~lT~~G~~   77 (90)
                      ..|+..| -.+++.+..|+...|-.+              +-+-.+++.||+.|||+.    +++++|    .||++|+.
T Consensus        41 ~~iL~~l-~~~~~t~~eLa~~l~~~~--------------~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~  105 (151)
T 3kp7_A           41 SHVLNML-SIEALTVGQITEKQGVNK--------------AAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKK  105 (151)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHHCSCS--------------SHHHHHHHHHHHTTSEEC-----------CCBEECHHHHH
T ss_pred             HHHHHHH-HcCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHH
Confidence            4577778 789999999999887543              467789999999999996    555555    59999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       106 ~~~~~~~~  113 (151)
T 3kp7_A          106 YIKERKAI  113 (151)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887554

>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=97.14  E-value=0.00095  Score=43.17  Aligned_cols=69  Identities=13%  Similarity=0.044  Sum_probs=52.8

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      --..|+..|+-.+++.+..|+...+-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+.
T Consensus        37 ~q~~vL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~  102 (140)
T 3hsr_A           37 TGYIVLMAIENDEKLNIKKLGERVFLD--------------SGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKA  102 (140)
T ss_dssp             HHHHHHHHSCTTCEEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHH
Confidence            345678888888999999999988653              367788999999999998665  3444    58999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+....
T Consensus       103 ~~~~~~~~~  111 (140)
T 3hsr_A          103 IKSPLAEIS  111 (140)
T ss_dssp             THHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876543

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

Probab=97.14  E-value=0.0014  Score=41.69  Aligned_cols=69  Identities=16%  Similarity=0.103  Sum_probs=54.3

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      ..-..|+..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..+  +++|    .||++|+
T Consensus        36 ~~~~~iL~~l~~~~~~t~~ela~~l~~s--------------~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~  101 (142)
T 2fbi_A           36 EQQWRVIRILRQQGEMESYQLANQACIL--------------RPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQ  101 (142)
T ss_dssp             HHHHHHHHHHHHHCSEEHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------HhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHH
Confidence            3445688888888999999999987643              357888999999999998654  3344    4999999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++++...
T Consensus       102 ~~~~~~~~~  110 (142)
T 2fbi_A          102 QCFVSMSGD  110 (142)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887654

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

Probab=97.12  E-value=0.0018  Score=40.98  Aligned_cols=69  Identities=12%  Similarity=0.181  Sum_probs=53.8

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      ..-..|+..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..+  .++|    .||++|+
T Consensus        38 ~~~~~iL~~l~~~~~~t~~ela~~l~~~--------------~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~  103 (140)
T 2nnn_A           38 PTQWAALVRLGETGPCPQNQLGRLTAMD--------------AATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGR  103 (140)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHTTCC--------------HHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHH
Confidence            3445688888888999999999987643              356788999999999998754  2233    5999999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++++...
T Consensus       104 ~~~~~~~~~  112 (140)
T 2nnn_A          104 AELEAGLAA  112 (140)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887554

>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=97.10  E-value=0.0021  Score=41.45  Aligned_cols=67  Identities=15%  Similarity=0.214  Sum_probs=53.4

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~~   78 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+..+|+.||+.|||+..++  ++|    .||++|+..
T Consensus        42 ~~~iL~~l~~~~~~t~~ela~~l~~~--------------~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~  107 (152)
T 3bj6_A           42 QRAILEGLSLTPGATAPQLGAALQMK--------------RQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAI  107 (152)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHH
Confidence            45678888888999999999988753              3578889999999999987542  333    589999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++.+...
T Consensus       108 ~~~~~~~  114 (152)
T 3bj6_A          108 ITAIRAD  114 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876544

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

Probab=97.10  E-value=0.0029  Score=40.74  Aligned_cols=68  Identities=13%  Similarity=0.141  Sum_probs=52.7

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CC----CeeeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KG----GRRITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~----GR~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .+    .=.||++|+.
T Consensus        41 ~~~~iL~~l~~~~~~t~~ela~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~  106 (148)
T 3nrv_A           41 TEWRIISVLSSASDCSVQKISDILGLD--------------KAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQE  106 (148)
T ss_dssp             HHHHHHHHHHHSSSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEC---------CCBEECHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHH
Confidence            345688889999999999999988743              357888999999999998664  22    3369999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       107 ~~~~~~~~  114 (148)
T 3nrv_A          107 LYEVASDF  114 (148)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99987654

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

Probab=97.09  E-value=0.0021  Score=42.19  Aligned_cols=68  Identities=16%  Similarity=0.169  Sum_probs=53.7

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+..+|+.||+.|||+..+  +++|    .||++|+.
T Consensus        53 ~~~~iL~~l~~~~~~t~~ela~~l~is--------------~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~  118 (162)
T 3cjn_A           53 AKMRALAILSAKDGLPIGTLGIFAVVE--------------QSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRA  118 (162)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHH
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence            345688888888999999999988643              357888999999999998754  2333    59999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       119 ~~~~~~~~  126 (162)
T 3cjn_A          119 VYDRLWPH  126 (162)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887554

>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=97.03  E-value=0.0028  Score=40.54  Aligned_cols=67  Identities=9%  Similarity=0.085  Sum_probs=53.3

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  .++|    .||++|+..
T Consensus        31 ~~~iL~~l~~~~~~t~~~la~~l~~s--------------~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~   96 (144)
T 1lj9_A           31 QYLYLVRVCENPGIIQEKIAELIKVD--------------RTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNV   96 (144)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHH
T ss_pred             HHHHHHHHHHCcCcCHHHHHHHHCCC--------------HhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHH
Confidence            35678888888999999999988643              357888999999999998654  3343    599999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++.+...
T Consensus        97 ~~~~~~~  103 (144)
T 1lj9_A           97 YPIIVRE  103 (144)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9877554

>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=97.01  E-value=0.003  Score=42.43  Aligned_cols=68  Identities=13%  Similarity=0.111  Sum_probs=51.3

Q ss_pred             HHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            5 VTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      -..||..|+- .+++.+..|+...|-.              .+-+-.+++.||+.|||++.+  +++|    .||++|+.
T Consensus        55 q~~vL~~L~~~~~~~t~~eLa~~l~i~--------------~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~  120 (166)
T 3deu_A           55 HWVTLHNIHQLPPDQSQIQLAKAIGIE--------------QPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEP  120 (166)
T ss_dssp             HHHHHHHHHHSCSSEEHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHH
Confidence            3567888887 6789999999988753              256778999999999999765  3444    49999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus       121 ~~~~~~~~~  129 (166)
T 3deu_A          121 LIAEMEEVI  129 (166)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876543

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

Probab=97.00  E-value=0.0047  Score=39.33  Aligned_cols=67  Identities=10%  Similarity=0.094  Sum_probs=51.8

Q ss_pred             HHHHHHHH-hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            5 VTSMARKI-YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~Rkl-Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      -..|+..| +-.+++.+..|+...|-.              .+-+..+++.||+.|||+..++  ++|    .||++|+.
T Consensus        39 ~~~iL~~l~~~~~~~t~~~la~~l~~s--------------~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~  104 (146)
T 2fbh_A           39 RWLVLLHLARHRDSPTQRELAQSVGVE--------------GPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADV  104 (146)
T ss_dssp             HHHHHHHHHHCSSCCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCC--------------hhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHH
Confidence            34678888 557889999999988643              3578889999999999987642  333    68999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       105 ~~~~~~~~  112 (146)
T 2fbh_A          105 LIADIEAI  112 (146)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887544

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

Probab=97.00  E-value=0.0028  Score=38.51  Aligned_cols=67  Identities=15%  Similarity=0.197  Sum_probs=51.4

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVA   83 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~iA   83 (90)
                      .|+..|.-.+++.+..|+...|-              |.+-+...|+.||+.|||+..+++.   ..||++|...+-...
T Consensus        28 ~il~~l~~~~~~s~~ela~~l~i--------------s~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l   93 (99)
T 3cuo_A           28 LILCMLSGSPGTSAGELTRITGL--------------SASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATL   93 (99)
T ss_dssp             HHHHHHTTCCSEEHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHH
Confidence            46666666668999999998874              3468999999999999999876432   268999977776665


Q ss_pred             HHhh
Q 034587           84 GRIV   87 (90)
Q Consensus        84 ~~v~   87 (90)
                      .+++
T Consensus        94 ~~~~   97 (99)
T 3cuo_A           94 KNVY   97 (99)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            5543

>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=96.98  E-value=0.0026  Score=40.63  Aligned_cols=68  Identities=19%  Similarity=0.319  Sum_probs=53.8

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+.
T Consensus        34 ~~~~iL~~l~~~~~~~~~~la~~l~~--------------s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~   99 (145)
T 2a61_A           34 AQFDILQKIYFEGPKRPGELSVLLGV--------------AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEE   99 (145)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCC--------------CchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHH
Confidence            34568888888899999999998864              2357888999999999998754  2333    58999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       100 ~~~~~~~~  107 (145)
T 2a61_A          100 VIEKVIER  107 (145)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876544

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

Probab=96.97  E-value=0.004  Score=40.51  Aligned_cols=67  Identities=10%  Similarity=0.128  Sum_probs=50.9

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..|+..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..+  +++|    .||++|+..
T Consensus        45 ~~~iL~~l~~~~~~t~~ela~~l~i~--------------~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~  110 (155)
T 3cdh_A           45 EWRVLACLVDNDAMMITRLAKLSLME--------------QSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRAL  110 (155)
T ss_dssp             HHHHHHHHSSCSCBCHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHH
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHH
Confidence            34678888888899999999987643              256778999999999999754  2333    599999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++.+...
T Consensus       111 ~~~~~~~  117 (155)
T 3cdh_A          111 AESLVAS  117 (155)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887544

>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=96.93  E-value=0.0022  Score=38.92  Aligned_cols=66  Identities=8%  Similarity=0.103  Sum_probs=50.6

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC----eeeCcchHhhHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSSGQRDLD   80 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G----R~lT~~G~~~lD   80 (90)
                      .|+..|+-.++..+..|+...|-              +.+-+-..|+.||+.|||+...  ..+    -.||++|...+.
T Consensus        20 ~iL~~L~~~~~~~~~ela~~l~i--------------s~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~   85 (100)
T 1ub9_A           20 GIMIFLLPRRKAPFSQIQKVLDL--------------TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAK   85 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHhcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHH
Confidence            46777777789999999998864              3367888999999999998533  223    358999998888


Q ss_pred             HHHHHh
Q 034587           81 QVAGRI   86 (90)
Q Consensus        81 ~iA~~v   86 (90)
                      .+...+
T Consensus        86 ~~~~~~   91 (100)
T 1ub9_A           86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776654

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

Probab=96.93  E-value=0.0036  Score=40.09  Aligned_cols=63  Identities=13%  Similarity=0.135  Sum_probs=49.2

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..|+..|+-.+ +.+..|+...|-.              .+-+..+|+.||+.|||+..+  .++|    .||++|+..+
T Consensus        41 ~~iL~~l~~~~-~t~~eLa~~l~~s--------------~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~  105 (146)
T 3tgn_A           41 EHILMLLSEES-LTNSELARRLNVS--------------QAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIA  105 (146)
T ss_dssp             HHHHHHHTTCC-CCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHH
T ss_pred             HHHHHHHHhCC-CCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHH
Confidence            56888888777 9999999998753              367899999999999998665  2444    4999999999


Q ss_pred             HHHH
Q 034587           80 DQVA   83 (90)
Q Consensus        80 D~iA   83 (90)
                      +.+.
T Consensus       106 ~~~~  109 (146)
T 3tgn_A          106 EEHH  109 (146)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8886

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=96.92  E-value=0.0043  Score=47.66  Aligned_cols=70  Identities=14%  Similarity=0.115  Sum_probs=53.0

Q ss_pred             hhhHHHHHH-----HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-CeeeCcch
Q 034587            2 SELVTSMAR-----KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-GRRITSSG   75 (90)
Q Consensus         2 ~~r~ASi~R-----klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-GR~lT~~G   75 (90)
                      +.|--.|++     .|--.+|||+..|++.|+=            .-|..-||+-|..||++|++++.-.+ ||..|.+|
T Consensus        16 ~eR~~~IL~~i~~~yl~~~~pV~s~~La~~~~l------------~VS~aTIRrDL~~LE~~GlL~r~HgsAgript~~g   83 (338)
T 1stz_A           16 NDRQRKVLYCIVREYIENKKPVSSQRVLEVSNI------------EFSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDKG   83 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCC------------CSCHHHHHHHHHHHHHTTSEECCSSCSCBEECHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCccHHHHHHHhCC------------CCCHHHHHHHHHHHHHCCCEEEccCcceecCCccc
Confidence            467777887     4444699999999998842            12558999999999999999976643 68888888


Q ss_pred             -HhhHHHHH
Q 034587           76 -QRDLDQVA   83 (90)
Q Consensus        76 -~~~lD~iA   83 (90)
                       +.+.|.+.
T Consensus        84 ~r~yvd~l~   92 (338)
T 1stz_A           84 LRFYYEEML   92 (338)
T ss_dssp             HHHHHHHHH
T ss_pred             chhhhhhhh
Confidence             44566554

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=96.92  E-value=0.0025  Score=45.43  Aligned_cols=63  Identities=11%  Similarity=0.178  Sum_probs=52.6

Q ss_pred             HHHHHhh----cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHH
Q 034587            8 MARKIYL----RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA   83 (90)
Q Consensus         8 i~RklYl----~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA   83 (90)
                      .|.-||.    .+++.+..|+...|-.+              +-+..+|+.||+.|||+..+.++=.||++|+....++.
T Consensus         7 YL~~I~~l~~~~~~~~~~~lA~~l~vs~--------------~tvs~~l~~Le~~GlV~r~~~~~i~LT~~G~~~~~~~~   72 (214)
T 3hrs_A            7 YLKCLYELGTRHNKITNKEIAQLMQVSP--------------PAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVSDLY   72 (214)
T ss_dssp             HHHHHHHTTSSCSCCCHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHCCCh--------------hHHHHHHHHHHHCCCEEEecCCCeEECHHHHHHHHHHH
Confidence            3556665    46899999999887643              67889999999999999988778899999999988876


Q ss_pred             H
Q 034587           84 G   84 (90)
Q Consensus        84 ~   84 (90)
                      .
T Consensus        73 ~   73 (214)
T 3hrs_A           73 R   73 (214)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=96.92  E-value=0.0023  Score=41.44  Aligned_cols=68  Identities=13%  Similarity=0.144  Sum_probs=53.3

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-.              .+-+..+++.||+.|||+..++  ++|    .||++|+.
T Consensus        38 ~~~~iL~~l~~~~~~t~~ela~~l~~s--------------~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~  103 (155)
T 1s3j_A           38 AQLFVLASLKKHGSLKVSEIAERMEVK--------------PSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDI  103 (155)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHH
Confidence            345678888888999999999988642              3678889999999999986542  333    68999999


Q ss_pred             hHHHHHHH
Q 034587           78 DLDQVAGR   85 (90)
Q Consensus        78 ~lD~iA~~   85 (90)
                      .++.+...
T Consensus       104 ~~~~~~~~  111 (155)
T 1s3j_A          104 KFEEVLAG  111 (155)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99886554

>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=96.91  E-value=0.0023  Score=40.78  Aligned_cols=64  Identities=8%  Similarity=0.061  Sum_probs=49.2

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CC----eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~G----R~lT~~G~~~l   79 (90)
                      ..|+..|+ .++..+..|.+...             .-|.+.+-..|+.||+.|||+....  ++    -.||++|+..+
T Consensus        17 ~~IL~~L~-~~~~~~~eLa~~l~-------------~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l~   82 (107)
T 2hzt_A           17 XVILXHLT-HGKKRTSELKRLMP-------------NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   82 (107)
T ss_dssp             HHHHHHHT-TCCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHHH
Confidence            35777887 89999999998761             2345788999999999999986542  23    48999999877


Q ss_pred             HHHH
Q 034587           80 DQVA   83 (90)
Q Consensus        80 D~iA   83 (90)
                      +.+.
T Consensus        83 ~~~~   86 (107)
T 2hzt_A           83 GILD   86 (107)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

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

Probab=96.90  E-value=0.0031  Score=39.48  Aligned_cols=64  Identities=16%  Similarity=0.127  Sum_probs=50.7

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCcchHhhHHH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ   81 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~lD~   81 (90)
                      ..|+..| -.+|+.+..|+...|-              |.+-+...|+.||+.|||+..++ ||    .||++|...+..
T Consensus        24 ~~IL~~L-~~~~~~~~ela~~l~i--------------s~~tv~~~l~~L~~~gli~~~~~-gr~~~y~l~~~~~~~~~~   87 (114)
T 2oqg_A           24 WEILTEL-GRADQSASSLATRLPV--------------SRQAIAKHLNALQACGLVESVKV-GREIRYRALGAELNKTAR   87 (114)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHSSS--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECSHHHHHHHH
T ss_pred             HHHHHHH-HcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeEEec-CCEEEEEechHHHHHHHH
Confidence            3577777 6799999999998863              34689999999999999987764 54    799999877765


Q ss_pred             HHHH
Q 034587           82 VAGR   85 (90)
Q Consensus        82 iA~~   85 (90)
                      ....
T Consensus        88 ~~~~   91 (114)
T 2oqg_A           88 TLER   91 (114)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5444

>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=96.88  E-value=0.0047  Score=40.06  Aligned_cols=68  Identities=15%  Similarity=0.149  Sum_probs=49.4

Q ss_pred             HHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            5 VTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      -..||..|+-.+ ++.+..|+...|-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+.
T Consensus        41 q~~vL~~l~~~~~~~t~~eLa~~l~i~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~  106 (150)
T 3fm5_A           41 SYSVLVLACEQAEGVNQRGVAATMGLD--------------PSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRR  106 (150)
T ss_dssp             HHHHHHHHHHSTTCCCSHHHHHHHTCC--------------HHHHHHHHHHHHTTTSEEC-----------CEECHHHHH
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHCCC--------------HhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHH
Confidence            456777777654 78999999988743              356778899999999998755  3343    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus       107 ~~~~~~~~~  115 (150)
T 3fm5_A          107 LRDDAKARV  115 (150)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876553

>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=96.85  E-value=0.0023  Score=40.62  Aligned_cols=63  Identities=19%  Similarity=0.189  Sum_probs=49.0

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CC----eeeCcchHhhHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRDLD   80 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~G----R~lT~~G~~~lD   80 (90)
                      .|+..|+ .++..+..|++..++             -+.+.+-..|+.||+.|||+..+.  ++    -.||++|+..++
T Consensus        29 ~IL~~L~-~~~~~~~eL~~~l~g-------------is~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~   94 (107)
T 2fsw_A           29 LIIFQIN-RRIIRYGELKRAIPG-------------ISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVLP   94 (107)
T ss_dssp             HHHHHHT-TSCEEHHHHHHHSTT-------------CCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTHH
T ss_pred             HHHHHHH-hCCcCHHHHHHHccc-------------CCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECccHHHHHH
Confidence            4777777 889999999987742             244788999999999999986542  23    379999998877


Q ss_pred             HHH
Q 034587           81 QVA   83 (90)
Q Consensus        81 ~iA   83 (90)
                      .+.
T Consensus        95 ~l~   97 (107)
T 2fsw_A           95 IID   97 (107)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=96.82  E-value=0.002  Score=41.31  Aligned_cols=63  Identities=14%  Similarity=0.221  Sum_probs=48.8

Q ss_pred             HHHHHHHhhcCCCchhHHHHHh-cCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CC----eeeCcchHhh
Q 034587            6 TSMARKIYLRQGLGVGSFRRIY-GGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRD   78 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~Y-Gg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~G----R~lT~~G~~~   78 (90)
                      ..|+..|+ .++..+..|+... |              -+.+.+-..|+.||+.|||+..+.  ++    -.||++|+..
T Consensus        25 ~~IL~~L~-~~~~~~~eLa~~l~~--------------is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~   89 (112)
T 1z7u_A           25 LSLMDELF-QGTKRNGELMRALDG--------------ITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYAL   89 (112)
T ss_dssp             HHHHHHHH-HSCBCHHHHHHHSTT--------------CCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHhcc--------------CCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHH
Confidence            35777777 6899999999977 3              244788899999999999986552  23    3789999987


Q ss_pred             HHHHH
Q 034587           79 LDQVA   83 (90)
Q Consensus        79 lD~iA   83 (90)
                      ++.+.
T Consensus        90 ~~~~~   94 (112)
T 1z7u_A           90 YDALS   94 (112)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76653

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

Probab=96.73  E-value=0.0042  Score=41.23  Aligned_cols=68  Identities=10%  Similarity=0.139  Sum_probs=51.5

Q ss_pred             HHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            5 VTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      -..||..|+-.  +++.+..|+...|-.+              +-+-.+++.||+.|||++.+  .++|    .||++|+
T Consensus        48 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~--------------~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~  113 (168)
T 3u2r_A           48 QYNTLRLLRSVHPEGMATLQIADRLISRA--------------PDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGL  113 (168)
T ss_dssp             HHHHHHHHHHHTTSCEEHHHHHHHC---C--------------THHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHHCCCh--------------hhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHH
Confidence            35688888885  5899999999886532              46778999999999998654  3344    4999999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++.+...+
T Consensus       114 ~~~~~~~~~~  123 (168)
T 3u2r_A          114 KLLKDLEEPV  123 (168)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998876543

>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=96.69  E-value=0.0046  Score=45.27  Aligned_cols=62  Identities=21%  Similarity=0.330  Sum_probs=49.7

Q ss_pred             HHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHH
Q 034587            8 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG   84 (90)
Q Consensus         8 i~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~   84 (90)
                      .+--||. .+|+|...|+..-|-+              -..+|..++-|++.|||+..+ +|=.||++|++...++-.
T Consensus        20 YLk~I~~L~~~V~~~~LA~~LgvS--------------~~SV~~~lkkL~e~GLV~~~~-~Gv~LTe~G~~~A~~i~~   82 (200)
T 2p8t_A           20 VLAVIFLLKEPLGRKQISERLELG--------------EGSVRTLLRKLSHLDIIRSKQ-RGHFLTLKGKEIRDKLLS   82 (200)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCccHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEEEeC-CCeEECHHHHHHHHHHHH
Confidence            3444554 6899999999998843              368999999999999999888 899999999998777654

>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=96.67  E-value=0.0021  Score=40.73  Aligned_cols=62  Identities=8%  Similarity=0.092  Sum_probs=50.7

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchh-HHHHHHHHHHhCCcccccCCCCe---eeCcchHhhH
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGA-IARHILQQLQNMNIIDIEPKGGR---RITSSGQRDL   79 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~-iiR~~LqqLE~~glV~k~~~~GR---~lT~~G~~~l   79 (90)
                      .-..|+.-|.-+||..+..|++..|-.+              . -+|..|+.||+.|+|++.. .||   .||++|+..|
T Consensus        12 ~~~~IL~~Lk~~g~~ta~eiA~~Lgit~--------------~~aVr~hL~~Le~eGlV~~~~-~gRP~w~LT~~g~~~~   76 (79)
T 1xmk_A           12 IKEKICDYLFNVSDSSALNLAKNIGLTK--------------ARDINAVLIDMERQGDVYRQG-TTPPIWHLTDKKRERM   76 (79)
T ss_dssp             HHHHHHHHHHHTCCEEHHHHHHHHCGGG--------------HHHHHHHHHHHHHTTSEEEEC-SSSCEEEECHHHHTTT
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHcCCCc--------------HHHHHHHHHHHHHCCCEEecC-CCCCCeEeCHhHHhHh
Confidence            3456788888899999999999998643              4 7999999999999998663 466   7899998765


Q ss_pred             H
Q 034587           80 D   80 (90)
Q Consensus        80 D   80 (90)
                      +
T Consensus        77 ~   77 (79)
T 1xmk_A           77 Q   77 (79)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=96.65  E-value=0.0051  Score=41.46  Aligned_cols=62  Identities=18%  Similarity=0.260  Sum_probs=49.1

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-----CeeeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----GRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-----GR~lT~~G~~~lD~   81 (90)
                      .|++.++ .|+..+..|.+..|-              |.+.+-..|+.||+.|||++.+..     .-.||++|+..+..
T Consensus        28 ~IL~~L~-~g~~~~~eLa~~lgi--------------s~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l~~~   92 (146)
T 2f2e_A           28 LIVRDAF-EGLTRFGEFQKSLGL--------------AKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALFPL   92 (146)
T ss_dssp             HHHHHHH-TTCCSHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHHHHH
Confidence            4778886 789999999997754              447899999999999999976532     34799999987665


Q ss_pred             HH
Q 034587           82 VA   83 (90)
Q Consensus        82 iA   83 (90)
                      +.
T Consensus        93 l~   94 (146)
T 2f2e_A           93 LV   94 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=96.64  E-value=0.0027  Score=40.27  Aligned_cols=62  Identities=15%  Similarity=0.047  Sum_probs=49.6

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+.
T Consensus        32 ~~~~iL~~l~~~~~~~~~ela~~l~i--------------s~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~   97 (142)
T 3bdd_A           32 TRYSILQTLLKDAPLHQLALQERLQI--------------DRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQARE   97 (142)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence            34568888888899999999998864              33678889999999999986542  333    58999999


Q ss_pred             hH
Q 034587           78 DL   79 (90)
Q Consensus        78 ~l   79 (90)
                      .+
T Consensus        98 ~~   99 (142)
T 3bdd_A           98 AL   99 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            98

>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=96.62  E-value=0.00031  Score=53.23  Aligned_cols=65  Identities=22%  Similarity=0.319  Sum_probs=0.0

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      .|-..|+..||-.+++++..|+..+|-.+              .-||..|+.||+.|||+... .|=.||++|+..++.+
T Consensus        20 ~r~~~iL~~l~~~~~~t~~eLa~~l~vs~--------------~Tv~r~l~~Le~~Glv~~~~-~gi~LT~~G~~~~~~~   84 (345)
T 2o0m_A           20 QERFQILRNIYWMQPIGRRSLSETMGITE--------------RVLRTETDVLKQLNLIEPSK-SGMTLTERGLEVYQGL   84 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEEe-cceEEcHHHHHHHHHH
Confidence            45568999999999999999999998743              57999999999999998554 4789999999766543

>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=96.62  E-value=0.0085  Score=41.04  Aligned_cols=68  Identities=15%  Similarity=0.205  Sum_probs=52.8

Q ss_pred             HHHHHHHHhh--cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            5 VTSMARKIYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl--~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      -..||..|+-  .+++.+..|+...|-.              .+-+-.+++.||+.|||+..+  ..+|    .||++|+
T Consensus        43 q~~vL~~L~~~~~~~~t~~eLa~~l~is--------------~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~  108 (189)
T 3nqo_A           43 QYMTILSILHLPEEETTLNNIARKMGTS--------------KQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGK  108 (189)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHH
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHH
Confidence            3467788887  5689999999988753              256778999999999998654  3444    5899999


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++.+....
T Consensus       109 ~~~~~~~~~~  118 (189)
T 3nqo_A          109 KVMVTCSRTG  118 (189)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999876543

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

Probab=96.60  E-value=0.0055  Score=40.50  Aligned_cols=65  Identities=12%  Similarity=0.182  Sum_probs=46.8

Q ss_pred             HHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            7 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      .+|..||..  +++.++.|+...+-.+              +-+=.++..||+.|||+..+  +.+|    .||++|+..
T Consensus        39 ~vL~~L~~~~~~~~t~~eLa~~l~~~~--------------~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~  104 (147)
T 4b8x_A           39 EALVLLTFSKSGELPMSKIGERLMVHP--------------TSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREV  104 (147)
T ss_dssp             HHHHHHHTSGGGEEEHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHH
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHH
Confidence            466677764  5688888888776543              45667899999999998655  3444    389999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++++...
T Consensus       105 ~~~~~~~  111 (147)
T 4b8x_A          105 VEAATRD  111 (147)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9987654

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

Probab=96.53  E-value=0.0086  Score=38.41  Aligned_cols=66  Identities=12%  Similarity=0.099  Sum_probs=51.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~~l   79 (90)
                      ..|+..|+-.++ .+..|+...|-.              .+-+-.+++.||+.|||++.++  ++|    .||++|+..+
T Consensus        40 ~~iL~~l~~~~~-~~~~la~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~  104 (144)
T 3f3x_A           40 FSILKATSEEPR-SMVYLANRYFVT--------------QSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVL  104 (144)
T ss_dssp             HHHHHHHHHSCE-EHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHCCC-CHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHH
Confidence            467888888888 999999987653              2567789999999999986653  333    5999999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +.+....
T Consensus       105 ~~~~~~~  111 (144)
T 3f3x_A          105 LEANEVL  111 (144)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876543

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

Probab=96.53  E-value=0.0035  Score=40.68  Aligned_cols=66  Identities=12%  Similarity=0.091  Sum_probs=49.9

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-              +.+-+..+|+.||+.|||+..++  ++|    .||++|+.
T Consensus        48 ~~~~iL~~l~~~~~~t~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~  113 (153)
T 2pex_A           48 PQYLVMLVLWETDERSVSEIGERLYL--------------DSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRA  113 (153)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHhCC--------------CcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHH
Confidence            34567888888899999999998874              23578889999999999987542  333    58999998


Q ss_pred             hHHHHH
Q 034587           78 DLDQVA   83 (90)
Q Consensus        78 ~lD~iA   83 (90)
                      .++.+.
T Consensus       114 ~~~~~~  119 (153)
T 2pex_A          114 LRSKAG  119 (153)
T ss_dssp             GGGGST
T ss_pred             HHHHHH
Confidence            877643

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

Probab=96.51  E-value=0.0068  Score=39.44  Aligned_cols=68  Identities=12%  Similarity=0.168  Sum_probs=49.8

Q ss_pred             HHHHHHHHh-hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            5 VTSMARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~RklY-l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      -..|+..|| -.+++.+..|+...|-.+              +-+-.+++.||+.|||++.+  .++|    .||++|+.
T Consensus        49 ~~~iL~~L~~~~~~~~~~ela~~l~i~~--------------~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~  114 (160)
T 3boq_A           49 KFDAMAQLARNPDGLSMGKLSGALKVTN--------------GNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLT  114 (160)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHCSSCC--------------SCHHHHHHHHHHHTSEEEC--------CEEEECHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCh--------------hhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHH
Confidence            346788885 468999999999876533              34667899999999998754  2333    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++.+...+
T Consensus       115 ~~~~~~~~~  123 (160)
T 3boq_A          115 TFKQASEAH  123 (160)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998875543

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=96.50  E-value=0.0077  Score=40.77  Aligned_cols=64  Identities=17%  Similarity=0.123  Sum_probs=49.7

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..|++.|+ .|+...+.|++.-.+             -|.+.+-..|..||+.|||+...  ...|    .||++|++.+
T Consensus        29 l~IL~~L~-~g~~rf~eL~~~l~g-------------Is~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~   94 (131)
T 4a5n_A           29 GILFYHMI-DGKKRFNEFRRICPS-------------ITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLE   94 (131)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHCTT-------------SCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhcc-------------cCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHH
Confidence            35778887 889999999987622             34579999999999999998664  2222    6999999988


Q ss_pred             HHHH
Q 034587           80 DQVA   83 (90)
Q Consensus        80 D~iA   83 (90)
                      ..+.
T Consensus        95 ~~l~   98 (131)
T 4a5n_A           95 PIVL   98 (131)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=96.48  E-value=0.0043  Score=38.45  Aligned_cols=54  Identities=15%  Similarity=0.065  Sum_probs=45.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      .|+..|  .+++.+..|+..+|-              |.+-++..|+.||+.|+|+... +...||+.|+.
T Consensus        35 ~Il~~L--~~~~~~~eLa~~l~i--------------s~~tv~~~L~~L~~~Glv~~~~-g~y~l~~~g~~   88 (96)
T 1y0u_A           35 KILRML--DKGRSEEEIMQTLSL--------------SKKQLDYHLKVLEAGFCIERVG-ERWVVTDAGKI   88 (96)
T ss_dssp             HHHHHH--HTTCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECTTTCC
T ss_pred             HHHHHH--cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEC-CEEEECCCchH
Confidence            467777  899999999998865              3468999999999999999877 66789999864

>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=96.47  E-value=0.0057  Score=42.96  Aligned_cols=67  Identities=10%  Similarity=0.121  Sum_probs=52.3

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~~   78 (90)
                      -..||..|+-.+++.+..|+...|-.              .+-+-.+|+.||+.|||+..++  ++|    .||++|+..
T Consensus        50 q~~iL~~L~~~~~~t~~eLa~~l~i~--------------~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~  115 (207)
T 2fxa_A           50 EHHILWIAYQLNGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEV  115 (207)
T ss_dssp             HHHHHHHHHHHTSEEHHHHHHHTTCC--------------HHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHH
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHH
Confidence            45688888888999999999988653              3567779999999999987553  344    599999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++.+...
T Consensus       116 ~~~~~~~  122 (207)
T 2fxa_A          116 FWSLLEE  122 (207)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9987654

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=96.46  E-value=0.0033  Score=40.39  Aligned_cols=68  Identities=13%  Similarity=0.118  Sum_probs=46.3

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe-----eeCcchHhhH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR-----RITSSGQRDL   79 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR-----~lT~~G~~~l   79 (90)
                      .||.-|.- +|.--..+.+....          +..-+.+.+-.+|+.||+.|||+...  .+||     .||++|+..+
T Consensus        13 ~IL~~L~~-~~~~gyel~~~l~~----------~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l   81 (108)
T 3l7w_A           13 LILAIVSK-HDSYGYDISQTIKL----------IASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHL   81 (108)
T ss_dssp             HHHHHHHH-SCEEHHHHHHHHTT----------TCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHc-CCCcHHHHHHHHHH----------HhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHH
Confidence            35555553 55544455555443          12356678999999999999998654  2454     4999999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      ++....
T Consensus        82 ~~~~~~   87 (108)
T 3l7w_A           82 VYLTKE   87 (108)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=96.44  E-value=0.0022  Score=41.16  Aligned_cols=66  Identities=11%  Similarity=0.087  Sum_probs=51.1

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHh
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~   77 (90)
                      .-..|+..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+.
T Consensus        41 ~~~~iL~~l~~~~~~~~~~la~~l~~--------------~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~  106 (147)
T 1z91_A           41 PQYLALLLLWEHETLTVKKMGEQLYL--------------DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGAL  106 (147)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHTTTC--------------CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHS
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCC--------------CcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHH
Confidence            34567888888889999999997753              23678889999999999987653  343    58999999


Q ss_pred             hHHHHH
Q 034587           78 DLDQVA   83 (90)
Q Consensus        78 ~lD~iA   83 (90)
                      .++.+.
T Consensus       107 ~~~~~~  112 (147)
T 1z91_A          107 LKEKAV  112 (147)
T ss_dssp             GGGGTT
T ss_pred             HHHHHH
Confidence            887653

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=96.43  E-value=0.0064  Score=39.22  Aligned_cols=62  Identities=11%  Similarity=0.124  Sum_probs=49.4

Q ss_pred             HHHHHHhhcCCCc--hhHHHHHh-cCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLG--VGSFRRIY-GGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vG--V~~Lr~~Y-Gg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~lD~   81 (90)
                      .|++.++ .|+..  ++.|++.. |-              |.+.+-..|+.||+.|||++..  ..-..||++|++.++.
T Consensus        31 ~IL~~L~-~g~~~~~~~eL~~~l~gi--------------s~~~ls~~L~~Le~~GlV~r~~~r~~~y~LT~~G~~l~~~   95 (111)
T 3df8_A           31 LIISVLG-NGSTRQNFNDIRSSIPGI--------------SSTILSRRIKDLIDSGLVERRSGQITTYALTEKGMNVRNS   95 (111)
T ss_dssp             HHHHHHT-SSSSCBCHHHHHHTSTTC--------------CHHHHHHHHHHHHHTTSEEEEESSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHh-cCCCCCCHHHHHHHccCC--------------CHHHHHHHHHHHHHCCCEEEeecCcEEEEECccHHHHHHH
Confidence            4777777 88888  99999866 33              4578999999999999999764  2345899999988776


Q ss_pred             HH
Q 034587           82 VA   83 (90)
Q Consensus        82 iA   83 (90)
                      +.
T Consensus        96 l~   97 (111)
T 3df8_A           96 LM   97 (111)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=96.39  E-value=0.014  Score=40.30  Aligned_cols=77  Identities=16%  Similarity=0.128  Sum_probs=55.9

Q ss_pred             ChhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---C-----CeeeC
Q 034587            1 MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---G-----GRRIT   72 (90)
Q Consensus         1 ~~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~-----GR~lT   72 (90)
                      ||.+-+ ||.-|. .+|.-...|.+.+...      -.++...|-+.|-..|+.||+.|||+....   +     =..||
T Consensus         1 M~l~~~-iL~lL~-~~~~~gyel~~~l~~~------~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT   72 (179)
T 1yg2_A            1 MSLPHV-ILTVLS-TRDATGYDITKEFSAS------IGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSIT   72 (179)
T ss_dssp             -CHHHH-HHHHHH-HCCBCHHHHHHHHTTG------GGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEEC
T ss_pred             CchHHH-HHHHHh-cCCCCHHHHHHHHHHH------hCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeC
Confidence            454443 666665 4888888999988642      134566777899999999999999985431   2     25799


Q ss_pred             cchHhhHHHHHHH
Q 034587           73 SSGQRDLDQVAGR   85 (90)
Q Consensus        73 ~~G~~~lD~iA~~   85 (90)
                      ++|+..+.+...+
T Consensus        73 ~~G~~~l~~~~~~   85 (179)
T 1yg2_A           73 QAGRSALGEWFDQ   85 (179)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHhC
Confidence            9999999886554

>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=96.32  E-value=0.012  Score=41.98  Aligned_cols=68  Identities=13%  Similarity=0.185  Sum_probs=52.4

Q ss_pred             hhHHHHHHHHhhc--CCCch--hHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587            3 ELVTSMARKIYLR--QGLGV--GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD   78 (90)
Q Consensus         3 ~r~ASi~RklYl~--g~vGV--~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~   78 (90)
                      ...-.+++-||.-  .++.+  ..|+...|-.              .+-+..+|+.||+.|||+..++.+=.||++|+..
T Consensus         6 ~~~e~~L~~L~~l~~~~~~~~~~~La~~l~vs--------------~~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~   71 (230)
T 1fx7_A            6 DTTEMYLRTIYDLEEEGVTPLRARIAERLDQS--------------GPTVSQTVSRMERDGLLRVAGDRHLELTEKGRAL   71 (230)
T ss_dssp             SHHHHHHHHHHHHHHHTSCCCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEECTTSCEEECHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCCCCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEeCCccEEECHHHHHH
Confidence            3445567777752  35556  8898887653              3678899999999999998887778899999999


Q ss_pred             HHHHHH
Q 034587           79 LDQVAG   84 (90)
Q Consensus        79 lD~iA~   84 (90)
                      ++.+..
T Consensus        72 ~~~~~~   77 (230)
T 1fx7_A           72 AIAVMR   77 (230)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887643

>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=96.32  E-value=0.011  Score=38.75  Aligned_cols=68  Identities=15%  Similarity=0.124  Sum_probs=53.3

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHH-HhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRR-IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~-~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      +.--.|||+.|+-++++.+..|+. .-+-.+              +.+=.-++-||+.|||+.+. ++=.||++|+..+.
T Consensus        15 ~~~QfsiL~~L~~~~~~t~~~Lae~~l~~dr--------------stvsrnl~~L~r~GlVe~~~-~Dl~LT~~G~~~l~   79 (95)
T 1bja_A           15 NEKTATILITIAKKDFITAAEVREVHPDLGN--------------AVVNSNIGVLIKKGLVEKSG-DGLIITGEAQDIIS   79 (95)
T ss_dssp             CHHHHHHHHHHHHSTTBCHHHHHHTCTTSCH--------------HHHHHHHHHHHTTTSEEEET-TEEEECHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHhcccH--------------HHHHHHHHHHHHCCCeecCC-CCeeeCHhHHHHHH
Confidence            344579999999999999999998 544432              45556789999999999443 35679999999998


Q ss_pred             HHHH
Q 034587           81 QVAG   84 (90)
Q Consensus        81 ~iA~   84 (90)
                      ..+.
T Consensus        80 ~a~~   83 (95)
T 1bja_A           80 NAAT   83 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8754

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=96.31  E-value=0.004  Score=39.30  Aligned_cols=54  Identities=13%  Similarity=0.079  Sum_probs=43.0

Q ss_pred             HHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc----CCCCeeeC
Q 034587            5 VTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE----PKGGRRIT   72 (90)
Q Consensus         5 ~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~----~~~GR~lT   72 (90)
                      ...|+..++-.| ++.+..|+..+|-.              .+-+|.+|+.|++.|||+..    +.+|+.+.
T Consensus        20 ~l~Il~~l~~~g~~~s~~eLa~~lgvs--------------~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~   78 (110)
T 1q1h_A           20 VIDVLRILLDKGTEMTDEEIANQLNIK--------------VNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIY   78 (110)
T ss_dssp             THHHHHHHHHHCSCBCHHHHHHTTTSC--------------HHHHHHHHHHHHHHTSCEEEEEC---CCCCEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEecccCCCceEEE
Confidence            446788887777 89999999998874              37899999999999999987    66675554

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=96.24  E-value=0.012  Score=39.05  Aligned_cols=60  Identities=15%  Similarity=0.086  Sum_probs=48.5

Q ss_pred             HHHHHHhhcCCCchhHHHHHh--cCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIY--GGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~Y--Gg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      .||..|--+|+..+..|....  |-              |...++.-|+.||+.|||+....+=-.||++|+..+.
T Consensus        17 ~IL~~L~~~g~~s~~eLA~~l~~gi--------------S~~aVs~rL~~Le~~GLV~~~~rg~Y~LT~~G~~~l~   78 (111)
T 3b73_A           17 RILEIIHEEGNGSPKELEDRDEIRI--------------SKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLN   78 (111)
T ss_dssp             HHHHHHHHHSCBCHHHHHTSTTCCS--------------CHHHHHHHHHHHHHTTSEEECSTTCEEECHHHHHHHT
T ss_pred             HHHHHHHHcCCCCHHHHHHHHhcCC--------------CHHHHHHHHHHHHHCCCEEecCCceEEECchHHHHHH
Confidence            467666667999999999866  33              4478999999999999999875444799999998875

>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=96.19  E-value=0.005  Score=39.81  Aligned_cols=51  Identities=14%  Similarity=0.175  Sum_probs=43.6

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchHhhHHHHH
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQVA   83 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~lD~iA   83 (90)
                      .+..|+..||-              |..-+|.+|+.||+.|||+..+  ..|-.+++....++..+.
T Consensus        45 s~~eLa~~lgV--------------Sr~tVr~al~~L~~~GlI~~~~gG~~G~~V~~~~~~~~~~~~   97 (102)
T 2b0l_A           45 VASKIADRVGI--------------TRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELE   97 (102)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSSCEEEEECCHHHHHHHH
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEeCCCCcEEEecCCHHHHHHHH
Confidence            78888888876              3579999999999999999888  569999998888887764

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

Probab=96.18  E-value=0.038  Score=36.72  Aligned_cols=66  Identities=18%  Similarity=0.179  Sum_probs=46.0

Q ss_pred             HHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            7 SMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         7 Si~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      .||..|+-.+ +.....|+...|-.+              +-+=.+++.||+.|||++.+  +++|    .||++|+..+
T Consensus        35 ~vL~~L~~~~~~~~~~eLa~~l~~~~--------------~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~  100 (151)
T 4aik_A           35 VTLYNINRLPPEQSQIQLAKAIGIEQ--------------PSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPII  100 (151)
T ss_dssp             HHHHHHHHSCTTSCHHHHHHHHTSCH--------------HHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHH
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHCcCH--------------HHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHH
Confidence            4566666543 344567777666532              56677899999999998544  4455    4799999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +++...+
T Consensus       101 ~~~~~~~  107 (151)
T 4aik_A          101 EQVDGVI  107 (151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876543

>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=96.16  E-value=0.011  Score=37.28  Aligned_cols=69  Identities=9%  Similarity=0.065  Sum_probs=52.7

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCcchHhhH
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDL   79 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~l   79 (90)
                      .-..|+..|+-.+|+.+..|....+-.  .++        +.+-+-.+|+.||+.|||+..+++.|    .||++|+...
T Consensus        11 ~~~~vL~~l~~~~~~t~~ela~~l~~~--~~~--------s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~lT~~g~~~~   80 (123)
T 1okr_A           11 AEWEVMNIIWMKKYASANNIIEEIQMQ--KDW--------SPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKY   80 (123)
T ss_dssp             HHHHHHHHHHHHSSEEHHHHHHHHHHH--CCC--------CHHHHHHHHHHHHHHTSEEEEEETTEEEEEESSCHHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHhcc--CCC--------cHhhHHHHHHHHHHCCCeEEEecCCeEEEEEecCHHHHHH
Confidence            345688888888999999999988742  111        33678899999999999998775332    3799999877


Q ss_pred             HHH
Q 034587           80 DQV   82 (90)
Q Consensus        80 D~i   82 (90)
                      +.+
T Consensus        81 ~~~   83 (123)
T 1okr_A           81 KTS   83 (123)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            655

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=96.11  E-value=0.045  Score=33.90  Aligned_cols=61  Identities=15%  Similarity=0.217  Sum_probs=46.6

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQV   82 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~i   82 (90)
                      .|++.| ..+|..++.|....|-.+              +.+.+.|+.||+.|||+...++.   ..||+.+-..+=..
T Consensus        27 ~Il~~L-~~~~~~~~ela~~l~is~--------------~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~~   90 (102)
T 3pqk_A           27 MLVCTL-VEGEFSVGELEQQIGIGQ--------------PTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNA   90 (102)
T ss_dssp             HHHHHH-HTCCBCHHHHHHHHTCCT--------------THHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHHH
T ss_pred             HHHHHH-HhCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHHH
Confidence            577777 478999999999987633              57899999999999998776432   56888766554333

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

Probab=96.06  E-value=0.017  Score=38.31  Aligned_cols=64  Identities=16%  Similarity=0.244  Sum_probs=38.7

Q ss_pred             HHHHHHhhcC-----CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc-CCCCe----eeCcchH
Q 034587            7 SMARKIYLRQ-----GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-PKGGR----RITSSGQ   76 (90)
Q Consensus         7 Si~RklYl~g-----~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~-~~~GR----~lT~~G~   76 (90)
                      +||..|+..+     ++.+..|+...|-.+              +-+=.+++.||+.|||+.. +.++|    .||++|+
T Consensus        37 ~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~--------------~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~  102 (148)
T 4fx0_A           37 STLAVISLSEGSAGIDLTMSELAARIGVER--------------TTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGR  102 (148)
T ss_dssp             HHHHHHHC---------CHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSBC-----------CCBCHHHH
T ss_pred             HHHHHHHHhcCCCCCCcCHHHHHHHHCCCh--------------hhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHH
Confidence            3455555442     356666766655432              4566789999999999643 23344    5899999


Q ss_pred             hhHHHHHH
Q 034587           77 RDLDQVAG   84 (90)
Q Consensus        77 ~~lD~iA~   84 (90)
                      ..++++..
T Consensus       103 ~~~~~~~~  110 (148)
T 4fx0_A          103 AALQKAVP  110 (148)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99988754

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=96.06  E-value=0.0072  Score=40.27  Aligned_cols=63  Identities=21%  Similarity=0.208  Sum_probs=48.7

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CC----eeeCcchHhhHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRDLD   80 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~G----R~lT~~G~~~lD   80 (90)
                      .||..|+ .|+..+..|.+..++             -+.+.+-..|+.||+.|||+....  .+    -.||++|+..++
T Consensus        39 ~IL~~L~-~g~~~~~eLa~~l~g-------------is~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~  104 (131)
T 1yyv_A           39 LILVALR-DGTHRFSDLRRXMGG-------------VSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD  104 (131)
T ss_dssp             HHHHHGG-GCCEEHHHHHHHSTT-------------CCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHhcc-------------CCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHHH
Confidence            4777887 899999999997731             245789999999999999986542  23    369999998776


Q ss_pred             HHH
Q 034587           81 QVA   83 (90)
Q Consensus        81 ~iA   83 (90)
                      .+.
T Consensus       105 ~l~  107 (131)
T 1yyv_A          105 XVA  107 (131)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=96.02  E-value=0.025  Score=36.69  Aligned_cols=60  Identities=12%  Similarity=0.108  Sum_probs=46.7

Q ss_pred             hHHHHHHHHhhc---CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchHh
Q 034587            4 LVTSMARKIYLR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~---g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~   77 (90)
                      .|-.++..|..+   +++.+..|+..+|-.              -..++++|++|+++|||+...  .||..|+.....
T Consensus        10 ~al~iL~~la~~~~~~~~s~~ela~~~~i~--------------~~~v~~il~~L~~~Glv~~~~g~~ggy~L~~~~~~   74 (129)
T 2y75_A           10 YGLTIMIELAKKHGEGPTSLKSIAQTNNLS--------------EHYLEQLVSPLRNAGLVKSIRGAYGGYVLGSEPDA   74 (129)
T ss_dssp             HHHHHHHHHHHTTTSCCBCHHHHHHHTTSC--------------HHHHHHHHHHHHHTTSEEEC----CCEEESSCGGG
T ss_pred             HHHHHHHHHHhCCCCCcCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCceEecCCCCCceEeCCCHHH
Confidence            466777777764   579999999988764              379999999999999998764  478899876543

>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=96.00  E-value=0.01  Score=38.71  Aligned_cols=44  Identities=20%  Similarity=0.235  Sum_probs=33.7

Q ss_pred             cCchhHHHHHHHHHHhCCcccccC---CCCe-----eeCcchHhhHHHHHHH
Q 034587           42 KSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQRDLDQVAGR   85 (90)
Q Consensus        42 ~asg~iiR~~LqqLE~~glV~k~~---~~GR-----~lT~~G~~~lD~iA~~   85 (90)
                      .-+.+.+-.+|+.||+.|||+...   .+|+     .||++|++.++.....
T Consensus        44 ~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~   95 (116)
T 3f8b_A           44 ELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENMRLAFES   95 (116)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEECHHHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECHHHHHHHHHHHHH
Confidence            456688999999999999998652   2342     6999999999886554

>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=95.91  E-value=0.017  Score=41.19  Aligned_cols=68  Identities=12%  Similarity=0.173  Sum_probs=52.0

Q ss_pred             hhHHHHHHHHhhc--CCCch--hHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhh
Q 034587            3 ELVTSMARKIYLR--QGLGV--GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD   78 (90)
Q Consensus         3 ~r~ASi~RklYl~--g~vGV--~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~   78 (90)
                      ...-.+|+-||.-  .++.+  ..|+...|-.+              +-+..+|+.||+.|||+..++.+=.||++|+..
T Consensus         6 ~~~e~yL~~i~~l~~~~~~~~~~~la~~l~vs~--------------~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~   71 (226)
T 2qq9_A            6 ATTEMYLRTIYELEEEGVTPLRARIAERLEQSG--------------PTVSQTVARMERDGLVVVASDRSLQMTPTGRTL   71 (226)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCBHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEECTTSBEEECHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCCCccHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEeCCCCeEECHHHHHH
Confidence            3445678888873  23444  88888776532              567779999999999998887778999999998


Q ss_pred             HHHHHH
Q 034587           79 LDQVAG   84 (90)
Q Consensus        79 lD~iA~   84 (90)
                      ..++..
T Consensus        72 ~~~~~~   77 (226)
T 2qq9_A           72 ATAVMR   77 (226)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887764

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=95.79  E-value=0.039  Score=33.86  Aligned_cols=66  Identities=12%  Similarity=0.107  Sum_probs=49.7

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVA   83 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~iA   83 (90)
                      .|+..|. +++..+..|+...|-              |.+-+.+-|+.||+.|||+...++.   ..||+.+-..+-...
T Consensus        27 ~Il~~L~-~~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l   91 (98)
T 3jth_A           27 QILCMLH-NQELSVGELCAKLQL--------------SQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLL   91 (98)
T ss_dssp             HHHHHTT-TSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHH
T ss_pred             HHHHHHh-cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHH
Confidence            4666665 489999999998865              3468999999999999998776432   358888877666665


Q ss_pred             HHhh
Q 034587           84 GRIV   87 (90)
Q Consensus        84 ~~v~   87 (90)
                      .+++
T Consensus        92 ~~~~   95 (98)
T 3jth_A           92 HSLY   95 (98)
T ss_dssp             HHHC
T ss_pred             HHHh
Confidence            5554

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

Probab=95.70  E-value=0.021  Score=38.40  Aligned_cols=67  Identities=13%  Similarity=0.143  Sum_probs=49.0

Q ss_pred             HHHHHHHHhhcCC---CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcch
Q 034587            5 VTSMARKIYLRQG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSG   75 (90)
Q Consensus         5 ~ASi~RklYl~g~---vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G   75 (90)
                      -..||..|+-.++   +.+..|+...|-.+              +-+-.+|+.||+.|||+..++  ++|    .||++|
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is~--------------~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G  136 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAISG--------------PSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQG  136 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCS--------------GGGSSHHHHHHHHTSEECCC-------CCBEECHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHH
Confidence            3567888888775   89999999776432              344558999999999987642  333    699999


Q ss_pred             HhhHHHHHHH
Q 034587           76 QRDLDQVAGR   85 (90)
Q Consensus        76 ~~~lD~iA~~   85 (90)
                      +..++++...
T Consensus       137 ~~~~~~~~~~  146 (181)
T 2fbk_A          137 RALVTHLLPA  146 (181)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999886554

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=95.68  E-value=0.019  Score=39.22  Aligned_cols=65  Identities=12%  Similarity=0.203  Sum_probs=51.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC----eeeCcchHhhHHH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG----RRITSSGQRDLDQ   81 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G----R~lT~~G~~~lD~   81 (90)
                      -.|++.|. ++|..+..|+...|-.              .+-+.+-|+.||++|||+...+ |    -.||+.|...+-.
T Consensus        61 ~~IL~~L~-~~~~t~~eLa~~lgls--------------~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~lt~~~~~~l~~  124 (151)
T 3f6v_A           61 RRLVQLLT-SGEQTVNNLAAHFPAS--------------RSAISQHLRVLTEAGLVTPRKD-GRFRYYRLDPQGLAQLRA  124 (151)
T ss_dssp             HHHHHHGG-GCCEEHHHHHTTSSSC--------------HHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHHHHHHH
Confidence            35788887 8999999999987753              3689999999999999987754 4    4699999877766


Q ss_pred             HHHHh
Q 034587           82 VAGRI   86 (90)
Q Consensus        82 iA~~v   86 (90)
                      +..++
T Consensus       125 ~l~~~  129 (151)
T 3f6v_A          125 LFDSF  129 (151)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>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=95.63  E-value=0.037  Score=36.06  Aligned_cols=63  Identities=17%  Similarity=0.203  Sum_probs=48.4

Q ss_pred             HHHHHHHhhc------CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCe---eeCcch
Q 034587            6 TSMARKIYLR------QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGR---RITSSG   75 (90)
Q Consensus         6 ASi~RklYl~------g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR---~lT~~G   75 (90)
                      -++++.|+.-      +++-...|++.-+-              +.+-++..|..||+.|||+..+. .||   .||++|
T Consensus        19 ~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l--------------~~stLsR~l~rLe~~GLV~r~~~~D~R~~v~LT~~G   84 (96)
T 2obp_A           19 VEVLLVLREAGIENGATPWSLPKIAKRAQL--------------PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEG   84 (96)
T ss_dssp             HHHHHHHHHHTSSTTCCCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHH
T ss_pred             HHHHHHHHHHHhhCCCCCcCHHHHHHHhCC--------------chhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHH
Confidence            3567777765      67778888876554              45789999999999999986442 344   599999


Q ss_pred             HhhHHHH
Q 034587           76 QRDLDQV   82 (90)
Q Consensus        76 ~~~lD~i   82 (90)
                      +..+++.
T Consensus        85 ~~~l~~~   91 (96)
T 2obp_A           85 AALAAQL   91 (96)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9998865

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

Probab=95.59  E-value=0.041  Score=40.40  Aligned_cols=66  Identities=14%  Similarity=0.226  Sum_probs=53.8

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcchHhhHH
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQRDLD   80 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~~lD   80 (90)
                      +...-.||..|.-++++.+..|++..|-.              .+-+...|+.||+.|||+..+. .--.||++|+....
T Consensus       151 ~~~~~~IL~~L~~~~~~s~~eLA~~lgls--------------ksTv~r~L~~Le~~GlV~r~~r~~~~~LT~~G~~l~~  216 (244)
T 2wte_A          151 SREEMKLLNVLYETKGTGITELAKMLDKS--------------EKTLINKIAELKKFGILTQKGKDRKVELNELGLNVIK  216 (244)
T ss_dssp             CHHHHHHHHHHHHHTCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEETTTTEEEECHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEeCCccEEEECHHHHHHHH
Confidence            34566789988889999999999999863              3678889999999999998643 34689999999765


Q ss_pred             H
Q 034587           81 Q   81 (90)
Q Consensus        81 ~   81 (90)
                      .
T Consensus       217 ~  217 (244)
T 2wte_A          217 L  217 (244)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=95.51  E-value=0.018  Score=40.30  Aligned_cols=51  Identities=22%  Similarity=0.251  Sum_probs=42.8

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +-...|+..||-              |...+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus        40 L~E~~La~~lgV--------------SRtpVREAl~~L~~eGlv~~~~~~G~~V~~~~~~~~~e~   90 (222)
T 3ihu_A           40 LVETDLVAHFGV--------------GRNSVREALQRLAAEGIVDLQRHRGAVIRRLSLQETLDV   90 (222)
T ss_dssp             ECHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECSTTCEEECCCCHHHHHHH
T ss_pred             cCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHHHHHH
Confidence            446779999986              458999999999999999999988999988777766654

>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=95.49  E-value=0.024  Score=43.18  Aligned_cols=68  Identities=9%  Similarity=0.170  Sum_probs=51.6

Q ss_pred             HHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe----eeCcchHh
Q 034587            6 TSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR----~lT~~G~~   77 (90)
                      -.||+.|+-+  +++.+..|+...+-.              .+-+=.+|+.||+.|||++.  ++..|    .||++|+.
T Consensus       407 ~~vl~~l~~~~~~~~~~~~l~~~~~~~--------------~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~  472 (487)
T 1hsj_A          407 IYILNHILRSESNEISSKEIAKCSEFK--------------PYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKA  472 (487)
T ss_dssp             HHHHHHHHTCSCSEEEHHHHHHSSCCC--------------HHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHH
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHH
Confidence            3578888888  888899998855443              24566789999999999864  34455    37999999


Q ss_pred             hHHHHHHHhh
Q 034587           78 DLDQVAGRIV   87 (90)
Q Consensus        78 ~lD~iA~~v~   87 (90)
                      .++++...+.
T Consensus       473 ~~~~~~~~~~  482 (487)
T 1hsj_A          473 NIQKLISELE  482 (487)
T ss_dssp             HHHHHHHHHG
T ss_pred             HHHHHHHHHH
Confidence            9998876653

>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=95.42  E-value=0.093  Score=33.03  Aligned_cols=66  Identities=14%  Similarity=0.122  Sum_probs=48.8

Q ss_pred             hHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--C--CCeeeCcchHhh
Q 034587            4 LVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--K--GGRRITSSGQRD   78 (90)
Q Consensus         4 r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~--~GR~lT~~G~~~   78 (90)
                      --..++.-|++ .+|+.+..|+...|-.              .+-+..+|+.||+.|||+..+  .  ....++..|...
T Consensus        27 ~~~~il~~L~~~~~~~t~~ela~~l~~~--------------~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~~~~~~~   92 (152)
T 1ku9_A           27 SVGAVYAILYLSDKPLTISDIMEELKIS--------------KGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSS   92 (152)
T ss_dssp             HHHHHHHHHHHCSSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHHH
T ss_pred             hHHHHHHHHHHcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEecCCCceEEEeecchHHH
Confidence            34567777776 6899999999998753              357889999999999999763  2  234678777655


Q ss_pred             HHHHH
Q 034587           79 LDQVA   83 (90)
Q Consensus        79 lD~iA   83 (90)
                      ++.+.
T Consensus        93 ~~~~~   97 (152)
T 1ku9_A           93 IKDIA   97 (152)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55444

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=95.39  E-value=0.03  Score=36.55  Aligned_cols=70  Identities=16%  Similarity=0.115  Sum_probs=47.1

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCC-----eeeCcchHhhH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDL   79 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~G-----R~lT~~G~~~l   79 (90)
                      ||--|. .+|.---.|.+....   .     .+..-+.+.+-.+|+.||+.|||+...   .+|     -.||++|+..+
T Consensus        14 IL~~L~-~~~~~Gyei~~~l~~---~-----~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l   84 (115)
T 4esb_A           14 ILYIIS-QEEVYGYELSTKLNK---H-----GFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGLEQL   84 (115)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHHH---T-----TCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHH---c-----CCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHHHHH
Confidence            444444 455544455555543   1     244567789999999999999998542   234     24999999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +......
T Consensus        85 ~~~~~~~   91 (115)
T 4esb_A           85 EEFKQSW   91 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876553

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.32  E-value=0.024  Score=35.99  Aligned_cols=61  Identities=16%  Similarity=0.154  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQV   82 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~i   82 (90)
                      .|+.-|. .++..+..|+...|-.              .+-+...|+.||+.|||+...++.   ..||+++...+=+.
T Consensus        29 ~IL~~L~-~~~~s~~eLa~~lgis--------------~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~   92 (108)
T 2kko_A           29 QILDLLA-QGERAVEAIATATGMN--------------LTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFAL   92 (108)
T ss_dssp             HHHHHHT-TCCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHH
Confidence            4666665 6899999999988753              368999999999999998776432   36899886554433

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=95.30  E-value=0.022  Score=36.69  Aligned_cols=50  Identities=14%  Similarity=0.129  Sum_probs=42.2

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      .+..|+..||-              |...+|.+|+.||+.|||+..+..|-.+++....++..+
T Consensus        35 s~~~La~~~~v--------------Sr~tvr~al~~L~~~Gli~~~~~~G~~V~~~~~~~~~~~   84 (113)
T 3tqn_A           35 SIRKISTEYQI--------------NPLTVSKAYQSLLDDNVIEKRRGLGMLVKAGARQRLLTQ   84 (113)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECTTHHHHHHHH
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCCeEEEeCCchHHHHHH
Confidence            67889999986              347999999999999999999888999998877665543

>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=95.20  E-value=0.092  Score=32.89  Aligned_cols=59  Identities=12%  Similarity=0.174  Sum_probs=45.1

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~l   79 (90)
                      -.|+..|. +++..+..|+...|-.              .+-+.+.|+.||+.|||+...++.   -.||+.+-..+
T Consensus        29 ~~IL~~L~-~~~~~~~ela~~l~is--------------~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~~~   90 (106)
T 1r1u_A           29 IRIMELLS-VSEASVGHISHQLNLS--------------QSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATM   90 (106)
T ss_dssp             HHHHHHHH-HCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHH
Confidence            35777776 8999999999988763              368899999999999998776432   35788775443

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=95.20  E-value=0.016  Score=38.24  Aligned_cols=40  Identities=13%  Similarity=0.076  Sum_probs=34.1

Q ss_pred             chhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHH
Q 034587           44 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA   83 (90)
Q Consensus        44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA   83 (90)
                      |...+|.+|+.||+.|||+..+..|-.+++....++..+.
T Consensus        48 Sr~tvr~Al~~L~~~G~i~~~~~~G~~V~~~~~~~~~~~~   87 (126)
T 3ic7_A           48 NANTVMRSYEYLQSQEVIYNKRGIGFFVASGAKMLIHSLR   87 (126)
T ss_dssp             CSGGGHHHHHHHHTTTSEEEETTTEEEECTTHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCcEEEEcCCccEEccCcHHHHHHHH
Confidence            4578999999999999999999889999998876665543

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=95.13  E-value=0.049  Score=34.90  Aligned_cols=64  Identities=9%  Similarity=0.082  Sum_probs=49.0

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVA   83 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~iA   83 (90)
                      .|+..|. ++|..++.|....|-.              .+-+.+-|+.||+.|||+....+.   -.||+.|...+....
T Consensus        22 ~Il~~L~-~~~~~~~eLa~~l~is--------------~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~   86 (118)
T 3f6o_A           22 AVLGRLS-RGPATVSELAKPFDMA--------------LPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWL   86 (118)
T ss_dssp             HHHHHHH-TCCEEHHHHHTTCCSC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhCcC--------------HHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHH
Confidence            4667776 7999999999977653              367889999999999998766422   468999988776554


Q ss_pred             HH
Q 034587           84 GR   85 (90)
Q Consensus        84 ~~   85 (90)
                      ..
T Consensus        87 ~~   88 (118)
T 3f6o_A           87 AE   88 (118)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3sxy_A Transcriptional regulator, GNTR family; transcription factor, metal-binding, structur genomics, PSI-2, protein structure initiative; 1.65A {Thermotoga maritima} PDB: 3dbw_A 3fms_A*

Probab=95.12  E-value=0.017  Score=40.41  Aligned_cols=66  Identities=20%  Similarity=0.263  Sum_probs=49.9

Q ss_pred             hHHHHHHHHhhcC------CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587            4 LVTSMARKIYLRQ------GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus         4 r~ASi~RklYl~g------~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      .++.-+|.-=+.|      .+....|+..||-              |...+|.+|+.||..|||+..+..|-.+++-...
T Consensus        16 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~   81 (218)
T 3sxy_A           16 KVYNLLKEMILNHELKLGEKLNVRELSEKLGI--------------SFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEK   81 (218)
T ss_dssp             HHHHHHHHHHHTTSSCTTCEECHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEEETTTEEEECCCCHH
T ss_pred             HHHHHHHHHHHhCCCCCCCEeCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCHH
Confidence            3444445444444      2457789999987              4589999999999999999999889999987777


Q ss_pred             hHHHHH
Q 034587           78 DLDQVA   83 (90)
Q Consensus        78 ~lD~iA   83 (90)
                      ++..+-
T Consensus        82 ~~~el~   87 (218)
T 3sxy_A           82 FIRETI   87 (218)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>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=95.08  E-value=0.1  Score=33.67  Aligned_cols=60  Identities=18%  Similarity=0.267  Sum_probs=44.8

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~lD~   81 (90)
                      .|+..|.-.++..+..|....|-.              .+-+.+.|+.||+.|||+...+ ||    .||+.+-..+-.
T Consensus        46 ~IL~~L~~~~~~s~~eLa~~l~is--------------~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~~~~~~~~  109 (122)
T 1u2w_A           46 KITYALCQDEELCVCDIANILGVT--------------IANASHHLRTLYKQGVVNFRKE-GKLALYSLGDEHIRQIMM  109 (122)
T ss_dssp             HHHHHHHHSSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEC-----CCEEEESCHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEEEE-CCEEEEEECHHHHHHHHH
Confidence            467777667999999999988753              3688899999999999987754 44    788887655433

>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=95.01  E-value=0.029  Score=38.12  Aligned_cols=72  Identities=11%  Similarity=0.017  Sum_probs=45.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCe-----eeCcchHhh
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGR-----RITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR-----~lT~~G~~~   78 (90)
                      .||.-|+ .+|.--..|.+.....-.      .+..-+-+.+-.+|+.||+.|||+....   +|+     .||++|++.
T Consensus        45 ~IL~~L~-~~~~~gyeI~~~l~~~~~------~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~  117 (145)
T 1xma_A           45 IILSLLI-EGDSYGYEISKNIRIKTD------ELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKY  117 (145)
T ss_dssp             HHHHHHH-HCCEEHHHHHHHHHHHHT------TSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHHHHhhC------CccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECHHHHHH
Confidence            4555554 356544444444432100      1123556789999999999999986531   232     799999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      +......
T Consensus       118 l~~~~~~  124 (145)
T 1xma_A          118 YKQKCEE  124 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876554

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=95.00  E-value=0.14  Score=33.69  Aligned_cols=42  Identities=17%  Similarity=0.112  Sum_probs=36.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .+..|+..||-.              ..-+|.+|+.|+..|||+..+..|-.+++.
T Consensus        37 se~~La~~~~vS--------------r~tvr~Al~~L~~~Gli~~~~g~G~~V~~~   78 (126)
T 3by6_A           37 SVRETALQEKIN--------------PNTVAKAYKELEAQKVIRTIPGKGTFITGN   78 (126)
T ss_dssp             CHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEETTTEEEECSC
T ss_pred             CHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEecCCeEEEccC
Confidence            788899988863              478999999999999999998889999883

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=94.98  E-value=0.024  Score=40.54  Aligned_cols=51  Identities=16%  Similarity=0.144  Sum_probs=43.4

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +....|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus        52 L~e~~La~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~el  102 (239)
T 2hs5_A           52 LSEPDICAALDV--------------SRNTVREAFQILIEDRLVAHELNRGVFVRVPTAEDITEL  102 (239)
T ss_dssp             ECHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCCCHHHHHHH
T ss_pred             eCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEeCCCHHHHHHH
Confidence            567788888887              457999999999999999999988999998877776654

>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=94.97  E-value=0.044  Score=35.40  Aligned_cols=44  Identities=14%  Similarity=0.225  Sum_probs=34.8

Q ss_pred             CchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHHHHHHh
Q 034587           43 SSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        43 asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~iA~~v   86 (90)
                      -+-+.+=-+|+.||+.|||+...+..   -.||++|+..+++...+.
T Consensus        42 is~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~   88 (99)
T 2co5_A           42 ISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFF   88 (99)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhH
Confidence            34567888999999999998765222   479999999999877654

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=94.96  E-value=0.035  Score=36.43  Aligned_cols=69  Identities=23%  Similarity=0.240  Sum_probs=45.9

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCC-----eeeCcchHhhH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDL   79 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~G-----R~lT~~G~~~l   79 (90)
                      ||--|. .+|.---.|.+....   .     .+..-+-+.+-.+|+.||+.|||+...   .+|     -.||++|+..|
T Consensus        18 IL~lL~-~~p~~Gyei~~~l~~---~-----g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l   88 (116)
T 3hhh_A           18 VLAIIQ-RKETYGYEITKILND---Q-----GFTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAEL   88 (116)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHT---T-----SCSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHH
T ss_pred             HHHHHh-cCCCCHHHHHHHHHH---c-----CCCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHH
Confidence            444444 455544456665544   1     244556788999999999999998543   234     35999999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +.....
T Consensus        89 ~~~~~~   94 (116)
T 3hhh_A           89 ADFWQR   94 (116)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886554

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=94.79  E-value=0.044  Score=35.94  Aligned_cols=44  Identities=18%  Similarity=0.357  Sum_probs=33.7

Q ss_pred             cCchhHHHHHHHHHHhCCcccccC---CCC-----eeeCcchHhhHHHHHHH
Q 034587           42 KSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDLDQVAGR   85 (90)
Q Consensus        42 ~asg~iiR~~LqqLE~~glV~k~~---~~G-----R~lT~~G~~~lD~iA~~   85 (90)
                      .-+-+.+-.+|+.||+.|||+...   .+|     -.||++|+..|+.....
T Consensus        41 ~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~~~~~   92 (117)
T 4esf_A           41 EVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQELELFWKK   92 (117)
T ss_dssp             TCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHHHHHHHH
Confidence            456688999999999999998653   233     35999999999886554

>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=94.77  E-value=0.17  Score=36.18  Aligned_cols=60  Identities=8%  Similarity=-0.061  Sum_probs=49.5

Q ss_pred             hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587            3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~   76 (90)
                      .|+-.||..|.-.+ ++++..|....|-.+              +-+..+|+.||+.|||+.+.++...|+++..
T Consensus         8 ~r~l~iL~~l~~~~~~~~~~ela~~~gl~~--------------stv~r~l~~L~~~G~v~~~~~~~Y~lg~~~~   68 (249)
T 1mkm_A            8 KKAFEILDFIVKNPGDVSVSEIAEKFNMSV--------------SNAYKYMVVLEEKGFVLRKKDKRYVPGYKLI   68 (249)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEECTTSCEEECTHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCcEEECCCCcEEECHHHH
Confidence            57888998887765 799999999887744              6788999999999999988556678988654

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=94.69  E-value=0.035  Score=39.81  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      .+....|+..||-              |..-+|.+|+.||..|||+..+.+|-.+++....++..+
T Consensus        49 ~L~e~~La~~lgV--------------Sr~~VReAL~~L~~~Glv~~~~~~G~~V~~~~~~~~~~~  100 (237)
T 3c7j_A           49 ALRQQELATLFGV--------------SRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDA  100 (237)
T ss_dssp             BCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCCHHHHHHHH
T ss_pred             eeCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCceEEecCCHHHHHHH
Confidence            4678899999987              457999999999999999999888999998877665543

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

Probab=94.67  E-value=0.06  Score=32.37  Aligned_cols=45  Identities=13%  Similarity=0.141  Sum_probs=37.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .|+.-|.-.+++.+..|+..+|-.              .+-++..|+.||+.|+|+..+
T Consensus         4 ~Il~~L~~~~~~s~~eLa~~lgvs--------------~~tv~r~L~~L~~~GlI~~~~   48 (81)
T 2htj_A            4 EILEFLNRHNGGKTAEIAEALAVT--------------DYQARYYLLLLEKAGMVQRSP   48 (81)
T ss_dssp             HHHHHHHHSCCCCHHHHHHHHTSC--------------HHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEec
Confidence            466667767899999999999863              367999999999999998543

>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=94.65  E-value=0.21  Score=30.00  Aligned_cols=46  Identities=11%  Similarity=0.149  Sum_probs=37.1

Q ss_pred             HHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            6 TSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         6 ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      ..++..++- .+++.+..|+..+|-.              .+-+...|+.||+.|||+..+
T Consensus        24 ~~~l~~l~~~~~~~t~~ela~~l~is--------------~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           24 VAVLLKMVEIEKPITSEELADIFKLS--------------KTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEeec
Confidence            345666665 7899999999998753              368999999999999998654

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=94.62  E-value=0.052  Score=35.38  Aligned_cols=46  Identities=13%  Similarity=0.089  Sum_probs=35.6

Q ss_pred             ccCchhHHHHHHHHHHhCCcccccC----CCC-----eeeCcchHhhHHHHHHHh
Q 034587           41 CKSSGAIARHILQQLQNMNIIDIEP----KGG-----RRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        41 ~~asg~iiR~~LqqLE~~glV~k~~----~~G-----R~lT~~G~~~lD~iA~~v   86 (90)
                      ..-+-+.+-.+|+.||+.|||+...    .+|     -.||++|++.++....+.
T Consensus        52 ~~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~  106 (115)
T 2dql_A           52 YRLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQAEDLARLW  106 (115)
T ss_dssp             EECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            3556688999999999999998542    124     479999999998876543

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=94.60  E-value=0.15  Score=33.72  Aligned_cols=47  Identities=15%  Similarity=0.060  Sum_probs=39.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL   79 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l   79 (90)
                      ....|+..||-              |...+|.+|+.||..|||+..+..|-.+++....++
T Consensus        30 se~~La~~~gv--------------Sr~tVr~Al~~L~~~Gli~~~~g~G~~V~~~~~~~~   76 (129)
T 2ek5_A           30 STNELAAFHRI--------------NPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALI   76 (129)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHTTTSEEEETTTEEEECTTHHHHH
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEecCCEEEEecCchHhh
Confidence            67788888886              347999999999999999999888999998765554

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=94.57  E-value=0.063  Score=35.16  Aligned_cols=43  Identities=16%  Similarity=0.085  Sum_probs=37.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      .+..|+..||-              |...+|.+|+.|++.|||+..+..|-.+++.-
T Consensus        39 s~~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~~~   81 (125)
T 3neu_A           39 SVREMGVKLAV--------------NPNTVSRAYQELERAGYIYAKRGMGSFVTSDK   81 (125)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCCH
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCeEEEecCCEEEEecCc
Confidence            58889998886              34799999999999999999988898998854

>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=94.50  E-value=0.071  Score=39.03  Aligned_cols=67  Identities=10%  Similarity=0.075  Sum_probs=49.4

Q ss_pred             HHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            6 TSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      ..||..|+-.+  ++.++.|+...+-.              .+-+=.+++.||+.|||+..+  ++.|    .||++|+.
T Consensus       161 ~~vL~~L~~~~~~~~t~~eLa~~l~i~--------------~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~  226 (250)
T 1p4x_A          161 FTILAIITSQNKNIVLLKDLIETIHHK--------------YPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQD  226 (250)
T ss_dssp             HHHHHHHHTTTTCCEEHHHHHHHSSSC--------------HHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHH
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHH
Confidence            35677777765  47888888866543              245667899999999998654  4555    38999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++++...+
T Consensus       227 ~~~~~~~~~  235 (250)
T 1p4x_A          227 HAEQLLAQV  235 (250)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999886654

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=94.49  E-value=0.026  Score=36.53  Aligned_cols=72  Identities=13%  Similarity=0.029  Sum_probs=47.7

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCch-hHHHHHHHHHHhCCcccccCC--CC-----eeeCcchHhh
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSG-AIARHILQQLQNMNIIDIEPK--GG-----RRITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg-~iiR~~LqqLE~~glV~k~~~--~G-----R~lT~~G~~~   78 (90)
                      .||.-|.- +|.-...|.+....   .|.-.   ..-+- +.+-.+|+.||+.|||+....  .|     -.||++|+..
T Consensus        17 ~IL~~L~~-~~~~gyel~~~l~~---~g~~~---~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~~G~~~   89 (118)
T 2esh_A           17 TILLLVAE-KPSHGYELAERLAE---FGIEI---PGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLY   89 (118)
T ss_dssp             HHHHHHHH-SCBCHHHHHHHHHT---TCCSS---TTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHH
T ss_pred             HHHHHHHc-CCCCHHHHHHHHHH---hCCcc---cCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHH
Confidence            45666643 67766677777653   22110   12344 578889999999999985531  23     2799999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      +......
T Consensus        90 l~~~~~~   96 (118)
T 2esh_A           90 LREILRS   96 (118)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9886554

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=94.23  E-value=0.035  Score=39.94  Aligned_cols=65  Identities=18%  Similarity=0.196  Sum_probs=46.9

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC---CCC-----eeeCcchHhhHHHHHHH
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDLDQVAGR   85 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~---~~G-----R~lT~~G~~~lD~iA~~   85 (90)
                      .+|.---.|.+.+...-      .++...+-+-|-.+|+.||+.|||+...   .+|     ..||++|+..|.+...+
T Consensus        47 ~~p~~GYeL~~~l~~~~------~~~~~~s~g~lY~~L~rLe~~GlI~~~~~~~~~~p~rk~Y~iT~~Gr~~l~~~l~~  119 (204)
T 3l9f_A           47 KKERSGYEINDILQNQL------SYFYDGTYGMIYPTLRKLEKDGKITKEVVIQDGRPNKNIYAITESGKKELASYLQS  119 (204)
T ss_dssp             SCCEEHHHHHHHHHHTS------TTTEECCTTCHHHHHHHHHHTTSEEEEEECCTTSCCEEEEEECHHHHHHHHHHHHS
T ss_pred             cCCCCHHHHHHHHHHHh------CCccCCCcchHHHHHHHHHHCCCeEEEeeccCCCCCceEEEEChHHHHHHHHHHhc
Confidence            56666666777765431      2455667788999999999999998543   233     36999999999876654

>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=94.23  E-value=0.16  Score=31.92  Aligned_cols=54  Identities=11%  Similarity=0.070  Sum_probs=42.6

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      ..|+.-|+-.+|+.+..|....+-.  ++.        +.+-+-.+|+.||+.|||+..+++.+
T Consensus        13 ~~vL~~L~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~R~~~~r~   66 (126)
T 1sd4_A           13 WDVMNIIWDKKSVSANEIVVEIQKY--KEV--------SDKTIRTLITRLYKKEIIKRYKSENI   66 (126)
T ss_dssp             HHHHHHHHHSSSEEHHHHHHHHHTT--SCC--------CHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHhhc--CCC--------ChhhHHHHHHHHHHCCceEEEeCCCe
Confidence            4688999999999999999998753  222        23678899999999999997775333

>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=94.16  E-value=0.082  Score=37.85  Aligned_cols=59  Identities=17%  Similarity=0.312  Sum_probs=48.7

Q ss_pred             hhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcch
Q 034587            3 ELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSG   75 (90)
Q Consensus         3 ~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~G   75 (90)
                      .|+-.||..|.-.+ ++++..|....|-.|              +-+..+|+.||+.|||+.+++ +...|+++.
T Consensus         6 ~r~l~iL~~l~~~~~~~s~~ela~~~gl~~--------------stv~r~l~~L~~~G~v~~~~~~~~Y~lg~~~   66 (241)
T 2xrn_A            6 ARAASIMRALGSHPHGLSLAAIAQLVGLPR--------------STVQRIINALEEEFLVEALGPAGGFRLGPAL   66 (241)
T ss_dssp             HHHHHHHHHHHTCTTCEEHHHHHHHTTSCH--------------HHHHHHHHHHHTTTSEEECGGGCEEEECSHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEeCCCCeEEECHHH
Confidence            57888999887664 799999999887754              689999999999999998875 556787764

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=94.16  E-value=0.058  Score=33.72  Aligned_cols=43  Identities=14%  Similarity=0.228  Sum_probs=36.2

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      .+..|+..||-.              ...+|.+|+.||+.|+|+..+..|..+++..
T Consensus        37 s~~eLa~~~~vS--------------r~tvr~al~~L~~~Gli~~~~g~G~~v~~~~   79 (102)
T 1v4r_A           37 SVADIRAQFGVA--------------AKTVSRALAVLKSEGLVSSRGALGTVVEKNP   79 (102)
T ss_dssp             CHHHHHHHSSSC--------------TTHHHHHTTTTTTSSCCEEETTTEEESCSCC
T ss_pred             CHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEeCCCeEEEccCC
Confidence            788999988863              3689999999999999998887788877654

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

Probab=94.09  E-value=0.11  Score=32.25  Aligned_cols=53  Identities=19%  Similarity=0.243  Sum_probs=41.2

Q ss_pred             hHHHHHHHHhhc------CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587            4 LVTSMARKIYLR------QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI   71 (90)
Q Consensus         4 r~ASi~RklYl~------g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l   71 (90)
                      |...|+--|--.      +|+.|..++..+|=+              -.-||.-|..||+.|+|+.++ +||.+
T Consensus         5 r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS--------------~~TVrr~L~~Le~kG~I~R~~-ggr~~   63 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGAPVKTRDIADAAGLS--------------IYQVRLYLEQLHDVGVLEKVN-AGKGV   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEES-CSSSS
T ss_pred             HHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCcEEecC-CCCCc
Confidence            344556555555      899999999988752              356999999999999999987 56655

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=93.75  E-value=0.047  Score=35.96  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=35.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .+..|+..||-              |..-+|.+|++||..|||+..+..|-.+++.
T Consensus        40 ser~La~~~gV--------------Sr~tVReAl~~L~~eGlv~~~~g~G~~V~~~   81 (134)
T 4ham_A           40 SIREFASRIGV--------------NPNTVSKAYQELERQEVIITVKGKGTFIANQ   81 (134)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCC
T ss_pred             cHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCcEEEEeCC
Confidence            56778888886              4479999999999999999988778777654

>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=93.60  E-value=0.16  Score=33.03  Aligned_cols=53  Identities=23%  Similarity=0.418  Sum_probs=40.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe----eeCcch
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSG   75 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR----~lT~~G   75 (90)
                      .|+..|+ +++..+..|+...|-.              .+-+.+.|+.||+.|||....+ ||    .+|+++
T Consensus        50 ~IL~~L~-~~~~s~~ela~~lgis--------------~stvs~~L~~Le~~Glv~~~~~-gr~~~y~l~~~~  106 (122)
T 1r1t_A           50 RLLSLLA-RSELCVGDLAQAIGVS--------------ESAVSHQLRSLRNLRLVSYRKQ-GRHVYYQLQDHH  106 (122)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEE-TTEEEEEESSHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEEEe-CCEEEEEEChHH
Confidence            4666665 6889999999988753              3688999999999999987654 43    356554

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=93.56  E-value=0.12  Score=37.83  Aligned_cols=58  Identities=14%  Similarity=0.204  Sum_probs=48.1

Q ss_pred             hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587            3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .|+-.||.-|--. +++++..|+..-|-.|              +-+..+|+.|++.|||++++++...|+++
T Consensus        30 ~Ral~IL~~l~~~~~~ltl~eia~~lgl~k--------------sTv~RlL~tL~~~G~v~~~~~~~Y~LG~~   88 (275)
T 3mq0_A           30 RRAVRILDLVAGSPRDLTAAELTRFLDLPK--------------SSAHGLLAVMTELDLLARSADGTLRIGPH   88 (275)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCC----------------CHHHHHHHHHHTTSEEECTTSEEEECTH
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEECCCCcEEehHH
Confidence            5788899988875 4799999999998765              56889999999999999998666788876

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=93.43  E-value=0.067  Score=36.86  Aligned_cols=44  Identities=18%  Similarity=0.166  Sum_probs=34.4

Q ss_pred             cCchhHHHHHHHHHHhCCcccccCC----CC-----eeeCcchHhhHHHHHHH
Q 034587           42 KSSGAIARHILQQLQNMNIIDIEPK----GG-----RRITSSGQRDLDQVAGR   85 (90)
Q Consensus        42 ~asg~iiR~~LqqLE~~glV~k~~~----~G-----R~lT~~G~~~lD~iA~~   85 (90)
                      .-+-+.+-.+|+.||+.|||+....    +|     -.||++|++.++.....
T Consensus        75 ~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~  127 (148)
T 2zfw_A           75 RLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQL  127 (148)
T ss_dssp             ECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESSSSCSTTHHHHHH
T ss_pred             CCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECHHHHHHHHHHHHH
Confidence            4556789999999999999986431    24     47999999988877654

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=93.41  E-value=0.076  Score=36.00  Aligned_cols=46  Identities=15%  Similarity=0.107  Sum_probs=35.7

Q ss_pred             ccCchhHHHHHHHHHHhCCcccccC--C--CC-----eeeCcchHhhHHHHHHHh
Q 034587           41 CKSSGAIARHILQQLQNMNIIDIEP--K--GG-----RRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        41 ~~asg~iiR~~LqqLE~~glV~k~~--~--~G-----R~lT~~G~~~lD~iA~~v   86 (90)
                      ..-+-+.+-.+|+.||+.|||+...  .  +|     -.||++|++.++....+.
T Consensus        64 ~~is~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~  118 (138)
T 2e1n_A           64 YRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLW  118 (138)
T ss_dssp             EECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEESCSCCHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            3556688999999999999998542  1  24     479999999988876543

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=93.33  E-value=0.045  Score=38.66  Aligned_cols=44  Identities=20%  Similarity=0.253  Sum_probs=36.9

Q ss_pred             hhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc--cCC--CCeeeCcchHh
Q 034587           20 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPK--GGRRITSSGQR   77 (90)
Q Consensus        20 V~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k--~~~--~GR~lT~~G~~   77 (90)
                      -..|+..||-              |...+|.+|+.||..|||+.  .+.  +|-.+++....
T Consensus        31 E~~La~~lgV--------------SRtpVREAL~~L~~~GlV~~~~~~~~~~G~~V~~~~~~   78 (239)
T 2di3_A           31 ERALSETLGV--------------SRSSLREALRVLEALGTISTATGSGPRSGTIITAAPGQ   78 (239)
T ss_dssp             HHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEECCSTTSGGGCCEECCCCCS
T ss_pred             HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEeecccCCCCCceeeCCcch
Confidence            4589999986              45799999999999999999  887  78888876553

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=93.23  E-value=0.054  Score=35.47  Aligned_cols=38  Identities=18%  Similarity=0.259  Sum_probs=29.9

Q ss_pred             hHHHHHHHHHHhCCcccccC---CCC-----eeeCcchHhhHHHHH
Q 034587           46 AIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDLDQVA   83 (90)
Q Consensus        46 ~iiR~~LqqLE~~glV~k~~---~~G-----R~lT~~G~~~lD~iA   83 (90)
                      +.+-.+|+.||+.|||+...   .+|     -.||++|+..|++..
T Consensus        48 gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l~~~~   93 (117)
T 3elk_A           48 GSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFLCDHS   93 (117)
T ss_dssp             THHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHHHHTS
T ss_pred             chHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHHHH
Confidence            68899999999999998543   123     359999999998753

>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=93.14  E-value=0.25  Score=33.03  Aligned_cols=57  Identities=9%  Similarity=0.104  Sum_probs=42.4

Q ss_pred             HHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcchH
Q 034587            6 TSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ   76 (90)
Q Consensus         6 ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G~   76 (90)
                      -.++-.|..+  +++.+..++..++-.              -..++++|++|+++|||+... .||..|+....
T Consensus        17 l~~L~~La~~~~~~~~~~~iA~~~~i~--------------~~~l~kil~~L~~~Glv~s~rG~GGy~L~~~p~   76 (149)
T 1ylf_A           17 VHILSILKNNPSSLCTSDYMAESVNTN--------------PVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLH   76 (149)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEC---CCEEESSCGG
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEEccCCCceEeCCChh
Confidence            3455555553  478899999988874              379999999999999998654 57888887643

>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=93.10  E-value=0.38  Score=30.91  Aligned_cols=70  Identities=17%  Similarity=0.135  Sum_probs=51.9

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc-----C-CCCeeeCc-----
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGRRITS-----   73 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~-----~-~~GR~lT~-----   73 (90)
                      --.|++.|.-++++....|+..+|-              |.+-++..|+.||+.|+|+..     + +-|..+|.     
T Consensus         6 ~~~il~~L~~~~~~~~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~~~v~~~   71 (141)
T 1i1g_A            6 DKIILEILEKDARTPFTEIAKKLGI--------------SETAVRKRVKALEEKGIIEGYTIKINPKKLGYSLVTITGVD   71 (141)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTSSCCCCCCCCSGGGTCCEEEEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEeccccccChHHhCccEEEEEEEE
Confidence            3467887777889999999999875              347899999999999999742     2 23666655     


Q ss_pred             -chHhhHHHHHHHhhcC
Q 034587           74 -SGQRDLDQVAGRIVVA   89 (90)
Q Consensus        74 -~G~~~lD~iA~~v~~~   89 (90)
                       .+ ..++.++..+..-
T Consensus        72 ~~~-~~~~~~~~~l~~~   87 (141)
T 1i1g_A           72 TKP-EKLFEVAEKLKEY   87 (141)
T ss_dssp             ECG-GGHHHHHHHHHHS
T ss_pred             ECc-hhHHHHHHHHhcC
Confidence             44 4678888777543

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=93.09  E-value=0.3  Score=35.25  Aligned_cols=60  Identities=5%  Similarity=-0.007  Sum_probs=48.2

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~   76 (90)
                      .|+-.||.-|.- .+++++..|....|-.|              +-+..+|+.||+.|||+.++++...|+++.-
T Consensus        23 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~k--------------stv~r~l~tL~~~G~v~~~~~~~Y~lg~~~~   83 (260)
T 2o0y_A           23 TRVIDLLELFDAAHPTRSLKELVEGTKLPK--------------TTVVRLVATMCARSVLTSRADGSYSLGPEML   83 (260)
T ss_dssp             HHHHHHHTTCBTTBSSBCHHHHHHHHCCCH--------------HHHHHHHHHHHHTTSEEECTTSCEEECHHHH
T ss_pred             HHHHHHHHHHhhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEECCCCeEEecHHHH
Confidence            467778877653 57899999999988754              6888999999999999998765667877643

>3aaf_A Werner syndrome ATP-dependent helicase; helix-turn-helix, winged-helix, protein-DNA complex, DNA-BIN helicase; HET: DNA; 1.90A {Homo sapiens} PDB: 2axl_A

Probab=93.09  E-value=0.62  Score=31.27  Aligned_cols=80  Identities=13%  Similarity=0.070  Sum_probs=58.3

Q ss_pred             hHHHHHHHHh-hcCCCchhHHHHHhcCCCCCCCCCCcccc---C-----chhHHHHHHHHHHhCCcccccCCC----C-e
Q 034587            4 LVTSMARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCK---S-----SGAIARHILQQLQNMNIIDIEPKG----G-R   69 (90)
Q Consensus         4 r~ASi~RklY-l~g~vGV~~Lr~~YGg~krrG~~P~h~~~---a-----sg~iiR~~LqqLE~~glV~k~~~~----G-R   69 (90)
                      -|-.+|.-|| +.+..|++.+..+.-|+++.-+.-.|...   |     +-.-++.++.||...|+++.+...    + =
T Consensus        17 ~AqkiLs~V~r~~~rfG~~~iidvLrGs~~~ki~~~~~~l~tfGigk~~s~~~w~~lirqLi~~G~L~~~~~~~~~~~~L   96 (134)
T 3aaf_A           17 QAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKIC   96 (134)
T ss_dssp             HHHHHHHHHHHTTTCSCTHHHHHHHTTCCCTTSCGGGGGSTTTTTTTTSCHHHHHHHHHHHHHTTSEEEEECSSTTCEEE
T ss_pred             HHHHHHHHHHHHcCcccccchhhhhcCCcHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHHHHcCCceeecCcCccCceE
Confidence            3444555555 36789999999999999887665522211   2     234799999999999999876533    2 6


Q ss_pred             eeCcchHhhHHHHH
Q 034587           70 RITSSGQRDLDQVA   83 (90)
Q Consensus        70 ~lT~~G~~~lD~iA   83 (90)
                      .||++|+..|..--
T Consensus        97 ~Lt~~g~~vL~~~~  110 (134)
T 3aaf_A           97 ALTKKGRNWLHKAN  110 (134)
T ss_dssp             EECHHHHHHHHHHT
T ss_pred             EECHHHHHHHhCCc
Confidence            89999999987643

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=92.85  E-value=0.12  Score=36.23  Aligned_cols=62  Identities=18%  Similarity=0.164  Sum_probs=43.5

Q ss_pred             HHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC------CCCe-----eeCc
Q 034587            7 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGR-----RITS   73 (90)
Q Consensus         7 Si~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~------~~GR-----~lT~   73 (90)
                      +|+..|.-+  ++..+..|....+             .=|-.-|+.-|+.|++.|+|++..      ..||     .||+
T Consensus        33 ~IL~~Ll~~p~~~~ta~eL~~~l~-------------~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~   99 (151)
T 3u1d_A           33 DVLHQILAQPDGVLSVEELLYRNP-------------DETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTG   99 (151)
T ss_dssp             HHHHHHHHSTTSCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHhcC-------------CCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECH
Confidence            345555444  2356777765432             135679999999999999998542      1254     8999


Q ss_pred             chHhhHHH
Q 034587           74 SGQRDLDQ   81 (90)
Q Consensus        74 ~G~~~lD~   81 (90)
                      +|+..++.
T Consensus       100 ~Gr~~l~~  107 (151)
T 3u1d_A          100 EGIALLRA  107 (151)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999987

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=92.68  E-value=0.36  Score=30.28  Aligned_cols=60  Identities=12%  Similarity=0.087  Sum_probs=44.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~~lD~   81 (90)
                      .|+..|+- ++..+..++...|-.+              +-+...|+.||+.|+|....+ ....+|..|...++.
T Consensus        36 ~il~~L~~-~~~s~~ela~~l~is~--------------stvsr~l~~Le~~Glv~~~~~~r~~~~~~~~~~~~~~   96 (119)
T 2lkp_A           36 MILTQLRN-GPLPVTDLAEAIGMEQ--------------SAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQL   96 (119)
T ss_dssp             HHHHHHHH-CCCCHHHHHHHHSSCH--------------HHHHHHHHHHHHHCSEEEEEETTEEEEEESCHHHHHH
T ss_pred             HHHHHHHH-CCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEEecCCEEEEEEchHHHHHH
Confidence            46666664 7899999999887643              688999999999999987653 234577777655443

>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=92.67  E-value=0.31  Score=34.33  Aligned_cols=66  Identities=20%  Similarity=0.105  Sum_probs=47.5

Q ss_pred             HHHHHHHhhcCC------CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC---CCeeeCcchH
Q 034587            6 TSMARKIYLRQG------LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQ   76 (90)
Q Consensus         6 ASi~RklYl~g~------vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~---~GR~lT~~G~   76 (90)
                      -.+++.|+..+.      +.+..++...+-.+              +-+=..+++||+.|||+..++   .+=.||++|+
T Consensus        10 l~~l~~l~~~~~l~~~~~~s~s~aA~~L~isq--------------~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G~   75 (230)
T 3cta_A           10 YRAIKKIKEAAEASNRAYLTSSKLADMLGISQ--------------QSASRIIIDLEKNGYITRTVTKRGQILNITEKGL   75 (230)
T ss_dssp             HHHHHHHHHHTTTSSEEECCHHHHHHHHTSCH--------------HHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHH
T ss_pred             HHHHHHHHHhcccccCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHHH
Confidence            345555555443      56888888776643              567778899999999997732   3557999999


Q ss_pred             hhHHHHHHH
Q 034587           77 RDLDQVAGR   85 (90)
Q Consensus        77 ~~lD~iA~~   85 (90)
                      ..++.+...
T Consensus        76 ~l~~~~~~~   84 (230)
T 3cta_A           76 DVLYTEFAD   84 (230)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876543

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=92.50  E-value=0.12  Score=37.43  Aligned_cols=58  Identities=16%  Similarity=0.265  Sum_probs=48.6

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CCeeeCcc
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~GR~lT~~   74 (90)
                      .|+-.||.-|-- .+++++..|...-|-.|              +-+..+|+.|++.|||+++++ +...|+++
T Consensus         6 ~Ral~IL~~l~~~~~~lsl~eia~~lgl~k--------------sT~~RlL~tL~~~G~v~~~~~~~~Y~lG~~   65 (260)
T 3r4k_A            6 SKALTLLTYFNHGRLEIGLSDLTRLSGMNK--------------ATVYRLMSELQEAGFVEQVEGARSYRLGPQ   65 (260)
T ss_dssp             HHHHHHHTTCBTTBSEEEHHHHHHHHCSCH--------------HHHHHHHHHHHHTTSEEECSSSSEEEECTT
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEEcCHH
Confidence            578888888875 57899999999988754              788999999999999999886 55677765

>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=92.35  E-value=0.23  Score=36.34  Aligned_cols=66  Identities=8%  Similarity=0.062  Sum_probs=46.7

Q ss_pred             HHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCee----eCcchHhh
Q 034587            7 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRR----ITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~----lT~~G~~~   78 (90)
                      .||..||-.  +++.+..|....+-.             ++.+- .+|+.||+.|||++.  +++.|.    ||++|+..
T Consensus        38 ~vL~~L~~~~~~~~~~~el~~~l~~~-------------~~t~t-~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~  103 (250)
T 1p4x_A           38 ILLTYLFHQQENTLPFKKIVSDLCYK-------------QSDLV-QHIKVLVKHSYISKVRSKIDERNTYISISEEQREK  103 (250)
T ss_dssp             HHHHHHHSCSCSEEEHHHHHHHSSSC-------------GGGTH-HHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHH
T ss_pred             HHHHHHHhcCCCCcCHHHHHHHHCCC-------------HhhHH-HHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHH
Confidence            467777764  478888888755443             33343 689999999999854  444443    89999998


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++.+...+
T Consensus       104 ~~~~~~~~  111 (250)
T 1p4x_A          104 IAERVTLF  111 (250)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88776554

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=92.20  E-value=0.28  Score=32.84  Aligned_cols=56  Identities=14%  Similarity=0.202  Sum_probs=42.2

Q ss_pred             HHHHHHhhc---CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchH
Q 034587            7 SMARKIYLR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ   76 (90)
Q Consensus         7 Si~RklYl~---g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~   76 (90)
                      .++-.|..+   +++.+..++..+|-.              -..++++|++|.++|||+...  .||-.|+..-.
T Consensus        15 ~~L~~La~~~~~~~~s~~~IA~~~~i~--------------~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p~   75 (143)
T 3t8r_A           15 TLMISLAKKEGQGCISLKSIAEENNLS--------------DLYLEQLVGPLRNAGLIRSVRGAKGGYQLRVPAE   75 (143)
T ss_dssp             HHHHHHHTTTTSCCEEHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEECSSSSSEEEESSCGG
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCEEEecCCCCCCeeecCCcc
Confidence            344455543   378999999988764              379999999999999998554  47888886554

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=92.16  E-value=0.082  Score=36.93  Aligned_cols=42  Identities=14%  Similarity=0.229  Sum_probs=35.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .-..|+..||-              |..-+|.+|+.||..|||+..+..|-.+++.
T Consensus        33 sE~eLa~~~gV--------------SR~tVReAL~~L~~eGlv~~~~g~G~~V~~~   74 (239)
T 1hw1_A           33 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNNF   74 (239)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTEEEEECCH
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEecCCCcEeeCc
Confidence            56788888886              4579999999999999999998778888763

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

Probab=91.91  E-value=0.58  Score=30.41  Aligned_cols=61  Identities=8%  Similarity=0.041  Sum_probs=45.0

Q ss_pred             HHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe-----eeCcchH
Q 034587            6 TSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR-----RITSSGQ   76 (90)
Q Consensus         6 ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR-----~lT~~G~   76 (90)
                      ..|+.-|+- .+|+.+..|....+..  ++.        +-+-+-.+|+.||+.|||+..+++.+     .+|++|.
T Consensus        12 ~~vL~~L~~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~r~~~~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A           12 RAVMDHLWSRTEPQTVRQVHEALSAR--RDL--------AYTTVMAVLQRLAKKNLVLQIRDDRAHRYAPVHGRDEL   78 (138)
T ss_dssp             HHHHHHHHTCSSCEEHHHHHHHHTTT--CCC--------CHHHHHHHHHHHHHTTSEEEEC---CCEEEESSCHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHhcc--CCC--------CHHHHHHHHHHHHHCCCEEEEecCCeEEEEeCCCHHHH
Confidence            468888988 5999999999999753  222        23578889999999999998775322     2577764

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=91.52  E-value=0.35  Score=34.75  Aligned_cols=58  Identities=19%  Similarity=0.137  Sum_probs=47.2

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      .|+-.||..|.- .+++++..|.+..|-.|              +-+..+|+.|++.|||+.+. +...|+++.
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~~--------------stv~r~l~~L~~~G~v~~~~-~~Y~Lg~~~   72 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGLSR--------------PAVRRILLTLQKLGYVAGSG-GRWSLTPRV   72 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEET-TEEEECGGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeCC-CEEEEcHHH
Confidence            467778887764 46899999999998754              67889999999999999874 567888875

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=91.50  E-value=0.38  Score=32.97  Aligned_cols=46  Identities=13%  Similarity=0.158  Sum_probs=37.6

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG   75 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G   75 (90)
                      +++.+..++..++-..              ..++++|++|.++|||+...  .||-.|+..-
T Consensus        27 ~~~s~~~IA~~~~is~--------------~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p   74 (162)
T 3k69_A           27 SKVASRELAQSLHLNP--------------VMIRNILSVLHKHGYLTGTVGKNGGYQLDLAL   74 (162)
T ss_dssp             SCBCHHHHHHHHTSCG--------------GGTHHHHHHHHHTTSSEEECSTTCEEECCSCG
T ss_pred             CCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeecCCCCCeEecCCh
Confidence            4789999999888743              68999999999999998654  4678887554

>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=91.43  E-value=0.71  Score=30.04  Aligned_cols=71  Identities=8%  Similarity=0.075  Sum_probs=52.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc-----C-CCCee------eCc
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGRR------ITS   73 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~-----~-~~GR~------lT~   73 (90)
                      -.|++.|.-++++.+..|+...|-.              .+-++..|+.||+.|+|+..     + +-|+.      ++.
T Consensus         6 ~~il~~L~~~~~~~~~ela~~lg~s--------------~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~   71 (150)
T 2pn6_A            6 LRILKILQYNAKYSLDEIAREIRIP--------------KATLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKA   71 (150)
T ss_dssp             HHHHHHHTTCTTSCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSSCCCCCCCCGGGGTCCEEEEEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEEEEeecCHHHhCCceEEEEEEEe
Confidence            4578877778899999999998763              46899999999999999852     2 22544      354


Q ss_pred             ch-HhhHHHHHHHhhcCC
Q 034587           74 SG-QRDLDQVAGRIVVAP   90 (90)
Q Consensus        74 ~G-~~~lD~iA~~v~~~~   90 (90)
                      .+ ...++.++..+.+-|
T Consensus        72 ~~~~~~~~~~~~~l~~~p   89 (150)
T 2pn6_A           72 KYGKNYHVELGNKLAQIP   89 (150)
T ss_dssp             CCCTTHHHHHHHHHHTST
T ss_pred             cCChhHHHHHHHHHhcCc
Confidence            44 567888888776543

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

Probab=91.39  E-value=0.43  Score=29.57  Aligned_cols=44  Identities=16%  Similarity=0.177  Sum_probs=38.8

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE   64 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~   64 (90)
                      .|+..|--+|.+.|..|+..|+-              |-.-||.-|..||+.|+|+..
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~V--------------S~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLNT--------------PQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEe
Confidence            47777888999999999998876              457999999999999999887

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

Probab=91.36  E-value=0.41  Score=28.21  Aligned_cols=46  Identities=4%  Similarity=0.018  Sum_probs=37.1

Q ss_pred             HHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587            7 SMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK   66 (90)
Q Consensus         7 Si~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~   66 (90)
                      .||.-|--. +|+.+..|+...|-.              .+.+.++|+.||+.|+|+..++
T Consensus        14 ~IL~~L~~~~~~~s~~eLA~~lgls--------------r~tv~~~l~~L~~~G~I~~~~~   60 (67)
T 2heo_A           14 KILQVLSDDGGPVAIFQLVKKCQVP--------------KKTLNQVLYRLKKEDRVSSPSP   60 (67)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHCSC--------------HHHHHHHHHHHHHTTSEEEEET
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEecCCC
Confidence            466666545 589999999999875              4789999999999999987543

>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=91.07  E-value=0.26  Score=34.67  Aligned_cols=67  Identities=12%  Similarity=0.261  Sum_probs=49.6

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe-------------e
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR-------------R   70 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR-------------~   70 (90)
                      ..|++.|. ++++.+..|+...|-.              .+-++.-|+.||+.|+|+..  ...|+             .
T Consensus        23 ~~IL~~L~-~~~~s~~eLA~~lglS--------------~stv~~~l~~Le~~GlI~~~~~~~~~~~~~~~~g~~~~~~~   87 (192)
T 1uly_A           23 RKILKLLR-NKEMTISQLSEILGKT--------------PQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADVFY   87 (192)
T ss_dssp             HHHHHHHT-TCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSEEE
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEeccccccchhhhcCcceEEEE
Confidence            46788888 8999999999988753              36799999999999999876  22233             3


Q ss_pred             eCcchH-hhHHHHHHHhh
Q 034587           71 ITSSGQ-RDLDQVAGRIV   87 (90)
Q Consensus        71 lT~~G~-~~lD~iA~~v~   87 (90)
                      ||.++. ..++.++..+.
T Consensus        88 v~~~~~~~~~~~~~~~~~  105 (192)
T 1uly_A           88 INLYLGDEELRYIARSRL  105 (192)
T ss_dssp             ECSCSSCHHHHHHHHHHH
T ss_pred             EecCCchhHHHHHHHHHH
Confidence            677763 45666665543

>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, STRU genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum}

Probab=90.66  E-value=0.098  Score=37.13  Aligned_cols=37  Identities=16%  Similarity=0.331  Sum_probs=27.4

Q ss_pred             HHHHHHhCCcccccC-CCC------eeeCcchHhhHHHHHHHhh
Q 034587           51 ILQQLQNMNIIDIEP-KGG------RRITSSGQRDLDQVAGRIV   87 (90)
Q Consensus        51 ~LqqLE~~glV~k~~-~~G------R~lT~~G~~~lD~iA~~v~   87 (90)
                      +|.+||+.|||+... .+|      ..||++|+..+.+.-.+.+
T Consensus        54 ~l~~Le~~GlI~~~~~~~~rpektvY~ITe~Gr~~l~~~l~~~~   97 (180)
T 2rkh_A           54 SIELLRYEGLVEAVDDGQGMEDDAMLAISAAGRRELHSLLTARL   97 (180)
T ss_dssp             CTHHHHHTTSEECCC--------CEEEECHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHCCCeeeeecCCCCCccceeeeCHHHHHHHHHHHHHHh
Confidence            789999999997555 333      4799999999987655443

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

Probab=90.61  E-value=1.9  Score=29.29  Aligned_cols=70  Identities=10%  Similarity=0.167  Sum_probs=52.8

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc-----C-CCCe-------eeCc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGR-------RITS   73 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~-----~-~~GR-------~lT~   73 (90)
                      .|+..|.-++++.+..|++..|-              |.+-++..|+.||+.|+|+..     + +-|+       .+++
T Consensus        21 ~IL~~L~~~~~~s~~eLA~~lgl--------------S~~tv~~~l~~L~~~G~I~~~~~~~d~~~lG~~~a~v~v~~~~   86 (171)
T 2ia0_A           21 NILRLLKKDARLTISELSEQLKK--------------PESTIHFRIKKLQERGVIERYTIILGEQLKPKHLALIVLEVGK   86 (171)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEEEEECTTTSCSEEEEEEEEESC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeecccCCHHHhhcceEEEEEEECC
Confidence            57788888899999999999885              346899999999999999742     2 2354       3455


Q ss_pred             c-----hHhhHHHHHHHhhcCC
Q 034587           74 S-----GQRDLDQVAGRIVVAP   90 (90)
Q Consensus        74 ~-----G~~~lD~iA~~v~~~~   90 (90)
                      .     ....+|.++..+..-|
T Consensus        87 ~~~~~f~~~~~~~~~~~l~~~p  108 (171)
T 2ia0_A           87 PVIEDFLERYISYISSTLSALP  108 (171)
T ss_dssp             C--CHHHHHHHHHHHHHHHTST
T ss_pred             ccccccchhHHHHHHHHHHCCC
Confidence            5     5557888888876544

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=90.56  E-value=0.6  Score=32.13  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=37.4

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcch
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG   75 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G   75 (90)
                      +|+.+..++..++-.              -..+|++|++|.++|||+...  .||-.|+..-
T Consensus        43 ~~~s~~eIA~~~~i~--------------~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p   90 (159)
T 3lwf_A           43 GPISLRSIAQDKNLS--------------EHYLEQLIGPLRNAGIVKSIRGAHGGYVLNGDP   90 (159)
T ss_dssp             CCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECSTTCEEEECSCT
T ss_pred             CCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCeEEEecCCCCceEecCCH
Confidence            478999999988774              479999999999999998554  4688887544

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

Probab=89.87  E-value=0.49  Score=30.15  Aligned_cols=44  Identities=7%  Similarity=0.106  Sum_probs=38.6

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE   64 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~   64 (90)
                      .|+..|--+|.+.|..|+..|+-              |-.-||.-|..||+.|+|...
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l~V--------------S~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARLQT--------------PQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHTTC--------------CHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEE
Confidence            47777788999999999998876              457999999999999999876

>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=89.80  E-value=0.4  Score=28.47  Aligned_cols=51  Identities=8%  Similarity=0.120  Sum_probs=40.7

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK   66 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~   66 (90)
                      ..|+.-|+-.+|+.+..|....+-.  .+.        +-+-+..+|+.||+.|||+..++
T Consensus        12 ~~vL~~L~~~~~~t~~ei~~~l~~~--~~~--------s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A           12 LEVMKVIWKHSSINTNEVIKELSKT--STW--------SPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             HHHHHHHHTSSSEEHHHHHHHHHHH--SCC--------CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHhhc--CCc--------cHHHHHHHHHHHHHCCCeEEEec
Confidence            4678888888999999999988742  111        34678999999999999998764

>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=89.44  E-value=1.9  Score=28.16  Aligned_cols=71  Identities=11%  Similarity=0.165  Sum_probs=53.0

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc-----cC-CCCee------eCc
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI-----EP-KGGRR------ITS   73 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k-----~~-~~GR~------lT~   73 (90)
                      -.|+..|.-++++.+..|+...|-              |.+-++..|+.||+.|+|..     ++ +-|+.      ++.
T Consensus        11 ~~il~~L~~~~~~s~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~   76 (152)
T 2cg4_A           11 RGILEALMGNARTAYAELAKQFGV--------------SPETIHVRVEKMKQAGIITGARIDVSPKQLGYDVGCFIGIIL   76 (152)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTSEEEEEEEECTTTTTCCEEEEEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHcCCcceEEEecCHHHcCCeEEEEEEEEE
Confidence            367888888899999999998875              34689999999999999984     23 24654      344


Q ss_pred             chHhhHHHHHHHhhcCC
Q 034587           74 SGQRDLDQVAGRIVVAP   90 (90)
Q Consensus        74 ~G~~~lD~iA~~v~~~~   90 (90)
                      .....+|.++..+.+-|
T Consensus        77 ~~~~~~~~~~~~l~~~p   93 (152)
T 2cg4_A           77 KSAKDYPSALAKLESLD   93 (152)
T ss_dssp             SSGGGHHHHHHHHHTCT
T ss_pred             CCCCCHHHHHHHHhCCc
Confidence            44456888888876544

>3l09_A Putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG, protein structure initiative transcription regulator; 2.81A {Jannaschia SP}

Probab=89.33  E-value=0.22  Score=37.53  Aligned_cols=75  Identities=19%  Similarity=0.120  Sum_probs=55.3

Q ss_pred             hhHHHHHHHHhh---c---CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC---CeeeCc
Q 034587            3 ELVTSMARKIYL---R---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS   73 (90)
Q Consensus         3 ~r~ASi~RklYl---~---g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~---GR~lT~   73 (90)
                      .++-|++-.||-   .   +.+-++.|-.....-   |        =+...+|.+|.-|++.||++....|   +..||+
T Consensus        22 ~~a~Sli~tl~Gd~~~~~g~~i~~~~Li~l~~~~---G--------i~~~avR~Al~RL~~~G~l~~~~~Gr~~~Y~Lt~   90 (266)
T 3l09_A           22 LKLWSVLVTCLGDVSRDGVIEVSGVALSSFVERM---G--------LQPQAMRVALHRLKRDGWVESRRLGRVGFHRLSD   90 (266)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCCEEHHHHHHHHHHT---T--------CCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECH
T ss_pred             CChhHHHHHHHHHHhccCCCcccHHHHHHHHHHc---C--------CCchHHHHHHHHHHHCCCeeeeecCCcceEEECH
Confidence            367788888883   2   467788766554431   1        1236899999999999999877544   578999


Q ss_pred             chHhhHHHHHHHhhc
Q 034587           74 SGQRDLDQVAGRIVV   88 (90)
Q Consensus        74 ~G~~~lD~iA~~v~~   88 (90)
                      .|++.+++....|..
T Consensus        91 ~g~~~l~~~~~ri~~  105 (266)
T 3l09_A           91 SALTQTRAVAGRIYG  105 (266)
T ss_dssp             HHHHHHHTTHHHHHS
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999887776653

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=88.96  E-value=0.48  Score=34.91  Aligned_cols=50  Identities=16%  Similarity=0.309  Sum_probs=38.9

Q ss_pred             cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHH-HHHhCCcccccCCCCeeeCcchHhhH
Q 034587           15 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDL   79 (90)
Q Consensus        15 ~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~Lq-qLE~~glV~k~~~~GR~lT~~G~~~l   79 (90)
                      .+|+|+..|+..+|-..              .-++.+.+ .|..+|+|+..+. ||++|++|-+.|
T Consensus       274 ~~~~~~~~l~~~~~~~~--------------~t~~~~~~~~l~~~g~i~~~~~-gr~~~~~~~~~~  324 (334)
T 1in4_A          274 GGPVGLNALAASLGVEA--------------DTLSEVYEPYLLQAGFLARTPR-GRIVTEKAYKHL  324 (334)
T ss_dssp             TCCBCHHHHHHHHTSCH--------------HHHHHHTHHHHHHTTSEEEETT-EEEECHHHHHHT
T ss_pred             CCcchHHHHHHHhCCCc--------------chHHHHHHHHHHHcCCeecccc-cHHhhHHHHHHh
Confidence            47889999998877532              22444444 8999999999985 999999998876

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=88.88  E-value=0.92  Score=33.46  Aligned_cols=47  Identities=13%  Similarity=0.168  Sum_probs=40.5

Q ss_pred             hHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccc-cc
Q 034587            4 LVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID-IE   64 (90)
Q Consensus         4 r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~-k~   64 (90)
                      |-+..+-.+|-.+++++..|++.+|-              |..-||.-|+.||+.|+|+ +.
T Consensus         8 ~~~~~ia~l~~~~~~~~~ela~~l~v--------------S~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A            8 RLIVKIAQLYYEQDMTQAQIARELGI--------------YRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEEe
Confidence            55566777888999999999999986              5579999999999999997 44

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=88.59  E-value=0.41  Score=34.32  Aligned_cols=42  Identities=17%  Similarity=0.207  Sum_probs=35.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      ....|+..||-              |..-+|.+|++|++.|+|+..+..|-.+++.
T Consensus        36 se~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~~   77 (243)
T 2wv0_A           36 SEREYAEQFGI--------------SRMTVRQALSNLVNEGLLYRLKGRGTFVSKP   77 (243)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECCC
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEeCCCeEEEeCC
Confidence            67888888886              3578999999999999999888778777754

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=88.59  E-value=0.36  Score=35.37  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=34.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      ....|+..||-              |...+|.+|++|++.|+|+..+..|-.+++.
T Consensus        55 se~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~~   96 (272)
T 3eet_A           55 SQARIREEYGV--------------SDTVALEARKVLMAEGLVEGRSGSGTYVRER   96 (272)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECCC--EEECCC
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceEEEecC
Confidence            67889999886              4579999999999999999888777777654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=88.23  E-value=0.46  Score=34.36  Aligned_cols=57  Identities=16%  Similarity=0.118  Sum_probs=45.6

Q ss_pred             hhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587            3 ELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus         3 ~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      .|+-.||.-|.- .+++++..|....|-.|              +-+..+|+.|++.|||+++. +...|+++
T Consensus        21 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~~--------------stv~r~l~tL~~~G~v~~~~-~~Y~Lg~~   78 (265)
T 2ia2_A           21 ARGLAVIRCFDHRNQRRTLSDVARATDLTR--------------ATARRFLLTLVELGYVATDG-SAFWLTPR   78 (265)
T ss_dssp             HHHHHHHHTCCSSCSSEEHHHHHHHHTCCH--------------HHHHHHHHHHHHHTSEEESS-SEEEECGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEecC-CEEEEcHH
Confidence            467778877654 46899999999988754              67889999999999999874 55677765

>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=88.12  E-value=0.47  Score=31.49  Aligned_cols=54  Identities=9%  Similarity=0.167  Sum_probs=38.1

Q ss_pred             HHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcch
Q 034587            7 SMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG   75 (90)
Q Consensus         7 Si~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~G   75 (90)
                      .++-.|..+ ++ .+..++..++-              +-..++++|++|.++|||+... .||-.|+..-
T Consensus        13 ~~L~~La~~~~~-s~~~IA~~~~i--------------~~~~l~kIl~~L~~aGlv~s~rG~GGy~Lar~p   68 (145)
T 1xd7_A           13 HILSLISMDEKT-SSEIIADSVNT--------------NPVVVRRMISLLKKADILTSRAGVPGASLKKDP   68 (145)
T ss_dssp             HHHHHHHTCSCC-CHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEECCSSSSSCEESSCG
T ss_pred             HHHHHHHhCCCC-CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEeecCCCCceecCCH
Confidence            344444443 23 67777777665              3479999999999999998554 5788887654

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=88.01  E-value=0.36  Score=34.54  Aligned_cols=42  Identities=14%  Similarity=0.204  Sum_probs=35.6

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      ....|+..||-              |..-+|.+|+.|++.|+|+..+..|-.+++.
T Consensus        35 se~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~~   76 (236)
T 3edp_A           35 NETALQEIYSS--------------SRTTIRRAVDLLVEEGLVVRKNGVGLYVQPK   76 (236)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCC
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEECCceEEEccC
Confidence            67788888876              4579999999999999999988778777764

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

Probab=87.70  E-value=0.53  Score=30.12  Aligned_cols=52  Identities=19%  Similarity=0.162  Sum_probs=40.9

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCe
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR   69 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR   69 (90)
                      .||+-|+-.+|+.+..|....+..  .+        -+-+-+-.+|+.||+.|||+..+. ||
T Consensus        39 ~VL~~L~~~~~~t~~eL~~~l~~~--~~--------~s~sTVt~~L~rLe~KGlV~R~~~-gR   90 (99)
T 2k4b_A           39 IVMRVIWSLGEARVDEIYAQIPQE--LE--------WSLATVKTLLGRLVKKEMLSTEKE-GR   90 (99)
T ss_dssp             HHHHHHHHHSCEEHHHHHHTCCGG--GC--------CCHHHHHHHHHHHHHTTSCEEEEE-TT
T ss_pred             HHHHHHHhCCCCCHHHHHHHHhcc--cC--------CCHhhHHHHHHHHHHCCCEEEEeC-CC
Confidence            578888888999999999987642  11        234678899999999999998763 54

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

Probab=87.51  E-value=3.2  Score=27.33  Aligned_cols=70  Identities=14%  Similarity=0.077  Sum_probs=52.0

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc-----C-CCCee--------e
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGRR--------I   71 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~-----~-~~GR~--------l   71 (90)
                      -.|+..|.-++++.+..|+...|-              |.+-++..|+.||+.|+|+..     + +-|..        +
T Consensus        13 ~~il~~L~~~~~~s~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~   78 (162)
T 2p5v_A           13 IKILQVLQENGRLTNVELSERVAL--------------SPSPCLRRLKQLEDAGIVRQYAALLSPESVNLGLQAFIRVSI   78 (162)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEEEEECTGGGTCCEEEEEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEeeecccCChHHhcccEEEEEEEEE
Confidence            468888888899999999998875              346789999999999999842     1 12442        2


Q ss_pred             CcchHhhHHHHHHHhhcCC
Q 034587           72 TSSGQRDLDQVAGRIVVAP   90 (90)
Q Consensus        72 T~~G~~~lD~iA~~v~~~~   90 (90)
                      ++.. ..++.++..+.+-|
T Consensus        79 ~~~~-~~~~~~~~~l~~~p   96 (162)
T 2p5v_A           79 RKAK-DAREDFAASVRKWP   96 (162)
T ss_dssp             CSST-THHHHHHHHHTTCT
T ss_pred             cCCc-hHHHHHHHHHhcCh
Confidence            4544 66888888775543

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=87.09  E-value=0.44  Score=34.00  Aligned_cols=41  Identities=12%  Similarity=0.037  Sum_probs=34.2

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      ....|+..||-              |..-+|.+|+.|++.|+|+..+..|-.+++
T Consensus        31 se~~La~~~~v--------------Sr~tvr~Al~~L~~~g~i~~~~g~G~~V~~   71 (239)
T 3bwg_A           31 VLETLMAQFEV--------------SKSTITKSLELLEQKGAIFQVRGSGIFVRK   71 (239)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEeCCceEEEec
Confidence            67889998886              457999999999999999988866766654

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=86.93  E-value=0.39  Score=34.59  Aligned_cols=41  Identities=7%  Similarity=0.045  Sum_probs=33.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS   74 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~   74 (90)
                      ....|+..||-              |...+|.+|++|++.|||+. +..|-.+++.
T Consensus        38 se~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~-~g~Gt~V~~~   78 (248)
T 3f8m_A           38 AEREIAEQFEV--------------ARETVRQALRELLIDGRVER-RGRTTVVARP   78 (248)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEE-ETTEEEECCC
T ss_pred             CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEe-CCCEEEEccC
Confidence            66788888876              45799999999999999999 8777766653

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=86.41  E-value=0.94  Score=26.74  Aligned_cols=54  Identities=7%  Similarity=-0.003  Sum_probs=40.1

Q ss_pred             hHHHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC
Q 034587            4 LVTSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK   66 (90)
Q Consensus         4 r~ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~   66 (90)
                      +--.|+.-|.-.  +++.+..|........     |    .-|-+-++..|+.||+.|+|.+...
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~-----~----~is~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMG-----E----EIGLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTT-----C----CCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhC-----C----CCCHhhHHHHHHHHHHCCCeEEEee
Confidence            345677777654  6899999999884321     1    2355789999999999999987653

>3kfw_X Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.50A {Mycobacterium tuberculosis}

Probab=85.52  E-value=1.1  Score=33.11  Aligned_cols=75  Identities=12%  Similarity=0.065  Sum_probs=56.4

Q ss_pred             ChhhHHHHHHHHhhc---CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHh
Q 034587            1 MSELVTSMARKIYLR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR   77 (90)
Q Consensus         1 ~~~r~ASi~RklYl~---g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~   77 (90)
                      |..++=|++=.||+-   +.+-++.|-.....   =|+        +...+|.+|--|-+.||++... .|..||+.|++
T Consensus         1 ~~~~arSlIlsll~g~~g~~i~~~~Li~l~~~---~Gi--------~e~avRtAlsRL~~~G~L~~~~-~GY~LT~~~~~   68 (247)
T 3kfw_X            1 MSLTARSVVLSVLLGAHPAWATASELIQLTAD---FGI--------KETTLRVALTRMVGAGDLVRSA-DGYRLSDRLLA   68 (247)
T ss_dssp             -CCCHHHHHHHHHTTTTTSCBCHHHHHHHHTT---TTC--------CHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHH
T ss_pred             CCCCCceeeEeeecCCCCCcccHHHHHHHHHH---cCC--------ChHHHHHHHHHHHHcCCeeccC-CceeeCHHHHH
Confidence            556677777777653   46888888777653   232        2368999999999999999765 57999999999


Q ss_pred             hHHHHHHHhh
Q 034587           78 DLDQVAGRIV   87 (90)
Q Consensus        78 ~lD~iA~~v~   87 (90)
                      .+++....|.
T Consensus        69 ~~~~~~~rI~   78 (247)
T 3kfw_X           69 RQRRQDEAMR   78 (247)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHHhc
Confidence            8887766554

>1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4 cluster; HET: SAM; 2.07A {Escherichia coli} SCOP: c.1.28.2

Probab=84.59  E-value=0.64  Score=36.16  Aligned_cols=62  Identities=13%  Similarity=0.213  Sum_probs=42.1

Q ss_pred             hcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHHh
Q 034587           14 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        14 l~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~v   86 (90)
                      ...++-...+...||-.         +..--.. .-..|++|++.|||+.+. +.=+||++|+-.+|.|+...
T Consensus       379 ~~~g~~~~~~~~~~g~~---------~~~~~~~-~~~~l~~~~~~gll~~~~-~~~~lT~~G~~~~~~i~~~f  440 (457)
T 1olt_A          379 CNFRLDYSPIEQQWDLL---------FADYFAE-DLKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICMCF  440 (457)
T ss_dssp             HHSEEEHHHHHHHTTCC---------HHHHTHH-HHHHHHHHHHTTSEEECS-SEEEECTTTGGGHHHHHHTT
T ss_pred             HcCCCCHHHHHHHhCCC---------HHHHHHH-HHHHHHHHHHCCCEEEEC-CEEEECHhhHHHHHHHHHHH
Confidence            34566667777777642         0000011 123478999999998764 46689999999999999875

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=84.56  E-value=1.6  Score=26.95  Aligned_cols=60  Identities=12%  Similarity=0.201  Sum_probs=44.9

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC---eeeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G---R~lT~~G~~~lD~   81 (90)
                      .|++.+.-+++..+..|+...|-.              .+-+.+-|+.||++ +|+...+|.   -.||+.+...+-+
T Consensus        31 ~IL~~l~~~~~~~~~ela~~l~is--------------~stvs~hL~~L~~~-lv~~~~~gr~~~y~l~~~~~~~~~~   93 (99)
T 2zkz_A           31 KIVNELYKHKALNVTQIIQILKLP--------------QSTVSQHLCKMRGK-VLKRNRQGLEIYYSINNPKVEGIIK   93 (99)
T ss_dssp             HHHHHHHHHSCEEHHHHHHHHTCC--------------HHHHHHHHHHHBTT-TBEEEEETTEEEEECCCHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHH-hhhheEeCcEEEEEEChHHHHHHHH
Confidence            466666678999999999988764              36888999999999 998665432   3478877655543

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=84.10  E-value=1.8  Score=32.48  Aligned_cols=57  Identities=12%  Similarity=0.218  Sum_probs=46.2

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ   81 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~   81 (90)
                      .++|.|  ++|..+..|+..+|-.              -..++..|++|.++|+++...  |-++|+.+...|.+
T Consensus        47 ~ll~~L--~~~~t~~eLa~~~g~~--------------~~~v~~~L~~l~~~gll~~~~--~~~lt~~~~~~l~~  103 (373)
T 2qm3_A           47 NVLSAV--LASDDIWRIVDLSEEP--------------LPLVVAILESLNELGYVTFED--GVKLTEKGEELVAE  103 (373)
T ss_dssp             HHHHHH--HHCSCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEECSS--SSEECHHHHHHHHH
T ss_pred             HHHHHh--cCCCCHHHHHHHhCCC--------------hHHHHHHHHHHhhCCcEEECC--CEEECHHHHHHHHh
Confidence            357777  7888999999888653              357999999999999998754  59999999877765

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

Probab=84.06  E-value=4.8  Score=25.71  Aligned_cols=46  Identities=4%  Similarity=0.123  Sum_probs=37.8

Q ss_pred             HHHHHHHhhcCC--CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            6 TSMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         6 ASi~RklYl~g~--vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      ..|+..|+-.++  +.+..|+...|-              |.+-+...|+.||+.|+|+..+
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~--------------s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKL--------------DVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeeC
Confidence            567888887665  899999998873              5578999999999999998643

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

Probab=82.08  E-value=0.59  Score=34.12  Aligned_cols=42  Identities=5%  Similarity=0.002  Sum_probs=33.3

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI   63 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k   63 (90)
                      .|++.|+ .+|..+..|+...|-              |.+-+.+.|+.||++|||+.
T Consensus        16 ~IL~~L~-~g~~s~~ELa~~lgl--------------S~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A           16 DLLSHLT-CMECYFSLLSSKVSV--------------SSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             HHHHHHT-TTTTCSSSSCTTCCC--------------CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHH-hCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEE
Confidence            4777776 688888888776543              45789999999999999987

>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=80.58  E-value=2.7  Score=29.72  Aligned_cols=44  Identities=14%  Similarity=0.143  Sum_probs=36.0

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      .|+..| ..+|..+..|+...|              -|.+-+-..|+.||+.|||+...
T Consensus        19 ~IL~~L-~~~~~s~~eLa~~l~--------------is~stvs~hLk~Le~~GLV~~~~   62 (202)
T 2p4w_A           19 RILFLL-TKRPYFVSELSRELG--------------VGQKAVLEHLRILEEAGLIESRV   62 (202)
T ss_dssp             HHHHHH-HHSCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHH-HhCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCceEEEe
Confidence            466666 378999999999885              35578999999999999998654

---

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	90
d2v7fa1	149	a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococ	7e-38

>d2v7fa1 a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococcus abyssi [TaxId: 29292]} Length = 149

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rps19E-like
domain: Ribosomal protein S19e
species: Pyrococcus abyssi [TaxId: 29292]

 Score =  121 bits (306), Expect = 7e-38
 Identities = 30/81 (37%), Positives = 44/81 (54%)

Query: 6   TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 65
            S+ R++YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  P
Sbjct: 55  ASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVP 114

Query: 66  KGGRRITSSGQRDLDQVAGRI 86
             GR IT  G+  LD++A  +
Sbjct: 115 GKGRVITPKGRSFLDKIATEL 135

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	90
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	100.0
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	97.97
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.33
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.29
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.26
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	97.24
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.23
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.23
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.11
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	97.08
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.03
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.77
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	96.63
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.61
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	96.59
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.59
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.57
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.56
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	96.54
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.51
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.45
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.37
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	96.04
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	95.97
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	95.97
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.95
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	95.73
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	95.65
d1ixsb1	76	Holliday junction helicase RuvB {Thermus thermophi	95.64
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	95.5
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	95.46
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	95.43
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	95.34
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.13
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	94.89
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	94.66
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.64
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.6
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	94.54
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	94.48
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	94.46
d2axla1	144	Werner syndrome ATP-dependent helicase WRN {Human	93.86
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	93.21
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	93.09
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.91
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.69
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	91.58
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	91.43
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	89.94
d1olta_	441	Oxygen-independent coproporphyrinogen III oxidase	89.89
d2fnaa1	73	Hypothetical protein SSO1545, C-terminal domain {S	88.94
d1bjaa_	95	Transcription factor MotA, activation domain {Bact	88.83
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	86.62
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	85.5
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	84.68
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	84.26
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	83.68

>d2v7fa1 a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococcus abyssi [TaxId: 29292]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rps19E-like
domain: Ribosomal protein S19e
species: Pyrococcus abyssi [TaxId: 29292]

Probab=100.00  E-value=2.3e-44  Score=255.47  Aligned_cols=86  Identities=36%  Similarity=0.620  Sum_probs=80.4

Q ss_pred             hhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            3 ELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         3 ~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +||||||||||++||+||++|++.|||+||||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+|
T Consensus        52 ~RaASilRkiY~~gpvGv~~Lr~~YGg~k~rG~~P~h~~~~Sg~iiR~~LQqLE~~glVek~~~~GR~lT~~G~~~LD~i  131 (149)
T d2v7fa1          52 YRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKI  131 (149)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHCCCCCCCCCCCCcCCCccHHHHHHHHHHHhCCCeeEcCCCCcEECHHHHHHHHHH
Confidence            69999999999999999999999999999999999999999999999999999999999999989999999999999999


Q ss_pred             HHHhhc
Q 034587           83 AGRIVV   88 (90)
Q Consensus        83 A~~v~~   88 (90)
                      |.+|.+
T Consensus       132 A~~v~~  137 (149)
T d2v7fa1         132 ATELKK  137 (149)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999975

>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=97.97  E-value=1.4e-05  Score=50.23  Aligned_cols=66  Identities=17%  Similarity=0.157  Sum_probs=51.4

Q ss_pred             ChhhHHHHHHH---Hhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcc
Q 034587            1 MSELVTSMARK---IYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSS   74 (90)
Q Consensus         1 ~~~r~ASi~Rk---lYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~   74 (90)
                      |+.|-..||+-   .|+.  -|+|...+.+.||-+            -|.+-||+.|++||+.|+|++.. ..||..|++
T Consensus         2 Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~------------~S~aTIRn~m~~LE~~G~l~~~h~s~GriPT~~   69 (87)
T d1stza1           2 LNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIE------------FSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDK   69 (87)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCC------------SCHHHHHHHHHHHHHTTSEECCSSCSCBEECHH
T ss_pred             cCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCC------------CCHHHHHHHHHHHHHCCcccCCCCCCCCcccHH
Confidence            34566666654   4664  599999999987653            26689999999999999998644 579999999


Q ss_pred             hHhh
Q 034587           75 GQRD   78 (90)
Q Consensus        75 G~~~   78 (90)
                      |.+.
T Consensus        70 g~r~   73 (87)
T d1stza1          70 GLRF   73 (87)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9753

>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=97.33  E-value=0.00018  Score=43.98  Aligned_cols=66  Identities=8%  Similarity=0.087  Sum_probs=52.3

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC----eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G----R~lT~~G~~~l   79 (90)
                      -+|+..|+-+|++.++.|+...|-.+              +-+-..|..||+.|||+..+  .++    -.||++|+..+
T Consensus        19 ~~IL~~L~~~~~~~~~eLa~~l~is~--------------~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~   84 (100)
T d1ub9a_          19 LGIMIFLLPRRKAPFSQIQKVLDLTP--------------GNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEA   84 (100)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHhccCCCeeHHHHHHHHhhcc--------------ccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHH
Confidence            46888999999999999999887643              56777899999999998554  233    35999999888


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      .+....
T Consensus        85 ~~~~~~   90 (100)
T d1ub9a_          85 KRFLSS   90 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876544

>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=97.29  E-value=0.00032  Score=44.70  Aligned_cols=66  Identities=21%  Similarity=0.363  Sum_probs=54.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..+|..||-.||+.+..|+..-|-.+              +-+-.+++.||+.|||++.+  +++|    .||++|+..+
T Consensus        33 ~~iL~~i~~~~~~t~~~la~~l~i~~--------------~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~   98 (139)
T d2a61a1          33 FDILQKIYFEGPKRPGELSVLLGVAK--------------STVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVI   98 (139)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCc--------------ccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHH
Confidence            46889999999999999999887753              56888999999999998554  3455    4899999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +++...
T Consensus        99 ~~~~~~  104 (139)
T d2a61a1          99 EKVIER  104 (139)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=97.26  E-value=0.0005  Score=44.05  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=52.8

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..||..|+-.+++.+..|++.-+-.+              +-+-.+++.||+.|||++.+  +.+|    .||++|+..+
T Consensus        39 ~~vL~~l~~~~~~t~~~la~~l~~~~--------------~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~  104 (141)
T d1lnwa_          39 VHVLKLIDEQRGLNLQDLGRQMCRDK--------------ALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIH  104 (141)
T ss_dssp             HHHHHHHHSSTTCBHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCccH--------------hHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHH
Confidence            45777888888899999998776643              67888999999999998555  4455    5899999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +.+...
T Consensus       105 ~~~~~~  110 (141)
T d1lnwa_         105 QHAEAI  110 (141)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=97.24  E-value=0.00052  Score=41.61  Aligned_cols=60  Identities=22%  Similarity=0.346  Sum_probs=50.4

Q ss_pred             HHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587            8 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus         8 i~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      +++-+|+ +.|+|=..|+..-|-.              =.++|.-+.-|-+.|+|+..+ .|=.||++|+++++++
T Consensus         7 vl~~l~ll~qPiGRr~La~~L~l~--------------Er~vRte~~~Lk~~gLI~~~~-~Gm~lTe~G~~~l~~L   67 (69)
T d2p8ta1           7 VLAVIFLLKEPLGRKQISERLELG--------------EGSVRTLLRKLSHLDIIRSKQ-RGHFLTLKGKEIRDKL   67 (69)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHHcCCc--------------HHHHHHHHHHHHHCCCeeeeC-CCCEECHhHHHHHHHH
Confidence            4566664 8999999999987763              359999999999999999886 7999999999999876

>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=97.23  E-value=0.0004  Score=44.08  Aligned_cols=71  Identities=15%  Similarity=0.136  Sum_probs=57.2

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG   75 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G   75 (90)
                      +.--..||..|+-.|++.+..|+...+-.+              +-+=.+++.||+.|||++.+  .++|    .||++|
T Consensus        29 t~~q~~vL~~l~~~~~~t~~~la~~~~i~~--------------~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G   94 (136)
T d2fbia1          29 TEQQWRVIRILRQQGEMESYQLANQACILR--------------PSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKG   94 (136)
T ss_dssp             CHHHHHHHHHHHHHCSEEHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHH
Confidence            445678899999999999999999877643              56778999999999998554  4455    479999


Q ss_pred             HhhHHHHHHHh
Q 034587           76 QRDLDQVAGRI   86 (90)
Q Consensus        76 ~~~lD~iA~~v   86 (90)
                      +..++.+-...
T Consensus        95 ~~~~~~~~~~~  105 (136)
T d2fbia1          95 QQCFVSMSGDM  105 (136)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999876543

>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=97.23  E-value=0.00038  Score=44.44  Aligned_cols=66  Identities=15%  Similarity=0.174  Sum_probs=54.3

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..+|..||-.+|+.++.|++..+-.              .+-+-.+++.||+.|||++.+  +.+|    .||++|+..+
T Consensus        38 ~~iL~~l~~~~~~t~~~la~~~~i~--------------~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~  103 (143)
T d1s3ja_          38 LFVLASLKKHGSLKVSEIAERMEVK--------------PSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKF  103 (143)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHH
Confidence            3688999999999999999988774              367888999999999998544  4455    6999999998


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +.+-..
T Consensus       104 ~~~~~~  109 (143)
T d1s3ja_         104 EEVLAG  109 (143)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876544

>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=97.11  E-value=0.0012  Score=41.95  Aligned_cols=66  Identities=12%  Similarity=0.127  Sum_probs=54.1

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR----~lT~~G~~~l   79 (90)
                      ..+|..|+-++++.+..|+..-+-.              .+-+-.+++.||+.|||++.  ++++|    .||++|+..+
T Consensus        37 ~~vL~~l~~~~~~t~~ela~~~~i~--------------~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~  102 (138)
T d1jgsa_          37 FKVLCSIRCAACITPVELKKVLSVD--------------LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAIC  102 (138)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHH
T ss_pred             HHHHHhHHhCcCCCHHHHHHHHCCC--------------HhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHH
Confidence            4688889999999999999987764              36788899999999999854  44566    6899999998


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +++...
T Consensus       103 ~~~~~~  108 (138)
T d1jgsa_         103 EQCHQL  108 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886543

>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=97.08  E-value=0.001  Score=41.79  Aligned_cols=69  Identities=7%  Similarity=0.070  Sum_probs=52.3

Q ss_pred             HHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchH
Q 034587            5 VTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQ   76 (90)
Q Consensus         5 ~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~   76 (90)
                      -..||..||..+  ++.+..|++..+-.              .+-+=.+++.||+.|||++.+  +++|    .|||+|+
T Consensus        35 q~~vL~~l~~~~~~~~t~~~la~~l~~~--------------~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~  100 (115)
T d2frha1          35 EFAVLTYISENKEKEYYLKDIINHLNYK--------------QPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQR  100 (115)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSSH--------------HHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHCCC--------------HhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHH
Confidence            345777777754  46788888866543              356778999999999998665  4455    4999999


Q ss_pred             hhHHHHHHHhh
Q 034587           77 RDLDQVAGRIV   87 (90)
Q Consensus        77 ~~lD~iA~~v~   87 (90)
                      +.++.+..++-
T Consensus       101 ~~~~~~~~~~~  111 (115)
T d2frha1         101 KKIESLLSRVN  111 (115)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887764

>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=97.03  E-value=0.0012  Score=41.88  Aligned_cols=67  Identities=10%  Similarity=0.112  Sum_probs=54.7

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      .-||-.||-.|++.+..|+...+-.+              +-+-.++..||+.|||++.+  .++|    .||++|+..+
T Consensus        35 ~~iL~~l~~~~~~t~~~La~~l~i~~--------------~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~  100 (140)
T d2etha1          35 LYAFLYVALFGPKKMKEIAEFLSTTK--------------SNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIF  100 (140)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHTTSCH--------------HHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHH
Confidence            45788899999999999999887643              67888999999999998554  4444    5899999999


Q ss_pred             HHHHHHh
Q 034587           80 DQVAGRI   86 (90)
Q Consensus        80 D~iA~~v   86 (90)
                      +++...+
T Consensus       101 ~~~~~~~  107 (140)
T d2etha1         101 GEILSNF  107 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876654

>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=96.77  E-value=0.0028  Score=39.73  Aligned_cols=66  Identities=9%  Similarity=0.123  Sum_probs=50.4

Q ss_pred             HHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            7 SMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         7 Si~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      .|+..||-.+  ++.+..|+..-+-.+              +-+-.+++.||+.|||++..  +.+|    .|||+|+..
T Consensus        33 ~vL~~l~~~~~~~it~~ela~~~~~~~--------------~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~   98 (135)
T d3broa1          33 TIIDYLSRNKNKEVLQRDLESEFSIKS--------------STATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKL   98 (135)
T ss_dssp             HHHHHHHHTTTSCCBHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTT
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCH--------------hHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHH
Confidence            4677777764  488888988776643              56778999999999997543  4443    689999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      .+++...+
T Consensus        99 ~~~~~~~~  106 (135)
T d3broa1          99 ETIILSYM  106 (135)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887654

>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=96.63  E-value=0.0044  Score=39.60  Aligned_cols=68  Identities=9%  Similarity=0.088  Sum_probs=55.1

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      -..+|..|+-++|+.+..|+...+-.+              +-+-.+++.||+.|||++.+  +++|    .||++|+..
T Consensus        31 q~~iL~~i~~~~~~t~~~la~~l~i~~--------------~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~   96 (144)
T d1lj9a_          31 QYLYLVRVCENPGIIQEKIAELIKVDR--------------TTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNV   96 (144)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCccH--------------hhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHH
Confidence            356888899999999999999887753              67888999999999998555  3444    589999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      .+++...+
T Consensus        97 ~~~~~~~~  104 (144)
T d1lj9a_          97 YPIIVREN  104 (144)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88876654

>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=96.61  E-value=0.0014  Score=39.85  Aligned_cols=56  Identities=21%  Similarity=0.176  Sum_probs=43.6

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCee----eCcchHhhHHHHHHHh
Q 034587           16 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR----ITSSGQRDLDQVAGRI   86 (90)
Q Consensus        16 g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~----lT~~G~~~lD~iA~~v   86 (90)
                      +++.+..|+..-|-.+              +-+-.+|+.||+.|||+..++ ||.    ||++|+..+.+...++
T Consensus        20 ~~lt~~eLa~~l~i~~--------------~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~G~~~l~~~~~~~   79 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQ--------------QSASRIIIDLEKNGYITRTVT-KRGQILNITEKGLDVLYTEFADL   79 (85)
T ss_dssp             EECCHHHHHHHHTSCH--------------HHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeeeecc-cccccceECHHHHHHHHHHHHHH
Confidence            4677788887666543              567789999999999998665 443    7999999999887665

>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=96.59  E-value=0.00053  Score=43.64  Aligned_cols=63  Identities=11%  Similarity=0.115  Sum_probs=49.4

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..||-.|+..+++.+..|+..-+-.+              +-+=.+++.||+.|||+..+  +++|    .||++|+...
T Consensus        36 ~~vL~~l~~~~~~t~~~La~~~~i~~--------------~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~  101 (137)
T d1z91a1          36 YLALLLLWEHETLTVKKMGEQLYLDS--------------GTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLK  101 (137)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHTTTCCH--------------HHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGG
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHH
Confidence            45788888889999999998665532              34556999999999998554  5577    7999999887


Q ss_pred             HHH
Q 034587           80 DQV   82 (90)
Q Consensus        80 D~i   82 (90)
                      +++
T Consensus       102 ~~~  104 (137)
T d1z91a1         102 EKA  104 (137)
T ss_dssp             GGT
T ss_pred             HHH
Confidence            764

>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=96.59  E-value=0.009  Score=35.08  Aligned_cols=60  Identities=8%  Similarity=-0.065  Sum_probs=50.8

Q ss_pred             hhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchH
Q 034587            3 ELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ   76 (90)
Q Consensus         3 ~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~   76 (90)
                      .|+-.|+..|.-. +|+++..+++.-|-.+              +-+..+|+.|++.|||++++++--.|+++--
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~~~--------------st~~rll~tL~~~g~l~~~~~g~y~lG~~l~   65 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNMSV--------------SNAYKYMVVLEEKGFVLRKKDKRYVPGYKLI   65 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEECTTSCEEECTHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEECCCCCEeecHHHH
Confidence            5788999988875 6899999999877643              7899999999999999999877678888754

>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=96.57  E-value=0.003  Score=39.90  Aligned_cols=65  Identities=9%  Similarity=0.136  Sum_probs=51.8

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..|+..|+-.+|+.++.|+..-|-.+              +-+-.+++.||+.|||++.+  .++|    .||++|+..+
T Consensus        37 ~~vL~~i~~~~~~t~~~la~~l~~~~--------------~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~  102 (136)
T d2bv6a1          37 FLVLTILWDESPVNVKKVVTELALDT--------------GTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIR  102 (136)
T ss_dssp             HHHHHHHHHSSEEEHHHHHHHTTCCT--------------TTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCCH--------------hHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHH
Confidence            46788899999999999999887754              45778999999999998544  3454    4699999988


Q ss_pred             HHHHH
Q 034587           80 DQVAG   84 (90)
Q Consensus        80 D~iA~   84 (90)
                      +++..
T Consensus       103 ~~~~~  107 (136)
T d2bv6a1         103 PELSN  107 (136)
T ss_dssp             HHHTT
T ss_pred             HHHHH
Confidence            87653

>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=96.56  E-value=0.001  Score=41.58  Aligned_cols=41  Identities=22%  Similarity=0.306  Sum_probs=34.3

Q ss_pred             ccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHH
Q 034587           41 CKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV   82 (90)
Q Consensus        41 ~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~i   82 (90)
                      ++=|-..+...|+.|++.|+|++.. +...||++|+.+|+.+
T Consensus        28 aNLs~~~~~kyl~~L~~~GLI~~~~-~~Y~iT~kG~~~L~~~   68 (90)
T d1r7ja_          28 ANLSYALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDI   68 (90)
T ss_dssp             HTCCHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHCCCeeecC-CEEEECccHHHHHHHH
Confidence            3345568889999999999998764 5789999999998875

>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=96.54  E-value=0.0039  Score=39.05  Aligned_cols=68  Identities=9%  Similarity=0.177  Sum_probs=52.5

Q ss_pred             HHHHHHHhhc--CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            6 TSMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~--g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      ..||..||..  +++.+..|+...+-.              .+-+=.+++.||+.|||++.+  +++|    .||++|+.
T Consensus        35 ~~vL~~l~~~~~~~~t~~ela~~l~~~--------------~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~  100 (115)
T d1hsja1          35 IYILNHILRSESNEISSKEIAKCSEFK--------------PYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKA  100 (115)
T ss_dssp             HHHHHHHHTCSCSEEEHHHHHHSSCCC--------------HHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHH
T ss_pred             HHHHHHHHccCCCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHH
Confidence            4678888874  468888998866653              245667899999999998655  4566    48999999


Q ss_pred             hHHHHHHHhh
Q 034587           78 DLDQVAGRIV   87 (90)
Q Consensus        78 ~lD~iA~~v~   87 (90)
                      .++++..++-
T Consensus       101 ~~~~~~~~~~  110 (115)
T d1hsja1         101 NIQKLISELE  110 (115)
T ss_dssp             HHHHHHHHHG
T ss_pred             HHHHHHHHHH
Confidence            9999887763

>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=96.51  E-value=0.0053  Score=38.96  Aligned_cols=66  Identities=15%  Similarity=0.157  Sum_probs=51.1

Q ss_pred             HHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhh
Q 034587            6 TSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD   78 (90)
Q Consensus         6 ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~   78 (90)
                      ..+|..||-. |++.+..|+...|-.+              +-+-.+++.||+.|||++.+  .+.|    .||++|+..
T Consensus        37 ~~vL~~L~~~~g~~t~~~La~~~~~~~--------------~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~  102 (145)
T d2hr3a1          37 LVVLGAIDRLGGDVTPSELAAAERMRS--------------SNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN  102 (145)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTCCH--------------HHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHH
Confidence            5678888865 5799999999888753              57888999999999998665  3333    589999999


Q ss_pred             HHHHHHH
Q 034587           79 LDQVAGR   85 (90)
Q Consensus        79 lD~iA~~   85 (90)
                      ++++...
T Consensus       103 ~~~~~~~  109 (145)
T d2hr3a1         103 LYGNRAK  109 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887644

>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=96.45  E-value=0.0037  Score=38.41  Aligned_cols=71  Identities=13%  Similarity=0.172  Sum_probs=54.1

Q ss_pred             hhhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC----CC--eeeCcc
Q 034587            2 SELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK----GG--RRITSS   74 (90)
Q Consensus         2 ~~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~----~G--R~lT~~   74 (90)
                      |..-..|+..|+- .+|+.+..|+...|-.+              +-+...|+.||+.|||+..+.    +|  ..+|..
T Consensus        20 s~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~--------------~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~~~~   85 (109)
T d2d1ha1          20 TDTDVAVLLKMVEIEKPITSEELADIFKLSK--------------TTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSI   85 (109)
T ss_dssp             CHHHHHHHHHHHHHCSCEEHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEEEC-------CCEEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHHCccH--------------hHHHHHHHHHHHCCCEEEeecCCCCCceeEEEeeC
Confidence            4455678888875 57899999999888753              689999999999999986542    23  367888


Q ss_pred             hHhhHHHHHHHh
Q 034587           75 GQRDLDQVAGRI   86 (90)
Q Consensus        75 G~~~lD~iA~~v   86 (90)
                      |.+..+++...+
T Consensus        86 ~~~~~~~i~~~~   97 (109)
T d2d1ha1          86 SSNILEKIRNDL   97 (109)
T ss_dssp             CTTHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            888777776654

>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=96.37  E-value=0.01  Score=37.04  Aligned_cols=67  Identities=7%  Similarity=0.041  Sum_probs=51.9

Q ss_pred             HHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC--CCe----eeCcchHhh
Q 034587            6 TSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRD   78 (90)
Q Consensus         6 ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~~   78 (90)
                      -.+|..|+-.+ ++.++.|+...+-.+              +-+-.++..||+.|||++.++  .+|    .||++|+..
T Consensus        31 ~~iL~~l~~~~~~~t~~~la~~~~~~~--------------~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~   96 (137)
T d2fbha1          31 WLVLLHLARHRDSPTQRELAQSVGVEG--------------PTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVL   96 (137)
T ss_dssp             HHHHHHHHHCSSCCBHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCH--------------HHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHH
Confidence            35677777655 588899999887643              568889999999999996653  344    599999999


Q ss_pred             HHHHHHHh
Q 034587           79 LDQVAGRI   86 (90)
Q Consensus        79 lD~iA~~v   86 (90)
                      ++++....
T Consensus        97 ~~~~~~~~  104 (137)
T d2fbha1          97 IADIEAIA  104 (137)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

>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=96.04  E-value=0.0047  Score=38.42  Aligned_cols=46  Identities=17%  Similarity=0.161  Sum_probs=34.3

Q ss_pred             cccCchhHHHHHHHHHHhCCccccc---CCCC-----eeeCcchHhhHHHHHHH
Q 034587           40 FCKSSGAIARHILQQLQNMNIIDIE---PKGG-----RRITSSGQRDLDQVAGR   85 (90)
Q Consensus        40 ~~~asg~iiR~~LqqLE~~glV~k~---~~~G-----R~lT~~G~~~lD~iA~~   85 (90)
                      +..-|-+.|=.+|..||+.|||+..   ..+|     -.||++|+..|.+...+
T Consensus        37 ~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~~~~~~   90 (103)
T d1xmaa_          37 LYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKCEE   90 (103)
T ss_dssp             SCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHHHH
T ss_pred             eecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHHHHHHH
Confidence            3455667888999999999999732   2344     37999999999876654

>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=95.97  E-value=0.0093  Score=37.64  Aligned_cols=69  Identities=9%  Similarity=-0.001  Sum_probs=51.9

Q ss_pred             hHHHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcch
Q 034587            4 LVTSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG   75 (90)
Q Consensus         4 r~ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G   75 (90)
                      --..||..||-.+  ++.+..|+...+-.+              +-+-.+++.||+.|||++.+  ++.|    .||++|
T Consensus        35 ~q~~iL~~l~~~~~~~~t~~eia~~~~~~~--------------~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G  100 (125)
T d1p4xa1          35 KEFILLTYLFHQQENTLPFKKIVSDLCYKQ--------------SDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQ  100 (125)
T ss_dssp             HHHHHHHHHHSCSCSEEEHHHHHHHSSSCG--------------GGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHH
T ss_pred             HHHHHHHHHHHhccCCcCHHHHHHHhCCCc--------------chHHHHHHHHHHCCCceeecccCCCCeEEEEECHHH
Confidence            3456788888764  678889998776543              45677899999999998655  3455    489999


Q ss_pred             HhhHHHHHHHh
Q 034587           76 QRDLDQVAGRI   86 (90)
Q Consensus        76 ~~~lD~iA~~v   86 (90)
                      +..+..+...+
T Consensus       101 ~~~~~~~~~~~  111 (125)
T d1p4xa1         101 REKIAERVTLF  111 (125)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99998876654

>d1in4a1 a.4.5.11 (A:255-329) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=95.97  E-value=0.0026  Score=39.03  Aligned_cols=55  Identities=18%  Similarity=0.303  Sum_probs=40.2

Q ss_pred             HHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587           11 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL   79 (90)
Q Consensus        11 klYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l   79 (90)
                      +-|--||||+.+|+-.-|-.+             ..|.=.+===|-+.|+|++++ .||++|++|.+.|
T Consensus        16 ~~f~ggPvGl~tlAa~l~e~~-------------~TiEdviEPyLiq~G~i~RTp-RGR~~T~~~~~hl   70 (75)
T d1in4a1          16 EIYRGGPVGLNALAASLGVEA-------------DTLSEVYEPYLLQAGFLARTP-RGRIVTEKAYKHL   70 (75)
T ss_dssp             HHSTTCCBCHHHHHHHHTSCH-------------HHHHHHTHHHHHHTTSEEEET-TEEEECHHHHHHT
T ss_pred             HHhCCCCCcHHHHHHHHcCCh-------------hHHHHHhhHHHHHhhHHhhCC-chHHhHHHHHHHc
Confidence            334568999999999877643             123333333467899999999 4999999998765

>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=95.95  E-value=0.018  Score=35.99  Aligned_cols=68  Identities=13%  Similarity=0.123  Sum_probs=48.2

Q ss_pred             HHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            5 VTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         5 ~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      -..+|..|+- .+++-+..|....+-.+              +-+=.+++.||+.|||++.+  +.+|    .||++|+.
T Consensus        33 ~~~~L~~l~~~~~~~t~~~la~~l~i~~--------------~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~   98 (140)
T d3deua1          33 HWVTLHNIHQLPPDQSQIQLAKAIGIEQ--------------PSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEP   98 (140)
T ss_dssp             HHHHHHHHHHSCSSEEHHHHHHHHTSCH--------------HHHHHHHHHHHHTTSEEEC--------CEEEECGGGHH
T ss_pred             HHHHHHHHHHcCCCccHHHHHHHHCCCH--------------hHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHH
Confidence            3467777775 45588888888776643              34567999999999998544  4454    49999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++++...+
T Consensus        99 ~~~~~~~~~  107 (140)
T d3deua1          99 LIAEMEEVI  107 (140)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999877654

>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=95.73  E-value=0.014  Score=37.06  Aligned_cols=67  Identities=10%  Similarity=0.084  Sum_probs=50.5

Q ss_pred             HHHHHHHhhcC--CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            6 TSMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         6 ASi~RklYl~g--~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      ..||-.||-.+  ++.++.++..-|-.+              +-+-.+++.||+.|||++.+  ++.|    .||++|++
T Consensus        36 ~~vL~~l~~~~~~~~~~~~ia~~l~~~~--------------~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~  101 (125)
T d1p4xa2          36 FTILAIITSQNKNIVLLKDLIETIHHKY--------------PQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQD  101 (125)
T ss_dssp             HHHHHHHHTTTTCCEEHHHHHHHSSSCH--------------HHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHH
T ss_pred             HHHHHHHHHccCCCccHHHHHHHHCCCc--------------chHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHH
Confidence            45677777643  567788888776543              56778999999999998544  4566    48999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++++..++
T Consensus       102 ~~~~l~~~~  110 (125)
T d1p4xa2         102 HAEQLLAQV  110 (125)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988765

>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=95.65  E-value=0.0069  Score=39.98  Aligned_cols=66  Identities=14%  Similarity=0.180  Sum_probs=46.2

Q ss_pred             HHHHHHhhcCC---CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHh
Q 034587            7 SMARKIYLRQG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQR   77 (90)
Q Consensus         7 Si~RklYl~g~---vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~   77 (90)
                      .||..||..++   +.++.|+...+-.+              +-+=.+++.||+.|||++.+  .++|    .||++|+.
T Consensus        66 ~vL~~L~~~~~~~~lt~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~  131 (172)
T d2fbka1          66 DLLLTLYRSAPPEGLRPTELSALAAISG--------------PSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRA  131 (172)
T ss_dssp             HHHHHHHHHCCSSCBCHHHHHHHCSCCS--------------GGGSSHHHHHHHHTSEECCC-------CCBEECHHHHH
T ss_pred             HHHHHHHhhCCCCCcCHHHHHHHHCcCH--------------hHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHH
Confidence            56777777654   67888888776643              22334689999999999665  3344    59999999


Q ss_pred             hHHHHHHHh
Q 034587           78 DLDQVAGRI   86 (90)
Q Consensus        78 ~lD~iA~~v   86 (90)
                      .++++....
T Consensus       132 l~~~~~~~~  140 (172)
T d2fbka1         132 LVTHLLPAH  140 (172)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999876543

>d1ixsb1 a.4.5.11 (B:243-318) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=95.64  E-value=0.0051  Score=37.78  Aligned_cols=53  Identities=15%  Similarity=0.204  Sum_probs=39.1

Q ss_pred             hhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhH
Q 034587           13 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL   79 (90)
Q Consensus        13 Yl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~l   79 (90)
                      |=-||||+.+|+-.-|-.+.             .|.=.+===|-+.|+|++.+ .||++|++|.+.|
T Consensus        18 f~ggPVGl~tlA~~lgE~~~-------------TiEdviEPyLiq~G~i~RTp-rGR~~T~~a~~hL   70 (76)
T d1ixsb1          18 FGGGPVGLATLATALSEDPG-------------TLEEVHEPYLIRQGLLKRTP-RGRVATELAYRHL   70 (76)
T ss_dssp             SCSSCCCSHHHHGGGSSCTT-------------HHHHTSHHHHHHTTSEEECS-SSEEECHHHHHHH
T ss_pred             hCCCCccHHHHHHHHcCChh-------------HHHHHhhHHHHHHhHHhhCC-ChHHhHHHHHHHc
Confidence            34479999999998877542             23322233466789999999 5999999998766

>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=95.50  E-value=0.0078  Score=39.73  Aligned_cols=71  Identities=13%  Similarity=0.159  Sum_probs=48.9

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe------eeCcchHhhH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR------RITSSGQRDL   79 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR------~lT~~G~~~l   79 (90)
                      ||=-|.- +|.-==.|++.+-.      ...+|.+.|-+-|=..|+.||+.|||+...  .+|+      .||++|+..|
T Consensus         6 iLg~L~~-~~~~GYei~~~~~~------~~~~~w~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~~Gr~~l   78 (178)
T d1yg2a_           6 ILTVLST-RDATGYDITKEFSA------SIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSAL   78 (178)
T ss_dssp             HHHHHHH-CCBCHHHHHHHHTT------GGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHH
T ss_pred             HHHHHhh-CCCCHHHHHHHHHH------HhCCccCCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHH
Confidence            3334443 44444457777743      245788899999999999999999997432  2233      7999999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      .+...+
T Consensus        79 ~~wl~~   84 (178)
T d1yg2a_          79 GEWFDQ   84 (178)
T ss_dssp             HHHHHS
T ss_pred             HHHHhc
Confidence            886554

>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=95.46  E-value=0.015  Score=36.68  Aligned_cols=62  Identities=13%  Similarity=0.215  Sum_probs=46.7

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC------eeeCcchHhhHH
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG------RRITSSGQRDLD   80 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G------R~lT~~G~~~lD   80 (90)
                      -|++.|+ .|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.....      ..||+.|++.+.
T Consensus        23 ~Il~~L~-~g~~RF~el~~~l~-------------gIS~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~~G~~L~p   88 (108)
T d1z7ua1          23 SLMDELF-QGTKRNGELMRALD-------------GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   88 (108)
T ss_dssp             HHHHHHH-HSCBCHHHHHHHST-------------TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHCc-------------CCChhHHHHHHHHHHHCCcceeeccCCCcceehhhhchhHHHHHH
Confidence            4677775 57777777777543             246679999999999999998765222      789999998876


Q ss_pred             HH
Q 034587           81 QV   82 (90)
Q Consensus        81 ~i   82 (90)
                      -+
T Consensus        89 il   90 (108)
T d1z7ua1          89 AL   90 (108)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=95.43  E-value=0.028  Score=34.52  Aligned_cols=63  Identities=8%  Similarity=0.095  Sum_probs=48.1

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCC------eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG------RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~G------R~lT~~G~~~l   79 (90)
                      .-|++.+ ..||...+.|.+.-.             .-|.+++=.-|++||+.|+|++.....      ..||++|++.+
T Consensus        14 l~Il~~L-~~g~~rF~el~~~l~-------------gis~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          14 CVILCHL-THGKKRTSELKRLMP-------------NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             HHHHHHH-TTCCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHH-HcCCCCHHHHHHHhh-------------cCChhHHHHHHHHHHHhHHHhheeccccccchhhhhhhhHHHHH
Confidence            4578887 478888888877442             346679999999999999999665222      78999999987


Q ss_pred             HHH
Q 034587           80 DQV   82 (90)
Q Consensus        80 D~i   82 (90)
                      .-+
T Consensus        80 pil   82 (95)
T d2hzta1          80 GIL   82 (95)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=95.34  E-value=0.017  Score=38.11  Aligned_cols=66  Identities=11%  Similarity=0.130  Sum_probs=50.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCe----eeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~l   79 (90)
                      ..||.-|+-.+++.++.|++.-+-.+              +-+=.+++.||+.|||++.+  ++.|    .||++|+..+
T Consensus        44 ~~vL~~l~~~~~~t~~~la~~~~l~~--------------~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~  109 (162)
T d2fxaa1          44 HHILWIAYQLNGASISEIAKFGVMHV--------------STAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVF  109 (162)
T ss_dssp             HHHHHHHHHHTSEEHHHHHHHTTCCH--------------HHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHH
T ss_pred             HHHHhhhccCCCcCHHHHHHHHcCCc--------------hhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHH
Confidence            45777888888999999998766643              56778999999999998655  3455    4899999999


Q ss_pred             HHHHHH
Q 034587           80 DQVAGR   85 (90)
Q Consensus        80 D~iA~~   85 (90)
                      +++-..
T Consensus       110 ~~~~~~  115 (162)
T d2fxaa1         110 WSLLEE  115 (162)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=95.13  E-value=0.031  Score=35.09  Aligned_cols=54  Identities=9%  Similarity=0.184  Sum_probs=41.5

Q ss_pred             HHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCCeeeCcchH
Q 034587            8 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ   76 (90)
Q Consensus         8 i~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~GR~lT~~G~   76 (90)
                      +|=-+..++|+....++..++-              +-.++|++|++|.++|||+...  .||+ |+..-.
T Consensus         9 ~L~~la~~~~~ss~~IA~~~~~--------------~~~~v~kIl~~L~~aglV~s~rG~~GGy-Lar~p~   64 (127)
T d1xd7a_           9 ILSLISMDEKTSSEIIADSVNT--------------NPVVVRRMISLLKKADILTSRAGVPGAS-LKKDPA   64 (127)
T ss_dssp             HHHHHHTCSCCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEECCSSSSSCE-ESSCGG
T ss_pred             HHHHHhcCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHhCcccccCCCCCcc-ccCCHH
Confidence            3444566789999999998876              3469999999999999998544  5676 876543

>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=94.89  E-value=0.02  Score=36.36  Aligned_cols=63  Identities=17%  Similarity=0.150  Sum_probs=48.5

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCC-CC-----eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GG-----RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~-~G-----R~lT~~G~~~l   79 (90)
                      .-|++.|+ .|+...+.|.+.-.             .-|.+++=.-|.+||+.|+|++... ..     ..||+.|++++
T Consensus        27 l~Il~~L~-~g~~RF~el~~~l~-------------gis~~~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~G~~L~   92 (114)
T d1yyva1          27 VLILVALR-DGTHRFSDLRRKMG-------------GVSEKMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVS   92 (114)
T ss_dssp             HHHHHHGG-GCCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHHh-cCCCCHHHHHHHcc-------------ccchhHHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHhHHHHH
Confidence            45788876 68888888887543             2456788889999999999997652 22     78999999987


Q ss_pred             HHH
Q 034587           80 DQV   82 (90)
Q Consensus        80 D~i   82 (90)
                      .-+
T Consensus        93 ~il   95 (114)
T d1yyva1          93 DKV   95 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=94.66  E-value=0.015  Score=36.55  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=35.0

Q ss_pred             cccCchhHHHHHHHHHHhCCcccccC--CCC-----eeeCcchHhhHHHHHHHh
Q 034587           40 FCKSSGAIARHILQQLQNMNIIDIEP--KGG-----RRITSSGQRDLDQVAGRI   86 (90)
Q Consensus        40 ~~~asg~iiR~~LqqLE~~glV~k~~--~~G-----R~lT~~G~~~lD~iA~~v   86 (90)
                      ....+-+.|=.+|+.||+.|||+...  .+|     -.||++|+..|+....++
T Consensus        41 ~~~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~~~~~~~   94 (114)
T d2esha1          41 PGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSL   94 (114)
T ss_dssp             TTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             cccCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            33444467889999999999997422  234     379999999998876664

>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=94.64  E-value=0.085  Score=32.17  Aligned_cols=71  Identities=18%  Similarity=0.175  Sum_probs=50.6

Q ss_pred             hhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc--CCCCee--eC-cchH
Q 034587            2 SELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRR--IT-SSGQ   76 (90)
Q Consensus         2 ~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~--~~~GR~--lT-~~G~   76 (90)
                      +.-=|.|+.-|+-+|+..+..+++.-|-.              .+-+..+|+.||+.|||++.  ++++|.  .+ ....
T Consensus        19 t~~e~~v~~~L~~~g~~t~~eia~~~~i~--------------~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~   84 (109)
T d1sfxa_          19 KPSDVRIYSLLLERGGMRVSEIARELDLS--------------ARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPE   84 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHH
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHhCCC--------------cchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHH
Confidence            34457788888889999999999988764              36799999999999999854  344542  22 2234


Q ss_pred             hhHHHHHHHh
Q 034587           77 RDLDQVAGRI   86 (90)
Q Consensus        77 ~~lD~iA~~v   86 (90)
                      ..++++...+
T Consensus        85 e~l~~~~~~~   94 (109)
T d1sfxa_          85 KVLKEFKSSI   94 (109)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5566665543

>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=94.60  E-value=0.031  Score=32.64  Aligned_cols=42  Identities=21%  Similarity=0.185  Sum_probs=34.2

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeee
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI   71 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~l   71 (90)
                      |..+..+++.+|-             .|-+-++..|++||+.|||++.+...|.|
T Consensus        24 ~Ps~rei~~~~g~-------------~S~stv~~~l~~Le~kG~I~r~~~~~R~i   65 (71)
T d1jhfa1          24 PPTRAEIAQRLGF-------------RSPNAAEEHLKALARKGVIEIVSGASRGI   65 (71)
T ss_dssp             CCCHHHHHHHTTC-------------SSHHHHHHHHHHHHHTTSEEECSSSSSCE
T ss_pred             CCCHHHHHHHcCC-------------CCHHHHHHHHHHHHHCcCeecCCCCCcee
Confidence            6788999987774             25578999999999999999988655554

>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=94.54  E-value=0.037  Score=34.39  Aligned_cols=63  Identities=17%  Similarity=0.143  Sum_probs=46.4

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-C-----eeeCcchHhhH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-G-----RRITSSGQRDL   79 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-G-----R~lT~~G~~~l   79 (90)
                      .-|++.+. .|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.... .     ..||+.|++.+
T Consensus        23 l~Il~~L~-~g~~rF~el~~~l~-------------gIs~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          23 LLIIFQIN-RRIIRYGELKRAIP-------------GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             HHHHHHHT-TSCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHHHc-cCCCCHHHHHhhCc-------------ccchhHHHHHHHHHHHCCceeecccCCCCCeehhhhhHhHHHHH
Confidence            35677765 67877777777442             34567888889999999999876522 1     66999999987


Q ss_pred             HHH
Q 034587           80 DQV   82 (90)
Q Consensus        80 D~i   82 (90)
                      .-+
T Consensus        89 pil   91 (102)
T d2fswa1          89 PII   91 (102)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>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=94.48  E-value=0.015  Score=33.67  Aligned_cols=41  Identities=17%  Similarity=0.101  Sum_probs=34.5

Q ss_pred             CchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeC
Q 034587           18 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT   72 (90)
Q Consensus        18 vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT   72 (90)
                      +-...|+..||-              |...+|.+|+.||+.|||+..+..|-.+.
T Consensus        26 l~~~~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~~~G~~V~   66 (69)
T d2hs5a1          26 LSEPDICAALDV--------------SRNTVREAFQILIEDRLVAHELNRGVFVR   66 (69)
T ss_dssp             ECHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEEC
T ss_pred             cCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCCEEEec
Confidence            447789998887              44799999999999999999987777664

>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=94.46  E-value=0.015  Score=34.21  Aligned_cols=43  Identities=12%  Similarity=0.025  Sum_probs=36.4

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcch
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG   75 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G   75 (90)
                      ....|+..||-              |...+|.+|+.|++.|||+..+..|-.+++.-
T Consensus        24 se~~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~g~G~~V~~~~   66 (78)
T d3bwga1          24 VLETLMAQFEV--------------SKSTITKSLELLEQKGAIFQVRGSGIFVRKHK   66 (78)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCCC
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCcEEEEccCC
Confidence            67888888886              45799999999999999999988787777643

>d2axla1 a.4.5.43 (A:1-144) Werner syndrome ATP-dependent helicase WRN {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RecQ helicase DNA-binding domain-like
domain: Werner syndrome ATP-dependent helicase WRN
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.86  E-value=0.046  Score=35.55  Aligned_cols=80  Identities=13%  Similarity=0.133  Sum_probs=58.9

Q ss_pred             hhhHHHHHHHHhh-cCCCchhHHHHHhcCCCCCCCCCCc-----cccC---chhHHHHHHHHHHhCCcccccCCCCe---
Q 034587            2 SELVTSMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPH-----FCKS---SGAIARHILQQLQNMNIIDIEPKGGR---   69 (90)
Q Consensus         2 ~~r~ASi~RklYl-~g~vGV~~Lr~~YGg~krrG~~P~h-----~~~a---sg~iiR~~LqqLE~~glV~k~~~~GR---   69 (90)
                      ++-|-.||.-||- .+..|++.+..++-|.++.-.+..|     |-.+   +-.-++.++.||-..|+++.....|.   
T Consensus        12 T~eA~~iLs~V~~~~~rfg~~~iidiL~Gs~~~kI~~~~~~l~~yG~Gk~~s~~~w~~li~qli~~G~L~e~~~~~~~~~   91 (144)
T d2axla1          12 GPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMK   91 (144)
T ss_dssp             HHHHHHHHHHHHHTTTCSCSHHHHHHHTCCSCSHHHHHTCSCTTTTGGGGSCHHHHHHHHHHHHHHSSEEEETTSCTTTC
T ss_pred             HHHHHHHHHHHHHhcccccchHHHHHHHhcccHHHHHHhhcccccCCCCcCCHHHHHHHHHHHHHcCcceeecccCccee
Confidence            4556666666665 5789999999999998876554322     2222   33489999999999999976655553   


Q ss_pred             --eeCcchHhhHHH
Q 034587           70 --RITSSGQRDLDQ   81 (90)
Q Consensus        70 --~lT~~G~~~lD~   81 (90)
                        .||++|+..|..
T Consensus        92 ~l~lt~kg~~~L~g  105 (144)
T d2axla1          92 ICALTKKGRNWLHK  105 (144)
T ss_dssp             EEEECHHHHHHHHH
T ss_pred             eeeECHHHHHHHhc
Confidence              799999999864

>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=93.21  E-value=0.11  Score=33.92  Aligned_cols=62  Identities=18%  Similarity=0.269  Sum_probs=47.1

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCC-----CeeeCcchHhhHH
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----GRRITSSGQRDLD   80 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~-----GR~lT~~G~~~lD   80 (90)
                      .-|+|.++ .|+...+.|.+.-|              -|.+++-.-|++||+.|+|++....     -..||++|++++.
T Consensus        23 l~Il~~l~-~G~~rf~el~~~lg--------------is~~vLs~rL~~L~~~gLv~r~~~~~p~r~~Y~LT~~G~~L~p   87 (142)
T d2f2ea1          23 MLIVRDAF-EGLTRFGEFQKSLG--------------LAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALFP   87 (142)
T ss_dssp             HHHHHHHH-TTCCSHHHHHHHHC--------------CCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHhh--------------ccHHHHHHHHHHHHHhcceeeecCCCCCeeEEecCcCcchHHH
Confidence            45788875 68888888888553              3457898999999999999973321     2789999998866


Q ss_pred             HH
Q 034587           81 QV   82 (90)
Q Consensus        81 ~i   82 (90)
                      -+
T Consensus        88 il   89 (142)
T d2f2ea1          88 LL   89 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=93.09  E-value=0.094  Score=29.83  Aligned_cols=46  Identities=11%  Similarity=0.040  Sum_probs=40.5

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE   64 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~   64 (90)
                      .+.|++.|+-+||+....|++..|-.              ..-+..++..|++.|||+..
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS--------------~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELA--------------PASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEe
Confidence            46799999999999999999988874              47899999999999999744

>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=92.91  E-value=0.28  Score=30.29  Aligned_cols=61  Identities=11%  Similarity=0.098  Sum_probs=47.5

Q ss_pred             hhhHHHHHHHHhhcC-CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC--CCC----eeeCcc
Q 034587            2 SELVTSMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSS   74 (90)
Q Consensus         2 ~~r~ASi~RklYl~g-~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~--~~G----R~lT~~   74 (90)
                      +.-++.|+--||+.+ |+.+..|+..-|-.              .+-+-.+|+.||+.|+|...+  ...    ..+|++
T Consensus        25 ~~~~~~i~~~L~~~~~plt~~ela~~l~vs--------------k~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~t~~   90 (151)
T d1ku9a_          25 NKSVGAVYAILYLSDKPLTISDIMEELKIS--------------KGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGF   90 (151)
T ss_dssp             CHHHHHHHHHHHHCSSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHH
T ss_pred             CHHHHHHHHHHHhCCCCcCHHHHHHHhCCC--------------cchHHHHHHHHHHCCCEEEEEcCCCCceeEEeCCHH
Confidence            455788888999875 79999999987764              367889999999999997554  222    257888


Q ss_pred             hH
Q 034587           75 GQ   76 (90)
Q Consensus        75 G~   76 (90)
                      |+
T Consensus        91 g~   92 (151)
T d1ku9a_          91 SS   92 (151)
T ss_dssp             HH
T ss_pred             HH
Confidence            85

>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=92.69  E-value=0.17  Score=28.59  Aligned_cols=54  Identities=13%  Similarity=0.097  Sum_probs=41.6

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCc-ccccCCCCeeeCc
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITS   73 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~gl-V~k~~~~GR~lT~   73 (90)
                      -.|+.-|-=.+.+....|+..+|-.              ..-||.-++.||+.|+ |+..+..|.+|++
T Consensus         8 ~~iL~~L~~~~~~s~~eLa~~l~vS--------------~~ti~r~i~~L~~~G~~I~~~~g~GY~L~~   62 (63)
T d1biaa1           8 LKLIALLANGEFHSGEQLGETLGMS--------------RAAINKHIQTLRDWGVDVFTVPGKGYSLPE   62 (63)
T ss_dssp             HHHHHHHTTSSCBCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTCCCEEETTTEEECSS
T ss_pred             HHHHHHHHHCCcCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCcEEEeCCCeEEeCC
Confidence            3566666556779999999999874              3689999999999998 5666655777763

>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=91.58  E-value=0.057  Score=31.63  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=34.3

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      ....|+..||-              |...+|.+|+.|++.|||+..+..|-.++.
T Consensus        29 s~~eLa~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   69 (74)
T d1hw1a1          29 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN   69 (74)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTEEEEECC
T ss_pred             cHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEeCceEEECC
Confidence            67788888887              457999999999999999999877776653

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.43  E-value=0.3  Score=27.36  Aligned_cols=57  Identities=14%  Similarity=0.156  Sum_probs=44.8

Q ss_pred             hhhHHHHHHHHhhc-CCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCc-ccccCCCCeeeCc
Q 034587            2 SELVTSMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITS   73 (90)
Q Consensus         2 ~~r~ASi~RklYl~-g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~gl-V~k~~~~GR~lT~   73 (90)
                      ++|--.|+..|.-. +++.+..|+..+|-.              ..-||.=++.|++.|+ |+..+ +|.+|.+
T Consensus         6 ~eR~~~Il~~L~~~~~~vs~~~La~~l~VS--------------~~TI~rdi~~L~~~G~~I~~~~-gGY~L~~   64 (65)
T d1j5ya1           6 QERLKSIVRILERSKEPVSGAQLAEELSVS--------------RQVIVQDIAYLRSLGYNIVATP-RGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHTSC--------------HHHHHHHHHHHHHHTCCCEEET-TEEECCT
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEEeC-CCEEeCC
Confidence            35666788888654 679999999999874              3579999999999998 76655 6888764

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=89.94  E-value=0.036  Score=34.01  Aligned_cols=41  Identities=15%  Similarity=0.245  Sum_probs=34.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           19 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        19 GV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      .+..|+..||-.              ...+|.+|+.|++.|||+..+..|-.+++
T Consensus        35 s~r~La~~~~vS--------------r~tvr~Al~~L~~~Gli~~~~g~G~~V~~   75 (100)
T d1v4ra1          35 SVADIRAQFGVA--------------AKTVSRALAVLKSEGLVSSRGALGTVVEK   75 (100)
T ss_dssp             CHHHHHHHSSSC--------------TTHHHHHTTTTTTSSCCEEETTTEEESCS
T ss_pred             cHHHHHHHHCCC--------------HHHHHHHHHHHHHCCcEEEecCCEEEECC
Confidence            677888888764              36999999999999999988877888875

>d1olta_ c.1.28.2 (A:) Oxygen-independent coproporphyrinogen III oxidase HemN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Radical SAM enzymes
family: Oxygen-independent coproporphyrinogen III oxidase HemN
domain: Oxygen-independent coproporphyrinogen III oxidase HemN
species: Escherichia coli [TaxId: 562]

Probab=89.89  E-value=0.13  Score=38.43  Aligned_cols=63  Identities=11%  Similarity=0.143  Sum_probs=44.0

Q ss_pred             HhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHHHHHHH
Q 034587           12 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR   85 (90)
Q Consensus        12 lYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD~iA~~   85 (90)
                      |=....+-...+...||-.-         ..--... -..|++|++.|||+.+. +.=+||++|+-++|.||..
T Consensus       374 L~~~~~ld~~~~~~~fg~~~---------~~~f~~~-~~~L~~l~~~GLv~~~~-~~l~lT~~Gr~l~~~I~~~  436 (441)
T d1olta_         374 LICNFRLDYSPIEQQWDLLF---------ADYFAED-LKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICMC  436 (441)
T ss_dssp             HHHHSEEEHHHHHHHTTCCH---------HHHTHHH-HHHHHHHHHTTSEEECS-SEEEECTTTGGGHHHHHHT
T ss_pred             HHHhCCcCHHHHHHHHCCCH---------HHHHHHH-HHHHHHHHHCCCEEEEC-CEEEECHhHHHHHHHHHHH
Confidence            33445666777777776531         1111122 25788899999999886 5789999999999999864

>d2fnaa1 a.4.5.11 (A:284-356) Hypothetical protein SSO1545, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Hypothetical protein SSO1545, C-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=88.94  E-value=0.2  Score=29.97  Aligned_cols=29  Identities=21%  Similarity=0.016  Sum_probs=23.2

Q ss_pred             chhHHHHHHHHHHhCCcccccCCCCeeeCc
Q 034587           44 SGAIARHILQQLQNMNIIDIEPKGGRRITS   73 (90)
Q Consensus        44 sg~iiR~~LqqLE~~glV~k~~~~GR~lT~   73 (90)
                      +.+.+=.+|++|+++|||+|.. ++..||.
T Consensus        37 ~d~~ls~lL~nL~k~~~iek~~-~~Y~i~D   65 (73)
T d2fnaa1          37 SDSEIYNYLTQLTKHSWIIKEG-EKYCPSE   65 (73)
T ss_dssp             CHHHHHHHHHHHHHTTSEEESS-SCEEESS
T ss_pred             ChHHHHHHHHHHHHcCceeecC-CeeccCc
Confidence            3467788999999999999874 5677764

>d1bjaa_ a.4.5.9 (A:) Transcription factor MotA, activation domain {Bacteriophage T4 [TaxId: 10665]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor MotA, activation domain
domain: Transcription factor MotA, activation domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=88.83  E-value=1.3  Score=27.41  Aligned_cols=72  Identities=14%  Similarity=0.151  Sum_probs=55.9

Q ss_pred             ChhhHHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccCCCCeeeCcchHhhHH
Q 034587            1 MSELVTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD   80 (90)
Q Consensus         1 ~~~r~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~lD   80 (90)
                      +++.+|+|+-+|.-+.-+.+...|..             +..-+-.+.-+=+--|-+-|||||.- +|-+.|..|+..+-
T Consensus        14 lnekta~I~i~iaKk~FiTa~ev~e~-------------~~~~~~avvnSNIGVliKKgliEKSG-DG~v~T~e~~~il~   79 (95)
T d1bjaa_          14 LNEKTATILITIAKKDFITAAEVREV-------------HPDLGNAVVNSNIGVLIKKGLVEKSG-DGLIITGEAQDIIS   79 (95)
T ss_dssp             SCHHHHHHHHHHHHSTTBCHHHHHHT-------------CTTSCHHHHHHHHHHHHTTTSEEEET-TEEEECHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHhhchhHHHHHHH-------------hHHhccceeecceeeeeecchhhccC-CceEeeccHHHHHH
Confidence            36789999999988888888888762             12223356666677899999999996 59999999999998


Q ss_pred             HHHHHh
Q 034587           81 QVAGRI   86 (90)
Q Consensus        81 ~iA~~v   86 (90)
                      +.|.--
T Consensus        80 ~AA~l~   85 (95)
T d1bjaa_          80 NAATLY   85 (95)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877543

>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=86.62  E-value=0.46  Score=30.78  Aligned_cols=43  Identities=9%  Similarity=0.366  Sum_probs=35.8

Q ss_pred             HHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587            7 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE   64 (90)
Q Consensus         7 Si~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~   64 (90)
                      -|++.| ..+|..|+.|+...|-.+              +-+++-|+.||++|+|+..
T Consensus        23 ~Il~~L-~~~~~s~~ela~~lg~s~--------------~~v~~hl~~L~~~glv~~~   65 (190)
T d1ulya_          23 KILKLL-RNKEMTISQLSEILGKTP--------------QTIYHHIEKLKEAGLVEVK   65 (190)
T ss_dssp             HHHHHH-TTCCBCHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHH-HhCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCeEEE
Confidence            367766 489999999999987653              6789999999999999744

>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=85.50  E-value=0.21  Score=28.12  Aligned_cols=45  Identities=11%  Similarity=0.140  Sum_probs=36.9

Q ss_pred             HHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC
Q 034587            6 TSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP   65 (90)
Q Consensus         6 ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~   65 (90)
                      |-|++.|+ ++|+.-..|++.-|=.              ..-+..++..|++.|||+...
T Consensus         2 s~Il~~i~-~~pisr~eLa~~~gls--------------~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1           2 SRILKRIM-KSPVSRVELAEELGLT--------------KTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             CCSHHHHH-HSCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHH-HCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEECC
Confidence            45788887 6899999999987764              368999999999999996443

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=84.68  E-value=0.36  Score=29.51  Aligned_cols=37  Identities=30%  Similarity=0.434  Sum_probs=28.4

Q ss_pred             hhHHHHHHHHHHhCCcccc--cCC--CCeeeCcchHhhHHH
Q 034587           45 GAIARHILQQLQNMNIIDI--EPK--GGRRITSSGQRDLDQ   81 (90)
Q Consensus        45 g~iiR~~LqqLE~~glV~k--~~~--~GR~lT~~G~~~lD~   81 (90)
                      =|.+|..|-||+.+|+++.  +++  |-=.||++|+..-+.
T Consensus        38 MS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lca~   78 (81)
T d2obpa1          38 MSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAAQ   78 (81)
T ss_dssp             HHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHHHH
Confidence            3799999999999999984  332  234799999976443

>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=84.26  E-value=0.81  Score=25.81  Aligned_cols=46  Identities=11%  Similarity=0.054  Sum_probs=39.7

Q ss_pred             HHHHHHHHhhcCCCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCccccc
Q 034587            5 VTSMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE   64 (90)
Q Consensus         5 ~ASi~RklYl~g~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~   64 (90)
                      ...|++.|+-+||+.-..|++.-|=.              ..-+-.++++|++.|||+..
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS--------------~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLA--------------PASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCC--------------HHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEee
Confidence            45799999999999999999987764              36789999999999999743

>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=83.68  E-value=0.5  Score=29.49  Aligned_cols=44  Identities=11%  Similarity=0.181  Sum_probs=34.8

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCccccCchhHHHHHHHHHHhCCcccccC-CCCeeeCcc
Q 034587           17 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSS   74 (90)
Q Consensus        17 ~vGV~~Lr~~YGg~krrG~~P~h~~~asg~iiR~~LqqLE~~glV~k~~-~~GR~lT~~   74 (90)
                      ++.+..++..+|-.              -..+|++|++|.++|||+... .||-.|...
T Consensus        23 ~vss~~IA~~~~i~--------------~~~l~kil~~L~~aGlv~S~rG~GG~~L~~~   67 (138)
T d1ylfa1          23 LCTSDYMAESVNTN--------------PVVIRKIMSYLKQAGFVYVNRGPGGAGLLKD   67 (138)
T ss_dssp             GCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEC---CCEEESSC
T ss_pred             cCcHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEeecCCCCceecCC
Confidence            68889999888764              368999999999999998554 478888743