Citrus Sinensis ID: 032244

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140----
Protein Sequence
METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVVAP
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHHHccccccccccHHHcccccccccccccccHHHHHHHHHHHHHHHcccccccHHHHHccccccccccccccccccHHHHHHHHHHHHcccEEcccccccEEcHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccEEEcccHHHHHHHHHHHHHHccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccEEEcccccEEEccccHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
metaknvkdvspHEFVKAYAAHLKrsgkielptwndivktgtlkelapydpdwYYIRAASMARKIYLRGglgvgsfrriygggkrngsrpphfskssgsVARHILHQlqdtniieldskggrritssgqrdlDQVAGRIAVVAP
Flexible Loop (DISEMBL)
metaknvkdvspheFVKAYAAHlkrsgkielptwndivktgtlkelapydPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGgrritssgqrdldqvagriavvap
Low Complexity Region (SEG)
METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVVAP
Disordered region (IsUnstruct)
*************EFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGG*********************ILHQLQDTNII******************************
Disordered Region (DISOPRED)
***AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGG*************SSGSVARHILHQLQDTNIIELDS****RITSSGQRDLDQVAGRIAVV**
Disordered Region (DISEMBL)
*********VSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK***************VARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVVAP
Disordered Region (DISPRO)
****KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRN*SRPP******GSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVVAP
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	144	2.2.26 [Sep-21-2011]
Q9SGA6	143	40S ribosomal protein S19	yes	no	0.979	0.986	0.865	5e-69
Q9FNP8	143	40S ribosomal protein S19	no	no	0.972	0.979	0.871	9e-69
Q9LF30	143	40S ribosomal protein S19	yes	no	0.972	0.979	0.857	2e-67
P40978	146	40S ribosomal protein S19	yes	no	0.972	0.958	0.728	5e-57
Q94613	149	40S ribosomal protein S19	N/A	no	0.937	0.906	0.562	4e-44
Q8T5Z4	147	40S ribosomal protein S19	N/A	no	0.944	0.925	0.573	3e-43
Q9Y0H3	145	40S ribosomal protein S19	N/A	no	0.958	0.951	0.557	7e-42
P17074	145	40S ribosomal protein S19	yes	no	0.937	0.931	0.577	1e-41
Q9CZX8	145	40S ribosomal protein S19	yes	no	0.937	0.931	0.577	1e-41
Q5R8M9	145	40S ribosomal protein S19	yes	no	0.937	0.931	0.570	6e-41

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

 Score =  259 bits (661), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 122/141 (86%), Positives = 130/141 (92%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M T K VKDVSPH+FVKAYA+HLKRSGKIELPTW DIVKTG LKELAPYDPDWYYIRAAS
Sbjct: 1   MATGKTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  NI+ELD+KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAV 141
           GRRITSSGQRDLDQVAGRIAV
Sbjct: 121 GRRITSSGQRDLDQVAGRIAV 141

Arabidopsis thaliana (taxid: 3702)

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

 Score =  258 bits (659), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 122/140 (87%), Positives = 128/140 (91%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M T K VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTG LKELAPYDPDWYYIRAAS
Sbjct: 1   MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG VARHIL QLQ  NI++LD+KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKG 120

Query: 121 GRRITSSGQRDLDQVAGRIA 140
           GR+ITSSGQRDLDQVAGRIA
Sbjct: 121 GRKITSSGQRDLDQVAGRIA 140

Arabidopsis thaliana (taxid: 3702)

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

 Score =  253 bits (647), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 120/140 (85%), Positives = 128/140 (91%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M T K VKDVSPH+FVKAYA+HLKRSGKIELP W DIVKTG LKELAPYDPDWYYIRAAS
Sbjct: 1   MATGKTVKDVSPHDFVKAYASHLKRSGKIELPLWTDIVKTGRLKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  +I+ELD+KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELDTKG 120

Query: 121 GRRITSSGQRDLDQVAGRIA 140
           GRRITSSGQRDLDQVAGRIA
Sbjct: 121 GRRITSSGQRDLDQVAGRIA 140

Arabidopsis thaliana (taxid: 3702)

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

 Score =  219 bits (557), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 102/140 (72%), Positives = 119/140 (85%)

Query: 3   TAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMA 62
           TA+ VKDV+PHEFVKAY+AHLKRSGK+ELP W DIVKT   KEL PYDPDWYY RAAS+A
Sbjct: 5   TARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIA 64

Query: 63  RKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122
           RKIYLR G+GVG F++IYGG +RNGSRPPHF KSSG+++R+IL QLQ   II++D KGGR
Sbjct: 65  RKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGR 124

Query: 123 RITSSGQRDLDQVAGRIAVV 142
            ITS G+RDLDQVAGR+ V 
Sbjct: 125 LITSQGRRDLDQVAGRVDVT 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 =  176 bits (446), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 76/135 (56%), Positives = 105/135 (77%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
           +VKDVS HEF +A+AA LK+SGK+++P W D VKTG  KEL+PY+PDWY+IRAAS+ R +
Sbjct: 4   SVKDVSSHEFTRAFAAFLKKSGKMKVPEWTDFVKTGMFKELSPYEPDWYFIRAASICRHL 63

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           Y+R   G+GSF +IYGG +R G+ P HF K++GS++R +L  L+   I+E D  GGRR+T
Sbjct: 64  YIRSPAGIGSFEKIYGGRRRRGTAPSHFCKANGSISRRLLQSLEGLKIVEKDPNGGRRLT 123

Query: 126 SSGQRDLDQVAGRIA 140
           S G+RDLD++A +IA
Sbjct: 124 SQGRRDLDRIAAQIA 138

Mya arenaria (taxid: 6604)

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

 Score =  173 bits (438), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 78/136 (57%), Positives = 104/136 (76%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  EFVKA+AA LK+SGK++LP W D+VKT   KELAPYDPDW+Y+RAAS AR +
Sbjct: 6   TVKDVNQQEFVKAFAAFLKKSGKLKLPEWVDLVKTAPHKELAPYDPDWFYLRAASTARHL 65

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           Y+RGG+GVG+  +IYGG KR G++P  F   S  V+R +L  L+   ++E D+ GGRR+T
Sbjct: 66  YMRGGVGVGAMCKIYGGRKRRGTKPAKFRVCSRGVSRTVLQSLEGIKMVEKDAAGGRRLT 125

Query: 126 SSGQRDLDQVAGRIAV 141
           S GQRDLD++AG++A 
Sbjct: 126 SQGQRDLDRIAGQVAT 141

Branchiostoma belcheri (taxid: 7741)

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

 Score =  169 bits (427), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 77/138 (55%), Positives = 105/138 (76%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  EFVKA AA  K+SGK++ P W D VK G  KELAP+D DWYYIR AS+AR +
Sbjct: 5   TVKDVNQQEFVKALAAFFKKSGKLKKPDWVDTVKLGKHKELAPFDIDWYYIRTASVARHL 64

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           Y+RGG+GVG+  +IYGG +RNG+RP H+S+ S +VAR +L  L+   ++E D  GGRR+T
Sbjct: 65  YMRGGVGVGAMTKIYGGRQRNGTRPSHYSRGSRNVARKVLQSLEMLKMVEKDPNGGRRLT 124

Query: 126 SSGQRDLDQVAGRIAVVA 143
           S GQRD+D++AG++ V++
Sbjct: 125 SIGQRDMDRIAGQVVVLS 142

Myxine glutinosa (taxid: 7769)

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

 Score =  167 bits (424), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/135 (57%), Positives = 100/135 (74%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YLRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 126 SSGQRDLDQVAGRIA 140
             GQRDLD++AG++A
Sbjct: 125 PQGQRDLDRIAGQVA 139

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 =  167 bits (424), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 78/135 (57%), Positives = 100/135 (74%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YLRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 126 SSGQRDLDQVAGRIA 140
             GQRDLD++AG++A
Sbjct: 125 PQGQRDLDRIAGQVA 139

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

Mus musculus (taxid: 10090)

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

 Score =  165 bits (418), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 77/135 (57%), Positives = 99/135 (73%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +
Sbjct: 5   TVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHL 64

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YLRGG GVGS  +IYGG +RNG  P HFS+ S SVAR +L  L+   ++E D  GGR++T
Sbjct: 65  YLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLT 124

Query: 126 SSGQRDLDQVAGRIA 140
             GQRDLD++AG++A
Sbjct: 125 PQGQRDLDRIAGQVA 139

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	144
225457277	143	PREDICTED: 40S ribosomal protein S19-3 [	0.979	0.986	0.886	5e-68
255570268	143	40S ribosomal protein S19, putative [Ric	0.993	1.0	0.868	1e-67
255560408	143	40S ribosomal protein S19, putative [Ric	0.993	1.0	0.861	1e-67
255570270	143	40S ribosomal protein S19-3, putative [R	0.993	1.0	0.861	2e-67
15232844	143	40S ribosomal protein S19-1 [Arabidopsis	0.979	0.986	0.865	3e-67
224141061	143	predicted protein [Populus trichocarpa]	0.993	1.0	0.861	4e-67
15240154	143	40S ribosomal protein S19-3 [Arabidopsis	0.972	0.979	0.871	6e-67
388508852	144	unknown [Lotus japonicus]	1.0	1.0	0.840	1e-66
224077760	143	predicted protein [Populus trichocarpa]	0.993	1.0	0.861	2e-66
297832838	142	40S ribosomal protein S19 [Arabidopsis l	0.951	0.964	0.875	5e-66

>gi|225457277|ref|XP_002284393.1| PREDICTED: 40S ribosomal protein S19-3 [Vitis vinifera] gi|147858266|emb|CAN83920.1| hypothetical protein VITISV_028810 [Vitis vinifera] gi|297733901|emb|CBI15148.3| unnamed protein product [Vitis vinifera]

 Score =  261 bits (668), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 125/141 (88%), Positives = 129/141 (91%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TA+ VKDVSPHEFV AYAAHLKRSGKIELP W DIVKT T KELAPYDPDWYYIRAAS
Sbjct: 1   MATARTVKDVSPHEFVNAYAAHLKRSGKIELPHWTDIVKTATFKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGG+GVG+FRRIYGG KRNGSRPPHF KSSGS+ARHIL QLQ  NIIELDSKG
Sbjct: 61  MARKIYLRGGIGVGAFRRIYGGSKRNGSRPPHFCKSSGSIARHILQQLQTMNIIELDSKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAV 141
           GRRITSSGQRDLDQVAGRIAV
Sbjct: 121 GRRITSSGQRDLDQVAGRIAV 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 125/144 (86%), Positives = 134/144 (93%), Gaps = 1/144 (0%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TAK VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTGTLKELAPYDPDWY++RAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPPWTDIVKTGTLKELAPYDPDWYFVRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG++ARHIL QLQ+ NI+++D KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDPKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GRRITSSGQRDLDQVAGRI VVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRI-VVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 124/144 (86%), Positives = 134/144 (93%), Gaps = 1/144 (0%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TAK VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTGTLKELAPYDPDWYY+RAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGTLKELAPYDPDWYYVRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG++ARHIL QLQ+ NI+++DSKG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDSKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GRRITS+GQRDLDQVAG I +VAP
Sbjct: 121 GRRITSTGQRDLDQVAGHI-IVAP 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 =  259 bits (662), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 124/144 (86%), Positives = 134/144 (93%), Gaps = 1/144 (0%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TAK VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTGTLKELAPYDPDWY++RAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYAAHLKRSGKIELPPWTDIVKTGTLKELAPYDPDWYFVRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG++ARHIL QLQ+ NI+++D KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFGKSSGAIARHILQQLQNMNIVDIDPKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GR+ITSSGQRDLDQVAGRI VVAP
Sbjct: 121 GRKITSSGQRDLDQVAGRI-VVAP 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232844|ref|NP_186857.1| 40S ribosomal protein S19-1 [Arabidopsis thaliana] gi|27923843|sp|Q9SGA6.1|RS191_ARATH RecName: Full=40S ribosomal protein S19-1 gi|6513924|gb|AAF14828.1|AC011664_10 putative 40S ribosomal protein S19 [Arabidopsis thaliana] gi|13878029|gb|AAK44092.1|AF370277_1 putative 40S ribosomal protein S19 [Arabidopsis thaliana] gi|17104595|gb|AAL34186.1| putative 40S ribosomal protein S19 [Arabidopsis thaliana] gi|21593712|gb|AAM65679.1| putative 40S ribosomal protein S19 [Arabidopsis thaliana] gi|332640239|gb|AEE73760.1| 40S ribosomal protein S19-1 [Arabidopsis thaliana]

 Score =  259 bits (661), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 122/141 (86%), Positives = 130/141 (92%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M T K VKDVSPH+FVKAYA+HLKRSGKIELPTW DIVKTG LKELAPYDPDWYYIRAAS
Sbjct: 1   MATGKTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  NI+ELD+KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAV 141
           GRRITSSGQRDLDQVAGRIAV
Sbjct: 121 GRRITSSGQRDLDQVAGRIAV 141

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  258 bits (660), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 124/144 (86%), Positives = 133/144 (92%), Gaps = 1/144 (0%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TAK+VKDVSPHEFVKAY+AHLKRSGKIELP W DIVKTG  KELAPYDPDWYY+RAAS
Sbjct: 1   MATAKSVKDVSPHEFVKAYSAHLKRSGKIELPLWTDIVKTGKFKELAPYDPDWYYVRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIY+RGGLGVG+FRRIYGG KRNGSRPPHF KSSGS+ARHIL QLQ+ NII++D KG
Sbjct: 61  MARKIYIRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGSIARHILQQLQNVNIIDIDPKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GRRITSSGQRDLDQVAGRI VVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRI-VVAP 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15240154|ref|NP_200925.1| 40S ribosomal protein S19-3 [Arabidopsis thaliana] gi|297793669|ref|XP_002864719.1| 40S ribosomal protein S19 [Arabidopsis lyrata subsp. lyrata] gi|27923837|sp|Q9FNP8.1|RS193_ARATH RecName: Full=40S ribosomal protein S19-3 gi|9759463|dbj|BAB10379.1| 40S ribosomal protein S19 [Arabidopsis thaliana] gi|34365671|gb|AAQ65147.1| At5g61170 [Arabidopsis thaliana] gi|51970120|dbj|BAD43752.1| 40S ribosomal protein S19 - like [Arabidopsis thaliana] gi|297310554|gb|EFH40978.1| 40S ribosomal protein S19 [Arabidopsis lyrata subsp. lyrata] gi|332010047|gb|AED97430.1| 40S ribosomal protein S19-3 [Arabidopsis thaliana]

 Score =  258 bits (659), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 122/140 (87%), Positives = 128/140 (91%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M T K VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTG LKELAPYDPDWYYIRAAS
Sbjct: 1   MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG VARHIL QLQ  NI++LD+KG
Sbjct: 61  MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKG 120

Query: 121 GRRITSSGQRDLDQVAGRIA 140
           GR+ITSSGQRDLDQVAGRIA
Sbjct: 121 GRKITSSGQRDLDQVAGRIA 140

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508852|gb|AFK42492.1| unknown [Lotus japonicus]

 Score =  256 bits (655), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 121/144 (84%), Positives = 131/144 (90%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TA+ VKDVSPHEFVKAYAAHLKRSGK+ELP W DIVKT   KELAPYDPDWYYIRAAS
Sbjct: 1   MSTARTVKDVSPHEFVKAYAAHLKRSGKMELPEWTDIVKTARFKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+F+RIYGG +RNGSRPPHF KSSGS+ARHIL QLQ  +IIELD+KG
Sbjct: 61  MARKIYLRGGLGVGAFQRIYGGSQRNGSRPPHFCKSSGSIARHILQQLQTMHIIELDNKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GR+ITSSG+RDLDQVAGRI VVAP
Sbjct: 121 GRKITSSGRRDLDQVAGRIVVVAP 144

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 124/144 (86%), Positives = 131/144 (90%), Gaps = 1/144 (0%)

Query: 1   METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
           M TAK VKDVSPHEFVKAY+AHLKRSGK+ELP W DIVKT   KELAPYDPDWYYIRAAS
Sbjct: 1   MATAKTVKDVSPHEFVKAYSAHLKRSGKVELPPWTDIVKTAKFKELAPYDPDWYYIRAAS 60

Query: 61  MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
           MARKIYLRGGLGVG+FRRIYGG +RNGSRPPHF KSSGSVARHIL QLQ+ NII++D KG
Sbjct: 61  MARKIYLRGGLGVGAFRRIYGGSQRNGSRPPHFCKSSGSVARHILQQLQNMNIIDVDPKG 120

Query: 121 GRRITSSGQRDLDQVAGRIAVVAP 144
           GRRITSSGQRDLDQVAGRI VVAP
Sbjct: 121 GRRITSSGQRDLDQVAGRI-VVAP 143

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832838|ref|XP_002884301.1| 40S ribosomal protein S19 [Arabidopsis lyrata subsp. lyrata] gi|297330141|gb|EFH60560.1| 40S ribosomal protein S19 [Arabidopsis lyrata subsp. lyrata]

 Score =  255 bits (651), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 120/137 (87%), Positives = 128/137 (93%)

Query: 5   KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARK 64
           K VKDVSPH+FVKAYA+HLKRSGKIELPTW DIVKTG LKELAPYDPDWYYIRAASMARK
Sbjct: 4   KTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAASMARK 63

Query: 65  IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
           +YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  NI+ELD+KGGRRI
Sbjct: 64  VYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKGGRRI 123

Query: 125 TSSGQRDLDQVAGRIAV 141
           TSSGQRDLDQVAGRIAV
Sbjct: 124 TSSGQRDLDQVAGRIAV 140

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	144
TAIR|locus:2078633	143	AT3G02080 [Arabidopsis thalian	0.979	0.986	0.865	4.7e-64
TAIR|locus:2159486	143	AT5G61170 [Arabidopsis thalian	0.972	0.979	0.871	2e-63
TAIR|locus:2180912	143	AT5G15520 [Arabidopsis thalian	0.972	0.979	0.857	1.4e-62
MGI|MGI:1333780	145	Rps19 "ribosomal protein S19"	0.930	0.924	0.582	2.9e-39
RGD|68440	145	Rps19 "ribosomal protein S19"	0.930	0.924	0.582	2.9e-39
RGD|2318347	145	LOC100362339 "ribosomal protei	0.930	0.924	0.582	4.8e-39
RGD|2321315	145	LOC100360843 "ribosomal protei	0.930	0.924	0.582	7.8e-39
UNIPROTKB|Q32PD5	145	RPS19 "40S ribosomal protein S	0.930	0.924	0.574	1.3e-38
UNIPROTKB|J9P425	153	RPS19 "Uncharacterized protein	0.930	0.875	0.574	1.3e-38
UNIPROTKB|P39019	145	RPS19 "40S ribosomal protein S	0.930	0.924	0.574	1.3e-38

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

 Score = 653 (234.9 bits), Expect = 4.7e-64, P = 4.7e-64
 Identities = 122/141 (86%), Positives = 130/141 (92%)

Query:     1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
             M T K VKDVSPH+FVKAYA+HLKRSGKIELPTW DIVKTG LKELAPYDPDWYYIRAAS
Sbjct:     1 MATGKTVKDVSPHDFVKAYASHLKRSGKIELPTWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query:    61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
             MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  NI+ELD+KG
Sbjct:    61 MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMNIVELDTKG 120

Query:   121 GRRITSSGQRDLDQVAGRIAV 141
             GRRITSSGQRDLDQVAGRIAV
Sbjct:   121 GRRITSSGQRDLDQVAGRIAV 141

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 647 (232.8 bits), Expect = 2.0e-63, P = 2.0e-63
 Identities = 122/140 (87%), Positives = 128/140 (91%)

Query:     1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
             M T K VKDVSPHEFVKAYAAHLKRSGKIELP W DIVKTG LKELAPYDPDWYYIRAAS
Sbjct:     1 MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAAS 60

Query:    61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
             MARK+YLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG VARHIL QLQ  NI++LD+KG
Sbjct:    61 MARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKG 120

Query:   121 GRRITSSGQRDLDQVAGRIA 140
             GR+ITSSGQRDLDQVAGRIA
Sbjct:   121 GRKITSSGQRDLDQVAGRIA 140

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

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

GO:0005829 "cytosol" evidence=IDA

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

 Score = 639 (230.0 bits), Expect = 1.4e-62, P = 1.4e-62
 Identities = 120/140 (85%), Positives = 128/140 (91%)

Query:     1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAAS 60
             M T K VKDVSPH+FVKAYA+HLKRSGKIELP W DIVKTG LKELAPYDPDWYYIRAAS
Sbjct:     1 MATGKTVKDVSPHDFVKAYASHLKRSGKIELPLWTDIVKTGRLKELAPYDPDWYYIRAAS 60

Query:    61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120
             MARKIYLRGGLGVG+FRRIYGG KRNGSRPPHF KSSG +ARHIL QL+  +I+ELD+KG
Sbjct:    61 MARKIYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGIARHILQQLETMSIVELDTKG 120

Query:   121 GRRITSSGQRDLDQVAGRIA 140
             GRRITSSGQRDLDQVAGRIA
Sbjct:   121 GRRITSSGQRDLDQVAGRIA 140

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 = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 78/134 (58%), Positives = 100/134 (74%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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 = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 78/134 (58%), Positives = 100/134 (74%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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 = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 78/134 (58%), Positives = 100/134 (74%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMMEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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 = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 78/134 (58%), Positives = 99/134 (73%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWLYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG RP HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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 = 413 (150.4 bits), Expect = 1.3e-38, P = 1.3e-38
 Identities = 77/134 (57%), Positives = 99/134 (73%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG  P HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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 = 413 (150.4 bits), Expect = 1.3e-38, P = 1.3e-38
 Identities = 77/134 (57%), Positives = 99/134 (73%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:    14 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 73

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG  P HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    74 LRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 133

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   134 QGQRDLDRIAGQVA 147

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 = 413 (150.4 bits), Expect = 1.3e-38, P = 1.3e-38
 Identities = 77/134 (57%), Positives = 99/134 (73%)

Query:     7 VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
             VKDV+  EFV+A AA LK+SGK+++P W D VK    KELAPYD +W+Y RAAS AR +Y
Sbjct:     6 VKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLY 65

Query:    67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
             LRGG GVGS  +IYGG +RNG  P HFS+ S SVAR +L  L+   ++E D  GGR++T 
Sbjct:    66 LRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTP 125

Query:   127 SGQRDLDQVAGRIA 140
              GQRDLD++AG++A
Sbjct:   126 QGQRDLDRIAGQVA 139

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	0.4701	0.9236	0.9236	yes	no
Q9V0G8	RS19E_PYRAB	No assigned EC number	0.3880	0.9305	0.8933	yes	no
Q90YQ4	RS19_ICTPU	No assigned EC number	0.5703	0.9375	0.9183	N/A	no
P39019	RS19_HUMAN	No assigned EC number	0.5703	0.9375	0.9310	yes	no
P39018	RS19A_DROME	No assigned EC number	0.4925	0.9305	0.8589	yes	no
P40978	RS19_ORYSJ	No assigned EC number	0.7285	0.9722	0.9589	yes	no
Q5R8M9	RS19_PONAB	No assigned EC number	0.5703	0.9375	0.9310	yes	no
Q54X51	RS19_DICDI	No assigned EC number	0.5217	0.9513	0.9256	yes	no
O28210	RS19E_ARCFU	No assigned EC number	0.3955	0.9097	0.8911	yes	no
Q8T5Z4	RS19_BRABE	No assigned EC number	0.5735	0.9444	0.9251	N/A	no
Q9LF30	RS192_ARATH	No assigned EC number	0.8571	0.9722	0.9790	yes	no
Q8ITC3	RS19_ARGIR	No assigned EC number	0.5074	0.9305	0.9305	N/A	no
P19952	RS19E_HALMA	No assigned EC number	0.3703	0.9097	0.8562	yes	no
Q9HM21	RS19E_THEAC	No assigned EC number	0.3432	0.9236	0.8866	yes	no
Q9DFR5	RS19_GILMI	No assigned EC number	0.5434	0.9583	0.9387	N/A	no
O27653	RS19E_METTH	No assigned EC number	0.4060	0.9166	0.9103	yes	no
Q9FNP8	RS193_ARATH	No assigned EC number	0.8714	0.9722	0.9790	no	no
Q9Y0H3	RS19_MYXGL	No assigned EC number	0.5579	0.9583	0.9517	N/A	no
P07280	RS19A_YEAST	No assigned EC number	0.4701	0.9236	0.9236	yes	no
Q9CZX8	RS19_MOUSE	No assigned EC number	0.5777	0.9375	0.9310	yes	no
P61155	RS19_PAGMA	No assigned EC number	0.5481	0.9375	0.9246	N/A	no
Q29308	RS19_PIG	No assigned EC number	0.5757	0.9166	0.9705	yes	no
Q94613	RS19_MYAAR	No assigned EC number	0.5629	0.9375	0.9060	N/A	no
P58234	RS19A_SCHPO	No assigned EC number	0.5648	0.9097	0.9097	yes	no
Q9SGA6	RS191_ARATH	No assigned EC number	0.8652	0.9791	0.9860	yes	no
O59041	RS19E_PYRHO	No assigned EC number	0.3805	0.9305	0.8933	yes	no
O18650	RS19_CAEEL	No assigned EC number	0.4671	0.9375	0.9246	yes	no
Q9YD22	RS19E_AERPE	No assigned EC number	0.3897	0.9305	0.8758	yes	no
P17074	RS19_RAT	No assigned EC number	0.5777	0.9375	0.9310	yes	no
P27073	RS19_EMENI	No assigned EC number	0.5303	0.9097	0.8851	yes	no
Q32PD5	RS19_BOVIN	No assigned EC number	0.5703	0.9375	0.9310	yes	no
P54057	RS19E_METJA	No assigned EC number	0.3955	0.9166	0.8918	yes	no
P79016	RS19B_SCHPO	No assigned EC number	0.5648	0.9097	0.9160	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	144
pfam01090	140	pfam01090, Ribosomal_S19e, Ribosomal protein S19e	2e-75
COG2238	147	COG2238, RPS19A, Ribosomal protein S19E (S16A) [Tr	1e-52
PRK09333	150	PRK09333, PRK09333, 30S ribosomal protein S19e; Pr	4e-49
PTZ00095	169	PTZ00095, PTZ00095, 40S ribosomal protein S19; Pro	3e-43

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

 Score =  220 bits (563), Expect = 2e-75
 Identities = 76/134 (56%), Positives = 95/134 (70%)

Query: 7   VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
           VKDV   E +KA A  LK+SGKI++P W D VKTG  KEL P DPDW+Y+RAAS+ RK+Y
Sbjct: 3   VKDVPADELIKALAEFLKKSGKIKVPEWADFVKTGVHKELPPEDPDWWYVRAASILRKLY 62

Query: 67  LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
           LRG +GVG  R+IYGG KR G RP HF K SGS+ R  L QL+   ++E D KGGRR+T 
Sbjct: 63  LRGPVGVGRLRKIYGGRKRRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDPKGGRRLTP 122

Query: 127 SGQRDLDQVAGRIA 140
            G+ DLD++A  + 
Sbjct: 123 QGRSDLDRIAAEVL 136

Length = 140

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

 Score =  162 bits (413), Expect = 1e-52
 Identities = 60/135 (44%), Positives = 83/135 (61%), Gaps = 1/135 (0%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            V DV     ++A A++LK +GK++ P W DIVKTG  KE  P   DW+Y+RAAS+ RKI
Sbjct: 3   TVYDVPADLLIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKI 62

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           Y+ G +G+   R  YGG K  GSRP  F K SGS+ R +L QL+   ++E  +  GR +T
Sbjct: 63  YIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVE-KTPKGRVLT 121

Query: 126 SSGQRDLDQVAGRIA 140
             G+  LD++A  I 
Sbjct: 122 PKGRSLLDRIATEIK 136

Length = 147

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

 Score =  154 bits (391), Expect = 4e-49
 Identities = 58/135 (42%), Positives = 77/135 (57%), Gaps = 1/135 (0%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            V DV     ++  A +LK   +I+ P W   VKTG  KE  P   DW+Y+RAAS+ RK+
Sbjct: 3   TVYDVPADLLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKV 62

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           Y+ G +GV   R  YGG K  G RP HF K SGS+ R IL QL+   ++E  +K GR IT
Sbjct: 63  YIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVE-KTKKGRVIT 121

Query: 126 SSGQRDLDQVAGRIA 140
             G+  LD +A  + 
Sbjct: 122 PKGRSLLDNLAAEVK 136

Length = 150

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

 Score =  139 bits (353), Expect = 3e-43
 Identities = 58/135 (42%), Positives = 81/135 (60%), Gaps = 1/135 (0%)

Query: 7   VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
           +KDVSP  F+KA+A H K  GKI +P   +IVKT   +ELAP +PDWYYIR A++ R +Y
Sbjct: 28  LKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALY 87

Query: 67  LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-GRRIT 125
           LR  +G G  R+ +   KR GS P H  ++SG + R I  QL+   ++E   K  GRR+T
Sbjct: 88  LRPDVGYGGLRKRFSSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLT 147

Query: 126 SSGQRDLDQVAGRIA 140
             G    +  A ++ 
Sbjct: 148 RKGCNFANAFARQVT 162

Length = 169

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
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
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	97.49
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	97.43
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	97.04
COG3388	101	Predicted transcriptional regulator [Transcription	96.85
COG1420	346	HrcA Transcriptional regulator of heat shock gene	96.79
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.72
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	96.49
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.48
PRK11050	152	manganese transport regulator MntR; Provisional	96.44
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.41
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.31
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.28
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.25
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	96.11
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	96.1
PRK03911	260	heat-inducible transcription repressor; Provisiona	96.02
COG1846	126	MarR Transcriptional regulators [Transcription]	95.95
PRK10870	176	transcriptional repressor MprA; Provisional	95.88
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.76
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	95.65
PRK03573	144	transcriptional regulator SlyA; Provisional	95.63
PRK13777	185	transcriptional regulator Hpr; Provisional	95.55
PRK03902	142	manganese transport transcriptional regulator; Pro	95.12
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.96
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	94.81
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	94.78
PF14338	92	Mrr_N: Mrr N-terminal domain	94.77
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	94.7
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.66
PRK05638	442	threonine synthase; Validated	94.63
COG3432	95	Predicted transcriptional regulator [Transcription	94.4
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.08
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	93.88
COG1693	325	Repressor of nif and glnA expression [Transcriptio	93.88
PF10711	102	DUF2513: Hypothetical protein (DUF2513); InterPro:	93.78
TIGR03338	212	phnR_burk phosphonate utilization associated trans	93.54
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	93.52
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.38
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.25
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	93.12
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	93.09
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.06
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.01
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	92.93
COG1733	120	Predicted transcriptional regulators [Transcriptio	92.79
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	92.78
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	92.54
PF03551	75	PadR: Transcriptional regulator PadR-like family;	92.5
PRK11014	141	transcriptional repressor NsrR; Provisional	92.47
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	92.35
COG1725	125	Predicted transcriptional regulators [Transcriptio	91.97
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	91.62
COG1802	230	GntR Transcriptional regulators [Transcription]	91.58
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	91.39
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	91.23
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	91.16
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	91.02
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	90.94
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	90.75
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	90.73
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	90.65
PF09114	96	MotA_activ: Transcription factor MotA, activation	90.64
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	90.28
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	90.22
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	90.13
PRK03837	241	transcriptional regulator NanR; Provisional	90.12
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	89.74
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	89.71
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	89.67
PRK08599	377	coproporphyrinogen III oxidase; Provisional	89.22
PRK09057	380	coproporphyrinogen III oxidase; Provisional	88.85
PRK11569	274	transcriptional repressor IclR; Provisional	88.43
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	88.07
PRK14165	217	winged helix-turn-helix domain-containing protein/	88.02
COG1414	246	IclR Transcriptional regulator [Transcription]	87.97
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	87.92
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	87.88
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	87.87
COG3355	126	Predicted transcriptional regulator [Transcription	87.83
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	87.75
PRK04984	239	fatty acid metabolism regulator; Provisional	87.72
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	87.57
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	87.2
PRK09416	135	lstR lineage-specific thermal regulator protein; P	86.85
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	86.83
COG1695	138	Predicted transcriptional regulators [Transcriptio	86.71
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	86.64
PF13814	191	Replic_Relax: Replication-relaxation	86.62
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	86.48
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	86.3
PF09382	106	RQC: RQC domain; InterPro: IPR018982 This entry re	86.16
PRK13347	453	coproporphyrinogen III oxidase; Provisional	86.12
PRK08208	430	coproporphyrinogen III oxidase; Validated	85.8
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	85.46
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	85.31
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	84.95
PRK05628	375	coproporphyrinogen III oxidase; Validated	84.25
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	83.95
PRK14999	241	histidine utilization repressor; Provisional	83.75
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	83.23
PRK05799	374	coproporphyrinogen III oxidase; Provisional	83.02
PRK09334	86	30S ribosomal protein S25e; Provisional	82.35
PRK06294	370	coproporphyrinogen III oxidase; Provisional	82.18
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	81.97
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	81.92
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	81.71
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	81.42
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	81.27
PRK08898	394	coproporphyrinogen III oxidase; Provisional	81.03
COG2186	241	FadR Transcriptional regulators [Transcription]	80.67
COG2188	236	PhnF Transcriptional regulators [Transcription]	80.57
PRK05660	378	HemN family oxidoreductase; Provisional	80.45

>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=1.3e-75  Score=450.49  Aligned_cols=138  Identities=62%  Similarity=1.084  Sum_probs=126.8

Q ss_pred             CceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCC
Q 032244            5 KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK   84 (144)
Q Consensus         5 ~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k   84 (144)
                      +||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+|
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            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           85 RNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        85 ~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      |||++|+||++|||+|||+||||||++|||++++++||+||++||++||+||.||++.
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            9999999999999999999999999999999999889999999999999999999863

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.

>PTZ00095 40S ribosomal protein S19; Provisional

Probab=100.00  E-value=3.1e-74  Score=454.24  Aligned_cols=141  Identities=41%  Similarity=0.724  Sum_probs=137.0

Q ss_pred             CCCCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHh
Q 032244            1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY   80 (144)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~Y   80 (144)
                      |..++||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|
T Consensus        22 ~~~~~tvkDVpa~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~Y  101 (169)
T PTZ00095         22 RRKNATLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRF  101 (169)
T ss_pred             ccCCCceeeCCHHHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHH
Confidence            44679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHhhHHHHHHHHhh
Q 032244           81 GGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQRDLDQVAGRIAV  141 (144)
Q Consensus        81 Gg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~~lD~iA~~i~~  141 (144)
                      ||+||||++|+||++|||+|||+||||||++|||++++ ++||+||++||++||+||.+|++
T Consensus       102 Gg~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~  163 (169)
T PTZ00095        102 SSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTI  163 (169)
T ss_pred             CCCCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999996 48999999999999999999975

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=100.00  E-value=5.3e-73  Score=440.59  Aligned_cols=138  Identities=41%  Similarity=0.708  Sum_probs=135.6

Q ss_pred             CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244            4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG   83 (144)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~   83 (144)
                      |+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+
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            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      ||||++|+||++|||+|||++|||||++|||++++ +||+||++||++||+||.+|++.
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            99999999999999999999999999999999999 79999999999999999999754

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

Probab=100.00  E-value=5.7e-72  Score=427.61  Aligned_cols=141  Identities=62%  Similarity=1.080  Sum_probs=138.4

Q ss_pred             CCCCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHh
Q 032244            1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY   80 (144)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~Y   80 (144)
                      ||. +|||||+|++|+++||.|||++|||++|+|+|+||||.+||+||+||||||+|||||+||||+++++|||.|+++|
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            774 8999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           81 GGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        81 Gg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      ||+||||++|+||+.+||+|+|++||+||++||||++++|||+||++||++||+||++|.+.
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            99999999999999999999999999999999999999999999999999999999999764

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

Probab=100.00  E-value=7.5e-71  Score=424.85  Aligned_cols=137  Identities=44%  Similarity=0.768  Sum_probs=135.0

Q ss_pred             CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244            4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG   83 (144)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~   83 (144)
                      |+||||||+|+||+++|++||++++|++|+|++|||||+|||+||+|+||||+||||||||||++||+||++|++.|||+
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            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhh
Q 032244           84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAV  141 (144)
Q Consensus        84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~  141 (144)
                      |+||++|+||++|||+|+|++|||||++|||++++ +||+|||+||++||+||.+|++
T Consensus        81 k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~e  137 (147)
T COG2238          81 KNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKE  137 (147)
T ss_pred             ccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHH
Confidence            99999999999999999999999999999999999 5999999999999999999975

>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=97.49  E-value=0.00024  Score=50.52  Aligned_cols=57  Identities=23%  Similarity=0.440  Sum_probs=47.1

Q ss_pred             HHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCceeCcchHhhHHH
Q 032244           64 KIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRRITSSGQRDLDQ  134 (144)
Q Consensus        64 klYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~lT~~G~~~lD~  134 (144)
                      ..|++  .|||=..+....+              -|..-||+.++.||++|||++.  +.+||+-|.+|-+.+++
T Consensus        15 ~~Y~~~~~PVgSk~ia~~l~--------------~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~   75 (78)
T PF03444_consen   15 ELYIETGEPVGSKTIAEELG--------------RSPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR   75 (78)
T ss_pred             HHHHhcCCCcCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence            45775  5999999998764              1346899999999999999964  47899999999998864

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

>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=97.43  E-value=0.00029  Score=47.78  Aligned_cols=63  Identities=21%  Similarity=0.243  Sum_probs=51.3

Q ss_pred             HHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244           61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l  132 (144)
                      ||+.|+-. +|+|=..|+....-.   |      ..-|-.-+|.-|..||..||+++...+||.||++|...|
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~---g------~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~G~~~L   66 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLR---G------EELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL   66 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhc---C------hhhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence            78888875 689999999988632   2      233456799999999999999988778999999998764

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

Probab=97.04  E-value=0.002  Score=44.40  Aligned_cols=62  Identities=18%  Similarity=0.305  Sum_probs=44.5

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      +.||.-+- .++.+..++..              .+.=|-+.+...|+.|++.|+|++ .++.-.||++|...|+.+-
T Consensus         9 ~~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~lTekG~~~l~~l~   70 (77)
T PF14947_consen    9 FDILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKK-KDGKYRLTEKGKEFLEELE   70 (77)
T ss_dssp             HHHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEE-ETTEEEE-HHHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEECccHHHHHHHHH
Confidence            34555444 67777777764              556778899999999999999977 4458999999999999883

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=96.85  E-value=0.0024  Score=47.33  Aligned_cols=68  Identities=22%  Similarity=0.320  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      |--+||..+.=.+|+|+..|+..-|       .|.|.       +|+.|.-||..+++.-+.. |-.+|+.+-.++++|.
T Consensus        15 RHl~Vl~~v~eeqPiGI~klS~~TG-------mp~HK-------VRYSLRVLEq~~iI~PS~~-GAi~td~~~e~ie~i~   79 (101)
T COG3388          15 RHLSVLKVVLEEQPIGIIKLSDETG-------MPEHK-------VRYSLRVLEQENIISPSRQ-GAILTDDFPEFIEEII   79 (101)
T ss_pred             HHHHHHHHHHHhCCceeEeechhcC-------Cchhh-------hhhhhhhhhhcCccCcccc-CCccCccHHHHHHHHH
Confidence            5556676667789999999999999       67664       7899999999999987776 9999999999998887


Q ss_pred             HHH
Q 032244          137 GRI  139 (144)
Q Consensus       137 ~~i  139 (144)
                      +++
T Consensus        80 ~dl   82 (101)
T COG3388          80 GDL   82 (101)
T ss_pred             HHH
Confidence            765

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

Probab=96.79  E-value=0.003  Score=55.26  Aligned_cols=63  Identities=27%  Similarity=0.379  Sum_probs=51.6

Q ss_pred             HHHHHHHHH---HHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244           57 RAASMARKI---YLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRkl---Yl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~  130 (144)
                      |...|||.|   |+.  .|||=..|.+.|+            -.-|.+-||+.+++||++||++|.. .+||+-|+.|-+
T Consensus         7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~------------l~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr   74 (346)
T COG1420           7 RQRLILRAIVEDYLATGEPVGSKTLSEKYN------------LDLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR   74 (346)
T ss_pred             HHHHHHHHHHHHHHhcCCccchHHHHHHhC------------CCCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence            556677654   775  5999999999886            2346788999999999999999876 569999999976


Q ss_pred             h
Q 032244          131 D  131 (144)
Q Consensus       131 ~  131 (144)
                      .
T Consensus        75 ~   75 (346)
T COG1420          75 Y   75 (346)
T ss_pred             H
Confidence            4

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.72  E-value=0.011  Score=42.71  Aligned_cols=65  Identities=15%  Similarity=0.172  Sum_probs=52.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|.+..|-.+              +-+-.+++.||+.|||++.+  .+.|    .||++|++.+++
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            677778889999999999887433              35678999999999999765  3345    699999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +....
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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=96.49  E-value=0.017  Score=43.07  Aligned_cols=63  Identities=14%  Similarity=0.143  Sum_probs=50.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++....|+...|-.+              +-+=.+++.||+.|||++.+  .++|    .||++|+..+++
T Consensus        45 vL~~l~~~~~~t~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         45 VLCSIRCAACITPVELKKVLSVDL--------------GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             HHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            677788888999999999887533              45777899999999999765  4455    589999999888


Q ss_pred             HHH
Q 032244          135 VAG  137 (144)
Q Consensus       135 iA~  137 (144)
                      +..
T Consensus       111 ~~~  113 (144)
T PRK11512        111 CHQ  113 (144)
T ss_pred             HHH
Confidence            643

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.48  E-value=0.0069  Score=48.06  Aligned_cols=60  Identities=17%  Similarity=0.316  Sum_probs=49.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhh
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----RITSSGQRD  131 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----~lT~~G~~~  131 (144)
                      +||.-|.-.+++.+..|....|-              +..-+|..|+.||+.|||+...   ..||     .||++|+..
T Consensus         5 ~IL~~L~~~~~~t~~eLA~~lgi--------------s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~   70 (203)
T TIGR02702         5 DILSYLLKQGQATAAALAEALAI--------------SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ   70 (203)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence            57877877899999999998874              3468999999999999998763   2478     999999876


Q ss_pred             HH
Q 032244          132 LD  133 (144)
Q Consensus       132 lD  133 (144)
                      +.
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.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.44  E-value=0.02  Score=43.96  Aligned_cols=63  Identities=17%  Similarity=0.194  Sum_probs=52.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      |++.++-.+++.+..|...+|-              |.+-+..+|++||+.|||...+.+|-.||++|+..+..+..
T Consensus        42 I~~~l~~~~~~t~~eLA~~l~i--------------s~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~  104 (152)
T PRK11050         42 IADLIAEVGEARQVDIAARLGV--------------SQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE  104 (152)
T ss_pred             HHHHHHhcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence            5556666788999999998874              34689999999999999998876689999999999777654

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.41  E-value=0.017  Score=35.54  Aligned_cols=59  Identities=24%  Similarity=0.329  Sum_probs=44.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCc-chHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITS-SGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~-~G~~~lD~  134 (144)
                      |++.|+ .+++.+..+...+|-              |.+-++.+|++|++.|+|+...++   ...+|. .|...++.
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            567777 889999999999872              445799999999999999976642   234666 55555543

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

Probab=96.31  E-value=0.0093  Score=41.17  Aligned_cols=42  Identities=19%  Similarity=0.378  Sum_probs=36.4

Q ss_pred             chhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q 032244           97 SGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGR  138 (144)
Q Consensus        97 sg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~  138 (144)
                      |.+-++.+|+.||+.|||++.+.++-.||+.|+...+.+...
T Consensus        12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~   53 (96)
T smart00529       12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRK   53 (96)
T ss_pred             ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHH
Confidence            456899999999999999999877999999999988776543

iron dependent repressor

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.28  E-value=0.035  Score=37.41  Aligned_cols=65  Identities=18%  Similarity=0.280  Sum_probs=51.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC------CceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------GRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g------GR~lT~~G~~~lD~  134 (144)
                      ||..|+..+++.+..+....+-.              ..-|..+|+.|++.|||+...++      .-.||++|.+.+..
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            67778888999999999876522              23478999999999999876542      35699999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus        81 ~~~~~   85 (101)
T smart00347       81 LLEAR   85 (101)
T ss_pred             HHHHH
Confidence            77665

>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=96.25  E-value=0.011  Score=38.26  Aligned_cols=54  Identities=22%  Similarity=0.399  Sum_probs=39.5

Q ss_pred             HHHHHH-HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcch
Q 032244           61 MARKIY-LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSG  128 (144)
Q Consensus        61 ilRklY-l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G  128 (144)
                      ||+.|+ -.++.....|+...+-              +..-+..++++|++.|||++.+  .++|    .||++|
T Consensus         8 vL~~l~~~~~~~t~~~l~~~~~~--------------~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    8 VLRALAHSDGPMTQSDLAERLGI--------------SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHT--TS-BEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHccCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            688888 7789999999998774              3346779999999999998664  3365    578877

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

Probab=96.11  E-value=0.017  Score=40.49  Aligned_cols=65  Identities=17%  Similarity=0.260  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC------CceeCcchHhh
Q 032244           58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------GRRITSSGQRD  131 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g------GR~lT~~G~~~  131 (144)
                      +..||+.|.. |+...+.|.+.-             ...|.+++-.-|+.||+.|+|++....      -..||+.|+++
T Consensus         7 ~~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l   72 (90)
T PF01638_consen    7 TLLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKEL   72 (90)
T ss_dssp             HHHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHH
T ss_pred             HHHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHH
Confidence            3568888888 888888888743             246788999999999999999986422      27899999998


Q ss_pred             HHHHH
Q 032244          132 LDQVA  136 (144)
Q Consensus       132 lD~iA  136 (144)
                      +.-+.
T Consensus        73 ~~~l~   77 (90)
T PF01638_consen   73 LPVLE   77 (90)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            86554

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.

>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=96.10  E-value=0.0057  Score=43.32  Aligned_cols=68  Identities=19%  Similarity=0.224  Sum_probs=43.0

Q ss_pred             chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244           52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRD  131 (144)
Q Consensus        52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~  131 (144)
                      |+.-.|.-..|..-|-.||+|+..|+..-|-.+.             .|.=.+===|-+.|+|+++++ ||++|++|.+-
T Consensus         7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~-------------Tie~v~EPyLiq~G~I~RT~r-GR~~T~~a~~~   72 (76)
T PF05491_consen    7 DELDRRYLKTLIENFKGGPVGLDTLAAALGEDKE-------------TIEDVIEPYLIQIGFIQRTPR-GRVATPKAYEH   72 (76)
T ss_dssp             BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HH-------------HHHHTTHHHHHHTTSEEEETT-EEEE-HHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHh-------------HHHHHhhHHHHHhhhHhhCcc-HHHhHHHHHHH
Confidence            3444455555666677899999999987774332             111111123456899999998 99999999876


Q ss_pred             HH
Q 032244          132 LD  133 (144)
Q Consensus       132 lD  133 (144)
                      |.
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.

>PRK03911 heat-inducible transcription repressor; Provisional

Probab=96.02  E-value=0.018  Score=49.07  Aligned_cols=63  Identities=19%  Similarity=0.343  Sum_probs=49.7

Q ss_pred             HHHHHHHH---HHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244           57 RAASMARK---IYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRk---lYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~  130 (144)
                      |.-.||+.   -|+.  .|||-..|.+.|+-            .-|.+-||+.++.||++|++++.. .+||+-|.+|-+
T Consensus         4 R~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr   71 (260)
T PRK03911          4 KKDLLLDSIIQTYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMK   71 (260)
T ss_pred             HHHHHHHHHHHHHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHH
Confidence            34445554   4775  59999999998872            346678999999999999999765 569999999986


Q ss_pred             h
Q 032244          131 D  131 (144)
Q Consensus       131 ~  131 (144)
                      .
T Consensus        72 ~   72 (260)
T PRK03911         72 N   72 (260)
T ss_pred             H
Confidence            3

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=95.95  E-value=0.043  Score=37.84  Aligned_cols=65  Identities=26%  Similarity=0.392  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ..+|..||..++.+.+.|....+-              +.+-+=.+++.||+.|||+...  .++|    .||++|+..+
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            457888888888776778876663              3356778899999999998665  4455    7999999999


Q ss_pred             HHHHH
Q 032244          133 DQVAG  137 (144)
Q Consensus       133 D~iA~  137 (144)
                      .++..
T Consensus        91 ~~~~~   95 (126)
T COG1846          91 EQLLP   95 (126)
T ss_pred             HHhcc
Confidence            88755

>PRK10870 transcriptional repressor MprA; Provisional

Probab=95.88  E-value=0.042  Score=43.01  Aligned_cols=64  Identities=17%  Similarity=0.178  Sum_probs=49.5

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRR----ITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~----lT~~G~~~l  132 (144)
                      ||..|+-.  +++.+..|+...|-.              .+-+=.+++.||+.|||++.+  .++|.    ||++|+..+
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            57777753  467778999988743              246677899999999999764  45777    999999999


Q ss_pred             HHHHHH
Q 032244          133 DQVAGR  138 (144)
Q Consensus       133 D~iA~~  138 (144)
                      +++-..
T Consensus       126 ~~i~~~  131 (176)
T PRK10870        126 REVLPP  131 (176)
T ss_pred             HHHHHH
Confidence            998544

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.76  E-value=0.055  Score=36.75  Aligned_cols=60  Identities=27%  Similarity=0.362  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchH
Q 032244           56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQ  129 (144)
Q Consensus        56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~  129 (144)
                      -|+-.|+..|.-. +++++..+....|-              +.+-++..|+.||+.|+|++++ ++...|++...
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            3788899988887 79999999998863              4578999999999999999875 44567777543

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=95.65  E-value=0.062  Score=38.70  Aligned_cols=66  Identities=12%  Similarity=0.142  Sum_probs=51.6

Q ss_pred             HHHHHH----HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHh
Q 032244           61 MARKIY----LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQR  130 (144)
Q Consensus        61 ilRklY----l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~  130 (144)
                      ||..|+    -.+++....|+...+-.              .+-+=.++..||+.|||++.+  ++.|    .||++|++
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    34789999999977732              245777899999999999765  4355    39999999


Q ss_pred             hHHHHHHHHh
Q 032244          131 DLDQVAGRIA  140 (144)
Q Consensus       131 ~lD~iA~~i~  140 (144)
                      .++.+..++-
T Consensus        96 ~~~~~~~~~~  105 (109)
T TIGR01889        96 KIESLISEIE  105 (109)
T ss_pred             HHHHHHHHHH
Confidence            9999988764

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=95.63  E-value=0.077  Score=39.33  Aligned_cols=65  Identities=15%  Similarity=0.173  Sum_probs=48.7

Q ss_pred             HHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      +|..|+-. +++....|+...|-.+              +-+=.+++.||+.|||++.+  .+.|    .||++|+..++
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            56667754 4578889998877433              34668999999999999765  4455    49999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+....
T Consensus       102 ~~~~~~  107 (144)
T PRK03573        102 EVEAVI  107 (144)
T ss_pred             HHHHHH
Confidence            866543

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=95.55  E-value=0.07  Score=42.83  Aligned_cols=65  Identities=14%  Similarity=0.152  Sum_probs=49.9

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~lD~  134 (144)
                      ||-.||-.+++....|++..+-.              .+-+=.+++.||+.|||++.  +++.|    .||++|++.+++
T Consensus        50 iL~~L~~~~~itq~eLa~~l~l~--------------~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~  115 (185)
T PRK13777         50 ILWIAYHLKGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE  115 (185)
T ss_pred             HHHHHHhCCCcCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            67778888999999999965532              13366699999999999965  44455    399999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       116 l~~~~  120 (185)
T PRK13777        116 TMEEY  120 (185)
T ss_pred             HHHHH
Confidence            86543

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=95.12  E-value=0.094  Score=39.26  Aligned_cols=61  Identities=13%  Similarity=0.144  Sum_probs=45.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      |.+.+.-.|++-+..|+...|-              |.+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus        13 I~~l~~~~~~~~~~ela~~l~v--------------s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~   73 (142)
T PRK03902         13 IYLLIEEKGYARVSDIAEALSV--------------HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL   73 (142)
T ss_pred             HHHHHhcCCCcCHHHHHHHhCC--------------ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence            3333444577888888886663              335678889999999999976656899999998876655

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

Probab=94.96  E-value=0.09  Score=36.58  Aligned_cols=65  Identities=12%  Similarity=0.318  Sum_probs=46.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC-----ceeCcchHhhHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG-----RRITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG-----R~lT~~G~~~lD  133 (144)
                      |+=-|+-.+.+-...|+..-|              -+.+-+.+-|+.||++|+|+..+  .++     -.||++|++.+.
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            444455567777788887554              46678999999999999998654  333     269999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      +.-..+
T Consensus        71 ~~~~~L   76 (80)
T PF13601_consen   71 RYVAAL   76 (80)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876654

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=94.81  E-value=0.067  Score=38.23  Aligned_cols=47  Identities=19%  Similarity=0.309  Sum_probs=35.8

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceec--C-CCCc-----eeCcchHhhHHHHHHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELD--S-KGGR-----RITSSGQRDLDQVAGRI  139 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~--~-~gGR-----~lT~~G~~~lD~iA~~i  139 (144)
                      +..-+-+-+-.+|..||+.|||+..  + .+||     .||++|+..|+......
T Consensus        34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~   88 (100)
T TIGR03433        34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW   88 (100)
T ss_pred             ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            3444556688999999999999973  2 2232     59999999999987765

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

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=94.78  E-value=0.079  Score=45.85  Aligned_cols=52  Identities=25%  Similarity=0.275  Sum_probs=44.1

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-CceeCcchHhh
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-GRRITSSGQRD  131 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-GR~lT~~G~~~  131 (144)
                      .+|+|+..|.+.|+-            .-|..-||+-|.+||+.|++++...+ ||.-|.+|-+.
T Consensus        19 ~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~   71 (337)
T TIGR00331        19 GQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRY   71 (337)
T ss_pred             CCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHH
Confidence            589999999998762            34567899999999999999987644 99999998776

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

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=94.77  E-value=0.035  Score=39.09  Aligned_cols=35  Identities=29%  Similarity=0.388  Sum_probs=31.4

Q ss_pred             hhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244           99 SVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD  133 (144)
Q Consensus        99 ~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD  133 (144)
                      +-|+++++-|.++|+|++..+|--.||++|++.|-
T Consensus        55 ~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~   89 (92)
T PF14338_consen   55 NRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA   89 (92)
T ss_pred             HhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence            46899999999999999888877999999999874

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=94.70  E-value=0.086  Score=45.65  Aligned_cols=63  Identities=24%  Similarity=0.376  Sum_probs=48.3

Q ss_pred             HHHHHHH---HHHH--hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244           57 RAASMAR---KIYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilR---klYl--~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~  130 (144)
                      |--.||.   ..|+  .+|+|...|.+.|+-            .-|..-||+-+..||++|++++.. ..||.-|.+|-+
T Consensus         7 R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR   74 (339)
T PRK00082          7 RQREILRAIVEDYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYR   74 (339)
T ss_pred             HHHHHHHHHHHHHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHH
Confidence            3344554   2456  479999999987652            235678999999999999999765 459999999976


Q ss_pred             h
Q 032244          131 D  131 (144)
Q Consensus       131 ~  131 (144)
                      .
T Consensus        75 ~   75 (339)
T PRK00082         75 Y   75 (339)
T ss_pred             H
Confidence            4

>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=94.66  E-value=0.072  Score=33.68  Aligned_cols=49  Identities=22%  Similarity=0.300  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      -|+.+||+.|.-.+ ++++..+...-|-              +.+-+..+|+.|++.|||++++
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            48899999888865 5799999998884              3468999999999999999875

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.

>PRK05638 threonine synthase; Validated

Probab=94.63  E-value=0.24  Score=43.88  Aligned_cols=93  Identities=19%  Similarity=0.209  Sum_probs=62.3

Q ss_pred             HcCCCCCCCcchhcccCCC--------ccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCC
Q 032244           25 RSGKIELPTWNDIVKTGTL--------KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKS   96 (144)
Q Consensus        25 ~~gki~~P~w~d~vKTg~~--------kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~a   96 (144)
                      ++|.|..-+=+=++=||.+        ||.-..++-+.     .||+.|. +++.-+..|.+..+.            .-
T Consensus       337 ~~g~i~~~~~Vv~i~tG~g~k~~~~~~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~  398 (442)
T PRK05638        337 EEGYIEKGDKVVLVVTGSGLKGYGEGGREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PL  398 (442)
T ss_pred             HcCCCCCCCeEEEEeCCCCCCCCCCCchhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cC
Confidence            4444444344444555554        33334455433     3666555 678999999998883            13


Q ss_pred             chhhHHHHHHHHHhCCcceecCCCCce----eCcchHhhHHHH
Q 032244           97 SGSVARHILHQLQDTNIIELDSKGGRR----ITSSGQRDLDQV  135 (144)
Q Consensus        97 sg~iiR~~LqqLE~~glv~k~~~gGR~----lT~~G~~~lD~i  135 (144)
                      |...++..|+.||++|||+...+.||+    ||++|+..+..+
T Consensus       399 s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~  441 (442)
T PRK05638        399 KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL  441 (442)
T ss_pred             CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence            677999999999999999864222444    999999998764

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=94.40  E-value=0.063  Score=39.47  Aligned_cols=43  Identities=19%  Similarity=0.271  Sum_probs=34.7

Q ss_pred             CCCchhhHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHH
Q 032244           94 SKSSGSVARHILHQLQDTNIIELDSKG---GRRITSSGQRDLDQVA  136 (144)
Q Consensus        94 ~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~G~~~lD~iA  136 (144)
                      +.=+=.+++++++.|++.|++++.+.+   .-.||++|.++|.++-
T Consensus        41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~   86 (95)
T COG3432          41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS   86 (95)
T ss_pred             cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence            344557999999999999988888764   3579999999987653

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

Probab=94.08  E-value=0.13  Score=33.32  Aligned_cols=48  Identities=25%  Similarity=0.390  Sum_probs=40.4

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      .|++.|-..+|..++.|....|-              +-+-+.+=|+.||++|||+.... ||
T Consensus        14 ~Il~~L~~~~~~t~~ela~~l~~--------------~~~t~s~hL~~L~~aGli~~~~~-gr   61 (61)
T PF12840_consen   14 RILRLLASNGPMTVSELAEELGI--------------SQSTVSYHLKKLEEAGLIEVERE-GR   61 (61)
T ss_dssp             HHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEEE-TT
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEecc-CC
Confidence            58888888999999999999983              44679999999999999998775 44

...

>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=93.88  E-value=0.13  Score=35.29  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=36.0

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ  129 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~  129 (144)
                      ++.+..++..+|-              |-..+|++|++|++.|+|+..+  .||-.|+..-.
T Consensus        25 ~~s~~eiA~~~~i--------------~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~   72 (83)
T PF02082_consen   25 PVSSKEIAERLGI--------------SPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPE   72 (83)
T ss_dssp             -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CC
T ss_pred             CCCHHHHHHHHCc--------------CHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHH
Confidence            4899999998874              4469999999999999999664  57888876543

(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.

>COG1693 Repressor of nif and glnA expression [Transcription]

Probab=93.88  E-value=0.059  Score=46.97  Aligned_cols=65  Identities=20%  Similarity=0.277  Sum_probs=50.4

Q ss_pred             HHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244           61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~  134 (144)
                      |||=|.-.+ |+|-+.....--   +||+.      =+---+|+=||-||+.||++|+--.||.||.+|-+.|.+
T Consensus        11 Il~il~esd~plgak~Ia~el~---kRGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~   76 (325)
T COG1693          11 ILRILAESDEPLGAKIIALELR---KRGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR   76 (325)
T ss_pred             HHHHHHhcCCccchHHHHHHHH---hcccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence            566555554 888877766554   23432      233468999999999999999998899999999999998

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

Probab=93.78  E-value=0.12  Score=37.41  Aligned_cols=47  Identities=28%  Similarity=0.344  Sum_probs=38.2

Q ss_pred             CCCCCCCCchhhHHHHHHHHHhCCcceecCCC---C------ceeCcchHhhHHHH
Q 032244           89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKG---G------RRITSSGQRDLDQV  135 (144)
Q Consensus        89 ~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---G------R~lT~~G~~~lD~i  135 (144)
                      ....+..-+-.-|-+-+++|+++|||+.....   |      ..||.+|..+||.|
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            44556667777999999999999999976632   2      48999999999986

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=93.54  E-value=0.11  Score=40.44  Aligned_cols=65  Identities=14%  Similarity=0.242  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHhCC------CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244           57 RAASMARKIYLRGG------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRklYl~g~------~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~  130 (144)
                      .++..||..-+.|.      +.-..|+..||              -|.+-+|.+|+.||..|||+..+..|-.+++-...
T Consensus        15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg--------------VSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~   80 (212)
T TIGR03338        15 LVQDEIERAILSGELPPGAKLNESDIAARLG--------------VSRGPVREAFRALEEAGLVRNEKNRGVFVREISLA   80 (212)
T ss_pred             HHHHHHHHHHHcCCCCCCCEecHHHHHHHhC--------------CChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence            34445555555543      44567888888              36679999999999999999998889888887776


Q ss_pred             hHHHH
Q 032244          131 DLDQV  135 (144)
Q Consensus       131 ~lD~i  135 (144)
                      ++..+
T Consensus        81 ~~~ei   85 (212)
T TIGR03338        81 EADEI   85 (212)
T ss_pred             HHHHH
Confidence            66543

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.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=93.52  E-value=0.15  Score=39.84  Aligned_cols=54  Identities=17%  Similarity=0.295  Sum_probs=43.3

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      .|++.++.++..-+=              |.+-+-..|+.|++.|||+..+.+|-.||++|.+..-++
T Consensus        22 ~~~~~~~diA~~L~V--------------sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~   75 (154)
T COG1321          22 KGFARTKDIAERLKV--------------SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL   75 (154)
T ss_pred             cCcccHHHHHHHhCC--------------CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHH
Confidence            467888888886652              234677889999999999999999999999999654443

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.38  E-value=0.46  Score=34.83  Aligned_cols=68  Identities=13%  Similarity=0.193  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcch-HhhH
Q 032244           58 AASMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSG-QRDL  132 (144)
Q Consensus        58 aASilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G-~~~l  132 (144)
                      |-.+|..|...  +++.+..|+..+|-              |.+.++++|+.|++.|+|+...  .||..|.... +-.+
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            44566666554  46899999998874              5579999999999999998653  5687887665 3346


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .+|...|
T Consensus        77 ~~v~~~l   83 (130)
T TIGR02944        77 ADIVKAV   83 (130)
T ss_pred             HHHHHHH
Confidence            6666555

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.

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.25  E-value=0.19  Score=38.92  Aligned_cols=44  Identities=23%  Similarity=0.338  Sum_probs=33.9

Q ss_pred             CchhhHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHH
Q 032244           96 SSGSVARHILHQLQDTNIIELD---SKGGR-----RITSSGQRDLDQVAGRI  139 (144)
Q Consensus        96 asg~iiR~~LqqLE~~glv~k~---~~gGR-----~lT~~G~~~lD~iA~~i  139 (144)
                      .+-+-+=.+|+.||+.|||+..   ..+||     .||+.|++.|+....++
T Consensus        55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w  106 (138)
T TIGR02719        55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF  106 (138)
T ss_pred             CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            4456678899999999999863   23354     49999999988877664

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).

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

Probab=93.12  E-value=0.46  Score=29.60  Aligned_cols=62  Identities=19%  Similarity=0.209  Sum_probs=46.6

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA  136 (144)
                      .|+..++-.+ +....+.+..|-              +.+-++.+|.+|++.|++.....   .-..+|+ |+..++.+.
T Consensus        11 ~il~~l~~~~-~~~~ei~~~~~i--------------~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~   74 (78)
T cd00090          11 RILRLLLEGP-LTVSELAERLGL--------------SQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLE   74 (78)
T ss_pred             HHHHHHHHCC-cCHHHHHHHHCc--------------CHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHH
Confidence            3566666555 999999997763              34678999999999999986543   2457898 888888765


Q ss_pred             H
Q 032244          137 G  137 (144)
Q Consensus       137 ~  137 (144)
                      .
T Consensus        75 ~   75 (78)
T cd00090          75 S   75 (78)
T ss_pred             H
Confidence            3

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.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=93.09  E-value=0.36  Score=39.55  Aligned_cols=62  Identities=19%  Similarity=0.249  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q 032244           56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQRD  131 (144)
Q Consensus        56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~~  131 (144)
                      -|+..||+.|.-.+ ++++..|.+..|-              +.+-+..+|+.|++.|||++++ .+...||++..+.
T Consensus        11 ~ral~iL~~l~~~~~~ls~~eia~~lgl--------------~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l   74 (263)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELTGL--------------HRTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL   74 (263)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence            38889999887654 5999999998874              3468999999999999999986 4467788876543

>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=93.06  E-value=0.36  Score=30.47  Aligned_cols=51  Identities=24%  Similarity=0.402  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCce
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRR  123 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~  123 (144)
                      ..+|..||-.+++.+..|....+-              +.+-+-.++++||+.|||++..  ++.|.
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            347888999999999999998874              4467888999999999998654  44553

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 ....

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.01  E-value=0.34  Score=38.40  Aligned_cols=55  Identities=18%  Similarity=0.248  Sum_probs=44.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC--CceeCcch
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG--GRRITSSG  128 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g--GR~lT~~G  128 (144)
                      .||..|.-++++.+..+....|-              |.+-+++.|+.||+.|||++..+.  .-.||++|
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            57877777789999999998874              456889999999999999988622  34578876

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.

>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=92.93  E-value=0.27  Score=31.11  Aligned_cols=46  Identities=15%  Similarity=0.217  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhCC--CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           59 ASMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        59 ASilRklYl~g~--~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      ..||..|+-.++  +.++.|....|-.              .+-+-.+++.||+.|||++.+
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            358999999998  9999999988843              357888999999999999775

...

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=92.79  E-value=0.37  Score=36.14  Aligned_cols=62  Identities=23%  Similarity=0.347  Sum_probs=48.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC------CCCceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS------KGGRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~------~gGR~lT~~G~~~lD~  134 (144)
                      ||+++.- |+.--+.|++.-++             =|.+++=.-|+.||+.|+|++..      +-...||+.|++++.-
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            6777766 77777777776554             56678888899999999999775      2268899999998765


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus        94 l~   95 (120)
T COG1733          94 LL   95 (120)
T ss_pred             HH
Confidence            54

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

Probab=92.78  E-value=0.55  Score=30.59  Aligned_cols=39  Identities=26%  Similarity=0.386  Sum_probs=31.0

Q ss_pred             CC-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           70 GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        70 ~~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      .+ ....|...||              -|...+|.+|+.|++.|+|+..+..|-
T Consensus        23 ~lps~~~la~~~~--------------vsr~tvr~al~~L~~~g~i~~~~~~G~   62 (64)
T PF00392_consen   23 RLPSERELAERYG--------------VSRTTVREALRRLEAEGLIERRPGRGT   62 (64)
T ss_dssp             BE--HHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             EeCCHHHHHHHhc--------------cCCcHHHHHHHHHHHCCcEEEECCceE
Confidence            35 7788888888              466799999999999999998886553

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 ....

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

Probab=92.54  E-value=0.16  Score=31.87  Aligned_cols=39  Identities=18%  Similarity=0.267  Sum_probs=31.4

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT  125 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT  125 (144)
                      +..|+..||-              |..-++++|+.|++.|+|+..+..|-.||
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            7778887763              55799999999999999997775576665

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

>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=92.50  E-value=0.094  Score=35.24  Aligned_cols=42  Identities=31%  Similarity=0.431  Sum_probs=32.9

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceecCC---CC-----ceeCcchHhhHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELDSK---GG-----RRITSSGQRDLDQ  134 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~~~---gG-----R~lT~~G~~~lD~  134 (144)
                      +..-|-+-|=.+|+.||+.|||+....   +|     -.||++|+..|..
T Consensus        26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E   75 (75)
T PF03551_consen   26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE   75 (75)
T ss_dssp             TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred             CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence            456677889999999999999986542   22     4699999998763

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 ....

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=92.47  E-value=0.33  Score=36.39  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=34.6

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCc
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITS  126 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~  126 (144)
                      ++.+..|+..+|-              |...+|++|++|++.|||+..+  .||-.|+.
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            5778889998884              4569999999999999999776  34666654

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=92.35  E-value=0.19  Score=42.49  Aligned_cols=61  Identities=18%  Similarity=0.203  Sum_probs=46.6

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHhh
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVAGRIAV  141 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA~~i~~  141 (144)
                      .+.++.|-..-+           ...=+...+|.+|.-|++.|||+....   ....||++|++.++..+.-|..
T Consensus        17 ~i~~~~Li~l~~-----------~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~   80 (280)
T TIGR02277        17 AIWLGSLIEFLA-----------GLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD   80 (280)
T ss_pred             ceeHHHHHHHHH-----------hcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence            455566655554           223345689999999999999997654   3678999999999999888865

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=91.97  E-value=0.3  Score=37.38  Aligned_cols=38  Identities=21%  Similarity=0.336  Sum_probs=32.8

Q ss_pred             hhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           98 GSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        98 g~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      -.-+.++.|.||..|+|+.....|..+|++|+..+|..
T Consensus        49 pnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~   86 (125)
T COG1725          49 PNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQL   86 (125)
T ss_pred             HHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHH
Confidence            35788999999999999988877999999999877654

>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=91.62  E-value=1.2  Score=28.16  Aligned_cols=44  Identities=16%  Similarity=0.239  Sum_probs=33.8

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      +++....|....|-              |.+-+..+|++|++.|+|+....++-.|+|
T Consensus        24 ~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~   67 (67)
T cd00092          24 LPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP   67 (67)
T ss_pred             CCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence            45677777777763              556889999999999999988755666654

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.58  E-value=1  Score=35.88  Aligned_cols=65  Identities=17%  Similarity=0.288  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHhC------CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244           57 RAASMARKIYLRG------GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRklYl~g------~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~  130 (144)
                      .+...||.--+.|      .+....|...||-              |..-||.+|++|+..|||+..+..|-.+++-..+
T Consensus        20 ~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gv--------------SrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~   85 (230)
T COG1802          20 QVYEELREAILSGELAPGERLSEEELAEELGV--------------SRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLA   85 (230)
T ss_pred             HHHHHHHHHHHhCCCCCCCCccHHHHHHHhCC--------------CCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHH
Confidence            4445556555554      5788999999995              4468999999999999999999889999988888


Q ss_pred             hHHHH
Q 032244          131 DLDQV  135 (144)
Q Consensus       131 ~lD~i  135 (144)
                      ++..+
T Consensus        86 ~~~ei   90 (230)
T COG1802          86 EAREI   90 (230)
T ss_pred             HHHHH
Confidence            87774

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=91.39  E-value=1.2  Score=32.26  Aligned_cols=49  Identities=24%  Similarity=0.312  Sum_probs=39.3

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCceeCcchHhh
Q 032244           69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRRITSSGQRD  131 (144)
Q Consensus        69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~lT~~G~~~  131 (144)
                      +++.+..|+..+|-              +.+.+|++|+.|++.|||...  ..||-.|+......
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            38999999998774              457999999999999999864  35678888776544

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.

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=91.23  E-value=0.37  Score=38.30  Aligned_cols=42  Identities=10%  Similarity=0.256  Sum_probs=35.8

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      .-..|+..||              -|..-+|-+|+.||..|||+..+..|-.+++-
T Consensus        32 sE~~La~~lg--------------VSRtpVREAL~~Le~eGlV~~~~~~G~~V~~~   73 (235)
T TIGR02812        32 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNNF   73 (235)
T ss_pred             CHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence            4667888888              46789999999999999999998778888773

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=91.16  E-value=0.35  Score=38.18  Aligned_cols=51  Identities=20%  Similarity=0.289  Sum_probs=40.2

Q ss_pred             CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        71 ~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      +....|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-...++..+
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            455688888883              557999999999999999999877888877666555443

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

Probab=91.02  E-value=0.71  Score=29.96  Aligned_cols=48  Identities=17%  Similarity=0.253  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      -..|+..|--++.+.+..|...||-              |-.=||.=|+.||+.|+|.+.-.
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~V--------------S~~TiRRDl~~L~~~g~i~r~~G   49 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGV--------------SEMTIRRDLNKLEKQGLIKRTHG   49 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcC
Confidence            3457888888999999999999984              55689999999999999998875

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

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

Probab=90.94  E-value=0.75  Score=33.46  Aligned_cols=44  Identities=18%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      ||.|||--||--...+++..              ..+-.-++.+|..||++||||...
T Consensus        12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~   55 (92)
T PF10007_consen   12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE   55 (92)
T ss_pred             HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec
Confidence            89999999998888887754              455578999999999999999877

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

Probab=90.75  E-value=0.79  Score=30.76  Aligned_cols=45  Identities=11%  Similarity=0.062  Sum_probs=38.3

Q ss_pred             HHHHHHHHhCC--CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           60 SMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        60 SilRklYl~g~--~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      .||..|.-+|+  +....|.+..|=.+              +.++.+|..||+.|+|++..
T Consensus        10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~--------------~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550       10 KILEFLENSGDETSTALQLAKNLGLPK--------------KEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecC
Confidence            47777777877  99999999988543              58999999999999999865

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

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=90.73  E-value=0.3  Score=30.08  Aligned_cols=36  Identities=17%  Similarity=0.295  Sum_probs=29.1

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG  121 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG  121 (144)
                      .+..|+..||              -|..-+|.+|++||+.|+|+..+.+|
T Consensus        22 s~~~la~~~~--------------vs~~tv~~~l~~L~~~g~i~~~~~~g   57 (60)
T smart00345       22 SERELAAQLG--------------VSRTTVREALSRLEAEGLVQRRPGSG   57 (60)
T ss_pred             CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            6777788776              35679999999999999998776544

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=90.65  E-value=0.33  Score=39.01  Aligned_cols=45  Identities=22%  Similarity=0.170  Sum_probs=36.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR  130 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~  130 (144)
                      .-..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-...
T Consensus        33 sE~eLa~~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~   77 (251)
T PRK09990         33 SERRLCEKLG--------------FSRSALREGLTVLRGRGIIETAQGRGSFVARLNRV   77 (251)
T ss_pred             CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence            4567888888              46789999999999999999998778777765543

>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=90.64  E-value=1.6  Score=32.23  Aligned_cols=70  Identities=17%  Similarity=0.141  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      .+++|+-++|-+.=+..+.++-.-            +...+...+-+=++-|-+-|||||.-+ |-++|..|+..+-++|
T Consensus        17 ~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~~AA   83 (96)
T PF09114_consen   17 NAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIIIQAA   83 (96)
T ss_dssp             HHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHHHHH
Confidence            578899888888888888888733            234455677777899999999999998 8999999999999887


Q ss_pred             HHH
Q 032244          137 GRI  139 (144)
Q Consensus       137 ~~i  139 (144)
                      .--
T Consensus        84 ~l~   86 (96)
T PF09114_consen   84 ELW   86 (96)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            643

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.

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=90.28  E-value=0.46  Score=37.53  Aligned_cols=49  Identities=18%  Similarity=0.262  Sum_probs=37.8

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      ...|+..||-              |..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus        37 e~~La~~lgV--------------SRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei   85 (221)
T PRK11414         37 TKNLAEQLGM--------------SITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI   85 (221)
T ss_pred             HHHHHHHHCC--------------CchhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence            3568888883              557899999999999999998877877766555555443

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

Probab=90.22  E-value=0.84  Score=29.60  Aligned_cols=55  Identities=20%  Similarity=0.386  Sum_probs=39.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ  129 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~  129 (144)
                      |+=.|=+..++-+..+...||..             --......|++|++.|||+.+.. .=+||++|+
T Consensus        11 i~~~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~~-~l~lT~~G~   65 (66)
T PF06969_consen   11 IMLGLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDGG-RLRLTEKGR   65 (66)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-SS-EEEE-TTTG
T ss_pred             HHHHHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeCC-EEEECcccC
Confidence            34445556788999999999854             22355788999999999998774 778999996

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=90.13  E-value=0.93  Score=27.08  Aligned_cols=46  Identities=15%  Similarity=0.248  Sum_probs=37.0

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      .|+..|.-++++.+..|...+|-              |-.-+++.|+.|++.|+|+....
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGV--------------SEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeec
Confidence            36666666788999999999863              34568999999999999997664

>PRK03837 transcriptional regulator NanR; Provisional

Probab=90.12  E-value=2.3  Score=33.62  Aligned_cols=57  Identities=12%  Similarity=0.292  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           57 RAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        57 RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      ..+.-||.--+.|.      + ....|+..||              -|...+|.+|+.||..|||+..+..|-.+++-
T Consensus        17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~g--------------VSRt~VREAL~~L~~eGlv~~~~~~G~~V~~~   80 (241)
T PRK03837         17 EVEERLEQMIRSGEFGPGDQLPSERELMAFFG--------------VGRPAVREALQALKRKGLVQISHGERARVSRP   80 (241)
T ss_pred             HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence            34444454444542      4 4667899888              47789999999999999999888667666653

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=89.74  E-value=0.92  Score=36.93  Aligned_cols=58  Identities=7%  Similarity=0.115  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCceeCcc
Q 032244           56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGRRITSS  127 (144)
Q Consensus        56 ~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR~lT~~  127 (144)
                      -|+-.||..|.-.+++++..|.+.-|-.              .+-+..+|+.|++.|||++++. +...|+++
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            4888999999877889999999977743              4689999999999999998863 43455543

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=89.71  E-value=1.1  Score=33.32  Aligned_cols=46  Identities=15%  Similarity=0.305  Sum_probs=36.6

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cCCCCceeCcch
Q 032244           69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGGRRITSSG  128 (144)
Q Consensus        69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~~gGR~lT~~G  128 (144)
                      +++.+..++..++              -+...++++|++|.++|||+.  ...||-.|+..-
T Consensus        24 ~~~s~~~ia~~~~--------------ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~   71 (135)
T TIGR02010        24 GPVTLADISERQG--------------ISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA   71 (135)
T ss_pred             CcCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH
Confidence            4789999998776              455799999999999999985  346687887643

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

>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=89.67  E-value=1.4  Score=26.93  Aligned_cols=42  Identities=17%  Similarity=0.206  Sum_probs=34.8

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE  115 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~  115 (144)
                      .||..|.-++++.+..++...|-              |.+-+++.|++|++.|+|+
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            47777888899999999998884              5578999999999999986

...

>PRK08599 coproporphyrinogen III oxidase; Provisional

Probab=89.22  E-value=1.4  Score=37.79  Aligned_cols=59  Identities=20%  Similarity=0.331  Sum_probs=44.8

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      ..++-...+...||..             -.......+++|++.||++.+.. .=+||++|+-.+|.|+.+++
T Consensus       316 ~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~~-~~~lt~~G~~~~~~i~~~~~  374 (377)
T PRK08599        316 KSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDDD-HVRLTKKGKFLGNEVFEAFL  374 (377)
T ss_pred             hCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEECC-EEEECccHhHHHHHHHHHHh
Confidence            4455566666666521             13456778899999999997654 67999999999999999875

>PRK09057 coproporphyrinogen III oxidase; Provisional

Probab=88.85  E-value=2  Score=37.25  Aligned_cols=57  Identities=26%  Similarity=0.387  Sum_probs=44.2

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      ..++-...+...||-.-                ....|+.|++.||++.+.++.=+||++|+-.+|.|+.+++
T Consensus       323 ~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~  379 (380)
T PRK09057        323 REGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA  379 (380)
T ss_pred             hCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence            35677788888888421                1257999999999986553246899999999999999876

>PRK11569 transcriptional repressor IclR; Provisional

Probab=88.43  E-value=1.4  Score=36.46  Aligned_cols=59  Identities=15%  Similarity=0.196  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC-ceeCcc
Q 032244           55 YIRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG-RRITSS  127 (144)
Q Consensus        55 y~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG-R~lT~~  127 (144)
                      --|+..||+.|-- .+++++..|.+.-|-.|              +-+..+|+.|++.|||+++++.| ..|.+.
T Consensus        27 l~ral~IL~~l~~~~~~~~lseia~~lglpk--------------sTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   87 (274)
T PRK11569         27 LTRGLKLLEWIAESNGSVALTELAQQAGLPN--------------STTHRLLTTMQQQGFVRQVGELGHWAIGAH   87 (274)
T ss_pred             HHHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence            3599999999876 46899999999887543              68999999999999999887433 345443

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=88.07  E-value=1.5  Score=36.20  Aligned_cols=57  Identities=19%  Similarity=0.144  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC-ceeCc
Q 032244           56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG-RRITS  126 (144)
Q Consensus        56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG-R~lT~  126 (144)
                      -|+.+||+.|.-. +++++..+.+.-|-.|              +-+..+|+.|+..|||++++..| ..|++
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpk--------------Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~   83 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDLPL--------------STTFRLLKVLQAADFVYQDSQLGWWHIGL   83 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence            3888999998764 5799999999888544              67899999999999999987433 33443

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

Probab=88.02  E-value=0.72  Score=38.05  Aligned_cols=55  Identities=25%  Similarity=0.204  Sum_probs=42.7

Q ss_pred             CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHH
Q 032244           71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        71 ~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA~~i  139 (144)
                      +..+.|.+..|-              |.+-+-..|++||+.|||++...   .--.||++|+..+.+...+.
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            446788886653              55678899999999999987652   23579999999998887664

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=87.97  E-value=1.6  Score=35.92  Aligned_cols=51  Identities=20%  Similarity=0.254  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHHhCCC--chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244           56 IRAASMARKIYLRGGL--GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG  121 (144)
Q Consensus        56 ~RaASilRklYl~g~~--Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG  121 (144)
                      .|+..||..|.- +|.  ++..|.+.-|-              +.+=++.+|+.|++.|||++++++|
T Consensus         4 ~ral~iL~~l~~-~~~~l~l~ela~~~gl--------------pksT~~RlL~tL~~~G~v~~d~~~g   56 (246)
T COG1414           4 ERALAILDLLAE-GPGGLSLAELAERLGL--------------PKSTVHRLLQTLVELGYVEQDPEDG   56 (246)
T ss_pred             HHHHHHHHHHHh-CCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEcCCCC
Confidence            488899988887 444  59999998774              3467999999999999999999654

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=87.92  E-value=1.9  Score=34.21  Aligned_cols=58  Identities=19%  Similarity=0.216  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        55 y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      |..-+..||+-=..|..       +-..|+..||-              |..-+|++|+.|+..|+|.+.+..|-.+++
T Consensus         3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~   67 (230)
T TIGR02018         3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAE   67 (230)
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEcc
Confidence            55666666665555532       45678898884              667999999999999999999866766654

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.

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=87.88  E-value=0.88  Score=36.58  Aligned_cols=41  Identities=15%  Similarity=0.259  Sum_probs=33.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .-..|+..||              -|...+|.+|+.||..|||+..+..|-.+++
T Consensus        36 sE~eLa~~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~   76 (254)
T PRK09464         36 PERELAKQFD--------------VSRPSLREAIQRLEAKGLLLRRQGGGTFVQS   76 (254)
T ss_pred             CHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence            4556888888              4678999999999999999988877866665

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

Probab=87.87  E-value=0.7  Score=30.29  Aligned_cols=47  Identities=17%  Similarity=0.193  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      +.|+..|--+|+..+..+.+.-|-              +.+-++.+|+.|++.|||++.+.
T Consensus        11 ~~vy~~Ll~~~~~t~~eIa~~l~i--------------~~~~v~~~L~~L~~~GlV~~~~~   57 (68)
T PF01978_consen   11 AKVYLALLKNGPATAEEIAEELGI--------------SRSTVYRALKSLEEKGLVEREEG   57 (68)
T ss_dssp             HHHHHHHHHHCHEEHHHHHHHHTS--------------SHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcC
Confidence            445656656899999999997764              45789999999999999998773

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=87.83  E-value=1.4  Score=33.95  Aligned_cols=60  Identities=27%  Similarity=0.388  Sum_probs=47.4

Q ss_pred             HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----------eeCcchHhhH
Q 032244           67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----------RITSSGQRDL  132 (144)
Q Consensus        67 l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----------~lT~~G~~~l  132 (144)
                      -+||.+|..|+..-+              =+.+-+=++||.|..+|+|++.+   ++||           .++....++|
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            489999999999765              35678999999999999998665   4443           3567788888


Q ss_pred             HHHHHHHh
Q 032244          133 DQVAGRIA  140 (144)
Q Consensus       133 D~iA~~i~  140 (144)
                      |..|.++.
T Consensus       105 ~~w~~~~~  112 (126)
T COG3355         105 DEWYDKMK  112 (126)
T ss_pred             HHHHHHHH
Confidence            88887763

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=87.75  E-value=0.54  Score=37.96  Aligned_cols=41  Identities=20%  Similarity=0.184  Sum_probs=34.5

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      -..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-
T Consensus        29 E~eLae~~g--------------VSRtpVREAL~~Le~~GlV~~~~~~G~~V~~~   69 (253)
T PRK10421         29 ERQLAMQLG--------------VSRNSLREALAKLVSEGVLLSRRGGGTFIRWR   69 (253)
T ss_pred             HHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence            457888888              46789999999999999999888778888764

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=87.72  E-value=0.61  Score=37.10  Aligned_cols=41  Identities=10%  Similarity=0.285  Sum_probs=34.5

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .-..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++
T Consensus        33 sE~eLae~~g--------------VSRt~VReAL~~L~~eGlv~~~~g~G~~V~~   73 (239)
T PRK04984         33 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNN   73 (239)
T ss_pred             CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence            4557888888              4678999999999999999998877877765

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=87.57  E-value=0.53  Score=37.99  Aligned_cols=59  Identities=17%  Similarity=0.259  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHhC------CC-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244           57 RAASMARKIYLRG------GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ  129 (144)
Q Consensus        57 RaASilRklYl~g------~~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~  129 (144)
                      ..+..||.--+.|      .+ ....|+..||=              |..-+|.+|+.||..|||+..+..|-.+++...
T Consensus        13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~   78 (257)
T PRK10225         13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDV--------------TRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG   78 (257)
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence            4445555555555      24 36689999983              668999999999999999998877877766543

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

Probab=87.20  E-value=0.84  Score=33.99  Aligned_cols=39  Identities=21%  Similarity=0.353  Sum_probs=33.2

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      ++.+..|+....+..|              -.|.+|++|++.|||+-.+.-||
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            5789999998887665              68999999999999999985565

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=86.85  E-value=1.1  Score=34.86  Aligned_cols=44  Identities=18%  Similarity=0.335  Sum_probs=33.7

Q ss_pred             CCchhhHHHHHHHHHhCCcceecCCC-C---ceeCcchHhhHHHHHHH
Q 032244           95 KSSGSVARHILHQLQDTNIIELDSKG-G---RRITSSGQRDLDQVAGR  138 (144)
Q Consensus        95 ~asg~iiR~~LqqLE~~glv~k~~~g-G---R~lT~~G~~~lD~iA~~  138 (144)
                      ..|-+-|=-+|+.||+.|||+....+ .   -.||+.|+..|+....+
T Consensus        74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~  121 (135)
T PRK09416         74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN  121 (135)
T ss_pred             cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence            33556677899999999999865432 2   36999999999987653

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=86.83  E-value=0.75  Score=35.43  Aligned_cols=46  Identities=24%  Similarity=0.323  Sum_probs=37.4

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ  129 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~  129 (144)
                      ++.+..++..++-              |...+++|||+|.++|||+...  .||-.|+..-.
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            5778888887763              5579999999999999998665  67999987654

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=86.71  E-value=1.1  Score=33.17  Aligned_cols=44  Identities=25%  Similarity=0.419  Sum_probs=32.9

Q ss_pred             CchhhHHHHHHHHHhCCcceecC--CCC------ceeCcchHhhHHHHHHHH
Q 032244           96 SSGSVARHILHQLQDTNIIELDS--KGG------RRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        96 asg~iiR~~LqqLE~~glv~k~~--~gG------R~lT~~G~~~lD~iA~~i  139 (144)
                      .|-+.|=-+|+.||+.|||+...  .+|      -.||++|+..|.+...+.
T Consensus        42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~   93 (138)
T COG1695          42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEW   93 (138)
T ss_pred             CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            34445667999999999999652  222      379999999999876553

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=86.64  E-value=2.8  Score=33.10  Aligned_cols=61  Identities=11%  Similarity=0.211  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      -|..-+..|+.-=..|..       .-..|+..||              -|..-+|++|+.|+..|+|++.+..|-.+++
T Consensus         9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~   74 (238)
T TIGR02325         9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFG--------------VNRHTVRRAIAALVERGLLRAEQGRGTFVAA   74 (238)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence            466777777666555533       3457888888              4667999999999999999998866877775


Q ss_pred             ch
Q 032244          127 SG  128 (144)
Q Consensus       127 ~G  128 (144)
                      ..
T Consensus        75 ~~   76 (238)
T TIGR02325        75 RR   76 (238)
T ss_pred             Cc
Confidence            43

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

>PF13814 Replic_Relax: Replication-relaxation

Probab=86.62  E-value=1.8  Score=33.00  Aligned_cols=62  Identities=21%  Similarity=0.285  Sum_probs=46.9

Q ss_pred             HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-----CC-----ceeCcchHhh
Q 032244           62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-----GG-----RRITSSGQRD  131 (144)
Q Consensus        62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-----gG-----R~lT~~G~~~  131 (144)
                      |+-||-.+-+....|...++...++           ..-+|..|++|++.|+|+....     +|     -.||++|.+.
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            3556777788888898888854432           1279999999999999987653     13     3799999998


Q ss_pred             HHH
Q 032244          132 LDQ  134 (144)
Q Consensus       132 lD~  134 (144)
                      |..
T Consensus        70 l~~   72 (191)
T PF13814_consen   70 LAD   72 (191)
T ss_pred             HHh
Confidence            874

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=86.48  E-value=2.2  Score=33.39  Aligned_cols=46  Identities=15%  Similarity=0.255  Sum_probs=37.5

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cCCCCceeCcch
Q 032244           69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGGRRITSSG  128 (144)
Q Consensus        69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~~gGR~lT~~G  128 (144)
                      +++.+..++..+|-              +...++++|++|.++|||+.  .+.||-.|...-
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            47899999997774              55699999999999999985  456788887654

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=86.30  E-value=0.72  Score=37.22  Aligned_cols=41  Identities=17%  Similarity=0.165  Sum_probs=33.6

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      -..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-
T Consensus        35 E~eLae~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~   75 (253)
T PRK11523         35 ERFIADEKN--------------VSRTVVREAIIMLEVEGYVEVRKGSGIHVVSN   75 (253)
T ss_pred             HHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCeeEEecC
Confidence            457888888              46789999999999999999888667666654

>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=86.16  E-value=3  Score=29.25  Aligned_cols=76  Identities=16%  Similarity=0.176  Sum_probs=50.3

Q ss_pred             HHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCC------CCC---chhhHHHHHHHHHhCCcceecCC----CCce
Q 032244           58 AASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHF------SKS---SGSVARHILHQLQDTNIIELDSK----GGRR  123 (144)
Q Consensus        58 aASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~------~~a---sg~iiR~~LqqLE~~glv~k~~~----gGR~  123 (144)
                      |..||+-|+- .+.+|...+..++=|.++....-.++      -.+   |..-++.++++|...|+++....    .-=.
T Consensus         6 a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~   85 (106)
T PF09382_consen    6 AKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLK   85 (106)
T ss_dssp             HHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEE
T ss_pred             HHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEE
Confidence            3446666665 46899999999999998877543322      222   44689999999999999965543    1357


Q ss_pred             eCcchHhhHH
Q 032244          124 ITSSGQRDLD  133 (144)
Q Consensus       124 lT~~G~~~lD  133 (144)
                      +|++|++.|.
T Consensus        86 ~~~~~~~~l~   95 (106)
T PF09382_consen   86 LTPKGKELLN   95 (106)
T ss_dssp             E-GGGHHHHC
T ss_pred             ECHHHHHHHC
Confidence            8999998875

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.

>PRK13347 coproporphyrinogen III oxidase; Provisional

Probab=86.12  E-value=2.5  Score=37.56  Aligned_cols=63  Identities=16%  Similarity=0.109  Sum_probs=44.7

Q ss_pred             HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHH
Q 032244           65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i  139 (144)
                      |-...++-...+...||-..      ..     -.-....|++|++.|||+.+.. +=+||++|+-.+|.|+..+
T Consensus       376 L~~~~~ld~~~~~~~~g~~~------~~-----~~~~~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~f  438 (453)
T PRK13347        376 LMCNFPVDLAAIAARHGFFA------RY-----FLDELARLEPLAADGLVTIDGG-GIRVTPEGRPLIRAVAAAF  438 (453)
T ss_pred             HHhhCCcCHHHHHHHHCCCH------HH-----HHHHHHHHHHHHHCCCEEEECC-EEEECcchhHHHHHHHHHH
Confidence            44455666777888887320      00     0012457899999999997654 6799999999999999865

>PRK08208 coproporphyrinogen III oxidase; Validated

Probab=85.80  E-value=2.8  Score=37.04  Aligned_cols=59  Identities=22%  Similarity=0.293  Sum_probs=45.2

Q ss_pred             HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244           67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus        67 l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      +..++-...+...||..      +       .. ....|++|++.|||+.+.+ .=+||++|+-..|.|+.+++
T Consensus       358 ~~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~~-~l~lT~~G~~~~d~i~~~~~  416 (430)
T PRK08208        358 QAQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNGG-RLRLTEEGLALSDAIGPVFI  416 (430)
T ss_pred             HhCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEECC-EEEECcchhhHHHHHHHHHc
Confidence            34677777888888731      1       12 3458899999999987653 56899999999999999885

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=85.46  E-value=1.1  Score=37.62  Aligned_cols=57  Identities=16%  Similarity=0.281  Sum_probs=42.3

Q ss_pred             HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHH-HHHhCCcceecCCCCceeCcchHhhHH
Q 032244           62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILH-QLQDTNIIELDSKGGRRITSSGQRDLD  133 (144)
Q Consensus        62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~Lq-qLE~~glv~k~~~gGR~lT~~G~~~lD  133 (144)
                      +...|-.+++|+..+...-|-...              -+-.++. .|-+.|||++++. ||++|++|.+.|.
T Consensus       268 ~~~~~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~~-gr~~~~~~~~~~~  325 (328)
T PRK00080        268 IIEKFGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTPR-GRVATPKAYEHLG  325 (328)
T ss_pred             HHHHcCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCCc-hHHHHHHHHHHhC
Confidence            344455679999999998885443              2333333 8889999997776 9999999998774

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

Probab=85.31  E-value=0.77  Score=34.53  Aligned_cols=77  Identities=22%  Similarity=0.340  Sum_probs=47.6

Q ss_pred             CCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHH
Q 032244           29 IELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQL  108 (144)
Q Consensus        29 i~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqL  108 (144)
                      =+.-.|.+=-++...+--.-.|+.-+    ..|+--+--..-|.+..|...||-              ++||.|.+|..|
T Consensus        22 k~kKK~~~k~~k~~~~~av~vdee~~----~ki~KEV~~~r~VTpy~la~r~gI--------------~~SvAr~vLR~L   83 (107)
T COG4901          22 KDKKKWSKKKKKEEARRAVTVDEELL----DKIRKEVPRERVVTPYVLASRYGI--------------NGSVARIVLRHL   83 (107)
T ss_pred             hhhhccccccccchhhhhhhccHHHH----HHHHHhcccceeecHHHHHHHhcc--------------chHHHHHHHHHH
Confidence            34456766544443333333333221    123333333345778888888883              679999999999


Q ss_pred             HhCCcceecCCCCcee
Q 032244          109 QDTNIIELDSKGGRRI  124 (144)
Q Consensus       109 E~~glv~k~~~gGR~l  124 (144)
                      |+.|+|....+ +|+.
T Consensus        84 eeeGvv~lvsk-nrR~   98 (107)
T COG4901          84 EEEGVVQLVSK-NRRQ   98 (107)
T ss_pred             HhCCceeeecc-Cccc
Confidence            99999988776 5554

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

Probab=84.95  E-value=3.6  Score=29.12  Aligned_cols=48  Identities=15%  Similarity=0.106  Sum_probs=34.5

Q ss_pred             HHHHHHHHHH--------HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           57 RAASMARKIY--------LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        57 RaASilRklY--------l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      |-|++|-.|.        ...++.-..|....|-              |..-+.++|++||+.|||+...
T Consensus        26 r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~--------------sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        26 REFRVLLAIIRLTYGWNKKQDRVTATVIAELTGL--------------SRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             HHHHHHHHHHHHHhCccccCCccCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeeec
Confidence            5566665554        4456677777777763              3456889999999999998654

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

>PRK05628 coproporphyrinogen III oxidase; Validated

Probab=84.25  E-value=1.4  Score=37.86  Aligned_cols=38  Identities=13%  Similarity=0.130  Sum_probs=32.6

Q ss_pred             HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244          102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus       102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      +..|++|++.|++..+.. .=+||++|+-.+|.|+.+++
T Consensus       337 ~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~~~  374 (375)
T PRK05628        337 RARAARVVADGLLAAEGG-RLVLTLRGRLLADAVVRDLL  374 (375)
T ss_pred             HHHHHHHHHCCCEEEECC-EEEEChhhhHHHHHHHHHHh
Confidence            468899999999987654 57899999999999998864

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=83.95  E-value=4.3  Score=32.25  Aligned_cols=58  Identities=17%  Similarity=0.206  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        55 y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      |...+..|++-=..|..       .=..|+..||              -|..-+|++|+.|+..|+|++.+..|--+++
T Consensus         2 y~qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~g--------------VSR~TVR~Al~~L~~eGli~r~~G~GTfV~~   66 (233)
T TIGR02404         2 YEQIYQDLEQKITHGQYKEGDYLPSEHELMDQYG--------------ASRETVRKALNLLTEAGYIQKIQGKGSIVLN   66 (233)
T ss_pred             HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence            44455555554444433       2456888888              4678999999999999999999866877754

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.

>PRK14999 histidine utilization repressor; Provisional

Probab=83.75  E-value=7.9  Score=31.01  Aligned_cols=60  Identities=17%  Similarity=0.153  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+..|++-=..|.      + +-..|+..||              -|..-+|++|+.|+..|+|.+.+..|--+++
T Consensus        13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~g--------------VSR~TVR~Al~~L~~eGli~r~~GkGTfV~~   78 (241)
T PRK14999         13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYG--------------FSRMTINRALRELTDEGWLVRLQGVGTFVAE   78 (241)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence            46677777766555542      2 5678899998              4667999999999999999988866777765


Q ss_pred             c
Q 032244          127 S  127 (144)
Q Consensus       127 ~  127 (144)
                      .
T Consensus        79 ~   79 (241)
T PRK14999         79 P   79 (241)
T ss_pred             C
Confidence            4

>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=83.23  E-value=1.4  Score=29.65  Aligned_cols=40  Identities=23%  Similarity=0.194  Sum_probs=30.7

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      |-.|..+...+|-             .|-+-+..-|++||+.|+|+.++...|
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            5588888888883             367889999999999999999885433

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.

>PRK05799 coproporphyrinogen III oxidase; Provisional

Probab=83.02  E-value=1.8  Score=37.02  Aligned_cols=40  Identities=5%  Similarity=0.090  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244          100 VARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus       100 iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      .....|++|++.||++.+.. .=+||++|+-.+|.|+.+++
T Consensus       334 ~~~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~~~  373 (374)
T PRK05799        334 VYGEVINKYIKLGLLIEKEG-RIYLSERGIEVSNSIMSDFL  373 (374)
T ss_pred             HHHHHHHHHHHCCCEEEECC-EEEEChhHHHHHHHHHHHHh
Confidence            35567899999999986543 46899999999999998874

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=82.35  E-value=1.5  Score=31.68  Aligned_cols=36  Identities=28%  Similarity=0.343  Sum_probs=27.3

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      -+....|...|+              =.||+.|.+|++||+-|+|.....
T Consensus        41 ~ITps~lserlk--------------I~~SlAr~~Lr~L~~kG~Ik~V~~   76 (86)
T PRK09334         41 IVTPYTLASKYG--------------IKISVAKKVLRELEKRGVLVLYSK   76 (86)
T ss_pred             EEcHHHHHHHhc--------------chHHHHHHHHHHHHHCCCEEEEec
Confidence            355666666665              357899999999999999976554

>PRK06294 coproporphyrinogen III oxidase; Provisional

Probab=82.18  E-value=1.9  Score=37.32  Aligned_cols=39  Identities=10%  Similarity=0.166  Sum_probs=32.3

Q ss_pred             HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244          101 ARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus       101 iR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      ....+++|++.||++.+.+ .=.||++|+-.+|.|+.+++
T Consensus       332 ~~~~l~~~~~~gll~~~~~-~i~lT~~G~~~~~~i~~~~~  370 (370)
T PRK06294        332 TSELIMHPIIQELFTKNDQ-ALSLNKKGRLFHDTIAEEIM  370 (370)
T ss_pred             HHHHHHHHHHCCCEEEECC-EEEECcchhhHHHHHHHHhC
Confidence            4567889999999986653 56899999999999998763

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=81.97  E-value=6.7  Score=31.49  Aligned_cols=61  Identities=25%  Similarity=0.344  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+..|++-=..|..       .-..|+..||              -|..-+|.+|+.|+..|+|.+.+..|-.+++
T Consensus         6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~   71 (240)
T PRK09764          6 LYRQIADRIREQIARGELKPGDALPTESALQTEFG--------------VSRVTVRQALRQLVEQQILESIQGSGTYVKE   71 (240)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEEcc
Confidence            466677777666555532       3467888888              3668999999999999999988866877765


Q ss_pred             ch
Q 032244          127 SG  128 (144)
Q Consensus       127 ~G  128 (144)
                      ..
T Consensus        72 ~~   73 (240)
T PRK09764         72 ER   73 (240)
T ss_pred             cc
Confidence            44

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

Probab=81.92  E-value=3.5  Score=36.36  Aligned_cols=68  Identities=16%  Similarity=0.196  Sum_probs=48.0

Q ss_pred             chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244           52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRD  131 (144)
Q Consensus        52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~  131 (144)
                      ||.=.+--+.+-.-|--||||+..++-.-|--+.             .|-=.+===|-..|+++++++ ||++|+++.+.
T Consensus       259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTpR-GR~aT~~ay~h  324 (332)
T COG2255         259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTPR-GRIATAKAYEH  324 (332)
T ss_pred             cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCCC-cceecHHHHHH
Confidence            5666666556666666799999999998885432             121122223556899999998 99999999876


Q ss_pred             HH
Q 032244          132 LD  133 (144)
Q Consensus       132 lD  133 (144)
                      |-
T Consensus       325 l~  326 (332)
T COG2255         325 LG  326 (332)
T ss_pred             hc
Confidence            53

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=81.71  E-value=1.9  Score=25.50  Aligned_cols=35  Identities=14%  Similarity=0.244  Sum_probs=26.7

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      ++.+..+....|-              |..-++.+|++|++.|+|+...
T Consensus         8 ~~s~~~la~~l~~--------------s~~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419        8 PLTRQEIAELLGL--------------TRETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             ccCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeC
Confidence            4556666676663              4467899999999999998765

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=81.42  E-value=6  Score=27.09  Aligned_cols=61  Identities=31%  Similarity=0.390  Sum_probs=41.4

Q ss_pred             HHHHHHHHHH---Hh---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCcc
Q 032244           57 RAASMARKIY---LR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITSS  127 (144)
Q Consensus        57 RaASilRklY---l~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~  127 (144)
                      |+-|++--||   +.   +++-++.|-...+.           --=+-+-+|.+|--|-+.||++....|   +-.||++
T Consensus         1 ~a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~-----------~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~   69 (70)
T PF07848_consen    1 RARSLIVTLLGDYLRPRGGWIWVASLIRLLAA-----------FGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTER   69 (70)
T ss_dssp             -HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCC-----------TT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred             CcceehHHHHHHHhccCCCceeHHHHHHHHHH-----------cCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence            4567777777   43   46677777776662           223456899999999999999998874   3678887


Q ss_pred             h
Q 032244          128 G  128 (144)
Q Consensus       128 G  128 (144)
                      |
T Consensus        70 g   70 (70)
T PF07848_consen   70 G   70 (70)
T ss_dssp             H
T ss_pred             C
Confidence            6

PaaX is a transcriptional regulator that 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 []. ; PDB: 3KFW_X 3L09_B.

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=81.27  E-value=1.6  Score=37.14  Aligned_cols=60  Identities=20%  Similarity=0.228  Sum_probs=44.3

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-C-CCceeCcchHhhHHH
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-K-GGRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~-gGR~lT~~G~~~lD~  134 (144)
                      ||+.|=- +|-+.-..|+..+|              =|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
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            4444444 24555666666666              47789999999999999999888 4 377888877777775

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.

>PRK08898 coproporphyrinogen III oxidase; Provisional

Probab=81.03  E-value=7.7  Score=33.88  Aligned_cols=39  Identities=23%  Similarity=0.235  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244          101 ARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus       101 iR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~  140 (144)
                      +...|+.|++.||++.+.+ .=+||++|+-.+|.|+.+++
T Consensus       355 ~~~~l~~l~~~gll~~~~~-~~~LT~~G~~~~d~i~~~~~  393 (394)
T PRK08898        355 IEPQLAAAEQRGLLERDHT-RIRPTPLGQRFLNDLQELFL  393 (394)
T ss_pred             HHHHHHHHHHCCCEEEECC-EEEEChhHhHHHHHHHHHHh
Confidence            4568899999999986542 34899999999999999875

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=80.67  E-value=1.8  Score=35.38  Aligned_cols=40  Identities=20%  Similarity=0.400  Sum_probs=31.5

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      -..|...||              -|..++|-+|+.||..|||+.-+..|=.+++
T Consensus        37 EreLae~fg--------------VSR~~vREAl~~L~a~Glve~r~G~Gt~V~~   76 (241)
T COG2186          37 ERELAERFG--------------VSRTVVREALKRLEAKGLVEIRQGSGTFVRP   76 (241)
T ss_pred             HHHHHHHHC--------------CCcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence            346777777              4668999999999999999988765655544

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=80.57  E-value=7.1  Score=31.63  Aligned_cols=71  Identities=21%  Similarity=0.274  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHHhCCCchh-------HHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           55 YIRAASMARKIYLRGGLGVG-------SFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        55 y~RaASilRklYl~g~~Gv~-------~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      |.+-+.-|+.-=..|-...|       .|+..||-              |.--+|++|++|++.|+|......|--+++.
T Consensus         9 Y~qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~V--------------SR~TvRkAL~~L~~eGli~r~~G~GtfV~~~   74 (236)
T COG2188           9 YQQIAEDIRQRIESGELPPGDKLPSERELAEQFGV--------------SRMTVRKALDELVEEGLIVRRQGKGTFVASP   74 (236)
T ss_pred             HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCC--------------cHHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence            45555566665555543333       67888874              6679999999999999999888668777764


Q ss_pred             ----hHhhHHHHHHHH
Q 032244          128 ----GQRDLDQVAGRI  139 (144)
Q Consensus       128 ----G~~~lD~iA~~i  139 (144)
                          ....+..+...+
T Consensus        75 ~~~~~~~~~~~f~e~~   90 (236)
T COG2188          75 KEQSPLLELTSFSEEL   90 (236)
T ss_pred             cccccccccccHHHHH
Confidence                333344444443

>PRK05660 HemN family oxidoreductase; Provisional

Probab=80.45  E-value=2.6  Score=36.59  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=32.6

Q ss_pred             HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhh
Q 032244          102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAV  141 (144)
Q Consensus       102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~  141 (144)
                      ...+++|++.||++.+.. .=+||++|+-++|.|+.+++.
T Consensus       339 ~~~l~~l~~~gl~~~~~~-~~~lt~~G~~~~d~i~~~~~~  377 (378)
T PRK05660        339 RPQLDEALAQGYLTETAD-HWQITEHGKLFLNDLLELFLA  377 (378)
T ss_pred             HHHHHHHHHCCCEEEeCC-EEEECcchhHHHHHHHHHHhc
Confidence            467899999999986543 467999999999999998864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	144
3iz6_S	146	Localization Of The Small Subunit Ribosomal Protein		5e-58
3izb_S	144	Localization Of The Small Subunit Ribosomal Protein		2e-32
3jyv_T	141	Structure Of The 40s Rrna And Proteins And PE TRNA		2e-32
2xzm_T	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		1e-23
3zey_O	167	High-resolution Cryo-electron Microscopy Structure		1e-21
2v7f_A	150	Structure Of P. Abyssi Rps19 Protein Length = 150		4e-20
3j20_U	150	Promiscuous Behavior Of Proteins In Archaeal Riboso		4e-20

>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 =  219 bits (557), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 102/140 (72%), Positives = 119/140 (85%)
Query: 3   TAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMA 62
           TA+ VKDV+PHEFVKAY+AHLKRSGK+ELP W DIVKT   KEL PYDPDWYY RAAS+A
Sbjct: 5   TARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIA 64
Query: 63  RKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122
           RKIYLR G+GVG F++IYGG +RNGSRPPHF KSSG+++R+IL QLQ   II++D KGGR
Sbjct: 65  RKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGR 124
Query: 123 RITSSGQRDLDQVAGRIAVV 142
            ITS G+RDLDQVAGR+ V 
Sbjct: 125 LITSQGRRDLDQVAGRVDVT 144

>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 =  134 bits (337), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 63/134 (47%), Positives = 93/134 (69%), Gaps = 1/134 (0%)
Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARK 64
           +V+DV+  +F+ AYA+ L+R GK+E+P + DIVKT +  E+ P D + W+Y RAAS+AR 
Sbjct: 5   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64
Query: 65  IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
           IY+R  +GVG   ++YGG K  G RP     +SGS+ R +L  L+   I+E+  KGGRRI
Sbjct: 65  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124
Query: 125 TSSGQRDLDQVAGR 138
           + +GQRDLD++A +
Sbjct: 125 SENGQRDLDRIAAQ 138

>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 =  134 bits (337), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 63/134 (47%), Positives = 93/134 (69%), Gaps = 1/134 (0%)
Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARK 64
           +V+DV+  +F+ AYA+ L+R GK+E+P + DIVKT +  E+ P D + W+Y RAAS+AR 
Sbjct: 2   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 61
Query: 65  IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
           IY+R  +GVG   ++YGG K  G RP     +SGS+ R +L  L+   I+E+  KGGRRI
Sbjct: 62  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 121
Query: 125 TSSGQRDLDQVAGR 138
           + +GQRDLD++A +
Sbjct: 122 SENGQRDLDRIAAQ 135

>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 =  105 bits (261), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/140 (36%), Positives = 79/140 (56%), Gaps = 5/140 (3%)
Query: 7   VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
           VKDV+  +F++ YA+HLK++ K+ +P +     T   +ELAP D DW YIR A++ARK+Y
Sbjct: 10  VKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVY 69
Query: 67  LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-----SKGG 121
           L+   G+ + + I+G  K  G+         G + R  L  L+D  II  D      K  
Sbjct: 70  LKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFS 129
Query: 122 RRITSSGQRDLDQVAGRIAV 141
           R IT  G  +L+++A +IA+
Sbjct: 130 RVITKEGMTELNRIATQIAI 149

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

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 76/136 (55%)
Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            ++DV P  +VK  + H K+ GK+ +P   +IVKT   +E AP +PDWYYIR A++ R +
Sbjct: 22  TLRDVHPWRWVKICSQHFKQEGKMMVPNCAEIVKTSHGRERAPQNPDWYYIRCAAVLRAV 81
Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YLR G+G G   + +   K  GSRP   +++S  +       L    ++E     G R+T
Sbjct: 82  YLRPGVGYGGLSKRFSSKKNRGSRPEITTRASKGLLHWCCKSLTKLELLEKCKGAGHRVT 141
Query: 126 SSGQRDLDQVAGRIAV 141
             G++  D +A +IA+
Sbjct: 142 KLGRKVADTIAFKIAL 157

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

Iteration: 1
 Score = 93.2 bits (230), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 52/134 (38%), Positives = 69/134 (51%)
Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            V DV     V+  A  LK   +I+ P W   VKTG  KE  P   DW+Y R AS+ R++
Sbjct: 3   TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62
Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YL G +G+   R  YGG K  G  P  F K+ GS+ R  L QL+    +E     GR IT
Sbjct: 63  YLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122
Query: 126 SSGQRDLDQVAGRI 139
             G+  LD++A  +
Sbjct: 123 PKGRSFLDKIATEL 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 = 93.2 bits (230), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 52/134 (38%), Positives = 69/134 (51%)
Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            V DV     V+  A  LK   +I+ P W   VKTG  KE  P   DW+Y R AS+ R++
Sbjct: 3   TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62
Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YL G +G+   R  YGG K  G  P  F K+ GS+ R  L QL+    +E     GR IT
Sbjct: 63  YLDGPVGIERLRTYYGGRKNRGHAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122
Query: 126 SSGQRDLDQVAGRI 139
             G+  LD++A  +
Sbjct: 123 PKGRSFLDKIATEL 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	144
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	1e-63
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	2e-63
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	3e-60
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	2e-58
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04

>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 =  190 bits (484), Expect = 1e-63
 Identities = 52/135 (38%), Positives = 69/135 (51%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            V DV     V+  A  LK   +I+ P W   VKTG  KE  P   DW+Y R AS+ R++
Sbjct: 3   TVYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRV 62

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125
           YL G +G+   R  YGG K  G  P  F K+ GS+ R  L QL+    +E     GR IT
Sbjct: 63  YLDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVIT 122

Query: 126 SSGQRDLDQVAGRIA 140
             G+  LD++A  + 
Sbjct: 123 PKGRSFLDKIATELK 137

>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 =  190 bits (483), Expect = 2e-63
 Identities = 101/139 (72%), Positives = 118/139 (84%)

Query: 2   ETAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASM 61
            TA+ VKDV+PHEFVKAY+AHLKRSGK+ELP W DIVKT   KEL PYDPDWYY RAAS+
Sbjct: 4   STARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASI 63

Query: 62  ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG 121
           ARKIYLR G+GVG F++IYGG +RNGSRPPHF KSSG+++R+IL QLQ   II++D KGG
Sbjct: 64  ARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGG 123

Query: 122 RRITSSGQRDLDQVAGRIA 140
           R ITS G+RDLDQVAGR+ 
Sbjct: 124 RLITSQGRRDLDQVAGRVD 142

>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 =  181 bits (461), Expect = 3e-60
 Identities = 63/136 (46%), Positives = 93/136 (68%), Gaps = 1/136 (0%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARK 64
           +V+DV+  +F+ AYA+ L+R GK+E+P + DIVKT +  E+ P D + W+Y RAAS+AR 
Sbjct: 5   SVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARH 64

Query: 65  IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124
           IY+R  +GVG   ++YGG K  G RP     +SGS+ R +L  L+   I+E+  KGGRRI
Sbjct: 65  IYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRI 124

Query: 125 TSSGQRDLDQVAGRIA 140
           + +GQRDLD++A +  
Sbjct: 125 SENGQRDLDRIAAQTL 140

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

 Score =  177 bits (451), Expect = 2e-58
 Identities = 51/140 (36%), Positives = 78/140 (55%), Gaps = 5/140 (3%)

Query: 6   NVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKI 65
            VKDV+  +F++ YA+HLK++ K+ +P +     T   +ELAP D DW YIR A++ARK+
Sbjct: 9   TVKDVAAADFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKV 68

Query: 66  YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-----SKG 120
           YL+   G+ + + I+G  K  G+         G + R  L  L+D  II  D      K 
Sbjct: 69  YLKPHTGISTLKHIFGSNKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKF 128

Query: 121 GRRITSSGQRDLDQVAGRIA 140
            R IT  G  +L+++A +IA
Sbjct: 129 SRVITKEGMTELNRIATQIA 148

>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 = 37.9 bits (87), Expect = 6e-04
 Identities = 21/134 (15%), Positives = 43/134 (32%), Gaps = 35/134 (26%)

Query: 3   TAKNVKDV--SPHEFVKAYAAH--LKRSGKIELPTWNDIVKTGTLKELAPYDPDWYY--- 55
           + + +  +  S             L    +       ++V+   ++E+   +  +     
Sbjct: 47  SKEEIDHIIMSKDAVSGTLRLFWTLLSKQE-------EMVQK-FVEEVLRINYKFLMSPI 98

Query: 56  ---IRAASMARKIYLRGGLGVGSFR-RIYGGG----KRNGSRPPHFSKSSGSVARHILHQ 107
               R  SM  ++Y+         R R+Y       K N SR   + K      R  L +
Sbjct: 99  KTEQRQPSMMTRMYI-------EQRDRLYNDNQVFAKYNVSRLQPYLK-----LRQALLE 146

Query: 108 LQDTNIIELDSKGG 121
           L+    + +D   G
Sbjct: 147 LRPAKNVLIDGVLG 160

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	144
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	97.35
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.3
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.18
2h09_A	155	Transcriptional regulator MNTR; transcription regu	97.17
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.13
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	97.07
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.06
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.05
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.02
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.99
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.98
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.93
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	96.93
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.92
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.9
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.89
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.88
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.87
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.86
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.85
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.82
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.8
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.79
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.78
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.78
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.76
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.75
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.74
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.72
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.7
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.68
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	96.66
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.66
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.64
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.62
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.61
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.6
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.54
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.53
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.52
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.52
2nnn_A	140	Probable transcriptional regulator; structural gen	96.5
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.5
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	96.49
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.47
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.43
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	96.43
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.39
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.38
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.37
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.36
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.35
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.26
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.24
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.23
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.2
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.2
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.18
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.15
2o0m_A	345	Transcriptional regulator, SORC family; structural	96.09
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.05
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	96.02
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.0
3nqo_A	189	MARR-family transcriptional regulator; structural	95.99
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.95
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	95.87
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.83
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	95.8
3f3x_A	144	Transcriptional regulator, MARR family, putative;	95.78
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.78
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	95.76
2fxa_A	207	Protease production regulatory protein HPR; protea	95.7
2obp_A	96	Putative DNA-binding protein; structural genomics,	95.67
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.65
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.64
1bja_A	95	Transcription regulatory protein MOTA; activation	95.56
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.55
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.55
1hsj_A	487	Fusion protein consisting of staphylococcus access	95.48
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	95.38
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	95.36
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	95.24
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	95.23
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.19
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.14
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	95.03
3by6_A	126	Predicted transcriptional regulator; structural ge	95.02
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	95.01
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.84
4fx0_A	148	Probable transcriptional repressor protein; helix-	94.79
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	94.48
2kko_A	108	Possible transcriptional regulatory protein (possi	94.36
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	94.33
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	94.29
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.27
3jth_A	98	Transcription activator HLYU; transcription factor	94.22
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	94.2
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	93.88
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	93.86
1xma_A	145	Predicted transcriptional regulator; southea colla	93.83
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	93.75
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	93.73
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	93.72
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	93.68
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	93.65
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	93.65
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	93.52
2co5_A	99	Viral protein F93; viral protein-winged helix comp	93.49
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.46
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.27
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.27
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	93.25
4esf_A	117	PADR-like transcriptional regulator; PADR family,	93.24
1ku9_A	152	Hypothetical protein MJ223; putative transcription	93.17
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	93.11
3l09_A	266	Putative transcriptional regulator; structural gen	93.08
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	92.83
2dql_A	115	PEX protein; circadian clock associated protein, c	92.82
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	92.8
3cta_A	230	Riboflavin kinase; structural genomics, transferas	92.56
1ylf_A	149	RRF2 family protein; structural genomics, transcri	92.56
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	92.54
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	92.46
3c7j_A	237	Transcriptional regulator, GNTR family; structural	92.42
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	92.25
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	91.92
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	91.6
3k69_A	162	Putative transcription regulator; putative transcr	91.57
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	91.38
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	91.38
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	91.37
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	91.21
3eet_A	272	Putative GNTR-family transcriptional regulator; st	90.91
3elk_A	117	Putative transcriptional regulator TA0346; structu	90.78
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	90.74
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	90.17
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	90.15
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	90.14
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	90.04
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	90.04
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	89.81
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	89.8
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	89.78
3kfw_X	247	Uncharacterized protein; structural genomics, PSI-	89.73
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	89.65
3aaf_A	134	Werner syndrome ATP-dependent helicase; helix-turn	89.58
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	89.41
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	89.01
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	88.91
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	88.54
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	88.48
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.25
2g7u_A	257	Transcriptional regulator; ICLR family, structural	87.07
1p6r_A	82	Penicillinase repressor; transcription regulation,	86.87
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	86.87
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	86.19
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	86.07
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.64
2rkh_A	180	Putative APHA-like transcription factor; ZP_002083	85.52
1xd7_A	145	YWNA; structural genomics, protein structure initi	85.45
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	85.45
3r0a_A	123	Putative transcriptional regulator; structural gen	84.21
2qm3_A	373	Predicted methyltransferase; putative methyltransf	83.38
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	83.23
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	82.87
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	82.29
1lva_A	258	Selenocysteine-specific elongation factor; winged-	82.19

>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=5.5e-77  Score=459.17  Aligned_cols=141  Identities=45%  Similarity=0.849  Sum_probs=137.4

Q ss_pred             CCCCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCc-hHHHHHHHHHHHHHHhCCCchhHHHHH
Q 032244            1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPD-WYYIRAASMARKIYLRGGLGVGSFRRI   79 (144)
Q Consensus         1 m~~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~D-W~y~RaASilRklYl~g~~Gv~~l~~~   79 (144)
                      ||+ +||||||||+||++||+|||++|||++|+|+||||||++||+||+||| |||+||||||||||++||+||++|+++
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            775 899999999999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             hcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           80 YGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        80 YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      |||+||||++|+||++|||+|||+||||||++||||+++++||+||++||++||+||.||++.
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            999999999999999999999999999999999999999889999999999999999999763

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

Probab=100.00  E-value=1.1e-75  Score=456.36  Aligned_cols=140  Identities=36%  Similarity=0.677  Sum_probs=137.0

Q ss_pred             CCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcC
Q 032244            3 TAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGG   82 (144)
Q Consensus         3 ~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg   82 (144)
                      .|+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||
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            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHHHHHHHHhhc
Q 032244           83 GKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-----GRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        83 ~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-----GR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      +||||++|+||++|||+|||+||||||++||||++++|     ||+||++||++||+||.||+..
T Consensus        86 ~krrG~~P~h~~~asg~iiR~~LQqLE~~g~Vek~~~g~~~k~GR~lT~~G~~~LDriA~~i~~~  150 (155)
T 2xzm_T           86 NKDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQIAIK  150 (155)
T ss_dssp             EECCSSSCCEECCCCHHHHHHHHHHHHHTTSEEECSSCSSSTTCEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcccCCCcHHHHHHHHHHHHCCCEeecCCCCcCCCCCEECHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999887     9999999999999999999753

>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=2.1e-76  Score=456.72  Aligned_cols=139  Identities=73%  Similarity=1.239  Sum_probs=136.3

Q ss_pred             CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244            4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG   83 (144)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~   83 (144)
                      .+||||||||+||++||+|||++|||++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      ||||++|+||++|||+|||+||||||++||||+++++||+||++||++||+||.||++.
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            99999999999999999999999999999999999889999999999999999999753

>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=6.7e-54  Score=330.71  Aligned_cols=139  Identities=37%  Similarity=0.626  Sum_probs=125.4

Q ss_pred             CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244            4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG   83 (144)
Q Consensus         4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~   83 (144)
                      |+||||||||+||++||+|||++|+|++|+|+||||||.++|++|+|+||||.|||++||++|++|+.|++.|++.|||+
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            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      ||||++|+||+++|+++||.+||+||++|||++.+.+|+.+|+.|+++||+||.+|++.
T Consensus        81 k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~~~G~~Vt~~~~~~l~~ia~~i~~~  139 (150)
T 2v7f_A           81 KNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKE  139 (150)
T ss_dssp             ---CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHHH
T ss_pred             ccCCcCCccccccchHHHHHHHHHHHHCCCEEEeCCCceEECCCCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999998889999999999999999999753

>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=97.35  E-value=0.00047  Score=46.66  Aligned_cols=71  Identities=14%  Similarity=0.158  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhh-HHHHHHHHHhCCcceecCCCCc----eeCcch
Q 032244           55 YIRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSV-ARHILHQLQDTNIIELDSKGGR----RITSSG  128 (144)
Q Consensus        55 y~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~i-iR~~LqqLE~~glv~k~~~gGR----~lT~~G  128 (144)
                      .+|...+|..++-.+ ++.+..|.+..|-              +.+- +-.+++.||+.|||+.++.++|    .||++|
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            457777888787787 8999999998883              3356 7778899999999996654454    799999


Q ss_pred             HhhHHHHHHHH
Q 032244          129 QRDLDQVAGRI  139 (144)
Q Consensus       129 ~~~lD~iA~~i  139 (144)
                      ++.++.+....
T Consensus        80 ~~~~~~~~~~~   90 (95)
T 2pg4_A           80 RRLAECLEKCR   90 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

>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=97.30  E-value=0.00041  Score=48.47  Aligned_cols=63  Identities=16%  Similarity=0.123  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      ...||+.|+ .+ +|...|...-|=              |-+.+|..+..||+.|||++... |-.||++|+..|+.+..
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--------------SYALTGRYIKMLMDLEIIRQEGK-QYMLTKKGEELLEDIRK   72 (95)
T ss_dssp             HHHHHHHHT-TC-BCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETT-EEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCeEEECC-eeEEChhHHHHHHHHHH
Confidence            356888777 45 999999986663              45699999999999999999864 89999999987776543

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

Probab=97.18  E-value=0.0017  Score=45.72  Aligned_cols=66  Identities=11%  Similarity=0.153  Sum_probs=53.8

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++
T Consensus        35 ~iL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  100 (145)
T 3g3z_A           35 AVLYTLATEGSRTQKHIGEKWSL--------------PKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAA  100 (145)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHH
Confidence            37888999999999999998873              3457788999999999999755  3355    49999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus       101 ~~~~~~  106 (145)
T 3g3z_A          101 PLTESA  106 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=97.17  E-value=0.0015  Score=47.25  Aligned_cols=60  Identities=18%  Similarity=0.164  Sum_probs=50.5

Q ss_pred             HHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           64 KIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        64 klYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      .|+-.+++.+..|...+|-              |.+-++.+|+.||+.|||+..+..|-.||+.|+..+..+..
T Consensus        48 ~l~~~~~~~~~~la~~l~v--------------s~~tvs~~l~~Le~~Glv~r~~~~~~~lT~~g~~~~~~~~~  107 (155)
T 2h09_A           48 LIREVGEARQVDMAARLGV--------------SQPTVAKMLKRLATMGLIEMIPWRGVFLTAEGEKLAQESRE  107 (155)
T ss_dssp             HHHHHSCCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTCEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEecCCceEEChhHHHHHHHHHH
Confidence            4444688999999999874              45789999999999999998876688999999998887654

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

Probab=97.13  E-value=0.0018  Score=45.58  Aligned_cols=65  Identities=11%  Similarity=0.154  Sum_probs=52.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++.
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            7888888899999999998873              3457788999999999999765  3355    499999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       108 ~~~~~  112 (143)
T 3oop_A          108 LRDIV  112 (143)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

>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=97.07  E-value=0.0028  Score=45.04  Aligned_cols=59  Identities=15%  Similarity=0.160  Sum_probs=49.9

Q ss_pred             HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      +.-.+++.+..|+...|-              |.+-++.+|+.||+.|||+..+.++-.||++|+..+..+..
T Consensus        17 ~~~~~~~~~~ela~~l~v--------------s~~tvs~~l~~Le~~Glv~r~~~~~~~LT~~g~~~~~~~~~   75 (142)
T 1on2_A           17 IEEKGYARVSDIAEALAV--------------HPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVY   75 (142)
T ss_dssp             HHHHSSCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HhhcCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeeCceEEEchhHHHHHHHHHH
Confidence            334689999999998873              45689999999999999998886678999999999887654

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=97.06  E-value=0.0022  Score=45.13  Aligned_cols=65  Identities=14%  Similarity=0.165  Sum_probs=49.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+..+++
T Consensus        42 vL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  107 (142)
T 3ech_A           42 VLKLIDEQRGLNLQDLGRQMCRD--------------KALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLH  107 (142)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHC-----------------CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHH
T ss_pred             HHHHHHhCCCcCHHHHHHHhCCC--------------HHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHH
Confidence            78888889999999999988743              246778999999999999765  3344    599999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       108 ~~~~~  112 (142)
T 3ech_A          108 AELIM  112 (142)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=97.05  E-value=0.0029  Score=45.68  Aligned_cols=65  Identities=22%  Similarity=0.188  Sum_probs=52.9

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-.              .+-+-.+++.||+.|||++..  .++|    .||++|+..+++
T Consensus        51 iL~~l~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  116 (162)
T 3k0l_A           51 ALSVLAAKPNLSNAKLAERSFIK--------------PQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQ  116 (162)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSC--------------GGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHH
Confidence            78888888999999999988743              346778999999999998654  3354    599999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       117 ~~~~~  121 (162)
T 3k0l_A          117 CNQVV  121 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77653

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=97.02  E-value=0.004  Score=43.24  Aligned_cols=65  Identities=12%  Similarity=0.124  Sum_probs=52.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+...  .++|    .||++|+..+++
T Consensus        39 iL~~l~~~~~~~~~~la~~l~~--------------~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  104 (138)
T 1jgs_A           39 VLCSIRCAACITPVELKKVLSV--------------DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             HHHHHHHHSSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhcCCCCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHHH
Confidence            6777888899999999988763              3456788999999999998753  3454    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       105 ~~~~~  109 (138)
T 1jgs_A          105 CHQLV  109 (138)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76544

>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=96.99  E-value=0.003  Score=44.29  Aligned_cols=67  Identities=18%  Similarity=0.211  Sum_probs=52.6

Q ss_pred             HHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q 032244           59 ASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRD  131 (144)
Q Consensus        59 ASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~  131 (144)
                      ..||..|+- .+++.+..|....|-              +.+-+..+++.||+.|||++.+  .++|    .||++|+..
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            447888998 899999999998762              4467888999999999999765  3344    599999999


Q ss_pred             HHHHHHHH
Q 032244          132 LDQVAGRI  139 (144)
Q Consensus       132 lD~iA~~i  139 (144)
                      ++.+...+
T Consensus       104 ~~~~~~~~  111 (147)
T 2hr3_A          104 LYGNRAKR  111 (147)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876543

>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=96.98  E-value=0.0027  Score=44.37  Aligned_cols=64  Identities=14%  Similarity=0.146  Sum_probs=52.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+ .+++.+..|....|-              +.+-+..+|+.||+.|||+..+  .++|    .||++|+..++.
T Consensus        42 iL~~l~-~~~~~~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  106 (146)
T 2gxg_A           42 VLRATS-DGPKTMAYLANRYFV--------------TQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNK  106 (146)
T ss_dssp             HHHHHT-TSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHh-cCCcCHHHHHHHhCC--------------CchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHH
Confidence            677888 999999999998763              4568889999999999998654  3343    699999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       107 ~~~~~  111 (146)
T 2gxg_A          107 GIEIY  111 (146)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.93  E-value=0.0036  Score=43.27  Aligned_cols=65  Identities=12%  Similarity=0.193  Sum_probs=51.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-.              .+-+-.+|+.||+.|||+...  .++|    .||++|+..+++
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            67778888999999999988732              245778999999999998753  3344    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       104 ~~~~~  108 (139)
T 3bja_A          104 VDVQY  108 (139)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.93  E-value=0.0024  Score=45.18  Aligned_cols=65  Identities=6%  Similarity=0.088  Sum_probs=52.1

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.  +++.+..|....|-              +.+-+-.+|+.||+.|||++.  +.++|    .||++|++.+
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            67778888  88999999997773              335677789999999999875  34455    6999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +++...+
T Consensus       108 ~~~~~~~  114 (127)
T 2frh_A          108 ESLLSRV  114 (127)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887654

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

Probab=96.92  E-value=0.0031  Score=45.55  Aligned_cols=65  Identities=20%  Similarity=0.268  Sum_probs=52.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+++
T Consensus        58 vL~~l~~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  123 (161)
T 3e6m_A           58 LLSSLSAYGELTVGQLATLGVM--------------EQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE  123 (161)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHH
Confidence            7777888899999999997763              3467888999999999999765  3344    599999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       124 ~~~~~  128 (161)
T 3e6m_A          124 ISPLI  128 (161)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            86654

>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=96.90  E-value=0.0043  Score=43.26  Aligned_cols=66  Identities=17%  Similarity=0.283  Sum_probs=51.9

Q ss_pred             HHHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q 032244           60 SMARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRD  131 (144)
Q Consensus        60 SilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~  131 (144)
                      .||..|+-.+  ++.+..|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..
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            3788888886  9999999998873              3456778999999999998653  4455    499999999


Q ss_pred             HHHHHHHH
Q 032244          132 LDQVAGRI  139 (144)
Q Consensus       132 lD~iA~~i  139 (144)
                      ++.+...+
T Consensus       101 ~~~~~~~~  108 (139)
T 3eco_A          101 VEAFTSIF  108 (139)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876543

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

Probab=96.89  E-value=0.004  Score=44.72  Aligned_cols=65  Identities=14%  Similarity=0.183  Sum_probs=51.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++.
T Consensus        55 vL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  120 (159)
T 3s2w_A           55 FLMRLYREDGINQESLSDYLKI--------------DKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPD  120 (159)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHH
Confidence            6778888899999999998873              3467888999999999998654  3455    499999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       121 ~~~~~  125 (159)
T 3s2w_A          121 MKKIA  125 (159)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=96.88  E-value=0.0045  Score=43.71  Aligned_cols=62  Identities=15%  Similarity=0.189  Sum_probs=50.5

Q ss_pred             HHHHHHH----hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           61 MARKIYL----RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        61 ilRklYl----~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      +|+.||.    .+++.+..|+...|-              |.+-++.+|+.||+.|||++.+ ++-.||++|+...+.+.
T Consensus        18 ~L~~l~~l~~~~~~~s~~ela~~l~i--------------s~~tv~~~l~~Le~~Gli~r~~-~~~~Lt~~g~~~~~~~~   82 (139)
T 2x4h_A           18 YLLTIKRYNDSGEGAKINRIAKDLKI--------------APSSVFEEVSHLEEKGLVKKKE-DGVWITNNGTRSINYLI   82 (139)
T ss_dssp             HHHHHHHHHTTTSCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCcCHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEecC-CeEEEChhHHHHHHHHH
Confidence            4444543    578999999998883              4578999999999999999888 58899999999887765


Q ss_pred             H
Q 032244          137 G  137 (144)
Q Consensus       137 ~  137 (144)
                      .
T Consensus        83 ~   83 (139)
T 2x4h_A           83 K   83 (139)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=96.87  E-value=0.0044  Score=45.22  Aligned_cols=65  Identities=15%  Similarity=0.239  Sum_probs=52.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+++
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            6778888899999999998873              3456778999999999998743  3344    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       116 ~~~~~  120 (168)
T 2nyx_A          116 VTEHR  120 (168)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.86  E-value=0.003  Score=45.02  Aligned_cols=66  Identities=17%  Similarity=0.257  Sum_probs=51.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++.
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            7888888899999999998873              3467888999999999999764  3355    499999999998


Q ss_pred             HHHHHh
Q 032244          135 VAGRIA  140 (144)
Q Consensus       135 iA~~i~  140 (144)
                      +...+.
T Consensus       112 ~~~~~~  117 (149)
T 4hbl_A          112 VFEAIS  117 (149)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876553

>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=96.85  E-value=0.0045  Score=41.04  Aligned_cols=66  Identities=18%  Similarity=0.224  Sum_probs=53.8

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCc----eeCcchHhhHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGR----RITSSGQRDLDQ  134 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR----~lT~~G~~~lD~  134 (144)
                      .|+..|.-.+++.+..|....|-              +.+-+..+|+.||+.|||+.... ++|    .+|+.|+..++.
T Consensus        24 ~il~~l~~~~~~s~~ela~~l~i--------------s~~tv~~~l~~L~~~glv~~~~~~~~r~~~~~~t~~g~~~~~~   89 (109)
T 1sfx_A           24 RIYSLLLERGGMRVSEIARELDL--------------SARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLKE   89 (109)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEeecCCceEEEEecCcHHHHHHH
Confidence            47777877899999999998863              55789999999999999987542 455    699999999888


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus        90 ~~~~~   94 (109)
T 1sfx_A           90 FKSSI   94 (109)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=96.82  E-value=0.0066  Score=42.66  Aligned_cols=65  Identities=15%  Similarity=0.265  Sum_probs=51.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+|+.||+.|||+...  .++|    .||++|+..++.
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            6788888899999999998863              4467888999999999998753  3344    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       113 ~~~~~  117 (150)
T 2rdp_A          113 VIEKR  117 (150)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.80  E-value=0.0033  Score=44.60  Aligned_cols=64  Identities=16%  Similarity=0.224  Sum_probs=51.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++  .+  .++|    .||++|+..+
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            6888888899999999998873              34577889999999999998  43  3344    5999999998


Q ss_pred             HHHHHH
Q 032244          133 DQVAGR  138 (144)
Q Consensus       133 D~iA~~  138 (144)
                      +++...
T Consensus       112 ~~~~~~  117 (154)
T 2qww_A          112 KRSTAN  117 (154)
T ss_dssp             HHHHSC
T ss_pred             HHHHhh
Confidence            876543

>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=96.79  E-value=0.0037  Score=44.27  Aligned_cols=65  Identities=18%  Similarity=0.335  Sum_probs=45.8

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRR----ITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~----lT~~G~~~l  132 (144)
                      ||..|+-.  +++.+..|....|-.              .+-+-.+++.||+.|||++..  .++|.    ||++|+..+
T Consensus        46 vL~~l~~~~~~~~t~~eLa~~l~~~--------------~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~  111 (148)
T 3jw4_A           46 MIGYIYENQESGIIQKDLAQFFGRR--------------GASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALV  111 (148)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHC--------------------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHH
T ss_pred             HHHHHHhCCCCCCCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHH
Confidence            78888887  899999999977632              235678999999999998764  33553    999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +.+...+
T Consensus       112 ~~~~~~~  118 (148)
T 3jw4_A          112 EEFNNIF  118 (148)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876554

>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=96.78  E-value=0.0072  Score=41.92  Aligned_cols=64  Identities=9%  Similarity=0.100  Sum_probs=51.4

Q ss_pred             HHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.+  ++.+..|....|-              +.+-+..+++.||+.|||+..+  .++|    .||++|+..+
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            688888887  8999999998873              3467888999999999998654  3343    3899999998


Q ss_pred             HHHHHH
Q 032244          133 DQVAGR  138 (144)
Q Consensus       133 D~iA~~  138 (144)
                      +.+...
T Consensus       105 ~~~~~~  110 (141)
T 3bro_A          105 TIILSY  110 (141)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877554

>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=96.78  E-value=0.0062  Score=43.23  Aligned_cols=64  Identities=14%  Similarity=0.312  Sum_probs=48.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee----cCCCCc----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL----DSKGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k----~~~gGR----~lT~~G~~~l  132 (144)
                      ||..| -.+++.++.|+...|-.+              +-+-.+++.||+.|||+.    ++.++|    .||++|+..+
T Consensus        43 iL~~l-~~~~~t~~eLa~~l~~~~--------------~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~  107 (151)
T 3kp7_A           43 VLNML-SIEALTVGQITEKQGVNK--------------AAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYI  107 (151)
T ss_dssp             HHHHH-HHSCBCHHHHHHHHCSCS--------------SHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHH
T ss_pred             HHHHH-HcCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHH
Confidence            67777 789999999999887432              467789999999999996    555455    6999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +.+...+
T Consensus       108 ~~~~~~~  114 (151)
T 3kp7_A          108 KERKAIM  114 (151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876543

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

Probab=96.76  E-value=0.0035  Score=43.50  Aligned_cols=65  Identities=17%  Similarity=0.194  Sum_probs=52.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+..+++.||+.|||++.+  .++|    .||++|+..+++
T Consensus        41 iL~~l~~~~~~t~~ela~~l~~--------------s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  106 (142)
T 2fbi_A           41 VIRILRQQGEMESYQLANQACI--------------LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  106 (142)
T ss_dssp             HHHHHHHHCSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCC--------------CHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHH
Confidence            7888888899999999998763              4467888999999999998764  3344    499999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       107 ~~~~~  111 (142)
T 2fbi_A          107 MSGDM  111 (142)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.75  E-value=0.0041  Score=41.88  Aligned_cols=70  Identities=10%  Similarity=0.006  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~G~~~lD~iA  136 (144)
                      .||..|+-.+++.+..|.+....          ...-+.+-+-.+|+.||+.|||++..+.   .-.||++|+..++.+.
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~----------~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~   81 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNA----------EFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLK   81 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHT----------TSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHH----------HcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHH
Confidence            36777777889999999322210          1223456788899999999999976532   2369999999998876


Q ss_pred             HHH
Q 032244          137 GRI  139 (144)
Q Consensus       137 ~~i  139 (144)
                      ..+
T Consensus        82 ~~~   84 (99)
T 1tbx_A           82 TAI   84 (99)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

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

Probab=96.74  E-value=0.0049  Score=42.08  Aligned_cols=63  Identities=17%  Similarity=0.177  Sum_probs=51.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G~~~lD~i  135 (144)
                      .||+.| ..+++.+..|....|              -|.+-+...|+.||+.|+|+.... ||    .||++|...+...
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            478777 689999999999886              355789999999999999998765 54    7999998877665


Q ss_pred             HHH
Q 032244          136 AGR  138 (144)
Q Consensus       136 A~~  138 (144)
                      ...
T Consensus        89 ~~~   91 (114)
T 2oqg_A           89 LER   91 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=96.72  E-value=0.0024  Score=43.24  Aligned_cols=68  Identities=21%  Similarity=0.300  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHH-hCC---CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcch
Q 032244           57 RAASMARKIYL-RGG---LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSG  128 (144)
Q Consensus        57 RaASilRklYl-~g~---~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G  128 (144)
                      ++..||-.|+- .++   +.+..|....|-              +.+-+-.+|+.||+.||| .++.++|    .||++|
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--------------PHSYVWLIIKKFEEAKMV-ECELEGRTKIIRLTDKG   77 (95)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEHHHHHHHSSS--------------CHHHHHHHHHHHHHTTSE-EEEEETTEEEEEECHHH
T ss_pred             hHHHHHHHHHHccCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCcCc-cCCCCCCeEEEEEChhH
Confidence            44556766665 355   889999998763              345677889999999999 4444466    799999


Q ss_pred             HhhHHHHHHHH
Q 032244          129 QRDLDQVAGRI  139 (144)
Q Consensus       129 ~~~lD~iA~~i  139 (144)
                      +..++++...+
T Consensus        78 ~~~~~~~~~~~   88 (95)
T 2qvo_A           78 QKIAQQIKSII   88 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999887665

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

Probab=96.70  E-value=0.0061  Score=42.14  Aligned_cols=66  Identities=14%  Similarity=0.225  Sum_probs=53.0

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+-.+++.+..|....|-              +.+-+..+++.||+.|||++.+  .++|    .||++|+..++
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            37778888899999999998873              4567888999999999999754  3343    69999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus        99 ~~~~~~  104 (138)
T 3bpv_A           99 LILKVE  104 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.68  E-value=0.0091  Score=42.57  Aligned_cols=66  Identities=11%  Similarity=0.156  Sum_probs=52.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..++
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            37888888899999999998762              4457788999999999998753  3344    58999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus       114 ~~~~~~  119 (154)
T 2eth_A          114 EILSNF  119 (154)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.66  E-value=0.0034  Score=44.27  Aligned_cols=66  Identities=14%  Similarity=0.081  Sum_probs=51.9

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+-.+++.++.|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++
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            37878888899999999998873              4567889999999999999765  3354    58999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++....
T Consensus       106 ~~~~~~  111 (140)
T 3hsr_A          106 PLAEIS  111 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

>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=96.66  E-value=0.0037  Score=43.31  Aligned_cols=63  Identities=17%  Similarity=0.159  Sum_probs=49.6

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+ .++..++.|....+             .-|.+.+-..|+.||+.|||++..  .++|    .||++|+..++
T Consensus        29 ~IL~~L~-~~~~~~~eL~~~l~-------------gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~   94 (107)
T 2fsw_A           29 LIIFQIN-RRIIRYGELKRAIP-------------GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVLP   94 (107)
T ss_dssp             HHHHHHT-TSCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTHH
T ss_pred             HHHHHHH-hCCcCHHHHHHHcc-------------cCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECccHHHHHH
Confidence            3677776 89999999998764             135678999999999999998664  2233    79999999877


Q ss_pred             HHH
Q 032244          134 QVA  136 (144)
Q Consensus       134 ~iA  136 (144)
                      .+.
T Consensus        95 ~l~   97 (107)
T 2fsw_A           95 IID   97 (107)
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=96.64  E-value=0.0081  Score=44.01  Aligned_cols=65  Identities=15%  Similarity=0.167  Sum_probs=49.6

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      ||..|+- .+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..++
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            6777887 678999999998873              3467788999999999999765  3354    49999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus       124 ~~~~~~  129 (166)
T 3deu_A          124 EMEEVI  129 (166)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.62  E-value=0.0042  Score=43.45  Aligned_cols=64  Identities=8%  Similarity=0.144  Sum_probs=50.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-.              .+-+..+|+.||+.|||+..+  .++|    .||++|+..++.
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            67778888999999999988732              346788999999999998654  3344    579999999988


Q ss_pred             HHHH
Q 032244          135 VAGR  138 (144)
Q Consensus       135 iA~~  138 (144)
                      +...
T Consensus       108 ~~~~  111 (142)
T 2bv6_A          108 LSNA  111 (142)
T ss_dssp             HTTH
T ss_pred             HHHH
Confidence            7543

>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=96.61  E-value=0.0064  Score=42.37  Aligned_cols=66  Identities=21%  Similarity=0.363  Sum_probs=52.7

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||..|+-.+++.+..|....|-              +.+-+..+++.||+.|||+..+  .++|    .||++|+..++
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            37888888899999999998873              4467888999999999999764  3333    69999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus       103 ~~~~~~  108 (145)
T 2a61_A          103 KVIERR  108 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            865543

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

Probab=96.60  E-value=0.007  Score=43.02  Aligned_cols=65  Identities=12%  Similarity=0.165  Sum_probs=49.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+++
T Consensus        48 iL~~l~~~~~~t~~ela~~l~i--------------~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  113 (155)
T 3cdh_A           48 VLACLVDNDAMMITRLAKLSLM--------------EQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAES  113 (155)
T ss_dssp             HHHHHSSCSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHH
Confidence            6777777889999999997762              3456788999999999999764  3343    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       114 ~~~~~  118 (155)
T 3cdh_A          114 LVASA  118 (155)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            75543

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

Probab=96.54  E-value=0.0082  Score=39.72  Aligned_cols=67  Identities=16%  Similarity=0.201  Sum_probs=52.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~iA  136 (144)
                      .|+..|.-.+++.+..|....|-              |.+-+...|++||+.|+|+...++.   -.||++|...+-...
T Consensus        28 ~il~~l~~~~~~s~~ela~~l~i--------------s~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l   93 (99)
T 3cuo_A           28 LILCMLSGSPGTSAGELTRITGL--------------SASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATL   93 (99)
T ss_dssp             HHHHHHTTCCSEEHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHH
Confidence            47777766669999999998873              4578999999999999999877532   268999977776665


Q ss_pred             HHHh
Q 032244          137 GRIA  140 (144)
Q Consensus       137 ~~i~  140 (144)
                      .+++
T Consensus        94 ~~~~   97 (99)
T 3cuo_A           94 KNVY   97 (99)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            5543

>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=96.53  E-value=0.0096  Score=41.90  Aligned_cols=65  Identities=15%  Similarity=0.210  Sum_probs=52.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+..+|+.||+.|||+...  .++|    .||++|+..++.
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            6878888899999999998873              3467888999999999999764  2333    589999999888


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       111 ~~~~~  115 (152)
T 3bj6_A          111 IRADE  115 (152)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

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

Probab=96.52  E-value=0.013  Score=41.76  Aligned_cols=65  Identities=11%  Similarity=0.146  Sum_probs=49.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-              +.+-+-.+|+.||+.|||++..  .++    -.||++|+..++.
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            6777777889999999998863              4467888999999999999754  233    3599999999987


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       120 ~~~~~  124 (162)
T 2fa5_A          120 VAPLV  124 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.52  E-value=0.013  Score=41.24  Aligned_cols=65  Identities=14%  Similarity=0.197  Sum_probs=51.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|....|-              +.+-+-.+++.||+.|||++.+  .++    -.||++|+..++.
T Consensus        45 iL~~l~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~  110 (148)
T 3nrv_A           45 IISVLSSASDCSVQKISDILGL--------------DKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV  110 (148)
T ss_dssp             HHHHHHHSSSBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHH
Confidence            7888888999999999998873              3467889999999999999764  223    4699999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       111 ~~~~~  115 (148)
T 3nrv_A          111 ASDFA  115 (148)
T ss_dssp             HHHHT
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=96.50  E-value=0.0097  Score=41.08  Aligned_cols=65  Identities=12%  Similarity=0.263  Sum_probs=52.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+|+.||+.|||+..+  .++|    .||++|+..+++
T Consensus        43 iL~~l~~~~~~t~~ela~~l~~--------------~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  108 (140)
T 2nnn_A           43 ALVRLGETGPCPQNQLGRLTAM--------------DAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEA  108 (140)
T ss_dssp             HHHHHHHHSSBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHH
Confidence            7888888899999999998763              4467888999999999999754  3233    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       109 ~~~~~  113 (140)
T 2nnn_A          109 GLAAA  113 (140)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

>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=96.50  E-value=0.0061  Score=42.26  Aligned_cols=63  Identities=10%  Similarity=0.141  Sum_probs=49.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD  133 (144)
                      .||+.|+ .++..++.|.+...             .-|.+.+-..|+.||+.|||++..  .++    -.||++|++.++
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            3677777 89999999999751             346678999999999999998654  223    479999999877


Q ss_pred             HHH
Q 032244          134 QVA  136 (144)
Q Consensus       134 ~iA  136 (144)
                      .+.
T Consensus        84 ~~~   86 (107)
T 2hzt_A           84 ILD   86 (107)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            553

>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=96.49  E-value=0.0092  Score=50.12  Aligned_cols=68  Identities=15%  Similarity=0.111  Sum_probs=53.1

Q ss_pred             HHHHHHH-----HHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-CceeCcch-H
Q 032244           57 RAASMAR-----KIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-GRRITSSG-Q  129 (144)
Q Consensus        57 RaASilR-----klYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-GR~lT~~G-~  129 (144)
                      |-..||+     .|--.+|+|+..|.+.|+            -.-|..-||+-|+.||++|++++...+ ||.-|.+| +
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 RQRKVLYCIVREYIENKKPVSSQRVLEVSN------------IEFSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDKGLR   85 (338)
T ss_dssp             HHHHHHHHHHHHHHHHCSCBCHHHHHHHSC------------CCSCHHHHHHHHHHHHHTTSEECCSSCSCBEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCccHHHHHHHhC------------CCCCHHHHHHHHHHHHHCCCEEEccCcceecCCcccch
Confidence            7777887     344458999999999884            123778999999999999999987754 68889888 4


Q ss_pred             hhHHHHH
Q 032244          130 RDLDQVA  136 (144)
Q Consensus       130 ~~lD~iA  136 (144)
                      ...|++.
T Consensus        86 ~yvd~l~   92 (338)
T 1stz_A           86 FYYEEML   92 (338)
T ss_dssp             HHHHHHH
T ss_pred             hhhhhhh
Confidence            4566554

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

Probab=96.47  E-value=0.011  Score=41.38  Aligned_cols=61  Identities=13%  Similarity=0.150  Sum_probs=48.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+ +.++.|....|-              +.+-+..+|+.||+.|||++.+  .++|    .||++|+..+..
T Consensus        43 iL~~l~~~~-~t~~eLa~~l~~--------------s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~  107 (146)
T 3tgn_A           43 ILMLLSEES-LTNSELARRLNV--------------SQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEE  107 (146)
T ss_dssp             HHHHHTTCC-CCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHH
T ss_pred             HHHHHHhCC-CCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHH
Confidence            788888777 999999999873              4578899999999999999765  2354    499999999998


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus       108 ~~  109 (146)
T 3tgn_A          108 HH  109 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            86

>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=96.43  E-value=0.008  Score=39.74  Aligned_cols=66  Identities=8%  Similarity=0.113  Sum_probs=51.8

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD  133 (144)
                      .||..|+-.++..+..|....|              -|.+-+-..|+.||+.|+|+...  .+|    -.||++|+..+.
T Consensus        20 ~iL~~L~~~~~~~~~ela~~l~--------------is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~   85 (100)
T 1ub9_A           20 GIMIFLLPRRKAPFSQIQKVLD--------------LTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAK   85 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHhcCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHH
Confidence            4777787789999999999876              34567889999999999998543  223    358999998888


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus        86 ~~~~~~   91 (100)
T 1ub9_A           86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776654

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

Probab=96.43  E-value=0.01  Score=42.41  Aligned_cols=65  Identities=17%  Similarity=0.230  Sum_probs=51.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+..+|+.||+.|||++..  .++|    .||++|+..++.
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            6777888899999999998873              3467888999999999999754  3344    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +....
T Consensus       123 ~~~~~  127 (162)
T 3cjn_A          123 LWPHM  127 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.39  E-value=0.0082  Score=44.30  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=50.6

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      .||+.|. .|+...+.|++.-.             .-|.+.+-..|+.||+.|||++..  ...|    .||++|++.+.
T Consensus        30 ~IL~~L~-~g~~rf~eL~~~l~-------------gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~~   95 (131)
T 4a5n_A           30 ILFYHMI-DGKKRFNEFRRICP-------------SITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEP   95 (131)
T ss_dssp             HHHHHHT-TSCBCHHHHHHHCT-------------TSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGHH
T ss_pred             HHHHHHh-cCCcCHHHHHHHhc-------------ccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHHH
Confidence            4778887 89999999999762             246679999999999999999764  2233    69999999887


Q ss_pred             HHHH
Q 032244          134 QVAG  137 (144)
Q Consensus       134 ~iA~  137 (144)
                      .+..
T Consensus        96 ~l~~   99 (131)
T 4a5n_A           96 IVLQ   99 (131)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6643

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

Probab=96.38  E-value=0.018  Score=39.98  Aligned_cols=64  Identities=11%  Similarity=0.156  Sum_probs=50.6

Q ss_pred             HHHHH-HHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKI-YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRkl-Yl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      ||..| +-.+++.+..|....|-              +.+-+..+++.||+.|||+..+  .++|    .||++|+..++
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            67777 45789999999998873              4467888999999999999765  2233    68999999998


Q ss_pred             HHHHH
Q 032244          134 QVAGR  138 (144)
Q Consensus       134 ~iA~~  138 (144)
                      .+...
T Consensus       108 ~~~~~  112 (146)
T 2fbh_A          108 DIEAI  112 (146)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87544

>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=96.37  E-value=0.014  Score=40.72  Aligned_cols=65  Identities=9%  Similarity=0.112  Sum_probs=52.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||+...  .++|    .||++|+..++.
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            6777888899999999998873              4467888999999999998754  3344    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       100 ~~~~~  104 (144)
T 1lj9_A          100 IVREN  104 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.36  E-value=0.0096  Score=46.31  Aligned_cols=62  Identities=13%  Similarity=0.206  Sum_probs=51.8

Q ss_pred             HHHHHH----hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           62 ARKIYL----RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        62 lRklYl----~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      |+.||.    .+++.+..|+...|-              |.+-+..+|+.||+.|||+..+.++=.||++|++...++..
T Consensus         8 L~~I~~l~~~~~~~~~~~lA~~l~v--------------s~~tvs~~l~~Le~~GlV~r~~~~~i~LT~~G~~~~~~~~~   73 (214)
T 3hrs_A            8 LKCLYELGTRHNKITNKEIAQLMQV--------------SPPAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVSDLYR   73 (214)
T ss_dssp             HHHHHHTTSSCSCCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCcCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEEecCCCeEECHHHHHHHHHHHH
Confidence            445555    468999999998884              34678999999999999999987788999999999888765

>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=96.35  E-value=0.0068  Score=42.35  Aligned_cols=63  Identities=16%  Similarity=0.270  Sum_probs=49.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD  133 (144)
                      .||..|+ ++++.++.|.....             .-+.+.+-..|+.||+.|||++..  .++    -.||++|+..++
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            4777777 69999999999771             245678999999999999998665  223    378999998777


Q ss_pred             HHH
Q 032244          134 QVA  136 (144)
Q Consensus       134 ~iA  136 (144)
                      .+.
T Consensus        92 ~~~   94 (112)
T 1z7u_A           92 ALS   94 (112)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

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

Probab=96.26  E-value=0.0053  Score=43.55  Aligned_cols=62  Identities=11%  Similarity=0.152  Sum_probs=48.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|              -+.+-+..+|+.||+.|||++..  .++|    .||++|+..++.
T Consensus        52 iL~~l~~~~~~t~~ela~~l~--------------~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  117 (153)
T 2pex_A           52 VMLVLWETDERSVSEIGERLY--------------LDSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRSK  117 (153)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGGG
T ss_pred             HHHHHHhCCCcCHHHHHHHhC--------------CCcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHHH
Confidence            677788889999999999887              24567888999999999999765  2343    589999988776


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus       118 ~~  119 (153)
T 2pex_A          118 AG  119 (153)
T ss_dssp             ST
T ss_pred             HH
Confidence            53

>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=96.24  E-value=0.0064  Score=41.82  Aligned_cols=60  Identities=5%  Similarity=0.073  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchh-hHHHHHHHHHhCCcceecCCCCc---eeCcchHhhH
Q 032244           58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGS-VARHILHQLQDTNIIELDSKGGR---RITSSGQRDL  132 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~-iiR~~LqqLE~~glv~k~~~gGR---~lT~~G~~~l  132 (144)
                      ...||.-|.-+||..+..|++..|=              +.. -+|..|+.||+.|+|++... ||   .||++|+..|
T Consensus        13 ~~~IL~~Lk~~g~~ta~eiA~~Lgi--------------t~~~aVr~hL~~Le~eGlV~~~~~-gRP~w~LT~~g~~~~   76 (79)
T 1xmk_A           13 KEKICDYLFNVSDSSALNLAKNIGL--------------TKARDINAVLIDMERQGDVYRQGT-TPPIWHLTDKKRERM   76 (79)
T ss_dssp             HHHHHHHHHHTCCEEHHHHHHHHCG--------------GGHHHHHHHHHHHHHTTSEEEECS-SSCEEEECHHHHTTT
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHcCC--------------CcHHHHHHHHHHHHHCCCEEecCC-CCCCeEeCHhHHhHh
Confidence            3458888888999999999999884              334 79999999999999997653 66   7899998765

>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=96.23  E-value=0.012  Score=41.48  Aligned_cols=65  Identities=18%  Similarity=0.248  Sum_probs=52.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+..+++.||+.|||+..+  .++|    .||++|+..++.
T Consensus        42 iL~~l~~~~~~t~~ela~~l~~--------------s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (155)
T 1s3j_A           42 VLASLKKHGSLKVSEIAERMEV--------------KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  107 (155)
T ss_dssp             HHHHHHHHSEEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHHH
Confidence            6778888899999999998873              4567888999999999998764  2343    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       108 ~~~~~  112 (155)
T 1s3j_A          108 VLAGR  112 (155)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76543

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

Probab=96.20  E-value=0.0096  Score=43.16  Aligned_cols=65  Identities=12%  Similarity=0.180  Sum_probs=49.9

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.  +++.++.|....|-.              .+-+-.+++.||+.|||++..  .++|    .||++|+..+
T Consensus        51 vL~~l~~~~~~~~t~~eLa~~l~~~--------------~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  116 (168)
T 3u2r_A           51 TLRLLRSVHPEGMATLQIADRLISR--------------APDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLL  116 (168)
T ss_dssp             HHHHHHHHTTSCEEHHHHHHHC-----------------CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCC--------------hhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHH
Confidence            78888885  489999999987632              246778999999999999754  3344    5999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +.+...+
T Consensus       117 ~~~~~~~  123 (168)
T 3u2r_A          117 KDLEEPV  123 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876643

>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=96.20  E-value=0.02  Score=40.51  Aligned_cols=65  Identities=15%  Similarity=0.193  Sum_probs=47.8

Q ss_pred             HHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      ||..|+-.+ ++.+..|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++
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 7899999998873              3456778999999999999765  3344    59999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+...+
T Consensus       110 ~~~~~~  115 (150)
T 3fm5_A          110 DAKARV  115 (150)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886654

>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=96.18  E-value=0.014  Score=42.91  Aligned_cols=62  Identities=16%  Similarity=0.284  Sum_probs=49.7

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-----GRRITSSGQRDLDQ  134 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-----GR~lT~~G~~~lD~  134 (144)
                      .||+.|+ .|+..++.|.+..|              -|.+.+-..|+.||+.|||++....     .-.||++|+..+..
T Consensus        28 ~IL~~L~-~g~~~~~eLa~~lg--------------is~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l~~~   92 (146)
T 2f2e_A           28 LIVRDAF-EGLTRFGEFQKSLG--------------LAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALFPL   92 (146)
T ss_dssp             HHHHHHH-TTCCSHHHHHHHHC--------------CCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHHHHH
Confidence            3788885 79999999999776              3567999999999999999976532     34799999987665


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus        93 l~   94 (146)
T 2f2e_A           93 LV   94 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=96.15  E-value=0.0072  Score=41.86  Aligned_cols=58  Identities=12%  Similarity=0.097  Sum_probs=48.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.+++.+..|....|-              |.+-+..+++.||+.|||++.+  .++|    .||++|+..+
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            7888888899999999998863              4467888999999999998664  2343    5999999998

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=96.09  E-value=0.00096  Score=55.34  Aligned_cols=64  Identities=23%  Similarity=0.300  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      |-..||..||..+++++..|...+|-              |..-||..|+.||+.|+|+.... |=.||++|+..+..+
T Consensus        21 r~~~iL~~l~~~~~~t~~eLa~~l~v--------------s~~Tv~r~l~~Le~~Glv~~~~~-gi~LT~~G~~~~~~~   84 (345)
T 2o0m_A           21 ERFQILRNIYWMQPIGRRSLSETMGI--------------TERVLRTETDVLKQLNLIEPSKS-GMTLTERGLEVYQGL   84 (345)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEec-ceEEcHHHHHHHHHH
Confidence            44568999999999999999999885              34579999999999999985554 789999999766544

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

Probab=96.05  E-value=0.014  Score=40.95  Aligned_cols=63  Identities=14%  Similarity=0.168  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCc--hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC--CCceeCcchHhhHHHH
Q 032244           60 SMARKIYLRGGLG--VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GGRRITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~g~~G--v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~--gGR~lT~~G~~~lD~i  135 (144)
                      .||+.|. .|+..  ++.|.+...             .-|.+.+-..|+.||+.|||++...  ---.||++|++.+..+
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            4777777 88988  999999651             2466789999999999999997742  2468999999987765


Q ss_pred             H
Q 032244          136 A  136 (144)
Q Consensus       136 A  136 (144)
                      .
T Consensus        97 ~   97 (111)
T 3df8_A           97 M   97 (111)
T ss_dssp             H
T ss_pred             H
Confidence            4

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

Probab=96.02  E-value=0.013  Score=42.21  Aligned_cols=65  Identities=12%  Similarity=0.202  Sum_probs=47.9

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      +|..||..  +++.++.|....|-.              .+-+=.+++.||+.|||++.+  .++|    .||++|+..+
T Consensus        40 vL~~L~~~~~~~~t~~eLa~~l~~~--------------~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  105 (147)
T 4b8x_A           40 ALVLLTFSKSGELPMSKIGERLMVH--------------PTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVV  105 (147)
T ss_dssp             HHHHHHTSGGGEEEHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHH
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHH
Confidence            67777764  578999999988743              345667999999999998664  4355    4899999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +++...+
T Consensus       106 ~~~~~~~  112 (147)
T 4b8x_A          106 EAATRDL  112 (147)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876543

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

Probab=96.00  E-value=0.013  Score=39.51  Aligned_cols=54  Identities=17%  Similarity=0.076  Sum_probs=46.0

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR  130 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~  130 (144)
                      .||+.|  .+++.++.|....|-              |.+-+++.|+.||+.|+|+... |.-.||+.|+.
T Consensus        35 ~Il~~L--~~~~~~~eLa~~l~i--------------s~~tv~~~L~~L~~~Glv~~~~-g~y~l~~~g~~   88 (96)
T 1y0u_A           35 KILRML--DKGRSEEEIMQTLSL--------------SKKQLDYHLKVLEAGFCIERVG-ERWVVTDAGKI   88 (96)
T ss_dssp             HHHHHH--HTTCCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECTTTCC
T ss_pred             HHHHHH--cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEC-CEEEECCCchH
Confidence            477777  899999999998863              4578999999999999999877 67789999864

>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=95.99  E-value=0.03  Score=41.89  Aligned_cols=65  Identities=12%  Similarity=0.181  Sum_probs=51.9

Q ss_pred             HHHHHHH--hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl--~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-  .+++.++.|+...|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+
T Consensus        46 vL~~L~~~~~~~~t~~eLa~~l~i--------------s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~  111 (189)
T 3nqo_A           46 TILSILHLPEEETTLNNIARKMGT--------------SKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVM  111 (189)
T ss_dssp             HHHHHHHSCGGGCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHH
T ss_pred             HHHHHHhccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHH
Confidence            7877887  679999999998873              3456778999999999998654  3455    5999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +++....
T Consensus       112 ~~~~~~~  118 (189)
T 3nqo_A          112 VTCSRTG  118 (189)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876553

>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=95.95  E-value=0.0066  Score=42.52  Aligned_cols=62  Identities=11%  Similarity=0.144  Sum_probs=49.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|              -+.+-+..+++.||+.|||+..+  .++|    .||++|+..++.
T Consensus        45 iL~~l~~~~~~~~~~la~~l~--------------~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~~  110 (147)
T 1z91_A           45 ALLLLWEHETLTVKKMGEQLY--------------LDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  110 (147)
T ss_dssp             HHHHHHHHSEEEHHHHHHTTT--------------CCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHHCCCCCHHHHHHHHC--------------CCcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            677888889999999999765              24567888999999999999765  2344    589999998876


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus       111 ~~  112 (147)
T 1z91_A          111 AV  112 (147)
T ss_dssp             TT
T ss_pred             HH
Confidence            54

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

Probab=95.87  E-value=0.008  Score=42.06  Aligned_cols=68  Identities=15%  Similarity=0.143  Sum_probs=48.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc-----eeCcchHhhHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR-----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR-----~lT~~G~~~lD  133 (144)
                      ||..|. .+|.--..+.+....          +..-|.+.+-.+|+.||+.|||+...  .+||     .||++|+..++
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            555554 466555566665542          23457788999999999999998654  2464     59999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      +.....
T Consensus        83 ~~~~~~   88 (108)
T 3l7w_A           83 YLTKEW   88 (108)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876553

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

Probab=95.83  E-value=0.021  Score=40.62  Aligned_cols=65  Identities=12%  Similarity=0.203  Sum_probs=48.1

Q ss_pred             HHHHHH-HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIY-LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklY-l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      ||..|+ -.+++.+..|....|-.+              +-+-.+++.||+.|||++..  .++|    .||++|+..++
T Consensus        52 iL~~L~~~~~~~~~~ela~~l~i~~--------------~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  117 (160)
T 3boq_A           52 AMAQLARNPDGLSMGKLSGALKVTN--------------GNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFK  117 (160)
T ss_dssp             HHHHHHHCTTCEEHHHHHHHCSSCC--------------SCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCCCh--------------hhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHH
Confidence            677785 468999999999876332              35677899999999999765  3343    59999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus       118 ~~~~~~  123 (160)
T 3boq_A          118 QASEAH  123 (160)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

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

Probab=95.80  E-value=0.064  Score=37.66  Aligned_cols=68  Identities=15%  Similarity=0.169  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|-..+.-++..-+.|..       ....|+..||-              |..-+|.+|+.||+.|+|+..+..|-.+++
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            456667667766666533       67789999983              567999999999999999998877999998


Q ss_pred             chHhhHHHH
Q 032244          127 SGQRDLDQV  135 (144)
Q Consensus       127 ~G~~~lD~i  135 (144)
                      ....++..+
T Consensus        76 ~~~~~~~~~   84 (113)
T 3tqn_A           76 GARQRLLTQ   84 (113)
T ss_dssp             THHHHHHHH
T ss_pred             CchHHHHHH
Confidence            877665543

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

Probab=95.78  E-value=0.025  Score=39.54  Aligned_cols=64  Identities=14%  Similarity=0.127  Sum_probs=50.9

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.++ .+..|....|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..+++
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            6778888888 99999998873              3456778999999999999765  3333    599999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       107 ~~~~~  111 (144)
T 3f3x_A          107 ANEVL  111 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=95.78  E-value=0.028  Score=40.49  Aligned_cols=63  Identities=19%  Similarity=0.168  Sum_probs=50.3

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD  133 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD  133 (144)
                      -.||..|--+|+..++.|.....            ..-|..-+++-|+.||+.|||+....+=-.||++|++.|.
T Consensus        16 ~~IL~~L~~~g~~s~~eLA~~l~------------~giS~~aVs~rL~~Le~~GLV~~~~rg~Y~LT~~G~~~l~   78 (111)
T 3b73_A           16 DRILEIIHEEGNGSPKELEDRDE------------IRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLN   78 (111)
T ss_dssp             HHHHHHHHHHSCBCHHHHHTSTT------------CCSCHHHHHHHHHHHHHTTSEEECSTTCEEECHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHh------------cCCCHHHHHHHHHHHHHCCCEEecCCceEEECchHHHHHH
Confidence            45787776679999999998651            0236678999999999999999875534699999998875

>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=95.76  E-value=0.025  Score=45.04  Aligned_cols=55  Identities=20%  Similarity=0.259  Sum_probs=46.2

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      .+|+|...|+..-|=              |-..+|..++-|++.|||+..+ +|=.||++|++...++-.
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            589999999999883              3458999999999999999888 799999999988776643

>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=95.70  E-value=0.022  Score=43.68  Aligned_cols=65  Identities=12%  Similarity=0.165  Sum_probs=51.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|....|-              +.+-+-.+|+.||+.|||++..  .++|    .||++|+..+++
T Consensus        53 iL~~L~~~~~~t~~eLa~~l~i--------------~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  118 (207)
T 2fxa_A           53 ILWIAYQLNGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  118 (207)
T ss_dssp             HHHHHHHHTSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHH
Confidence            7888888899999999998773              3456777999999999999765  3344    599999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       119 ~~~~~  123 (207)
T 2fxa_A          119 LLEEF  123 (207)
T ss_dssp             HHHHC
T ss_pred             HHHHH
Confidence            76543

>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=95.67  E-value=0.024  Score=40.23  Aligned_cols=62  Identities=19%  Similarity=0.205  Sum_probs=49.2

Q ss_pred             HHHHHHHHh------CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCc---eeCcchH
Q 032244           60 SMARKIYLR------GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGR---RITSSGQ  129 (144)
Q Consensus        60 SilRklYl~------g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR---~lT~~G~  129 (144)
                      ++|+.|...      +++-...|++.-+              =+.+-+++.|..||+.|||+... .+||   .||++|+
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            577777766      6788888888555              46689999999999999998654 2355   6999999


Q ss_pred             hhHHHH
Q 032244          130 RDLDQV  135 (144)
Q Consensus       130 ~~lD~i  135 (144)
                      ..+.+.
T Consensus        86 ~~l~~~   91 (96)
T 2obp_A           86 ALAAQL   91 (96)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            998765

>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=95.65  E-value=0.014  Score=40.18  Aligned_cols=53  Identities=13%  Similarity=0.142  Sum_probs=42.5

Q ss_pred             HHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec----CCCCceeC
Q 032244           59 ASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD----SKGGRRIT  125 (144)
Q Consensus        59 ASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~----~~gGR~lT  125 (144)
                      ..|+..++-.| ++.+..|+..+|-              |.+-+|.+|+.|++.|+|+..    +.+|+.+.
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lgv--------------s~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~   78 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLNI--------------KVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIY   78 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTS--------------CHHHHHHHHHHHHHHTSCEEEEEC---CCCCEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecccCCCceEEE
Confidence            45888888777 8999999998884              557899999999999999987    66675544

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

Probab=95.64  E-value=0.02  Score=41.52  Aligned_cols=62  Identities=23%  Similarity=0.279  Sum_probs=48.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+ .|+..++.|....+|             -|.+.+-..|+.||+.|||++..  .++|    .||++|++.+..
T Consensus        40 IL~~L~-~g~~~~~eLa~~l~g-------------is~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~~  105 (131)
T 1yyv_A           40 ILVALR-DGTHRFSDLRRXMGG-------------VSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSDX  105 (131)
T ss_dssp             HHHHGG-GCCEEHHHHHHHSTT-------------CCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHhcc-------------CCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHHHH
Confidence            677777 899999999997621             36678999999999999998654  3233    699999987765


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus       106 l~  107 (131)
T 1yyv_A          106 VA  107 (131)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=95.56  E-value=0.02  Score=40.75  Aligned_cols=65  Identities=17%  Similarity=0.141  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHhCCCchhHHHH-HhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           58 AASMARKIYLRGGLGVGSFRR-IYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~-~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      -.|||++|+-++++.++.|.. .-+-              ..+.+=.-++-||+.|||+.+.+ +=.||++|+..+...+
T Consensus        18 QfsiL~~L~~~~~~t~~~Lae~~l~~--------------drstvsrnl~~L~r~GlVe~~~~-Dl~LT~~G~~~l~~a~   82 (95)
T 1bja_A           18 TATILITIAKKDFITAAEVREVHPDL--------------GNAVVNSNIGVLIKKGLVEKSGD-GLIITGEAQDIISNAA   82 (95)
T ss_dssp             HHHHHHHHHHSTTBCHHHHHHTCTTS--------------CHHHHHHHHHHHHTTTSEEEETT-EEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHhcc--------------cHHHHHHHHHHHHHCCCeecCCC-CeeeCHhHHHHHHHHH
Confidence            368999999999999999998 4443              22456667899999999994444 5679999999998875


Q ss_pred             H
Q 032244          137 G  137 (144)
Q Consensus       137 ~  137 (144)
                      .
T Consensus        83 ~   83 (95)
T 1bja_A           83 T   83 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=95.55  E-value=0.023  Score=39.12  Aligned_cols=67  Identities=7%  Similarity=0.081  Sum_probs=51.7

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G~~~lD~i  135 (144)
                      .||..|+-.+++.+..|....|-.  .        .-+.+-+-.+|+.||+.|||++.+++.|    .||++|+..++.+
T Consensus        14 ~vL~~l~~~~~~t~~ela~~l~~~--~--------~~s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~lT~~g~~~~~~~   83 (123)
T 1okr_A           14 EVMNIIWMKKYASANNIIEEIQMQ--K--------DWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTS   83 (123)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHHHH--C--------CCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESSCHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHhcc--C--------CCcHhhHHHHHHHHHHCCCeEEEecCCeEEEEEecCHHHHHHHHH
Confidence            367777778999999999998732  1        1245678999999999999998776332    4899999887665


Q ss_pred             H
Q 032244          136 A  136 (144)
Q Consensus       136 A  136 (144)
                      .
T Consensus        84 ~   84 (123)
T 1okr_A           84 K   84 (123)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=95.55  E-value=0.049  Score=38.51  Aligned_cols=60  Identities=12%  Similarity=0.159  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHh---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchHh
Q 032244           57 RAASMARKIYLR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRklYl~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~~  130 (144)
                      +|..+|..|..+   +++.+..|+..+|-              |.+.++++|++|+++|||+...  .||..|+.....
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            466778777764   57999999998874              4579999999999999999764  478899876544

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=95.48  E-value=0.033  Score=46.65  Aligned_cols=66  Identities=11%  Similarity=0.218  Sum_probs=46.0

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~l  132 (144)
                      ||+.|+-+  +++.+..|+..              ..-+.+-+=.+|+.||+.|||++.  +++.|    .||++|+..+
T Consensus       409 vl~~l~~~~~~~~~~~~l~~~--------------~~~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~  474 (487)
T 1hsj_A          409 ILNHILRSESNEISSKEIAKC--------------SEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  474 (487)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHS--------------SCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHhCCCCCcCHHHHHHH--------------HCCCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHH
Confidence            55555555  55566666653              233445677789999999999864  44455    4799999999


Q ss_pred             HHHHHHHh
Q 032244          133 DQVAGRIA  140 (144)
Q Consensus       133 D~iA~~i~  140 (144)
                      +++...+.
T Consensus       475 ~~~~~~~~  482 (487)
T 1hsj_A          475 QKLISELE  482 (487)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHHHHH
Confidence            98877654

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

Probab=95.38  E-value=0.029  Score=41.25  Aligned_cols=65  Identities=15%  Similarity=0.238  Sum_probs=46.3

Q ss_pred             HHHHHHHhCC---CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q 032244           61 MARKIYLRGG---LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRD  131 (144)
Q Consensus        61 ilRklYl~g~---~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~  131 (144)
                      ||..|+-.++   +.+..|....|-.              .+-+-.+|+.||+.|||++..  .++|    .||++|+..
T Consensus        74 iL~~L~~~~~~~~~t~~eLa~~l~is--------------~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  139 (181)
T 2fbk_A           74 LLLTLYRSAPPEGLRPTELSALAAIS--------------GPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  139 (181)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSCC--------------SGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHH
Confidence            6777777664   8888888876532              234556889999999999764  2233    699999999


Q ss_pred             HHHHHHHH
Q 032244          132 LDQVAGRI  139 (144)
Q Consensus       132 lD~iA~~i  139 (144)
                      ++++...+
T Consensus       140 ~~~~~~~~  147 (181)
T 2fbk_A          140 VTHLLPAH  147 (181)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98875543

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

Probab=95.36  E-value=0.12  Score=36.85  Aligned_cols=61  Identities=15%  Similarity=0.159  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+.-|+.--+.|..       ....|+..||-              |..-+|.+|+.|+..|+|+..+..|-.+++
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            566677777776666533       58899999983              567999999999999999999877888888


Q ss_pred             ch
Q 032244          127 SG  128 (144)
Q Consensus       127 ~G  128 (144)
                      .-
T Consensus        80 ~~   81 (125)
T 3neu_A           80 DK   81 (125)
T ss_dssp             CH
T ss_pred             Cc
Confidence            54

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

Probab=95.24  E-value=0.13  Score=37.26  Aligned_cols=65  Identities=18%  Similarity=0.193  Sum_probs=47.7

Q ss_pred             HHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      +|..|+-.+ ++..+.|....|-              +.+-+=.+++.||+.|||++.+  .++|    .||++|+..++
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~~--------------~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~  101 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIGI--------------EQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIE  101 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCc--------------CHHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHH
Confidence            677777654 4555788887773              3345777899999999998554  4455    48999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus       102 ~~~~~~  107 (151)
T 4aik_A          102 QVDGVI  107 (151)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

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

Probab=95.23  E-value=0.056  Score=40.63  Aligned_cols=72  Identities=13%  Similarity=0.122  Sum_probs=53.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGG-----RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gG-----R~lT~~G~~~l  132 (144)
                      ||.-|. .+|.--..|.+.+...-      .++...|-+.|-..|+.||+.|||+...   ++|     -.||++|+..+
T Consensus         7 iL~lL~-~~~~~gyel~~~l~~~~------~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l   79 (179)
T 1yg2_A            7 ILTVLS-TRDATGYDITKEFSASI------GYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSAL   79 (179)
T ss_dssp             HHHHHH-HCCBCHHHHHHHHTTGG------GGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHH
T ss_pred             HHHHHh-cCCCCHHHHHHHHHHHh------CCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHH
Confidence            565555 58888888999886322      2466778889999999999999998654   222     47999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .+...+.
T Consensus        80 ~~~~~~~   86 (179)
T 1yg2_A           80 GEWFDQP   86 (179)
T ss_dssp             HHHHHSC
T ss_pred             HHHHhCc
Confidence            8865543

>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=95.19  E-value=0.027  Score=40.01  Aligned_cols=72  Identities=14%  Similarity=0.106  Sum_probs=45.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----~lT~~G~~~l  132 (144)
                      ||.-|. .+|.---.+.+.....-      ..+-.-|.+.+-.+|+.||+.|||+...   .+|+     .||++|++.+
T Consensus        17 IL~~L~-~~~~~Gyei~~~l~~~~------~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l   89 (116)
T 3f8b_A           17 LLNVLK-QGDNYVYGIIKQVKEAS------NGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENM   89 (116)
T ss_dssp             HHHHHH-HCCBCHHHHHHHHHHHT------TTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEECHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHHHHHh------CCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECHHHHHHH
Confidence            454444 45643344444433211      1234567788999999999999998652   2342     6999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +......
T Consensus        90 ~~~~~~~   96 (116)
T 3f8b_A           90 RLAFESW   96 (116)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876553

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=95.14  E-value=0.03  Score=41.68  Aligned_cols=64  Identities=16%  Similarity=0.269  Sum_probs=51.4

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC----ceeCcchHhhHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG----RRITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG----R~lT~~G~~~lD~i  135 (144)
                      .||+.|. +++..++.|....|-              |.+-+.+-|+.||++|||+...+ |    -.||++|...+-.+
T Consensus        62 ~IL~~L~-~~~~t~~eLa~~lgl--------------s~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~lt~~~~~~l~~~  125 (151)
T 3f6v_A           62 RLVQLLT-SGEQTVNNLAAHFPA--------------SRSAISQHLRVLTEAGLVTPRKD-GRFRYYRLDPQGLAQLRAL  125 (151)
T ss_dssp             HHHHHGG-GCCEEHHHHHTTSSS--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHHHHHHHH
Confidence            4787777 899999999997763              45789999999999999998775 5    46999998877665


Q ss_pred             HHHH
Q 032244          136 AGRI  139 (144)
Q Consensus       136 A~~i  139 (144)
                      ..++
T Consensus       126 l~~~  129 (151)
T 3f6v_A          126 FDSF  129 (151)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=95.03  E-value=0.18  Score=33.92  Aligned_cols=64  Identities=17%  Similarity=0.232  Sum_probs=48.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~iA  136 (144)
                      .||+.| .+|+..++.|....|-              |.+-+.+.|+.||+.|||+....|.   ..||+.+-..+=+..
T Consensus        27 ~Il~~L-~~~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~~l   91 (102)
T 3pqk_A           27 MLVCTL-VEGEFSVGELEQQIGI--------------GQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNAL   91 (102)
T ss_dssp             HHHHHH-HTCCBCHHHHHHHHTC--------------CTTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHHHH
T ss_pred             HHHHHH-HhCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHHHH
Confidence            477777 5799999999998874              3357999999999999999877632   568887665544333


Q ss_pred             HH
Q 032244          137 GR  138 (144)
Q Consensus       137 ~~  138 (144)
                      .+
T Consensus        92 ~~   93 (102)
T 3pqk_A           92 YT   93 (102)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

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

Probab=95.02  E-value=0.11  Score=37.22  Aligned_cols=59  Identities=14%  Similarity=0.079  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|-..+..||..-+.|.      + ....|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++
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            46677777777666653      3 78899999983              567999999999999999999877988988

>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=95.01  E-value=0.021  Score=40.07  Aligned_cols=51  Identities=22%  Similarity=0.195  Sum_probs=44.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchHhhHHHHH
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~~~lD~iA  136 (144)
                      .+..|...||-              |..-+|.+|+.||+.|+|+..+  ..|-.+++.+..++..+.
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            78899999983              5689999999999999999888  459999998888877664

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=94.84  E-value=0.15  Score=35.99  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=45.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G~~~lD~  134 (144)
                      .||..|.-.++..++.|....|-              |.+-+.+.|+.||+.|||+.... ||    .||+.+...+-+
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            47777766799999999998873              45688999999999999998775 44    688887655433

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

Probab=94.79  E-value=0.081  Score=38.23  Aligned_cols=63  Identities=14%  Similarity=0.219  Sum_probs=40.3

Q ss_pred             HHHHHHHhC-----CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec-CCCCc----eeCcchHh
Q 032244           61 MARKIYLRG-----GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-SKGGR----RITSSGQR  130 (144)
Q Consensus        61 ilRklYl~g-----~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~-~~gGR----~lT~~G~~  130 (144)
                      ||..|+..+     ++.++.|....|-              +.+-+=.+++.||+.|||+.. +.++|    .||++|+.
T Consensus        38 vL~~l~~~~~~~~~~~t~~eLa~~l~~--------------~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~  103 (148)
T 4fx0_A           38 TLAVISLSEGSAGIDLTMSELAARIGV--------------ERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRA  103 (148)
T ss_dssp             HHHHHHC---------CHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSBC-----------CCBCHHHHH
T ss_pred             HHHHHHHhcCCCCCCcCHHHHHHHHCC--------------ChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHH
Confidence            566666553     4677888887763              234566789999999999643 23354    58999999


Q ss_pred             hHHHHHH
Q 032244          131 DLDQVAG  137 (144)
Q Consensus       131 ~lD~iA~  137 (144)
                      .++++..
T Consensus       104 ~~~~~~~  110 (148)
T 4fx0_A          104 ALQKAVP  110 (148)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988754

>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=94.48  E-value=0.16  Score=34.76  Aligned_cols=57  Identities=14%  Similarity=0.205  Sum_probs=45.1

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcchHhhH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSGQRDL  132 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G~~~l  132 (144)
                      .|+..|. +++..++.|....|-              |.+-+.+.|+.||+.|+|+.... ||    .||+.+-..+
T Consensus        30 ~IL~~L~-~~~~~~~ela~~l~i--------------s~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~~~~~~   90 (106)
T 1r1u_A           30 RIMELLS-VSEASVGHISHQLNL--------------SQSNVSHQLKLLKSVHLVKAKRQ-GQSMIYSLDDIHVATM   90 (106)
T ss_dssp             HHHHHHH-HCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEESSHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEEChHHHHHH
Confidence            4777776 899999999998873              44689999999999999997765 44    5787775433

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=94.36  E-value=0.092  Score=36.31  Aligned_cols=61  Identities=18%  Similarity=0.209  Sum_probs=46.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~i  135 (144)
                      .||.-|. .+++.++.|....|-              |.+-+...|+.||+.|+|+...+|.   ..||+++...+=+.
T Consensus        29 ~IL~~L~-~~~~s~~eLa~~lgi--------------s~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~   92 (108)
T 2kko_A           29 QILDLLA-QGERAVEAIATATGM--------------NLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFAL   92 (108)
T ss_dssp             HHHHHHT-TCCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHH
Confidence            4666565 689999999998873              4468999999999999999776532   36899886554333

>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=94.33  E-value=0.056  Score=42.02  Aligned_cols=54  Identities=11%  Similarity=0.190  Sum_probs=45.1

Q ss_pred             CCch--hHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244           70 GLGV--GSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG  137 (144)
Q Consensus        70 ~~Gv--~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~  137 (144)
                      ++..  ..|+...|-              |.+-+..+|+.||+.|||+..++.+=.||++|+..+..+..
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            5666  899998763              45678999999999999999887678999999999887653

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=94.29  E-value=0.16  Score=36.66  Aligned_cols=64  Identities=16%  Similarity=0.161  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           55 YIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        55 y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      |-..+.-++..-+.|.      + ....|+..||-              |..-+|.+|+.||..|+|+..+..|-.+++.
T Consensus         6 ~~~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gv--------------Sr~tVr~Al~~L~~~Gli~~~~g~G~~V~~~   71 (129)
T 2ek5_A            6 YKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRI--------------NPATARNGLTLLVEAGILYKKRGIGMFVSAQ   71 (129)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTC--------------CHHHHHHHHHHHHTTTSEEEETTTEEEECTT
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEecCCEEEEecC
Confidence            4455555555555543      2 67788998883              5679999999999999999998779899887


Q ss_pred             hHhhH
Q 032244          128 GQRDL  132 (144)
Q Consensus       128 G~~~l  132 (144)
                      ...++
T Consensus        72 ~~~~~   76 (129)
T 2ek5_A           72 APALI   76 (129)
T ss_dssp             HHHHH
T ss_pred             chHhh
Confidence            65554

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

Probab=94.27  E-value=0.12  Score=34.90  Aligned_cols=53  Identities=19%  Similarity=0.235  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHh------CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244           57 RAASMARKIYLR------GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI  124 (144)
Q Consensus        57 RaASilRklYl~------g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l  124 (144)
                      |...||--|--.      +|+.|..++..+|           .   |-+-||.-|..||+.|+|+.++ |||.+
T Consensus         5 r~~~IL~~I~~~i~~~~g~~psv~EIa~~lg-----------v---S~~TVrr~L~~Le~kG~I~R~~-ggr~~   63 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGAPVKTRDIADAAG-----------L---SIYQVRLYLEQLHDVGVLEKVN-AGKGV   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCEEHHHHHHHHT-----------C---CHHHHHHHHHHHHHTTSEEEES-CSSSS
T ss_pred             HHHHHHHHHHHHHhhccCCCcCHHHHHHHHC-----------C---CHHHHHHHHHHHHHCCcEEecC-CCCCc
Confidence            555666666666      8999999999998           3   3456999999999999999998 46654

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=94.22  E-value=0.18  Score=33.59  Aligned_cols=65  Identities=12%  Similarity=0.111  Sum_probs=49.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~iA  136 (144)
                      .|++.|. +++..++.|....|-              |.+-+.+-|+.||+.|+|+....|.   ..||+.+-..+-...
T Consensus        27 ~Il~~L~-~~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l   91 (98)
T 3jth_A           27 QILCMLH-NQELSVGELCAKLQL--------------SQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLL   91 (98)
T ss_dssp             HHHHHTT-TSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHH
T ss_pred             HHHHHHh-cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHH
Confidence            4676665 489999999998873              5578999999999999999887632   358888766655554


Q ss_pred             HHH
Q 032244          137 GRI  139 (144)
Q Consensus       137 ~~i  139 (144)
                      .++
T Consensus        92 ~~~   94 (98)
T 3jth_A           92 HSL   94 (98)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

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

Probab=94.20  E-value=0.078  Score=37.68  Aligned_cols=70  Identities=17%  Similarity=0.133  Sum_probs=49.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----~lT~~G~~~l  132 (144)
                      ||--|. .+|.---.|.+....   .     .+..-|.+.|-.+|+.||+.|||+...   .+|+     .||++|++.|
T Consensus        14 IL~~L~-~~~~~Gyei~~~l~~---~-----~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l   84 (115)
T 4esb_A           14 ILYIIS-QEEVYGYELSTKLNK---H-----GFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGLEQL   84 (115)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHHH---T-----TCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHH---c-----CCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHHHHH
Confidence            454444 566655566666553   1     245667889999999999999998643   2342     4999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +....+.
T Consensus        85 ~~~~~~~   91 (115)
T 4esb_A           85 EEFKQSW   91 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876654

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

Probab=93.88  E-value=0.13  Score=33.71  Aligned_cols=45  Identities=11%  Similarity=0.105  Sum_probs=37.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      .|+.-|.-.+++.+..|+..+|-              |.+-+|..|+.||+.|+|+...
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            46776776789999999999984              4568999999999999999654

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

Probab=93.86  E-value=0.21  Score=40.03  Aligned_cols=64  Identities=13%  Similarity=0.221  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCceeCcchHhhHHH
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGRRITSSGQRDLDQ  134 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR~lT~~G~~~lD~  134 (144)
                      ....||..|.-++++++..|++..|-              +.+-+...|+.||+.|||++..+ ..-.||++|+.....
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            45568988888999999999999884              44678899999999999998743 246899999997654

>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=93.83  E-value=0.071  Score=39.51  Aligned_cols=72  Identities=13%  Similarity=0.062  Sum_probs=47.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCc-----eeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGR-----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR-----~lT~~G~~~l  132 (144)
                      ||.-|. .+|.--..|.+..+..-.      .+..-+-+.|-.+|+.||+.|||+....   +|+     .||++|++.+
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            666665 467655555554432110      1234677899999999999999986531   242     7999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .....+.
T Consensus       119 ~~~~~~~  125 (145)
T 1xma_A          119 KQKCEEW  125 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876554

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=93.75  E-value=0.19  Score=35.09  Aligned_cols=64  Identities=14%  Similarity=0.194  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQVA  136 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~iA  136 (144)
                      .||+.|. +++..++.|....|              -|.+-+.+-|+.||+.|||+....|.   -.||+.|...+....
T Consensus        22 ~Il~~L~-~~~~~~~eLa~~l~--------------is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~   86 (118)
T 3f6o_A           22 AVLGRLS-RGPATVSELAKPFD--------------MALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWL   86 (118)
T ss_dssp             HHHHHHH-TCCEEHHHHHTTCC--------------SCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHH
Confidence            3777776 89999999999665              35578889999999999998776532   468999988776655


Q ss_pred             HH
Q 032244          137 GR  138 (144)
Q Consensus       137 ~~  138 (144)
                      .+
T Consensus        87 ~~   88 (118)
T 3f6o_A           87 AE   88 (118)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=93.73  E-value=0.078  Score=41.27  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=48.8

Q ss_pred             HHHHHHHHh--CCCch--hHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           60 SMARKIYLR--GGLGV--GSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        60 SilRklYl~--g~~Gv--~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      .+|+.||.-  .++.+  ..|+...|-              +.+-+..+|+.||+.|||+..+..+=.||++|+....++
T Consensus        10 ~yL~~i~~l~~~~~~~~~~~la~~l~v--------------s~~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~~~~~   75 (226)
T 2qq9_A           10 MYLRTIYELEEEGVTPLRARIAERLEQ--------------SGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAV   75 (226)
T ss_dssp             HHHHHHHHHHHHTCCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEECTTSBEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCCeEECHHHHHHHHHH
Confidence            346666652  24444  889887773              335677799999999999998876789999999998877


Q ss_pred             HH
Q 032244          136 AG  137 (144)
Q Consensus       136 A~  137 (144)
                      ..
T Consensus        76 ~~   77 (226)
T 2qq9_A           76 MR   77 (226)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=93.72  E-value=0.065  Score=36.54  Aligned_cols=61  Identities=18%  Similarity=0.276  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHhC-----C-C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRG-----G-L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g-----~-~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|-..+.-+|..-+.+     . + .+..|+..||-              |..-+|.+|+.||+.|+|+..+..|..+++
T Consensus        12 ~~~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~v--------------Sr~tvr~al~~L~~~Gli~~~~g~G~~v~~   77 (102)
T 1v4r_A           12 GYADVATHFRTLIKSGELAPGDTLPSVADIRAQFGV--------------AAKTVSRALAVLKSEGLVSSRGALGTVVEK   77 (102)
T ss_dssp             CHHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSS--------------CTTHHHHHTTTTTTSSCCEEETTTEEESCS
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEcc
Confidence            3556666565544442     2 3 78899998884              456999999999999999988866877776


Q ss_pred             ch
Q 032244          127 SG  128 (144)
Q Consensus       127 ~G  128 (144)
                      ..
T Consensus        78 ~~   79 (102)
T 1v4r_A           78 NP   79 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=93.65  E-value=0.13  Score=36.62  Aligned_cols=70  Identities=21%  Similarity=0.240  Sum_probs=48.2

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGG-----RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gG-----R~lT~~G~~~l  132 (144)
                      ||.-|. .+|.---.|.+....   .     .+..-|-+.|-.+|+.||+.|||+...   .+|     -.||++|++.|
T Consensus        18 IL~lL~-~~p~~Gyei~~~l~~---~-----g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l   88 (116)
T 3hhh_A           18 VLAIIQ-RKETYGYEITKILND---Q-----GFTEIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAEL   88 (116)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHT---T-----SCSSCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHH
T ss_pred             HHHHHh-cCCCCHHHHHHHHHH---c-----CCCCCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHH
Confidence            444443 566544566666653   2     245667889999999999999998653   234     35999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .....+.
T Consensus        89 ~~~~~~~   95 (116)
T 3hhh_A           89 ADFWQRW   95 (116)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8866553

>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=93.65  E-value=0.082  Score=40.41  Aligned_cols=67  Identities=16%  Similarity=0.107  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHhCC------CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcch
Q 032244           55 YIRAASMARKIYLRGG------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSG  128 (144)
Q Consensus        55 y~RaASilRklYl~g~------~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G  128 (144)
                      +-.++.-||.--+.|.      +....|+..||              -|...+|.+|+.||..|||+..+..|-.+++-.
T Consensus        18 ~~~v~~~l~~~I~~g~l~pG~~L~E~~La~~lg--------------VSRtpVREAl~~L~~eGlv~~~~~~G~~V~~~~   83 (222)
T 3ihu_A           18 SDTVFFGIMSGLELGTFVPGQRLVETDLVAHFG--------------VGRNSVREALQRLAAEGIVDLQRHRGAVIRRLS   83 (222)
T ss_dssp             HHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEECSTTCEEECCCC
T ss_pred             HHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCCeEEecCC
Confidence            3344445555555542      44677999998              467899999999999999999987798888877


Q ss_pred             HhhHHHH
Q 032244          129 QRDLDQV  135 (144)
Q Consensus       129 ~~~lD~i  135 (144)
                      ..++..+
T Consensus        84 ~~~~~e~   90 (222)
T 3ihu_A           84 LQETLDV   90 (222)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6666554

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=93.52  E-value=0.067  Score=38.39  Aligned_cols=68  Identities=16%  Similarity=0.154  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        55 y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      |-..+.-|+..-+.|..       ....|+..||              -|..-+|.+|+.||..|+|+..+..|-.+++.
T Consensus        13 ~~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~~~G~~V~~~   78 (126)
T 3ic7_A           13 YLQIADRICDDILLGQYEEEGRIPSVREYASIVE--------------VNANTVMRSYEYLQSQEVIYNKRGIGFFVASG   78 (126)
T ss_dssp             TTHHHHHHHHHHHTTSSCBTSEECCTTTTTTCC---------------CCSGGGHHHHHHHHTTTSEEEETTTEEEECTT
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEEcCCccEEccC
Confidence            34555556665555532       3445666555              36679999999999999999999779999998


Q ss_pred             hHhhHHHHH
Q 032244          128 GQRDLDQVA  136 (144)
Q Consensus       128 G~~~lD~iA  136 (144)
                      ...++..+.
T Consensus        79 ~~~~~~~~~   87 (126)
T 3ic7_A           79 AKMLIHSLR   87 (126)
T ss_dssp             HHHHHHHHH
T ss_pred             cHHHHHHHH
Confidence            776655543

>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=93.49  E-value=0.12  Score=36.21  Aligned_cols=45  Identities=16%  Similarity=0.258  Sum_probs=35.9

Q ss_pred             CchhhHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHHHHHh
Q 032244           96 SSGSVARHILHQLQDTNIIELDSKGG---RRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus        96 asg~iiR~~LqqLE~~glv~k~~~gG---R~lT~~G~~~lD~iA~~i~  140 (144)
                      -|-+.|=.+|+.||+.|||+...+..   -.||++|++.|.+...+..
T Consensus        42 is~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~~   89 (99)
T 2co5_A           42 ISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFFK   89 (99)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhHH
Confidence            45677888999999999999776223   4799999999998877653

>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=93.46  E-value=0.29  Score=32.10  Aligned_cols=44  Identities=11%  Similarity=0.130  Sum_probs=36.2

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      +|..++- .+++.+..|...+|-              |.+-++.+|+.||+.|||+...
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            5555655 789999999999873              4568999999999999998764

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.27  E-value=0.064  Score=37.84  Aligned_cols=72  Identities=11%  Similarity=0.074  Sum_probs=49.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCch-hhHHHHHHHHHhCCcceecC--CCC-----ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSG-SVARHILHQLQDTNIIELDS--KGG-----RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg-~iiR~~LqqLE~~glv~k~~--~gG-----R~lT~~G~~~l  132 (144)
                      ||.-|. .+|.-...|.+....   .|.-  . ..-+- +.+-.+|+.||+.|||+...  .+|     -.||++|++.+
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---FGIE--I-PGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYL   90 (118)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHT---TCCS--S-TTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHH---hCCc--c-cCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHHH
Confidence            566564 477777777777753   2210  0 12455 67889999999999998653  124     27999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .....+.
T Consensus        91 ~~~~~~~   97 (118)
T 2esh_A           91 REILRSL   97 (118)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876553

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=93.27  E-value=0.36  Score=37.75  Aligned_cols=60  Identities=12%  Similarity=-0.024  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244           56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ  129 (144)
Q Consensus        56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~  129 (144)
                      -|+..||..|.-.+ ++++..|....|-              +.+-+..+|+.||+.|||+++..+.-.|+++..
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            48889998887665 7999999998874              446888999999999999988545678888643

>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=93.25  E-value=0.2  Score=40.10  Aligned_cols=65  Identities=9%  Similarity=0.099  Sum_probs=45.7

Q ss_pred             HHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..|+-.+  ++..+.|....+              -+.+-+=.+++.||+.|||++.+  .++|    .||++|+..+
T Consensus       163 vL~~L~~~~~~~~t~~eLa~~l~--------------i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~  228 (250)
T 1p4x_A          163 ILAIITSQNKNIVLLKDLIETIH--------------HKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHA  228 (250)
T ss_dssp             HHHHHHTTTTCCEEHHHHHHHSS--------------SCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHH
T ss_pred             HHHHHHhCCCCCcCHHHHHHHHC--------------CChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHH
Confidence            555555544  366666666544              23345667899999999998654  4465    4899999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +++...+
T Consensus       229 ~~~~~~~  235 (250)
T 1p4x_A          229 EQLLAQV  235 (250)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887665

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=93.24  E-value=0.11  Score=37.02  Aligned_cols=69  Identities=16%  Similarity=0.250  Sum_probs=45.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGG-----RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gG-----R~lT~~G~~~l  132 (144)
                      ||--|. .+|.---.|.+.....   |     +..-|-+.|-.+|+.||+.|||+...   .+|     -.||++|++.|
T Consensus        16 IL~lL~-~~p~~Gyei~~~l~~~---g-----~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l   86 (117)
T 4esf_A           16 VLEIIS-RRETYGYEITRHLNDL---G-----FTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQEL   86 (117)
T ss_dssp             HHHHHH-HSCBCHHHHHHHHHHH---T-----CTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHHc---C-----CCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHH
Confidence            443333 5665444555554321   2     34567789999999999999998653   234     35999999999


Q ss_pred             HHHHHH
Q 032244          133 DQVAGR  138 (144)
Q Consensus       133 D~iA~~  138 (144)
                      .....+
T Consensus        87 ~~~~~~   92 (117)
T 4esf_A           87 ELFWKK   92 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            886654

>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=93.17  E-value=0.52  Score=32.26  Aligned_cols=63  Identities=13%  Similarity=0.107  Sum_probs=47.0

Q ss_pred             HHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CC--CceeCcchHhhHHH
Q 032244           60 SMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KG--GRRITSSGQRDLDQ  134 (144)
Q Consensus        60 SilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~g--GR~lT~~G~~~lD~  134 (144)
                      .++.-|++ .+++.+..|....|-              +.+-+..+|+.||+.|||+..+  .+  ...++..|...+..
T Consensus        30 ~il~~L~~~~~~~t~~ela~~l~~--------------~~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~~~~~~~~~~   95 (152)
T 1ku9_A           30 AVYAILYLSDKPLTISDIMEELKI--------------SKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSIKD   95 (152)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecCCCceEEEeecchHHHHHH
Confidence            36666775 689999999999883              4467889999999999999863  22  34677777655555


Q ss_pred             HH
Q 032244          135 VA  136 (144)
Q Consensus       135 iA  136 (144)
                      +.
T Consensus        96 ~~   97 (152)
T 1ku9_A           96 IA   97 (152)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=93.11  E-value=0.25  Score=35.43  Aligned_cols=61  Identities=13%  Similarity=0.226  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+.-||..-+.|.      + ....|+..||              -|..-+|.+|++||..|||+..+..|-.+++
T Consensus        15 lY~QI~~~i~~~I~~G~l~pG~~LPser~La~~~g--------------VSr~tVReAl~~L~~eGlv~~~~g~G~~V~~   80 (134)
T 4ham_A           15 IYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIG--------------VNPNTVSKAYQELERQEVIITVKGKGTFIAN   80 (134)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEEcCcEEEEeC
Confidence            57777777777767653      2 5668999998              3667999999999999999988866877765


Q ss_pred             ch
Q 032244          127 SG  128 (144)
Q Consensus       127 ~G  128 (144)
                      ..
T Consensus        81 ~~   82 (134)
T 4ham_A           81 QT   82 (134)
T ss_dssp             CS
T ss_pred             Cc
Confidence            43

>3l09_A Putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG, protein structure initiative transcription regulator; 2.81A {Jannaschia SP}

Probab=93.08  E-value=0.098  Score=43.05  Aligned_cols=75  Identities=20%  Similarity=0.143  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHH---h---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCc
Q 032244           56 IRAASMARKIYL---R---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITS  126 (144)
Q Consensus        56 ~RaASilRklYl---~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~  126 (144)
                      +|+-|++--||-   .   +.+-++.|-...+.           -.=+...+|.+|.-|++.||++....|   +..||+
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 LKLWSVLVTCLGDVSRDGVIEVSGVALSSFVER-----------MGLQPQAMRVALHRLKRDGWVESRRLGRVGFHRLSD   90 (266)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCCEEHHHHHHHHHH-----------TTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECH
T ss_pred             CChhHHHHHHHHHHhccCCCcccHHHHHHHHHH-----------cCCCchHHHHHHHHHHHCCCeeeeecCCcceEEECH
Confidence            588999999993   2   46888887766652           223457899999999999999987764   578999


Q ss_pred             chHhhHHHHHHHHhh
Q 032244          127 SGQRDLDQVAGRIAV  141 (144)
Q Consensus       127 ~G~~~lD~iA~~i~~  141 (144)
                      .|++.+++....|..
T Consensus        91 ~g~~~l~~~~~ri~~  105 (266)
T 3l09_A           91 SALTQTRAVAGRIYG  105 (266)
T ss_dssp             HHHHHHHTTHHHHHS
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999988877765

>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=92.83  E-value=0.078  Score=40.41  Aligned_cols=65  Identities=17%  Similarity=0.248  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHhCC------CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244           57 RAASMARKIYLRGG------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR  130 (144)
Q Consensus        57 RaASilRklYl~g~------~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~  130 (144)
                      .++.-||.--+.|.      +....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-...
T Consensus        16 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~   81 (218)
T 3sxy_A           16 KVYNLLKEMILNHELKLGEKLNVRELSEKLG--------------ISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEK   81 (218)
T ss_dssp             HHHHHHHHHHHTTSSCTTCEECHHHHHHHHT--------------CCHHHHHHHHHHHHHHTSEEEETTTEEEECCCCHH
T ss_pred             HHHHHHHHHHHhCCCCCCCEeCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCHH
Confidence            34445555555542      45678999999              46789999999999999999998779888887776


Q ss_pred             hHHHH
Q 032244          131 DLDQV  135 (144)
Q Consensus       131 ~lD~i  135 (144)
                      ++..+
T Consensus        82 ~~~el   86 (218)
T 3sxy_A           82 FIRET   86 (218)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66654

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=92.82  E-value=0.14  Score=36.30  Aligned_cols=47  Identities=17%  Similarity=0.112  Sum_probs=36.9

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceecC----CCC-----ceeCcchHhhHHHHHHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELDS----KGG-----RRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~~----~gG-----R~lT~~G~~~lD~iA~~i  139 (144)
                      +..-|-+.|-.+|+.||+.|||+...    .+|     -.||++|++.+.....+.
T Consensus        51 ~~~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~  106 (115)
T 2dql_A           51 TYRLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQAEDLARLW  106 (115)
T ss_dssp             TEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHHHHHHHHHH
T ss_pred             CCCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            34567788999999999999998652    224     379999999998876654

>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=92.80  E-value=0.25  Score=38.64  Aligned_cols=59  Identities=25%  Similarity=0.382  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCceeCcch
Q 032244           56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGRRITSSG  128 (144)
Q Consensus        56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR~lT~~G  128 (144)
                      -|+..||+.|.-.+ ++++..|....|-              +.+-+..+|+.||+.|||+++++ +...|+++.
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            48889998887654 7999999998874              44789999999999999999874 456777664

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=92.56  E-value=0.088  Score=40.71  Aligned_cols=74  Identities=19%  Similarity=0.113  Sum_probs=51.3

Q ss_pred             chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcch
Q 032244           52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSG  128 (144)
Q Consensus        52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G  128 (144)
                      .+-+.++-+....++-.+++.+..++...|-              |.+-+=..+++||+.||++..++   .+=.||++|
T Consensus         9 ~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~i--------------sq~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G   74 (230)
T 3cta_A            9 YYRAIKKIKEAAEASNRAYLTSSKLADMLGI--------------SQQSASRIIIDLEKNGYITRTVTKRGQILNITEKG   74 (230)
T ss_dssp             HHHHHHHHHHHTTTSSEEECCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHH
T ss_pred             HHHHHHHHHHhcccccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHH
Confidence            3444444443444444455778999997774              33567778899999999998732   256799999


Q ss_pred             HhhHHHHHHHH
Q 032244          129 QRDLDQVAGRI  139 (144)
Q Consensus       129 ~~~lD~iA~~i  139 (144)
                      +..++.+...+
T Consensus        75 ~~l~~~~~~~~   85 (230)
T 3cta_A           75 LDVLYTEFADL   85 (230)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99998776543

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=92.56  E-value=0.25  Score=36.11  Aligned_cols=58  Identities=12%  Similarity=0.125  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchH
Q 032244           58 AASMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQ  129 (144)
Q Consensus        58 aASilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~  129 (144)
                      |-.+|..|..+  +++.+..++..+|-              |-..+|++|++|+++|||+... .||-.|+....
T Consensus        16 Al~~L~~La~~~~~~~~~~~iA~~~~i--------------~~~~l~kil~~L~~~Glv~s~rG~GGy~L~~~p~   76 (149)
T 1ylf_A           16 AVHILSILKNNPSSLCTSDYMAESVNT--------------NPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDLH   76 (149)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEC---CCEEESSCGG
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEccCCCceEeCCChh
Confidence            44456555553  47899999998884              4569999999999999998655 67888887653

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=92.54  E-value=0.16  Score=37.44  Aligned_cols=47  Identities=19%  Similarity=0.116  Sum_probs=37.0

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceecC--C--CC-----ceeCcchHhhHHHHHHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELDS--K--GG-----RRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~~--~--gG-----R~lT~~G~~~lD~iA~~i  139 (144)
                      +..-|-+.|-.+|+.||+.|||+...  .  +|     -.||++|++.+.....+.
T Consensus        63 ~~~is~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~  118 (138)
T 2e1n_A           63 NYRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLW  118 (138)
T ss_dssp             TEECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEESCSCCHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            34567789999999999999998652  1  34     379999999998876654

>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=92.46  E-value=0.12  Score=40.43  Aligned_cols=68  Identities=15%  Similarity=0.224  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHHhC------CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           54 YYIRAASMARKIYLRG------GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        54 ~y~RaASilRklYl~g------~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      .+-.++..||..-+.|      .+....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-
T Consensus        29 ~~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~   94 (239)
T 2hs5_A           29 RTTRVAGILRDAIIDGTFRPGARLSEPDICAALD--------------VSRNTVREAFQILIEDRLVAHELNRGVFVRVP   94 (239)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECCC
T ss_pred             HHHHHHHHHHHHHHcCCCCCcCEeCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEEeCC
Confidence            3445556666555554      356778999999              46789999999999999999999779899888


Q ss_pred             hHhhHHHH
Q 032244          128 GQRDLDQV  135 (144)
Q Consensus       128 G~~~lD~i  135 (144)
                      ...++..+
T Consensus        95 ~~~~~~el  102 (239)
T 2hs5_A           95 TAEDITEL  102 (239)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            77766554

>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=92.42  E-value=0.13  Score=40.35  Aligned_cols=52  Identities=17%  Similarity=0.302  Sum_probs=43.9

Q ss_pred             CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      .+....|+..||              -|..-+|.+|+.||..|+|+..+.+|-.+++-...++..+
T Consensus        49 ~L~e~~La~~lg--------------VSr~~VReAL~~L~~~Glv~~~~~~G~~V~~~~~~~~~~~  100 (237)
T 3c7j_A           49 ALRQQELATLFG--------------VSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDA  100 (237)
T ss_dssp             BCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEETTTEEEECCCHHHHHHHH
T ss_pred             eeCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCceEEecCCHHHHHHH
Confidence            467889999998              4678999999999999999999888989988877665543

>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=92.25  E-value=0.59  Score=31.99  Aligned_cols=50  Identities=12%  Similarity=0.101  Sum_probs=40.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG  120 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g  120 (144)
                      ||+.|+-.+|+.++.|....+-.  +|        -+.+-+-.+|+.||+.|||+..+++
T Consensus        15 vL~~L~~~~~~t~~el~~~l~~~--~~--------~~~~Tvt~~l~rLe~kGlv~R~~~~   64 (126)
T 1sd4_A           15 VMNIIWDKKSVSANEIVVEIQKY--KE--------VSDKTIRTLITRLYKKEIIKRYKSE   64 (126)
T ss_dssp             HHHHHHHSSSEEHHHHHHHHHTT--SC--------CCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHhcCCCCHHHHHHHHhhc--CC--------CChhhHHHHHHHHHHCCceEEEeCC
Confidence            68888889999999999999842  11        2356788999999999999987763

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=91.92  E-value=0.32  Score=35.52  Aligned_cols=56  Identities=14%  Similarity=0.236  Sum_probs=42.5

Q ss_pred             HHHHHHHHh---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244           60 SMARKIYLR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ  129 (144)
Q Consensus        60 SilRklYl~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~  129 (144)
                      .+|..|..+   +++.+..++..+|-              |-..+|++|++|.++|||+...  .||-.|+..-.
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            345445543   36899999997774              5569999999999999998654  57888886554

>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=91.60  E-value=0.44  Score=33.75  Aligned_cols=53  Identities=23%  Similarity=0.393  Sum_probs=40.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcch
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSG  128 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G  128 (144)
                      .||+.|. +++..++.|....|-              |.+-+.+.|+.||+.|+|..... ||    .||+++
T Consensus        50 ~IL~~L~-~~~~s~~ela~~lgi--------------s~stvs~~L~~Le~~Glv~~~~~-gr~~~y~l~~~~  106 (122)
T 1r1t_A           50 RLLSLLA-RSELCVGDLAQAIGV--------------SESAVSHQLRSLRNLRLVSYRKQ-GRHVYYQLQDHH  106 (122)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEESSHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEEChHH
Confidence            3666664 689999999998873              45689999999999999997765 43    355554

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=91.57  E-value=0.34  Score=36.34  Aligned_cols=55  Identities=11%  Similarity=0.079  Sum_probs=41.3

Q ss_pred             HHHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcch
Q 032244           60 SMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSG  128 (144)
Q Consensus        60 SilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G  128 (144)
                      .+|-.|..+  +++.+..++..+|-              |...+|++|++|.++|||+...  .||-+|+..-
T Consensus        16 r~l~~La~~~~~~~s~~~IA~~~~i--------------s~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p   74 (162)
T 3k69_A           16 HSILYLDAHRDSKVASRELAQSLHL--------------NPVMIRNILSVLHKHGYLTGTVGKNGGYQLDLAL   74 (162)
T ss_dssp             HHHHHHHTTTTSCBCHHHHHHHHTS--------------CGGGTHHHHHHHHHTTSSEEECSTTCEEECCSCG
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeecCCCCCeEecCCh
Confidence            344444433  47899999998885              3468999999999999998665  5688887654

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=91.38  E-value=0.18  Score=37.84  Aligned_cols=46  Identities=20%  Similarity=0.141  Sum_probs=36.0

Q ss_pred             CCCchhhHHHHHHHHHhCCcceecC--C--CC-----ceeCcchHhhHHHHHHHH
Q 032244           94 SKSSGSVARHILHQLQDTNIIELDS--K--GG-----RRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        94 ~~asg~iiR~~LqqLE~~glv~k~~--~--gG-----R~lT~~G~~~lD~iA~~i  139 (144)
                      ..-+-+.|-.+|+.||+.|||+...  .  +|     -.||++|++.|.....+.
T Consensus        74 ~~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~  128 (148)
T 2zfw_A           74 YRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLW  128 (148)
T ss_dssp             EECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESSSSCSTTHHHHHHH
T ss_pred             CCCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            3456678999999999999998653  1  24     479999999988876654

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

Probab=91.38  E-value=0.37  Score=32.56  Aligned_cols=45  Identities=13%  Similarity=0.194  Sum_probs=39.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      .|+..|--+|.+.|..|...|+              -|-.-||.-|..||+.|+|++.+
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~--------------VS~~TIRrdL~~Le~~G~l~R~~   50 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLN--------------TPQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTT--------------CCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEec
Confidence            3677777789999999999887              46789999999999999999883

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=91.37  E-value=0.33  Score=38.89  Aligned_cols=58  Identities=19%  Similarity=0.218  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      -|+..||..|--. +++++..|...-|-.|              +-+..+|+.|++.|||++++++...|++.
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            4788899888875 4799999999888544              46889999999999999998655777765

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=91.21  E-value=0.41  Score=32.85  Aligned_cols=59  Identities=17%  Similarity=0.164  Sum_probs=44.3

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-CceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-GRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-GR~lT~~G~~~lD~  134 (144)
                      ||..|+- ++..+..+....|-              |.+-+.+.|+.||+.|+|....++ +..+|..|...+..
T Consensus        37 il~~L~~-~~~s~~ela~~l~i--------------s~stvsr~l~~Le~~Glv~~~~~~r~~~~~~~~~~~~~~   96 (119)
T 2lkp_A           37 ILTQLRN-GPLPVTDLAEAIGM--------------EQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQL   96 (119)
T ss_dssp             HHHHHHH-CCCCHHHHHHHHSS--------------CHHHHHHHHHHHHHHCSEEEEEETTEEEEEESCHHHHHH
T ss_pred             HHHHHHH-CCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEecCCEEEEEEchHHHHHH
Confidence            6666664 78999999998874              446899999999999999876542 34577777655443

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=90.91  E-value=0.75  Score=36.84  Aligned_cols=60  Identities=28%  Similarity=0.369  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+..|+.--..|-      + ....|+..||              -|..-+|.+|++|++.|+|+..+..|-.+++
T Consensus        30 ~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   95 (272)
T 3eet_A           30 AYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYG--------------VSDTVALEARKVLMAEGLVEGRSGSGTYVRE   95 (272)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTSBCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEECCC--EEECC
T ss_pred             HHHHHHHHHHHHHHcCCCCCcCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceEEEec
Confidence            56777777777666653      3 6788999999              4668999999999999999998866766665


Q ss_pred             c
Q 032244          127 S  127 (144)
Q Consensus       127 ~  127 (144)
                      .
T Consensus        96 ~   96 (272)
T 3eet_A           96 R   96 (272)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=90.78  E-value=0.14  Score=36.55  Aligned_cols=67  Identities=10%  Similarity=0.129  Sum_probs=42.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGG-----RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gG-----R~lT~~G~~~l  132 (144)
                      ||--|. .+|.---.|.+.....-. +     +  -+-+.|-.+|+.||+.|||+...   .+|     -.||++|++.|
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-KRPMHGYELQKSMFETTG-Q-----A--LPQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFL   89 (117)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHHHHHS-C-----C--CCTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHHHHhC-C-----C--CCcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHH
Confidence            454443 566655555555542211 0     1  13378999999999999998553   223     35999999999


Q ss_pred             HHHH
Q 032244          133 DQVA  136 (144)
Q Consensus       133 D~iA  136 (144)
                      .+..
T Consensus        90 ~~~~   93 (117)
T 3elk_A           90 CDHS   93 (117)
T ss_dssp             HHTS
T ss_pred             HHHH
Confidence            8753

>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=90.74  E-value=0.46  Score=37.91  Aligned_cols=65  Identities=8%  Similarity=0.049  Sum_probs=47.6

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCce----eCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRR----ITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~----lT~~G~~~l  132 (144)
                      ||..||-.  +++.+..|....+-.             ++.+ =.+|+.||+.|||++.  +.+.|.    ||++|+..+
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-------------QSDL-VQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (250)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSSSC-------------GGGT-HHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCC-------------HhhH-HHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHH
Confidence            67778874  478899998865532             3333 4689999999999865  444553    899999988


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +.+...+
T Consensus       105 ~~~~~~~  111 (250)
T 1p4x_A          105 AERVTLF  111 (250)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876654

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=90.17  E-value=0.69  Score=34.74  Aligned_cols=46  Identities=15%  Similarity=0.228  Sum_probs=37.8

Q ss_pred             CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcch
Q 032244           69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSG  128 (144)
Q Consensus        69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G  128 (144)
                      +++.+..++..+|-              |-..+|++|++|.++|||+...  .||-.|+..-
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            47899999998874              4579999999999999998655  5688887654

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=90.15  E-value=0.3  Score=37.20  Aligned_cols=61  Identities=20%  Similarity=0.191  Sum_probs=43.5

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC------CCCc-----eeCcc
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS------KGGR-----RITSS  127 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~------~gGR-----~lT~~  127 (144)
                      ||..|.-+  +...+..|....             -.=|-+-|+.-|+.|+++|+|++..      ..||     .||++
T Consensus        34 IL~~Ll~~p~~~~ta~eL~~~l-------------~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~  100 (151)
T 3u1d_A           34 VLHQILAQPDGVLSVEELLYRN-------------PDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGE  100 (151)
T ss_dssp             HHHHHHHSTTSCBCHHHHHHHC-------------TTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHhc-------------CCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHH
Confidence            55555444  235677775432             1246789999999999999999652      1244     89999


Q ss_pred             hHhhHHH
Q 032244          128 GQRDLDQ  134 (144)
Q Consensus       128 G~~~lD~  134 (144)
                      |+..|+.
T Consensus       101 Gr~~l~~  107 (151)
T 3u1d_A          101 GIALLRA  107 (151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999987

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=90.04  E-value=0.18  Score=38.94  Aligned_cols=44  Identities=25%  Similarity=0.259  Sum_probs=36.8

Q ss_pred             hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cCC--CCceeCcchHh
Q 032244           73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSK--GGRRITSSGQR  130 (144)
Q Consensus        73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~~--gGR~lT~~G~~  130 (144)
                      -..|+..||              -|..-+|.+|+.||..|||+.  .+.  .|-.+++-...
T Consensus        31 E~~La~~lg--------------VSRtpVREAL~~L~~~GlV~~~~~~~~~~G~~V~~~~~~   78 (239)
T 2di3_A           31 ERALSETLG--------------VSRSSLREALRVLEALGTISTATGSGPRSGTIITAAPGQ   78 (239)
T ss_dssp             HHHHHHHHT--------------CCHHHHHHHHHHHHHHTSEECCSTTSGGGCCEECCCCCS
T ss_pred             HHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEeecccCCCCCceeeCCcch
Confidence            458999998              467899999999999999998  887  78888776554

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=90.04  E-value=0.63  Score=36.69  Aligned_cols=59  Identities=3%  Similarity=-0.002  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcch
Q 032244           56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSG  128 (144)
Q Consensus        56 ~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G  128 (144)
                      -|+..||+.|.- .+++++..|....|-              +.+-+..+|+.||+.|||++++++...|+++.
T Consensus        23 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~kstv~r~l~tL~~~G~v~~~~~~~Y~lg~~~   82 (260)
T 2o0y_A           23 TRVIDLLELFDAAHPTRSLKELVEGTKL--------------PKTTVVRLVATMCARSVLTSRADGSYSLGPEM   82 (260)
T ss_dssp             HHHHHHHTTCBTTBSSBCHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECHHH
T ss_pred             HHHHHHHHHHhhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEECCCCeEEecHHH
Confidence            477788876653 468999999998884              34688899999999999999886556777654

>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=89.81  E-value=0.81  Score=34.83  Aligned_cols=59  Identities=10%  Similarity=0.133  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           55 YIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        55 y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      |-.++..||..-+.|.      + .-..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++.
T Consensus         9 ~~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~g--------------VSR~tVReAL~~L~~eGlv~~~~g~G~~V~~~   74 (239)
T 1hw1_A            9 AGFAEEYIIESIWNNRFPPGTILPAERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNNF   74 (239)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTEEEEECCH
T ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEecCCCcEeeCc
Confidence            4455555665555542      4 5678999998              36789999999999999999988768778753

>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=89.80  E-value=0.89  Score=35.54  Aligned_cols=60  Identities=17%  Similarity=0.228  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+..||.--..|.      + ....|+..||              -|..-+|.+|+.|++.|+|+..+..|-.+++
T Consensus        10 ~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   75 (236)
T 3edp_A           10 LFEVIASKIKDSINRDEYKTGMLMPNETALQEIYS--------------SSRTTIRRAVDLLVEEGLVVRKNGVGLYVQP   75 (236)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCC--CCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEECCceEEEcc
Confidence            35666777776666542      3 6778999888              4668999999999999999998866877766


Q ss_pred             c
Q 032244          127 S  127 (144)
Q Consensus       127 ~  127 (144)
                      .
T Consensus        76 ~   76 (236)
T 3edp_A           76 K   76 (236)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=89.78  E-value=0.22  Score=39.06  Aligned_cols=65  Identities=17%  Similarity=0.172  Sum_probs=47.8

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhHHHHHHH
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGG-----RRITSSGQRDLDQVAGR  138 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gG-----R~lT~~G~~~lD~iA~~  138 (144)
                      .+|.---.|.+.+...-      .++...|-+-|-.+|+.||+.|||+...   .+|     -.||++|+..|.+...+
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            56766667777776432      2355677788999999999999998543   233     36999999999876654

>3kfw_X Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.50A {Mycobacterium tuberculosis}

Probab=89.73  E-value=1  Score=36.33  Aligned_cols=72  Identities=10%  Similarity=0.041  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHh---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244           57 RAASMARKIYLR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD  133 (144)
Q Consensus        57 RaASilRklYl~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD  133 (144)
                      +|-|++=-|++-   +.+.++.|-...+           ---=|...+|.+|--|-+.||++.... |..||+.|++.++
T Consensus         4 ~arSlIlsll~g~~g~~i~~~~Li~l~~-----------~~Gi~e~avRtAlsRL~~~G~L~~~~~-GY~LT~~~~~~~~   71 (247)
T 3kfw_X            4 TARSVVLSVLLGAHPAWATASELIQLTA-----------DFGIKETTLRVALTRMVGAGDLVRSAD-GYRLSDRLLARQR   71 (247)
T ss_dssp             CHHHHHHHHHTTTTTSCBCHHHHHHHHT-----------TTTCCHHHHHHHHHHHHHTTSEEEETT-EEEECHHHHHHHH
T ss_pred             CCceeeEeeecCCCCCcccHHHHHHHHH-----------HcCCChHHHHHHHHHHHHcCCeeccCC-ceeeCHHHHHHHH
Confidence            566777666542   4688888887776           222355789999999999999998776 7999999999888


Q ss_pred             HHHHHHh
Q 032244          134 QVAGRIA  140 (144)
Q Consensus       134 ~iA~~i~  140 (144)
                      +....|.
T Consensus        72 ~~~~rI~   78 (247)
T 3kfw_X           72 RQDEAMR   78 (247)
T ss_dssp             HHHHHHS
T ss_pred             HHHHHhc
Confidence            7776664

>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=89.65  E-value=1  Score=31.47  Aligned_cols=67  Identities=18%  Similarity=0.171  Sum_probs=50.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC------CCCceeCc------c
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS------KGGRRITS------S  127 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~------~gGR~lT~------~  127 (144)
                      .||+.|.-++++....|...+|-              |.+-++..|+.||+.|+|+...      +-|..+|.      .
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            47777777889999999999873              5678999999999999997432      22666655      4


Q ss_pred             hHhhHHHHHHHHhh
Q 032244          128 GQRDLDQVAGRIAV  141 (144)
Q Consensus       128 G~~~lD~iA~~i~~  141 (144)
                      + ..++.++..+.+
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 467888777643

>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=89.58  E-value=1.5  Score=32.04  Aligned_cols=77  Identities=13%  Similarity=0.083  Sum_probs=56.7

Q ss_pred             HHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCC--------CCchhhHHHHHHHHHhCCcceecCCC----C-ceeC
Q 032244           60 SMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFS--------KSSGSVARHILHQLQDTNIIELDSKG----G-RRIT  125 (144)
Q Consensus        60 SilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~--------~asg~iiR~~LqqLE~~glv~k~~~g----G-R~lT  125 (144)
                      .+|..||- .+..|++.+-.+.=|+++.-++-.|..        .=+-.-+|.++.||...|+++.+...    + =.||
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            35666664 678999999999999887665442111        12334799999999999999876532    2 7899


Q ss_pred             cchHhhHHHHH
Q 032244          126 SSGQRDLDQVA  136 (144)
Q Consensus       126 ~~G~~~lD~iA  136 (144)
                      ++|+..|..--
T Consensus       100 ~~g~~vL~~~~  110 (134)
T 3aaf_A          100 KKGRNWLHKAN  110 (134)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHhCCc
Confidence            99999987643

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

Probab=89.41  E-value=0.52  Score=32.71  Aligned_cols=45  Identities=9%  Similarity=0.144  Sum_probs=39.1

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      .|+.-|--+|.+.|..|...||              -|-.-||.-|..||+.|+|.+..
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l~--------------VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARLQ--------------TPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHTT--------------CCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEe
Confidence            3677777789999999999888              46689999999999999999873

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

Probab=89.01  E-value=1.3  Score=31.33  Aligned_cols=58  Identities=9%  Similarity=0.068  Sum_probs=43.6

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc------eeCcchH
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR------RITSSGQ  129 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR------~lT~~G~  129 (144)
                      ||..|+- .+++.+..|....+..  ++        =+.+-+-.+|+.||+.|||+..++ ||      .||++|.
T Consensus        14 vL~~L~~~~~~~t~~el~~~l~~~--~~--------~~~~Tvt~~l~rLe~kGlv~r~~~-~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A           14 VMDHLWSRTEPQTVRQVHEALSAR--RD--------LAYTTVMAVLQRLAKKNLVLQIRD-DRAHRYAPVHGRDEL   78 (138)
T ss_dssp             HHHHHHTCSSCEEHHHHHHHHTTT--CC--------CCHHHHHHHHHHHHHTTSEEEEC----CCEEEESSCHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHhcc--CC--------CCHHHHHHHHHHHHHCCCEEEEec-CCeEEEEeCCCHHHH
Confidence            6888887 5999999999999843  11        245678899999999999998876 44      2677774

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=88.91  E-value=1.5  Score=34.26  Aligned_cols=60  Identities=15%  Similarity=0.213  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      .|...+..|+.--..|.      + ....|+..||-              |..-+|.+|++|++.|+|+..+..|-.+++
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            46677776666555542      3 67899999983              567999999999999999988876877765


Q ss_pred             c
Q 032244          127 S  127 (144)
Q Consensus       127 ~  127 (144)
                      .
T Consensus        77 ~   77 (243)
T 2wv0_A           77 P   77 (243)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=88.54  E-value=0.99  Score=34.57  Aligned_cols=66  Identities=14%  Similarity=0.250  Sum_probs=49.5

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc-------------ee
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR-------------RI  124 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR-------------~l  124 (144)
                      .||+.|. ++++.+..|....|-              |.+-++..|+.||+.|+|+..  ...|+             .|
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            4788887 899999999998873              456899999999999999876  22243             36


Q ss_pred             CcchH-hhHHHHHHHHh
Q 032244          125 TSSGQ-RDLDQVAGRIA  140 (144)
Q Consensus       125 T~~G~-~~lD~iA~~i~  140 (144)
                      |.+|. ..++.++..+.
T Consensus        89 ~~~~~~~~~~~~~~~~~  105 (192)
T 1uly_A           89 NLYLGDEELRYIARSRL  105 (192)
T ss_dssp             CSCSSCHHHHHHHHHHH
T ss_pred             ecCCchhHHHHHHHHHH
Confidence            77773 45666666543

>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=88.48  E-value=0.32  Score=38.51  Aligned_cols=58  Identities=16%  Similarity=0.271  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCceeCcc
Q 032244           56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGRRITSS  127 (144)
Q Consensus        56 ~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR~lT~~  127 (144)
                      -|+..||+.|-- .+++++..|...-|-              +.+-+..+|+.|++.|||++++. +...|+++
T Consensus         6 ~Ral~IL~~l~~~~~~lsl~eia~~lgl--------------~ksT~~RlL~tL~~~G~v~~~~~~~~Y~lG~~   65 (260)
T 3r4k_A            6 SKALTLLTYFNHGRLEIGLSDLTRLSGM--------------NKATVYRLMSELQEAGFVEQVEGARSYRLGPQ   65 (260)
T ss_dssp             HHHHHHHTTCBTTBSEEEHHHHHHHHCS--------------CHHHHHHHHHHHHHTTSEEECSSSSEEEECTT
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEcCCCCcEEcCHH
Confidence            378889988875 478999999998884              34789999999999999999986 45566664

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

Probab=88.25  E-value=1.1  Score=28.78  Aligned_cols=46  Identities=9%  Similarity=0.096  Sum_probs=37.5

Q ss_pred             HHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           60 SMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        60 SilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      .||..|--. +++++..|....|-              |.+.+.++|+.||+.|+|+..++
T Consensus        14 ~IL~~L~~~~~~~s~~eLA~~lgl--------------sr~tv~~~l~~L~~~G~I~~~~~   60 (67)
T 2heo_A           14 KILQVLSDDGGPVAIFQLVKKCQV--------------PKKTLNQVLYRLKKEDRVSSPSP   60 (67)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHCS--------------CHHHHHHHHHHHHHTTSEEEEET
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEecCCC
Confidence            467666555 58999999999984              35789999999999999987555

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=87.07  E-value=0.78  Score=36.04  Aligned_cols=58  Identities=19%  Similarity=0.126  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcch
Q 032244           56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSG  128 (144)
Q Consensus        56 ~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G  128 (144)
                      -|+..||+.|.- .+++++..|.+..|-              +.+-+..+|+.|++.|||+++. +...|+++.
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~~stv~r~l~~L~~~G~v~~~~-~~Y~Lg~~~   72 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGL--------------SRPAVRRILLTLQKLGYVAGSG-GRWSLTPRV   72 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECGGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCC-CEEEEcHHH
Confidence            377778877754 368999999998884              3468889999999999999874 466788765

>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=86.87  E-value=0.68  Score=29.91  Aligned_cols=51  Identities=12%  Similarity=0.204  Sum_probs=40.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      ||.-|+-.+++.+..|....+-.  .        .-+.+-+..+|+.||+.|||+.... ||
T Consensus        14 vL~~L~~~~~~t~~ei~~~l~~~--~--------~~s~~Tv~~~l~rL~~kGlv~r~~~-gr   64 (82)
T 1p6r_A           14 VMKVIWKHSSINTNEVIKELSKT--S--------TWSPKTIQTMLLRLIKKGALNHHKE-GR   64 (82)
T ss_dssp             HHHHHHTSSSEEHHHHHHHHHHH--S--------CCCHHHHHHHHHHHHHTTSEEEEEE-TT
T ss_pred             HHHHHHcCCCCCHHHHHHHHhhc--C--------CccHHHHHHHHHHHHHCCCeEEEec-CC
Confidence            67777778999999999998732  1        1255789999999999999998775 44

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

Probab=86.87  E-value=0.75  Score=32.05  Aligned_cols=51  Identities=18%  Similarity=0.232  Sum_probs=40.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR  122 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR  122 (144)
                      ||+-|+-.+++.+..|....+..          ..-+.+-+..+|+.||+.|||++.+. ||
T Consensus        40 VL~~L~~~~~~t~~eL~~~l~~~----------~~~s~sTVt~~L~rLe~KGlV~R~~~-gR   90 (99)
T 2k4b_A           40 VMRVIWSLGEARVDEIYAQIPQE----------LEWSLATVKTLLGRLVKKEMLSTEKE-GR   90 (99)
T ss_dssp             HHHHHHHHSCEEHHHHHHTCCGG----------GCCCHHHHHHHHHHHHHTTSCEEEEE-TT
T ss_pred             HHHHHHhCCCCCHHHHHHHHhcc----------cCCCHhhHHHHHHHHHHCCCEEEEeC-CC
Confidence            67778889999999999987632          11345778999999999999998775 55

>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=86.19  E-value=0.82  Score=36.89  Aligned_cols=53  Identities=19%  Similarity=0.362  Sum_probs=41.3

Q ss_pred             HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHH-HHHhCCcceecCCCCceeCcchHhhH
Q 032244           65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILH-QLQDTNIIELDSKGGRRITSSGQRDL  132 (144)
Q Consensus        65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~Lq-qLE~~glv~k~~~gGR~lT~~G~~~l  132 (144)
                      .|-.+|+|+..++..+|-..              .-++.+.. .|..+|+|+..++ ||++|++|-+.|
T Consensus       271 ~~~~~~~~~~~l~~~~~~~~--------------~t~~~~~~~~l~~~g~i~~~~~-gr~~~~~~~~~~  324 (334)
T 1in4_A          271 IYRGGPVGLNALAASLGVEA--------------DTLSEVYEPYLLQAGFLARTPR-GRIVTEKAYKHL  324 (334)
T ss_dssp             HSTTCCBCHHHHHHHHTSCH--------------HHHHHHTHHHHHHTTSEEEETT-EEEECHHHHHHT
T ss_pred             HhCCCcchHHHHHHHhCCCc--------------chHHHHHHHHHHHcCCeecccc-cHHhhHHHHHHh
Confidence            34357899999999888432              23555555 8999999999998 999999998776

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=86.07  E-value=1.4  Score=35.62  Aligned_cols=50  Identities=14%  Similarity=0.184  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce-ecC
Q 032244           55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE-LDS  118 (144)
Q Consensus        55 y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~-k~~  118 (144)
                      -.|-+..+-.+|-.+++++..|.+.+|-              |..-||+-|+.||+.|+|+ +..
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            4577777888899999999999999984              6789999999999999998 554

>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=85.64  E-value=1.9  Score=30.55  Aligned_cols=68  Identities=6%  Similarity=0.040  Sum_probs=51.0

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec-----C-CCCce------eCcc
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-----S-KGGRR------ITSS  127 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~-----~-~gGR~------lT~~  127 (144)
                      .||+.|--++++.+..|....|-              |.+-++..|+.||+.|+|+..     + +-|+.      ++..
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            47777777889999999998883              557899999999999999862     1 22544      3545


Q ss_pred             h-HhhHHHHHHHHhh
Q 032244          128 G-QRDLDQVAGRIAV  141 (144)
Q Consensus       128 G-~~~lD~iA~~i~~  141 (144)
                      + ...+++++..+.+
T Consensus        73 ~~~~~~~~~~~~l~~   87 (150)
T 2pn6_A           73 YGKNYHVELGNKLAQ   87 (150)
T ss_dssp             CCTTHHHHHHHHHHT
T ss_pred             CChhHHHHHHHHHhc
Confidence            4 5678888877754

>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, STRU genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum}

Probab=85.52  E-value=0.21  Score=38.66  Aligned_cols=37  Identities=19%  Similarity=0.303  Sum_probs=27.5

Q ss_pred             HHHHHHhCCcceecC-CCC------ceeCcchHhhHHHHHHHHh
Q 032244          104 ILHQLQDTNIIELDS-KGG------RRITSSGQRDLDQVAGRIA  140 (144)
Q Consensus       104 ~LqqLE~~glv~k~~-~gG------R~lT~~G~~~lD~iA~~i~  140 (144)
                      +|.+||+.|||+... .+|      -.||++|+..+.+.-.+.+
T Consensus        54 ~l~~Le~~GlI~~~~~~~~rpektvY~ITe~Gr~~l~~~l~~~~   97 (180)
T 2rkh_A           54 SIELLRYEGLVEAVDDGQGMEDDAMLAISAAGRRELHSLLTARL   97 (180)
T ss_dssp             CTHHHHHTTSEECCC--------CEEEECHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHCCCeeeeecCCCCCccceeeeCHHHHHHHHHHHHHHh
Confidence            788999999997666 444      3799999999987655443

>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=85.45  E-value=0.71  Score=33.45  Aligned_cols=56  Identities=11%  Similarity=0.137  Sum_probs=39.9

Q ss_pred             HHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchH
Q 032244           59 ASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQ  129 (144)
Q Consensus        59 ASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~  129 (144)
                      -.+|..|..+ +. .+..++..++-              |-..++++|++|.++|||+... .||-.|+..-.
T Consensus        12 l~~L~~La~~~~~-s~~~IA~~~~i--------------~~~~l~kIl~~L~~aGlv~s~rG~GGy~Lar~p~   69 (145)
T 1xd7_A           12 IHILSLISMDEKT-SSEIIADSVNT--------------NPVVVRRMISLLKKADILTSRAGVPGASLKKDPA   69 (145)
T ss_dssp             HHHHHHHHTCSCC-CHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEECCSSSSSCEESSCGG
T ss_pred             HHHHHHHHhCCCC-CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEeecCCCCceecCCHH
Confidence            3445444443 23 67778887764              5579999999999999998654 67888876543

>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=85.45  E-value=1.7  Score=33.76  Aligned_cols=58  Identities=16%  Similarity=0.076  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHHhC------CC-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           55 YIRAASMARKIYLRG------GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        55 y~RaASilRklYl~g------~~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      |...+..|+.--..|      .+ ....|+..||-              |..-+|.+|++|+..|+|+..+..|-.+++
T Consensus         7 ~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~v--------------Sr~tvr~Al~~L~~~g~i~~~~g~G~~V~~   71 (239)
T 3bwg_A            7 YQQIATEIETYIEEHQLQQGDKLPVLETLMAQFEV--------------SKSTITKSLELLEQKGAIFQVRGSGIFVRK   71 (239)
T ss_dssp             -CHHHHHHHHHHHHTTCCTTCBCCCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEeCCceEEEec
Confidence            334555555444443      23 67789998883              668999999999999999988866765554

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

Probab=84.21  E-value=3.9  Score=28.60  Aligned_cols=45  Identities=7%  Similarity=0.185  Sum_probs=37.4

Q ss_pred             HHHHHHHHhCC--CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244           60 SMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS  118 (144)
Q Consensus        60 SilRklYl~g~--~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~  118 (144)
                      .|+..|+-.++  +.+..|....|              -|.+-+...|+.||+.|+|++..
T Consensus        30 ~il~~L~~~~~~~~t~~eLa~~l~--------------~s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           30 NVMKSFLNEPDRWIDTDALSKSLK--------------LDVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHSTTCCEEHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEeeC
Confidence            47777777665  99999999887              26788999999999999998753

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=83.38  E-value=1.5  Score=36.07  Aligned_cols=56  Identities=11%  Similarity=0.189  Sum_probs=47.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~  134 (144)
                      ++|.|  ++|..+..|...+|-.              -..++..|++|.++|+++...  |-++|+.+...|.+
T Consensus        48 ll~~L--~~~~t~~eLa~~~g~~--------------~~~v~~~L~~l~~~gll~~~~--~~~lt~~~~~~l~~  103 (373)
T 2qm3_A           48 VLSAV--LASDDIWRIVDLSEEP--------------LPLVVAILESLNELGYVTFED--GVKLTEKGEELVAE  103 (373)
T ss_dssp             HHHHH--HHCSCHHHHHHHHTSC--------------HHHHHHHHHHHHHTTSEECSS--SSEECHHHHHHHHH
T ss_pred             HHHHh--cCCCCHHHHHHHhCCC--------------hHHHHHHHHHHhhCCcEEECC--CEEECHHHHHHHHh
Confidence            68888  7899999999988743              358999999999999998754  58999998877765

>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=83.23  E-value=5.2  Score=28.45  Aligned_cols=68  Identities=10%  Similarity=0.167  Sum_probs=51.6

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee-----cC-CCCce------eCcc
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL-----DS-KGGRR------ITSS  127 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k-----~~-~gGR~------lT~~  127 (144)
                      .||+.|.-++.+.+..|....|-              |.+-++..|+.||+.|+|..     ++ +-|+.      ++-.
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            57888888899999999998883              56789999999999999985     22 23654      3444


Q ss_pred             hHhhHHHHHHHHhh
Q 032244          128 GQRDLDQVAGRIAV  141 (144)
Q Consensus       128 G~~~lD~iA~~i~~  141 (144)
                      +...+++++..+.+
T Consensus        78 ~~~~~~~~~~~l~~   91 (152)
T 2cg4_A           78 SAKDYPSALAKLES   91 (152)
T ss_dssp             SGGGHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHhC
Confidence            44567888887754

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

Probab=82.87  E-value=8.4  Score=28.44  Aligned_cols=68  Identities=12%  Similarity=0.182  Sum_probs=51.9

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec-----C-CCCc-------eeCc
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD-----S-KGGR-------RITS  126 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~-----~-~gGR-------~lT~  126 (144)
                      .||+.|.-++.+.+..|.+..|-              |.+-++..|+.||+.|+|+..     + +-|+       .+++
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            47888888899999999998883              557899999999999999742     2 2254       3455


Q ss_pred             c-----hHhhHHHHHHHHhh
Q 032244          127 S-----GQRDLDQVAGRIAV  141 (144)
Q Consensus       127 ~-----G~~~lD~iA~~i~~  141 (144)
                      .     ....+|+++..+.+
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     55578888887653

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=82.29  E-value=0.96  Score=35.72  Aligned_cols=57  Identities=16%  Similarity=0.135  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244           56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS  127 (144)
Q Consensus        56 ~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~  127 (144)
                      -|+..||..|.- .+++++..|....|-              +.+-+..+|+.|++.|||+++. +...|++.
T Consensus        21 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~~stv~r~l~tL~~~G~v~~~~-~~Y~Lg~~   78 (265)
T 2ia2_A           21 ARGLAVIRCFDHRNQRRTLSDVARATDL--------------TRATARRFLLTLVELGYVATDG-SAFWLTPR   78 (265)
T ss_dssp             HHHHHHHHTCCSSCSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEESS-SEEEECGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEecC-CEEEEcHH
Confidence            477778876653 468999999998884              3468889999999999999874 45567664

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=82.19  E-value=3.2  Score=32.85  Aligned_cols=98  Identities=14%  Similarity=0.267  Sum_probs=72.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCCCcchhcc-cCCC--------------ccCCCCCCchHHH-----HHHHHHHHHHHhCC
Q 032244           11 SPHEFVKAYAAHLKRSGKIELPTWNDIVK-TGTL--------------KELAPYDPDWYYI-----RAASMARKIYLRGG   70 (144)
Q Consensus        11 ~~~~fI~~~A~~LK~~gki~~P~w~d~vK-Tg~~--------------kE~~P~d~DW~y~-----RaASilRklYl~g~   70 (144)
                      ..+.+.+.+...|++.| +.||.+.|+.. +|..              ..+-+.++|-||.     .++.+++.+.-+|+
T Consensus       138 ~~~~~~~~i~~~~~~~g-~~pp~~~dl~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~~~~~~~~~~~~~~~l~~~~~~~~  216 (258)
T 1lva_A          138 TQKKLLKDLEDKYRVSR-WQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGP  216 (258)
T ss_dssp             HHHHHHHHHHHHHHHHT-TSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBEEEHHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHHHHHHHCC-CCCCCHHHHHhHhCCCHHHHHHHHHHHHHCCCEEEecCCeEEcHHHHHHHHHHHHHHHhcCC
Confidence            56678888888887655 99998888775 4432              2366777887764     45666666555578


Q ss_pred             CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244           71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI  124 (144)
Q Consensus        71 ~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l  124 (144)
                      +.|..+|...|.              |.+.+=-+|.-|.+.|+.....+ .|+|
T Consensus       217 it~a~~Rd~lg~--------------SRK~aIplLE~~Dr~g~TrR~gd-~Rvl  255 (258)
T 1lva_A          217 FGLAEARDALGS--------------SRKYVLPLLEYLDQVKFTRRVGD-KRVV  255 (258)
T ss_dssp             BCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETT-EEEE
T ss_pred             cCHHHHHHHhCC--------------cHHHHHHHHHHHhhcCceeeeCC-EEee
Confidence            999999999985              55666788999999999987764 5655

---

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	144
d2v7fa1	149	a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococ	2e-68

>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 =  201 bits (513), Expect = 2e-68
 Identities = 52/134 (38%), Positives = 69/134 (51%)

Query: 7   VKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIY 66
           V DV     V+  A  LK   +I+ P W   VKTG  KE  P   DW+Y R AS+ R++Y
Sbjct: 3   VYDVPGDLLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVY 62

Query: 67  LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126
           L G +G+   R  YGG K  G  P  F K+ GS+ R  L QL+    +E     GR IT 
Sbjct: 63  LDGPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITP 122

Query: 127 SGQRDLDQVAGRIA 140
            G+  LD++A  + 
Sbjct: 123 KGRSFLDKIATELK 136

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	144
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	100.0
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	97.61
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	97.11
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.89
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.88
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.87
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.86
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	96.81
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	96.67
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.59
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	96.54
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	96.35
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	96.31
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.27
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.23
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.21
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.2
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	96.07
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	95.98
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	95.91
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	95.81
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	95.47
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.41
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.37
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	95.25
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.15
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	95.07
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	95.05
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	95.03
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	94.81
d1ixsb1	76	Holliday junction helicase RuvB {Thermus thermophi	94.54
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.13
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	93.97
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	93.83
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	93.78
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	93.77
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	92.58
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.48
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	92.22
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.12
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	92.07
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	92.07
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	91.93
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	91.53
d2axla1	144	Werner syndrome ATP-dependent helicase WRN {Human	91.21
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	89.48
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	88.98
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	87.76
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	86.91
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	86.75
d1olta_	441	Oxygen-independent coproporphyrinogen III oxidase	86.6
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	85.44
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	84.0
d2fnaa1	73	Hypothetical protein SSO1545, C-terminal domain {S	82.6
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	81.84
d1bjaa_	95	Transcription factor MotA, activation domain {Bact	81.59
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	81.3
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	81.08
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	80.66

>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=4.9e-75  Score=448.56  Aligned_cols=138  Identities=38%  Similarity=0.632  Sum_probs=125.4

Q ss_pred             CceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCC
Q 032244            5 KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK   84 (144)
Q Consensus         5 ~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k   84 (144)
                      .||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|++.|||+|
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            49999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244           85 RNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV  142 (144)
Q Consensus        85 ~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~  142 (144)
                      |||++|+||++|||+|||+||||||++|||++++++||+||++||++||+||.+|.+.
T Consensus        81 ~rG~~P~h~~~~Sg~iiR~~LQqLE~~glVek~~~~GR~lT~~G~~~LD~iA~~v~~~  138 (149)
T d2v7fa1          81 NRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKE  138 (149)
T ss_dssp             --CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCCccHHHHHHHHHHHhCCCeeEcCCCCcEECHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999889999999999999999999753

>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=97.61  E-value=0.00012  Score=49.83  Aligned_cols=56  Identities=18%  Similarity=0.165  Sum_probs=46.0

Q ss_pred             HHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q 032244           64 KIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQRD  131 (144)
Q Consensus        64 klYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~~  131 (144)
                      ..|+.  -|+|...+.+.||-            .-|.+-||+.|++||+.|||++.. .+||..|.+|-+.
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            45664  49999999998773            236789999999999999999754 5699999999754

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=97.11  E-value=0.00053  Score=45.06  Aligned_cols=60  Identities=23%  Similarity=0.370  Sum_probs=50.5

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      +++-+++ +.|+|=..|+..-|-.-              .++|.-+.-|-+.|+|+..+. |-.||++|++.|+++
T Consensus         7 vl~~l~ll~qPiGRr~La~~L~l~E--------------r~vRte~~~Lk~~gLI~~~~~-Gm~lTe~G~~~l~~L   67 (69)
T d2p8ta1           7 VLAVIFLLKEPLGRKQISERLELGE--------------GSVRTLLRKLSHLDIIRSKQR-GHFLTLKGKEIRDKL   67 (69)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHHTCCH--------------HHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHHcCCcH--------------HHHHHHHHHHHHCCCeeeeCC-CCEECHhHHHHHHHH
Confidence            4555664 89999999999887544              499999999999999998885 999999999999875

>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=96.89  E-value=0.00081  Score=44.60  Aligned_cols=66  Identities=8%  Similarity=0.102  Sum_probs=52.2

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG----R~lT~~G~~~lD  133 (144)
                      +||..|+-+|++.++.|+...|-              +.+-+-..|..||+.|||+...  .++    -.||++|+..+.
T Consensus        20 ~IL~~L~~~~~~~~~eLa~~l~i--------------s~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~   85 (100)
T d1ub9a_          20 GIMIFLLPRRKAPFSQIQKVLDL--------------TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAK   85 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHhccCCCeeHHHHHHHHhh--------------ccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHH
Confidence            48999999999999999998774              3356777799999999998654  223    259999999888


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus        86 ~~~~~~   91 (100)
T d1ub9a_          86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765543

>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=96.88  E-value=0.0019  Score=44.84  Aligned_cols=65  Identities=18%  Similarity=0.248  Sum_probs=53.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+-.+|+.++.|.+..+-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++.
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            7888999999999999998874              4567889999999999998554  4466    699999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +-..+
T Consensus       106 ~~~~~  110 (143)
T d1s3ja_         106 VLAGR  110 (143)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

>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=96.87  E-value=0.0013  Score=45.98  Aligned_cols=64  Identities=14%  Similarity=0.207  Sum_probs=51.9

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.+..|.+.-+-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++.
T Consensus        41 vL~~l~~~~~~t~~~la~~l~~--------------~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          41 VLKLIDEQRGLNLQDLGRQMCR--------------DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHSSTTCBHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCc--------------cHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            6777888888999999997664              4468889999999999998654  4465    589999999888


Q ss_pred             HHHH
Q 032244          135 VAGR  138 (144)
Q Consensus       135 iA~~  138 (144)
                      +...
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=96.86  E-value=0.0014  Score=45.47  Aligned_cols=65  Identities=22%  Similarity=0.363  Sum_probs=53.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+-.|++.+..|+..-|-.              .+-+-.+++.||+.|||++..  +++|    .||++|+..+++
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            78889999999999999988743              356889999999999998664  4455    589999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +....
T Consensus       101 ~~~~~  105 (139)
T d2a61a1         101 VIERR  105 (139)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            86543

>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=96.81  E-value=0.003  Score=43.76  Aligned_cols=64  Identities=13%  Similarity=0.110  Sum_probs=53.1

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+-++++.++.|+..-+-              +.+-+-.+++.||+.|||++.  +.++|    .||++|+..+++
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            6888999999999999998774              446788899999999999864  45566    699999999988


Q ss_pred             HHHH
Q 032244          135 VAGR  138 (144)
Q Consensus       135 iA~~  138 (144)
                      +...
T Consensus       105 ~~~~  108 (138)
T d1jgsa_         105 CHQL  108 (138)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7543

>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=96.67  E-value=0.0027  Score=43.34  Aligned_cols=66  Identities=6%  Similarity=0.094  Sum_probs=52.4

Q ss_pred             HHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||.+||..+  ++.+..|++..+              -+.+-+=.+++.||+.|||++.+  +++|    .||++|++.+
T Consensus        38 vL~~l~~~~~~~~t~~~la~~l~--------------~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  103 (115)
T d2frha1          38 VLTYISENKEKEYYLKDIINHLN--------------YKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKI  103 (115)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSS--------------SHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHC--------------CCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHH
Confidence            677888864  478889999666              34567888999999999998765  4455    4999999999


Q ss_pred             HHHHHHHh
Q 032244          133 DQVAGRIA  140 (144)
Q Consensus       133 D~iA~~i~  140 (144)
                      +.+..++-
T Consensus       104 ~~~~~~~~  111 (115)
T d2frha1         104 ESLLSRVN  111 (115)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887763

>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=96.59  E-value=0.0049  Score=42.43  Aligned_cols=65  Identities=11%  Similarity=0.168  Sum_probs=53.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||-.|+-.|++.++.|+...|-              +.+-+-.++..||+.|||++.+  .++|    .||++|+..+++
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            6888999999999999998774              4467888999999999998654  4454    589999999998


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
T Consensus       103 ~~~~~  107 (140)
T d2etha1         103 ILSNF  107 (140)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

>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=96.54  E-value=0.0023  Score=44.13  Aligned_cols=66  Identities=17%  Similarity=0.190  Sum_probs=53.6

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      ++|..|+-.|++.++.|+...|-              +.+-+=.+++.||+.|||++.+  .++|    .||++|++.++
T Consensus        34 ~vL~~l~~~~~~t~~~la~~~~i--------------~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~   99 (136)
T d2fbia1          34 RVIRILRQQGEMESYQLANQACI--------------LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFV   99 (136)
T ss_dssp             HHHHHHHHHCSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHH
Confidence            47888999999999999997774              3456788999999999998664  4455    47999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      .+-...
T Consensus       100 ~~~~~~  105 (136)
T d2fbia1         100 SMSGDM  105 (136)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.35  E-value=0.0039  Score=42.61  Aligned_cols=66  Identities=9%  Similarity=0.185  Sum_probs=52.5

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      +|..||..  +++.++.|....|-              +.+-+=.+++.||+.|||++..  .++|    .||++|+..+
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            78889874  57888999996553              4456778999999999998654  4466    4899999999


Q ss_pred             HHHHHHHh
Q 032244          133 DQVAGRIA  140 (144)
Q Consensus       133 D~iA~~i~  140 (144)
                      +.+..++-
T Consensus       103 ~~~~~~~~  110 (115)
T d1hsja1         103 QKLISELE  110 (115)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHHHHH
Confidence            99987763

>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=96.31  E-value=0.0067  Score=42.30  Aligned_cols=65  Identities=9%  Similarity=0.112  Sum_probs=53.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+-++++.++.|+...+-              +.+-+-.+++.||+.|||++.+  +++|    .||++|+...++
T Consensus        34 iL~~i~~~~~~t~~~la~~l~i--------------~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          34 YLVRVCENPGIIQEKIAELIKV--------------DRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCc--------------cHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHH
Confidence            6888898999999999998874              4467889999999999998654  4454    589999999988


Q ss_pred             HHHHH
Q 032244          135 VAGRI  139 (144)
Q Consensus       135 iA~~i  139 (144)
                      +...+
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=96.27  E-value=0.014  Score=37.24  Aligned_cols=60  Identities=13%  Similarity=0.021  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244           56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ  129 (144)
Q Consensus        56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~  129 (144)
                      -|+.+||..|.-. +|+++..+.+.-|-              +.+-+..+|+.||+.|||+++++|--.|+++--
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            4889999988875 68999999997663              457899999999999999999876677777654

>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=96.23  E-value=0.0075  Score=41.13  Aligned_cols=65  Identities=9%  Similarity=0.111  Sum_probs=51.2

Q ss_pred             HHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244           61 MARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l  132 (144)
                      ||..||-.+  ++.+..|...-|-              +.+-+-.+++.||+.|||++..  .++|    .||++|+..+
T Consensus        34 vL~~l~~~~~~~it~~ela~~~~~--------------~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~   99 (135)
T d3broa1          34 IIDYLSRNKNKEVLQRDLESEFSI--------------KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLE   99 (135)
T ss_dssp             HHHHHHHTTTSCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCc--------------CHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHH
Confidence            677788764  4889999997764              3456778999999999997553  4453    6999999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .++...+
T Consensus       100 ~~~~~~~  106 (135)
T d3broa1         100 TIILSYM  106 (135)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887654

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.21  E-value=0.0053  Score=40.38  Aligned_cols=71  Identities=23%  Similarity=0.222  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHH---hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCce----eCcc
Q 032244           55 YIRAASMARKIYL---RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRR----ITSS  127 (144)
Q Consensus        55 y~RaASilRklYl---~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~----lT~~  127 (144)
                      |.||-.-++-+.-   ++++.++.|...-|-              +.+-+-.+|+.||+.|||+...+ ||.    ||++
T Consensus         3 ~~~~l~~l~~~~~~~~~~~lt~~eLa~~l~i--------------~~~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~   67 (85)
T d3ctaa1           3 YYRAIKKIKEAAEASNRAYLTSSKLADMLGI--------------SQQSASRIIIDLEKNGYITRTVT-KRGQILNITEK   67 (85)
T ss_dssp             HHHHHHHHHHHTTTSSEEECCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHH
T ss_pred             HHHHHHHHHHhhhccCCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeecc-cccccceECHH
Confidence            3455433433333   247889999997763              44578889999999999998665 553    7999


Q ss_pred             hHhhHHHHHHHHh
Q 032244          128 GQRDLDQVAGRIA  140 (144)
Q Consensus       128 G~~~lD~iA~~i~  140 (144)
                      |+..+.+...++.
T Consensus        68 G~~~l~~~~~~~~   80 (85)
T d3ctaa1          68 GLDVLYTEFADLS   80 (85)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887653

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.20  E-value=0.01  Score=40.48  Aligned_cols=65  Identities=9%  Similarity=0.114  Sum_probs=51.4

Q ss_pred             HHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      +|..|+-.+ ++.++.|....+-.              .+-+-.++..||+.|||++.+  .++|    .||++|+..++
T Consensus        33 iL~~l~~~~~~~t~~~la~~~~~~--------------~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~   98 (137)
T d2fbha1          33 VLLHLARHRDSPTQRELAQSVGVE--------------GPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA   98 (137)
T ss_dssp             HHHHHHHCSSCCBHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHH
Confidence            677777655 68999999988743              356889999999999999776  3344    59999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++....
T Consensus        99 ~~~~~~  104 (137)
T d2fbha1          99 DIEAIA  104 (137)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876653

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.07  E-value=0.0025  Score=44.09  Aligned_cols=61  Identities=11%  Similarity=0.133  Sum_probs=48.8

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+..+++.+..|...-|-              +.+-+=.+++.||+.|||++.+  +++|    .||++|+...++
T Consensus        38 vL~~l~~~~~~t~~~La~~~~i--------------~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  103 (137)
T d1z91a1          38 ALLLLWEHETLTVKKMGEQLYL--------------DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  103 (137)
T ss_dssp             HHHHHHHHSEEEHHHHHHTTTC--------------CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHHHH
Confidence            6778888999999999996553              3345566999999999998654  5577    799999998875


Q ss_pred             H
Q 032244          135 V  135 (144)
Q Consensus       135 i  135 (144)
                      +
T Consensus       104 ~  104 (137)
T d1z91a1         104 A  104 (137)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=95.98  E-value=0.0081  Score=41.27  Aligned_cols=63  Identities=8%  Similarity=0.156  Sum_probs=50.6

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      +|..|+..+++.++.|+..-|-.+              +-+-.+++.||+.|||++..  .++|    .||++|+..+++
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            688899999999999999887433              35788999999999998554  4454    569999998887


Q ss_pred             HHH
Q 032244          135 VAG  137 (144)
Q Consensus       135 iA~  137 (144)
                      +..
T Consensus       105 ~~~  107 (136)
T d2bv6a1         105 LSN  107 (136)
T ss_dssp             HTT
T ss_pred             HHH
Confidence            643

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.91  E-value=0.0032  Score=42.71  Aligned_cols=41  Identities=22%  Similarity=0.323  Sum_probs=34.6

Q ss_pred             CCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244           94 SKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV  135 (144)
Q Consensus        94 ~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i  135 (144)
                      +.=|=..+.+.|+.|++.|+|++... ...||++|+.+|+.+
T Consensus        28 aNLs~~~~~kyl~~L~~~GLI~~~~~-~Y~iT~kG~~~L~~~   68 (90)
T d1r7ja_          28 ANLSYALTGRYIKMLMDLEIIRQEGK-QYMLTKKGEELLEDI   68 (90)
T ss_dssp             HTCCHHHHHHHHHHHHHTTSEEEETT-EEEECHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHCCCeeecCC-EEEECccHHHHHHHH
Confidence            44456788999999999999997664 789999999998875

>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=95.81  E-value=0.02  Score=39.50  Aligned_cols=65  Identities=18%  Similarity=0.222  Sum_probs=50.2

Q ss_pred             HHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      +|..||-. |++.+..|+...|-              +.+-+-.+++.||+.|||++.+  .++|    .||++|+..++
T Consensus        39 vL~~L~~~~g~~t~~~La~~~~~--------------~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~  104 (145)
T d2hr3a1          39 VLGAIDRLGGDVTPSELAAAERM--------------RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLY  104 (145)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHH
Confidence            78888865 57999999998874              3457888999999999999665  3344    58999999998


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++....
T Consensus       105 ~~~~~~  110 (145)
T d2hr3a1         105 GNRAKR  110 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.47  E-value=0.013  Score=40.40  Aligned_cols=66  Identities=9%  Similarity=0.005  Sum_probs=50.8

Q ss_pred             HHHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q 032244           60 SMARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRD  131 (144)
Q Consensus        60 SilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~  131 (144)
                      .||..|+-.+  ++.+..|+...+-              +.+-+-.+++.||+.|||++..  .+.|    .||++|++.
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            3788887763  6788999997663              3456778999999999998764  3355    489999999


Q ss_pred             HHHHHHHH
Q 032244          132 LDQVAGRI  139 (144)
Q Consensus       132 lD~iA~~i  139 (144)
                      +..+...+
T Consensus       104 ~~~~~~~~  111 (125)
T d1p4xa1         104 IAERVTLF  111 (125)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98877654

>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=95.41  E-value=0.016  Score=38.65  Aligned_cols=66  Identities=12%  Similarity=0.152  Sum_probs=50.7

Q ss_pred             HHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC----CC--ceeCcchHhhH
Q 032244           60 SMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK----GG--RRITSSGQRDL  132 (144)
Q Consensus        60 SilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~----gG--R~lT~~G~~~l  132 (144)
                      .||+.|+- .||+.+..|+...|-              +.+-+..+|+.||+.|||++.+.    +|  ..+|..|.+..
T Consensus        25 ~iL~~L~~~~~~~t~~eLa~~~~i--------------~~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~~~~~~~~~   90 (109)
T d2d1ha1          25 AVLLKMVEIEKPITSEELADIFKL--------------SKTTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSISSNIL   90 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEC-------CCEEEEECTTHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCc--------------cHhHHHHHHHHHHHCCCEEEeecCCCCCceeEEEeeCCHHHH
Confidence            47888875 578999999998874              44689999999999999986541    23  36788888877


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      .+|..++
T Consensus        91 ~~i~~~~   97 (109)
T d2d1ha1          91 EKIRNDL   97 (109)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776665

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.37  E-value=0.038  Score=37.62  Aligned_cols=65  Identities=15%  Similarity=0.162  Sum_probs=47.8

Q ss_pred             HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244           61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD  133 (144)
Q Consensus        61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD  133 (144)
                      +|..|+- .+++.++.|....+-.              .+-+-.+++.||+.|||++.+  +++|    .||++|++.++
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            6777875 4568999999988743              334667999999999998554  4454    49999999999


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus       102 ~~~~~~  107 (140)
T d3deua1         102 EMEEVI  107 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>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=95.25  E-value=0.012  Score=38.95  Aligned_cols=57  Identities=18%  Similarity=0.296  Sum_probs=40.9

Q ss_pred             HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244           62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL  132 (144)
Q Consensus        62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l  132 (144)
                      |-+-|--||||+..|+..-|-.+.             .|.=.+===|-+.|+|+++++ ||++|++|.+.|
T Consensus        14 l~~~f~ggPvGl~tlAa~l~e~~~-------------TiEdviEPyLiq~G~i~RTpR-GR~~T~~~~~hl   70 (75)
T d1in4a1          14 IIEIYRGGPVGLNALAASLGVEAD-------------TLSEVYEPYLLQAGFLARTPR-GRIVTEKAYKHL   70 (75)
T ss_dssp             HHHHSTTCCBCHHHHHHHHTSCHH-------------HHHHHTHHHHHHTTSEEEETT-EEEECHHHHHHT
T ss_pred             HHHHhCCCCCcHHHHHHHHcCChh-------------HHHHHhhHHHHHhhHHhhCCc-hHHhHHHHHHHc
Confidence            444455689999999998885432             222222223556999999998 999999998765

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=95.15  E-value=0.033  Score=38.18  Aligned_cols=57  Identities=12%  Similarity=0.165  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244           58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ  129 (144)
Q Consensus        58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~  129 (144)
                      |.-+|=-|..++++....++..+|-              |-.++|++|++|.++|||+...  .||+ |+..-.
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            4445544566789999999998873              5579999999999999998554  6686 876543

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=95.07  E-value=0.02  Score=41.25  Aligned_cols=64  Identities=13%  Similarity=0.162  Sum_probs=50.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ  134 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~  134 (144)
                      ||..|+-.+++.++.|.+.-+-              +.+-+=.+++.||+.|||++.+  .+.|    .||++|+..++.
T Consensus        46 vL~~l~~~~~~t~~~la~~~~l--------------~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          46 ILWIAYQLNGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             HHHHHHHHTSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHhhhccCCCcCHHHHHHHHcC--------------CchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHH
Confidence            6888888999999999997663              3456788999999999999765  3455    589999999988


Q ss_pred             HHHH
Q 032244          135 VAGR  138 (144)
Q Consensus       135 iA~~  138 (144)
                      +-..
T Consensus       112 ~~~~  115 (162)
T d2fxaa1         112 LLEE  115 (162)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>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=95.05  E-value=0.016  Score=39.14  Aligned_cols=47  Identities=17%  Similarity=0.198  Sum_probs=35.8

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELD---SKGGR-----RITSSGQRDLDQVAGRI  139 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~---~~gGR-----~lT~~G~~~lD~iA~~i  139 (144)
                      +..-|-+.|=.+|+.||+.|||+..   ..+||     .||++|++.|.+...+.
T Consensus        37 ~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~~~~~~~   91 (103)
T d1xmaa_          37 LYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKCEEW   91 (103)
T ss_dssp             SCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHHHHH
T ss_pred             eecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            4566778889999999999999743   23453     79999999998876653

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.03  E-value=0.017  Score=41.51  Aligned_cols=65  Identities=14%  Similarity=0.199  Sum_probs=45.1

Q ss_pred             HHHHHHHhCC---CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q 032244           61 MARKIYLRGG---LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRD  131 (144)
Q Consensus        61 ilRklYl~g~---~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~  131 (144)
                      ||..||..++   +.++.|....|-.+              +-+=.+++.||+.|||++..  .++|    .||++|+..
T Consensus        67 vL~~L~~~~~~~~lt~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l  132 (172)
T d2fbka1          67 LLLTLYRSAPPEGLRPTELSALAAISG--------------PSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  132 (172)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSCCS--------------GGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHCcCH--------------hHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHH
Confidence            6777777654   67788888666433              22334688999999999775  3354    599999999


Q ss_pred             HHHHHHHH
Q 032244          132 LDQVAGRI  139 (144)
Q Consensus       132 lD~iA~~i  139 (144)
                      ++++...+
T Consensus       133 ~~~~~~~~  140 (172)
T d2fbka1         133 VTHLLPAH  140 (172)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99876554

>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=94.81  E-value=0.027  Score=38.92  Aligned_cols=65  Identities=9%  Similarity=0.101  Sum_probs=50.1

Q ss_pred             HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhH
Q 032244           61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~l  132 (144)
                      ||-.||..  +++.++.++..-|-              +.+-+-.+++.||+.|||++.  +.++|    .||++|++.+
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            67777764  35778889886663              335678899999999999865  44466    4899999999


Q ss_pred             HHHHHHH
Q 032244          133 DQVAGRI  139 (144)
Q Consensus       133 D~iA~~i  139 (144)
                      +.+..++
T Consensus       104 ~~l~~~~  110 (125)
T d1p4xa2         104 EQLLAQV  110 (125)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988765

>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=94.54  E-value=0.014  Score=38.70  Aligned_cols=53  Identities=15%  Similarity=0.229  Sum_probs=38.6

Q ss_pred             HHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244           66 YLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL  132 (144)
Q Consensus        66 Yl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l  132 (144)
                      |--||||+..|+..-|-.+.             .|.=-+===|-+.|+|+++++ ||++|++|.+-|
T Consensus        18 f~ggPVGl~tlA~~lgE~~~-------------TiEdviEPyLiq~G~i~RTpr-GR~~T~~a~~hL   70 (76)
T d1ixsb1          18 FGGGPVGLATLATALSEDPG-------------TLEEVHEPYLIRQGLLKRTPR-GRVATELAYRHL   70 (76)
T ss_dssp             SCSSCCCSHHHHGGGSSCTT-------------HHHHTSHHHHHHTTSEEECSS-SEEECHHHHHHH
T ss_pred             hCCCCccHHHHHHHHcCChh-------------HHHHHhhHHHHHHhHHhhCCC-hHHhHHHHHHHc
Confidence            34579999999998886554             122212223456899999998 999999998766

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.13  E-value=0.11  Score=34.48  Aligned_cols=67  Identities=19%  Similarity=0.252  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCce--eC-cchHhhHH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRR--IT-SSGQRDLD  133 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~--lT-~~G~~~lD  133 (144)
                      +.|+..|+-+|+..+..+.+.-|-              +.+-+..+|+.||+.|||++.  +++||.  .+ ..+...|+
T Consensus        23 ~~v~~~L~~~g~~t~~eia~~~~i--------------~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l~   88 (109)
T d1sfxa_          23 VRIYSLLLERGGMRVSEIARELDL--------------SARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLK   88 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHhCC--------------CcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHHH
Confidence            457888888999999999998773              446899999999999999864  344542  22 22345666


Q ss_pred             HHHHHH
Q 032244          134 QVAGRI  139 (144)
Q Consensus       134 ~iA~~i  139 (144)
                      ++...+
T Consensus        89 ~~~~~~   94 (109)
T d1sfxa_          89 EFKSSI   94 (109)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            665544

>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=93.97  E-value=0.079  Score=33.04  Aligned_cols=55  Identities=16%  Similarity=0.231  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHhC------CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244           57 RAASMARKIYLRG------GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT  125 (144)
Q Consensus        57 RaASilRklYl~g------~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT  125 (144)
                      +.+..||.--+.|      .+....|+..||-              |...+|.+|+.||..|+|+..+..|-.+.
T Consensus         6 qi~~~l~~~I~~g~~~~G~~l~~~~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~~~G~~V~   66 (69)
T d2hs5a1           6 RVAGILRDAIIDGTFRPGARLSEPDICAALDV--------------SRNTVREAFQILIEDRLVAHELNRGVFVR   66 (69)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTEEEEC
T ss_pred             HHHHHHHHHHHcCCCCCcCccCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEEcCCEEEec
Confidence            4444455444443      2346788998884              66799999999999999999887676664

>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=93.83  E-value=0.06  Score=36.80  Aligned_cols=62  Identities=16%  Similarity=0.255  Sum_probs=48.3

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-C-----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-G-----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-G-----R~lT~~G~~~lD  133 (144)
                      -||+.|+ .|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.... .     ..||+.|++++.
T Consensus        23 ~Il~~L~-~g~~RF~el~~~l~-------------gIS~~~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~~G~~L~p   88 (108)
T d1z7ua1          23 SLMDELF-QGTKRNGELMRALD-------------GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   88 (108)
T ss_dssp             HHHHHHH-HSCBCHHHHHHHST-------------TCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHCc-------------CCChhHHHHHHHHHHHCCcceeeccCCCcceehhhhchhHHHHHH
Confidence            4788886 58888888887542             35778999999999999999986522 2     789999998876


Q ss_pred             HH
Q 032244          134 QV  135 (144)
Q Consensus       134 ~i  135 (144)
                      -+
T Consensus        89 il   90 (108)
T d1z7ua1          89 AL   90 (108)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=93.78  E-value=0.11  Score=34.58  Aligned_cols=63  Identities=10%  Similarity=0.130  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-C-----ceeCcchHhhH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-G-----RRITSSGQRDL  132 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-G-----R~lT~~G~~~l  132 (144)
                      .-|++.| ..|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.... .     ..||+.|++++
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            3478887 478888888877432             36778999999999999999977522 2     78999999987


Q ss_pred             HHH
Q 032244          133 DQV  135 (144)
Q Consensus       133 D~i  135 (144)
                      .-+
T Consensus        80 pil   82 (95)
T d2hzta1          80 GIL   82 (95)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>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=93.77  E-value=0.028  Score=40.33  Aligned_cols=65  Identities=14%  Similarity=0.168  Sum_probs=47.1

Q ss_pred             hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc------eeCcchHhhHHHHHHH
Q 032244           68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR------RITSSGQRDLDQVAGR  138 (144)
Q Consensus        68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR------~lT~~G~~~lD~iA~~  138 (144)
                      .+|.-=-.|++.+..      ...++...|-+-|=..|+.||+.|||+...  .+|+      .||++|+..|.+-..+
T Consensus        12 ~~~~~GYei~~~~~~------~~~~~w~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~~Gr~~l~~wl~~   84 (178)
T d1yg2a_          12 TRDATGYDITKEFSA------SIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWFDQ   84 (178)
T ss_dssp             HCCBCHHHHHHHHTT------GGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHHHHS
T ss_pred             hCCCCHHHHHHHHHH------HhCCccCCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHhc
Confidence            355555557777743      235688899999999999999999998542  2233      7999999999886544

>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=92.58  E-value=0.062  Score=36.60  Aligned_cols=47  Identities=15%  Similarity=0.222  Sum_probs=35.9

Q ss_pred             CCCCchhhHHHHHHHHHhCCcceec--CCCC-----ceeCcchHhhHHHHHHHH
Q 032244           93 FSKSSGSVARHILHQLQDTNIIELD--SKGG-----RRITSSGQRDLDQVAGRI  139 (144)
Q Consensus        93 ~~~asg~iiR~~LqqLE~~glv~k~--~~gG-----R~lT~~G~~~lD~iA~~i  139 (144)
                      ....+-+.|=.+|+.||+.|||+..  +.+|     -.||++|+..|+....++
T Consensus        41 ~~~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~~~~~~~   94 (114)
T d2esha1          41 PGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSL   94 (114)
T ss_dssp             TTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             cccCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            3445556789999999999999743  2334     379999999998877665

>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=92.48  E-value=0.1  Score=32.96  Aligned_cols=50  Identities=26%  Similarity=0.304  Sum_probs=37.1

Q ss_pred             HHHHHHh-C-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244           62 ARKIYLR-G-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI  124 (144)
Q Consensus        62 lRklYl~-g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l  124 (144)
                      ++..|.. | |-++..+...+|           +  .|-+-++..|++||+.|||++.+...|.|
T Consensus        14 I~~~~~~~G~~Ps~rei~~~~g-----------~--~S~stv~~~l~~Le~kG~I~r~~~~~R~i   65 (71)
T d1jhfa1          14 IRDHISQTGMPPTRAEIAQRLG-----------F--RSPNAAEEHLKALARKGVIEIVSGASRGI   65 (71)
T ss_dssp             HHHHHHHHSSCCCHHHHHHHTT-----------C--SSHHHHHHHHHHHHHTTSEEECSSSSSCE
T ss_pred             HHHHHHHhCCCCCHHHHHHHcC-----------C--CCHHHHHHHHHHHHHCcCeecCCCCCcee
Confidence            3344443 3 678888888877           2  36788999999999999999987545544

>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=92.22  E-value=0.16  Score=34.87  Aligned_cols=63  Identities=19%  Similarity=0.196  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CC-----ceeCcchHhhH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GG-----RRITSSGQRDL  132 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gG-----R~lT~~G~~~l  132 (144)
                      .-||+.|+ .|+...+.|.+.-.             .-|.+++=.-|.+||+.|+|++... ..     ..||+.|++++
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            34888875 68888888887543             3566788889999999999997752 22     78999999987


Q ss_pred             HHH
Q 032244          133 DQV  135 (144)
Q Consensus       133 D~i  135 (144)
                      .-+
T Consensus        93 ~il   95 (114)
T d1yyva1          93 DKV   95 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=92.12  E-value=0.36  Score=32.58  Aligned_cols=78  Identities=10%  Similarity=0.111  Sum_probs=60.5

Q ss_pred             chHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCC
Q 032244           12 PHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRP   90 (144)
Q Consensus        12 ~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P   90 (144)
                      ...|++.+++.++.-| +..                         -++.|+-.||+.+ |+.+..|...-|-        
T Consensus         8 ~~~~~~~~~~~~~~~G-l~~-------------------------~~~~i~~~L~~~~~plt~~ela~~l~v--------   53 (151)
T d1ku9a_           8 KKLIIELFSELAKIHG-LNK-------------------------SVGAVYAILYLSDKPLTISDIMEELKI--------   53 (151)
T ss_dssp             HHHHHHHHHHHHHHTT-CCH-------------------------HHHHHHHHHHHCSSCEEHHHHHHHHTC--------
T ss_pred             HHHHHHHHHHHHHHcC-CCH-------------------------HHHHHHHHHHhCCCCcCHHHHHHHhCC--------
Confidence            4678888888888876 221                         5678888999875 7999999998774        


Q ss_pred             CCCCCCchhhHHHHHHHHHhCCcceecCCC--C----ceeCcchH
Q 032244           91 PHFSKSSGSVARHILHQLQDTNIIELDSKG--G----RRITSSGQ  129 (144)
Q Consensus        91 ~h~~~asg~iiR~~LqqLE~~glv~k~~~g--G----R~lT~~G~  129 (144)
                            |.+-+-.+|+.||+.|+|.+....  .    ..+|++|+
T Consensus        54 ------sk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~t~~g~   92 (151)
T d1ku9a_          54 ------SKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSS   92 (151)
T ss_dssp             ------CHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHHH
T ss_pred             ------CcchHHHHHHHHHHCCCEEEEEcCCCCceeEEeCCHHHH
Confidence                  556789999999999999866422  2    36888885

>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=92.07  E-value=0.25  Score=35.04  Aligned_cols=62  Identities=16%  Similarity=0.280  Sum_probs=47.8

Q ss_pred             HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHH
Q 032244           59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-----GRRITSSGQRDLD  133 (144)
Q Consensus        59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-----GR~lT~~G~~~lD  133 (144)
                      .-|||.++ .|+...+.|.+.-|              -|.+++-.=|++||+.|+|++....     -..||++|++++.
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            35888874 68988888888654              4567899999999999999974321     2689999998866


Q ss_pred             HH
Q 032244          134 QV  135 (144)
Q Consensus       134 ~i  135 (144)
                      -+
T Consensus        88 il   89 (142)
T d2f2ea1          88 LL   89 (142)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=92.07  E-value=0.054  Score=34.44  Aligned_cols=43  Identities=14%  Similarity=0.064  Sum_probs=35.9

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcch
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSG  128 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G  128 (144)
                      ....|+..||              -|...+|.+|+.||..|+|+..+..|-.+++.-
T Consensus        24 se~~La~~~~--------------vSr~tvr~Al~~L~~~Gli~~~~g~G~~V~~~~   66 (78)
T d3bwga1          24 VLETLMAQFE--------------VSKSTITKSLELLEQKGAIFQVRGSGIFVRKHK   66 (78)
T ss_dssp             CHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECCCC
T ss_pred             CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEEcCcEEEEccCC
Confidence            5778888888              466899999999999999999987787776543

>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=91.93  E-value=0.23  Score=30.60  Aligned_cols=47  Identities=15%  Similarity=0.140  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD  117 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~  117 (144)
                      ..+.||+.|+-+|++....|.+..|-              |.+-++.++..|++.|+|+..
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            45789999999999999999998884              557899999999999999754

>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=91.53  E-value=0.19  Score=33.74  Aligned_cols=62  Identities=18%  Similarity=0.141  Sum_probs=46.9

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-C-----ceeCcchHhhHH
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-G-----RRITSSGQRDLD  133 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-G-----R~lT~~G~~~lD  133 (144)
                      -|++.|. .|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.... .     ..||+.|++++.
T Consensus        24 ~Il~~L~-~g~~rF~el~~~l~-------------gIs~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~~G~~L~p   89 (102)
T d2fswa1          24 LIIFQIN-RRIIRYGELKRAIP-------------GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVLP   89 (102)
T ss_dssp             HHHHHHT-TSCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTHH
T ss_pred             HHHHHHc-cCCCCHHHHHhhCc-------------ccchhHHHHHHHHHHHCCceeecccCCCCCeehhhhhHhHHHHHH
Confidence            4777775 68888888877432             35667888889999999999987522 2     569999999876


Q ss_pred             HH
Q 032244          134 QV  135 (144)
Q Consensus       134 ~i  135 (144)
                      -+
T Consensus        90 il   91 (102)
T d2fswa1          90 II   91 (102)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=91.21  E-value=0.46  Score=33.30  Aligned_cols=77  Identities=16%  Similarity=0.162  Sum_probs=56.3

Q ss_pred             HHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCC-----CCCCCC---chhhHHHHHHHHHhCCcceecCCCCc-----e
Q 032244           58 AASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRP-----PHFSKS---SGSVARHILHQLQDTNIIELDSKGGR-----R  123 (144)
Q Consensus        58 aASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P-----~h~~~a---sg~iiR~~LqqLE~~glv~k~~~gGR-----~  123 (144)
                      |-.||..|+- .+..|++.+..++-|.++.-.+.     +.|-.|   +-.-++.++.||-..|+++.....|.     .
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            3346666766 57899999999999987764432     223222   33479999999999999976665453     8


Q ss_pred             eCcchHhhHHH
Q 032244          124 ITSSGQRDLDQ  134 (144)
Q Consensus       124 lT~~G~~~lD~  134 (144)
                      ||++|+..|..
T Consensus        95 lt~kg~~~L~g  105 (144)
T d2axla1          95 LTKKGRNWLHK  105 (144)
T ss_dssp             ECHHHHHHHHH
T ss_pred             ECHHHHHHHhc
Confidence            99999999854

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=89.48  E-value=0.16  Score=33.73  Aligned_cols=64  Identities=20%  Similarity=0.319  Sum_probs=48.0

Q ss_pred             CCCCCchHHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244           47 APYDPDWYYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK  119 (144)
Q Consensus        47 ~P~d~DW~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~  119 (144)
                      +|..+-  |...+.-||..-..|.      + ....|+..||-              |...+|.+|+.|+..|||+..+.
T Consensus         5 ~p~~~~--y~qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~v--------------Sr~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1           5 APEGKG--YADVATHFRTLIKSGELAPGDTLPSVADIRAQFGV--------------AAKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             CCSSCC--HHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSS--------------CTTHHHHHTTTTTTSSCCEEETT
T ss_pred             CCCCCH--HHHHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEEecC
Confidence            444444  5566677777666652      4 67889998884              44699999999999999998886


Q ss_pred             CCceeCc
Q 032244          120 GGRRITS  126 (144)
Q Consensus       120 gGR~lT~  126 (144)
                      .|-.+++
T Consensus        69 ~G~~V~~   75 (100)
T d1v4ra1          69 LGTVVEK   75 (100)
T ss_dssp             TEEESCS
T ss_pred             CEEEECC
Confidence            6877775

>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=88.98  E-value=0.55  Score=28.61  Aligned_cols=53  Identities=9%  Similarity=0.027  Sum_probs=40.4

Q ss_pred             HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCc-ceecCCCCceeCc
Q 032244           60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNI-IELDSKGGRRITS  126 (144)
Q Consensus        60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~gl-v~k~~~gGR~lT~  126 (144)
                      .||+-|-=.+.+....|...+|-              |..-||+-++.||+.|+ |+..+..|-+|+.
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~v--------------S~~ti~r~i~~L~~~G~~I~~~~g~GY~L~~   62 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGM--------------SRAAINKHIQTLRDWGVDVFTVPGKGYSLPE   62 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTCCCEEETTTEEECSS
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCcEEEeCCCeEEeCC
Confidence            46666655667999999999985              45689999999999998 5555544777753

>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=87.76  E-value=1.8  Score=29.22  Aligned_cols=57  Identities=12%  Similarity=0.120  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcch
Q 032244           58 AASMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSG  128 (144)
Q Consensus        58 aASilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G  128 (144)
                      |--+|..|..+  .++.+..++..+|-              +-..+|++|++|.++|+|+... .||-.|...-
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i--------------~~~~l~kil~~L~~aGlv~S~rG~GG~~L~~~p   68 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNT--------------NPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDL   68 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEC---CCEEESSCG
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEeecCCCCceecCCH
Confidence            44456555443  36899999997774              4569999999999999998654 4788887543

>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=86.91  E-value=0.33  Score=32.18  Aligned_cols=38  Identities=26%  Similarity=0.356  Sum_probs=29.4

Q ss_pred             CchhhHHHHHHHHHhCCcceec--CCC--CceeCcchHhhHH
Q 032244           96 SSGSVARHILHQLQDTNIIELD--SKG--GRRITSSGQRDLD  133 (144)
Q Consensus        96 asg~iiR~~LqqLE~~glv~k~--~~g--GR~lT~~G~~~lD  133 (144)
                      -.=|.+|..|-||+.+|+++..  ++|  --.||++|+..-+
T Consensus        36 ~PMS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lca   77 (81)
T d2obpa1          36 LPMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAA   77 (81)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHHH
Confidence            3457999999999999999844  442  2479999997644

>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=86.75  E-value=0.19  Score=31.79  Aligned_cols=41  Identities=10%  Similarity=0.267  Sum_probs=34.0

Q ss_pred             chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      ....|+..||-              |..-+|.+|+.|++.|||+..+..|-.++.
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            57778888884              567999999999999999999876766653

>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=86.60  E-value=0.27  Score=40.02  Aligned_cols=67  Identities=12%  Similarity=0.162  Sum_probs=46.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGR  138 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~  138 (144)
                      |+-.|-...++-...+...||-.-.         .-- .-....|++|++.|||+.+.. +=+||++|+-++|.||..
T Consensus       370 vi~~L~~~~~ld~~~~~~~fg~~~~---------~~f-~~~~~~L~~l~~~GLv~~~~~-~l~lT~~Gr~l~~~I~~~  436 (441)
T d1olta_         370 VIKSLICNFRLDYSPIEQQWDLLFA---------DYF-AEDLKLLAPLAKDGLVDVDEK-GIQVTAKGRLLIRNICMC  436 (441)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTCCHH---------HHT-HHHHHHHHHHHHTTSEEECSS-EEEECTTTGGGHHHHHHT
T ss_pred             HHHHHHHhCCcCHHHHHHHHCCCHH---------HHH-HHHHHHHHHHHHCCCEEEECC-EEEECHhHHHHHHHHHHH
Confidence            3333445567777888888873210         001 122357888999999998775 889999999999999863

>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=85.44  E-value=1.1  Score=27.11  Aligned_cols=55  Identities=15%  Similarity=0.079  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCc-ceecCCCCceeCc
Q 032244           57 RAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNI-IELDSKGGRRITS  126 (144)
Q Consensus        57 RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~gl-v~k~~~gGR~lT~  126 (144)
                      |-..|+..|.-. +++.+..|...+|-              |..-||+=++.||+.|+ |+..+ +|-+|.+
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~V--------------S~~TI~rdi~~L~~~G~~I~~~~-gGY~L~~   64 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELSV--------------SRQVIVQDIAYLRSLGYNIVATP-RGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTS--------------CHHHHHHHHHHHHHHTCCCEEET-TEEECCT
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEEeC-CCEEeCC
Confidence            445677777654 57999999999984              44579999999999998 76655 4888764

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.00  E-value=1  Score=27.62  Aligned_cols=47  Identities=15%  Similarity=0.185  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD  117 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~  117 (144)
                      ....|++.|+-+|++.-..|.+.-|=              |..-+..++++|++.|||+..
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            45679999999999999999997773              456799999999999999754

>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=82.60  E-value=0.59  Score=30.24  Aligned_cols=29  Identities=21%  Similarity=0.091  Sum_probs=23.0

Q ss_pred             chhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244           97 SGSVARHILHQLQDTNIIELDSKGGRRITS  126 (144)
Q Consensus        97 sg~iiR~~LqqLE~~glv~k~~~gGR~lT~  126 (144)
                      +.+.+=.+|++|+++|||+|..+ +-.|+.
T Consensus        37 ~d~~ls~lL~nL~k~~~iek~~~-~Y~i~D   65 (73)
T d2fnaa1          37 SDSEIYNYLTQLTKHSWIIKEGE-KYCPSE   65 (73)
T ss_dssp             CHHHHHHHHHHHHHTTSEEESSS-CEEESS
T ss_pred             ChHHHHHHHHHHHHcCceeecCC-eeccCc
Confidence            45677789999999999999765 666663

>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=81.84  E-value=0.75  Score=29.36  Aligned_cols=57  Identities=18%  Similarity=0.196  Sum_probs=45.4

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l  132 (144)
                      |..+| -.||..+..|...-|              .+-..++.+|..|..+|+++.+..+--.+|+.|+-+.
T Consensus        26 ifd~l-~~gp~s~~eLA~~~g--------------~~~~~l~rlLr~l~a~gl~~e~~~~~y~lt~~s~~L~   82 (85)
T d1tw3a1          26 LVDHI-LAGARTVKALAARTD--------------TRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLA   82 (85)
T ss_dssp             HHHHH-HTTCCBHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEETTEEEECTTGGGGS
T ss_pred             cHHHh-ccCCCCHHHHHHHhC--------------cChhHHHHHHHHHHHCCCeEecCCCeEecCHHHHHhh
Confidence            44445 478999999999766              3446899999999999999887776788999987653

>d1bjaa_ a.4.5.9 (A:) Transcription factor MotA, activation domain {Bacteriophage T4 [TaxId: 10665]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor MotA, activation domain
domain: Transcription factor MotA, activation domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=81.59  E-value=2.7  Score=28.09  Aligned_cols=69  Identities=16%  Similarity=0.186  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244           57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA  136 (144)
Q Consensus        57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA  136 (144)
                      .+|+|+-++..+.=+..+..|..             +..-+.++.-+=+--|-+-|||||.-+ |-+.|..|+..|-+.|
T Consensus        17 kta~I~i~iaKk~FiTa~ev~e~-------------~~~~~~avvnSNIGVliKKgliEKSGD-G~v~T~e~~~il~~AA   82 (95)
T d1bjaa_          17 KTATILITIAKKDFITAAEVREV-------------HPDLGNAVVNSNIGVLIKKGLVEKSGD-GLIITGEAQDIISNAA   82 (95)
T ss_dssp             HHHHHHHHHHHSTTBCHHHHHHT-------------CTTSCHHHHHHHHHHHHTTTSEEEETT-EEEECHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHhhchhHHHHHHH-------------hHHhccceeecceeeeeecchhhccCC-ceEeeccHHHHHHHHH
Confidence            68899988887888888888762             223344566666778999999999998 9999999999988877


Q ss_pred             HHH
Q 032244          137 GRI  139 (144)
Q Consensus       137 ~~i  139 (144)
                      .--
T Consensus        83 ~l~   85 (95)
T d1bjaa_          83 TLY   85 (95)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=81.30  E-value=1.4  Score=29.33  Aligned_cols=53  Identities=17%  Similarity=0.263  Sum_probs=38.7

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcch
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSG  128 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G  128 (144)
                      |++.|.-.++..|+.|....|-              |.+-+=+=|+.|+.+|||....+ ||    .|.++.
T Consensus        36 Il~~L~~~~~~~v~ela~~l~~--------------s~s~vS~HL~~L~~aGlv~~~r~-G~~~~Y~l~~~~   92 (108)
T d1u2wa1          36 ITYALCQDEELCVCDIANILGV--------------TIANASHHLRTLYKQGVVNFRKE-GKLALYSLGDEH   92 (108)
T ss_dssp             HHHHHHHSSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEC-----CCEEEESCHH
T ss_pred             HHHHHHhCCCccHHHHHHHHcc--------------ChhHHHHHHHHHHHCCeeEEEEE-CCEEEEEECHHH
Confidence            6666766799999999999884              34566677899999999998776 53    455554

>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=81.08  E-value=1.1  Score=29.21  Aligned_cols=57  Identities=16%  Similarity=0.166  Sum_probs=42.0

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC--ceeCcchHhhH
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG--RRITSSGQRDL  132 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG--R~lT~~G~~~l  132 (144)
                      |.-+| -.||..+..|...-|.              +-..++.+|..|..+|++++++++.  -.+|+.|.-..
T Consensus        32 ifd~L-~~gp~t~~eLA~~~g~--------------~~~~l~rLlr~L~a~gll~~~~d~~~~~~~t~~g~lL~   90 (92)
T d1qzza1          32 LVDHL-LAGADTLAGLADRTDT--------------HPQALSRLVRHLTVVGVLEGGEKQGRPLRPTRLGMLLA   90 (92)
T ss_dssp             HHHHH-HTTCCSHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEECCCC-CCCCEECTTGGGGS
T ss_pred             chHHH-hCCCCCHHHHHHHHCc--------------CchHHHHHHHHHHHCCCeeeecCCCceecccHHHHhcc
Confidence            33344 3689999999997664              3357999999999999999988654  34577776543

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.66  E-value=1.2  Score=31.45  Aligned_cols=42  Identities=12%  Similarity=0.338  Sum_probs=35.5

Q ss_pred             HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec
Q 032244           61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD  117 (144)
Q Consensus        61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~  117 (144)
                      ||+.| ..+|..++.|....|-.              -+-+++-|+.||++|||+..
T Consensus        24 Il~~L-~~~~~s~~ela~~lg~s--------------~~~v~~hl~~L~~~glv~~~   65 (190)
T d1ulya_          24 ILKLL-RNKEMTISQLSEILGKT--------------PQTIYHHIEKLKEAGLVEVK   65 (190)
T ss_dssp             HHHHH-TTCCBCHHHHHHHHTCC--------------HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHH-HhCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEE
Confidence            77766 48999999999998843              36799999999999999754