Psyllid ID: psy5605

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
Protein Sequence
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPTGAV
Secondary Structure (PSIPRED)
cccHHHHHHcccccccccccccHHHHHcccccccccccccHHHHHHHHHHHHHHHcccccccHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccEEEccccccEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccEEEcccccEEEccccHHHHHHHHHHHHHHHHHHcHHHHHHHccEEcccccc
Coil and Loop (DISEMBL)
mvsvsyigfrpsksgkmkvpeWVDIVKSakfkelapydpdwfYTRCAALARHIymrspvgvkTVTKIfggrkrngvcpshfcrssgSVARKALQALEQVNIIeksddggrkitshgrrDMDRIAAQIRVSKKEAALQALAAQgitvvptgav
Flexible Loop (DISEMBL)
mvsvsyigfrpsksgkmkvpeWVDIVKSAkfkelapydpDWFYTRCAALARHIYMRSPVGVKTVTKIfggrkrngvcpSHFCRSSGSVARKALQALEQvniieksddggrkitshgrrdmdRIAAQIRVSKKEAALQAlaaqgitvvptgav
Low Complexity Region (SEG)
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEaalqalaaqGITVVPTGAV
Disordered region (IsUnstruct)
*****************KVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNII*********************************LQALAAQGIT*******
Disordered Region (DISOPRED)
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFG****************GSVARKALQALEQVNIIEKSDD**RKITSHGRRDMDRIAAQIRV**************ITVVP****
Disordered Region (DISEMBL)
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPTGAV
Disordered Region (DISPRO)
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRN*VCPS******GSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPTGAV
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	152	2.2.26 [Sep-21-2011]
P39018	156	40S ribosomal protein S19	yes	N/A	0.822	0.801	0.656	3e-46
Q8ITC3	144	40S ribosomal protein S19	N/A	N/A	0.763	0.805	0.646	3e-44
Q5R8M9	145	40S ribosomal protein S19	yes	N/A	0.796	0.834	0.636	7e-43
P39019	145	40S ribosomal protein S19	yes	N/A	0.796	0.834	0.636	7e-43
Q32PD5	145	40S ribosomal protein S19	yes	N/A	0.796	0.834	0.636	7e-43
P17074	145	40S ribosomal protein S19	yes	N/A	0.796	0.834	0.636	1e-42
Q9CZX8	145	40S ribosomal protein S19	yes	N/A	0.796	0.834	0.636	1e-42
Q94613	149	40S ribosomal protein S19	N/A	N/A	0.756	0.771	0.6	7e-42
Q29308	136	40S ribosomal protein S19	yes	N/A	0.743	0.830	0.654	7e-41
Q90YQ4	147	40S ribosomal protein S19	N/A	N/A	0.802	0.829	0.598	2e-39

>sp|P39018|RS19A_DROME 40S ribosomal protein S19a OS=Drosophila melanogaster GN=RpS19a PE=2 SV=3

 Score =  184 bits (466), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 82/125 (65%), Positives = 104/125 (83%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GK+KVP+ +DIVK+AKFKELAPYDPDWFY RCA++ RH+Y RSP GV ++TKI+GGRK
Sbjct: 24  KTGKLKVPDQMDIVKTAKFKELAPYDPDWFYVRCASILRHLYHRSPAGVGSITKIYGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCR++   ARKALQALE   ++EK  DGGRK++S G+RD+DRIA QI   ++
Sbjct: 84  RNGVHPSHFCRAADGAARKALQALEHARLVEKHPDGGRKLSSIGQRDLDRIANQIVFKQR 143

Query: 133 EAALQ 137
           +AA Q
Sbjct: 144 DAAKQ 148

Drosophila melanogaster (taxid: 7227)

>sp|Q8ITC3|RS19_ARGIR 40S ribosomal protein S19 OS=Argopecten irradians GN=RPS19 PE=2 SV=1

 Score =  176 bits (447), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 75/116 (64%), Positives = 96/116 (82%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGKMK+PEW  I+K +KF EL+PYD DWFYTR A++ RH+Y+RSP GV  +TKI+G RK
Sbjct: 23  KSGKMKIPEWATIIKLSKFNELSPYDEDWFYTRAASICRHLYIRSPAGVGALTKIYGDRK 82

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128
           RNG  PSH+CRSSGSVAR+ LQALE   ++EK  +GGRK+TS G++D+DRIAAQ++
Sbjct: 83  RNGTVPSHYCRSSGSVARRVLQALETQKLVEKDANGGRKLTSQGQKDLDRIAAQVK 138

Aequipecten irradians (taxid: 31199)

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

 Score =  172 bits (436), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct: 84  RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query: 133 E 133
           +
Sbjct: 144 K 144

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

Pongo abelii (taxid: 9601)

>sp|P39019|RS19_HUMAN 40S ribosomal protein S19 OS=Homo sapiens GN=RPS19 PE=1 SV=2

 Score =  172 bits (436), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct: 84  RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query: 133 E 133
           +
Sbjct: 144 K 144

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

Homo sapiens (taxid: 9606)

>sp|Q32PD5|RS19_BOVIN 40S ribosomal protein S19 OS=Bos taurus GN=RPS19 PE=2 SV=3

 Score =  172 bits (436), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct: 84  RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query: 133 E 133
           +
Sbjct: 144 K 144

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

Bos taurus (taxid: 9913)

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

 Score =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct: 84  RNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query: 133 E 133
           +
Sbjct: 144 K 144

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 =  171 bits (433), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct: 84  RNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query: 133 E 133
           +
Sbjct: 144 K 144

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

Mus musculus (taxid: 10090)

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

 Score =  169 bits (428), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 69/115 (60%), Positives = 95/115 (82%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGKMKVPEW D VK+  FKEL+PY+PDW++ R A++ RH+Y+RSP G+ +  KI+GGR+
Sbjct: 23  KSGKMKVPEWTDFVKTGMFKELSPYEPDWYFIRAASICRHLYIRSPAGIGSFEKIYGGRR 82

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQI 127
           R G  PSHFC+++GS++R+ LQ+LE + I+EK  +GGR++TS GRRD+DRIAAQI
Sbjct: 83  RRGTAPSHFCKANGSISRRLLQSLEGLKIVEKDPNGGRRLTSQGRRDLDRIAAQI 137

Mya arenaria (taxid: 6604)

>sp|Q29308|RS19_PIG 40S ribosomal protein S19 (Fragment) OS=Sus scrofa GN=RPS19 PE=2 SV=3

 Score =  166 bits (419), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 74/113 (65%), Positives = 90/113 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEWVD VK A  KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct: 24  KSGKLKVPEWVDTVKLAXHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA 125
           RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA 
Sbjct: 84  RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAG 136

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

Sus scrofa (taxid: 9823)

>sp|Q90YQ4|RS19_ICTPU 40S ribosomal protein S19 OS=Ictalurus punctatus GN=rps19 PE=2 SV=1

 Score =  160 bits (405), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 73/122 (59%), Positives = 94/122 (77%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVP+WVDIVK AK KELAP D +WFY R A+  RH+Y+R  VGV ++ KI+GGRK
Sbjct: 26  KSGKLKVPDWVDIVKLAKHKELAPCDDNWFYIRAASTVRHLYLRGGVGVGSMIKIYGGRK 85

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGVCPSHF   S +VARK LQALE + ++EK  +GGR++T  G RD+DRIA Q+  + K
Sbjct: 86  RNGVCPSHFSVGSKNVARKVLQALEALKMVEKDPNGGRRLTPQGTRDLDRIAGQVAAASK 145

Query: 133 EA 134
           ++
Sbjct: 146 KS 147

Ictalurus punctatus (taxid: 7998)

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	152
332024106	154	40S ribosomal protein S19a [Acromyrmex e	0.822	0.811	0.769	4e-52
307184609	153	40S ribosomal protein S19a [Camponotus f	0.822	0.816	0.761	6e-52
156542773	154	PREDICTED: 40S ribosomal protein S19a-li	0.822	0.811	0.753	6e-52
342356371	153	ribosomal protein S19 [Heliconius melpom	0.835	0.830	0.732	1e-51
112983980	153	ribosomal protein S19 [Bombyx mori] gi|5	0.835	0.830	0.724	1e-51
268306368	153	ribosomal protein S19 [Manduca sexta]	0.835	0.830	0.732	1e-51
48140499	154	PREDICTED: 40S ribosomal protein S19a-li	0.822	0.811	0.761	1e-51
15213826	153	ribosomal protein S19 [Spodoptera frugip	0.822	0.816	0.744	2e-51
307185027	154	40S ribosomal protein S19a [Camponotus f	0.848	0.837	0.738	2e-51
315115381	153	ribosomal protein S19 [Euphydryas aurini	0.835	0.830	0.732	2e-51

>gi|332024106|gb|EGI64322.1| 40S ribosomal protein S19a [Acromyrmex echinatior]

 Score =  209 bits (531), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 97/126 (76%), Positives = 112/126 (88%), Gaps = 1/126 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GKM+VPEWVDIVK+AKFKELAPYDPDW+Y RCAAL RHIY+RSPVGV  VTKIFGGRK
Sbjct: 24  KTGKMRVPEWVDIVKTAKFKELAPYDPDWYYIRCAALVRHIYIRSPVGVGAVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV-SK 131
           RNG  PSHFCRS+GSVARKALQ+LEQ+ +IEK+  GGRK+TS GRRD+DRIAAQ++  SK
Sbjct: 84  RNGTHPSHFCRSAGSVARKALQSLEQLKLIEKAPLGGRKLTSQGRRDLDRIAAQVKAKSK 143

Query: 132 KEAALQ 137
           K+  LQ
Sbjct: 144 KQLKLQ 149

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307184609|gb|EFN70947.1| 40S ribosomal protein S19a [Camponotus floridanus]

 Score =  208 bits (529), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 96/126 (76%), Positives = 112/126 (88%), Gaps = 1/126 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GKM+VPEWVDIVK+AKFKELAPYDPDW+Y RCAAL RHIY+RSP+GV  VTKIFGGRK
Sbjct: 24  KTGKMRVPEWVDIVKTAKFKELAPYDPDWYYIRCAALVRHIYIRSPIGVGAVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV-SK 131
           RNG  PSHFCRS+GSVARKALQ+LEQ+ +IEK+  GGRK+TS GRRD+DRIAAQ++  SK
Sbjct: 84  RNGTHPSHFCRSAGSVARKALQSLEQLKLIEKAPLGGRKLTSQGRRDLDRIAAQVKAKSK 143

Query: 132 KEAALQ 137
           K+  LQ
Sbjct: 144 KQLKLQ 149

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156542773|ref|XP_001602816.1| PREDICTED: 40S ribosomal protein S19a-like [Nasonia vitripennis]

 Score =  208 bits (529), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 95/126 (75%), Positives = 112/126 (88%), Gaps = 1/126 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GKM+VPEW+DIVKSA+FKELAPYDPDW+YTRCAAL RHIY+RSP+GV  VTKIFGGRK
Sbjct: 24  KTGKMRVPEWIDIVKSARFKELAPYDPDWYYTRCAALVRHIYIRSPIGVGAVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV-SK 131
           RNG  PSHFCRS+G VARKALQ+LEQ+ +IEK+  GGRK+TS GRRD+DRIAAQ++  SK
Sbjct: 84  RNGTHPSHFCRSAGGVARKALQSLEQLKLIEKTPVGGRKLTSQGRRDLDRIAAQVKAKSK 143

Query: 132 KEAALQ 137
           K+  LQ
Sbjct: 144 KQLKLQ 149

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|342356371|gb|AEL28844.1| ribosomal protein S19 [Heliconius melpomene cythera]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 93/127 (73%), Positives = 112/127 (88%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K GK+KVPE +D+VK+ +FKELAPYDPDWFY RCAA+ RHIY+RSPVGVKTVTKIFGGRK
Sbjct: 24  KMGKVKVPEHMDLVKTGRFKELAPYDPDWFYVRCAAVLRHIYIRSPVGVKTVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCRSSGS+ARKALQALE + ++EK  DGGR +T+ GRRD+DRIAAQ+R+  K
Sbjct: 84  RNGVTPSHFCRSSGSIARKALQALEALKLVEKIQDGGRILTTQGRRDLDRIAAQVRLKAK 143

Query: 133 EAALQAL 139
           +AA Q++
Sbjct: 144 QAAKQSV 150

Source: Heliconius melpomene cythera

Species: Heliconius melpomene

Genus: Heliconius

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112983980|ref|NP_001037271.1| ribosomal protein S19 [Bombyx mori] gi|54609323|gb|AAV34877.1| ribosomal protein S19 [Bombyx mori]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 92/127 (72%), Positives = 112/127 (88%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GK+KVPE +D+VK+A+FKELAPYDPDWFY RCAA+ RHIY+RSPVGVKTVTKIFGGRK
Sbjct: 24  KTGKVKVPEHMDLVKTARFKELAPYDPDWFYVRCAAILRHIYIRSPVGVKTVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCRSSGS+ARKALQ+LE + ++EK  DGGR +T+ GRRD+DRIAAQ+R+  K
Sbjct: 84  RNGVTPSHFCRSSGSIARKALQSLEALKLVEKVQDGGRILTTQGRRDLDRIAAQVRLKAK 143

Query: 133 EAALQAL 139
           + A Q +
Sbjct: 144 QQAKQQV 150

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|268306368|gb|ACY95305.1| ribosomal protein S19 [Manduca sexta]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 93/127 (73%), Positives = 111/127 (87%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K GK+KVPE +D+VK+A+FKELAPYDPDWFY RCAA+ RHIY+RSPVGVKTVTKIFGGRK
Sbjct: 24  KMGKVKVPEHMDLVKTARFKELAPYDPDWFYVRCAAILRHIYIRSPVGVKTVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCRSSGS+ARKALQALE + ++EK  DGGR +T+ GRRD+DRIAAQ+R+  K
Sbjct: 84  RNGVTPSHFCRSSGSIARKALQALEALKLVEKVQDGGRILTTQGRRDLDRIAAQVRLKAK 143

Query: 133 EAALQAL 139
           + A Q +
Sbjct: 144 QQAKQQV 150

Source: Manduca sexta

Species: Manduca sexta

Genus: Manduca

Family: Sphingidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48140499|ref|XP_393511.1| PREDICTED: 40S ribosomal protein S19a-like [Apis mellifera] gi|110774476|ref|XP_001120315.1| PREDICTED: 40S ribosomal protein S19a isoform 1 [Apis mellifera] gi|328794080|ref|XP_003251983.1| PREDICTED: 40S ribosomal protein S19a isoform 2 [Apis mellifera] gi|328794082|ref|XP_003251984.1| PREDICTED: 40S ribosomal protein S19a isoform 3 [Apis mellifera] gi|380015271|ref|XP_003691630.1| PREDICTED: 40S ribosomal protein S19a-like [Apis florea]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 96/126 (76%), Positives = 111/126 (88%), Gaps = 1/126 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GKM+VPEWVDIVKSA+FKELAPYDPDW+Y RCAAL RHIY+RSP+GV  VTKIFGGRK
Sbjct: 24  KTGKMRVPEWVDIVKSARFKELAPYDPDWYYIRCAALVRHIYIRSPIGVGAVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV-SK 131
           RNG  PSHFCRS+G VARKALQ+LEQ+ +IEKS  GGRK+TS GRRD+DRIAAQ++  SK
Sbjct: 84  RNGTHPSHFCRSAGGVARKALQSLEQLKLIEKSPVGGRKLTSQGRRDLDRIAAQVKAKSK 143

Query: 132 KEAALQ 137
           K+  LQ
Sbjct: 144 KQLKLQ 149

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|15213826|gb|AAK92188.1|AF400216_1 ribosomal protein S19 [Spodoptera frugiperda]

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 93/125 (74%), Positives = 110/125 (88%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GK+KVPE +D+VK+ +FKELAPYDPDWFY RCAA+ RHIY+RSPVGVKTVTKIFGGRK
Sbjct: 24  KTGKVKVPEHMDLVKTGRFKELAPYDPDWFYVRCAAILRHIYIRSPVGVKTVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCRSSGS+ARKALQALE + ++EK  DGGR +T  GRRD+DRIAAQ+R+  K
Sbjct: 84  RNGVTPSHFCRSSGSIARKALQALEALKMVEKVQDGGRILTVQGRRDLDRIAAQVRLKAK 143

Query: 133 EAALQ 137
           +AA Q
Sbjct: 144 QAAKQ 148

Source: Spodoptera frugiperda

Species: Spodoptera frugiperda

Genus: Spodoptera

Family: Noctuidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307185027|gb|EFN71256.1| 40S ribosomal protein S19a [Camponotus floridanus]

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 96/130 (73%), Positives = 112/130 (86%), Gaps = 1/130 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+GKM+VPEWVDIVK+AKFKELAPYDPDW+Y RCAAL RHIY+RSP+GV  VTKIFGGRK
Sbjct: 24  KTGKMRVPEWVDIVKTAKFKELAPYDPDWYYIRCAALVRHIYIRSPIGVGAVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV-SK 131
           RNG  PSHFCRS+G VARKALQ+LEQ+ +IEK+  GGRK+TS GRRD+DRIAAQ++  SK
Sbjct: 84  RNGTHPSHFCRSAGGVARKALQSLEQLKLIEKAPLGGRKLTSQGRRDLDRIAAQVKAKSK 143

Query: 132 KEAALQALAA 141
           K+  LQ   A
Sbjct: 144 KQLKLQETIA 153

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|315115381|gb|ADT80663.1| ribosomal protein S19 [Euphydryas aurinia]

 Score =  206 bits (524), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 93/127 (73%), Positives = 112/127 (88%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K GK+K+PE +D+VK+A+FKELAPYDPDWFY RCAA+ RHIY+RSPVGVKTVTKIFGGRK
Sbjct: 24  KMGKVKLPEHMDLVKTARFKELAPYDPDWFYVRCAAILRHIYIRSPVGVKTVTKIFGGRK 83

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           RNGV PSHFCRSSGS+ARKALQALE + ++EK  DGGR +T  GRRD+DRIAAQ+R+  K
Sbjct: 84  RNGVTPSHFCRSSGSIARKALQALEALKLVEKIPDGGRILTVQGRRDLDRIAAQVRLKAK 143

Query: 133 EAALQAL 139
           +AA Q++
Sbjct: 144 QAAKQSV 150

Source: Euphydryas aurinia

Species: Euphydryas aurinia

Genus: Euphydryas

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

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	152
FB|FBgn0010412	156	RpS19a "Ribosomal protein S19a	0.796	0.775	0.652	8.4e-42
UNIPROTKB|Q32PD5	145	RPS19 "40S ribosomal protein S	0.796	0.834	0.636	1.4e-39
UNIPROTKB|J9P425	153	RPS19 "Uncharacterized protein	0.796	0.790	0.636	1.4e-39
UNIPROTKB|P39019	145	RPS19 "40S ribosomal protein S	0.796	0.834	0.636	1.4e-39
UNIPROTKB|F1RGG1	145	RPS19 "40S ribosomal protein S	0.796	0.834	0.636	1.4e-39
MGI|MGI:1333780	145	Rps19 "ribosomal protein S19"	0.796	0.834	0.636	2.3e-39
RGD|68440	145	Rps19 "ribosomal protein S19"	0.796	0.834	0.636	2.3e-39
RGD|2318347	145	LOC100362339 "ribosomal protei	0.796	0.834	0.636	3.7e-39
RGD|2321315	145	LOC100360843 "ribosomal protei	0.796	0.834	0.628	9.9e-39
RGD|1562153	160	Rps19l1 "ribosomal protein S19	0.796	0.756	0.619	2.1e-38

FB|FBgn0010412 RpS19a "Ribosomal protein S19a" [Drosophila melanogaster (taxid:7227)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 79/121 (65%), Positives = 101/121 (83%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             K+GK+KVP+ +DIVK+AKFKELAPYDPDWFY RCA++ RH+Y RSP GV ++TKI+GGRK
Sbjct:    24 KTGKLKVPDQMDIVKTAKFKELAPYDPDWFYVRCASILRHLYHRSPAGVGSITKIYGGRK 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHFCR++   ARKALQALE   ++EK  DGGRK++S G+RD+DRIA QI   ++
Sbjct:    84 RNGVHPSHFCRAADGAARKALQALEHARLVEKHPDGGRKLSSIGQRDLDRIANQIVFKQR 143

Query:   133 E 133
             +
Sbjct:   144 D 144

GO:0006412 "translation" evidence=ISS;NAS

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

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

GO:0005840 "ribosome" evidence=IDA;NAS

GO:0005811 "lipid particle" evidence=IDA

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

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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 = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    32 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 91

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    92 RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 151

Query:   133 E 133
             +
Sbjct:   152 K 152

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 = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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

UNIPROTKB|F1RGG1 RPS19 "40S ribosomal protein S19" [Sus scrofa (taxid:9823)]

 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

GO:0006412 "translation" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

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

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

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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 = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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 = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 77/121 (63%), Positives = 96/121 (79%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVRPSHFSRGSKSVARRVLQALEGLKMMEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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 = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 76/121 (62%), Positives = 95/121 (78%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVPEWVD VK AK KELAPYD +W YTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    24 KSGKLKVPEWVDTVKLAKHKELAPYDENWLYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 83

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVAR+ LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    84 RNGVRPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 143

Query:   133 E 133
             +
Sbjct:   144 K 144

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

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

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 75/121 (61%), Positives = 95/121 (78%)

Query:    13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
             KSGK+KVP+WVD VK AK KELAPYD +WFYTR A+ ARH+Y+R   GV ++TKI+GGR+
Sbjct:    39 KSGKLKVPKWVDTVKLAKHKELAPYDENWFYTRAASTARHLYLRGGAGVGSMTKIYGGRQ 98

Query:    73 RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             RNGV PSHF R S SVA + LQALE + ++EK  DGGRK+T  G+RD+DRIA Q+  + K
Sbjct:    99 RNGVRPSHFSRGSKSVAHRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANK 158

Query:   133 E 133
             +
Sbjct:   159 K 159

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

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P07281	RS19B_YEAST	No assigned EC number	0.5217	0.75	0.7916	yes	N/A
Q9V0G8	RS19E_PYRAB	No assigned EC number	0.3983	0.7763	0.7866	yes	N/A
Q90YQ4	RS19_ICTPU	No assigned EC number	0.5983	0.8026	0.8299	N/A	N/A
P39019	RS19_HUMAN	No assigned EC number	0.6363	0.7960	0.8344	yes	N/A
P39018	RS19A_DROME	No assigned EC number	0.656	0.8223	0.8012	yes	N/A
P40978	RS19_ORYSJ	No assigned EC number	0.5762	0.7763	0.8082	yes	N/A
Q5R8M9	RS19_PONAB	No assigned EC number	0.6363	0.7960	0.8344	yes	N/A
Q54X51	RS19_DICDI	No assigned EC number	0.4827	0.7565	0.7770	yes	N/A
O28210	RS19E_ARCFU	No assigned EC number	0.3853	0.7105	0.7346	yes	N/A
Q8T5Z4	RS19_BRABE	No assigned EC number	0.5655	0.8026	0.8299	N/A	N/A
Q9LF30	RS192_ARATH	No assigned EC number	0.5478	0.7565	0.8041	yes	N/A
P19952	RS19E_HALMA	No assigned EC number	0.3046	0.8157	0.8104	yes	N/A
Q9HM21	RS19E_THEAC	No assigned EC number	0.2536	0.8881	0.9	yes	N/A
P24494	RS19G_ASCSU	No assigned EC number	0.5238	0.8223	0.8445	N/A	N/A
O27653	RS19E_METTH	No assigned EC number	0.4513	0.7368	0.7724	yes	N/A
P39698	RS19S_ASCSU	No assigned EC number	0.5538	0.8486	0.86	N/A	N/A
P07280	RS19A_YEAST	No assigned EC number	0.5217	0.75	0.7916	yes	N/A
Q9CZX8	RS19_MOUSE	No assigned EC number	0.6363	0.7960	0.8344	yes	N/A
Q29308	RS19_PIG	No assigned EC number	0.6548	0.7434	0.8308	yes	N/A
P58234	RS19A_SCHPO	No assigned EC number	0.5371	0.7960	0.8402	yes	N/A
Q9SGA6	RS191_ARATH	No assigned EC number	0.5555	0.7697	0.8181	yes	N/A
O59041	RS19E_PYRHO	No assigned EC number	0.3983	0.7763	0.7866	yes	N/A
O18650	RS19_CAEEL	No assigned EC number	0.5528	0.7960	0.8287	yes	N/A
Q9YD22	RS19E_AERPE	No assigned EC number	0.3846	0.7631	0.7581	yes	N/A
P17074	RS19_RAT	No assigned EC number	0.6363	0.7960	0.8344	yes	N/A
P27073	RS19_EMENI	No assigned EC number	0.4754	0.7894	0.8108	yes	N/A
Q32PD5	RS19_BOVIN	No assigned EC number	0.6363	0.7960	0.8344	yes	N/A
P54057	RS19E_METJA	No assigned EC number	0.4482	0.7565	0.7770	yes	N/A
P79016	RS19B_SCHPO	No assigned EC number	0.5714	0.7368	0.7832	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	152
pfam01090	140	pfam01090, Ribosomal_S19e, Ribosomal protein S19e	8e-69
COG2238	147	COG2238, RPS19A, Ribosomal protein S19E (S16A) [Tr	1e-47
PRK09333	150	PRK09333, PRK09333, 30S ribosomal protein S19e; Pr	2e-41
PTZ00095	169	PTZ00095, PTZ00095, 40S ribosomal protein S19; Pro	1e-35

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

 Score =  203 bits (520), Expect = 8e-69
 Identities = 67/120 (55%), Positives = 86/120 (71%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           KSGK+KVPEW D VK+   KEL P DPDW+Y R A++ R +Y+R PVGV  + KI+GGRK
Sbjct: 21  KSGKIKVPEWADFVKTGVHKELPPEDPDWWYVRAASILRKLYLRGPVGVGRLRKIYGGRK 80

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
           R GV PSHF + SGS+ RKALQ LE+  ++EK   GGR++T  GR D+DRIAA++     
Sbjct: 81  RRGVRPSHFVKGSGSIIRKALQQLEKAGLVEKDPKGGRRLTPQGRSDLDRIAAEVLKELA 140

Length = 140

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

 Score =  150 bits (382), Expect = 1e-47
 Identities = 54/124 (43%), Positives = 77/124 (62%), Gaps = 1/124 (0%)

Query: 14  SGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKR 73
           +GK+K PEW DIVK+   KE  P   DW+Y R A++ R IY+  PVG++ +   +GGRK 
Sbjct: 23  TGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKN 82

Query: 74  NGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133
            G  P  F + SGS+ RK LQ LE+  ++EK+   GR +T  GR  +DRIA +I+   +E
Sbjct: 83  RGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKT-PKGRVLTPKGRSLLDRIATEIKEELEE 141

Query: 134 AALQ 137
             L+
Sbjct: 142 PELE 145

Length = 147

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

 Score =  134 bits (341), Expect = 2e-41
 Identities = 53/123 (43%), Positives = 74/123 (60%), Gaps = 4/123 (3%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
              ++K PEW   VK+   KE  P   DW+Y R A++ R +Y+  PVGV+ +   +GGRK
Sbjct: 22  NVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRK 81

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             GV P HF + SGS+ RK LQ LE+  ++EK+   GR IT  GR  +D +AA++   KK
Sbjct: 82  NRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTKK-GRVITPKGRSLLDNLAAEV---KK 137

Query: 133 EAA 135
           E A
Sbjct: 138 ELA 140

Length = 150

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

 Score =  121 bits (304), Expect = 1e-35
 Identities = 46/122 (37%), Positives = 72/122 (59%), Gaps = 1/122 (0%)

Query: 15  GKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRN 74
           GK+ VP+  +IVK++  +ELAP +PDW+Y RCAA+ R +Y+R  VG   + K F  +KR 
Sbjct: 48  GKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSKKRR 107

Query: 75  GVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHGRRDMDRIAAQIRVSKKE 133
           G  P+H  R+SG + R   Q LE++ ++E+     GR++T  G    +  A Q+ + K  
Sbjct: 108 GSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIRKFG 167

Query: 134 AA 135
             
Sbjct: 168 KE 169

Length = 169

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
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|consensus	143		100.0
COG2238	147	RPS19A Ribosomal protein S19E (S16A) [Translation,	100.0
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	97.35
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	97.28
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.84
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	96.81
COG3388	101	Predicted transcriptional regulator [Transcription	96.62
COG1420	346	HrcA Transcriptional regulator of heat shock gene	96.58
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	96.56
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.56
COG1725	125	Predicted transcriptional regulators [Transcriptio	96.5
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.2
PRK11050	152	manganese transport regulator MntR; Provisional	96.19
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.07
COG1846	126	MarR Transcriptional regulators [Transcription]	96.02
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.0
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.92
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.9
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	95.84
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	95.72
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.71
PRK10870	176	transcriptional repressor MprA; Provisional	95.66
PRK13777	185	transcriptional regulator Hpr; Provisional	95.36
PRK03911	260	heat-inducible transcription repressor; Provisiona	95.3
PRK03573	144	transcriptional regulator SlyA; Provisional	95.25
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	95.19
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	95.18
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.78
PRK03902	142	manganese transport transcriptional regulator; Pro	94.68
TIGR03338	212	phnR_burk phosphonate utilization associated trans	94.6
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	94.44
COG3432	95	Predicted transcriptional regulator [Transcription	94.02
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	93.93
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	93.88
PF14338	92	Mrr_N: Mrr N-terminal domain	93.72
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	93.69
PRK05638	442	threonine synthase; Validated	93.4
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.24
PF10711	102	DUF2513: Hypothetical protein (DUF2513); InterPro:	93.23
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	92.82
COG1693	325	Repressor of nif and glnA expression [Transcriptio	92.81
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	92.71
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	92.64
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	92.59
PF03551	75	PadR: Transcriptional regulator PadR-like family;	92.53
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	92.24
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.02
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	91.99
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	91.98
COG1802	230	GntR Transcriptional regulators [Transcription]	91.95
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	91.8
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	91.71
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	91.58
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	91.48
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	91.39
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	91.36
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.33
PF09114	96	MotA_activ: Transcription factor MotA, activation	91.29
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	91.23
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	91.13
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	90.5
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	90.15
PRK11014	141	transcriptional repressor NsrR; Provisional	90.04
PRK04984	239	fatty acid metabolism regulator; Provisional	89.92
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	89.87
COG1733	120	Predicted transcriptional regulators [Transcriptio	89.78
COG3355	126	Predicted transcriptional regulator [Transcription	89.53
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	89.51
PF09382	106	RQC: RQC domain; InterPro: IPR018982 This entry re	89.42
PRK11569	274	transcriptional repressor IclR; Provisional	89.3
PRK03837	241	transcriptional regulator NanR; Provisional	89.2
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	89.13
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	89.05
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	88.08
COG1485	367	Predicted ATPase [General function prediction only	88.02
PRK07379	400	coproporphyrinogen III oxidase; Provisional	87.86
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	87.83
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	87.65
PRK14165	217	winged helix-turn-helix domain-containing protein/	87.53
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	87.43
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	87.25
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	87.04
PRK08629	433	coproporphyrinogen III oxidase; Provisional	86.46
COG1695	138	Predicted transcriptional regulators [Transcriptio	86.07
COG2186	241	FadR Transcriptional regulators [Transcription]	85.95
PRK08599	377	coproporphyrinogen III oxidase; Provisional	85.84
PRK09416	135	lstR lineage-specific thermal regulator protein; P	85.78
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	85.53
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	85.06
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	84.96
PRK09057	380	coproporphyrinogen III oxidase; Provisional	84.77
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	84.64
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	84.08
COG1414	246	IclR Transcriptional regulator [Transcription]	83.92
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	83.74
PRK13509	251	transcriptional repressor UlaR; Provisional	83.37
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	83.33
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	83.3
PF13814	191	Replic_Relax: Replication-relaxation	82.77
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	82.64
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	82.21
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	82.21
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	82.03
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	81.68
PRK14999	241	histidine utilization repressor; Provisional	81.58
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	80.64
PRK08208	430	coproporphyrinogen III oxidase; Validated	80.23

>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=3.3e-68  Score=414.20  Aligned_cols=130  Identities=52%  Similarity=0.931  Sum_probs=118.6

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||++|||++|+||
T Consensus        10 ~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~~~DW~Y~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~   89 (139)
T PF01090_consen   10 EFIKALAEFLKKSGKIEPPEWADIVKTGSHKELAPYDPDWWYIRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHF   89 (139)
T ss_dssp             HHHHHHHHHHTCSSTS--TSCGGGTSSSSS-SSTTCHHTHHHHHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE
T ss_pred             HHHHHHHHHHHHcCCcCCcchHHHHhhcccccCCCCCCCeeeeeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK  131 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~  131 (152)
                      ++|||+|||+||||||++|||++++++||+|||+||++||+||.+|++++
T Consensus        90 ~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~~~~  139 (139)
T PF01090_consen   90 VKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVAKEL  139 (139)
T ss_dssp             --CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHHHcC
Confidence            99999999999999999999999998999999999999999999998764

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=8.7e-67  Score=416.87  Aligned_cols=132  Identities=35%  Similarity=0.610  Sum_probs=128.2

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||++|||++|+||
T Consensus        35 ~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h~  114 (169)
T PTZ00095         35 RFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHT  114 (169)
T ss_pred             HHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCcc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRDMDRIAAQIRVSKKE  133 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~LD~iA~~i~~~~~~  133 (152)
                      ++|||+|||+||||||++|||+++++ +||+|||+||++||+||.+|++++..
T Consensus       115 ~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~~l~~  167 (169)
T PTZ00095        115 VRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIRKFG  167 (169)
T ss_pred             cCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999964 89999999999999999999987754

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=100.00  E-value=1.4e-65  Score=403.70  Aligned_cols=132  Identities=38%  Similarity=0.713  Sum_probs=129.1

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+||||++|+||
T Consensus        11 ~~I~~~A~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~   90 (150)
T PRK09333         11 LLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHF   90 (150)
T ss_pred             HHHHHHHHHHHhcCCcCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCcc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA  134 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~  134 (152)
                      ++|||+|||++|||||++|||++++ +||+||++||++||+||.+|++++.+.
T Consensus        91 ~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~iA~~i~~~~~~~  142 (150)
T PRK09333         91 VKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNLAAEVKKELAEE  142 (150)
T ss_pred             ccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999 899999999999999999999988654

>KOG3411|consensus

Probab=100.00  E-value=2.3e-65  Score=396.70  Aligned_cols=129  Identities=60%  Similarity=1.030  Sum_probs=127.0

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .|+++||.|||++|||++|+|+|+||||.+||+||+||||||+|||||+||||+++|+||+.|+++|||+||||++|+||
T Consensus        13 ~f~~a~asfLK~sgkv~vp~~~DivKtg~~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiYGg~krrGvrPsh~   92 (143)
T KOG3411|consen   13 KFTKAYASFLKRSGKVEVPQWVDIVKTGKGKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIYGGSKRRGVRPSHF   92 (143)
T ss_pred             HHHHHHHHHHHhcCCccCcchhhhhhcccCcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHhcccccCCCCChhh
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS  130 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~  130 (152)
                      +.+||+|+|++||+||++||||++++|||+||++||+|||+||++|.++
T Consensus        93 ~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~  141 (143)
T KOG3411|consen   93 CDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE  141 (143)
T ss_pred             hccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999999865

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

Probab=100.00  E-value=1.7e-63  Score=389.16  Aligned_cols=130  Identities=41%  Similarity=0.751  Sum_probs=128.3

Q ss_pred             hHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccC
Q psy5605           3 SVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFC   82 (152)
Q Consensus         3 ~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~   82 (152)
                      +|+++|++||++++|++|+|+||||||.+||+||.|+||||+||||||||||++||+||++|++.|||++|||++|+||+
T Consensus        12 lI~~lA~~LK~~~kv~pP~wa~~vKTG~~kE~~P~~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~   91 (147)
T COG2238          12 LIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFR   91 (147)
T ss_pred             HHHHHHHHHHhcCCcCChhhhhhhhccccccCCCCCCchHHHHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhh
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE  133 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~  133 (152)
                      +|||+|+|++|||||++|||++++ +||+|||+||++||+||.+|++++.+
T Consensus        92 ~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~eel~~  141 (147)
T COG2238          92 KGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKEELEE  141 (147)
T ss_pred             cCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHHHhcc
Confidence            999999999999999999999999 79999999999999999999999876

>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=97.35  E-value=0.00038  Score=50.22  Aligned_cols=57  Identities=32%  Similarity=0.623  Sum_probs=46.6

Q ss_pred             hHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcchHhhHHH
Q psy5605          52 HIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSHGRRDMDR  122 (152)
Q Consensus        52 kiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~G~~~LD~  122 (152)
                      ..|++  .|||-..+....+              -|..-||+.++.||++|||++.  +.+||+-|.+|-+.+++
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            45764  6999999998753              2347899999999999999964  46899999999998864

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=97.28  E-value=0.00045  Score=47.45  Aligned_cols=63  Identities=27%  Similarity=0.400  Sum_probs=50.6

Q ss_pred             HHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605          49 LARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L  120 (152)
                      ||+.|+- .+|+|-..|+....-+   |      ..-|-.-+|.-|..||..|++++.-.+||.||++|...|
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            6777775 4789999999887432   2      234557899999999999999987778999999998764

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.84  E-value=0.0054  Score=49.10  Aligned_cols=60  Identities=18%  Similarity=0.320  Sum_probs=48.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGGR-----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gGR-----~lT~~G~~~  119 (152)
                      +||..|.-.+++.+..|....|-              +.+-+|..|+.||+.|||+..+   ..||     .||++|+..
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            57777777899999999998743              3578999999999999998763   2478     999999875


Q ss_pred             HH
Q psy5605         120 MD  121 (152)
Q Consensus       120 LD  121 (152)
                      +.
T Consensus        71 ~~   72 (203)
T TIGR02702        71 FP   72 (203)
T ss_pred             cc
Confidence            43

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.

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

Probab=96.81  E-value=0.0064  Score=42.31  Aligned_cols=60  Identities=18%  Similarity=0.306  Sum_probs=42.0

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      .||.-+- .++.....+..              .+.=|-+.+...|..|++.|+|++. ++.-.||++|...|+.+
T Consensus        10 ~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l   69 (77)
T PF14947_consen   10 DILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEEL   69 (77)
T ss_dssp             HHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHH
Confidence            4454443 66666665553              2556778999999999999999774 46899999999999988

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=96.62  E-value=0.0078  Score=45.31  Aligned_cols=73  Identities=25%  Similarity=0.371  Sum_probs=60.7

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      |--+++..+-=.+|+|+..|+..-|       .|+|.       +|+.|.=||+.++|.-+. .|-.+|+.+-.++++|-
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-------VRYSLRVLEQENIISPSR-QGAILTDDFPEFIEEII   79 (101)
T ss_pred             HHHHHHHHHHHhCCceeEeechhcC-------Cchhh-------hhhhhhhhhhcCccCccc-cCCccCccHHHHHHHHH
Confidence            5556676666789999999999876       48876       799999999999998777 59999999999999998


Q ss_pred             HHHHHHHH
Q psy5605         125 AQIRVSKK  132 (152)
Q Consensus       125 ~~i~~~~~  132 (152)
                      +++-+-+.
T Consensus        80 ~dl~ei~e   87 (101)
T COG3388          80 GDLSEINE   87 (101)
T ss_pred             HHHHHHHH
Confidence            88754333

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

Probab=96.58  E-value=0.0047  Score=54.70  Aligned_cols=63  Identities=33%  Similarity=0.533  Sum_probs=51.7

Q ss_pred             HHHHHHhhH---hhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHh
Q psy5605          45 RCAALARHI---YMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRR  118 (152)
Q Consensus        45 RaASilRki---Yl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~  118 (152)
                      |-..|||.|   |+.  -|||-..|.+.|+            -.-|..-||+.+++||++|+++|... .||+-|..|-+
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   764  5999999999984            24677899999999999999998764 79999999976


Q ss_pred             h
Q psy5605         119 D  119 (152)
Q Consensus       119 ~  119 (152)
                      .
T Consensus        75 ~   75 (346)
T COG1420          75 Y   75 (346)
T ss_pred             H
Confidence            4

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=96.56  E-value=0.02  Score=43.08  Aligned_cols=65  Identities=14%  Similarity=0.124  Sum_probs=47.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++....|+...|-              +.+-+=.+++.||+.|||++.++  ++|    .||++|+..++
T Consensus        44 ~vL~~l~~~~~~t~~eLa~~l~i--------------~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~  109 (144)
T PRK11512         44 KVLCSIRCAACITPVELKKVLSV--------------DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE  109 (144)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence            35666676777888888887643              33556678899999999997653  455    58999999988


Q ss_pred             HHHHH
Q psy5605         122 RIAAQ  126 (152)
Q Consensus       122 ~iA~~  126 (152)
                      ++...
T Consensus       110 ~~~~~  114 (144)
T PRK11512        110 QCHQL  114 (144)
T ss_pred             HHHHH
Confidence            76443

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.56  E-value=0.029  Score=40.85  Aligned_cols=68  Identities=13%  Similarity=0.141  Sum_probs=52.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|+...|-.              .+-+-.+++.||+.|||+..++  +.|    .||++|++.+++
T Consensus        33 iL~~l~~~~~~t~~ela~~~~~~--------------~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~   98 (118)
T TIGR02337        33 ILRILAEQGSMEFTQLANQACIL--------------RPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS   98 (118)
T ss_pred             HHHHHHHcCCcCHHHHHHHhCCC--------------chhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            66667778888999999887542              2345688999999999997653  344    699999999998


Q ss_pred             HHHHHHHH
Q psy5605         123 IAAQIRVS  130 (152)
Q Consensus       123 iA~~i~~~  130 (152)
                      +.....+.
T Consensus        99 ~~~~~~~~  106 (118)
T TIGR02337        99 LSPQIEEI  106 (118)
T ss_pred             hhHHHHHH
Confidence            87665443

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=96.50  E-value=0.011  Score=45.75  Aligned_cols=60  Identities=20%  Similarity=0.351  Sum_probs=51.3

Q ss_pred             hhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCce
Q psy5605          86 GSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGIT  145 (152)
Q Consensus        86 g~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~  145 (152)
                      -.-+.++.|.||..|+|++....|..+|++++..+|..=.+..++..+.--..+.+.|++
T Consensus        49 pnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~s  108 (125)
T COG1725          49 PNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLS  108 (125)
T ss_pred             HHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            367889999999999999998889999999999888887777777777777777777775

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

Probab=96.20  E-value=0.012  Score=41.02  Aligned_cols=43  Identities=26%  Similarity=0.343  Sum_probs=37.1

Q ss_pred             CchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQ  126 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~  126 (152)
                      -|.+-++.+++.||+.|||++.++++-.||+.|+...+.+...
T Consensus        11 is~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~   53 (96)
T smart00529       11 VSPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRK   53 (96)
T ss_pred             CChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHH
Confidence            3567899999999999999999977999999999988776543

iron dependent repressor

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.19  E-value=0.03  Score=43.37  Aligned_cols=63  Identities=17%  Similarity=0.168  Sum_probs=51.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      |++.++-.+++.+..|...+|              -|.+-+...++.||+.|||...+.+|-.||++|+..+..+..
T Consensus        42 I~~~l~~~~~~t~~eLA~~l~--------------is~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~  104 (152)
T PRK11050         42 IADLIAEVGEARQVDIAARLG--------------VSQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE  104 (152)
T ss_pred             HHHHHHhcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence            445555568888888888873              456789999999999999998877789999999998887663

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.07  E-value=0.052  Score=36.78  Aligned_cols=67  Identities=22%  Similarity=0.342  Sum_probs=51.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC------CceeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG------GRKITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g------GR~lT~~G~~~LD~  122 (152)
                      |+..|+..+++.+..+....+-              |..-+...|+.|++.|||+...++      .-.||++|.+.+..
T Consensus        15 il~~l~~~~~~~~~~la~~~~~--------------s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       15 VLRILYEEGPLSVSELAKRLGV--------------SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCC--------------CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            6777888888999999887631              233477999999999999876542      35699999998888


Q ss_pred             HHHHHHH
Q psy5605         123 IAAQIRV  129 (152)
Q Consensus       123 iA~~i~~  129 (152)
                      +...+..
T Consensus        81 ~~~~~~~   87 (101)
T smart00347       81 LLEARHE   87 (101)
T ss_pred             HHHHHHH
Confidence            7666543

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=96.02  E-value=0.053  Score=37.62  Aligned_cols=65  Identities=23%  Similarity=0.401  Sum_probs=49.5

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      ..++..||..++.+.+.|+...+              -+.+-+=.+++.||+.|||+..++  ++|    .||++|+..+
T Consensus        25 ~~~L~~l~~~~~~~~~~la~~l~--------------i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~   90 (126)
T COG1846          25 YQVLLALYEAGGITVKELAERLG--------------LDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL   90 (126)
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence            45777888888766566766653              344667778999999999996653  455    7999999999


Q ss_pred             HHHHH
Q psy5605         121 DRIAA  125 (152)
Q Consensus       121 D~iA~  125 (152)
                      .++..
T Consensus        91 ~~~~~   95 (126)
T COG1846          91 EQLLP   95 (126)
T ss_pred             HHhcc
Confidence            88776

>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=96.00  E-value=0.013  Score=38.17  Aligned_cols=54  Identities=24%  Similarity=0.421  Sum_probs=38.8

Q ss_pred             HHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcch
Q psy5605          49 LARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHG  116 (152)
Q Consensus        49 ilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G  116 (152)
                      ||+.|+ -.++.....|+...|-              +..-+..++++|++.|||++.++  .+|    .|||+|
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            677888 7789999999998743              44566799999999999986643  455    578877

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.92  E-value=0.033  Score=34.42  Aligned_cols=59  Identities=17%  Similarity=0.280  Sum_probs=43.4

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC---CceeCc-chHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---GRKITS-HGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~-~G~~~LD~  122 (152)
                      |++.++ .+++.+..+...+|              -|.+-++.+|++|++.|+|+...++   .-.+|+ .|...++.
T Consensus         2 il~~l~-~~~~~~~~i~~~l~--------------is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~   64 (66)
T smart00418        2 ILKLLA-EGELCVCELAEILG--------------LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE   64 (66)
T ss_pred             HHHHhh-cCCccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence            566677 88999999999985              3446799999999999999976642   234666 55554443

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.90  E-value=0.11  Score=35.62  Aligned_cols=60  Identities=18%  Similarity=0.273  Sum_probs=48.8

Q ss_pred             HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchH
Q psy5605          44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGR  117 (152)
Q Consensus        44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~  117 (152)
                      -|+-.|+..|.-. +++++..+....|-              +.+-++..|+.|++.|+|+.++. +...|++...
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            3788899988877 79999999999743              56889999999999999998753 4567877544

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

Probab=95.84  E-value=0.014  Score=41.93  Aligned_cols=68  Identities=19%  Similarity=0.277  Sum_probs=45.6

Q ss_pred             chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605          40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD  119 (152)
Q Consensus        40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~  119 (152)
                      |+.=.|.-..+..-|--||+|+..|+..-|--             ...|.=.+=-=|-+.|+|++++ .||++|++|.+-
T Consensus         7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed-------------~~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~   72 (76)
T PF05491_consen    7 DELDRRYLKTLIENFKGGPVGLDTLAAALGED-------------KETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEH   72 (76)
T ss_dssp             BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS--------------HHHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCC-------------HhHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHH
Confidence            45555655667777788999999999876432             2233333334566799999999 599999999876


Q ss_pred             HH
Q psy5605         120 MD  121 (152)
Q Consensus       120 LD  121 (152)
                      |.
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.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=95.72  E-value=0.066  Score=38.93  Aligned_cols=68  Identities=15%  Similarity=0.168  Sum_probs=50.7

Q ss_pred             HHhhHh----hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHh
Q psy5605          49 LARHIY----MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRR  118 (152)
Q Consensus        49 ilRkiY----l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~  118 (152)
                      +|..|+    -.+++....|+..-+-              +.+-+=.++..||+.|||.+.++  +.|    .||++|++
T Consensus        30 vL~~l~~~~~~~~~~t~~eL~~~l~~--------------~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~   95 (109)
T TIGR01889        30 ILYYLGKLENNEGKLTLKEIIKEILI--------------KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS   95 (109)
T ss_pred             HHHHHHhhhccCCcCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence            666666    3467888888887632              33556678899999999997653  344    29999999


Q ss_pred             hHHHHHHHHHHH
Q psy5605         119 DMDRIAAQIRVS  130 (152)
Q Consensus       119 ~LD~iA~~i~~~  130 (152)
                      .++.+-.++-+-
T Consensus        96 ~~~~~~~~~~~~  107 (109)
T TIGR01889        96 KIESLISEIEQI  107 (109)
T ss_pred             HHHHHHHHHHHH
Confidence            999998887543

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.

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

Probab=95.71  E-value=0.04  Score=38.96  Aligned_cols=64  Identities=16%  Similarity=0.276  Sum_probs=49.1

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC------CceeCcchHhhH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG------GRKITSHGRRDM  120 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g------GR~lT~~G~~~L  120 (152)
                      ..|++.++. |+...+.|.+.-             ...|.+++-.-|+.||+.|+|++....      -..||+.|++++
T Consensus         8 ~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~   73 (90)
T PF01638_consen    8 LLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL   73 (90)
T ss_dssp             HHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred             HHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence            568888888 888888888764             246789999999999999999976432      278999999988


Q ss_pred             HHHH
Q psy5605         121 DRIA  124 (152)
Q Consensus       121 D~iA  124 (152)
                      +-+.
T Consensus        74 ~~l~   77 (90)
T PF01638_consen   74 PVLE   77 (90)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

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.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=95.66  E-value=0.093  Score=41.51  Aligned_cols=65  Identities=15%  Similarity=0.220  Sum_probs=45.9

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRK----ITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~----lT~~G~~~L  120 (152)
                      +|..|+-.  +++.+..|+...|-              +.+-+=.+++.||+.|||++.+  +++|.    ||++|+..+
T Consensus        60 iL~~L~~~~~~~it~~eLa~~l~l--------------~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~  125 (176)
T PRK10870         60 ALITLESQENHSIQPSELSCALGS--------------SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL  125 (176)
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            45555532  34566677776642              3356667889999999999765  45777    999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +++-...
T Consensus       126 ~~i~~~~  132 (176)
T PRK10870        126 REVLPPQ  132 (176)
T ss_pred             HHHHHHH
Confidence            9975443

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=95.36  E-value=0.12  Score=41.91  Aligned_cols=66  Identities=17%  Similarity=0.119  Sum_probs=48.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR----~lT~~G~~~LD  121 (152)
                      .||-.||-.+++....|++..+-              ..+-+-.+++.||+.|||+..  ++..|    .||++|+..++
T Consensus        49 ~iL~~L~~~~~itq~eLa~~l~l--------------~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~  114 (185)
T PRK13777         49 HILWIAYHLKGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL  114 (185)
T ss_pred             HHHHHHHhCCCcCHHHHHHHHCC--------------CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            36667788888888999886432              123355689999999999965  43444    39999999999


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       115 ~l~~~~  120 (185)
T PRK13777        115 ETMEEY  120 (185)
T ss_pred             HHHHHH
Confidence            876543

>PRK03911 heat-inducible transcription repressor; Provisional

Probab=95.30  E-value=0.025  Score=48.85  Aligned_cols=64  Identities=17%  Similarity=0.350  Sum_probs=49.9

Q ss_pred             HHHHHhh---Hhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q psy5605          46 CAALARH---IYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD-DGGRKITSHGRRD  119 (152)
Q Consensus        46 aASilRk---iYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~-~gGR~lT~~G~~~  119 (152)
                      --.||+.   -|+.  .|||-..|.+.|+-            .-|.+-||+.++.||++|++++.. ..||.-|.+|-+.
T Consensus         5 ~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr~   72 (260)
T PRK03911          5 KDLLLDSIIQTYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMKN   72 (260)
T ss_pred             HHHHHHHHHHHHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHHH
Confidence            3344443   4664  59999999998853            356689999999999999998765 4799999999864


Q ss_pred             -HH
Q psy5605         120 -MD  121 (152)
Q Consensus       120 -LD  121 (152)
                       +|
T Consensus        73 Yvd   75 (260)
T PRK03911         73 YWQ   75 (260)
T ss_pred             HHH
Confidence             44

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=95.25  E-value=0.17  Score=37.86  Aligned_cols=64  Identities=17%  Similarity=0.187  Sum_probs=44.1

Q ss_pred             HHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          49 LARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      +|..|+-. ++.....|+...|-              +.+-+=.+++.||+.|||++.++  +.|    .||++|+..++
T Consensus        36 vL~~l~~~~~~~t~~eLa~~l~~--------------~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  101 (144)
T PRK03573         36 TLHNIHQLPPEQSQIQLAKAIGI--------------EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS  101 (144)
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCC--------------ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH
Confidence            44455543 34566677766543              23455688999999999997753  455    49999999998


Q ss_pred             HHHHH
Q psy5605         122 RIAAQ  126 (152)
Q Consensus       122 ~iA~~  126 (152)
                      .+...
T Consensus       102 ~~~~~  106 (144)
T PRK03573        102 EVEAV  106 (144)
T ss_pred             HHHHH
Confidence            76544

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=95.19  E-value=0.081  Score=38.23  Aligned_cols=49  Identities=18%  Similarity=0.277  Sum_probs=36.7

Q ss_pred             cCCCchhHHHHHHHHHHhCCcceec--C-CCCc-----eeCcchHhhHHHHHHHHHH
Q psy5605          81 FCRSSGSVARKALQALEQVNIIEKS--D-DGGR-----KITSHGRRDMDRIAAQIRV  129 (152)
Q Consensus        81 ~~~asg~iiR~~LQqLE~~glVek~--~-~gGR-----~lT~~G~~~LD~iA~~i~~  129 (152)
                      +..-+-+-+-.+|..||+.|||+..  + .+||     .||++|+..|+........
T Consensus        34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~~~   90 (100)
T TIGR03433        34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESWAR   90 (100)
T ss_pred             ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHH
Confidence            3344556688899999999999973  2 2232     5999999999998777643

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=95.18  E-value=0.044  Score=47.88  Aligned_cols=58  Identities=31%  Similarity=0.444  Sum_probs=47.2

Q ss_pred             hhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-CceeCcchHhh-HHHH
Q psy5605          54 YMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHGRRD-MDRI  123 (152)
Q Consensus        54 Yl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-GR~lT~~G~~~-LD~i  123 (152)
                      --.+|+|+..|.+.|+-            .-|..-||+-+.+||+.|++++.-.+ ||.-|.+|-+. .|.+
T Consensus        17 ~~~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~   76 (337)
T TIGR00331        17 KTGQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHL   76 (337)
T ss_pred             hcCCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHh
Confidence            34689999999999743            45678999999999999999987654 99999998876 4443

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

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

Probab=94.78  E-value=0.056  Score=38.07  Aligned_cols=62  Identities=19%  Similarity=0.350  Sum_probs=43.0

Q ss_pred             hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC-----ceeCcchHhhHHHHH
Q psy5605          52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG-----RKITSHGRRDMDRIA  124 (152)
Q Consensus        52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG-----R~lT~~G~~~LD~iA  124 (152)
                      -++-.+.+-...|+..-              .-+.+-+.+-|+.||++|+|+..+.  ++     -.||++|+..+++.-
T Consensus         8 ~L~~~~~~~f~~L~~~l--------------~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~   73 (80)
T PF13601_consen    8 LLYANEEATFSELKEEL--------------GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV   73 (80)
T ss_dssp             HHHHHSEEEHHHHHHHT--------------T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred             HHhhcCCCCHHHHHHHh--------------CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence            34445666666666664              4566788899999999999986542  33     269999999988876


Q ss_pred             HHH
Q psy5605         125 AQI  127 (152)
Q Consensus       125 ~~i  127 (152)
                      ..+
T Consensus        74 ~~L   76 (80)
T PF13601_consen   74 AAL   76 (80)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=94.68  E-value=0.16  Score=38.33  Aligned_cols=57  Identities=18%  Similarity=0.209  Sum_probs=43.0

Q ss_pred             HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      +.-.|++-+..|+...|              -|.+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus        17 ~~~~~~~~~~ela~~l~--------------vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~   73 (142)
T PRK03902         17 IEEKGYARVSDIAEALS--------------VHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL   73 (142)
T ss_pred             HhcCCCcCHHHHHHHhC--------------CChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence            33457777777777653              2345677778999999999976667899999999876655

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=94.60  E-value=0.14  Score=40.20  Aligned_cols=65  Identities=15%  Similarity=0.250  Sum_probs=47.9

Q ss_pred             HHHHHHhhHhhcCC------cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          45 RCAALARHIYMRSP------VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        45 RaASilRkiYl~g~------vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      .++..+|..-+.|.      +.-..|+..||              -|.+-+|.+|+.||..|||+..+..|-.+++-...
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            34445555544442      34456788874              57899999999999999999999889888887777


Q ss_pred             hHHHH
Q psy5605         119 DMDRI  123 (152)
Q Consensus       119 ~LD~i  123 (152)
                      ++..+
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.

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=94.44  E-value=0.11  Score=45.56  Aligned_cols=59  Identities=34%  Similarity=0.563  Sum_probs=46.8

Q ss_pred             Hhh--cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhh-HHHH
Q psy5605          53 IYM--RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRD-MDRI  123 (152)
Q Consensus        53 iYl--~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~-LD~i  123 (152)
                      .|+  .+|+|+..|.+.|+=            .-|..-||+-+..||++|++++.-. .||.-|.+|-+. +|.+
T Consensus        18 ~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L   80 (339)
T PRK00082         18 DYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHL   80 (339)
T ss_pred             HHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence            354  589999999988632            3456889999999999999997654 599999999764 4444

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=94.02  E-value=0.083  Score=39.38  Aligned_cols=42  Identities=24%  Similarity=0.359  Sum_probs=34.1

Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDG---GRKITSHGRRDMDRI  123 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~~G~~~LD~i  123 (152)
                      +.=+=.+++++++.|++.|++++.+++   .-.||++|.++|.++
T Consensus        41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y   85 (95)
T COG3432          41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKY   85 (95)
T ss_pred             cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHH
Confidence            444558999999999999998888754   357999999997654

>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=93.93  E-value=0.14  Score=32.70  Aligned_cols=49  Identities=16%  Similarity=0.323  Sum_probs=40.4

Q ss_pred             HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605          44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD  106 (152)
Q Consensus        44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~  106 (152)
                      -|+.+||+.|.-. +++++..+...-|              =+.+-+..+|+.|++.|||++++
T Consensus         3 ~ral~iL~~l~~~~~~~t~~eia~~~g--------------l~~stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    3 ERALRILEALAESGGPLTLSEIARALG--------------LPKSTVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHHHHHCHHCTBSCEEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCcCeecCc
Confidence            4888999988865 4589999999865              34578999999999999999875

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.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=93.88  E-value=0.47  Score=39.28  Aligned_cols=66  Identities=15%  Similarity=0.217  Sum_probs=52.6

Q ss_pred             HHHHHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhhHH
Q psy5605          44 TRCAALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRDMD  121 (152)
Q Consensus        44 iRaASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~LD  121 (152)
                      -|+..||+.|.-.+ ++++..|.+..|              -+.+-+..+|+.|++.|||+++++ +...||++..+.-.
T Consensus        11 ~ral~iL~~l~~~~~~ls~~eia~~lg--------------l~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l~~   76 (263)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELTG--------------LHRTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQLSE   76 (263)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHHHH
Confidence            38889999887654 599999999974              345789999999999999999864 56789988876544


Q ss_pred             HH
Q psy5605         122 RI  123 (152)
Q Consensus       122 ~i  123 (152)
                      .+
T Consensus        77 ~~   78 (263)
T PRK09834         77 GF   78 (263)
T ss_pred             hh
Confidence            43

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=93.72  E-value=0.081  Score=37.58  Aligned_cols=37  Identities=27%  Similarity=0.373  Sum_probs=31.9

Q ss_pred             chhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q psy5605          85 SGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMD  121 (152)
Q Consensus        85 sg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD  121 (152)
                      .-+-++.+++.|.++|+|++...|--.||+.|++.|-
T Consensus        53 ~~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~   89 (92)
T PF14338_consen   53 FKNRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA   89 (92)
T ss_pred             HHHhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence            3457899999999999999877667999999999874

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=93.69  E-value=0.27  Score=39.17  Aligned_cols=50  Identities=24%  Similarity=0.296  Sum_probs=38.6

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      -...|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus        36 ~e~~La~~lg--------------VSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei   85 (221)
T PRK11414         36 ITKNLAEQLG--------------MSITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI   85 (221)
T ss_pred             CHHHHHHHHC--------------CCchhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence            3456778774              5778999999999999999999877877766655555443

>PRK05638 threonine synthase; Validated

Probab=93.40  E-value=0.24  Score=44.22  Aligned_cols=75  Identities=17%  Similarity=0.245  Sum_probs=54.1

Q ss_pred             CcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          31 FKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        31 ~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      +||.-+.++.+.     .||+.|. +++.-+..|.+..+.            .-|.+.++..|+.||+.|||+.....||
T Consensus       363 ~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~  424 (442)
T PRK05638        363 GREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGR  424 (442)
T ss_pred             chhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCC
Confidence            344444555544     4666554 678889999998863            1477899999999999999986422344


Q ss_pred             e----eCcchHhhHHHH
Q psy5605         111 K----ITSHGRRDMDRI  123 (152)
Q Consensus       111 ~----lT~~G~~~LD~i  123 (152)
                      +    ||++|+..+..+
T Consensus       425 ~~~Y~Lt~~g~~~l~~~  441 (442)
T PRK05638        425 RVYYKLTEKGRRLLENL  441 (442)
T ss_pred             cEEEEECcHHHHHHHhc
Confidence            3    999999998764

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.24  E-value=0.33  Score=38.03  Aligned_cols=45  Identities=20%  Similarity=0.304  Sum_probs=34.8

Q ss_pred             CchhHHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKS---DDGGR-----KITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~---~~gGR-----~lT~~G~~~LD~iA~~i~  128 (152)
                      .+-+-+=.+|+.||+.|||+..   ..+||     .||+.|++.|+....+..
T Consensus        55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~  107 (138)
T TIGR02719        55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFE  107 (138)
T ss_pred             CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHH
Confidence            4456677899999999999863   22354     499999999999887753

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).

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

Probab=93.23  E-value=0.16  Score=37.03  Aligned_cols=50  Identities=24%  Similarity=0.291  Sum_probs=40.2

Q ss_pred             CCCccCCCchhHHHHHHHHHHhCCcceecCCC---C------ceeCcchHhhHHHHHHH
Q psy5605          77 CPSHFCRSSGSVARKALQALEQVNIIEKSDDG---G------RKITSHGRRDMDRIAAQ  126 (152)
Q Consensus        77 ~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---G------R~lT~~G~~~LD~iA~~  126 (152)
                      .+..+..-+-.-+-+-+++|.++|+|+-....   |      ..||.+|..+||.|=.+
T Consensus        25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~   83 (102)
T PF10711_consen   25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDD   83 (102)
T ss_pred             chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCc
Confidence            45556667777999999999999999976532   2      48999999999998655

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=92.82  E-value=0.25  Score=40.05  Aligned_cols=45  Identities=24%  Similarity=0.316  Sum_probs=36.2

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      .-..|+..||              -|...+|.+|+.||..|||+..+..|-.+++-...
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            4457777774              58899999999999999999999878777765443

>COG1693 Repressor of nif and glnA expression [Transcription]

Probab=92.81  E-value=0.11  Score=45.94  Aligned_cols=70  Identities=23%  Similarity=0.425  Sum_probs=52.1

Q ss_pred             HHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH--HHH
Q psy5605          49 LARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR--IAA  125 (152)
Q Consensus        49 ilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~--iA~  125 (152)
                      |||=|-=. .|+|-......--   +||+.      =+---+|+=||-||+.|+++|+--.||.||++|-+.|.+  +..
T Consensus        11 Il~il~esd~plgak~Ia~el~---kRGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~~~~~~   81 (325)
T COG1693          11 ILRILAESDEPLGAKIIALELR---KRGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKRALISE   81 (325)
T ss_pred             HHHHHHhcCCccchHHHHHHHH---hcccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhhhhhHH
Confidence            45555543 4888887776652   22543      233468999999999999999988899999999999998  555


Q ss_pred             HH
Q psy5605         126 QI  127 (152)
Q Consensus       126 ~i  127 (152)
                      ++
T Consensus        82 R~   83 (325)
T COG1693          82 RL   83 (325)
T ss_pred             HH
Confidence            54

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=92.71  E-value=0.18  Score=39.75  Aligned_cols=53  Identities=21%  Similarity=0.359  Sum_probs=42.7

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR  122 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~  122 (152)
                      .|++.++.++..-+      +.        .+-+-..|+.|++.|||+..+.+|=.||++|.+..-.
T Consensus        22 ~~~~~~~diA~~L~------Vs--------p~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~   74 (154)
T COG1321          22 KGFARTKDIAERLK------VS--------PPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKE   74 (154)
T ss_pred             cCcccHHHHHHHhC------CC--------cHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHH
Confidence            57788888888752      33        3567788999999999999999999999999865443

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=92.64  E-value=0.48  Score=37.71  Aligned_cols=50  Identities=14%  Similarity=0.232  Sum_probs=39.4

Q ss_pred             cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605          59 VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR  122 (152)
Q Consensus        59 vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~  122 (152)
                      +....|+..||              -|..-+|.+|+.||..|+|+..+..|-.+++-...++..
T Consensus        31 L~e~eLae~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~e   80 (224)
T PRK11534         31 LRMSLLTSRYA--------------LGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLD   80 (224)
T ss_pred             CCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHH
Confidence            34567777774              467899999999999999999998887887766665544

>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=92.59  E-value=0.39  Score=33.30  Aligned_cols=45  Identities=36%  Similarity=0.527  Sum_probs=35.1

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG  116 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G  116 (152)
                      ++.+..++..+|              -+-..+|+++++|++.|+|+..+  .||-.|+..-
T Consensus        25 ~~s~~eiA~~~~--------------i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~   71 (83)
T PF02082_consen   25 PVSSKEIAERLG--------------ISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPP   71 (83)
T ss_dssp             -BEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred             CCCHHHHHHHHC--------------cCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence            488999999874              46689999999999999999665  4788887643

(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.

>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=92.53  E-value=0.1  Score=35.41  Aligned_cols=41  Identities=32%  Similarity=0.475  Sum_probs=32.2

Q ss_pred             cCCCchhHHHHHHHHHHhCCcceecCC---CC-----ceeCcchHhhHH
Q psy5605          81 FCRSSGSVARKALQALEQVNIIEKSDD---GG-----RKITSHGRRDMD  121 (152)
Q Consensus        81 ~~~asg~iiR~~LQqLE~~glVek~~~---gG-----R~lT~~G~~~LD  121 (152)
                      +..-|-+-+=.+|+.||+.|||+....   +|     -.||++|+..|.
T Consensus        26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~   74 (75)
T PF03551_consen   26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR   74 (75)
T ss_dssp             TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred             CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence            345667888999999999999985542   22     469999999876

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 ....

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

Probab=92.24  E-value=0.19  Score=31.91  Aligned_cols=39  Identities=23%  Similarity=0.419  Sum_probs=31.0

Q ss_pred             hhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605          61 VKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT  113 (152)
Q Consensus        61 V~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT  113 (152)
                      +..|+..||              -|..-++++|+.|++.|+|+..++.|-.||
T Consensus        28 ~~~la~~~~--------------is~~~v~~~l~~L~~~G~i~~~~~~~~~l~   66 (66)
T cd07377          28 ERELAEELG--------------VSRTTVREALRELEAEGLVERRPGRGTFVA   66 (66)
T ss_pred             HHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence            667777763              467899999999999999998776666664

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

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

Probab=92.02  E-value=0.49  Score=30.15  Aligned_cols=51  Identities=22%  Similarity=0.359  Sum_probs=40.0

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCce
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRK  111 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~  111 (152)
                      ..+|..||-.|++.+..|....+-              +.+-+-.++++||+.|||++..  +..|.
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            357888999999999999998744              5567778899999999998664  33453

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 ....

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=91.99  E-value=0.48  Score=29.38  Aligned_cols=36  Identities=19%  Similarity=0.356  Sum_probs=28.7

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG  109 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG  109 (152)
                      .+..|+..|              .-|.+-+|.+|++|++.|+|+..+++|
T Consensus        22 s~~~la~~~--------------~vs~~tv~~~l~~L~~~g~i~~~~~~g   57 (60)
T smart00345       22 SERELAAQL--------------GVSRTTVREALSRLEAEGLVQRRPGSG   57 (60)
T ss_pred             CHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            566677776              346789999999999999999877544

>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=91.98  E-value=0.42  Score=31.28  Aligned_cols=47  Identities=23%  Similarity=0.344  Sum_probs=39.3

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      ..|++.|-..+|..++.|....|              -+.+-+.+=|+.||++|+|+....
T Consensus        13 ~~Il~~L~~~~~~t~~ela~~l~--------------~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   13 LRILRLLASNGPMTVSELAEELG--------------ISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHHHCSTBEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEEecc
Confidence            35888887899999999999986              345678899999999999998763

...

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.95  E-value=0.65  Score=37.26  Aligned_cols=64  Identities=16%  Similarity=0.217  Sum_probs=51.7

Q ss_pred             HHHHHHhhHhhcC------CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          45 RCAALARHIYMRS------PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        45 RaASilRkiYl~g------~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      .+...+|.-=+.|      .+....|+..||-              |..-+|.+|+.|+..|+|+..+..|-.+++-..+
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            4445555555544      5778889999964              6678999999999999999999889999999888


Q ss_pred             hHHH
Q psy5605         119 DMDR  122 (152)
Q Consensus       119 ~LD~  122 (152)
                      +++.
T Consensus        86 ~~~e   89 (230)
T COG1802          86 EARE   89 (230)
T ss_pred             HHHH
Confidence            8887

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=91.80  E-value=0.53  Score=37.67  Aligned_cols=55  Identities=22%  Similarity=0.295  Sum_probs=44.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC--CceeCcch
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG--GRKITSHG  116 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g--GR~lT~~G  116 (152)
                      .|+..+.-+|++.+..+....|-              |.+-+++.|+.||+.|||+..++.  .-.||++|
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            67877777789999999999853              456889999999999999988632  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.

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

Probab=91.71  E-value=0.78  Score=30.20  Aligned_cols=37  Identities=24%  Similarity=0.407  Sum_probs=29.7

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      ....|...|              .-|...+|.+|+.|++.|+|+..+..|-
T Consensus        26 s~~~la~~~--------------~vsr~tvr~al~~L~~~g~i~~~~~~G~   62 (64)
T PF00392_consen   26 SERELAERY--------------GVSRTTVREALRRLEAEGLIERRPGRGT   62 (64)
T ss_dssp             -HHHHHHHH--------------TS-HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             CHHHHHHHh--------------ccCCcHHHHHHHHHHHCCcEEEECCceE
Confidence            667788887              4688999999999999999999886553

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 ....

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=91.58  E-value=0.34  Score=38.88  Aligned_cols=42  Identities=14%  Similarity=0.281  Sum_probs=35.5

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      .-..|+..||              -|..-+|.+|+.||..|+|+..+..|-.+++-
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            4557777774              57899999999999999999999888888773

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.

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

Probab=91.48  E-value=1  Score=28.14  Aligned_cols=61  Identities=18%  Similarity=0.271  Sum_probs=45.0

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIA  124 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA  124 (152)
                      .|+..++-.+ +....+.+..|              -+.+-++..|.+|++.|+|.....   .-..+|+ |+..++.+.
T Consensus        11 ~il~~l~~~~-~~~~ei~~~~~--------------i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~   74 (78)
T cd00090          11 RILRLLLEGP-LTVSELAERLG--------------LSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLE   74 (78)
T ss_pred             HHHHHHHHCC-cCHHHHHHHHC--------------cCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHH
Confidence            3565566555 88888888763              345778999999999999986553   2357898 888777654

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.

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=91.39  E-value=0.53  Score=38.35  Aligned_cols=59  Identities=17%  Similarity=0.334  Sum_probs=43.0

Q ss_pred             HHHHHHhhHhhcC------Cc-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchH
Q psy5605          45 RCAALARHIYMRS------PV-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGR  117 (152)
Q Consensus        45 RaASilRkiYl~g------~v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~  117 (152)
                      ..+..+|.-=+.|      .+ ....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++...
T Consensus        13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~   78 (257)
T PRK10225         13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLD--------------VTRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG   78 (257)
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence            4444455554554      24 3567888884              5789999999999999999999977877766543

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=91.36  E-value=1.1  Score=33.23  Aligned_cols=68  Identities=13%  Similarity=0.253  Sum_probs=46.6

Q ss_pred             HHHHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch-HhhH
Q psy5605          46 CAALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG-RRDM  120 (152)
Q Consensus        46 aASilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G-~~~L  120 (152)
                      |-.++..+...  +++.+..|+..+|              -|.+.++++|+.|++.|+|+...  ++|..|.... +-.+
T Consensus        11 al~~l~~la~~~~~~~s~~eia~~l~--------------is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~   76 (130)
T TIGR02944        11 ATLVLTTLAQNDSQPYSAAEIAEQTG--------------LNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITV   76 (130)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCH
Confidence            34455555543  4688888888874              56789999999999999998653  5677776644 2224


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      ++|...+
T Consensus        77 ~~v~~~l   83 (130)
T TIGR02944        77 ADIVKAV   83 (130)
T ss_pred             HHHHHHH
Confidence            4444443

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.

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

Probab=91.33  E-value=0.7  Score=29.45  Aligned_cols=47  Identities=15%  Similarity=0.217  Sum_probs=38.2

Q ss_pred             HHHHhhHhhcCC--cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          47 AALARHIYMRSP--VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        47 ASilRkiYl~g~--vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      ..||..|+-.++  +.+..|+...|-              +.+-+-.+++.||+.|||++.++
T Consensus         8 ~~vL~~l~~~~~~~~t~~~la~~l~~--------------~~~~vs~~v~~L~~~Glv~r~~~   56 (62)
T PF12802_consen    8 FRVLMALARHPGEELTQSELAERLGI--------------SKSTVSRIVKRLEKKGLVERERD   56 (62)
T ss_dssp             HHHHHHHHHSTTSGEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE-
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCC
Confidence            368889999988  899999998743              44677889999999999997764

...

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

Probab=91.29  E-value=2  Score=32.29  Aligned_cols=78  Identities=17%  Similarity=0.158  Sum_probs=57.5

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      .+++|+-.+|-+.=+..+.++..-            +...+-..+-+=.+-|-+-|||||+-| |-++|..|+..+-++|
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            578888888888777777777643            123455666666799999999999996 7999999999999988


Q ss_pred             HHHHHHHHHHH
Q psy5605         125 AQIRVSKKEAA  135 (152)
Q Consensus       125 ~~i~~~~~~~~  135 (152)
                      .--..+..++.
T Consensus        84 ~l~a~en~pel   94 (96)
T PF09114_consen   84 ELWAQENAPEL   94 (96)
T ss_dssp             HHHHHHTHHHH
T ss_pred             HHHHhcCChhh
Confidence            77666665543

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.

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=91.23  E-value=0.57  Score=38.14  Aligned_cols=33  Identities=24%  Similarity=0.244  Sum_probs=28.8

Q ss_pred             CCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      .-|..-+|.+|+.||..|||+..+.+|-.+++-
T Consensus        37 gVSRtpVREAL~~Le~~GlV~~~~~~G~~V~~~   69 (253)
T PRK10421         37 GVSRNSLREALAKLVSEGVLLSRRGGGTFIRWR   69 (253)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence            358899999999999999999988778887764

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=91.13  E-value=0.87  Score=37.38  Aligned_cols=58  Identities=10%  Similarity=0.182  Sum_probs=46.4

Q ss_pred             HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcc
Q psy5605          44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSH  115 (152)
Q Consensus        44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~  115 (152)
                      -|+-.||..|.-.+++++..|++.-|              -+.+-+..+|+.|++.|||+.++. +...|+++
T Consensus        14 ~r~l~IL~~l~~~~~l~l~eia~~lg--------------l~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~~   72 (257)
T PRK15090         14 LKVFGILQALGEEREIGITELSQRVM--------------MSKSTVYRFLQTMKTLGYVAQEGESEKYSLTLK   72 (257)
T ss_pred             HHHHHHHHHhhcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence            38889999988778899999999864              345788999999999999998864 44555544

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=90.50  E-value=0.45  Score=38.72  Aligned_cols=33  Identities=27%  Similarity=0.342  Sum_probs=28.1

Q ss_pred             CchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          84 SSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      -|..-+|.+|+.||..|+|+..+..|-.+++--
T Consensus        44 VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~   76 (253)
T PRK11523         44 VSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ   76 (253)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence            578999999999999999999987776666543

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=90.15  E-value=0.36  Score=41.24  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=38.2

Q ss_pred             CchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA~~i~  128 (152)
                      =+...+|.+|.-|++.|||+....   +...||++|++.++..+..|.
T Consensus        32 i~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy   79 (280)
T TIGR02277        32 INERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIY   79 (280)
T ss_pred             CCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhc
Confidence            355789999999999999997654   467899999999999887764

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.

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=90.04  E-value=0.96  Score=34.24  Aligned_cols=43  Identities=19%  Similarity=0.368  Sum_probs=34.3

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCc
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITS  114 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~  114 (152)
                      ++.+..|+..+|              -|...+|++|++|++.|||+..++  ||-.|+.
T Consensus        25 ~~s~~~ia~~~~--------------is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~   69 (141)
T PRK11014         25 MTSISEVTEVYG--------------VSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK   69 (141)
T ss_pred             ccCHHHHHHHHC--------------cCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence            567788888874              467899999999999999997774  4656664

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=89.92  E-value=0.9  Score=36.41  Aligned_cols=41  Identities=15%  Similarity=0.289  Sum_probs=34.1

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .-..|+..||              -|.+-+|.+|+.||..|+|+..+..|-.+++
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            3456777774              6889999999999999999999987877765

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=89.87  E-value=2.4  Score=31.04  Aligned_cols=48  Identities=27%  Similarity=0.437  Sum_probs=37.8

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcchHh
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSHGRR  118 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~G~~  118 (152)
                      +|+.+..|+..+|              -+.+.+|++|+.|++.|||...  ..||-.|+.....
T Consensus        24 ~~~s~~eia~~~~--------------i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~   73 (132)
T TIGR00738        24 GPVSVKEIAERQG--------------ISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEE   73 (132)
T ss_pred             CcCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHH
Confidence            4788889988874              4678999999999999999864  3457788766543

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.

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=89.78  E-value=1.3  Score=33.61  Aligned_cols=63  Identities=21%  Similarity=0.358  Sum_probs=47.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC------CCceeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD------GGRKITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~------gGR~lT~~G~~~LD~  122 (152)
                      |++++.- |+.--+.|++.-++             =|.+++=.-|+.||+.|+|++..-      -...||+.|++++.-
T Consensus        28 Il~~L~~-g~~RF~eL~r~i~~-------------Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~v   93 (120)
T COG1733          28 ILRDLFD-GPKRFNELRRSIGG-------------ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPV   93 (120)
T ss_pred             HHHHHhc-CCCcHHHHHHHccc-------------cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHH
Confidence            5666665 77677777776543             566888888999999999997752      268899999998765


Q ss_pred             HHH
Q psy5605         123 IAA  125 (152)
Q Consensus       123 iA~  125 (152)
                      +..
T Consensus        94 l~~   96 (120)
T COG1733          94 LLA   96 (120)
T ss_pred             HHH
Confidence            543

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.53  E-value=1.7  Score=33.82  Aligned_cols=65  Identities=23%  Similarity=0.399  Sum_probs=47.4

Q ss_pred             hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCCc-----------eeCcchHhhH
Q psy5605          55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGGR-----------KITSHGRRDM  120 (152)
Q Consensus        55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gGR-----------~lT~~G~~~L  120 (152)
                      .+||..|..|+..-              .=+.|-+-++||.|..+|+|++.+   ++||           .++....++|
T Consensus        39 ~~~~~tvdelae~l--------------nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l  104 (126)
T COG3355          39 ENGPLTVDELAEIL--------------NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL  104 (126)
T ss_pred             hcCCcCHHHHHHHH--------------CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence            47999999999985              456788999999999999998664   3343           2455566667


Q ss_pred             HHHHHHHHHHHHH
Q psy5605         121 DRIAAQIRVSKKE  133 (152)
Q Consensus       121 D~iA~~i~~~~~~  133 (152)
                      |..+.++...+.+
T Consensus       105 ~~w~~~~~~~i~~  117 (126)
T COG3355         105 DEWYDKMKQLIEE  117 (126)
T ss_pred             HHHHHHHHHHHHH
Confidence            7666666554443

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

Probab=89.51  E-value=0.28  Score=33.55  Aligned_cols=40  Identities=28%  Similarity=0.434  Sum_probs=30.5

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      |..|..++..+|-             .|-+-+..-|++||+.|+|+.++...|
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            5577777777754             577889999999999999999986444

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

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

Probab=89.42  E-value=1.6  Score=30.90  Aligned_cols=76  Identities=11%  Similarity=0.221  Sum_probs=51.2

Q ss_pred             HHHHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCc------cCC---CchhHHHHHHHHHHhCCcceecCC--C--Cce
Q psy5605          46 CAALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSH------FCR---SSGSVARKALQALEQVNIIEKSDD--G--GRK  111 (152)
Q Consensus        46 aASilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h------~~~---asg~iiR~~LQqLE~~glVek~~~--g--GR~  111 (152)
                      |..|++-|+ +.+.+|...+..++=|.++......+      |-.   =|..-++.++++|...|+++...+  .  -=.
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            446677777 46789999999999998887754322      211   245689999999999999976653  1  346


Q ss_pred             eCcchHhhHH
Q psy5605         112 ITSHGRRDMD  121 (152)
Q Consensus       112 lT~~G~~~LD  121 (152)
                      +|++|++.|.
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.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=89.30  E-value=2.3  Score=35.42  Aligned_cols=58  Identities=21%  Similarity=0.300  Sum_probs=46.4

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcc
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSH  115 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~  115 (152)
                      -|+..||+.|-- .+|+++..|.+.-|-              +.+-+..+|+.|++.|||+.+++ +...|.+.
T Consensus        28 ~ral~IL~~l~~~~~~~~lseia~~lgl--------------pksTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   87 (274)
T PRK11569         28 TRGLKLLEWIAESNGSVALTELAQQAGL--------------PNSTTHRLLTTMQQQGFVRQVGELGHWAIGAH   87 (274)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence            599999999875 578999999998653              45789999999999999998875 33455544

>PRK03837 transcriptional regulator NanR; Provisional

Probab=89.20  E-value=2.6  Score=33.63  Aligned_cols=42  Identities=21%  Similarity=0.399  Sum_probs=34.5

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      ....|+..||              -|.+.+|.+|+.||..|||+..+..|-.+++-
T Consensus        39 ~E~~Lae~~g--------------VSRt~VREAL~~L~~eGlv~~~~~~G~~V~~~   80 (241)
T PRK03837         39 SERELMAFFG--------------VGRPAVREALQALKRKGLVQISHGERARVSRP   80 (241)
T ss_pred             CHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence            4567888874              68899999999999999999988767666653

>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=89.13  E-value=1.2  Score=29.28  Aligned_cols=48  Identities=23%  Similarity=0.374  Sum_probs=41.3

Q ss_pred             HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      -..|+..|--++.+.+..|...||              -|-.=||.=|+.||+.|+|.+.-+
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~--------------VS~~TiRRDl~~L~~~g~i~r~~G   49 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFG--------------VSEMTIRRDLNKLEKQGLIKRTHG   49 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEcC
Confidence            345777788899999999999994              467889999999999999998884

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

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=89.05  E-value=2.7  Score=35.09  Aligned_cols=58  Identities=14%  Similarity=0.116  Sum_probs=45.6

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC-ceeCcc
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG-RKITSH  115 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG-R~lT~~  115 (152)
                      -|+.+||+.|.- .+++++..+++.-|-              +.+-+..+|+.|+..|||+.++..| ..|++.
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lgl--------------pkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~   84 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDL--------------PLSTTFRLLKVLQAADFVYQDSQLGWWHIGLG   84 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence            388999999875 467999999998654              4578899999999999999986433 345544

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=88.08  E-value=1.9  Score=32.48  Aligned_cols=45  Identities=16%  Similarity=0.259  Sum_probs=35.6

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcc
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSH  115 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~  115 (152)
                      +++.+..++..+              .-+...++++|++|.++|||+..  +.||-.|+..
T Consensus        24 ~~~s~~~ia~~~--------------~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~   70 (135)
T TIGR02010        24 GPVTLADISERQ--------------GISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRP   70 (135)
T ss_pred             CcCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCC
Confidence            478888888876              45678999999999999999853  3467777654

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

>COG1485 Predicted ATPase [General function prediction only]

Probab=88.02  E-value=0.91  Score=41.04  Aligned_cols=97  Identities=23%  Similarity=0.322  Sum_probs=65.2

Q ss_pred             chHHHHHHHHHhhHhhcCCcchhh---HHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          40 DWFYTRCAALARHIYMRSPVGVKT---VTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        40 DW~YiRaASilRkiYl~g~vGV~~---L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      -|+|-|.....|-||+.||||.|.   |-..|.+-.-..-+.-||+    ..++.+-|.|..+.        |+.  .-+
T Consensus        55 ~~lf~r~~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh----~FM~~vH~~l~~l~--------g~~--dpl  120 (367)
T COG1485          55 GWLFGRDHGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFH----RFMARVHQRLHTLQ--------GQT--DPL  120 (367)
T ss_pred             ccccccCCCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHH----HHHHHHHHHHHHHc--------CCC--Ccc
Confidence            699999889999999999999986   5667766554444455654    47888888888776        222  223


Q ss_pred             HhhHHHHHHH-------------HHHHH-HHHHHHHHhhcCceeeccC
Q psy5605         117 RRDMDRIAAQ-------------IRVSK-KEAALQALAAQGITVVPTG  150 (152)
Q Consensus       117 ~~~LD~iA~~-------------i~~~~-~~~~~~~~~~~~~~~~~~~  150 (152)
                      ...-|++|.+             |...+ ----..+|-++||++|-|.
T Consensus       121 ~~iA~~~~~~~~vLCfDEF~VtDI~DAMiL~rL~~~Lf~~GV~lvaTS  168 (367)
T COG1485         121 PPIADELAAETRVLCFDEFEVTDIADAMILGRLLEALFARGVVLVATS  168 (367)
T ss_pred             HHHHHHHHhcCCEEEeeeeeecChHHHHHHHHHHHHHHHCCcEEEEeC
Confidence            3444555544             22222 2233568889999999875

>PRK07379 coproporphyrinogen III oxidase; Provisional

Probab=87.86  E-value=0.71  Score=40.83  Aligned_cols=59  Identities=20%  Similarity=0.203  Sum_probs=43.8

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc--eeCc-chHhhHHHHHHHHHHH
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR--KITS-HGRRDMDRIAAQIRVS  130 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR--~lT~-~G~~~LD~iA~~i~~~  130 (152)
                      .++-...+...||..             .-......|++|++.||++.+.  +|  +||+ +|+-.+|.|+.+++..
T Consensus       334 ~Gl~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~gll~~~~--~~~~~lT~~~G~~~~~~i~~~~~~~  395 (400)
T PRK07379        334 EGVSLSALTERFGKE-------------IVEQILQCLQPYFQQGWVELEG--DRRLRLTDPEGFLFSNTVLASLFEA  395 (400)
T ss_pred             CCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEeC--CeEEEECchHHhHHHHHHHHHHHHH
Confidence            445566677777531             2234567789999999998654  55  8995 9999999999999843

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=87.83  E-value=2.1  Score=25.72  Aligned_cols=46  Identities=17%  Similarity=0.361  Sum_probs=36.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      .|+..+.-++++.+..|+..+|              -|.+-+++.|+.|++.|+|+...+
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~--------------~s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLG--------------VSEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeec
Confidence            3566666678899999999983              245678999999999999997763

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

Probab=87.65  E-value=1.2  Score=29.11  Aligned_cols=52  Identities=19%  Similarity=0.326  Sum_probs=37.0

Q ss_pred             hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchH
Q psy5605          52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGR  117 (152)
Q Consensus        52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~  117 (152)
                      .+=+..++-+..+...||..             --......|+.|++.|||+.+. +.=+||++|+
T Consensus        14 ~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~   65 (66)
T PF06969_consen   14 GLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR   65 (66)
T ss_dssp             HHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred             HHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence            34456788888999998764             2244577899999999999887 4778999996

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.

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

Probab=87.53  E-value=1.1  Score=37.54  Aligned_cols=48  Identities=21%  Similarity=0.088  Sum_probs=38.3

Q ss_pred             CchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIAAQIRVSK  131 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA~~i~~~~  131 (152)
                      -|.+-+-..|+.||+.|||+...+   .--.||++|+..+++...+....+
T Consensus        33 iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~~~if   83 (217)
T PRK14165         33 TSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADYSRIF   83 (217)
T ss_pred             cCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHHHHHh
Confidence            466778889999999999987653   245799999999988887765544

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=87.43  E-value=0.58  Score=37.96  Aligned_cols=41  Identities=27%  Similarity=0.396  Sum_probs=33.4

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .-..|+..|              .-|...+|.+|+.||..|||+..+.+|-.+++
T Consensus        36 sE~eLa~~l--------------gVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~   76 (254)
T PRK09464         36 PERELAKQF--------------DVSRPSLREAIQRLEAKGLLLRRQGGGTFVQS   76 (254)
T ss_pred             CHHHHHHHh--------------CCCHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence            345577777              46889999999999999999999877866655

>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=87.25  E-value=0.85  Score=29.22  Aligned_cols=44  Identities=16%  Similarity=0.399  Sum_probs=32.4

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      +++....|....|              -|.+-+..+|++|++.|+|+....++-.|+|
T Consensus        24 ~~~s~~ela~~~g--------------~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~   67 (67)
T cd00092          24 LPLTRQEIADYLG--------------LTRETVSRTLKELEEEGLISRRGRGKYRVNP   67 (67)
T ss_pred             CCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence            4556666666654              3567889999999999999988755566654

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

Probab=87.04  E-value=1.7  Score=32.07  Aligned_cols=44  Identities=20%  Similarity=0.406  Sum_probs=36.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD  106 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~  106 (152)
                      ||.++|-.||---..+++..              ...-.-++.+|..||++|||+..+
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            88899988886666666653              455678999999999999999887

>PRK08629 coproporphyrinogen III oxidase; Provisional

Probab=86.46  E-value=4.4  Score=36.53  Aligned_cols=71  Identities=14%  Similarity=0.136  Sum_probs=51.0

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA  135 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~  135 (152)
                      .+++-...+...||..             ........|++|+..|++..+. +.=.||++|+-.+|.|..+++.-+-+.+
T Consensus       356 ~~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~f~~g~~~~r  421 (433)
T PRK08629        356 SGRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKEFYTGMDNVR  421 (433)
T ss_pred             hCCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHHHhChHHHH
Confidence            4566677888887631             2345677889999999999765 2458999999999999999985333333


Q ss_pred             HHHHh
Q psy5605         136 LQALA  140 (152)
Q Consensus       136 ~~~~~  140 (152)
                      .++.+
T Consensus       422 ~~~~~  426 (433)
T PRK08629        422 AQFRD  426 (433)
T ss_pred             HHHHh
Confidence            34333

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=86.07  E-value=1.8  Score=32.20  Aligned_cols=44  Identities=23%  Similarity=0.400  Sum_probs=33.2

Q ss_pred             CchhHHHHHHHHHHhCCcceecC--CCC------ceeCcchHhhHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSD--DGG------RKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~--~gG------R~lT~~G~~~LD~iA~~i  127 (152)
                      .|-+-|=-+|+.||+.|||+...  .++      -.||++|+..|.+...+.
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            34455667899999999999652  122      379999999999877654

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=85.95  E-value=2.5  Score=34.90  Aligned_cols=32  Identities=28%  Similarity=0.402  Sum_probs=26.6

Q ss_pred             CCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .-|+.++|-+|+.||..|||+..++.|=.+++
T Consensus        45 gVSR~~vREAl~~L~a~Glve~r~G~Gt~V~~   76 (241)
T COG2186          45 GVSRTVVREALKRLEAKGLVEIRQGSGTFVRP   76 (241)
T ss_pred             CCCcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence            35889999999999999999988876655543

>PRK08599 coproporphyrinogen III oxidase; Provisional

Probab=85.84  E-value=3.3  Score=35.86  Aligned_cols=62  Identities=18%  Similarity=0.260  Sum_probs=47.6

Q ss_pred             HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605          53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~  128 (152)
                      +....++-...++..||..             ........+.+|++.||++.+. +.=+||++|+-.+|.|+.+++
T Consensus       313 Lr~~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~  374 (377)
T PRK08599        313 LRKKSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFL  374 (377)
T ss_pred             HHhhCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHh
Confidence            3345667777788777531             2355677889999999999766 467899999999999998875

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=85.78  E-value=1.2  Score=35.12  Aligned_cols=43  Identities=23%  Similarity=0.309  Sum_probs=33.3

Q ss_pred             CCchhHHHHHHHHHHhCCcceecCCC-C---ceeCcchHhhHHHHHH
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSDDG-G---RKITSHGRRDMDRIAA  125 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~~g-G---R~lT~~G~~~LD~iA~  125 (152)
                      ..|-+-|=-+|+.||+.|||+....+ .   -.||+.|+..|+....
T Consensus        74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~  120 (135)
T PRK09416         74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEK  120 (135)
T ss_pred             cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHh
Confidence            33556677899999999999865432 2   3699999999998765

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=85.53  E-value=3.1  Score=33.37  Aligned_cols=59  Identities=15%  Similarity=0.218  Sum_probs=42.4

Q ss_pred             HHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          43 YTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        43 YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      |.+.+..||+-=..|..       +-..|+..||              -|..-+|++|+.|++.|+|.+.++.|-.+++.
T Consensus         3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~--------------VSR~TVR~Al~~L~~eGli~r~~G~GtfV~~~   68 (230)
T TIGR02018         3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYG--------------CSRMTVNRALRELTDAGLLERRQGVGTFVAEP   68 (230)
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEEccC
Confidence            45555555544444321       4457777774              57899999999999999999999778777643

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.

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

Probab=85.06  E-value=3.4  Score=25.49  Aligned_cols=42  Identities=21%  Similarity=0.302  Sum_probs=34.2

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE  103 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe  103 (152)
                      .|+..|+-+|++....++...|              =|.+-+++.|++|++.|+|+
T Consensus         7 ~Il~~l~~~~~~t~~ela~~~~--------------is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    7 KILNYLRENPRITQKELAEKLG--------------ISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHCTTS-HHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCcCcC
Confidence            4777777789999999999874              46688999999999999985

...

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

Probab=84.96  E-value=3.7  Score=27.78  Aligned_cols=46  Identities=13%  Similarity=0.113  Sum_probs=37.8

Q ss_pred             HHHhhHhhcCC--cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          48 ALARHIYMRSP--VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        48 SilRkiYl~g~--vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      .||..|.-+|+  +....|.+..|=              +.+.++..|..||+.|+|++...
T Consensus        10 ~IL~~L~~~g~~~~ta~eLa~~lgl--------------~~~~v~r~L~~L~~~G~V~~~~~   57 (68)
T smart00550       10 KILEFLENSGDETSTALQLAKNLGL--------------PKKEVNRVLYSLEKKGKVCKQGG   57 (68)
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCC
Confidence            57777777777  999999998754              34689999999999999998763

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

>PRK09057 coproporphyrinogen III oxidase; Provisional

Probab=84.77  E-value=3.8  Score=35.88  Aligned_cols=58  Identities=19%  Similarity=0.308  Sum_probs=44.9

Q ss_pred             hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605          55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~  128 (152)
                      ...++-...+...||-.-                ....|+.|++.|+++.+.++.=+||++|+-.+|.|+.+++
T Consensus       322 ~~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~  379 (380)
T PRK09057        322 LREGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA  379 (380)
T ss_pred             HhCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence            346778889999987431                0247899999999997653346899999999999998874

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

Probab=84.64  E-value=1.5  Score=28.94  Aligned_cols=47  Identities=19%  Similarity=0.331  Sum_probs=37.5

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      +.|...|--+|+..+..+++.-              .-+.+-++.+|+.|++.|||+..+.
T Consensus        11 ~~vy~~Ll~~~~~t~~eIa~~l--------------~i~~~~v~~~L~~L~~~GlV~~~~~   57 (68)
T PF01978_consen   11 AKVYLALLKNGPATAEEIAEEL--------------GISRSTVYRALKSLEEKGLVEREEG   57 (68)
T ss_dssp             HHHHHHHHHHCHEEHHHHHHHH--------------TSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            3455555567999999999885              4567889999999999999998873

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.

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

Probab=84.08  E-value=1.9  Score=32.44  Aligned_cols=39  Identities=21%  Similarity=0.244  Sum_probs=31.5

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      ++.+..|+....+              |..-+|.+|++|++.|||+-.|.-||
T Consensus        19 ~vtl~elA~~l~c--------------S~Rn~r~lLkkm~~~gWi~W~pg~GR   57 (115)
T PF12793_consen   19 EVTLDELAELLFC--------------SRRNARTLLKKMQEEGWITWQPGRGR   57 (115)
T ss_pred             ceeHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeeeeCCCCC
Confidence            4677888887644              55668999999999999999997565

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=83.92  E-value=4.5  Score=33.57  Aligned_cols=77  Identities=17%  Similarity=0.289  Sum_probs=54.6

Q ss_pred             HHHHHHHhhHhhcCCc--chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC-ceeCc----ch
Q psy5605          44 TRCAALARHIYMRSPV--GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG-RKITS----HG  116 (152)
Q Consensus        44 iRaASilRkiYl~g~v--GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG-R~lT~----~G  116 (152)
                      .|+..||..|.- +|.  ++..|.+.-|              -+.+=++.+|+.|++.|||+.+++.| -.|++    -|
T Consensus         4 ~ral~iL~~l~~-~~~~l~l~ela~~~g--------------lpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~~~~lg   68 (246)
T COG1414           4 ERALAILDLLAE-GPGGLSLAELAERLG--------------LPKSTVHRLLQTLVELGYVEQDPEDGRYRLGPRLLELG   68 (246)
T ss_pred             HHHHHHHHHHHh-CCCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCEEEcCCCCcEeehHHHHHHH
Confidence            488889988886 444  5999999864              34578999999999999999999644 44544    45


Q ss_pred             HhhHHH-----HHHHHHHHHHHHH
Q psy5605         117 RRDMDR-----IAAQIRVSKKEAA  135 (152)
Q Consensus       117 ~~~LD~-----iA~~i~~~~~~~~  135 (152)
                      ...+++     +|..+++++.+..
T Consensus        69 ~~~l~~~~l~~~a~p~l~~L~~~t   92 (246)
T COG1414          69 AAALSSLDLVSLARPLLEELAEET   92 (246)
T ss_pred             HHHHhcCCHHHHhHHHHHHHHHHh
Confidence            555554     5555555554443

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=83.74  E-value=2.4  Score=35.72  Aligned_cols=55  Identities=24%  Similarity=0.376  Sum_probs=47.2

Q ss_pred             HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605          44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT  113 (152)
Q Consensus        44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT  113 (152)
                      -|-..|+..|--++.+.+..|...||              -|..-||.=|..||+.|++.... ||..+.
T Consensus        17 eR~~~Il~~L~~~~~vtv~eLa~~l~--------------VS~~TIRRDL~~Le~~G~l~r~~-GGa~~~   71 (269)
T PRK09802         17 ERREQIIQRLRQQGSVQVNDLSALYG--------------VSTVTIRNDLAFLEKQGIAVRAY-GGALIC   71 (269)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHHC--------------CCHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence            47788888888899999999999983              56688999999999999999888 676654

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=83.37  E-value=6.2  Score=32.78  Aligned_cols=56  Identities=25%  Similarity=0.329  Sum_probs=45.3

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      |-..|++.|--+|.+.+..|+..+|              -|..-||+=|++||+.|++.+.-.|-..+++
T Consensus         6 R~~~Il~~l~~~~~~~~~ela~~l~--------------vS~~TirRdL~~Le~~g~i~r~~gga~~~~~   61 (251)
T PRK13509          6 RHQILLELLAQLGFVTVEKVIERLG--------------ISPATARRDINKLDESGKLKKVRNGAEAITQ   61 (251)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCccccCC
Confidence            6677888888889999999999984              4667889999999999999987744333443

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=83.33  E-value=1.2  Score=38.39  Aligned_cols=40  Identities=25%  Similarity=0.311  Sum_probs=34.0

Q ss_pred             CCchhHHHHHHHHHHhCCcceecC-C-CCceeCcchHhhHHH
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSD-D-GGRKITSHGRRDMDR  122 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~-~-gGR~lT~~G~~~LD~  122 (152)
                      .-|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
T Consensus       209 GVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e  250 (251)
T TIGR02787       209 GITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE  250 (251)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence            357899999999999999999988 5 487888887777775

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.

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=83.30  E-value=1.3  Score=35.31  Aligned_cols=61  Identities=13%  Similarity=0.245  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      -|...+..++.-=..|..       .-..|+..||              -|..-+|++|+.|+..|+|+..++.|-.+++
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            466766666655444432       3456777774              5789999999999999999999987888875


Q ss_pred             ch
Q psy5605         115 HG  116 (152)
Q Consensus       115 ~G  116 (152)
                      ..
T Consensus        75 ~~   76 (238)
T TIGR02325        75 RR   76 (238)
T ss_pred             Cc
Confidence            54

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

>PF13814 Replic_Relax: Replication-relaxation

Probab=82.77  E-value=3.1  Score=31.97  Aligned_cols=61  Identities=16%  Similarity=0.328  Sum_probs=44.7

Q ss_pred             hhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-----CC-----ceeCcchHhhH
Q psy5605          51 RHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-----GG-----RKITSHGRRDM  120 (152)
Q Consensus        51 RkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-----gG-----R~lT~~G~~~L  120 (152)
                      +-||-.+.+....|...++...+.           .+-+|..|++|++.|+|+....     +|     -.||+.|.+.+
T Consensus         2 ~~L~~~r~lt~~Qi~~l~~~~~~~-----------~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l   70 (191)
T PF13814_consen    2 RLLARHRFLTTDQIARLLFPSSKS-----------ERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLL   70 (191)
T ss_pred             hhHHHhcCcCHHHHHHHHcCCCcc-----------hHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHH
Confidence            446666677788888888553221           1278999999999999986653     13     37999999999


Q ss_pred             HH
Q psy5605         121 DR  122 (152)
Q Consensus       121 D~  122 (152)
                      +.
T Consensus        71 ~~   72 (191)
T PF13814_consen   71 AD   72 (191)
T ss_pred             Hh
Confidence            74

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=82.64  E-value=3.5  Score=32.87  Aligned_cols=87  Identities=21%  Similarity=0.274  Sum_probs=54.4

Q ss_pred             CchHHHHHHHHHhhHh-hcCCc-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          39 PDWFYTRCAALARHIY-MRSPV-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        39 ~DW~YiRaASilRkiY-l~g~v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      ++|||.-    +|-+- +.+.. -...|.+.-        +|    .-|-.=+|.+|+-|+++|+|+++.+|.-..|.+.
T Consensus        22 ~~W~~~~----ir~l~~l~~~~~d~~~iak~l--------~p----~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~   85 (171)
T PF14394_consen   22 SSWYHPA----IRELLPLMPFAPDPEWIAKRL--------RP----KISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKS   85 (171)
T ss_pred             hhhHHHH----HHHHhhcCCCCCCHHHHHHHh--------cC----CCCHHHHHHHHHHHHHCCCeEECCCCcEEEecce
Confidence            4688753    44433 33322 455555543        23    4566789999999999999999998665655543


Q ss_pred             H----hhHHHHHHHHHHHHHHHHHHHHhh
Q psy5605         117 R----RDMDRIAAQIRVSKKEAALQALAA  141 (152)
Q Consensus       117 ~----~~LD~iA~~i~~~~~~~~~~~~~~  141 (152)
                      -    ...-....+.-.++-+.+.+||..
T Consensus        86 l~~~~~~~~~avr~~h~q~~~lA~~al~~  114 (171)
T PF14394_consen   86 LTTSSEIPSEAVRSYHKQMLELAQEALDR  114 (171)
T ss_pred             eeCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence            3    344444455556666666666653

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

Probab=82.21  E-value=1.3  Score=33.94  Aligned_cols=40  Identities=28%  Similarity=0.410  Sum_probs=30.8

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI  112 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l  112 (152)
                      -|.+..|...||              =++||.|.+|..||+.|+|....+ +|+.
T Consensus        59 ~VTpy~la~r~g--------------I~~SvAr~vLR~LeeeGvv~lvsk-nrR~   98 (107)
T COG4901          59 VVTPYVLASRYG--------------INGSVARIVLRHLEEEGVVQLVSK-NRRQ   98 (107)
T ss_pred             eecHHHHHHHhc--------------cchHHHHHHHHHHHhCCceeeecc-Cccc
Confidence            455666777774              468999999999999999987763 5543

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=82.21  E-value=1.6  Score=33.99  Aligned_cols=45  Identities=18%  Similarity=0.304  Sum_probs=35.8

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG  116 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G  116 (152)
                      ++.+..++..+              .-|.+.++++||+|.++|||+...  +||-.|+..-
T Consensus        24 ~~s~~eIA~~~--------------~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p   70 (153)
T PRK11920         24 LSRIPEIARAY--------------GVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPA   70 (153)
T ss_pred             cCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCH
Confidence            56777787776              356789999999999999999765  4788887654

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

Probab=82.03  E-value=5.6  Score=32.37  Aligned_cols=57  Identities=18%  Similarity=0.166  Sum_probs=44.7

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      -|+-.||.-|-- .+|+++..|.+.-|-              +.+-+..+|+.|++.|||+++. +.-.|++.
T Consensus         9 ~ral~IL~~l~~~~~~~~l~eia~~lgl--------------pksT~~RlL~tL~~~G~l~~~~-~~Y~lG~~   66 (248)
T TIGR02431         9 ARGLAVIEAFGAERPRLTLTDVAEATGL--------------TRAAARRFLLTLVELGYVTSDG-RLFWLTPR   66 (248)
T ss_pred             HHHHHHHHHHhcCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCC-CEEEecHH
Confidence            378888888864 678999999998653              4578899999999999999864 44556554

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

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=81.68  E-value=5.1  Score=31.72  Aligned_cols=45  Identities=16%  Similarity=0.220  Sum_probs=36.0

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcc
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSH  115 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~  115 (152)
                      +|+.+..++..+              .-+...++++|++|.++|||+..  ++||-.|...
T Consensus        24 ~~vs~~eIA~~~--------------~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~   70 (164)
T PRK10857         24 GPVPLADISERQ--------------GISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKD   70 (164)
T ss_pred             CcCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCC
Confidence            478888888887              45678999999999999999853  4578777644

>PRK14999 histidine utilization repressor; Provisional

Probab=81.58  E-value=11  Score=30.52  Aligned_cols=61  Identities=13%  Similarity=0.147  Sum_probs=45.9

Q ss_pred             HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|...+..||+-=..|.      + +-..|+..||              -|..-+|++|+.|+..|+|.+.++.|--+++
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            46677666665544442      2 5567888884              5789999999999999999999977887765


Q ss_pred             ch
Q psy5605         115 HG  116 (152)
Q Consensus       115 ~G  116 (152)
                      ..
T Consensus        79 ~~   80 (241)
T PRK14999         79 PK   80 (241)
T ss_pred             CC
Confidence            43

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=80.64  E-value=9.5  Score=31.78  Aligned_cols=54  Identities=24%  Similarity=0.409  Sum_probs=45.6

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT  113 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT  113 (152)
                      |-..|+..|--+|.+.+..|...||              -|..-||.=|+.||+.|+|...- ||=++.
T Consensus         6 R~~~Il~~L~~~~~v~v~eLa~~l~--------------VS~~TIRRDL~~Le~~g~l~r~~-Gga~~~   59 (256)
T PRK10434          6 RQAAILEYLQKQGKTSVEELAQYFD--------------TTGTTIRKDLVILEHAGTVIRTY-GGVVLN   59 (256)
T ss_pred             HHHHHHHHHHHcCCEEHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEEE-CCEEcC
Confidence            6778888888899999999999984              57788999999999999999887 454443

>PRK08208 coproporphyrinogen III oxidase; Validated

Probab=80.23  E-value=2.7  Score=37.45  Aligned_cols=62  Identities=18%  Similarity=0.213  Sum_probs=46.3

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK  132 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~  132 (152)
                      ..++-...+...||..      +       .. ....|++|++.|||+.+. +.=+||++|+-..|.|+.+++..-.
T Consensus       359 ~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~~~~  420 (430)
T PRK08208        359 AQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFISPEV  420 (430)
T ss_pred             hCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcCHHH
Confidence            4567777788887631      1       12 345789999999999765 3568999999999999999875443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	152
3iz6_S	146	Localization Of The Small Subunit Ribosomal Protein		2e-39
3izb_S	144	Localization Of The Small Subunit Ribosomal Protein		4e-30
3jyv_T	141	Structure Of The 40s Rrna And Proteins And PE TRNA		4e-30
2v7f_A	150	Structure Of P. Abyssi Rps19 Protein Length = 150		8e-23
3j20_U	150	Promiscuous Behavior Of Proteins In Archaeal Riboso		9e-23
2xzm_T	155	Crystal Structure Of The Eukaryotic 40s Ribosomal S		4e-18
3zey_O	167	High-resolution Cryo-electron Microscopy Structure		9e-18

>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 =  157 bits (398), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 68/118 (57%), Positives = 94/118 (79%)
Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           +SGKM++PEWVDIVK+A+FKEL PYDPDW+YTR A++AR IY+R  +GV    KI+GGR+
Sbjct: 27  RSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIARKIYLRQGIGVGGFQKIYGGRQ 86
Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS 130
           RNG  P HFC+SSG+++R  LQ L+++ II+    GGR ITS GRRD+D++A ++ V+
Sbjct: 87  RNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQVAGRVDVT 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 =  126 bits (317), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 60/116 (51%), Positives = 83/116 (71%), Gaps = 1/116 (0%)
Query: 12  SKSGKMKVPEWVDIVKSAKFKELAPYDPD-WFYTRCAALARHIYMRSPVGVKTVTKIFGG 70
            + GK++VP +VDIVK++   E+ P D + WFY R A++ARHIYMR  VGV  + K++GG
Sbjct: 23  QRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGG 82
Query: 71  RKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQ 126
            K  GV P     +SGS+ RK LQALE++ I+E S  GGR+I+ +G+RD+DRIAAQ
Sbjct: 83  AKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQ 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 =  126 bits (317), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 60/116 (51%), Positives = 83/116 (71%), Gaps = 1/116 (0%)
Query: 12  SKSGKMKVPEWVDIVKSAKFKELAPYDPD-WFYTRCAALARHIYMRSPVGVKTVTKIFGG 70
            + GK++VP +VDIVK++   E+ P D + WFY R A++ARHIYMR  VGV  + K++GG
Sbjct: 20  QRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGG 79
Query: 71  RKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQ 126
            K  GV P     +SGS+ RK LQALE++ I+E S  GGR+I+ +G+RD+DRIAAQ
Sbjct: 80  AKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQ 135

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

Iteration: 1
 Score =  102 bits (254), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 70/118 (59%)
Query: 16  KMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNG 75
           ++K PEW   VK+ + KE  P   DW+Y R A++ R +Y+  PVG++ +   +GGRK  G
Sbjct: 25  EIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRG 84
Query: 76  VCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133
             P  F ++ GS+ RKALQ LE    +EK    GR IT  GR  +D+IA +++   +E
Sbjct: 85  HAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEE 142

>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 =  102 bits (254), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 70/118 (59%)
Query: 16  KMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNG 75
           ++K PEW   VK+ + KE  P   DW+Y R A++ R +Y+  PVG++ +   +GGRK  G
Sbjct: 25  EIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRG 84
Query: 76  VCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133
             P  F ++ GS+ RKALQ LE    +EK    GR IT  GR  +D+IA +++   +E
Sbjct: 85  HAPEKFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEE 142

>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 = 87.0 bits (214), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 44/126 (34%), Positives = 69/126 (54%), Gaps = 5/126 (3%)
Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           K+ K+ +PE+     ++  +ELAP D DW Y R AALAR +Y++   G+ T+  IFG  K
Sbjct: 28  KANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVYLKPHTGISTLKHIFGSNK 87
Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRK-----ITSHGRRDMDRIAAQI 127
             G   +      G + R AL++LE + II K  +   K     IT  G  +++RIA QI
Sbjct: 88  DRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQI 147
Query: 128 RVSKKE 133
            + +++
Sbjct: 148 AIKQRQ 153

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

Iteration: 1
 Score = 85.9 bits (211), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 43/119 (36%), Positives = 69/119 (57%)
Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           + GKM VP   +IVK++  +E AP +PDW+Y RCAA+ R +Y+R  VG   ++K F  +K
Sbjct: 41  QEGKMMVPNCAEIVKTSHGRERAPQNPDWYYIRCAAVLRAVYLRPGVGYGGLSKRFSSKK 100
Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131
             G  P    R+S  +     ++L ++ ++EK    G ++T  GR+  D IA +I + K
Sbjct: 101 NRGSRPEITTRASKGLLHWCCKSLTKLELLEKCKGAGHRVTKLGRKVADTIAFKIALRK 159

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	4e-57
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	4e-55
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	4e-53
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	4e-52

>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 =  174 bits (442), Expect = 4e-57
 Identities = 47/122 (38%), Positives = 71/122 (58%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           +  ++K PEW   VK+ + KE  P   DW+Y R A++ R +Y+  PVG++ +   +GGRK
Sbjct: 22  EIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRK 81

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             G  P  F ++ GS+ RKALQ LE    +EK    GR IT  GR  +D+IA +++   +
Sbjct: 82  NRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELE 141

Query: 133 EA 134
           E 
Sbjct: 142 EI 143

>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 =  169 bits (429), Expect = 4e-55
 Identities = 68/118 (57%), Positives = 94/118 (79%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           +SGKM++PEWVDIVK+A+FKEL PYDPDW+YTR A++AR IY+R  +GV    KI+GGR+
Sbjct: 27  RSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIARKIYLRQGIGVGGFQKIYGGRQ 86

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS 130
           RNG  P HFC+SSG+++R  LQ L+++ II+    GGR ITS GRRD+D++A ++ V+
Sbjct: 87  RNGSRPPHFCKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQVAGRVDVT 144

>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 =  163 bits (415), Expect = 4e-53
 Identities = 60/121 (49%), Positives = 84/121 (69%), Gaps = 1/121 (0%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPD-WFYTRCAALARHIYMRSPVGVKTVTKIFGGR 71
           + GK++VP +VDIVK++   E+ P D + WFY R A++ARHIYMR  VGV  + K++GG 
Sbjct: 24  RQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGGA 83

Query: 72  KRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131
           K  GV P     +SGS+ RK LQALE++ I+E S  GGR+I+ +G+RD+DRIAAQ     
Sbjct: 84  KSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEED 143

Query: 132 K 132
           +
Sbjct: 144 E 144

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

 Score =  161 bits (409), Expect = 4e-52
 Identities = 45/128 (35%), Positives = 70/128 (54%), Gaps = 5/128 (3%)

Query: 12  SKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGR 71
            K+ K+ +PE+     ++  +ELAP D DW Y R AALAR +Y++   G+ T+  IFG  
Sbjct: 27  KKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVYLKPHTGISTLKHIFGSN 86

Query: 72  KRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-----GRKITSHGRRDMDRIAAQ 126
           K  G   +      G + R AL++LE + II K  +       R IT  G  +++RIA Q
Sbjct: 87  KDRGNLRNKHQACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQ 146

Query: 127 IRVSKKEA 134
           I + +++A
Sbjct: 147 IAIKQRQA 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	100.0
2xzm_T	155	RPS19E; ribosome, translation; 3.93A {Tetrahymena	100.0
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	100.0
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	100.0
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.45
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.2
2pg4_A	95	Uncharacterized protein; structural genomics, join	97.17
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.16
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	97.05
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.02
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.98
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.93
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.89
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.88
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.87
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.87
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.85
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.84
3by6_A	126	Predicted transcriptional regulator; structural ge	96.84
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.8
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.8
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.77
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.74
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.73
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.73
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.7
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.69
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.68
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.68
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.63
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.6
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.59
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.59
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.58
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	96.52
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.51
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.49
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.49
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	96.48
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.47
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.47
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.46
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.46
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.46
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.45
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.45
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	96.45
2nnn_A	140	Probable transcriptional regulator; structural gen	96.43
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.42
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.4
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.35
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.31
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.29
2o0m_A	345	Transcriptional regulator, SORC family; structural	96.27
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.27
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.26
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.26
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.22
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.22
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.2
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	96.19
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.13
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.13
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.08
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.06
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	96.06
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.93
3nqo_A	189	MARR-family transcriptional regulator; structural	95.77
3f3x_A	144	Transcriptional regulator, MARR family, putative;	95.75
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	95.71
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	95.67
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.61
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	95.6
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.53
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	95.44
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	95.41
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.31
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.31
1bja_A	95	Transcription regulatory protein MOTA; activation	95.27
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.27
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.24
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	95.17
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.16
2obp_A	96	Putative DNA-binding protein; structural genomics,	95.12
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	95.0
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	94.99
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	94.94
2fxa_A	207	Protease production regulatory protein HPR; protea	94.91
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	94.87
1yyv_A	131	Putative transcriptional regulator; reductive meth	94.82
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	94.68
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	94.64
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.59
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	94.5
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	94.48
3c7j_A	237	Transcriptional regulator, GNTR family; structural	94.41
1hsj_A	487	Fusion protein consisting of staphylococcus access	94.34
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.32
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	94.14
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	94.09
4fx0_A	148	Probable transcriptional repressor protein; helix-	94.06
1xma_A	145	Predicted transcriptional regulator; southea colla	94.06
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.02
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	93.99
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	93.96
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	93.96
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.87
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	93.8
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.54
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	93.4
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.4
2co5_A	99	Viral protein F93; viral protein-winged helix comp	93.36
4esf_A	117	PADR-like transcriptional regulator; PADR family,	93.28
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	93.15
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	93.12
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	93.05
2kko_A	108	Possible transcriptional regulatory protein (possi	92.9
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	92.87
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	92.81
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	92.73
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	92.68
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.52
3jth_A	98	Transcription activator HLYU; transcription factor	92.31
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	92.27
2dql_A	115	PEX protein; circadian clock associated protein, c	92.26
3aaf_A	134	Werner syndrome ATP-dependent helicase; helix-turn	92.07
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	92.0
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	91.67
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	91.54
2g7u_A	257	Transcriptional regulator; ICLR family, structural	91.54
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	91.52
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	91.32
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	91.16
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.02
3r0a_A	123	Putative transcriptional regulator; structural gen	90.98
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	90.36
3cta_A	230	Riboflavin kinase; structural genomics, transferas	90.19
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	90.15
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	90.11
1ylf_A	149	RRF2 family protein; structural genomics, transcri	90.01
3elk_A	117	Putative transcriptional regulator TA0346; structu	89.8
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	89.68
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	89.6
3l09_A	266	Putative transcriptional regulator; structural gen	89.53
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	89.2
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	88.72
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	88.69
3eet_A	272	Putative GNTR-family transcriptional regulator; st	88.44
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	88.0
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	87.51
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.24
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	86.88
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	86.74
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	86.65
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	85.94
1p6r_A	82	Penicillinase repressor; transcription regulation,	85.87
3k69_A	162	Putative transcription regulator; putative transcr	85.74
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	84.48
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	81.6
1xd7_A	145	YWNA; structural genomics, protein structure initi	81.54
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	81.24

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

Probab=100.00  E-value=1.8e-69  Score=423.04  Aligned_cols=130  Identities=53%  Similarity=0.990  Sum_probs=127.8

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+|||||+||||++||+||++|+++|||+||||++|+||
T Consensus        16 ~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KEl~P~d~DW~Y~RaASi~R~lYlrg~vGV~~lrk~YGg~krrG~~P~h~   95 (146)
T 3iz6_S           16 EFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPYDPDWYYTRAASIARKIYLRQGIGVGGFQKIYGGRQRNGSRPPHF   95 (146)
T ss_dssp             HHHHHHHTTGGGSSCCCCTTTGGGCCSSSSCSSSTHHHHTHHHHHHHHHHHHHHHCSBCHHHHHSSSCCCCCCCSSCCCC
T ss_pred             HHHHHHHHHHHHcCCCCCCchHHHhhccccccCCCCCCchHHHHHHHHHHHHHhcCCCcHHHHHHHHCCCCCCCCCCCcc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK  131 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~  131 (152)
                      ++|||+|||+||||||++||||+++++||+|||+||++||+||.||++++
T Consensus        96 ~~asg~iiR~~LQqLE~~g~Vek~~~gGR~lT~~G~~~LD~iA~~v~~~~  145 (146)
T 3iz6_S           96 CKSSGAISRNILQQLQKMGIIDVDPKGGRLITSQGRRDLDQVAGRVDVTI  145 (146)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSEEEETTTEEEECHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHCCCeEecCCCCcEECHhHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999998999999999999999999998875

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

Probab=100.00  E-value=3.3e-68  Score=419.22  Aligned_cols=132  Identities=33%  Similarity=0.592  Sum_probs=128.6

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+|||||+||||++||+||++|+++|||++|||++|+||
T Consensus        17 ~fI~~~A~~LKk~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASi~R~lYlrg~vGV~~lrk~YGg~krrG~~P~h~   96 (155)
T 2xzm_T           17 DFIREYASHLKKANKLSIPEFTQWTTTSVARELAPQDSDWVYIRTAALARKVYLKPHTGISTLKHIFGSNKDRGNLRNKH   96 (155)
T ss_dssp             HHHHHHHHHTTSSCCSCCCHHHHSCCCSSSCSSCCSSTTHHHHHHHHHHHHHHHSTTCCHHHHHHHTCCEECCSSSCCEE
T ss_pred             HHHHHHHHHHHhcCCCCCCchHhhhhccccccCCCCCCchHHHHHHHHHHHHhccCCCCHHHHHHHHCCCCCCCCCCCcc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHHHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDG-----GRKITSHGRRDMDRIAAQIRVSKKE  133 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~g-----GR~lT~~G~~~LD~iA~~i~~~~~~  133 (152)
                      ++|||+|||+||||||++||||++++|     ||+|||+||+|||+||.+|..+.+|
T Consensus        97 ~~asg~iiR~~LQqLE~~g~Vek~~~g~~~k~GR~lT~~G~~~LDriA~~i~~~~~~  153 (155)
T 2xzm_T           97 QACHGKILRWALKSLEDLKIIRKDKNSATKKFSRVITKEGMTELNRIATQIAIKQRQ  153 (155)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEECSSCSSSTTCEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHHHHHCCCEeecCCCCcCCCCCEECHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999877     9999999999999999999977665

>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=9.2e-69  Score=418.24  Aligned_cols=129  Identities=47%  Similarity=0.783  Sum_probs=127.0

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCc-hHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPD-WFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSH   80 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~D-W~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h   80 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||| |||+||||||||||++||+||++|+++|||+||||++|+|
T Consensus        13 ~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kEl~P~d~D~W~Y~RaASi~R~lYl~g~vGV~~lrk~YGg~krrG~~P~h   92 (144)
T 3u5c_T           13 DFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASVARHIYMRKQVGVGKLNKLYGGAKSRGVRPYK   92 (144)
T ss_dssp             HHHHHHHHHHHHHCCCCCTTTTTSCCSCTTCSSCCSSCSSSHHHHHHHHHHHHHTSSBCCHHHHHHHHCCEEEETTEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCCchHhHhhccccccCCCCCCcchHHHHHHHHHHHHHhcCCCcHHHHHHHHCCCCCCCCCCcc
Confidence            489999999999999999999999999999999999999 9999999999999999999999999999999999999999


Q ss_pred             cCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHH
Q psy5605          81 FCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS  130 (152)
Q Consensus        81 ~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~  130 (152)
                      |++|||+|||+||||||++|||++++++||+|||+||++||+||.||+++
T Consensus        93 ~~~asg~iiR~~LQqLE~~g~vek~~~~GR~lT~~G~~~LD~iA~~v~~~  142 (144)
T 3u5c_T           93 HIDASGSINRKVLQALEKIGIVEISPKGGRRISENGQRDLDRIAAQTLEE  142 (144)
T ss_dssp             ECCCCHHHHHHHHHHHHHTTSEECCSSSSCEECHHHHHHHHHHHHHHHHH
T ss_pred             ccccCcHHHHHHHHHHHHCCCeeecCCCCcEECHhHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999899999999999999999999876

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

Probab=100.00  E-value=2.7e-47  Score=296.67  Aligned_cols=132  Identities=37%  Similarity=0.702  Sum_probs=118.9

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||.++|++|+|+||||.|+|++||++|++|+.|+..|++.|||+||||++|+||
T Consensus        11 ~~i~~~a~~lk~~~ki~~P~w~~~vKt~~~ke~~p~~~~~~y~ria~~lr~~i~~g~~G~~~La~~~gg~k~~g~~p~~~   90 (150)
T 2v7f_A           11 LLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERF   90 (150)
T ss_dssp             HHHHHHHHHHTTCTTCCCCSCGGGCCC------CHHHHTHHHHHHHHHHHHHHHHCSBCHHHHHHHHCC----CCCTTSC
T ss_pred             HHHHHHHHHHHhcCCCCCcchhhhhcccccccCCCCCcchHHHHHHHHHHHHHHhCCCCHHHHHHHHCCCccCCcCCccc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE  133 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~  133 (152)
                      ++.|+++||.+||+||++|||++.+++|+.+|+.|+++||+||.+|.+++.+
T Consensus        91 ~~vSr~tVR~AL~~Le~~GlV~~~~~~G~~Vt~~~~~~l~~ia~~i~~~~~~  142 (150)
T 2v7f_A           91 YKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEE  142 (150)
T ss_dssp             CCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHCCCEEEeCCCceEECCCCHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999998889999999999999999999988755

>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=97.45  E-value=0.00089  Score=47.23  Aligned_cols=64  Identities=13%  Similarity=0.091  Sum_probs=53.0

Q ss_pred             HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      ...||+.++ .+ +|...|...-              .=|-+.+|..+..|++.|||++.. +|-.||++|+..|+.+..
T Consensus        10 i~~IL~~i~-~~-~~~t~La~~~--------------~ls~~~~~~~l~~L~~~GLI~~~~-~~~~LT~kG~~~l~~l~~   72 (95)
T 1r7j_A           10 IQAILEACK-SG-SPKTRIMYGA--------------NLSYALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDIRK   72 (95)
T ss_dssp             HHHHHHHHT-TC-BCHHHHHHHH--------------TCCHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-cC-CCHHHHHHHh--------------CcCHHHHHHHHHHHHHCCCeEEEC-CeeEEChhHHHHHHHHHH
Confidence            357888777 45 8888888875              456689999999999999999986 589999999988887765


Q ss_pred             H
Q psy5605         126 Q  126 (152)
Q Consensus       126 ~  126 (152)
                      -
T Consensus        73 ~   73 (95)
T 1r7j_A           73 F   73 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=97.20  E-value=0.0019  Score=46.02  Aligned_cols=71  Identities=14%  Similarity=0.201  Sum_probs=53.7

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~L  120 (152)
                      +|..|+-.  +++.+..|+...|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+..+
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            66677777  78888888887642              3456677889999999998754  3455    6999999999


Q ss_pred             HHHHHHHHHHHHH
Q psy5605         121 DRIAAQIRVSKKE  133 (152)
Q Consensus       121 D~iA~~i~~~~~~  133 (152)
                      +++...+...+.+
T Consensus       108 ~~~~~~~~~~~~~  120 (127)
T 2frh_A          108 ESLLSRVNKRITE  120 (127)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9987776555444

>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=97.17  E-value=0.0012  Score=45.05  Aligned_cols=71  Identities=15%  Similarity=0.116  Sum_probs=55.7

Q ss_pred             HHHHHHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhH-HHHHHHHHHhCCcceecCCCCc----eeCcch
Q psy5605          43 YTRCAALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSV-ARKALQALEQVNIIEKSDDGGR----KITSHG  116 (152)
Q Consensus        43 YiRaASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~i-iR~~LQqLE~~glVek~~~gGR----~lT~~G  116 (152)
                      .+|...+|..++-.+ ++.+..|++..|-              +.+- +-.+++.||+.|||+.++.++|    .||++|
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            357777887777777 8999999999852              3455 6778899999999996654454    799999


Q ss_pred             HhhHHHHHHHH
Q psy5605         117 RRDMDRIAAQI  127 (152)
Q Consensus       117 ~~~LD~iA~~i  127 (152)
                      ++.++.+....
T Consensus        80 ~~~~~~~~~~~   90 (95)
T 2pg4_A           80 RRLAECLEKCR   90 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99998876543

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

Probab=97.16  E-value=0.0028  Score=44.95  Aligned_cols=66  Identities=12%  Similarity=0.143  Sum_probs=52.7

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
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            47888888999999999998753              34667789999999999997653  344    49999999988


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       101 ~~~~~~  106 (145)
T 3g3z_A          101 PLTESA  106 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776554

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

Probab=97.05  E-value=0.0082  Score=43.55  Aligned_cols=89  Identities=16%  Similarity=0.221  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|...+.-++.--+.|.+       ....|+..||              -|..-+|.+|+.|+..|+|+..+..|-.+++
T Consensus        14 ~~~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   79 (125)
T 3neu_A           14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA--------------VNPNTVSRAYQELERAGYIYAKRGMGSFVTS   79 (125)
T ss_dssp             HHHHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCeEEEecCCEEEEec
Confidence            456666666666555532       5778888884              4779999999999999999999988989988


Q ss_pred             chHhhHHHHHHHHHHHHHHHHHHHHhhcCce
Q psy5605         115 HGRRDMDRIAAQIRVSKKEAALQALAAQGIT  145 (152)
Q Consensus       115 ~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~  145 (152)
                      .- ..++.+-.......-+.-.+.++++|++
T Consensus        80 ~~-~~~~~~~~~~~~~~le~~~~~~~~~g~~  109 (125)
T 3neu_A           80 DK-ALFDQLKKELADAITERFLEEAKSIGLD  109 (125)
T ss_dssp             CH-HHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             Cc-hhhHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            43 3444443333344445555667777765

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

Probab=97.02  E-value=0.0032  Score=44.55  Aligned_cols=67  Identities=13%  Similarity=0.258  Sum_probs=52.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|....|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..++
T Consensus        41 ~iL~~l~~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  106 (143)
T 3oop_A           41 SVLEGIEANEPISQKEIALWTKK--------------DTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETT  106 (143)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------CHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHH
Confidence            36777887899999999998742              44667789999999999997653  354    49999999999


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      .+...+.
T Consensus       107 ~~~~~~~  113 (143)
T 3oop_A          107 ELRDIVE  113 (143)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8766543

>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=0.0042  Score=43.68  Aligned_cols=65  Identities=15%  Similarity=0.241  Sum_probs=51.6

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .|+..|+ .+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        41 ~iL~~l~-~~~~~~~ela~~l~--------------~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  105 (146)
T 2gxg_A           41 LVLRATS-DGPKTMAYLANRYF--------------VTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFN  105 (146)
T ss_dssp             HHHHHHT-TSCBCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHh-cCCcCHHHHHHHhC--------------CCchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHH
Confidence            3677788 89999999999874              245778889999999999987543  343    69999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       106 ~~~~~~  111 (146)
T 2gxg_A          106 KGIEIY  111 (146)
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=96.93  E-value=0.003  Score=45.97  Aligned_cols=59  Identities=19%  Similarity=0.159  Sum_probs=49.5

Q ss_pred             HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      ++-.+++.+..|...+|              -|.+-++.+|+.||+.|||+..++.|-.||+.|+..++.+..
T Consensus        49 l~~~~~~~~~~la~~l~--------------vs~~tvs~~l~~Le~~Glv~r~~~~~~~lT~~g~~~~~~~~~  107 (155)
T 2h09_A           49 IREVGEARQVDMAARLG--------------VSQPTVAKMLKRLATMGLIEMIPWRGVFLTAEGEKLAQESRE  107 (155)
T ss_dssp             HHHHSCCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTCEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHhCCCcCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCEEEecCCceEEChhHHHHHHHHHH
Confidence            34458889999999884              356789999999999999998887788999999998887654

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

Probab=96.89  E-value=0.0064  Score=44.19  Aligned_cols=66  Identities=20%  Similarity=0.183  Sum_probs=50.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.++.|....|-              +.+-+-.+++.||+.|||++.++  .+|    .||++|+..++
T Consensus        50 ~iL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  115 (162)
T 3k0l_A           50 TALSVLAAKPNLSNAKLAERSFI--------------KPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLN  115 (162)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTS--------------CGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHH
Confidence            36667777788888888888743              33556788999999999996653  344    59999999999


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       116 ~~~~~~  121 (162)
T 3k0l_A          116 QCNQVV  121 (162)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877654

>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=96.88  E-value=0.0064  Score=40.53  Aligned_cols=69  Identities=12%  Similarity=0.142  Sum_probs=54.7

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCc----eeCcchHhhHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGR----KITSHGRRDMDR  122 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR----~lT~~G~~~LD~  122 (152)
                      .|+..|.-.+++.+..|....|              -+.+-+...|+.||+.|||+..++ ++|    .+|+.|+..++.
T Consensus        24 ~il~~l~~~~~~s~~ela~~l~--------------is~~tv~~~l~~L~~~glv~~~~~~~~r~~~~~~t~~g~~~~~~   89 (109)
T 1sfx_A           24 RIYSLLLERGGMRVSEIARELD--------------LSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLKE   89 (109)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEEeecCCceEEEEecCcHHHHHHH
Confidence            4777777789999999999984              356789999999999999987643 455    699999998887


Q ss_pred             HHHHHHHH
Q psy5605         123 IAAQIRVS  130 (152)
Q Consensus       123 iA~~i~~~  130 (152)
                      +...+...
T Consensus        90 ~~~~~~~~   97 (109)
T 1sfx_A           90 FKSSILGE   97 (109)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            76655443

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

Probab=96.87  E-value=0.0068  Score=42.31  Aligned_cols=67  Identities=13%  Similarity=0.136  Sum_probs=51.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      .++..|+-.+++.+..|+...|              -+.+-+-.+++.||+.|||+..+  +++|    .||++|+..++
T Consensus        38 ~iL~~l~~~~~~~~~~la~~l~--------------~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  103 (138)
T 1jgs_A           38 KVLCSIRCAACITPVELKKVLS--------------VDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICE  103 (138)
T ss_dssp             HHHHHHHHHSSBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHH
Confidence            3666777778888999988764              24466777999999999998754  3344    59999999998


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      ++...+.
T Consensus       104 ~~~~~~~  110 (138)
T 1jgs_A          104 QCHQLVG  110 (138)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8766554

>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=96.87  E-value=0.0067  Score=42.50  Aligned_cols=66  Identities=15%  Similarity=0.257  Sum_probs=50.9

Q ss_pred             HHHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q psy5605          48 ALARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~  119 (152)
                      .||..|+-.+  ++.+..|+...|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+..
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            4777888876  8999999998752              3466778999999999998664  3455    499999999


Q ss_pred             HHHHHHHH
Q psy5605         120 MDRIAAQI  127 (152)
Q Consensus       120 LD~iA~~i  127 (152)
                      ++.+....
T Consensus       101 ~~~~~~~~  108 (139)
T 3eco_A          101 VEAFTSIF  108 (139)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876554

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

Probab=96.85  E-value=0.0049  Score=43.63  Aligned_cols=66  Identities=11%  Similarity=0.169  Sum_probs=48.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.++.|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        41 ~vL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~  106 (142)
T 3ech_A           41 HVLKLIDEQRGLNLQDLGRQMCR--------------DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHL  106 (142)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHC-----------------CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHH
Confidence            47778888899999999998753              23567788999999999997653  344    59999999999


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       107 ~~~~~~  112 (142)
T 3ech_A          107 HAELIM  112 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876654

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

Probab=96.84  E-value=0.0066  Score=43.86  Aligned_cols=66  Identities=12%  Similarity=0.203  Sum_probs=49.9

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..++.
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            5666777788888888888743              34677789999999999986643  454    499999999988


Q ss_pred             HHHHHH
Q psy5605         123 IAAQIR  128 (152)
Q Consensus       123 iA~~i~  128 (152)
                      +...+.
T Consensus       121 ~~~~~~  126 (159)
T 3s2w_A          121 MKKIAS  126 (159)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766543

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

Probab=96.84  E-value=0.016  Score=42.26  Aligned_cols=88  Identities=14%  Similarity=0.165  Sum_probs=58.5

Q ss_pred             HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|-+.+..+|.--+.|.      + ....|+..||              -|..-+|.+|+.|+..|+|+..+..|-.+++
T Consensus        12 ~~~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~--------------vSr~tvr~Al~~L~~~Gli~~~~g~G~~V~~   77 (126)
T 3by6_A           12 VYLQLVDRIKNEVATDVLSANDQLPSVRETALQEK--------------INPNTVAKAYKELEAQKVIRTIPGKGTFITG   77 (126)
T ss_dssp             HHHHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECS
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCeEEEcc
Confidence            46677776666555543      2 6788888884              4678999999999999999999988989988


Q ss_pred             chHhhHHHHH-HHHHHHHHHHHHHHHhhcCce
Q psy5605         115 HGRRDMDRIA-AQIRVSKKEAALQALAAQGIT  145 (152)
Q Consensus       115 ~G~~~LD~iA-~~i~~~~~~~~~~~~~~~~~~  145 (152)
                       ...++..+. .++... -+.--..++++|++
T Consensus        78 -~~~~~~~~~~~~~r~~-le~~~~~~~~~~~~  107 (126)
T 3by6_A           78 -NTASVKNSNQNRLLAD-LSQVIAELIKSGVK  107 (126)
T ss_dssp             -CHHHHHHHHHHHHHHH-HHHHHHHHHHTTCC
T ss_pred             -CchhhhHhHHHHHHHH-HHHHHHHHHHcCCC
Confidence             444444432 222222 22233345556654

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

Probab=96.80  E-value=0.0066  Score=42.15  Aligned_cols=66  Identities=12%  Similarity=0.199  Sum_probs=50.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      .|+..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        37 ~iL~~l~~~~~~~~~ela~~l~~--------------~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~  102 (139)
T 3bja_A           37 GVIQVLAKSGKVSMSKLIENMGC--------------VPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKK  102 (139)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHCSS--------------CCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHH
Confidence            36777788899999999998743              2345677899999999998753  3344    59999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       103 ~~~~~~  108 (139)
T 3bja_A          103 QVDVQY  108 (139)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=96.80  E-value=0.0066  Score=44.59  Aligned_cols=65  Identities=15%  Similarity=0.310  Sum_probs=48.4

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|+...|              -+.+-+-.+++.||+.|||++.+  .++|    .||++|+..+++
T Consensus        50 iL~~L~~~~~~t~~eLa~~l~--------------is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  115 (168)
T 2nyx_A           50 TLVILSNHGPINLATLATLLG--------------VQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQ  115 (168)
T ss_dssp             HHHHHHHHCSEEHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            555666667788888888763              34566777899999999998754  3344    599999999988


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       116 ~~~~~  120 (168)
T 2nyx_A          116 VTEHR  120 (168)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

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

Probab=96.77  E-value=0.0064  Score=44.15  Aligned_cols=65  Identities=15%  Similarity=0.221  Sum_probs=48.7

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|....|              -+.+-+-.+++.||+.|||++.++  ++|    .||++|+..+++
T Consensus        58 vL~~l~~~~~~t~~eLa~~l~--------------~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  123 (161)
T 3e6m_A           58 LLSSLSAYGELTVGQLATLGV--------------MEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE  123 (161)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHH
Confidence            555566667777888877753              345677789999999999997653  344    599999999998


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       124 ~~~~~  128 (161)
T 3e6m_A          124 ISPLI  128 (161)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>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=96.74  E-value=0.0062  Score=41.31  Aligned_cols=66  Identities=14%  Similarity=0.123  Sum_probs=49.6

Q ss_pred             HHHhhHhhcCCcchhhH----HHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC---CceeCcchHhhH
Q psy5605          48 ALARHIYMRSPVGVKTV----TKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---GRKITSHGRRDM  120 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L----~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~~G~~~L  120 (152)
                      .||..|+-.+++.+..|    +...              .-+.+-+-.+|+.||+.|||++.++.   .-.||++|+..+
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~~l--------------~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~   77 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNAEF--------------PMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFA   77 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHTTS--------------CCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHHHc--------------CCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHH
Confidence            36667777888999888    4432              23556778899999999999976542   236999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +.+...+
T Consensus        78 ~~~~~~~   84 (99)
T 1tbx_A           78 ISLKTAI   84 (99)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876554

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

Probab=96.73  E-value=0.011  Score=41.85  Aligned_cols=66  Identities=11%  Similarity=0.227  Sum_probs=49.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|              -+.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        46 ~iL~~l~~~~~~t~~ela~~l~--------------~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  111 (150)
T 2rdp_A           46 VALQWLLEEGDLTVGELSNKMY--------------LACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIE  111 (150)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHH
Confidence            3666777778899999998874              245667789999999999987542  343    59999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       112 ~~~~~~  117 (150)
T 2rdp_A          112 EVIEKR  117 (150)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

>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=96.73  E-value=0.0095  Score=41.99  Aligned_cols=67  Identities=22%  Similarity=0.227  Sum_probs=51.7

Q ss_pred             HHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhh
Q psy5605          47 AALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRD  119 (152)
Q Consensus        47 ASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~  119 (152)
                      ..||..|+- .+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..
T Consensus        38 ~~iL~~l~~~~~~~~~~~la~~l~--------------i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~  103 (147)
T 2hr3_A           38 LVVLGAIDRLGGDVTPSELAAAER--------------MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN  103 (147)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhC--------------CChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHH
Confidence            357778888 89999999999874              345778889999999999997653  344    599999999


Q ss_pred             HHHHHHHH
Q psy5605         120 MDRIAAQI  127 (152)
Q Consensus       120 LD~iA~~i  127 (152)
                      ++.+...+
T Consensus       104 ~~~~~~~~  111 (147)
T 2hr3_A          104 LYGNRAKR  111 (147)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876554

>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=96.70  E-value=0.012  Score=41.09  Aligned_cols=66  Identities=17%  Similarity=0.157  Sum_probs=51.1

Q ss_pred             HHHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhh
Q psy5605          48 ALARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~  119 (152)
                      .||..|+-.+  ++.+..|+...|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+..
T Consensus        38 ~iL~~l~~~~~~~~~~~ela~~l~~--------------~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~  103 (141)
T 3bro_A           38 TIIDYLSRNKNKEVLQRDLESEFSI--------------KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKL  103 (141)
T ss_dssp             HHHHHHHHTTTSCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTT
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCC--------------CcchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHH
Confidence            3677788777  8999999998853              45678889999999999986542  343    489999999


Q ss_pred             HHHHHHHH
Q psy5605         120 MDRIAAQI  127 (152)
Q Consensus       120 LD~iA~~i  127 (152)
                      ++.+...+
T Consensus       104 ~~~~~~~~  111 (141)
T 3bro_A          104 ETIILSYM  111 (141)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88776543

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

Probab=96.69  E-value=0.0059  Score=43.50  Aligned_cols=65  Identities=23%  Similarity=0.302  Sum_probs=50.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee--cC--CCCc----eeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK--SD--DGGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek--~~--~gGR----~lT~~G~~~  119 (152)
                      .||..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+.  .+  .++|    .||++|+..
T Consensus        45 ~iL~~l~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~  110 (154)
T 2qww_A           45 AMINVIYSTPGISVADLTKRLII--------------TGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDL  110 (154)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHH
Confidence            36777888899999999998852              34567789999999999998  43  3344    599999999


Q ss_pred             HHHHHHH
Q psy5605         120 MDRIAAQ  126 (152)
Q Consensus       120 LD~iA~~  126 (152)
                      ++++...
T Consensus       111 ~~~~~~~  117 (154)
T 2qww_A          111 SKRSTAN  117 (154)
T ss_dssp             HHHHHSC
T ss_pred             HHHHHhh
Confidence            8877655

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

Probab=96.68  E-value=0.0058  Score=43.05  Aligned_cols=62  Identities=18%  Similarity=0.237  Sum_probs=48.4

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+ +.++.|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        42 ~iL~~l~~~~-~t~~eLa~~l~--------------~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~  106 (146)
T 3tgn_A           42 HILMLLSEES-LTNSELARRLN--------------VSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAE  106 (146)
T ss_dssp             HHHHHHTTCC-CCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHH
T ss_pred             HHHHHHHhCC-CCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHH
Confidence            4777888777 99999999985              355788999999999999997653  344    49999999999


Q ss_pred             HHH
Q psy5605         122 RIA  124 (152)
Q Consensus       122 ~iA  124 (152)
                      .+.
T Consensus       107 ~~~  109 (146)
T 3tgn_A          107 EHH  109 (146)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            886

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

Probab=96.68  E-value=0.0093  Score=41.47  Aligned_cols=66  Identities=20%  Similarity=0.262  Sum_probs=52.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .|+..|+-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        33 ~iL~~l~~~~~~~~~ela~~l~--------------~s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~   98 (138)
T 3bpv_A           33 ACLLRIHREPGIKQDELATFFH--------------VDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIP   98 (138)
T ss_dssp             HHHHHHHHSTTCBHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHH
Confidence            4677777789999999999874              245678889999999999997542  233    69999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus        99 ~~~~~~  104 (138)
T 3bpv_A           99 LILKVE  104 (138)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=96.63  E-value=0.014  Score=40.00  Aligned_cols=64  Identities=17%  Similarity=0.235  Sum_probs=52.4

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGRRDMDRI  123 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~~~LD~i  123 (152)
                      .|++.| ..||+.+..|....|              -|.+-+...|+.||+.|+|+..++ ||    .||++|...+...
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            477777 689999999999874              356789999999999999998765 54    7999999888776


Q ss_pred             HHHH
Q psy5605         124 AAQI  127 (152)
Q Consensus       124 A~~i  127 (152)
                      ...+
T Consensus        89 ~~~~   92 (114)
T 2oqg_A           89 LERI   92 (114)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6554

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=96.60  E-value=0.0062  Score=43.55  Aligned_cols=57  Identities=18%  Similarity=0.200  Sum_probs=48.9

Q ss_pred             hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      -.+++.+..|+...|              -|.+-++.+|+.||+.|||+..+.++-.||++|+..++.+..
T Consensus        19 ~~~~~~~~ela~~l~--------------vs~~tvs~~l~~Le~~Glv~r~~~~~~~LT~~g~~~~~~~~~   75 (142)
T 1on2_A           19 EKGYARVSDIAEALA--------------VHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVY   75 (142)
T ss_dssp             HHSSCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             hcCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEeeCceEEEchhHHHHHHHHHH
Confidence            468999999999984              356788999999999999999887778999999999887654

>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=96.59  E-value=0.014  Score=41.88  Aligned_cols=66  Identities=14%  Similarity=0.231  Sum_probs=50.2

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|....|              -+.+-+-.+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        48 ~iL~~l~~~~~~t~~ela~~l~--------------is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  113 (154)
T 2eth_A           48 YAFLYVALFGPKKMKEIAEFLS--------------TTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFG  113 (154)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHTT--------------SCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHH
Confidence            4666777778888888888764              24567778999999999998754  3344    58999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       114 ~~~~~~  119 (154)
T 2eth_A          114 EILSNF  119 (154)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=96.59  E-value=0.0055  Score=43.93  Aligned_cols=67  Identities=15%  Similarity=0.306  Sum_probs=49.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.++.|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        45 ~iL~~l~~~~~~~~~eLa~~l~~--------------~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  110 (149)
T 4hbl_A           45 LVMLTLWEENPQTLNSIGRHLDL--------------SSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQE  110 (149)
T ss_dssp             HHHHHHHHSSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHH
Confidence            46777787899999999998743              45677789999999999997653  355    49999999998


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      .+...+.
T Consensus       111 ~~~~~~~  117 (149)
T 4hbl_A          111 AVFEAIS  117 (149)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8766543

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

Probab=96.58  E-value=0.0086  Score=42.55  Aligned_cols=55  Identities=18%  Similarity=0.302  Sum_probs=47.2

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      .+++.+..|+...|              -+.+-++.+|+.||+.|||+..+ ++-.||++|+...+.+..
T Consensus        29 ~~~~s~~ela~~l~--------------is~~tv~~~l~~Le~~Gli~r~~-~~~~Lt~~g~~~~~~~~~   83 (139)
T 2x4h_A           29 GEGAKINRIAKDLK--------------IAPSSVFEEVSHLEEKGLVKKKE-DGVWITNNGTRSINYLIK   83 (139)
T ss_dssp             TSCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHhC--------------CChHHHHHHHHHHHHCCCEEecC-CeEEEChhHHHHHHHHHH
Confidence            57899999999985              35678999999999999999888 688999999998776654

>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=96.52  E-value=0.0079  Score=42.65  Aligned_cols=67  Identities=13%  Similarity=0.139  Sum_probs=51.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.++.|+...|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..++
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            47777887889999999998742              45677889999999999997653  344    58999999999


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      ++.....
T Consensus       106 ~~~~~~~  112 (140)
T 3hsr_A          106 PLAEISV  112 (140)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8775543

>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=96.51  E-value=0.011  Score=42.10  Aligned_cols=64  Identities=14%  Similarity=0.269  Sum_probs=47.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee----cCCCCc----eeCcchHhhH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK----SDDGGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek----~~~gGR----~lT~~G~~~L  120 (152)
                      ||..| -.+++.++.|+...|-              +.+-+-.+++.||+.|||+.    ++.++|    .||++|+..+
T Consensus        43 iL~~l-~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~  107 (151)
T 3kp7_A           43 VLNML-SIEALTVGQITEKQGV--------------NKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYI  107 (151)
T ss_dssp             HHHHH-HHSCBCHHHHHHHHCS--------------CSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHH
T ss_pred             HHHHH-HcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHH
Confidence            66667 7789999999998753              23556788999999999996    554455    6999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +.+...+
T Consensus       108 ~~~~~~~  114 (151)
T 3kp7_A          108 KERKAIM  114 (151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876554

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

Probab=96.49  E-value=0.012  Score=41.05  Aligned_cols=66  Identities=12%  Similarity=0.162  Sum_probs=50.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .|+..|+-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        40 ~iL~~l~~~~~~t~~ela~~l~--------------~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  105 (142)
T 2fbi_A           40 RVIRILRQQGEMESYQLANQAC--------------ILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFV  105 (142)
T ss_dssp             HHHHHHHHHCSEEHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHH
Confidence            3677777788899999988764              245678889999999999987642  344    49999999988


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       106 ~~~~~~  111 (142)
T 2fbi_A          106 SMSGDM  111 (142)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765553

>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=96.49  E-value=0.0059  Score=41.65  Aligned_cols=68  Identities=16%  Similarity=0.308  Sum_probs=50.1

Q ss_pred             HHHHHHhhHhh-cCC---cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcch
Q psy5605          45 RCAALARHIYM-RSP---VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHG  116 (152)
Q Consensus        45 RaASilRkiYl-~g~---vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G  116 (152)
                      +...+|-.++- .++   +.+..|+...|-              +.+-+-.+|+.||+.||| .++..+|    .||++|
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            44556666654 345   889999998642              446677788999999999 4444466    799999


Q ss_pred             HhhHHHHHHHH
Q psy5605         117 RRDMDRIAAQI  127 (152)
Q Consensus       117 ~~~LD~iA~~i  127 (152)
                      +..++++...+
T Consensus        78 ~~~~~~~~~~~   88 (95)
T 2qvo_A           78 QKIAQQIKSII   88 (95)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99988876654

>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=96.48  E-value=0.0034  Score=53.26  Aligned_cols=68  Identities=22%  Similarity=0.255  Sum_probs=53.4

Q ss_pred             HHHHHHh-----hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-CceeCcch-H
Q psy5605          45 RCAALAR-----HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHG-R  117 (152)
Q Consensus        45 RaASilR-----kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-GR~lT~~G-~  117 (152)
                      |--.||+     .+--.+|||+..|.+.|+=            .-|..-||+-|..||++|++++.-.+ ||.-|.+| +
T Consensus        18 R~~~IL~~i~~~yl~~~~pV~s~~La~~~~l------------~VS~aTIRrDL~~LE~~GlL~r~HgsAgript~~g~r   85 (338)
T 1stz_A           18 RQRKVLYCIVREYIENKKPVSSQRVLEVSNI------------EFSSATIRNDMKKLEYLGYIYQPHTSAGRIPTDKGLR   85 (338)
T ss_dssp             HHHHHHHHHHHHHHHHCSCBCHHHHHHHSCC------------CSCHHHHHHHHHHHHHTTSEECCSSCSCBEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCccHHHHHHHhCC------------CCCHHHHHHHHHHHHHCCCEEEccCcceecCCcccch
Confidence            7778887     4445699999999999842            34778999999999999999987754 68888888 4


Q ss_pred             hhHHHHH
Q psy5605         118 RDMDRIA  124 (152)
Q Consensus       118 ~~LD~iA  124 (152)
                      ...|++.
T Consensus        86 ~yvd~l~   92 (338)
T 1stz_A           86 FYYEEML   92 (338)
T ss_dssp             HHHHHHH
T ss_pred             hhhhhhh
Confidence            4555543

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

Probab=96.47  E-value=0.021  Score=40.96  Aligned_cols=65  Identities=11%  Similarity=0.170  Sum_probs=43.6

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|....|              -+.+-+..+++.||+.|||+..++  ++    -.||++|+..++.
T Consensus        54 iL~~l~~~~~~t~~ela~~l~--------------is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  119 (162)
T 2fa5_A           54 VITILALYPGSSASEVSDRTA--------------MDKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYET  119 (162)
T ss_dssp             HHHHHHHSTTCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHH
Confidence            444444456666666666653              345678889999999999997542  23    3599999999988


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       120 ~~~~~  124 (162)
T 2fa5_A          120 VAPLV  124 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>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=96.47  E-value=0.018  Score=42.45  Aligned_cols=65  Identities=17%  Similarity=0.201  Sum_probs=45.2

Q ss_pred             HHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          49 LARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      ||..|+- .+++.+..|+...|              -+.+-+-.+++.||+.|||++..+  ++|    .||++|+..++
T Consensus        58 vL~~L~~~~~~~t~~eLa~~l~--------------i~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  123 (166)
T 3deu_A           58 TLHNIHQLPPDQSQIQLAKAIG--------------IEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIA  123 (166)
T ss_dssp             HHHHHHHSCSSEEHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHC--------------CCHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHH
Confidence            5555555 45677777777653              345677789999999999997653  344    49999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       124 ~~~~~~  129 (166)
T 3deu_A          124 EMEEVI  129 (166)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=96.46  E-value=0.0062  Score=43.40  Aligned_cols=90  Identities=16%  Similarity=0.165  Sum_probs=61.3

Q ss_pred             HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|-..+.-++..-+.|.+       ....|+..||              -|..-+|.+|+.||..|+|+..+..|-.+++
T Consensus        10 ~~~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~--------------vSr~tvr~al~~L~~~Gli~~~~~~G~~V~~   75 (113)
T 3tqn_A           10 IYQQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQ--------------INPLTVSKAYQSLLDDNVIEKRRGLGMLVKA   75 (113)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECT
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCeEEEeC
Confidence            455666666665555432       6778999884              4778999999999999999999988999998


Q ss_pred             chHhhHHHHHH-HHHHHHHHHHHHHHhhcCce
Q psy5605         115 HGRRDMDRIAA-QIRVSKKEAALQALAAQGIT  145 (152)
Q Consensus       115 ~G~~~LD~iA~-~i~~~~~~~~~~~~~~~~~~  145 (152)
                      ....++..+.. ..+...-+...+.+++.|++
T Consensus        76 ~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~  107 (113)
T 3tqn_A           76 GARQRLLTQEKQYFLKKQWPQIKNKLERLGID  107 (113)
T ss_dssp             THHHHHHHHHHHHHHHHTSTTSTTTTTTSCCC
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            87766554332 22333333344445556654

>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=96.46  E-value=0.0056  Score=42.74  Aligned_cols=63  Identities=16%  Similarity=0.124  Sum_probs=49.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+ .|+..++.|.+..+             .-|.+.+-..|+.||+.|||+...+  ++|    .||++|+..++
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            4677776 88999999998763             1466888999999999999986543  233    79999998876


Q ss_pred             HHH
Q psy5605         122 RIA  124 (152)
Q Consensus       122 ~iA  124 (152)
                      .+.
T Consensus        95 ~l~   97 (107)
T 2fsw_A           95 IID   97 (107)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=96.46  E-value=0.0075  Score=42.95  Aligned_cols=67  Identities=22%  Similarity=0.306  Sum_probs=44.1

Q ss_pred             HHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhh
Q psy5605          48 ALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~  119 (152)
                      .+|..|+-.  +++.+..|+...|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..
T Consensus        45 ~vL~~l~~~~~~~~t~~eLa~~l~~--------------~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~  110 (148)
T 3jw4_A           45 RMIGYIYENQESGIIQKDLAQFFGR--------------RGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAAL  110 (148)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHC--------------------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHH
Confidence            366666666  67788888876532              23456678999999999987653  344    399999999


Q ss_pred             HHHHHHHHH
Q psy5605         120 MDRIAAQIR  128 (152)
Q Consensus       120 LD~iA~~i~  128 (152)
                      ++.+...+.
T Consensus       111 ~~~~~~~~~  119 (148)
T 3jw4_A          111 VEEFNNIFL  119 (148)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988766543

>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=96.45  E-value=0.017  Score=40.82  Aligned_cols=66  Identities=15%  Similarity=0.215  Sum_probs=51.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        44 ~iL~~l~~~~~~t~~ela~~l~~--------------~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  109 (152)
T 3bj6_A           44 AILEGLSLTPGATAPQLGAALQM--------------KRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIIT  109 (152)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHH
Confidence            36777788889999999998853              45678889999999999997653  333    58999999988


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+-..+
T Consensus       110 ~~~~~~  115 (152)
T 3bj6_A          110 AIRADE  115 (152)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765544

>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=96.45  E-value=0.0095  Score=39.66  Aligned_cols=70  Identities=11%  Similarity=0.225  Sum_probs=53.7

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gG----R~lT~~G~~~LD  121 (152)
                      .|+..++-.++..+..|....|              -|.+-+-..|+.||+.|+|+...  .++    -.||++|+..+.
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            4777777788999999999874              35567888899999999998543  223    358999999888


Q ss_pred             HHHHHHHHHH
Q psy5605         122 RIAAQIRVSK  131 (152)
Q Consensus       122 ~iA~~i~~~~  131 (152)
                      .+...+..-.
T Consensus        86 ~~~~~~~~~~   95 (100)
T 1ub9_A           86 RFLSSLKAVI   95 (100)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8777765443

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

Probab=96.45  E-value=0.015  Score=41.83  Aligned_cols=65  Identities=18%  Similarity=0.236  Sum_probs=48.7

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|....|              -+.+-+..+|+.||+.|||+..++  ++|    .||++|+..++.
T Consensus        57 iL~~l~~~~~~t~~ela~~l~--------------is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  122 (162)
T 3cjn_A           57 ALAILSAKDGLPIGTLGIFAV--------------VEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDR  122 (162)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHC--------------CChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            555666667788888887763              345678889999999999997542  343    599999999988


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +....
T Consensus       123 ~~~~~  127 (162)
T 3cjn_A          123 LWPHM  127 (162)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=96.43  E-value=0.014  Score=40.44  Aligned_cols=66  Identities=17%  Similarity=0.323  Sum_probs=50.2

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|....|              -+.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        42 ~iL~~l~~~~~~t~~ela~~l~--------------~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (140)
T 2nnn_A           42 AALVRLGETGPCPQNQLGRLTA--------------MDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELE  107 (140)
T ss_dssp             HHHHHHHHHSSBCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHH
Confidence            3667777778888888888764              244677889999999999997542  233    59999999988


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       108 ~~~~~~  113 (140)
T 2nnn_A          108 AGLAAA  113 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

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

Probab=96.42  E-value=0.026  Score=39.37  Aligned_cols=65  Identities=17%  Similarity=0.241  Sum_probs=49.4

Q ss_pred             HHhhH-hhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          49 LARHI-YMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRki-Yl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      ||..| +-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        42 iL~~l~~~~~~~t~~~la~~l~--------------~s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (146)
T 2fbh_A           42 VLLHLARHRDSPTQRELAQSVG--------------VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA  107 (146)
T ss_dssp             HHHHHHHCSSCCBHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHhC--------------CChhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHH
Confidence            56666 4567888899988874              345678889999999999997653  233    68999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       108 ~~~~~~  113 (146)
T 2fbh_A          108 DIEAIA  113 (146)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            875443

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

Probab=96.40  E-value=0.019  Score=40.58  Aligned_cols=66  Identities=15%  Similarity=0.232  Sum_probs=49.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|              -+.+-+-.+++.||+.|||+..++  ++    -.||++|+..++
T Consensus        44 ~iL~~l~~~~~~t~~ela~~l~--------------~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~  109 (148)
T 3nrv_A           44 RIISVLSSASDCSVQKISDILG--------------LDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE  109 (148)
T ss_dssp             HHHHHHHHSSSBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHH
Confidence            4777788888899999988874              345677889999999999997642  23    469999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+-..+
T Consensus       110 ~~~~~~  115 (148)
T 3nrv_A          110 VASDFA  115 (148)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            876554

>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=96.35  E-value=0.022  Score=39.94  Aligned_cols=65  Identities=14%  Similarity=0.209  Sum_probs=51.6

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      |+..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++.
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            6677788899999999998842              45678889999999999987542  344    599999999987


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       100 ~~~~~  104 (144)
T 1lj9_A          100 IVREN  104 (144)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

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

Probab=96.31  E-value=0.012  Score=41.02  Aligned_cols=59  Identities=14%  Similarity=0.237  Sum_probs=47.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      .|+..|+-.+++.+..|+...|              -|.+-+..+++.||+.|||+..++  ++|    .||++|+..+
T Consensus        35 ~iL~~l~~~~~~~~~ela~~l~--------------is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           35 SILQTLLKDAPLHQLALQERLQ--------------IDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            3777788889999999999874              355778889999999999987653  343    5999999999

>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=96.29  E-value=0.016  Score=40.52  Aligned_cols=66  Identities=18%  Similarity=0.364  Sum_probs=51.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        37 ~iL~~l~~~~~~~~~~la~~l~--------------~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  102 (145)
T 2a61_A           37 DILQKIYFEGPKRPGELSVLLG--------------VAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIE  102 (145)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHH
Confidence            4677777788999999999874              245678889999999999997642  333    69999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       103 ~~~~~~  108 (145)
T 2a61_A          103 KVIERR  108 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            765543

>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=96.27  E-value=0.0014  Score=54.83  Aligned_cols=66  Identities=26%  Similarity=0.443  Sum_probs=0.0

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      |-..||+.||-.+++++..|+..+|-              |..-+|..|+.||+.|+|+... .|=.||++|+..++.+-
T Consensus        21 r~~~iL~~l~~~~~~t~~eLa~~l~v--------------s~~Tv~r~l~~Le~~Glv~~~~-~gi~LT~~G~~~~~~~~   85 (345)
T 2o0m_A           21 ERFQILRNIYWMQPIGRRSLSETMGI--------------TERVLRTETDVLKQLNLIEPSK-SGMTLTERGLEVYQGLE   85 (345)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEe-cceEEcHHHHHHHHHHH
Confidence            55579999999999999999999853              5578999999999999998555 47899999998776553


Q ss_pred             H
Q psy5605         125 A  125 (152)
Q Consensus       125 ~  125 (152)
                      .
T Consensus        86 ~   86 (345)
T 2o0m_A           86 L   86 (345)
T ss_dssp             -
T ss_pred             H
Confidence            3

>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=96.27  E-value=0.013  Score=40.96  Aligned_cols=62  Identities=11%  Similarity=0.163  Sum_probs=48.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD  121 (152)
                      .||+.|+ .|+..++.|.+...             .-|.+.+-..|+.||+.|||+...+  ++    -.||++|++.++
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            3677776 89999999998751             3567889999999999999986543  23    489999999876


Q ss_pred             HH
Q psy5605         122 RI  123 (152)
Q Consensus       122 ~i  123 (152)
                      .+
T Consensus        84 ~~   85 (107)
T 2hzt_A           84 IL   85 (107)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=96.26  E-value=0.01  Score=41.71  Aligned_cols=66  Identities=20%  Similarity=0.286  Sum_probs=49.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .|+..|+-.+++.+..|+...|-              +.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        41 ~iL~~l~~~~~~~~~ela~~l~~--------------~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  106 (142)
T 2bv6_A           41 LVLTILWDESPVNVKKVVTELAL--------------DTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRP  106 (142)
T ss_dssp             HHHHHHHHSSEEEHHHHHHHTTC--------------CTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCC--------------ChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHH
Confidence            36667777788888888888743              23457789999999999987653  344    57999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       107 ~~~~~~  112 (142)
T 2bv6_A          107 ELSNAS  112 (142)
T ss_dssp             HHTTHH
T ss_pred             HHHHHH
Confidence            876443

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

Probab=96.26  E-value=0.024  Score=40.44  Aligned_cols=65  Identities=12%  Similarity=0.226  Sum_probs=45.7

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|....|              -+.+-+-.+++.||+.|||+..++  ++|    .||++|+..++.
T Consensus        48 iL~~l~~~~~~t~~ela~~l~--------------i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  113 (155)
T 3cdh_A           48 VLACLVDNDAMMITRLAKLSL--------------MEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAES  113 (155)
T ss_dssp             HHHHHSSCSCBCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHH
Confidence            555555566777777777653              344667789999999999997643  333    599999999988


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       114 ~~~~~  118 (155)
T 3cdh_A          114 LVASA  118 (155)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76554

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=96.25  E-value=0.0051  Score=42.75  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=42.3

Q ss_pred             HHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec----CCCCceeC
Q psy5605          47 AALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS----DDGGRKIT  113 (152)
Q Consensus        47 ASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~----~~gGR~lT  113 (152)
                      ..|+..++-.| ++.+..|+..+|              -|.+-+|.+|+.|++.|+|+..    +.+|+.+.
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lg--------------vs~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~   78 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLN--------------IKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIY   78 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTT--------------SCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEecccCCCceEEE
Confidence            35787787777 899999999984              4678899999999999999987    66676555

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

Probab=96.22  E-value=0.022  Score=37.84  Aligned_cols=66  Identities=14%  Similarity=0.169  Sum_probs=50.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDMDRIA  124 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~LD~iA  124 (152)
                      .|+..|.-.+++.+..|....|              -|.+-+...|+.||+.|+|+..+++.   -.||++|...+-...
T Consensus        28 ~il~~l~~~~~~s~~ela~~l~--------------is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l   93 (99)
T 3cuo_A           28 LILCMLSGSPGTSAGELTRITG--------------LSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATL   93 (99)
T ss_dssp             HHHHHHTTCCSEEHHHHHHHHC--------------CCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHH
Confidence            4777676667999999999985              35678999999999999999887532   268999877665554


Q ss_pred             HHH
Q psy5605         125 AQI  127 (152)
Q Consensus       125 ~~i  127 (152)
                      .++
T Consensus        94 ~~~   96 (99)
T 3cuo_A           94 KNV   96 (99)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            443

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

Probab=96.22  E-value=0.013  Score=41.85  Aligned_cols=64  Identities=13%  Similarity=0.194  Sum_probs=44.6

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||..|+-.+++.+..|....|              -+.+-+..+|+.||+.|||+..++  ++|    .||++|+..++.
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            455555566677777776653              355678889999999999997653  333    589999998877


Q ss_pred             HHHH
Q psy5605         123 IAAQ  126 (152)
Q Consensus       123 iA~~  126 (152)
                      +...
T Consensus       118 ~~~~  121 (153)
T 2pex_A          118 AGAV  121 (153)
T ss_dssp             STTH
T ss_pred             HHHH
Confidence            6543

>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=0.022  Score=41.53  Aligned_cols=65  Identities=8%  Similarity=0.164  Sum_probs=46.2

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      ||..|+-.  +++.+..|....|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..+
T Consensus        51 vL~~l~~~~~~~~t~~eLa~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  116 (168)
T 3u2r_A           51 TLRLLRSVHPEGMATLQIADRLIS--------------RAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLL  116 (168)
T ss_dssp             HHHHHHHHTTSCEEHHHHHHHC-----------------CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCC--------------ChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHH
Confidence            55566664  47777777777632              33567789999999999997643  344    5999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +.+...+
T Consensus       117 ~~~~~~~  123 (168)
T 3u2r_A          117 KDLEEPV  123 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876643

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=96.19  E-value=0.051  Score=39.81  Aligned_cols=64  Identities=17%  Similarity=0.232  Sum_probs=46.9

Q ss_pred             HHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          43 YTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        43 YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      |-+.+.-+|..-+.|.      + ....|+..||              -|..-+|.+|+.||..|+|+..+..|-.+++.
T Consensus         6 ~~~i~~~i~~~I~~g~l~~G~~LPse~~La~~~g--------------vSr~tVr~Al~~L~~~Gli~~~~g~G~~V~~~   71 (129)
T 2ek5_A            6 YKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHR--------------INPATARNGLTLLVEAGILYKKRGIGMFVSAQ   71 (129)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTT--------------CCHHHHHHHHHHHHTTTSEEEETTTEEEECTT
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEecCCEEEEecC
Confidence            3444554554444432      2 5677888874              47899999999999999999999889999987


Q ss_pred             hHhhH
Q psy5605         116 GRRDM  120 (152)
Q Consensus       116 G~~~L  120 (152)
                      ...++
T Consensus        72 ~~~~~   76 (129)
T 2ek5_A           72 APALI   76 (129)
T ss_dssp             HHHHH
T ss_pred             chHhh
Confidence            66554

>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=96.13  E-value=0.03  Score=39.84  Aligned_cols=65  Identities=22%  Similarity=0.245  Sum_probs=43.4

Q ss_pred             HHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          49 LARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      ||..|+-.+ ++.+..|....|              -+.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        44 vL~~l~~~~~~~t~~eLa~~l~--------------i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  109 (150)
T 3fm5_A           44 VLVLACEQAEGVNQRGVAATMG--------------LDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRD  109 (150)
T ss_dssp             HHHHHHHSTTCCCSHHHHHHHT--------------CCHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHH
T ss_pred             HHHHHHhCCCCcCHHHHHHHHC--------------CCHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHH
Confidence            454555443 566777776654              245667778999999999997653  343    59999999999


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       110 ~~~~~~  115 (150)
T 3fm5_A          110 DAKARV  115 (150)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876654

>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=96.13  E-value=0.019  Score=40.75  Aligned_cols=66  Identities=17%  Similarity=0.243  Sum_probs=51.6

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        41 ~iL~~l~~~~~~t~~ela~~l~--------------~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  106 (155)
T 1s3j_A           41 FVLASLKKHGSLKVSEIAERME--------------VKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFE  106 (155)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHH
Confidence            4677777788999999999874              245678889999999999987643  333    69999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+...+
T Consensus       107 ~~~~~~  112 (155)
T 1s3j_A          107 EVLAGR  112 (155)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            866554

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

Probab=96.08  E-value=0.014  Score=45.70  Aligned_cols=63  Identities=13%  Similarity=0.249  Sum_probs=51.4

Q ss_pred             HhhHhh----cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          50 ARHIYM----RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        50 lRkiYl----~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      |+.||.    .+++.+..|+...|              -|.+-+..+|+.||+.|||+..++++=.||++|++...++..
T Consensus         8 L~~I~~l~~~~~~~~~~~lA~~l~--------------vs~~tvs~~l~~Le~~GlV~r~~~~~i~LT~~G~~~~~~~~~   73 (214)
T 3hrs_A            8 LKCLYELGTRHNKITNKEIAQLMQ--------------VSPPAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVSDLYR   73 (214)
T ss_dssp             HHHHHHTTSSCSCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCcCHHHHHHHHC--------------CChhHHHHHHHHHHHCCCEEEecCCCeEECHHHHHHHHHHHH
Confidence            344553    46888999999874              345778899999999999999987788999999999888776


Q ss_pred             H
Q psy5605         126 Q  126 (152)
Q Consensus       126 ~  126 (152)
                      .
T Consensus        74 ~   74 (214)
T 3hrs_A           74 K   74 (214)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=96.06  E-value=0.022  Score=41.45  Aligned_cols=61  Identities=16%  Similarity=0.285  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|...+.-+|..=+.|-      + ....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++
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            57777777777666542      2 5567888884              5789999999999999999999977877776


Q ss_pred             ch
Q psy5605         115 HG  116 (152)
Q Consensus       115 ~G  116 (152)
                      ..
T Consensus        81 ~~   82 (134)
T 4ham_A           81 QT   82 (134)
T ss_dssp             CS
T ss_pred             Cc
Confidence            44

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

Probab=96.06  E-value=0.012  Score=41.52  Aligned_cols=69  Identities=12%  Similarity=0.159  Sum_probs=47.2

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc-----eeCcchHhhHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR-----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR-----~lT~~G~~~LD  121 (152)
                      ||.-|. .+|.--..+.+....          +..-|.+.+-.+|+.||+.|||+....  +||     .||++|+..++
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            454444 355444455555432          234567889999999999999986542  454     59999999999


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      +......
T Consensus        83 ~~~~~~~   89 (108)
T 3l7w_A           83 YLTKEWS   89 (108)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876653

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

Probab=95.93  E-value=0.016  Score=40.76  Aligned_cols=63  Identities=11%  Similarity=0.189  Sum_probs=49.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD  121 (152)
                      .||..|+ .|+..++.|.+...             .-+.+.+-..|+.||+.|||+...+  ++    -.||++|+..++
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            4777776 68999999999861             2466888999999999999986653  23    378999998877


Q ss_pred             HHH
Q psy5605         122 RIA  124 (152)
Q Consensus       122 ~iA  124 (152)
                      .+.
T Consensus        92 ~~~   94 (112)
T 1z7u_A           92 ALS   94 (112)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=95.77  E-value=0.047  Score=41.12  Aligned_cols=67  Identities=15%  Similarity=0.188  Sum_probs=51.4

Q ss_pred             HHHhhHhh--cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhh
Q psy5605          48 ALARHIYM--RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl--~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~  119 (152)
                      .||..|+-  .+++.++.|+...|              -+.+-+-.+++.||+.|||+..+  ..+|    .||++|+..
T Consensus        45 ~vL~~L~~~~~~~~t~~eLa~~l~--------------is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~  110 (189)
T 3nqo_A           45 MTILSILHLPEEETTLNNIARKMG--------------TSKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKV  110 (189)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHH
T ss_pred             HHHHHHHhccCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHH
Confidence            46767776  56899999999874              23466778899999999998754  3454    599999999


Q ss_pred             HHHHHHHHH
Q psy5605         120 MDRIAAQIR  128 (152)
Q Consensus       120 LD~iA~~i~  128 (152)
                      ++.+.....
T Consensus       111 ~~~~~~~~~  119 (189)
T 3nqo_A          111 MVTCSRTGI  119 (189)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998776543

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

Probab=95.75  E-value=0.042  Score=38.66  Aligned_cols=66  Identities=17%  Similarity=0.235  Sum_probs=50.2

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.++ .+..|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        41 ~iL~~l~~~~~-~~~~la~~l~~--------------~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  105 (144)
T 3f3x_A           41 SILKATSEEPR-SMVYLANRYFV--------------TQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLL  105 (144)
T ss_dssp             HHHHHHHHSCE-EHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCC-CHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHH
Confidence            36777777777 88999988742              44567789999999999997653  233    59999999998


Q ss_pred             HHHHHHH
Q psy5605         122 RIAAQIR  128 (152)
Q Consensus       122 ~iA~~i~  128 (152)
                      .+.....
T Consensus       106 ~~~~~~~  112 (144)
T 3f3x_A          106 EANEVLR  112 (144)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8765543

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

Probab=95.71  E-value=0.025  Score=42.12  Aligned_cols=64  Identities=16%  Similarity=0.124  Sum_probs=50.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||+.++ .|+...+.|++.-.             .-|.+.+-..|+.||+.|||+....  ..|    .||++|++.+.
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            4677776 88999999988752             2567899999999999999997642  233    69999999887


Q ss_pred             HHHH
Q psy5605         122 RIAA  125 (152)
Q Consensus       122 ~iA~  125 (152)
                      .+..
T Consensus        96 ~l~~   99 (131)
T 4a5n_A           96 IVLQ   99 (131)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6644

>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=95.67  E-value=0.029  Score=41.54  Aligned_cols=61  Identities=13%  Similarity=0.217  Sum_probs=49.4

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-----GRKITSHGRRDMDR  122 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-----GR~lT~~G~~~LD~  122 (152)
                      .||+.++ .|+..++.|.+..|              -|.+.+-..|+.||+.|||++.+..     .-.||++|+..+..
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            3777775 78999999998863              4678899999999999999976632     34799999988765


Q ss_pred             H
Q psy5605         123 I  123 (152)
Q Consensus       123 i  123 (152)
                      +
T Consensus        93 l   93 (146)
T 2f2e_A           93 L   93 (146)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=95.61  E-value=0.0093  Score=41.50  Aligned_cols=67  Identities=10%  Similarity=0.147  Sum_probs=51.0

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGRRDMDRI  123 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~~~LD~i  123 (152)
                      .||..|+-.+|+.+..|....|-.  .+        -+.+-+-.+|+.||+.|||+..+++.|    .||++|+...+.+
T Consensus        14 ~vL~~l~~~~~~t~~ela~~l~~~--~~--------~s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~lT~~g~~~~~~~   83 (123)
T 1okr_A           14 EVMNIIWMKKYASANNIIEEIQMQ--KD--------WSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTS   83 (123)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHHHH--CC--------CCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESSCHHHHHHHHH
T ss_pred             HHHHHHHhCCCcCHHHHHHHHhcc--CC--------CcHhhHHHHHHHHHHCCCeEEEecCCeEEEEEecCHHHHHHHHH
Confidence            366677778999999999998531  11        245778899999999999998876332    4899999887665


Q ss_pred             H
Q psy5605         124 A  124 (152)
Q Consensus       124 A  124 (152)
                      .
T Consensus        84 ~   84 (123)
T 1okr_A           84 K   84 (123)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=95.60  E-value=0.029  Score=40.73  Aligned_cols=64  Identities=13%  Similarity=0.216  Sum_probs=45.2

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      +|..||..  |++.++.|+...|-              +.+-+=.++..||+.|||+..++  .+|    .||++|+..+
T Consensus        40 vL~~L~~~~~~~~t~~eLa~~l~~--------------~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  105 (147)
T 4b8x_A           40 ALVLLTFSKSGELPMSKIGERLMV--------------HPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVV  105 (147)
T ss_dssp             HHHHHHTSGGGEEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHH
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHH
Confidence            55566653  56788888887643              33556668999999999987653  354    4899999999


Q ss_pred             HHHHHH
Q psy5605         121 DRIAAQ  126 (152)
Q Consensus       121 D~iA~~  126 (152)
                      +++...
T Consensus       106 ~~~~~~  111 (147)
T 4b8x_A          106 EAATRD  111 (147)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887554

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

Probab=95.53  E-value=0.038  Score=39.46  Aligned_cols=66  Identities=9%  Similarity=0.102  Sum_probs=46.5

Q ss_pred             HHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          48 ALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        48 SilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      .||..|+ -.+++.+..|....|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..+
T Consensus        51 ~iL~~L~~~~~~~~~~ela~~l~i--------------~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~  116 (160)
T 3boq_A           51 DAMAQLARNPDGLSMGKLSGALKV--------------TNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTF  116 (160)
T ss_dssp             HHHHHHHHCTTCEEHHHHHHHCSS--------------CCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCC--------------ChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHH
Confidence            3666674 4678888888888642              22445668899999999997653  343    5999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +.+...+
T Consensus       117 ~~~~~~~  123 (160)
T 3boq_A          117 KQASEAH  123 (160)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876554

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=95.44  E-value=0.021  Score=39.74  Aligned_cols=60  Identities=13%  Similarity=0.139  Sum_probs=49.2

Q ss_pred             HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchh-HHHHHHHHHHhCCcceecCCCCc---eeCcchHhhH
Q psy5605          46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGS-VARKALQALEQVNIIEKSDDGGR---KITSHGRRDM  120 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~-iiR~~LQqLE~~glVek~~~gGR---~lT~~G~~~L  120 (152)
                      .-.|+.-|.-+||..+..|++..|=              +.. -+|..|+.||+.|+|++.. .||   .||++|+..|
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--------------TKARDINAVLIDMERQGDVYRQG-TTPPIWHLTDKKRERM   76 (79)
T ss_dssp             HHHHHHHHHHTCCEEHHHHHHHHCG--------------GGHHHHHHHHHHHHHTTSEEEEC-SSSCEEEECHHHHTTT
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHcCC--------------CcHHHHHHHHHHHHHCCCEEecC-CCCCCeEeCHhHHhHh
Confidence            3467777888999999999999863              345 7999999999999999664 466   7899998765

>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=95.41  E-value=0.036  Score=44.64  Aligned_cols=54  Identities=22%  Similarity=0.428  Sum_probs=45.4

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      .+|+|...|+...|              =|-..+|..++-|++.|||+..+ +|=.||++|++...++-
T Consensus        28 ~~~V~~~~LA~~Lg--------------vS~~SV~~~lkkL~e~GLV~~~~-~Gv~LTe~G~~~A~~i~   81 (200)
T 2p8t_A           28 KEPLGRKQISERLE--------------LGEGSVRTLLRKLSHLDIIRSKQ-RGHFLTLKGKEIRDKLL   81 (200)
T ss_dssp             TSCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHHH
T ss_pred             cCCccHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEeC-CCeEECHHHHHHHHHHH
Confidence            58999999999986              34578999999999999999888 89999999998766553

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

Probab=95.31  E-value=0.028  Score=39.77  Aligned_cols=63  Identities=8%  Similarity=0.154  Sum_probs=49.8

Q ss_pred             HHHhhHhhcCCcc--hhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCcchHhhHHHH
Q psy5605          48 ALARHIYMRSPVG--VKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITSHGRRDMDRI  123 (152)
Q Consensus        48 SilRkiYl~g~vG--V~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~G~~~LD~i  123 (152)
                      .|++.+. .|+..  ++.|.+...             .-|.+.+-..|+.||+.|||++...  .--.||++|++.++.+
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 88888  999998751             2467889999999999999998753  2458999999987765


Q ss_pred             H
Q psy5605         124 A  124 (152)
Q Consensus       124 A  124 (152)
                      .
T Consensus        97 ~   97 (111)
T 3df8_A           97 M   97 (111)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=95.31  E-value=0.049  Score=39.06  Aligned_cols=47  Identities=17%  Similarity=0.168  Sum_probs=36.0

Q ss_pred             CCCchhHHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhhHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSD---DGGR-----KITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~---~gGR-----~lT~~G~~~LD~iA~~i~  128 (152)
                      ..-+.+.+-.+|+.||+.|||+...   .+||     .||++|++.++.......
T Consensus        43 ~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~~   97 (116)
T 3f8b_A           43 MELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENMRLAFESWS   97 (116)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECHHHHHHHHHHHHHHH
Confidence            3556788999999999999998652   2342     699999999998776543

>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=95.27  E-value=0.036  Score=39.95  Aligned_cols=67  Identities=19%  Similarity=0.193  Sum_probs=51.9

Q ss_pred             HHHHHhhHhhcCCcchhhHHH-HhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          46 CAALARHIYMRSPVGVKTVTK-IFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~-~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      -.|||+.|+-+++..++.|.. .-+              =..+.+=.-++-||+.|||+.+.+ +=.||++|+..+...+
T Consensus        18 QfsiL~~L~~~~~~t~~~Lae~~l~--------------~drstvsrnl~~L~r~GlVe~~~~-Dl~LT~~G~~~l~~a~   82 (95)
T 1bja_A           18 TATILITIAKKDFITAAEVREVHPD--------------LGNAVVNSNIGVLIKKGLVEKSGD-GLIITGEAQDIISNAA   82 (95)
T ss_dssp             HHHHHHHHHHSTTBCHHHHHHTCTT--------------SCHHHHHHHHHHHHTTTSEEEETT-EEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHhc--------------ccHHHHHHHHHHHHHCCCeecCCC-CeeeCHhHHHHHHHHH
Confidence            368999999999999999998 422              234555566799999999994443 5679999999998876


Q ss_pred             HHH
Q psy5605         125 AQI  127 (152)
Q Consensus       125 ~~i  127 (152)
                      .-=
T Consensus        83 ~~W   85 (95)
T 1bja_A           83 TLY   85 (95)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=95.27  E-value=0.0057  Score=44.56  Aligned_cols=42  Identities=10%  Similarity=0.131  Sum_probs=35.5

Q ss_pred             CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      .-|..-+|.+|+.||..|+|+..+..|-.+++....++..+.
T Consensus        46 ~vSr~tvr~Al~~L~~~G~i~~~~~~G~~V~~~~~~~~~~~~   87 (126)
T 3ic7_A           46 EVNANTVMRSYEYLQSQEVIYNKRGIGFFVASGAKMLIHSLR   87 (126)
T ss_dssp             -CCSGGGHHHHHHHHTTTSEEEETTTEEEECTTHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHCCcEEEEcCCccEEccCcHHHHHHHH
Confidence            357789999999999999999999889999998876666554

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

Probab=95.24  E-value=0.029  Score=38.09  Aligned_cols=54  Identities=17%  Similarity=0.152  Sum_probs=45.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      .|++.|  .+++.++.|....|              -|.+-+++.|+.||+.|+|+... +.-.||+.|+.
T Consensus        35 ~Il~~L--~~~~~~~eLa~~l~--------------is~~tv~~~L~~L~~~Glv~~~~-g~y~l~~~g~~   88 (96)
T 1y0u_A           35 KILRML--DKGRSEEEIMQTLS--------------LSKKQLDYHLKVLEAGFCIERVG-ERWVVTDAGKI   88 (96)
T ss_dssp             HHHHHH--HTTCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEET-TEEEECTTTCC
T ss_pred             HHHHHH--cCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEC-CEEEECCCchH
Confidence            477777  89999999999883              35678999999999999999877 67789999864

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

Probab=95.17  E-value=0.2  Score=36.52  Aligned_cols=65  Identities=18%  Similarity=0.279  Sum_probs=44.8

Q ss_pred             HHhhHhhcCC-cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          49 LARHIYMRSP-VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl~g~-vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      +|..|+-.++ ...+.|+...|              -+.+-+=.+++.||+.|||+..+  .++|    .||++|+..++
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~--------------~~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~  101 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIG--------------IEQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIE  101 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHH
Confidence            5556664443 44466777653              23455667899999999998654  3455    48999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       102 ~~~~~~  107 (151)
T 4aik_A          102 QVDGVI  107 (151)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

>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=95.16  E-value=0.018  Score=40.55  Aligned_cols=65  Identities=14%  Similarity=0.173  Sum_probs=48.7

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|              -+.+-+..+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        44 ~iL~~l~~~~~~~~~~la~~l~--------------~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~  109 (147)
T 1z91_A           44 LALLLLWEHETLTVKKMGEQLY--------------LDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKE  109 (147)
T ss_dssp             HHHHHHHHHSEEEHHHHHHTTT--------------CCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGG
T ss_pred             HHHHHHHHCCCCCHHHHHHHHC--------------CCcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence            3566677677888888887653              345778889999999999997653  344    58999999988


Q ss_pred             HHHHH
Q psy5605         122 RIAAQ  126 (152)
Q Consensus       122 ~iA~~  126 (152)
                      .+...
T Consensus       110 ~~~~~  114 (147)
T 1z91_A          110 KAVDI  114 (147)
T ss_dssp             GTTTH
T ss_pred             HHHHH
Confidence            76443

>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=95.12  E-value=0.053  Score=38.89  Aligned_cols=62  Identities=19%  Similarity=0.272  Sum_probs=47.7

Q ss_pred             HHHhhHhhc------CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCc---eeCcchH
Q psy5605          48 ALARHIYMR------SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGR---KITSHGR  117 (152)
Q Consensus        48 SilRkiYl~------g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR---~lT~~G~  117 (152)
                      ++++.|...      +++-...|++.-              .=+.+-+++.|..||+.|||+.... .||   .||++|+
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 EVLLVLREAGIENGATPWSLPKIAKRA--------------QLPMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGA   85 (96)
T ss_dssp             HHHHHHHHHTSSTTCCCCBHHHHHHHH--------------TCCHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHH
T ss_pred             HHHHHHHHHHhhCCCCCcCHHHHHHHh--------------CCchhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHHH
Confidence            566666655      667777777764              4567899999999999999996543 355   6999999


Q ss_pred             hhHHHH
Q psy5605         118 RDMDRI  123 (152)
Q Consensus       118 ~~LD~i  123 (152)
                      ..+++.
T Consensus        86 ~~l~~~   91 (96)
T 2obp_A           86 ALAAQL   91 (96)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            988764

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=95.00  E-value=0.076  Score=40.93  Aligned_cols=67  Identities=15%  Similarity=0.083  Sum_probs=49.9

Q ss_pred             HHHHHHHHhhHhhcCC------cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          43 YTRCAALARHIYMRSP------VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        43 YiRaASilRkiYl~g~------vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      +-.++.-+|.--+.|-      +....|+..||              -|...+|.+|+.||..|||+..+..|-.+++-.
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            3344445555444442      44677888884              578999999999999999999998898888877


Q ss_pred             HhhHHHH
Q psy5605         117 RRDMDRI  123 (152)
Q Consensus       117 ~~~LD~i  123 (152)
                      ..++..+
T Consensus        84 ~~~~~e~   90 (222)
T 3ihu_A           84 LQETLDV   90 (222)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766654

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=94.99  E-value=0.096  Score=37.79  Aligned_cols=86  Identities=17%  Similarity=0.177  Sum_probs=53.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGG-----RKITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gG-----R~lT~~G~~~L  120 (152)
                      ||.-|. .+|.---.|.+....   .     .+..-|.+.+-.+|+.||+.|||+...   .+|     -.||++|+..|
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            443333 455433455555533   2     234567789999999999999998653   234     35999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCc
Q psy5605         121 DRIAAQIRVSKKEAALQALAAQGI  144 (152)
Q Consensus       121 D~iA~~i~~~~~~~~~~~~~~~~~  144 (152)
                      +....+.. .+.+...+.|...|+
T Consensus        89 ~~~~~~~~-~~~~~i~~il~~~~~  111 (116)
T 3hhh_A           89 ADFWQRWT-LLSKQVNKMKKNGGI  111 (116)
T ss_dssp             HHHHHHHH-HHHHHHHHHHHC---
T ss_pred             HHHHHHHH-HHHHHHHHHHCcCCc
Confidence            99876654 444444455554444

>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=94.94  E-value=0.024  Score=40.21  Aligned_cols=51  Identities=22%  Similarity=0.245  Sum_probs=43.5

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcchHhhHHHHH
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G~~~LD~iA  124 (152)
                      .+..|+..||              -|..-+|.+|+.||+.|+|+..+  ..|-.+++....++..+.
T Consensus        45 s~~eLa~~lg--------------VSr~tVr~al~~L~~~GlI~~~~gG~~G~~V~~~~~~~~~~~~   97 (102)
T 2b0l_A           45 VASKIADRVG--------------ITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELE   97 (102)
T ss_dssp             CHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECSSSCEEEEECCHHHHHHHH
T ss_pred             CHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEeCCCCcEEEecCCHHHHHHHH
Confidence            7888888884              47899999999999999999988  458999998888877654

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=94.91  E-value=0.061  Score=41.52  Aligned_cols=65  Identities=15%  Similarity=0.099  Sum_probs=49.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      .||..|+-.+++.+..|+...|-              +.+-+-.+++.||+.|||+..++  ++|    .||++|+..++
T Consensus        52 ~iL~~L~~~~~~t~~eLa~~l~i--------------~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  117 (207)
T 2fxa_A           52 HILWIAYQLNGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFW  117 (207)
T ss_dssp             HHHHHHHHHTSEEHHHHHHHTTC--------------CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHH
Confidence            36677777888999999988743              34666778999999999997653  344    59999999998


Q ss_pred             HHHHH
Q psy5605         122 RIAAQ  126 (152)
Q Consensus       122 ~iA~~  126 (152)
                      ++...
T Consensus       118 ~~~~~  122 (207)
T 2fxa_A          118 SLLEE  122 (207)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87644

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

Probab=94.87  E-value=0.09  Score=37.44  Aligned_cols=60  Identities=12%  Similarity=0.189  Sum_probs=46.0

Q ss_pred             HHHHHHhhHhhc---CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcchHh
Q psy5605          45 RCAALARHIYMR---SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHGRR  118 (152)
Q Consensus        45 RaASilRkiYl~---g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G~~  118 (152)
                      +|..++..|..+   +++.+..|+..+|              -|.+.+|++|++|+++|||+...  .||..|+.....
T Consensus        10 ~al~iL~~la~~~~~~~~s~~ela~~~~--------------i~~~~v~~il~~L~~~Glv~~~~g~~ggy~L~~~~~~   74 (129)
T 2y75_A           10 YGLTIMIELAKKHGEGPTSLKSIAQTNN--------------LSEHYLEQLVSPLRNAGLVKSIRGAYGGYVLGSEPDA   74 (129)
T ss_dssp             HHHHHHHHHHHTTTSCCBCHHHHHHHTT--------------SCHHHHHHHHHHHHHTTSEEEC----CCEEESSCGGG
T ss_pred             HHHHHHHHHHhCCCCCcCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCceEecCCCCCceEeCCCHHH
Confidence            456677777664   5789999999873              46689999999999999999774  368888876543

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

Probab=94.82  E-value=0.12  Score=37.81  Aligned_cols=63  Identities=19%  Similarity=0.224  Sum_probs=48.4

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD  121 (152)
                      .||..|+ .|+..++.|.+..+             .-|.+.+-..|+.||+.|||+...+  .+    -.||++|+..+.
T Consensus        39 ~IL~~L~-~g~~~~~eLa~~l~-------------gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~  104 (131)
T 1yyv_A           39 LILVALR-DGTHRFSDLRRXMG-------------GVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD  104 (131)
T ss_dssp             HHHHHGG-GCCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHhc-------------cCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHHH
Confidence            3666676 78999999998762             1467889999999999999986543  23    369999998776


Q ss_pred             HHH
Q psy5605         122 RIA  124 (152)
Q Consensus       122 ~iA  124 (152)
                      .+.
T Consensus       105 ~l~  107 (131)
T 1yyv_A          105 XVA  107 (131)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            553

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=94.68  E-value=0.027  Score=42.17  Aligned_cols=63  Identities=24%  Similarity=0.139  Sum_probs=38.2

Q ss_pred             CCCchhHHHHHHHHHHhCCcceecC----CCC-----ceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCcee
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSD----DGG-----RKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITV  146 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~----~gG-----R~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~  146 (152)
                      ..-|.+.+-.+|+.||+.|||+...    .+|     -.||++|++.+.....+... +.+. -++..+|.|.|
T Consensus        64 ~~is~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~~~-l~~~-~~~~~~~~~~~  135 (138)
T 2e1n_A           64 YRLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWER-YLSS-SAATDRQLIPV  135 (138)
T ss_dssp             EECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEESCSCCHHHHHHHHHHHH-HC--------------
T ss_pred             CCCCccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEECHHHHHHHHHHHHHHHH-HHhc-chhhhhccccc
Confidence            3567789999999999999998642    134     37999999999998766532 3222 55666666654

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

Probab=94.64  E-value=0.11  Score=37.55  Aligned_cols=60  Identities=18%  Similarity=0.265  Sum_probs=43.7

Q ss_pred             HHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc-----eeCcchH
Q psy5605          48 ALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR-----KITSHGR  117 (152)
Q Consensus        48 SilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR-----~lT~~G~  117 (152)
                      .||..|+- .+|+.+..|....+..  +++        +.+-+-.+|+.||+.|||+..+++.+     .||++|.
T Consensus        13 ~vL~~L~~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~r~~~~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A           13 AVMDHLWSRTEPQTVRQVHEALSAR--RDL--------AYTTVMAVLQRLAKKNLVLQIRDDRAHRYAPVHGRDEL   78 (138)
T ss_dssp             HHHHHHHTCSSCEEHHHHHHHHTTT--CCC--------CHHHHHHHHHHHHHTTSEEEEC---CCEEEESSCHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHhcc--CCC--------CHHHHHHHHHHHHHCCCEEEEecCCeEEEEeCCCHHHH
Confidence            37777887 5999999999998643  222        34678889999999999998876322     2677774

>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=94.59  E-value=0.47  Score=32.73  Aligned_cols=65  Identities=17%  Similarity=0.234  Sum_probs=48.6

Q ss_pred             HHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CC--CceeCcchHhhHHH
Q psy5605          48 ALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DG--GRKITSHGRRDMDR  122 (152)
Q Consensus        48 SilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~g--GR~lT~~G~~~LD~  122 (152)
                      .++.-+++ .+|+.+..|+...|-              +.+-+..+|+.||+.|||+..+  .+  ...++..|...+..
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            45666665 689999999999853              4567888999999999999863  22  34688888777766


Q ss_pred             HHHH
Q psy5605         123 IAAQ  126 (152)
Q Consensus       123 iA~~  126 (152)
                      +..+
T Consensus        96 ~~~~   99 (152)
T 1ku9_A           96 IAKR   99 (152)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

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

Probab=94.50  E-value=0.065  Score=40.22  Aligned_cols=67  Identities=15%  Similarity=0.290  Sum_probs=52.5

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC----ceeCcchHhhHHH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG----RKITSHGRRDMDR  122 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG----R~lT~~G~~~LD~  122 (152)
                      ..||+.|. ++|..++.|....|              -|.+-+.+-|+.||++|||+...+ |    -.||+.|...+-.
T Consensus        61 ~~IL~~L~-~~~~t~~eLa~~lg--------------ls~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~lt~~~~~~l~~  124 (151)
T 3f6v_A           61 RRLVQLLT-SGEQTVNNLAAHFP--------------ASRSAISQHLRVLTEAGLVTPRKD-GRFRYYRLDPQGLAQLRA  124 (151)
T ss_dssp             HHHHHHGG-GCCEEHHHHHTTSS--------------SCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHHHHHHH
Confidence            35777776 89999999999864              356789999999999999998764 5    4699999888876


Q ss_pred             HHHHHHH
Q psy5605         123 IAAQIRV  129 (152)
Q Consensus       123 iA~~i~~  129 (152)
                      +..++..
T Consensus       125 ~l~~~~~  131 (151)
T 3f6v_A          125 LFDSFWI  131 (151)
T ss_dssp             HHHHHSC
T ss_pred             HHHHHHH
Confidence            6554433

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

Probab=94.48  E-value=0.076  Score=38.66  Aligned_cols=64  Identities=17%  Similarity=0.152  Sum_probs=49.5

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR  122 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~  122 (152)
                      -.||..|--+|+..++.|....+            ..-|..-++.-|+.||+.|+|+....+=-.||++|++.+..
T Consensus        16 ~~IL~~L~~~g~~s~~eLA~~l~------------~giS~~aVs~rL~~Le~~GLV~~~~rg~Y~LT~~G~~~l~~   79 (111)
T 3b73_A           16 DRILEIIHEEGNGSPKELEDRDE------------IRISKSSVSRRLKKLADHDLLQPLANGVYVITEEGEAYLNG   79 (111)
T ss_dssp             HHHHHHHHHHSCBCHHHHHTSTT------------CCSCHHHHHHHHHHHHHTTSEEECSTTCEEECHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHh------------cCCCHHHHHHHHHHHHHCCCEEecCCceEEECchHHHHHHH
Confidence            35776666679999999998651            02366889999999999999998654336999999988753

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=94.41  E-value=0.11  Score=41.02  Aligned_cols=52  Identities=19%  Similarity=0.280  Sum_probs=43.8

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      .+....|+..||              -|..-+|.+|+.||..|+|+..+.+|-.+++-...++..+
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            467888888884              5789999999999999999999988989998877666544

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

Probab=94.34  E-value=0.085  Score=44.41  Aligned_cols=45  Identities=18%  Similarity=0.347  Sum_probs=33.6

Q ss_pred             CchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~iA~~i~  128 (152)
                      -+.+-+=.+|+.||+.|||++..  ...|    .||++|+..++++-..+.
T Consensus       432 ~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~~~~~~~~  482 (487)
T 1hsj_A          432 FKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKLISELE  482 (487)
T ss_dssp             CCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHHHHHHG
T ss_pred             CCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHHHHHHHHH
Confidence            34456667889999999998653  3455    479999999888766553

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

Probab=94.32  E-value=0.045  Score=37.34  Aligned_cols=57  Identities=14%  Similarity=0.190  Sum_probs=44.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~  119 (152)
                      .|++.| ..||..++.|....|-              |.+-+.+.|+.||+.|+|+...+|.   ..||+.+-..
T Consensus        27 ~Il~~L-~~~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~   86 (102)
T 3pqk_A           27 MLVCTL-VEGEFSVGELEQQIGI--------------GQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQ   86 (102)
T ss_dssp             HHHHHH-HTCCBCHHHHHHHHTC--------------CTTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHH
T ss_pred             HHHHHH-HhCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHH
Confidence            477777 4789999999999853              4467899999999999999877532   5688875443

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=94.14  E-value=0.31  Score=38.46  Aligned_cols=62  Identities=18%  Similarity=0.294  Sum_probs=49.5

Q ss_pred             HHHHHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhh
Q psy5605          44 TRCAALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRD  119 (152)
Q Consensus        44 iRaASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~  119 (152)
                      -|+..||+.|.-.+ ++++..|....|-              +.+-+..+|+.||+.|||+.+++ +...|+++....
T Consensus         6 ~r~l~iL~~l~~~~~~~s~~ela~~~gl--------------~~stv~r~l~~L~~~G~v~~~~~~~~Y~lg~~~~~l   69 (241)
T 2xrn_A            6 ARAASIMRALGSHPHGLSLAAIAQLVGL--------------PRSTVQRIINALEEEFLVEALGPAGGFRLGPALGQL   69 (241)
T ss_dssp             HHHHHHHHHHHTCTTCEEHHHHHHHTTS--------------CHHHHHHHHHHHHTTTSEEECGGGCEEEECSHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCCeEEECHHHHHH
Confidence            48889998887654 7999999998743              55789999999999999999875 456788775443

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

Probab=94.09  E-value=0.1  Score=38.55  Aligned_cols=65  Identities=18%  Similarity=0.320  Sum_probs=41.5

Q ss_pred             HHhhHhhcCC---cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhh
Q psy5605          49 LARHIYMRSP---VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRD  119 (152)
Q Consensus        49 ilRkiYl~g~---vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~  119 (152)
                      ||..|+-.++   +.+..|....|-              +.+-+-.+++.||+.|||+..++  ++    -.||++|+..
T Consensus        74 iL~~L~~~~~~~~~t~~eLa~~l~i--------------s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  139 (181)
T 2fbk_A           74 LLLTLYRSAPPEGLRPTELSALAAI--------------SGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  139 (181)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSC--------------CSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHH
Confidence            4444444443   666666665432              22334457899999999997653  23    3699999999


Q ss_pred             HHHHHHHH
Q psy5605         120 MDRIAAQI  127 (152)
Q Consensus       120 LD~iA~~i  127 (152)
                      ++++...+
T Consensus       140 ~~~~~~~~  147 (181)
T 2fbk_A          140 VTHLLPAH  147 (181)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876554

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

Probab=94.06  E-value=0.21  Score=36.31  Aligned_cols=42  Identities=12%  Similarity=0.324  Sum_probs=28.2

Q ss_pred             chhHHHHHHHHHHhCCcceecC-CCCc----eeCcchHhhHHHHHHH
Q psy5605          85 SGSVARKALQALEQVNIIEKSD-DGGR----KITSHGRRDMDRIAAQ  126 (152)
Q Consensus        85 sg~iiR~~LQqLE~~glVek~~-~gGR----~lT~~G~~~LD~iA~~  126 (152)
                      +.+-+=.+++.||+.|||+... .++|    .||++|+..++++...
T Consensus        65 ~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~~~~~~~~~  111 (148)
T 4fx0_A           65 ERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRAALQKAVPL  111 (148)
T ss_dssp             CHHHHHHHHHHHHHTTSBC-----------CCBCHHHHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            3455667789999999996432 2344    5899999999887643

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=94.06  E-value=0.11  Score=38.84  Aligned_cols=72  Identities=13%  Similarity=0.115  Sum_probs=46.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC---CCc-----eeCcchHhhH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD---GGR-----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~---gGR-----~lT~~G~~~L  120 (152)
                      ||.-|. .+|.--..|.+..+..-      ..+..-+.+.+-.+|+.||+.|||+....   +||     .||++|++.+
T Consensus        46 IL~~L~-~~~~~gyeI~~~l~~~~------~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l  118 (145)
T 1xma_A           46 ILSLLI-EGDSYGYEISKNIRIKT------DELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYY  118 (145)
T ss_dssp             HHHHHH-HCCEEHHHHHHHHHHHH------TTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHHHHhh------CCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECHHHHHHH
Confidence            555554 46655445544442210      11224567889999999999999986532   242     7999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      .......
T Consensus       119 ~~~~~~~  125 (145)
T 1xma_A          119 KQKCEEW  125 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9876554

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=94.02  E-value=0.25  Score=34.22  Aligned_cols=51  Identities=16%  Similarity=0.202  Sum_probs=40.6

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG  108 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g  108 (152)
                      .||+.|+-.+|+.++.|....+-.  +|.        +.+-+-.+|+.||+.|||+..+++
T Consensus        14 ~vL~~L~~~~~~t~~el~~~l~~~--~~~--------~~~Tvt~~l~rLe~kGlv~R~~~~   64 (126)
T 1sd4_A           14 DVMNIIWDKKSVSANEIVVEIQKY--KEV--------SDKTIRTLITRLYKKEIIKRYKSE   64 (126)
T ss_dssp             HHHHHHHHSSSEEHHHHHHHHHTT--SCC--------CHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHhcCCCCHHHHHHHHhhc--CCC--------ChhhHHHHHHHHHHCCceEEEeCC
Confidence            377788889999999999998642  222        347788899999999999988753

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

Probab=93.99  E-value=0.18  Score=36.17  Aligned_cols=70  Identities=16%  Similarity=0.144  Sum_probs=47.4

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhhH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGGR-----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gGR-----~lT~~G~~~L  120 (152)
                      ||--|. .+|.---.|.+....   .     .+..-|.+.+-.+|+.||+.|||+...   .+||     .||++|+..+
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            443333 455544455555432   1     234567789999999999999998643   2342     4999999999


Q ss_pred             HHHHHHH
Q psy5605         121 DRIAAQI  127 (152)
Q Consensus       121 D~iA~~i  127 (152)
                      +......
T Consensus        85 ~~~~~~~   91 (115)
T 4esb_A           85 EEFKQSW   91 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9987664

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=93.96  E-value=0.1  Score=41.07  Aligned_cols=68  Identities=16%  Similarity=0.218  Sum_probs=51.2

Q ss_pred             HHHHHHHHHhhHhhcC------CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          42 FYTRCAALARHIYMRS------PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        42 ~YiRaASilRkiYl~g------~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      .+-.++..+|..-+.|      .+....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-
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            3445555555544443      256778888884              57899999999999999999999889899888


Q ss_pred             hHhhHHHH
Q psy5605         116 GRRDMDRI  123 (152)
Q Consensus       116 G~~~LD~i  123 (152)
                      ...++..+
T Consensus        95 ~~~~~~el  102 (239)
T 2hs5_A           95 TAEDITEL  102 (239)
T ss_dssp             CHHHHHHH
T ss_pred             CHHHHHHH
Confidence            77766554

>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=93.96  E-value=0.072  Score=41.76  Aligned_cols=54  Identities=15%  Similarity=0.233  Sum_probs=44.7

Q ss_pred             Ccch--hhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          58 PVGV--KTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        58 ~vGV--~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      ++..  ..|+...|              -|.+-+..+|+.||+.|||+..++++=.||++|+..+..+..
T Consensus        22 ~~~~~~~~La~~l~--------------vs~~tvs~~l~~Le~~GlV~r~~~~~v~LT~~G~~~~~~~~~   77 (230)
T 1fx7_A           22 GVTPLRARIAERLD--------------QSGPTVSQTVSRMERDGLLRVAGDRHLELTEKGRALAIAVMR   77 (230)
T ss_dssp             TSCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEECTTSCEEECHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEeCCccEEECHHHHHHHHHHHH
Confidence            4555  88888763              355778899999999999999887778899999999887754

>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=93.87  E-value=0.81  Score=36.02  Aligned_cols=63  Identities=17%  Similarity=0.074  Sum_probs=50.4

Q ss_pred             HHHHHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605          44 TRCAALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM  120 (152)
Q Consensus        44 iRaASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L  120 (152)
                      -|+-.||..|.-.+ ++++..|....|-              +.+-+..+|+.||+.|||+.+.++.-.|+++....-
T Consensus         8 ~r~l~iL~~l~~~~~~~~~~ela~~~gl--------------~~stv~r~l~~L~~~G~v~~~~~~~Y~lg~~~~~l~   71 (249)
T 1mkm_A            8 KKAFEILDFIVKNPGDVSVSEIAEKFNM--------------SVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLIEYG   71 (249)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECTHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEECCCCcEEECHHHHHHH
Confidence            48889998887655 7999999998743              557888999999999999998545678988765443

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

Probab=93.80  E-value=0.21  Score=37.80  Aligned_cols=68  Identities=16%  Similarity=0.217  Sum_probs=49.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC---CC-----ceeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD---GG-----RKITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~---gG-----R~lT~~G~~~  119 (152)
                      .||.-|. .+|.--..|.+.+...      -.++...|-+-|-..|+.||+.|||+....   +|     -.||++|+..
T Consensus         6 ~iL~lL~-~~~~~gyel~~~l~~~------~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~   78 (179)
T 1yg2_A            6 VILTVLS-TRDATGYDITKEFSAS------IGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSA   78 (179)
T ss_dssp             HHHHHHH-HCCBCHHHHHHHHTTG------GGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHH
T ss_pred             HHHHHHh-cCCCCHHHHHHHHHHH------hCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHH
Confidence            3555554 4788888888888532      234556777899999999999999986532   22     4799999998


Q ss_pred             HHH
Q psy5605         120 MDR  122 (152)
Q Consensus       120 LD~  122 (152)
                      +.+
T Consensus        79 l~~   81 (179)
T 1yg2_A           79 LGE   81 (179)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            887

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.54  E-value=0.1  Score=37.13  Aligned_cols=73  Identities=14%  Similarity=0.135  Sum_probs=47.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCch-hHHHHHHHHHHhCCcceecCC--CC-----ceeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSG-SVARKALQALEQVNIIEKSDD--GG-----RKITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg-~iiR~~LQqLE~~glVek~~~--gG-----R~lT~~G~~~  119 (152)
                      .||.-|. .+|.-...|.+....   .|...   ..-+. +.+-.+|+.||+.|||+....  .|     -.||++|+..
T Consensus        17 ~IL~~L~-~~~~~gyel~~~l~~---~g~~~---~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~~G~~~   89 (118)
T 2esh_A           17 TILLLVA-EKPSHGYELAERLAE---FGIEI---PGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLY   89 (118)
T ss_dssp             HHHHHHH-HSCBCHHHHHHHHHT---TCCSS---TTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHHHH---hCCcc---cCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHH
Confidence            3555554 367666666666643   22110   12455 678889999999999986532  23     2799999999


Q ss_pred             HHHHHHHH
Q psy5605         120 MDRIAAQI  127 (152)
Q Consensus       120 LD~iA~~i  127 (152)
                      +.......
T Consensus        90 l~~~~~~~   97 (118)
T 2esh_A           90 LREILRSL   97 (118)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            98876654

>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=93.40  E-value=0.061  Score=41.36  Aligned_cols=65  Identities=15%  Similarity=0.216  Sum_probs=49.2

Q ss_pred             HHHHHHhhHhhcCC------cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          45 RCAALARHIYMRSP------VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        45 RaASilRkiYl~g~------vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      .++.-+|.--+.|-      +....|+..||              -|..-+|.+|+.||..|||+..+..|-.+++-...
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            34444555444442      45678888885              57899999999999999999999889888887776


Q ss_pred             hHHHH
Q psy5605         119 DMDRI  123 (152)
Q Consensus       119 ~LD~i  123 (152)
                      ++..+
T Consensus        82 ~~~el   86 (218)
T 3sxy_A           82 FIRET   86 (218)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>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=93.40  E-value=0.51  Score=31.09  Aligned_cols=45  Identities=13%  Similarity=0.322  Sum_probs=36.3

Q ss_pred             HHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          49 LARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        49 ilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      ++..++- .+++.+..|+..+|              -|.+-++..|+.||+.|+|+..++
T Consensus        26 ~l~~l~~~~~~~t~~ela~~l~--------------is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           26 VLLKMVEIEKPITSEELADIFK--------------LSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             HHHHHHHHCSCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEeecc
Confidence            4555555 78999999999984              356789999999999999987653

>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=93.36  E-value=0.16  Score=36.07  Aligned_cols=44  Identities=14%  Similarity=0.228  Sum_probs=35.2

Q ss_pred             CchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~LD~iA~~i  127 (152)
                      -|-+-+=.+|+.||+.|||+...+..   -.||++|+..+++...+.
T Consensus        42 is~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~   88 (99)
T 2co5_A           42 ISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFF   88 (99)
T ss_dssp             CCHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhH
Confidence            45677788999999999999776323   479999999999876654

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=93.28  E-value=0.26  Score=35.49  Aligned_cols=58  Identities=12%  Similarity=0.131  Sum_probs=40.1

Q ss_pred             CCCchhHHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhHHHHHHHHHHHHHHHHHHHHh
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSD---DGG-----RKITSHGRRDMDRIAAQIRVSKKEAALQALA  140 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~---~gG-----R~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~  140 (152)
                      ..-|.+.+-.+|+.||+.|||+...   .+|     -.||++|+..|+....... .+.+...+-+.
T Consensus        40 ~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~~~~~~~-~~~~~i~~il~  105 (117)
T 4esf_A           40 TEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQELELFWKKWD-FVSSKINVLKS  105 (117)
T ss_dssp             TTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHHHHHHHHHH-HHHHHHHHHHT
T ss_pred             CCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHHHHHHHHHH-HHHHHHHHHHc
Confidence            3467789999999999999998653   234     3599999999999776543 33333333343

>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=93.15  E-value=0.11  Score=40.84  Aligned_cols=65  Identities=17%  Similarity=0.260  Sum_probs=47.7

Q ss_pred             HHHhhHhhc--CCcch--hhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          48 ALARHIYMR--SPVGV--KTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        48 SilRkiYl~--g~vGV--~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      .+|+.||.-  .++.+  ..|+...|-              +.+-+..+++.||+.|||+..++.+=.||++|+....++
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            345556642  23333  788877632              445667799999999999998877789999999998887


Q ss_pred             HHH
Q psy5605         124 AAQ  126 (152)
Q Consensus       124 A~~  126 (152)
                      ...
T Consensus        76 ~~~   78 (226)
T 2qq9_A           76 MRK   78 (226)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=93.12  E-value=0.1  Score=35.84  Aligned_cols=61  Identities=16%  Similarity=0.264  Sum_probs=44.7

Q ss_pred             HHHHHHHHHhhHhhcC-----C-c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRS-----P-V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g-----~-v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|-..+.-+|..-+.+     . + .+..|+..||              -|.+-+|.+|+.||+.|+|+..+..|..+++
T Consensus        12 ~~~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~--------------vSr~tvr~al~~L~~~Gli~~~~g~G~~v~~   77 (102)
T 1v4r_A           12 GYADVATHFRTLIKSGELAPGDTLPSVADIRAQFG--------------VAAKTVSRALAVLKSEGLVSSRGALGTVVEK   77 (102)
T ss_dssp             CHHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSS--------------SCTTHHHHHTTTTTTSSCCEEETTTEEESCS
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEeCCCeEEEcc
Confidence            3556666555544432     2 2 7888888884              3678999999999999999998877877776


Q ss_pred             ch
Q psy5605         115 HG  116 (152)
Q Consensus       115 ~G  116 (152)
                      ..
T Consensus        78 ~~   79 (102)
T 1v4r_A           78 NP   79 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=93.05  E-value=0.063  Score=40.80  Aligned_cols=62  Identities=24%  Similarity=0.144  Sum_probs=37.6

Q ss_pred             CCchhHHHHHHHHHHhCCcceecC----CCC-----ceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCcee
Q psy5605          83 RSSGSVARKALQALEQVNIIEKSD----DGG-----RKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITV  146 (152)
Q Consensus        83 ~asg~iiR~~LQqLE~~glVek~~----~gG-----R~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~  146 (152)
                      .-+-+.+-.+|+.||+.|||+...    .+|     -.||++|++.++....+... +.+. .++..+|.|.|
T Consensus        75 ~is~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~~~~~~~-l~~~-~~~~~~~~~~~  145 (148)
T 2zfw_A           75 RLSDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRDLAQLWER-YLSS-SAATDRQLIPV  145 (148)
T ss_dssp             ECCSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESSSSCSTTHHHHHHHHH-HHCC------------
T ss_pred             CCChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECHHHHHHHHHHHHHHHH-HHhh-ccccccccccc
Confidence            456688999999999999998653    124     47999999999988765532 2222 44555555543

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=92.90  E-value=0.3  Score=33.96  Aligned_cols=58  Identities=17%  Similarity=0.261  Sum_probs=43.2

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDM  120 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~L  120 (152)
                      .|+..|. .++..++.|+...|              -|.+-+...|+.||+.|+|+...+|.   ..||+.+...+
T Consensus        29 ~IL~~L~-~~~~s~~eLa~~lg--------------is~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l   89 (108)
T 2kko_A           29 QILDLLA-QGERAVEAIATATG--------------MNLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARL   89 (108)
T ss_dssp             HHHHHHT-TCCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHH
Confidence            3555554 68999999999874              35578899999999999999776432   36888774443

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

Probab=92.87  E-value=0.23  Score=33.98  Aligned_cols=53  Identities=23%  Similarity=0.339  Sum_probs=41.7

Q ss_pred             HHHHHHhhHhhc------CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605          45 RCAALARHIYMR------SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI  112 (152)
Q Consensus        45 RaASilRkiYl~------g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l  112 (152)
                      |.-.|+--|--.      +|+.|..++..+|=              |-+-+|.-|..||+.|+|+.++ +||.+
T Consensus         5 r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgv--------------S~~TVrr~L~~Le~kG~I~R~~-ggr~~   63 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGAPVKTRDIADAAGL--------------SIYQVRLYLEQLHDVGVLEKVN-AGKGV   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEES-CSSSS
T ss_pred             HHHHHHHHHHHHHhhccCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCcEEecC-CCCCc
Confidence            455566666555      89999999999852              4466999999999999999998 56654

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=92.81  E-value=0.32  Score=34.19  Aligned_cols=65  Identities=20%  Similarity=0.209  Sum_probs=50.4

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDMDRIA  124 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~LD~iA  124 (152)
                      .|++.|. +||..++.|....|              -|.+-+.+-|+.||+.|+|+....|.   -.||+.|...+....
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            4677676 79999999998763              35677888999999999998776532   468999988886665


Q ss_pred             HHH
Q psy5605         125 AQI  127 (152)
Q Consensus       125 ~~i  127 (152)
                      ...
T Consensus        87 ~~~   89 (118)
T 3f6o_A           87 AEQ   89 (118)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=92.73  E-value=0.22  Score=40.24  Aligned_cols=46  Identities=15%  Similarity=0.229  Sum_probs=34.4

Q ss_pred             chhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHHHHHHHHHH
Q psy5605          85 SGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDRIAAQIRVS  130 (152)
Q Consensus        85 sg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~iA~~i~~~  130 (152)
                      +.+-+=.+++.||+.|||+..+  +++|    .||++|+..++++...+...
T Consensus       187 ~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~~~~~  238 (250)
T 1p4x_A          187 KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQVNQL  238 (250)
T ss_dssp             CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHHHHHHHHHH
Confidence            3455666889999999998654  3455    48999999999886665443

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=92.68  E-value=0.29  Score=39.15  Aligned_cols=58  Identities=12%  Similarity=0.305  Sum_probs=47.9

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcc
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSH  115 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~  115 (152)
                      -|+..||+.|-- .+++++..|.+.-|-              +.+-+..+|+.|++.|||+++++ +...|++.
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 578999999998753              55789999999999999999986 55677775

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=92.52  E-value=0.38  Score=33.05  Aligned_cols=54  Identities=15%  Similarity=0.223  Sum_probs=42.1

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGR  117 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~  117 (152)
                      .|+..|. +++..++.|....|              -|.+-+.+.|+.||+.|+|+...+ ||    .||+.+-
T Consensus        30 ~IL~~L~-~~~~~~~ela~~l~--------------is~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~~~   87 (106)
T 1r1u_A           30 RIMELLS-VSEASVGHISHQLN--------------LSQSNVSHQLKLLKSVHLVKAKRQ-GQSMIYSLDDIHV   87 (106)
T ss_dssp             HHHHHHH-HCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEESSHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEEChHHH
Confidence            5676666 88999999999874              355788999999999999997764 44    5676653

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=92.31  E-value=0.66  Score=31.03  Aligned_cols=60  Identities=12%  Similarity=0.112  Sum_probs=44.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhHHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDMDR  122 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~LD~  122 (152)
                      .|++.|. +|+..++.|....|-              |.+-+.+-|+.||+.|+|+...+|.   ..||+.+-..+-.
T Consensus        27 ~Il~~L~-~~~~~~~ela~~l~i--------------s~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~   89 (98)
T 3jth_A           27 QILCMLH-NQELSVGELCAKLQL--------------SQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIK   89 (98)
T ss_dssp             HHHHHTT-TSCEEHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHH
T ss_pred             HHHHHHh-cCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHH
Confidence            4666555 489999999999743              5678999999999999999887532   3577776554433

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=92.27  E-value=0.16  Score=39.49  Aligned_cols=44  Identities=27%  Similarity=0.400  Sum_probs=36.3

Q ss_pred             hhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee--cCC--CCceeCcchHh
Q psy5605          61 VKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK--SDD--GGRKITSHGRR  118 (152)
Q Consensus        61 V~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek--~~~--gGR~lT~~G~~  118 (152)
                      -..|+..||              -|..-+|.+|+.||..|+|+.  .+.  +|-.+++-...
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            347888874              578999999999999999999  887  78888776554

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=92.26  E-value=0.23  Score=35.60  Aligned_cols=46  Identities=20%  Similarity=0.224  Sum_probs=36.4

Q ss_pred             CCCchhHHHHHHHHHHhCCcceec--C--CCC-----ceeCcchHhhHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKS--D--DGG-----RKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~--~--~gG-----R~lT~~G~~~LD~iA~~i  127 (152)
                      ..-|.+.+-.+|+.||+.|||+..  +  .+|     -.||++|++.+.....+.
T Consensus        52 ~~is~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~  106 (115)
T 2dql_A           52 YRLSDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQAEDLARLW  106 (115)
T ss_dssp             EECCHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            356778899999999999999864  2  224     379999999999876654

>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=92.07  E-value=0.55  Score=34.81  Aligned_cols=77  Identities=10%  Similarity=0.071  Sum_probs=57.7

Q ss_pred             HHHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCccC--------CCchhHHHHHHHHHHhCCcceecCCCC-----cee
Q psy5605          47 AALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSHFC--------RSSGSVARKALQALEQVNIIEKSDDGG-----RKI  112 (152)
Q Consensus        47 ASilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h~~--------~asg~iiR~~LQqLE~~glVek~~~gG-----R~l  112 (152)
                      -.+|..|| +.+..|++.+..+.=|+++.-+.-.|..        .=+..-+|.++.||...|+++.+...+     =.|
T Consensus        19 qkiLs~V~r~~~rfG~~~iidvLrGs~~~ki~~~~~~l~tfGigk~~s~~~w~~lirqLi~~G~L~~~~~~~~~~~~L~L   98 (134)
T 3aaf_A           19 FKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICAL   98 (134)
T ss_dssp             HHHHHHHHHTTTCSCTHHHHHHHTTCCCTTSCGGGGGSTTTTTTTTSCHHHHHHHHHHHHHTTSEEEEECSSTTCEEEEE
T ss_pred             HHHHHHHHHHcCcccccchhhhhcCCcHHHHHHHhCCCCccCCCCCCCHHHHHHHHHHHHHcCCceeecCcCccCceEEE
Confidence            35677777 6789999999999999887665442211        123347999999999999999875432     689


Q ss_pred             CcchHhhHHHH
Q psy5605         113 TSHGRRDMDRI  123 (152)
Q Consensus       113 T~~G~~~LD~i  123 (152)
                      |++|+..|..-
T Consensus        99 t~~g~~vL~~~  109 (134)
T 3aaf_A           99 TKKGRNWLHKA  109 (134)
T ss_dssp             CHHHHHHHHHH
T ss_pred             CHHHHHHHhCC
Confidence            99999887754

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=92.00  E-value=0.26  Score=35.05  Aligned_cols=57  Identities=14%  Similarity=0.258  Sum_probs=41.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchHhh
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~~~  119 (152)
                      .|+..|.-.++..++.|....|              =|.+-+.+.|+.||+.|+|+...+ ||    .||+.+-..
T Consensus        46 ~IL~~L~~~~~~s~~eLa~~l~--------------is~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~~~~~  106 (122)
T 1u2w_A           46 KITYALCQDEELCVCDIANILG--------------VTIANASHHLRTLYKQGVVNFRKE-GKLALYSLGDEHIRQ  106 (122)
T ss_dssp             HHHHHHHHSSCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEC-----CCEEEESCHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEEEEE-CCEEEEEECHHHHHH
Confidence            4666665579999999999874              355788899999999999998764 44    677765443

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=91.67  E-value=0.68  Score=37.30  Aligned_cols=69  Identities=12%  Similarity=0.162  Sum_probs=47.2

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRK----ITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~----lT~~G~~~L  120 (152)
                      +|..||-.  +++.+..|....+             -.++.+- .+|+.||+.|||++..  ...|.    ||++|+..+
T Consensus        39 vL~~L~~~~~~~~~~~el~~~l~-------------~~~~t~t-~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~  104 (250)
T 1p4x_A           39 LLTYLFHQQENTLPFKKIVSDLC-------------YKQSDLV-QHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (250)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSS-------------SCGGGTH-HHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHC-------------CCHhhHH-HHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHH
Confidence            56666663  4677777776642             2234444 5789999999998653  33443    899999988


Q ss_pred             HHHHHHHHHHH
Q psy5605         121 DRIAAQIRVSK  131 (152)
Q Consensus       121 D~iA~~i~~~~  131 (152)
                      +.+-..+.+.+
T Consensus       105 ~~~~~~~~~~~  115 (250)
T 1p4x_A          105 AERVTLFDQII  115 (250)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88776665444

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

Probab=91.54  E-value=0.44  Score=38.48  Aligned_cols=66  Identities=12%  Similarity=0.195  Sum_probs=53.2

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhhHHHH
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRDMDRI  123 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~LD~i  123 (152)
                      ....||..|.-++++++..|++..|-              +.+-+...|+.||+.|||+.... +.-.||++|+......
T Consensus       153 ~~~~IL~~L~~~~~~s~~eLA~~lgl--------------sksTv~r~L~~Le~~GlV~r~~r~~~~~LT~~G~~l~~~~  218 (244)
T 2wte_A          153 EEMKLLNVLYETKGTGITELAKMLDK--------------SEKTLINKIAELKKFGILTQKGKDRKVELNELGLNVIKLN  218 (244)
T ss_dssp             HHHHHHHHHHHHTCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEETTTTEEEECHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCccEEEECHHHHHHHHHH
Confidence            34568888888899999999999863              55678889999999999998743 3468999999986654


Q ss_pred             H
Q psy5605         124 A  124 (152)
Q Consensus       124 A  124 (152)
                      .
T Consensus       219 ~  219 (244)
T 2wte_A          219 K  219 (244)
T ss_dssp             C
T ss_pred             h
Confidence            3

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=91.54  E-value=0.92  Score=35.94  Aligned_cols=60  Identities=18%  Similarity=0.164  Sum_probs=47.7

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR  118 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~  118 (152)
                      -|+..||+.|.- .+++++..|.+..|-              +.+-+..+|+.|++.|||+.+. +...|++....
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~~stv~r~l~~L~~~G~v~~~~-~~Y~Lg~~~~~   74 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGL--------------SRPAVRRILLTLQKLGYVAGSG-GRWSLTPRVLS   74 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEET-TEEEECGGGHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCC-CEEEEcHHHHH
Confidence            377788887764 468999999999753              4578889999999999999874 56788887543

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

Probab=91.52  E-value=0.4  Score=31.57  Aligned_cols=45  Identities=13%  Similarity=0.174  Sum_probs=37.0

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD  106 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~  106 (152)
                      .|+..|.-.+++.+..|+..+|-              |.+-+|..|+.||+.|+|+..+
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            46666666789999999999853              5678999999999999999653

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=91.32  E-value=0.31  Score=37.58  Aligned_cols=63  Identities=14%  Similarity=0.132  Sum_probs=43.9

Q ss_pred             HHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC------CCCc-----eeCc
Q psy5605          48 ALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD------DGGR-----KITS  114 (152)
Q Consensus        48 SilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~------~gGR-----~lT~  114 (152)
                      +|+..|.-+  +...+..|....             -.-|-+-|+.-|+.|++.|+|++..      ..||     .||+
T Consensus        33 ~IL~~Ll~~p~~~~ta~eL~~~l-------------~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~   99 (151)
T 3u1d_A           33 DVLHQILAQPDGVLSVEELLYRN-------------PDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTG   99 (151)
T ss_dssp             HHHHHHHHSTTSCBCHHHHHHHC-------------TTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHhc-------------CCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECH
Confidence            355555444  235666665432             1247789999999999999999652      1254     8999


Q ss_pred             chHhhHHHH
Q psy5605         115 HGRRDMDRI  123 (152)
Q Consensus       115 ~G~~~LD~i  123 (152)
                      +|+..|+..
T Consensus       100 ~Gr~~l~~y  108 (151)
T 3u1d_A          100 EGIALLRAV  108 (151)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999999873

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=91.16  E-value=0.83  Score=36.33  Aligned_cols=62  Identities=11%  Similarity=0.072  Sum_probs=48.9

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD  119 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~  119 (152)
                      -|+..||+.|.- .+++++..|.+..|-              +.+-+..+|+.|++.|||+.++++...|+++.-..
T Consensus        23 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~kstv~r~l~tL~~~G~v~~~~~~~Y~lg~~~~~l   85 (260)
T 2o0y_A           23 TRVIDLLELFDAAHPTRSLKELVEGTKL--------------PKTTVVRLVATMCARSVLTSRADGSYSLGPEMLRW   85 (260)
T ss_dssp             HHHHHHHTTCBTTBSSBCHHHHHHHHCC--------------CHHHHHHHHHHHHHTTSEEECTTSCEEECHHHHHH
T ss_pred             HHHHHHHHHHhhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEECCCCeEEecHHHHHH
Confidence            477888877753 578999999998753              45788899999999999999886556788775443

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

Probab=90.98  E-value=1.5  Score=31.20  Aligned_cols=78  Identities=17%  Similarity=0.258  Sum_probs=51.4

Q ss_pred             HHHhhHhhcCC--cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---C-CCc--eeCcchHhh
Q psy5605          48 ALARHIYMRSP--VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---D-GGR--KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~g~--vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~-gGR--~lT~~G~~~  119 (152)
                      .|+..|+-.++  +.+..|+...|              -|.+-+...|+.||+.|+|+..+   + +|+  ..++.....
T Consensus        30 ~il~~L~~~~~~~~t~~eLa~~l~--------------~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~~~~~y~~~~~~~   95 (123)
T 3r0a_A           30 NVMKSFLNEPDRWIDTDALSKSLK--------------LDVSTVQRSVKKLHEKEILQRSQQNLDGGGYVYIYKIYSKNQ   95 (123)
T ss_dssp             HHHHHHHHSTTCCEEHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECCHHH
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEeeCCccCCCcceEEEecCCHHH
Confidence            47777776655  99999999985              36788999999999999998753   2 342  334433444


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy5605         120 MDRIAAQIRVSKKEAALQAL  139 (152)
Q Consensus       120 LD~iA~~i~~~~~~~~~~~~  139 (152)
                      +.....++..+..+.-.+.|
T Consensus        96 ~~~~i~~~~~~~~~~~~~~l  115 (123)
T 3r0a_A           96 IRNIIQKIVQSWADRLGQEL  115 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            44444455555555444443

>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=90.19  E-value=0.34  Score=37.67  Aligned_cols=73  Identities=16%  Similarity=0.081  Sum_probs=51.5

Q ss_pred             chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC---CCceeCcch
Q psy5605          40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD---GGRKITSHG  116 (152)
Q Consensus        40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G  116 (152)
                      .+-+.++-+....++-.+++.+..++...|-              |.+-+=..+++||+.||++..++   .+=.||++|
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            4555555555555555566778888887643              44566777899999999998742   355799999


Q ss_pred             HhhHHHHHHH
Q psy5605         117 RRDMDRIAAQ  126 (152)
Q Consensus       117 ~~~LD~iA~~  126 (152)
                      +..++.+-..
T Consensus        75 ~~l~~~~~~~   84 (230)
T 3cta_A           75 LDVLYTEFAD   84 (230)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999776543

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=90.15  E-value=0.62  Score=35.75  Aligned_cols=59  Identities=10%  Similarity=0.143  Sum_probs=43.0

Q ss_pred             HHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605          43 YTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH  115 (152)
Q Consensus        43 YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~  115 (152)
                      |-.++..+|.--+.|-      + .-..|+..||              -|..-+|.+|+.||..|||+..+..|-.+++.
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            3445555555444442      3 4567888874              57899999999999999999999778778753

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=90.11  E-value=0.2  Score=39.69  Aligned_cols=64  Identities=20%  Similarity=0.267  Sum_probs=45.0

Q ss_pred             cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhHHHHHH
Q psy5605          56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGG-----RKITSHGRRDMDRIAA  125 (152)
Q Consensus        56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gG-----R~lT~~G~~~LD~iA~  125 (152)
                      .+|.---.|.+.+...      -.++...|-+-|-.+|+.||+.|||+...   ++|     -.||++|+..|.+...
T Consensus        47 ~~p~~GYeL~~~l~~~------~~~~~~~s~g~lY~~L~rLe~~GlI~~~~~~~~~~p~rk~Y~iT~~Gr~~l~~~l~  118 (204)
T 3l9f_A           47 KKERSGYEINDILQNQ------LSYFYDGTYGMIYPTLRKLEKDGKITKEVVIQDGRPNKNIYAITESGKKELASYLQ  118 (204)
T ss_dssp             SCCEEHHHHHHHHHHT------STTTEECCTTCHHHHHHHHHHTTSEEEEEECCTTSCCEEEEEECHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHH------hCCccCCCcchHHHHHHHHHHCCCeEEEeeccCCCCCceEEEEChHHHHHHHHHHh
Confidence            5666656666666432      22345667788999999999999998542   233     3699999999976443

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=90.01  E-value=0.75  Score=33.81  Aligned_cols=57  Identities=14%  Similarity=0.141  Sum_probs=41.6

Q ss_pred             HHHHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC-CCCceeCcch
Q psy5605          46 CAALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD-DGGRKITSHG  116 (152)
Q Consensus        46 aASilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~-~gGR~lT~~G  116 (152)
                      |-.+|..|..+  +++.+..++..+|              -|-+.+|++|++|+++|||+... .||-.|+...
T Consensus        16 Al~~L~~La~~~~~~~~~~~iA~~~~--------------i~~~~l~kil~~L~~~Glv~s~rG~GGy~L~~~p   75 (149)
T 1ylf_A           16 AVHILSILKNNPSSLCTSDYMAESVN--------------TNPVVIRKIMSYLKQAGFVYVNRGPGGAGLLKDL   75 (149)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEC---CCEEESSCG
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEccCCCceEeCCCh
Confidence            34455555543  4688888998874              46689999999999999998665 4788887754

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=89.80  E-value=0.2  Score=36.07  Aligned_cols=42  Identities=12%  Similarity=0.210  Sum_probs=32.5

Q ss_pred             hhHHHHHHHHHHhCCcceecC---CCC-----ceeCcchHhhHHHHHHHH
Q psy5605          86 GSVARKALQALEQVNIIEKSD---DGG-----RKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        86 g~iiR~~LQqLE~~glVek~~---~gG-----R~lT~~G~~~LD~iA~~i  127 (152)
                      .+.+-.+|+.||+.|||+...   .+|     -.||++|++.|++.....
T Consensus        47 ~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l~~~~~~~   96 (117)
T 3elk_A           47 QGSIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFLCDHSQAL   96 (117)
T ss_dssp             TTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHHHHTSTTH
T ss_pred             cchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            378899999999999998543   233     359999999999865543

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=89.68  E-value=0.83  Score=32.63  Aligned_cols=63  Identities=17%  Similarity=0.265  Sum_probs=42.3

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC-c--eeCcchHhhHHHHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG-R--KITSHGRRDMDRIAA  125 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG-R--~lT~~G~~~LD~iA~  125 (152)
                      |++.|. +++..++.|....|              -|.+-+.+.|+.||+.|+|....+|. .  .||+++   +..++.
T Consensus        51 IL~~L~-~~~~s~~ela~~lg--------------is~stvs~~L~~Le~~Glv~~~~~gr~~~y~l~~~~---l~~~~~  112 (122)
T 1r1t_A           51 LLSLLA-RSELCVGDLAQAIG--------------VSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHH---IVALYQ  112 (122)
T ss_dssp             HHHHHT-TCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHH---HHHHHH
T ss_pred             HHHHHH-cCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHH---HHHHHH
Confidence            455444 57889999998874              35678889999999999999776432 2  345443   444444


Q ss_pred             HHHH
Q psy5605         126 QIRV  129 (152)
Q Consensus       126 ~i~~  129 (152)
                      .+..
T Consensus       113 ~l~~  116 (122)
T 1r1t_A          113 NALD  116 (122)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=89.60  E-value=0.75  Score=33.89  Aligned_cols=56  Identities=13%  Similarity=0.204  Sum_probs=41.5

Q ss_pred             HHHhhHhhc---CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcchH
Q psy5605          48 ALARHIYMR---SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHGR  117 (152)
Q Consensus        48 SilRkiYl~---g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G~  117 (152)
                      .+|..|..+   +++.+..++..+|              -|...+|++|++|.++|+|+...  +||-.|+..-.
T Consensus        15 ~~L~~La~~~~~~~~s~~~IA~~~~--------------i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~p~   75 (143)
T 3t8r_A           15 TLMISLAKKEGQGCISLKSIAEENN--------------LSDLYLEQLVGPLRNAGLIRSVRGAKGGYQLRVPAE   75 (143)
T ss_dssp             HHHHHHHTTTTSCCEEHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEECSSSSSEEEESSCGG
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCEEEecCCCCCCeeecCCcc
Confidence            344444443   4688999998873              46689999999999999998665  46888876543

>3l09_A Putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG, protein structure initiative transcription regulator; 2.81A {Jannaschia SP}

Probab=89.53  E-value=0.32  Score=40.42  Aligned_cols=75  Identities=13%  Similarity=0.081  Sum_probs=58.3

Q ss_pred             HHHHHHHhhHhh---c---CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC---CceeCc
Q psy5605          44 TRCAALARHIYM---R---SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---GRKITS  114 (152)
Q Consensus        44 iRaASilRkiYl---~---g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~  114 (152)
                      +|+-|++-.||-   .   +.+-++.|-...+.           -.=+..-+|.+|.-|++.||++....|   +..||+
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            477789888883   2   46888887766532           123567899999999999999987654   578999


Q ss_pred             chHhhHHHHHHHHHH
Q psy5605         115 HGRRDMDRIAAQIRV  129 (152)
Q Consensus       115 ~G~~~LD~iA~~i~~  129 (152)
                      .|++.+++....|..
T Consensus        91 ~g~~~l~~~~~ri~~  105 (266)
T 3l09_A           91 SALTQTRAVAGRIYG  105 (266)
T ss_dssp             HHHHHHHTTHHHHHS
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999988887764

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=89.20  E-value=0.92  Score=36.59  Aligned_cols=59  Identities=17%  Similarity=0.286  Sum_probs=47.1

Q ss_pred             HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      -|+..||..|--. +++++..|.+.-|-              +.+-+..+|+.|++.|||++++++...|++.=
T Consensus        30 ~Ral~IL~~l~~~~~~ltl~eia~~lgl--------------~ksTv~RlL~tL~~~G~v~~~~~~~Y~LG~~~   89 (275)
T 3mq0_A           30 RRAVRILDLVAGSPRDLTAAELTRFLDL--------------PKSSAHGLLAVMTELDLLARSADGTLRIGPHS   89 (275)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTC--------------C--CHHHHHHHHHHTTSEEECTTSEEEECTHH
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEECCCCcEEehHHH
Confidence            4888899888865 57999999999754              33568899999999999999986567887763

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

Probab=88.72  E-value=0.81  Score=31.21  Aligned_cols=44  Identities=11%  Similarity=0.217  Sum_probs=38.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS  105 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~  105 (152)
                      .|+..|--+|.+.|..|...|              .-|..-||.-|..||+.|+|+..
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l--------------~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTL--------------NTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHT--------------TCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEEe
Confidence            466667778999999999998              46789999999999999999987

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=88.69  E-value=0.83  Score=31.52  Aligned_cols=67  Identities=10%  Similarity=0.181  Sum_probs=46.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-CceeCcchHhhHHHHHHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-GR~lT~~G~~~LD~iA~~i  127 (152)
                      |+..|+- ++..+..+....|              -|.+-+.+.|+.||+.|+|....++ +..+|..|...+ .++..+
T Consensus        37 il~~L~~-~~~s~~ela~~l~--------------is~stvsr~l~~Le~~Glv~~~~~~r~~~~~~~~~~~~-~~~~~~  100 (119)
T 2lkp_A           37 ILTQLRN-GPLPVTDLAEAIG--------------MEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVA-QLLDEA  100 (119)
T ss_dssp             HHHHHHH-CCCCHHHHHHHHS--------------SCHHHHHHHHHHHHHHCSEEEEEETTEEEEEESCHHHH-HHHHHH
T ss_pred             HHHHHHH-CCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEchHHHH-HHHHHH
Confidence            5555554 7889999988874              3567888999999999999876532 346777776543 344444


Q ss_pred             HHHH
Q psy5605         128 RVSK  131 (152)
Q Consensus       128 ~~~~  131 (152)
                      ...+
T Consensus       101 ~~~~  104 (119)
T 2lkp_A          101 IYHS  104 (119)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=88.44  E-value=1.2  Score=36.05  Aligned_cols=60  Identities=20%  Similarity=0.287  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|.+.+..++.--..|-      + ....|+..||              -|..-+|.+|+.|++.|+|+..+..|-.+++
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            56777777766555542      3 6778888884              5789999999999999999999977866665


Q ss_pred             c
Q psy5605         115 H  115 (152)
Q Consensus       115 ~  115 (152)
                      .
T Consensus        96 ~   96 (272)
T 3eet_A           96 R   96 (272)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=88.00  E-value=1.2  Score=33.85  Aligned_cols=45  Identities=13%  Similarity=0.310  Sum_probs=35.9

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcc
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSH  115 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~  115 (152)
                      +|+.+..++..+|              -|...+|++|++|.++|+|+...  .||-.|+..
T Consensus        43 ~~~s~~eIA~~~~--------------i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~   89 (159)
T 3lwf_A           43 GPISLRSIAQDKN--------------LSEHYLEQLIGPLRNAGIVKSIRGAHGGYVLNGD   89 (159)
T ss_dssp             CCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEECSTTCEEEECSC
T ss_pred             CCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCeEEEecCCCCceEecCC
Confidence            4788899998873              46789999999999999999665  367666643

>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=87.51  E-value=1.4  Score=34.73  Aligned_cols=60  Identities=15%  Similarity=0.284  Sum_probs=45.1

Q ss_pred             HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|...+..+|.--..|-      + ....|+..||              -|..-+|.+|+.|++.|+|+..+..|-.+++
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            35566666666555542      3 5677888874              5789999999999999999999977877776


Q ss_pred             c
Q psy5605         115 H  115 (152)
Q Consensus       115 ~  115 (152)
                      .
T Consensus        76 ~   76 (236)
T 3edp_A           76 K   76 (236)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=87.24  E-value=2  Score=30.23  Aligned_cols=66  Identities=20%  Similarity=0.285  Sum_probs=47.8

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec-----CC-CCceeCc------c
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS-----DD-GGRKITS------H  115 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~-----~~-gGR~lT~------~  115 (152)
                      .|++.+.-.+++....|+..+|              -|.+-++..|+.||+.|+|+..     +. -|..+|.      .
T Consensus         8 ~il~~L~~~~~~~~~ela~~lg--------------~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~~~v~~~~~   73 (141)
T 1i1g_A            8 IILEILEKDARTPFTEIAKKLG--------------ISETAVRKRVKALEEKGIIEGYTIKINPKKLGYSLVTITGVDTK   73 (141)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHT--------------SCHHHHHHHHHHHHHHTSSCCCCCCCCSGGGTCCEEEEEEEEEC
T ss_pred             HHHHHHHHcCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEeccccccChHHhCccEEEEEEEEEC
Confidence            4677666778899999999984              3668899999999999999743     21 2666654      4


Q ss_pred             hHhhHHHHHHHHH
Q psy5605         116 GRRDMDRIAAQIR  128 (152)
Q Consensus       116 G~~~LD~iA~~i~  128 (152)
                      + ..++.++..+.
T Consensus        74 ~-~~~~~~~~~l~   85 (141)
T 1i1g_A           74 P-EKLFEVAEKLK   85 (141)
T ss_dssp             G-GGHHHHHHHHH
T ss_pred             c-hhHHHHHHHHh
Confidence            4 35666666553

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=86.88  E-value=2  Score=34.13  Aligned_cols=58  Identities=16%  Similarity=0.129  Sum_probs=45.6

Q ss_pred             HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      -|+..||..|.- .+++++..|....|-              +.+-+..+|+.|++.|||+++. +...|++.-
T Consensus        21 ~r~l~iL~~l~~~~~~~~~~eia~~~gl--------------~~stv~r~l~tL~~~G~v~~~~-~~Y~Lg~~~   79 (265)
T 2ia2_A           21 ARGLAVIRCFDHRNQRRTLSDVARATDL--------------TRATARRFLLTLVELGYVATDG-SAFWLTPRV   79 (265)
T ss_dssp             HHHHHHHHTCCSSCSSEEHHHHHHHHTC--------------CHHHHHHHHHHHHHHTSEEESS-SEEEECGGG
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEecC-CEEEEcHHH
Confidence            477788877663 478999999998753              4578889999999999999974 556777653

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=86.74  E-value=2.9  Score=32.24  Aligned_cols=67  Identities=12%  Similarity=0.212  Sum_probs=49.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCc-------------ee
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGR-------------KI  112 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR-------------~l  112 (152)
                      .|++.|. ++++.+..|+...|              -|.+-++.-|+.||+.|+|+..  ...|+             .|
T Consensus        24 ~IL~~L~-~~~~s~~eLA~~lg--------------lS~stv~~~l~~Le~~GlI~~~~~~~~~~~~~~~~g~~~~~~~v   88 (192)
T 1uly_A           24 KILKLLR-NKEMTISQLSEILG--------------KTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADVFYI   88 (192)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSEEEE
T ss_pred             HHHHHHH-cCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEeccccccchhhhcCcceEEEEE
Confidence            5787787 89999999999874              3567899999999999999876  22243             36


Q ss_pred             CcchH-hhHHHHHHHHHH
Q psy5605         113 TSHGR-RDMDRIAAQIRV  129 (152)
Q Consensus       113 T~~G~-~~LD~iA~~i~~  129 (152)
                      |.+|. ..++.++..+..
T Consensus        89 ~~~~~~~~~~~~~~~~~~  106 (192)
T 1uly_A           89 NLYLGDEELRYIARSRLK  106 (192)
T ss_dssp             CSCSSCHHHHHHHHHHHH
T ss_pred             ecCCchhHHHHHHHHHHH
Confidence            77773 456666655443

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

Probab=86.65  E-value=0.98  Score=31.70  Aligned_cols=45  Identities=7%  Similarity=0.200  Sum_probs=38.9

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD  106 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~  106 (152)
                      .|+..|--+|.+.|..|...|              .-|..-||.-|..||+.|+|....
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l--------------~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARL--------------QTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHT--------------TCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEEEe
Confidence            366667778999999999998              467899999999999999998763

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=85.94  E-value=2.2  Score=33.63  Aligned_cols=60  Identities=17%  Similarity=0.266  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhhHhhcC------Cc-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          42 FYTRCAALARHIYMRS------PV-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        42 ~YiRaASilRkiYl~g------~v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      .|...+..+|.--..|      .+ ....|+..||              -|..-+|.+|+.|++.|+|+..++.|-.+++
T Consensus        11 ~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   76 (243)
T 2wv0_A           11 IYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFG--------------ISRMTVRQALSNLVNEGLLYRLKGRGTFVSK   76 (243)
T ss_dssp             HHHHHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEECTTSCEEECC
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEeCCCeEEEeC
Confidence            4666666665544443      13 6678888884              4788999999999999999999877877776


Q ss_pred             c
Q psy5605         115 H  115 (152)
Q Consensus       115 ~  115 (152)
                      .
T Consensus        77 ~   77 (243)
T 2wv0_A           77 P   77 (243)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=85.87  E-value=0.65  Score=30.33  Aligned_cols=49  Identities=14%  Similarity=0.188  Sum_probs=39.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      ||.-|+-.+|+.+..|....+-.  .+        -+.+-+..+|+.||+.|+|+..++
T Consensus        14 vL~~L~~~~~~t~~ei~~~l~~~--~~--------~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A           14 VMKVIWKHSSINTNEVIKELSKT--ST--------WSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             HHHHHHTSSSEEHHHHHHHHHHH--SC--------CCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHcCCCCCHHHHHHHHhhc--CC--------ccHHHHHHHHHHHHHCCCeEEEec
Confidence            66677778999999999998531  11        245788999999999999998774

>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=85.74  E-value=1.4  Score=33.19  Aligned_cols=45  Identities=16%  Similarity=0.258  Sum_probs=35.9

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcc
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSH  115 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~  115 (152)
                      +++.+..++..+|              -|...+|++|++|.++|||+...  .||-.|+..
T Consensus        27 ~~~s~~~IA~~~~--------------is~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~   73 (162)
T 3k69_A           27 SKVASRELAQSLH--------------LNPVMIRNILSVLHKHGYLTGTVGKNGGYQLDLA   73 (162)
T ss_dssp             SCBCHHHHHHHHT--------------SCGGGTHHHHHHHHHTTSSEEECSTTCEEECCSC
T ss_pred             CCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEeecCCCCCeEecCC
Confidence            4688999999884              45678999999999999998665  357777654

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

Probab=84.48  E-value=0.81  Score=32.27  Aligned_cols=51  Identities=16%  Similarity=0.191  Sum_probs=40.2

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      ||+-|+-.+|+.+..|....+..  +        .-+.+-+..+|..||+.|||+..++ ||
T Consensus        40 VL~~L~~~~~~t~~eL~~~l~~~--~--------~~s~sTVt~~L~rLe~KGlV~R~~~-gR   90 (99)
T 2k4b_A           40 VMRVIWSLGEARVDEIYAQIPQE--L--------EWSLATVKTLLGRLVKKEMLSTEKE-GR   90 (99)
T ss_dssp             HHHHHHHHSCEEHHHHHHTCCGG--G--------CCCHHHHHHHHHHHHHTTSCEEEEE-TT
T ss_pred             HHHHHHhCCCCCHHHHHHHHhcc--c--------CCCHhhHHHHHHHHHHCCCEEEEeC-CC
Confidence            77778878999999999987542  1        1345778899999999999998774 55

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

Probab=81.60  E-value=2.8  Score=27.04  Aligned_cols=46  Identities=11%  Similarity=0.131  Sum_probs=36.7

Q ss_pred             HHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          48 ALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        48 SilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      .||.-|--. +|+.+..|+...|-              |.+.+.++|+.||+.|+|+..+.
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            466655544 58999999999854              47899999999999999987553

>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=81.54  E-value=1.3  Score=32.30  Aligned_cols=54  Identities=13%  Similarity=0.238  Sum_probs=37.5

Q ss_pred             HHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC-CCCceeCcch
Q psy5605          48 ALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD-DGGRKITSHG  116 (152)
Q Consensus        48 SilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~-~gGR~lT~~G  116 (152)
                      .+|..|..+ ++ .+..++..+              .-|-..++++|++|.++|||+... .||-.|+..-
T Consensus        13 ~~L~~La~~~~~-s~~~IA~~~--------------~i~~~~l~kIl~~L~~aGlv~s~rG~GGy~Lar~p   68 (145)
T 1xd7_A           13 HILSLISMDEKT-SSEIIADSV--------------NTNPVVVRRMISLLKKADILTSRAGVPGASLKKDP   68 (145)
T ss_dssp             HHHHHHHTCSCC-CHHHHHHHH--------------TSCHHHHHHHHHHHHHTTSEECCSSSSSCEESSCG
T ss_pred             HHHHHHHhCCCC-CHHHHHHHH--------------CcCHHHHHHHHHHHHHCCceEeecCCCCceecCCH
Confidence            344444433 23 566677765              456789999999999999998655 5677776543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=81.24  E-value=2.7  Score=34.20  Aligned_cols=50  Identities=10%  Similarity=0.161  Sum_probs=43.2

Q ss_pred             HHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce-ecC
Q psy5605          43 YTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE-KSD  106 (152)
Q Consensus        43 YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe-k~~  106 (152)
                      -.|-+..+-.+|-.+++++..|++.+|              -|..-||+-|+.||+.|+|+ +..
T Consensus         6 ~~~~~~~ia~l~~~~~~~~~ela~~l~--------------vS~~tIrRdL~~l~~~G~v~iri~   56 (315)
T 2w48_A            6 DIRLIVKIAQLYYEQDMTQAQIARELG--------------IYRTTISRLLKRGREQGIVTIAIN   56 (315)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEEec
Confidence            356677777889999999999999985              47899999999999999998 554

---

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	152
d2v7fa1	149	a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococ	1e-62

>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 =  186 bits (475), Expect = 1e-62
 Identities = 47/122 (38%), Positives = 71/122 (58%)

Query: 13  KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRK 72
           +  ++K PEW   VK+ + KE  P   DW+Y R A++ R +Y+  PVG++ +   +GGRK
Sbjct: 21  EIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRK 80

Query: 73  RNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132
             G  P  F ++ GS+ RKALQ LE    +EK    GR IT  GR  +D+IA +++   +
Sbjct: 81  NRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELE 140

Query: 133 EA 134
           E 
Sbjct: 141 EI 142

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	152
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	100.0
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	97.37
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.04
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.0
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.91
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.85
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.83
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	96.6
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	96.54
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.45
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	96.43
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.36
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.2
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	96.13
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.02
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.92
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.88
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	95.86
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.78
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	95.69
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.63
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	95.45
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	95.39
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.39
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.31
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	95.12
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	94.73
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	94.5
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	94.33
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	94.28
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	94.24
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	94.09
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	93.79
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.68
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	93.59
d1ixsb1	76	Holliday junction helicase RuvB {Thermus thermophi	93.52
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.39
d2axla1	144	Werner syndrome ATP-dependent helicase WRN {Human	92.9
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	92.82
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	92.8
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	92.03
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	91.53
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	91.44
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	90.12
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	88.38
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	87.68
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	86.78
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	86.55
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	84.39
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	84.32
d1olta_	441	Oxygen-independent coproporphyrinogen III oxidase	83.75
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	82.4
d1oywa1	110	DNA helicase RecQ DNA-binding domain {Escherichia	80.74

>d2v7fa1 a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococcus abyssi [TaxId: 29292]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rps19E-like
domain: Ribosomal protein S19e
species: Pyrococcus abyssi [TaxId: 29292]

Probab=100.00  E-value=1.9e-68  Score=416.59  Aligned_cols=133  Identities=37%  Similarity=0.695  Sum_probs=120.3

Q ss_pred             chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605           2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF   81 (152)
Q Consensus         2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~   81 (152)
                      .||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||++|||++|+||
T Consensus        10 ~~I~~lA~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~y~RaASilRkiY~~gpvGv~~Lr~~YGg~k~rG~~P~h~   89 (149)
T d2v7fa1          10 LLVERVAQRLKEIPEIKPPEWAPFVKTGRHKERLPEQEDWWYYRVASILRRVYLDGPVGIERLRTYYGGRKNRGHAPERF   89 (149)
T ss_dssp             HHHHHHHHHHTTCTTCCCCSCGGGCCC------CHHHHTHHHHHHHHHHHHHHHHCSBCHHHHHHHHCC----CCCTTSC
T ss_pred             HHHHHHHHHHHhcCCCCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCCCCCCCCCCc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA  134 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~  134 (152)
                      ++|||+|||+||||||++|||++++++||+||++||++||+||.+|.+++.+.
T Consensus        90 ~~~Sg~iiR~~LQqLE~~glVek~~~~GR~lT~~G~~~LD~iA~~v~~~~~~~  142 (149)
T d2v7fa1          90 YKAGGSIIRKALQQLEAAGFVEKVPGKGRVITPKGRSFLDKIATELKKELEEI  142 (149)
T ss_dssp             CCHHHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHHhCCCeeEcCCCCcEECHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999998999999999999999999999988764

>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=97.37  E-value=0.00013  Score=50.19  Aligned_cols=56  Identities=25%  Similarity=0.337  Sum_probs=45.9

Q ss_pred             hHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q psy5605          52 HIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD-DGGRKITSHGRRD  119 (152)
Q Consensus        52 kiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~-~gGR~lT~~G~~~  119 (152)
                      ..|+.  -|+|...+.+.||-            .-|.+-||+.|++||+.|+|++.. .+||..|.+|-+.
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            44653  59999999998853            347899999999999999999754 4799999999754

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=97.04  E-value=0.0013  Score=45.90  Aligned_cols=66  Identities=17%  Similarity=0.328  Sum_probs=52.6

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      .+|..|+-.||+.+..|+..-|-              +.+-+-.+++.||+.|||++.+  +++|    .||++|+..++
T Consensus        34 ~iL~~i~~~~~~t~~~la~~l~i--------------~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~   99 (139)
T d2a61a1          34 DILQKIYFEGPKRPGELSVLLGV--------------AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIE   99 (139)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCC--------------CcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHH
Confidence            47888999999999999998743              3456888999999999998664  3355    58999999988


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++....
T Consensus       100 ~~~~~~  105 (139)
T d2a61a1         100 KVIERR  105 (139)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            875543

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=97.00  E-value=0.0018  Score=45.40  Aligned_cols=68  Identities=13%  Similarity=0.120  Sum_probs=54.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      +|..|+-+|++.++.|+..-+-              +.+-+-.+++.||+.|||++.+  +++|    .||++|+..+++
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            6778888999999999998643              5577888999999999999654  4466    699999999988


Q ss_pred             HHHHHHHH
Q psy5605         123 IAAQIRVS  130 (152)
Q Consensus       123 iA~~i~~~  130 (152)
                      +...+...
T Consensus       105 ~~~~~~~~  112 (138)
T d1jgsa_         105 CHQLVGQD  112 (138)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            76544433

>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=96.91  E-value=0.002  Score=45.00  Aligned_cols=66  Identities=17%  Similarity=0.223  Sum_probs=53.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      .+|..|+-.||+.++.|++..+-              +.+-+-.+++.||+.|||++.+  ..+|    .||++|+..++
T Consensus        39 ~iL~~l~~~~~~t~~~la~~~~i--------------~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~  104 (143)
T d1s3ja_          39 FVLASLKKHGSLKVSEIAERMEV--------------KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFE  104 (143)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHH
Confidence            37788998999999999998743              4577888999999999998554  3466    69999999888


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+-..+
T Consensus       105 ~~~~~~  110 (143)
T d1s3ja_         105 EVLAGR  110 (143)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766544

>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=96.85  E-value=0.0015  Score=43.61  Aligned_cols=66  Identities=12%  Similarity=0.215  Sum_probs=51.0

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~~~LD  121 (152)
                      +||..|+-+|++.++.|+...|-              +.+-+-..|..||+.|||+...+  ++    -.||++|+..+.
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            58889999999999999998743              34556667999999999986542  33    259999998877


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus        86 ~~~~~~   91 (100)
T d1ub9a_          86 RFLSSL   91 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            665443

>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=96.83  E-value=0.0035  Score=43.96  Aligned_cols=64  Identities=13%  Similarity=0.205  Sum_probs=49.1

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      +|..|+-.+++.+..|.+.-+              -+.+-+-.+++.||+.|||++.+  +.+|    .||++|+..++.
T Consensus        41 vL~~l~~~~~~t~~~la~~l~--------------~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          41 VLKLIDEQRGLNLQDLGRQMC--------------RDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHSSTTCBHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHC--------------ccHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            555667777788888888753              45577888999999999998665  3455    589999998887


Q ss_pred             HHHH
Q psy5605         123 IAAQ  126 (152)
Q Consensus       123 iA~~  126 (152)
                      +...
T Consensus       107 ~~~~  110 (141)
T d1lnwa_         107 AEAI  110 (141)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6544

>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=96.60  E-value=0.0044  Score=42.94  Aligned_cols=66  Identities=12%  Similarity=0.152  Sum_probs=52.5

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      ++|..|+-.|++.++.|+...|-              +.+-+=.+++.||+.|||++.+  .++|    .||++|++.++
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            57778888999999999998743              3466778899999999998664  3454    48999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      .+-...
T Consensus       100 ~~~~~~  105 (136)
T d2fbia1         100 SMSGDM  105 (136)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>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=96.54  E-value=0.0055  Score=42.13  Aligned_cols=68  Identities=13%  Similarity=0.221  Sum_probs=50.9

Q ss_pred             HHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          49 LARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      +|..||..+  ++.+..|++..+              -+.+-+=.+++.||+.|||++.++  .+|    .||++|++.+
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            566777653  467778888753              455677788999999999997753  455    4999999999


Q ss_pred             HHHHHHHHHH
Q psy5605         121 DRIAAQIRVS  130 (152)
Q Consensus       121 D~iA~~i~~~  130 (152)
                      +.+..++-+.
T Consensus       104 ~~~~~~~~~~  113 (115)
T d2frha1         104 ESLLSRVNKR  113 (115)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            9987776543

>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=96.45  E-value=0.0085  Score=41.52  Aligned_cols=65  Identities=14%  Similarity=0.246  Sum_probs=53.0

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      +|-.|+-.||+.++.|+...|              -+.+-+-.++..||+.|||++.+  .++|    .||++|+..+++
T Consensus        37 iL~~l~~~~~~t~~~La~~l~--------------i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d2etha1          37 AFLYVALFGPKKMKEIAEFLS--------------TTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  102 (140)
T ss_dssp             HHHHHHHHCCBCHHHHHHHTT--------------SCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHH
Confidence            677889999999999999874              35577888999999999998664  3454    589999999888


Q ss_pred             HHHHH
Q psy5605         123 IAAQI  127 (152)
Q Consensus       123 iA~~i  127 (152)
                      +...+
T Consensus       103 ~~~~~  107 (140)
T d2etha1         103 ILSNF  107 (140)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.43  E-value=0.0048  Score=40.91  Aligned_cols=60  Identities=22%  Similarity=0.447  Sum_probs=50.4

Q ss_pred             HHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605          49 LARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI  123 (152)
Q Consensus        49 ilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i  123 (152)
                      +++-+| ++.|+|=..|+..-|              =+-.++|.-+.-|-+.|+|+..+ .|-.||++|++.|+++
T Consensus         7 vl~~l~ll~qPiGRr~La~~L~--------------l~Er~vRte~~~Lk~~gLI~~~~-~Gm~lTe~G~~~l~~L   67 (69)
T d2p8ta1           7 VLAVIFLLKEPLGRKQISERLE--------------LGEGSVRTLLRKLSHLDIIRSKQ-RGHFLTLKGKEIRDKL   67 (69)
T ss_dssp             HHHHHHHTTSCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEC---CEEECHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHHcC--------------CcHHHHHHHHHHHHHCCCeeeeC-CCCEECHhHHHHHHHH
Confidence            556666 589999999999864              35679999999999999999988 6999999999999875

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=96.36  E-value=0.0042  Score=42.03  Aligned_cols=76  Identities=16%  Similarity=0.263  Sum_probs=59.0

Q ss_pred             HHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC----CC--ceeCcchHhhH
Q psy5605          48 ALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD----GG--RKITSHGRRDM  120 (152)
Q Consensus        48 SilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~----gG--R~lT~~G~~~L  120 (152)
                      .||+.|+- .||+.+..|+...|              =+.+-++..|+.||+.|||+..+.    +|  ..+|..|.+..
T Consensus        25 ~iL~~L~~~~~~~t~~eLa~~~~--------------i~~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~~~~~~~~~   90 (109)
T d2d1ha1          25 AVLLKMVEIEKPITSEELADIFK--------------LSKTTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSISSNIL   90 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEC-------CCEEEEECTTHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHC--------------ccHhHHHHHHHHHHHCCCEEEeecCCCCCceeEEEeeCCHHHH
Confidence            57777874 67899999999874              356789999999999999986643    23  47899999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q psy5605         121 DRIAAQIRVSKKEAALQ  137 (152)
Q Consensus       121 D~iA~~i~~~~~~~~~~  137 (152)
                      ++|..++.+..++.+.+
T Consensus        91 ~~i~~~~~~~~~k~~~~  107 (109)
T d2d1ha1          91 EKIRNDLLNCAKRMELA  107 (109)
T ss_dssp             HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99988877766665543

>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=96.20  E-value=0.014  Score=39.95  Aligned_cols=66  Identities=17%  Similarity=0.166  Sum_probs=49.6

Q ss_pred             HHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q psy5605          49 LARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~L  120 (152)
                      +|..||-.+  ++.+..|+..-|              -+.+-+-.+++.||+.|||++..  +.+|    .||++|+..+
T Consensus        34 vL~~l~~~~~~~it~~ela~~~~--------------~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~   99 (135)
T d3broa1          34 IIDYLSRNKNKEVLQRDLESEFS--------------IKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLE   99 (135)
T ss_dssp             HHHHHHHTTTSCCBHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHC--------------cCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHH
Confidence            666777664  488888888753              34566778999999999998554  3443    6999999999


Q ss_pred             HHHHHHHH
Q psy5605         121 DRIAAQIR  128 (152)
Q Consensus       121 D~iA~~i~  128 (152)
                      .++...+.
T Consensus       100 ~~~~~~~~  107 (135)
T d3broa1         100 TIILSYMD  107 (135)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88776553

>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=96.13  E-value=0.019  Score=40.15  Aligned_cols=66  Identities=14%  Similarity=0.225  Sum_probs=52.8

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      +|..|+-++|+.+..|+...+              -+.+-+-.+++.||+.|||++.++  ++|    .||++|++..++
T Consensus        34 iL~~i~~~~~~t~~~la~~l~--------------i~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          34 YLVRVCENPGIIQEKIAELIK--------------VDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHSTTEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHC--------------ccHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHH
Confidence            667788889999999999874              355778889999999999986653  344    589999998888


Q ss_pred             HHHHHH
Q psy5605         123 IAAQIR  128 (152)
Q Consensus       123 iA~~i~  128 (152)
                      +...+.
T Consensus       100 ~~~~~~  105 (144)
T d1lj9a_         100 IVRENQ  105 (144)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776543

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.02  E-value=0.0074  Score=41.30  Aligned_cols=42  Identities=17%  Similarity=0.256  Sum_probs=35.8

Q ss_pred             CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA  124 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA  124 (152)
                      +.=|-..+.+.|+.|++.|+|++.. +...||++|+++|+.+-
T Consensus        28 aNLs~~~~~kyl~~L~~~GLI~~~~-~~Y~iT~kG~~~L~~~~   69 (90)
T d1r7ja_          28 ANLSYALTGRYIKMLMDLEIIRQEG-KQYMLTKKGEELLEDIR   69 (90)
T ss_dssp             HTCCHHHHHHHHHHHHHTTSEEEET-TEEEECHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHCCCeeecC-CEEEECccHHHHHHHHH
Confidence            4556678899999999999999866 57899999999999863

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.92  E-value=0.029  Score=38.40  Aligned_cols=65  Identities=15%  Similarity=0.200  Sum_probs=49.9

Q ss_pred             HHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605          49 LARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD  121 (152)
                      +|..|+-.+ ++.++.|+...|-              +.+-+-.++..||+.|||++.++  .+|    .||++|+..++
T Consensus        33 iL~~l~~~~~~~t~~~la~~~~~--------------~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~   98 (137)
T d2fbha1          33 VLLHLARHRDSPTQRELAQSVGV--------------EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA   98 (137)
T ss_dssp             HHHHHHHCSSCCBHHHHHHHHTC--------------CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCC--------------CHHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHH
Confidence            666776544 5888999998743              44668889999999999997764  344    59999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++....
T Consensus        99 ~~~~~~  104 (137)
T d2fbha1          99 DIEAIA  104 (137)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=95.88  E-value=0.014  Score=38.64  Aligned_cols=57  Identities=19%  Similarity=0.239  Sum_probs=44.4

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHHHHHHHH
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~~~LD~iA~~i~  128 (152)
                      +++.++.|...-|              -+.+-+-.+|+.||+.|||+..++ ||    .||++|+..+.+...++.
T Consensus        20 ~~lt~~eLa~~l~--------------i~~~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~G~~~l~~~~~~~~   80 (85)
T d3ctaa1          20 AYLTSSKLADMLG--------------ISQQSASRIIIDLEKNGYITRTVT-KRGQILNITEKGLDVLYTEFADLS   80 (85)
T ss_dssp             EECCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeeeecc-cccccceECHHHHHHHHHHHHHHH
Confidence            4677888888753              345667789999999999998665 44    379999999888776654

>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=95.86  E-value=0.029  Score=39.00  Aligned_cols=68  Identities=22%  Similarity=0.206  Sum_probs=50.6

Q ss_pred             HHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605          48 ALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM  120 (152)
Q Consensus        48 SilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L  120 (152)
                      .+|..||-. |++.+..|+...|-              +.+-+-.+++.||+.|||++.++  ++|    .||++|+..+
T Consensus        38 ~vL~~L~~~~g~~t~~~La~~~~~--------------~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~  103 (145)
T d2hr3a1          38 VVLGAIDRLGGDVTPSELAAAERM--------------RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNL  103 (145)
T ss_dssp             HHHHHHHHTTSCBCHHHHHHHTTC--------------CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHH
Confidence            367778754 57999999998754              45677888999999999997653  343    5899999999


Q ss_pred             HHHHHHHHH
Q psy5605         121 DRIAAQIRV  129 (152)
Q Consensus       121 D~iA~~i~~  129 (152)
                      +++......
T Consensus       104 ~~~~~~~~~  112 (145)
T d2hr3a1         104 YGNRAKREE  112 (145)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            887655433

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.78  E-value=0.034  Score=35.75  Aligned_cols=60  Identities=18%  Similarity=0.122  Sum_probs=49.9

Q ss_pred             HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchH
Q psy5605          44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGR  117 (152)
Q Consensus        44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~  117 (152)
                      -|+.+|+..+.-. +|+++..+.+.-|              -+.+-+..+|+.|++.|||++++++--.|+++--
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~--------------~~~st~~rll~tL~~~g~l~~~~~g~y~lG~~l~   65 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFN--------------MSVSNAYKYMVVLEEKGFVLRKKDKRYVPGYKLI   65 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTT--------------CCHHHHHHHHHHHHHTTSEEECTTSCEEECTHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEECCCCCEeecHHHH
Confidence            3888999988864 6899999999853              4568899999999999999999876677887653

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.69  E-value=0.012  Score=40.43  Aligned_cols=66  Identities=18%  Similarity=0.329  Sum_probs=48.5

Q ss_pred             HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q psy5605          49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~L  120 (152)
                      +|..||..  +++.+..|+...|              -+.+-+=.+++.||+.|||++.+  +.+|    .||++|+..+
T Consensus        37 vL~~l~~~~~~~~t~~ela~~l~--------------~~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  102 (115)
T d1hsja1          37 ILNHILRSESNEISSKEIAKCSE--------------FKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  102 (115)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHSSC--------------CCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHccCCCCcCHHHHHHHHC--------------CChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHH
Confidence            66677753  4577777777643              34456677899999999998665  3466    4899999999


Q ss_pred             HHHHHHHH
Q psy5605         121 DRIAAQIR  128 (152)
Q Consensus       121 D~iA~~i~  128 (152)
                      +.+..++-
T Consensus       103 ~~~~~~~~  110 (115)
T d1hsja1         103 QKLISELE  110 (115)
T ss_dssp             HHHHHHHG
T ss_pred             HHHHHHHH
Confidence            98876653

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=95.63  E-value=0.0039  Score=43.38  Aligned_cols=62  Identities=15%  Similarity=0.199  Sum_probs=47.5

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      +|..|+..+++.+..|+..-|-              +.+-+=.+++.||+.|||+..+  +++|    .||++|+...++
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            5667777888888888887532              3344555899999999998664  4577    799999998887


Q ss_pred             HH
Q psy5605         123 IA  124 (152)
Q Consensus       123 iA  124 (152)
                      +.
T Consensus       104 ~~  105 (137)
T d1z91a1         104 AV  105 (137)
T ss_dssp             TT
T ss_pred             HH
Confidence            53

>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=95.45  E-value=0.014  Score=40.34  Aligned_cols=63  Identities=21%  Similarity=0.294  Sum_probs=48.7

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~  122 (152)
                      +|..|+..+|+.++.|+..-|-.              .+-+-.+++.||+.|||++.+  .++|    .||++|+..+++
T Consensus        39 vL~~i~~~~~~t~~~la~~l~~~--------------~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~  104 (136)
T d2bv6a1          39 VLTILWDESPVNVKKVVTELALD--------------TGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  104 (136)
T ss_dssp             HHHHHHHSSEEEHHHHHHHTTCC--------------TTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHCCC--------------HhHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHH
Confidence            66778888999999999986542              245778899999999998554  3454    569999998887


Q ss_pred             HHH
Q psy5605         123 IAA  125 (152)
Q Consensus       123 iA~  125 (152)
                      +..
T Consensus       105 ~~~  107 (136)
T d2bv6a1         105 LSN  107 (136)
T ss_dssp             HTT
T ss_pred             HHH
Confidence            654

>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=95.39  E-value=0.024  Score=39.29  Aligned_cols=70  Identities=13%  Similarity=0.135  Sum_probs=50.2

Q ss_pred             HHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhh
Q psy5605          48 ALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRD  119 (152)
Q Consensus        48 SilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~  119 (152)
                      .||..||-.  +++.+..|+...+              -+.+-+-.+++.||+.|||++..+  ..|    .||++|++.
T Consensus        38 ~iL~~l~~~~~~~~t~~eia~~~~--------------~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~  103 (125)
T d1p4xa1          38 ILLTYLFHQQENTLPFKKIVSDLC--------------YKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREK  103 (125)
T ss_dssp             HHHHHHHSCSCSEEEHHHHHHHSS--------------SCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHH
T ss_pred             HHHHHHHHhccCCcCHHHHHHHhC--------------CCcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHH
Confidence            467677765  3577778887753              344566778999999999987653  355    589999999


Q ss_pred             HHHHHHHHHHHH
Q psy5605         120 MDRIAAQIRVSK  131 (152)
Q Consensus       120 LD~iA~~i~~~~  131 (152)
                      +..+...+-+-+
T Consensus       104 ~~~~~~~~~~~i  115 (125)
T d1p4xa1         104 IAERVTLFDQII  115 (125)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            988766654433

>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=95.39  E-value=0.051  Score=37.23  Aligned_cols=65  Identities=17%  Similarity=0.206  Sum_probs=45.7

Q ss_pred             HHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q psy5605          49 LARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMD  121 (152)
Q Consensus        49 ilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD  121 (152)
                      +|..|+- .+++-++.|....+-              +.+-+-.+++.||+.|||++.+  +.+|    .||++|++.++
T Consensus        36 ~L~~l~~~~~~~t~~~la~~l~i--------------~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~  101 (140)
T d3deua1          36 TLHNIHQLPPDQSQIQLAKAIGI--------------EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIA  101 (140)
T ss_dssp             HHHHHHHSCSSEEHHHHHHHHTS--------------CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHH
T ss_pred             HHHHHHHcCCCccHHHHHHHHCC--------------CHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHH
Confidence            6666774 456888888887643              3344567999999999998555  3454    49999999998


Q ss_pred             HHHHHH
Q psy5605         122 RIAAQI  127 (152)
Q Consensus       122 ~iA~~i  127 (152)
                      ++...+
T Consensus       102 ~~~~~~  107 (140)
T d3deua1         102 EMEEVI  107 (140)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877654

>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=95.31  E-value=0.039  Score=37.26  Aligned_cols=73  Identities=11%  Similarity=0.176  Sum_probs=51.5

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCce--eC-cchHhhHH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRK--IT-SHGRRDMD  121 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~--lT-~~G~~~LD  121 (152)
                      +.|+..|+-+|+..+..+++.-|              =+.+-+..+|+.||+.|||++.  ++++|.  .+ ......++
T Consensus        23 ~~v~~~L~~~g~~t~~eia~~~~--------------i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l~   88 (109)
T d1sfxa_          23 VRIYSLLLERGGMRVSEIARELD--------------LSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLK   88 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHhC--------------CCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHHH
Confidence            45777888899999999999865              3557899999999999999864  334442  22 22345566


Q ss_pred             HHHHHHHHHHHH
Q psy5605         122 RIAAQIRVSKKE  133 (152)
Q Consensus       122 ~iA~~i~~~~~~  133 (152)
                      ++-..+.+.+.+
T Consensus        89 ~~~~~~~~~l~e  100 (109)
T d1sfxa_          89 EFKSSILGEIER  100 (109)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666555554443

>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=95.12  E-value=0.015  Score=39.65  Aligned_cols=48  Identities=17%  Similarity=0.243  Sum_probs=35.9

Q ss_pred             ccCCCchhHHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHH
Q psy5605          80 HFCRSSGSVARKALQALEQVNIIEKS---DDGGR-----KITSHGRRDMDRIAAQI  127 (152)
Q Consensus        80 h~~~asg~iiR~~LQqLE~~glVek~---~~gGR-----~lT~~G~~~LD~iA~~i  127 (152)
                      ++..-|-+.|=.+|..||+.|||+..   .++||     .||++|++.|.+...+.
T Consensus        36 ~~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l~~~~~~~   91 (103)
T d1xmaa_          36 ELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKCEEW   91 (103)
T ss_dssp             TSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHHHHH
T ss_pred             CeecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence            33456678889999999999999743   23453     79999999998876653

>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=94.73  E-value=0.031  Score=37.45  Aligned_cols=58  Identities=19%  Similarity=0.345  Sum_probs=43.2

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM  120 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L  120 (152)
                      .+-.-|--||||+..|+..-|-             ....|.=-+=-=|-+.|+|++++ .||++|++|.+.|
T Consensus        13 ~l~~~f~ggPvGl~tlAa~l~e-------------~~~TiEdviEPyLiq~G~i~RTp-RGR~~T~~~~~hl   70 (75)
T d1in4a1          13 TIIEIYRGGPVGLNALAASLGV-------------EADTLSEVYEPYLLQAGFLARTP-RGRIVTEKAYKHL   70 (75)
T ss_dssp             HHHHHSTTCCBCHHHHHHHHTS-------------CHHHHHHHTHHHHHHTTSEEEET-TEEEECHHHHHHT
T ss_pred             HHHHHhCCCCCcHHHHHHHHcC-------------ChhHHHHHhhHHHHHhhHHhhCC-chHHhHHHHHHHc
Confidence            4445566799999999998754             23344444445577799999999 5999999998765

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=94.50  E-value=0.058  Score=37.24  Aligned_cols=57  Identities=12%  Similarity=0.244  Sum_probs=42.8

Q ss_pred             HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcchH
Q psy5605          46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHGR  117 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G~  117 (152)
                      |.-+|=-+..++++....++..+|              -+-+++|++|++|.++|+|+...  +||+ |+..-.
T Consensus         6 Av~~L~~la~~~~~ss~~IA~~~~--------------~~~~~v~kIl~~L~~aglV~s~rG~~GGy-Lar~p~   64 (127)
T d1xd7a_           6 AIHILSLISMDEKTSSEIIADSVN--------------TNPVVVRRMISLLKKADILTSRAGVPGAS-LKKDPA   64 (127)
T ss_dssp             HHHHHHHHHTCSCCCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTSEECCSSSSSCE-ESSCGG
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHhCcccccCCCCCcc-ccCCHH
Confidence            334444455678999999999874              35689999999999999998654  4676 876543

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=94.33  E-value=0.037  Score=40.01  Aligned_cols=38  Identities=21%  Similarity=0.373  Sum_probs=28.2

Q ss_pred             HHHHHHHhCCcceecCC--CCc----eeCcchHhhHHHHHHHHH
Q psy5605          91 KALQALEQVNIIEKSDD--GGR----KITSHGRRDMDRIAAQIR  128 (152)
Q Consensus        91 ~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~iA~~i~  128 (152)
                      .+++.||+.|||++.++  ++|    .||++|+..++.+.....
T Consensus        98 r~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~~~~~~~  141 (172)
T d2fbka1          98 NRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPAHL  141 (172)
T ss_dssp             SHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHHHHHHHH
Confidence            45899999999997753  344    599999999998765544

>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=94.28  E-value=0.23  Score=33.93  Aligned_cols=59  Identities=14%  Similarity=0.224  Sum_probs=45.6

Q ss_pred             HHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC----ceeCcchH
Q psy5605          45 RCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG----RKITSHGR  117 (152)
Q Consensus        45 RaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG----R~lT~~G~  117 (152)
                      -++.|+--+|+. +|+.+..|+..-|              -|.+-+-.+|+.||+.|+|....+  ..    ..+|++|+
T Consensus        27 ~~~~i~~~L~~~~~plt~~ela~~l~--------------vsk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~t~~g~   92 (151)
T d1ku9a_          27 SVGAVYAILYLSDKPLTISDIMEELK--------------ISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSS   92 (151)
T ss_dssp             HHHHHHHHHHHCSSCEEHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHHH
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHhC--------------CCcchHHHHHHHHHHCCCEEEEEcCCCCceeEEeCCHHHH
Confidence            356788888877 4799999999864              366778899999999999986643  22    36788885

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.24  E-value=0.13  Score=35.81  Aligned_cols=80  Identities=19%  Similarity=0.126  Sum_probs=55.5

Q ss_pred             HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CC-----ceeCcchHhh
Q psy5605          46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GG-----RKITSHGRRD  119 (152)
Q Consensus        46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gG-----R~lT~~G~~~  119 (152)
                      ..-|++.++ .|+...+.|.+.-.             .-|.+++=.-|.+||+.|+|++... ..     ..||+.|+++
T Consensus        26 ~l~Il~~L~-~g~~RF~el~~~l~-------------gis~~~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~G~~L   91 (114)
T d1yyva1          26 GVLILVALR-DGTHRFSDLRRKMG-------------GVSEKMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQV   91 (114)
T ss_dssp             HHHHHHHGG-GCCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHH
T ss_pred             HHHHHHHHh-cCCCCHHHHHHHcc-------------ccchhHHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHhHHHH
Confidence            345788875 68888888887642             3677888899999999999997753 22     7899999988


Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q psy5605         120 MDRIAAQIRVSKKEAALQALA  140 (152)
Q Consensus       120 LD~iA~~i~~~~~~~~~~~~~  140 (152)
                      +. +-..+..=..++..+-.+
T Consensus        92 ~~-il~~l~~W~~~~~~~i~~  111 (114)
T d1yyva1          92 SD-KVAALADWIELNLPQVLA  111 (114)
T ss_dssp             HH-HHHHHHHHHHHHHHHHHT
T ss_pred             HH-HHHHHHHHHHHHHHHHHH
Confidence            75 344444433333333333

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=94.09  E-value=0.05  Score=39.48  Aligned_cols=64  Identities=16%  Similarity=0.115  Sum_probs=49.6

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR  122 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~  122 (152)
                      ||.-|+-.+++.++.|++.-+              =+.+-+=.+++.||+.|||++.++  +.|    .||++|+..++.
T Consensus        46 vL~~l~~~~~~t~~~la~~~~--------------l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          46 ILWIAYQLNGASISEIAKFGV--------------MHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             HHHHHHHHTSEEHHHHHHHTT--------------CCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHhhhccCCCcCHHHHHHHHc--------------CCchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHH
Confidence            677788889999999998853              345667788999999999997653  454    589999999988


Q ss_pred             HHHH
Q psy5605         123 IAAQ  126 (152)
Q Consensus       123 iA~~  126 (152)
                      +-..
T Consensus       112 ~~~~  115 (162)
T d2fxaa1         112 LLEE  115 (162)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>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=93.79  E-value=0.094  Score=35.29  Aligned_cols=62  Identities=11%  Similarity=0.171  Sum_probs=47.9

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC------ceeCcchHhhH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG------RKITSHGRRDM  120 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG------R~lT~~G~~~L  120 (152)
                      .-|++.+ ..|+...+.|.+.-.             .-|.+++=.-|++||+.|+|++.....      ..||+.|++++
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            4578877 478888888877542             367789999999999999999765322      78999999987


Q ss_pred             HH
Q psy5605         121 DR  122 (152)
Q Consensus       121 D~  122 (152)
                      .-
T Consensus        80 pi   81 (95)
T d2hzta1          80 GI   81 (95)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>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=93.68  E-value=0.017  Score=37.28  Aligned_cols=42  Identities=26%  Similarity=0.333  Sum_probs=33.8

Q ss_pred             CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605          58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI  112 (152)
Q Consensus        58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l  112 (152)
                      |.++..+.+.+|-             .|-+-++..|++||+.|||++.+...|.|
T Consensus        24 ~Ps~rei~~~~g~-------------~S~stv~~~l~~Le~kG~I~r~~~~~R~i   65 (71)
T d1jhfa1          24 PPTRAEIAQRLGF-------------RSPNAAEEHLKALARKGVIEIVSGASRGI   65 (71)
T ss_dssp             CCCHHHHHHHTTC-------------SSHHHHHHHHHHHHHTTSEEECSSSSSCE
T ss_pred             CCCHHHHHHHcCC-------------CCHHHHHHHHHHHHHCcCeecCCCCCcee
Confidence            5677788777752             47788999999999999999998656654

>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=93.59  E-value=0.064  Score=37.06  Aligned_cols=62  Identities=11%  Similarity=0.216  Sum_probs=47.3

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC------ceeCcchHhhHH
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG------RKITSHGRRDMD  121 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG------R~lT~~G~~~LD  121 (152)
                      -|++.++ .|+.--+.|.+.-.             .-|.+++=.-|++||+.|+|++.....      ..||+.|++++.
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            4777775 57777777777642             367889999999999999999765322      789999998876


Q ss_pred             HH
Q psy5605         122 RI  123 (152)
Q Consensus       122 ~i  123 (152)
                      -+
T Consensus        89 il   90 (108)
T d1z7ua1          89 AL   90 (108)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=93.52  E-value=0.042  Score=36.89  Aligned_cols=55  Identities=18%  Similarity=0.313  Sum_probs=40.3

Q ss_pred             hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605          52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM  120 (152)
Q Consensus        52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L  120 (152)
                      .-|--||||+..|+..-|-.             .+.|.=-+=-=|-+.|+|++++ .||++|++|.+-|
T Consensus        16 ~~f~ggPVGl~tlA~~lgE~-------------~~TiEdviEPyLiq~G~i~RTp-rGR~~T~~a~~hL   70 (76)
T d1ixsb1          16 LRFGGGPVGLATLATALSED-------------PGTLEEVHEPYLIRQGLLKRTP-RGRVATELAYRHL   70 (76)
T ss_dssp             SSSCSSCCCSHHHHGGGSSC-------------TTHHHHTSHHHHHHTTSEEECS-SSEEECHHHHHHH
T ss_pred             HHhCCCCccHHHHHHHHcCC-------------hhHHHHHhhHHHHHHhHHhhCC-ChHHhHHHHHHHc
Confidence            33456899999999987653             2233333334566789999999 5999999998765

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.39  E-value=0.031  Score=39.03  Aligned_cols=49  Identities=14%  Similarity=0.197  Sum_probs=37.7

Q ss_pred             CchhHHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHHHHHHHHHHHH
Q psy5605          84 SSGSVARKALQALEQVNIIEKSD--DGGR----KITSHGRRDMDRIAAQIRVSKK  132 (152)
Q Consensus        84 asg~iiR~~LQqLE~~glVek~~--~gGR----~lT~~G~~~LD~iA~~i~~~~~  132 (152)
                      -+.+-+-.+++.||+.|||++..  ++.|    .||++|++.++.+..++-+-++
T Consensus        61 ~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~~~~~~~i~  115 (125)
T d1p4xa2          61 HKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQVNQLLA  115 (125)
T ss_dssp             SCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHHHHHHHHHHh
Confidence            34566778899999999998654  4465    4899999999988877765443

>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=92.90  E-value=0.074  Score=38.08  Aligned_cols=81  Identities=12%  Similarity=0.178  Sum_probs=59.2

Q ss_pred             hHHHH-HHHHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCc-----cCCC---chhHHHHHHHHHHhCCcceecCCCCc
Q psy5605          41 WFYTR-CAALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSH-----FCRS---SGSVARKALQALEQVNIIEKSDDGGR  110 (152)
Q Consensus        41 W~YiR-aASilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h-----~~~a---sg~iiR~~LQqLE~~glVek~~~gGR  110 (152)
                      |-++. |-.||..|+ +.+..|++.+..++-|.++.-.+..|     |..|   +-.-+|.++.||-..|+++.....|.
T Consensus         9 ~D~T~eA~~iLs~V~~~~~rfg~~~iidiL~Gs~~~kI~~~~~~l~~yG~Gk~~s~~~w~~li~qli~~G~L~e~~~~~~   88 (144)
T d2axla1           9 WDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNK   88 (144)
T ss_dssp             EECHHHHHHHHHHHHHTTTCSCSHHHHHHHTCCSCSHHHHHTCSCTTTTGGGGSCHHHHHHHHHHHHHHSSEEEETTSCT
T ss_pred             eehHHHHHHHHHHHHHhcccccchHHHHHHHhcccHHHHHHhhcccccCCCCcCCHHHHHHHHHHHHHcCcceeecccCc
Confidence            44443 445777777 57899999999999998776543322     3222   33589999999999999976665553


Q ss_pred             -----eeCcchHhhHH
Q psy5605         111 -----KITSHGRRDMD  121 (152)
Q Consensus       111 -----~lT~~G~~~LD  121 (152)
                           .||++|+..|.
T Consensus        89 ~~~~l~lt~kg~~~L~  104 (144)
T d2axla1          89 FMKICALTKKGRNWLH  104 (144)
T ss_dssp             TTCEEEECHHHHHHHH
T ss_pred             ceeeeeECHHHHHHHh
Confidence                 79999999884

>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=92.82  E-value=0.052  Score=39.21  Aligned_cols=62  Identities=18%  Similarity=0.233  Sum_probs=44.0

Q ss_pred             CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCc------eeCcchHhhHHHHH
Q psy5605          57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGR------KITSHGRRDMDRIA  124 (152)
Q Consensus        57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR------~lT~~G~~~LD~iA  124 (152)
                      +|.-=-.|++.+-.      ...++...|-+-|=..|+.||+.|||+...  .+|+      .||++|+..|.+..
T Consensus        13 ~~~~GYei~~~~~~------~~~~~w~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~~Gr~~l~~wl   82 (178)
T d1yg2a_          13 RDATGYDITKEFSA------SIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWF   82 (178)
T ss_dssp             CCBCHHHHHHHHTT------GGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH------HhCCccCCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHH
Confidence            44444456777632      346777889999999999999999998532  2232      79999999887743

>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=92.80  E-value=0.092  Score=36.09  Aligned_cols=46  Identities=15%  Similarity=0.188  Sum_probs=35.9

Q ss_pred             CCCchhHHHHHHHHHHhCCcceec--CCCC-----ceeCcchHhhHHHHHHHH
Q psy5605          82 CRSSGSVARKALQALEQVNIIEKS--DDGG-----RKITSHGRRDMDRIAAQI  127 (152)
Q Consensus        82 ~~asg~iiR~~LQqLE~~glVek~--~~gG-----R~lT~~G~~~LD~iA~~i  127 (152)
                      ...+-+.|=.+|+.||+.|||+..  +.+|     -.||++|+..|+....++
T Consensus        42 ~~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~~~~~~~   94 (114)
T d2esha1          42 GIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSL   94 (114)
T ss_dssp             TCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             ccCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence            345556788999999999999743  2234     379999999999887775

>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=92.03  E-value=0.055  Score=34.79  Aligned_cols=43  Identities=28%  Similarity=0.275  Sum_probs=35.6

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG  116 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G  116 (152)
                      ....|+..||              -|.+.+|.+|+.|+..|+|+..+..|-.+++.-
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            5677888874              578999999999999999999997787776543

>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=91.53  E-value=0.066  Score=33.81  Aligned_cols=40  Identities=15%  Similarity=0.196  Sum_probs=33.2

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT  113 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT  113 (152)
                      -...|+..||              -|...+|.+|+.||..|+|+..+..|-.+.
T Consensus        27 ~~~~La~~~~--------------vSr~tvr~Al~~L~~~Gli~~~~~~G~~V~   66 (69)
T d2hs5a1          27 SEPDICAALD--------------VSRNTVREAFQILIEDRLVAHELNRGVFVR   66 (69)
T ss_dssp             CHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTTEEEEC
T ss_pred             CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEEcCCEEEec
Confidence            4567888884              577999999999999999999987776654

>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=91.44  E-value=0.19  Score=34.18  Aligned_cols=63  Identities=16%  Similarity=0.115  Sum_probs=46.7

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-C-----ceeCcchHhhH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-G-----RKITSHGRRDM  120 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-G-----R~lT~~G~~~L  120 (152)
                      .-|++.+. .|+..-+.|.+.-.             .-|.+++=.-|++||+.|+|++.... .     ..||+.|++++
T Consensus        23 l~Il~~L~-~g~~rF~el~~~l~-------------gIs~~~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          23 LLIIFQIN-RRIIRYGELKRAIP-------------GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             HHHHHHHT-TSCEEHHHHHHHST-------------TCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHHHc-cCCCCHHHHHhhCc-------------ccchhHHHHHHHHHHHCCceeecccCCCCCeehhhhhHhHHHHH
Confidence            34677764 67777777777641             36778888889999999999976532 1     56999999987


Q ss_pred             HHH
Q psy5605         121 DRI  123 (152)
Q Consensus       121 D~i  123 (152)
                      .-+
T Consensus        89 pil   91 (102)
T d2fswa1          89 PII   91 (102)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            643

>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=90.12  E-value=0.27  Score=35.31  Aligned_cols=60  Identities=12%  Similarity=0.171  Sum_probs=46.3

Q ss_pred             HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-----CceeCcchHhhHH
Q psy5605          47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-----GRKITSHGRRDMD  121 (152)
Q Consensus        47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-----GR~lT~~G~~~LD  121 (152)
                      .-|+|.++ .|+...+.|.+.-              .-|.+++-.-|++||+.|+|++....     -..||++|++++.
T Consensus        23 l~Il~~l~-~G~~rf~el~~~l--------------gis~~vLs~rL~~L~~~gLv~r~~~~~p~r~~Y~LT~~G~~L~p   87 (142)
T d2f2ea1          23 MLIVRDAF-EGLTRFGEFQKSL--------------GLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALFP   87 (142)
T ss_dssp             HHHHHHHH-TTCCSHHHHHHHH--------------CCCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHh--------------hccHHHHHHHHHHHHHhcceeeecCCCCCeeEEecCcCcchHHH
Confidence            35788874 6888888887764              35668898999999999999974322     2689999998865

>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=88.38  E-value=0.24  Score=33.22  Aligned_cols=65  Identities=18%  Similarity=0.319  Sum_probs=48.3

Q ss_pred             CCCCCchHHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605          35 APYDPDWFYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD  107 (152)
Q Consensus        35 aP~d~DW~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~  107 (152)
                      +|..+-  |...+.-+|..-..|-      + ....|+..||              -|...+|.+|+.|+..|||+..+.
T Consensus         5 ~p~~~~--y~qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~--------------vSr~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1           5 APEGKG--YADVATHFRTLIKSGELAPGDTLPSVADIRAQFG--------------VAAKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             CCSSCC--HHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSS--------------SCTTHHHHHTTTTTTSSCCEEETT
T ss_pred             CCCCCH--HHHHHHHHHHHHHcCCCCCcCCCccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEecC
Confidence            444444  5566777776666652      3 6677888874              567899999999999999999987


Q ss_pred             CCceeCcc
Q psy5605         108 GGRKITSH  115 (152)
Q Consensus       108 gGR~lT~~  115 (152)
                      .|-.+++.
T Consensus        69 ~G~~V~~~   76 (100)
T d1v4ra1          69 LGTVVEKN   76 (100)
T ss_dssp             TEEESCSC
T ss_pred             CEEEECCC
Confidence            78777753

>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=87.68  E-value=0.7  Score=28.58  Aligned_cols=47  Identities=13%  Similarity=0.173  Sum_probs=41.1

Q ss_pred             HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec
Q psy5605          45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS  105 (152)
Q Consensus        45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~  105 (152)
                      ..+.|++.|+-+||+....|++..|              =|.+-++.++..|++.|+|+..
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~g--------------lS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESE--------------LAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEe
Confidence            4568999999999999999999974              4668899999999999999754

>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=86.78  E-value=0.94  Score=27.86  Aligned_cols=53  Identities=13%  Similarity=0.129  Sum_probs=40.6

Q ss_pred             HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCc-ceecCCCCceeCc
Q psy5605          48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNI-IEKSDDGGRKITS  114 (152)
Q Consensus        48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~gl-Vek~~~gGR~lT~  114 (152)
                      .|++-|-=.+.+....|+..+|              -|..-||+-++.||+.|+ |+..+..|-+|++
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~--------------vS~~ti~r~i~~L~~~G~~I~~~~g~GY~L~~   62 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLG--------------MSRAAINKHIQTLRDWGVDVFTVPGKGYSLPE   62 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHT--------------SCHHHHHHHHHHHHHTTCCCEEETTTEEECSS
T ss_pred             HHHHHHHHCCcCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCcEEEeCCCeEEeCC
Confidence            4666665567789999999985              466789999999999998 5666655777753

>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=86.55  E-value=0.2  Score=32.12  Aligned_cols=41  Identities=15%  Similarity=0.289  Sum_probs=33.2

Q ss_pred             chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605          60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS  114 (152)
Q Consensus        60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~  114 (152)
                      ....|+..||              -|..-+|.+|+.|++.|||+..+..|-.++.
T Consensus        29 s~~eLa~~~~--------------vSr~tvr~Al~~L~~~G~i~~~~g~G~~V~~   69 (74)
T d1hw1a1          29 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNN   69 (74)
T ss_dssp             CHHHHHHHHT--------------CCHHHHHHHHHHHHHTTSEEEETTEEEEECC
T ss_pred             cHHHHHHHHC--------------CCHHHHHHHHHHHHHCCcEEEEeCceEEECC
Confidence            4566777773              5779999999999999999999977766653

>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=84.39  E-value=1.2  Score=27.28  Aligned_cols=55  Identities=16%  Similarity=0.236  Sum_probs=42.7

Q ss_pred             HHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCc-ceecCCCCceeCc
Q psy5605          45 RCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNI-IEKSDDGGRKITS  114 (152)
Q Consensus        45 RaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~gl-Vek~~~gGR~lT~  114 (152)
                      |--.|+..|.- ++++.+..|+..+|              -|..-||+=++.|++.|+ |+..+ +|-+|.+
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~--------------VS~~TI~rdi~~L~~~G~~I~~~~-gGY~L~~   64 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELS--------------VSRQVIVQDIAYLRSLGYNIVATP-RGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHT--------------SCHHHHHHHHHHHHHHTCCCEEET-TEEECCT
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEEEeC-CCEEeCC
Confidence            44567777764 46799999999984              466789999999999998 77666 5888764

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=84.32  E-value=0.5  Score=31.78  Aligned_cols=38  Identities=26%  Similarity=0.358  Sum_probs=29.5

Q ss_pred             chhHHHHHHHHHHhCCcceec--CCC--CceeCcchHhhHHH
Q psy5605          85 SGSVARKALQALEQVNIIEKS--DDG--GRKITSHGRRDMDR  122 (152)
Q Consensus        85 sg~iiR~~LQqLE~~glVek~--~~g--GR~lT~~G~~~LD~  122 (152)
                      -=|.+|..|-||+.+|+++..  ++|  --.||++|+..-+.
T Consensus        37 PMS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lca~   78 (81)
T d2obpa1          37 PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAAQ   78 (81)
T ss_dssp             CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHHHH
Confidence            348999999999999999854  432  24799999976543

>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=83.75  E-value=0.43  Score=39.21  Aligned_cols=66  Identities=12%  Similarity=0.162  Sum_probs=45.6

Q ss_pred             HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605          49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA  125 (152)
Q Consensus        49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~  125 (152)
                      ++-.|-...++-...+...||-.-.     ..    .... ...|++|++.|||+.++ ++=+||++|+-++|.||.
T Consensus       370 vi~~L~~~~~ld~~~~~~~fg~~~~-----~~----f~~~-~~~L~~l~~~GLv~~~~-~~l~lT~~Gr~l~~~I~~  435 (441)
T d1olta_         370 VIKSLICNFRLDYSPIEQQWDLLFA-----DY----FAED-LKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICM  435 (441)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTCCHH-----HH----THHH-HHHHHHHHHTTSEEECS-SEEEECTTTGGGHHHHHH
T ss_pred             HHHHHHHhCCcCHHHHHHHHCCCHH-----HH----HHHH-HHHHHHHHHCCCEEEEC-CEEEECHhHHHHHHHHHH
Confidence            3333444566777788888754210     01    1122 25678899999999887 578999999999999986

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=82.40  E-value=2.1  Score=27.52  Aligned_cols=48  Identities=25%  Similarity=0.342  Sum_probs=31.3

Q ss_pred             hhHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605          86 GSVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA  135 (152)
Q Consensus        86 g~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~  135 (152)
                      -+-+-+.+++||+   ..|++.+. +|=.+|+.|+..+.. |.+|+.......
T Consensus        29 q~avs~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~-a~~il~~~~~~~   79 (89)
T d1ixca1          29 QPPITRQMQALEADLGVVLLERSH-RGIELTAAGHAFLED-ARRILELAGRSG   79 (89)
T ss_dssp             HHHHHHHHHHHHHHHTSCCBC------CCBCHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCceeeEecC-CccCccHhHHHHHHH-HHHHHHHHHHHH
Confidence            3567788899998   56777765 588999999988876 455655544433

>d1oywa1 a.4.5.43 (A:407-516) DNA helicase RecQ 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: RecQ helicase DNA-binding domain-like
domain: DNA helicase RecQ DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=80.74  E-value=0.8  Score=30.86  Aligned_cols=74  Identities=11%  Similarity=0.102  Sum_probs=54.9

Q ss_pred             HHHhhHh-hcCCcchhhHHHHhCCCCCCCCC-------CCcc--CCCchhHHHHHHHHHHhCCcceecCC--CCceeCcc
Q psy5605          48 ALARHIY-MRSPVGVKTVTKIFGGRKRNGVC-------PSHF--CRSSGSVARKALQALEQVNIIEKSDD--GGRKITSH  115 (152)
Q Consensus        48 SilRkiY-l~g~vGV~~L~~~YGg~krrG~~-------P~h~--~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~  115 (152)
                      .+|..|+ +.+..|++.+..++-|.++.-+.       |.|-  ..-|-.-++.++.||...|+++++..  +-=.||++
T Consensus        12 ~iLs~V~~~~~rfg~~~ivdiL~Gs~~~kI~~~~h~~l~~yG~gk~~~~~~w~~li~qLv~~g~L~~~~~~y~~l~lt~~   91 (110)
T d1oywa1          12 IALSTIGRVNQRFGMGYVVEVIRGANNQRIRDYGHDKLKVYGMGRDKSHEHWVSVIRQLIHLGLVTQNIAQHSALQLTEA   91 (110)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHHHHTCCCHHHHHHTGGGSTTTTTTTTSCHHHHHHHHHHHHHTTSEEEEGGGTTEEEECGG
T ss_pred             HHHHHHHHhcCccCcceehhhHhcCccHHHHHhCCCcCCcccCcCCCCHHHHHHHHHHHHHcCCceeccCcCCeEEECHH
Confidence            4667777 57899999999999887776322       2221  12245689999999999999998753  34579999


Q ss_pred             hHhhHH
Q psy5605         116 GRRDMD  121 (152)
Q Consensus       116 G~~~LD  121 (152)
                      |+..|.
T Consensus        92 g~~~l~   97 (110)
T d1oywa1          92 ARPVLR   97 (110)
T ss_dssp             GHHHHH
T ss_pred             HHHHhC
Confidence            999885