Citrus Sinensis ID: 033029

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHcccccccccHHcccccccccccccccccccHHHHHHHHHHHHHcccEEcccccccEEcHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccEEEcccccEEEccccHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
matartvkdvsphEFVKAYSAHLKrsgkfkelapydpdwYYVRAASMARKIYLRQGlgvgsfrriyggskrngsrpphfckssGAIARHILQQLQNmniidiepkggrritssgqrdldQVAGRIVVAP
Flexible Loop (DISEMBL)
matartvkdvsphefVKAYSahlkrsgkfkelapydPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGgrritssgqrdldqvagrivvap
Low Complexity Region (SEG)
MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Disordered region (IsUnstruct)
**************FVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGG**********FCKSSGAIARHILQQLQNMNIIDI***************************
Disordered Region (DISOPRED)
***ARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGG*************SSGAIARHILQQLQNMNIIDIEPK***RITSSGQRDLDQVAGRIVVA*
Disordered Region (DISEMBL)
**********SPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
Disordered Region (DISPRO)
***ARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRN*SRPP******GAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV**
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVAP
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	129	2.2.26 [Sep-21-2011]
Q9FNP8	143	40S ribosomal protein S19	yes	no	0.992	0.895	0.774	3e-60
Q9SGA6	143	40S ribosomal protein S19	no	no	1.0	0.902	0.762	7e-60
Q9LF30	143	40S ribosomal protein S19	no	no	0.968	0.874	0.769	4e-58
P40978	146	40S ribosomal protein S19	yes	no	0.984	0.869	0.737	2e-55
Q94613	149	40S ribosomal protein S19	N/A	no	0.930	0.805	0.507	2e-37
Q9Y0H3	145	40S ribosomal protein S19	N/A	no	0.945	0.841	0.5	2e-35
P17074	145	40S ribosomal protein S19	yes	no	0.953	0.848	0.496	3e-34
Q9CZX8	145	40S ribosomal protein S19	yes	no	0.953	0.848	0.496	3e-34
Q8T5Z4	147	40S ribosomal protein S19	N/A	no	0.953	0.836	0.496	3e-34
Q5R8M9	145	40S ribosomal protein S19	yes	no	0.953	0.848	0.489	2e-33

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

 Score =  229 bits (585), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 110/142 (77%), Positives = 120/142 (84%), Gaps = 14/142 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MAT +TVKDVSPHEFVKAY+AHLKRSGK               KELAPYDPDWYY+RAAS
Sbjct: 1   MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG +ARHILQQLQ MNI+D++ KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVA 128
           GR+ITSSGQRDLDQVAGRI  A
Sbjct: 121 GRKITSSGQRDLDQVAGRIAAA 142

Arabidopsis thaliana (taxid: 3702)

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

 Score =  228 bits (581), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 109/143 (76%), Positives = 121/143 (84%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MAT +TVKDVSPH+FVKAY++HLKRSGK               KELAPYDPDWYY+RAAS
Sbjct: 1   MATGKTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ MNI++++ KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSGQRDLDQVAGRI V P
Sbjct: 121 GRRITSSGQRDLDQVAGRIAVEP 143

Arabidopsis thaliana (taxid: 3702)

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

 Score =  223 bits (567), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 107/139 (76%), Positives = 119/139 (85%), Gaps = 14/139 (10%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MAT +TVKDVSPH+FVKAY++HLKRSGK               KELAPYDPDWYY+RAAS
Sbjct: 1   MATGKTVKDVSPHDFVKAYASHLKRSGKIELPLWTDIVKTGRLKELAPYDPDWYYIRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ M+I++++ KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELDTKG 120

Query: 107 GRRITSSGQRDLDQVAGRI 125
           GRRITSSGQRDLDQVAGRI
Sbjct: 121 GRRITSSGQRDLDQVAGRI 139

Arabidopsis thaliana (taxid: 3702)

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

 Score =  214 bits (544), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 104/141 (73%), Positives = 117/141 (82%), Gaps = 14/141 (9%)

Query: 2   ATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASM 47
           +TARTVKDV+PHEFVKAYSAHLKRSGK              FKEL PYDPDWYY RAAS+
Sbjct: 4   STARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASI 63

Query: 48  ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107
           ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++PKGG
Sbjct: 64  ARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGG 123

Query: 108 RRITSSGQRDLDQVAGRIVVA 128
           R ITS G+RDLDQVAGR+ V 
Sbjct: 124 RLITSQGRRDLDQVAGRVDVT 144

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  154 bits (389), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 68/134 (50%), Positives = 99/134 (73%), Gaps = 14/134 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKI 51
           +VKDVS HEF +A++A LK+SGK              FKEL+PY+PDWY++RAAS+ R +
Sbjct: 4   SVKDVSSHEFTRAFAAFLKKSGKMKVPEWTDFVKTGMFKELSPYEPDWYFIRAASICRHL 63

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           Y+R   G+GSF +IYGG +R G+ P HFCK++G+I+R +LQ L+ + I++ +P GGRR+T
Sbjct: 64  YIRSPAGIGSFEKIYGGRRRRGTAPSHFCKANGSISRRLLQSLEGLKIVEKDPNGGRRLT 123

Query: 112 SSGQRDLDQVAGRI 125
           S G+RDLD++A +I
Sbjct: 124 SQGRRDLDRIAAQI 137

Mya arenaria (taxid: 6604)

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

 Score =  147 bits (371), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 68/136 (50%), Positives = 97/136 (71%), Gaps = 14/136 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
           TVKDV+  EFVKA +A  K+SGK K              ELAP+D DWYY+R AS+AR +
Sbjct: 5   TVKDVNQQEFVKALAAFFKKSGKLKKPDWVDTVKLGKHKELAPFDIDWYYIRTASVARHL 64

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           Y+R G+GVG+  +IYGG +RNG+RP H+ + S  +AR +LQ L+ + +++ +P GGRR+T
Sbjct: 65  YMRGGVGVGAMTKIYGGRQRNGTRPSHYSRGSRNVARKVLQSLEMLKMVEKDPNGGRRLT 124

Query: 112 SSGQRDLDQVAGRIVV 127
           S GQRD+D++AG++VV
Sbjct: 125 SIGQRDMDRIAGQVVV 140

Myxine glutinosa (taxid: 7769)

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

 Score =  143 bits (360), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 68/137 (49%), Positives = 93/137 (67%), Gaps = 14/137 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
           TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 112 SSGQRDLDQVAGRIVVA 128
             GQRDLD++AG++  A
Sbjct: 125 PQGQRDLDRIAGQVAAA 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 =  143 bits (360), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 68/137 (49%), Positives = 93/137 (67%), Gaps = 14/137 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
           TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 112 SSGQRDLDQVAGRIVVA 128
             GQRDLD++AG++  A
Sbjct: 125 PQGQRDLDRIAGQVAAA 141

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

Mus musculus (taxid: 10090)

>sp|Q8T5Z4|RS19_BRABE 40S ribosomal protein S19 OS=Branchiostoma belcheri GN=RPS19 PE=2 SV=1

 Score =  143 bits (360), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 68/137 (49%), Positives = 95/137 (69%), Gaps = 14/137 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
           TVKDV+  EFVKA++A LK+SGK K              ELAPYDPDW+Y+RAAS AR +
Sbjct: 6   TVKDVNQQEFVKAFAAFLKKSGKLKLPEWVDLVKTAPHKELAPYDPDWFYLRAASTARHL 65

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           Y+R G+GVG+  +IYGG KR G++P  F   S  ++R +LQ L+ + +++ +  GGRR+T
Sbjct: 66  YMRGGVGVGAMCKIYGGRKRRGTKPAKFRVCSRGVSRTVLQSLEGIKMVEKDAAGGRRLT 125

Query: 112 SSGQRDLDQVAGRIVVA 128
           S GQRDLD++AG++  A
Sbjct: 126 SQGQRDLDRIAGQVATA 142

Branchiostoma belcheri (taxid: 7741)

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

 Score =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 67/137 (48%), Positives = 92/137 (67%), Gaps = 14/137 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
           TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 112 SSGQRDLDQVAGRIVVA 128
             GQRDLD++AG++  A
Sbjct: 125 PQGQRDLDRIAGQVAAA 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	129
224077760	143	predicted protein [Populus trichocarpa]	1.0	0.902	0.839	2e-63
224141061	143	predicted protein [Populus trichocarpa]	1.0	0.902	0.846	6e-63
255570268	143	40S ribosomal protein S19, putative [Ric	1.0	0.902	0.839	7e-62
255570270	143	40S ribosomal protein S19-3, putative [R	1.0	0.902	0.832	2e-61
449491502	143	PREDICTED: 40S ribosomal protein S19-3-l	1.0	0.902	0.825	2e-61
351722849	143	uncharacterized protein LOC100305587 [Gl	1.0	0.902	0.818	4e-61
449447418	143	PREDICTED: 40S ribosomal protein S19-3-l	1.0	0.902	0.811	7e-61
351722318	143	uncharacterized protein LOC100499800 [Gl	1.0	0.902	0.825	7e-61
255560408	143	40S ribosomal protein S19, putative [Ric	1.0	0.902	0.818	2e-60
449462326	143	PREDICTED: 40S ribosomal protein S19-3-l	1.0	0.902	0.811	2e-60

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

 Score =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 120/143 (83%), Positives = 128/143 (89%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA+TVKDVSPHEFVKAYSAHLKRSGK              FKELAPYDPDWYY+RAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYSAHLKRSGKVELPPWTDIVKTAKFKELAPYDPDWYYIRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+FRRIYGGS+RNGSRPPHFCKSSG++ARHILQQLQNMNIID++PKG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSQRNGSRPPHFCKSSGSVARHILQQLQNMNIIDVDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSGQRDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRIVVAP 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 =  244 bits (624), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 121/143 (84%), Positives = 128/143 (89%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA++VKDVSPHEFVKAYSAHLKRSGK              FKELAPYDPDWYYVRAAS
Sbjct: 1   MATAKSVKDVSPHEFVKAYSAHLKRSGKIELPLWTDIVKTGKFKELAPYDPDWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIY+R GLGVG+FRRIYGGSKRNGSRPPHFCKSSG+IARHILQQLQN+NIIDI+PKG
Sbjct: 61  MARKIYIRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGSIARHILQQLQNVNIIDIDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSGQRDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRIVVAP 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 =  241 bits (615), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 120/143 (83%), Positives = 126/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA+TVKDVSPHEFVKAY+AHLKRSGK               KELAPYDPDWY+VRAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPPWTDIVKTGTLKELAPYDPDWYFVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+PKG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSGQRDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRIVVAP 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 =  240 bits (612), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 119/143 (83%), Positives = 126/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA+TVKDVSPHEFVKAY+AHLKRSGK               KELAPYDPDWY+VRAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPPWTDIVKTGTLKELAPYDPDWYFVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+PKG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GR+ITSSGQRDLDQVAGRIVVAP
Sbjct: 121 GRKITSSGQRDLDQVAGRIVVAP 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 =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 118/143 (82%), Positives = 126/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATARTVKDVSPHEFVKAY+AHLKRSGK              FKELAPYD DWYYVRAAS
Sbjct: 1   MATARTVKDVSPHEFVKAYAAHLKRSGKVELPPWADIVKTARFKELAPYDADWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFC+SSGAIARHILQQLQ MNI+D++PKG
Sbjct: 61  MARKIYLRGGLGVGAFKRIYGGSKRNGSRPPHFCESSGAIARHILQQLQEMNIVDVDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSG+RDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGRRDLDQVAGRIVVAP 143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722849|ref|NP_001237514.1| uncharacterized protein LOC100305587 [Glycine max] gi|255625993|gb|ACU13341.1| unknown [Glycine max]

 Score =  238 bits (608), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 117/143 (81%), Positives = 127/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATARTVKDVSPHEFVKAYS+HLKRSGK              FKELAPYDPDWYYVRAAS
Sbjct: 1   MATARTVKDVSPHEFVKAYSSHLKRSGKMELPEWTDIVKTARFKELAPYDPDWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFCKSSGA+ARHILQQLQNM+II+++ KG
Sbjct: 61  MARKIYLRGGLGVGAFQRIYGGSKRNGSRPPHFCKSSGAVARHILQQLQNMSIIELDTKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GR+ITSSG+RDLDQVAGRIVVAP
Sbjct: 121 GRKITSSGRRDLDQVAGRIVVAP 143

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  238 bits (607), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 116/143 (81%), Positives = 126/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA+TVKDVSPHEFVKAY+AHLKRSGK              FKELAPYD DWYY+RAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKVELPPWTDIVKTARFKELAPYDADWYYLRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFC+SSGAIARHILQQLQ MNI+D++PKG
Sbjct: 61  MARKIYLRGGLGVGAFKRIYGGSKRNGSRPPHFCESSGAIARHILQQLQEMNIVDVDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSG+RDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGRRDLDQVAGRIVVAP 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 =  238 bits (606), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 118/143 (82%), Positives = 126/143 (88%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATARTVKDVSPH FVKAYS+HLKRSGK              FKELAPYDPDWYYVRAAS
Sbjct: 1   MATARTVKDVSPHGFVKAYSSHLKRSGKMELPEWTDIVKTARFKELAPYDPDWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+F+RIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII+++ KG
Sbjct: 61  MARKIYLRGGLGVGAFQRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIELDTKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GR+ITSSG+RDLDQVAGRIVVAP
Sbjct: 121 GRKITSSGRRDLDQVAGRIVVAP 143

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  236 bits (603), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 117/143 (81%), Positives = 124/143 (86%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATA+TVKDVSPHEFVKAY+AHLKRSGK               KELAPYDPDWYYVRAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGTLKELAPYDPDWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+FRRIYGGSKRNGSRPPHF KSSGAIARHILQQLQNMNI+DI+ KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDSKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITS+GQRDLDQVAG I+VAP
Sbjct: 121 GRRITSTGQRDLDQVAGHIIVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 116/143 (81%), Positives = 124/143 (86%), Gaps = 14/143 (9%)

Query: 1   MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAAS 46
           MATARTVKDVSPHEFVKAY+AHLKRSGK              FKELAPYD DWYYVRAAS
Sbjct: 1   MATARTVKDVSPHEFVKAYAAHLKRSGKVELPPWADIVKTARFKELAPYDADWYYVRAAS 60

Query: 47  MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
           MARKIYLR GLGVG+F+RIY GSKRNGSRPPHFC+SSGAI RHILQQLQ MNI+D++PKG
Sbjct: 61  MARKIYLRGGLGVGAFKRIYNGSKRNGSRPPHFCESSGAIVRHILQQLQEMNIVDVDPKG 120

Query: 107 GRRITSSGQRDLDQVAGRIVVAP 129
           GRRITSSG+RDLDQVAGRIVVAP
Sbjct: 121 GRRITSSGRRDLDQVAGRIVVAP 143

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	129
TAIR|locus:2159486	143	AT5G61170 [Arabidopsis thalian	0.992	0.895	0.774	9.9e-55
TAIR|locus:2078633	143	AT3G02080 [Arabidopsis thalian	1.0	0.902	0.762	2.1e-54
TAIR|locus:2180912	143	AT5G15520 [Arabidopsis thalian	0.968	0.874	0.769	6.3e-53
MGI|MGI:1333780	145	Rps19 "ribosomal protein S19"	0.953	0.848	0.496	2.6e-31
RGD|68440	145	Rps19 "ribosomal protein S19"	0.953	0.848	0.496	2.6e-31
RGD|2318347	145	LOC100362339 "ribosomal protei	0.953	0.848	0.496	4.2e-31
RGD|2321315	145	LOC100360843 "ribosomal protei	0.953	0.848	0.496	6.9e-31
UNIPROTKB|Q32PD5	145	RPS19 "40S ribosomal protein S	0.953	0.848	0.489	1.1e-30
UNIPROTKB|J9P425	153	RPS19 "Uncharacterized protein	0.953	0.803	0.489	1.1e-30
UNIPROTKB|P39019	145	RPS19 "40S ribosomal protein S	0.953	0.848	0.489	1.1e-30

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 110/142 (77%), Positives = 120/142 (84%)

Query:     1 MATARTVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAAS 46
             MAT +TVKDVSPHEFVKAY+AHLKRSGK               KELAPYDPDWYY+RAAS
Sbjct:     1 MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query:    47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
             MARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG +ARHILQQLQ MNI+D++ KG
Sbjct:    61 MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKG 120

Query:   107 GRRITSSGQRDLDQVAGRIVVA 128
             GR+ITSSGQRDLDQVAGRI  A
Sbjct:   121 GRKITSSGQRDLDQVAGRIAAA 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:2078633 AT3G02080 [Arabidopsis thaliana (taxid:3702)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 109/143 (76%), Positives = 121/143 (84%)

Query:     1 MATARTVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAAS 46
             MAT +TVKDVSPH+FVKAY++HLKRSGK               KELAPYDPDWYY+RAAS
Sbjct:     1 MATGKTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query:    47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
             MARK+YLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ MNI++++ KG
Sbjct:    61 MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKG 120

Query:   107 GRRITSSGQRDLDQVAGRIVVAP 129
             GRRITSSGQRDLDQVAGRI V P
Sbjct:   121 GRRITSSGQRDLDQVAGRIAVEP 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:2180912 AT5G15520 [Arabidopsis thaliana (taxid:3702)]

 Score = 548 (198.0 bits), Expect = 6.3e-53, P = 6.3e-53
 Identities = 107/139 (76%), Positives = 119/139 (85%)

Query:     1 MATARTVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAAS 46
             MAT +TVKDVSPH+FVKAY++HLKRSGK               KELAPYDPDWYY+RAAS
Sbjct:     1 MATGKTVKDVSPHDFVKAYASHLKRSGKIELPLWTDIVKTGRLKELAPYDPDWYYIRAAS 60

Query:    47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG 106
             MARKIYLR GLGVG+FRRIYGGSKRNGSRPPHFCKSSG IARHILQQL+ M+I++++ KG
Sbjct:    61 MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELDTKG 120

Query:   107 GRRITSSGQRDLDQVAGRI 125
             GRRITSSGQRDLDQVAGRI
Sbjct:   121 GRRITSSGQRDLDQVAGRI 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 = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 68/137 (49%), Positives = 93/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 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|68440 Rps19 "ribosomal protein S19" [Rattus norvegicus (taxid:10116)]

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 68/137 (49%), Positives = 93/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 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 = 342 (125.4 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 68/137 (49%), Positives = 93/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMMEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 141

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 68/137 (49%), Positives = 92/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWLYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG RP HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 141

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|Q32PD5 RPS19 "40S ribosomal protein S19" [Bos taurus (taxid:9913)]

 Score = 338 (124.0 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 67/137 (48%), Positives = 92/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 141

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

GO:0030218 "erythrocyte differentiation" evidence=IEA

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

GO:0015669 "gas transport" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0006412 "translation" evidence=IEA

UNIPROTKB|J9P425 RPS19 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 338 (124.0 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 67/137 (48%), Positives = 92/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:    13 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 72

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    73 YLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 132

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   133 PQGQRDLDRIAGQVAAA 149

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

UNIPROTKB|P39019 RPS19 "40S ribosomal protein S19" [Homo sapiens (taxid:9606)]

 Score = 338 (124.0 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 67/137 (48%), Positives = 92/137 (67%)

Query:     6 TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPDWYYVRAASMARKI 51
             TVKDV+  EFV+A +A LK+SGK K              ELAPYD +W+Y RAAS AR +
Sbjct:     5 TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query:    52 YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
             YLR G GVGS  +IYGG +RNG  P HF + S ++AR +LQ L+ + +++ +  GGR++T
Sbjct:    65 YLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query:   112 SSGQRDLDQVAGRIVVA 128
               GQRDLD++AG++  A
Sbjct:   125 PQGQRDLDRIAGQVAAA 141

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

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

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

GO:0006364 "rRNA processing" evidence=IMP

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

GO:0006412 "translation" evidence=IC;TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005840 "ribosome" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0009991 "response to extracellular stimulus" evidence=TAS

GO:0030218 "erythrocyte differentiation" evidence=IMP

GO:0051272 "positive regulation of cellular component movement" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

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

---

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)
P07281	RS19B_YEAST	No assigned EC number	0.4191	0.9379	0.8402	yes	no
P39019	RS19_HUMAN	No assigned EC number	0.4890	0.9534	0.8482	yes	no
P40978	RS19_ORYSJ	No assigned EC number	0.7375	0.9844	0.8698	yes	no
Q5R8M9	RS19_PONAB	No assigned EC number	0.4890	0.9534	0.8482	yes	no
Q54X51	RS19_DICDI	No assigned EC number	0.4460	0.9612	0.8378	yes	no
Q9LF30	RS192_ARATH	No assigned EC number	0.7697	0.9689	0.8741	no	no
Q9FNP8	RS193_ARATH	No assigned EC number	0.7746	0.9922	0.8951	yes	no
P07280	RS19A_YEAST	No assigned EC number	0.4191	0.9379	0.8402	yes	no
Q9CZX8	RS19_MOUSE	No assigned EC number	0.4963	0.9534	0.8482	yes	no
Q29308	RS19_PIG	No assigned EC number	0.5	0.9147	0.8676	yes	no
Q94613	RS19_MYAAR	No assigned EC number	0.5074	0.9302	0.8053	N/A	no
P58234	RS19A_SCHPO	No assigned EC number	0.4885	0.9069	0.8125	yes	no
Q9SGA6	RS191_ARATH	No assigned EC number	0.7622	1.0	0.9020	no	no
O18650	RS19_CAEEL	No assigned EC number	0.4233	0.9379	0.8287	yes	no
Q9YD22	RS19E_AERPE	No assigned EC number	0.408	0.9534	0.8039	yes	no
P17074	RS19_RAT	No assigned EC number	0.4963	0.9534	0.8482	yes	no
P27073	RS19_EMENI	No assigned EC number	0.4852	0.9379	0.8175	yes	no
Q32PD5	RS19_BOVIN	No assigned EC number	0.4890	0.9534	0.8482	yes	no
P54057	RS19E_METJA	No assigned EC number	0.3458	0.9224	0.8040	yes	no
P79016	RS19B_SCHPO	No assigned EC number	0.4885	0.9069	0.8181	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

Your Input:
	eugene3.00041113	hypothetical protein (144 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XVI.1998.1	SubName- Full=Putative uncharacterized protein; (204 aa)			•	•	•	•	•		0.804
	eugene3.00061162	SubName- Full=Putative uncharacterized protein; (208 aa)			•	•	•	•	•		0.802
	estExt_fgenesh4_pg.C_LG_X2153	SubName- Full=Putative uncharacterized protein; (105 aa)			•	•		•	•		0.776
	estExt_fgenesh4_pg.C_LG_VII0715	SubName- Full=Putative uncharacterized protein; (106 aa)			•	•		•	•		0.773
	grail3.0189002602	SubName- Full=Putative uncharacterized protein; (220 aa)			•	•		•	•		0.771
	estExt_fgenesh4_pm.C_LG_XIX0276	SubName- Full=Putative uncharacterized protein; (220 aa)			•	•		•	•		0.771
	fgenesh4_kg.C_LG_V000020	SubName- Full=Putative uncharacterized protein; (106 aa)			•	•		•	•		0.770
	estExt_Genewise1_v1.C_2040015	SubName- Full=Putative uncharacterized protein; (129 aa)	•								0.766
	grail3.0072001304	SubName- Full=Putative uncharacterized protein; (133 aa)			•	•		•	•		0.753
	estExt_Genewise1_v1.C_2040056	SubName- Full=Putative uncharacterized protein; (133 aa)			•	•		•	•		0.753

---

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	129
pfam01090	140	pfam01090, Ribosomal_S19e, Ribosomal protein S19e	1e-65
COG2238	147	COG2238, RPS19A, Ribosomal protein S19E (S16A) [Tr	3e-43
PRK09333	150	PRK09333, PRK09333, 30S ribosomal protein S19e; Pr	6e-39
PTZ00095	169	PTZ00095, PTZ00095, 40S ribosomal protein S19; Pro	2e-35

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

 Score =  195 bits (497), Expect = 1e-65
 Identities = 68/135 (50%), Positives = 88/135 (65%), Gaps = 14/135 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKI 51
           TVKDV   E +KA +  LK+SGK               KEL P DPDW+YVRAAS+ RK+
Sbjct: 2   TVKDVPADELIKALAEFLKKSGKIKVPEWADFVKTGVHKELPPEDPDWWYVRAASILRKL 61

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YLR  +GVG  R+IYGG KR G RP HF K SG+I R  LQQL+   +++ +PKGGRR+T
Sbjct: 62  YLRGPVGVGRLRKIYGGRKRRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDPKGGRRLT 121

Query: 112 SSGQRDLDQVAGRIV 126
             G+ DLD++A  ++
Sbjct: 122 PQGRSDLDRIAAEVL 136

Length = 140

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

 Score =  138 bits (350), Expect = 3e-43
 Identities = 54/134 (40%), Positives = 75/134 (55%), Gaps = 15/134 (11%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKI 51
           TV DV     ++A +++LK +GK               KE  P   DW+YVRAAS+ RKI
Sbjct: 3   TVYDVPADLLIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKI 62

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           Y+   +G+   R  YGG K  GSRP  F K SG+I R +LQQL+   +++  PK GR +T
Sbjct: 63  YIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTPK-GRVLT 121

Query: 112 SSGQRDLDQVAGRI 125
             G+  LD++A  I
Sbjct: 122 PKGRSLLDRIATEI 135

Length = 147

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

 Score =  127 bits (322), Expect = 6e-39
 Identities = 52/134 (38%), Positives = 71/134 (52%), Gaps = 15/134 (11%)

Query: 6   TVKDVSPHEFVKAYSAHLK--------------RSGKFKELAPYDPDWYYVRAASMARKI 51
           TV DV     ++  + +LK              ++G  KE  P   DW+YVRAAS+ RK+
Sbjct: 3   TVYDVPADLLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKV 62

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           Y+   +GV   R  YGG K  G RP HF K SG+I R ILQQL+   +++   K GR IT
Sbjct: 63  YIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK-GRVIT 121

Query: 112 SSGQRDLDQVAGRI 125
             G+  LD +A  +
Sbjct: 122 PKGRSLLDNLAAEV 135

Length = 150

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

 Score =  119 bits (301), Expect = 2e-35
 Identities = 53/135 (39%), Positives = 77/135 (57%), Gaps = 15/135 (11%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAASMARKI 51
           T+KDVSP  F+KA++ H K  GK               +ELAP +PDWYY+R A++ R +
Sbjct: 27  TLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRAL 86

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-GRRI 110
           YLR  +G G  R+ +   KR GS P H  ++SG I R I QQL+ + +++  PK  GRR+
Sbjct: 87  YLRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRL 146

Query: 111 TSSGQRDLDQVAGRI 125
           T  G    +  A ++
Sbjct: 147 TRKGCNFANAFARQV 161

Length = 169

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	129
PF01090	139	Ribosomal_S19e: Ribosomal protein S19e; InterPro:	100.0
PTZ00095	169	40S ribosomal protein S19; Provisional	100.0
PRK09333	150	30S ribosomal protein S19e; Provisional	100.0
KOG3411	143	consensus 40S ribosomal protein S19 [Translation,	100.0
COG2238	147	RPS19A Ribosomal protein S19E (S16A) [Translation,	100.0
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	97.52
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	97.23
COG1420	346	HrcA Transcriptional regulator of heat shock gene	96.98
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	96.96
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.55
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.52
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.48
PRK10870	176	transcriptional repressor MprA; Provisional	96.42
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.42
PRK11050	152	manganese transport regulator MntR; Provisional	96.32
COG3388	101	Predicted transcriptional regulator [Transcription	96.3
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	96.27
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	96.21
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.19
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.12
PRK03911	260	heat-inducible transcription repressor; Provisiona	96.01
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.88
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.85
PRK03573	144	transcriptional regulator SlyA; Provisional	95.81
COG1846	126	MarR Transcriptional regulators [Transcription]	95.79
PRK03902	142	manganese transport transcriptional regulator; Pro	95.56
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	95.16
PRK13777	185	transcriptional regulator Hpr; Provisional	95.01
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	94.92
PF14338	92	Mrr_N: Mrr N-terminal domain	94.87
COG3432	95	Predicted transcriptional regulator [Transcription	94.8
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	94.77
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	94.6
TIGR03338	212	phnR_burk phosphonate utilization associated trans	94.48
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.41
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.33
PRK05638	442	threonine synthase; Validated	94.28
COG1725	125	Predicted transcriptional regulators [Transcriptio	94.19
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	94.19
PF10711	102	DUF2513: Hypothetical protein (DUF2513); InterPro:	94.11
COG1693	325	Repressor of nif and glnA expression [Transcriptio	94.01
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.96
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	93.81
PF03551	75	PadR: Transcriptional regulator PadR-like family;	93.74
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.64
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	93.44
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	93.37
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	93.01
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	92.83
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	92.76
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	92.64
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.45
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	92.36
COG1733	120	Predicted transcriptional regulators [Transcriptio	92.03
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	92.02
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	91.91
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	91.9
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	91.7
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	91.53
PRK11014	141	transcriptional repressor NsrR; Provisional	91.38
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.33
PF09114	96	MotA_activ: Transcription factor MotA, activation	91.2
COG1802	230	GntR Transcriptional regulators [Transcription]	91.06
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	90.77
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	90.45
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	90.39
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	90.36
PRK04984	239	fatty acid metabolism regulator; Provisional	90.35
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	90.31
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	90.07
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	90.07
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	89.91
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	89.88
PRK03837	241	transcriptional regulator NanR; Provisional	89.86
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	89.68
PRK09416	135	lstR lineage-specific thermal regulator protein; P	89.63
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	89.28
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.24
PRK14165	217	winged helix-turn-helix domain-containing protein/	88.87
PF09382	106	RQC: RQC domain; InterPro: IPR018982 This entry re	88.57
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	88.48
PRK11569	274	transcriptional repressor IclR; Provisional	88.37
PRK09057	380	coproporphyrinogen III oxidase; Provisional	88.29
COG3355	126	Predicted transcriptional regulator [Transcription	88.04
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	87.67
PF13814	191	Replic_Relax: Replication-relaxation	87.51
PRK08599	377	coproporphyrinogen III oxidase; Provisional	87.37
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.3
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	87.17
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	87.16
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	87.14
COG1695	138	Predicted transcriptional regulators [Transcriptio	87.03
PRK07379	400	coproporphyrinogen III oxidase; Provisional	86.87
COG1414	246	IclR Transcriptional regulator [Transcription]	86.85
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	86.55
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	86.44
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	85.97
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	85.93
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	85.71
PRK05799	374	coproporphyrinogen III oxidase; Provisional	85.53
COG2186	241	FadR Transcriptional regulators [Transcription]	85.38
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	84.47
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	84.36
PRK05628	375	coproporphyrinogen III oxidase; Validated	83.89
PRK05660	378	HemN family oxidoreductase; Provisional	83.87
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	83.65
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	83.47
PRK09334	86	30S ribosomal protein S25e; Provisional	82.52
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	82.38
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	82.3
PRK08208	430	coproporphyrinogen III oxidase; Validated	82.21
COG0635	416	HemN Coproporphyrinogen III oxidase and related Fe	81.58
PRK13347	453	coproporphyrinogen III oxidase; Provisional	81.39
PRK14999	241	histidine utilization repressor; Provisional	81.33
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	81.24
PRK10079	241	phosphonate metabolism transcriptional regulator P	81.06
PRK06294	370	coproporphyrinogen III oxidase; Provisional	81.04
COG2524	294	Predicted transcriptional regulator, contains C-te	80.11

>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=6.7e-67  Score=395.37  Aligned_cols=124  Identities=59%  Similarity=1.064  Sum_probs=114.5

Q ss_pred             CcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccC
Q 033029            5 RTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSK   70 (129)
Q Consensus         5 ~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k   70 (129)
                      +||||||||+||++||+|||++|+              +||+||+||||||+|||||||||||+||+||++||++|||+|
T Consensus         1 vtvkDV~a~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~~~DW~Y~RaASilRklY~~g~~GV~~lr~~YGg~k   80 (139)
T PF01090_consen    1 VTVKDVPADEFIKALAEFLKKSGKIEPPEWADIVKTGSHKELAPYDPDWWYIRAASILRKLYIRGPVGVGRLRKIYGGRK   80 (139)
T ss_dssp             HCGGGSSHHHHHHHHHHHHTCSSTS--TSCGGGTSSSSS-SSTTCHHTHHHHHHHHHHHHHHHCTSB-HHHHHHHH--EE
T ss_pred             CcceecCHHHHHHHHHHHHHHcCCcCCcchHHHHhhcccccCCCCCCCeeeeeHHHHHHHHHHhcCcchHHHHHHhCCCC
Confidence            599999999999999999999987              999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           71 RNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        71 ~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      |||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+||.||+++
T Consensus        81 ~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~~~  138 (139)
T PF01090_consen   81 RRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVAKE  138 (139)
T ss_dssp             EETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999999999899999999999999999999864

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=7.4e-66  Score=399.75  Aligned_cols=126  Identities=42%  Similarity=0.781  Sum_probs=121.8

Q ss_pred             CCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcc
Q 033029            3 TARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGG   68 (129)
Q Consensus         3 ~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg   68 (129)
                      .++||||||||+||++||+|||++|+              +||+||+||||||+||||||||||++||+||++||++|||
T Consensus        24 ~~~tvkDVpa~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg  103 (169)
T PTZ00095         24 KNATLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSS  103 (169)
T ss_pred             CCCceeeCCHHHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCC
Confidence            46899999999999999999999987              9999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhhHHHHHHHhhhC
Q 033029           69 SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        69 ~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      +||||++|+||++|||+|||+||||||++|||++++ ++||+|||+||++||+||.+|+++
T Consensus       104 ~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~~  164 (169)
T PTZ00095        104 KKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIR  164 (169)
T ss_pred             CCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999996 489999999999999999999764

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=100.00  E-value=1.5e-64  Score=386.49  Aligned_cols=124  Identities=40%  Similarity=0.667  Sum_probs=120.9

Q ss_pred             CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029            4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS   69 (129)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~   69 (129)
                      |+||||||||+||++||+|||++|+              +||+||+||||||+||||||||||++||+||++|+++|||+
T Consensus         1 m~tv~DVpa~~~I~~~A~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~   80 (150)
T PRK09333          1 MVTVYDVPADLLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGR   80 (150)
T ss_pred             CCCcccCCHHHHHHHHHHHHHhcCCcCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCC
Confidence            7899999999999999999999987              99999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      ||||++|+||++|||+|||++|||||++|||++++ +||+||++||++||+||.+|+.+
T Consensus        81 k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~iA~~i~~~  138 (150)
T PRK09333         81 KNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNLAAEVKKE  138 (150)
T ss_pred             cCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999998 89999999999999999999753

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

Probab=100.00  E-value=2.2e-64  Score=379.75  Aligned_cols=127  Identities=65%  Similarity=1.116  Sum_probs=124.7

Q ss_pred             CCCCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHh
Q 033029            1 MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIY   66 (129)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~Y   66 (129)
                      ||+ +|||||+|++|+++||.|||++||              +||+||+||||||+|||||+||||++||+||++|+++|
T Consensus         1 m~g-vtVkdV~~~~f~~a~asfLK~sgkv~vp~~~DivKtg~~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiY   79 (143)
T KOG3411|consen    1 MPG-VTVKDVDPHKFTKAYASFLKRSGKVEVPQWVDIVKTGKGKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIY   79 (143)
T ss_pred             CCc-cchhhcCHHHHHHHHHHHHHhcCCccCcchhhhhhcccCcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHh
Confidence            787 899999999999999999999998              99999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           67 GGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        67 Gg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      ||+|||||+|+||+.+||+|+|++||+||++||||++++|||+||++||++||+||++|..+
T Consensus        80 Gg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~  141 (143)
T KOG3411|consen   80 GGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE  141 (143)
T ss_pred             cccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999875

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

Probab=100.00  E-value=9.8e-63  Score=373.67  Aligned_cols=124  Identities=43%  Similarity=0.717  Sum_probs=121.1

Q ss_pred             CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029            4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS   69 (129)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~   69 (129)
                      |+||||||+|+||++||++||++++              |||+||+++||||+|||||||||||+|||||++||+.|||+
T Consensus         1 m~tv~dVpad~lI~~lA~~LK~~~kv~pP~wa~~vKTG~~kE~~P~~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~   80 (147)
T COG2238           1 MVTVYDVPADLLIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGR   80 (147)
T ss_pred             CCchhcCCHHHHHHHHHHHHHhcCCcCChhhhhhhhccccccCCCCCCchHHHHHHHHHHHHHhcCchhHHHHHHHHCcc
Confidence            7899999999999999999999976              99999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      +|||++|+||.+|||+|+|++|||||++|||+|++ +||+|||+||++||+||.+|+++
T Consensus        81 k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~ee  138 (147)
T COG2238          81 KNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKEE  138 (147)
T ss_pred             ccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999998 79999999999999999999764

>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=97.52  E-value=0.00019  Score=47.86  Aligned_cols=63  Identities=21%  Similarity=0.238  Sum_probs=51.1

Q ss_pred             HHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029           47 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      ||+.|+-. +|+|-..|+....-.   |.      .-|-.-+|+-|..||..||+++...+||.||++|...|
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---GE------ELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL   66 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhc---Ch------hhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence            67777775 689999999987653   32      33456899999999999999987778999999998764

>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=97.23  E-value=0.00027  Score=49.43  Aligned_cols=57  Identities=25%  Similarity=0.514  Sum_probs=46.2

Q ss_pred             HHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchHhhHHH
Q 033029           50 KIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ  120 (129)
Q Consensus        50 ~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~~lD~  120 (129)
                      ..|++  .|||-..+....+-              |-.-||+.++.||++|||++.+  .+||+-|.+|-+.+++
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            45775  49999999987531              2368999999999999999643  6899999999998864

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

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

Probab=96.98  E-value=0.0015  Score=56.03  Aligned_cols=63  Identities=27%  Similarity=0.402  Sum_probs=50.6

Q ss_pred             hHHHHHHHH---HHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHh
Q 033029           43 RAASMARKI---YLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQR  116 (129)
Q Consensus        43 R~ASilR~l---Yl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~  116 (129)
                      |-..|||.|   |+.  -|||-..|.+.|+-            .-|..-||+.+++||++|+++|.. ..||+-|+.|-+
T Consensus         7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l------------~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr   74 (346)
T COG1420           7 RQRLILRAIVEDYLATGEPVGSKTLSEKYNL------------DLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR   74 (346)
T ss_pred             HHHHHHHHHHHHHHhcCCccchHHHHHHhCC------------CCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence            455566654   775  49999999998763            345678999999999999999865 479999999976


Q ss_pred             h
Q 033029          117 D  117 (129)
Q Consensus       117 ~  117 (129)
                      .
T Consensus        75 ~   75 (346)
T COG1420          75 Y   75 (346)
T ss_pred             H
Confidence            4

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

Probab=96.96  E-value=0.0026  Score=42.98  Aligned_cols=62  Identities=15%  Similarity=0.247  Sum_probs=43.7

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA  122 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA  122 (129)
                      +.||.-+- .++.....+...              +.=|-+.+.+.|..|++.|+|++. ++.-.||++|...|+.+-
T Consensus         9 ~~IL~~l~-~~~~~~t~i~~~--------------~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l~   70 (77)
T PF14947_consen    9 FDILKILS-KGGAKKTEIMYK--------------ANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEELE   70 (77)
T ss_dssp             HHHHHHH--TT-B-HHHHHTT--------------ST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHH--------------hCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHHH
Confidence            34555554 677777666532              345667999999999999999774 578999999999999874

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

Probab=96.55  E-value=0.0059  Score=41.36  Aligned_cols=41  Identities=22%  Similarity=0.398  Sum_probs=35.9

Q ss_pred             chhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           83 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      +.+-+..+|+.||+.|||++.++++-.||+.|+...+.+..
T Consensus        12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~   52 (96)
T smart00529       12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLR   52 (96)
T ss_pred             ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHH
Confidence            45689999999999999999887799999999998877654

iron dependent repressor

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.52  E-value=0.016  Score=41.04  Aligned_cols=65  Identities=14%  Similarity=0.133  Sum_probs=51.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-++++.+..|+...|-.+              +-+-.+++.||+.|||+..+  ...|    .||++|+..+++
T Consensus        33 iL~~l~~~~~~t~~ela~~~~~~~--------------~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~   98 (118)
T TIGR02337        33 ILRILAEQGSMEFTQLANQACILR--------------PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS   98 (118)
T ss_pred             HHHHHHHcCCcCHHHHHHHhCCCc--------------hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            666777889999999999876532              24568999999999999754  3344    699999999998


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +....
T Consensus        99 ~~~~~  103 (118)
T TIGR02337        99 LSPQI  103 (118)
T ss_pred             hhHHH
Confidence            87654

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.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.48  E-value=0.0059  Score=47.51  Aligned_cols=60  Identities=15%  Similarity=0.256  Sum_probs=49.1

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCc-----eeCcchHhh
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR-----~lT~~G~~~  117 (129)
                      +||..|.-.|++.+..|....|-.              ..-+|+.|+.||+.|||+...   ..||     .||++|...
T Consensus         5 ~IL~~L~~~~~~t~~eLA~~lgis--------------~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~   70 (203)
T TIGR02702         5 DILSYLLKQGQATAAALAEALAIS--------------PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ   70 (203)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence            578888778999999999987543              358999999999999998762   3578     999999876


Q ss_pred             HH
Q 033029          118 LD  119 (129)
Q Consensus       118 lD  119 (129)
                      +.
T Consensus        71 ~~   72 (203)
T TIGR02702        71 FP   72 (203)
T ss_pred             cc
Confidence            54

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.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=96.42  E-value=0.021  Score=43.88  Aligned_cols=64  Identities=17%  Similarity=0.184  Sum_probs=49.1

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce----eCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~----lT~~G~~~l  118 (129)
                      ||..|+-.  +++.+..|+...|-.              .+-+=.+++.||+.|||++.+  +.+|.    ||++|+..+
T Consensus        60 iL~~L~~~~~~~it~~eLa~~l~l~--------------~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~  125 (176)
T PRK10870         60 ALITLESQENHSIQPSELSCALGSS--------------RTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL  125 (176)
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            56777753  467778999987753              235667899999999999754  45777    999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      +++-..
T Consensus       126 ~~i~~~  131 (176)
T PRK10870        126 REVLPP  131 (176)
T ss_pred             HHHHHH
Confidence            998544

>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=96.42  E-value=0.0035  Score=39.84  Aligned_cols=54  Identities=19%  Similarity=0.322  Sum_probs=38.4

Q ss_pred             HHHHHH-HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcch
Q 033029           47 MARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG  114 (129)
Q Consensus        47 ilR~lY-l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G  114 (129)
                      ||+.|+ -+++.....|+...+-.              ..-+.+++++|++.|||++.+  ..+|    .|||+|
T Consensus         8 vL~~l~~~~~~~t~~~l~~~~~~~--------------~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    8 VLRALAHSDGPMTQSDLAERLGIS--------------KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHT--TS-BEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHccCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            777788 67899999999987653              245669999999999998654  3455    578877

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.32  E-value=0.02  Score=43.13  Aligned_cols=64  Identities=16%  Similarity=0.164  Sum_probs=52.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      .|++.++-.+++.+..|...+|-.              .+-+..+++.||+.|+|...+.+|-.||++|+..+..+..
T Consensus        41 ~I~~~l~~~~~~t~~eLA~~l~is--------------~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~  104 (152)
T PRK11050         41 LIADLIAEVGEARQVDIAARLGVS--------------QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE  104 (152)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence            366666667889999999887643              3589999999999999998776789999999999777653

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=96.30  E-value=0.0093  Score=43.51  Aligned_cols=69  Identities=23%  Similarity=0.294  Sum_probs=57.8

Q ss_pred             HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      .|--+++..+-=.+|+|+..|+..-|-       |+|.       +|+.|.=||+.+++.-+. .|-++|+.+-..+++|
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            355677777777899999999998774       8776       799999999999998664 5999999999998888


Q ss_pred             HHHh
Q 033029          122 AGRI  125 (129)
Q Consensus       122 A~~i  125 (129)
                      .+.+
T Consensus        79 ~~dl   82 (101)
T COG3388          79 IGDL   82 (101)
T ss_pred             HHHH
Confidence            7664

>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=96.27  E-value=0.0049  Score=42.93  Aligned_cols=68  Identities=21%  Similarity=0.216  Sum_probs=44.9

Q ss_pred             chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029           38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD  117 (129)
Q Consensus        38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~  117 (129)
                      |+.=.|.-..+...|-.||||+..|+..-|--+             ..|.=.+===|-+.|+|++++ .||++|++|.+-
T Consensus         7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~-------------~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~   72 (76)
T PF05491_consen    7 DELDRRYLKTLIENFKGGPVGLDTLAAALGEDK-------------ETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEH   72 (76)
T ss_dssp             BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-H-------------HHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCH-------------hHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHH
Confidence            445556566677777889999999998765421             123322333467899999998 599999999876


Q ss_pred             HH
Q 033029          118 LD  119 (129)
Q Consensus       118 lD  119 (129)
                      |.
T Consensus        73 l~   74 (76)
T PF05491_consen   73 LG   74 (76)
T ss_dssp             TT
T ss_pred             hC
Confidence            53

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=96.21  E-value=0.028  Score=41.18  Aligned_cols=64  Identities=14%  Similarity=0.163  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++....|+...|-.              .+-+=.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        44 ~vL~~l~~~~~~t~~eLa~~l~i~--------------~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~  109 (144)
T PRK11512         44 KVLCSIRCAACITPVELKKVLSVD--------------LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE  109 (144)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence            367778888999999999987653              235667899999999999754  3455    58999999988


Q ss_pred             HHHH
Q 033029          120 QVAG  123 (129)
Q Consensus       120 ~iA~  123 (129)
                      ++..
T Consensus       110 ~~~~  113 (144)
T PRK11512        110 QCHQ  113 (144)
T ss_pred             HHHH
Confidence            8643

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.19  E-value=0.039  Score=36.44  Aligned_cols=65  Identities=18%  Similarity=0.276  Sum_probs=50.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC------CceeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~------GR~lT~~G~~~lD~  120 (129)
                      |+..|+..+++.+..+....+-.              ..-|..+|+.|++.|||++..++      .-.||++|...+..
T Consensus        15 il~~l~~~~~~~~~~la~~~~~s--------------~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       15 VLRILYEEGPLSVSELAKRLGVS--------------PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            77778888899999998875421              22478999999999999876532      35699999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus        81 ~~~~~   85 (101)
T smart00347       81 LLEAR   85 (101)
T ss_pred             HHHHH
Confidence            77664

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.12  E-value=0.026  Score=33.95  Aligned_cols=59  Identities=19%  Similarity=0.260  Sum_probs=43.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCc-chHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS-SGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~-~G~~~lD~  120 (129)
                      |++.|+ .+++.+..+...+|-              |.+-++.+|++|++.|+|+...++   .-.+|+ .|...++.
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 889999999999872              335799999999999999976532   233666 55555543

>PRK03911 heat-inducible transcription repressor; Provisional

Probab=96.01  E-value=0.0099  Score=49.68  Aligned_cols=55  Identities=22%  Similarity=0.383  Sum_probs=45.2

Q ss_pred             HHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029           51 IYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD  117 (129)
Q Consensus        51 lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~  117 (129)
                      -|+.  -|||-..|.+.|+-            .-|.+-||+.++.||++|++++.. ..||+-|.+|-+.
T Consensus        15 ~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr~   72 (260)
T PRK03911         15 TYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMKN   72 (260)
T ss_pred             HHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHHH
Confidence            3775  49999999998764            334578999999999999999754 4799999999863

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

Probab=95.88  E-value=0.028  Score=38.58  Aligned_cols=64  Identities=13%  Similarity=0.182  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC------CceeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~------GR~lT~~G~~~l  118 (129)
                      ..|++.|.. |+...+.|.+.-             ...|.+++-.-|..||+.|+|++....      -..||+.|++++
T Consensus         8 ~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~   73 (90)
T PF01638_consen    8 LLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL   73 (90)
T ss_dssp             HHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred             HHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence            568888888 888878877753             245678999999999999999976422      268999999988


Q ss_pred             HHHH
Q 033029          119 DQVA  122 (129)
Q Consensus       119 D~iA  122 (129)
                      .-+.
T Consensus        74 ~~l~   77 (90)
T PF01638_consen   74 PVLE   77 (90)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6554

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.85  E-value=0.046  Score=36.38  Aligned_cols=60  Identities=20%  Similarity=0.297  Sum_probs=48.5

Q ss_pred             HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchH
Q 033029           42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ  115 (129)
Q Consensus        42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~  115 (129)
                      -|+-.|+..|.-. +++++..+....|-              +.+-+++.|+.||+.|+|++++ ++...|++...
T Consensus         5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i--------------~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~   66 (91)
T smart00346        5 ERGLAVLRALAEEPGGLTLAELAERLGL--------------SKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL   66 (91)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence            3788899998887 79999999998754              3468999999999999999875 34567777544

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=95.81  E-value=0.081  Score=38.43  Aligned_cols=64  Identities=14%  Similarity=0.146  Sum_probs=47.5

Q ss_pred             HHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      +|..|+-. ++.....|+...|-.+              +-+=.++..||+.|||++.+  +..|    .||++|+..++
T Consensus        36 vL~~l~~~~~~~t~~eLa~~l~~~~--------------~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  101 (144)
T PRK03573         36 TLHNIHQLPPEQSQIQLAKAIGIEQ--------------PSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS  101 (144)
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCh--------------hhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH
Confidence            56666654 4577889998876542              24558999999999999764  3455    49999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       102 ~~~~~  106 (144)
T PRK03573        102 EVEAV  106 (144)
T ss_pred             HHHHH
Confidence            86654

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=95.79  E-value=0.053  Score=36.62  Aligned_cols=65  Identities=20%  Similarity=0.326  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      ..++..||..++.+.+.|....+-              +.+-+=.+++.||+.|||+...  ..+|    .||++|+..+
T Consensus        25 ~~~L~~l~~~~~~~~~~la~~l~i--------------~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~   90 (126)
T COG1846          25 YQVLLALYEAGGITVKELAERLGL--------------DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL   90 (126)
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence            568888899888765677766443              2346678899999999998655  3455    7999999999


Q ss_pred             HHHHH
Q 033029          119 DQVAG  123 (129)
Q Consensus       119 D~iA~  123 (129)
                      .++..
T Consensus        91 ~~~~~   95 (126)
T COG1846          91 EQLLP   95 (126)
T ss_pred             HHhcc
Confidence            88755

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=95.56  E-value=0.068  Score=39.25  Aligned_cols=61  Identities=13%  Similarity=0.077  Sum_probs=44.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      |.+.+.-.|++-+..|+...|-.              .+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus        13 I~~l~~~~~~~~~~ela~~l~vs--------------~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~   73 (142)
T PRK03902         13 IYLLIEEKGYARVSDIAEALSVH--------------PSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL   73 (142)
T ss_pred             HHHHHhcCCCcCHHHHHHHhCCC--------------hhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence            44444445667777777765432              23577889999999999876667899999998876655

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=95.16  E-value=0.11  Score=36.58  Aligned_cols=66  Identities=11%  Similarity=0.106  Sum_probs=50.6

Q ss_pred             HHHHHH----HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce----eCcchHh
Q 033029           47 MARKIY----LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQR  116 (129)
Q Consensus        47 ilR~lY----l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~----lT~~G~~  116 (129)
                      +|..|+    -.+++....|+..-+-.              .+-+=.++..||+.|||++..  +..|.    ||++|++
T Consensus        30 vL~~l~~~~~~~~~~t~~eL~~~l~~~--------------~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~   95 (109)
T TIGR01889        30 ILYYLGKLENNEGKLTLKEIIKEILIK--------------QSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS   95 (109)
T ss_pred             HHHHHHhhhccCCcCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence            677777    34789999999876542              235667899999999999754  34553    8999999


Q ss_pred             hHHHHHHHhh
Q 033029          117 DLDQVAGRIV  126 (129)
Q Consensus       117 ~lD~iA~~i~  126 (129)
                      .++.+..++-
T Consensus        96 ~~~~~~~~~~  105 (109)
T TIGR01889        96 KIESLISEIE  105 (109)
T ss_pred             HHHHHHHHHH
Confidence            9999988763

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.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=95.01  E-value=0.12  Score=40.72  Aligned_cols=66  Identities=12%  Similarity=0.137  Sum_probs=49.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR----~lT~~G~~~lD  119 (129)
                      .||-.||-++++....|++..+-.              .+-+=.+++.||+.|||+..  ++..|    .||++|+..++
T Consensus        49 ~iL~~L~~~~~itq~eLa~~l~l~--------------~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~  114 (185)
T PRK13777         49 HILWIAYHLKGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL  114 (185)
T ss_pred             HHHHHHHhCCCcCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            367778888999999999964432              12355699999999999964  34455    39999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      ++...+
T Consensus       115 ~l~~~~  120 (185)
T PRK13777        115 ETMEEY  120 (185)
T ss_pred             HHHHHH
Confidence            886543

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=94.92  E-value=0.056  Score=37.90  Aligned_cols=45  Identities=20%  Similarity=0.293  Sum_probs=34.1

Q ss_pred             CCchhHHHHHHHHHHhCCceeec--C-CCCc-----eeCcchHhhHHHHHHHh
Q 033029           81 KSSGAIARHILQQLQNMNIIDIE--P-KGGR-----RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~--~-~~GR-----~lT~~G~~~lD~iA~~i  125 (129)
                      .-+-+-+=.+|..||+.|||+..  + .+||     .||++|+..|+......
T Consensus        36 ~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~   88 (100)
T TIGR03433        36 QVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW   88 (100)
T ss_pred             ccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            34445688899999999999973  2 2232     59999999999887654

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

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=94.87  E-value=0.033  Score=38.45  Aligned_cols=36  Identities=25%  Similarity=0.332  Sum_probs=31.6

Q ss_pred             hhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029           84 GAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD  119 (129)
Q Consensus        84 g~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD  119 (129)
                      -+-++++++-|.++|+|++...|--.||+.|++.|-
T Consensus        54 ~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~   89 (92)
T PF14338_consen   54 KNRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA   89 (92)
T ss_pred             HHhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence            357999999999999999877667899999999874

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=94.80  E-value=0.049  Score=39.33  Aligned_cols=42  Identities=19%  Similarity=0.233  Sum_probs=33.5

Q ss_pred             CCchhHHHHHHHHHHhCCceeecCCC---CceeCcchHhhHHHHH
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA  122 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~~G~~~lD~iA  122 (129)
                      .=+-.+++++++.|++.|++++...+   .-.||++|.++|..+-
T Consensus        42 Nlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~   86 (95)
T COG3432          42 NLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS   86 (95)
T ss_pred             CcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence            33457899999999999988877643   2579999999987653

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=94.77  E-value=0.075  Score=45.09  Aligned_cols=53  Identities=25%  Similarity=0.293  Sum_probs=44.0

Q ss_pred             HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcchHhh
Q 033029           53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQRD  117 (129)
Q Consensus        53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~G~~~  117 (129)
                      -.+|||+..|.+.|+-            .-|..-||+-+.+||+.|++++... .||.-|.+|-+.
T Consensus        18 ~~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~   71 (337)
T TIGR00331        18 TGQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRY   71 (337)
T ss_pred             cCCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHH
Confidence            3579999999998664            3345689999999999999998653 599999998776

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

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=94.60  E-value=0.087  Score=44.73  Aligned_cols=55  Identities=24%  Similarity=0.389  Sum_probs=44.2

Q ss_pred             HHH--hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029           51 IYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD  117 (129)
Q Consensus        51 lYl--~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~  117 (129)
                      .|+  .+|+|+..|.+.|+-            .-|-.-||+-+..||++|++++.. ..||+-|.+|-+.
T Consensus        18 ~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~   75 (339)
T PRK00082         18 DYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRY   75 (339)
T ss_pred             HHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHH
Confidence            355  579999999987654            233468999999999999999755 4699999999764

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=94.48  E-value=0.063  Score=41.05  Aligned_cols=51  Identities=16%  Similarity=0.229  Sum_probs=40.7

Q ss_pred             CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      +.-..|+..||-              |.+-+|.+|+.||..|||+..++.|-.+++-...++..+
T Consensus        35 L~e~~La~~lgV--------------SRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei   85 (212)
T TIGR03338        35 LNESDIAARLGV--------------SRGPVREAFRALEEAGLVRNEKNRGVFVREISLAEADEI   85 (212)
T ss_pred             ecHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHHHHHH
Confidence            344578888765              446899999999999999999888999988777766543

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.

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

Probab=94.41  E-value=0.092  Score=32.57  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=40.3

Q ss_pred             HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      -|+..||+.|.-.+ ++++..+...-|-              +.+-+.++|+.|++.|||++++
T Consensus         3 ~ral~iL~~l~~~~~~~t~~eia~~~gl--------------~~stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    3 ERALRILEALAESGGPLTLSEIARALGL--------------PKSTVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHHHHHCHHCTBSCEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCcCeecCc
Confidence            48889999888865 4799999998664              2367899999999999999874

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.

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

Probab=94.33  E-value=0.095  Score=35.79  Aligned_cols=65  Identities=12%  Similarity=0.320  Sum_probs=43.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCC-----ceeCcchHhhHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG-----RRITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~G-----R~lT~~G~~~lD  119 (129)
                      |+=-|+-.+.+-...|+..-|              -+.+-+.+-|+.||++|+|+..+  .++     -.||++|+..+.
T Consensus         5 Il~~L~~~~~~~f~~L~~~l~--------------lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~   70 (80)
T PF13601_consen    5 ILALLYANEEATFSELKEELG--------------LTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE   70 (80)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred             HHHHHhhcCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence            344445556666666666533              34567889999999999998654  233     269999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      +.-..+
T Consensus        71 ~~~~~L   76 (80)
T PF13601_consen   71 RYVAAL   76 (80)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

>PRK05638 threonine synthase; Validated

Probab=94.28  E-value=0.11  Score=44.95  Aligned_cols=75  Identities=15%  Similarity=0.198  Sum_probs=54.6

Q ss_pred             CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ++|.-+.++-+.     .||+.|. +++.-+..|.+..+.            .-|...++..|+.||+.|||+...+.||
T Consensus       363 ~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~  424 (442)
T PRK05638        363 GREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGR  424 (442)
T ss_pred             chhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCC
Confidence            555555566443     3666665 668889999998873            1366799999999999999986422344


Q ss_pred             e----eCcchHhhHHHH
Q 033029          109 R----ITSSGQRDLDQV  121 (129)
Q Consensus       109 ~----lT~~G~~~lD~i  121 (129)
                      +    ||++|+..+..+
T Consensus       425 ~~~Y~Lt~~g~~~l~~~  441 (442)
T PRK05638        425 RVYYKLTEKGRRLLENL  441 (442)
T ss_pred             cEEEEECcHHHHHHHhc
Confidence            4    999999998764

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=94.19  E-value=0.082  Score=39.75  Aligned_cols=37  Identities=22%  Similarity=0.343  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           85 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        85 ~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      +-+.++.|.||..|+|+.....|..+|++|+..+|..
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            4889999999999999988878999999999877654

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=94.19  E-value=0.28  Score=38.00  Aligned_cols=85  Identities=19%  Similarity=0.228  Sum_probs=57.7

Q ss_pred             CCCCCcccccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCccc
Q 033029            1 MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFC   80 (129)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~   80 (129)
                      ||+..+   ++...+-+.++++|++.=...+++|-+.                   +-...|+..||-.           
T Consensus         1 ~~~~~~---~~~~~~~e~v~~~l~~~I~~g~l~pG~~-------------------L~e~~La~~lgVS-----------   47 (221)
T PRK11414          1 MPGTEK---TQHISLTLQVENDLKHQLSIGALKPGAR-------------------LITKNLAEQLGMS-----------   47 (221)
T ss_pred             CCCCcc---cCCCCHHHHHHHHHHHHHHhCCCCCCCc-------------------cCHHHHHHHHCCC-----------
Confidence            555333   3344455666777776544567788663                   2235688888753           


Q ss_pred             CCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                         ..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus        48 ---RtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei   85 (221)
T PRK11414         48 ---ITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI   85 (221)
T ss_pred             ---chhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence               35899999999999999998877877776655555443

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

Probab=94.11  E-value=0.097  Score=37.10  Aligned_cols=47  Identities=26%  Similarity=0.280  Sum_probs=37.6

Q ss_pred             CCCcccCCchhHHHHHHHHHHhCCceeecCCC---C------ceeCcchHhhHHHH
Q 033029           75 RPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---G------RRITSSGQRDLDQV  121 (129)
Q Consensus        75 ~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---G------R~lT~~G~~~lD~i  121 (129)
                      .+..+..-+-.-|-+-+++|.++|||+-....   |      ..||.+|..+||.|
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            34555666677999999999999999866532   1      48999999999986

>COG1693 Repressor of nif and glnA expression [Transcription]

Probab=94.01  E-value=0.053  Score=46.46  Aligned_cols=65  Identities=20%  Similarity=0.230  Sum_probs=48.9

Q ss_pred             HHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029           47 MARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~  120 (129)
                      |||=|.=.+ |+|-......---   ||+.-      +---+|+=||-||+.||++|+.-.||.||++|-+.|.+
T Consensus        11 Il~il~esd~plgak~Ia~el~k---RGy~i------geRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~   76 (325)
T COG1693          11 ILRILAESDEPLGAKIIALELRK---RGYNI------GERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR   76 (325)
T ss_pred             HHHHHHhcCCccchHHHHHHHHh---cccch------hHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence            555555544 7887766655422   25432      23469999999999999999988899999999999998

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.96  E-value=0.082  Score=40.17  Aligned_cols=43  Identities=21%  Similarity=0.332  Sum_probs=32.6

Q ss_pred             chhHHHHHHHHHHhCCceeec---CCCCc-----eeCcchHhhHHHHHHHh
Q 033029           83 SGAIARHILQQLQNMNIIDIE---PKGGR-----RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~---~~~GR-----~lT~~G~~~lD~iA~~i  125 (129)
                      +-+-+=.+|+.||+.|||+..   ..+||     .||+.|+..|+....++
T Consensus        56 ~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w  106 (138)
T TIGR02719        56 DQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF  106 (138)
T ss_pred             CcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            334677899999999999863   23354     49999999888876654

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).

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=93.81  E-value=0.13  Score=39.40  Aligned_cols=54  Identities=17%  Similarity=0.374  Sum_probs=43.2

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      .|++.++.++..-+      +.|        +-+-..++.|++.|||+..+.+|=.||++|....-.+
T Consensus        22 ~~~~~~~diA~~L~------Vsp--------~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~   75 (154)
T COG1321          22 KGFARTKDIAERLK------VSP--------PSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL   75 (154)
T ss_pred             cCcccHHHHHHHhC------CCc--------HHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHH
Confidence            56788888887643      445        3677899999999999999999999999999655443

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

Probab=93.74  E-value=0.063  Score=35.43  Aligned_cols=41  Identities=27%  Similarity=0.362  Sum_probs=31.6

Q ss_pred             cCCchhHHHHHHHHHHhCCceeecCC---CC-----ceeCcchHhhHHH
Q 033029           80 CKSSGAIARHILQQLQNMNIIDIEPK---GG-----RRITSSGQRDLDQ  120 (129)
Q Consensus        80 ~~asg~iiR~~lqqLE~~g~vek~~~---~G-----R~lT~~G~~~lD~  120 (129)
                      ..-|-+-+=.+|+.||+.|+|+....   +|     -.||++|+..|.+
T Consensus        27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E   75 (75)
T PF03551_consen   27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE   75 (75)
T ss_dssp             EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred             cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence            45566788999999999999986442   22     3699999998763

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 ....

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.64  E-value=0.23  Score=38.55  Aligned_cols=55  Identities=13%  Similarity=0.175  Sum_probs=43.7

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC--CceeCcch
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG--GRRITSSG  114 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~--GR~lT~~G  114 (129)
                      .|+..|.-+|++.+..+....|-              |.+-+++.|+.||+.|||++..+.  .-.||++|
T Consensus       147 ~IL~~l~~~g~~s~~eia~~l~i--------------s~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G  203 (203)
T TIGR01884       147 KVLEVLKAEGEKSVKNIAKKLGK--------------SLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG  203 (203)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence            57877777789999999998864              345789999999999999987522  34578776

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.

>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=93.44  E-value=0.19  Score=33.90  Aligned_cols=45  Identities=24%  Similarity=0.346  Sum_probs=34.7

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG  114 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G  114 (129)
                      ++.+..++..+|-.              -..+|+++++|++.|+|+..+  .||-.|+..-
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            48888999887653              358999999999999999654  4788887654

(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.

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

Probab=93.37  E-value=0.12  Score=31.94  Aligned_cols=39  Identities=18%  Similarity=0.303  Sum_probs=30.3

Q ss_pred             hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029           59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT  111 (129)
Q Consensus        59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT  111 (129)
                      +..|+..||-              |..-++++|+.|++.|+|+..++.|-.||
T Consensus        28 ~~~la~~~~i--------------s~~~v~~~l~~L~~~G~i~~~~~~~~~l~   66 (66)
T cd07377          28 ERELAEELGV--------------SRTTVREALRELEAEGLVERRPGRGTFVA   66 (66)
T ss_pred             HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence            6677777644              34689999999999999997765666665

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

>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=93.01  E-value=0.27  Score=31.24  Aligned_cols=46  Identities=17%  Similarity=0.229  Sum_probs=38.9

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      ..|++.|-..+|..++.|....|-              +-+-+.+=|+.||++|+|+...
T Consensus        13 ~~Il~~L~~~~~~t~~ela~~l~~--------------~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   13 LRILRLLASNGPMTVSELAEELGI--------------SQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEec
Confidence            358888888999999999999873              3357899999999999999875

...

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=92.83  E-value=0.2  Score=39.04  Aligned_cols=42  Identities=14%  Similarity=0.229  Sum_probs=34.9

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      .-..|+..||-              |..-+|.+|+.||..|+|+..++.|-.+++-
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            45577777765              4578999999999999999988889998873

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.

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=92.76  E-value=0.19  Score=38.86  Aligned_cols=51  Identities=20%  Similarity=0.279  Sum_probs=40.0

Q ss_pred             CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      +-...|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++-...++..+
T Consensus        31 L~e~eLae~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei   81 (224)
T PRK11534         31 LRMSLLTSRYAL--------------GVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDI   81 (224)
T ss_pred             CCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHHH
Confidence            345678888875              336899999999999999998888888887766655443

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=92.64  E-value=0.42  Score=38.42  Aligned_cols=62  Identities=19%  Similarity=0.226  Sum_probs=49.7

Q ss_pred             HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029           42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD  117 (129)
Q Consensus        42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~  117 (129)
                      -|+..||+.|.-++ ++++..|.+..|-.              .+-+.++|+.|++.|||++++ ++...||++....
T Consensus        11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~--------------kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l   74 (263)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELTGLH--------------RTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL   74 (263)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence            48889999987755 59999999987542              357899999999999999886 4567788877543

>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=92.45  E-value=0.46  Score=29.38  Aligned_cols=51  Identities=20%  Similarity=0.333  Sum_probs=40.0

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR  109 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~  109 (129)
                      ..+|..||-.|++.+..|....+-              +.+-+-.++++||+.|||++..  +..|.
T Consensus         6 ~~iL~~l~~~~~~~~~~la~~~~~--------------~~~~~t~~i~~L~~~g~I~r~~~~~D~R~   58 (59)
T PF01047_consen    6 FRILRILYENGGITQSELAEKLGI--------------SRSTVTRIIKRLEKKGLIERERDPDDRRQ   58 (59)
T ss_dssp             HHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEEETTETTS
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeccCCCCCCc
Confidence            357888999999999999998765              3356778999999999998654  34443

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 ....

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=92.36  E-value=0.18  Score=39.63  Aligned_cols=45  Identities=18%  Similarity=0.129  Sum_probs=36.3

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHh
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR  116 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~  116 (129)
                      .-..|+..||-              |...+|.+|+.||..|||+..++.|-.+++-...
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            45677887775              4579999999999999999988888888776544

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=92.03  E-value=0.54  Score=34.59  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=47.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC------CCCceeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRRITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~------~~GR~lT~~G~~~lD~  120 (129)
                      |++++.- |+.--+.|++.-++             =|-+++=.-|+.||+.|+|++..      +-...||+.|++++.-
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            7777776 77777777776544             45578888899999999999765      2367899999998765


Q ss_pred             HH
Q 033029          121 VA  122 (129)
Q Consensus       121 iA  122 (129)
                      +.
T Consensus        94 l~   95 (120)
T COG1733          94 LL   95 (120)
T ss_pred             HH
Confidence            43

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=92.02  E-value=0.68  Score=33.27  Aligned_cols=68  Identities=15%  Similarity=0.212  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch-HhhH
Q 033029           44 AASMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG-QRDL  118 (129)
Q Consensus        44 ~ASilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G-~~~l  118 (129)
                      |-.+|..|...  +++.+..|+..+|-              |.+.++++|+.|++.|+|+...  .+|..|.... +-.+
T Consensus        11 al~~l~~la~~~~~~~s~~eia~~l~i--------------s~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~   76 (130)
T TIGR02944        11 ATLVLTTLAQNDSQPYSAAEIAEQTGL--------------NAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITV   76 (130)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCH
Confidence            34456666554  46888889888765              3469999999999999998643  5677777655 3336


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      ..|...|
T Consensus        77 ~~v~~~l   83 (130)
T TIGR02944        77 ADIVKAV   83 (130)
T ss_pred             HHHHHHH
Confidence            6666554

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.

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

Probab=91.91  E-value=0.83  Score=27.84  Aligned_cols=61  Identities=16%  Similarity=0.197  Sum_probs=45.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~  123 (129)
                      |+..++-.+ +.+..+.+..|-              +.+-++.+|.+|++.|+|.....   .-..+|+ |+..++.+..
T Consensus        12 il~~l~~~~-~~~~ei~~~~~i--------------~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~~   75 (78)
T cd00090          12 ILRLLLEGP-LTVSELAERLGL--------------SQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLES   75 (78)
T ss_pred             HHHHHHHCC-cCHHHHHHHHCc--------------CHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHHH
Confidence            666666655 889999887643              23578999999999999986542   2447898 8888877653

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=91.90  E-value=0.21  Score=30.15  Aligned_cols=36  Identities=19%  Similarity=0.310  Sum_probs=27.4

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG  107 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G  107 (129)
                      .+..|+..||-              |..-+|++|++|++.|+|+..+++|
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            56666776643              4568999999999999998776444

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=91.70  E-value=0.26  Score=40.82  Aligned_cols=44  Identities=23%  Similarity=0.271  Sum_probs=37.5

Q ss_pred             hhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHHHhhh
Q 033029           84 GAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRIVV  127 (129)
Q Consensus        84 g~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~~i~~  127 (129)
                      ...+|.+|.-|++.|+|+....   ....||++|++.++..+.-|..
T Consensus        34 ~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~   80 (280)
T TIGR02277        34 ERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD   80 (280)
T ss_pred             cchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence            3589999999999999997653   4678999999999998887764

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.

>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=91.53  E-value=0.24  Score=31.71  Aligned_cols=37  Identities=24%  Similarity=0.398  Sum_probs=28.8

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ....|...||-              |...+|.+|+.|++.|+|+..+..|-
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            56677777764              45699999999999999998876553

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 ....

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=91.38  E-value=0.41  Score=35.23  Aligned_cols=43  Identities=21%  Similarity=0.310  Sum_probs=33.4

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCceeCc
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITS  112 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR~lT~  112 (129)
                      ++.+..|+..+|-              |...+|++|++|++.|+|+..+.  ||-.|+.
T Consensus        25 ~~s~~~ia~~~~i--------------s~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~   69 (141)
T PRK11014         25 MTSISEVTEVYGV--------------SRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK   69 (141)
T ss_pred             ccCHHHHHHHHCc--------------CHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence            5677888888775              34589999999999999997763  4656654

>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=91.33  E-value=0.43  Score=29.54  Aligned_cols=46  Identities=15%  Similarity=0.219  Sum_probs=38.1

Q ss_pred             HHHHHHHHHhCC--CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           45 ASMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        45 ASilR~lYl~g~--vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      ..||..|+-+++  +.+..|+...|-.              .+-+-.+++.||+.|||++.+
T Consensus         8 ~~vL~~l~~~~~~~~t~~~la~~l~~~--------------~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    8 FRVLMALARHPGEELTQSELAERLGIS--------------KSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             HHHHHHHHHSTTSGEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEeC
Confidence            358899999998  8999999987653              346788999999999999765

...

>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=91.20  E-value=1.4  Score=32.03  Aligned_cols=71  Identities=17%  Similarity=0.106  Sum_probs=53.3

Q ss_pred             HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      =.+|+|+=+||-+.=+..+.++-.-            +...+...+-+=++-|-+-|||||..| |-++|..|+..+-++
T Consensus        16 E~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~~A   82 (96)
T PF09114_consen   16 ENAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIIIQA   82 (96)
T ss_dssp             HHHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHHHH
Confidence            3578899999988888888887742            224455667777899999999999964 899999999999998


Q ss_pred             HHHh
Q 033029          122 AGRI  125 (129)
Q Consensus       122 A~~i  125 (129)
                      |.--
T Consensus        83 A~l~   86 (96)
T PF09114_consen   83 AELW   86 (96)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8643

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.

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.06  E-value=0.33  Score=37.90  Aligned_cols=52  Identities=19%  Similarity=0.324  Sum_probs=45.1

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      .+....|+..||-.              ..-||.+|+.|+..|+|+..+..|-.+++-..+++..+
T Consensus        39 ~l~e~~La~~~gvS--------------rtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei   90 (230)
T COG1802          39 RLSEEELAEELGVS--------------RTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI   90 (230)
T ss_pred             CccHHHHHHHhCCC--------------CccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence            57788899999864              24799999999999999999989999999888888774

>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=90.77  E-value=0.6  Score=29.74  Aligned_cols=48  Identities=17%  Similarity=0.220  Sum_probs=40.7

Q ss_pred             hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      |-..|+..|--++.+.+..|...||-              |-.-||+=|+.||+.|+|.+.-
T Consensus         1 R~~~Il~~l~~~~~~s~~ela~~~~V--------------S~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    1 RQQQILELLKEKGKVSVKELAEEFGV--------------SEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             CHHHHHHHHHHcCCEEHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc
Confidence            34567888888999999999999875              3458999999999999999875

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

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=90.45  E-value=0.29  Score=38.76  Aligned_cols=41  Identities=20%  Similarity=0.135  Sum_probs=33.5

Q ss_pred             hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      -..|+..||=              |..-+|.+|+.||..|||+..+.+|-.+++-
T Consensus        29 E~eLae~~gV--------------SRtpVREAL~~Le~~GlV~~~~~~G~~V~~~   69 (253)
T PRK10421         29 ERQLAMQLGV--------------SRNSLREALAKLVSEGVLLSRRGGGTFIRWR   69 (253)
T ss_pred             HHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence            4567777764              5579999999999999999888788888764

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=90.39  E-value=1.2  Score=31.61  Aligned_cols=49  Identities=20%  Similarity=0.308  Sum_probs=38.5

Q ss_pred             CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCceeCcchHhh
Q 033029           55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRD  117 (129)
Q Consensus        55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR~lT~~G~~~  117 (129)
                      +++.+..|+..+|-              +.+.++++|+.|++.|||...  ..||-.|+......
T Consensus        24 ~~~s~~eia~~~~i--------------~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i   74 (132)
T TIGR00738        24 GPVSVKEIAERQGI--------------SRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI   74 (132)
T ss_pred             CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC
Confidence            37889999888765              346999999999999999864  34677888776544

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.

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

Probab=90.36  E-value=0.87  Score=32.52  Aligned_cols=48  Identities=19%  Similarity=0.203  Sum_probs=35.9

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI  110 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l  110 (129)
                      ||.|+|--||---..+++..              ...-.-++.+|..||++||||...  |..|
T Consensus        12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~--g~~i   59 (92)
T PF10007_consen   12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE--GKTI   59 (92)
T ss_pred             HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec--Cccc
Confidence            78888888876555565543              344468999999999999999875  4444

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=90.35  E-value=0.33  Score=37.83  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=33.8

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .-..|+..||-              |.+-+|.+|+.||..|+|+..+..|-.+++
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            34567787765              557999999999999999998878888865

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=90.31  E-value=0.28  Score=38.77  Aligned_cols=44  Identities=11%  Similarity=0.186  Sum_probs=35.8

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ  115 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~  115 (129)
                      ....|+..||=              |..-+|.+|+.||..|+|+..++.|-.+++...
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            35678888875              456899999999999999988877888876543

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=90.07  E-value=0.85  Score=36.37  Aligned_cols=58  Identities=10%  Similarity=0.149  Sum_probs=45.9

Q ss_pred             HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcc
Q 033029           42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS  113 (129)
Q Consensus        42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~  113 (129)
                      -|+..||..|.-.+++++..|++.-|-.              .+-+..+|+.|++.|||++++. +...|+++
T Consensus        14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~--------------kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~~   72 (257)
T PRK15090         14 LKVFGILQALGEEREIGITELSQRVMMS--------------KSTVYRFLQTMKTLGYVAQEGESEKYSLTLK   72 (257)
T ss_pred             HHHHHHHHHhhcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence            4888899999877889999999986653              3578999999999999998753 44455544

>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=90.07  E-value=0.47  Score=29.57  Aligned_cols=45  Identities=16%  Similarity=0.230  Sum_probs=33.4

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .+++....|....|-              |.+-+.++|++|++.|+|+....++-.|||
T Consensus        23 ~~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~   67 (67)
T cd00092          23 QLPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP   67 (67)
T ss_pred             cCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence            356677777777664              346789999999999999987645566654

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

Probab=89.91  E-value=0.98  Score=29.73  Aligned_cols=45  Identities=7%  Similarity=-0.036  Sum_probs=37.1

Q ss_pred             HHHHHHHHhCC--CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           46 SMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        46 SilR~lYl~g~--vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      .||..|.-+|+  +....|.+..|=.              .+.++++|..||+.|+|++..
T Consensus        10 ~IL~~L~~~g~~~~ta~eLa~~lgl~--------------~~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550       10 KILEFLENSGDETSTALQLAKNLGLP--------------KKEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecC
Confidence            46777777777  9999999987753              248999999999999999865

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

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

Probab=89.88  E-value=0.93  Score=28.81  Aligned_cols=52  Identities=21%  Similarity=0.425  Sum_probs=36.6

Q ss_pred             HHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029           50 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ  115 (129)
Q Consensus        50 ~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~  115 (129)
                      .|=+..++-+..+...||..             --......|+.|++.|||+.+. +.=+||++|+
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            34446688888899988864             1235578899999999999875 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.

>PRK03837 transcriptional regulator NanR; Provisional

Probab=89.86  E-value=0.38  Score=37.38  Aligned_cols=43  Identities=16%  Similarity=0.294  Sum_probs=34.4

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      ....|+..||=              |.+.+|.+|+.||..|+|+..++.|-.+++-.
T Consensus        39 ~E~~Lae~~gV--------------SRt~VREAL~~L~~eGlv~~~~~~G~~V~~~~   81 (241)
T PRK03837         39 SERELMAFFGV--------------GRPAVREALQALKRKGLVQISHGERARVSRPS   81 (241)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCceeEecCC
Confidence            45678888764              55799999999999999998887777776543

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=89.68  E-value=0.36  Score=38.02  Aligned_cols=42  Identities=19%  Similarity=0.237  Sum_probs=33.4

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      .-..|+..||-              |...+|.+|+.||..|||+..+.+|-.+++.
T Consensus        36 sE~eLa~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~   77 (254)
T PRK09464         36 PERELAKQFDV--------------SRPSLREAIQRLEAKGLLLRRQGGGTFVQSS   77 (254)
T ss_pred             CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEecC
Confidence            34567777764              4579999999999999999888778777653

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=89.63  E-value=0.41  Score=36.51  Aligned_cols=42  Identities=17%  Similarity=0.253  Sum_probs=32.1

Q ss_pred             chhHHHHHHHHHHhCCceeecCCC-C---ceeCcchHhhHHHHHHH
Q 033029           83 SGAIARHILQQLQNMNIIDIEPKG-G---RRITSSGQRDLDQVAGR  124 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~~-G---R~lT~~G~~~lD~iA~~  124 (129)
                      |-+-|=-+|+.||+.|||+....+ .   -.||+.|+..|+....+
T Consensus        76 s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~  121 (135)
T PRK09416         76 NEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN  121 (135)
T ss_pred             CCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence            445677899999999999864322 2   36999999999987653

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=89.28  E-value=0.4  Score=37.91  Aligned_cols=42  Identities=12%  Similarity=0.122  Sum_probs=33.5

Q ss_pred             hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      -..|+..||=              |..-+|.+|+.||..|+|+..+..|-.+++-.
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            4567777765              45689999999999999998887787776643

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=89.24  E-value=1.7  Score=25.35  Aligned_cols=45  Identities=13%  Similarity=0.182  Sum_probs=35.5

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      .|+..+.-++++.+..|+..+|-              |-+-+++.|+.|++.|+|+...
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGV--------------SEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEee
Confidence            35666666788999999998843              2346899999999999999765

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

Probab=88.87  E-value=0.67  Score=37.54  Aligned_cols=55  Identities=24%  Similarity=0.170  Sum_probs=40.7

Q ss_pred             CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHHHh
Q 033029           57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~~i  125 (129)
                      +..+.|++..|-              |.+-+-+.|+.||+.|||++...   .--.||++|+..+.+.....
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            335577776543              45678889999999999987642   24579999999998877553

>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=88.57  E-value=2  Score=29.59  Aligned_cols=76  Identities=16%  Similarity=0.144  Sum_probs=50.0

Q ss_pred             HHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcc------cC---CchhHHHHHHHHHHhCCceeecCC----CCcee
Q 033029           45 ASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHF------CK---SSGAIARHILQQLQNMNIIDIEPK----GGRRI  110 (129)
Q Consensus        45 ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~------~~---asg~iiR~~lqqLE~~g~vek~~~----~GR~l  110 (129)
                      ..|++-|+- .+.+|...+..++=|.++......++      -.   =+..-++.++++|...|+++...+    .-=.+
T Consensus         7 ~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~   86 (106)
T PF09382_consen    7 KKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKL   86 (106)
T ss_dssp             HHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEEE
Confidence            345555555 56899999999999988877543322      11   255789999999999999976543    13468


Q ss_pred             CcchHhhHHH
Q 033029          111 TSSGQRDLDQ  120 (129)
Q Consensus       111 T~~G~~~lD~  120 (129)
                      |++|++.|..
T Consensus        87 ~~~~~~~l~g   96 (106)
T PF09382_consen   87 TPKGKELLNG   96 (106)
T ss_dssp             -GGGHHHHCT
T ss_pred             CHHHHHHHCC
Confidence            9999988753

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.

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

Probab=88.48  E-value=0.61  Score=34.10  Aligned_cols=39  Identities=26%  Similarity=0.399  Sum_probs=32.4

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ++.+..|+....+..|              -+|.+|++|++.|||+-.+..||
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            5788888888776544              68999999999999999987676

>PRK11569 transcriptional repressor IclR; Provisional

Probab=88.37  E-value=1.4  Score=35.67  Aligned_cols=59  Identities=12%  Similarity=0.157  Sum_probs=46.0

Q ss_pred             HHhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcc
Q 033029           41 YVRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS  113 (129)
Q Consensus        41 Y~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~  113 (129)
                      --|+..||+.|-- .+++++..|.+.-|-.              .+-+..+|+.|++.|||+++++ +...|.+.
T Consensus        27 l~ral~IL~~l~~~~~~~~lseia~~lglp--------------ksTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   87 (274)
T PRK11569         27 LTRGLKLLEWIAESNGSVALTELAQQAGLP--------------NSTTHRLLTTMQQQGFVRQVGELGHWAIGAH   87 (274)
T ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence            3588999999876 4689999999986653              3688999999999999998764 33345443

>PRK09057 coproporphyrinogen III oxidase; Provisional

Probab=88.29  E-value=2.2  Score=36.30  Aligned_cols=57  Identities=21%  Similarity=0.351  Sum_probs=44.0

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV  126 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~  126 (129)
                      ..++-...+...||-.      .          ....|+.|++.|+++.+.++.=+||++|+-.+|.|+..++
T Consensus       323 ~~gid~~~~~~~~g~~------~----------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~  379 (380)
T PRK09057        323 REGIDLARYAALSGRP------L----------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA  379 (380)
T ss_pred             hCCCCHHHHHHHHCCC------c----------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence            4567778888888743      1          1247999999999997542246899999999999999875

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=88.04  E-value=1.6  Score=32.97  Aligned_cols=60  Identities=25%  Similarity=0.315  Sum_probs=46.2

Q ss_pred             HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCc-----------eeCcchHhhH
Q 033029           53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----------RITSSGQRDL  118 (129)
Q Consensus        53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR-----------~lT~~G~~~l  118 (129)
                      .+||..|..|+..-+              =+.|-+=++||.|..+|+|++.+   ++||           .++....++|
T Consensus        39 ~~~~~tvdelae~ln--------------r~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l  104 (126)
T COG3355          39 ENGPLTVDELAEILN--------------RSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL  104 (126)
T ss_pred             hcCCcCHHHHHHHHC--------------ccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence            489999999998743              35578899999999999998655   3444           2566788888


Q ss_pred             HHHHHHhh
Q 033029          119 DQVAGRIV  126 (129)
Q Consensus       119 D~iA~~i~  126 (129)
                      |..+.++.
T Consensus       105 ~~w~~~~~  112 (126)
T COG3355         105 DEWYDKMK  112 (126)
T ss_pred             HHHHHHHH
Confidence            88887763

>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=87.67  E-value=0.8  Score=30.35  Aligned_cols=40  Identities=20%  Similarity=0.216  Sum_probs=29.3

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      |-.|..++..+|-             .|-+-+..-|++||+.|+|+.++...|
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            3467777777765             355789999999999999999875443

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.

>PF13814 Replic_Relax: Replication-relaxation

Probab=87.51  E-value=1.5  Score=32.75  Aligned_cols=62  Identities=24%  Similarity=0.338  Sum_probs=46.2

Q ss_pred             HHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-----CCc-----eeCcchHhh
Q 033029           48 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-----GGR-----RITSSGQRD  117 (129)
Q Consensus        48 lR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-----~GR-----~lT~~G~~~  117 (129)
                      |+-||-.+-+....|...++...+.           ..-++..|++|++.|+|+....     +|.     .||++|...
T Consensus         1 L~~L~~~r~lt~~Qi~~l~~~~~~~-----------~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~   69 (191)
T PF13814_consen    1 LRLLARHRFLTTDQIARLLFPSSKS-----------ERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARL   69 (191)
T ss_pred             ChhHHHhcCcCHHHHHHHHcCCCcc-----------hHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHH
Confidence            3456677778888888888765332           1278999999999999987653     122     699999998


Q ss_pred             HHH
Q 033029          118 LDQ  120 (129)
Q Consensus       118 lD~  120 (129)
                      |..
T Consensus        70 l~~   72 (191)
T PF13814_consen   70 LAD   72 (191)
T ss_pred             HHh
Confidence            874

>PRK08599 coproporphyrinogen III oxidase; Provisional

Probab=87.37  E-value=2.2  Score=35.84  Aligned_cols=62  Identities=18%  Similarity=0.300  Sum_probs=46.3

Q ss_pred             HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      ...++=...+...||..             ........+++|++.|+++.+. +.=+||++|+-.+|.|+.+++.+
T Consensus       315 ~~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~~~  376 (377)
T PRK08599        315 KKSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFLLD  376 (377)
T ss_pred             hhCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHhhh
Confidence            34556666666666531             1345677889999999999764 46789999999999999987643

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

Probab=87.30  E-value=2.5  Score=25.32  Aligned_cols=42  Identities=12%  Similarity=0.177  Sum_probs=34.3

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCcee
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID  101 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ve  101 (129)
                      .|+..|.-+|++.+..++...|-              |.+-+++.|++|++.|+|+
T Consensus         7 ~Il~~l~~~~~~t~~ela~~~~i--------------s~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    7 KILNYLRENPRITQKELAEKLGI--------------SRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHCTTS-HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCcCcC
Confidence            47777888899999999998765              4468999999999999985

...

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=87.17  E-value=1.9  Score=34.95  Aligned_cols=57  Identities=12%  Similarity=0.066  Sum_probs=44.6

Q ss_pred             HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC-ceeCc
Q 033029           42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITS  112 (129)
Q Consensus        42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G-R~lT~  112 (129)
                      -|+.+||+.|.-. +++++..|++.-|-.              .+-+..+|+.|+..|||++++..| -.|++
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglp--------------kStv~RlL~tL~~~G~l~~~~~~~~Y~lG~   83 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDLP--------------LSTTFRLLKVLQAADFVYQDSQLGWWHIGL   83 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence            3889999998764 579999999987653              357899999999999999876433 33444

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=87.16  E-value=0.73  Score=35.71  Aligned_cols=61  Identities=11%  Similarity=0.139  Sum_probs=43.3

Q ss_pred             HHHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      -|...+..++.-=..|..       .-..|+..||-              |..-+|++|+.|++.|+|++.+..|-.+++
T Consensus         9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~   74 (238)
T TIGR02325         9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGV--------------NRHTVRRAIAALVERGLLRAEQGRGTFVAA   74 (238)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence            355555555554444432       33567777775              456899999999999999998877888876


Q ss_pred             ch
Q 033029          113 SG  114 (129)
Q Consensus       113 ~G  114 (129)
                      ..
T Consensus        75 ~~   76 (238)
T TIGR02325        75 RR   76 (238)
T ss_pred             Cc
Confidence            54

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.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=87.14  E-value=1.5  Score=32.00  Aligned_cols=46  Identities=13%  Similarity=0.257  Sum_probs=35.4

Q ss_pred             CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCceeCcch
Q 033029           55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSG  114 (129)
Q Consensus        55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR~lT~~G  114 (129)
                      +++.+..++..++-              +...++++|++|.++|||+..  ..||-.|+..-
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            47888888887654              346899999999999999853  35687887643

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

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=87.03  E-value=0.99  Score=32.69  Aligned_cols=40  Identities=23%  Similarity=0.444  Sum_probs=30.9

Q ss_pred             hHHHHHHHHHHhCCceeecC--CCC------ceeCcchHhhHHHHHHH
Q 033029           85 AIARHILQQLQNMNIIDIEP--KGG------RRITSSGQRDLDQVAGR  124 (129)
Q Consensus        85 ~iiR~~lqqLE~~g~vek~~--~~G------R~lT~~G~~~lD~iA~~  124 (129)
                      ..|=-+|+.||+.|||+...  .++      -.||++|+..|.+...+
T Consensus        45 gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~   92 (138)
T COG1695          45 GTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREE   92 (138)
T ss_pred             CcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHH
Confidence            35667999999999998642  222      37999999999987655

>PRK07379 coproporphyrinogen III oxidase; Provisional

Probab=86.87  E-value=0.8  Score=39.30  Aligned_cols=40  Identities=23%  Similarity=0.289  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHhCCceeecCCCCc--eeCc-chHhhHHHHHHHhh
Q 033029           85 AIARHILQQLQNMNIIDIEPKGGR--RITS-SGQRDLDQVAGRIV  126 (129)
Q Consensus        85 ~iiR~~lqqLE~~g~vek~~~~GR--~lT~-~G~~~lD~iA~~i~  126 (129)
                      ......|++|++.||++.+  ++|  +||+ +|.-.+|.|+.+++
T Consensus       351 ~~~~~~l~~l~~~gll~~~--~~~~~~lT~~~G~~~~~~i~~~~~  393 (400)
T PRK07379        351 EQILQCLQPYFQQGWVELE--GDRRLRLTDPEGFLFSNTVLASLF  393 (400)
T ss_pred             HHHHHHHHHHHHCCCEEEe--CCeEEEECchHHhHHHHHHHHHHH
Confidence            3456778999999999865  456  8995 99999999999875

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=86.85  E-value=2  Score=34.56  Aligned_cols=56  Identities=16%  Similarity=0.257  Sum_probs=43.5

Q ss_pred             HhHHHHHHHHHHhCCC--chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC-ceeCc
Q 033029           42 VRAASMARKIYLRQGL--GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITS  112 (129)
Q Consensus        42 ~R~ASilR~lYl~g~v--GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G-R~lT~  112 (129)
                      .|+..||..|.- +|.  ++..|.+.-|-.              .+=++.+|+.|++.|||+++++.| -.|++
T Consensus         4 ~ral~iL~~l~~-~~~~l~l~ela~~~glp--------------ksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~   62 (246)
T COG1414           4 ERALAILDLLAE-GPGGLSLAELAERLGLP--------------KSTVHRLLQTLVELGYVEQDPEDGRYRLGP   62 (246)
T ss_pred             HHHHHHHHHHHh-CCCCCCHHHHHHHhCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCcEeehH
Confidence            588899998887 454  499999986642              357899999999999999998554 34444

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=86.55  E-value=0.76  Score=38.42  Aligned_cols=60  Identities=12%  Similarity=0.169  Sum_probs=42.9

Q ss_pred             HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-C-CCceeCcchHhhHHH
Q 033029           47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-K-GGRRITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~-~GR~lT~~G~~~lD~  120 (129)
                      |++.|=- +|-+.-..|+..+|              -|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
T Consensus       188 IL~~L~~~egrlse~eLAerlG--------------VSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e  250 (251)
T TIGR02787       188 IFEELDGNEGLLVASKIADRVG--------------ITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE  250 (251)
T ss_pred             HHHHhccccccccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence            4444433 24455555555554              35679999999999999999887 5 488888888888775

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.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=86.44  E-value=0.88  Score=34.40  Aligned_cols=46  Identities=24%  Similarity=0.325  Sum_probs=35.8

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchH
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ  115 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~  115 (129)
                      ++.+..++..++-              |.+.++++||+|.++|||+...  +||-.|+..-.
T Consensus        24 ~~s~~eIA~~~~i--------------s~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~   71 (153)
T PRK11920         24 LSRIPEIARAYGV--------------SELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAA   71 (153)
T ss_pred             cCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHH
Confidence            4677777777654              3468999999999999998665  57989986554

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=85.97  E-value=0.85  Score=35.56  Aligned_cols=59  Identities=14%  Similarity=0.153  Sum_probs=41.3

Q ss_pred             HHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           41 YVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        41 Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      |...+..|++-=..|..       +-..|+..||-              |..-+|++|+.|++.|+|.+.+..|-.+++.
T Consensus         3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~   68 (230)
T TIGR02018         3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAEP   68 (230)
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEccC
Confidence            44445555544334422       44577888875              4569999999999999999988778777643

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=85.93  E-value=1.6  Score=35.95  Aligned_cols=64  Identities=19%  Similarity=0.309  Sum_probs=45.2

Q ss_pred             chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHH-HHHhCCceeecCCCCceeCcchHh
Q 033029           38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQR  116 (129)
Q Consensus        38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lq-qLE~~g~vek~~~~GR~lT~~G~~  116 (129)
                      |..|+|+   +...|-.+|+|+..+...-|-...              -+-.++. .|-..|+|++.+ .||++|++|.+
T Consensus       261 ~~~~l~~---~~~~~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~  322 (328)
T PRK00080        261 DRKYLRT---IIEKFGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTP-RGRVATPKAYE  322 (328)
T ss_pred             HHHHHHH---HHHHcCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCC-chHHHHHHHHH
Confidence            4556643   233355779999999988765322              2333444 889999999775 69999999998


Q ss_pred             hHH
Q 033029          117 DLD  119 (129)
Q Consensus       117 ~lD  119 (129)
                      .|.
T Consensus       323 ~~~  325 (328)
T PRK00080        323 HLG  325 (328)
T ss_pred             HhC
Confidence            774

>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=85.71  E-value=1.4  Score=28.26  Aligned_cols=46  Identities=13%  Similarity=0.114  Sum_probs=36.4

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      +.|...|--+|+..+..+.+.-|-              +.+-++.+|+.|++.|||++.+
T Consensus        11 ~~vy~~Ll~~~~~t~~eIa~~l~i--------------~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen   11 AKVYLALLKNGPATAEEIAEELGI--------------SRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHHCHEEHHHHHHHHTS--------------SHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc
Confidence            345555556889999999987554              4468999999999999999875

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.

>PRK05799 coproporphyrinogen III oxidase; Provisional

Probab=85.53  E-value=0.67  Score=38.87  Aligned_cols=40  Identities=5%  Similarity=0.200  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029           86 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV  126 (129)
Q Consensus        86 iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~  126 (129)
                      .....|+.|++.|+++.+. +.=+||++|+-.+|.|+.+++
T Consensus       334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~  373 (374)
T PRK05799        334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMSDFL  373 (374)
T ss_pred             HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHHHHh
Confidence            4556789999999999753 346889999999999998864

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=85.38  E-value=0.96  Score=36.28  Aligned_cols=30  Identities=20%  Similarity=0.438  Sum_probs=24.8

Q ss_pred             chhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           83 SGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      |..++|-+|+.||..|||+..++.|=.+++
T Consensus        47 SR~~vREAl~~L~a~Glve~r~G~Gt~V~~   76 (241)
T COG2186          47 SRTVVREALKRLEAKGLVEIRQGSGTFVRP   76 (241)
T ss_pred             CcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence            456999999999999999987766666654

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

Probab=84.47  E-value=0.96  Score=33.45  Aligned_cols=40  Identities=23%  Similarity=0.384  Sum_probs=30.5

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI  110 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l  110 (129)
                      -|.+..|...||-              ++||.|.+|..||+.|+|.... ++|+.
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            4556667777664              4789999999999999998775 35553

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=84.36  E-value=1.5  Score=25.49  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=18.5

Q ss_pred             chhHHHHHHHHHHhCCceeecC
Q 033029           83 SGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~  104 (129)
                      |.+-++++|++|++.|+|+...
T Consensus        21 s~~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419       21 TRETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             CHHHHHHHHHHHHHCCCEEEeC
Confidence            3457899999999999999764

>PRK05628 coproporphyrinogen III oxidase; Validated

Probab=83.89  E-value=1.6  Score=36.77  Aligned_cols=38  Identities=18%  Similarity=0.194  Sum_probs=32.3

Q ss_pred             HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029           88 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV  126 (129)
Q Consensus        88 R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~  126 (129)
                      +..|++|++.|++..+. +.=+||++|+-.+|.|+..++
T Consensus       337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~  374 (375)
T PRK05628        337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVRDLL  374 (375)
T ss_pred             HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHHHHh
Confidence            46889999999998764 356899999999999998764

>PRK05660 HemN family oxidoreductase; Provisional

Probab=83.87  E-value=1.8  Score=36.79  Aligned_cols=40  Identities=15%  Similarity=0.155  Sum_probs=33.2

Q ss_pred             HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           88 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        88 R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      ...++.|++.||++.+. +.=+||++|+-++|.|+..++.+
T Consensus       339 ~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~~~~~~  378 (378)
T PRK05660        339 RPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLELFLAE  378 (378)
T ss_pred             HHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHHHHhcC
Confidence            45789999999998753 34578999999999999988754

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=83.65  E-value=1.3  Score=34.80  Aligned_cols=60  Identities=22%  Similarity=0.290  Sum_probs=41.7

Q ss_pred             HHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           41 YVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        41 Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      |...+..|+.-=..|..       .-..|+..||-              |..-+|+||+.|++.|+|.+.+..|-.+++.
T Consensus         7 y~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~   72 (240)
T PRK09764          7 YRQIADRIREQIARGELKPGDALPTESALQTEFGV--------------SRVTVRQALRQLVEQQILESIQGSGTYVKEE   72 (240)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEccc
Confidence            45555555554444422       33567777764              4568999999999999999888778787765


Q ss_pred             h
Q 033029          114 G  114 (129)
Q Consensus       114 G  114 (129)
                      .
T Consensus        73 ~   73 (240)
T PRK09764         73 R   73 (240)
T ss_pred             c
Confidence            4

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=83.47  E-value=1.3  Score=34.47  Aligned_cols=40  Identities=20%  Similarity=0.237  Sum_probs=32.5

Q ss_pred             hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      ..|+..||-              |..-+|++|+.|++.|+|++.+..|-.+++.
T Consensus        28 ~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~G~GTfV~~~   67 (233)
T TIGR02404        28 HELMDQYGA--------------SRETVRKALNLLTEAGYIQKIQGKGSIVLNR   67 (233)
T ss_pred             HHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCceEEEecC
Confidence            457777764              5569999999999999999988778888653

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.

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=82.52  E-value=1.6  Score=30.94  Aligned_cols=22  Identities=14%  Similarity=0.373  Sum_probs=19.1

Q ss_pred             chhHHHHHHHHHHhCCceeecC
Q 033029           83 SGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~  104 (129)
                      .||++|.+|..||+-|+|.-..
T Consensus        54 ~~SlAr~~Lr~L~~kG~Ik~V~   75 (86)
T PRK09334         54 KISVAKKVLRELEKRGVLVLYS   75 (86)
T ss_pred             hHHHHHHHHHHHHHCCCEEEEe
Confidence            4789999999999999997554

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=82.38  E-value=3.1  Score=31.93  Aligned_cols=46  Identities=13%  Similarity=0.230  Sum_probs=36.3

Q ss_pred             CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee--cCCCCceeCcch
Q 033029           55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG  114 (129)
Q Consensus        55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek--~~~~GR~lT~~G  114 (129)
                      +++.+..++..+|-              +...++++|++|.++|||+.  .++||-.|...-
T Consensus        24 ~~vs~~eIA~~~~i--------------p~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p   71 (164)
T PRK10857         24 GPVPLADISERQGI--------------SLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA   71 (164)
T ss_pred             CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH
Confidence            47888888888765              34689999999999999985  346788887553

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

Probab=82.30  E-value=4.4  Score=28.18  Aligned_cols=48  Identities=15%  Similarity=0.090  Sum_probs=33.1

Q ss_pred             hHHHHHHHHH--------HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           43 RAASMARKIY--------LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        43 R~ASilR~lY--------l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      |-|++|-.|.        ...++.-..|....|-.              ..-+.++|++||+.|+|+...
T Consensus        26 r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~s--------------r~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        26 REFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLS--------------RTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             HHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeeeec
Confidence            5556555554        44566666777766553              335889999999999998753

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

>PRK08208 coproporphyrinogen III oxidase; Validated

Probab=82.21  E-value=1.9  Score=37.36  Aligned_cols=59  Identities=22%  Similarity=0.342  Sum_probs=43.7

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhh
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV  127 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~  127 (129)
                      ..++-...+...||..      +       .. ....|++|++.|||+.+. +.=+||++|+-..|.|+.+++.
T Consensus       359 ~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~  417 (430)
T PRK08208        359 AQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFIS  417 (430)
T ss_pred             hCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcC
Confidence            3566667777777642      1       12 345789999999999764 3558999999999999998754

>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]

Probab=81.58  E-value=8  Score=33.80  Aligned_cols=79  Identities=22%  Similarity=0.288  Sum_probs=58.5

Q ss_pred             CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ..+++|.|.    +|-+ ++=.+=+.-++-+..+...||- -.            -..+...|+.+++.|+++.+. +.-
T Consensus       332 ~~~l~~~d~----~~e~-~i~gLr~~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~-~~~  392 (416)
T COG0635         332 GEELTPDDL----IREA-LILGLRLNFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDG-DRL  392 (416)
T ss_pred             eeeCCHHHH----HHHH-HHHHHHHhcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecC-CEE
Confidence            677888774    2221 2223334558888899998875 22            357889999999999999875 578


Q ss_pred             eeCcchHhhHHHHHHHhh
Q 033029          109 RITSSGQRDLDQVAGRIV  126 (129)
Q Consensus       109 ~lT~~G~~~lD~iA~~i~  126 (129)
                      .||+.|+-++|.||....
T Consensus       393 ~lt~~g~~~~~~i~~~f~  410 (416)
T COG0635         393 RLTEKGRLLLRSIAEAFD  410 (416)
T ss_pred             EECCcchhHHHHHHHHHH
Confidence            999999999999998753

>PRK13347 coproporphyrinogen III oxidase; Provisional

Probab=81.39  E-value=2.3  Score=37.00  Aligned_cols=63  Identities=19%  Similarity=0.221  Sum_probs=42.7

Q ss_pred             HHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHh
Q 033029           51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        51 lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i  125 (129)
                      |-...++-...+...||-.      +..+     .-....|++|++.|||+.+. ++=+||++|+-.+|.|+..+
T Consensus       376 L~~~~~ld~~~~~~~~g~~------~~~~-----~~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~f  438 (453)
T PRK13347        376 LMCNFPVDLAAIAARHGFF------ARYF-----LDELARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAAAF  438 (453)
T ss_pred             HHhhCCcCHHHHHHHHCCC------HHHH-----HHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHH
Confidence            3344555556666666632      1111     01245789999999999764 45689999999999999864

>PRK14999 histidine utilization repressor; Provisional

Probab=81.33  E-value=1.8  Score=34.01  Aligned_cols=61  Identities=13%  Similarity=0.073  Sum_probs=43.5

Q ss_pred             HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+..|++-=..|.      + .-..|+..||-              |..-+|++|+.|+..|+|.+.+..|--+++
T Consensus        13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~GkGTfV~~   78 (241)
T PRK14999         13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGF--------------SRMTINRALRELTDEGWLVRLQGVGTFVAE   78 (241)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence            35555555555444432      2 45678888875              456899999999999999998877888865


Q ss_pred             ch
Q 033029          113 SG  114 (129)
Q Consensus       113 ~G  114 (129)
                      ..
T Consensus        79 ~~   80 (241)
T PRK14999         79 PK   80 (241)
T ss_pred             CC
Confidence            43

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=81.24  E-value=3.5  Score=35.74  Aligned_cols=68  Identities=18%  Similarity=0.173  Sum_probs=48.8

Q ss_pred             chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029           38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD  117 (129)
Q Consensus        38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~  117 (129)
                      ||.=.+--+.+-.-|--||||+..++-.-|--..             .|-=.+===|-..|++++++ .||++|+++.+-
T Consensus       259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTp-RGR~aT~~ay~h  324 (332)
T COG2255         259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTP-RGRIATAKAYEH  324 (332)
T ss_pred             cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCC-CcceecHHHHHH
Confidence            6666666666666677899999999998775322             12222333466789999998 599999999776


Q ss_pred             HH
Q 033029          118 LD  119 (129)
Q Consensus       118 lD  119 (129)
                      |-
T Consensus       325 l~  326 (332)
T COG2255         325 LG  326 (332)
T ss_pred             hc
Confidence            53

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=81.06  E-value=1.8  Score=34.09  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=32.3

Q ss_pred             hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      ..|+..||-              |..-+|++|+.|++.|+|+..+..|-.+++.
T Consensus        39 ~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~   78 (241)
T PRK10079         39 QQLAARYEV--------------NRHTLRRAIDQLVEKGWVQRRQGVGVLVLMR   78 (241)
T ss_pred             HHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEecC
Confidence            467777765              4569999999999999999988778777643

>PRK06294 coproporphyrinogen III oxidase; Provisional

Probab=81.04  E-value=2.4  Score=35.96  Aligned_cols=38  Identities=11%  Similarity=0.136  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHh
Q 033029           87 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        87 iR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i  125 (129)
                      ....+++|++.||++.+. +.=.||++|+-.+|.|+.++
T Consensus       332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~~~  369 (370)
T PRK06294        332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAEEI  369 (370)
T ss_pred             HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHh
Confidence            456788999999998763 35689999999999999875

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

Probab=80.11  E-value=1.4  Score=37.52  Aligned_cols=36  Identities=28%  Similarity=0.454  Sum_probs=31.0

Q ss_pred             hHHHHHHHHHHhCCceeecC--CCCceeCcchHhhHHH
Q 033029           85 AIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ  120 (129)
Q Consensus        85 ~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~~lD~  120 (129)
                      .-+|+.+|.|-++||||-.+  +||.+-|.+.-..|+.
T Consensus        40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~i   77 (294)
T COG2524          40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSI   77 (294)
T ss_pred             chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhcc
Confidence            36899999999999999765  7999999998877653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	129
3iz6_S	146	Localization Of The Small Subunit Ribosomal Protein		1e-56
3jyv_T	141	Structure Of The 40s Rrna And Proteins And PE TRNA		6e-28
3izb_S	144	Localization Of The Small Subunit Ribosomal Protein		9e-28
2xzm_T	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-18
3zey_O	167	High-resolution Cryo-electron Microscopy Structure		5e-17
2v7f_A	150	Structure Of P. Abyssi Rps19 Protein Length = 150		2e-16
3j20_U	150	Promiscuous Behavior Of Proteins In Archaeal Riboso		2e-16

>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 =  214 bits (544), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 104/141 (73%), Positives = 117/141 (82%), Gaps = 14/141 (9%)
Query: 2   ATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASM 47
           +TARTVKDV+PHEFVKAYSAHLKRSGK              FKEL PYDPDWYY RAAS+
Sbjct: 4   STARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASI 63
Query: 48  ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107
           ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++PKGG
Sbjct: 64  ARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGG 123
Query: 108 RRITSSGQRDLDQVAGRIVVA 128
           R ITS G+RDLDQVAGR+ V 
Sbjct: 124 RLITSQGRRDLDQVAGRVDVT 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 =  119 bits (297), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 57/136 (41%), Positives = 89/136 (65%), Gaps = 15/136 (11%)
Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPD-WYYVRAASMARK 50
           +V+DV+  +F+ AY++ L+R GK +              E+ P D + W+Y RAAS+AR 
Sbjct: 2   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 61
Query: 51  IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110
           IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I PKGGRRI
Sbjct: 62  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 121
Query: 111 TSSGQRDLDQVAGRIV 126
           + +GQRDLD++A + +
Sbjct: 122 SENGQRDLDRIAAQTL 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 =  118 bits (296), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 57/136 (41%), Positives = 89/136 (65%), Gaps = 15/136 (11%)
Query: 6   TVKDVSPHEFVKAYSAHLKRSGKFK--------------ELAPYDPD-WYYVRAASMARK 50
           +V+DV+  +F+ AY++ L+R GK +              E+ P D + W+Y RAAS+AR 
Sbjct: 5   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64
Query: 51  IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110
           IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I PKGGRRI
Sbjct: 65  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124
Query: 111 TSSGQRDLDQVAGRIV 126
           + +GQRDLD++A + +
Sbjct: 125 SENGQRDLDRIAAQTL 140

>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 = 88.2 bits (217), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 76/141 (53%), Gaps = 19/141 (13%)
Query: 6   TVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAASMARKI 51
           TVKDV+  +F++ Y++HLK++ K               +ELAP D DW Y+R A++ARK+
Sbjct: 9   TVKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKV 68
Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNII-----DIEPKG 106
           YL+   G+ + + I+G +K  G+         G I R  L+ L+++ II         K 
Sbjct: 69  YLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKF 128
Query: 107 GRRITSSGQRDLDQVAGRIVV 127
            R IT  G  +L+++A +I +
Sbjct: 129 SRVITKEGMTELNRIATQIAI 149

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 42/136 (30%), Positives = 69/136 (50%), Gaps = 14/136 (10%)
Query: 6   TVKDVSPHEFVKAYSAHLKRSGKF--------------KELAPYDPDWYYVRAASMARKI 51
           T++DV P  +VK  S H K+ GK               +E AP +PDWYY+R A++ R +
Sbjct: 22  TLRDVHPWRWVKICSQHFKQEGKMMVPNCAEIVKTSHGRERAPQNPDWYYIRCAAVLRAV 81
Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YLR G+G G   + +   K  GSRP    ++S  +     + L  + +++     G R+T
Sbjct: 82  YLRPGVGYGGLSKRFSSKKNRGSRPEITTRASKGLLHWCCKSLTKLELLEKCKGAGHRVT 141
Query: 112 SSGQRDLDQVAGRIVV 127
             G++  D +A +I +
Sbjct: 142 KLGRKVADTIAFKIAL 157

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

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 65/121 (53%), Gaps = 5/121 (4%)
Query: 5   RTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRR 64
           + + ++ P E+     A   ++G+ KE  P   DW+Y R AS+ R++YL   +G+   R 
Sbjct: 21  KEIPEIKPPEW-----APFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRT 75
Query: 65  IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR 124
            YGG K  G  P  F K+ G+I R  LQQL+    ++  P  GR IT  G+  LD++A  
Sbjct: 76  YYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATE 135
Query: 125 I 125
           +
Sbjct: 136 L 136

>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 = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 65/121 (53%), Gaps = 5/121 (4%)
Query: 5   RTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRR 64
           + + ++ P E+     A   ++G+ KE  P   DW+Y R AS+ R++YL   +G+   R 
Sbjct: 21  KEIPEIKPPEW-----APFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRT 75
Query: 65  IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR 124
            YGG K  G  P  F K+ G+I R  LQQL+    ++  P  GR IT  G+  LD++A  
Sbjct: 76  YYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATE 135
Query: 125 I 125
           +
Sbjct: 136 L 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	129
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	1e-54
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	1e-53
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	4e-52
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	6e-50
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

>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 =  167 bits (423), Expect = 1e-54
 Identities = 103/138 (74%), Positives = 116/138 (84%), Gaps = 14/138 (10%)

Query: 2   ATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASM 47
           +TARTVKDV+PHEFVKAYSAHLKRSGK              FKEL PYDPDWYY RAAS+
Sbjct: 4   STARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASI 63

Query: 48  ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107
           ARKIYLRQG+GVG F++IYGG +RNGSRPPHFCKSSGAI+R+ILQQLQ M IID++PKGG
Sbjct: 64  ARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGG 123

Query: 108 RRITSSGQRDLDQVAGRI 125
           R ITS G+RDLDQVAGR+
Sbjct: 124 RLITSQGRRDLDQVAGRV 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 =  164 bits (417), Expect = 1e-53
 Identities = 45/134 (33%), Positives = 63/134 (47%), Gaps = 14/134 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKI 51
           TV DV     V+  +  LK   +               KE  P   DW+Y R AS+ R++
Sbjct: 3   TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  P  GR IT
Sbjct: 63  YLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122

Query: 112 SSGQRDLDQVAGRI 125
             G+  LD++A  +
Sbjct: 123 PKGRSFLDKIATEL 136

>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 =  160 bits (406), Expect = 4e-52
 Identities = 54/136 (39%), Positives = 87/136 (63%), Gaps = 15/136 (11%)

Query: 6   TVKDVSPHEFVKAYSAHLK--------------RSGKFKELAPYDPD-WYYVRAASMARK 50
           +V+DV+  +F+ AY++ L+              ++    E+ P D + W+Y RAAS+AR 
Sbjct: 5   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64

Query: 51  IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110
           IY+R+ +GVG   ++YGG+K  G RP     +SG+I R +LQ L+ + I++I PKGGRRI
Sbjct: 65  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124

Query: 111 TSSGQRDLDQVAGRIV 126
           + +GQRDLD++A + +
Sbjct: 125 SENGQRDLDRIAAQTL 140

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

 Score =  155 bits (392), Expect = 6e-50
 Identities = 45/142 (31%), Positives = 75/142 (52%), Gaps = 19/142 (13%)

Query: 6   TVKDVSPHEFVKAYSAHLK--------------RSGKFKELAPYDPDWYYVRAASMARKI 51
           TVKDV+  +F++ Y++HLK               +   +ELAP D DW Y+R A++ARK+
Sbjct: 9   TVKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKV 68

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-----KG 106
           YL+   G+ + + I+G +K  G+         G I R  L+ L+++ II  +      K 
Sbjct: 69  YLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKF 128

Query: 107 GRRITSSGQRDLDQVAGRIVVA 128
            R IT  G  +L+++A +I + 
Sbjct: 129 SRVITKEGMTELNRIATQIAIK 150

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.2 bits (93), Expect = 7e-05
 Identities = 20/125 (16%), Positives = 38/125 (30%), Gaps = 31/125 (24%)

Query: 3   TARTVKDV--SPHEFVKAYSAH--LKRSGK------FKELAPYDPDWYY------VRAAS 46
           +   +  +  S             L    +       +E+   +  +         R  S
Sbjct: 47  SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS 106

Query: 47  MARKIYLRQGLGVGSFRRIYGG----SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102
           M  ++Y+ Q        R+Y      +K N SR   + K      R  L +L+    + I
Sbjct: 107 MMTRMYIEQ------RDRLYNDNQVFAKYNVSRLQPYLK-----LRQALLELRPAKNVLI 155

Query: 103 EPKGG 107
           +   G
Sbjct: 156 DGVLG 160

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 37.1 bits (85), Expect = 7e-04
 Identities = 27/138 (19%), Positives = 46/138 (33%), Gaps = 40/138 (28%)

Query: 13  H-EFVKAYSAHLKRSGKFKELAPYDPDWY-YV----RAASMARKIYLRQGLGVGSFRRIY 66
           H   V  Y+               D  +Y ++    +      ++ L        FR ++
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL--------FRMVF 497

Query: 67  G-----GSK-RNGSRPPHFCKSSGAIARHILQQLQNMN--IIDIEPKGGRRITS------ 112
                   K R+ S       +SG+I  + LQQL+     I D +PK  R + +      
Sbjct: 498 LDFRFLEQKIRHDSTA---WNASGSIL-NTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553

Query: 113 --------SGQRDLDQVA 122
                   S   DL ++A
Sbjct: 554 KIEENLICSKYTDLLRIA 571

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	129
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	100.0
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	100.0
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	100.0
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	100.0
2pg4_A	95	Uncharacterized protein; structural genomics, join	97.37
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.36
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	97.1
2h09_A	155	Transcriptional regulator MNTR; transcription regu	97.1
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.09
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.03
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.98
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.95
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.92
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.9
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	96.89
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.86
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.81
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.81
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.81
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.8
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.76
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.75
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.72
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.72
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.65
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.64
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.63
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.63
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.62
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.62
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.61
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	96.59
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.59
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.58
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.57
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.56
2nnn_A	140	Probable transcriptional regulator; structural gen	96.55
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.55
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.54
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.54
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.53
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.52
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.51
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.5
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.46
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.44
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.44
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.44
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.43
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	96.41
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	96.4
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.32
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.28
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.27
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.25
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.23
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.23
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.07
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.05
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.03
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	95.98
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.96
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	95.95
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	95.93
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.92
2o0m_A	345	Transcriptional regulator, SORC family; structural	95.91
3nqo_A	189	MARR-family transcriptional regulator; structural	95.79
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.75
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.72
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.65
3f3x_A	144	Transcriptional regulator, MARR family, putative;	95.61
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	95.59
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.58
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.56
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	95.54
1bja_A	95	Transcription regulatory protein MOTA; activation	95.53
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.44
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.44
2obp_A	96	Putative DNA-binding protein; structural genomics,	95.35
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.34
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.25
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	95.24
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.18
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	94.98
2fxa_A	207	Protease production regulatory protein HPR; protea	94.9
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	94.79
3by6_A	126	Predicted transcriptional regulator; structural ge	94.69
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	94.66
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.65
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	94.59
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	94.5
1hsj_A	487	Fusion protein consisting of staphylococcus access	94.36
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	94.36
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	94.35
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	94.32
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	94.15
1xma_A	145	Predicted transcriptional regulator; southea colla	94.13
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	94.11
3jth_A	98	Transcription activator HLYU; transcription factor	94.01
2co5_A	99	Viral protein F93; viral protein-winged helix comp	93.96
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	93.93
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	93.81
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	93.76
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	93.75
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.74
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	93.68
3c7j_A	237	Transcriptional regulator, GNTR family; structural	93.63
4esf_A	117	PADR-like transcriptional regulator; PADR family,	93.6
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.39
1ku9_A	152	Hypothetical protein MJ223; putative transcription	93.3
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	93.15
2dql_A	115	PEX protein; circadian clock associated protein, c	93.05
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	92.88
1mkm_A	249	ICLR transcriptional regulator; structural genomic	92.82
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	92.74
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	92.74
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	92.71
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	92.69
2kko_A	108	Possible transcriptional regulatory protein (possi	92.49
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.43
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	92.28
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	92.26
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	92.2
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	91.93
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	91.9
1ylf_A	149	RRF2 family protein; structural genomics, transcri	91.9
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	91.8
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	91.45
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	91.4
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	91.21
3cta_A	230	Riboflavin kinase; structural genomics, transferas	91.21
3aaf_A	134	Werner syndrome ATP-dependent helicase; helix-turn	91.19
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	91.17
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	91.15
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.02
3elk_A	117	Putative transcriptional regulator TA0346; structu	90.97
3l09_A	266	Putative transcriptional regulator; structural gen	90.94
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	90.9
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	90.67
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	90.54
3k69_A	162	Putative transcription regulator; putative transcr	89.83
3eet_A	272	Putative GNTR-family transcriptional regulator; st	89.73
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	89.65
1p6r_A	82	Penicillinase repressor; transcription regulation,	89.55
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	89.01
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	88.73
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	88.69
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	88.16
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	88.13
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	87.97
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.79
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	86.9
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	86.57
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	86.49
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	86.28
1xd7_A	145	YWNA; structural genomics, protein structure initi	86.25
2rkh_A	180	Putative APHA-like transcription factor; ZP_002083	86.14
2g7u_A	257	Transcriptional regulator; ICLR family, structural	86.07
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	85.84
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.45
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	85.23
3r0a_A	123	Putative transcriptional regulator; structural gen	85.21
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	84.99
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	84.94
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	84.87
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	84.59
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	83.43
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	83.34
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	83.22
2qm3_A	373	Predicted methyltransferase; putative methyltransf	82.12
3kfw_X	247	Uncharacterized protein; structural genomics, PSI-	81.94
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	80.54
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	80.12

>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=1.4e-68  Score=405.34  Aligned_cols=127  Identities=46%  Similarity=0.900  Sum_probs=123.2

Q ss_pred             CCCCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCc-hHHHhHHHHHHHHHHhCCCchhhhHHH
Q 033029            1 MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPD-WYYVRAASMARKIYLRQGLGVGSFRRI   65 (129)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~D-W~Y~R~ASilR~lYl~g~vGV~~lr~~   65 (129)
                      ||+ +||||||||+||++||+|||++||              +||+||+||| |||+|||||||||||+||+||++|+++
T Consensus         1 m~~-~tvkDV~a~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kEl~P~d~D~W~Y~RaASi~R~lYl~g~vGV~~lrk~   79 (144)
T 3u5c_T            1 MPG-VSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKL   79 (144)
T ss_dssp             -CC-CCSTTSCHHHHHHHHHHHHHHHCCCCCTTTTTSCCSCTTCSSCCSSCSSSHHHHHHHHHHHHHTSSBCCHHHHHHH
T ss_pred             CCC-CceeecCHHHHHHHHHHHHHHcCCCCCCchHhHhhccccccCCCCCCcchHHHHHHHHHHHHHhcCCCcHHHHHHH
Confidence            787 899999999999999999999987              9999999999 999999999999999999999999999


Q ss_pred             hcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           66 YGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        66 YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      |||+||||++|+||++|||+|||+||||||++||||+++++||+|||+||++||+||.||+.+
T Consensus        80 YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g~vek~~~~GR~lT~~G~~~LD~iA~~v~~~  142 (144)
T 3u5c_T           80 YGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEE  142 (144)
T ss_dssp             HCCEEEETTEEEEECCCCHHHHHHHHHHHHHTTSEECCSSSSCEECHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCCCCCCccccccCcHHHHHHHHHHHHCCCeeecCCCCcEECHhHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999899999999999999999999764

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

Probab=100.00  E-value=4.5e-67  Score=400.97  Aligned_cols=125  Identities=36%  Similarity=0.698  Sum_probs=121.8

Q ss_pred             CCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcc
Q 033029            3 TARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGG   68 (129)
Q Consensus         3 ~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg   68 (129)
                      .|+||||||||+||++||+|||++|+              +||+||+||||||||||||||||||+||+||++|+++|||
T Consensus         6 ~m~tvkDV~a~~fI~~~A~~LKk~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASi~R~lYlrg~vGV~~lrk~YGg   85 (155)
T 2xzm_T            6 SFFTVKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVYLKPHTGISTLKHIFGS   85 (155)
T ss_dssp             CCCCGGGSCHHHHHHHHHHHTTSSCCSCCCHHHHSCCCSSSCSSCCSSTTHHHHHHHHHHHHHHHSTTCCHHHHHHHTCC
T ss_pred             CCceeeecCHHHHHHHHHHHHHhcCCCCCCchHhhhhccccccCCCCCCchHHHHHHHHHHHHhccCCCCHHHHHHHHCC
Confidence            48999999999999999999999987              9999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC-----CceeCcchHhhHHHHHHHhhh
Q 033029           69 SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----GRRITSSGQRDLDQVAGRIVV  127 (129)
Q Consensus        69 ~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~-----GR~lT~~G~~~lD~iA~~i~~  127 (129)
                      +||||++|+||++|||+|||+||||||++||||+++++     ||+|||+||++||+||.||+.
T Consensus        86 ~krrG~~P~h~~~asg~iiR~~LQqLE~~g~Vek~~~g~~~k~GR~lT~~G~~~LDriA~~i~~  149 (155)
T 2xzm_T           86 NKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQIAI  149 (155)
T ss_dssp             EECCSSSCCEECCCCHHHHHHHHHHHHHTTSEEECSSCSSSTTCEEECHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcccCCCcHHHHHHHHHHHHCCCEeecCCCCcCCCCCEECHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999998877     999999999999999999975

>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=1.1e-67  Score=401.17  Aligned_cols=125  Identities=82%  Similarity=1.362  Sum_probs=121.7

Q ss_pred             CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029            4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS   69 (129)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~   69 (129)
                      .+||||||||+||++||+|||++||              +||+||+||||||+|||||||||||+||+||++|+++|||+
T Consensus         6 ~~tvkDV~a~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KEl~P~d~DW~Y~RaASi~R~lYlrg~vGV~~lrk~YGg~   85 (146)
T 3iz6_S            6 ARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIARKIYLRQGIGVGGFQKIYGGR   85 (146)
T ss_dssp             HHHHHHSCHHHHHHHHHTTGGGSSCCCCTTTGGGCCSSSSCSSSTHHHHTHHHHHHHHHHHHHHHCSBCHHHHHSSSCCC
T ss_pred             CCeeeecCHHHHHHHHHHHHHHcCCCCCCchHHHhhccccccCCCCCCchHHHHHHHHHHHHHhcCCCcHHHHHHHHCCC
Confidence            3699999999999999999999987              99999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029           70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA  128 (129)
Q Consensus        70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~  128 (129)
                      ||||++|+||++|||+|||+||||||++||||+++++||+|||+||++||+||.||+++
T Consensus        86 krrG~~P~h~~~asg~iiR~~LQqLE~~g~Vek~~~gGR~lT~~G~~~LD~iA~~v~~~  144 (146)
T 3iz6_S           86 QRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQVAGRVDVT  144 (146)
T ss_dssp             CCCCSSCCCCCCCCHHHHHHHHHHHHHHTSEEEETTTEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcccCCCcHHHHHHHHHHHHCCCeEecCCCCcEECHhHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999899999999999999999999753

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

Probab=100.00  E-value=2.6e-46  Score=283.18  Aligned_cols=124  Identities=36%  Similarity=0.605  Sum_probs=112.4

Q ss_pred             CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029            4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS   69 (129)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~   69 (129)
                      |+||||||||+||++||+|||++|+              ++|++|+|+||||.|||++||++|++|+.|+..|++.|||+
T Consensus         1 m~tv~dv~~~~~i~~~a~~lk~~~ki~~P~w~~~vKt~~~ke~~p~~~~~~y~ria~~lr~~i~~g~~G~~~La~~~gg~   80 (150)
T 2v7f_A            1 MATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGR   80 (150)
T ss_dssp             -CCGGGSCHHHHHHHHHHHHTTCTTCCCCSCGGGCCC------CHHHHTHHHHHHHHHHHHHHHHCSBCHHHHHHHHCC-
T ss_pred             CCCccccCHHHHHHHHHHHHHhcCCCCCcchhhhhcccccccCCCCCcchHHHHHHHHHHHHHHhCCCCHHHHHHHHCCC
Confidence            6899999999999999999999986              99999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhh
Q 033029           70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV  127 (129)
Q Consensus        70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~  127 (129)
                      ||||++|+||+++|+++||.+||+||++|||++.+++|+.||+.|+++||+||.+|+.
T Consensus        81 k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~~~G~~Vt~~~~~~l~~ia~~i~~  138 (150)
T 2v7f_A           81 KNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKK  138 (150)
T ss_dssp             ---CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHH
T ss_pred             ccCCcCCccccccchHHHHHHHHHHHHCCCEEEeCCCceEECCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999998888999999999999999999875

>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=97.37  E-value=0.00052  Score=45.55  Aligned_cols=71  Identities=13%  Similarity=0.107  Sum_probs=56.3

Q ss_pred             HHhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhH-HHHHHHHHHhCCceeecCCCCc----eeCcch
Q 033029           41 YVRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAI-ARHILQQLQNMNIIDIEPKGGR----RITSSG  114 (129)
Q Consensus        41 Y~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~i-iR~~lqqLE~~g~vek~~~~GR----~lT~~G  114 (129)
                      .+|+..+|..++-.+ ++.+..|++..|-              +.+- +-.+++.||+.|||+.++.++|    .||++|
T Consensus        14 ~~~~l~~L~~l~~~~~~~t~~eLa~~l~i--------------s~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G   79 (95)
T 2pg4_A           14 LIRILPTLLEFEKKGYEPSLAEIVKASGV--------------SEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKG   79 (95)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHCC--------------CHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHH
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHCC--------------CchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhH
Confidence            457777888888888 8999999998773              2345 6778999999999996654444    699999


Q ss_pred             HhhHHHHHHHh
Q 033029          115 QRDLDQVAGRI  125 (129)
Q Consensus       115 ~~~lD~iA~~i  125 (129)
                      +..++.+....
T Consensus        80 ~~~~~~~~~~~   90 (95)
T 2pg4_A           80 RRLAECLEKCR   90 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887653

>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=97.36  E-value=0.00052  Score=47.04  Aligned_cols=63  Identities=14%  Similarity=0.074  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           44 AASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        44 ~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      ...||+.++ .+ +|...|...-|=              |-+.+|..+..||+.|||++.. +|-.||++|+..|+.+..
T Consensus        10 i~~IL~~i~-~~-~~~t~La~~~~l--------------s~~~~~~~l~~L~~~GLI~~~~-~~~~LT~kG~~~l~~l~~   72 (95)
T 1r7j_A           10 IQAILEACK-SG-SPKTRIMYGANL--------------SYALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDIRK   72 (95)
T ss_dssp             HHHHHHHHT-TC-BCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCeEEEC-CeeEEChhHHHHHHHHHH
Confidence            356888887 45 888888887543              3469999999999999999984 689999999987776543

>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=97.10  E-value=0.0025  Score=44.39  Aligned_cols=63  Identities=14%  Similarity=0.066  Sum_probs=51.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      |++-+.-.+++.+..|+...|-              |.+-++.+|+.||+.|||+..+.++-.||++|+..+..+..
T Consensus        13 i~~l~~~~~~~~~~ela~~l~v--------------s~~tvs~~l~~Le~~Glv~r~~~~~~~LT~~g~~~~~~~~~   75 (142)
T 1on2_A           13 IYMLIEEKGYARVSDIAEALAV--------------HPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVY   75 (142)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeeCceEEEchhHHHHHHHHHH
Confidence            4444445689999999998864              34678999999999999998876778999999999887654

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

Probab=97.10  E-value=0.002  Score=45.70  Aligned_cols=63  Identities=17%  Similarity=0.200  Sum_probs=51.0

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      |+..|+-.+++.+..|...+|-              |.+-++.+|+.||+.|||+..++.|-.||+.|+..+..+..
T Consensus        45 i~~~l~~~~~~~~~~la~~l~v--------------s~~tvs~~l~~Le~~Glv~r~~~~~~~lT~~g~~~~~~~~~  107 (155)
T 2h09_A           45 ISDLIREVGEARQVDMAARLGV--------------SQPTVAKMLKRLATMGLIEMIPWRGVFLTAEGEKLAQESRE  107 (155)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTCEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEecCCceEEChhHHHHHHHHHH
Confidence            3334455688999999998865              34689999999999999998877788999999998887654

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

Probab=97.09  E-value=0.0025  Score=43.96  Aligned_cols=66  Identities=8%  Similarity=0.101  Sum_probs=52.9

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-.              .+-+-.+++.||+.|||+..+  ..+|    .||++|+..++
T Consensus        35 ~iL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  100 (145)
T 3g3z_A           35 AVLYTLATEGSRTQKHIGEKWSLP--------------KQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAA  100 (145)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHH
Confidence            488888999999999999987642              346778999999999999754  3455    49999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       101 ~~~~~~  106 (145)
T 3g3z_A          101 PLTESA  106 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876553

>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=97.03  E-value=0.0025  Score=43.67  Aligned_cols=64  Identities=13%  Similarity=0.103  Sum_probs=51.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+ .+++.+..|+...|-              +.+-+..+++.||+.|||+...  .++|    .||++|+..++
T Consensus        41 ~iL~~l~-~~~~~~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  105 (146)
T 2gxg_A           41 LVLRATS-DGPKTMAYLANRYFV--------------TQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFN  105 (146)
T ss_dssp             HHHHHHT-TSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHh-cCCcCHHHHHHHhCC--------------CchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHH
Confidence            3777788 999999999998753              3457888999999999998654  2343    68999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       106 ~~~~~  110 (146)
T 2gxg_A          106 KGIEI  110 (146)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

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

Probab=96.98  E-value=0.0027  Score=43.71  Aligned_cols=65  Identities=12%  Similarity=0.155  Sum_probs=51.4

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++.
T Consensus        42 iL~~l~~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  107 (143)
T 3oop_A           42 VLEGIEANEPISQKEIALWTKK--------------DTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTE  107 (143)
T ss_dssp             HHHHHHHHSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHCC--------------CHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHH
Confidence            7778888899999999998753              2356778999999999999754  3444    499999999998


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       108 ~~~~~  112 (143)
T 3oop_A          108 LRDIV  112 (143)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76553

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

Probab=96.95  E-value=0.0038  Score=43.24  Aligned_cols=55  Identities=13%  Similarity=0.218  Sum_probs=46.7

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      .+++.+..|+...|-              +.+-++.+|+.||+.|||+..+ ++-.||++|+...+.+..
T Consensus        29 ~~~~s~~ela~~l~i--------------s~~tv~~~l~~Le~~Gli~r~~-~~~~Lt~~g~~~~~~~~~   83 (139)
T 2x4h_A           29 GEGAKINRIAKDLKI--------------APSSVFEEVSHLEEKGLVKKKE-DGVWITNNGTRSINYLIK   83 (139)
T ss_dssp             TSCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEecC-CeEEEChhHHHHHHHHHH
Confidence            578999999998763              3468899999999999999887 688999999998876654

>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=96.92  E-value=0.0034  Score=43.26  Aligned_cols=66  Identities=17%  Similarity=0.188  Sum_probs=49.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.++.|....|-.      |        +-+-.+++.||+.|||++.++  .+|    .||++|+..++
T Consensus        41 ~vL~~l~~~~~~t~~eLa~~l~~~------~--------~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~  106 (142)
T 3ech_A           41 HVLKLIDEQRGLNLQDLGRQMCRD------K--------ALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHL  106 (142)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHC-----------------CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHhCCC------H--------HHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHH
Confidence            378888889999999999988643      2        367789999999999997542  344    59999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       107 ~~~~~~  112 (142)
T 3ech_A          107 HAELIM  112 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.90  E-value=0.0056  Score=41.62  Aligned_cols=66  Identities=12%  Similarity=0.154  Sum_probs=51.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+...  +++|    .||++|+..++
T Consensus        38 ~iL~~l~~~~~~~~~~la~~l~~--------------~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  103 (138)
T 1jgs_A           38 KVLCSIRCAACITPVELKKVLSV--------------DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICE  103 (138)
T ss_dssp             HHHHHHHHHSSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHH
Confidence            36777788899999999987653              2346778999999999998743  3444    59999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       104 ~~~~~~  109 (138)
T 1jgs_A          104 QCHQLV  109 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.89  E-value=0.0026  Score=44.04  Aligned_cols=65  Identities=8%  Similarity=0.101  Sum_probs=51.2

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      ||..|+-+  +++.+..|+...|-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..+
T Consensus        42 vL~~l~~~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~  107 (127)
T 2frh_A           42 VLTYISENKEKEYYLKDIINHLNY--------------KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKI  107 (127)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSS--------------HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHH
T ss_pred             HHHHHHhccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            77778888  88999999998663              2345667899999999998743  3455    6999999999


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      +++...+
T Consensus       108 ~~~~~~~  114 (127)
T 2frh_A          108 ESLLSRV  114 (127)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876654

>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=96.86  E-value=0.0041  Score=40.39  Aligned_cols=85  Identities=16%  Similarity=0.184  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHH
Q 033029           15 FVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQL   94 (129)
Q Consensus        15 fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqL   94 (129)
                      .+..+.+.|+.-|    +   ++     .-..|+..|.-.+++.+..|....|-              +.+-+..+|+.|
T Consensus         5 ~~~~~~~~l~~~~----l---~~-----~~~~il~~l~~~~~~s~~ela~~l~i--------------s~~tv~~~l~~L   58 (109)
T 1sfx_A            5 PLGELVKALEKLS----F---KP-----SDVRIYSLLLERGGMRVSEIARELDL--------------SARFVRDRLKVL   58 (109)
T ss_dssp             HHHHHHHHHHHTC----C---CH-----HHHHHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcC----C---CH-----HHHHHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHH
Confidence            4566777777543    1   11     11347777777899999999998853              446899999999


Q ss_pred             HhCCceeecCC-CCc----eeCcchHhhHHHHHHHh
Q 033029           95 QNMNIIDIEPK-GGR----RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        95 E~~g~vek~~~-~GR----~lT~~G~~~lD~iA~~i  125 (129)
                      |+.|+|+.... ++|    .+|+.|+..++.+...+
T Consensus        59 ~~~glv~~~~~~~~r~~~~~~t~~g~~~~~~~~~~~   94 (109)
T 1sfx_A           59 LKRGFVRREIVEKGWVGYIYSAEKPEKVLKEFKSSI   94 (109)
T ss_dssp             HHTTSEEEEEEESSSEEEEEEECCHHHHHHHHHHHH
T ss_pred             HHCCCEEEEeecCCceEEEEecCcHHHHHHHHHHHH
Confidence            99999987542 455    69999999988776543

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

Probab=96.81  E-value=0.0038  Score=43.37  Aligned_cols=64  Identities=14%  Similarity=0.239  Sum_probs=50.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee--cC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek--~~--~~GR----~lT~~G~~~l  118 (129)
                      ||..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+.  .+  ..+|    .||++|+..+
T Consensus        46 iL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~  111 (154)
T 2qww_A           46 MINVIYSTPGISVADLTKRLII--------------TGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLS  111 (154)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHH
Confidence            7777888899999999998863              23467789999999999998  33  3344    5999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      +++...
T Consensus       112 ~~~~~~  117 (154)
T 2qww_A          112 KRSTAN  117 (154)
T ss_dssp             HHHHSC
T ss_pred             HHHHhh
Confidence            887544

>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=96.81  E-value=0.0051  Score=41.99  Aligned_cols=66  Identities=18%  Similarity=0.293  Sum_probs=51.0

Q ss_pred             HHHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhh
Q 033029           46 SMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~  117 (129)
                      .||..|+-.+  ++.+..|+...|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..
T Consensus        35 ~vL~~l~~~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~  100 (139)
T 3eco_A           35 HTLGYLYAHQQDGLTQNDIAKALQR--------------TGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKL  100 (139)
T ss_dssp             HHHHHHHHSTTTCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHH
T ss_pred             HHHHHHHhcCCCCcCHHHHHHHhCC--------------CcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHH
Confidence            3788888887  9999999998764              2346778999999999998653  3455    499999999


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      ++.+...+
T Consensus       101 ~~~~~~~~  108 (139)
T 3eco_A          101 VEAFTSIF  108 (139)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

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

Probab=96.81  E-value=0.0044  Score=41.96  Aligned_cols=65  Identities=12%  Similarity=0.152  Sum_probs=50.3

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      |+..|+-.+++.+..|....|-.              .+-+-.+++.||+.|||+...  ..+|    .||++|+..++.
T Consensus        38 iL~~l~~~~~~~~~ela~~l~~~--------------~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~~  103 (139)
T 3bja_A           38 VIQVLAKSGKVSMSKLIENMGCV--------------PSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKKQ  103 (139)
T ss_dssp             HHHHHHHSCSEEHHHHHHHCSSC--------------CTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHHH
Confidence            77777888999999999987532              235677899999999998743  3344    599999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       104 ~~~~~  108 (139)
T 3bja_A          104 VDVQY  108 (139)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.80  E-value=0.0057  Score=42.01  Aligned_cols=66  Identities=15%  Similarity=0.160  Sum_probs=51.5

Q ss_pred             HHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhh
Q 033029           45 ASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRD  117 (129)
Q Consensus        45 ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~  117 (129)
                      ..||..|+- .+++.+..|....|-              +.+-+..+++.||+.|||++.++  .+|    .||++|+..
T Consensus        38 ~~iL~~l~~~~~~~~~~~la~~l~i--------------~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~  103 (147)
T 2hr3_A           38 LVVLGAIDRLGGDVTPSELAAAERM--------------RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN  103 (147)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCC--------------ChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHH
Confidence            458888888 899999999998753              33578889999999999997642  344    599999999


Q ss_pred             HHHHHHH
Q 033029          118 LDQVAGR  124 (129)
Q Consensus       118 lD~iA~~  124 (129)
                      ++.+...
T Consensus       104 ~~~~~~~  110 (147)
T 2hr3_A          104 LYGNRAK  110 (147)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887654

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

Probab=96.76  E-value=0.0059  Score=43.65  Aligned_cols=65  Identities=15%  Similarity=0.240  Sum_probs=51.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+++
T Consensus        50 iL~~L~~~~~~t~~eLa~~l~i--------------s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  115 (168)
T 2nyx_A           50 TLVILSNHGPINLATLATLLGV--------------QPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQ  115 (168)
T ss_dssp             HHHHHHHHCSEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            6777888899999999998753              3346777999999999998743  3344    599999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       116 ~~~~~  120 (168)
T 2nyx_A          116 VTEHR  120 (168)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.75  E-value=0.0075  Score=41.00  Aligned_cols=64  Identities=9%  Similarity=0.108  Sum_probs=50.5

Q ss_pred             HHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      ||..|+-.+  ++.+..|+...|-              +.+-+..+++.||+.|||+..+  +++|    .||++|+..+
T Consensus        39 iL~~l~~~~~~~~~~~ela~~l~~--------------~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~~  104 (141)
T 3bro_A           39 IIDYLSRNKNKEVLQRDLESEFSI--------------KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLE  104 (141)
T ss_dssp             HHHHHHHTTTSCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTH
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCC--------------CcchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHHH
Confidence            777788887  8999999998864              2357888999999999998654  2333    3899999998


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      +.+...
T Consensus       105 ~~~~~~  110 (141)
T 3bro_A          105 TIILSY  110 (141)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877554

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

Probab=96.72  E-value=0.0058  Score=41.41  Aligned_cols=66  Identities=14%  Similarity=0.207  Sum_probs=52.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        33 ~iL~~l~~~~~~~~~ela~~l~~--------------s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~   98 (138)
T 3bpv_A           33 ACLLRIHREPGIKQDELATFFHV--------------DKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIP   98 (138)
T ss_dssp             HHHHHHHHSTTCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHH
Confidence            37777888899999999998753              3457888999999999999754  2233    59999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus        99 ~~~~~~  104 (138)
T 3bpv_A           99 LILKVE  104 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

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

Probab=96.72  E-value=0.0042  Score=43.34  Aligned_cols=65  Identities=18%  Similarity=0.233  Sum_probs=49.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++.
T Consensus        46 iL~~l~~~~~~~~~eLa~~l~~--------------~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  111 (149)
T 4hbl_A           46 VMLTLWEENPQTLNSIGRHLDL--------------SSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEA  111 (149)
T ss_dssp             HHHHHHHSSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHH
Confidence            7777888899999999998764              2356778999999999999754  3455    499999999998


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       112 ~~~~~  116 (149)
T 4hbl_A          112 VFEAI  116 (149)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

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

Probab=96.65  E-value=0.006  Score=43.11  Aligned_cols=66  Identities=15%  Similarity=0.188  Sum_probs=52.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-++++.+..|....|-              +.+-+-.+++.||+.|||++..  ..+|    .||++|+..++
T Consensus        57 ~vL~~l~~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~  122 (161)
T 3e6m_A           57 RLLSSLSAYGELTVGQLATLGVM--------------EQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLA  122 (161)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHH
Confidence            37788888899999999997653              2356778999999999999765  2344    59999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       123 ~~~~~~  128 (161)
T 3e6m_A          123 EISPLI  128 (161)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876643

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

Probab=96.64  E-value=0.0074  Score=42.40  Aligned_cols=65  Identities=14%  Similarity=0.166  Sum_probs=50.8

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-.              .+-+-.+++.||+.|||++.+  ..+|    .||++|+..++.
T Consensus        55 vL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  120 (159)
T 3s2w_A           55 FLMRLYREDGINQESLSDYLKID--------------KGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPD  120 (159)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHH
Confidence            77778888999999999987642              357778999999999998654  3444    499999999998


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       121 ~~~~~  125 (159)
T 3s2w_A          121 MKKIA  125 (159)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76553

>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=96.63  E-value=0.0076  Score=42.59  Aligned_cols=66  Identities=23%  Similarity=0.227  Sum_probs=52.6

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-+|++.+..|....|-.              .+-+-.+++.||+.|||++..  ..+|    .||++|+..++
T Consensus        50 ~iL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  115 (162)
T 3k0l_A           50 TALSVLAAKPNLSNAKLAERSFIK--------------PQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLN  115 (162)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSC--------------GGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHH
Confidence            378888889999999999988642              235678999999999998654  3444    59999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      ++...+
T Consensus       116 ~~~~~~  121 (162)
T 3k0l_A          116 QCNQVV  121 (162)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876643

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

Probab=96.63  E-value=0.013  Score=40.03  Aligned_cols=92  Identities=9%  Similarity=0.042  Sum_probs=60.4

Q ss_pred             hHHHHHHHHHHHhcCC------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhH
Q 033029           13 HEFVKAYSAHLKRSGK------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAI   86 (129)
Q Consensus        13 ~~fI~~~A~~LK~~gk------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~i   86 (129)
                      +++-+.+...|.....      .+.+.+.+=+.   .-..||..|+-.+ +.+..|+...|-              +.+-
T Consensus         6 ~el~~~l~~ll~~~~~~~~~~~~~~~~~~~lt~---~~~~iL~~l~~~~-~t~~eLa~~l~~--------------s~~t   67 (146)
T 3tgn_A            6 KDINAFLNEVILQAENQHEILIGHCTSEVALTN---TQEHILMLLSEES-LTNSELARRLNV--------------SQAA   67 (146)
T ss_dssp             HHHHHHHHHHHHHTTTCSSCCSSCCCCSSCCCH---HHHHHHHHHTTCC-CCHHHHHHHHTC--------------CHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCH---HHHHHHHHHHhCC-CCHHHHHHHHCC--------------CHHH
Confidence            4444555555555433      44444443221   1123778888777 999999999864              3467


Q ss_pred             HHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHHHH
Q 033029           87 ARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQVA  122 (129)
Q Consensus        87 iR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~iA  122 (129)
                      +..+++.||+.|||++.+  ..+|    .||++|+..+..+.
T Consensus        68 vs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~~~  109 (146)
T 3tgn_A           68 VTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEHH  109 (146)
T ss_dssp             HHHHHHHHHHTTSEEC----------CCEECGGGHHHHHHHH
T ss_pred             HHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHHHH
Confidence            899999999999998755  2344    49999999999886

>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=96.62  E-value=0.0057  Score=40.36  Aligned_cols=70  Identities=11%  Similarity=0.044  Sum_probs=48.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCcchHhhHHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA  122 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~~G~~~lD~iA  122 (129)
                      .||..|+-.+++.+..|.+....  .        ..-+.+-+-.+|+.||+.|||++..+.   .-.||++|+..++.+.
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~--~--------l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~   81 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNA--E--------FPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLK   81 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHT--T--------SCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHH--H--------cCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHH
Confidence            36777777888999888322211  1        112345778899999999999875432   3359999999998876


Q ss_pred             HHh
Q 033029          123 GRI  125 (129)
Q Consensus       123 ~~i  125 (129)
                      ..+
T Consensus        82 ~~~   84 (99)
T 1tbx_A           82 TAI   84 (99)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>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=96.62  E-value=0.0037  Score=42.45  Aligned_cols=63  Identities=19%  Similarity=0.194  Sum_probs=49.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+ .|+..++.|....+|             -+.+.+-..|+.||+.|||+....  .+|    .||++|+..++
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            3778887 899999999987641             245688999999999999986542  233    79999999877


Q ss_pred             HHH
Q 033029          120 QVA  122 (129)
Q Consensus       120 ~iA  122 (129)
                      .+.
T Consensus        95 ~l~   97 (107)
T 2fsw_A           95 IID   97 (107)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=96.61  E-value=0.009  Score=41.49  Aligned_cols=63  Identities=14%  Similarity=0.284  Sum_probs=47.0

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee----cCCCCc----eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI----EPKGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek----~~~~GR----~lT~~G~~~l  118 (129)
                      ||..| -.+++.+..|+...|-.              .+-+-.+++.||+.|||+.    ++..+|    .||++|+..+
T Consensus        43 iL~~l-~~~~~t~~eLa~~l~~~--------------~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~  107 (151)
T 3kp7_A           43 VLNML-SIEALTVGQITEKQGVN--------------KAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYI  107 (151)
T ss_dssp             HHHHH-HHSCBCHHHHHHHHCSC--------------SSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHH
T ss_pred             HHHHH-HcCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHH
Confidence            66777 78999999999987643              2367789999999999996    444555    5999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      +.+...
T Consensus       108 ~~~~~~  113 (151)
T 3kp7_A          108 KERKAI  113 (151)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=96.59  E-value=0.0042  Score=42.94  Aligned_cols=66  Identities=14%  Similarity=0.079  Sum_probs=51.1

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-++++.+..|+...|-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        40 ~vL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  105 (140)
T 3hsr_A           40 IVLMAIENDEKLNIKKLGERVFL--------------DSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKS  105 (140)
T ss_dssp             HHHHHSCTTCEEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------ChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHH
Confidence            47788888899999999998763              3457778999999999999765  3344    58999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+....
T Consensus       106 ~~~~~~  111 (140)
T 3hsr_A          106 PLAEIS  111 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.59  E-value=0.0069  Score=39.27  Aligned_cols=66  Identities=8%  Similarity=0.103  Sum_probs=50.9

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCC----ceeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~G----R~lT~~G~~~lD  119 (129)
                      .|+..|+-+++..+..|....|-              |.+-+-..|+.||+.|+|+...  ..|    -.||++|...+.
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            47888887899999999998752              3457888999999999998543  123    358999998888


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus        86 ~~~~~~   91 (100)
T 1ub9_A           86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776654

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

Probab=96.58  E-value=0.0044  Score=41.14  Aligned_cols=68  Identities=19%  Similarity=0.324  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHH-hCC---CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcch
Q 033029           43 RAASMARKIYL-RQG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSG  114 (129)
Q Consensus        43 R~ASilR~lYl-~g~---vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G  114 (129)
                      ++..+|-.|+- .++   +.+..|+...|-              +.+-+-.+|+.||+.|||. ++..+|    .||++|
T Consensus        13 ~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i--------------~~~tvs~~l~~Le~~Glv~-~~~d~R~~~v~LT~~G   77 (95)
T 2qvo_A           13 KALEILMTIYYESLGGNDVYIQYIASKVNS--------------PHSYVWLIIKKFEEAKMVE-CELEGRTKIIRLTDKG   77 (95)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEHHHHHHHSSS--------------CHHHHHHHHHHHHHTTSEE-EEEETTEEEEEECHHH
T ss_pred             hHHHHHHHHHHccCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCcCcc-CCCCCCeEEEEEChhH
Confidence            44456666654 345   889999998654              2346777899999999994 444466    799999


Q ss_pred             HhhHHHHHHHh
Q 033029          115 QRDLDQVAGRI  125 (129)
Q Consensus       115 ~~~lD~iA~~i  125 (129)
                      +..++++...+
T Consensus        78 ~~~~~~~~~~~   88 (95)
T 2qvo_A           78 QKIAQQIKSII   88 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

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

Probab=96.57  E-value=0.01  Score=40.83  Aligned_cols=65  Identities=14%  Similarity=0.182  Sum_probs=50.6

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CC----CceeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KG----GRRITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~----GR~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.+  ..    .-.||++|+..++
T Consensus        44 ~iL~~l~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~  109 (148)
T 3nrv_A           44 RIISVLSSASDCSVQKISDILGL--------------DKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE  109 (148)
T ss_dssp             HHHHHHHHSSSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHH
Confidence            37888888999999999998763              2357788999999999999764  22    3469999999999


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       110 ~~~~~  114 (148)
T 3nrv_A          110 VASDF  114 (148)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

>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=96.56  E-value=0.024  Score=38.69  Aligned_cols=65  Identities=9%  Similarity=0.101  Sum_probs=51.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+...  .++|    .||++|+..++.
T Consensus        34 iL~~l~~~~~~t~~~la~~l~~--------------s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~   99 (144)
T 1lj9_A           34 YLVRVCENPGIIQEKIAELIKV--------------DRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCcCcCHHHHHHHHCC--------------CHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHHH
Confidence            6777888899999999998763              3457788999999999998754  2344    599999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       100 ~~~~~  104 (144)
T 1lj9_A          100 IVREN  104 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.55  E-value=0.0086  Score=40.52  Aligned_cols=65  Identities=12%  Similarity=0.227  Sum_probs=51.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        42 ~iL~~l~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (140)
T 2nnn_A           42 AALVRLGETGPCPQNQLGRLTAM--------------DAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELE  107 (140)
T ss_dssp             HHHHHHHHHSSBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHH
Confidence            37888888899999999998753              3356788999999999999753  2233    59999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       108 ~~~~~  112 (140)
T 2nnn_A          108 AGLAA  112 (140)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87554

>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=96.55  E-value=0.012  Score=41.02  Aligned_cols=65  Identities=9%  Similarity=0.095  Sum_probs=51.3

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-++++.+..|....|-              +.+-+-.+++.||+.|||+...  ..+|    .||++|+..++
T Consensus        48 ~iL~~l~~~~~~t~~ela~~l~i--------------s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  113 (154)
T 2eth_A           48 YAFLYVALFGPKKMKEIAEFLST--------------TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFG  113 (154)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHTTS--------------CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHH
Confidence            47788888899999999998753              3346778999999999998743  3344    58999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       114 ~~~~~  118 (154)
T 2eth_A          114 EILSN  118 (154)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

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

Probab=96.54  E-value=0.0083  Score=40.10  Aligned_cols=63  Identities=16%  Similarity=0.160  Sum_probs=50.5

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQV  121 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~i  121 (129)
                      .|+..| .+|++.+..|....|              -|.+-+...|+.||+.|+|+...+ ||    .||++|...+...
T Consensus        25 ~IL~~L-~~~~~~~~ela~~l~--------------is~~tv~~~l~~L~~~gli~~~~~-gr~~~y~l~~~~~~~~~~~   88 (114)
T 2oqg_A           25 EILTEL-GRADQSASSLATRLP--------------VSRQAIAKHLNALQACGLVESVKV-GREIRYRALGAELNKTART   88 (114)
T ss_dssp             HHHHHH-HHSCBCHHHHHHHSS--------------SCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECSHHHHHHHHH
T ss_pred             HHHHHH-HcCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeeEEec-CCEEEEEechHHHHHHHHH
Confidence            488877 789999999999875              244689999999999999987654 55    7999998777655


Q ss_pred             HHH
Q 033029          122 AGR  124 (129)
Q Consensus       122 A~~  124 (129)
                      ...
T Consensus        89 ~~~   91 (114)
T 2oqg_A           89 LER   91 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

>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=96.54  E-value=0.0049  Score=42.23  Aligned_cols=64  Identities=9%  Similarity=0.160  Sum_probs=50.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD~  120 (129)
                      |+..|+-.+++.+..|+...|-.              .+-+..+++.||+.|||+..++  ++|    .||++|+..++.
T Consensus        42 iL~~l~~~~~~~~~ela~~l~~~--------------~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (142)
T 2bv6_A           42 VLTILWDESPVNVKKVVTELALD--------------TGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  107 (142)
T ss_dssp             HHHHHHHSSEEEHHHHHHHTTCC--------------TTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHHH
Confidence            77778888999999999988642              2357789999999999987542  344    579999999988


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       108 ~~~~  111 (142)
T 2bv6_A          108 LSNA  111 (142)
T ss_dssp             HTTH
T ss_pred             HHHH
Confidence            7543

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

Probab=96.53  E-value=0.012  Score=41.17  Aligned_cols=64  Identities=13%  Similarity=0.119  Sum_probs=48.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCC----ceeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG----RRITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~G----R~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  ..+    -.||++|+..++.
T Consensus        54 iL~~l~~~~~~t~~ela~~l~i--------------s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  119 (162)
T 2fa5_A           54 VITILALYPGSSASEVSDRTAM--------------DKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYET  119 (162)
T ss_dssp             HHHHHHHSTTCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHH
Confidence            7777777899999999998763              3357888999999999998754  223    3599999999987


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       120 ~~~~  123 (162)
T 2fa5_A          120 VAPL  123 (162)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

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

Probab=96.52  E-value=0.012  Score=40.44  Aligned_cols=65  Identities=12%  Similarity=0.209  Sum_probs=50.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+-.+|+.||+.|||+...  ..+|    .||++|+..++.
T Consensus        47 iL~~l~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  112 (150)
T 2rdp_A           47 ALQWLLEEGDLTVGELSNKMYL--------------ACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEE  112 (150)
T ss_dssp             HHHHHHHHCSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCC--------------CchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHH
Confidence            7777888899999999998753              3356778999999999998753  2344    599999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       113 ~~~~~  117 (150)
T 2rdp_A          113 VIEKR  117 (150)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.51  E-value=0.0052  Score=42.61  Aligned_cols=66  Identities=18%  Similarity=0.288  Sum_probs=45.8

Q ss_pred             HHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce----eCcchHhh
Q 033029           46 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~----lT~~G~~~  117 (129)
                      .||..|+-.  +++.+..|+...|-.      |        +-+-.+++.||+.|||++..  ..+|.    ||++|+..
T Consensus        45 ~vL~~l~~~~~~~~t~~eLa~~l~~~------~--------~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~  110 (148)
T 3jw4_A           45 RMIGYIYENQESGIIQKDLAQFFGRR------G--------ASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAAL  110 (148)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHC--------------------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHCCC------h--------hHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHH
Confidence            377788887  899999999976532      2        24668999999999998754  34553    99999999


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      ++.+...+
T Consensus       111 ~~~~~~~~  118 (148)
T 3jw4_A          111 VEEFNNIF  118 (148)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876553

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

Probab=96.50  E-value=0.0097  Score=38.59  Aligned_cols=65  Identities=15%  Similarity=0.231  Sum_probs=51.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQV  121 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~i  121 (129)
                      .|+..|.-.+++.+..|....|-              |.+-+.+.|+.||+.|+|+...+ ||    .||++|...+-..
T Consensus        28 ~il~~l~~~~~~s~~ela~~l~i--------------s~~tvs~~l~~L~~~glv~~~~~-~r~~~y~l~~~~~~~l~~~   92 (99)
T 3cuo_A           28 LILCMLSGSPGTSAGELTRITGL--------------SASATSQHLARMRDEGLIDSQRD-AQRILYSIKNEAVNAIIAT   92 (99)
T ss_dssp             HHHHHHTTCCSEEHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEEEEC-SSCEEEEECCHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHHHHHHHH
Confidence            47777766679999999998863              34689999999999999998764 44    6899997776666


Q ss_pred             HHHh
Q 033029          122 AGRI  125 (129)
Q Consensus       122 A~~i  125 (129)
                      ..++
T Consensus        93 l~~~   96 (99)
T 3cuo_A           93 LKNV   96 (99)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5554

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

Probab=96.46  E-value=0.015  Score=39.59  Aligned_cols=64  Identities=11%  Similarity=0.138  Sum_probs=49.7

Q ss_pred             HHHHH-HHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           47 MARKI-YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~l-Yl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      ||..| +-.+++.+..|....|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        42 iL~~l~~~~~~~t~~~la~~l~~--------------s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (146)
T 2fbh_A           42 VLLHLARHRDSPTQRELAQSVGV--------------EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA  107 (146)
T ss_dssp             HHHHHHHCSSCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCC--------------ChhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHH
Confidence            66777 45789999999998753              33578889999999999997542  333    68999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       108 ~~~~~  112 (146)
T 2fbh_A          108 DIEAI  112 (146)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87544

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

Probab=96.44  E-value=0.0093  Score=40.43  Aligned_cols=66  Identities=15%  Similarity=0.135  Sum_probs=51.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..+  ..+|    .||++|+..++
T Consensus        40 ~iL~~l~~~~~~t~~ela~~l~~--------------s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  105 (142)
T 2fbi_A           40 RVIRILRQQGEMESYQLANQACI--------------LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFV  105 (142)
T ss_dssp             HHHHHHHHHCSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHH
Confidence            37788888899999999998653              3357888999999999998753  3344    49999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       106 ~~~~~~  111 (142)
T 2fbi_A          106 SMSGDM  111 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.44  E-value=0.0095  Score=40.48  Aligned_cols=63  Identities=8%  Similarity=0.081  Sum_probs=48.9

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CC----ceeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~G----R~lT~~G~~~lD  119 (129)
                      .||+.|+ +|+..+..|.....             .-|.+.+-..|+.||+.|||++...  .+    -.||++|++.++
T Consensus        18 ~IL~~L~-~~~~~~~eLa~~l~-------------~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l~~   83 (107)
T 2hzt_A           18 VILXHLT-HGKKRTSELKRLMP-------------NITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLEG   83 (107)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHHHH
Confidence            3777787 89999999998751             2355788999999999999986542  23    479999999877


Q ss_pred             HHH
Q 033029          120 QVA  122 (129)
Q Consensus       120 ~iA  122 (129)
                      .+.
T Consensus        84 ~~~   86 (107)
T 2hzt_A           84 ILD   86 (107)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            553

>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=96.44  E-value=0.011  Score=40.71  Aligned_cols=64  Identities=16%  Similarity=0.227  Sum_probs=51.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|+...|-              +.+-+..+|+.||+.|||+...+  ++|    .||++|+..++.
T Consensus        45 iL~~l~~~~~~t~~ela~~l~~--------------~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  110 (152)
T 3bj6_A           45 ILEGLSLTPGATAPQLGAALQM--------------KRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITA  110 (152)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHH
Confidence            7777888899999999998864              23578889999999999997542  233    589999999887


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       111 ~~~~  114 (152)
T 3bj6_A          111 IRAD  114 (152)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6554

>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=96.43  E-value=0.01  Score=40.45  Aligned_cols=65  Identities=20%  Similarity=0.358  Sum_probs=51.4

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        37 ~iL~~l~~~~~~~~~~la~~l~~--------------s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  102 (145)
T 2a61_A           37 DILQKIYFEGPKRPGELSVLLGV--------------AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIE  102 (145)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHH
Confidence            37777888899999999998753              3357888999999999998754  2333    69999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       103 ~~~~~  107 (145)
T 2a61_A          103 KVIER  107 (145)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=96.41  E-value=0.01  Score=41.54  Aligned_cols=64  Identities=17%  Similarity=0.199  Sum_probs=50.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+..+|+.||+.|||+...  .++|    .||++|+..++.
T Consensus        57 iL~~l~~~~~~t~~ela~~l~i--------------s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  122 (162)
T 3cjn_A           57 ALAILSAKDGLPIGTLGIFAVV--------------EQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDR  122 (162)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            7777888899999999998753              2357888999999999998753  2333    599999999988


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       123 ~~~~  126 (162)
T 3cjn_A          123 LWPH  126 (162)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7554

>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=96.40  E-value=0.012  Score=48.40  Aligned_cols=68  Identities=16%  Similarity=0.139  Sum_probs=52.3

Q ss_pred             hHHHHHH-----HHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC-CceeCcch-H
Q 033029           43 RAASMAR-----KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-GRRITSSG-Q  115 (129)
Q Consensus        43 R~ASilR-----~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~-GR~lT~~G-~  115 (129)
                      |-..||+     .|--.+|||+..|.+.|+=            .-|-.-||+-|..||++|++++...+ ||.-|.+| +
T Consensus        18 R~~~IL~~i~~~yl~~~~pV~s~~La~~~~l------------~VS~aTIRrDL~~LE~~GlL~r~HgsAgript~~g~r   85 (338)
T 1stz_A           18 RQRKVLYCIVREYIENKKPVSSQRVLEVSNI------------EFSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDKGLR   85 (338)
T ss_dssp             HHHHHHHHHHHHHHHHCSCBCHHHHHHHSCC------------CSCHHHHHHHHHHHHHTTSEECCSSCSCBEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCccHHHHHHHhCC------------CCCHHHHHHHHHHHHHCCCEEEccCcceecCCcccch
Confidence            6677887     4444689999999998852            23557999999999999999986643 68889888 4


Q ss_pred             hhHHHHH
Q 033029          116 RDLDQVA  122 (129)
Q Consensus       116 ~~lD~iA  122 (129)
                      ...|++.
T Consensus        86 ~yvd~l~   92 (338)
T 1stz_A           86 FYYEEML   92 (338)
T ss_dssp             HHHHHHH
T ss_pred             hhhhhhh
Confidence            4566554

>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=96.32  E-value=0.0076  Score=41.29  Aligned_cols=63  Identities=13%  Similarity=0.188  Sum_probs=48.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CC----ceeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GG----RRITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~G----R~lT~~G~~~lD  119 (129)
                      .||..|+ +|++.++.|.....             .-+.+.+-..|+.||+.|||+....  .+    -.||++|+..++
T Consensus        26 ~IL~~L~-~~~~~~~eLa~~l~-------------~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~~~   91 (112)
T 1z7u_A           26 SLMDELF-QGTKRNGELMRALD-------------GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   91 (112)
T ss_dssp             HHHHHHH-HSCBCHHHHHHHST-------------TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhc-------------cCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHHHH
Confidence            4788887 69999999999862             2345688899999999999986542  23    378999998777


Q ss_pred             HHH
Q 033029          120 QVA  122 (129)
Q Consensus       120 ~iA  122 (129)
                      .+.
T Consensus        92 ~~~   94 (112)
T 1z7u_A           92 ALS   94 (112)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=96.28  E-value=0.011  Score=42.41  Aligned_cols=65  Identities=14%  Similarity=0.149  Sum_probs=48.9

Q ss_pred             HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      ||..|+- .+++.+..|+...|-              +.+-+-.+++.||+.|||++..  ..+|    .||++|+..++
T Consensus        58 vL~~L~~~~~~~t~~eLa~~l~i--------------~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  123 (166)
T 3deu_A           58 TLHNIHQLPPDQSQIQLAKAIGI--------------EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIA  123 (166)
T ss_dssp             HHHHHHHSCSSEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCC--------------CHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHH
Confidence            7777887 678999999998764              2356778999999999999765  2344    49999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       124 ~~~~~~  129 (166)
T 3deu_A          124 EMEEVI  129 (166)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.27  E-value=0.011  Score=40.85  Aligned_cols=65  Identities=14%  Similarity=0.171  Sum_probs=51.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+...+  ++|    .||++|+..++
T Consensus        41 ~iL~~l~~~~~~t~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  106 (155)
T 1s3j_A           41 FVLASLKKHGSLKVSEIAERMEV--------------KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFE  106 (155)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHH
Confidence            37777888899999999998753              34578889999999999987542  333    58999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       107 ~~~~~  111 (155)
T 1s3j_A          107 EVLAG  111 (155)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            86654

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

Probab=96.25  E-value=0.017  Score=40.12  Aligned_cols=65  Identities=11%  Similarity=0.159  Sum_probs=49.3

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..++
T Consensus        47 ~iL~~l~~~~~~t~~ela~~l~i--------------~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  112 (155)
T 3cdh_A           47 RVLACLVDNDAMMITRLAKLSLM--------------EQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAE  112 (155)
T ss_dssp             HHHHHHSSCSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHH
Confidence            37777888899999999998653              2356778999999999999754  2333    59999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       113 ~~~~~  117 (155)
T 3cdh_A          113 SLVAS  117 (155)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87554

>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=96.23  E-value=0.019  Score=39.80  Aligned_cols=65  Identities=14%  Similarity=0.160  Sum_probs=47.4

Q ss_pred             HHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      ||..|+-.+ ++.+..|....|-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        44 vL~~l~~~~~~~t~~eLa~~l~i--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  109 (150)
T 3fm5_A           44 VLVLACEQAEGVNQRGVAATMGL--------------DPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRD  109 (150)
T ss_dssp             HHHHHHHSTTCCCSHHHHHHHTC--------------CHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHH
T ss_pred             HHHHHHhCCCCcCHHHHHHHHCC--------------CHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHH
Confidence            677777654 7899999998763              2346778899999999998754  2344    59999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       110 ~~~~~~  115 (150)
T 3fm5_A          110 DAKARV  115 (150)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876553

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

Probab=96.23  E-value=0.013  Score=44.62  Aligned_cols=56  Identities=11%  Similarity=0.157  Sum_probs=47.6

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      .+++.+..|+...|-.              .+-+..+|+.||+.|||+..+.++=.||++|+....++..
T Consensus        18 ~~~~~~~~lA~~l~vs--------------~~tvs~~l~~Le~~GlV~r~~~~~i~LT~~G~~~~~~~~~   73 (214)
T 3hrs_A           18 HNKITNKEIAQLMQVS--------------PPAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVSDLYR   73 (214)
T ss_dssp             CSCCCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEEecCCCeEECHHHHHHHHHHHH
Confidence            4688899999887653              3478899999999999999887788999999999888765

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

Probab=96.07  E-value=0.02  Score=41.35  Aligned_cols=65  Identities=17%  Similarity=0.123  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      ..||+.|. .|+...+.|++.-.             .-|.+.+-..|..||+.|||++..  ...|    .||++|++++
T Consensus        29 l~IL~~L~-~g~~rf~eL~~~l~-------------gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~   94 (131)
T 4a5n_A           29 GILFYHMI-DGKKRFNEFRRICP-------------SITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLE   94 (131)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhc-------------ccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHH
Confidence            34888887 89999999998752             235579999999999999999754  2233    6999999988


Q ss_pred             HHHHH
Q 033029          119 DQVAG  123 (129)
Q Consensus       119 D~iA~  123 (129)
                      ..+..
T Consensus        95 ~~l~~   99 (131)
T 4a5n_A           95 PIVLQ   99 (131)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76643

>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=96.05  E-value=0.019  Score=41.37  Aligned_cols=62  Identities=18%  Similarity=0.260  Sum_probs=48.9

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC-----CceeCcchHhhHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG-----GRRITSSGQRDLDQ  120 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~-----GR~lT~~G~~~lD~  120 (129)
                      .||+.|+ +|+..++.|.+..|-              |.+.+-..|+.||+.|||++....     .-.||++|+..+..
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            3788886 899999999987643              456899999999999999976532     34799999987765


Q ss_pred             HH
Q 033029          121 VA  122 (129)
Q Consensus       121 iA  122 (129)
                      +.
T Consensus        93 l~   94 (146)
T 2f2e_A           93 LV   94 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=96.03  E-value=0.0096  Score=40.19  Aligned_cols=59  Identities=7%  Similarity=0.062  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchh-HHHHHHHHHHhCCceeecCCCCc---eeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGA-IARHILQQLQNMNIIDIEPKGGR---RITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~-iiR~~lqqLE~~g~vek~~~~GR---~lT~~G~~~l  118 (129)
                      ..|+..|.-+||..+..|++..|-.              .. -+|..|+.||+.|+|++.. .||   .||++|+..|
T Consensus        14 ~~IL~~Lk~~g~~ta~eiA~~Lgit--------------~~~aVr~hL~~Le~eGlV~~~~-~gRP~w~LT~~g~~~~   76 (79)
T 1xmk_A           14 EKICDYLFNVSDSSALNLAKNIGLT--------------KARDINAVLIDMERQGDVYRQG-TTPPIWHLTDKKRERM   76 (79)
T ss_dssp             HHHHHHHHHTCCEEHHHHHHHHCGG--------------GHHHHHHHHHHHHHTTSEEEEC-SSSCEEEECHHHHTTT
T ss_pred             HHHHHHHHHcCCcCHHHHHHHcCCC--------------cHHHHHHHHHHHHHCCCEEecC-CCCCCeEeCHhHHhHh
Confidence            4577778888999999999988753              34 7999999999999999763 467   7899998765

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

Probab=95.98  E-value=0.0078  Score=41.33  Aligned_cols=67  Identities=13%  Similarity=0.154  Sum_probs=45.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc-----eeCcchHhhHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR-----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR-----~lT~~G~~~lD  119 (129)
                      ||.-|. .+|.--..+.+....          +..-+.+.+-.+|+.||+.|||+...  .+||     .||++|+..++
T Consensus        14 IL~~L~-~~~~~gyel~~~l~~----------~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l~   82 (108)
T 3l7w_A           14 ILAIVS-KHDSYGYDISQTIKL----------IASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHLV   82 (108)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHTT----------TCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHHH
T ss_pred             HHHHHH-cCCCcHHHHHHHHHH----------HhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHHH
Confidence            555555 356444444444432          12456678999999999999998653  2454     49999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      ++...
T Consensus        83 ~~~~~   87 (108)
T 3l7w_A           83 YLTKE   87 (108)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87655

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

Probab=95.96  E-value=0.0088  Score=41.54  Aligned_cols=62  Identities=13%  Similarity=0.138  Sum_probs=47.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|....|-              +.+-+..+|+.||+.|||+...+  .+|    .||++|+..++.
T Consensus        52 iL~~l~~~~~~t~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  117 (153)
T 2pex_A           52 VMLVLWETDERSVSEIGERLYL--------------DSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRSK  117 (153)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGGG
T ss_pred             HHHHHHhCCCcCHHHHHHHhCC--------------CcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHHH
Confidence            7777888899999999998762              34577889999999999997542  333    589999988776


Q ss_pred             HH
Q 033029          121 VA  122 (129)
Q Consensus       121 iA  122 (129)
                      +.
T Consensus       118 ~~  119 (153)
T 2pex_A          118 AG  119 (153)
T ss_dssp             ST
T ss_pred             HH
Confidence            43

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

Probab=95.95  E-value=0.016  Score=41.19  Aligned_cols=65  Identities=11%  Similarity=0.162  Sum_probs=49.3

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      ||..|+-.  +++.+..|....|-.      +        +-+-.+++.||+.|||++..  ..+|    .||++|+..+
T Consensus        51 vL~~l~~~~~~~~t~~eLa~~l~~~------~--------~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  116 (168)
T 3u2r_A           51 TLRLLRSVHPEGMATLQIADRLISR------A--------PDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLL  116 (168)
T ss_dssp             HHHHHHHHTTSCEEHHHHHHHC---------C--------THHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCC------h--------hhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHH
Confidence            77888885  489999999987532      2        36778999999999999754  3344    5999999999


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      +.+...+
T Consensus       117 ~~~~~~~  123 (168)
T 3u2r_A          117 KDLEEPV  123 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876543

>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=95.93  E-value=0.019  Score=44.91  Aligned_cols=55  Identities=20%  Similarity=0.305  Sum_probs=46.1

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      .+|+|...|+..-|=              |-..+|..++-|++.|||+..+ +|=.||++|++...++-.
T Consensus        28 ~~~V~~~~LA~~Lgv--------------S~~SV~~~lkkL~e~GLV~~~~-~Gv~LTe~G~~~A~~i~~   82 (200)
T 2p8t_A           28 KEPLGRKQISERLEL--------------GEGSVRTLLRKLSHLDIIRSKQ-RGHFLTLKGKEIRDKLLS   82 (200)
T ss_dssp             TSCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHHHT
T ss_pred             cCCccHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeC-CCeEECHHHHHHHHHHHH
Confidence            589999999999872              3358999999999999999887 899999999998777654

>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=95.92  E-value=0.0085  Score=40.58  Aligned_cols=66  Identities=9%  Similarity=0.098  Sum_probs=50.4

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQVA  122 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~iA  122 (129)
                      ||..|+-.+|+.+..|....|-.  .++        +.+-+-.+|+.||+.|||++.+++.|    .||++|+..++.+.
T Consensus        15 vL~~l~~~~~~t~~ela~~l~~~--~~~--------s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~lT~~g~~~~~~~~   84 (123)
T 1okr_A           15 VMNIIWMKKYASANNIIEEIQMQ--KDW--------SPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSK   84 (123)
T ss_dssp             HHHHHHHHSSEEHHHHHHHHHHH--CCC--------CHHHHHHHHHHHHHHTSEEEEEETTEEEEEESSCHHHHHHHHHH
T ss_pred             HHHHHHhCCCcCHHHHHHHHhcc--CCC--------cHhhHHHHHHHHHHCCCeEEEecCCeEEEEEecCHHHHHHHHHH
Confidence            66777778999999999998742  222        34578899999999999998765332    47999998876653

>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=95.91  E-value=0.0013  Score=53.47  Aligned_cols=64  Identities=22%  Similarity=0.329  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      |-..||..||-.+++++..|+..+|-.              ..-||+.|+.||+.|+|+... .|=.||++|+..+..+
T Consensus        21 r~~~iL~~l~~~~~~t~~eLa~~l~vs--------------~~Tv~r~l~~Le~~Glv~~~~-~gi~LT~~G~~~~~~~   84 (345)
T 2o0m_A           21 ERFQILRNIYWMQPIGRRSLSETMGIT--------------ERVLRTETDVLKQLNLIEPSK-SGMTLTERGLEVYQGL   84 (345)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEe-cceEEcHHHHHHHHHH
Confidence            445699999999999999999998753              347999999999999998544 4789999999766544

>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=95.79  E-value=0.04  Score=40.31  Aligned_cols=66  Identities=15%  Similarity=0.228  Sum_probs=51.2

Q ss_pred             HHHHHHHH--hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhh
Q 033029           46 SMARKIYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl--~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~  117 (129)
                      .||..|+-  .+++.++.|+...|-              +.+-+-.+++.||+.|||++..  ..+|    .||++|+..
T Consensus        45 ~vL~~L~~~~~~~~t~~eLa~~l~i--------------s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~  110 (189)
T 3nqo_A           45 MTILSILHLPEEETTLNNIARKMGT--------------SKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKV  110 (189)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHH
T ss_pred             HHHHHHHhccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHH
Confidence            37777887  679999999998763              2346778999999999998644  3455    589999999


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      ++.+....
T Consensus       111 ~~~~~~~~  118 (189)
T 3nqo_A          111 MVTCSRTG  118 (189)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

>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=95.75  E-value=0.02  Score=39.40  Aligned_cols=63  Identities=10%  Similarity=0.093  Sum_probs=49.6

Q ss_pred             HHHHHHHHhCCCc--hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCceeCcchHhhHHHH
Q 033029           46 SMARKIYLRQGLG--VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDLDQV  121 (129)
Q Consensus        46 SilR~lYl~g~vG--V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR~lT~~G~~~lD~i  121 (129)
                      .|++.|. .|+..  ++.|.+...             .-|.+.+-..|+.||+.|+|++...  .--.||++|++.+..+
T Consensus        31 ~IL~~L~-~g~~~~~~~eL~~~l~-------------gis~~~ls~~L~~Le~~GlV~r~~~r~~~y~LT~~G~~l~~~l   96 (111)
T 3df8_A           31 LIISVLG-NGSTRQNFNDIRSSIP-------------GISSTILSRRIKDLIDSGLVERRSGQITTYALTEKGMNVRNSL   96 (111)
T ss_dssp             HHHHHHT-SSSSCBCHHHHHHTST-------------TCCHHHHHHHHHHHHHTTSEEEEESSSEEEEECHHHHHHHHHH
T ss_pred             HHHHHHh-cCCCCCCHHHHHHHcc-------------CCCHHHHHHHHHHHHHCCCEEEeecCcEEEEECccHHHHHHHH
Confidence            4788887 88988  999998751             2355789999999999999997642  3458999999987765


Q ss_pred             H
Q 033029          122 A  122 (129)
Q Consensus       122 A  122 (129)
                      .
T Consensus        97 ~   97 (111)
T 3df8_A           97 M   97 (111)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=95.72  E-value=0.014  Score=39.57  Aligned_cols=58  Identities=14%  Similarity=0.067  Sum_probs=47.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~l  118 (129)
                      |+..|+-.+++.+..|....|-              +.+-+..+++.||+.|||+...+  .+|    .||++|+..+
T Consensus        36 iL~~l~~~~~~~~~ela~~l~i--------------s~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           36 ILQTLLKDAPLHQLALQERLQI--------------DRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHHCSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            7778888899999999998753              33578889999999999987542  343    5899999998

>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=95.65  E-value=0.023  Score=37.52  Aligned_cols=55  Identities=15%  Similarity=0.060  Sum_probs=45.7

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHh
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR  116 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~  116 (129)
                      ..|+..|  ++++.++.|....|-              |.+-+++.|+.||+.|+|+... +.-.||+.|+.
T Consensus        34 ~~Il~~L--~~~~~~~eLa~~l~i--------------s~~tv~~~L~~L~~~Glv~~~~-g~y~l~~~g~~   88 (96)
T 1y0u_A           34 RKILRML--DKGRSEEEIMQTLSL--------------SKKQLDYHLKVLEAGFCIERVG-ERWVVTDAGKI   88 (96)
T ss_dssp             HHHHHHH--HTTCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECTTTCC
T ss_pred             HHHHHHH--cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEC-CEEEECCCchH
Confidence            3478877  899999999998843              3468999999999999999876 66789999864

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

Probab=95.61  E-value=0.036  Score=37.98  Aligned_cols=64  Identities=11%  Similarity=0.102  Sum_probs=49.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.++ .+..|+...|-              +.+-+-.+++.||+.|||++.++  .+|    .||++|+..++.
T Consensus        42 iL~~l~~~~~-~~~~la~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (144)
T 3f3x_A           42 ILKATSEEPR-SMVYLANRYFV--------------TQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLE  106 (144)
T ss_dssp             HHHHHHHSCE-EHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCC-CHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHHH
Confidence            7777888888 99999998763              23467789999999999987542  333    599999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       107 ~~~~~  111 (144)
T 3f3x_A          107 ANEVL  111 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=95.59  E-value=0.013  Score=40.50  Aligned_cols=51  Identities=14%  Similarity=0.175  Sum_probs=42.9

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchHhhHHHHH
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQVA  122 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~~lD~iA  122 (129)
                      .+..|+..||-              |..-+|.+|+.||+.|+|+..+  ..|-.+++....++..+.
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            67888888875              3568999999999999999888  469999999888887764

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

Probab=95.58  E-value=0.025  Score=39.34  Aligned_cols=65  Identities=12%  Similarity=0.184  Sum_probs=47.2

Q ss_pred             HHHHHH-HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lY-l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      ||..|+ -.+++.+..|....|-.      +        +-+-.+++.||+.|||++..  .++|    .||++|+..++
T Consensus        52 iL~~L~~~~~~~~~~ela~~l~i~------~--------~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  117 (160)
T 3boq_A           52 AMAQLARNPDGLSMGKLSGALKVT------N--------GNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFK  117 (160)
T ss_dssp             HHHHHHHCTTCEEHHHHHHHCSSC------C--------SCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCCC------h--------hhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHH
Confidence            677775 46899999999987532      2        24667899999999999754  2343    59999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       118 ~~~~~~  123 (160)
T 3boq_A          118 QASEAH  123 (160)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            875543

>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=95.56  E-value=0.01  Score=40.71  Aligned_cols=63  Identities=11%  Similarity=0.121  Sum_probs=49.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        44 ~iL~~l~~~~~~~~~~la~~l~~--------------~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~  109 (147)
T 1z91_A           44 LALLLLWEHETLTVKKMGEQLYL--------------DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKE  109 (147)
T ss_dssp             HHHHHHHHHSEEEHHHHHHTTTC--------------CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGG
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCC--------------CcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence            37777888899999999987642              33578889999999999997543  344    58999999887


Q ss_pred             HHH
Q 033029          120 QVA  122 (129)
Q Consensus       120 ~iA  122 (129)
                      .+.
T Consensus       110 ~~~  112 (147)
T 1z91_A          110 KAV  112 (147)
T ss_dssp             GTT
T ss_pred             HHH
Confidence            653

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=95.54  E-value=0.092  Score=36.12  Aligned_cols=68  Identities=12%  Similarity=0.111  Sum_probs=50.6

Q ss_pred             HHHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|-..+.-++..-+.|..       .+..|+..||-              |..-+|.+|+.||+.|+|+..+..|-.+++
T Consensus        10 ~~~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~v--------------Sr~tvr~al~~L~~~Gli~~~~~~G~~V~~   75 (113)
T 3tqn_A           10 IYQQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQI--------------NPLTVSKAYQSLLDDNVIEKRRGLGMLVKA   75 (113)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECT
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCCeEEEeC
Confidence            355555556555555432       56788888865              346899999999999999998888999998


Q ss_pred             chHhhHHHH
Q 033029          113 SGQRDLDQV  121 (129)
Q Consensus       113 ~G~~~lD~i  121 (129)
                      ....++..+
T Consensus        76 ~~~~~~~~~   84 (113)
T 3tqn_A           76 GARQRLLTQ   84 (113)
T ss_dssp             THHHHHHHH
T ss_pred             CchHHHHHH
Confidence            877665543

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=95.53  E-value=0.033  Score=38.93  Aligned_cols=64  Identities=16%  Similarity=0.126  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhCCCchhhhHH-HhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           45 ASMARKIYLRQGLGVGSFRR-IYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~-~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      .|||++|+-+++..++.|.. .-+-              ..+.+=+-++-||+.|||+.+. .+=.||++|+..+...+.
T Consensus        19 fsiL~~L~~~~~~t~~~Lae~~l~~--------------drstvsrnl~~L~r~GlVe~~~-~Dl~LT~~G~~~l~~a~~   83 (95)
T 1bja_A           19 ATILITIAKKDFITAAEVREVHPDL--------------GNAVVNSNIGVLIKKGLVEKSG-DGLIITGEAQDIISNAAT   83 (95)
T ss_dssp             HHHHHHHHHSTTBCHHHHHHTCTTS--------------CHHHHHHHHHHHHTTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHhcc--------------cHHHHHHHHHHHHHCCCeecCC-CCeeeCHhHHHHHHHHHH
Confidence            68999999999999999998 4332              2245556689999999999443 356799999999988653

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=95.44  E-value=0.023  Score=39.67  Aligned_cols=44  Identities=20%  Similarity=0.235  Sum_probs=33.7

Q ss_pred             CCchhHHHHHHHHHHhCCceeecC---CCCc-----eeCcchHhhHHHHHHH
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQRDLDQVAGR  124 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~---~~GR-----~lT~~G~~~lD~iA~~  124 (129)
                      .-+.+.+-.+|+.||+.|||+...   .+|+     .||++|+..++.....
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            445678999999999999998652   2343     6999999999886654

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.44  E-value=0.037  Score=39.14  Aligned_cols=63  Identities=14%  Similarity=0.075  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD  119 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD  119 (129)
                      -.||..|--+|+..+..|.....    -|+        |..-+++-|+.||+.|+|+....+=-.||++|+..|.
T Consensus        16 ~~IL~~L~~~g~~s~~eLA~~l~----~gi--------S~~aVs~rL~~Le~~GLV~~~~rg~Y~LT~~G~~~l~   78 (111)
T 3b73_A           16 DRILEIIHEEGNGSPKELEDRDE----IRI--------SKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLN   78 (111)
T ss_dssp             HHHHHHHHHHSCBCHHHHHTSTT----CCS--------CHHHHHHHHHHHHHTTSEEECSTTCEEECHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHh----cCC--------CHHHHHHHHHHHHHCCCEEecCCceEEECchHHHHHH
Confidence            45787777779999999998651    122        4468999999999999999864333699999998875

>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=95.35  E-value=0.053  Score=37.74  Aligned_cols=62  Identities=18%  Similarity=0.219  Sum_probs=47.0

Q ss_pred             HHHHHHHHh------CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCc---eeCcchH
Q 033029           46 SMARKIYLR------QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGR---RITSSGQ  115 (129)
Q Consensus        46 SilR~lYl~------g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR---~lT~~G~  115 (129)
                      ++++.|...      +++-...|++.-+              =+.+-+++.|..||+.|||+.... .||   .||++|+
T Consensus        20 ~vL~~L~~~~~~~~g~~~s~~eLa~~l~--------------l~~stLsR~l~rLe~~GLV~r~~~~D~R~~v~LT~~G~   85 (96)
T 2obp_A           20 EVLLVLREAGIENGATPWSLPKIAKRAQ--------------LPMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGA   85 (96)
T ss_dssp             HHHHHHHHHTSSTTCCCCBHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHH
T ss_pred             HHHHHHHHHHhhCCCCCcCHHHHHHHhC--------------CchhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHHH
Confidence            567777665      6677777777533              356799999999999999986442 355   5999999


Q ss_pred             hhHHHH
Q 033029          116 RDLDQV  121 (129)
Q Consensus       116 ~~lD~i  121 (129)
                      ..+.+.
T Consensus        86 ~~l~~~   91 (96)
T 2obp_A           86 ALAAQL   91 (96)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            998875

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=95.34  E-value=0.039  Score=38.26  Aligned_cols=60  Identities=12%  Similarity=0.119  Sum_probs=45.8

Q ss_pred             hHHHHHHHHHHh---CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchHh
Q 033029           43 RAASMARKIYLR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQR  116 (129)
Q Consensus        43 R~ASilR~lYl~---g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~  116 (129)
                      +|..+|..|..+   +++.+..|+..+|-              |-+.++++|++|+++|||+...  .||..|+.....
T Consensus        10 ~al~iL~~la~~~~~~~~s~~ela~~~~i--------------~~~~v~~il~~L~~~Glv~~~~g~~ggy~L~~~~~~   74 (129)
T 2y75_A           10 YGLTIMIELAKKHGEGPTSLKSIAQTNNL--------------SEHYLEQLVSPLRNAGLVKSIRGAYGGYVLGSEPDA   74 (129)
T ss_dssp             HHHHHHHHHHHTTTSCCBCHHHHHHHTTS--------------CHHHHHHHHHHHHHTTSEEEC----CCEEESSCGGG
T ss_pred             HHHHHHHHHHhCCCCCcCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEecCCCCCceEeCCCHHH
Confidence            466677777764   57899999998754              3469999999999999999764  378899876543

>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=95.25  E-value=0.022  Score=38.31  Aligned_cols=53  Identities=11%  Similarity=0.058  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec----CCCCceeC
Q 033029           45 ASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE----PKGGRRIT  111 (129)
Q Consensus        45 ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~----~~~GR~lT  111 (129)
                      ..|+..++-.| ++.+..|+..+|-.              .+-+|.+|+.|++.|+|+..    +.+|+.+.
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lgvs--------------~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~   78 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLNIK--------------VNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIY   78 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSC--------------HHHHHHHHHHHHHHTSCEEEEEC---CCCCEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEEecccCCCceEEE
Confidence            45888888778 89999999988753              46899999999999999987    66675554

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

Probab=95.24  E-value=0.045  Score=38.61  Aligned_cols=85  Identities=14%  Similarity=0.178  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHH
Q 033029           14 EFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHIL   91 (129)
Q Consensus        14 ~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~l   91 (129)
                      .+...+.+.|+..|    +.+  +.|.      +|..||..  |++.++.|....|-.              .+-+=.++
T Consensus        19 ~l~~~~~~~l~~~g----Lt~--~q~~------vL~~L~~~~~~~~t~~eLa~~l~~~--------------~~tvs~~v   72 (147)
T 4b8x_A           19 ILLGEVDAVVKPYG----LTF--ARYE------ALVLLTFSKSGELPMSKIGERLMVH--------------PTSVTNTV   72 (147)
T ss_dssp             HHHHHHHHHHGGGT----CCH--HHHH------HHHHHHTSGGGEEEHHHHHHHHTCC--------------HHHHHHHH
T ss_pred             HHHHHHHHHHHHcC----CCH--HHHH------HHHHHHHCCCCCcCHHHHHHHHCCC--------------HHHHHHHH
Confidence            34455566666543    222  2344      67777764  578999999987653              23566689


Q ss_pred             HHHHhCCceeecC--CCCc----eeCcchHhhHHHHHHH
Q 033029           92 QQLQNMNIIDIEP--KGGR----RITSSGQRDLDQVAGR  124 (129)
Q Consensus        92 qqLE~~g~vek~~--~~GR----~lT~~G~~~lD~iA~~  124 (129)
                      ..||+.|||++.+  ..+|    .||++|+..++.+...
T Consensus        73 ~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~  111 (147)
T 4b8x_A           73 DRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEAATRD  111 (147)
T ss_dssp             HHHHHTTSEEEEECC----CEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHhCCCEEEeecCCcCceeEEEECHHHHHHHHHHHHH
Confidence            9999999998654  3455    3899999999987654

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=95.18  E-value=0.027  Score=40.09  Aligned_cols=63  Identities=21%  Similarity=0.212  Sum_probs=48.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+ .|+..++.|....+|             -|.+.+-..|+.||+.|||++...  .+|    .||++|+..+.
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            3677777 899999999987631             255789999999999999986542  233    69999998776


Q ss_pred             HHH
Q 033029          120 QVA  122 (129)
Q Consensus       120 ~iA  122 (129)
                      .+.
T Consensus       105 ~l~  107 (131)
T 1yyv_A          105 XVA  107 (131)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=94.98  E-value=0.2  Score=35.08  Aligned_cols=61  Identities=15%  Similarity=0.119  Sum_probs=46.1

Q ss_pred             HHHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+..++.--+.|..       .+..|+..||-              |..-+|.+|+.|++.|+|+..+..|-.+++
T Consensus        14 ~~~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   79 (125)
T 3neu_A           14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAV--------------NPNTVSRAYQELERAGYIYAKRGMGSFVTS   79 (125)
T ss_dssp             HHHHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCeEEEecCCEEEEec
Confidence            455556666655555532       47788888875              346999999999999999998888999988


Q ss_pred             ch
Q 033029          113 SG  114 (129)
Q Consensus       113 ~G  114 (129)
                      .-
T Consensus        80 ~~   81 (125)
T 3neu_A           80 DK   81 (125)
T ss_dssp             CH
T ss_pred             Cc
Confidence            54

>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=94.90  E-value=0.053  Score=40.68  Aligned_cols=65  Identities=11%  Similarity=0.135  Sum_probs=50.6

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~lD  119 (129)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+...+  .+|    .||++|+..++
T Consensus        52 ~iL~~L~~~~~~t~~eLa~~l~i--------------~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  117 (207)
T 2fxa_A           52 HILWIAYQLNGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFW  117 (207)
T ss_dssp             HHHHHHHHHTSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHH
Confidence            37788888899999999998764              23466779999999999987553  344    59999999999


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      .+...
T Consensus       118 ~~~~~  122 (207)
T 2fxa_A          118 SLLEE  122 (207)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

>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=94.79  E-value=0.041  Score=41.97  Aligned_cols=54  Identities=11%  Similarity=0.167  Sum_probs=43.8

Q ss_pred             CCch--hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029           56 GLGV--GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG  123 (129)
Q Consensus        56 ~vGV--~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~  123 (129)
                      ++..  ..|+...|-              |.+-+..+|+.||+.|||+..++++=.||++|+..+..+..
T Consensus        22 ~~~~~~~~La~~l~v--------------s~~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~~~~~~~   77 (230)
T 1fx7_A           22 GVTPLRARIAERLDQ--------------SGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMR   77 (230)
T ss_dssp             TSCCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCccEEECHHHHHHHHHHHH
Confidence            4556  888887643              33578899999999999999887778899999999887653

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=94.69  E-value=0.16  Score=35.70  Aligned_cols=60  Identities=15%  Similarity=0.117  Sum_probs=46.5

Q ss_pred             HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+..+|.--+.|.      + .+..|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++
T Consensus        12 ~~~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~g~G~~V~~   77 (126)
T 3by6_A           12 VYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKI--------------NPNTVAKAYKELEAQKVIRTIPGKGTFITG   77 (126)
T ss_dssp             HHHHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECS
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCCeEEEcc
Confidence            46666666666555553      2 67888888875              346899999999999999998888999988


Q ss_pred             c
Q 033029          113 S  113 (129)
Q Consensus       113 ~  113 (129)
                      .
T Consensus        78 ~   78 (126)
T 3by6_A           78 N   78 (126)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=94.66  E-value=0.11  Score=38.17  Aligned_cols=72  Identities=14%  Similarity=0.145  Sum_probs=52.6

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CC-----ceeCcchHhh
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GG-----RRITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~G-----R~lT~~G~~~  117 (129)
                      .||.-|. .+|.--..|.+.+...      -.++...|-+-|-..|+.||+.|||+....   +|     -.||++|+..
T Consensus         6 ~iL~lL~-~~~~~gyel~~~l~~~------~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~   78 (179)
T 1yg2_A            6 VILTVLS-TRDATGYDITKEFSAS------IGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSA   78 (179)
T ss_dssp             HHHHHHH-HCCBCHHHHHHHHTTG------GGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHH
T ss_pred             HHHHHHh-cCCCCHHHHHHHHHHH------hCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHH
Confidence            3566665 4888888888888643      234556777899999999999999986431   22     4699999999


Q ss_pred             HHHHHHH
Q 033029          118 LDQVAGR  124 (129)
Q Consensus       118 lD~iA~~  124 (129)
                      +.+...+
T Consensus        79 l~~~~~~   85 (179)
T 1yg2_A           79 LGEWFDQ   85 (179)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhC
Confidence            9886544

>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=94.65  E-value=0.21  Score=32.89  Aligned_cols=60  Identities=15%  Similarity=0.206  Sum_probs=45.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC---ceeCcchHhhHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQ  120 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G---R~lT~~G~~~lD~  120 (129)
                      .|++.| .+|+..++.|....|-.              .+.+.+.|+.||+.|+|+...++.   -.||+.+...+=+
T Consensus        27 ~Il~~L-~~~~~~~~ela~~l~is--------------~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~   89 (102)
T 3pqk_A           27 MLVCTL-VEGEFSVGELEQQIGIG--------------QPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVN   89 (102)
T ss_dssp             HHHHHH-HTCCBCHHHHHHHHTCC--------------TTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHH
T ss_pred             HHHHHH-HhCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHH
Confidence            588888 57999999999988652              247899999999999998776432   4688876655433

>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=94.59  E-value=0.045  Score=41.06  Aligned_cols=51  Identities=22%  Similarity=0.251  Sum_probs=41.8

Q ss_pred             CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      +....|+..||-              |...+|.+|+.||..|||+..+..|-.+++-...++..+
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            346778888875              457999999999999999998888999988777666554

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=94.50  E-value=0.069  Score=37.24  Aligned_cols=70  Identities=17%  Similarity=0.158  Sum_probs=47.4

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCc-----eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR-----~lT~~G~~~l  118 (129)
                      ||--|. .+|.---.|.+....   .|     +..-|.+.|-.+|+.||+.|||+...   .+||     .||++|+..|
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---HG-----FTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGLEQL   84 (115)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHHH---TT-----CTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHH---cC-----CCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHHHHH
Confidence            555554 566544455555443   12     34556788999999999999998642   2342     4999999999


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      +......
T Consensus        85 ~~~~~~~   91 (115)
T 4esb_A           85 EEFKQSW   91 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876553

>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=94.36  E-value=0.076  Score=43.48  Aligned_cols=66  Identities=9%  Similarity=0.200  Sum_probs=45.6

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc----eeCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR----~lT~~G~~~l  118 (129)
                      ||+.|+-+  +++.+..|+...+              -+.+-+=.+|+.||+.|||++.  ++..|    .||++|+..+
T Consensus       409 vl~~l~~~~~~~~~~~~l~~~~~--------------~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~  474 (487)
T 1hsj_A          409 ILNHILRSESNEISSKEIAKCSE--------------FKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  474 (487)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHSSC--------------CCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHhCCCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHH
Confidence            55566666  5666666665422              2334566789999999999864  34455    3799999999


Q ss_pred             HHHHHHhh
Q 033029          119 DQVAGRIV  126 (129)
Q Consensus       119 D~iA~~i~  126 (129)
                      +++...+.
T Consensus       475 ~~~~~~~~  482 (487)
T 1hsj_A          475 QKLISELE  482 (487)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHHHHH
Confidence            98877653

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=94.36  E-value=0.035  Score=39.16  Aligned_cols=68  Identities=15%  Similarity=0.096  Sum_probs=48.0

Q ss_pred             HHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           41 YVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        41 Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      |-..+.-++..-+.|..       .+..|+..||-              |..-+|.+|+.||+.|+|+..+..|-.+++.
T Consensus        13 ~~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~~~G~~V~~~   78 (126)
T 3ic7_A           13 YLQIADRICDDILLGQYEEEGRIPSVREYASIVEV--------------NANTVMRSYEYLQSQEVIYNKRGIGFFVASG   78 (126)
T ss_dssp             TTHHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-C--------------CSGGGHHHHHHHHTTTSEEEETTTEEEECTT
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEEcCCccEEccC
Confidence            44555566665555533       34455555543              4468999999999999999998889999998


Q ss_pred             hHhhHHHHH
Q 033029          114 GQRDLDQVA  122 (129)
Q Consensus       114 G~~~lD~iA  122 (129)
                      ....+..+.
T Consensus        79 ~~~~~~~~~   87 (126)
T 3ic7_A           79 AKMLIHSLR   87 (126)
T ss_dssp             HHHHHHHHH
T ss_pred             cHHHHHHHH
Confidence            876665543

>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=94.35  E-value=0.057  Score=41.18  Aligned_cols=63  Identities=14%  Similarity=0.242  Sum_probs=46.4

Q ss_pred             HHHHHHHh--CCCch--hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHH
Q 033029           47 MARKIYLR--QGLGV--GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA  122 (129)
Q Consensus        47 ilR~lYl~--g~vGV--~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA  122 (129)
                      +|+.||.-  .++.+  ..|+...|-.              .+-+..+++.||+.|||+..++.+=.||++|+....++.
T Consensus        11 yL~~i~~l~~~~~~~~~~~la~~l~vs--------------~~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~~~~~~   76 (226)
T 2qq9_A           11 YLRTIYELEEEGVTPLRARIAERLEQS--------------GPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVM   76 (226)
T ss_dssp             HHHHHHHHHHHTCCCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEECTTSBEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCccHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEeCCCCeEECHHHHHHHHHHH
Confidence            45555542  23444  7888876542              345677999999999999987777899999999988776


Q ss_pred             H
Q 033029          123 G  123 (129)
Q Consensus       123 ~  123 (129)
                      .
T Consensus        77 ~   77 (226)
T 2qq9_A           77 R   77 (226)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=94.32  E-value=0.21  Score=35.37  Aligned_cols=65  Identities=18%  Similarity=0.170  Sum_probs=46.6

Q ss_pred             HHHHHHHhCC-CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYLRQG-LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~g~-vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      +|..|+-.++ +....|+...|-.              .+-+=.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~~~--------------~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~  101 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIGIE--------------QPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIE  101 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCcC--------------HHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHH
Confidence            6777776544 5557788876542              245667899999999998644  4455    47999999998


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+...+
T Consensus       102 ~~~~~~  107 (151)
T 4aik_A          102 QVDGVI  107 (151)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

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

Probab=94.15  E-value=0.07  Score=38.37  Aligned_cols=64  Identities=14%  Similarity=0.180  Sum_probs=43.4

Q ss_pred             HHHHHHHhCC---CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCc----eeCcchHhh
Q 033029           47 MARKIYLRQG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGR----RITSSGQRD  117 (129)
Q Consensus        47 ilR~lYl~g~---vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR----~lT~~G~~~  117 (129)
                      ||..|+-.++   +.+..|....|-.      +        +-+-.+|+.||+.|||+...+  .+|    .||++|+..
T Consensus        74 iL~~L~~~~~~~~~t~~eLa~~l~is------~--------~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  139 (181)
T 2fbk_A           74 LLLTLYRSAPPEGLRPTELSALAAIS------G--------PSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  139 (181)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSCC------S--------GGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHCCC------H--------HHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHH
Confidence            5666666654   7777777765421      1        244558899999999997542  233    699999999


Q ss_pred             HHHHHHH
Q 033029          118 LDQVAGR  124 (129)
Q Consensus       118 lD~iA~~  124 (129)
                      ++.+...
T Consensus       140 ~~~~~~~  146 (181)
T 2fbk_A          140 VTHLLPA  146 (181)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887554

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=94.13  E-value=0.062  Score=39.05  Aligned_cols=71  Identities=11%  Similarity=0.025  Sum_probs=46.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CCc-----eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGR-----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~GR-----~lT~~G~~~l  118 (129)
                      ||.-|. .+|.--..|.+..+..-.      .+..-+-+.+-.+|+.||+.|||+....   +|+     .||++|+..+
T Consensus        46 IL~~L~-~~~~~gyeI~~~l~~~~~------~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l  118 (145)
T 1xma_A           46 ILSLLI-EGDSYGYEISKNIRIKTD------ELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYY  118 (145)
T ss_dssp             HHHHHH-HCCEEHHHHHHHHHHHHT------TSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHHHHhhC------CccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECHHHHHHH
Confidence            777775 467655555554432211      1123456789999999999999986531   232     7999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      ......
T Consensus       119 ~~~~~~  124 (145)
T 1xma_A          119 KQKCEE  124 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886554

>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=94.11  E-value=0.041  Score=41.14  Aligned_cols=52  Identities=21%  Similarity=0.256  Sum_probs=42.6

Q ss_pred             CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHH
Q 033029           57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA  122 (129)
Q Consensus        57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA  122 (129)
                      +....|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-...++..+-
T Consensus        36 L~e~~La~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~el~   87 (218)
T 3sxy_A           36 LNVRELSEKLGI--------------SFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEKFIRETI   87 (218)
T ss_dssp             ECHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEEETTTEEEECCCCHHHHHHHH
T ss_pred             eCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCHHHHHHHH
Confidence            456788888875              4579999999999999999988889999987777666543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=94.01  E-value=0.21  Score=32.57  Aligned_cols=66  Identities=12%  Similarity=0.091  Sum_probs=49.1

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC---ceeCcchHhhHHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVA  122 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G---R~lT~~G~~~lD~iA  122 (129)
                      .|++.|.- |++.++.|....|-              |.+-+.+-|+.||+.|+|+...+|.   -.||+.+-..+-...
T Consensus        27 ~Il~~L~~-~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l   91 (98)
T 3jth_A           27 QILCMLHN-QELSVGELCAKLQL--------------SQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLL   91 (98)
T ss_dssp             HHHHHTTT-SCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHH
T ss_pred             HHHHHHhc-CCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHH
Confidence            47777654 99999999998754              3468899999999999999876432   358888776665555


Q ss_pred             HHhh
Q 033029          123 GRIV  126 (129)
Q Consensus       123 ~~i~  126 (129)
                      .+++
T Consensus        92 ~~~~   95 (98)
T 3jth_A           92 HSLY   95 (98)
T ss_dssp             HHHC
T ss_pred             HHHh
Confidence            4443

>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=93.96  E-value=0.099  Score=36.03  Aligned_cols=43  Identities=14%  Similarity=0.244  Sum_probs=34.2

Q ss_pred             chhHHHHHHHHHHhCCceeecCCCC---ceeCcchHhhHHHHHHHh
Q 033029           83 SGAIARHILQQLQNMNIIDIEPKGG---RRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~~G---R~lT~~G~~~lD~iA~~i  125 (129)
                      +-+.|=-+|+.||+.|||+...+..   -.||++|+..|.+...+.
T Consensus        43 s~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~   88 (99)
T 2co5_A           43 SDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFF   88 (99)
T ss_dssp             CHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhH
Confidence            4467778999999999999765223   379999999999877654

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=93.93  E-value=0.22  Score=35.25  Aligned_cols=47  Identities=15%  Similarity=0.060  Sum_probs=38.5

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      ....|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++.....+
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            56678887765              346899999999999999998888999998765554

>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=93.81  E-value=0.063  Score=41.13  Aligned_cols=67  Identities=16%  Similarity=0.166  Sum_probs=49.4

Q ss_pred             HHhHHHHHHHHHHhC------CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           41 YVRAASMARKIYLRQ------GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        41 Y~R~ASilR~lYl~g------~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      +-.++..+|.-=+.|      .+....|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-.
T Consensus        30 ~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~   95 (239)
T 2hs5_A           30 TTRVAGILRDAIIDGTFRPGARLSEPDICAALDV--------------SRNTVREAFQILIEDRLVAHELNRGVFVRVPT   95 (239)
T ss_dssp             HHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCCC
T ss_pred             HHHHHHHHHHHHHcCCCCCcCEeCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEeCCC
Confidence            344444555444444      2456778888875              45689999999999999999988899999887


Q ss_pred             HhhHHHH
Q 033029          115 QRDLDQV  121 (129)
Q Consensus       115 ~~~lD~i  121 (129)
                      ..++..+
T Consensus        96 ~~~~~el  102 (239)
T 2hs5_A           96 AEDITEL  102 (239)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766654

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=93.76  E-value=0.087  Score=36.90  Aligned_cols=69  Identities=25%  Similarity=0.279  Sum_probs=45.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCC-----ceeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~G-----R~lT~~G~~~l  118 (129)
                      ||--|. .+|.---.|.+....   .|     +..-+-+.+-.+|+.||+.|||+...   .+|     -.||++|+..|
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---QG-----FTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAEL   88 (116)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHT---TS-----CSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHH
T ss_pred             HHHHHh-cCCCCHHHHHHHHHH---cC-----CCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHH
Confidence            555554 456533455555543   22     33556678999999999999998642   234     25999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      .....+
T Consensus        89 ~~~~~~   94 (116)
T 3hhh_A           89 ADFWQR   94 (116)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886654

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

Probab=93.75  E-value=0.18  Score=39.64  Aligned_cols=64  Identities=13%  Similarity=0.245  Sum_probs=52.1

Q ss_pred             hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcchHhhHHH
Q 033029           43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQRDLDQ  120 (129)
Q Consensus        43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~G~~~lD~  120 (129)
                      ....||..|.-++++.+..|+...|-              +.+-+.+.|+.||+.|||++... ..-.||++|+.....
T Consensus       153 ~~~~IL~~L~~~~~~s~~eLA~~lgl--------------sksTv~r~L~~Le~~GlV~r~~r~~~~~LT~~G~~l~~~  217 (244)
T 2wte_A          153 EEMKLLNVLYETKGTGITELAKMLDK--------------SEKTLINKIAELKKFGILTQKGKDRKVELNELGLNVIKL  217 (244)
T ss_dssp             HHHHHHHHHHHHTCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCccEEEECHHHHHHHHH
Confidence            35568888888999999999999874              34578889999999999998642 346899999997654

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

Probab=93.74  E-value=0.11  Score=36.77  Aligned_cols=64  Identities=16%  Similarity=0.225  Sum_probs=40.7

Q ss_pred             HHHHHHHHhC-----CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec-CCCCc----eeCcchH
Q 033029           46 SMARKIYLRQ-----GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-PKGGR----RITSSGQ  115 (129)
Q Consensus        46 SilR~lYl~g-----~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~-~~~GR----~lT~~G~  115 (129)
                      ++|..|+..+     ++.++.|....|-.              .+-+=.+++.||+.|||+.. +..+|    .||++|+
T Consensus        37 ~vL~~l~~~~~~~~~~~t~~eLa~~l~~~--------------~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~  102 (148)
T 4fx0_A           37 STLAVISLSEGSAGIDLTMSELAARIGVE--------------RTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGR  102 (148)
T ss_dssp             HHHHHHHC---------CHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSBC-----------CCBCHHHH
T ss_pred             HHHHHHHHhcCCCCCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHH
Confidence            3677777653     46778888876542              23566789999999999643 23344    5899999


Q ss_pred             hhHHHHHH
Q 033029          116 RDLDQVAG  123 (129)
Q Consensus       116 ~~lD~iA~  123 (129)
                      ..++++..
T Consensus       103 ~~~~~~~~  110 (148)
T 4fx0_A          103 AALQKAVP  110 (148)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99988754

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=93.68  E-value=0.12  Score=37.53  Aligned_cols=64  Identities=14%  Similarity=0.233  Sum_probs=50.4

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~  120 (129)
                      ..||+.|. +++..++.|....|-              |.+-+.+-|+.||++|||+...+ ||    .||++|...+-.
T Consensus        61 ~~IL~~L~-~~~~t~~eLa~~lgl--------------s~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~lt~~~~~~l~~  124 (151)
T 3f6v_A           61 RRLVQLLT-SGEQTVNNLAAHFPA--------------SRSAISQHLRVLTEAGLVTPRKD-GRFRYYRLDPQGLAQLRA  124 (151)
T ss_dssp             HHHHHHGG-GCCEEHHHHHTTSSS--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHHHHHHH
Confidence            35888887 899999999997654              34688999999999999997653 53    699999877766


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +..+
T Consensus       125 ~l~~  128 (151)
T 3f6v_A          125 LFDS  128 (151)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>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=93.63  E-value=0.075  Score=40.80  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=42.7

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      .+....|+..||-              |..-+|.+|+.||..|+|+..+.+|-.+++-...++..+
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            4677888888875              456899999999999999999888999998877665543

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=93.60  E-value=0.1  Score=36.53  Aligned_cols=44  Identities=18%  Similarity=0.357  Sum_probs=33.5

Q ss_pred             CCchhHHHHHHHHHHhCCceeecC---CCC-----ceeCcchHhhHHHHHHH
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDLDQVAGR  124 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~---~~G-----R~lT~~G~~~lD~iA~~  124 (129)
                      .-|-+.+-.+|+.||+.|||+...   .+|     -.||++|+..|......
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            456678999999999999998643   234     25999999999886554

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.39  E-value=0.06  Score=37.25  Aligned_cols=71  Identities=13%  Similarity=0.034  Sum_probs=46.8

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCch-hHHHHHHHHHHhCCceeecCC--CC-----ceeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSG-AIARHILQQLQNMNIIDIEPK--GG-----RRITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg-~iiR~~lqqLE~~g~vek~~~--~G-----R~lT~~G~~~l  118 (129)
                      ||.-|. .+|.-...|.+....   .|.-.  + .-+- +.+-.+|+.||+.|||+....  .|     -.||++|+..+
T Consensus        18 IL~~L~-~~~~~gyel~~~l~~---~g~~~--~-~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~~G~~~l   90 (118)
T 2esh_A           18 ILLLVA-EKPSHGYELAERLAE---FGIEI--P-GIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYL   90 (118)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHT---TCCSS--T-TCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHH---hCCcc--c-CCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHHH
Confidence            666664 367666666666643   22110  1 1344 568889999999999986531  23     27999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      ......
T Consensus        91 ~~~~~~   96 (118)
T 2esh_A           91 REILRS   96 (118)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886554

>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=93.30  E-value=0.42  Score=32.09  Aligned_cols=84  Identities=14%  Similarity=0.156  Sum_probs=58.3

Q ss_pred             hHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHH
Q 033029           13 HEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHIL   91 (129)
Q Consensus        13 ~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~l   91 (129)
                      ..|...+.+.++..|    +.|.        -..++.-|++ .+|+.+..|+...|-              +.+-+..+|
T Consensus         9 ~~~~~~~~~~~~~~g----l~~~--------~~~il~~L~~~~~~~t~~ela~~l~~--------------~~stvs~~l   62 (152)
T 1ku9_A            9 KLIIELFSELAKIHG----LNKS--------VGAVYAILYLSDKPLTISDIMEELKI--------------SKGNVSMSL   62 (152)
T ss_dssp             HHHHHHHHHHHHHTT----CCHH--------HHHHHHHHHHCSSCEEHHHHHHHHTC--------------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC----CChh--------HHHHHHHHHHcCCCCCHHHHHHHHCc--------------CHHHHHHHH
Confidence            456677777777654    3332        2346666675 689999999999874              335788899


Q ss_pred             HHHHhCCceeecC--CC--CceeCcchHhhHHHHH
Q 033029           92 QQLQNMNIIDIEP--KG--GRRITSSGQRDLDQVA  122 (129)
Q Consensus        92 qqLE~~g~vek~~--~~--GR~lT~~G~~~lD~iA  122 (129)
                      +.||+.|||+..+  ..  ...++..|...+..+.
T Consensus        63 ~~L~~~G~v~r~~~~~d~r~~~~~~~~~~~~~~~~   97 (152)
T 1ku9_A           63 KKLEELGFVRKVWIKGERKNYYEAVDGFSSIKDIA   97 (152)
T ss_dssp             HHHHHTTSEEEECCTTCSSCEEEECCHHHHHHHHH
T ss_pred             HHHHHCCCEEEEecCCCceEEEeecchHHHHHHHH
Confidence            9999999999763  22  3467777765555444

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=93.15  E-value=0.1  Score=34.86  Aligned_cols=43  Identities=14%  Similarity=0.228  Sum_probs=35.5

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      .+..|+..||-.              .+.+|.+|+.||+.|+|+..+..|..+++..
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            678888888753              3589999999999999998887788887654

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=93.05  E-value=0.14  Score=35.59  Aligned_cols=45  Identities=13%  Similarity=0.095  Sum_probs=35.1

Q ss_pred             CCchhHHHHHHHHHHhCCceeecC----CCC-----ceeCcchHhhHHHHHHHh
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEP----KGG-----RRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~----~~G-----R~lT~~G~~~lD~iA~~i  125 (129)
                      ..|-+.|-.+|+.||+.|||+...    .+|     -.||++|+..+.....+.
T Consensus        53 ~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~  106 (115)
T 2dql_A           53 RLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQAEDLARLW  106 (115)
T ss_dssp             ECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            456678899999999999998642    124     379999999998876553

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=92.88  E-value=0.26  Score=33.67  Aligned_cols=64  Identities=9%  Similarity=0.082  Sum_probs=49.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCcchHhhHHHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA  122 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~~G~~~lD~iA  122 (129)
                      .|++.|. +||+.++.|....|-              |.+-+.+-|+.||+.|+|+....|   --.||+.|...+....
T Consensus        22 ~Il~~L~-~~~~~~~eLa~~l~i--------------s~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~   86 (118)
T 3f6o_A           22 AVLGRLS-RGPATVSELAKPFDM--------------ALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWL   86 (118)
T ss_dssp             HHHHHHH-TCCEEHHHHHTTCCS--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHH
Confidence            3788887 899999999987643              345788999999999999876542   2368999988776554


Q ss_pred             HH
Q 033029          123 GR  124 (129)
Q Consensus       123 ~~  124 (129)
                      ..
T Consensus        87 ~~   88 (118)
T 3f6o_A           87 AE   88 (118)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=92.82  E-value=0.54  Score=35.98  Aligned_cols=60  Identities=10%  Similarity=-0.047  Sum_probs=48.4

Q ss_pred             HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029           42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ  115 (129)
Q Consensus        42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~  115 (129)
                      -|+..||..|.-.+ ++++..|....|-              +.+-+.++|+.||+.|||+++.++.-.|+++..
T Consensus         8 ~r~l~iL~~l~~~~~~~~~~ela~~~gl--------------~~stv~r~l~~L~~~G~v~~~~~~~Y~lg~~~~   68 (249)
T 1mkm_A            8 KKAFEILDFIVKNPGDVSVSEIAEKFNM--------------SVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLI   68 (249)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECTHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEECCCCcEEECHHHH
Confidence            47888999887765 7999999998754              336788999999999999988545678888654

>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=92.74  E-value=0.53  Score=32.39  Aligned_cols=60  Identities=18%  Similarity=0.267  Sum_probs=44.0

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~  120 (129)
                      .|+..|.-+++..+..|....|-              |.+-+.+.|+.||+.|+|+...+ ||    .||+.+...+-.
T Consensus        46 ~IL~~L~~~~~~s~~eLa~~l~i--------------s~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~~~~~~~~  109 (122)
T 1u2w_A           46 KITYALCQDEELCVCDIANILGV--------------TIANASHHLRTLYKQGVVNFRKE-GKLALYSLGDEHIRQIMM  109 (122)
T ss_dssp             HHHHHHHHSSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEC-----CCEEEESCHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEE-CCEEEEEECHHHHHHHHH
Confidence            47777766799999999998764              33578899999999999998754 54    688887554433

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

Probab=92.74  E-value=0.31  Score=32.31  Aligned_cols=53  Identities=15%  Similarity=0.178  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHh------CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029           43 RAASMARKIYLR------QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI  110 (129)
Q Consensus        43 R~ASilR~lYl~------g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l  110 (129)
                      |...|+--|--.      +|+.|..++..+|=              |-+-||+-|..||+.|+|+.+. +||.+
T Consensus         5 r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgv--------------S~~TVrr~L~~Le~kG~I~R~~-ggr~~   63 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGAPVKTRDIADAAGL--------------SIYQVRLYLEQLHDVGVLEKVN-AGKGV   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEES-CSSSS
T ss_pred             HHHHHHHHHHHHHhhccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEecC-CCCCc
Confidence            455566666666      89999999998874              2346999999999999999987 56654

>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=92.71  E-value=0.088  Score=37.10  Aligned_cols=61  Identities=13%  Similarity=0.172  Sum_probs=45.1

Q ss_pred             HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+.-+|.-=+.|-      + .+..|+..||-              |..-+|.+|++||..|+|+..+..|-.+++
T Consensus        15 lY~QI~~~i~~~I~~G~l~pG~~LPser~La~~~gV--------------Sr~tVReAl~~L~~eGlv~~~~g~G~~V~~   80 (134)
T 4ham_A           15 IYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGV--------------NPNTVSKAYQELERQEVIITVKGKGTFIAN   80 (134)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCcEEEEeC
Confidence            46666666666655552      2 45678888875              346899999999999999998877887776


Q ss_pred             ch
Q 033029          113 SG  114 (129)
Q Consensus       113 ~G  114 (129)
                      ..
T Consensus        81 ~~   82 (134)
T 4ham_A           81 QT   82 (134)
T ss_dssp             CS
T ss_pred             Cc
Confidence            43

>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=92.69  E-value=0.26  Score=33.19  Aligned_cols=50  Identities=12%  Similarity=0.109  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG  106 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~  106 (129)
                      ||..|+-++|+.+..|....+-.  +|.        +.+-+-.+|+.||+.|||+..+++
T Consensus        15 vL~~L~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~R~~~~   64 (126)
T 1sd4_A           15 VMNIIWDKKSVSANEIVVEIQKY--KEV--------SDKTIRTLITRLYKKEIIKRYKSE   64 (126)
T ss_dssp             HHHHHHHSSSEEHHHHHHHHHTT--SCC--------CHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHhcCCCCHHHHHHHHhhc--CCC--------ChhhHHHHHHHHHHCCceEEEeCC
Confidence            77888889999999999998742  232        235788999999999999987653

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=92.49  E-value=0.16  Score=34.32  Aligned_cols=81  Identities=15%  Similarity=0.114  Sum_probs=58.2

Q ss_pred             ChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHH
Q 033029           11 SPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHI   90 (129)
Q Consensus        11 ~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~   90 (129)
                      +.++..+.++..+|--+        ||    +| ..|+..|. .|++.+..|....|-              |.+-+.+.
T Consensus         7 ~~~~~~~~~~~~~~al~--------~~----~r-~~IL~~L~-~~~~s~~eLa~~lgi--------------s~stvs~~   58 (108)
T 2kko_A            7 RKAALLDQVARVGKALA--------NG----RR-LQILDLLA-QGERAVEAIATATGM--------------NLTTASAN   58 (108)
T ss_dssp             THHHHHHHHHHHHHHHT--------TS----TT-HHHHHHHT-TCCEEHHHHHHHHTC--------------CHHHHHHH
T ss_pred             cChhhHHHHHHHHHHhC--------CH----HH-HHHHHHHH-cCCcCHHHHHHHHCc--------------CHHHHHHH
Confidence            34566777888888653        44    22 24777665 699999999998764              23588999


Q ss_pred             HHHHHhCCceeecCCCCc----eeCcchHhhHHH
Q 033029           91 LQQLQNMNIIDIEPKGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        91 lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~  120 (129)
                      |+.||+.|+|+...+ ||    .||+++...+=+
T Consensus        59 L~~L~~~GlV~~~~~-gr~~~y~l~~~~~~~l~~   91 (108)
T 2kko_A           59 LQALKSGGLVEARRE-GTRQYYRIAGEDVARLFA   91 (108)
T ss_dssp             HHHHHHHTSEEEEEE-TTEEEEEESCHHHHHHHH
T ss_pred             HHHHHHCCCeEEEEe-CCEEEEEEChHHHHHHHH
Confidence            999999999987654 44    689888655433

>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=92.43  E-value=0.65  Score=30.92  Aligned_cols=77  Identities=14%  Similarity=0.212  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHH
Q 033029           13 HEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ   92 (129)
Q Consensus        13 ~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lq   92 (129)
                      ++-.+.++..++--+        ||    +| ..|+..|. +++..++.|....|-              |.+-+.+.|+
T Consensus        10 ~~~~~~~~~~~~~l~--------~~----~r-~~IL~~L~-~~~~~~~ela~~l~i--------------s~stvs~~L~   61 (106)
T 1r1u_A           10 TDTLERVTEIFKALG--------DY----NR-IRIMELLS-VSEASVGHISHQLNL--------------SQSNVSHQLK   61 (106)
T ss_dssp             HHHHHHHHHHHHHTC--------SH----HH-HHHHHHHH-HCCBCHHHHHHHHTC--------------CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC--------CH----HH-HHHHHHHH-hCCCCHHHHHHHHCc--------------CHHHHHHHHH
Confidence            444566777777542        43    22 35787777 899999999998764              2357899999


Q ss_pred             HHHhCCceeecCCCCc----eeCcchHhhH
Q 033029           93 QLQNMNIIDIEPKGGR----RITSSGQRDL  118 (129)
Q Consensus        93 qLE~~g~vek~~~~GR----~lT~~G~~~l  118 (129)
                      .||+.|+|+...+ ||    .||+.+-..+
T Consensus        62 ~L~~~Glv~~~~~-gr~~~y~l~~~~~~~~   90 (106)
T 1r1u_A           62 LLKSVHLVKAKRQ-GQSMIYSLDDIHVATM   90 (106)
T ss_dssp             HHHHTTSEEEEEE-TTEEEEEESSHHHHHH
T ss_pred             HHHHCCCeEEEEe-CCEEEEEEChHHHHHH
Confidence            9999999987654 44    5787775433

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=92.28  E-value=0.14  Score=37.11  Aligned_cols=46  Identities=15%  Similarity=0.112  Sum_probs=35.6

Q ss_pred             cCCchhHHHHHHHHHHhCCceeecC----CCC-----ceeCcchHhhHHHHHHHh
Q 033029           80 CKSSGAIARHILQQLQNMNIIDIEP----KGG-----RRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        80 ~~asg~iiR~~lqqLE~~g~vek~~----~~G-----R~lT~~G~~~lD~iA~~i  125 (129)
                      ..-+-+.|-.+|+.||+.|||+...    .+|     -.||++|+..+.....+.
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            3556678999999999999998642    134     379999999998876553

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

Probab=92.26  E-value=0.19  Score=32.21  Aligned_cols=45  Identities=13%  Similarity=0.141  Sum_probs=36.7

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      .|+..|.-.+++.+..|+..+|-              |.+-+|+.|+.||+.|+|+...
T Consensus         4 ~Il~~L~~~~~~s~~eLa~~lgv--------------s~~tv~r~L~~L~~~GlI~~~~   48 (81)
T 2htj_A            4 EILEFLNRHNGGKTAEIAEALAV--------------TDYQARYYLLLLEKAGMVQRSP   48 (81)
T ss_dssp             HHHHHHHHSCCCCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEec
Confidence            46777776789999999999865              3357999999999999998543

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

Probab=92.20  E-value=0.26  Score=34.42  Aligned_cols=59  Identities=10%  Similarity=0.079  Sum_probs=43.4

Q ss_pred             HHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc------eeCcchH
Q 033029           46 SMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR------RITSSGQ  115 (129)
Q Consensus        46 SilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR------~lT~~G~  115 (129)
                      .||..|+- .+|+.+..|....+..  ++.        +.+-+-.+|+.||+.|||+..++ ||      .||++|.
T Consensus        13 ~vL~~L~~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~r~~~-~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A           13 AVMDHLWSRTEPQTVRQVHEALSAR--RDL--------AYTTVMAVLQRLAKKNLVLQIRD-DRAHRYAPVHGRDEL   78 (138)
T ss_dssp             HHHHHHHTCSSCEEHHHHHHHHTTT--CCC--------CHHHHHHHHHHHHHTTSEEEEC----CCEEEESSCHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHhcc--CCC--------CHHHHHHHHHHHHHCCCEEEEec-CCeEEEEeCCCHHHH
Confidence            37777887 5999999999998753  232        23578889999999999998765 44      2677774

>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=91.93  E-value=0.89  Score=29.03  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=35.4

Q ss_pred             HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      ++..++- .+++.+..|...+|-              |.+-++.+|+.||+.|+|+...
T Consensus        26 ~l~~l~~~~~~~t~~ela~~l~i--------------s~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           26 VLLKMVEIEKPITSEELADIFKL--------------SKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             HHHHHHHHCSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEeec
Confidence            5555555 789999999998863              3467999999999999998754

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=91.90  E-value=0.097  Score=39.63  Aligned_cols=44  Identities=20%  Similarity=0.253  Sum_probs=35.9

Q ss_pred             hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee--cCC--CCceeCcchHh
Q 033029           59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPK--GGRRITSSGQR  116 (129)
Q Consensus        59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek--~~~--~GR~lT~~G~~  116 (129)
                      -..|+..||-              |..-+|.+|+.||..|+|+.  .+.  +|-.+++-...
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            4478888865              45689999999999999999  887  78888876554

>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=91.90  E-value=0.32  Score=34.78  Aligned_cols=58  Identities=10%  Similarity=0.117  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchH
Q 033029           44 AASMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ  115 (129)
Q Consensus        44 ~ASilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~  115 (129)
                      |-.+|-.|..+  +++.+..++..+|-.              -+.++++|++|.++|||+... .||-.|+....
T Consensus        16 Al~~L~~La~~~~~~~~~~~iA~~~~i~--------------~~~l~kil~~L~~~Glv~s~rG~GGy~L~~~p~   76 (149)
T 1ylf_A           16 AVHILSILKNNPSSLCTSDYMAESVNTN--------------PVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLH   76 (149)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEC---CCEEESSCGG
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCcEEEccCCCceEeCCChh
Confidence            44455555553  468888999887653              358999999999999998654 57888887643

>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=91.80  E-value=0.42  Score=37.41  Aligned_cols=41  Identities=15%  Similarity=0.233  Sum_probs=32.1

Q ss_pred             hHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHHHHHHh
Q 033029           85 AIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        85 ~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~iA~~i  125 (129)
                      +-+=.+++.||+.|||++.+  +.+|    .||++|+..++++...+
T Consensus       189 ~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~~  235 (250)
T 1p4x_A          189 PQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQV  235 (250)
T ss_dssp             HHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            45566899999999998654  4455    38999999999886654

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=91.40  E-value=0.19  Score=37.04  Aligned_cols=45  Identities=16%  Similarity=0.118  Sum_probs=34.6

Q ss_pred             CCchhHHHHHHHHHHhCCceeecC----CCC-----ceeCcchHhhHHHHHHHh
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEP----KGG-----RRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~----~~G-----R~lT~~G~~~lD~iA~~i  125 (129)
                      .-+-+.|-.+|+.||+.|||+...    .+|     -.||++|+..|.....+.
T Consensus        75 ~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~  128 (148)
T 2zfw_A           75 RLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLW  128 (148)
T ss_dssp             ECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESSSSCSTTHHHHHHH
T ss_pred             CCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            445578899999999999998643    124     379999999988776543

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=91.21  E-value=0.24  Score=37.05  Aligned_cols=62  Identities=18%  Similarity=0.156  Sum_probs=43.6

Q ss_pred             HHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC------CCCc-----eeCc
Q 033029           46 SMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGR-----RITS  112 (129)
Q Consensus        46 SilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~------~~GR-----~lT~  112 (129)
                      +|+..|--+  +...+..|....             ..-|-+-|+.-|+.|+++|+|++..      ..||     .||+
T Consensus        33 ~IL~~Ll~~p~~~~ta~eL~~~l-------------~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~   99 (151)
T 3u1d_A           33 DVLHQILAQPDGVLSVEELLYRN-------------PDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTG   99 (151)
T ss_dssp             HHHHHHHHSTTSCBCHHHHHHHC-------------TTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHhc-------------CCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECH
Confidence            456655554  235666665432             1246689999999999999999642      1255     8999


Q ss_pred             chHhhHHH
Q 033029          113 SGQRDLDQ  120 (129)
Q Consensus       113 ~G~~~lD~  120 (129)
                      +|+..|+.
T Consensus       100 ~Gr~~l~~  107 (151)
T 3u1d_A          100 EGIALLRA  107 (151)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99999987

>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=91.21  E-value=0.22  Score=37.63  Aligned_cols=73  Identities=18%  Similarity=0.069  Sum_probs=50.1

Q ss_pred             chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCceeCcch
Q 033029           38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGRRITSSG  114 (129)
Q Consensus        38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR~lT~~G  114 (129)
                      .|-+.++-+....++-.+++.+..++...|-.              .+-+=+.+++||+.|||+...   ..+=.||++|
T Consensus         9 ~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~is--------------q~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G   74 (230)
T 3cta_A            9 YYRAIKKIKEAAEASNRAYLTSSKLADMLGIS--------------QQSASRIIIDLEKNGYITRTVTKRGQILNITEKG   74 (230)
T ss_dssp             HHHHHHHHHHHTTTSSEEECCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHH
T ss_pred             HHHHHHHHHHhcccccCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHH
Confidence            34444444444444444557788888876543              346677889999999999873   2355799999


Q ss_pred             HhhHHHHHHH
Q 033029          115 QRDLDQVAGR  124 (129)
Q Consensus       115 ~~~lD~iA~~  124 (129)
                      +..++.+...
T Consensus        75 ~~l~~~~~~~   84 (230)
T 3cta_A           75 LDVLYTEFAD   84 (230)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999876543

>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=91.19  E-value=1  Score=32.32  Aligned_cols=77  Identities=12%  Similarity=0.082  Sum_probs=55.7

Q ss_pred             HHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCccc--------CCchhHHHHHHHHHHhCCceeecCCC----C-ceeC
Q 033029           46 SMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFC--------KSSGAIARHILQQLQNMNIIDIEPKG----G-RRIT  111 (129)
Q Consensus        46 SilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~--------~asg~iiR~~lqqLE~~g~vek~~~~----G-R~lT  111 (129)
                      .+|..||- .+..|++.+..+.=|+++.-+.-.|..        .=+-.-++.++.||...|+++.+...    + =.||
T Consensus        20 kiLs~V~r~~~rfG~~~iidvLrGs~~~ki~~~~~~l~tfGigk~~s~~~w~~lirqLi~~G~L~~~~~~~~~~~~L~Lt   99 (134)
T 3aaf_A           20 KLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALT   99 (134)
T ss_dssp             HHHHHHHHTTTCSCTHHHHHHHTTCCCTTSCGGGGGSTTTTTTTTSCHHHHHHHHHHHHHTTSEEEEECSSTTCEEEEEC
T ss_pred             HHHHHHHHHcCcccccchhhhhcCCcHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHHHHcCCceeecCcCccCceEEEC
Confidence            35555553 678999999999988887665442111        12335699999999999999876533    2 6899


Q ss_pred             cchHhhHHHHH
Q 033029          112 SSGQRDLDQVA  122 (129)
Q Consensus       112 ~~G~~~lD~iA  122 (129)
                      ++|+..|..--
T Consensus       100 ~~g~~vL~~~~  110 (134)
T 3aaf_A          100 KKGRNWLHKAN  110 (134)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHhCCc
Confidence            99999987643

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=91.17  E-value=0.16  Score=39.07  Aligned_cols=65  Identities=18%  Similarity=0.196  Sum_probs=45.5

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCC-----ceeCcchHhhHHHHHHH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDLDQVAGR  124 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~G-----R~lT~~G~~~lD~iA~~  124 (129)
                      .+|.---.|.+.+...-      .++...|-+-|-.+|+.||+.|||+...   .+|     -.||++|+..|.+...+
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            46655556666665431      2345566678999999999999998542   233     26999999999876554

>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=91.15  E-value=0.24  Score=37.98  Aligned_cols=59  Identities=22%  Similarity=0.354  Sum_probs=47.4

Q ss_pred             HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcch
Q 033029           42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSG  114 (129)
Q Consensus        42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~G  114 (129)
                      -|+..||+.|.-.+ ++++..|....|-              +.+-+.++|+.||+.|||+++++ +.-.|+++.
T Consensus         6 ~r~l~iL~~l~~~~~~~s~~ela~~~gl--------------~~stv~r~l~~L~~~G~v~~~~~~~~Y~lg~~~   66 (241)
T 2xrn_A            6 ARAASIMRALGSHPHGLSLAAIAQLVGL--------------PRSTVQRIINALEEEFLVEALGPAGGFRLGPAL   66 (241)
T ss_dssp             HHHHHHHHHHHTCTTCEEHHHHHHHTTS--------------CHHHHHHHHHHHHTTTSEEECGGGCEEEECSHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCCeEEECHHH
Confidence            47889999887664 7999999998754              34689999999999999999864 456777764

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=90.97  E-value=0.14  Score=35.79  Aligned_cols=67  Identities=10%  Similarity=0.153  Sum_probs=42.0

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCC-----ceeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGG-----RRITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~G-----R~lT~~G~~~l  118 (129)
                      ||--|. .+|.---.|.+.....-...        -+-+.+-.+|+.||+.|||+...   .+|     -.||++|+..|
T Consensus        19 IL~lL~-~~p~~gyel~~~l~~~~~~~--------i~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l   89 (117)
T 3elk_A           19 ILKELV-KRPMHGYELQKSMFETTGQA--------LPQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFL   89 (117)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHHHHHSCC--------CCTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHHHhCCC--------CCcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHH
Confidence            555444 46654445555544321111        12268899999999999998543   223     24999999999


Q ss_pred             HHHH
Q 033029          119 DQVA  122 (129)
Q Consensus       119 D~iA  122 (129)
                      ....
T Consensus        90 ~~~~   93 (117)
T 3elk_A           90 CDHS   93 (117)
T ss_dssp             HHTS
T ss_pred             HHHH
Confidence            8753

>3l09_A Putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG, protein structure initiative transcription regulator; 2.81A {Jannaschia SP}

Probab=90.94  E-value=0.26  Score=39.76  Aligned_cols=74  Identities=19%  Similarity=0.165  Sum_probs=58.3

Q ss_pred             HhHHHHHHHHHH---h---CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCc
Q 033029           42 VRAASMARKIYL---R---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS  112 (129)
Q Consensus        42 ~R~ASilR~lYl---~---g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~  112 (129)
                      +|+-|++-.||-   .   +.+-++.|-...+.-   |+        +...+|.+|.-|++.|||+....|   +-.||+
T Consensus        22 ~~a~Sli~tl~Gd~~~~~g~~i~~~~Li~l~~~~---Gi--------~~~avR~Al~RL~~~G~l~~~~~Gr~~~Y~Lt~   90 (266)
T 3l09_A           22 LKLWSVLVTCLGDVSRDGVIEVSGVALSSFVERM---GL--------QPQAMRVALHRLKRDGWVESRRLGRVGFHRLSD   90 (266)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCCEEHHHHHHHHHHT---TC--------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEECH
T ss_pred             CChhHHHHHHHHHHhccCCCcccHHHHHHHHHHc---CC--------CchHHHHHHHHHHHCCCeeeeecCCcceEEECH
Confidence            788999999993   2   468888877776542   32        346899999999999999977544   578999


Q ss_pred             chHhhHHHHHHHhh
Q 033029          113 SGQRDLDQVAGRIV  126 (129)
Q Consensus       113 ~G~~~lD~iA~~i~  126 (129)
                      .|+..+++....|.
T Consensus        91 ~g~~~l~~~~~ri~  104 (266)
T 3l09_A           91 SALTQTRAVAGRIY  104 (266)
T ss_dssp             HHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999988777665

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=90.90  E-value=0.32  Score=34.86  Aligned_cols=56  Identities=14%  Similarity=0.202  Sum_probs=41.2

Q ss_pred             HHHHHHHHh---CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchH
Q 033029           46 SMARKIYLR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ  115 (129)
Q Consensus        46 SilR~lYl~---g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~  115 (129)
                      .+|-.|..+   +++.+..++..+|-              |-..+|++|++|.++|+|+...  +||-.|+..-.
T Consensus        15 ~~L~~La~~~~~~~~s~~~IA~~~~i--------------~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p~   75 (143)
T 3t8r_A           15 TLMISLAKKEGQGCISLKSIAEENNL--------------SDLYLEQLVGPLRNAGLIRSVRGAKGGYQLRVPAE   75 (143)
T ss_dssp             HHHHHHHTTTTSCCEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECSSSSSEEEESSCGG
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCEEEecCCCCCCeeecCCcc
Confidence            344455543   36888889888765              3358999999999999998654  46888886554

>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=90.67  E-value=0.15  Score=38.19  Aligned_cols=42  Identities=14%  Similarity=0.229  Sum_probs=34.8

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      .-..|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++.
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            46778888875              4568999999999999999988778888763

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=90.54  E-value=0.39  Score=37.69  Aligned_cols=58  Identities=17%  Similarity=0.233  Sum_probs=46.9

Q ss_pred             HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      -|+..||..|--.+ ++++..|.+.-|-.+              +-+..+|+.|++.|||++++++...|++.
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            47888999888754 799999999877532              46889999999999999988655777775

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=89.83  E-value=0.48  Score=34.78  Aligned_cols=54  Identities=11%  Similarity=0.085  Sum_probs=39.9

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG  114 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G  114 (129)
                      +|-.|..+  +++.+..++..+|-.              ...+|++|++|.++|||+...  .||-.|+..-
T Consensus        17 ~l~~La~~~~~~~s~~~IA~~~~is--------------~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p   74 (162)
T 3k69_A           17 SILYLDAHRDSKVASRELAQSLHLN--------------PVMIRNILSVLHKHGYLTGTVGKNGGYQLDLAL   74 (162)
T ss_dssp             HHHHHHTTTTSCBCHHHHHHHHTSC--------------GGGTHHHHHHHHHTTSSEEECSTTCEEECCSCG
T ss_pred             HHHHHHhCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeecCCCCCeEecCCh
Confidence            34444433  468899999988763              248999999999999998654  4678887654

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=89.73  E-value=1  Score=35.33  Aligned_cols=60  Identities=22%  Similarity=0.284  Sum_probs=44.5

Q ss_pred             HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+..++.--..|-      + ....|+..||-              |..-+|++|++|++.|+|+..+..|-.+++
T Consensus        30 ~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   95 (272)
T 3eet_A           30 AYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGV--------------SDTVALEARKVLMAEGLVEGRSGSGTYVRE   95 (272)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTSBCCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECCC--EEECC
T ss_pred             HHHHHHHHHHHHHHcCCCCCcCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceEEEec
Confidence            56667777766655553      3 56788998875              456999999999999999998877877775


Q ss_pred             c
Q 033029          113 S  113 (129)
Q Consensus       113 ~  113 (129)
                      .
T Consensus        96 ~   96 (272)
T 3eet_A           96 R   96 (272)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=89.65  E-value=0.88  Score=31.53  Aligned_cols=75  Identities=21%  Similarity=0.369  Sum_probs=52.7

Q ss_pred             ChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHH
Q 033029           11 SPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHI   90 (129)
Q Consensus        11 ~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~   90 (129)
                      +.++.++.++..||--+        ||    +| ..|++.|. +++..++.|....|-              |.+-+.+.
T Consensus        28 ~~~~~~~~~~~~~kaL~--------~~----~r-l~IL~~L~-~~~~s~~ela~~lgi--------------s~stvs~~   79 (122)
T 1r1t_A           28 IAPEVAQSLAEFFAVLA--------DP----NR-LRLLSLLA-RSELCVGDLAQAIGV--------------SESAVSHQ   79 (122)
T ss_dssp             CCHHHHHHHHHHHHHHC--------CH----HH-HHHHHHHT-TCCBCHHHHHHHHTC--------------CHHHHHHH
T ss_pred             CCHhHHHHHHHHHHHhC--------CH----HH-HHHHHHHH-cCCCCHHHHHHHHCc--------------CHHHHHHH
Confidence            44567777777777642        33    22 24777775 689999999998764              33588899


Q ss_pred             HHHHHhCCceeecCCCCc----eeCcch
Q 033029           91 LQQLQNMNIIDIEPKGGR----RITSSG  114 (129)
Q Consensus        91 lqqLE~~g~vek~~~~GR----~lT~~G  114 (129)
                      |+.||+.|+|....+ ||    .||+++
T Consensus        80 L~~Le~~Glv~~~~~-gr~~~y~l~~~~  106 (122)
T 1r1t_A           80 LRSLRNLRLVSYRKQ-GRHVYYQLQDHH  106 (122)
T ss_dssp             HHHHHHTTSEEEEEE-TTEEEEEESSHH
T ss_pred             HHHHHHCCCeEEEEe-CCEEEEEEChHH
Confidence            999999999987653 43    355554

>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=89.55  E-value=0.27  Score=31.27  Aligned_cols=51  Identities=12%  Similarity=0.201  Sum_probs=39.6

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ||.-|+-.+++.+..|....+-.  .+.        +.+-+..+|+.||+.|+|+...+ ||
T Consensus        14 vL~~L~~~~~~t~~ei~~~l~~~--~~~--------s~~Tv~~~l~rL~~kGlv~r~~~-gr   64 (82)
T 1p6r_A           14 VMKVIWKHSSINTNEVIKELSKT--STW--------SPKTIQTMLLRLIKKGALNHHKE-GR   64 (82)
T ss_dssp             HHHHHHTSSSEEHHHHHHHHHHH--SCC--------CHHHHHHHHHHHHHTTSEEEEEE-TT
T ss_pred             HHHHHHcCCCCCHHHHHHHHhhc--CCc--------cHHHHHHHHHHHHHCCCeEEEec-CC
Confidence            66667778999999999998752  222        34678999999999999998764 44

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=89.01  E-value=1.1  Score=34.65  Aligned_cols=60  Identities=3%  Similarity=-0.011  Sum_probs=46.9

Q ss_pred             HhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029           42 VRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ  115 (129)
Q Consensus        42 ~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~  115 (129)
                      -|+..||+.|.- .+++++..|....|-.              .+-+.++|+.||+.|||++++++...|+++.-
T Consensus        23 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~--------------kstv~r~l~tL~~~G~v~~~~~~~Y~lg~~~~   83 (260)
T 2o0y_A           23 TRVIDLLELFDAAHPTRSLKELVEGTKLP--------------KTTVVRLVATMCARSVLTSRADGSYSLGPEML   83 (260)
T ss_dssp             HHHHHHHTTCBTTBSSBCHHHHHHHHCCC--------------HHHHHHHHHHHHHTTSEEECTTSCEEECHHHH
T ss_pred             HHHHHHHHHHhhCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEECCCCeEEecHHHH
Confidence            477788887753 5689999999987652              36788999999999999998755567877643

>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=88.73  E-value=1.2  Score=34.03  Aligned_cols=59  Identities=15%  Similarity=0.192  Sum_probs=43.1

Q ss_pred             HHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           41 YVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        41 Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      |...+..++.-=..|-      + ....|+..||-              |..-+|++|+.|++.|+|+..+..|-.+++.
T Consensus        11 ~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~~   76 (236)
T 3edp_A           11 FEVIASKIKDSINRDEYKTGMLMPNETALQEIYSS--------------SRTTIRRAVDLLVEEGLVVRKNGVGLYVQPK   76 (236)
T ss_dssp             HHHHHHHHHHHHHTTSSCCCC--CCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCC
T ss_pred             HHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEECCceEEEccC
Confidence            4555555555545442      3 56778888765              4568999999999999999988778888764

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=88.69  E-value=1.1  Score=29.91  Aligned_cols=81  Identities=11%  Similarity=0.085  Sum_probs=56.1

Q ss_pred             hhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHH
Q 033029           12 PHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHIL   91 (129)
Q Consensus        12 ~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~l   91 (129)
                      .+..++.++..+|--.        |+.+     ..|+..|+- ++..+..+....|-              +.+-+.+.|
T Consensus        15 ~~~~~~~~~~~~~~l~--------~~~~-----~~il~~L~~-~~~s~~ela~~l~i--------------s~stvsr~l   66 (119)
T 2lkp_A           15 DSQAAAQVASTLQALA--------TPSR-----LMILTQLRN-GPLPVTDLAEAIGM--------------EQSAVSHQL   66 (119)
T ss_dssp             HHHHHHHHHHHHHHHC--------CHHH-----HHHHHHHHH-CCCCHHHHHHHHSS--------------CHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC--------CHHH-----HHHHHHHHH-CCCCHHHHHHHHCc--------------CHHHHHHHH
Confidence            3566777888888652        3322     236666664 78999999998754              335888999


Q ss_pred             HHHHhCCceeecCC-CCceeCcchHhhHHH
Q 033029           92 QQLQNMNIIDIEPK-GGRRITSSGQRDLDQ  120 (129)
Q Consensus        92 qqLE~~g~vek~~~-~GR~lT~~G~~~lD~  120 (129)
                      +.||+.|+|....+ .+..+|..|...+..
T Consensus        67 ~~Le~~Glv~~~~~~r~~~~~~~~~~~~~~   96 (119)
T 2lkp_A           67 RVLRNLGLVVGDRAGRSIVYSLYDTHVAQL   96 (119)
T ss_dssp             HHHHHHCSEEEEEETTEEEEEESCHHHHHH
T ss_pred             HHHHHCCCEEEEecCCEEEEEEchHHHHHH
Confidence            99999999987643 234677777655443

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=88.16  E-value=0.84  Score=33.63  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=36.6

Q ss_pred             CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch
Q 033029           55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG  114 (129)
Q Consensus        55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G  114 (129)
                      +++.+..++..+|-              |-..+|++|++|.++|+|+...  .||-.|+..-
T Consensus        43 ~~~s~~eIA~~~~i--------------~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p   90 (159)
T 3lwf_A           43 GPISLRSIAQDKNL--------------SEHYLEQLIGPLRNAGIVKSIRGAHGGYVLNGDP   90 (159)
T ss_dssp             CCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECSTTCEEEECSCT
T ss_pred             CCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCeEEEecCCCCceEecCCH
Confidence            47888889888765              3369999999999999998654  4688887654

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=88.13  E-value=0.47  Score=36.75  Aligned_cols=58  Identities=16%  Similarity=0.275  Sum_probs=46.9

Q ss_pred             HhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcc
Q 033029           42 VRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS  113 (129)
Q Consensus        42 ~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~  113 (129)
                      -|+..||+.|-- .+++++..|...-|-.              .+-+.++|+.|++.|||+++++ +...|+++
T Consensus         6 ~Ral~IL~~l~~~~~~lsl~eia~~lgl~--------------ksT~~RlL~tL~~~G~v~~~~~~~~Y~lG~~   65 (260)
T 3r4k_A            6 SKALTLLTYFNHGRLEIGLSDLTRLSGMN--------------KATVYRLMSELQEAGFVEQVEGARSYRLGPQ   65 (260)
T ss_dssp             HHHHHHHTTCBTTBSEEEHHHHHHHHCSC--------------HHHHHHHHHHHHHTTSEEECSSSSEEEECTT
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCcEEcCHH
Confidence            378889988875 5789999999987653              3688999999999999999875 55577665

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

Probab=87.97  E-value=0.35  Score=33.13  Aligned_cols=51  Identities=20%  Similarity=0.177  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR  108 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR  108 (129)
                      ||+-|+-.+++.+..|....+..  .+        -+.+-+..+|+.||+.|||+..+. ||
T Consensus        40 VL~~L~~~~~~t~~eL~~~l~~~--~~--------~s~sTVt~~L~rLe~KGlV~R~~~-gR   90 (99)
T 2k4b_A           40 VMRVIWSLGEARVDEIYAQIPQE--LE--------WSLATVKTLLGRLVKKEMLSTEKE-GR   90 (99)
T ss_dssp             HHHHHHHHSCEEHHHHHHTCCGG--GC--------CCHHHHHHHHHHHHHTTSCEEEEE-TT
T ss_pred             HHHHHHhCCCCCHHHHHHHHhcc--cC--------CCHhhHHHHHHHHHHCCCEEEEeC-CC
Confidence            77778889999999999987642  12        234678899999999999998753 55

>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=87.79  E-value=1.6  Score=29.91  Aligned_cols=67  Identities=16%  Similarity=0.128  Sum_probs=49.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC------CCCceeCc------c
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRRITS------S  113 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~------~~GR~lT~------~  113 (129)
                      .|++.|.-++++....|...+|-              |.+-++..|+.||+.|+|+...      +-|..+|.      .
T Consensus         8 ~il~~L~~~~~~~~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~~~v~~~~~   73 (141)
T 1i1g_A            8 IILEILEKDARTPFTEIAKKLGI--------------SETAVRKRVKALEEKGIIEGYTIKINPKKLGYSLVTITGVDTK   73 (141)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTSSCCCCCCCCSGGGTCCEEEEEEEEEC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEeccccccChHHhCccEEEEEEEEEC
Confidence            47777777889999999998864              3468999999999999997431      13665654      4


Q ss_pred             hHhhHHHHHHHhhh
Q 033029          114 GQRDLDQVAGRIVV  127 (129)
Q Consensus       114 G~~~lD~iA~~i~~  127 (129)
                      + ..++.++..+..
T Consensus        74 ~-~~~~~~~~~l~~   86 (141)
T 1i1g_A           74 P-EKLFEVAEKLKE   86 (141)
T ss_dssp             G-GGHHHHHHHHHH
T ss_pred             c-hhHHHHHHHHhc
Confidence            4 467788777653

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

Probab=86.90  E-value=1.2  Score=29.40  Aligned_cols=44  Identities=16%  Similarity=0.177  Sum_probs=38.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE  103 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~  103 (129)
                      .|+..|--+|.+.|..|...|+-              |-.-||.-|..||+.|+|+..
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            46777778999999999998764              457999999999999999987

>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=86.57  E-value=1.6  Score=32.76  Aligned_cols=65  Identities=12%  Similarity=0.261  Sum_probs=48.4

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc-------------ee
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR-------------RI  110 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR-------------~l  110 (129)
                      .|++.|. +|++.+..|....|-              |.+-+++-|+.||+.|+|+..  ...|+             .|
T Consensus        24 ~IL~~L~-~~~~s~~eLA~~lgl--------------S~stv~~~l~~Le~~GlI~~~~~~~~~~~~~~~~g~~~~~~~v   88 (192)
T 1uly_A           24 KILKLLR-NKEMTISQLSEILGK--------------TPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADVFYI   88 (192)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSEEEE
T ss_pred             HHHHHHH-cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEeccccccchhhhcCcceEEEEE
Confidence            4888888 899999999998764              345789999999999999876  22343             36


Q ss_pred             CcchH-hhHHHHHHHh
Q 033029          111 TSSGQ-RDLDQVAGRI  125 (129)
Q Consensus       111 T~~G~-~~lD~iA~~i  125 (129)
                      |.+|. ..++.++..+
T Consensus        89 ~~~~~~~~~~~~~~~~  104 (192)
T 1uly_A           89 NLYLGDEELRYIARSR  104 (192)
T ss_dssp             CSCSSCHHHHHHHHHH
T ss_pred             ecCCchhHHHHHHHHH
Confidence            77773 4566666554

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=86.49  E-value=0.61  Score=35.82  Aligned_cols=60  Identities=15%  Similarity=0.171  Sum_probs=43.5

Q ss_pred             HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      .|...+..++.--..|.      + ....|+..||-              |..-+|++|++|++.|+|+..+..|-.+++
T Consensus        11 ~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~v--------------Sr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   76 (243)
T 2wv0_A           11 IYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGI--------------SRMTVRQALSNLVNEGLLYRLKGRGTFVSK   76 (243)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECC
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEeCCCeEEEeC
Confidence            35555655555444432      3 56788888875              346899999999999999998877887775


Q ss_pred             c
Q 033029          113 S  113 (129)
Q Consensus       113 ~  113 (129)
                      .
T Consensus        77 ~   77 (243)
T 2wv0_A           77 P   77 (243)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=86.28  E-value=0.69  Score=36.15  Aligned_cols=65  Identities=8%  Similarity=0.072  Sum_probs=47.9

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCce----eCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRR----ITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR~----lT~~G~~~l  118 (129)
                      +|..||-+  +++.+..|....+-.             ++.+. .+|+.||+.|||++.  ++..|.    ||++|+..+
T Consensus        39 vL~~L~~~~~~~~~~~el~~~l~~~-------------~~t~t-~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~  104 (250)
T 1p4x_A           39 LLTYLFHQQENTLPFKKIVSDLCYK-------------QSDLV-QHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (250)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSSSC-------------GGGTH-HHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCC-------------HhhHH-HHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHH
Confidence            78888875  478899999865432             33344 589999999999864  344443    899999988


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      +.+...+
T Consensus       105 ~~~~~~~  111 (250)
T 1p4x_A          105 AERVTLF  111 (250)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876654

>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=86.25  E-value=0.69  Score=32.87  Aligned_cols=54  Identities=9%  Similarity=0.169  Sum_probs=37.1

Q ss_pred             HHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcch
Q 033029           46 SMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSG  114 (129)
Q Consensus        46 SilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G  114 (129)
                      .+|..|..++ + .+..++..++-              |-..++++|++|.++|||+... .||-.|+..-
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            3444444432 3 56666666554              4469999999999999998654 5788887654

>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, STRU genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum}

Probab=86.14  E-value=0.25  Score=37.48  Aligned_cols=36  Identities=17%  Similarity=0.328  Sum_probs=26.4

Q ss_pred             HHHHHHhCCceeecC-CCCc------eeCcchHhhHHHHHHHh
Q 033029           90 ILQQLQNMNIIDIEP-KGGR------RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        90 ~lqqLE~~g~vek~~-~~GR------~lT~~G~~~lD~iA~~i  125 (129)
                      +|.+||+.|+|+... .+||      .||++|+..+.+.-.+.
T Consensus        54 ~l~~Le~~GlI~~~~~~~~rpektvY~ITe~Gr~~l~~~l~~~   96 (180)
T 2rkh_A           54 SIELLRYEGLVEAVDDGQGMEDDAMLAISAAGRRELHSLLTAR   96 (180)
T ss_dssp             CTHHHHHTTSEECCC--------CEEEECHHHHHHHHHHHSCC
T ss_pred             HHHHHHHCCCeeeeecCCCCCccceeeeCHHHHHHHHHHHHHH
Confidence            789999999997655 3443      69999999998765543

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=86.07  E-value=0.88  Score=35.01  Aligned_cols=58  Identities=19%  Similarity=0.145  Sum_probs=45.8

Q ss_pred             HhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           42 VRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        42 ~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      -|+..||+.|.- .+++++..|.+..|-.              .+-+.++|+.|++.|||+++. +.-.|+++.
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~--------------~stv~r~l~~L~~~G~v~~~~-~~Y~Lg~~~   72 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGLS--------------RPAVRRILLTLQKLGYVAGSG-GRWSLTPRV   72 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEET-TEEEECGGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeCC-CEEEEcHHH
Confidence            367778877764 3689999999987652              357889999999999999874 567888875

>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=85.84  E-value=1  Score=35.60  Aligned_cols=53  Identities=19%  Similarity=0.329  Sum_probs=40.9

Q ss_pred             HHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHH-HHHhCCceeecCCCCceeCcchHhhH
Q 033029           51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        51 lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lq-qLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      .|-.+|+|+..++...|-..              .-++.+.. .|..+|+|+..+ .||++|++|-+.|
T Consensus       271 ~~~~~~~~~~~l~~~~~~~~--------------~t~~~~~~~~l~~~g~i~~~~-~gr~~~~~~~~~~  324 (334)
T 1in4_A          271 IYRGGPVGLNALAASLGVEA--------------DTLSEVYEPYLLQAGFLARTP-RGRIVTEKAYKHL  324 (334)
T ss_dssp             HSTTCCBCHHHHHHHHTSCH--------------HHHHHHTHHHHHHTTSEEEET-TEEEECHHHHHHT
T ss_pred             HhCCCcchHHHHHHHhCCCc--------------chHHHHHHHHHHHcCCeeccc-ccHHhhHHHHHHh
Confidence            34457899999999877531              13555555 899999999998 4999999998776

>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=85.45  E-value=2  Score=29.81  Aligned_cols=68  Identities=7%  Similarity=0.051  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec-----C-CCCce------eCcc
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGRR------ITSS  113 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~-----~-~~GR~------lT~~  113 (129)
                      .|++.|--++++.+..|....|-              |.+-++..|+.||+.|+|+..     + +-|+.      ++..
T Consensus         7 ~il~~L~~~~~~~~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~~   72 (150)
T 2pn6_A            7 RILKILQYNAKYSLDEIAREIRI--------------PKATLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKAK   72 (150)
T ss_dssp             HHHHHHTTCTTSCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSSCCCCCCCCGGGGTCCEEEEEEEEEC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEEEeecCHHHhCCceEEEEEEEec
Confidence            47777777889999999998764              346889999999999999862     1 22544      3544


Q ss_pred             h-HhhHHHHHHHhhh
Q 033029          114 G-QRDLDQVAGRIVV  127 (129)
Q Consensus       114 G-~~~lD~iA~~i~~  127 (129)
                      + ...++.++..+..
T Consensus        73 ~~~~~~~~~~~~l~~   87 (150)
T 2pn6_A           73 YGKNYHVELGNKLAQ   87 (150)
T ss_dssp             CCTTHHHHHHHHHHT
T ss_pred             CChhHHHHHHHHHhc
Confidence            4 5678888877754

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

Probab=85.23  E-value=2  Score=26.91  Aligned_cols=46  Identities=4%  Similarity=0.018  Sum_probs=36.8

Q ss_pred             HHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029           46 SMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK  105 (129)
Q Consensus        46 SilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~  105 (129)
                      .||..|--+ +|+.+..|+...|-.              .+.+.++|+.||+.|+|+..+.
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            366666555 589999999998763              4689999999999999987543

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

Probab=85.21  E-value=2.8  Score=28.85  Aligned_cols=45  Identities=4%  Similarity=0.135  Sum_probs=37.0

Q ss_pred             HHHHHHHHhCC--CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029           46 SMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        46 SilR~lYl~g~--vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                      .|+..|.-.++  +.+..|....|-              |.+-+.+.|+.||+.|+|++..
T Consensus        30 ~il~~L~~~~~~~~t~~eLa~~l~~--------------s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           30 NVMKSFLNEPDRWIDTDALSKSLKL--------------DVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHSTTCCEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeeC
Confidence            47777777665  899999998762              5678999999999999998743

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

Probab=84.99  E-value=1.2  Score=30.34  Aligned_cols=44  Identities=7%  Similarity=0.106  Sum_probs=38.1

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE  103 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~  103 (129)
                      .|+..|--+|.+.|..|...||-              |-.-||.-|..||+.|+|...
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            36777778899999999998864              457999999999999999876

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=84.94  E-value=1.4  Score=29.77  Aligned_cols=61  Identities=15%  Similarity=0.070  Sum_probs=36.0

Q ss_pred             CCCCCcccccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCccc
Q 033029            1 MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFC   80 (129)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~   80 (129)
                      |..++++.|+........+-++|+++                            | +.+..|.+..|=            
T Consensus         4 ~~~~~~~~d~~~~~~~~~IL~lL~~~----------------------------g-~sa~eLAk~Lgi------------   42 (82)
T 1oyi_A            4 MASKIYIDERSNAEIVCEAIKTIGIE----------------------------G-ATAAQLTRQLNM------------   42 (82)
T ss_dssp             ---------CCSHHHHHHHHHHHSSS----------------------------T-EEHHHHHHHSSS------------
T ss_pred             cccccCccccchHHHHHHHHHHHHHc----------------------------C-CCHHHHHHHHCc------------
Confidence            34445666776666666666666643                            1 445555555442            


Q ss_pred             CCchhHHHHHHHHHHhCCceeecC
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEP  104 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~  104 (129)
                        |.+-+|+.|+.||+.|+|.+..
T Consensus        43 --Sk~aVr~~L~~Le~eG~I~~~~   64 (82)
T 1oyi_A           43 --EKREVNKALYDLQRSAMVYSSD   64 (82)
T ss_dssp             --CHHHHHHHHHHHHHHTSSEECS
T ss_pred             --CHHHHHHHHHHHHHCCCEEeCC
Confidence              3468999999999999998863

>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=84.87  E-value=0.68  Score=35.41  Aligned_cols=42  Identities=12%  Similarity=0.034  Sum_probs=33.8

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      ....|+..||-              |..-+|.+|+.|++.|+|+..+..|-.+++.
T Consensus        31 se~~La~~~~v--------------Sr~tvr~Al~~L~~~g~i~~~~g~G~~V~~~   72 (239)
T 3bwg_A           31 VLETLMAQFEV--------------SKSTITKSLELLEQKGAIFQVRGSGIFVRKH   72 (239)
T ss_dssp             CHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECCC
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEeCCceEEEecC
Confidence            56778888775              4568999999999999999888777766543

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=84.59  E-value=0.62  Score=35.98  Aligned_cols=41  Identities=7%  Similarity=0.045  Sum_probs=33.5

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      ....|+..||-              |..-+|++|+.|++.|+|+. +..|-.+++.
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            56778887764              45799999999999999999 8778777654

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=83.43  E-value=2.3  Score=33.60  Aligned_cols=50  Identities=14%  Similarity=0.179  Sum_probs=42.8

Q ss_pred             HHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCcee-ecC
Q 033029           41 YVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID-IEP  104 (129)
Q Consensus        41 Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ve-k~~  104 (129)
                      -.|-+..+-.+|-.+++++..|++.+|-              |..-||+-|+.||+.|+|+ +..
T Consensus         6 ~~~~~~~ia~l~~~~~~~~~ela~~l~v--------------S~~tIrRdL~~l~~~G~v~iri~   56 (315)
T 2w48_A            6 DIRLIVKIAQLYYEQDMTQAQIARELGI--------------YRTTISRLLKRGREQGIVTIAIN   56 (315)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEEec
Confidence            4566777788899999999999999875              5679999999999999998 553

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

Probab=83.34  E-value=8.4  Score=27.90  Aligned_cols=68  Identities=9%  Similarity=0.140  Sum_probs=51.4

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec-----C-CCCc-------eeCc
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE-----P-KGGR-------RITS  112 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~-----~-~~GR-------~lT~  112 (129)
                      .|++.|.-++++.+..|....|-              |.+-++..|+.||+.|+|+..     + +-|+       .+++
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            47888888899999999998874              346889999999999999742     2 2254       3455


Q ss_pred             c-----hHhhHHHHHHHhhh
Q 033029          113 S-----GQRDLDQVAGRIVV  127 (129)
Q Consensus       113 ~-----G~~~lD~iA~~i~~  127 (129)
                      .     ....+|.++..+..
T Consensus        87 ~~~~~f~~~~~~~~~~~l~~  106 (171)
T 2ia0_A           87 PVIEDFLERYISYISSTLSA  106 (171)
T ss_dssp             C--CHHHHHHHHHHHHHHHT
T ss_pred             ccccccchhHHHHHHHHHHC
Confidence            5     55578888888754

>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=83.22  E-value=5.2  Score=27.86  Aligned_cols=68  Identities=12%  Similarity=0.183  Sum_probs=50.9

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee-----cC-CCCce------eCcc
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI-----EP-KGGRR------ITSS  113 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek-----~~-~~GR~------lT~~  113 (129)
                      .|++.|.-++++.+..|....|-              |.+-++..|+.||+.|+|..     ++ +-|+.      ++-.
T Consensus        12 ~il~~L~~~~~~s~~ela~~lg~--------------s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~~   77 (152)
T 2cg4_A           12 GILEALMGNARTAYAELAKQFGV--------------SPETIHVRVEKMKQAGIITGARIDVSPKQLGYDVGCFIGIILK   77 (152)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTSEEEEEEEECTTTTTCCEEEEEEEEES
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHcCCcceEEEecCHHHcCCeEEEEEEEEEC
Confidence            57888878899999999998764              34689999999999999985     22 23654      3444


Q ss_pred             hHhhHHHHHHHhhh
Q 033029          114 GQRDLDQVAGRIVV  127 (129)
Q Consensus       114 G~~~lD~iA~~i~~  127 (129)
                      ....++.++..+..
T Consensus        78 ~~~~~~~~~~~l~~   91 (152)
T 2cg4_A           78 SAKDYPSALAKLES   91 (152)
T ss_dssp             SGGGHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHhC
Confidence            44568888887754

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=82.12  E-value=1.8  Score=34.78  Aligned_cols=57  Identities=12%  Similarity=0.218  Sum_probs=46.8

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ  120 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~  120 (129)
                      .++|.|  ++|..+..|...+|-.              -..++..|++|.++|+++...  |-.+|+.+...|.+
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            367877  7899999999987652              348999999999999998754  59999998877765

>3kfw_X Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.50A {Mycobacterium tuberculosis}

Probab=81.94  E-value=1.7  Score=34.36  Aligned_cols=72  Identities=11%  Similarity=0.076  Sum_probs=53.4

Q ss_pred             hHHHHHHHHHH---hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029           43 RAASMARKIYL---RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD  119 (129)
Q Consensus        43 R~ASilR~lYl---~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD  119 (129)
                      ++=|++=.|++   -+.+-++.|-...+.   -|+.        ...+|.+|--|-+.|+++... .|..||+.|++.++
T Consensus         4 ~arSlIlsll~g~~g~~i~~~~Li~l~~~---~Gi~--------e~avRtAlsRL~~~G~L~~~~-~GY~LT~~~~~~~~   71 (247)
T 3kfw_X            4 TARSVVLSVLLGAHPAWATASELIQLTAD---FGIK--------ETTLRVALTRMVGAGDLVRSA-DGYRLSDRLLARQR   71 (247)
T ss_dssp             CHHHHHHHHHTTTTTSCBCHHHHHHHHTT---TTCC--------HHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHH
T ss_pred             CCceeeEeeecCCCCCcccHHHHHHHHHH---cCCC--------hHHHHHHHHHHHHcCCeeccC-CceeeCHHHHHHHH
Confidence            44566666554   246777887777653   2443        368999999999999999865 58999999999888


Q ss_pred             HHHHHhh
Q 033029          120 QVAGRIV  126 (129)
Q Consensus       120 ~iA~~i~  126 (129)
                      +....|.
T Consensus        72 ~~~~rI~   78 (247)
T 3kfw_X           72 RQDEAMR   78 (247)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhc
Confidence            7766653

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=80.54  E-value=1.1  Score=34.74  Aligned_cols=57  Identities=18%  Similarity=0.160  Sum_probs=44.4

Q ss_pred             HhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029           42 VRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS  113 (129)
Q Consensus        42 ~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~  113 (129)
                      -|+..||..|.- .+++++..|....|-.              .+-+.++|+.|++.|||+++. +...|+++
T Consensus        21 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~--------------~stv~r~l~tL~~~G~v~~~~-~~Y~Lg~~   78 (265)
T 2ia2_A           21 ARGLAVIRCFDHRNQRRTLSDVARATDLT--------------RATARRFLLTLVELGYVATDG-SAFWLTPR   78 (265)
T ss_dssp             HHHHHHHHTCCSSCSSEEHHHHHHHHTCC--------------HHHHHHHHHHHHHHTSEEESS-SEEEECGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEecC-CEEEEcHH
Confidence            467778877654 4689999999987652              367889999999999999873 55677765

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=80.12  E-value=0.8  Score=32.78  Aligned_cols=23  Identities=35%  Similarity=0.485  Sum_probs=19.8

Q ss_pred             chhHHHHHHHHHHhCCceeecCC
Q 033029           83 SGAIARHILQQLQNMNIIDIEPK  105 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~  105 (129)
                      .||+.|.+|+.||+-|+|.....
T Consensus        72 ~gSLAR~aLreL~~kGlIk~V~k   94 (108)
T 3u5c_Z           72 GGSLARIALRHLEKEGIIKPISK   94 (108)
T ss_dssp             CTTHHHHHHHHHSSSSSCEEEEC
T ss_pred             hHHHHHHHHHHHHHCCCEEEEec
Confidence            57899999999999999986543

---

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	129
d2v7fa1	149	a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococ	4e-59

>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 =  177 bits (450), Expect = 4e-59
 Identities = 45/134 (33%), Positives = 63/134 (47%), Gaps = 14/134 (10%)

Query: 6   TVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKI 51
           TV DV     V+  +  LK   +               KE  P   DW+Y R AS+ R++
Sbjct: 2   TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 61

Query: 52  YLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111
           YL   +G+   R  YGG K  G  P  F K+ G+I R  LQQL+    ++  P  GR IT
Sbjct: 62  YLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 121

Query: 112 SSGQRDLDQVAGRI 125
             G+  LD++A  +
Sbjct: 122 PKGRSFLDKIATEL 135

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	129
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	100.0
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	97.53
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	96.85
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.78
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	96.71
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.68
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.67
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.66
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	96.36
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	96.27
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.27
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	96.23
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.2
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.06
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.05
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.87
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	95.79
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.75
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.68
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	95.64
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	95.61
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	95.48
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	95.33
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.92
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	94.91
d1ixsb1	76	Holliday junction helicase RuvB {Thermus thermophi	94.76
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.72
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	94.71
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	94.48
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	94.26
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	94.0
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	93.59
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	93.49
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	93.38
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	93.35
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	93.3
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.22
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.87
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	92.76
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.04
d2axla1	144	Werner syndrome ATP-dependent helicase WRN {Human	91.81
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	91.61
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	91.36
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	90.27
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	90.11
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	89.6
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	88.63
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	88.25
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	87.27
d1olta_	441	Oxygen-independent coproporphyrinogen III oxidase	86.64
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	85.22
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	83.37
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	83.03
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	82.86
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	82.07
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	81.19
d2fnaa1	73	Hypothetical protein SSO1545, C-terminal domain {S	80.78

>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=1.6e-66  Score=394.14  Aligned_cols=123  Identities=37%  Similarity=0.612  Sum_probs=112.5

Q ss_pred             CcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccC
Q 033029            5 RTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSK   70 (129)
Q Consensus         5 ~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k   70 (129)
                      .||||||||+||++||+|||++|+              |||+||+||||||+||||||||||++||+||++|++.|||+|
T Consensus         1 aTv~DVpa~~~I~~lA~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~y~RaASilRkiY~~gpvGv~~Lr~~YGg~k   80 (149)
T d2v7fa1           1 ATVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRK   80 (149)
T ss_dssp             CCGGGSCHHHHHHHHHHHHTTCTTCCCCSCGGGCCC------CHHHHTHHHHHHHHHHHHHHHHCSBCHHHHHHHHCC--
T ss_pred             CCccccCHHHHHHHHHHHHHhcCCCCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCC
Confidence            499999999999999999999987              999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhh
Q 033029           71 RNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV  127 (129)
Q Consensus        71 ~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~  127 (129)
                      |||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+||.+|..
T Consensus        81 ~rG~~P~h~~~~Sg~iiR~~LQqLE~~glVek~~~~GR~lT~~G~~~LD~iA~~v~~  137 (149)
T d2v7fa1          81 NRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKK  137 (149)
T ss_dssp             --CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCccHHHHHHHHHHHhCCCeeEcCCCCcEECHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999989999999999999999999975

>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=97.53  E-value=6.6e-05  Score=50.17  Aligned_cols=56  Identities=20%  Similarity=0.216  Sum_probs=45.5

Q ss_pred             HHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029           50 KIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD  117 (129)
Q Consensus        50 ~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~  117 (129)
                      ..|+.  -|+|...+...||-            +-|-+-||+.|++||+.|+|++.. .+||+.|.+|-+.
T Consensus        15 e~y~~~g~Pv~s~~i~~~~~l------------~~S~aTIRn~m~~LE~~G~l~~~h~s~GriPT~~g~r~   73 (87)
T d1stza1          15 REYIENKKPVSSQRVLEVSNI------------EFSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDKGLRF   73 (87)
T ss_dssp             HHHHHHCSCBCHHHHHHHSCC------------CSCHHHHHHHHHHHHHTTSEECCSSCSCBEECHHHHHH
T ss_pred             HHHHHcCCccCHHHHHHHhCC------------CCCHHHHHHHHHHHHHCCcccCCCCCCCCcccHHHHHH
Confidence            44664  49999999998764            336689999999999999999744 5799999999753

>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=96.85  E-value=0.0012  Score=42.52  Aligned_cols=60  Identities=22%  Similarity=0.346  Sum_probs=49.9

Q ss_pred             HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      +++-+++ +.|+|=..|+..-|-.              =.++|.-+.-|-+.|+|+..+ .|-.||++|++.|+++
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            5566664 7999999999987653              349999999999999999886 7999999999999876

>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=96.78  E-value=0.00095  Score=43.40  Aligned_cols=66  Identities=8%  Similarity=0.108  Sum_probs=51.5

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      +||..|+-+|++.++.|+...|-.              .+-+-..|..||+.|||+...  .++|    .||++|+..+.
T Consensus        20 ~IL~~L~~~~~~~~~eLa~~l~is--------------~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~   85 (100)
T d1ub9a_          20 GIMIFLLPRRKAPFSQIQKVLDLT--------------PGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAK   85 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHhccCCCeeHHHHHHHHhhc--------------cccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHH
Confidence            489999999999999999987553              246677799999999998654  2332    59999999888


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      ++...+
T Consensus        86 ~~~~~~   91 (100)
T d1ub9a_          86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765543

>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=96.71  E-value=0.0039  Score=42.30  Aligned_cols=64  Identities=13%  Similarity=0.142  Sum_probs=52.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+-+|++.++.|+..-+-              +.+-+-.+++.||+.|||++.  ++.+|    .||++|+..+++
T Consensus        39 vL~~l~~~~~~t~~ela~~~~i--------------~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  104 (138)
T d1jgsa_          39 VLCSIRCAACITPVELKKVLSV--------------DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             HHHHHHHHSSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             HHHhHHhCcCCCHHHHHHHHCC--------------CHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHH
Confidence            7888899999999999998665              345778899999999999864  44566    689999999988


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       105 ~~~~  108 (138)
T d1jgsa_         105 CHQL  108 (138)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7543

>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=96.68  E-value=0.0027  Score=43.28  Aligned_cols=64  Identities=17%  Similarity=0.227  Sum_probs=51.2

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.+..|.+.-+-.              .+-+-++++.||+.|||++.+  +.+|    .||++|+..++.
T Consensus        41 vL~~l~~~~~~t~~~la~~l~~~--------------~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          41 VLKLIDEQRGLNLQDLGRQMCRD--------------KALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHSSTTCBHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCcc--------------HhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            67777888889999999986543              357888999999999998654  4465    589999999888


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       107 ~~~~  110 (141)
T d1lnwa_         107 AEAI  110 (141)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>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=96.67  E-value=0.0015  Score=44.40  Aligned_cols=64  Identities=20%  Similarity=0.361  Sum_probs=52.1

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+-.||+.+..|+..-|-.              .+-+-.+++.||+.|||++..  +.+|    .||++|+..+++
T Consensus        35 iL~~i~~~~~~t~~~la~~l~i~--------------~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~  100 (139)
T d2a61a1          35 ILQKIYFEGPKRPGELSVLLGVA--------------KSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  100 (139)
T ss_dssp             HHHHHHHHCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHhCCC--------------cccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHH
Confidence            78888999999999999986653              245788999999999998654  3455    489999999998


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +...
T Consensus       101 ~~~~  104 (139)
T d2a61a1         101 VIER  104 (139)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8654

>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=96.66  E-value=0.0031  Score=42.80  Aligned_cols=64  Identities=16%  Similarity=0.201  Sum_probs=52.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+-.||+.++.|++..+-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++.
T Consensus        40 iL~~l~~~~~~t~~~la~~~~i--------------~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~~  105 (143)
T d1s3ja_          40 VLASLKKHGSLKVSEIAERMEV--------------KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  105 (143)
T ss_dssp             HHHHHHHHSEEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHHH
Confidence            7888999999999999998765              2457888999999999998544  4466    699999999888


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +-..
T Consensus       106 ~~~~  109 (143)
T d1s3ja_         106 VLAG  109 (143)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

>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=96.36  E-value=0.0063  Score=40.63  Aligned_cols=66  Identities=8%  Similarity=0.089  Sum_probs=51.3

Q ss_pred             HHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      +|.+||..+  ++.+..|++..+-              +.+-+=.+++.||+.|||++.+  +.+|    .|||+|++.+
T Consensus        38 vL~~l~~~~~~~~t~~~la~~l~~--------------~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  103 (115)
T d2frha1          38 VLTYISENKEKEYYLKDIINHLNY--------------KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKI  103 (115)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSS--------------HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHCC--------------CHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHH
Confidence            677888864  4778889987553              3456778999999999998765  3455    4999999999


Q ss_pred             HHHHHHhh
Q 033029          119 DQVAGRIV  126 (129)
Q Consensus       119 D~iA~~i~  126 (129)
                      +.+..++-
T Consensus       104 ~~~~~~~~  111 (115)
T d2frha1         104 ESLLSRVN  111 (115)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887763

>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=96.27  E-value=0.0032  Score=42.49  Aligned_cols=66  Identities=15%  Similarity=0.135  Sum_probs=52.4

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      ++|..|+-.|++.+..|+...|-.              .+-+=.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        34 ~vL~~l~~~~~~t~~~la~~~~i~--------------~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~   99 (136)
T d2fbia1          34 RVIRILRQQGEMESYQLANQACIL--------------RPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFV   99 (136)
T ss_dssp             HHHHHHHHHCSEEHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHH
Confidence            478888889999999999986653              246778999999999998654  4455    47999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      .+-...
T Consensus       100 ~~~~~~  105 (136)
T d2fbia1         100 SMSGDM  105 (136)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.27  E-value=0.0094  Score=40.13  Aligned_cols=65  Identities=9%  Similarity=0.110  Sum_probs=52.8

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||-.|+-.|++.++.|+...|-              +.+-+-.++..||+.|||++.+  ..+|    .||++|+..++.
T Consensus        37 iL~~l~~~~~~t~~~La~~l~i--------------~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d2etha1          37 AFLYVALFGPKKMKEIAEFLST--------------TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  102 (140)
T ss_dssp             HHHHHHHHCCBCHHHHHHHTTS--------------CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHH
Confidence            7888899999999999998664              3357788999999999998654  3454    589999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       103 ~~~~~  107 (140)
T d2etha1         103 ILSNF  107 (140)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

>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=96.23  E-value=0.018  Score=39.15  Aligned_cols=65  Identities=9%  Similarity=0.101  Sum_probs=52.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+-++|+.+..|+...+-.              .+-+-.+++.||+.|||++.+  +.+|    .||++|+...++
T Consensus        34 iL~~i~~~~~~t~~~la~~l~i~--------------~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          34 YLVRVCENPGIIQEKIAELIKVD--------------RTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCcc--------------HhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHH
Confidence            77788889999999999987653              357888999999999998654  3454    589999999988


Q ss_pred             HHHHh
Q 033029          121 VAGRI  125 (129)
Q Consensus       121 iA~~i  125 (129)
                      +...+
T Consensus       100 ~~~~~  104 (144)
T d1lj9a_         100 IVREN  104 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>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=96.20  E-value=0.018  Score=35.97  Aligned_cols=60  Identities=10%  Similarity=-0.051  Sum_probs=49.5

Q ss_pred             HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029           42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ  115 (129)
Q Consensus        42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~  115 (129)
                      -|+.+||..|.-. +|+++..+.+.-|-              +.+-+.++|+.||+.|||++++++--.|+++--
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~--------------~~st~~rll~tL~~~g~l~~~~~g~y~lG~~l~   65 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNM--------------SVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLI   65 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECTHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEECCCCCEeecHHHH
Confidence            4889999998875 58999999998554              346899999999999999998876677887654

>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=96.06  E-value=0.0029  Score=42.12  Aligned_cols=40  Identities=23%  Similarity=0.309  Sum_probs=34.0

Q ss_pred             CCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029           81 KSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV  121 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i  121 (129)
                      .=|-..+.+.|+.|++.|+|++.. +.-.||++|+.+|+.+
T Consensus        29 NLs~~~~~kyl~~L~~~GLI~~~~-~~Y~iT~kG~~~L~~~   68 (90)
T d1r7ja_          29 NLSYALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDI   68 (90)
T ss_dssp             TCCHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCeeecC-CEEEECccHHHHHHHH
Confidence            444568899999999999999864 5789999999998875

>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=96.05  E-value=0.014  Score=38.89  Aligned_cols=87  Identities=9%  Similarity=0.141  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHH
Q 033029           13 HEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHI   90 (129)
Q Consensus        13 ~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~   90 (129)
                      ..+...+.+.|++.|    +.  .+.|.      ||..||-++  ++.+..|+..-|-              +.+-+-.+
T Consensus        12 ~~~~~~~~~~l~~~g----lt--~~q~~------vL~~l~~~~~~~it~~ela~~~~~--------------~~~~vs~~   65 (135)
T d3broa1          12 NQMSTRFDIFAKKYD----LT--GTQMT------IIDYLSRNKNKEVLQRDLESEFSI--------------KSSTATVL   65 (135)
T ss_dssp             HHHHHHHHHHHHTTT----CC--HHHHH------HHHHHHHTTTSCCBHHHHHHHHTC--------------CHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC----CC--HHHHH------HHHHHHHcCCCCCCHHHHHHHHCc--------------CHhHHHHH
Confidence            344555666666543    22  22344      677778764  4888899997654              33567789


Q ss_pred             HHHHHhCCceeecC--CCCc----eeCcchHhhHHHHHHHh
Q 033029           91 LQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQVAGRI  125 (129)
Q Consensus        91 lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~iA~~i  125 (129)
                      ++.||+.|||++..  +.+|    .|||+|+..+.++...+
T Consensus        66 l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~  106 (135)
T d3broa1          66 LQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYM  106 (135)
T ss_dssp             HHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHHHHHHH
Confidence            99999999997543  3453    68999999999887654

>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=95.87  E-value=0.0048  Score=39.83  Aligned_cols=56  Identities=21%  Similarity=0.161  Sum_probs=43.7

Q ss_pred             CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCce----eCcchHhhHHHHHHHh
Q 033029           55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR----ITSSGQRDLDQVAGRI  125 (129)
Q Consensus        55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~----lT~~G~~~lD~iA~~i  125 (129)
                      +++.++.|+..-|-              +.+-+-.+|+.||+.|||+...+ ||.    ||++|+..+.+...++
T Consensus        20 ~~lt~~eLa~~l~i--------------~~~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~G~~~l~~~~~~~   79 (85)
T d3ctaa1          20 AYLTSSKLADMLGI--------------SQQSASRIIIDLEKNGYITRTVT-KRGQILNITEKGLDVLYTEFADL   79 (85)
T ss_dssp             EECCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeecc-cccccceECHHHHHHHHHHHHHH
Confidence            46778888887554              23467789999999999998654 453    7999999999887665

>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=95.79  E-value=0.01  Score=39.97  Aligned_cols=63  Identities=10%  Similarity=0.163  Sum_probs=49.8

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+-++++.++.|+..-|-.+              +-+-.+++.||+.|||++..  ..+|    .||++|+..++.
T Consensus        39 vL~~i~~~~~~t~~~la~~l~~~~--------------~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~  104 (136)
T d2bv6a1          39 VLTILWDESPVNVKKVVTELALDT--------------GTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  104 (136)
T ss_dssp             HHHHHHHSSEEEHHHHHHHTTCCT--------------TTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHCCCH--------------hHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHH
Confidence            778889999999999999866532              35778999999999998543  3455    469999998887


Q ss_pred             HHH
Q 033029          121 VAG  123 (129)
Q Consensus       121 iA~  123 (129)
                      +..
T Consensus       105 ~~~  107 (136)
T d2bv6a1         105 LSN  107 (136)
T ss_dssp             HTT
T ss_pred             HHH
Confidence            643

>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=95.75  E-value=0.0041  Score=42.08  Aligned_cols=61  Identities=11%  Similarity=0.142  Sum_probs=47.7

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      +|..|+.++++.+..|+..-|-.              .+-+=++++.||+.|||+..+  +.+|    .||++|+...++
T Consensus        38 vL~~l~~~~~~t~~~La~~~~i~--------------~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  103 (137)
T d1z91a1          38 ALLLLWEHETLTVKKMGEQLYLD--------------SGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  103 (137)
T ss_dssp             HHHHHHHHSEEEHHHHHHTTTCC--------------HHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHHHH
Confidence            66788889999999999965432              234556999999999998654  4577    799999998776


Q ss_pred             H
Q 033029          121 V  121 (129)
Q Consensus       121 i  121 (129)
                      +
T Consensus       104 ~  104 (137)
T d1z91a1         104 A  104 (137)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=95.68  E-value=0.019  Score=38.28  Aligned_cols=69  Identities=10%  Similarity=0.187  Sum_probs=52.9

Q ss_pred             CchHHHhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----e
Q 033029           37 PDWYYVRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----R  109 (129)
Q Consensus        37 ~DW~Y~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~  109 (129)
                      +.|.      +|..|+-.+ ++.++.|+...+-.              .+-+-.++..||+.|||++.+  ..+|    .
T Consensus        29 ~q~~------iL~~l~~~~~~~t~~~la~~~~~~--------------~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~   88 (137)
T d2fbha1          29 ARWL------VLLHLARHRDSPTQRELAQSVGVE--------------GPTLARLLDGLESQGLVRRLAVAEDRRAKHIV   88 (137)
T ss_dssp             THHH------HHHHHHHCSSCCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCBTTBCSCEEE
T ss_pred             HHHH------HHHHHHHcCCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHcCCccccCCCCCCCchhhh
Confidence            4676      677777555 58899999987653              246888999999999999765  3344    5


Q ss_pred             eCcchHhhHHHHHHHh
Q 033029          110 ITSSGQRDLDQVAGRI  125 (129)
Q Consensus       110 lT~~G~~~lD~iA~~i  125 (129)
                      ||++|+..++++....
T Consensus        89 lT~~G~~~~~~~~~~~  104 (137)
T d2fbha1          89 LTPKADVLIADIEAIA  104 (137)
T ss_dssp             ECTTHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHH
Confidence            9999999999876543

>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=95.64  E-value=0.025  Score=38.21  Aligned_cols=64  Identities=16%  Similarity=0.175  Sum_probs=48.9

Q ss_pred             HHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      +|..||-. |++.+..|+...|-.              .+-+-.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        39 vL~~L~~~~g~~t~~~La~~~~~~--------------~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~  104 (145)
T d2hr3a1          39 VLGAIDRLGGDVTPSELAAAERMR--------------SSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLY  104 (145)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHTTCC--------------HHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHH
Confidence            77778765 579999999987653              346778999999999999765  2344    58999999998


Q ss_pred             HHHHH
Q 033029          120 QVAGR  124 (129)
Q Consensus       120 ~iA~~  124 (129)
                      ++...
T Consensus       105 ~~~~~  109 (145)
T d2hr3a1         105 GNRAK  109 (145)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87644

>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=95.61  E-value=0.01  Score=39.59  Aligned_cols=66  Identities=9%  Similarity=0.195  Sum_probs=51.4

Q ss_pred             HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029           47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l  118 (129)
                      +|..||..  +++.+..|+...|-              +.+-+=.+++.||+.|||++..  +.+|    .||++|+..+
T Consensus        37 vL~~l~~~~~~~~t~~ela~~l~~--------------~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  102 (115)
T d1hsja1          37 ILNHILRSESNEISSKEIAKCSEF--------------KPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  102 (115)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHSSCC--------------CHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHccCCCCcCHHHHHHHHCC--------------ChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHH
Confidence            88889874  46888899986554              2345667899999999998654  4566    4899999999


Q ss_pred             HHHHHHhh
Q 033029          119 DQVAGRIV  126 (129)
Q Consensus       119 D~iA~~i~  126 (129)
                      +.+..++-
T Consensus       103 ~~~~~~~~  110 (115)
T d1hsja1         103 QKLISELE  110 (115)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHHHHH
Confidence            99887753

>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=95.48  E-value=0.011  Score=39.28  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=33.6

Q ss_pred             cCCchhHHHHHHHHHHhCCceeec---CCCCc-----eeCcchHhhHHHHHHH
Q 033029           80 CKSSGAIARHILQQLQNMNIIDIE---PKGGR-----RITSSGQRDLDQVAGR  124 (129)
Q Consensus        80 ~~asg~iiR~~lqqLE~~g~vek~---~~~GR-----~lT~~G~~~lD~iA~~  124 (129)
                      ..-|-+.|=.+|..||+.|||+..   ..+||     .||++|+..|.+...+
T Consensus        38 ~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~~~~~~   90 (103)
T d1xmaa_          38 YVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKCEE   90 (103)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHHHH
T ss_pred             ecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHHHHHHH
Confidence            445557888999999999999732   23453     7999999999876654

>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=95.33  E-value=0.012  Score=38.31  Aligned_cols=57  Identities=18%  Similarity=0.274  Sum_probs=41.7

Q ss_pred             HHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029           48 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        48 lR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      +-.-|--||||+..|+..-|-.+             ..|.=-+===|-+.|+|++++ .||++|++|.+.|
T Consensus        14 l~~~f~ggPvGl~tlAa~l~e~~-------------~TiEdviEPyLiq~G~i~RTp-RGR~~T~~~~~hl   70 (75)
T d1in4a1          14 IIEIYRGGPVGLNALAASLGVEA-------------DTLSEVYEPYLLQAGFLARTP-RGRIVTEKAYKHL   70 (75)
T ss_dssp             HHHHSTTCCBCHHHHHHHHTSCH-------------HHHHHHTHHHHHHTTSEEEET-TEEEECHHHHHHT
T ss_pred             HHHHhCCCCCcHHHHHHHHcCCh-------------hHHHHHhhHHHHHhhHHhhCC-chHHhHHHHHHHc
Confidence            34445668999999999877532             233333334577899999998 5999999998765

>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=94.92  E-value=0.035  Score=36.11  Aligned_cols=67  Identities=13%  Similarity=0.171  Sum_probs=50.0

Q ss_pred             HHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC----CCc--eeCcchHhh
Q 033029           45 ASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK----GGR--RITSSGQRD  117 (129)
Q Consensus        45 ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~----~GR--~lT~~G~~~  117 (129)
                      ..||..|+- .||+.+..|+...|-.              .+-+..+|+.||+.|||++.+.    +||  .+|..|.+.
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~--------------~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~~~~~~~~   89 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLS--------------KTTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSISSNI   89 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEEC-------CCEEEEECTTH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcc--------------HhHHHHHHHHHHHCCCEEEeecCCCCCceeEEEeeCCHHH
Confidence            347777775 5789999999987653              4589999999999999986542    233  678888888


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      ..+|...+
T Consensus        90 ~~~i~~~~   97 (109)
T d2d1ha1          90 LEKIRNDL   97 (109)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77776654

>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=94.91  E-value=0.04  Score=36.99  Aligned_cols=57  Identities=11%  Similarity=0.183  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchH
Q 033029           44 AASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ  115 (129)
Q Consensus        44 ~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~  115 (129)
                      |.-+|=.|..++++....++..+|-              +-+++|++|++|.++|+|+...  .||+ |+..-.
T Consensus         6 Av~~L~~la~~~~~ss~~IA~~~~~--------------~~~~v~kIl~~L~~aglV~s~rG~~GGy-Lar~p~   64 (127)
T d1xd7a_           6 AIHILSLISMDEKTSSEIIADSVNT--------------NPVVVRRMISLLKKADILTSRAGVPGAS-LKKDPA   64 (127)
T ss_dssp             HHHHHHHHHTCSCCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEECCSSSSSCE-ESSCGG
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHhCcccccCCCCCcc-ccCCHH
Confidence            4444555566889999999998765              3369999999999999998654  4686 876543

>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=94.76  E-value=0.016  Score=37.84  Aligned_cols=54  Identities=15%  Similarity=0.185  Sum_probs=39.7

Q ss_pred             HHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029           51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        51 lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      -|--||||+..|+..-|-.+.             .|.=-+===|-+.|+|++++ .||++|++|.+-|
T Consensus        17 ~f~ggPVGl~tlA~~lgE~~~-------------TiEdviEPyLiq~G~i~RTp-rGR~~T~~a~~hL   70 (76)
T d1ixsb1          17 RFGGGPVGLATLATALSEDPG-------------TLEEVHEPYLIRQGLLKRTP-RGRVATELAYRHL   70 (76)
T ss_dssp             SSCSSCCCSHHHHGGGSSCTT-------------HHHHTSHHHHHHTTSEEECS-SSEEECHHHHHHH
T ss_pred             HhCCCCccHHHHHHHHcCChh-------------HHHHHhhHHHHHHhHHhhCC-ChHHhHHHHHHHc
Confidence            345689999999998776432             23333333467899999998 5999999998765

>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=94.72  E-value=0.069  Score=35.50  Aligned_cols=65  Identities=14%  Similarity=0.149  Sum_probs=46.5

Q ss_pred             HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029           47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD  119 (129)
Q Consensus        47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD  119 (129)
                      +|..|+- .+++-++.|....+-.              .+-+=.+++.||+.|||++.+  +.+|    .||++|+..++
T Consensus        36 ~L~~l~~~~~~~t~~~la~~l~i~--------------~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~  101 (140)
T d3deua1          36 TLHNIHQLPPDQSQIQLAKAIGIE--------------QPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIA  101 (140)
T ss_dssp             HHHHHHHSCSSEEHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCccHHHHHHHHCCC--------------HhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHH
Confidence            6677775 4568888999976653              234557999999999998654  3454    49999999999


Q ss_pred             HHHHHh
Q 033029          120 QVAGRI  125 (129)
Q Consensus       120 ~iA~~i  125 (129)
                      ++...+
T Consensus       102 ~~~~~~  107 (140)
T d3deua1         102 EMEEVI  107 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=94.71  E-value=0.027  Score=37.89  Aligned_cols=66  Identities=9%  Similarity=0.017  Sum_probs=49.8

Q ss_pred             HHHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhh
Q 033029           46 SMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD  117 (129)
Q Consensus        46 SilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~  117 (129)
                      .||..||-.+  ++.+..|+...+-              +.+-+-.+++.||+.|||++..  +..|    .||++|+..
T Consensus        38 ~iL~~l~~~~~~~~t~~eia~~~~~--------------~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~  103 (125)
T d1p4xa1          38 ILLTYLFHQQENTLPFKKIVSDLCY--------------KQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREK  103 (125)
T ss_dssp             HHHHHHHSCSCSEEEHHHHHHHSSS--------------CGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHH
T ss_pred             HHHHHHHHhccCCcCHHHHHHHhCC--------------CcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHH
Confidence            4788888864  6788899987553              2345667899999999998754  3455    489999999


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      +..+...+
T Consensus       104 ~~~~~~~~  111 (125)
T d1p4xa1         104 IAERVTLF  111 (125)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876654

>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=94.48  E-value=0.039  Score=38.90  Aligned_cols=64  Identities=11%  Similarity=0.129  Sum_probs=49.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ  120 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~  120 (129)
                      ||..|+-.+++.++.|++.-+-.              .+-+=.+++.||+.|||++.+  ...|    .||++|+..++.
T Consensus        46 vL~~l~~~~~~t~~~la~~~~l~--------------~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          46 ILWIAYQLNGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             HHHHHHHHTSEEHHHHHHHTTCC--------------HHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHhhhccCCCcCHHHHHHHHcCC--------------chhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHH
Confidence            78888889999999999975542              346778999999999999655  3455    489999999988


Q ss_pred             HHHH
Q 033029          121 VAGR  124 (129)
Q Consensus       121 iA~~  124 (129)
                      +-..
T Consensus       112 ~~~~  115 (162)
T d2fxaa1         112 LLEE  115 (162)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>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=94.26  E-value=0.024  Score=39.85  Aligned_cols=65  Identities=14%  Similarity=0.174  Sum_probs=45.6

Q ss_pred             HHHHHHHhCC---CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhh
Q 033029           47 MARKIYLRQG---LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRD  117 (129)
Q Consensus        47 ilR~lYl~g~---vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~  117 (129)
                      ||..||..|+   +.++.|+...|-.+.              -+=.+++.||+.|||++..  ..+|    .||++|+..
T Consensus        67 vL~~L~~~~~~~~lt~~eLa~~l~i~~~--------------tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l  132 (172)
T d2fbka1          67 LLLTLYRSAPPEGLRPTELSALAAISGP--------------STSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  132 (172)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSCCSG--------------GGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHCcCHh--------------HHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHH
Confidence            7788887764   678888887655321              2224689999999999765  3344    599999999


Q ss_pred             HHHHHHHh
Q 033029          118 LDQVAGRI  125 (129)
Q Consensus       118 lD~iA~~i  125 (129)
                      ++.+...+
T Consensus       133 ~~~~~~~~  140 (172)
T d2fbka1         133 VTHLLPAH  140 (172)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876553

>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=94.00  E-value=0.031  Score=39.29  Aligned_cols=71  Identities=13%  Similarity=0.159  Sum_probs=48.5

Q ss_pred             HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc------eeCcchHhhH
Q 033029           47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR------RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR------~lT~~G~~~l  118 (129)
                      ||=-|.- +|.-=-.|++.+..      ...+|...|-+-|=.+|+.||+.|||+...  .+|+      .||++|+..|
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            3444443 44444447777643      246777888899999999999999997432  2233      7999999999


Q ss_pred             HHHHHH
Q 033029          119 DQVAGR  124 (129)
Q Consensus       119 D~iA~~  124 (129)
                      .+...+
T Consensus        79 ~~wl~~   84 (178)
T d1yg2a_          79 GEWFDQ   84 (178)
T ss_dssp             HHHHHS
T ss_pred             HHHHhc
Confidence            886544

>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=93.59  E-value=0.029  Score=35.15  Aligned_cols=43  Identities=12%  Similarity=0.025  Sum_probs=35.3

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG  114 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G  114 (129)
                      ....|+..||-              |.+.+|.+|+.||+.|+|+..+..|-.+++.-
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            56778887765              45799999999999999999887788877653

>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=93.49  E-value=0.15  Score=33.19  Aligned_cols=83  Identities=19%  Similarity=0.231  Sum_probs=55.9

Q ss_pred             HHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHh
Q 033029           17 KAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQN   96 (129)
Q Consensus        17 ~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~   96 (129)
                      ..+.+.|++-|    +.|.+        +.|+..|+-+|+..+..+++.-|-              +.+-+..+|+.||+
T Consensus         7 ~~l~~~L~~lG----lt~~e--------~~v~~~L~~~g~~t~~eia~~~~i--------------~~~~v~~~l~~L~~   60 (109)
T d1sfxa_           7 GELVKALEKLS----FKPSD--------VRIYSLLLERGGMRVSEIARELDL--------------SARFVRDRLKVLLK   60 (109)
T ss_dssp             HHHHHHHHHTC----CCHHH--------HHHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC----CCHHH--------HHHHHHHHhcCCCCHHHHHHHhCC--------------CcchHHHHHHHHHh
Confidence            44556666654    33333        668888888999999999998664              33578999999999


Q ss_pred             CCceeec--CCCCce--eC-cchHhhHHHHHHHh
Q 033029           97 MNIIDIE--PKGGRR--IT-SSGQRDLDQVAGRI  125 (129)
Q Consensus        97 ~g~vek~--~~~GR~--lT-~~G~~~lD~iA~~i  125 (129)
                      .|||++.  +++||.  .+ ......|+++...+
T Consensus        61 ~GlV~r~~~~~~~r~~~~~a~~~~e~l~~~~~~~   94 (109)
T d1sfxa_          61 RGFVRREIVEKGWVGYIYSAEKPEKVLKEFKSSI   94 (109)
T ss_dssp             TTSEEEEEEESSSEEEEEEECCHHHHHHHHHHHH
T ss_pred             CCCEEEEeccCCCccccccCCCHHHHHHHHHHHH
Confidence            9999854  344542  22 22345566665443

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=93.38  E-value=0.033  Score=34.29  Aligned_cols=41  Identities=15%  Similarity=0.061  Sum_probs=33.2

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      -...|+..||-              |...+|.+|+.||+.|+|+..++.|-.+++
T Consensus        27 ~~~~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~~~G~~V~~   67 (69)
T d2hs5a1          27 SEPDICAALDV--------------SRNTVREAFQILIEDRLVAHELNRGVFVRV   67 (69)
T ss_dssp             CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCCEEEecC
Confidence            35678888875              446999999999999999998877877653

>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=93.35  E-value=0.083  Score=35.36  Aligned_cols=63  Identities=13%  Similarity=0.205  Sum_probs=47.6

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC------ceeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG------RRITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G------R~lT~~G~~~l  118 (129)
                      .-|++.|+ .|+.--+.|.+.-.             .-|.+++=.-|++||+.|+|++.....      ..||+.|++++
T Consensus        22 ~~Il~~L~-~g~~RF~el~~~l~-------------gIS~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~~G~~L~   87 (108)
T d1z7ua1          22 LSLMDELF-QGTKRNGELMRALD-------------GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALY   87 (108)
T ss_dssp             HHHHHHHH-HSCBCHHHHHHHST-------------TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHCc-------------CCChhHHHHHHHHHHHCCcceeeccCCCcceehhhhchhHHHHH
Confidence            34888886 58877777777532             346689999999999999999754222      78999999887


Q ss_pred             HHH
Q 033029          119 DQV  121 (129)
Q Consensus       119 D~i  121 (129)
                      .-+
T Consensus        88 pil   90 (108)
T d1z7ua1          88 DAL   90 (108)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>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=93.30  E-value=0.15  Score=33.13  Aligned_cols=63  Identities=8%  Similarity=0.101  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC------ceeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG------RRITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G------R~lT~~G~~~l  118 (129)
                      .-|++.+ ..|+...+.|.+.-.             .-|-+++=.-|++||+.|+|++.....      ..||+.|++++
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            4588887 478887777776431             356679999999999999999765222      78999999987


Q ss_pred             HHH
Q 033029          119 DQV  121 (129)
Q Consensus       119 D~i  121 (129)
                      .-+
T Consensus        80 pil   82 (95)
T d2hzta1          80 GIL   82 (95)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=93.22  E-value=0.036  Score=37.53  Aligned_cols=65  Identities=11%  Similarity=0.086  Sum_probs=48.6

Q ss_pred             HHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc----eeCcchHhhH
Q 033029           47 MARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDL  118 (129)
Q Consensus        47 ilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR----~lT~~G~~~l  118 (129)
                      ||-.||-.+  ++.++.++..-|-              +.+-+-.+++.||+.|||++.  ++.+|    .||++|++.+
T Consensus        38 vL~~l~~~~~~~~~~~~ia~~l~~--------------~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~  103 (125)
T d1p4xa2          38 ILAIITSQNKNIVLLKDLIETIHH--------------KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHA  103 (125)
T ss_dssp             HHHHHHTTTTCCEEHHHHHHHSSS--------------CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHH
T ss_pred             HHHHHHHccCCCccHHHHHHHHCC--------------CcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHH
Confidence            677777643  5667788886553              234677899999999999864  34566    4899999999


Q ss_pred             HHHHHHh
Q 033029          119 DQVAGRI  125 (129)
Q Consensus       119 D~iA~~i  125 (129)
                      +.+..++
T Consensus       104 ~~l~~~~  110 (125)
T d1p4xa2         104 EQLLAQV  110 (125)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9987765

>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=92.87  E-value=0.66  Score=30.51  Aligned_cols=77  Identities=13%  Similarity=0.136  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHH
Q 033029           13 HEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHIL   91 (129)
Q Consensus        13 ~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~l   91 (129)
                      ..|++.+++.++.-|    +++        -++.|+-.||+.+ |+.+..|+..-|-              |.+-+-.+|
T Consensus         9 ~~~~~~~~~~~~~~G----l~~--------~~~~i~~~L~~~~~plt~~ela~~l~v--------------sk~~vs~~l   62 (151)
T d1ku9a_           9 KLIIELFSELAKIHG----LNK--------SVGAVYAILYLSDKPLTISDIMEELKI--------------SKGNVSMSL   62 (151)
T ss_dssp             HHHHHHHHHHHHHTT----CCH--------HHHHHHHHHHHCSSCEEHHHHHHHHTC--------------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC----CCH--------HHHHHHHHHHhCCCCcCHHHHHHHhCC--------------CcchHHHHH
Confidence            679999999999886    333        4588999999875 7999999998654              446788999


Q ss_pred             HHHHhCCceeecCC--CC----ceeCcchH
Q 033029           92 QQLQNMNIIDIEPK--GG----RRITSSGQ  115 (129)
Q Consensus        92 qqLE~~g~vek~~~--~G----R~lT~~G~  115 (129)
                      +.||+.|+|....+  ..    ..+|++|+
T Consensus        63 ~~L~~~GlV~r~~~~~drr~~~~~~t~~g~   92 (151)
T d1ku9a_          63 KKLEELGFVRKVWIKGERKNYYEAVDGFSS   92 (151)
T ss_dssp             HHHHHTTSEEEECCTTCSSCEEEECCHHHH
T ss_pred             HHHHHCCCEEEEEcCCCCceeEEeCCHHHH
Confidence            99999999986542  22    36788885

>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=92.76  E-value=0.055  Score=36.20  Aligned_cols=45  Identities=18%  Similarity=0.226  Sum_probs=34.0

Q ss_pred             CCchhHHHHHHHHHHhCCceeec--CCCC-----ceeCcchHhhHHHHHHHh
Q 033029           81 KSSGAIARHILQQLQNMNIIDIE--PKGG-----RRITSSGQRDLDQVAGRI  125 (129)
Q Consensus        81 ~asg~iiR~~lqqLE~~g~vek~--~~~G-----R~lT~~G~~~lD~iA~~i  125 (129)
                      ..+-+.|=.+|+.||+.|||+..  +.+|     -.||++|+..|+....++
T Consensus        43 ~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~~~~~~~   94 (114)
T d2esha1          43 IGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSL   94 (114)
T ss_dssp             CCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            34445788999999999999742  2334     269999999998876664

>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=92.04  E-value=0.075  Score=33.03  Aligned_cols=42  Identities=21%  Similarity=0.185  Sum_probs=32.8

Q ss_pred             CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029           56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI  110 (129)
Q Consensus        56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l  110 (129)
                      |..+..++..+|-             .|-+-++..|.+||+.|||++.+...|.|
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            5677777777663             25678999999999999999987655654

>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=91.81  E-value=0.11  Score=35.97  Aligned_cols=77  Identities=14%  Similarity=0.155  Sum_probs=55.8

Q ss_pred             HHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCc-----ccCC---chhHHHHHHHHHHhCCceeecCCCCc-----e
Q 033029           44 AASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPH-----FCKS---SGAIARHILQQLQNMNIIDIEPKGGR-----R  109 (129)
Q Consensus        44 ~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h-----~~~a---sg~iiR~~lqqLE~~g~vek~~~~GR-----~  109 (129)
                      |-.||..|+- .+..|++.+..++-|.++.-++..|     |..|   +-.-++.++.||-..|+++.....|.     .
T Consensus        15 A~~iLs~V~~~~~rfg~~~iidiL~Gs~~~kI~~~~~~l~~yG~Gk~~s~~~w~~li~qli~~G~L~e~~~~~~~~~~l~   94 (144)
T d2axla1          15 AFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICA   94 (144)
T ss_dssp             HHHHHHHHHHTTTCSCSHHHHHHHTCCSCSHHHHHTCSCTTTTGGGGSCHHHHHHHHHHHHHHSSEEEETTSCTTTCEEE
T ss_pred             HHHHHHHHHHhcccccchHHHHHHHhcccHHHHHHhhcccccCCCCcCCHHHHHHHHHHHHHcCcceeecccCcceeeee
Confidence            3446666665 5689999999999888776443222     2222   34679999999999999976655553     7


Q ss_pred             eCcchHhhHHH
Q 033029          110 ITSSGQRDLDQ  120 (129)
Q Consensus       110 lT~~G~~~lD~  120 (129)
                      ||++|+..|..
T Consensus        95 lt~kg~~~L~g  105 (144)
T d2axla1          95 LTKKGRNWLHK  105 (144)
T ss_dssp             ECHHHHHHHHH
T ss_pred             ECHHHHHHHhc
Confidence            99999999864

>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=91.61  E-value=0.19  Score=33.82  Aligned_cols=63  Identities=17%  Similarity=0.150  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CC-----ceeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GG-----RRITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~G-----R~lT~~G~~~l  118 (129)
                      .-|++.|+ .|+...+.|.+.-.             .-|.+++=.-|.+||+.|+|++... ..     ..||+.|++++
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            45888886 78887788877532             3456788888999999999997652 22     68999999987


Q ss_pred             HHH
Q 033029          119 DQV  121 (129)
Q Consensus       119 D~i  121 (129)
                      .-+
T Consensus        93 ~il   95 (114)
T d1yyva1          93 DKV   95 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=91.36  E-value=0.23  Score=34.66  Aligned_cols=62  Identities=18%  Similarity=0.275  Sum_probs=46.1

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-C----CceeCcchHhhHH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-G----GRRITSSGQRDLD  119 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~----GR~lT~~G~~~lD  119 (129)
                      .-|+|.++ .|+...+.|.+.-|              -|.+++-.-|++||+.|+|++... .    -..||++|++++.
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            45888875 68887888877542              344688888999999999997332 1    2689999998865


Q ss_pred             HH
Q 033029          120 QV  121 (129)
Q Consensus       120 ~i  121 (129)
                      -+
T Consensus        88 il   89 (142)
T d2f2ea1          88 LL   89 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=90.27  E-value=0.14  Score=33.39  Aligned_cols=73  Identities=18%  Similarity=0.248  Sum_probs=49.6

Q ss_pred             CCCCCchHHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029           33 APYDPDWYYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK  105 (129)
Q Consensus        33 aP~d~DW~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~  105 (129)
                      +|..+-  |...+.-+|..=..|-      + .+..|+..||-.              ...+|.+|+.|++.|||+..+.
T Consensus         5 ~p~~~~--y~qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~vS--------------r~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1           5 APEGKG--YADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVA--------------AKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             CCSSCC--HHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSC--------------TTHHHHHTTTTTTSSCCEEETT
T ss_pred             CCCCCH--HHHHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCCC--------------HHHHHHHHHHHHHCCcEEEecC
Confidence            344444  4455666666655552      3 567788888653              3589999999999999998887


Q ss_pred             CCceeCcc--hHhhHHHH
Q 033029          106 GGRRITSS--GQRDLDQV  121 (129)
Q Consensus       106 ~GR~lT~~--G~~~lD~i  121 (129)
                      .|-.+++.  -....|++
T Consensus        69 ~G~~V~~~~~~~~~~~~~   86 (100)
T d1v4ra1          69 LGTVVEKNPIVITGADRL   86 (100)
T ss_dssp             TEEESCSCCCCCSSHHHH
T ss_pred             CEEEECCCCcccchHHHH
Confidence            78888753  22344444

>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=90.11  E-value=0.45  Score=28.62  Aligned_cols=47  Identities=13%  Similarity=0.069  Sum_probs=40.7

Q ss_pred             hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029           43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE  103 (129)
Q Consensus        43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~  103 (129)
                      ..+.|++.|+-+|++....|.+.-|-              |.+-++.++..|++.|+|+..
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~gl--------------S~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESEL--------------APASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEe
Confidence            45689999999999999999998765              346899999999999999754

>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=89.60  E-value=0.11  Score=32.32  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=33.1

Q ss_pred             chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      ....|+..||-              |..-+|.+|+.|++.|||+..++.|-.++.
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            46677787765              446999999999999999998877777653

>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=88.63  E-value=0.36  Score=28.96  Aligned_cols=53  Identities=13%  Similarity=0.107  Sum_probs=40.1

Q ss_pred             HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCc-eeecCCCCceeCc
Q 033029           46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITS  112 (129)
Q Consensus        46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~-vek~~~~GR~lT~  112 (129)
                      .|++-|-=++.+....|...+|-.              ..-||+-++.||+.|+ |+..+..|-+|++
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~vS--------------~~ti~r~i~~L~~~G~~I~~~~g~GY~L~~   62 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGMS--------------RAAINKHIQTLRDWGVDVFTVPGKGYSLPE   62 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTCCCEEETTTEEECSS
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCcEEEeCCCeEEeCC
Confidence            466666556678899999988763              4589999999999998 6666555777753

>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=88.25  E-value=0.23  Score=32.64  Aligned_cols=63  Identities=17%  Similarity=0.157  Sum_probs=46.3

Q ss_pred             HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC------ceeCcchHhhH
Q 033029           45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG------RRITSSGQRDL  118 (129)
Q Consensus        45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G------R~lT~~G~~~l  118 (129)
                      .-|++.|. .|+..-+.|.+.-.             .-|.+++=.-|++||+.|+|++....+      ..||+.|++++
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            45788875 67877777766531             345578888899999999999764221      56999999987


Q ss_pred             HHH
Q 033029          119 DQV  121 (129)
Q Consensus       119 D~i  121 (129)
                      .-+
T Consensus        89 pil   91 (102)
T d2fswa1          89 PII   91 (102)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>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=87.27  E-value=0.35  Score=31.48  Aligned_cols=37  Identities=30%  Similarity=0.434  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHHhCCceee--cCC--CCceeCcchHhhHHH
Q 033029           84 GAIARHILQQLQNMNIIDI--EPK--GGRRITSSGQRDLDQ  120 (129)
Q Consensus        84 g~iiR~~lqqLE~~g~vek--~~~--~GR~lT~~G~~~lD~  120 (129)
                      =|.+|+.|-||+.+|+++.  +++  |--.||++|+..-+.
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  333  234799999976543

>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=86.64  E-value=0.3  Score=38.96  Aligned_cols=64  Identities=11%  Similarity=0.141  Sum_probs=44.2

Q ss_pred             HHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHH
Q 033029           50 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGR  124 (129)
Q Consensus        50 ~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~  124 (129)
                      .|=...++=...+...||-.-         ..-...+ ...|++|++.|||+.+. ++=+||++|+-++|.||..
T Consensus       373 ~L~~~~~ld~~~~~~~fg~~~---------~~~f~~~-~~~L~~l~~~GLv~~~~-~~l~lT~~Gr~l~~~I~~~  436 (441)
T d1olta_         373 SLICNFRLDYSPIEQQWDLLF---------ADYFAED-LKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICMC  436 (441)
T ss_dssp             HHHHHSEEEHHHHHHHTTCCH---------HHHTHHH-HHHHHHHHHTTSEEECS-SEEEECTTTGGGHHHHHHT
T ss_pred             HHHHhCCcCHHHHHHHHCCCH---------HHHHHHH-HHHHHHHHHCCCEEEEC-CEEEECHhHHHHHHHHHHH
Confidence            343455666677777776531         0111122 25788899999999875 5889999999999999864

>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=85.22  E-value=0.94  Score=30.16  Aligned_cols=56  Identities=11%  Similarity=0.140  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcc
Q 033029           44 AASMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSS  113 (129)
Q Consensus        44 ~ASilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~  113 (129)
                      |--+|..+..+  .++.+..++...|-              +-..+|++|++|.++|+|+... .||-.|...
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i--------------~~~~l~kil~~L~~aGlv~S~rG~GG~~L~~~   67 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNT--------------NPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKD   67 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEC---CCEEESSC
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEeecCCCCceecCC
Confidence            34445555443  35888888887765              3358999999999999998654 477788743

>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=83.37  E-value=0.88  Score=27.06  Aligned_cols=55  Identities=15%  Similarity=0.177  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCc-eeecCCCCceeCc
Q 033029           43 RAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITS  112 (129)
Q Consensus        43 R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~-vek~~~~GR~lT~  112 (129)
                      |-..|+..|.- ++++.+..|...+|-.              ..-||+=++.|++.|+ |+..+ +|-+|.+
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~VS--------------~~TI~rdi~~L~~~G~~I~~~~-gGY~L~~   64 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELSVS--------------RQVIVQDIAYLRSLGYNIVATP-RGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSC--------------HHHHHHHHHHHHHHTCCCEEET-TEEECCT
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeEEEeC-CCEEeCC
Confidence            44567777765 3579999999998764              3479999999999998 77655 6888764

>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=83.03  E-value=1.2  Score=26.71  Aligned_cols=47  Identities=13%  Similarity=0.082  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029           43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE  103 (129)
Q Consensus        43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~  103 (129)
                      ....|++.|+-+||+.-..|.+.-|=              |..-+..++++|++.|||+..
T Consensus         6 N~~~Il~~i~~~g~~sr~eLa~~~gL--------------S~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           6 NAGAVYRLIDQLGPVSRIDLSRLAQL--------------APASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHHSSCSCCHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEee
Confidence            45679999999999999999998554              345789999999999999753

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=82.86  E-value=0.98  Score=28.22  Aligned_cols=56  Identities=13%  Similarity=0.118  Sum_probs=43.7

Q ss_pred             HHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029           48 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL  118 (129)
Q Consensus        48 lR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l  118 (129)
                      .-+| -.||..++.|...=|.              +-..++.+|..|..+|+++.++++--.+||.|+-+.
T Consensus        27 fd~l-~~gp~s~~eLA~~~g~--------------~~~~l~rlLr~l~a~gl~~e~~~~~y~lt~~s~~L~   82 (85)
T d1tw3a1          27 VDHI-LAGARTVKALAARTDT--------------RPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLA   82 (85)
T ss_dssp             HHHH-HTTCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEETTEEEECTTGGGGS
T ss_pred             HHHh-ccCCCCHHHHHHHhCc--------------ChhHHHHHHHHHHHCCCeEecCCCeEecCHHHHHhh
Confidence            3344 4789999999987553              335799999999999999877666788999987543

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=82.07  E-value=4.4  Score=25.69  Aligned_cols=67  Identities=24%  Similarity=0.418  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHH
Q 033029           14 EFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQ   93 (129)
Q Consensus        14 ~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqq   93 (129)
                      +-++.+|+.||-=+        ||    +|. .|++.| ..++..|+.|....|-.              .+.+-+=|+.
T Consensus         8 e~~~~la~~~kaL~--------~p----~Rl-~Il~~L-~~~~~~v~ela~~l~is--------------~stvS~HL~~   59 (98)
T d1r1ta_           8 EVAQSLAEFFAVLA--------DP----NRL-RLLSLL-ARSELCVGDLAQAIGVS--------------ESAVSHQLRS   59 (98)
T ss_dssp             HHHHHHHHHHHHHC--------CH----HHH-HHHHHH-TTCCBCHHHHHHHHTCC--------------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--------CH----HHH-HHHHHH-HcCCcCHHHHHHHHCcC--------------HHHHHHHHHH
Confidence            45788899998754        66    674 588877 47899999999988753              3567777999


Q ss_pred             HHhCCceeecCCCCce
Q 033029           94 LQNMNIIDIEPKGGRR  109 (129)
Q Consensus        94 LE~~g~vek~~~~GR~  109 (129)
                      |+++|+|....+ ||.
T Consensus        60 L~~aglV~~~r~-G~~   74 (98)
T d1r1ta_          60 LRNLRLVSYRKQ-GRH   74 (98)
T ss_dssp             HHHTTSEEEEEE-TTE
T ss_pred             HHHCCceEEEEE-CCE
Confidence            999999987654 554

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=81.19  E-value=1.4  Score=28.13  Aligned_cols=51  Identities=12%  Similarity=0.074  Sum_probs=38.8

Q ss_pred             hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCce--eCcchHhhH
Q 033029           54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR--ITSSGQRDL  118 (129)
Q Consensus        54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~--lT~~G~~~l  118 (129)
                      .||..+..|...-|.              +-..++.+|..|..+|++++++++.+.  +|+.|.-+.
T Consensus        38 ~gp~t~~eLA~~~g~--------------~~~~l~rLlr~L~a~gll~~~~d~~~~~~~t~~g~lL~   90 (92)
T d1qzza1          38 AGADTLAGLADRTDT--------------HPQALSRLVRHLTVVGVLEGGEKQGRPLRPTRLGMLLA   90 (92)
T ss_dssp             TTCCSHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEECCCC-CCCCEECTTGGGGS
T ss_pred             CCCCCHHHHHHHHCc--------------CchHHHHHHHHHHHCCCeeeecCCCceecccHHHHhcc
Confidence            689999999997554              224799999999999999998765444  477776543

>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=80.78  E-value=0.81  Score=29.03  Aligned_cols=29  Identities=21%  Similarity=0.016  Sum_probs=22.9

Q ss_pred             chhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029           83 SGAIARHILQQLQNMNIIDIEPKGGRRITS  112 (129)
Q Consensus        83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~  112 (129)
                      +.+.+=.+|++|+++|||+|.. ++-.|+.
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            4567888999999999999974 4666653