Psyllid ID: psy15513

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-------
Protein Sequence
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLVI
Secondary Structure (PSIPRED)
ccccccccccccHHHHcccccHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
HHHccccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHcccccccccHHHHHHHHHc
Coil and Loop (DISEMBL)
maaagvrpcvisrqlrvshGCVSKILNRYqetgsirpgviggskprvatpdVERRIEeykgenpamfsWEIRDRLVI
Flexible Loop (DISEMBL)
maaagvrpcvisrqlrvshgCVSKILNRyqetgsirpgviggskprvatpdVERRieeykgenpamfsweirdrlvi
Low Complexity Region (SEG)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLVI
Disordered region (IsUnstruct)
*****VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI****************************W********
Disordered Region (DISOPRED)
***********SRQLRVSHGCVSKILNRYQE*********************ERRIEEYKGENPAMFSWEIRDRLVI
Disordered Region (DISEMBL)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLVI
Disordered Region (DISPRO)
****GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLVI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLVI
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	77	2.2.26 [Sep-21-2011]
P06601	613	Segmentation protein pair	yes	N/A	0.987	0.123	0.828	1e-33
P09082	427	Protein gooseberry OS=Dro	no	N/A	0.987	0.177	0.842	1e-32
P47239	503	Paired box protein Pax-7	yes	N/A	0.987	0.151	0.857	3e-32
P23759	520	Paired box protein Pax-7	no	N/A	0.987	0.146	0.857	3e-32
P09083	449	Protein gooseberry-neuro	no	N/A	0.987	0.169	0.789	9e-32
P23760	479	Paired box protein Pax-3	yes	N/A	0.987	0.158	0.818	2e-31
P24610	479	Paired box protein Pax-3	no	N/A	0.987	0.158	0.818	3e-31
Q0IH87	483	Paired box protein Pax-3-	N/A	N/A	0.987	0.157	0.789	3e-31
Q645N4	484	Paired box protein Pax-3-	N/A	N/A	0.987	0.157	0.779	1e-29
Q02650	391	Paired box protein Pax-5	no	N/A	0.987	0.194	0.763	1e-28

>sp|P06601|PRD_DROME Segmentation protein paired OS=Drosophila melanogaster GN=prd PE=1 SV=1

 Score =  141 bits (355), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 63/76 (82%), Positives = 71/76 (93%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 55  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 114

Query: 61  GENPAMFSWEIRDRLV 76
             +P MFSWEIR++L+
Sbjct: 115 RSSPGMFSWEIREKLI 130

Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.
Drosophila melanogaster (taxid: 7227)

>sp|P09082|GSB_DROME Protein gooseberry OS=Drosophila melanogaster GN=gsb PE=2 SV=1

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 64/76 (84%), Positives = 69/76 (90%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNR+QETGSIRPGVIGGSKPRVATPD+E RIEE K
Sbjct: 47  MAAAGVRPCVISRQLRVSHGCVSKILNRFQETGSIRPGVIGGSKPRVATPDIESRIEELK 106

Query: 61  GENPAMFSWEIRDRLV 76
              P +FSWEIR +L+
Sbjct: 107 QSQPGIFSWEIRAKLI 122

Expressed in segmentally repeating pattern to define the polarity of embryonic segments.

Drosophila melanogaster (taxid: 7227)

>sp|P47239|PAX7_MOUSE Paired box protein Pax-7 OS=Mus musculus GN=Pax7 PE=2 SV=2

 Score =  137 bits (344), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 66/77 (85%), Positives = 70/77 (90%), Gaps = 1/77 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query: 60  KGENPAMFSWEIRDRLV 76
           K ENP MFSWEIRDRL+
Sbjct: 122 KRENPGMFSWEIRDRLL 138

Probable transcription factor. May have a role in myogenesis.

Mus musculus (taxid: 10090)

>sp|P23759|PAX7_HUMAN Paired box protein Pax-7 OS=Homo sapiens GN=PAX7 PE=2 SV=3

 Score =  136 bits (343), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 66/77 (85%), Positives = 70/77 (90%), Gaps = 1/77 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query: 60  KGENPAMFSWEIRDRLV 76
           K ENP MFSWEIRDRL+
Sbjct: 122 KRENPGMFSWEIRDRLL 138

Probable transcription factor. May have a role in myogenesis.

Homo sapiens (taxid: 9606)

>sp|P09083|GSBN_DROME Protein gooseberry-neuro OS=Drosophila melanogaster GN=gsb-n PE=1 SV=2

 Score =  135 bits (339), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 60/76 (78%), Positives = 72/76 (94%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP+V +P++E RI+E +
Sbjct: 48  MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPKVTSPEIETRIDELR 107

Query: 61  GENPAMFSWEIRDRLV 76
            ENP++FSWEIR++L+
Sbjct: 108 KENPSIFSWEIREKLI 123

Expressed in a segmentally repeating pattern to define the polarity of embryonic segments.

Drosophila melanogaster (taxid: 7227)

>sp|P23760|PAX3_HUMAN Paired box protein Pax-3 OS=Homo sapiens GN=PAX3 PE=1 SV=2

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 63/77 (81%), Positives = 69/77 (89%), Gaps = 1/77 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TPDVE++IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPDVEKKIEEY 121

Query: 60  KGENPAMFSWEIRDRLV 76
           K ENP MFSWEIRD+L+
Sbjct: 122 KRENPGMFSWEIRDKLL 138

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Homo sapiens (taxid: 9606)

>sp|P24610|PAX3_MOUSE Paired box protein Pax-3 OS=Mus musculus GN=Pax3 PE=1 SV=2

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 63/77 (81%), Positives = 69/77 (89%), Gaps = 1/77 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TPDVE++IEEY
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPDVEKKIEEY 121

Query: 60  KGENPAMFSWEIRDRLV 76
           K ENP MFSWEIRD+L+
Sbjct: 122 KRENPGMFSWEIRDKLL 138

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Mus musculus (taxid: 10090)

>sp|Q0IH87|PAX3B_XENLA Paired box protein Pax-3-B OS=Xenopus laevis GN=pax3-b PE=2 SV=2

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 60/76 (78%), Positives = 69/76 (90%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+V TP+VE++IEE+K
Sbjct: 62  MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKVTTPEVEKKIEEFK 121

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MFSWEIRD+L+
Sbjct: 122 RDNPGMFSWEIRDKLL 137

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|Q645N4|PAX3A_XENLA Paired box protein Pax-3-A OS=Xenopus laevis GN=pax3-a PE=2 SV=1

 Score =  128 bits (322), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 60/77 (77%), Positives = 69/77 (89%), Gaps = 1/77 (1%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
           MA  GVRPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKP+ V TP+VE+++EE+
Sbjct: 62  MAHHGVRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPKQVTTPEVEKKMEEF 121

Query: 60  KGENPAMFSWEIRDRLV 76
           K +NP MFSWEIRD+L+
Sbjct: 122 KRDNPGMFSWEIRDKLL 138

Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.

Xenopus laevis (taxid: 8355)

>sp|Q02650|PAX5_MOUSE Paired box protein Pax-5 OS=Mus musculus GN=Pax5 PE=1 SV=1

 Score =  125 bits (313), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 58/76 (76%), Positives = 65/76 (85%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V  +I EYK
Sbjct: 44  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MF+WEIRDRL+
Sbjct: 104 RQNPTMFAWEIRDRLL 119

May play an important role in B-cell differentiation as well as neural development and spermatogenesis. Involved in the regulation of the CD19 gene, a B-lymphoid-specific target gene.

Mus musculus (taxid: 10090)

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	77
328713660	440	PREDICTED: protein gooseberry-like [Acyr	0.987	0.172	0.960	8e-36
328719097	574	PREDICTED: paired box protein Pax-3-B-li	0.961	0.128	0.959	6e-35
322794106	486	hypothetical protein SINV_02934 [Solenop	0.987	0.156	0.921	1e-34
391327510	665	PREDICTED: paired box protein Pax-7-like	0.987	0.114	0.921	2e-34
307197090	481	Segmentation protein paired [Harpegnatho	0.987	0.158	0.907	4e-34
350397864	522	PREDICTED: LOW QUALITY PROTEIN: protein	0.987	0.145	0.907	5e-34
340724544	502	PREDICTED: LOW QUALITY PROTEIN: segmenta	0.987	0.151	0.907	6e-34
383854529	483	PREDICTED: paired box protein Pax-3-B-li	0.987	0.157	0.907	6e-34
307180596	516	Segmentation protein paired [Camponotus	0.987	0.147	0.907	7e-34
328782878	531	PREDICTED: paired box protein Pax-3-B [A	0.987	0.143	0.907	9e-34

>gi|328713660|ref|XP_001942974.2| PREDICTED: protein gooseberry-like [Acyrthosiphon pisum]

 Score =  154 bits (388), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 73/76 (96%), Positives = 74/76 (97%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK
Sbjct: 47  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 106

Query: 61  GENPAMFSWEIRDRLV 76
             NPAMFSWEIRD+LV
Sbjct: 107 KANPAMFSWEIRDKLV 122

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328719097|ref|XP_001949018.2| PREDICTED: paired box protein Pax-3-B-like [Acyrthosiphon pisum]

 Score =  151 bits (381), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 71/74 (95%), Positives = 72/74 (97%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK
Sbjct: 48  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 107

Query: 61  GENPAMFSWEIRDR 74
            ENP +FSWEIRDR
Sbjct: 108 TENPGIFSWEIRDR 121

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322794106|gb|EFZ17315.1| hypothetical protein SINV_02934 [Solenopsis invicta]

 Score =  150 bits (378), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 48  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEEYK 107

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MFSWEIRDRL+
Sbjct: 108 RDNPGMFSWEIRDRLI 123

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|391327510|ref|XP_003738241.1| PREDICTED: paired box protein Pax-7-like [Metaseiulus occidentalis]

 Score =  149 bits (377), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 70/76 (92%), Positives = 74/76 (97%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE+RIE+Y+
Sbjct: 230 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEDYR 289

Query: 61  GENPAMFSWEIRDRLV 76
            ENP +FSWEIRDRLV
Sbjct: 290 KENPGIFSWEIRDRLV 305

Source: Metaseiulus occidentalis

Species: Metaseiulus occidentalis

Genus: Metaseiulus

Family: Phytoseiidae

Order: Mesostigmata

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307197090|gb|EFN78458.1| Segmentation protein paired [Harpegnathos saltator]

 Score =  148 bits (373), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 74/76 (97%)

Query: 1  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
          MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE +IEEYK
Sbjct: 1  MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEAKIEEYK 60

Query: 61 GENPAMFSWEIRDRLV 76
           ENP++FSWEIRDRLV
Sbjct: 61 RENPSVFSWEIRDRLV 76

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350397864|ref|XP_003485014.1| PREDICTED: LOW QUALITY PROTEIN: protein gooseberry-like [Bombus impatiens]

 Score =  148 bits (373), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 85  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVESRIEEYK 144

Query: 61  GENPAMFSWEIRDRLV 76
            +NP +FSWEIRDRL+
Sbjct: 145 RDNPGIFSWEIRDRLI 160

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340724544|ref|XP_003400641.1| PREDICTED: LOW QUALITY PROTEIN: segmentation protein paired-like [Bombus terrestris]

 Score =  147 bits (372), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 60  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVESRIEEYK 119

Query: 61  GENPAMFSWEIRDRLV 76
            +NP +FSWEIRDRL+
Sbjct: 120 RDNPGIFSWEIRDRLI 135

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383854529|ref|XP_003702773.1| PREDICTED: paired box protein Pax-3-B-like [Megachile rotundata]

 Score =  147 bits (372), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 40  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEEYK 99

Query: 61  GENPAMFSWEIRDRLV 76
            +NP +FSWEIRDRL+
Sbjct: 100 RDNPGIFSWEIRDRLI 115

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180596|gb|EFN68551.1| Segmentation protein paired [Camponotus floridanus]

 Score =  147 bits (371), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 47  MAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEEYK 106

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MFSWEIRDRL+
Sbjct: 107 RDNPGMFSWEIRDRLI 122

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782878|ref|XP_003250208.1| PREDICTED: paired box protein Pax-3-B [Apis mellifera]

 Score =  147 bits (370), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 69/76 (90%), Positives = 73/76 (96%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP+VE RIEEYK
Sbjct: 88  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEVEARIEEYK 147

Query: 61  GENPAMFSWEIRDRLV 76
            +NP +FSWEIRDRL+
Sbjct: 148 RDNPGIFSWEIRDRLI 163

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	77
FB|FBgn0003145	613	prd "paired" [Drosophila melan	0.987	0.123	0.828	5.3e-31
MGI|MGI:97491	503	Pax7 "paired box gene 7" [Mus	0.987	0.151	0.857	1.1e-30
RGD|1564360	503	Pax7 "paired box 7" [Rattus no	0.987	0.151	0.857	1.1e-30
UNIPROTKB|E1BKL5	505	PAX7 "Uncharacterized protein"	0.987	0.150	0.857	1.2e-30
UNIPROTKB|F1PNX6	505	PAX7 "Uncharacterized protein"	0.987	0.150	0.857	1.2e-30
UNIPROTKB|E9PFV9	505	PAX7 "Paired box protein Pax-7	0.987	0.150	0.857	1.2e-30
ZFIN|ZDB-GENE-990415-201	507	pax7a "paired box gene 7a" [Da	0.987	0.149	0.857	1.2e-30
FB|FBgn0001148	427	gsb "gooseberry" [Drosophila m	0.987	0.177	0.842	1.4e-30
UNIPROTKB|P23759	520	PAX7 "Paired box protein Pax-7	0.987	0.146	0.857	1.6e-30
UNIPROTKB|O42349	524	Pax-7 "PAX7 protein" [Gallus g	0.987	0.145	0.857	1.7e-30

FB|FBgn0003145 prd "paired" [Drosophila melanogaster (taxid:7227)]

 Score = 347 (127.2 bits), Expect = 5.3e-31, P = 5.3e-31
 Identities = 63/76 (82%), Positives = 71/76 (93%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
             MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct:    55 MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 114

Query:    61 GENPAMFSWEIRDRLV 76
               +P MFSWEIR++L+
Sbjct:   115 RSSPGMFSWEIREKLI 130

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0005667 "transcription factor complex" evidence=ISS

GO:0007366 "periodic partitioning by pair rule gene" evidence=NAS;TAS

GO:0003677 "DNA binding" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA

MGI|MGI:97491 Pax7 "paired box gene 7" [Mus musculus (taxid:10090)]

 Score = 339 (124.4 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0000983 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=TAS

GO:0006338 "chromatin remodeling" evidence=IMP

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IMP

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0010453 "regulation of cell fate commitment" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0014813 "satellite cell commitment" evidence=IMP

GO:0021527 "spinal cord association neuron differentiation" evidence=IGI

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IDA

GO:0031062 "positive regulation of histone methylation" evidence=IGI;IDA

GO:0043393 "regulation of protein binding" evidence=IMP

GO:0043403 "skeletal muscle tissue regeneration" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0048663 "neuron fate commitment" evidence=IGI

GO:0048706 "embryonic skeletal system development" evidence=IMP

GO:0051216 "cartilage development" evidence=IMP

GO:0060415 "muscle tissue morphogenesis" evidence=IGI

GO:2000288 "positive regulation of myoblast proliferation" evidence=IMP

RGD|1564360 Pax7 "paired box 7" [Rattus norvegicus (taxid:10116)]

 Score = 339 (124.4 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0000983 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006338 "chromatin remodeling" evidence=ISO

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

GO:0007519 "skeletal muscle tissue development" evidence=ISO

GO:0010453 "regulation of cell fate commitment" evidence=ISO

GO:0010468 "regulation of gene expression" evidence=ISO

GO:0014813 "satellite cell commitment" evidence=IEA;ISO

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA;ISO

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA;ISO

GO:0031062 "positive regulation of histone methylation" evidence=ISO

GO:0043393 "regulation of protein binding" evidence=ISO

GO:0043403 "skeletal muscle tissue regeneration" evidence=IEA;ISO

GO:0043565 "sequence-specific DNA binding" evidence=IEA;ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0048663 "neuron fate commitment" evidence=IEA;ISO

GO:0048706 "embryonic skeletal system development" evidence=IEA;ISO

GO:0051216 "cartilage development" evidence=IEA;ISO

GO:0060415 "muscle tissue morphogenesis" evidence=IEA;ISO

GO:2000288 "positive regulation of myoblast proliferation" evidence=ISO

UNIPROTKB|E1BKL5 PAX7 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 339 (124.4 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0005634 "nucleus" evidence=IEA

GO:0060415 "muscle tissue morphogenesis" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0043403 "skeletal muscle tissue regeneration" evidence=IEA

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0014813 "satellite cell commitment" evidence=IEA

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|F1PNX6 PAX7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 339 (124.4 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|E9PFV9 PAX7 "Paired box protein Pax-7" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-990415-201 pax7a "paired box gene 7a" [Danio rerio (taxid:7955)]

 Score = 339 (124.4 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE+RIEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKRIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRD+L+
Sbjct:   122 KRENPGMFSWEIRDKLL 138

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

FB|FBgn0001148 gsb "gooseberry" [Drosophila melanogaster (taxid:7227)]

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 64/76 (84%), Positives = 69/76 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
             MAAAGVRPCVISRQLRVSHGCVSKILNR+QETGSIRPGVIGGSKPRVATPD+E RIEE K
Sbjct:    47 MAAAGVRPCVISRQLRVSHGCVSKILNRFQETGSIRPGVIGGSKPRVATPDIESRIEELK 106

Query:    61 GENPAMFSWEIRDRLV 76
                P +FSWEIR +L+
Sbjct:   107 QSQPGIFSWEIRAKLI 122

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0005667 "transcription factor complex" evidence=ISS

GO:0007367 "segment polarity determination" evidence=NAS

GO:0005634 "nucleus" evidence=IMP;NAS

GO:0007419 "ventral cord development" evidence=TAS

GO:0007435 "salivary gland morphogenesis" evidence=IMP

GO:0005737 "cytoplasm" evidence=IMP

GO:0007268 "synaptic transmission" evidence=IDA

GO:0060025 "regulation of synaptic activity" evidence=IDA

UNIPROTKB|P23759 PAX7 "Paired box protein Pax-7" [Homo sapiens (taxid:9606)]

 Score = 339 (124.4 bits), Expect = 1.6e-30, P = 1.6e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0014813 "satellite cell commitment" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0021904 "dorsal/ventral neural tube patterning" evidence=IEA

GO:0043403 "skeletal muscle tissue regeneration" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0060415 "muscle tissue morphogenesis" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=TAS

GO:0009653 "anatomical structure morphogenesis" evidence=TAS

UNIPROTKB|O42349 Pax-7 "PAX7 protein" [Gallus gallus (taxid:9031)]

 Score = 339 (124.4 bits), Expect = 1.7e-30, P = 1.7e-30
 Identities = 66/77 (85%), Positives = 70/77 (90%)

Query:     1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEY 59
             MA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIRPG IGGSKPR VATPDVE++IEEY
Sbjct:    62 MAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIRPGAIGGSKPRQVATPDVEKKIEEY 121

Query:    60 KGENPAMFSWEIRDRLV 76
             K ENP MFSWEIRDRL+
Sbjct:   122 KRENPGMFSWEIRDRLL 138

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

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

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0048663 "neuron fate commitment" evidence=IEA

GO:0060415 "muscle tissue morphogenesis" evidence=IEA

GO:0014813 "satellite cell commitment" evidence=ISS

GO:0043403 "skeletal muscle tissue regeneration" evidence=ISS

GO:0048706 "embryonic skeletal system development" evidence=ISS

GO:0007519 "skeletal muscle tissue development" evidence=ISS

GO:0021904 "dorsal/ventral neural tube patterning" evidence=ISS

GO:0051216 "cartilage development" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

---

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)
P47239	PAX7_MOUSE	No assigned EC number	0.8571	0.9870	0.1510	yes	N/A
P06601	PRD_DROME	No assigned EC number	0.8289	0.9870	0.1239	yes	N/A
P23760	PAX3_HUMAN	No assigned EC number	0.8181	0.9870	0.1586	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	77
pfam00292	125	pfam00292, PAX, 'Paired box' domain	7e-47
cd00131	128	cd00131, PAX, Paired Box domain	1e-45
smart00351	125	smart00351, PAX, Paired Box domain	8e-44

>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain

 Score =  144 bits (366), Expect = 7e-47
 Identities = 60/76 (78%), Positives = 69/76 (90%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A +GVRPC ISRQLRVSHGCVSKIL RYQETGSIRPGVIGGSKP+VATP+V ++I EYK
Sbjct: 29  LAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSIRPGVIGGSKPKVATPEVVKKIAEYK 88

Query: 61  GENPAMFSWEIRDRLV 76
            ENP +F+WEIRDRL+
Sbjct: 89  RENPGIFAWEIRDRLL 104

Length = 125

>gnl|CDD|238076 cd00131, PAX, Paired Box domain

 Score =  141 bits (358), Expect = 1e-45
 Identities = 60/76 (78%), Positives = 68/76 (89%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A +G+RPC ISRQLRVSHGCVSKILNRY ETGSIRPG IGGSKPRVATP+V ++IE YK
Sbjct: 29  LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYK 88

Query: 61  GENPAMFSWEIRDRLV 76
            ENP MF+WEIRDRL+
Sbjct: 89  QENPGMFAWEIRDRLL 104

Length = 128

>gnl|CDD|128645 smart00351, PAX, Paired Box domain

 Score =  137 bits (346), Expect = 8e-44
 Identities = 56/76 (73%), Positives = 64/76 (84%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQL VSHGCVSKIL RY ETGSIRPG IGGSKP+VATP V ++I +YK
Sbjct: 29  LAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88

Query: 61  GENPAMFSWEIRDRLV 76
            ENP +F+WEIRDRL+
Sbjct: 89  QENPGIFAWEIRDRLL 104

Length = 125

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	77
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	99.95
cd00131	128	PAX Paired Box domain	99.93
smart00351	125	PAX Paired Box domain.	99.91
KOG3517|consensus	334		99.85
COG3415	138	Transposase and inactivated derivatives [DNA repli	99.76
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	99.72
KOG3862|consensus	327		99.7
PF13551	112	HTH_29: Winged helix-turn helix	99.58
KOG0849|consensus	354		99.31
PF13565	77	HTH_32: Homeodomain-like domain	99.15
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	99.1
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	98.95
PF13518	52	HTH_28: Helix-turn-helix domain	98.88
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	98.68
PRK09413	121	IS2 repressor TnpA; Reviewed	98.61
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	98.55
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	98.5
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	98.21
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	98.15
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	98.14
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	98.07
PF14493	91	HTH_40: Helix-turn-helix domain	98.04
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	97.92
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	97.88
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	97.88
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	97.85
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	97.84
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	97.84
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	97.84
COG2963	116	Transposase and inactivated derivatives [DNA repli	97.79
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	97.78
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	97.77
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.76
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	97.75
TIGR01764	49	excise DNA binding domain, excisionase family. An	97.73
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	97.72
PRK15418	318	transcriptional regulator LsrR; Provisional	97.71
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	97.71
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	97.7
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	97.67
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	97.67
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	97.66
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	97.65
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	97.64
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	97.63
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	97.61
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.57
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	97.57
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	97.55
PF12728	51	HTH_17: Helix-turn-helix domain	97.55
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	97.55
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	97.54
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	97.54
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.54
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	97.53
PRK13182	175	racA polar chromosome segregation protein; Reviewe	97.52
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	97.52
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.5
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	97.5
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	97.49
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	97.49
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	97.47
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	97.45
PRK11050	152	manganese transport regulator MntR; Provisional	97.44
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	97.44
PHA02591	83	hypothetical protein; Provisional	97.43
PRK00118	104	putative DNA-binding protein; Validated	97.42
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	97.41
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	97.4
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.4
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	97.37
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	97.37
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	97.36
PRK13413	200	mpi multiple promoter invertase; Provisional	97.36
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	97.35
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.35
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	97.33
PRK13749	121	transcriptional regulator MerD; Provisional	97.33
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	97.33
TIGR02054	120	MerD mercuric resistence transcriptional repressor	97.33
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	97.31
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	97.29
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	97.29
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	97.28
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	97.28
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.28
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	97.27
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	97.27
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	97.26
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	97.25
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	97.24
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	97.24
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	97.23
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	97.22
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.21
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	97.2
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	97.2
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	97.19
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	97.18
PHA00738	108	putative HTH transcription regulator	97.18
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	97.17
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	97.14
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	97.12
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	97.12
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	97.11
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	97.11
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	97.1
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	97.09
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	97.09
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	97.08
PF13730	55	HTH_36: Helix-turn-helix domain	97.08
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	97.08
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	97.07
PRK04217	110	hypothetical protein; Provisional	97.07
PHA00542	82	putative Cro-like protein	97.06
PRK11014	141	transcriptional repressor NsrR; Provisional	97.05
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	97.04
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	97.04
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	97.03
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	97.03
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	97.01
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	96.99
PRK10870	176	transcriptional repressor MprA; Provisional	96.98
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	96.98
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.97
PRK03573	144	transcriptional regulator SlyA; Provisional	96.96
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	96.94
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	96.94
COG2522	119	Predicted transcriptional regulator [General funct	96.94
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.93
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	96.93
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.92
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	96.89
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	96.88
PHA01976	67	helix-turn-helix protein	96.85
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	96.84
PRK01381	99	Trp operon repressor; Provisional	96.84
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	96.83
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	96.82
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.81
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.81
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	96.79
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	96.78
PRK10072	96	putative transcriptional regulator; Provisional	96.77
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	96.76
PRK03975	141	tfx putative transcriptional regulator; Provisiona	96.76
COG2944	104	Predicted transcriptional regulator [Transcription	96.76
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	96.75
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.75
PHA00675	78	hypothetical protein	96.74
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	96.74
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	96.74
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	96.73
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	96.73
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.7
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	96.69
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	96.69
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	96.65
PRK11169	164	leucine-responsive transcriptional regulator; Prov	96.65
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	96.63
PF07638	185	Sigma70_ECF: ECF sigma factor	96.63
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.63
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	96.62
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.57
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	96.55
TIGR02844	80	spore_III_D sporulation transcriptional regulator	96.55
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	96.54
PRK15043	243	transcriptional regulator MirA; Provisional	96.53
PRK06759	154	RNA polymerase factor sigma-70; Validated	96.52
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	96.52
PRK14987	331	gluconate operon transcriptional regulator; Provis	96.51
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	96.5
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	96.5
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.49
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	96.48
TIGR02607	78	antidote_HigA addiction module antidote protein, H	96.47
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.46
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	96.46
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	96.43
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	96.42
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.42
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	96.41
PRK13919	186	putative RNA polymerase sigma E protein; Provision	96.41
PRK08241	339	RNA polymerase factor sigma-70; Validated	96.41
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	96.38
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	96.38
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	96.37
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	96.37
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	96.36
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	96.35
PRK11924	179	RNA polymerase sigma factor; Provisional	96.34
PRK12537	182	RNA polymerase sigma factor; Provisional	96.32
PRK13752	144	putative transcriptional regulator MerR; Provision	96.31
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	96.29
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	96.28
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	96.28
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	96.28
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	96.28
PRK08301	234	sporulation sigma factor SigE; Reviewed	96.28
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	96.28
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	96.27
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	96.27
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	96.26
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	96.25
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	96.24
PRK12514	179	RNA polymerase sigma factor; Provisional	96.24
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	96.24
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	96.23
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	96.23
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	96.23
PRK00215	205	LexA repressor; Validated	96.22
PRK14165	217	winged helix-turn-helix domain-containing protein/	96.22
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	96.21
PRK10046	225	dpiA two-component response regulator DpiA; Provis	96.2
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	96.2
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	96.19
PRK10423	327	transcriptional repressor RbsR; Provisional	96.17
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	96.17
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	96.16
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	96.15
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	96.15
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	96.14
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	96.12
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	96.12
PRK12519	194	RNA polymerase sigma factor; Provisional	96.11
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	96.11
PRK09726	88	antitoxin HipB; Provisional	96.1
PRK09492	315	treR trehalose repressor; Provisional	96.08
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	96.08
PRK12536	181	RNA polymerase sigma factor; Provisional	96.07
PRK09047	161	RNA polymerase factor sigma-70; Validated	96.06
COG3355	126	Predicted transcriptional regulator [Transcription	96.05
TIGR03338	212	phnR_burk phosphonate utilization associated trans	96.02
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	96.02
PRK09409	301	IS2 transposase TnpB; Reviewed	96.02
PRK13777	185	transcriptional regulator Hpr; Provisional	96.02
PRK12423	202	LexA repressor; Provisional	96.0
PRK12534	187	RNA polymerase sigma factor; Provisional	95.99
COG1959	150	Predicted transcriptional regulator [Transcription	95.99
PRK09706	135	transcriptional repressor DicA; Reviewed	95.98
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	95.94
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	95.93
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	95.93
PRK09526	342	lacI lac repressor; Reviewed	95.92
PRK12547	164	RNA polymerase sigma factor; Provisional	95.91
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	95.91
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	95.91
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	95.89
PF13309	64	HTH_22: HTH domain	95.89
PRK06704	228	RNA polymerase factor sigma-70; Validated	95.89
PRK12530	189	RNA polymerase sigma factor; Provisional	95.88
PRK12511	182	RNA polymerase sigma factor; Provisional	95.86
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	95.86
PF10654	126	DUF2481: Protein of unknown function (DUF2481) ; I	95.85
PRK12528	161	RNA polymerase sigma factor; Provisional	95.85
PRK12513	194	RNA polymerase sigma factor; Provisional	95.83
PHA02535	581	P terminase ATPase subunit; Provisional	95.82
COG3677	129	Transposase and inactivated derivatives [DNA repli	95.82
PRK12532	195	RNA polymerase sigma factor; Provisional	95.82
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	95.81
PRK15320	251	transcriptional activator SprB; Provisional	95.79
COG1846	126	MarR Transcriptional regulators [Transcription]	95.79
PRK12516	187	RNA polymerase sigma factor; Provisional	95.78
PRK13509	251	transcriptional repressor UlaR; Provisional	95.78
PRK12524	196	RNA polymerase sigma factor; Provisional	95.78
PRK12542	185	RNA polymerase sigma factor; Provisional	95.78
PRK12518	175	RNA polymerase sigma factor; Provisional	95.76
PRK09415	179	RNA polymerase factor sigma C; Reviewed	95.76
PRK03902	142	manganese transport transcriptional regulator; Pro	95.75
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	95.75
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	95.75
PRK12533	216	RNA polymerase sigma factor; Provisional	95.75
PRK01905	77	DNA-binding protein Fis; Provisional	95.74
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	95.74
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	95.71
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	95.71
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	95.71
PRK08583	257	RNA polymerase sigma factor SigB; Validated	95.7
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	95.68
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	95.67
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	95.67
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	95.64
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	95.64
PRK12525	168	RNA polymerase sigma factor; Provisional	95.63
PRK12522	173	RNA polymerase sigma factor; Provisional	95.63
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	95.61
PRK06811	189	RNA polymerase factor sigma-70; Validated	95.6
COG2452	193	Predicted site-specific integrase-resolvase [DNA r	95.6
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	95.58
PRK09906	296	DNA-binding transcriptional regulator HcaR; Provis	95.57
PRK11013	309	DNA-binding transcriptional regulator LysR; Provis	95.57
PRK12682	309	transcriptional regulator CysB-like protein; Revie	95.57
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	95.56
TIGR03339	279	phn_lysR aminoethylphosphonate catabolism associat	95.55
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	95.55
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.55
PRK12529	178	RNA polymerase sigma factor; Provisional	95.54
PRK06930	170	positive control sigma-like factor; Validated	95.54
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	95.54
PRK12523	172	RNA polymerase sigma factor; Reviewed	95.53
COG1342	99	Predicted DNA-binding proteins [General function p	95.53
PRK09483	217	response regulator; Provisional	95.52
PF08765	108	Mor: Mor transcription activator family; InterPro:	95.51
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	95.51
PRK13890	120	conjugal transfer protein TrbA; Provisional	95.5
PRK05602	186	RNA polymerase sigma factor; Reviewed	95.49
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	95.49
PRK12520	191	RNA polymerase sigma factor; Provisional	95.48
PRK12541	161	RNA polymerase sigma factor; Provisional	95.48
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	95.48
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	95.47
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	95.47
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	95.47
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	95.46
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	95.45
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	95.43
PRK12517	188	RNA polymerase sigma factor; Provisional	95.41
PRK12512	184	RNA polymerase sigma factor; Provisional	95.39
PRK15201	198	fimbriae regulatory protein FimW; Provisional	95.39
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	95.38
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	95.37
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	95.37
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	95.36
PRK12543	179	RNA polymerase sigma factor; Provisional	95.35
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	95.35
PRK12540	182	RNA polymerase sigma factor; Provisional	95.33
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	95.32
PRK12526	206	RNA polymerase sigma factor; Provisional	95.31
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	95.31
COG5484	279	Uncharacterized conserved protein [Function unknow	95.3
PRK09954	362	putative kinase; Provisional	95.3
PF04645	181	DUF603: Protein of unknown function, DUF603; Inter	95.29
PRK12527	159	RNA polymerase sigma factor; Reviewed	95.29
PRK05572	252	sporulation sigma factor SigF; Validated	95.28
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	95.26
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	95.25
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	95.24
PRK00430	95	fis global DNA-binding transcriptional dual regula	95.23
PRK12539	184	RNA polymerase sigma factor; Provisional	95.23
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	95.22
PRK08295	208	RNA polymerase factor sigma-70; Validated	95.22
PRK05803	233	sporulation sigma factor SigK; Reviewed	95.21
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	95.2
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	95.18
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	95.17
PRK12545	201	RNA polymerase sigma factor; Provisional	95.16
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	95.15
PRK12538	233	RNA polymerase sigma factor; Provisional	95.14
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	95.13
PRK12544	206	RNA polymerase sigma factor; Provisional	95.13
PRK12515	189	RNA polymerase sigma factor; Provisional	95.1
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	95.1
PRK10840	216	transcriptional regulator RcsB; Provisional	95.1
TIGR02424	300	TF_pcaQ pca operon transcription factor PcaQ. Memb	95.1
TIGR00180	187	parB_part ParB-like partition proteins. This model	95.08
PRK12546	188	RNA polymerase sigma factor; Provisional	95.07
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	95.05
PRK13348	294	chromosome replication initiation inhibitor protei	95.05
PRK15369	211	two component system sensor kinase SsrB; Provision	95.04
PRK12531	194	RNA polymerase sigma factor; Provisional	95.02
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	95.02
PRK12535	196	RNA polymerase sigma factor; Provisional	95.01
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	94.99
PRK11151	305	DNA-binding transcriptional regulator OxyR; Provis	94.99
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	94.97
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	94.96
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	94.95
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	94.95
PRK12684	313	transcriptional regulator CysB-like protein; Revie	94.95
COG1414	246	IclR Transcriptional regulator [Transcription]	94.94
PRK11608	326	pspF phage shock protein operon transcriptional ac	94.94
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	94.92
COG2345	218	Predicted transcriptional regulator [Transcription	94.92
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	94.91
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	94.9
PRK03601	275	transcriptional regulator HdfR; Provisional	94.88
PRK11922	231	RNA polymerase sigma factor; Provisional	94.87
PRK11569	274	transcriptional repressor IclR; Provisional	94.86
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	94.85
PRK11482	317	putative DNA-binding transcriptional regulator; Pr	94.85
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	94.84
TIGR03418	291	chol_sulf_TF putative choline sulfate-utilization	94.81
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	94.81
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	94.81
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	94.81
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	94.79
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	94.78
PRK15431	78	ferrous iron transport protein FeoC; Provisional	94.76
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	94.74
PRK11233	305	nitrogen assimilation transcriptional regulator; P	94.73
PRK12683	309	transcriptional regulator CysB-like protein; Revie	94.72
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	94.72
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	94.72
PF14502	48	HTH_41: Helix-turn-helix domain	94.7
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	94.7
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	94.68
PRK04984	239	fatty acid metabolism regulator; Provisional	94.67
COG2964	220	Uncharacterized protein conserved in bacteria [Fun	94.67
PRK06424	144	transcription factor; Provisional	94.66
PRK09391	230	fixK transcriptional regulator FixK; Provisional	94.66
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	94.65
PRK09791	302	putative DNA-binding transcriptional regulator; Pr	94.63
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	94.62
PRK10216	319	DNA-binding transcriptional regulator YidZ; Provis	94.61
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	94.61
COG2197	211	CitB Response regulator containing a CheY-like rec	94.58
COG1802	230	GntR Transcriptional regulators [Transcription]	94.57
PRK13698	323	plasmid-partitioning protein; Provisional	94.55
PHA02517	277	putative transposase OrfB; Reviewed	94.53
PRK14999	241	histidine utilization repressor; Provisional	94.53
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	94.52
PRK08215	258	sporulation sigma factor SigG; Reviewed	94.51
PRK06474	178	hypothetical protein; Provisional	94.51
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	94.48
CHL00180	305	rbcR LysR transcriptional regulator; Provisional	94.47
PRK12681	324	cysB transcriptional regulator CysB; Reviewed	94.47
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	94.46
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	94.42
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	94.41
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	94.41
PRK03837	241	transcriptional regulator NanR; Provisional	94.39
PRK12680	327	transcriptional regulator CysB-like protein; Revie	94.39
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	94.39
PRK10079	241	phosphonate metabolism transcriptional regulator P	94.37
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	94.32
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	94.29
PRK09801	310	transcriptional activator TtdR; Provisional	94.27
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	94.25
PRK10403	215	transcriptional regulator NarP; Provisional	94.25
PRK10094	308	DNA-binding transcriptional activator AllS; Provis	94.24
PRK10341	312	DNA-binding transcriptional activator TdcA; Provis	94.24
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	94.23
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	94.21
PRK12679	316	cbl transcriptional regulator Cbl; Reviewed	94.2
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	94.2
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	94.18
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	94.17
PRK14997	301	LysR family transcriptional regulator; Provisional	94.16
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	94.14
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	94.09
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	94.08
PRK10837	290	putative DNA-binding transcriptional regulator; Pr	94.06
PRK10651	216	transcriptional regulator NarL; Provisional	94.05
PF03428	177	RP-C: Replication protein C N-terminal domain; Int	94.03
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	94.03
PRK11557	278	putative DNA-binding transcriptional regulator; Pr	94.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	94.0
COG1725	125	Predicted transcriptional regulators [Transcriptio	93.94
PRK09191	261	two-component response regulator; Provisional	93.91
COG2186	241	FadR Transcriptional regulators [Transcription]	93.89
TIGR00270	154	conserved hypothetical protein TIGR00270.	93.88
PRK15482	285	transcriptional regulator MurR; Provisional	93.84
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	93.81
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	93.77
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	93.77
COG1339	214	Transcriptional regulator of a riboflavin/FAD bios	93.75
PRK10082	303	cell density-dependent motility repressor; Provisi	93.74
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	93.73
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	93.66
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	93.66
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	93.64
PRK09775	442	putative DNA-binding transcriptional regulator; Pr	93.63
PRK09508	314	leuO leucine transcriptional activator; Reviewed	93.61
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	93.6
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	93.58
PHA02943	165	hypothetical protein; Provisional	93.58
PRK10632	309	transcriptional regulator; Provisional	93.52
PRK09935	210	transcriptional regulator FimZ; Provisional	93.52
PRK10086	311	DNA-binding transcriptional regulator DsdC; Provis	93.47
PRK04140	317	hypothetical protein; Provisional	93.46
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	93.46
COG1609	333	PurR Transcriptional regulators [Transcription]	93.44
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	93.42
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	93.41
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	93.41
COG1737	281	RpiR Transcriptional regulators [Transcription]	93.41
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	93.38
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	93.36
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	93.33
PRK11062	296	nhaR transcriptional activator NhaR; Provisional	93.32
PF12964	96	DUF3853: Protein of unknown function (DUF3853); In	93.32
COG1710	139	Uncharacterized protein conserved in archaea [Func	93.27
PRK11074	300	putative DNA-binding transcriptional regulator; Pr	93.25
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	93.17
PRK15092	310	DNA-binding transcriptional repressor LrhA; Provis	93.15
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.15
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	93.09
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	93.09
PRK13870	234	transcriptional regulator TraR; Provisional	93.05
PRK03635	294	chromosome replication initiation inhibitor protei	93.05
PRK15424	538	propionate catabolism operon regulatory protein Pr	93.04
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	92.98
TIGR03298	292	argP transcriptional regulator, ArgP family. ArgP	92.9
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	92.87
PF05043	87	Mga: Mga helix-turn-helix domain; InterPro: IPR007	92.85
COG2188	236	PhnF Transcriptional regulators [Transcription]	92.81
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	92.78
PRK09986	294	DNA-binding transcriptional activator XapR; Provis	92.78
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	92.78
PRK09863	584	putative frv operon regulatory protein; Provisiona	92.72

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=99.95  E-value=8.4e-28  Score=152.25  Aligned_cols=76  Identities=78%  Similarity=1.323  Sum_probs=57.9

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |++.|+++|+||++|.||++||+||++||++||++.|++.||.+|++.+|+++.+|.++..+||.+|+|||+++|+
T Consensus        29 la~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~  104 (125)
T PF00292_consen   29 LAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLI  104 (125)
T ss_dssp             HHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHH
T ss_pred             HhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999985

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

>cd00131 PAX Paired Box domain

Probab=99.93  E-value=3.8e-26  Score=144.91  Aligned_cols=76  Identities=79%  Similarity=1.327  Sum_probs=70.9

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |+++|+|+++||++|+||.+||++|+++|++||+++|++.||++|+..++++.++|..++++|||+|++||+++|.
T Consensus        29 ~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~  104 (128)
T cd00131          29 LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLL  104 (128)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            3578999999999999999999999999999999999999987788888888899999999999999999999874

>smart00351 PAX Paired Box domain

Probab=99.91  E-value=1.8e-24  Score=136.56  Aligned_cols=75  Identities=75%  Similarity=1.263  Sum_probs=70.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      +++|.|.++||++||||.+||++|+++|+++|+++|+++||++|+..++++.++|.+++++|||+|++||++.|.
T Consensus        30 ~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~  104 (125)
T smart00351       30 AQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLL  104 (125)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence            468999999999999999999999999999999999999988888888888999999999999999999999884

>KOG3517|consensus

Probab=99.85  E-value=2.3e-22  Score=139.96  Aligned_cols=76  Identities=68%  Similarity=1.176  Sum_probs=74.0

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |++.|.++|||+++|.||++||+|++.||.|||++.|...||.+|++.||.++..|+++.+..|.||.|||+|+|+
T Consensus        32 LarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLl  107 (334)
T KOG3517|consen   32 LARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLL  107 (334)
T ss_pred             HHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhh
Confidence            5778999999999999999999999999999999999999999999999999999999999999999999999986

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=99.76  E-value=2.8e-18  Score=110.45  Aligned_cols=72  Identities=22%  Similarity=0.207  Sum_probs=65.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      .|||+++||++||||.|||++|++||+++|...|.+.++++|+.+++++.+.|++.+++.. .|+.+++..|.
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~   91 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELG   91 (138)
T ss_pred             cCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHh
Confidence            7999999999999999999999999999999988888889999999998888888887765 99999998763

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=99.72  E-value=1.4e-17  Score=104.22  Aligned_cols=67  Identities=24%  Similarity=0.303  Sum_probs=58.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      +.|.|+++||++|+||.+||++|++ ..++|++.|++.|+.    ..  +.+.|.++|++|||+|+.||++.|-
T Consensus        16 ~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~----Ki--d~~~L~~~v~~~pd~tl~Ela~~l~   82 (119)
T PF01710_consen   16 EKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRK----KI--DRDELKALVEENPDATLRELAERLG   82 (119)
T ss_pred             HccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccc----cc--cHHHHHHHHHHCCCcCHHHHHHHcC
Confidence            5789999999999999999999999 788999999987643    22  2567999999999999999998863

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>KOG3862|consensus

Probab=99.70  E-value=1.1e-17  Score=117.30  Aligned_cols=76  Identities=76%  Similarity=1.279  Sum_probs=74.0

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      ||+.|+.+|+||+++.||++||++++.+|+|||+++|+..||.++++.++.+++.|-.++++||.++.||++++|.
T Consensus        37 La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~  112 (327)
T KOG3862|consen   37 LAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLL  112 (327)
T ss_pred             HHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhh
Confidence            6889999999999999999999999999999999999999999999999999999999999999999999999985

>PF13551 HTH_29: Winged helix-turn helix

Probab=99.58  E-value=9.4e-15  Score=88.27  Aligned_cols=75  Identities=31%  Similarity=0.446  Sum_probs=62.7

Q ss_pred             CccCCCC-HHHHHHHhccCHHHHHHHHHHHHHhc--CCCccccCCCCCCC-CCHHHHHHHHHHHHhCC-----CCcHHHH
Q psy15513          1 MAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRV-ATPDVERRIEEYKGENP-----AMFSWEI   71 (77)
Q Consensus         1 l~~~G~s-~~~iA~rf~VS~stv~r~~~r~r~tG--~v~pk~~gg~~~~~-~~~~~~~~i~~~v~~~p-----d~tl~El   71 (77)
                      |+.+|++ +.+||+.||||..||++|+++|+++|  .+.+...++++++. +++++.+.|.+++.++|     ..|+.++
T Consensus         7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l   86 (112)
T PF13551_consen    7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEEL   86 (112)
T ss_pred             HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHH
Confidence            4568996 99999999999999999999999999  66773233345554 78999999999999999     5889998


Q ss_pred             HHHh
Q psy15513         72 RDRL   75 (77)
Q Consensus        72 ~~~L   75 (77)
                      ++.|
T Consensus        87 ~~~l   90 (112)
T PF13551_consen   87 AEWL   90 (112)
T ss_pred             HHHH
Confidence            8865

>KOG0849|consensus

Probab=99.31  E-value=1.2e-12  Score=94.68  Aligned_cols=76  Identities=80%  Similarity=1.337  Sum_probs=71.7

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC-CCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~-~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |+..|+++|.+++.+.||+.||++++.+|.+||++.|...||.+++ +.+++++.+|.++..++|++|.|||++.|+
T Consensus        27 ~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~  103 (354)
T KOG0849|consen   27 MAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLL  103 (354)
T ss_pred             ccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhccc
Confidence            5678999999999999999999999999999999999999998886 888999999999999999999999999874

>PF13565 HTH_32: Homeodomain-like domain

Probab=99.15  E-value=1.7e-10  Score=66.28  Aligned_cols=54  Identities=31%  Similarity=0.457  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHhc-----CCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513         21 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus        21 tv~r~~~r~r~tG-----~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      ||++|+++|++.|     +..+++.+| +|+. ++++.+.|.+++.++|++|+.+|++.|.
T Consensus         1 Tv~rw~~ry~~~G~~gL~~~~~~~~~G-rp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~   59 (77)
T PF13565_consen    1 TVYRWLKRYREEGLEGLKDRKRRPRPG-RPRK-DPEQRERIIALIEEHPRWTPREIAEYLE   59 (77)
T ss_pred             CHHHHHHHHHhhCchhhhcccccCCCC-CCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            7999999999999     655555554 5555 7877799999999999999999999874

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=99.10  E-value=2.6e-11  Score=64.82  Aligned_cols=32  Identities=31%  Similarity=0.457  Sum_probs=21.4

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ..+|+|.++||+.||||++||++|+++|+++|
T Consensus        14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G   45 (50)
T PF13384_consen   14 LREGWSIREIAKRLGVSRSTVYRWIKRYREEG   45 (50)
T ss_dssp             HHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence            34699999999999999999999999999988

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=98.95  E-value=4.4e-09  Score=62.91  Aligned_cols=58  Identities=29%  Similarity=0.401  Sum_probs=41.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC--CccccCCC-CCCCCCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGS-KPRVATPDVERRIEEYK   60 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v--~pk~~gg~-~~~~~~~~~~~~i~~~v   60 (77)
                      ++|.+..++|+.||||..|++||+.||++.|..  ..+..-+. .|..+.++.+..|.++.
T Consensus        23 ~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~lR   83 (85)
T PF13011_consen   23 EQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIELR   83 (85)
T ss_pred             HcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHHh
Confidence            579999999999999999999999999999865  22222222 23344465566666553

>PF13518 HTH_28: Helix-turn-helix domain

Probab=98.88  E-value=1.9e-09  Score=57.48  Aligned_cols=32  Identities=28%  Similarity=0.449  Sum_probs=30.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      .+|.|..++|+.||||.+||++|+++|.+.|.
T Consensus        10 ~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen   10 LEGESVREIAREFGISRSTVYRWIKRYREGGI   41 (52)
T ss_pred             HcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence            47889999999999999999999999999884

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

Probab=98.68  E-value=1.3e-08  Score=53.68  Aligned_cols=27  Identities=30%  Similarity=0.347  Sum_probs=20.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .+.|+|.++||+.||+|++||+++++|
T Consensus        17 ~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen   17 LEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            468999999999999999999999987

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=98.61  E-value=7e-08  Score=60.33  Aligned_cols=36  Identities=19%  Similarity=0.187  Sum_probs=32.2

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      .+.|++..++|+.||||.+|+++|+++|++.|....
T Consensus        26 ~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~   61 (121)
T PRK09413         26 FEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLTAV   61 (121)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccccc
Confidence            457999999999999999999999999998776554

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=98.55  E-value=4e-08  Score=51.95  Aligned_cols=27  Identities=33%  Similarity=0.444  Sum_probs=21.8

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |.++|+|..+||+.||||.+||+|+++
T Consensus        17 l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   17 LYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            457899999999999999999999975

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=98.50  E-value=1.1e-06  Score=49.14  Aligned_cols=64  Identities=16%  Similarity=0.127  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L   75 (77)
                      +|..++|+.+|||++|+.+|.+++   |-+.|....++. +.-++.+...+   ..+.+  -++++.|+++.|
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r~~~~~-r~yt~~~v~~l~~i~~l~~--~g~~l~~i~~~~   67 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQRTDGGH-RLYSEADVARLRLIRRLTS--EGVRISQAAALA   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCCCCC-eecCHHHHHHHHHHHHHHH--CCCCHHHHHHHh
Confidence            578999999999999999998764   666654433222 33444444444   34443  589999998765

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=98.21  E-value=1.2e-06  Score=48.84  Aligned_cols=33  Identities=21%  Similarity=0.194  Sum_probs=29.3

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      |+-.|+++.+||+.|||+.+||+.|.+++.-.+
T Consensus         9 LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~   41 (58)
T PF06056_consen    9 LYLQGWSIKEIAEELGVPRSTVYSWKDRYKWDE   41 (58)
T ss_pred             HHHcCCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence            456899999999999999999999999987544

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=98.15  E-value=2.5e-05  Score=43.86  Aligned_cols=64  Identities=11%  Similarity=0.146  Sum_probs=43.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||.+|+..|-+.+   |-+.|....++. +.-+..+...   |..+.+  .++++.|++..|
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r~~~g~-R~yt~~di~~l~~i~~l~~--~g~~l~~i~~~l   67 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQRSDGGH-RLFNDADIDRILEIKRWID--NGVQVSKVKKLL   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCCCC-cccCHHHHHHHHHHHHHHH--cCCCHHHHHHHh
Confidence            478899999999999999884433   777675543333 3344434443   445544  789999998765

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=98.14  E-value=6.9e-06  Score=42.26  Aligned_cols=32  Identities=13%  Similarity=0.135  Sum_probs=26.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ++..++|+.||||.+|+.+|.++    |.+.+.+.+
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~~~   32 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIRTP   32 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCceeCC
Confidence            57899999999999999999886    777554443

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=98.07  E-value=1.6e-06  Score=47.44  Aligned_cols=28  Identities=32%  Similarity=0.345  Sum_probs=22.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+.|.|.++||+.|||+.+||+.|++..
T Consensus        19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen   19 LEEGESKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence            4689999999999999999999999863

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF14493 HTH_40: Helix-turn-helix domain

Probab=98.04  E-value=2.7e-05  Score=46.34  Aligned_cols=69  Identities=13%  Similarity=0.071  Sum_probs=58.2

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |+++|+|.-+||+.-+++.+||..-+-.+...|..-+-.      ....++..+.|.+.++..+...+.++.+.|
T Consensus         9 l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~------~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l   77 (91)
T PF14493_consen    9 LFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE------ELLSEEEIKQIEDAIEKLGSEKLKPIKEAL   77 (91)
T ss_pred             HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH------HhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence            578999999999999999999999999999999833221      346666778899999999988899988876

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=97.92  E-value=8.4e-06  Score=46.28  Aligned_cols=28  Identities=14%  Similarity=0.287  Sum_probs=25.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..|.|..++|+.+||+++|+++|+++|+
T Consensus        21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen   21 ESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HCCCceEeeecccccccccccHHHHHHh
Confidence            4689999999999999999999999999

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=97.88  E-value=0.00015  Score=40.42  Aligned_cols=63  Identities=16%  Similarity=0.083  Sum_probs=41.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||++|+..|-++..-   ..|+..||.  +.-++++...   |..+.+  -.+++.|+.+.|
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~g~l---~~~~~~~g~--R~y~~~~l~~l~~i~~l~~--~g~~l~~i~~~l   66 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFNL---YIPRTENGR--RYYTDEDIELLKKIKTLLE--KGLSIKEIKEIL   66 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCC---CCCCCCCCc--eeeCHHHHHHHHHHHHHHH--CCCCHHHHHHHh
Confidence            57889999999999999999765331   223333433  3344434443   445554  569999998765

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=97.88  E-value=0.00016  Score=43.95  Aligned_cols=67  Identities=10%  Similarity=-0.009  Sum_probs=47.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHhh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRLV   76 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L~   76 (77)
                      ++..++|+.+|||.+|+..|-+.   .|-+.|...+|+ .+.-++++...|..+..  .+-.+++.++++.|.
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~~g-~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~   69 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRAGG-RRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALK   69 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCCCC-CeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            57889999999999999988544   355666544333 34455666776666553  466799999988763

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators

Probab=97.85  E-value=0.00015  Score=43.03  Aligned_cols=65  Identities=18%  Similarity=0.085  Sum_probs=45.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++++.++|+.+|||.+|+..|    .+.|-+.|....++..+.-++.+...   |..+.+  -++++.|+++.+
T Consensus         1 ~~ti~evA~~~gvs~~tLR~y----e~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~--~G~sl~~i~~~l   68 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYW----EEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLD--EGFTLAAAVEKL   68 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHH--CCCCHHHHHHHH
Confidence            578999999999999999998    44588887664321223344444443   445543  679999998766

Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=97.84  E-value=9.1e-05  Score=41.29  Aligned_cols=64  Identities=20%  Similarity=0.145  Sum_probs=45.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHhh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |+..++|+.+|||.+|+..|.++    |-+.|....++. +.-++++...   |..+.+  -.+++.|+++.|.
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~----gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~--~G~sl~~I~~~l~   67 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYERE----GLLPPPRDENGY-RYYSEEDVERLREIKELRK--QGMSLEEIKKLLK   67 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHT----TSSTTBESTTSS-EEE-HHHHHHHHHHHHHHH--TTTHHHHHHHHH-
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHh----cCcccccccCce-eeccHHHHHHHHHHHHHHH--CcCCHHHHHHHHc
Confidence            57889999999999999999665    668887743333 4455555554   445544  5799999998764

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=97.84  E-value=0.00018  Score=40.00  Aligned_cols=63  Identities=17%  Similarity=0.106  Sum_probs=43.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc-ccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG-VIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk-~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||.+|+.+|.+    .|-+.|. +..++. +.-+..+..   .|..+.+  -++++.++...|
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~g~-r~y~~~dl~~l~~i~~lr~--~g~~~~~i~~~l   67 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEGGY-RLYSDEDLERLRFIKRLKE--LGFSLEEIKELL   67 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCC-EecCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            5789999999999999999965    7988875 332222 233333343   3445543  568888887654

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=97.84  E-value=2.3e-05  Score=43.75  Aligned_cols=38  Identities=29%  Similarity=0.316  Sum_probs=32.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ..++..+||+.|+||++||+..++++.+.|-|.-.+-+
T Consensus        21 ~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y~   58 (60)
T PF01325_consen   21 GPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPYK   58 (60)
T ss_dssp             SSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred             CCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCC
Confidence            34889999999999999999999999999988766543

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=97.79  E-value=8.5e-05  Score=45.57  Aligned_cols=37  Identities=16%  Similarity=0.142  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhcc-CHHHHHHHHHHHHHhcCCCccc
Q psy15513          3 AAGVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         3 ~~G~s~~~iA~rf~V-S~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +.|.+..++|+.||| +.++.++|+++|++.+...+..
T Consensus        22 ~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~   59 (116)
T COG2963          22 RGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSG   59 (116)
T ss_pred             hcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccC
Confidence            468899999999995 9999999999999988776653

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=97.78  E-value=0.00019  Score=44.06  Aligned_cols=66  Identities=14%  Similarity=0.049  Sum_probs=42.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh-CCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE-NPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~-~pd~tl~El~~~L   75 (77)
                      |+..++|+.+|||++|+..|-+    .|-+.|....++..+.-++.+...+.....- .-++++.||++.|
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l   67 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVV   67 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            6889999999999999999844    5988876543222233444445443322221 2358888887655

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=97.77  E-value=2.9e-05  Score=48.76  Aligned_cols=59  Identities=15%  Similarity=0.151  Sum_probs=48.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      .+++.+++|..|++|++||++-++-.++.|=|...+.|....-.+.+...+|+..++.+
T Consensus        29 ~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~   87 (117)
T PRK10141         29 GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ   87 (117)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH
Confidence            35899999999999999999999999999999999888655545566566667665544

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.76  E-value=3.8e-05  Score=40.39  Aligned_cols=30  Identities=23%  Similarity=0.259  Sum_probs=27.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ...|+|..+||+.|+||.+||++++++.++
T Consensus        15 ~~~g~s~~eia~~l~is~~tv~~~~~~~~~   44 (58)
T smart00421       15 LAEGLTNKEIAERLGISEKTVKTHLSNIMR   44 (58)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            347999999999999999999999998764

lux regulon (activates the bioluminescence operon

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=97.75  E-value=0.00033  Score=42.36  Aligned_cols=64  Identities=19%  Similarity=0.102  Sum_probs=43.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.||||++|+..|-+    .|-+.|...+++..+.-++.+...+   ..+. . -++++.|++.-+
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr-~-~g~~l~~i~~~~   67 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLK-E-LGFSLKEIKELL   67 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHH-H-cCCCHHHHHHHH
Confidence            5789999999999999998865    6888775433223344555555443   3333 3 579999998765

Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip

>TIGR01764 excise DNA binding domain, excisionase family

Probab=97.73  E-value=4.2e-05  Score=39.48  Aligned_cols=32  Identities=19%  Similarity=0.276  Sum_probs=26.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ++..++|+.||||.+|+++|++    .|.+.+-..|
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~----~g~i~~~~~g   33 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIH----EGELPAYRVG   33 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH----cCCCCeEEeC
Confidence            5789999999999999999985    4777654444

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

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

Probab=97.72  E-value=4.2e-05  Score=43.25  Aligned_cols=40  Identities=13%  Similarity=0.163  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      .+++.+|||..||+|..+|.+|+......|.|...|.+.+
T Consensus        14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG   53 (62)
T PF04703_consen   14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRG   53 (62)
T ss_dssp             S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSS
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCC
Confidence            5689999999999999999999999999999987665433

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=97.71  E-value=3.9e-05  Score=54.96  Aligned_cols=36  Identities=25%  Similarity=0.383  Sum_probs=33.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+|+++.|||++||||+++|+|++++-|++|=|.=.
T Consensus        27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~   62 (318)
T PRK15418         27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQ   62 (318)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEE
Confidence            579999999999999999999999999999998655

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=97.71  E-value=0.00027  Score=42.68  Aligned_cols=65  Identities=11%  Similarity=0.082  Sum_probs=45.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||.+|+..|.    +.|-+.|....+ ..+.-++.+.+.+.....  .+-++++.++..-|
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~-g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l   68 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNG-GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRII   68 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCC-CCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            578999999999999999994    468888843322 223455556666655443  33589999998765

Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=97.70  E-value=0.00018  Score=45.38  Aligned_cols=64  Identities=16%  Similarity=0.169  Sum_probs=45.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH--HhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK--GENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v--~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||++|+..|-+.    |-+.|...+|.  +.-++++...|..+.  ..+.++++.||++-|
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~----GLl~p~r~~G~--R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L   67 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH----GLIKPARRNGQ--RLYSNNDLKRLRFIKKLINEKGLNIAGVKQIL   67 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcCCCCc--EEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            68899999999999999988764    98988765443  334444455443222  234689999999876

Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=97.67  E-value=0.00017  Score=37.48  Aligned_cols=44  Identities=14%  Similarity=0.055  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER   54 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~   54 (77)
                      |+..++|+.||||.+|+.+|.++    |.+.|...+| ..+.-++++..
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~----g~l~~~~~~~-~~~~y~~~~v~   44 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERI----GLLSPARTEG-GYRLYSDADLE   44 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCEEeCHHHHH
Confidence            57899999999999999999644    7776654433 22334444443

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator

Probab=97.67  E-value=0.00033  Score=42.26  Aligned_cols=65  Identities=15%  Similarity=0.166  Sum_probs=44.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L   75 (77)
                      |++.++|+++|||.+|+..|-+    .|-+.|....++ .+.-++.+...+.....  +.-++++.|++.-|
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~~~g-~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l   67 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERSEGR-YRLYSEEDLKRLERILRLREVLGFSLQEVTHFL   67 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCC-CEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            5789999999999999999954    498887654332 33444445554443222  22479999998655

Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=97.66  E-value=7.6e-05  Score=39.88  Aligned_cols=33  Identities=24%  Similarity=0.295  Sum_probs=30.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |..++|++|+||.+||.+.+++..+.|-+...+
T Consensus        22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            899999999999999999999999999887554

>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length

Probab=97.65  E-value=0.00012  Score=46.38  Aligned_cols=55  Identities=16%  Similarity=0.199  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC-CCCHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEYK   60 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~-~~~~~~~~~i~~~v   60 (77)
                      |.+.++|..+|+|.-||+||++..-=+-+..|+..||.-+- ..++.+.+||...-
T Consensus         1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s~~   56 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRSIP   56 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHhhH
Confidence            68899999999999999999998876666777777775443 45566677776544

The function of this family is unknown.

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

Probab=97.64  E-value=7.7e-05  Score=40.62  Aligned_cols=40  Identities=20%  Similarity=0.373  Sum_probs=33.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      +++.+||+.+++|+++|++.++++.+.|-|.-.+..++++
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~R   61 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDRR   61 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence            8999999999999999999999999999997766555543

...

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=97.63  E-value=3.5e-05  Score=36.36  Aligned_cols=25  Identities=36%  Similarity=0.417  Sum_probs=22.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +..|.+..++|+.|+||.+||++|+
T Consensus        18 ~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569          18 LAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            3578899999999999999999985

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

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

Probab=97.61  E-value=0.00013  Score=36.27  Aligned_cols=29  Identities=24%  Similarity=0.350  Sum_probs=24.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      |+..|||..+|.|.-||+|.++++++.|-
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~gl   31 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGL   31 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCC
Confidence            68899999999999999999999999884

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.57  E-value=5.1e-05  Score=46.19  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=23.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.|+|.++||+.+|||.+||+||-+-
T Consensus        53 ~~~~tQrEIa~~lGiS~atIsR~sn~   78 (94)
T TIGR01321        53 NGNMSQREIASKLGVSIATITRGSNN   78 (94)
T ss_pred             hCCCCHHHHHHHhCCChhhhhHHHhh
Confidence            46899999999999999999998654

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=97.57  E-value=6.3e-05  Score=45.17  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=22.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ..|+|..+||+.||||.+||+||.
T Consensus        48 ~~G~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        48 KQGKTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHH
Confidence            579999999999999999999966

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=97.55  E-value=0.001  Score=40.85  Aligned_cols=64  Identities=14%  Similarity=0.053  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |+..++|+.+|||++|+..|-+    .|-+.|.+...+..+.=++.+...   |..+.  +-+++|.||.+-|
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l   67 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLR--NTGMSIKDIKEYA   67 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            5789999999999999988854    588855433222223344444443   44443  3579999998755

Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=97.55  E-value=0.00013  Score=38.66  Aligned_cols=32  Identities=25%  Similarity=0.325  Sum_probs=26.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      +|..|+|..||||.+||++|+++    |.+.+-+.|
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~----g~i~~~~~g   33 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ----GKIPPFKIG   33 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCeEEeC
Confidence            57899999999999999999964    777555443

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=97.55  E-value=0.0012  Score=40.95  Aligned_cols=64  Identities=17%  Similarity=0.138  Sum_probs=42.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.||||.+|+.-    |-+.|-+.|.....+..+.=++.+..   .|..+  .+-++++.||.+-+
T Consensus         1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~l--r~~G~sl~eI~~~l   67 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRA--QALGFSLAEIRELL   67 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence            6789999999999999843    56679888644322222334444444   34444  34578999988654

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=97.54  E-value=0.00063  Score=40.30  Aligned_cols=65  Identities=11%  Similarity=0.053  Sum_probs=45.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||++|+..|.+    .|-+.|....+ ..+.-++.+...+.....  .+-++++.+++.-|
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l   68 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRIL   68 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            5788999999999999999964    59999865433 234455656665554433  33579999887654

Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=97.54  E-value=0.0009  Score=41.11  Aligned_cols=66  Identities=14%  Similarity=-0.007  Sum_probs=46.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||..|+..|-+.    |-+.|.....+..+.-++.+..++.-... .+-++.+.||++.+
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~----GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l   67 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLR----GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLC   67 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            57889999999999999877655    99988544322334455656665554333 44578999988765

Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,

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

Probab=97.54  E-value=0.00017  Score=37.80  Aligned_cols=32  Identities=22%  Similarity=0.414  Sum_probs=27.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .++|..++|+.+|+|.+||++.+++..+.|=+
T Consensus        16 ~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen   16 PRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            45999999999999999999999999998854

...

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=97.53  E-value=0.00078  Score=40.57  Aligned_cols=66  Identities=15%  Similarity=0.132  Sum_probs=47.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh--CCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE--NPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~--~pd~tl~El~~~L   75 (77)
                      |+..++|+.+|||.+|+..|.+    .|-+.|....+...+.-++.+...|.....-  +=++++.|+++.+
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l   68 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVL   68 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            6789999999999999988876    5888885433222345667677766654332  2479999998765

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=97.52  E-value=0.00063  Score=45.39  Aligned_cols=63  Identities=11%  Similarity=0.038  Sum_probs=42.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH-HhCCCCcHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK-GENPAMFSWEIRD   73 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v-~~~pd~tl~El~~   73 (77)
                      |++.++|+++|||..|+.+|.++    |.+.+.+..++. +.-++.+..+|..+. ..+-++++.+++.
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~----g~L~~~R~~~G~-R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~   64 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQ----LNLPCEKNEYGH-YIFTEEDLQLLEYVKSQIEEGQNMQDTQK   64 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCC-EEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            57899999999999999999886    556444333323 334455566655443 3445677887755

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=97.52  E-value=0.0002  Score=37.28  Aligned_cols=36  Identities=22%  Similarity=0.207  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..++|+.|+||.+||++.++.+.+.|-+....
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence            469999999999999999999999999999887543

>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=97.50  E-value=0.00014  Score=39.00  Aligned_cols=33  Identities=21%  Similarity=0.356  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+++..+||+++|+++|||+|+++.+.+.|=+.
T Consensus        17 ~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~   49 (52)
T PF09339_consen   17 GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE   49 (52)
T ss_dssp             SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence            457999999999999999999999999999765

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.

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=97.50  E-value=0.00025  Score=36.44  Aligned_cols=29  Identities=24%  Similarity=0.263  Sum_probs=26.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..|++..+||..+|+|.++|++|+.+.++
T Consensus        24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          24 GEGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37899999999999999999999998765

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=97.49  E-value=0.00019  Score=38.42  Aligned_cols=29  Identities=24%  Similarity=0.306  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -+|+|..+||+.+|+|.++|.+|+.+-++
T Consensus        24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   24 FQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            37999999999999999999999998765

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=97.49  E-value=0.00014  Score=39.34  Aligned_cols=28  Identities=14%  Similarity=0.243  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|.+-.++|.+||||+|||+||......
T Consensus        18 ~~~~~~~La~~FgIs~stvsri~~~~~~   45 (53)
T PF13613_consen   18 LNLTFQDLAYRFGISQSTVSRIFHEWIP   45 (53)
T ss_pred             cCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence            5778899999999999999999988754

>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator

Probab=97.47  E-value=0.0017  Score=38.99  Aligned_cols=64  Identities=17%  Similarity=0.113  Sum_probs=42.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||.+|+..|-+    .|-+.|...+.+..+.-++.+..   .|..+.  .-++++.||.+.+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr--~~G~~l~eI~~~l   67 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLK--ELGISLKEIKDYL   67 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            5788999999999999988744    59998864322223334444433   344443  2369999998755

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=97.45  E-value=0.0018  Score=39.11  Aligned_cols=65  Identities=17%  Similarity=0.153  Sum_probs=42.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDR   74 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~   74 (77)
                      +++.++|+.+|||.+|+..|    -+.|-+.|...+....+.=++.+..++.-...-..++.+.++++.
T Consensus         1 y~i~e~A~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~   65 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNY----ESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRI   65 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHH
Confidence            36789999999999999877    446988764332222344556566665443333257888887653

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=97.44  E-value=0.0004  Score=44.87  Aligned_cols=37  Identities=27%  Similarity=0.336  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .+.++.++|+.|+||+++|+++++++.+.|-+...+.
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~   86 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY   86 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            5689999999999999999999999999998876553

>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators

Probab=97.44  E-value=0.0014  Score=39.01  Aligned_cols=63  Identities=17%  Similarity=0.157  Sum_probs=43.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L   75 (77)
                      |+..++|+.+||+.+|+..|.+    .|-+.|.+.+++. +.-+..+...+   ..+..  .++++.++...+
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~--~g~~~~~i~~~l   66 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSENGY-RLYSEEDLERLRLIRRLRE--LGLSLKEIRELL   66 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCCCC-cccCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            5789999999999999999965    4888776544333 33444444443   34433  688998887654

Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PHA02591 hypothetical protein; Provisional

Probab=97.43  E-value=0.00012  Score=43.22  Aligned_cols=27  Identities=30%  Similarity=0.254  Sum_probs=24.9

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |.+.|+|..+||..||||+.+|++++.
T Consensus        55 L~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         55 LARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            567899999999999999999999875

>PRK00118 putative DNA-binding protein; Validated

Probab=97.42  E-value=8.5e-05  Score=45.88  Aligned_cols=63  Identities=13%  Similarity=0.050  Sum_probs=41.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA   65 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd   65 (77)
                      ..|+|..+||+.||||.+||++++.+-+..=.=.-.+.|+-.+.....+.-+.+....+..||
T Consensus        31 ~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (104)
T PRK00118         31 LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLKEKYPD   93 (104)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHcccc
Confidence            479999999999999999999999987754333333445433332323333445555555554

>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator

Probab=97.41  E-value=0.0013  Score=39.92  Aligned_cols=65  Identities=11%  Similarity=-0.051  Sum_probs=42.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHH-HHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEY-KGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~-v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||++|+..|-+    .|-+.|....+ ..+.=++.+.+++.-. .-.+-++++.|+++.+
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~----~Gll~~~r~~~-g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l   67 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEK----LGLITGTRNAN-GYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL   67 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            6889999999999999986654    59998754332 2233444445443311 1234479999988754

Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators

Probab=97.40  E-value=0.0014  Score=39.78  Aligned_cols=63  Identities=17%  Similarity=0.050  Sum_probs=41.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.||||++|+.-|-+    .|-+.|....++ .+.=++.+..   +|..+  .+-++++.|++..+
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~r~~~g-~R~Y~~~dl~~l~~I~~l--~~~G~~l~ei~~~~   67 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSARSEAN-YRLYSEADLSRLEKIVFL--QAGGLPLEEIAGCL   67 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCCCCC-CeeeCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence            6889999999999999955544    488855433222 2333333343   44455  34579999998754

Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.40  E-value=0.00024  Score=37.41  Aligned_cols=29  Identities=24%  Similarity=0.188  Sum_probs=26.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..|++..+||+.|++|.+||.+++.+.++
T Consensus        13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            47899999999999999999999998765

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

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

Probab=97.37  E-value=0.00017  Score=39.09  Aligned_cols=42  Identities=19%  Similarity=0.380  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|++..++|+.++++++++++++++..+.|=+.-.+...+++
T Consensus        16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R   57 (59)
T PF01047_consen   16 GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRR   57 (59)
T ss_dssp             SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence            568999999999999999999999999999997776655554

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 ....

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=97.37  E-value=0.0002  Score=37.71  Aligned_cols=34  Identities=21%  Similarity=0.363  Sum_probs=29.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .+.-++.+++|+.|++|+++|++-++..++.|=|
T Consensus        12 ~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV   45 (47)
T PF01022_consen   12 SEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV   45 (47)
T ss_dssp             TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence            3444889999999999999999999999998855

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=97.36  E-value=0.0018  Score=39.58  Aligned_cols=66  Identities=14%  Similarity=0.109  Sum_probs=43.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC-CCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG-SKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg-~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      ++..++|+.||||.+|+.-|-++    |=+.|....+ +..+.=++.+...|..... .+=++++.|+..-+
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~----GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~   68 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI----GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL   68 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            57889999999999999887664    9998865321 2334445555554442222 22368999988654

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=97.36  E-value=0.00014  Score=48.35  Aligned_cols=27  Identities=26%  Similarity=0.399  Sum_probs=24.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ...|+|..+||+.||||.+||+|+++.
T Consensus       169 ~~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        169 LDKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            357999999999999999999999985

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=97.35  E-value=0.002  Score=38.62  Aligned_cols=62  Identities=16%  Similarity=0.152  Sum_probs=43.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||.+|+..|-+    .|-+.|...  +|.|  .=++.+.   .+|..+.+  -++++.||.+.+
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~--~G~~l~eI~~~l   67 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHR--LYDRADIRRLHQIIALRR--LGFSLREIGRAL   67 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCce--eeCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            6789999999999999988754    698888533  3333  3344444   34555543  369999998765

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.35  E-value=0.00016  Score=42.17  Aligned_cols=32  Identities=22%  Similarity=0.301  Sum_probs=28.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +|+|..+||+.+|||.+||..|+.+....|-+
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~   62 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKGETKAGGL   62 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence            79999999999999999999999986655543

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=97.33  E-value=0.00017  Score=38.74  Aligned_cols=29  Identities=17%  Similarity=0.284  Sum_probs=26.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      .+|..++|..|+||..||.+-++..++.|
T Consensus        15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   15 PITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            48999999999999999999999999999

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK13749 transcriptional regulator MerD; Provisional

Probab=97.33  E-value=0.0028  Score=40.00  Aligned_cols=68  Identities=10%  Similarity=-0.058  Sum_probs=48.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHhh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRLV   76 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L~   76 (77)
                      .+++.++|+++|||..|+.-|    -+.|=+.|-....+..+.=++.+..++.-... ..-++++.||++.|.
T Consensus         3 ~~tIgelA~~~gvS~~tiR~Y----E~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~   71 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRDY----LLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCR   71 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHHH----HHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            489999999999999998544    34587777544333344556666776654443 567899999998763

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

Probab=97.33  E-value=0.0003  Score=38.37  Aligned_cols=38  Identities=21%  Similarity=0.349  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..++|+.|++|.++|++++++..+.|-+.....+
T Consensus        19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~   56 (78)
T cd00090          19 GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG   56 (78)
T ss_pred             CCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence            34889999999999999999999999999988766544

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.

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=97.33  E-value=0.0024  Score=40.16  Aligned_cols=68  Identities=13%  Similarity=0.004  Sum_probs=46.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      ..+++.++|+.+|||..|+.-|-+    .|=+.|.....+..+.=++.+..+|.-... ..-++++.||++-+
T Consensus         2 ~~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll   70 (120)
T TIGR02054         2 NAYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLC   70 (120)
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            368999999999999999876644    488887655322334455556665543333 44679999998754

This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=97.31  E-value=0.0025  Score=39.93  Aligned_cols=62  Identities=18%  Similarity=0.111  Sum_probs=41.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|-+    .|-+.|...  +|.|  .=++.+...   |..+  .+-++++.||++-+
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~----~GLl~~~~r~~~g~R--~Y~~~~~~~l~~I~~l--r~~G~sL~eI~~~l   67 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEE----IGLIPPPSRSDNGYR--VYNQRDIEELRFIRRA--RDLGFSLEEIRELL   67 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCce--ecCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence            6889999999999999876654    488875332  3333  333434443   4444  34678999988754

Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=97.29  E-value=0.00036  Score=36.87  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=19.1

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .| +|.+++|+.|||+.+|+++.++.
T Consensus        14 ~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen   14 NGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            45 99999999999999999977654

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=97.29  E-value=0.0022  Score=41.04  Aligned_cols=65  Identities=22%  Similarity=0.163  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||.+|+..|-+.    |-+.|....++ .+.=++.+..+|..... .+-++++.||++.|
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~~----GLl~p~r~~~g-~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l   67 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQK----GLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEAL   67 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCCC-CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            78999999999999999877655    88887554333 23344545554332211 34568899988765

Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=97.28  E-value=0.0027  Score=40.07  Aligned_cols=64  Identities=19%  Similarity=0.132  Sum_probs=42.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+++|||..|+.-|-+.    |-+.|.....+..+.=++.+..   +|..+.  +-++++.|+.+-+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~----GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr--~~G~sl~eI~~~l   68 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKN----GLIKPAGRTDSGYRLYTDEDQKRLRFILKAK--ELGFTLDEIKELL   68 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCCcCCCCceecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            68999999999999999877654    9998854322222233333444   344443  4578999988755

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=97.28  E-value=0.0031  Score=39.51  Aligned_cols=62  Identities=18%  Similarity=0.159  Sum_probs=41.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |+..++|+++|||..|+.-|-    +.|-+.|...  +|.|  .=++++...   |..+  ..-++++.||++.|
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~p~~r~~~gyR--~Y~~~~l~~l~~I~~l--r~~G~sL~eI~~~l   67 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYE----EKGLIPPPLRSEGGYR--TYTQQHLDELRLISRA--RQVGFSLEECKELL   67 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCe--ecCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence            688999999999999987554    4588877543  3333  333434443   4343  34578899988754

This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.28  E-value=0.0019  Score=37.38  Aligned_cols=59  Identities=20%  Similarity=0.282  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP   64 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p   64 (77)
                      .+++..+||+.++||.+||++.++.+.+.|-+...+.+| + ....+...++-..+...++
T Consensus        19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~-~-y~l~~~~~~~~~~~~~~~~   77 (91)
T smart00346       19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNG-R-YRLGPKVLELGQSYLSSLD   77 (91)
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCC-c-eeecHHHHHHHHHHHhcCC
Confidence            469999999999999999999999999999997654332 2 2344444444445544443

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=97.27  E-value=0.0017  Score=39.50  Aligned_cols=62  Identities=19%  Similarity=0.233  Sum_probs=42.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-    |-+.|=+.|...+|++.  =++.+.   .+|..+.+-  ++++.||++-+
T Consensus         1 m~Ige~a~~~gvs~~tlRy----Ye~~GLl~p~~~~g~r~--Y~~~~~~~l~~I~~lr~~--G~sL~eI~~~l   65 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRH----YIDLGLLIPEKKGGQYF--FDEKCQDDLEFILELKGL--GFSLIEIQKIF   65 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCcCCccCCCccc--cCHHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            6889999999999999754    34668888876555443  233333   344444433  68999988754

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=97.27  E-value=0.00024  Score=38.18  Aligned_cols=34  Identities=24%  Similarity=0.495  Sum_probs=23.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGS   43 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~   43 (77)
                      ++..++++.+|||.+|+++|++    .|.. .|-+.|+.
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k----~g~FP~pvklg~r   38 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIK----DGKFPKPVKLGGR   38 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHH----HHH---SEESSS-
T ss_pred             ccHHHHHHHHCCCHHHHHHHHh----cccCCCCEEECCC
Confidence            3678999999999999999999    3544 55556653

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=97.26  E-value=0.0027  Score=40.59  Aligned_cols=64  Identities=20%  Similarity=0.155  Sum_probs=43.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||..|+.-|-+    .|-+.|.....+..+.=++.+...   |..+  .+-++++.||++.+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~l--r~~G~sL~eI~~~l   68 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRA--KQLGFTLEEIRELL   68 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence            6889999999999999988754    498888543222223344444443   3343  34578999998765

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=97.25  E-value=0.00074  Score=35.70  Aligned_cols=29  Identities=28%  Similarity=0.361  Sum_probs=24.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||.++|.++.++-.+
T Consensus        18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~   46 (50)
T PF04545_consen   18 FEGLTLEEIAERLGISRSTVRRILKRALK   46 (50)
T ss_dssp             TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            46899999999999999999999987653

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=97.24  E-value=0.00091  Score=41.71  Aligned_cols=62  Identities=21%  Similarity=0.126  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc--cCCCCCCCCC-HHHHHHHHHHHHhCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVAT-PDVERRIEEYKGENPAM   66 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~--~gg~~~~~~~-~~~~~~i~~~v~~~pd~   66 (77)
                      .+|..+||.+++||+++|.+.++..++.|=+...+  .||....... ......|.+.++..+.+
T Consensus        25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l~~~~~v   89 (130)
T TIGR02944        25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAVEGPVAL   89 (130)
T ss_pred             CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHHcCCCCc
Confidence            48999999999999999999999999999986543  3444331111 11233455556655543

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.

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=97.24  E-value=0.0038  Score=39.01  Aligned_cols=63  Identities=19%  Similarity=0.185  Sum_probs=41.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-ccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR-PGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.||||.+|+.    -|-+.|-+. |.+..+ ..+.-++.+...   |..+.  +=++++.||.+-+
T Consensus         1 m~I~e~a~~~gvs~~tlR----~Ye~~GLl~~~~r~~~-gyR~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l   67 (126)
T cd04783           1 LTIGELAKAAGVNVETIR----YYQRRGLLPEPPRPEG-GYRRYPEETVTRLRFIKRAQ--ELGFTLDEIAELL   67 (126)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCC-CCeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            678999999999999993    335668887 443222 233444444444   44443  3468899888755

Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=97.23  E-value=0.0003  Score=37.46  Aligned_cols=26  Identities=23%  Similarity=0.380  Sum_probs=21.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.|+|..++|+.+|||+++|++|.+-
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            57999999999999999999999753

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=97.22  E-value=0.00035  Score=50.45  Aligned_cols=38  Identities=24%  Similarity=0.450  Sum_probs=34.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .+|+++.+||++||||..+|+|++++-++.|-|.-.-.
T Consensus        24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~   61 (321)
T COG2390          24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN   61 (321)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence            57999999999999999999999999999999876543

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.21  E-value=0.00072  Score=42.80  Aligned_cols=43  Identities=21%  Similarity=0.300  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~   46 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.
T Consensus        53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~   95 (144)
T PRK11512         53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRG   95 (144)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCe
Confidence            5699999999999999999999999999999988877667663

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=97.20  E-value=0.00067  Score=34.85  Aligned_cols=34  Identities=24%  Similarity=0.305  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .++..++|+.+++|+++|++.++++.+.|-+...
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4789999999999999999999999999998754

>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators

Probab=97.20  E-value=0.0038  Score=39.45  Aligned_cols=64  Identities=14%  Similarity=0.059  Sum_probs=42.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|    -+.|-+.|....++..+.=++.+..   +|..+.  +-+++|.||++-+
T Consensus         1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr--~~G~sL~eI~~~l   67 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSAR--QLGFSLKDIKEIL   67 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            68899999999999998443    5679888865431222333343443   344443  4569999988765

Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=97.19  E-value=0.0046  Score=37.06  Aligned_cols=64  Identities=16%  Similarity=0.033  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++..++|+.+|||.+|+.-|-+.    |-+.|.....+..+.-+..+..   .|..+.+  -++++.||++.+
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~----Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~--~G~~l~~I~~~l   67 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI----GLFKPAKIAENGYRYYSYAQLYQLQFILFLRE--LGFSLAEIKELL   67 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            57889999999999999877654    9998865422222333333333   3444433  469999998765

Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>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=97.18  E-value=0.00087  Score=36.69  Aligned_cols=36  Identities=22%  Similarity=0.219  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      ..++..++|..+|+|.+||++.++++.+.|-+...+
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            358999999999999999999999999999887653

>PHA00738 putative HTH transcription regulator

Probab=97.18  E-value=0.00037  Score=43.39  Aligned_cols=41  Identities=24%  Similarity=0.139  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+++++++..|++|+++||+-++-.++.|=|...+.|....
T Consensus        26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vy   66 (108)
T PHA00738         26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLY   66 (108)
T ss_pred             CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEE
Confidence            48999999999999999999999999999999998875443

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=97.17  E-value=0.0012  Score=34.97  Aligned_cols=39  Identities=23%  Similarity=0.378  Sum_probs=33.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ....+..+|++.|+||.++|++.++++.+.|-+.....+
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~   46 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG   46 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence            345889999999999999999999999999998755433

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=97.14  E-value=0.0048  Score=39.33  Aligned_cols=66  Identities=9%  Similarity=0.069  Sum_probs=43.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      |++.++|+++|||..|+.-|    -+.|-+.|.....+..+.=++.+..+|.-... .+-++++.||++-+
T Consensus         1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l   67 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELV   67 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            68899999999999998554    45588877544222234445555555543322 34579999987754

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=97.12  E-value=0.0043  Score=38.75  Aligned_cols=64  Identities=14%  Similarity=0.081  Sum_probs=41.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|-    +.|-+.|.....+..+.=++.+..   +|..+.+  =++++.||.+-|
T Consensus         1 m~IgevA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~G~sL~eI~~~l   67 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYE----KEGLLPAPARSANNYRLYDEEHLERLLFIRRCRS--LDMSLDEIRTLL   67 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            678999999999999986554    458887543322223344444454   4444433  369999988754

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>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=97.12  E-value=0.00076  Score=39.27  Aligned_cols=34  Identities=26%  Similarity=0.395  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      ++..+||++++||++++.+++++..+.|=+...+
T Consensus        26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~   59 (83)
T PF02082_consen   26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSR   59 (83)
T ss_dssp             BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC
Confidence            7999999999999999999999999999987654

(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.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=97.11  E-value=0.0006  Score=36.13  Aligned_cols=24  Identities=33%  Similarity=0.462  Sum_probs=22.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .|..+||+.+|||.+||.+++.+|
T Consensus        28 ~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   28 RSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHhh
Confidence            589999999999999999999886

>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=97.11  E-value=0.0052  Score=38.98  Aligned_cols=64  Identities=13%  Similarity=0.066  Sum_probs=41.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+++|||.+|+.-|-    +.|-+.|....++..+.=++.+..   +|..+.  .-+++|.||.+-|
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr--~~GfsL~eI~~ll   67 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQ--QAGFSLDEIRQLL   67 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            688999999999999986654    458887743322222333343443   344433  3468999998765

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su

>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=97.10  E-value=0.00064  Score=37.43  Aligned_cols=39  Identities=23%  Similarity=0.298  Sum_probs=33.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ..+++..++|+.|+++++|+++-++...+.|=|...+.|
T Consensus        22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~g   60 (61)
T PF12840_consen   22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVEREG   60 (61)
T ss_dssp             CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeccC
Confidence            567999999999999999999999999999988766544

...

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=97.09  E-value=0.0062  Score=37.26  Aligned_cols=66  Identities=17%  Similarity=0.100  Sum_probs=44.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|    -+.|-+.|.....+..+.=++++...+..... .+-++++.|+.+.|
T Consensus         1 ~~I~eva~~~gvs~~tLRyY----E~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l   67 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFY----ERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELL   67 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHH----HHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            57899999999999998655    45688888766532334445555444332221 24579999998866

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=97.09  E-value=0.0032  Score=35.61  Aligned_cols=43  Identities=21%  Similarity=0.224  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP   64 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p   64 (77)
                      ++..+||++.|||.+||+++++               +++. .+++..+.|.+..++..
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln---------------~~~~-v~~~t~~~i~~~~~~~g   43 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLN---------------GNGR-VSEETREKVLAAMEELG   43 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHC---------------CCCC-CCHHHHHHHHHHHHHhC
Confidence            3678999999999999999882               1222 34556677777666653

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=97.08  E-value=0.0055  Score=38.47  Aligned_cols=62  Identities=19%  Similarity=0.130  Sum_probs=41.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|-+    .|-+.|...  +|.|  .=++.+.   .+|..+.  .=++++.||.+.|
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR--~Y~~~~l~~l~~I~~lr--~lG~sL~eI~~~l   67 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYR--VYTVGHVERLAFIRNCR--TLDMSLAEIRQLL   67 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCC--cCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            6789999999999999877654    588865332  3333  3334343   3444443  3468888888754

This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=97.08  E-value=0.0011  Score=35.39  Aligned_cols=28  Identities=21%  Similarity=0.373  Sum_probs=26.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      |...+|+.+|+|.+||+++++...+.|-
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~   54 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEKGL   54 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence            8899999999999999999999999884

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=97.08  E-value=0.005  Score=38.47  Aligned_cols=61  Identities=15%  Similarity=0.131  Sum_probs=39.9

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++.++|+.+|||+.|+.-|    -+.|-+.|...  +|.|.  -++.+...   |..+  ..-++++.||.+.|
T Consensus         1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~--Y~~~~l~~l~~I~~l--~~~G~sl~eI~~~l   66 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRR--YPEETVKRLRFIKRA--QELGFSLEEIGGLL   66 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEe--ECHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence            4689999999999999555    45688865322  44332  33434443   4444  44579999998765

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=97.07  E-value=0.0063  Score=37.41  Aligned_cols=63  Identities=19%  Similarity=0.124  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||.+|+.-|-+    .|-+.|....++ .+.=++.+...   |..+.  .-++++.||.+.+
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~~~g-~R~Y~~~~~~~l~~I~~lr--~~G~sl~eI~~~l   66 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERSANG-YRDYDEAAVDRVRQIRRLL--AAGLTLEEIREFL   66 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcCCCC-CeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            6789999999999999988755    498888544322 23344444443   44443  3468888888654

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK04217 hypothetical protein; Provisional

Probab=97.07  E-value=0.0011  Score=41.38  Aligned_cols=29  Identities=21%  Similarity=0.296  Sum_probs=26.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .+|+|..+||+.||||.+||++.+.+.++
T Consensus        56 ~eGlS~~EIAk~LGIS~sTV~r~L~RArk   84 (110)
T PRK04217         56 YEGLTQEEAGKRMGVSRGTVWRALTSARK   84 (110)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37899999999999999999999987654

>PHA00542 putative Cro-like protein

Probab=97.06  E-value=0.00046  Score=40.51  Aligned_cols=25  Identities=24%  Similarity=0.260  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||+++|++|..
T Consensus        29 ~~glTq~elA~~lgIs~~tIsr~e~   53 (82)
T PHA00542         29 RAGWSQEQIADATDVSQPTICRIYS   53 (82)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            5789999999999999999999974

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=97.05  E-value=0.0012  Score=41.94  Aligned_cols=35  Identities=17%  Similarity=0.177  Sum_probs=32.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .|..++|++|+||+.+|.+.+++....|=|...+.
T Consensus        26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G   60 (141)
T PRK11014         26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG   60 (141)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence            68899999999999999999999999999977764

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.04  E-value=0.0007  Score=36.00  Aligned_cols=40  Identities=30%  Similarity=0.280  Sum_probs=30.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      +..+||+..|||.+||+|.+.-.                ....++..+.|.+.+++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~----------------~~vs~~tr~rI~~~a~~   40 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGP----------------PRVSEETRERILEAAEE   40 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTC----------------SSSTHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCC----------------CCCCHHHHHHHHHHHHH
Confidence            35799999999999999998631                12445667778777665

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=97.04  E-value=0.0004  Score=41.21  Aligned_cols=25  Identities=16%  Similarity=0.101  Sum_probs=18.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +...+.|++|+.||||.|||.+=+.
T Consensus        17 ~~~aTVR~~Ak~FGvSKSTVHkDvt   41 (82)
T PF12116_consen   17 ETKATVRQAAKVFGVSKSTVHKDVT   41 (82)
T ss_dssp             HH---HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcccHHHHHHHHHCCcHHHHHHHHH
Confidence            3467899999999999999998663

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=97.03  E-value=0.0043  Score=37.74  Aligned_cols=56  Identities=13%  Similarity=0.249  Sum_probs=45.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCC---CCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRV---ATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~---~~~~~~~~i~~~   59 (77)
                      .+++..++|..+++++++|++.+++..+.|=|.-.+...+++..   +++.-.+.+..+
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~  100 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL  100 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence            45999999999999999999999999999999877777777643   556555544443

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.

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=97.03  E-value=0.0045  Score=38.52  Aligned_cols=62  Identities=21%  Similarity=0.224  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHH---HHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIE---EYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~---~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||..|+.-|=+    .|-+.|...+|.  +.=++.+..+|.   .+.  +-++++.||.+.+
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~----~GLl~p~r~~gy--R~Y~~~~l~~l~~I~~lr--~~G~~L~~I~~~l   65 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYED----KGLLSPERRGQT--RVYSRRDRARLKLILRGK--RLGFSLEEIRELL   65 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCCCCc--cccCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence            5788999999999999876644    499999766543  344555555443   433  4579999988755

Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=97.01  E-value=0.0089  Score=37.41  Aligned_cols=64  Identities=16%  Similarity=0.079  Sum_probs=40.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |+..++|+.+|||.+|+.-|-    +.|-+.|.....+..+.-++.+...   |..+.  +=++++.||.+-+
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l   67 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGYRLYGAAHVERLRFIRRAR--DLGFSLEEIRALL   67 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCccccCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence            678999999999999987554    4588876433211223344444443   43433  4458888888654

Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

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

Probab=96.99  E-value=0.0014  Score=35.47  Aligned_cols=32  Identities=19%  Similarity=0.260  Sum_probs=29.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.+++|..|+||.++|.+.++++.+.|-+...
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            48899999999999999999999999988644

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

>PRK10870 transcriptional repressor MprA; Provisional

Probab=96.98  E-value=0.0042  Score=40.96  Aligned_cols=50  Identities=16%  Similarity=0.187  Sum_probs=41.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      ++++.++|+.++++++||++.+++..+.|=|...+...+++.   .+|++-.+
T Consensus        71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~  123 (176)
T PRK10870         71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHE  123 (176)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence            488899999999999999999999999999988887777664   35554333

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=96.98  E-value=0.0049  Score=39.37  Aligned_cols=63  Identities=21%  Similarity=0.175  Sum_probs=43.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||.+|+..|-    +.|-+.|....++. +.-++.+..   +|..+.  +=++++.||.+.+
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~g~-R~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l   66 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDSNY-RYYDETALDRLQLIEHLK--GQRLSLAEIKDQL   66 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCC-eeECHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence            578899999999999998885    45999887653322 223333333   455553  3569999998765

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

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

Probab=96.97  E-value=0.002  Score=36.50  Aligned_cols=34  Identities=12%  Similarity=0.252  Sum_probs=31.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      |++..+||+.+||+.++|.|.+..+.+.|-|...
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~   55 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ   55 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            5999999999999999999999999999999764

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.96  E-value=0.0045  Score=38.92  Aligned_cols=42  Identities=10%  Similarity=0.245  Sum_probs=38.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|.++.++|+.++++++||++.+++..+.|=|.-.+...+++
T Consensus        45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR   86 (144)
T PRK03573         45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRR   86 (144)
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcC
Confidence            468999999999999999999999999999998887766666

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=96.94  E-value=0.001  Score=42.86  Aligned_cols=29  Identities=28%  Similarity=0.371  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..|+|..+||++||+|+++|+++.++.++
T Consensus        19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~k   47 (137)
T TIGR00721        19 EKGLSQKEIAKELKTTRANVSAIEKRAME   47 (137)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence            58999999999999999999998887554

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>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=96.94  E-value=0.0012  Score=36.61  Aligned_cols=35  Identities=20%  Similarity=0.178  Sum_probs=30.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      |..++|++|+||.+||.+-+.+..+.|-+...+..
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~   60 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAEGLIERRPGR   60 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence            78999999999999999999999999999777543

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 ....

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=96.94  E-value=0.00043  Score=43.76  Aligned_cols=30  Identities=20%  Similarity=0.356  Sum_probs=26.1

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      |.+.|+|+.+||+-||||++.||++++-.+
T Consensus        18 L~eeG~Sq~~iA~LLGltqaAVS~Yls~kr   47 (119)
T COG2522          18 LIEEGLSQYRIAKLLGLTQAAVSQYLSGKR   47 (119)
T ss_pred             HHHcCCcHHHHHHHhCCCHHHHHHHHccCC
Confidence            345799999999999999999999997543

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

Probab=96.93  E-value=0.0031  Score=36.94  Aligned_cols=34  Identities=24%  Similarity=0.370  Sum_probs=30.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ++.++|+.|+||++||++.+++..+.|=+...+.
T Consensus         1 ~~~ela~~l~is~stvs~~l~~L~~~glI~r~~~   34 (96)
T smart00529        1 RTSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY   34 (96)
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence            3679999999999999999999999998877654

iron dependent repressor

>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=96.93  E-value=0.0069  Score=37.56  Aligned_cols=63  Identities=19%  Similarity=0.129  Sum_probs=42.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHH---HHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIE---EYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~---~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|-++    |-+.|....+ ..+.=++.+..+|.   .+.  .=++++.|+++.+
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~----GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr--~~G~~L~eI~~~l   66 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEK----GLIASIGRRG-LRRQYDPQVLDRLALIALGR--AAGFSLDEIQAML   66 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CceecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            67899999999999999776654    8888754433 22334444455443   332  2379999998754

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.92  E-value=0.0049  Score=37.67  Aligned_cols=54  Identities=15%  Similarity=0.168  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIE   57 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~   57 (77)
                      .+++..++|+.+++++++|++.+++..+.|=|.-.+...+++.   .+|++-.+.+.
T Consensus        41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~   97 (118)
T TIGR02337        41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYA   97 (118)
T ss_pred             CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence            5689999999999999999999999999999987665555542   45565444333

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.

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=96.89  E-value=0.0011  Score=35.06  Aligned_cols=24  Identities=13%  Similarity=0.147  Sum_probs=22.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|++..++|+..|||+++|++|.
T Consensus        13 ~~gltq~~lA~~~gvs~~~vs~~e   36 (58)
T TIGR03070        13 ALGLTQADLADLAGVGLRFIRDVE   36 (58)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            468999999999999999999997

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=96.88  E-value=0.00057  Score=37.40  Aligned_cols=27  Identities=33%  Similarity=0.517  Sum_probs=20.9

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |.+.|++..++|+..|||.+|+++|++
T Consensus         6 m~~~~it~~~La~~~gis~~tl~~~~~   32 (63)
T PF13443_consen    6 MAERGITQKDLARKTGISRSTLSRILN   32 (63)
T ss_dssp             HHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            356899999999999999999999987

>PHA01976 helix-turn-helix protein

Probab=96.85  E-value=0.0013  Score=36.33  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=22.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|+|..++|+.+|||+++|++|.
T Consensus        13 ~~glt~~~lA~~~gvs~~~v~~~e   36 (67)
T PHA01976         13 ARAWSAPELSRRAGVRHSLIYDFE   36 (67)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            478999999999999999999995

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=96.84  E-value=0.0037  Score=43.18  Aligned_cols=44  Identities=16%  Similarity=0.114  Sum_probs=30.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      |+..+||+..|||.+||||.++..            +..+ ...++.++.|++.+++
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~~------------~~~~-~Vs~~tr~rV~~~a~e   44 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGK------------AKQY-RVSDKTVEKVMAVVRE   44 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC------------CCCC-CcCHHHHHHHHHHHHH
Confidence            578999999999999999999621            0001 2345566777766665

>PRK01381 Trp operon repressor; Provisional

Probab=96.84  E-value=0.00038  Score=42.75  Aligned_cols=26  Identities=15%  Similarity=0.164  Sum_probs=21.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.++|.|+||..+|||.+||+|=-+-
T Consensus        53 ~g~~sQREIa~~lGvSiaTITRgsn~   78 (99)
T PRK01381         53 RGELSQREIKQELGVGIATITRGSNS   78 (99)
T ss_pred             cCCcCHHHHHHHhCCceeeehhhHHH
Confidence            34599999999999999999985443

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=96.83  E-value=0.0028  Score=38.97  Aligned_cols=47  Identities=17%  Similarity=0.292  Sum_probs=34.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~   66 (77)
                      +.|++..++|+.+|+|++||++|     ++|...|.           . ....+..++..+|+.
T Consensus        76 ~~gltq~~lA~~lg~~~~tis~~-----e~g~~~p~-----------~-~~~~l~~~l~~~p~~  122 (127)
T TIGR03830        76 KLGLSQREAAELLGGGVNAFSRY-----ERGEVRPS-----------K-ALDKLLRLLDKHPEL  122 (127)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHH-----HCCCCCCC-----------H-HHHHHHHHHHHChHH
Confidence            46899999999999999999999     55654432           1 134466777778754

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=96.82  E-value=0.0023  Score=36.53  Aligned_cols=36  Identities=14%  Similarity=0.267  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHH-------hcCCCcccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQE-------TGSIRPGVI   40 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~-------tG~v~pk~~   40 (77)
                      -+|..++|+++|+++.+|.+|+..||+       +|+.+++-+
T Consensus        13 ~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~E~RVR   55 (65)
T PF05344_consen   13 QISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHWEARVR   55 (65)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCChHHHhh
Confidence            378999999999999999999999997       466555544

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.81  E-value=0.0022  Score=39.74  Aligned_cols=28  Identities=18%  Similarity=0.280  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+++.++|.+.|||.+|+.+++..-|.
T Consensus        56 egl~QeeaA~~MgVSR~T~~ril~~ARk   83 (106)
T PF02001_consen   56 EGLSQEEAAERMGVSRPTFQRILESARK   83 (106)
T ss_pred             cCCCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6899999999999999999999998775

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=96.81  E-value=0.0018  Score=36.41  Aligned_cols=26  Identities=23%  Similarity=0.247  Sum_probs=23.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ++.-.+||..||||.+||.+|-.+..
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK~~dk   47 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWKSRDK   47 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHhhhcc
Confidence            48999999999999999999987744

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=96.79  E-value=0.0013  Score=36.40  Aligned_cols=25  Identities=32%  Similarity=0.446  Sum_probs=20.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|+|..++|+++|||+++|++|-+
T Consensus        12 ~~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen   12 RAGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             CHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4689999999999999999999743

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=96.78  E-value=0.013  Score=36.06  Aligned_cols=63  Identities=16%  Similarity=0.106  Sum_probs=43.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |+..++|+.+|||+.|+.-|-    +.|-+.|....+ ..+.-++.+..+   |..+.  +-++++.||.+.+
T Consensus         1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr--~~G~sl~eI~~~l   66 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEAR--QLGFTLAELKAIF   66 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            688999999999999987664    459998866554 334444545554   44443  3468899988654

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK10072 putative transcriptional regulator; Provisional

Probab=96.77  E-value=0.0015  Score=39.74  Aligned_cols=51  Identities=20%  Similarity=0.266  Sum_probs=36.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEI   71 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El   71 (77)
                      +.|++..++|+.+|||.+||++|.+     |...|.        .  + . ..+.+++..+| -++.+|
T Consensus        44 ~~glTQ~elA~~lGvS~~TVs~WE~-----G~r~P~--------~--~-~-l~Ll~~L~~~P-~~~~~l   94 (96)
T PRK10072         44 GTGLKIDDFARVLGVSVAMVKEWES-----RRVKPS--------S--A-E-LKLMRLIQANP-ALSKQL   94 (96)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc-----CCCCCC--------H--H-H-HHHHHHHhhCH-HHHHHH
Confidence            4699999999999999999999964     333332        1  2 2 33788899999 444443

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=96.76  E-value=0.001  Score=34.37  Aligned_cols=27  Identities=22%  Similarity=0.331  Sum_probs=21.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..|-...++|+.||||.+|+++-+++|
T Consensus        16 ~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen   16 RCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            356688999999999999999999875

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=96.76  E-value=0.0018  Score=41.89  Aligned_cols=30  Identities=30%  Similarity=0.294  Sum_probs=26.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..|+|..+||+.||+|+++|++|.++.++.
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kk   48 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEKRAREN   48 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            589999999999999999999999876553

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=96.76  E-value=0.0061  Score=37.74  Aligned_cols=45  Identities=29%  Similarity=0.407  Sum_probs=35.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA   65 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd   65 (77)
                      .|+|+-+-|+.||||.+||++|     |.|...|-  |        +  +..++.+|+.+|-
T Consensus        56 ~~lSQ~vFA~~L~vs~~Tv~~W-----EqGr~kPs--g--------~--AlkLL~ivq~~p~  100 (104)
T COG2944          56 LGLSQPVFARYLGVSVSTVRKW-----EQGRKKPS--G--------A--ALKLLRIVQNHPL  100 (104)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHH-----HcCCcCCC--C--------H--HHHHHHHHHhcch
Confidence            5799999999999999999999     45544432  1        2  5678999999884

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=96.75  E-value=0.0017  Score=38.96  Aligned_cols=29  Identities=14%  Similarity=0.142  Sum_probs=25.2

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ...|+|.++||+.+|||.+||+|--+-..
T Consensus        46 L~~g~syreIa~~tgvS~aTItRvsr~Lk   74 (87)
T PF01371_consen   46 LDEGKSYREIAEETGVSIATITRVSRCLK   74 (87)
T ss_dssp             HHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            45899999999999999999999766544

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.75  E-value=0.0031  Score=42.16  Aligned_cols=36  Identities=17%  Similarity=0.242  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ..++|..++|+.|+||++||++.++++.+.|-|...
T Consensus        13 ~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~   48 (203)
T TIGR02702        13 QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE   48 (203)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence            356999999999999999999999999999999654

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.

>PHA00675 hypothetical protein

Probab=96.74  E-value=0.0015  Score=38.44  Aligned_cols=33  Identities=21%  Similarity=0.402  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|.|.-+||+.||||.|||+.+....+ =|++.
T Consensus        37 r~G~s~~~IA~~fGVsrstV~~I~~gk~-W~~~~   69 (78)
T PHA00675         37 VEGMSYAVLAEKFEQSKGAIAKICRYER-RGQFA   69 (78)
T ss_pred             hcCccHHHHHHHhCCCHHHHHHHHccch-hhhee
Confidence            4789999999999999999999876543 34443

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=96.74  E-value=0.012  Score=38.46  Aligned_cols=62  Identities=18%  Similarity=0.153  Sum_probs=41.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc-CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~-gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+++|||..|+..|    -+.|-+.|... +|+  +.-++.+..+   |..+.  +=+++|.||++.|
T Consensus        12 ~~IgevAk~~gvs~~TlRyY----E~~GLi~~~r~~~g~--R~Y~~~~i~~L~~I~~lr--~lG~sL~eIk~ll   77 (154)
T PRK15002         12 LTPGEVAKRSGVAVSALHFY----ESKGLITSIRNSGNQ--RRYKRDVLRYVAIIKIAQ--RIGIPLATIGEAF   77 (154)
T ss_pred             ccHHHHHHHHCcCHHHHHHH----HHCCCCCCccCCCCC--EEECHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            78999999999999998665    45598888544 333  3334444443   33333  3458888888765

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=96.74  E-value=0.0027  Score=35.60  Aligned_cols=32  Identities=19%  Similarity=0.147  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .-++..++|.+|+||.+||++-+++..+.|-.
T Consensus        12 ~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~   43 (69)
T TIGR00122        12 NPFSGEKLGEALGMSRTAVNKHIQTLREWGVD   43 (69)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence            34778999999999999999999999998875

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

>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]

Probab=96.73  E-value=0.0024  Score=46.05  Aligned_cols=72  Identities=19%  Similarity=0.127  Sum_probs=49.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC---------CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI---------RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR   72 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v---------~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~   72 (77)
                      .+.|+|.++||++||..+|||+|=++|=+..+..         .-.+.+.-++...+++-.+.|.+.+++.  +.-.+|+
T Consensus        20 ~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~L~~~--wSPEQI~   97 (318)
T COG2826          20 LKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEKLKSK--WSPEQII   97 (318)
T ss_pred             HHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHHHHhh--CCHHHHH
Confidence            4679999999999999999999988874433312         1111222344567788888888887663  5555555


Q ss_pred             HHh
Q psy15513         73 DRL   75 (77)
Q Consensus        73 ~~L   75 (77)
                      -.|
T Consensus        98 g~l  100 (318)
T COG2826          98 GRL  100 (318)
T ss_pred             HHH
Confidence            444

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=96.73  E-value=0.0026  Score=34.57  Aligned_cols=30  Identities=23%  Similarity=0.254  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..|++..+||..++||.+||+..++..+..
T Consensus        16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~K   45 (58)
T PF00196_consen   16 AQGMSNKEIAEELGISEKTVKSHRRRIMKK   45 (58)
T ss_dssp             HTTS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred             HhcCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence            479999999999999999999999987764

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>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=96.70  E-value=0.00091  Score=37.40  Aligned_cols=36  Identities=19%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+.+++|.++|++.++...+.|-|...+
T Consensus        21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen   21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            458999999999999999999999999999997765

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.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=96.69  E-value=0.0017  Score=37.68  Aligned_cols=25  Identities=24%  Similarity=0.396  Sum_probs=20.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||++.|+++.+
T Consensus        29 ~~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   29 ERGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCChhHHHHHHc
Confidence            5799999999999999999999875

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=96.69  E-value=0.011  Score=38.08  Aligned_cols=63  Identities=17%  Similarity=0.126  Sum_probs=42.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+.-|=+.    |-+.|....++. +.=++.+..   +|..+.+  =++++.||++.+
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~~----GLl~~~r~~~g~-R~Y~~~di~~l~~I~~lr~--~G~sL~eI~~~l   67 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYESK----GLITSIRNSGNQ-RRYKRDVLRRVAVIKAAQR--VGIPLATIGEAL   67 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCccCCCCC-EEECHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            68899999999999998776554    989885543332 333344443   3444432  368999998765

SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.

>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA

Probab=96.65  E-value=0.0013  Score=35.22  Aligned_cols=28  Identities=29%  Similarity=0.274  Sum_probs=25.0

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      |+.+|..+|+.|+.|+||.+||.|=+|.
T Consensus        17 ma~nG~GiRdtaRvL~I~~nTVlrtLK~   44 (46)
T PF12759_consen   17 MAFNGSGIRDTARVLKISINTVLRTLKN   44 (46)
T ss_pred             HHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence            5678999999999999999999988764

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=96.65  E-value=0.003  Score=41.08  Aligned_cols=67  Identities=16%  Similarity=0.257  Sum_probs=45.8

Q ss_pred             CccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-------ccccCCCCC---CC----CCHHHHHHHHHHHHhCCC
Q psy15513          1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR-------PGVIGGSKP---RV----ATPDVERRIEEYKGENPA   65 (77)
Q Consensus         1 l~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-------pk~~gg~~~---~~----~~~~~~~~i~~~v~~~pd   65 (77)
                      |.++| +|..+||+++|+|.+||.+=+++..+.|-+.       |.+.|-+-.   .+    ..+...+.+.+.+.+.|.
T Consensus        23 Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~~~~~~~l~~~p~  102 (164)
T PRK11169         23 LQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNAAVQKLEE  102 (164)
T ss_pred             hccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHHHHHHHHHhcCcc
Confidence            34556 9999999999999999999999999999874       444443211   01    123333445566677776


Q ss_pred             Cc
Q psy15513         66 MF   67 (77)
Q Consensus        66 ~t   67 (77)
                      +.
T Consensus       103 V~  104 (164)
T PRK11169        103 IQ  104 (164)
T ss_pred             ee
Confidence            54

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=96.63  E-value=0.0036  Score=39.75  Aligned_cols=28  Identities=21%  Similarity=0.217  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||+.++.+-+.
T Consensus       143 ~~~s~~eIA~~lgis~~tV~~~l~ra~~  170 (182)
T PRK09652        143 EGLSYEEIAEIMGCPIGTVRSRIFRARE  170 (182)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887654

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=96.63  E-value=0.0033  Score=41.37  Aligned_cols=29  Identities=24%  Similarity=0.291  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.+||+|.++..+.
T Consensus       149 ~~Gls~~EIA~~lgiS~~tV~r~l~~aR~  177 (185)
T PF07638_consen  149 FEGLSVEEIAERLGISERTVRRRLRRARA  177 (185)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37999999999999999999999988764

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.63  E-value=0.013  Score=33.80  Aligned_cols=52  Identities=19%  Similarity=0.239  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~   55 (77)
                      .+++..++|+.+++|+++|++.++.+.+.|-|...+.+++++   -.+++.-...
T Consensus        23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~   77 (101)
T smart00347       23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGREL   77 (101)
T ss_pred             CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHH
Confidence            358999999999999999999999999999997655444433   2345543433

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=96.62  E-value=0.021  Score=37.66  Aligned_cols=62  Identities=16%  Similarity=0.182  Sum_probs=42.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||..|+..|-+    .|-+.|...  +|.|  .=++.+..   .|..+  .+=++++.||+.-|
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~----~GLl~p~~r~~~gyR--~Y~~~dl~rL~~I~~l--r~~G~sL~eI~~ll   68 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER----IGLLSPSARSESNYR--LYGERDLERLEQICAY--RSAGVSLEDIRSLL   68 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCc--cCCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence            5889999999999999877654    598888543  3333  33333333   34444  33468899988765

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

>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=96.57  E-value=0.0019  Score=35.38  Aligned_cols=36  Identities=25%  Similarity=0.392  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ++..++|..|+||.+||.|=+....+.|-+.- ..||
T Consensus        15 ~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r-~~GG   50 (57)
T PF08220_consen   15 VSVKELAEEFGVSEMTIRRDLNKLEKQGLIKR-THGG   50 (57)
T ss_pred             EEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE-EcCE
Confidence            78999999999999999999999999997653 3444

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

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=96.55  E-value=0.0042  Score=38.58  Aligned_cols=29  Identities=17%  Similarity=0.113  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||||.+||..++.+.++
T Consensus       127 ~~~~~~~eIA~~lgis~~tv~~~~~ra~~  155 (161)
T TIGR02985       127 FEGKSYKEIAEELGISVKTVEYHISKALK  155 (161)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36999999999999999999999988764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=96.55  E-value=0.011  Score=34.87  Aligned_cols=41  Identities=17%  Similarity=0.227  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      ++..++|+.||||.+||++-+.             + +.+ ...++..+.|.+.++
T Consensus        20 ~ti~dvA~~~gvS~~TVsr~L~-------------~-~~~-~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844        20 ATVRETAKVFGVSKSTVHKDVT-------------E-RLP-EINPELAEEVKEVLD   60 (80)
T ss_pred             CCHHHHHHHhCCCHHHHHHHhc-------------C-CCC-CCCHHHHHHHHHHHc
Confidence            7889999999999999999661             1 111 244667778888877

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators

Probab=96.54  E-value=0.0014  Score=34.55  Aligned_cols=18  Identities=44%  Similarity=0.506  Sum_probs=16.7

Q ss_pred             HHHHHhccCHHHHHHHHH
Q psy15513         10 VISRQLRVSHGCVSKILN   27 (77)
Q Consensus        10 ~iA~rf~VS~stv~r~~~   27 (77)
                      ++|+++|||.+||++|++
T Consensus         2 ~lA~~~gvs~~tvs~~l~   19 (52)
T cd01392           2 DIARAAGVSVATVSRVLN   19 (52)
T ss_pred             cHHHHHCcCHHHHHHHHc
Confidence            689999999999999983

HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre

>PRK15043 transcriptional regulator MirA; Provisional

Probab=96.53  E-value=0.015  Score=40.64  Aligned_cols=65  Identities=11%  Similarity=0.075  Sum_probs=44.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      -+++.++|+.+|||..|+..|-++   .|-+.|....|+. +.-++++.+   +|..+.+  -++++.|+++.+
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr---~GLL~P~Rt~~G~-R~Ys~~dv~rL~~I~~l~~--~G~~i~eIk~ll   70 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRR---YGLLKPQRTDGGH-RLFNDADIDRIREIKRWID--NGVQVSKVKMLL   70 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHh---cCCCCCccCCCCC-EEECHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            478999999999999999887654   4888886543322 333344444   3445543  468888887765

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=96.52  E-value=0.0046  Score=38.68  Aligned_cols=29  Identities=17%  Similarity=-0.001  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -+|+|..+||..+|||.+||..++.|-+.
T Consensus       120 ~~~~s~~EIA~~l~is~~tV~~~~~ra~~  148 (154)
T PRK06759        120 FVGKTMGEIALETEMTYYQVRWIYRQALE  148 (154)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999988654

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=96.52  E-value=0.0042  Score=40.52  Aligned_cols=37  Identities=30%  Similarity=0.448  Sum_probs=33.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ++..+||+.|+||++||+..+++..+-|=|.-.|.+|
T Consensus        25 ~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~g   61 (154)
T COG1321          25 ARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGG   61 (154)
T ss_pred             ccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCC
Confidence            7889999999999999999999999999998776655

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=96.51  E-value=0.0062  Score=42.25  Aligned_cols=22  Identities=18%  Similarity=0.152  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+..+||+..|||.+||||.++
T Consensus         6 ~ti~dIA~~agVS~~TVSrvLn   27 (331)
T PRK14987          6 PVLQDVADRVGVTKMTVSRFLR   27 (331)
T ss_pred             CcHHHHHHHhCCCHHHhhhhhC
Confidence            6889999999999999999995

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=96.50  E-value=0.0079  Score=41.75  Aligned_cols=23  Identities=22%  Similarity=0.141  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .++..+||+.+|||.+||||-++
T Consensus         6 ~~Ti~dIA~~agVS~~TVSr~Ln   28 (342)
T PRK10014          6 KITIHDVALAAGVSVSTVSLVLS   28 (342)
T ss_pred             CCcHHHHHHHhCCCHHHHHHHHC
Confidence            37899999999999999999986

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=96.50  E-value=0.0049  Score=37.30  Aligned_cols=29  Identities=28%  Similarity=0.335  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||.++|++++++.++
T Consensus       124 ~~g~s~~eIA~~l~~s~~~v~~~~~~~~~  152 (158)
T TIGR02937       124 LEGLSYKEIAEILGISVGTVKRRLKRARK  152 (158)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36999999999999999999999998764

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>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=96.49  E-value=0.0042  Score=34.11  Aligned_cols=43  Identities=19%  Similarity=0.282  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      ...++..++|..|++++++|++.+++..+-|=|.-.+...+++
T Consensus        16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R   58 (68)
T PF13463_consen   16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKR   58 (68)
T ss_dssp             TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence            4568999999999999999999999999999995554433333

>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=96.48  E-value=0.0092  Score=35.18  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=34.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC--ccccCCCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR   46 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~--pk~~gg~~~~   46 (77)
                      +.-++||+.+++|.+||.+-++...+-|-|+  |.+.||..|.
T Consensus        24 VgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT   66 (78)
T PF03444_consen   24 VGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT   66 (78)
T ss_pred             cCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence            5678899999999999999999999999996  4455665554

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

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=96.47  E-value=0.0028  Score=35.86  Aligned_cols=26  Identities=27%  Similarity=0.442  Sum_probs=23.3

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      -+.|++..++|+.+|||.++|++|.+
T Consensus        15 ~~~~~t~~~lA~~~gis~~tis~~~~   40 (78)
T TIGR02607        15 EPLGLSIRALAKALGVSRSTLSRIVN   40 (78)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            35789999999999999999999854

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

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

Probab=96.46  E-value=0.0072  Score=34.17  Aligned_cols=36  Identities=22%  Similarity=0.281  Sum_probs=30.3

Q ss_pred             CCC--CHHHHHHHhccC-HHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGV--RPCVISRQLRVS-HGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~--s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .|+  |.+|||+.||++ .++|...++...+.|-+.-.+
T Consensus        22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~   60 (65)
T PF01726_consen   22 NGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP   60 (65)
T ss_dssp             HSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred             cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence            454  568999999996 999999999999999997553

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=96.46  E-value=0.0035  Score=40.28  Aligned_cols=34  Identities=18%  Similarity=0.316  Sum_probs=31.1

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ++| .|..+||+.+|+|.+||.+=+++..+.|-+.
T Consensus        20 ~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~   54 (153)
T PRK11179         20 ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT   54 (153)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            455 8999999999999999999999999999774

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=96.43  E-value=0.0024  Score=35.68  Aligned_cols=24  Identities=21%  Similarity=0.187  Sum_probs=19.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +.|.+|+.|+|+..+|.+|+++--
T Consensus        27 ~~RAaarkf~V~r~~Vr~W~kqe~   50 (58)
T PF09607_consen   27 NQRAAARKFNVSRRQVRKWRKQEE   50 (58)
T ss_dssp             -HHHHHHHTTS-HHHHHHHHTTHH
T ss_pred             hHHHHHHHhCccHHHHHHHHHHHH
Confidence            458899999999999999998743

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=96.42  E-value=0.0057  Score=38.65  Aligned_cols=28  Identities=18%  Similarity=0.038  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~  148 (160)
T PRK09642        121 EEKSYQEIALQEKIEVKTVEMKLYRARK  148 (160)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999888887664

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.42  E-value=0.0039  Score=37.34  Aligned_cols=63  Identities=19%  Similarity=0.274  Sum_probs=43.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc-------cccCCCC-----CCCCCHHHHHHHHHHHHhCCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP-------GVIGGSK-----PRVATPDVERRIEEYKGENPAMF   67 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p-------k~~gg~~-----~~~~~~~~~~~i~~~v~~~pd~t   67 (77)
                      .++..++|+.+|+|.+||.+.+++..+.|-+..       ...|-+-     -....+...+.+.+.+.+.|.++
T Consensus        17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~v~~~l~~~p~v~   91 (108)
T smart00344       17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEEFLEKLEKLPEVV   91 (108)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHHHHHHHhCCcceE
Confidence            489999999999999999999999999998752       1112110     01111344566777788888654

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

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=96.41  E-value=0.0057  Score=38.37  Aligned_cols=28  Identities=29%  Similarity=0.335  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.+|||.+||...+.|-+.
T Consensus       126 ~g~~~~eIA~~l~is~~tv~~~l~Rar~  153 (159)
T TIGR02989       126 RGVSLTALAEQLGRTVNAVYKALSRLRV  153 (159)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999988764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=96.41  E-value=0.0054  Score=39.64  Aligned_cols=28  Identities=14%  Similarity=0.113  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|||.++|..++.|.++
T Consensus       150 ~~~s~~eIA~~lgis~~~V~~~l~ra~~  177 (186)
T PRK13919        150 QGYTHREAAQLLGLPLGTLKTRARRALS  177 (186)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999988764

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=96.41  E-value=0.032  Score=39.53  Aligned_cols=60  Identities=17%  Similarity=0.158  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      .|+|..+||..||+|.+||...+.|-++.=.-.+...-+-.+......+.+.+.++++.-
T Consensus       168 ~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~  227 (339)
T PRK08241        168 LGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAF  227 (339)
T ss_pred             hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHH
Confidence            799999999999999999999988877543321111111123334444555555555543

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=96.38  E-value=0.015  Score=38.16  Aligned_cols=39  Identities=21%  Similarity=0.267  Sum_probs=33.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc--ccCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGSK   44 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk--~~gg~~   44 (77)
                      +|..+||++++||..++.++++..++.|=|...  +.||..
T Consensus        26 vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~   66 (164)
T PRK10857         26 VPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYL   66 (164)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCee
Confidence            899999999999999999999999999999753  345544

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=96.38  E-value=0.014  Score=32.30  Aligned_cols=59  Identities=15%  Similarity=0.152  Sum_probs=41.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .+..++|+.||+|.+++.+.+++.  +| ..|+..       ......+.+..++..+ ++++.|+++.+
T Consensus         2 ~~~~~la~~~~~s~~~l~~~f~~~--~~-~s~~~~-------~~~~r~~~a~~~l~~~-~~~~~~ia~~~   60 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKE--TG-TTPKQY-------LRDRRLERARRLLRDT-DLSVTEIALRV   60 (84)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH--hC-cCHHHH-------HHHHHHHHHHHHHHcC-CCCHHHHHHHh
Confidence            477899999999999999998864  22 233321       1222345577788776 89999998764

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=96.37  E-value=0.025  Score=34.97  Aligned_cols=34  Identities=21%  Similarity=0.259  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+|..+||+.+++|.++|.++++...+.|=+...
T Consensus        25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            5899999999999999999999999999988653

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.

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=96.37  E-value=0.0031  Score=37.50  Aligned_cols=27  Identities=26%  Similarity=0.186  Sum_probs=20.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|+++.+||+++|-|+++|++.+.-.
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll   27 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLALL   27 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            369999999999999999999987643

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=96.36  E-value=0.014  Score=36.74  Aligned_cols=33  Identities=15%  Similarity=0.291  Sum_probs=30.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..+||++++||..++.+++.+.++.|=|...
T Consensus        26 ~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~   58 (135)
T TIGR02010        26 VTLADISERQGISLSYLEQLFAKLRKAGLVKSV   58 (135)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence            799999999999999999999999999988653

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

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=96.35  E-value=0.004  Score=34.87  Aligned_cols=19  Identities=26%  Similarity=0.281  Sum_probs=17.1

Q ss_pred             CHHHHHHHhccCHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~   25 (77)
                      +...+|+.||||+++|+.|
T Consensus        11 ~~~~lAkalGVs~~aVs~W   29 (60)
T PF14549_consen   11 GQSKLAKALGVSPQAVSQW   29 (60)
T ss_dssp             SHHHHHHHHTS-HHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHh
Confidence            6789999999999999999

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=96.34  E-value=0.0067  Score=38.37  Aligned_cols=28  Identities=29%  Similarity=0.319  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|++..+||..||+|.+||.+++.+.+.
T Consensus       140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~  167 (179)
T PRK11924        140 EGLSYREIAEILGVPVGTVKSRLRRARQ  167 (179)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999988764

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=96.32  E-value=0.0063  Score=39.49  Aligned_cols=28  Identities=21%  Similarity=0.319  Sum_probs=26.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||..++.|-++
T Consensus       148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~  175 (182)
T PRK12537        148 DGCSHAEIAQRLGAPLGTVKAWIKRSLK  175 (182)
T ss_pred             cCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence            7999999999999999999999998764

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=96.31  E-value=0.038  Score=35.60  Aligned_cols=63  Identities=11%  Similarity=0.004  Sum_probs=41.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      -+++.++|+++|||..|+.-|=    +.|-+.|...  +|.|  .-++.+..   +|..+.  +=+++|.||++.+
T Consensus         7 ~~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR--~Y~~~~l~rl~~I~~lr--~~G~sL~eI~~ll   74 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIR--RYGEADVTRVRFVKSAQ--RLGFSLDEIAELL   74 (144)
T ss_pred             cccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--ecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            3899999999999999986554    3487765433  3333  33444444   344444  3358899988755

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=96.29  E-value=0.012  Score=41.09  Aligned_cols=41  Identities=20%  Similarity=0.206  Sum_probs=29.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      +..+||+..|||.+||||.++.               +++ ..++.++.|++.+++.
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn~---------------~~~-Vs~~tr~rV~~~a~el   43 (343)
T PRK10727          3 TIKDVARLAGVSVATVSRVINN---------------SPK-ASEASRLAVHSAMESL   43 (343)
T ss_pred             CHHHHHHHhCCCHHHHHHHhCC---------------CCC-CCHHHHHHHHHHHHHH
Confidence            6889999999999999999951               111 3355566676666553

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.28  E-value=0.0085  Score=32.78  Aligned_cols=32  Identities=19%  Similarity=0.347  Sum_probs=26.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.| |...+|+.++||+++|++.+++..+.=.+
T Consensus        12 ~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~   43 (60)
T PF00126_consen   12 ETG-SISAAAEELGISQSAVSRQIKQLEEELGV   43 (60)
T ss_dssp             HHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred             HhC-CHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence            345 88999999999999999999999865433

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=96.28  E-value=0.0079  Score=38.06  Aligned_cols=28  Identities=21%  Similarity=0.278  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||.+.+.+-+.
T Consensus       126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~  153 (166)
T PRK09639        126 SGYSYKEIAEALGIKESSVGTTLARAKK  153 (166)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988664

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=96.28  E-value=0.005  Score=35.46  Aligned_cols=25  Identities=8%  Similarity=0.103  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+|..++|+..+||++||.|+.+..
T Consensus        34 ~~si~elA~~~~vS~sti~Rf~kkL   58 (77)
T PF01418_consen   34 FMSISELAEKAGVSPSTIVRFCKKL   58 (77)
T ss_dssp             T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred             HccHHHHHHHcCCCHHHHHHHHHHh
Confidence            4789999999999999999999874

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=96.28  E-value=0.009  Score=33.51  Aligned_cols=34  Identities=32%  Similarity=0.382  Sum_probs=31.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .++..++|..+|+|..||+|.++++++.|=+.-.
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~   61 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVK   61 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence            4788999999999999999999999999988743

...

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=96.28  E-value=0.0073  Score=40.76  Aligned_cols=29  Identities=14%  Similarity=0.201  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -+|+|..+||..||||.+||.+++.+-+.
T Consensus       196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~  224 (234)
T PRK08301        196 GEEKTQKEVADMLGISQSYISRLEKRIIK  224 (234)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            47999999999999999999999877654

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=96.28  E-value=0.016  Score=33.51  Aligned_cols=33  Identities=18%  Similarity=0.465  Sum_probs=25.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg   42 (77)
                      .+-.|++..+|+|.+|++|+++.    |+. .|.+.||
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~----~~FPkpvklG~   47 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKD----GTFPKPVKLGG   47 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHcc----CCCCCCeecCc
Confidence            45688999999999999999987    444 4555565

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=96.27  E-value=0.0081  Score=37.96  Aligned_cols=28  Identities=25%  Similarity=0.178  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.||||.+||...+.+-+.
T Consensus       124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037        124 HGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999877554

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=96.27  E-value=0.008  Score=38.69  Aligned_cols=28  Identities=25%  Similarity=0.134  Sum_probs=26.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|-+.
T Consensus       149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~  176 (183)
T TIGR02999       149 AGLTVEEIAELLGVSVRTVERDWRFARA  176 (183)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988765

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=96.26  E-value=0.0042  Score=31.29  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|+|..++|+.+++|.+++++|.+
T Consensus        10 ~~~~s~~~~a~~~~~~~~~v~~~~~   34 (58)
T cd00093          10 EKGLTQEELAEKLGVSRSTISRIEN   34 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4689999999999999999999854

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=96.25  E-value=0.031  Score=39.18  Aligned_cols=72  Identities=17%  Similarity=0.107  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc-CCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~-gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .|+|..+||..||+|.+||...+.|-+..=.-.-+.. +...+....+.+.+.+.++++.-..--+..|.+.|
T Consensus       157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD~~~l~~Ll  229 (324)
T TIGR02960       157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALL  229 (324)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCCHHHHHHHh
Confidence            7999999999999999999999888775432211111 11111223344555555555544333344444433

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=96.24  E-value=0.008  Score=38.44  Aligned_cols=29  Identities=17%  Similarity=0.189  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..||+|.++|...+.|-++.
T Consensus       141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~  169 (176)
T PRK09638        141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQ  169 (176)
T ss_pred             cCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence            69999999999999999999999887653

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=96.24  E-value=0.0079  Score=38.72  Aligned_cols=28  Identities=14%  Similarity=0.100  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||+|.+||...+.|-+.
T Consensus       144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~  171 (179)
T PRK12514        144 EGLSYKELAERHDVPLNTMRTWLRRSLL  171 (179)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence            7999999999999999999999988664

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=96.24  E-value=0.008  Score=39.26  Aligned_cols=29  Identities=21%  Similarity=0.190  Sum_probs=25.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -+|+|..+||..+|||.+||...+.|-+.
T Consensus       145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~  173 (193)
T TIGR02947       145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRK  173 (193)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999887654

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=96.23  E-value=0.0038  Score=33.87  Aligned_cols=27  Identities=30%  Similarity=0.480  Sum_probs=20.7

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |.+.|+|.++||++++=|..||.++++
T Consensus        16 m~qlG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen   16 MHQLGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             HHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred             HHHhchhHHHHHHHhCccHHHHHHHhc
Confidence            456899999999999999999999986

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=96.23  E-value=0.0083  Score=37.89  Aligned_cols=28  Identities=21%  Similarity=0.287  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|+|.+||..++.|-++
T Consensus       125 ~g~s~~eIA~~lgis~~tV~~~l~ra~~  152 (162)
T TIGR02983       125 EDLSEAQVAEALGISVGTVKSRLSRALA  152 (162)
T ss_pred             hcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999998775

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

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

Probab=96.23  E-value=0.011  Score=35.42  Aligned_cols=36  Identities=19%  Similarity=0.127  Sum_probs=32.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ..++|..++|..+|+|+.||+|.++++.+.|=|...
T Consensus        45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~   80 (95)
T TIGR01610        45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ   80 (95)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            357899999999999999999999999999999754

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

>PRK00215 LexA repressor; Validated

Probab=96.22  E-value=0.0089  Score=39.76  Aligned_cols=37  Identities=22%  Similarity=0.144  Sum_probs=32.6

Q ss_pred             CCCHHHHHHHhcc-CHHHHHHHHHHHHHhcCCCccccC
Q psy15513          5 GVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         5 G~s~~~iA~rf~V-S~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      +.+..++|+.||+ |++||++++++..+.|-+...+.+
T Consensus        23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~   60 (205)
T PRK00215         23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR   60 (205)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence            3588899999999 999999999999999999766533

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

Probab=96.22  E-value=0.013  Score=40.32  Aligned_cols=52  Identities=12%  Similarity=0.156  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI   56 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i   56 (77)
                      +.|..++|+.+++|++||++++++..+.|-|.....+.+..=.+|+.-.+.+
T Consensus        21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll   72 (217)
T PRK14165         21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVL   72 (217)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHH
Confidence            5899999999999999999999999999999766543222224555434433

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=96.21  E-value=0.012  Score=40.93  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||+..|||.+||||.++
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn   23 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVIN   23 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Confidence            3788999999999999999995

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=96.20  E-value=0.0076  Score=40.11  Aligned_cols=36  Identities=11%  Similarity=0.148  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |++..+||+.++||..||.+.+....+.|.+...-.
T Consensus       177 g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~  212 (225)
T PRK10046        177 QHTAETVAQALTISRTTARRYLEYCASRHLIIAEIV  212 (225)
T ss_pred             CcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEee
Confidence            689999999999999999999999999999977654

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

Probab=96.20  E-value=0.0027  Score=35.83  Aligned_cols=34  Identities=24%  Similarity=0.315  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +|..++|+.|++|+.+|.-.+.++...|.|+.-.
T Consensus        15 ~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen   15 VSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             EEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence            8999999999999999999999999999995443

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

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=96.19  E-value=0.0045  Score=30.94  Aligned_cols=24  Identities=25%  Similarity=0.356  Sum_probs=22.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ..|+|..++|+.++||.+++++|.
T Consensus         8 ~~~~s~~~la~~~~i~~~~i~~~~   31 (56)
T smart00530        8 EKGLTQEELAEKLGVSRSTLSRIE   31 (56)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            578999999999999999999985

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=96.17  E-value=0.012  Score=40.43  Aligned_cols=19  Identities=32%  Similarity=0.361  Sum_probs=17.9

Q ss_pred             HHHHHHhccCHHHHHHHHH
Q psy15513          9 CVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         9 ~~iA~rf~VS~stv~r~~~   27 (77)
                      .|||+..|||.+||||.++
T Consensus         2 ~dIA~~agVS~~TVSrvLn   20 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVIN   20 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhC
Confidence            5899999999999999996

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=96.17  E-value=0.0044  Score=42.81  Aligned_cols=22  Identities=32%  Similarity=0.347  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||+.+|||++||||.++
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln   23 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLN   23 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhC
Confidence            4789999999999999999995

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

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=96.16  E-value=0.01  Score=37.56  Aligned_cols=28  Identities=18%  Similarity=0.189  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.||||.+||...+.|-++
T Consensus       137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~  164 (170)
T TIGR02952       137 QNLPIAEVARILGKTEGAVKILQFRAIK  164 (170)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999988765

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=96.15  E-value=0.0046  Score=42.91  Aligned_cols=39  Identities=26%  Similarity=0.319  Sum_probs=33.4

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      .| ++..++|++|+||..||.|.+....+.|-+. +-+||-
T Consensus        17 ~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~-r~~GGa   56 (252)
T PRK10906         17 QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL-RHHGGA   56 (252)
T ss_pred             cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCE
Confidence            44 7899999999999999999999999999874 456663

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=96.15  E-value=0.0099  Score=37.08  Aligned_cols=28  Identities=21%  Similarity=0.071  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|.+.
T Consensus       120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~  147 (154)
T TIGR02950       120 KEFSYKEIAELLNLSLAKVKSNLFRARK  147 (154)
T ss_pred             ccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988764

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>TIGR01481 ccpA catabolite control protein A

Probab=96.14  E-value=0.016  Score=39.95  Aligned_cols=22  Identities=32%  Similarity=0.409  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||+..|||.+||||.++
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn   23 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVN   23 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhC
Confidence            4678999999999999999995

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=96.12  E-value=0.01  Score=37.89  Aligned_cols=28  Identities=18%  Similarity=0.194  Sum_probs=26.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~~  161 (169)
T TIGR02954       134 HDLTIKEIAEVMNKPEGTVKTYLHRALK  161 (169)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999998765

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=96.12  E-value=0.015  Score=37.64  Aligned_cols=34  Identities=29%  Similarity=0.208  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      ++..+||++++||++++.|+++..++.|=|...+
T Consensus        25 ~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r   58 (153)
T PRK11920         25 SRIPEIARAYGVSELFLFKILQPLVEAGLVETVR   58 (153)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            6899999999999999999999999999886655

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=96.11  E-value=0.0099  Score=38.72  Aligned_cols=28  Identities=18%  Similarity=0.229  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|++..+||..||+|.+||..++.|.+.
T Consensus       156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~  183 (194)
T PRK12519        156 EGLSQSEIAKRLGIPLGTVKARARQGLL  183 (194)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988664

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=96.11  E-value=0.053  Score=37.21  Aligned_cols=65  Identities=15%  Similarity=0.089  Sum_probs=47.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L   75 (77)
                      +++.++|+..|||.+||.-|-++    |-+.|....+ ..+.-++.|.+.|.-... ....+++.+|.+.|
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~~----GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l   67 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDR----GLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELL   67 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            68899999999999998776544    8887754433 334667778877765555 34678999998765

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09726 antitoxin HipB; Provisional

Probab=96.10  E-value=0.0062  Score=35.83  Aligned_cols=25  Identities=12%  Similarity=0.318  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|++.|||+++|++|.+
T Consensus        23 ~~gltq~elA~~~gvs~~tis~~e~   47 (88)
T PRK09726         23 QNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4689999999999999999999976

>PRK09492 treR trehalose repressor; Provisional

Probab=96.08  E-value=0.0046  Score=42.43  Aligned_cols=23  Identities=30%  Similarity=0.323  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+.+|||.+||||.++.
T Consensus         5 ~ti~dIA~~agVS~~TVSrvLn~   27 (315)
T PRK09492          5 LTIKDIARLSGVGKSTVSRVLNN   27 (315)
T ss_pred             CcHHHHHHHhCCCHHHHhHHhCC
Confidence            68899999999999999999974

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=96.08  E-value=0.0028  Score=41.72  Aligned_cols=33  Identities=33%  Similarity=0.392  Sum_probs=28.1

Q ss_pred             CccCCCCHHHHHHHhc-cCHHHHHHHHHHHHHhc
Q psy15513          1 MAAAGVRPCVISRQLR-VSHGCVSKILNRYQETG   33 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~-VS~stv~r~~~r~r~tG   33 (77)
                      |..+|+|..+||++|| ||.+.|+--+.|..=.+
T Consensus        14 lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~   47 (162)
T PF07750_consen   14 LWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG   47 (162)
T ss_pred             HHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence            4579999999999999 99999998888874333

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=96.07  E-value=0.011  Score=38.27  Aligned_cols=28  Identities=14%  Similarity=0.121  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||+.||||.+||...+.+-++
T Consensus       144 ~g~s~~EIA~~l~is~~tV~~~l~rar~  171 (181)
T PRK12536        144 EGLSVAETAQLTGLSESAVKVGIHRGLK  171 (181)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988664

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=96.06  E-value=0.011  Score=37.09  Aligned_cols=28  Identities=14%  Similarity=0.153  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~  148 (161)
T PRK09047        121 EDMDVAETAAAMGCSEGSVKTHCSRATH  148 (161)
T ss_pred             hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887654

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=96.05  E-value=0.0096  Score=37.98  Aligned_cols=36  Identities=17%  Similarity=0.159  Sum_probs=32.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.+++.-+||..++.|.|||+|-+++.-+.|=|.-.
T Consensus        40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re   75 (126)
T COG3355          40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE   75 (126)
T ss_pred             cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence            355899999999999999999999999999998433

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=96.02  E-value=0.024  Score=37.53  Aligned_cols=45  Identities=24%  Similarity=0.265  Sum_probs=36.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      .+-.++|++||||.++|..-+++....|=|...|..|-.-...+.
T Consensus        35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~   79 (212)
T TIGR03338        35 LNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISL   79 (212)
T ss_pred             ecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCH
Confidence            566789999999999999999999999999888766544344443

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.

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=96.02  E-value=0.021  Score=39.50  Aligned_cols=43  Identities=19%  Similarity=0.145  Sum_probs=29.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      +..+||+..|||.+||||.++.             .+......++.++.|.+.+++
T Consensus         1 ti~dIA~~aGVS~~TVSrvLn~-------------~~~~~~vs~~tr~rV~~~a~~   43 (327)
T TIGR02417         1 TLSDIAKLAGVSKTTASYVING-------------KAKEYRISQETVERVMAVVRE   43 (327)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC-------------CCCCCccCHHHHHHHHHHHHH
Confidence            4679999999999999999952             000012445567777777666

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

>PRK09409 IS2 transposase TnpB; Reviewed

Probab=96.02  E-value=0.024  Score=40.22  Aligned_cols=66  Identities=29%  Similarity=0.316  Sum_probs=42.6

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR   72 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~   72 (77)
                      |..+|++...+++.||||.|+.++|++++..-  . ..+   ..+.....+..+.|.++.+++|..=..-|.
T Consensus         7 ~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~--~-~~~---~~~~~~~~~l~~~I~~i~~~~~~yG~Rri~   72 (301)
T PRK09409          7 LIARGWGVSLVSRCLRVSRAQLHVILRRTDDW--M-DGR---RSRHTDDTDVLLRIHHVIGELPTYGYRRVW   72 (301)
T ss_pred             HHhcCCcHHHHHHhcCcChHHhhhhccccccc--c-ccc---cccCcchHHHHHHHHHHHHhCccCCHHHHH
Confidence            45678999999999999999999999986521  1 111   011122234456677777777765444333

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=96.02  E-value=0.036  Score=37.18  Aligned_cols=51  Identities=14%  Similarity=0.055  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|+++.++|+.++++++||++.+++..+.|=|.-.+...+++.   .+|+.-.+
T Consensus        58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~  111 (185)
T PRK13777         58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEE  111 (185)
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence            6899999999999999999999999999999987766666663   35554343

>PRK12423 LexA repressor; Provisional

Probab=96.00  E-value=0.0087  Score=40.13  Aligned_cols=37  Identities=22%  Similarity=0.185  Sum_probs=32.5

Q ss_pred             CCC--CHHHHHHHhc-cCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~--s~~~iA~rf~-VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .|.  |.+++|+.|| +|+++|++.+++..+.|-+...+.
T Consensus        22 ~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~   61 (202)
T PRK12423         22 AGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN   61 (202)
T ss_pred             cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence            454  8999999999 599999999999999999976654

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=95.99  E-value=0.012  Score=38.13  Aligned_cols=28  Identities=14%  Similarity=0.157  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.++|...+.|-+.
T Consensus       152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~  179 (187)
T PRK12534        152 EGITYEELAARTDTPIGTVKSWIRRGLA  179 (187)
T ss_pred             cCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence            7999999999999999999999998765

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=95.99  E-value=0.024  Score=36.69  Aligned_cols=35  Identities=20%  Similarity=0.303  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      +|..+||.+.+||++++.|++...++-|=|...+.
T Consensus        26 ~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG   60 (150)
T COG1959          26 VSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG   60 (150)
T ss_pred             ccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence            67899999999999999999999999999976654

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=95.98  E-value=0.0073  Score=37.97  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|++..++|..+|||++||++|.+
T Consensus        16 ~~gltq~~lA~~~gvs~~~is~~E~   40 (135)
T PRK09706         16 QLKLSQRSLAKAVKVSHVSISQWER   40 (135)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4689999999999999999999954

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=95.94  E-value=0.014  Score=37.87  Aligned_cols=29  Identities=28%  Similarity=0.322  Sum_probs=26.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..+|||.+||..++.+-+..
T Consensus       142 ~gls~~EIA~~l~i~~~tVks~l~ra~~~  170 (182)
T COG1595         142 EGLSYEEIAEILGISVGTVKSRLHRARKK  170 (182)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            69999999999999999999999987653

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=95.93  E-value=0.014  Score=38.14  Aligned_cols=29  Identities=10%  Similarity=0.130  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..||+|.+||...+.|-+..
T Consensus       145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~  173 (185)
T PRK09649        145 LGLSYADAAAVCGCPVGTIRSRVARARDA  173 (185)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            78999999999999999999999887653

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=95.93  E-value=0.0071  Score=35.37  Aligned_cols=26  Identities=15%  Similarity=0.183  Sum_probs=22.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |...+|+.||||+++|+.|       |++-|..
T Consensus        12 s~~kvA~aLGIs~~AVsQW-------Ge~VPe~   37 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW-------GELVPEG   37 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH-------hccCcHH
Confidence            6788999999999999999       6766653

>PRK09526 lacI lac repressor; Reviewed

Probab=95.92  E-value=0.0084  Score=41.61  Aligned_cols=23  Identities=35%  Similarity=0.365  Sum_probs=21.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..|||++.|||.+||||.++.
T Consensus         6 ~ti~dIA~~aGVS~~TVSrvLn~   28 (342)
T PRK09526          6 VTLYDVARYAGVSYQTVSRVLNQ   28 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhcC
Confidence            68999999999999999999963

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=95.91  E-value=0.015  Score=37.07  Aligned_cols=28  Identities=11%  Similarity=0.093  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|-+.
T Consensus       127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~  154 (164)
T PRK12547        127 SGFSYEDAAAICGCAVGTIKSRVSRARN  154 (164)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999998765

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=95.91  E-value=0.014  Score=38.06  Aligned_cols=28  Identities=18%  Similarity=0.175  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       121 ~g~~~~EIA~~lgis~~tV~~~l~Rar~  148 (181)
T PRK09637        121 EGLSQKEIAEKLGLSLSGAKSRVQRGRV  148 (181)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999988877654

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=95.91  E-value=0.015  Score=37.92  Aligned_cols=28  Identities=11%  Similarity=0.046  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||..++.|-+.
T Consensus       149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~  176 (188)
T PRK09640        149 AELEFQEIADIMHMGLSATKMRYKRALD  176 (188)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999988664

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=95.89  E-value=0.014  Score=37.50  Aligned_cols=29  Identities=24%  Similarity=0.228  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||+|.++|...+.|.+.
T Consensus       150 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~  178 (187)
T TIGR02948       150 MEDLSLKEISEILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999988764

This sigma factor is restricted to certain lineages of the order Bacillales.

>PF13309 HTH_22: HTH domain

Probab=95.89  E-value=0.0051  Score=34.61  Aligned_cols=21  Identities=19%  Similarity=0.260  Sum_probs=18.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +...+|+.||||..||+++++
T Consensus        44 av~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   44 AVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHcC
Confidence            566789999999999999874

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=95.89  E-value=0.011  Score=40.63  Aligned_cols=63  Identities=21%  Similarity=0.177  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFS   68 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl   68 (77)
                      .|+|..|||+.+|+|.+||...+.|-++.=.-.- ..|+..... ......++.++.++||.+-.
T Consensus       131 eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  193 (228)
T PRK06704        131 FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS-EEGIEIVEF-TDDMEVVVTSIREERPELLT  193 (228)
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH-HhcCCCCCc-cccHHHHHHHHHhcCHHHHH
Confidence            6899999999999999999999877665322111 123322222 23356678899999996544

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=95.88  E-value=0.015  Score=38.08  Aligned_cols=28  Identities=14%  Similarity=0.134  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||..++.|-+.
T Consensus       149 ~g~s~~EIA~~lgis~~tVk~~l~RAr~  176 (189)
T PRK12530        149 LELSSEQICQECDISTSNLHVLLYRARL  176 (189)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999888664

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=95.86  E-value=0.015  Score=38.04  Aligned_cols=28  Identities=14%  Similarity=0.177  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       126 eg~s~~EIA~~lgis~~tV~~~l~Rar~  153 (182)
T PRK12511        126 EGLSYQEAAAVLGIPIGTLMSRIGRARA  153 (182)
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999876554

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=95.86  E-value=0.01  Score=34.76  Aligned_cols=33  Identities=9%  Similarity=0.062  Sum_probs=27.8

Q ss_pred             cCCCCHHHHHHHhc------cCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          3 AAGVRPCVISRQLR------VSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         3 ~~G~s~~~iA~rf~------VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      +.|+++.++|+.+|      +|++||+||-+     |++.++.+
T Consensus        22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es-----~~ls~~n~   60 (75)
T smart00352       22 KLGFTQADVGLALGALYGPDFSQTTICRFEA-----LQLSFKNM   60 (75)
T ss_pred             HcCCCHHHHHHHhcccccCcCCHHHHHHHHh-----cCccHHHH
Confidence            47999999999999      49999999755     88877643

>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59

Probab=95.85  E-value=0.0092  Score=37.69  Aligned_cols=31  Identities=16%  Similarity=0.245  Sum_probs=26.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.+|.|+-+||..|+||.|+|-.+-++.+.+
T Consensus        77 R~AGlt~~aIAd~F~iS~s~~~nft~~n~~e  107 (126)
T PF10654_consen   77 RHAGLTCYAIADYFKISKSTVFNFTQNNKKE  107 (126)
T ss_pred             HhcCCChHHHHHHHhHHHHHHHHHHHHhHHH
Confidence            3589999999999999999999988776543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=95.85  E-value=0.016  Score=36.64  Aligned_cols=28  Identities=25%  Similarity=0.296  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.+-++
T Consensus       128 ~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528        128 DGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988764

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=95.83  E-value=0.016  Score=37.74  Aligned_cols=29  Identities=14%  Similarity=0.013  Sum_probs=25.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|+|.+||...+.|.+.
T Consensus       153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~  181 (194)
T PRK12513        153 HGDLELEEIAELTGVPEETVKSRLRYALQ  181 (194)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999988877654

>PHA02535 P terminase ATPase subunit; Provisional

Probab=95.82  E-value=0.0045  Score=47.95  Aligned_cols=28  Identities=14%  Similarity=0.079  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      -+|.|+.+||+.+||+.+||++|.++++
T Consensus        16 ~~G~sv~eIA~~LGv~~~Tl~~W~kr~~   43 (581)
T PHA02535         16 WQGWTVAEIAEELGLKSRTIYSWKERDG   43 (581)
T ss_pred             HcCCCHHHHHHHhCCChhHHHHHhcccc
Confidence            3599999999999999999999999977

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=95.82  E-value=0.006  Score=38.83  Aligned_cols=37  Identities=19%  Similarity=0.083  Sum_probs=31.6

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ...|++++++|+.++|+.++|.+|.+++.+...--+.
T Consensus        86 ~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~~~  122 (129)
T COG3677          86 YMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGLRL  122 (129)
T ss_pred             HHcCCCcccHHHHhcccHHHHHHHHHhhcchhhccCC
Confidence            4568999999999999999999999999887655443

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=95.82  E-value=0.016  Score=37.86  Aligned_cols=28  Identities=21%  Similarity=0.249  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~  178 (195)
T PRK12532        151 LGFSSDEIQQMCGISTSNYHTIMHRARE  178 (195)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999998887554

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=95.81  E-value=0.011  Score=30.63  Aligned_cols=24  Identities=17%  Similarity=0.250  Sum_probs=19.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .|..++|+.+|||.++|.+=+++.
T Consensus        18 ~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   18 RSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHHh
Confidence            889999999999999999877765

...

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.79  E-value=0.014  Score=40.52  Aligned_cols=39  Identities=8%  Similarity=0.092  Sum_probs=34.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ...|+|..+||.+|++|.+||++...+..+.=.+..-|-
T Consensus       176 LAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAkN~~~  214 (251)
T PRK15320        176 LSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMDSSPL  214 (251)
T ss_pred             HHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCCCCCch
Confidence            357999999999999999999999999999888876654

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=95.79  E-value=0.013  Score=34.67  Aligned_cols=37  Identities=16%  Similarity=0.263  Sum_probs=33.2

Q ss_pred             HHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          9 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         9 ~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .++|++++|++++|++++++..+.|-|.-.+...+++
T Consensus        40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR   76 (126)
T COG1846          40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRR   76 (126)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccc
Confidence            8999999999999999999999999998877665654

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=95.78  E-value=0.017  Score=37.89  Aligned_cols=28  Identities=14%  Similarity=0.156  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||+.||||.+||...+.+-+.
T Consensus       131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~  158 (187)
T PRK12516        131 SGFAYEEAAEICGCAVGTIKSRVNRARQ  158 (187)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999877654

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=95.78  E-value=0.011  Score=40.95  Aligned_cols=38  Identities=24%  Similarity=0.406  Sum_probs=32.2

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      .| ++..++|+.|+||.+||.|.++...+.|-+.- -+||
T Consensus        17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r-~~gg   55 (251)
T PRK13509         17 LGFVTVEKVIERLGISPATARRDINKLDESGKLKK-VRNG   55 (251)
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE-ecCC
Confidence            44 89999999999999999999999999888753 2344

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=95.78  E-value=0.017  Score=37.87  Aligned_cols=28  Identities=14%  Similarity=0.218  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.||||.+||..++.|-+.
T Consensus       151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~~  178 (196)
T PRK12524        151 EGLSNPEIAEVMEIGVEAVESLTARGKR  178 (196)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999998664

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=95.78  E-value=0.018  Score=37.37  Aligned_cols=28  Identities=18%  Similarity=0.181  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~  164 (185)
T PRK12542        137 YNLTYQEISSVMGITEANVRKQFERARK  164 (185)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887665

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=95.76  E-value=0.018  Score=36.76  Aligned_cols=28  Identities=18%  Similarity=0.140  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~  162 (175)
T PRK12518        135 EDLPQKEIAEILNIPVGTVKSRLFYARR  162 (175)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988664

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=95.76  E-value=0.018  Score=37.32  Aligned_cols=28  Identities=18%  Similarity=0.138  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|.++
T Consensus       142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~  169 (179)
T PRK09415        142 EELSIKEIAEVTGVNENTVKTRLKKAKE  169 (179)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999998775

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=95.75  E-value=0.017  Score=36.50  Aligned_cols=34  Identities=18%  Similarity=0.194  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ..+..+||+.|+||++||++.+++..+.|-|...
T Consensus        22 ~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         22 YARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            4788999999999999999999999999988643

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=95.75  E-value=0.012  Score=39.36  Aligned_cols=34  Identities=21%  Similarity=0.106  Sum_probs=29.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..+|+|..+||++++||.+||...+++..+.=.+
T Consensus       149 la~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        149 WMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             HHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            3589999999999999999999999988865444

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=95.75  E-value=0.019  Score=36.68  Aligned_cols=28  Identities=21%  Similarity=0.262  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~  160 (173)
T PRK09645        133 RGWSTAQIAADLGIPEGTVKSRLHYALR  160 (173)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6999999999999999999888776553

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=95.75  E-value=0.018  Score=39.03  Aligned_cols=28  Identities=21%  Similarity=0.134  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|-+.
T Consensus       149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~  176 (216)
T PRK12533        149 EDMSYREIAAIADVPVGTVMSRLARARR  176 (216)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999886654

>PRK01905 DNA-binding protein Fis; Provisional

Probab=95.74  E-value=0.012  Score=34.06  Aligned_cols=27  Identities=19%  Similarity=0.257  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..|-...++|+++|||++|+++.+++|
T Consensus        48 ~~~gn~s~aAr~LGIsrstL~rklkk~   74 (77)
T PRK01905         48 QAGGNQSLAAEYLGINRNTLRKKLQQH   74 (77)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            346678899999999999999999986

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=95.74  E-value=0.11  Score=35.98  Aligned_cols=65  Identities=20%  Similarity=0.091  Sum_probs=45.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCC-CCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGG-SKPRVATPDVERRIEEYKGENPAMFSWEIRDR   74 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg-~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~   74 (77)
                      .+..|+|..|++|..||++.++.|++. |.+-|...-- +-.+..+  |-.+|.++.-+.  .+..|++.+
T Consensus       106 LT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~t--HK~~ii~~~l~g--~~~~eiar~  172 (220)
T PF07900_consen  106 LTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVT--HKKIIIRLYLKG--KPTPEIARR  172 (220)
T ss_pred             ccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcch--HHHHHHHHHHcC--CCHHHHHHH
Confidence            788999999999999999999999987 9998875210 1222233  555566554442  455565543

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=95.71  E-value=0.018  Score=36.57  Aligned_cols=28  Identities=11%  Similarity=-0.052  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||..++.|.++
T Consensus       123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~  150 (165)
T PRK09644        123 HELTYEEAASVLDLKLNTYKSHLFRGRK  150 (165)
T ss_pred             hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999988765

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=95.71  E-value=0.019  Score=38.34  Aligned_cols=29  Identities=24%  Similarity=0.280  Sum_probs=26.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..||||.+||..++.|-+..
T Consensus       153 ~g~s~~EIA~~Lgis~~tV~~~l~RArk~  181 (203)
T PRK09647        153 EGLSYEEIAATLGVKLGTVRSRIHRGRQQ  181 (203)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999987653

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=95.71  E-value=0.027  Score=30.78  Aligned_cols=28  Identities=21%  Similarity=0.268  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .+.+..++|+.||||.+|++.-+++-..
T Consensus        22 R~~tl~elA~~lgis~st~~~~LRrae~   49 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLRRAER   49 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4578899999999999999999887543

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=95.70  E-value=0.019  Score=39.36  Aligned_cols=28  Identities=14%  Similarity=0.144  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||++++.+-+.
T Consensus       220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~  247 (257)
T PRK08583        220 ENLSQKETGERLGISQMHVSRLQRQAIK  247 (257)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999987654

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=95.68  E-value=0.076  Score=32.14  Aligned_cols=48  Identities=15%  Similarity=0.073  Sum_probs=33.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHh-cCCCcccc-CC--CCCCCCCHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVI-GG--SKPRVATPDVER   54 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~-gg--~~~~~~~~~~~~   54 (77)
                      |...+|++++||+++|++-+++..+. |..--... ||  ++...+|++-..
T Consensus        18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~   69 (99)
T TIGR00637        18 SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQR   69 (99)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHH
Confidence            88999999999999999999999854 44322222 21  344567775444

ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=95.67  E-value=0.021  Score=37.98  Aligned_cols=32  Identities=9%  Similarity=-0.021  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +++|-..+|..+|||.+|+.||-+.-++.|+=
T Consensus        18 ~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDD   49 (165)
T PF08822_consen   18 DRLSLEQAAAKCGVSYATARRWKREAKAKGDD   49 (165)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence            57889999999999999999999999999975

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=95.67  E-value=0.022  Score=36.67  Aligned_cols=28  Identities=18%  Similarity=0.216  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|++..+||..||+|.+||...+.|-+.
T Consensus       115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~  142 (170)
T TIGR02959       115 EGLSQQEIAEKLGLSLSGAKSRVQRGRK  142 (170)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999988776553

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=95.64  E-value=0.01  Score=41.47  Aligned_cols=23  Identities=35%  Similarity=0.403  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+..|||.+||+|.++.
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~   24 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNN   24 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCC
Confidence            47899999999999999999963

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=95.64  E-value=0.08  Score=36.91  Aligned_cols=66  Identities=12%  Similarity=0.048  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .|+|..+||+.||+|.++|...+.|-+..=.- .|.      .....+++.+.+.++++.--.--+..|.+.|
T Consensus       123 ~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~------~~~~~~~~~~~~~~f~~a~~~gD~~~l~~lL  189 (281)
T TIGR02957       123 FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPR------FEVSREESRQLLERFVEAAQTGDLDGLLELL  189 (281)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC------CCCChHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            68999999999999999999999988864321 111      1123344555566665554333344444433

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=95.63  E-value=0.023  Score=36.40  Aligned_cols=28  Identities=18%  Similarity=0.186  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||+|.+||...+.+-+.
T Consensus       133 eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525        133 EGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999987654

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=95.63  E-value=0.022  Score=36.53  Aligned_cols=29  Identities=21%  Similarity=0.120  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +|+|..+||..+|||.+||...+.|-+..
T Consensus       134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~  162 (173)
T PRK12522        134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQ  162 (173)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999887653

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=95.61  E-value=0.022  Score=37.00  Aligned_cols=28  Identities=21%  Similarity=0.232  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.++|...+.|-+.
T Consensus       153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~  180 (193)
T PRK11923        153 DGLSYEDIASVMQCPVGTVRSRIFRARE  180 (193)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999888764

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=95.60  E-value=0.022  Score=37.15  Aligned_cols=29  Identities=17%  Similarity=0.303  Sum_probs=26.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +|+|..+||+.||+|.++|...+.|-+..
T Consensus       146 ~g~s~~EIAe~lgis~~~V~~~l~Ra~~~  174 (189)
T PRK06811        146 LGEKIEEIAKKLGLTRSAIDNRLSRGRKK  174 (189)
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            79999999999999999999999887753

>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]

Probab=95.60  E-value=0.021  Score=38.79  Aligned_cols=51  Identities=20%  Similarity=0.230  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK   60 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v   60 (77)
                      .|.+.++|.++|||..|+++|.+-    |.+.+-...+++.....+ ....+...+
T Consensus         1 ~m~~~e~~~~lgis~~Tl~rw~r~----G~i~~~~~~~gr~~~~ee-~v~~~~~~~   51 (193)
T COG2452           1 LLRPKEACQLLGISYSTLLRWIRE----GKIRVVTTEGGKYRIPEE-EIKKYLGKR   51 (193)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHc----CcccceEecCceEeccHh-HHHHHhchh
Confidence            478999999999999999999875    888665555455443333 345555543

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=95.58  E-value=0.016  Score=35.90  Aligned_cols=28  Identities=18%  Similarity=0.176  Sum_probs=24.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..++..|+|++||||.+||.+.++++-=
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~   97 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIWRALKRLGI   97 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHHHHHHHcCc
Confidence            3578899999999999999999998643

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional

Probab=95.57  E-value=0.011  Score=40.40  Aligned_cols=31  Identities=10%  Similarity=0.063  Sum_probs=27.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ++.| |...+|++++||+++|+|.+++..+.=
T Consensus        13 ~~~g-s~s~AA~~L~isQ~avSr~i~~LE~~l   43 (296)
T PRK09906         13 AEEL-NFTKAAEKLHTAQPSLSQQIKDLENCV   43 (296)
T ss_pred             HhhC-CHHHHHHHhCCCCcHHHHHHHHHHHHh
Confidence            3556 899999999999999999999998643

>PRK11013 DNA-binding transcriptional regulator LysR; Provisional

Probab=95.57  E-value=0.012  Score=40.73  Aligned_cols=47  Identities=23%  Similarity=0.146  Sum_probs=33.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      ++.| |...+|++++||+++|++.++++.+. |.---.. .+ +.=.+|++
T Consensus        16 ~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R-~~-~~v~LT~~   63 (309)
T PRK11013         16 MTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKLFER-VR-GRLHPTVQ   63 (309)
T ss_pred             HHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeee-cC-CCcccCHH
Confidence            3455 89999999999999999999999954 4433332 22 33345554

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=95.57  E-value=0.013  Score=40.54  Aligned_cols=36  Identities=19%  Similarity=0.126  Sum_probs=29.6

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRP   37 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~p   37 (77)
                      ++.|.|...+|++++||+++|++.+++..+. |.---
T Consensus        13 ~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF   49 (309)
T PRK12682         13 VRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIF   49 (309)
T ss_pred             HHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeE
Confidence            4567799999999999999999999999854 44333

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=95.56  E-value=0.013  Score=31.95  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=19.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|..+|||.+++++|.+
T Consensus        10 ~~~lt~~~~a~~~~i~~~~i~~~e~   34 (64)
T PF12844_consen   10 EKGLTQKDLAEKLGISRSTISKIEN   34 (64)
T ss_dssp             HCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4689999999999999999999964

>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator

Probab=95.55  E-value=0.013  Score=39.28  Aligned_cols=33  Identities=18%  Similarity=0.240  Sum_probs=27.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ++.| |...+|++++||+++|++.+++..+.=.+
T Consensus         9 ~~~g-s~~~AA~~L~isqsavS~~i~~LE~~lg~   41 (279)
T TIGR03339         9 ARCG-SFTRAAERLGLSQPTVTDQVRKLEERYGV   41 (279)
T ss_pred             HhcC-CHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence            3456 88999999999999999999999854433

This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=95.55  E-value=0.023  Score=38.07  Aligned_cols=28  Identities=25%  Similarity=0.304  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.||||.++|++++++-+.
T Consensus       193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~  220 (227)
T TIGR02980       193 EDKTQSEIAERLGISQMHVSRLLRRALK  220 (227)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6899999999999999999999988654

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.55  E-value=0.016  Score=36.48  Aligned_cols=30  Identities=20%  Similarity=0.387  Sum_probs=28.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .|..++|+++|+|.++|.+-+++..+.|=+
T Consensus        23 ~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522          23 ISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            899999999999999999999999999955

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=95.54  E-value=0.025  Score=36.63  Aligned_cols=28  Identities=18%  Similarity=0.248  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.+-..
T Consensus       142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~  169 (178)
T PRK12529        142 DGMKQKDIAQALDIALPTVKKYIHQAYV  169 (178)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887543

>PRK06930 positive control sigma-like factor; Validated

Probab=95.54  E-value=0.023  Score=37.45  Aligned_cols=29  Identities=17%  Similarity=0.323  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||||.+||..++.+.+.
T Consensus       128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~  156 (170)
T PRK06930        128 GYGLSYSEIADYLNIKKSTVQSMIERAEK  156 (170)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47999999999999999999999988664

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=95.54  E-value=0.025  Score=30.37  Aligned_cols=34  Identities=24%  Similarity=0.197  Sum_probs=28.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ...|.|..+||..+++|..||...+.+....-.+
T Consensus        16 ~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~   49 (65)
T COG2771          16 VAQGKSNKEIARILGISEETVKTHLRNIYRKLGV   49 (65)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            4579999999999999999999999988654433

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=95.53  E-value=0.025  Score=36.30  Aligned_cols=28  Identities=25%  Similarity=0.242  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.+-+.
T Consensus       134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~  161 (172)
T PRK12523        134 DGMGHAEIAERLGVSVSRVRQYLAQGLR  161 (172)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887554

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=95.53  E-value=0.022  Score=34.87  Aligned_cols=29  Identities=10%  Similarity=0.187  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+++.++|.+.|||++|+.+.++.-|..
T Consensus        48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR~K   76 (99)
T COG1342          48 EGLTQEEAALRMGISRQTFWRLLTSARKK   76 (99)
T ss_pred             hhccHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            68999999999999999999999987753

>PRK09483 response regulator; Provisional

Probab=95.52  E-value=0.019  Score=36.91  Aligned_cols=33  Identities=27%  Similarity=0.206  Sum_probs=29.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||.+|+||.+||...+++.+..=.+
T Consensus       161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v  193 (217)
T PRK09483        161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI  193 (217)
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            479999999999999999999999998875444

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=95.51  E-value=0.024  Score=34.67  Aligned_cols=29  Identities=17%  Similarity=0.337  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +|++..++|++||+|...|++++++.+..
T Consensus        71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~   99 (108)
T PF08765_consen   71 NGMNVRELARKYGLSERQIYRIIKRVRRR   99 (108)
T ss_dssp             -SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            49999999999999999999999998763

It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=95.51  E-value=0.025  Score=38.33  Aligned_cols=29  Identities=24%  Similarity=0.143  Sum_probs=26.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.+|||.+||.+++.+-+.
T Consensus       198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~  226 (236)
T PRK06986        198 QEELNLKEIGAVLGVSESRVSQIHSQAIK  226 (236)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            47999999999999999999999887654

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=95.50  E-value=0.011  Score=37.00  Aligned_cols=26  Identities=15%  Similarity=0.093  Sum_probs=23.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|+|..++|++.|||.+++++|.+
T Consensus        15 ~~~Glsq~eLA~~~Gis~~~is~iE~   40 (120)
T PRK13890         15 DERHMTKKELSERSGVSISFLSDLTT   40 (120)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35799999999999999999999874

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=95.49  E-value=0.026  Score=36.54  Aligned_cols=28  Identities=14%  Similarity=0.239  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (186)
T PRK05602        143 QGLSNIEAAAVMDISVDALESLLARGRR  170 (186)
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            6999999999999999999999888764

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=95.49  E-value=0.025  Score=39.06  Aligned_cols=28  Identities=21%  Similarity=0.248  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|-+.
T Consensus       176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~  203 (244)
T TIGR03001       176 DGLSMDRIGAMYQVHRSTVSRWVAQARE  203 (244)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999888765

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=95.48  E-value=0.025  Score=36.85  Aligned_cols=28  Identities=14%  Similarity=0.140  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|+|.+||...+.|-+.
T Consensus       146 ~g~s~~EIA~~lgis~~tV~~~l~Rar~  173 (191)
T PRK12520        146 LELETEEICQELQITATNAWVLLYRARM  173 (191)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999887654

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=95.48  E-value=0.028  Score=35.50  Aligned_cols=28  Identities=21%  Similarity=0.071  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       127 ~~~s~~eIA~~lgis~~tv~~~l~Rar~  154 (161)
T PRK12541        127 YGFSYKEIAEMTGLSLAKVKIELHRGRK  154 (161)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988765

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=95.48  E-value=0.027  Score=36.20  Aligned_cols=28  Identities=25%  Similarity=0.245  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.++|...+.|.+.
T Consensus       151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~  178 (187)
T PRK09641        151 EDLSLKEISEILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999988764

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=95.47  E-value=0.064  Score=35.85  Aligned_cols=45  Identities=13%  Similarity=0.027  Sum_probs=36.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      .+..++|++||||.++|.--+++....|=|...|..|-.....+.
T Consensus        35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~   79 (221)
T PRK11414         35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSK   79 (221)
T ss_pred             cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCH
Confidence            577889999999999999999999999999887766544333443

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=95.47  E-value=0.027  Score=38.90  Aligned_cols=36  Identities=19%  Similarity=0.351  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+++|+++|||+|+++.+.+.|=+.-.+
T Consensus        25 ~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~   60 (263)
T PRK09834         25 GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA   60 (263)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            358999999999999999999999999999997544

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=95.47  E-value=0.016  Score=37.77  Aligned_cols=25  Identities=20%  Similarity=0.250  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|+|..++|.++|||+++|++|-+
T Consensus        36 ~lGmTq~eLAerlGVS~~tIs~iE~   60 (150)
T TIGR02612        36 ALGMSGAQLAGRLGVTPQRVEALEK   60 (150)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            3699999999999999999999974

Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=95.46  E-value=0.025  Score=38.37  Aligned_cols=27  Identities=15%  Similarity=0.206  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|+|..+||+.+|||.+||.+++.+-+
T Consensus       197 eg~s~~EIA~~Lgis~~tV~~~l~ra~  223 (234)
T TIGR02835       197 TEKTQKEVADMLGISQSYISRLEKRIL  223 (234)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            689999999999999999999987644

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=95.45  E-value=0.02  Score=39.41  Aligned_cols=38  Identities=26%  Similarity=0.352  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ..++..++|+.|+||.+||.|.++...+.|.+.-. .||
T Consensus        17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~-~Gg   54 (240)
T PRK10411         17 TSLTTEALAEQLNVSKETIRRDLNELQTQGKILRN-HGR   54 (240)
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe-cCe
Confidence            34899999999999999999999999998888643 444

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=95.43  E-value=0.015  Score=29.55  Aligned_cols=25  Identities=16%  Similarity=0.117  Sum_probs=19.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ++.++|+.+|||+.|+..|-+.    |-+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~----Gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYERE----GLL   25 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHT----TSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHHC----CCC
Confidence            4679999999999999887554    877

One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=95.41  E-value=0.028  Score=36.89  Aligned_cols=28  Identities=21%  Similarity=0.198  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..+|+|.+||...+.|.+.
T Consensus       143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (188)
T PRK12517        143 GGFSGEEIAEILDLNKNTVMTRLFRARN  170 (188)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999988765

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=95.39  E-value=0.029  Score=36.17  Aligned_cols=28  Identities=25%  Similarity=0.248  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.+-+.
T Consensus       146 ~g~s~~eIA~~l~is~~tV~~~l~ra~~  173 (184)
T PRK12512        146 EGASIKETAAKLSMSEGAVRVALHRGLA  173 (184)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999887654

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=95.39  E-value=0.025  Score=38.45  Aligned_cols=35  Identities=11%  Similarity=0.087  Sum_probs=30.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ...|++..+||..|+||.+||...+++..+.-.+.
T Consensus       145 LAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV~  179 (198)
T PRK15201        145 IASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK  179 (198)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            35799999999999999999999999998876553

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=95.38  E-value=0.031  Score=35.96  Aligned_cols=29  Identities=24%  Similarity=0.244  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||+|.+||..++.|-+.
T Consensus       152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       152 LEGLSYEDIARIMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37999999999999999999999988765

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=95.37  E-value=0.026  Score=36.29  Aligned_cols=33  Identities=9%  Similarity=0.166  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..+||..+|+|+.||+|.++++++.|-+.-.
T Consensus       144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~  176 (193)
T TIGR03697       144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH  176 (193)
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            689999999999999999999999999988654

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

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

Probab=95.37  E-value=0.029  Score=38.31  Aligned_cols=34  Identities=9%  Similarity=0.153  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      .+++..|||+++|+++|||+|+++-+.+.|=+..
T Consensus        23 ~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        23 PRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            5699999999999999999999999999999974

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.

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=95.36  E-value=0.033  Score=32.91  Aligned_cols=28  Identities=21%  Similarity=0.315  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhc-cCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLR-VSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~-VS~stv~r~~~r~r~   31 (77)
                      .|+|-.+|++.|| .++|||+.-+++..+
T Consensus        43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~   71 (90)
T cd06571          43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEE   71 (90)
T ss_pred             hCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence            4899999999999 999999999998765

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=95.35  E-value=0.031  Score=36.13  Aligned_cols=28  Identities=14%  Similarity=0.154  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.|-+.
T Consensus       132 e~~s~~EIA~~lgis~~tV~~~l~ra~~  159 (179)
T PRK12543        132 HDYSQEEIAQLLQIPIGTVKSRIHAALK  159 (179)
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7999999999999999999998877653

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=95.35  E-value=0.03  Score=36.65  Aligned_cols=28  Identities=18%  Similarity=0.177  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.+|||.++|..++.|-+.
T Consensus       157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~~  184 (194)
T PRK09646        157 GGLTYREVAERLAVPLGTVKTRMRDGLI  184 (194)
T ss_pred             cCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence            7899999999999999999999988664

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=95.33  E-value=0.032  Score=36.46  Aligned_cols=30  Identities=17%  Similarity=0.139  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..||+|.+||...+.|-++.
T Consensus       125 ~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~  154 (182)
T PRK12540        125 ASGFSYEDAAAICGCAVGTIKSRVNRARSK  154 (182)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            379999999999999999999998876653

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=95.32  E-value=0.03  Score=37.41  Aligned_cols=36  Identities=17%  Similarity=0.175  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..++|+.|++|++||++.+++..+.|-+...+
T Consensus       156 g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~  191 (203)
T TIGR01884       156 GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG  191 (203)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            357999999999999999999999999999997654

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.

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=95.31  E-value=0.03  Score=37.15  Aligned_cols=28  Identities=21%  Similarity=0.190  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||..++.+-+.
T Consensus       168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~  195 (206)
T PRK12526        168 QELSQEQLAQQLNVPLGTVKSRLRLALA  195 (206)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999999887654

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=95.31  E-value=0.032  Score=36.53  Aligned_cols=28  Identities=21%  Similarity=0.254  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||+|.+||...+.|-+.
T Consensus       146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~  173 (188)
T TIGR02943       146 LGFESDEICQELEISTSNCHVLLYRARL  173 (188)
T ss_pred             hCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887654

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=95.30  E-value=0.017  Score=40.99  Aligned_cols=27  Identities=22%  Similarity=0.218  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .||+..+||..+|||++||..|-+|+-
T Consensus        18 ~gmk~~dIAeklGvspntiksWKrr~g   44 (279)
T COG5484          18 KGMKLKDIAEKLGVSPNTIKSWKRRDG   44 (279)
T ss_pred             hhccHHHHHHHhCCChHHHHHHHHhcC
Confidence            689999999999999999999998864

>PRK09954 putative kinase; Provisional

Probab=95.30  E-value=0.023  Score=40.59  Aligned_cols=30  Identities=20%  Similarity=0.283  Sum_probs=28.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +|..++|+.|+||++||.+.+++.++.|-+
T Consensus        18 ~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954         18 IQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            899999999999999999999999999987

>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species

Probab=95.29  E-value=0.022  Score=38.16  Aligned_cols=35  Identities=20%  Similarity=0.280  Sum_probs=30.7

Q ss_pred             CccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         1 l~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +|..| .+-.+||..+|||.+.|.|.-++|...++-
T Consensus        14 yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~s   49 (181)
T PF04645_consen   14 YFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSEDS   49 (181)
T ss_pred             HHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCCc
Confidence            36788 999999999999999999999998876554

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=95.29  E-value=0.033  Score=35.11  Aligned_cols=28  Identities=21%  Similarity=0.254  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||+|.+||...+.|-+.
T Consensus       120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~  147 (159)
T PRK12527        120 EGLSHQQIAEHLGISRSLVEKHIVNAMK  147 (159)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999887553

>PRK05572 sporulation sigma factor SigF; Validated

Probab=95.28  E-value=0.032  Score=38.24  Aligned_cols=29  Identities=14%  Similarity=0.190  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||+++|+++.++-..
T Consensus       216 ~~~~s~~eIA~~lgis~~~V~~~~~ral~  244 (252)
T PRK05572        216 FKDKTQSEVAKRLGISQVQVSRLEKKILK  244 (252)
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37899999999999999999999887553

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=95.26  E-value=0.033  Score=34.28  Aligned_cols=29  Identities=17%  Similarity=0.259  Sum_probs=22.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .+.+|..+||..+|||...|+.+++|-..
T Consensus        31 ~eDlSlsEIAe~~~iSRqaV~d~ikr~~~   59 (101)
T PF04297_consen   31 EEDLSLSEIAEELGISRQAVYDSIKRAEK   59 (101)
T ss_dssp             TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46789999999999999999999999653

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=95.25  E-value=0.035  Score=36.01  Aligned_cols=28  Identities=18%  Similarity=0.165  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||+|.+||...+.|.++
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6999999999999999999998888765

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=95.24  E-value=0.035  Score=37.26  Aligned_cols=29  Identities=17%  Similarity=0.109  Sum_probs=26.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.++|.+++.+-++
T Consensus       189 ~~~~s~~eIA~~lgis~~tV~~~~~ra~~  217 (224)
T TIGR02479       189 YEELNLKEIGEVLGLTESRVSQIHSQALK  217 (224)
T ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999887654

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=95.23  E-value=0.022  Score=34.46  Aligned_cols=26  Identities=19%  Similarity=0.293  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .|-...++|+.+|||++|+++.+++|
T Consensus        67 ~~gn~s~AAr~LGIsRsTL~rKLkr~   92 (95)
T PRK00430         67 TRGNQTRAALMLGINRGTLRKKLKKY   92 (95)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            45678899999999999999999986

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=95.23  E-value=0.035  Score=36.00  Aligned_cols=28  Identities=14%  Similarity=0.144  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       146 ~g~s~~eIA~~lgis~~tV~~~l~ra~~  173 (184)
T PRK12539        146 EGLSVAEAATRSGMSESAVKVSVHRGLK  173 (184)
T ss_pred             cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999987654

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=95.22  E-value=0.037  Score=38.51  Aligned_cols=35  Identities=14%  Similarity=0.107  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..|||+++|+++|||+|+++-+.+.|-+.--
T Consensus        39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~   73 (271)
T PRK10163         39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD   73 (271)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            46899999999999999999999999999999543

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=95.22  E-value=0.036  Score=36.29  Aligned_cols=28  Identities=18%  Similarity=0.205  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..+|||.+||...+.|.+.
T Consensus       169 e~~s~~EIA~~lgis~~tV~~~l~rar~  196 (208)
T PRK08295        169 DGKSYQEIAEELNRHVKSIDNALQRVKR  196 (208)
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6899999999999999999998887664

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=95.21  E-value=0.035  Score=37.58  Aligned_cols=27  Identities=26%  Similarity=0.251  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +|+|..+||..+|||.+||++++.+-+
T Consensus       194 e~~S~~EIA~~lgis~~tV~~~~~rA~  220 (233)
T PRK05803        194 KEKTQREIAKALGISRSYVSRIEKRAL  220 (233)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            789999999999999999999987654

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=95.20  E-value=0.038  Score=35.51  Aligned_cols=28  Identities=29%  Similarity=0.345  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.+|||.+||...+.|-+.
T Consensus       134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (172)
T PRK09651        134 DGLTYSEIAHKLGVSVSSVKKYVAKATE  161 (172)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999987654

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=95.18  E-value=0.074  Score=36.19  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=33.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      +-.++|++||||.++|.--+++....|=|..+|.+|-
T Consensus        36 sE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~   72 (254)
T PRK09464         36 PERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGT   72 (254)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCcee
Confidence            6789999999999999999999999999988876553

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=95.17  E-value=0.028  Score=37.75  Aligned_cols=34  Identities=15%  Similarity=0.205  Sum_probs=31.1

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|++||||..||.+-+....+.|-+..++.
T Consensus        34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G   67 (238)
T TIGR02325        34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG   67 (238)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            6689999999999999999999999999987753

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.

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=95.16  E-value=0.036  Score=36.67  Aligned_cols=27  Identities=19%  Similarity=0.145  Sum_probs=24.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|+|..+||..||+|.+||...+.|-+
T Consensus       154 eg~s~~EIA~~lgis~~tVk~~l~RAr  180 (201)
T PRK12545        154 LDFEIDDICTELTLTANHCSVLLYRAR  180 (201)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            799999999999999999998777644

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=95.15  E-value=0.039  Score=35.41  Aligned_cols=28  Identities=21%  Similarity=0.269  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|||.+||.+-+.|.+.
T Consensus       155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~  182 (189)
T TIGR02984       155 EGLSFAEVAERMDRSEGAVSMLWVRGLA  182 (189)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999888664

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=95.14  E-value=0.037  Score=37.82  Aligned_cols=28  Identities=14%  Similarity=0.230  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~  213 (233)
T PRK12538        186 ENMSNGEIAEVMDTTVAAVESLLKRGRQ  213 (233)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7999999999999999999999888664

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=95.13  E-value=0.041  Score=35.70  Aligned_cols=28  Identities=14%  Similarity=0.156  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|||.+||...+.|-+.
T Consensus       154 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~  181 (189)
T PRK09648        154 VGLSAEETAEAVGSTPGAVRVAQHRALA  181 (189)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999988654

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=95.13  E-value=0.039  Score=36.92  Aligned_cols=28  Identities=14%  Similarity=0.135  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||+|.+||...+.|-+.
T Consensus       163 ~g~s~~EIAe~lgis~~tV~~~l~RAr~  190 (206)
T PRK12544        163 IELETNEICHAVDLSVSNLNVLLYRARL  190 (206)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6999999999999999999999887664

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=95.10  E-value=0.042  Score=35.74  Aligned_cols=28  Identities=4%  Similarity=-0.045  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||+.||||.+||...+.|-+.
T Consensus       146 ~~~s~~eIA~~lgis~~tV~~~l~Rar~  173 (189)
T PRK12515        146 HEKSVEEVGEIVGIPESTVKTRMFYARK  173 (189)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7899999999999999999988777654

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=95.10  E-value=0.023  Score=37.32  Aligned_cols=25  Identities=16%  Similarity=0.227  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+++|||++|+++|.+
T Consensus        18 ~~glt~~elA~~~gis~~~is~~E~   42 (185)
T PRK09943         18 QQGLSQRRAAELSGLTHSAISTIEQ   42 (185)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4799999999999999999999974

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=95.10  E-value=0.03  Score=36.77  Aligned_cols=33  Identities=18%  Similarity=0.090  Sum_probs=28.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||++++||.+||...+++..+.=.+
T Consensus       163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v  195 (216)
T PRK10840        163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV  195 (216)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            479999999999999999999999888765444

>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ

Probab=95.10  E-value=0.023  Score=38.87  Aligned_cols=33  Identities=24%  Similarity=0.302  Sum_probs=27.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~   36 (77)
                      +.| |...+|+.++||+++|++.+++..+. |.--
T Consensus        16 ~~g-S~s~AA~~L~isq~avS~~I~~LE~~lg~~L   49 (300)
T TIGR02424        16 RQG-SVKRAAEALHITQPAVSKTLRELEEILGTPL   49 (300)
T ss_pred             HhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence            455 88999999999999999999999854 4433

Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.

>TIGR00180 parB_part ParB-like partition proteins

Probab=95.08  E-value=0.028  Score=37.17  Aligned_cols=27  Identities=7%  Similarity=0.192  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|++..+||+.||+|.++|++.++-..
T Consensus       119 ~g~s~~~iA~~lg~s~~~V~r~l~l~~  145 (187)
T TIGR00180       119 FSMTQEDLAKKIGKSRAHITNLLRLLK  145 (187)
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHHc
Confidence            589999999999999999999998743

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=95.07  E-value=0.042  Score=36.18  Aligned_cols=30  Identities=23%  Similarity=0.173  Sum_probs=26.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..||||.+||...+.|-+..
T Consensus       127 ~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~  156 (188)
T PRK12546        127 ASGFSYEEAAEMCGVAVGTVKSRANRARAR  156 (188)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            379999999999999999999999887653

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=95.05  E-value=0.034  Score=36.31  Aligned_cols=32  Identities=22%  Similarity=0.340  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus       169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~  200 (211)
T PRK11753        169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLISA  200 (211)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            56789999999999999999999999997753

>PRK13348 chromosome replication initiation inhibitor protein; Provisional

Probab=95.05  E-value=0.024  Score=38.72  Aligned_cols=54  Identities=24%  Similarity=0.287  Sum_probs=36.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      +.| |...+|++++||+++|++.+++..+. |..--.+ +  ++-..|++ ...+.+.++
T Consensus        15 ~~g-s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R-~--r~i~lT~~-G~~l~~~a~   69 (294)
T PRK13348         15 ETG-SFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-G--RPCRPTPA-GQRLLRHLR   69 (294)
T ss_pred             HcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeec-C--CCCccChh-HHHHHHHHH
Confidence            455 88999999999999999999999854 4433332 3  23445554 344444443

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=95.04  E-value=0.038  Score=34.54  Aligned_cols=35  Identities=17%  Similarity=0.081  Sum_probs=30.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ..+|++..+||+.+++|..||..++++.+..-.+.
T Consensus       161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~  195 (211)
T PRK15369        161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVH  195 (211)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            35799999999999999999999999988876653

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=95.02  E-value=0.042  Score=35.98  Aligned_cols=28  Identities=14%  Similarity=0.137  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||..||||.+||...+.+.+.
T Consensus       156 eg~s~~EIA~~lgis~~tVk~rl~ra~~  183 (194)
T PRK12531        156 EELPHQQVAEMFDIPLGTVKSRLRLAVE  183 (194)
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            7999999999999999999988877654

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=95.02  E-value=0.032  Score=38.57  Aligned_cols=35  Identities=14%  Similarity=0.136  Sum_probs=30.3

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ...|++..+||++|+||.+||.+.+++..+.=.+.
T Consensus       155 ia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~  189 (217)
T PRK13719        155 YSFGFSHEYIAQLLNITVGSSKNKISEILKFFGIS  189 (217)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            35799999999999999999999999988765543

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=95.01  E-value=0.043  Score=36.32  Aligned_cols=28  Identities=14%  Similarity=0.110  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||...+.|-+.
T Consensus       148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~  175 (196)
T PRK12535        148 LGYTYEEAAKIADVRVGTIRSRVARARA  175 (196)
T ss_pred             hCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999876554

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=94.99  E-value=0.11  Score=34.79  Aligned_cols=45  Identities=9%  Similarity=0.115  Sum_probs=37.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      .+..++|++||||.+.|.--+++....|=|...|..|-.-+..+.
T Consensus        31 L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~   75 (224)
T PRK11534         31 LRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSE   75 (224)
T ss_pred             CCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCH
Confidence            577899999999999999999999999999877766554444443

>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional

Probab=94.99  E-value=0.025  Score=38.95  Aligned_cols=33  Identities=12%  Similarity=0.077  Sum_probs=27.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ++.| |...+|++++||+++|++-+++..+.=.+
T Consensus        13 ~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~   45 (305)
T PRK11151         13 AEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGV   45 (305)
T ss_pred             HHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence            3556 89999999999999999999999865433

>TIGR00498 lexA SOS regulatory protein LexA

Probab=94.97  E-value=0.042  Score=36.34  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhccC-HHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVS-HGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+.+++|+.|++| .+||++.+++..+.|-+....
T Consensus        26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498        26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence            5677999999998 999999999999999997653

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=94.96  E-value=0.16  Score=35.83  Aligned_cols=66  Identities=9%  Similarity=-0.010  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .|+|..+||+.+|+|.++|...+.|-++.=.- .|+      .....+++.+.+.++++...+--+..|.+.|
T Consensus       133 ~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~------~~~~~~~~~~~~~~f~~a~~~gd~~~l~~ll  199 (290)
T PRK09635        133 FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIA------ASVEPAQHRVVTRAFIEACSNGDLDTLLEVL  199 (290)
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCC------CCCChHHHHHHHHHHHHHHHhCCHHHHHHHh
Confidence            68999999999999999999999988764321 121      1122234556666666655444455555444

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=94.95  E-value=0.046  Score=36.78  Aligned_cols=28  Identities=14%  Similarity=0.154  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|++..+||..||||+++|+++.++-..
T Consensus       198 ~~~t~~eIA~~lgis~~~V~~~~~~al~  225 (231)
T TIGR02885       198 KDKTQTEVANMLGISQVQVSRLEKKVLK  225 (231)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6899999999999999999999887543

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=94.95  E-value=0.018  Score=39.88  Aligned_cols=23  Identities=30%  Similarity=0.244  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+..|||++||||-++.
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~   24 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLND   24 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcC
Confidence            36889999999999999999953

>PRK12684 transcriptional regulator CysB-like protein; Reviewed

Probab=94.95  E-value=0.023  Score=39.55  Aligned_cols=34  Identities=18%  Similarity=0.133  Sum_probs=28.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~   36 (77)
                      +.|-|...+|++++||+++|++.++++.+. |.--
T Consensus        14 ~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~L   48 (313)
T PRK12684         14 RQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEI   48 (313)
T ss_pred             HcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCee
Confidence            456799999999999999999999999854 4443

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=94.94  E-value=0.051  Score=37.52  Aligned_cols=38  Identities=16%  Similarity=0.302  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .|++..+||+++|+++|||+|++.-..+.|=+...+.+
T Consensus        18 ~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~   55 (246)
T COG1414          18 GGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED   55 (246)
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence            34789999999999999999999999999999877543

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=94.94  E-value=0.021  Score=40.77  Aligned_cols=27  Identities=11%  Similarity=0.066  Sum_probs=24.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|....++|++||||.+|.+|++++|
T Consensus       297 ~~~gn~~~aA~~LGIsR~tLyrklk~~  323 (326)
T PRK11608        297 QAKFNQKRAAELLGLTYHQLRALLKKH  323 (326)
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence            356688999999999999999999987

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=94.92  E-value=0.039  Score=35.85  Aligned_cols=31  Identities=16%  Similarity=0.255  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ++..+||..+|+|+.||+|.++++++.|-+.
T Consensus       150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        150 ATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            5788999999999999999999999999997

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=94.92  E-value=0.054  Score=37.40  Aligned_cols=43  Identities=19%  Similarity=0.273  Sum_probs=34.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc--cCCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKP   45 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~--~gg~~~   45 (77)
                      ..++|.-++|++||||..+|.+=+......|-|....  .|-+||
T Consensus        23 ~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP   67 (218)
T COG2345          23 SGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRP   67 (218)
T ss_pred             cCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCC
Confidence            3569999999999999999999999999999664333  333455

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=94.91  E-value=0.052  Score=37.28  Aligned_cols=35  Identities=14%  Similarity=0.229  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..+||+++|+++|||+|+++-+.+.|=+...
T Consensus        27 ~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~   61 (257)
T PRK15090         27 REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE   61 (257)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            35899999999999999999999999999998654

>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences

Probab=94.90  E-value=0.012  Score=33.03  Aligned_cols=22  Identities=18%  Similarity=0.235  Sum_probs=17.0

Q ss_pred             CHHHHHHHhccCHHHHH-HHHHH
Q psy15513          7 RPCVISRQLRVSHGCVS-KILNR   28 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~-r~~~r   28 (77)
                      +..+.|+.+|||++|++ .|.+|
T Consensus        14 ~~~~lA~~lgis~st~s~~~~~r   36 (66)
T PF07022_consen   14 SDKELAERLGISKSTLSNNWKKR   36 (66)
T ss_dssp             SCHHHHCCTT--HHHHH-HHHHS
T ss_pred             CHHHHHHHhCcCHHHhhHHHHhC
Confidence            55699999999999999 78764

The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.

>PRK03601 transcriptional regulator HdfR; Provisional

Probab=94.88  E-value=0.031  Score=38.16  Aligned_cols=32  Identities=13%  Similarity=0.095  Sum_probs=27.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v   35 (77)
                      +.| |...+|++++||+++|++.+++..+ -|.-
T Consensus        14 ~~g-s~s~AA~~L~isqpavS~~I~~LE~~lG~~   46 (275)
T PRK03601         14 RTR-HFGRAAESLYLTQSAVSFRIRQLENQLGVN   46 (275)
T ss_pred             HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCc
Confidence            445 8889999999999999999999986 4443

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=94.87  E-value=0.048  Score=36.86  Aligned_cols=27  Identities=15%  Similarity=0.133  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|+|..+||..||||.+||...+.|.+
T Consensus       164 ~g~s~~EIAe~lgis~~tVk~~l~Rar  190 (231)
T PRK11922        164 EELSVEETAQALGLPEETVKTRLHRAR  190 (231)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            799999999999999999998877654

>PRK11569 transcriptional repressor IclR; Provisional

Probab=94.86  E-value=0.054  Score=37.70  Aligned_cols=35  Identities=17%  Similarity=0.288  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..+||+++|+++|||+|++.-+.+.|=+...
T Consensus        42 ~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~   76 (274)
T PRK11569         42 GSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV   76 (274)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            46899999999999999999999999999999744

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=94.85  E-value=0.043  Score=36.75  Aligned_cols=33  Identities=9%  Similarity=0.011  Sum_probs=31.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||+.|++|..||.+.+.+....|-+
T Consensus       176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~  208 (239)
T PRK10430        176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHIL  208 (239)
T ss_pred             CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence            379999999999999999999999999999987

>PRK11482 putative DNA-binding transcriptional regulator; Provisional

Probab=94.85  E-value=0.031  Score=39.14  Aligned_cols=46  Identities=9%  Similarity=-0.026  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++.+++..+ -|.---...+  +.-.+|++
T Consensus        42 e~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~--r~v~lT~~   88 (317)
T PRK11482         42 VHK-GIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKG--QGVTPTAY   88 (317)
T ss_pred             HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCcceEecC--CCccCCHH
Confidence            445 8899999999999999999999985 4544333222  33345553

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=94.84  E-value=0.042  Score=28.81  Aligned_cols=23  Identities=30%  Similarity=0.343  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      -|..++|+.||+++++|++.++-
T Consensus        18 ~S~~eAa~~lg~~~~~I~~~~~~   40 (53)
T smart00497       18 SSIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             cCHHHHHHHhCCCHHHHHHHHhC
Confidence            37899999999999999988774

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor

Probab=94.81  E-value=0.033  Score=37.91  Aligned_cols=33  Identities=21%  Similarity=0.205  Sum_probs=27.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ++.| |...+|++|+||+++|++-+++..+.=.+
T Consensus        13 ~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~   45 (291)
T TIGR03418        13 ARLA-SFTAAARELGSTQPAVSQQVKRLEEELGT   45 (291)
T ss_pred             HHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence            3456 88999999999999999999999854433

Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=94.81  E-value=0.029  Score=27.90  Aligned_cols=20  Identities=30%  Similarity=0.260  Sum_probs=17.9

Q ss_pred             CCHHHHHHHhccCHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~   25 (77)
                      -|.+++|+-|+++++++++.
T Consensus        17 ~Si~eAa~~l~i~~~~I~~~   36 (37)
T PF07453_consen   17 DSIREAARYLGISHSTISKY   36 (37)
T ss_pred             cCHHHHHHHhCCCHHHHHHh
Confidence            37899999999999999875

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=94.81  E-value=0.2  Score=34.94  Aligned_cols=29  Identities=21%  Similarity=0.170  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..|||+.+|+|.++|...+.|-+..
T Consensus       130 ~g~s~~EIA~~lg~s~~tVk~~l~RAr~~  158 (293)
T PRK09636        130 FGVPFDEIASTLGRSPAACRQLASRARKH  158 (293)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            68999999999999999999999887754

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=94.81  E-value=0.04  Score=37.63  Aligned_cols=37  Identities=19%  Similarity=0.122  Sum_probs=33.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      +-+++|++||||.++|.--+++....|=|...+..|-
T Consensus        35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~   71 (257)
T PRK10225         35 PEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGI   71 (257)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEE
Confidence            5789999999999999999999999999988876554

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=94.79  E-value=0.041  Score=36.70  Aligned_cols=33  Identities=21%  Similarity=0.370  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            678899999999999999999999999998854

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=94.78  E-value=0.055  Score=36.52  Aligned_cols=28  Identities=25%  Similarity=0.194  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|+|..+||+.+|+|.+||.+++.+-+.
T Consensus       193 e~~S~~EIAe~lgis~~tV~~~~~rAl~  220 (227)
T TIGR02846       193 RRKTQREIAKILGISRSYVSRIEKRALM  220 (227)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999877543

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=94.76  E-value=0.04  Score=32.46  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=33.2

Q ss_pred             ccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         2 ~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +..| ++..++|++|+.|.+.|.-.+.++...|.|+--
T Consensus        12 ~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv   49 (78)
T PRK15431         12 ALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_pred             HHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence            3456 899999999999999999999999999999644

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=94.74  E-value=0.055  Score=37.35  Aligned_cols=28  Identities=14%  Similarity=0.120  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.++|++++.+-+.
T Consensus       218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~  245 (256)
T PRK07408        218 HDLTQKEAAERLGISPVTVSRRVKKGLD  245 (256)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6899999999999999999999887654

>PRK11233 nitrogen assimilation transcriptional regulator; Provisional

Probab=94.73  E-value=0.031  Score=38.62  Aligned_cols=30  Identities=10%  Similarity=0.118  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +.| |...+|++|+||+++|++-++++.+.=
T Consensus        14 ~~~-S~s~AA~~L~isQ~avS~~I~~LE~~l   43 (305)
T PRK11233         14 DIG-SLTQAAEVLHIAQPALSQQVATLEGEL   43 (305)
T ss_pred             HcC-CHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence            455 899999999999999999999998543

>PRK12683 transcriptional regulator CysB-like protein; Reviewed

Probab=94.72  E-value=0.032  Score=38.83  Aligned_cols=31  Identities=16%  Similarity=0.149  Sum_probs=27.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +.|.|...+|++++||+++|++-+++..+.=
T Consensus        14 ~~~~S~s~AA~~L~isQpavS~~I~~LE~~l   44 (309)
T PRK12683         14 RQNFNLTEVANALYTSQSGVSKQIKDLEDEL   44 (309)
T ss_pred             HccCCHHHHHHHhcCCcHHHHHHHHHHHHHh
Confidence            4567999999999999999999999998543

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

Probab=94.72  E-value=0.067  Score=32.29  Aligned_cols=38  Identities=24%  Similarity=0.302  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ..+|..+|...+     .||.+||||-++.+.+-|-+..-..+
T Consensus        15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~   57 (116)
T cd07153          15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG   57 (116)
T ss_pred             CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC
Confidence            348999999888     79999999999999999998765543

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=94.72  E-value=0.024  Score=39.39  Aligned_cols=39  Identities=26%  Similarity=0.306  Sum_probs=33.7

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      +.| ++..++|++|+||..||.|=+....+.|-+.-- +||
T Consensus        16 ~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~-hGG   55 (253)
T COG1349          16 EKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV-HGG   55 (253)
T ss_pred             HcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE-eCC
Confidence            455 889999999999999999999999999988743 455

>PF14502 HTH_41: Helix-turn-helix domain

Probab=94.70  E-value=0.062  Score=28.94  Aligned_cols=36  Identities=25%  Similarity=0.330  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+..+.++.|+||.+||++-++-..+.|-+.=.++|
T Consensus         7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rG   42 (48)
T PF14502_consen    7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRG   42 (48)
T ss_pred             CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecC
Confidence            357789999999999999999999999988665554

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=94.70  E-value=0.047  Score=36.97  Aligned_cols=34  Identities=21%  Similarity=0.220  Sum_probs=29.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ..|+|..+||+.|++|.+||..++.+....-.+.
T Consensus       168 ~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~  201 (216)
T PRK10100        168 RIGASNNEIARSLFISENTVKTHLYNLFKKIAVK  201 (216)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            3599999999999999999999999987765553

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=94.68  E-value=0.044  Score=36.92  Aligned_cols=34  Identities=15%  Similarity=0.118  Sum_probs=31.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|+.||||..||.+-+....+.|-+..++.
T Consensus        27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G   60 (230)
T TIGR02018        27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQG   60 (230)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            6789999999999999999999999999987753

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.

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=94.67  E-value=0.05  Score=36.66  Aligned_cols=36  Identities=14%  Similarity=0.122  Sum_probs=32.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |-+++|++||||.+||..=+++....|=|...+..|
T Consensus        33 sE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G   68 (239)
T PRK04984         33 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   68 (239)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            678999999999999999999999999998776544

>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.67  E-value=0.036  Score=38.39  Aligned_cols=25  Identities=20%  Similarity=0.485  Sum_probs=21.8

Q ss_pred             HHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          9 CVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         9 ~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -.+|.+|++|+.|||+++++++..|
T Consensus       195 ~~VA~~L~iSr~TVY~YL~~~k~~~  219 (220)
T COG2964         195 NIVADRLGISRHTVYRYLRKFKAGG  219 (220)
T ss_pred             HHHHHHhCCChHHHHHHHHHhhcCC
Confidence            3579999999999999999987655

>PRK06424 transcription factor; Provisional

Probab=94.66  E-value=0.037  Score=35.91  Aligned_cols=25  Identities=4%  Similarity=0.089  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|+.++|+++|||+++|++|-+
T Consensus        95 ~~GLSQ~eLA~~iGvs~stIskiE~  119 (144)
T PRK06424         95 RLSMSQADLAAKIFERKNVIASIER  119 (144)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4799999999999999999999954

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=94.66  E-value=0.048  Score=36.73  Aligned_cols=32  Identities=25%  Similarity=0.268  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..+||..+|+|+.||+|.++++++.|-+.-
T Consensus       180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~  211 (230)
T PRK09391        180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGL  211 (230)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            57889999999999999999999999998863

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=94.65  E-value=0.048  Score=36.72  Aligned_cols=34  Identities=26%  Similarity=0.149  Sum_probs=30.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|++||||..||.+-++...+.|-|..++.
T Consensus        26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G   59 (233)
T TIGR02404        26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQG   59 (233)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            5688999999999999999999999999987653

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

>PRK09791 putative DNA-binding transcriptional regulator; Provisional

Probab=94.63  E-value=0.037  Score=38.02  Aligned_cols=36  Identities=22%  Similarity=0.134  Sum_probs=29.1

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCcc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPG   38 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk   38 (77)
                      ++.| |...+|+.++||+++|++-++++.+ .|..--.
T Consensus        17 ~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~   53 (302)
T PRK09791         17 ARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFF   53 (302)
T ss_pred             HHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEE
Confidence            3456 8899999999999999999999984 4554433

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=94.62  E-value=0.063  Score=36.75  Aligned_cols=29  Identities=14%  Similarity=0.127  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.++|.+++.+-++
T Consensus       219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       219 EENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47999999999999999999999877553

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional

Probab=94.61  E-value=0.038  Score=38.47  Aligned_cols=32  Identities=16%  Similarity=0.185  Sum_probs=27.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v   35 (77)
                      +.| |...+|++|+||+++||+-+++..+ -|.-
T Consensus        21 e~g-s~t~AA~~L~iSQpavS~~I~~LE~~lg~~   53 (319)
T PRK10216         21 QER-SVTKAAKRMNVTPSAVSKSLAKLRAWFDDP   53 (319)
T ss_pred             HhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Confidence            455 8899999999999999999999986 4443

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=94.61  E-value=0.072  Score=36.19  Aligned_cols=38  Identities=18%  Similarity=0.145  Sum_probs=33.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      +-+++|++||||.++|.--+++....|=|...|..|-.
T Consensus        33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~   70 (251)
T PRK09990         33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSF   70 (251)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeE
Confidence            67899999999999999999999999999888765543

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=94.58  E-value=0.051  Score=36.61  Aligned_cols=36  Identities=19%  Similarity=0.220  Sum_probs=30.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ...|+|-.+||.+|++|.+||+..+.+....=.+..
T Consensus       160 la~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~  195 (211)
T COG2197         160 LAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRN  195 (211)
T ss_pred             HHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCC
Confidence            458999999999999999999999988876555543

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=94.57  E-value=0.14  Score=34.49  Aligned_cols=50  Identities=18%  Similarity=0.145  Sum_probs=41.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR   55 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~   55 (77)
                      .+..++|.+||||...|..-+.+....|=|.-.|+.|-.-...+......
T Consensus        40 l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~e   89 (230)
T COG1802          40 LSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEARE   89 (230)
T ss_pred             ccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHH
Confidence            67889999999999999999999999999998888776655555444443

>PRK13698 plasmid-partitioning protein; Provisional

Probab=94.55  E-value=0.054  Score=39.39  Aligned_cols=60  Identities=7%  Similarity=0.037  Sum_probs=42.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA   65 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd   65 (77)
                      +.|++..++|+++|+|+++|++.++-..=-..+...   ...|..++..|...|..+...+++
T Consensus       174 ~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP~~vi~~---~~~p~~Ls~gharaL~~ll~~~~~  233 (323)
T PRK13698        174 EFAGNISALADAENISRKIITRCINTAKLPKSVVAL---FAHPGELSARSGEALQKAFTDKEE  233 (323)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHH---hhccCCCChhHHHHHHHHhhhCHH
Confidence            347899999999999999999999886543333221   234455666678888888766653

>PHA02517 putative transposase OrfB; Reviewed

Probab=94.53  E-value=0.094  Score=36.06  Aligned_cols=55  Identities=9%  Similarity=0.029  Sum_probs=36.2

Q ss_pred             hccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh-CCCCcHHHHHHHhh
Q psy15513         15 LRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE-NPAMFSWEIRDRLV   76 (77)
Q Consensus        15 f~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~-~pd~tl~El~~~L~   76 (77)
                      ||||.||.++|+++...     |.  +...+....++..+.|.++..+ +|......|.+.|.
T Consensus         1 l~vsrs~yY~~~~~~~~-----p~--~~~~~~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~   56 (277)
T PHA02517          1 LGIAPSTYYRCQQQRHH-----PD--KRRARAQHDDWLKSEILRVYDENHQVYGVRKVWRQLN   56 (277)
T ss_pred             CCCChHHHHHHHhccCC-----cc--hhhhhhhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            79999999999987321     21  1111112345567788888766 57778888887764

>PRK14999 histidine utilization repressor; Provisional

Probab=94.53  E-value=0.051  Score=36.90  Aligned_cols=33  Identities=12%  Similarity=0.105  Sum_probs=30.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |-+++|++||||..||.+-+....+.|-|.-++
T Consensus        38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   70 (241)
T PRK14999         38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ   70 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            678999999999999999999999999997665

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=94.52  E-value=0.05  Score=36.66  Aligned_cols=34  Identities=12%  Similarity=-0.012  Sum_probs=29.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .-.|++..+||..|+||..||.....+..+.=.+
T Consensus       146 l~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv  179 (207)
T PRK11475        146 MSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV  179 (207)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            3479999999999999999999999998775544

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=94.51  E-value=0.068  Score=36.74  Aligned_cols=27  Identities=15%  Similarity=0.235  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +|+|..+||..||||.++|+++.++-.
T Consensus       224 ~~~t~~eIA~~lgis~~~V~~~~~~al  250 (258)
T PRK08215        224 QGKTQMEVAEEIGISQAQVSRLEKAAL  250 (258)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            689999999999999999999987644

>PRK06474 hypothetical protein; Provisional

Probab=94.51  E-value=0.051  Score=36.04  Aligned_cols=33  Identities=15%  Similarity=0.280  Sum_probs=30.7

Q ss_pred             CCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +++.+++..+ +||++|||+-++.+.+.|-|..-
T Consensus        27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~   60 (178)
T PRK06474         27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHVV   60 (178)
T ss_pred             CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence            8999999999 79999999999999999998643

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=94.48  E-value=0.17  Score=34.00  Aligned_cols=38  Identities=13%  Similarity=0.144  Sum_probs=33.8

Q ss_pred             C-CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          6 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         6 ~-s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      . |-+++|++||||.++|.--+++....|=|...|..|-
T Consensus        30 LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~   68 (235)
T TIGR02812        30 LPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPT   68 (235)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCcc
Confidence            5 6789999999999999999999999999988875543

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.

>CHL00180 rbcR LysR transcriptional regulator; Provisional

Probab=94.47  E-value=0.037  Score=38.22  Aligned_cols=32  Identities=19%  Similarity=0.170  Sum_probs=27.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.| |...+|++++||+++|++.+++..+.=.+
T Consensus        18 e~g-s~s~AA~~L~isqpavS~~i~~LE~~lg~   49 (305)
T CHL00180         18 TEG-SFKKAAESLYISQPAVSLQIKNLEKQLNI   49 (305)
T ss_pred             HcC-CHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence            455 88999999999999999999999865444

>PRK12681 cysB transcriptional regulator CysB; Reviewed

Probab=94.47  E-value=0.13  Score=36.18  Aligned_cols=33  Identities=15%  Similarity=0.133  Sum_probs=27.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.|-|...+|++++||+++|++-+++..+.=.+
T Consensus        14 e~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~   46 (324)
T PRK12681         14 NHNLNVSATAEGLYTSQPGISKQVRMLEDELGI   46 (324)
T ss_pred             HccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence            455699999999999999999999999855444

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=94.46  E-value=0.066  Score=37.40  Aligned_cols=29  Identities=7%  Similarity=-0.014  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||||.+||..++.+-++
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlk  268 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVEALK  268 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            47999999999999999999999988664

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=94.42  E-value=0.077  Score=34.79  Aligned_cols=28  Identities=25%  Similarity=0.246  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..||||.+||..-+.|-+.
T Consensus       149 ~g~s~~EIA~~lg~s~~tV~~rl~rar~  176 (192)
T PRK09643        149 QGYSVADAARMLGVAEGTVKSRCARGRA  176 (192)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            7899999999999999999888766543

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=94.41  E-value=0.07  Score=29.13  Aligned_cols=24  Identities=17%  Similarity=0.108  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .++..++|+.||||..+..|..++
T Consensus        15 hlp~~eAA~~Lgv~~T~LKr~CR~   38 (52)
T PF02042_consen   15 HLPIKEAAKELGVSVTTLKRRCRR   38 (52)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            478899999999999999887654

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=94.41  E-value=0.054  Score=37.60  Aligned_cols=27  Identities=11%  Similarity=0.038  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|+|..+||+.||||..+|+++.++-.
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al  261 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEKNAM  261 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            589999999999999999997776643

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>PRK03837 transcriptional regulator NanR; Provisional

Probab=94.39  E-value=0.067  Score=35.97  Aligned_cols=37  Identities=11%  Similarity=0.066  Sum_probs=33.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      +-+++|.+||||.++|..-+++....|=|...+..|-
T Consensus        39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~G~   75 (241)
T PRK03837         39 SERELMAFFGVGRPAVREALQALKRKGLVQISHGERA   75 (241)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCce
Confidence            6789999999999999999999999999988765443

>PRK12680 transcriptional regulator CysB-like protein; Reviewed

Probab=94.39  E-value=0.044  Score=38.68  Aligned_cols=33  Identities=12%  Similarity=0.182  Sum_probs=27.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.+.|...+|++++||+++|++.+++..+.=.+
T Consensus        14 e~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~   46 (327)
T PRK12680         14 DAELNITLAAARVHATQPGLSKQLKQLEDELGF   46 (327)
T ss_pred             HccCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence            334589999999999999999999999855333

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=94.39  E-value=0.06  Score=36.74  Aligned_cols=37  Identities=22%  Similarity=0.277  Sum_probs=33.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      +-+++|++||||.++|.--+++....|=|...|.+|-
T Consensus        28 sE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~   64 (253)
T PRK10421         28 AERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGT   64 (253)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeE
Confidence            4689999999999999999999999999988876553

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=94.37  E-value=0.057  Score=36.66  Aligned_cols=34  Identities=9%  Similarity=0.153  Sum_probs=30.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-.++|+.||||..||.+-+....+.|-+..++.
T Consensus        37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G   70 (241)
T PRK10079         37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG   70 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            4578999999999999999999999999986653

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=94.32  E-value=0.041  Score=40.08  Aligned_cols=27  Identities=15%  Similarity=0.091  Sum_probs=24.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|....++|++||||.+|.+|.+++|
T Consensus       428 ~~~gn~~~aA~~LGisr~tL~rkl~~~  454 (457)
T PRK11361        428 QQEGNRTRTALMLGISRRALMYKLQEY  454 (457)
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            456688999999999999999999987

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=94.29  E-value=0.065  Score=33.82  Aligned_cols=31  Identities=23%  Similarity=0.101  Sum_probs=27.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -.|++..+||+++++|.+||...+++.++.=
T Consensus       150 ~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl  180 (196)
T PRK10360        150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKL  180 (196)
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999988753

>PRK09801 transcriptional activator TtdR; Provisional

Probab=94.27  E-value=0.053  Score=37.84  Aligned_cols=32  Identities=16%  Similarity=0.131  Sum_probs=26.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.| |...+|+.|+||+++|++-+++..+.=.+
T Consensus        19 ~~g-s~t~AA~~L~iSQpavS~~I~~LE~~LG~   50 (310)
T PRK09801         19 HSG-SFSAAAATLGQTPAFVTKRIQILENTLAT   50 (310)
T ss_pred             HcC-CHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence            344 78899999999999999999999854333

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=94.25  E-value=0.066  Score=36.53  Aligned_cols=37  Identities=16%  Similarity=0.116  Sum_probs=32.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      +-+++|++||||.++|.--+++....|=|...|..|-
T Consensus        34 sE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~   70 (253)
T PRK11523         34 AERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGI   70 (253)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCee
Confidence            3689999999999999999999999999987776554

>PRK10403 transcriptional regulator NarP; Provisional

Probab=94.25  E-value=0.061  Score=33.93  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=28.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      ..|++..+||+.+++|.+||...+++.++.=.
T Consensus       166 ~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~  197 (215)
T PRK10403        166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLN  197 (215)
T ss_pred             HCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            46899999999999999999999999887543

>PRK10094 DNA-binding transcriptional activator AllS; Provisional

Probab=94.24  E-value=0.052  Score=37.77  Aligned_cols=30  Identities=13%  Similarity=0.135  Sum_probs=25.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +.| |..++|++++||+++|++.+++..+.=
T Consensus        15 e~g-s~s~AA~~L~iSQpavS~~I~~LE~~l   44 (308)
T PRK10094         15 ETG-SFSKAAERLCKTTATISYRIKLLEENT   44 (308)
T ss_pred             HhC-CHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence            445 889999999999999999999998543

>PRK10341 DNA-binding transcriptional activator TdcA; Provisional

Probab=94.24  E-value=0.051  Score=37.67  Aligned_cols=29  Identities=21%  Similarity=0.283  Sum_probs=25.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      |...+|++|+||+++|++-+++..+.=.+
T Consensus        23 s~s~AA~~L~iSQpavS~~I~~LE~~lg~   51 (312)
T PRK10341         23 SIGSAAKELGLTQPAVSKIINDIEDYFGV   51 (312)
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence            88999999999999999999999865444

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=94.23  E-value=0.068  Score=38.92  Aligned_cols=36  Identities=17%  Similarity=0.188  Sum_probs=32.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.|+||.+||.+-+.+..+.|-+..++..|
T Consensus        31 s~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~~G   66 (431)
T PRK15481         31 PVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNG   66 (431)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence            679999999999999999999999999998776544

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=94.21  E-value=0.096  Score=36.91  Aligned_cols=36  Identities=14%  Similarity=0.377  Sum_probs=33.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+..++|.+||||+++|..=++++.+.|-+..++-|
T Consensus       199 lse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG  234 (251)
T TIGR02787       199 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG  234 (251)
T ss_pred             ccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            899999999999999999999999999999988734

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.

>PRK12679 cbl transcriptional regulator Cbl; Reviewed

Probab=94.20  E-value=0.048  Score=37.99  Aligned_cols=34  Identities=18%  Similarity=0.181  Sum_probs=28.4

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v   35 (77)
                      ++.|-|...+|++++||+++|++-+++..+. |..
T Consensus        13 ~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~   47 (316)
T PRK12679         13 ARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIE   47 (316)
T ss_pred             HHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCE
Confidence            3456699999999999999999999999854 443

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=94.20  E-value=0.064  Score=36.53  Aligned_cols=32  Identities=25%  Similarity=0.210  Sum_probs=28.2

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ...|++..+||..|+||.+||...+++.+..=
T Consensus       183 ~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl  214 (232)
T TIGR03541       183 TALGRRQADIAAILGISERTVENHLRSARRKL  214 (232)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            35799999999999999999999999987543

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=94.18  E-value=0.04  Score=38.22  Aligned_cols=39  Identities=15%  Similarity=0.230  Sum_probs=33.0

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      +.| ++..++|+.|+||..||.|=++...+.|-+.-. +||
T Consensus        16 ~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~-~Gg   55 (256)
T PRK10434         16 KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT-YGG   55 (256)
T ss_pred             HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-ECC
Confidence            345 889999999999999999999999999987643 454

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=94.17  E-value=0.089  Score=36.61  Aligned_cols=29  Identities=17%  Similarity=0.241  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|++..+||..||||.++|.+++++-..
T Consensus       229 ~~~~t~~EIA~~lgis~~~V~~~~~ral~  257 (264)
T PRK07122        229 FESMTQTQIAERVGISQMHVSRLLAKTLA  257 (264)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36999999999999999999999887654

>PRK14997 LysR family transcriptional regulator; Provisional

Probab=94.16  E-value=0.058  Score=36.95  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=32.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++-+++..+. |..--.+.  +++-.+|++
T Consensus        15 ~~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~--~r~~~lT~~   61 (301)
T PRK14997         15 EEG-GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRT--TRQFNVTEV   61 (301)
T ss_pred             HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeec--cCcceEcHh
Confidence            344 78899999999999999999999854 43333322  233445554

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=94.14  E-value=0.09  Score=36.35  Aligned_cols=28  Identities=25%  Similarity=0.128  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|++..+||..||||.++|.+++.+-+.
T Consensus       220 e~~t~~EIA~~lgis~~~V~~~~~ral~  247 (257)
T PRK05911        220 EELVLKEIGKILGVSESRVSQIHSKALL  247 (257)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6899999999999999999999887654

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

Probab=94.09  E-value=0.07  Score=35.17  Aligned_cols=36  Identities=22%  Similarity=0.258  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ++..++|..+++|.+||+|.++.+.+.+=+...+.|
T Consensus        76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G  111 (165)
T PF05732_consen   76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNG  111 (165)
T ss_pred             eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCC
Confidence            478899999999999999999999999877655433

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=94.08  E-value=0.087  Score=27.31  Aligned_cols=23  Identities=26%  Similarity=0.294  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .++|.++||++.|||++++++..
T Consensus        15 ~~~s~~~Ia~~~gvs~~~~y~~f   37 (47)
T PF00440_consen   15 EAVSIRDIARRAGVSKGSFYRYF   37 (47)
T ss_dssp             TTSSHHHHHHHHTSCHHHHHHHC
T ss_pred             HhCCHHHHHHHHccchhhHHHHc
Confidence            46899999999999999999764

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>PRK10837 putative DNA-binding transcriptional regulator; Provisional

Probab=94.06  E-value=0.051  Score=36.82  Aligned_cols=30  Identities=23%  Similarity=0.204  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +.| |...+|++++||+++|++.+++..+.=
T Consensus        16 e~~-s~t~AA~~L~isqpavS~~I~~LE~~l   45 (290)
T PRK10837         16 KSG-STTQASVMLALSQSAVSAALTDLEGQL   45 (290)
T ss_pred             HcC-CHHHHHHHhCCCccHHHHHHHHHHHHh
Confidence            445 889999999999999999999998543

>PRK10651 transcriptional regulator NarL; Provisional

Probab=94.05  E-value=0.087  Score=33.33  Aligned_cols=33  Identities=18%  Similarity=0.297  Sum_probs=29.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||+.++||..||...+++.+..=.+
T Consensus       168 ~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~  200 (216)
T PRK10651        168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKL  200 (216)
T ss_pred             HcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence            478999999999999999999999999876544

>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []

Probab=94.03  E-value=0.12  Score=34.59  Aligned_cols=40  Identities=20%  Similarity=0.187  Sum_probs=34.5

Q ss_pred             CCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         6 ~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|..++|.++ |+|.+|+.+.+.+..+.|=+..+..+.+++
T Consensus        71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkR  111 (177)
T PF03428_consen   71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKR  111 (177)
T ss_pred             cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCc
Confidence            4778999999 999999999999999999998876544444

They may be involved in plasmid replication and stabilisation functions.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=94.03  E-value=0.062  Score=37.50  Aligned_cols=34  Identities=21%  Similarity=0.131  Sum_probs=29.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ..|+|..+||+.|+||.+||...+++.++.=.+.
T Consensus       203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~  236 (247)
T TIGR03020       203 RDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVR  236 (247)
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            4799999999999999999999999988755443

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK11557 putative DNA-binding transcriptional regulator; Provisional

Probab=94.00  E-value=0.063  Score=37.02  Aligned_cols=25  Identities=16%  Similarity=0.222  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+|..++|++.+||.+||.|..++.
T Consensus        30 ~~si~elA~~~~vS~aTv~Rf~kkl   54 (278)
T PRK11557         30 HLSSQQLANEAGVSQSSVVKFAQKL   54 (278)
T ss_pred             hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence            4899999999999999999998864

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=94.00  E-value=0.1  Score=35.74  Aligned_cols=29  Identities=17%  Similarity=0.130  Sum_probs=25.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -+|+|..+||..||||.++|..++.+-+.
T Consensus       215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~  243 (251)
T PRK07670        215 KEELTLTEIGQVLNLSTSRISQIHSKALF  243 (251)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37899999999999999999999887654

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=93.94  E-value=0.086  Score=33.56  Aligned_cols=34  Identities=12%  Similarity=0.194  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      =|.|+.|..++|+++||+|-.+...+.|=|..+.
T Consensus        36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~r   69 (125)
T COG1725          36 PSVRELAKDLGVNPNTVQRAYQELEREGIVETKR   69 (125)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            3889999999999999999999999999998764

>PRK09191 two-component response regulator; Provisional

Probab=93.91  E-value=0.1  Score=34.85  Aligned_cols=30  Identities=13%  Similarity=0.060  Sum_probs=26.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +|+|..+||..+|+|.+||...+.+.++.=
T Consensus       103 ~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l  132 (261)
T PRK09191        103 EGFSVEEAAEILGVDPAEAEALLDDARAEI  132 (261)
T ss_pred             hcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999998877643

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=93.89  E-value=0.093  Score=36.10  Aligned_cols=36  Identities=19%  Similarity=0.255  Sum_probs=32.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      +-+++|.+||||.++|.=-++.....|-|.+++..|
T Consensus        36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~G   71 (241)
T COG2186          36 SERELAERFGVSRTVVREALKRLEAKGLVEIRQGSG   71 (241)
T ss_pred             CHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCc
Confidence            368899999999999999999999999999987544

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=93.88  E-value=0.068  Score=34.94  Aligned_cols=30  Identities=17%  Similarity=0.321  Sum_probs=25.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      +.|+|..++|.++|||++++++|-     .|...|
T Consensus        80 ~~glSqeeLA~~lgvs~s~IsriE-----~G~~~P  109 (154)
T TIGR00270        80 KRGWSQEQLAKKIQEKESLIKKIE-----NAEIEP  109 (154)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH-----CCCCCC
Confidence            479999999999999999999984     465544

>PRK15482 transcriptional regulator MurR; Provisional

Probab=93.84  E-value=0.074  Score=36.95  Aligned_cols=25  Identities=20%  Similarity=0.369  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+|..++|++.+||.+||.|..++.
T Consensus        34 ~~si~elA~~~~vS~aTv~Rf~kkL   58 (285)
T PRK15482         34 SVSSRKMAKQLGISQSSIVKFAQKL   58 (285)
T ss_pred             hcCHHHHHHHhCCCHHHHHHHHHHh
Confidence            4799999999999999999998764

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=93.81  E-value=0.11  Score=35.86  Aligned_cols=28  Identities=14%  Similarity=0.143  Sum_probs=24.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      -.|+|..+||..||||.++|.+++.+-+
T Consensus       226 ~~~~s~~eIA~~lgis~~tV~~~~~ra~  253 (268)
T PRK06288        226 YEDLTLKEIGKVLGVTESRISQLHTKAV  253 (268)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3789999999999999999997776544

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=93.77  E-value=0.08  Score=35.44  Aligned_cols=33  Identities=15%  Similarity=0.220  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+..++|..+|+|+-||+|.++++++.|-+...
T Consensus       170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~  202 (226)
T PRK10402        170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS  202 (226)
T ss_pred             chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence            467899999999999999999999999988764

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=93.77  E-value=0.095  Score=35.59  Aligned_cols=34  Identities=15%  Similarity=0.095  Sum_probs=30.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|+.||||..||.+-+......|-|.-++.
T Consensus        31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G   64 (240)
T PRK09764         31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQG   64 (240)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            5689999999999999999999999999986653

>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]

Probab=93.75  E-value=0.13  Score=35.30  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.+..++|+++++|.-|++||++...+.|.+.-.
T Consensus        19 ~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~   52 (214)
T COG1339          19 KVTSSELAKRLGVSSQTAARKLKELEDEGYITRT   52 (214)
T ss_pred             cccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEE
Confidence            3789999999999999999999999999998644

>PRK10082 cell density-dependent motility repressor; Provisional

Probab=93.74  E-value=0.083  Score=36.41  Aligned_cols=46  Identities=11%  Similarity=0.029  Sum_probs=32.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |..++|+.++||+++|++-++++.+. |..--.+ . +++-.+|++
T Consensus        24 e~g-S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R-~-~r~~~lT~~   70 (303)
T PRK10082         24 KCR-NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNR-Q-VTPLQLSEQ   70 (303)
T ss_pred             hcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEe-c-CCCCccCHH
Confidence            445 88999999999999999999999854 4333322 2 233445554

>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data

Probab=93.73  E-value=0.078  Score=34.89  Aligned_cols=71  Identities=20%  Similarity=0.224  Sum_probs=17.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHH-HhcC-CCccc------cCCCCCC-CCCHHHHHHHHHHHHhC---CCCcHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQ-ETGS-IRPGV------IGGSKPR-VATPDVERRIEEYKGEN---PAMFSWEIRD   73 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r-~tG~-v~pk~------~gg~~~~-~~~~~~~~~i~~~v~~~---pd~tl~El~~   73 (77)
                      ++..+||..+||+.|||+|.++-.+ +|.. +-|-+      .+.+... .........|.++|++.   ..++=.+|++
T Consensus        50 Lt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~~  129 (160)
T PF04552_consen   50 LTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIAE  129 (160)
T ss_dssp             -----------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHHH
T ss_pred             CCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence            5678999999999999999876543 4432 22222      1111111 12233556789999873   3477788888


Q ss_pred             Hhh
Q psy15513         74 RLV   76 (77)
Q Consensus        74 ~L~   76 (77)
                      .|.
T Consensus       130 ~L~  132 (160)
T PF04552_consen  130 LLK  132 (160)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            774

This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=93.66  E-value=0.12  Score=35.22  Aligned_cols=29  Identities=7%  Similarity=0.100  Sum_probs=26.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..|+|..+||..+|||.+.|+++.++..+
T Consensus       197 ~~~~t~~EIA~~lgis~~~V~q~~~~~~~  225 (231)
T PRK12427        197 QHEMSLKEIALVLDLTEARICQLNKKIAQ  225 (231)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36899999999999999999999888764

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=93.66  E-value=0.1  Score=35.39  Aligned_cols=33  Identities=15%  Similarity=0.096  Sum_probs=30.1

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |-+++|+.||||..||.+-++...+.|-|..++
T Consensus        35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   67 (241)
T PRK11402         35 TENELCTQYNVSRITIRKAISDLVADGVLIRWQ   67 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            557899999999999999999999999998664

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=93.64  E-value=0.052  Score=38.97  Aligned_cols=27  Identities=11%  Similarity=0.066  Sum_probs=23.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..|....++|+++|||.+|.++.+++|
T Consensus       303 ~~~gn~~~aA~~LGisr~tL~rklkk~  329 (329)
T TIGR02974       303 EAQFNQRKAAELLGLTYHQLRGLLRKH  329 (329)
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            456788999999999999999999875

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK09775 putative DNA-binding transcriptional regulator; Provisional

Probab=93.63  E-value=0.087  Score=39.60  Aligned_cols=38  Identities=13%  Similarity=0.131  Sum_probs=32.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      +.-.+..++|.+|+||++||++-++..  .|.|...+.|.
T Consensus        11 ~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~~gr   48 (442)
T PRK09775         11 QGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRFGKAR   48 (442)
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEeccCc
Confidence            344899999999999999999999999  78887776654

>PRK09508 leuO leucine transcriptional activator; Reviewed

Probab=93.61  E-value=0.082  Score=36.69  Aligned_cols=32  Identities=16%  Similarity=0.122  Sum_probs=26.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v   35 (77)
                      +.| |...+|+.|+||+++|++=+++..+. |.-
T Consensus        35 e~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~   67 (314)
T PRK09508         35 QEQ-NITRAAHNLGMSQPAVSNAVARLKVMFNDE   67 (314)
T ss_pred             hcC-CHHHHHHHhCCCHHHHHHHHHHHHHhhCCC
Confidence            445 78899999999999999999999854 443

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=93.60  E-value=0.091  Score=34.18  Aligned_cols=25  Identities=8%  Similarity=0.147  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .+..+||+-.|||.+|.++|.++-+
T Consensus        35 ~T~~eiAee~Gis~~tLYrWr~~~~   59 (142)
T PF13022_consen   35 RTQAEIAEEVGISRSTLYRWRQQNK   59 (142)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred             chHHHHHHHhCCCHHHHHHHHhcCH
Confidence            6788999999999999999997644

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=93.58  E-value=0.084  Score=37.01  Aligned_cols=28  Identities=18%  Similarity=0.181  Sum_probs=25.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..+++..+||+.+|||.|.|+++.++.-
T Consensus       210 ~eelt~kEI~~~LgISes~VSql~kkai  237 (247)
T COG1191         210 KEELTQKEIAEVLGISESRVSRLHKKAI  237 (247)
T ss_pred             HhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence            4678999999999999999999998764

>PHA02943 hypothetical protein; Provisional

Probab=93.58  E-value=0.2  Score=33.18  Aligned_cols=42  Identities=26%  Similarity=0.331  Sum_probs=36.3

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      +.| .+..+||+++|+|.+-|.-.+......|-|..-+.|...
T Consensus        21 k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~t   63 (165)
T PHA02943         21 ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAA   63 (165)
T ss_pred             hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceE
Confidence            456 779999999999999999999999999999887766433

>PRK10632 transcriptional regulator; Provisional

Probab=93.52  E-value=0.09  Score=36.47  Aligned_cols=28  Identities=18%  Similarity=0.232  Sum_probs=25.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -|...+|++++||+++|++=+++..+.=
T Consensus        17 gS~t~AA~~L~isQpavS~~I~~LE~~l   44 (309)
T PRK10632         17 GSFTAAARQLQMSVSSISQTVSKLEDEL   44 (309)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence            3889999999999999999999998643

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=93.52  E-value=0.15  Score=32.24  Aligned_cols=32  Identities=22%  Similarity=0.124  Sum_probs=28.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      ..|+|..+||+.+++|..||..++.+.+..=.
T Consensus       162 ~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~  193 (210)
T PRK09935        162 VSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG  193 (210)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            36899999999999999999999999886543

>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional

Probab=93.47  E-value=0.088  Score=36.56  Aligned_cols=26  Identities=19%  Similarity=0.309  Sum_probs=24.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      |...+|+.++||+++|++=+++..+.
T Consensus        30 s~s~AA~~L~iSQpavS~~I~~LE~~   55 (311)
T PRK10086         30 SFALAADELSLTPSAVSHRINQLEEE   55 (311)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            88899999999999999999998854

>PRK04140 hypothetical protein; Provisional

Probab=93.46  E-value=0.077  Score=38.43  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++||++|.+
T Consensus       137 ~~GlSq~eLA~~lGVSr~tIskyE~  161 (317)
T PRK04140        137 ELGLSLGELASELGVSRRTISKYEN  161 (317)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4799999999999999999999964

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=93.46  E-value=0.064  Score=40.69  Aligned_cols=24  Identities=25%  Similarity=0.452  Sum_probs=22.2

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +.+++|++||||++|++|-++.|-
T Consensus       488 ~~~~aA~~LGisr~tL~rkl~~~g  511 (520)
T PRK10820        488 STRKLAKRLGVSHTAIANKLREYG  511 (520)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHcC
Confidence            788999999999999999999874

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=93.44  E-value=0.074  Score=37.95  Aligned_cols=41  Identities=20%  Similarity=0.216  Sum_probs=29.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      +..+||+..|||++||||-++..               + ...++.++.|++.+++-
T Consensus         2 TikDVA~~AGVS~sTVSrvln~~---------------~-~Vs~eTr~kV~~a~~el   42 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLNGS---------------P-YVSEETREKVLAAIKEL   42 (333)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHHH
Confidence            57899999999999999998641               1 23344566677666653

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=93.42  E-value=0.093  Score=36.74  Aligned_cols=36  Identities=22%  Similarity=0.175  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ++..++|+.|+||..||.|=+....+.|-+.- -+||
T Consensus        32 vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r-~~GG   67 (269)
T PRK09802         32 VQVNDLSALYGVSTVTIRNDLAFLEKQGIAVR-AYGG   67 (269)
T ss_pred             EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEE-EeCC
Confidence            78999999999999999999999999998873 3455

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=93.41  E-value=0.14  Score=35.12  Aligned_cols=27  Identities=15%  Similarity=0.238  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +|++..+||..||||.++|+++.++..
T Consensus       221 ~~~t~~eIA~~lgis~~~V~~~~~ral  247 (254)
T TIGR02850       221 EGKTQMEVAEEIGISQAQVSRLEKAAL  247 (254)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            689999999999999999999987754

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=93.41  E-value=0.071  Score=38.87  Aligned_cols=27  Identities=4%  Similarity=0.064  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|....++|+.||||.+|.+|-+++|
T Consensus       416 ~~~gn~~~aA~~Lgisr~tl~rkl~~~  442 (445)
T TIGR02915       416 RVDGNIARAAELLGITRPTLYDLMKKH  442 (445)
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            445678889999999999999999987

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>COG1737 RpiR Transcriptional regulators [Transcription]

Probab=93.41  E-value=0.067  Score=37.49  Aligned_cols=25  Identities=12%  Similarity=0.170  Sum_probs=22.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +|..++|++.|||++||.|..+++-
T Consensus        37 ~si~elA~~a~VS~aTv~Rf~~kLG   61 (281)
T COG1737          37 LSIAELAERAGVSPATVVRFARKLG   61 (281)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcC
Confidence            6789999999999999999988753

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

Probab=93.38  E-value=0.14  Score=36.36  Aligned_cols=31  Identities=16%  Similarity=0.092  Sum_probs=28.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .++..++|++|+||.+||.+-++..++.|-+
T Consensus        18 ~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~   48 (319)
T PRK11886         18 FHSGEQLGEELGISRAAIWKHIQTLEEWGLD   48 (319)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            4788899999999999999999999999983

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=93.36  E-value=0.2  Score=25.27  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=20.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ....+..++|..+|+|.+...|..+++
T Consensus         6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~   32 (42)
T PF00165_consen    6 QQKLTLEDIAEQAGFSPSYFSRLFKKE   32 (42)
T ss_dssp             -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            356899999999999999999988764

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=93.33  E-value=0.097  Score=36.00  Aligned_cols=25  Identities=12%  Similarity=0.142  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      -+|..++|+..+||.+||.|..++.
T Consensus        34 ~~si~~lA~~~~vS~aTv~Rf~kkl   58 (284)
T PRK11302         34 HSSIATLAKMANVSEPTVNRFCRSL   58 (284)
T ss_pred             hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence            3789999999999999999998763

>PRK11062 nhaR transcriptional activator NhaR; Provisional

Probab=93.32  E-value=0.099  Score=35.99  Aligned_cols=32  Identities=9%  Similarity=0.043  Sum_probs=26.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.| |...+|++|+||+++|++=+++..+.=.+
T Consensus        17 e~g-s~s~AA~~L~isqpavS~~I~~LE~~lg~   48 (296)
T PRK11062         17 KEG-SVVGAAEALFLTPQTITGQIKALEERLQG   48 (296)
T ss_pred             hcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence            344 88999999999999999999999854333

>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences []

Probab=93.32  E-value=0.064  Score=32.76  Aligned_cols=27  Identities=19%  Similarity=0.274  Sum_probs=21.6

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ...+|+-||+|.+||+||-+    +|-+.+.
T Consensus        48 ~~GlAklfgcSv~Ta~RiK~----sG~id~A   74 (96)
T PF12964_consen   48 LKGLAKLFGCSVPTANRIKK----SGKIDPA   74 (96)
T ss_pred             HHHHHHHhCCCchhHHHHHh----cCCccHH
Confidence            45699999999999999854    4777654

>COG1710 Uncharacterized protein conserved in archaea [Function unknown]

Probab=93.27  E-value=0.088  Score=33.65  Aligned_cols=31  Identities=26%  Similarity=0.382  Sum_probs=27.1

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      |+.+|+.+++||+-+||...||+-+++....
T Consensus       105 mlr~gk~preIsk~lGIpirTvyY~l~k~k~  135 (139)
T COG1710         105 MLRNGKTPREISKDLGIPIRTVYYLLKKLKK  135 (139)
T ss_pred             HHHcCCCHHHHHHhhCCchhhhHHHHHHHhh
Confidence            4678999999999999999999999886543

>PRK11074 putative DNA-binding transcriptional regulator; Provisional

Probab=93.25  E-value=0.1  Score=35.92  Aligned_cols=36  Identities=17%  Similarity=0.101  Sum_probs=28.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCcc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPG   38 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk   38 (77)
                      ++.| |...+|++|+||+++|++-+++..+ -|.---.
T Consensus        14 ~e~~-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~   50 (300)
T PRK11074         14 ARTG-SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFE   50 (300)
T ss_pred             HHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEE
Confidence            3455 8899999999999999999999984 4544433

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=93.17  E-value=0.16  Score=35.75  Aligned_cols=29  Identities=24%  Similarity=0.258  Sum_probs=25.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .+|+|..+||+.||||.++|..+..+-..
T Consensus       243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~  271 (289)
T PRK07500        243 EDGATLEALGEELGISKERVRQIEARALE  271 (289)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37899999999999999999999887654

>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional

Probab=93.15  E-value=0.11  Score=36.46  Aligned_cols=43  Identities=14%  Similarity=0.173  Sum_probs=31.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      |...+|++++||+++|++-+++..+. |.---.+ .+ ++-.+|++
T Consensus        27 s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R-~~-~~~~LT~~   70 (310)
T PRK15092         27 TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFAR-HG-RNKLLTEH   70 (310)
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEE-CC-CCceECHh
Confidence            78899999999999999999999854 4433332 22 33456664

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=93.15  E-value=0.17  Score=34.39  Aligned_cols=29  Identities=7%  Similarity=0.087  Sum_probs=25.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..|+|..+||..||||.++|.++.++-..
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~~al~  222 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIESKALR  222 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36899999999999999999999877554

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=93.09  E-value=0.17  Score=35.58  Aligned_cols=27  Identities=15%  Similarity=0.007  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|+|..+||+.||||.++|+.+.++..
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al  273 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAM  273 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            589999999999999999999988754

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=93.09  E-value=0.17  Score=36.41  Aligned_cols=29  Identities=10%  Similarity=0.062  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.+||..++.+-+.
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~  308 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVEALR  308 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47899999999999999999999877554

>PRK13870 transcriptional regulator TraR; Provisional

Probab=93.05  E-value=0.18  Score=34.60  Aligned_cols=34  Identities=21%  Similarity=0.063  Sum_probs=29.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|.+..|||..+|||.+||..-++.-++.=.+.
T Consensus       186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        186 AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            4799999999999999999999999988754443

>PRK03635 chromosome replication initiation inhibitor protein; Validated

Probab=93.05  E-value=0.14  Score=35.07  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=37.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      +.| |...+|++++||+++|++-+++..+. |..--.+ +  +.-..|++ .+.+...+++
T Consensus        15 e~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R-~--~~~~lT~~-G~~l~~~a~~   70 (294)
T PRK03635         15 REG-SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-T--QPCRPTEA-GQRLLRHARQ   70 (294)
T ss_pred             HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeec-C--CCCccCHH-HHHHHHHHHH
Confidence            344 88999999999999999999999855 4443333 2  34456664 4444444433

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=93.04  E-value=0.087  Score=40.48  Aligned_cols=28  Identities=11%  Similarity=-0.007  Sum_probs=24.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +.|....++|++||||.+|.+|++++|-
T Consensus       508 ~~~Gn~~~aA~~LGIsRtTL~RkLk~~g  535 (538)
T PRK15424        508 RFNGDKTAAANYLGISRTTLWRRLKAEA  535 (538)
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            4566788999999999999999999874

>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development

Probab=92.98  E-value=0.12  Score=31.28  Aligned_cols=24  Identities=13%  Similarity=0.217  Sum_probs=20.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ....+|+..||+.|+|+||-.-+.
T Consensus        25 gq~~vA~~~Gv~eStISR~k~~~~   48 (91)
T PF05269_consen   25 GQKKVAEAMGVDESTISRWKNDFI   48 (91)
T ss_dssp             HHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred             hhHHHHHHhCCCHHHHHHHHhhHH
Confidence            467899999999999999965443

CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.

>TIGR03298 argP transcriptional regulator, ArgP family

Probab=92.90  E-value=0.12  Score=35.20  Aligned_cols=55  Identities=18%  Similarity=0.088  Sum_probs=36.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      +.| |...+|++++||+++|++-+++..+.=.+ --- ++  ++-.+|++ .+.+.+.++.
T Consensus        14 ~~~-s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~-R~--r~~~lT~~-G~~l~~~~~~   69 (292)
T TIGR03298        14 EEG-SFERAAAALSVTPSAVSQRIKALEERLGQPLLV-RT--QPCRATEA-GQRLLRHARQ   69 (292)
T ss_pred             HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCchhee-cC--CCCcCCHh-HHHHHHHHHH
Confidence            344 88999999999999999999999865433 222 22  34456664 3444444433

ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).

>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins

Probab=92.87  E-value=0.2  Score=28.11  Aligned_cols=36  Identities=14%  Similarity=0.377  Sum_probs=30.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .-...||.++||+.|.+.+-++.+..-|-++.+..|
T Consensus         5 lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSlG   40 (61)
T PF08222_consen    5 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG   40 (61)
T ss_dssp             E-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEETT
T ss_pred             ehHHHHHHHhCccHHHHHHHHHHHHhcCceeecccC
Confidence            456789999999999999999999999999988765

CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.

>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=92.85  E-value=0.08  Score=30.63  Aligned_cols=29  Identities=10%  Similarity=0.132  Sum_probs=23.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +...+..++|..+.||.+|+.+.+++.++
T Consensus        28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~   56 (87)
T PF05043_consen   28 NEYVSIEDLAEELFISRSTIYRDIKKLNK   56 (87)
T ss_dssp             -SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45678899999999999999999998875

The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=92.81  E-value=0.15  Score=34.80  Aligned_cols=33  Identities=27%  Similarity=0.231  Sum_probs=29.9

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |-+++|++|+||..||.|-++...+.|-+....
T Consensus        33 sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~   65 (236)
T COG2188          33 SERELAEQFGVSRMTVRKALDELVEEGLIVRRQ   65 (236)
T ss_pred             CHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEe
Confidence            457899999999999999999999999987764

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=92.78  E-value=0.13  Score=35.30  Aligned_cols=35  Identities=20%  Similarity=0.133  Sum_probs=30.1

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ...|++..+||..|+||..||..-++..++.=.+.
T Consensus       191 ~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~  225 (240)
T PRK10188        191 TAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAP  225 (240)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            35799999999999999999999999988765443

>PRK09986 DNA-binding transcriptional activator XapR; Provisional

Probab=92.78  E-value=0.095  Score=35.57  Aligned_cols=30  Identities=10%  Similarity=-0.004  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      +.| |...+|+.++||+++|++-++++.+.=
T Consensus        20 ~~g-s~t~AA~~L~itq~avS~~i~~LE~~l   49 (294)
T PRK09986         20 EEL-HFGRAAARLNISQPPLSIHIKELEDQL   49 (294)
T ss_pred             Hhc-CHHHHHHHhCCCCCHHHHHHHHHHHHh
Confidence            455 889999999999999999999998543

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=92.78  E-value=0.17  Score=33.80  Aligned_cols=54  Identities=13%  Similarity=0.244  Sum_probs=39.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~   66 (77)
                      ++..+||..+|++..||+|.++.+++.| +. .  ++++-.+.   +.+.+.++...+|-+
T Consensus       174 ~t~~~iA~~lG~tretvsR~l~~L~~~g-l~-~--~~~~i~I~---d~~~L~~~~~~~~~~  227 (236)
T PRK09392        174 YEKRVLASYLGMTPENLSRAFAALASHG-VH-V--DGSAVTIT---DPAGLARFAKPSPLI  227 (236)
T ss_pred             CCHHHHHHHhCCChhHHHHHHHHHHhCC-eE-e--eCCEEEEc---CHHHHHHhhccCCCC
Confidence            4578999999999999999999999999 63 2  22222333   355577777777654

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=92.72  E-value=0.59  Score=35.71  Aligned_cols=72  Identities=10%  Similarity=-0.029  Sum_probs=45.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH----hcC-CCccccCCCCCCC------------CCHHHHHHHHHHHHhCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE----TGS-IRPGVIGGSKPRV------------ATPDVERRIEEYKGENPA   65 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~----tG~-v~pk~~gg~~~~~------------~~~~~~~~i~~~v~~~pd   65 (77)
                      +..++..++|+.||||..||.+-++...+    .|- +..+. +|.+-..            ..++....+..++. +..
T Consensus        15 ~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~-~Gy~l~~~~~~~~~~~~~~~~~e~~~il~~Ll~-~~~   92 (584)
T PRK09863         15 QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGS-AKYHLEILNRRSLFQLLQKSDNEDRLLLLRLLL-NTF   92 (584)
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecC-CceEEEeCCHHHHHHHHhcCCHHHHHHHHHHHH-cCC
Confidence            45689999999999999999999997754    232 12221 2333111            12222334445665 556


Q ss_pred             CcHHHHHHHhh
Q psy15513         66 MFSWEIRDRLV   76 (77)
Q Consensus        66 ~tl~El~~~L~   76 (77)
                      +++.+|++.|-
T Consensus        93 ~~~~~La~~l~  103 (584)
T PRK09863         93 TPMAQLASALN  103 (584)
T ss_pred             ccHHHHHHHhC
Confidence            89999999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	77
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		2e-33
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		3e-29
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		4e-29
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		3e-24

>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128

Iteration: 1
 Score =  137 bits (344), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 63/76 (82%), Positives = 71/76 (93%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 29  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 88
Query: 61  GENPAMFSWEIRDRLV 76
             +P MFSWEIR++L+
Sbjct: 89  RSSPGMFSWEIREKLI 104

>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149

Iteration: 1
 Score =  123 bits (309), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 58/76 (76%), Positives = 65/76 (85%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V  +I EYK
Sbjct: 44  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103
Query: 61  GENPAMFSWEIRDRLV 76
            +NP MF+WEIRDRL+
Sbjct: 104 RQNPTMFAWEIRDRLL 119

>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159

Iteration: 1
 Score =  122 bits (307), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 58/76 (76%), Positives = 65/76 (85%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSIRPGVIGGSKP+VATP V  +I +YK
Sbjct: 37  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYK 96
Query: 61  GENPAMFSWEIRDRLV 76
            +NP MF+WEIRDRL+
Sbjct: 97  RQNPTMFAWEIRDRLL 112

>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133

Iteration: 1
 Score =  106 bits (265), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 51/76 (67%), Positives = 62/76 (81%)
Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A +G RPC ISR L+VS+GCVSKIL RY  TGSIRP  IGGSKPRVATP+V  +I +YK
Sbjct: 29  LAHSGARPCDISRILQVSNGCVSKILGRYYATGSIRPRAIGGSKPRVATPEVVSKIAQYK 88
Query: 61  GENPAMFSWEIRDRLV 76
            E P++F+WEIRDRL+
Sbjct: 89  QECPSIFAWEIRDRLL 104
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	77
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	2e-26
2k27_A	159	Paired box protein PAX-8; paired domain, solution	6e-25
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	1e-24
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	3e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-04

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128

 Score = 92.5 bits (229), Expect = 2e-26
 Identities = 63/76 (82%), Positives = 71/76 (93%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 29  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 88

Query: 61  GENPAMFSWEIRDRLV 76
             +P MFSWEIR++L+
Sbjct: 89  RSSPGMFSWEIREKLI 104

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159

 Score = 89.5 bits (221), Expect = 6e-25
 Identities = 58/76 (76%), Positives = 65/76 (85%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSIRPGVIGGSKP+VATP V  +I +YK
Sbjct: 37  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYK 96

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MF+WEIRDRL+
Sbjct: 97  RQNPTMFAWEIRDRLL 112

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149

 Score = 89.1 bits (220), Expect = 1e-24
 Identities = 58/76 (76%), Positives = 65/76 (85%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PGVIGGSKP+VATP V  +I EYK
Sbjct: 44  LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYK 103

Query: 61  GENPAMFSWEIRDRLV 76
            +NP MF+WEIRDRL+
Sbjct: 104 RQNPTMFAWEIRDRLL 119

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194

 Score = 41.4 bits (96), Expect = 3e-06
 Identities = 4/27 (14%), Positives = 10/27 (37%)

Query: 50 PDVERRIEEYKGENPAMFSWEIRDRLV 76
             +  +E    E+P   +  ++  L 
Sbjct: 14 AHQKAVVETLLQEDPWRVAKMVKSYLQ 40

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 36.5 bits (83), Expect = 2e-04
 Identities = 3/26 (11%), Positives = 10/26 (38%)

Query: 50 PDVERRIEEYKGENPAMFSWEIRDRL 75
           +    ++    E+P   +  I+  +
Sbjct: 15 AEQRAEVDRMLSEDPWRAAKMIKGYM 40

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	77
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.72
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.7
2k27_A	159	Paired box protein PAX-8; paired domain, solution	99.63
1u78_A	141	TC3 transposase, transposable element TC3 transpos	99.44
3hot_A	345	Transposable element mariner, complete CDS; protei	99.31
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	98.84
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.82
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	98.53
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	98.32
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	98.32
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	98.28
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	98.22
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	98.08
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	98.06
3jth_A	98	Transcription activator HLYU; transcription factor	98.06
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	98.03
2kko_A	108	Possible transcriptional regulatory protein (possi	97.94
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.85
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	97.76
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	97.74
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	97.72
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	97.7
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.7
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	97.7
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.66
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	97.66
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	97.65
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	97.64
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	97.64
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	97.63
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	97.63
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	97.6
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	97.59
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	97.58
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	97.57
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	97.53
2jml_A	81	DNA binding domain/transcriptional regulator; anti	97.51
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.49
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	97.48
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	97.47
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	97.47
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.47
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	97.47
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	97.44
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.44
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	97.44
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.43
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.43
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	97.41
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	97.41
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	97.4
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	97.4
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.38
1ku9_A	152	Hypothetical protein MJ223; putative transcription	97.37
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	97.36
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	97.34
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	97.34
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.31
3gp4_A	142	Transcriptional regulator, MERR family; structural	97.31
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	97.28
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.28
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	97.27
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.27
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.27
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	97.26
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	97.25
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.24
1q06_A	135	Transcriptional regulator CUER; MERR family transc	97.24
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.24
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	97.23
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.22
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.22
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	97.22
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	97.22
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.21
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	97.21
2dg6_A	222	Putative transcriptional regulator; winged-helix m	97.2
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.19
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	97.19
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.19
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	97.18
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.18
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	97.18
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	97.17
2hin_A	71	GP39, repressor protein; transcription factor, dim	97.17
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	97.17
3hh0_A	146	Transcriptional regulator, MERR family; protein st	97.16
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.16
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	97.15
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.14
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.14
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	97.13
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	97.13
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	97.12
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.11
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.11
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	97.11
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.11
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	97.11
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.1
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	97.1
3nqo_A	189	MARR-family transcriptional regulator; structural	97.09
3c57_A	95	Two component transcriptional regulatory protein;	97.08
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	97.07
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	97.07
1z91_A	147	Organic hydroperoxide resistance transcriptional;	97.06
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	97.06
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	97.06
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	97.06
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	97.05
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	97.05
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	97.05
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.04
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	97.04
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	97.04
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.03
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.03
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	97.02
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	97.01
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	97.01
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.0
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	97.0
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.99
2nnn_A	140	Probable transcriptional regulator; structural gen	96.99
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	96.98
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	96.98
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.98
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	96.98
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	96.97
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.97
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.96
2pg4_A	95	Uncharacterized protein; structural genomics, join	96.96
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	96.96
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.96
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.96
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.96
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.95
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.95
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	96.95
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.95
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	96.94
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.94
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	96.94
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	96.92
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	96.92
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	96.92
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.91
3gpv_A	148	Transcriptional regulator, MERR family; protein st	96.91
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.9
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	96.9
2w25_A	150	Probable transcriptional regulatory protein; trans	96.9
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	96.9
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	96.9
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	96.89
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.89
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.88
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	96.88
3r0a_A	123	Putative transcriptional regulator; structural gen	96.88
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	96.87
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	96.87
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.87
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	96.85
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	96.84
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.83
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.83
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.82
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.82
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	96.81
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	96.81
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	96.8
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	96.78
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	96.78
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.78
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	96.78
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	96.77
3by6_A	126	Predicted transcriptional regulator; structural ge	96.77
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.76
4fx0_A	148	Probable transcriptional repressor protein; helix-	96.75
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.74
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	96.73
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	96.73
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	96.72
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	96.69
1ylf_A	149	RRF2 family protein; structural genomics, transcri	96.69
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	96.69
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.69
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	96.67
3iuo_A	122	ATP-dependent DNA helicase RECQ; C-terminal, GI PS	96.67
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	96.66
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	96.65
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	96.65
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.65
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	96.65
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	96.64
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	96.64
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	96.64
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	96.63
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.62
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	96.61
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.61
3f3x_A	144	Transcriptional regulator, MARR family, putative;	96.59
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	96.58
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	96.57
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	96.56
3t76_A	88	VANU, transcriptional regulator vanug; structural	96.56
3frw_A	107	Putative Trp repressor protein; structural genomic	96.56
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	96.56
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	96.53
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	96.52
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	96.51
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	96.5
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.49
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	96.49
2fxa_A	207	Protease production regulatory protein HPR; protea	96.49
3trb_A	104	Virulence-associated protein I; mobIle and extrach	96.47
1b0n_A	111	Protein (SINR protein); transcription regulator, a	96.47
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	96.46
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.46
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	96.46
3k69_A	162	Putative transcription regulator; putative transcr	96.44
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.43
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	96.42
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	96.42
3cec_A	104	Putative antidote protein of plasmid maintenance;	96.4
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	96.4
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.4
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	96.39
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	96.38
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.36
4ghj_A	101	Probable transcriptional regulator; structural gen	96.36
3cta_A	230	Riboflavin kinase; structural genomics, transferas	96.36
1xd7_A	145	YWNA; structural genomics, protein structure initi	96.35
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	96.34
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	96.33
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	96.31
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	96.3
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	96.29
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	96.28
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	96.28
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	96.28
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	96.28
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	96.25
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	96.23
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.21
1eto_A	98	FIS, factor for inversion stimulation; transcripti	96.18
3mlf_A	111	Transcriptional regulator; structural genomics, he	96.15
1z05_A	429	Transcriptional regulator, ROK family; structural	96.14
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	96.13
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	96.11
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	96.11
3c7j_A	237	Transcriptional regulator, GNTR family; structural	96.1
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.1
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	96.09
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	96.09
3ivp_A	126	Putative transposon-related DNA-binding protein; A	96.05
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	96.01
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	96.01
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	96.01
1hsj_A	487	Fusion protein consisting of staphylococcus access	96.0
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	95.95
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	95.93
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	95.91
2q0o_A	236	Probable transcriptional activator protein TRAR; h	95.9
3iwf_A	107	Transcription regulator RPIR family; transcription	95.87
4g6q_A	182	Putative uncharacterized protein; structural genom	95.85
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.84
2g7u_A	257	Transcriptional regulator; ICLR family, structural	95.84
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	95.83
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	95.83
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	95.82
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	95.82
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	95.77
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	95.77
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	95.76
2o0m_A	345	Transcriptional regulator, SORC family; structural	95.74
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	95.73
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	95.71
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	95.7
1u78_A	141	TC3 transposase, transposable element TC3 transpos	95.69
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	95.68
1rr7_A	129	Middle operon regulator; MOR, transcription; 2.20A	95.65
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	95.65
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	95.64
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	95.63
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	95.61
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	95.61
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	95.58
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	95.57
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.55
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	95.55
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	95.55
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	95.53
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	95.52
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	95.52
2wus_R	112	RODZ, putative uncharacterized protein; structural	95.51
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	95.5
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	95.5
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	95.48
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	95.48
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	95.47
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	95.47
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	95.46
3eet_A	272	Putative GNTR-family transcriptional regulator; st	95.45
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	95.44
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	95.42
3b02_A	195	Transcriptional regulator, CRP family; structural	95.4
3jvd_A	333	Transcriptional regulators; structural genomics, P	95.39
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.38
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	95.37
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	95.36
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	95.35
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	95.34
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	95.33
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	95.32
3hhg_A	306	Transcriptional regulator, LYSR family; transcript	95.32
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	95.31
2k27_A	159	Paired box protein PAX-8; paired domain, solution	95.31
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	95.26
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	95.24
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	95.23
1ft9_A	222	Carbon monoxide oxidation system transcription reg	95.23
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	95.22
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	95.21
2og0_A	52	Excisionase; protein-DNA complex, DNA architectura	95.15
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	95.14
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	95.13
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	95.12
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	95.09
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	95.08
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	95.06
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	95.05
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	95.04
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	95.04
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	95.0
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	94.99
1ixc_A	294	CBNR, LYSR-type regulatory protein; long alpha hel	94.99
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	94.97
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	94.96
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	94.95
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	94.89
2vn2_A	128	DNAD, chromosome replication initiation protein; D	94.88
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	94.85
3bil_A	348	Probable LACI-family transcriptional regulator; st	94.83
3e3m_A	355	Transcriptional regulator, LACI family; structural	94.83
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	94.81
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	94.8
1jye_A	349	Lactose operon repressor; gene regulation, protein	94.78
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	94.77
1bia_A	321	BIRA bifunctional protein; transcription regulatio	94.76
2esn_A	310	Probable transcriptional regulator; PA0477, APC582	94.74
3fxq_A	305	LYSR type regulator of TSAMBCD; transcriptional re	94.72
2obp_A	96	Putative DNA-binding protein; structural genomics,	94.67
1al3_A	324	Cys regulon transcriptional activator CYSB; LYSR f	94.6
3isp_A	303	HTH-type transcriptional regulator RV1985C/MT2039;	94.56
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	94.55
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	94.55
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	94.55
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.53
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	94.35
1pm6_A	72	Excisionase; antiparallel beta-sheet, winged-helix	94.27
3fzv_A	306	Probable transcriptional regulator; LYSR, structur	94.23
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	94.16
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	94.13
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	94.11
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	94.1
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	93.98
4ich_A	311	Transcriptional regulator; structural genomics, PS	93.98
3mz1_A	300	Putative transcriptional regulator; structural gen	93.87
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	93.82
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	93.78
2h9b_A	312	HTH-type transcriptional regulator BENM; LTTR, tra	93.75
2kfs_A	148	Conserved hypothetical regulatory protein; WHTH, D	93.74
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	93.67
2ra5_A	247	Putative transcriptional regulator; beta structure	93.49
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	93.48
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	93.48
2d6y_A	202	Putative TETR family regulatory protein; helix-tur	93.42
2zcm_A	192	Biofilm operon icaabcd HTH-type negative transcri	93.37
3vpr_A	190	Transcriptional regulator, TETR family; all alpha,	93.36
2h98_A	313	HTH-type transcriptional regulator CATM; BENM, LTT	93.34
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	93.23
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	93.23
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	93.23
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	93.16
3c3w_A	225	Two component transcriptional regulatory protein;	93.14
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	93.02
3egq_A	170	TETR family transcriptional regulator; DNA-binding	93.02
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	92.97
2w57_A	150	Ferric uptake regulation protein; gene regulation,	92.95
3lwj_A	202	Putative TETR-family transcriptional regulator; st	92.93
3ppb_A	195	Putative TETR family transcription regulator; DNA-	92.91
1uth_A	315	LYSR-type regulatory protein; transcription regula	92.87
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	92.84
2v57_A	190	TETR family transcriptional repressor LFRR; DNA-bi	92.84
3dew_A	206	Transcriptional regulator, TETR family; S genomics	92.83
3on4_A	191	Transcriptional regulator, TETR family; structural	92.83
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	92.79
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	92.77
3gzi_A	218	Transcriptional regulator, TETR family; TETR famil	92.75
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	92.73
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	92.71
3loc_A	212	HTH-type transcriptional regulator RUTR; helix-tur	92.67
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	92.67
1yio_A	208	Response regulatory protein; transcription regulat	92.64
2eh3_A	179	Transcriptional regulator; all alpha proteins, tet	92.58
2co5_A	99	Viral protein F93; viral protein-winged helix comp	92.53
4aci_A	191	HTH-type transcriptional repressor ACNR; aconitase	92.53
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	92.52
2yve_A	185	Transcriptional regulator; helix-turn-helix, TETR-	92.51
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	92.5
3rqi_A	184	Response regulator protein; structural genomics, s	92.49
2qtq_A	213	Transcriptional regulator, TETR family; transcript	92.46
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	92.44
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	92.43
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	92.42
1lva_A	258	Selenocysteine-specific elongation factor; winged-	92.42
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	92.4
3vib_A	210	MTRR; helix-turn-helix motif, DNA binding, DNA bin	92.38
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	92.33
3c2b_A	221	Transcriptional regulator, TETR family; structural	92.33
3bqz_B	194	HTH-type transcriptional regulator QACR; multidrug	92.32
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	92.28
2wui_A	210	MEXZ, transcriptional regulator; gene regulation,	92.26
3ljl_A	156	Transcriptional regulator LUXT; structural genomic	92.24
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	92.23
2jj7_A	186	Hemolysin II regulatory protein; DNA-binding prote	92.14
2oer_A	214	Probable transcriptional regulator; helix-turn-hel	92.14
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	92.13
3bqy_A	209	Putative TETR family transcriptional regulator; st	92.06
3f0c_A	216	TETR-molecule A, transcriptional regulator; MCSG,P	92.04
2i10_A	202	Putative TETR transcriptional regulator; structura	92.04
3rh2_A	212	Hypothetical TETR-like transcriptional regulator;	92.0
2hku_A	215	A putative transcriptional regulator; structural g	92.0
3bhq_A	211	Transcriptional regulator; bacterial RE proteins,	91.99
2o7t_A	199	Transcriptional regulator; transcription regulator	91.93
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	91.9
2opt_A	234	Actii protein; helical protein, TETR family, APO-p	91.89
2ibd_A	204	Possible transcriptional regulator; probable trans	91.88
3bjb_A	207	Probable transcriptional regulator, TETR family P;	91.83
3bru_A	222	Regulatory protein, TETR family; structural genomi	91.8
3frq_A	195	Repressor protein MPHR(A); macrolide antibiotic. r	91.8
2np5_A	203	Transcriptional regulator; TETR family, structural	91.77
3anp_C	204	Transcriptional repressor, TETR family; all alpha	91.75
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	91.73
3s5r_A	216	Transcriptional regulator TETR family; DNA/RNA-bin	91.71
3v6g_A	208	Probable transcriptional regulatory protein (PROB	91.71
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	91.69
1vi0_A	206	Transcriptional regulator; structural genomics; HE	91.68
3qbm_A	199	TETR transcriptional regulator; DNA/RNA-binding th	91.64
2f07_A	197	YVDT; helix-turn-helix, transcription; HET: BTB; 2	91.63
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	91.63
2hxi_A	241	Putative transcriptional regulator; structural gen	91.62
3cjd_A	198	Transcriptional regulator, TETR family; YP_510936.	91.62
2gen_A	197	Probable transcriptional regulator; APC6095, TETR	91.61
2nx4_A	194	Transcriptional regulator, TETR family protein; HT	91.6
1i3j_A	116	I-TEVI, intron-associated endonuclease 1; protein-	91.59
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	91.55
3col_A	196	Putative transcription regulator; structural genom	91.55
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	91.54
2zb9_A	214	Putative transcriptional regulator; transcription	91.52
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	91.5
3lsg_A	103	Two-component response regulator YESN; structural	91.48
3mnl_A	203	KSTR, transcriptional regulatory protein (probably	91.46
3pas_A	195	TETR family transcription regulator; structural ge	91.41
2hyt_A	197	TETR-family transcriptional regulator; structural	91.39
2rae_A	207	Transcriptional regulator, ACRR family protein; TE	91.33
3mn2_A	108	Probable ARAC family transcriptional regulator; st	91.28
3hot_A	345	Transposable element mariner, complete CDS; protei	91.28
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	91.27
3bni_A	229	Putative TETR-family transcriptional regulator; st	91.25
2qwt_A	196	Transcriptional regulator, TETR family; structural	91.23
1t33_A	224	Putative transcriptional repressor (TETR/ACRR FAM;	91.14
2zcx_A	231	SCO7815, TETR-family transcriptional regulator; he	91.14
3g7r_A	221	Putative transcriptional regulator; TETR, all-heli	91.11
2xpw_A	207	Tetracycline repressor protein class D; transcript	91.09
2rek_A	199	Putative TETR-family transcriptional regulator; su	91.09
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	91.07
1zk8_A	183	Transcriptional regulator, TETR family; TETR membe	91.06
1ui5_A	215	A-factor receptor homolog; helix-turn-helix, alpha	91.04
3crj_A	199	Transcription regulator; APC88200, TETR, structura	91.02
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	91.01
3nxc_A	212	HTH-type protein SLMA; nucleoid occlusion, cell di	90.98
3mvp_A	217	TETR/ACRR transcriptional regulator; PSI, MCSG, st	90.92
2guh_A	214	Putative TETR-family transcriptional regulator; he	90.92
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	90.91
1rkt_A	205	Protein YFIR; transcription regulator, structural	90.91
2id3_A	225	Putative transcriptional regulator; structural gen	90.89
3eqx_A	373	FIC domain containing transcriptional regulator; F	90.85
2ras_A	212	Transcriptional regulator, TETR family; bacterial	90.85
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.81
3cdl_A	203	Transcriptional regulator AEFR; APC88582, TETR, ps	90.78
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	90.74
3npi_A	251	TETR family regulatory protein; structural genomic	90.71
3nnr_A	228	Transcriptional regulator, TETR family; TETR-famil	90.71
1u8b_A	133	ADA polyprotein; protein-DNA complex, methylation,	90.69
2gfn_A	209	HTH-type transcriptional regulator PKSA related P;	90.65
3rd3_A	197	Probable transcriptional regulator; 2.40A {Pseudom	90.65
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	90.63
2oi8_A	216	Putative regulatory protein SCO4313; TETR, structu	90.59
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	90.58

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=99.72  E-value=1.3e-17  Score=100.62  Aligned_cols=74  Identities=84%  Similarity=1.417  Sum_probs=66.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...|+|.++||+.||||.+||++|+++|+++|.+.+++.+|.+++.+++++.+.|.+++.++|+++++||++.|
T Consensus        30 ~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~~i~~~~~~~~~~s~~~i~~~l  103 (128)
T 1pdn_C           30 AADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKL  103 (128)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            35799999999999999999999999999999998887766466677777888999999999999999999887

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=99.70  E-value=1.2e-16  Score=100.32  Aligned_cols=74  Identities=78%  Similarity=1.300  Sum_probs=66.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...|+|..+||+.||||.+||++|+++|+++|.+.+++.+|.+++..+++..+.|.+++.++|++++++|++.|
T Consensus        45 ~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l  118 (149)
T 1k78_A           45 AHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRL  118 (149)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCCHHHHHHHHHHHHhCcchhHHHHHHHH
Confidence            35799999999999999999999999999999998887766546777888899999999999999999999887

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=99.63  E-value=1.7e-16  Score=100.79  Aligned_cols=74  Identities=78%  Similarity=1.301  Sum_probs=65.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...|+|.++||+.||||.+||++|+++|+++|.+.+++.+|.+++..+++..+.|.+++.++|++++++|++.|
T Consensus        38 ~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l  111 (159)
T 2k27_A           38 AHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRL  111 (159)
T ss_dssp             HHHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTTHHHHHHHHHHHCSSSCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHHHHHHHHHHHHHCccchHHHHHHHH
Confidence            35799999999999999999999999999999998887766546666777888999999999999999999887

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=99.44  E-value=2.6e-13  Score=83.33  Aligned_cols=69  Identities=19%  Similarity=0.262  Sum_probs=58.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .+.|+|.++||+.||||.+||++|+++|.+.|...+    .++++.++++....|.++ ..+|+.+..+|++.|
T Consensus        19 ~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~----~gr~~~l~~~~~~~i~~~-~~~~~~s~~~i~~~l   87 (141)
T 1u78_A           19 KLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRKALSVRDERNVIRA-ASNSCKTARDIRNEL   87 (141)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCC----CCCCCSSCHHHHHHHHHH-HHHCCCCHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCC----CCCCCcCCHHHHHHHHHH-HhCCCCCHHHHHHHH
Confidence            468999999999999999999999999999886543    235667888777788887 788999999999876

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=99.31  E-value=5.2e-12  Score=87.16  Aligned_cols=69  Identities=13%  Similarity=0.177  Sum_probs=59.0

Q ss_pred             ccCCCCHHHHHHHhc-------cCHHHHHHHHHHHHHhcC--CCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513          2 AAAGVRPCVISRQLR-------VSHGCVSKILNRYQETGS--IRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR   72 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~-------VS~stv~r~~~r~r~tG~--v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~   72 (77)
                      ++.|.|..+||+.|+       ||.+||++|+++|++ |.  +.+++.+| +|+..++   +.|.++++++|+.|+.||+
T Consensus        19 ~~~G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~-g~~~l~~~~r~g-rp~~~~~---~~i~~~v~~~~~~t~~~ia   93 (345)
T 3hot_A           19 FHLKKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKS-GDFDVDDKEHGK-PPKRYED---AELQALLDEDDAQTQKQLA   93 (345)
T ss_dssp             HHTTCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTT-CCCCCSCCCCCC-CCCSSCH---HHHHHHHHHCSCCCHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhC-CCccccCCCCCC-CCCcccH---HHHHHHHHhCccchHHHHH
Confidence            568999999999977       999999999999997 64  78888776 6666654   5588899999999999999


Q ss_pred             HHh
Q psy15513         73 DRL   75 (77)
Q Consensus        73 ~~L   75 (77)
                      +.|
T Consensus        94 ~~l   96 (345)
T 3hot_A           94 EQL   96 (345)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            876

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

Probab=98.84  E-value=1.3e-09  Score=66.99  Aligned_cols=72  Identities=14%  Similarity=0.090  Sum_probs=63.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++.+++++|..|+++.+++..|++.+.++|.+.+.+.+..-.+....+..+.|.+++++|+++|++|+++.|
T Consensus        19 ~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~l   90 (121)
T 2pjp_A           19 EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRL   90 (121)
T ss_dssp             SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceECHHHHHHHHHHHHHHHHHCCCccHHHHHHHH
Confidence            577899999999999999999999999999999998765555555566788899999999999999999986

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=98.82  E-value=8.9e-10  Score=56.23  Aligned_cols=33  Identities=21%  Similarity=0.269  Sum_probs=29.9

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      ..+|+|..+||+.||||.+||++|+++|++.|.
T Consensus        18 ~~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g~   50 (51)
T 1tc3_C           18 KLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT   50 (51)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHCSTTTTC
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHhhHHhcCC
Confidence            357999999999999999999999999988774

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=98.53  E-value=7.7e-08  Score=56.30  Aligned_cols=30  Identities=13%  Similarity=0.235  Sum_probs=28.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      |.|..+||+.||||.+||++|+++|...|.
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~~~~~~g~   52 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWIIKYGSNHN   52 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHHHHCCCST
T ss_pred             CChHHHHHHHHCcCHHHHHHHHHHHhhcCc
Confidence            899999999999999999999999998764

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=98.32  E-value=4.5e-06  Score=50.64  Aligned_cols=69  Identities=10%  Similarity=0.063  Sum_probs=45.1

Q ss_pred             cCCCCH-HHHHHHhccCHHHHHHHHHHHHH-------hcCCCccccCCCCCCCCCHHHHHHHHHHHHhC----CCCcHHH
Q psy15513          3 AAGVRP-CVISRQLRVSHGCVSKILNRYQE-------TGSIRPGVIGGSKPRVATPDVERRIEEYKGEN----PAMFSWE   70 (77)
Q Consensus         3 ~~G~s~-~~iA~rf~VS~stv~r~~~r~r~-------tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~----pd~tl~E   70 (77)
                      +.|.+. +++|+.||||.+||++|++.+..       .+...+.. . ..+....++.++.|..+|.+.    -.+|-..
T Consensus        22 ~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~~~~~~~~~~~~~-k-r~r~~~~~~~E~~L~~Wi~~~~~~g~pvs~~~   99 (131)
T 1hlv_A           22 ENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCR-K-TNKLSPYDKLEGLLIAWFQQIRAAGLPVKGII   99 (131)
T ss_dssp             HCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHHHHHHHGGGGGTC-C-CCCCCTTHHHHHHHHHHHHHHGGGTCCCCHHH
T ss_pred             HCCCCcHHHHHHHhCCCHHHHHHHHhchhhhcchhhhccccchhh-c-ccCCCCCHHHHHHHHHHHHHHHHCCCCCCHHH
Confidence            456554 59999999999999999998765       45444321 1 123446677788787877543    2355444


Q ss_pred             HHH
Q psy15513         71 IRD   73 (77)
Q Consensus        71 l~~   73 (77)
                      |++
T Consensus       100 I~~  102 (131)
T 1hlv_A          100 LKE  102 (131)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=98.32  E-value=2.8e-07  Score=53.41  Aligned_cols=33  Identities=9%  Similarity=0.135  Sum_probs=28.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.|.|..+||+.||||.+||++|+++|.+.+..
T Consensus        36 ~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~~~~   68 (87)
T 2elh_A           36 HDGESKASVARDIGVPESTLRGWCKNEDKLRFM   68 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHHHHHhcccc
Confidence            468999999999999999999999999875443

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=98.28  E-value=2.3e-07  Score=50.21  Aligned_cols=32  Identities=13%  Similarity=0.075  Sum_probs=28.1

Q ss_pred             cCCCC----HHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          3 AAGVR----PCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         3 ~~G~s----~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      +.|.|    ..++|+.||||.+|+++|+++|.+.+.
T Consensus        19 ~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~~~   54 (59)
T 2glo_A           19 RNDNDCKGNQRATARKYNIHRRQIQKWLQCESNLRS   54 (59)
T ss_dssp             HHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHHHH
T ss_pred             HcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            35778    999999999999999999999987653

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=98.22  E-value=1.7e-07  Score=48.12  Aligned_cols=27  Identities=4%  Similarity=0.015  Sum_probs=24.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..|+|..+||+.||||.+||++|++++
T Consensus        19 ~~g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           19 EKGHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HTTCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            578999999999999999999998764

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=98.08  E-value=1.2e-06  Score=51.93  Aligned_cols=31  Identities=6%  Similarity=0.075  Sum_probs=28.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      |.+..+||+.||||.+|+++|+++|...|..
T Consensus        30 g~s~~~va~~~gIs~~tl~~W~~~~~~~~~~   60 (108)
T 2rn7_A           30 WATICSIAPKIGCTPETLRVWVRQHERDTGG   60 (108)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHTTSCC
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHHHHhcccc
Confidence            4789999999999999999999999988754

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=98.06  E-value=1.2e-06  Score=46.21  Aligned_cols=27  Identities=30%  Similarity=0.263  Sum_probs=24.3

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ...|+|..+||+.||||.+||++|+++
T Consensus        28 ~~~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           28 AKMGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            357999999999999999999999864

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=98.06  E-value=6.1e-06  Score=47.88  Aligned_cols=60  Identities=8%  Similarity=0.086  Sum_probs=44.8

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK   60 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v   60 (77)
                      |.+.+++..++|+.+|||++||++-++...+.|-|...+.|......++++....+.+.+
T Consensus        32 L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l   91 (98)
T 3jth_A           32 LHNQELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLL   91 (98)
T ss_dssp             TTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHH
Confidence            345558999999999999999999999999999998776654443344444444454444

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

Probab=98.03  E-value=3.5e-06  Score=48.44  Aligned_cols=57  Identities=16%  Similarity=0.088  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      +++..++|+.|+||++||++.+++..+.|-|...+.|....-.+++.....+.+.+.
T Consensus        38 ~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l~   94 (99)
T 3cuo_A           38 GTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATLK   94 (99)
T ss_dssp             SEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHH
Confidence            589999999999999999999999999999977664433233455545555555443

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=97.94  E-value=4.3e-06  Score=49.85  Aligned_cols=59  Identities=10%  Similarity=-0.018  Sum_probs=43.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      +.+++..++|+.||||++||++.++...+.|-|...+.|....-.+++.....+.+.+.
T Consensus        36 ~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~l~   94 (108)
T 2kko_A           36 QGERAVEAIATATGMNLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFALVQ   94 (108)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHH
Confidence            44589999999999999999999999999999987765543333344444444554443

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

Probab=97.85  E-value=2.9e-05  Score=43.91  Aligned_cols=35  Identities=17%  Similarity=0.199  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..++|+.||||.+||++.++...+.|-|...
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34899999999999999999999999999999743

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=97.76  E-value=3.3e-05  Score=42.55  Aligned_cols=53  Identities=15%  Similarity=0.114  Sum_probs=38.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      ++..++|+.+|||.+|+++|++.    |.+ .|.+.|+.. .-...+..+||.+.+++.
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~----g~fP~piklG~~~-~w~~~ev~~Wl~~~~~~~   64 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKS----GDLPKAKVIHGRA-RWLYRDHCEFKNKLLSRA   64 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHH----HHCCCSEESSSCE-EEEHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC----CCCCCCEEeCCCe-EEeHHHHHHHHHHHHHhh
Confidence            67889999999999999999986    554 456666533 344466677777665543

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=97.74  E-value=2.2e-05  Score=47.45  Aligned_cols=33  Identities=9%  Similarity=0.012  Sum_probs=30.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..++|..++|++|+||.+++.+|.+.|++.|.-
T Consensus        48 ~g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~~   80 (101)
T 2oa4_A           48 YGLITLAEAKQTYGLSDEEFNSWVSALAEHGKD   80 (101)
T ss_dssp             HTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSS
T ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHH
Confidence            356999999999999999999999999998854

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=97.72  E-value=2.1e-05  Score=47.48  Aligned_cols=54  Identities=17%  Similarity=0.174  Sum_probs=37.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC-CCCCCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK-PRVATPDVERRIE   57 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~-~~~~~~~~~~~i~   57 (77)
                      .+|+++.+||++||||.++|+|++++.++.-+-..-| .|-. -.+..|++..+++
T Consensus        32 v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~~~~~P-~g~~rv~v~lP~~~a~~v   86 (101)
T 2w7n_A           32 VDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDKNLP-EGYARVTAVLPEHQAYIV   86 (101)
T ss_dssp             TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTCCC-TTEEEEEEEECHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC-CCeeEEeeecCHHHHHHH
Confidence            4799999999999999999999999999763211122 2232 2444455555554

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=97.70  E-value=3.3e-05  Score=45.96  Aligned_cols=36  Identities=6%  Similarity=-0.119  Sum_probs=31.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ..+.|..++|++|+||.+++.+|.+.|.+.|.-..+
T Consensus        47 ~g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~~L~   82 (95)
T 2jrt_A           47 HGLITEREALDRYSLSEEEFALWRSAVAAHGEKALK   82 (95)
T ss_dssp             TTSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTTSCC
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHHh
Confidence            356899999999999999999999999998866543

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

Probab=97.70  E-value=2e-05  Score=46.43  Aligned_cols=58  Identities=19%  Similarity=0.156  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      .+++..++|+.|+||++||++.+++..+.|-|...+.|....-.+++.....+...+.
T Consensus        33 ~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l~~~~~~~~~~~~~   90 (114)
T 2oqg_A           33 ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKVGREIRYRALGAELNKTARTLE   90 (114)
T ss_dssp             SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEechHHHHHHHHHHH
Confidence            4589999999999999999999999999999987655432223455544444444443

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=97.70  E-value=0.00023  Score=42.47  Aligned_cols=63  Identities=16%  Similarity=0.051  Sum_probs=44.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ++++.++|+.+|||.+|+..|-+.    |-+.|...  +|.  +.-++.+...   |..+  .+-++++.|+++.+
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~----Gll~p~~r~~~g~--R~Y~~~dl~~l~~I~~l--r~~G~sl~~I~~~l   68 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDI----GLLVPSERSHAGH--RRYSDADLDRLQQILFY--RELGFPLDEVAALL   68 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHH----TSSCCSEECSSCC--EEBCHHHHHHHHHHHHH--HHTTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC----CCCCCCccCCCCC--eecCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence            578999999999999999988654    99888653  333  3344444443   4444  33479999998765

>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=97.66  E-value=2.5e-05  Score=45.57  Aligned_cols=48  Identities=13%  Similarity=0.047  Sum_probs=38.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      +..++..++|+.+|||++||++-++...+.|=|...+.|......+++
T Consensus        34 ~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~   81 (102)
T 3pqk_A           34 EGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTE   81 (102)
T ss_dssp             TCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECS
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECc
Confidence            345899999999999999999999999999999877666443333443

>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=97.66  E-value=2.6e-05  Score=47.33  Aligned_cols=51  Identities=18%  Similarity=0.102  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~   54 (77)
                      .+++..++|+.||||++||++.++...+.|-|...+.|....-.+++....
T Consensus        55 ~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~  105 (122)
T 1u2w_A           55 EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIR  105 (122)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEESCHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEECCEEEEEECHHHHH
Confidence            458999999999999999999999999999997766554333333433333

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

Probab=97.65  E-value=2.5e-05  Score=49.47  Aligned_cols=61  Identities=13%  Similarity=0.132  Sum_probs=48.3

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      .+..++..+||+.|+||++||++-++..++.|=|...+.|..+.-.+++.....+.+++..
T Consensus        68 ~~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~~~~~l~~~l~~  128 (151)
T 3f6v_A           68 TSGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLDPQGLAQLRALFDS  128 (151)
T ss_dssp             GGCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHHH
Confidence            3455899999999999999999999999999999877666444445676666666666654

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=97.64  E-value=3e-05  Score=46.78  Aligned_cols=29  Identities=7%  Similarity=0.141  Sum_probs=25.3

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      .| ++.++||+.+|||.|||+|. ++.-...
T Consensus        56 ~ge~TQREIA~~lGiS~stISRi-~r~L~~l   85 (101)
T 1jhg_A           56 RGEMSQRELKNELGAGIATITRG-SNSLKAA   85 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHH-HHHHHHS
T ss_pred             cCCcCHHHHHHHHCCChhhhhHH-HHHHHHc
Confidence            67 99999999999999999999 7766543

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=97.64  E-value=9e-05  Score=49.12  Aligned_cols=68  Identities=10%  Similarity=-0.034  Sum_probs=43.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH-HhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC--CCCcHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ-ETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN--PAMFSWEIRDR   74 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r-~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~--pd~tl~El~~~   74 (77)
                      ..|+++.+||++||||+++|+||++..+ ..|-+.-=|.-    ..+.-.....+..+.+..  .++++.||.+.
T Consensus        22 ~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~----~~ls~p~~~~L~k~~~~l~~~~~~l~eLi~~   92 (192)
T 1zx4_A           22 NDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQ----SELTFSDYKTLCAVGDEMGNKNLEFDQLIQN   92 (192)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCG----GGCCHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCc----ccCccchHHHHHHHHHHhhhcCCCHHHHHHH
Confidence            5799999999999999999999999988 66655544321    112222344455544432  33455555443

>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A

Probab=97.63  E-value=0.00014  Score=52.74  Aligned_cols=70  Identities=9%  Similarity=-0.037  Sum_probs=44.1

Q ss_pred             cCCCCHH----HHHHHhccCHHHHHHHHHHHHHhcC------CCccccCCC---CCCCCCHHHHHHHHHHHHhCCCCcHH
Q psy15513          3 AAGVRPC----VISRQLRVSHGCVSKILNRYQETGS------IRPGVIGGS---KPRVATPDVERRIEEYKGENPAMFSW   69 (77)
Q Consensus         3 ~~G~s~~----~iA~rf~VS~stv~r~~~r~r~tG~------v~pk~~gg~---~~~~~~~~~~~~i~~~v~~~pd~tl~   69 (77)
                      ..|.+..    .+|+.+|||.+|++||+++|+..|.      +.|+..+..   +.....++..+.|.+.....+..++.
T Consensus        46 ~~g~~~~~a~~~~a~~~gvS~~Tl~rW~~~y~~~~~~~gl~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~yl~~~~~s~~  125 (529)
T 4fcy_A           46 NQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVDGRGASRRNVHKSEFDEDAWQFLIADYLRPEKPAFR  125 (529)
T ss_dssp             HTTCCHHHHHHHHHHHTTSCHHHHHHHHHHHHTSCGGGHHHHHC------------CCCCHHHHHHHHHHHTSTTCCCHH
T ss_pred             hcCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCcccCceecccCCCCCCCCCCcCcCCHHHHHHHHHHHhCcCCCCHH
Confidence            3566654    4599999999999999999986553      355532221   12345677777888777666666665


Q ss_pred             HHH
Q psy15513         70 EIR   72 (77)
Q Consensus        70 El~   72 (77)
                      .+-
T Consensus       126 ~~~  128 (529)
T 4fcy_A          126 KCY  128 (529)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=97.63  E-value=2.4e-05  Score=43.21  Aligned_cols=29  Identities=14%  Similarity=0.141  Sum_probs=23.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ++..++|+.||||.+|+++|.+.    |.  |...
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~----G~--P~~~   31 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ----GM--PVLR   31 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT----TC--CCSS
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC----CC--CeEe
Confidence            46789999999999999999865    76  5443

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=97.60  E-value=1.9e-05  Score=47.54  Aligned_cols=59  Identities=10%  Similarity=0.142  Sum_probs=44.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG   61 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~   61 (77)
                      +..++..++|+.||||++||++-++...+.|-|...+.|....-.+++.....+.+++.
T Consensus        29 ~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~~   87 (118)
T 3f6o_A           29 RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWLA   87 (118)
T ss_dssp             TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHHH
Confidence            44589999999999999999999999999999987776644444455545555544443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=97.59  E-value=5e-05  Score=44.26  Aligned_cols=37  Identities=22%  Similarity=0.314  Sum_probs=34.1

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .++|++..+||+.||||.++|.+-+.+..+.|-|.-.
T Consensus        27 ~~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           27 GIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             SSSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            4678999999999999999999999999999999765

>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=97.58  E-value=3.9e-05  Score=45.26  Aligned_cols=39  Identities=23%  Similarity=0.215  Sum_probs=34.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      +.+++..++|+.+|||++||++.++...+.|-|...+.|
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~g   75 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQG   75 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            356899999999999999999999999999999876654

>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=97.57  E-value=7.6e-05  Score=44.03  Aligned_cols=67  Identities=21%  Similarity=0.131  Sum_probs=37.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc----ccCCCCCC--CCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG----VIGGSKPR--VATPDVERRIEEYKGENPAMFSWEIRDR   74 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk----~~gg~~~~--~~~~~~~~~i~~~v~~~pd~tl~El~~~   74 (77)
                      .++.+++|+.||||++||++-+++..+.|-|...    +.+|....  ..++.   .+.+++...-+..+..+..+
T Consensus        33 ~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~~~~~~~~---~i~~~~~~~~~~~~e~l~~~  105 (110)
T 1q1h_A           33 EMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYWKPNID---QINEILLNRKRLILDKLKTR  105 (110)
T ss_dssp             CBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEEECTHH---HHC-----------------
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecccCCCceEEEEeecCHH---HHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999999776    55543323  34432   24444433333444444433

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=97.53  E-value=6.1e-05  Score=43.33  Aligned_cols=38  Identities=13%  Similarity=0.156  Sum_probs=34.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+++..++|+.||||++||++.++...+.|-|...+.
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence            45689999999999999999999999999999976544

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=97.51  E-value=0.00043  Score=39.19  Aligned_cols=66  Identities=15%  Similarity=0.100  Sum_probs=44.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC-CCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG-GSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g-g~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      -+++.++|+.+|||.+|+..|-+.   .|-+.|.... ++. +.-++++...   |..+.. +-++++.|+++.|
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~~---~gl~~p~r~~~~g~-R~Y~~~dl~~l~~I~~l~~-~~G~sl~ei~~~l   74 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWERR---YGFPRPLRSEGNNY-RVYSREEVEAVRRVARLIQ-EEGLSVSEAIAQV   74 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHHH---TCCSCCBSSSCSSS-CEECHHHHHHHHHHHHHHH-HTSTHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHh---CCCCCCcCCCCCCe-eecCHHHHHHHHHHHHHHH-HCCCCHHHHHHHH
Confidence            478999999999999999988544   3666775432 222 3344444544   444431 3469999999876

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.49  E-value=0.00013  Score=38.59  Aligned_cols=33  Identities=18%  Similarity=0.096  Sum_probs=28.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||..+|||.+||...+++.++.=.+
T Consensus        11 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A           11 DEGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             HTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            479999999999999999999999998865433

>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=97.48  E-value=6.1e-05  Score=45.86  Aligned_cols=41  Identities=17%  Similarity=0.133  Sum_probs=35.6

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      .+.+++..++|+.||||+++|++.++...+.|-+...+.|.
T Consensus        56 ~~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~~gr   96 (122)
T 1r1t_A           56 ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGR   96 (122)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            34468999999999999999999999999999998766553

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=97.47  E-value=0.00057  Score=42.58  Aligned_cols=70  Identities=13%  Similarity=0.028  Sum_probs=46.1

Q ss_pred             CCCCHHHHHH----Hh--ccCHHHHHHHHHHHHHhcCC-Cccc-cCCCCCCCCCHHHHHHHHHHHHh---CCCCcHHHHH
Q psy15513          4 AGVRPCVISR----QL--RVSHGCVSKILNRYQETGSI-RPGV-IGGSKPRVATPDVERRIEEYKGE---NPAMFSWEIR   72 (77)
Q Consensus         4 ~G~s~~~iA~----rf--~VS~stv~r~~~r~r~tG~v-~pk~-~gg~~~~~~~~~~~~~i~~~v~~---~pd~tl~El~   72 (77)
                      .+++..++|+    .|  +||.+||++|++...+--+. ...+ ..-..+....++.++.+..++.+   ++.+|-..|+
T Consensus        29 ~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~~~~~~~~~kr~r~~~~~~le~~L~~Wi~~~~~~~~it~~~I~  108 (144)
T 1iuf_A           29 NRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDNTVEKPWDVKRNRPPKYPLLEAALFEWQVQQGDDATLSGETIK  108 (144)
T ss_dssp             SCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTTSCSSSSSSSCCCCCSCHHHHHHHHHHHHHTCTTCCCSSHHHH
T ss_pred             CCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhhcccccccccCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            4589999999    99  99999999999987653222 1111 11112345567777777777766   5567755555


Q ss_pred             H
Q psy15513         73 D   73 (77)
Q Consensus        73 ~   73 (77)
                      +
T Consensus       109 ~  109 (144)
T 1iuf_A          109 R  109 (144)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=97.47  E-value=0.00018  Score=38.78  Aligned_cols=30  Identities=10%  Similarity=0.112  Sum_probs=27.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..+|||.+||.+++.+.++.
T Consensus        29 ~~g~s~~eIA~~lgis~~tv~~~~~ra~~~   58 (70)
T 2o8x_A           29 LLGLSYADAAAVCGCPVGTIRSRVARARDA   58 (70)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            479999999999999999999999987653

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

Probab=97.47  E-value=9.2e-05  Score=40.92  Aligned_cols=34  Identities=12%  Similarity=0.236  Sum_probs=31.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+|..+||+.||||.+||.+.++.+++.|-|...
T Consensus        25 ~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~~   58 (67)
T 2heo_A           25 PVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSP   58 (67)
T ss_dssp             CEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEecC
Confidence            4899999999999999999999999999998653

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=97.47  E-value=0.00039  Score=41.43  Aligned_cols=64  Identities=17%  Similarity=0.099  Sum_probs=43.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||.+|+..|-+    .|-+.|.....+..+.-++.+...   |..+.  +-++++.|+.+.+
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~l~--~~G~~l~~I~~~l   69 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDN----IELLNPSALTDAGYRLYSDADLERLQQILFFK--EIGFRLDEIKEML   69 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH----TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHH--HTTCCHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----CCCCCCCeECCCCCeeeCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence            6889999999999999998854    598888652211223344544443   33432  3368899988765

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=97.44  E-value=0.00013  Score=39.71  Aligned_cols=30  Identities=13%  Similarity=0.107  Sum_probs=27.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..|+|..+||..||||.+||++++++.++.
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~k   53 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAMQK   53 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            479999999999999999999999997654

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=97.44  E-value=0.0001  Score=42.12  Aligned_cols=57  Identities=11%  Similarity=0.112  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERRIEEYK   60 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~i~~~v   60 (77)
                      .+++..++|+.++||++||++.+++..+.|-|...+..++++   -.+++.-.+.+..+.
T Consensus        29 ~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~~~~   88 (100)
T 1ub9_A           29 RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHHHHH
Confidence            458999999999999999999999999999997543222222   245665544444444

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=97.43  E-value=0.00013  Score=41.56  Aligned_cols=34  Identities=12%  Similarity=0.244  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +++..+||+.||||.+||.+.+.+..+.|-|.-.
T Consensus        31 ~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~   64 (77)
T 1qgp_A           31 ATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   64 (77)
T ss_dssp             CEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            6899999999999999999999999999998543

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

Probab=97.43  E-value=0.00014  Score=43.89  Aligned_cols=42  Identities=17%  Similarity=0.276  Sum_probs=32.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      ..|++..++|+.++||++||++.+++..+.|=|.-.+...++
T Consensus        49 ~~~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~~~d~   90 (146)
T 3tgn_A           49 EESLTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKDSKDA   90 (146)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-------
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccCCCCC
Confidence            445999999999999999999999999999999766543333

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

Probab=97.41  E-value=0.00016  Score=41.43  Aligned_cols=40  Identities=15%  Similarity=0.212  Sum_probs=33.9

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc-cCCC
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGS   43 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~-~gg~   43 (77)
                      .| ++..++|+.|+||.+||.+-+..+.+.|-+..-+ +||.
T Consensus        14 ~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~~~~Gga   55 (78)
T 1xn7_A           14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQEEPDG   55 (78)
T ss_dssp             SCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECCCCCC
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCcCCC
Confidence            44 8999999999999999999999999999986542 3443

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=97.41  E-value=0.00015  Score=50.14  Aligned_cols=40  Identities=20%  Similarity=0.320  Sum_probs=36.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ..|++..++|++|+||..||+|.++..++.|-|.-+-+||
T Consensus        19 ~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri~g~   58 (315)
T 2w48_A           19 EQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYD   58 (315)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEecCC
Confidence            4679999999999999999999999999999998555665

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=97.40  E-value=2.3e-05  Score=50.69  Aligned_cols=32  Identities=13%  Similarity=0.069  Sum_probs=0.0

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      |..+|+|..+||+.||||.+|++||++.....
T Consensus       154 l~~~G~s~~~Ia~~l~vs~~Tvyr~l~~~~~~  185 (193)
T 3uj3_X          154 LLAQGIPRKQVALIYDVALSTLYKKHPAKRAH  185 (193)
T ss_dssp             --------------------------------
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHHhhhc
Confidence            45689999999999999999999999986654

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=97.40  E-value=4e-05  Score=44.87  Aligned_cols=56  Identities=13%  Similarity=0.058  Sum_probs=40.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK   60 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v   60 (77)
                      .+++.+++|+.+|+|+++|++-++..++. -+...+.|....-.++++....+.+++
T Consensus        40 ~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~~gr~~~y~l~~~~~~~~~~~l   95 (99)
T 2zkz_A           40 KALNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNRQGLEIYYSINNPKVEGIIKLL   95 (99)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEEETTEEEEECCCHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheEeCcEEEEEEChHHHHHHHHHH
Confidence            45899999999999999999999999998 776665554333344444455454443

>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=97.38  E-value=0.00041  Score=41.76  Aligned_cols=56  Identities=11%  Similarity=0.035  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~   59 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.++
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~~  110 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESL  110 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence            5689999999999999999999999999999987665555542   4566544444443

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=97.37  E-value=0.00014  Score=43.66  Aligned_cols=42  Identities=29%  Similarity=0.377  Sum_probs=35.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      +.+++..++|+.+++|++||++.+++..+.|=|...+..+++
T Consensus        39 ~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~~d~   80 (152)
T 1ku9_A           39 DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGER   80 (152)
T ss_dssp             SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCS
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCc
Confidence            456999999999999999999999999999999766533333

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=97.36  E-value=0.00041  Score=41.51  Aligned_cols=52  Identities=19%  Similarity=0.123  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|+++.++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        46 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~  100 (139)
T 3eco_A           46 DGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKL  100 (139)
T ss_dssp             TCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHH
T ss_pred             CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHH
Confidence            4789999999999999999999999999999976655445543   355554443

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=97.34  E-value=0.0002  Score=40.66  Aligned_cols=31  Identities=19%  Similarity=0.284  Sum_probs=28.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ..|+|..+||+.||||.+||...+++.++.=
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   64 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHMLKKM   64 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999987654

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=97.34  E-value=0.00019  Score=39.72  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||++.|||++||+++++
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLn   22 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVIN   22 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4788999999999999999995

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

Probab=97.31  E-value=0.00082  Score=40.04  Aligned_cols=53  Identities=19%  Similarity=0.196  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .++++.++|+.+++|+++|++.+++..+.|-|.-.+.+.+++.   .+|+.-.+.+
T Consensus        47 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~  102 (138)
T 1jgs_A           47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAIC  102 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHH
Confidence            5689999999999999999999999999999976655444442   4566544433

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=97.31  E-value=0.002  Score=40.28  Aligned_cols=65  Identities=17%  Similarity=0.028  Sum_probs=44.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      .+++.++|+.+|||..|+..|-+.    |-+.|.....+..+.-++.+..   +|..+.  .-++++.||++.|
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~~----GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr--~~G~sL~eIk~~l   69 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYERI----GLIPPIHRNESGVRKFGAEDLRWILFTRQMR--RAGLSIEALIDYL   69 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHH----TSSCCCCBCTTSCBCBCHHHHHHHHHHHHHH--HTTCCHHHHHHHH
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCCCCCeeeCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            478999999999999999887554    9998833322222334444444   455553  3479999998765

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=97.28  E-value=0.0003  Score=41.80  Aligned_cols=38  Identities=13%  Similarity=0.177  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..++|+.++||++||++.+++..+.|-+.-.+.|
T Consensus        44 ~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~~~   81 (119)
T 2lkp_A           44 GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAG   81 (119)
T ss_dssp             CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEET
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            46899999999999999999999999999988655433

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=97.28  E-value=0.00059  Score=41.38  Aligned_cols=52  Identities=10%  Similarity=0.164  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|+++.++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        56 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~  110 (148)
T 3jw4_A           56 SGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAAL  110 (148)
T ss_dssp             TCCCHHHHHHC------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHH
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHH
Confidence            5799999999999999999999999999999987765555542   355544433

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=97.27  E-value=0.00045  Score=41.92  Aligned_cols=51  Identities=16%  Similarity=0.194  Sum_probs=37.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEI   71 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El   71 (77)
                      +.|+|+.++|+.+|||++||++|-+     |...|.           .. ...+..++..+|+. +.+|
T Consensus        82 ~~glsq~~la~~~g~s~~~i~~~E~-----g~~~p~-----------~~-~~~l~~~~~~~p~~-~~~l  132 (133)
T 3o9x_A           82 KLSLTQKEASEIFGGGVNAFSRYEK-----GNAQPH-----------PS-TIKLLRVLDKHPEL-LNEI  132 (133)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHH-----TSSCCC-----------HH-HHHHHHHHHHCGGG-HHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHC-----CCCCCC-----------HH-HHHHHHHHccCHHH-HHHh
Confidence            4799999999999999999999854     543332           11 35577888889875 4444

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

Probab=97.27  E-value=0.00039  Score=41.69  Aligned_cols=42  Identities=10%  Similarity=0.224  Sum_probs=35.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++
T Consensus        51 ~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~~d~R   92 (146)
T 2fbh_A           51 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRR   92 (146)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTTBC
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCCcccC
Confidence            568999999999999999999999999999997665443443

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=97.27  E-value=0.00099  Score=39.94  Aligned_cols=54  Identities=7%  Similarity=0.068  Sum_probs=41.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      ..+++..++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-...+
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~  104 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETF  104 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHH
Confidence            35689999999999999999999999999999976655444432   4566544433

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=97.26  E-value=0.00015  Score=38.96  Aligned_cols=24  Identities=17%  Similarity=0.411  Sum_probs=22.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.| |..++|+++|||+++|++|++
T Consensus        12 ~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A           12 EHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            468 999999999999999999993

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

Probab=97.25  E-value=0.00036  Score=39.92  Aligned_cols=34  Identities=18%  Similarity=0.123  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .|.+|||+.||||.+||.+-++...+.|-+.--+
T Consensus        25 psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A           25 VKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence            5799999999999999999999999999997654

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

Probab=97.24  E-value=0.00065  Score=40.90  Aligned_cols=52  Identities=10%  Similarity=0.024  Sum_probs=39.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|+++.++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~  104 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKE  104 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHH
Confidence            5689999999999999999999999999999976665445443   355554443

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=97.24  E-value=0.0018  Score=40.06  Aligned_cols=62  Identities=10%  Similarity=0.086  Sum_probs=42.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||..|+..|-+    .|-+.|...  +|.  +.-++.+..   +|..+.  +-++++.|+++.|
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~----~Gll~p~~r~~~g~--R~Y~~~dl~~l~~I~~lr--~~G~sl~eI~~~l   67 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE----KGLVTPPMRSENGY--RTYTQQHLNELTLLRQAR--QVGFNLEESGELV   67 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----TTCSCCCEECTTSC--EECCHHHHHHHHHHHHHH--HTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCC--eeeCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence            6889999999999999988854    588877532  333  334444444   344443  3479999998765

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

Probab=97.24  E-value=0.00086  Score=40.48  Aligned_cols=54  Identities=19%  Similarity=0.089  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERRIE   57 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~i~   57 (77)
                      .+++..++|+.++||+++|++.+++..+.|=|.-.+...+++   -.+|+.-.+.+.
T Consensus        53 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~  109 (148)
T 3nrv_A           53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE  109 (148)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHH
Confidence            468999999999999999999999999999997665444443   245555444333

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=97.23  E-value=0.00045  Score=39.64  Aligned_cols=29  Identities=21%  Similarity=0.242  Sum_probs=26.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..||||.+||..++.+.+.
T Consensus        51 ~~g~s~~eIA~~lgis~~tV~~~l~ra~~   79 (92)
T 3hug_A           51 YRGWSTAQIATDLGIAEGTVKSRLHYAVR   79 (92)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47999999999999999999999988764

>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=97.22  E-value=0.00027  Score=40.77  Aligned_cols=36  Identities=17%  Similarity=0.010  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..++|+.|+||++||++.++.+.+.|-|...+
T Consensus        42 ~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           42 KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            458999999999999999999999999999997655

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

Probab=97.22  E-value=0.00067  Score=40.87  Aligned_cols=53  Identities=9%  Similarity=0.069  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .|+++.++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+
T Consensus        50 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~  105 (142)
T 3ech_A           50 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIH  105 (142)
T ss_dssp             TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHH
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHH
Confidence            5799999999999999999999999999999976665444442   3555444433

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=97.22  E-value=0.00084  Score=37.22  Aligned_cols=42  Identities=19%  Similarity=0.203  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      ++..+||++.|||++||++++.             |  ++. ..++..+.|.+.+++.
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln-------------~--~~~-vs~~t~~rV~~~a~~l   51 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM-------------N--PDK-VSQATRNRVEKAAREV   51 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT-------------C--CCC-SCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc-------------C--CCC-CCHHHHHHHHHHHHHh
Confidence            6899999999999999999883             1  112 3466677777766653

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=97.22  E-value=0.00054  Score=37.22  Aligned_cols=29  Identities=10%  Similarity=0.117  Sum_probs=26.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..+|||.+||..++.+-++.
T Consensus        24 ~g~s~~eIA~~lgis~~tV~~~~~ra~~k   52 (68)
T 2p7v_B           24 TDYTLEEVGKQFDVTRERIRQIEAKALRK   52 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHG
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            79999999999999999999999987764

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

Probab=97.21  E-value=0.00048  Score=42.73  Aligned_cols=43  Identities=9%  Similarity=0.227  Sum_probs=37.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~   46 (77)
                      .|.++.++|+.++|+++||++.+++..+.|-|.-.+...+++.
T Consensus        45 ~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~~DrR~   87 (151)
T 4aik_A           45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSANDRRA   87 (151)
T ss_dssp             TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTC
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCCCCCcc
Confidence            5688899999999999999999999999999987776666653

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=97.21  E-value=0.00045  Score=41.28  Aligned_cols=41  Identities=12%  Similarity=0.148  Sum_probs=35.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      ++++.++|+.++||+++|++.+++..+.|-|.-.+...+++
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~d~R   90 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSR   90 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTT
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeCCCcCCC
Confidence            69999999999999999999999999999997665544443

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=97.20  E-value=0.0014  Score=44.05  Aligned_cols=66  Identities=20%  Similarity=0.171  Sum_probs=41.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH--HhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK--GENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v--~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||.+|+..|-+    .|-+.|.....+..+.-++.+...|....  ....++++.||++.|
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~----~GLl~p~~R~~~gyR~Y~~~dl~~L~~I~~lr~~~G~sL~eIk~~l   68 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLR----EGLLPPGRQVNATTAEYDEDHLRRLRLVRALIQVGKVPVATAREVL   68 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----HTSSCCC---------CCHHHHHHHHHHHHHHHTTCCCHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCeeCCCCceeeCHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            6889999999999999988754    49888743322222344555565554332  233369999998866

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

Probab=97.19  E-value=0.001  Score=41.08  Aligned_cols=53  Identities=15%  Similarity=0.159  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+
T Consensus        59 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~  114 (162)
T 3k0l_A           59 PNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKL  114 (162)
T ss_dssp             TTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHH
Confidence            5799999999999999999999999999999987665555553   4556544433

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=97.19  E-value=0.00048  Score=41.65  Aligned_cols=29  Identities=21%  Similarity=0.219  Sum_probs=26.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.+||++++.+-+.
T Consensus        36 ~~g~s~~EIA~~lgiS~~tV~~~l~ra~~   64 (113)
T 1s7o_A           36 ADDYSLAEIADEFGVSRQAVYDNIKRTEK   64 (113)
T ss_dssp             HTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47999999999999999999999998775

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

Probab=97.19  E-value=0.001  Score=40.09  Aligned_cols=53  Identities=11%  Similarity=0.004  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-.+.+
T Consensus        44 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~   99 (145)
T 3g3z_A           44 GSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYA   99 (145)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHH
Confidence            4699999999999999999999999999999976655444442   4566544433

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=97.18  E-value=0.00039  Score=38.40  Aligned_cols=31  Identities=19%  Similarity=0.087  Sum_probs=28.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -.|++..+||..||||.+||..++.+.++.=
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl   59 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHRANVMAKM   59 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999988653

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=97.18  E-value=0.00046  Score=39.73  Aligned_cols=34  Identities=12%  Similarity=0.244  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +++..+||+.||||.++|.+.+.+..+.|-|.-.
T Consensus        27 ~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~   60 (81)
T 1qbj_A           27 ATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   60 (81)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            4899999999999999999999999999998643

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=97.18  E-value=0.00024  Score=39.49  Aligned_cols=22  Identities=23%  Similarity=0.357  Sum_probs=20.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +..++|+.||||+++|++|++.
T Consensus        15 sq~~~A~~Lgvsq~aVS~~~~~   36 (65)
T 2cw1_A           15 NQEYAARALGLSQKLIEEVLKR   36 (65)
T ss_dssp             CHHHHHHHSSSCHHHHHHHHHT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHh
Confidence            8999999999999999999943

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=97.17  E-value=6.7e-05  Score=40.66  Aligned_cols=23  Identities=17%  Similarity=0.115  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .|.+..++|+.+|||+++|++|.
T Consensus         9 ~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            9 HFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HcCCHHHHHHHhCCCHHHHHHHH
Confidence            45699999999999999999996

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=97.17  E-value=0.00031  Score=39.65  Aligned_cols=21  Identities=19%  Similarity=0.131  Sum_probs=19.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +..++|+.||||+++|++|+.
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~   32 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQ   32 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHh
Confidence            578999999999999999996

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=97.17  E-value=0.00029  Score=37.13  Aligned_cols=25  Identities=16%  Similarity=0.198  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        12 ~~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A           12 KKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999964

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=97.16  E-value=0.0019  Score=40.58  Aligned_cols=66  Identities=14%  Similarity=0.029  Sum_probs=44.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      ..+++.++|+.+|||.+|+..|-+.    |-+.|.....+..+.=++.+...   |..+.  .-++++.|+++.|
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~~----GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr--~~G~sl~~I~~~l   71 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDKI----NLLKPSDYTEGGHRLYTKDDLYVLQQIQSFK--HLGFSLGEIQNII   71 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHT----TSSCCSEECTTSCEEBCHHHHHHHHHHHHHH--HTTCCHHHHHHHH
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHC----CCCCCCeECCCCCEeeCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            4589999999999999999877544    99987643212223344545544   34443  3468888888755

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.16  E-value=0.0012  Score=39.77  Aligned_cols=54  Identities=15%  Similarity=0.214  Sum_probs=38.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      ..+++..++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-...+
T Consensus        48 ~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~  104 (147)
T 2hr3_A           48 GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNL  104 (147)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHH
T ss_pred             CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHH
Confidence            35689999999999999999999999999999976654333332   4566544433

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

Probab=97.14  E-value=0.00087  Score=41.16  Aligned_cols=51  Identities=12%  Similarity=0.230  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+
T Consensus        63 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~  116 (159)
T 3s2w_A           63 DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKK  116 (159)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHH
Confidence            5689999999999999999999999999999977665555543   35554443

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=97.14  E-value=0.0013  Score=39.68  Aligned_cols=51  Identities=22%  Similarity=0.242  Sum_probs=39.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-..
T Consensus        53 ~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~  106 (152)
T 3bj6_A           53 PGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEA  106 (152)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHH
Confidence            4689999999999999999999999999999976655444432   35664433

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=97.13  E-value=0.0012  Score=39.65  Aligned_cols=51  Identities=20%  Similarity=0.225  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|++..++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-..
T Consensus        42 ~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~   95 (144)
T 1lj9_A           42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKN   95 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHH
T ss_pred             cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHH
Confidence            4689999999999999999999999999999976655444442   35655443

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=97.13  E-value=0.00076  Score=37.09  Aligned_cols=29  Identities=10%  Similarity=0.033  Sum_probs=26.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      .|+|..+||..+|||.+||..++.+-.+.
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~k   57 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALRK   57 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            68999999999999999999998886643

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

Probab=97.12  E-value=0.00061  Score=40.65  Aligned_cols=41  Identities=17%  Similarity=0.265  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...++
T Consensus        44 ~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~~d~   84 (142)
T 3bdd_A           44 APLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNPDNQ   84 (142)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSST
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCC
Confidence            46899999999999999999999999999999765543333

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

Probab=97.11  E-value=0.00077  Score=41.06  Aligned_cols=55  Identities=18%  Similarity=0.254  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEE   58 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~   58 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.+
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  111 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEA  111 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHH
Confidence            5689999999999999999999999999999977665445442   355554444433

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=97.11  E-value=0.001  Score=40.36  Aligned_cols=53  Identities=13%  Similarity=0.190  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .++++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-.+.+
T Consensus        53 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~  108 (150)
T 3fm5_A           53 EGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLR  108 (150)
T ss_dssp             TCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHH
Confidence            3579999999999999999999999999999977665555543   3555544433

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

Probab=97.11  E-value=0.00024  Score=41.67  Aligned_cols=33  Identities=15%  Similarity=0.269  Sum_probs=30.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|+.|+||.+||.+-+.++.+.|-+..-
T Consensus        17 vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A           17 MEAKQLSARLQTPQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEE
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            899999999999999999999999999998654

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

Probab=97.11  E-value=0.0015  Score=39.45  Aligned_cols=51  Identities=10%  Similarity=0.113  Sum_probs=38.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~   54 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++   -.+|+.-.+
T Consensus        55 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~  108 (150)
T 2rdp_A           55 GDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGER  108 (150)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHH
Confidence            468999999999999999999999999999997665444443   235555443

>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A

Probab=97.11  E-value=0.00025  Score=45.34  Aligned_cols=27  Identities=22%  Similarity=0.412  Sum_probs=24.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ..+|+|..+||+.||||.+||++|++.
T Consensus       155 ~~~G~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          155 WQQGLGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            457999999999999999999999974

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=97.10  E-value=0.0003  Score=42.51  Aligned_cols=51  Identities=6%  Similarity=0.078  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|++-.+
T Consensus        49 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~  102 (140)
T 3hsr_A           49 EKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKA  102 (140)
T ss_dssp             CEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHH
Confidence            4689999999999999999999999999999976665445442   35555443

>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=97.10  E-value=0.00029  Score=41.90  Aligned_cols=49  Identities=18%  Similarity=0.323  Sum_probs=40.0

Q ss_pred             cCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHH
Q psy15513          3 AAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~   51 (77)
                      +.+++..++|+.+ +||++||++.+++..+.|-|...+...+++.   .+|+.
T Consensus        33 ~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~   85 (112)
T 1z7u_A           33 QGTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPE   85 (112)
T ss_dssp             HSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHH
T ss_pred             hCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHh
Confidence            4568999999999 9999999999999999999987665544442   45664

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=97.09  E-value=0.0016  Score=41.51  Aligned_cols=52  Identities=12%  Similarity=0.093  Sum_probs=41.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      ..|+++.++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-.+
T Consensus        55 ~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~  109 (189)
T 3nqo_A           55 EEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKK  109 (189)
T ss_dssp             GGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHH
Confidence            35799999999999999999999999999999987666555553   35554333

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=97.08  E-value=0.00077  Score=39.15  Aligned_cols=33  Identities=12%  Similarity=0.201  Sum_probs=28.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      -.|+|..+||..+|||.+||..++.+.++.=.+
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            479999999999999999999999998865433

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=97.07  E-value=0.00058  Score=38.27  Aligned_cols=37  Identities=16%  Similarity=0.331  Sum_probs=33.1

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..++..+|+..|     +||.+||+|.++.+.+.|-|.....
T Consensus        32 ~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             SSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEee
Confidence            358999999999     9999999999999999999975544

>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=97.07  E-value=0.00039  Score=41.05  Aligned_cols=44  Identities=16%  Similarity=0.269  Sum_probs=36.6

Q ss_pred             ccCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         2 ~~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+.+++..++|+.+ +||++++++.+++..+.|=|...+...+++
T Consensus        24 ~~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~d~r   68 (107)
T 2hzt_A           24 THGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPP   68 (107)
T ss_dssp             TTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             HhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCCCCC
Confidence            34458999999999 999999999999999999997665544433

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=97.06  E-value=0.00057  Score=41.16  Aligned_cols=42  Identities=17%  Similarity=0.241  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++
T Consensus        53 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R   94 (147)
T 1z91_A           53 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDER   94 (147)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSSCTT
T ss_pred             CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCCCCCC
Confidence            458899999999999999999999999999997766544444

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=97.06  E-value=0.0002  Score=42.42  Aligned_cols=26  Identities=27%  Similarity=0.272  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.|++..++|+.||||.+||+|++..
T Consensus        18 ~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A           18 ETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            35689999999999999999999964

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=97.06  E-value=0.00041  Score=37.08  Aligned_cols=25  Identities=12%  Similarity=0.106  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||+++|++|.+
T Consensus        14 ~~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A           14 ALKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4799999999999999999999974

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=97.06  E-value=0.00042  Score=36.85  Aligned_cols=25  Identities=8%  Similarity=0.319  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||+++|++|.+
T Consensus        12 ~~glsq~~lA~~~gis~~~i~~~e~   36 (69)
T 1r69_A           12 QLGLNQAELAQKVGTTQQSIEQLEN   36 (69)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999953

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=97.05  E-value=0.00057  Score=42.32  Aligned_cols=63  Identities=13%  Similarity=0.177  Sum_probs=44.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc-------cccCCCCCC----CCCHHHHHHHHHHHHhCCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP-------GVIGGSKPR----VATPDVERRIEEYKGENPAMF   67 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p-------k~~gg~~~~----~~~~~~~~~i~~~v~~~pd~t   67 (77)
                      .+|..++|+.+|+|.+||.+.+++..+.|-+.-       .+.|-+-.-    ...+...+.+.+.+.+.|.++
T Consensus        21 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~G~~~~a~v~v~~~~~~~~~~~~~l~~~p~V~   94 (151)
T 2cyy_A           21 KAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGYSMLAFILVKVKAGKYSEVASNLAKYPEIV   94 (151)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCCCCCCCGGGGTCCEEEEEEEEECTTCHHHHHHHHHTCTTEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHCCccEEEEEEEEECcccHHHHHHHHhcCCCee
Confidence            489999999999999999999999999998853       333321000    111223455677777777653

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=97.05  E-value=0.00055  Score=39.26  Aligned_cols=31  Identities=13%  Similarity=0.047  Sum_probs=28.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -.|+|..+||..||||.+||..++.+.++.=
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   72 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVSNILSKL   72 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999988654

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=97.05  E-value=0.00057  Score=43.94  Aligned_cols=24  Identities=4%  Similarity=0.029  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      |.|..+||+.+|||.+|+++|.+.
T Consensus        48 ~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           48 KRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHc
Confidence            799999999999999999999995

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=97.04  E-value=0.0019  Score=39.41  Aligned_cols=53  Identities=11%  Similarity=0.103  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-...+
T Consensus        57 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~  112 (154)
T 2eth_A           57 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIF  112 (154)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHH
Confidence            4689999999999999999999999999999976654444442   3566544433

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=97.04  E-value=0.00035  Score=38.55  Aligned_cols=47  Identities=13%  Similarity=0.183  Sum_probs=35.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~   66 (77)
                      +.|+|..++|+.+|||++||++|-+     |...|.           .... .+......+|+.
T Consensus        22 ~~gltq~elA~~~gvs~~tis~~E~-----G~~~p~-----------~~~~-~l~~~l~~~p~~   68 (73)
T 3fmy_A           22 KLSLTQKEASEIFGGGVNAFSRYEK-----GNAXPH-----------PSTI-KLLRVLDKHPEL   68 (73)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHT-----TSSCCC-----------HHHH-HHHHHHHHCGGG
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc-----CCCCCC-----------HHHH-HHHHHHCCCHHH
Confidence            3699999999999999999999853     543332           2223 577888888864

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=97.04  E-value=0.00095  Score=38.05  Aligned_cols=30  Identities=7%  Similarity=-0.048  Sum_probs=27.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      .|+|..+||..+|||.+||..++.+-+..=
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~kL   66 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALRKL   66 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999999877643

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

Probab=97.03  E-value=0.0014  Score=40.15  Aligned_cols=52  Identities=19%  Similarity=0.192  Sum_probs=39.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        65 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~  119 (162)
T 3cjn_A           65 DGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAV  119 (162)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHH
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHH
Confidence            4689999999999999999999999999999976554333332   456654443

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

Probab=97.03  E-value=0.0019  Score=39.29  Aligned_cols=53  Identities=9%  Similarity=0.060  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~i   56 (77)
                      .+++..++|+.++|++++|++.+++..+.|-|.-.+...+++   -.+|+.-...+
T Consensus        56 ~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~  111 (155)
T 3cdh_A           56 DAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALA  111 (155)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHH
Confidence            568999999999999999999999999999997654433333   24566544433

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=97.02  E-value=0.00077  Score=41.47  Aligned_cols=62  Identities=13%  Similarity=0.200  Sum_probs=43.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc-------cccCCCCC---CCC-C--HHHHHHHHHHHHhCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP-------GVIGGSKP---RVA-T--PDVERRIEEYKGENPAM   66 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p-------k~~gg~~~---~~~-~--~~~~~~i~~~v~~~pd~   66 (77)
                      .++..++|+.+|||++||++.+++..+.|-+.-       .+.|..-.   ... .  +...+.+.+.+.+.|.+
T Consensus        17 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~~~~~~~~~~~~~~l~~~p~V   91 (150)
T 2pn6_A           17 KYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKAKYGKNYHVELGNKLAQIPGV   91 (150)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCCCCCCCGGGGTCCEEEEEEEEECCCTTHHHHHHHHHHTSTTE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEEeecCHHHhCCceEEEEEEEecCChhHHHHHHHHHhcCchh
Confidence            489999999999999999999999999998863       22332100   000 1  23455677777777765

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=97.01  E-value=0.0002  Score=40.33  Aligned_cols=25  Identities=16%  Similarity=0.197  Sum_probs=22.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|+|..++|++.|||++||++|.
T Consensus        19 ~~~glT~~~LA~~~Gvs~stls~~~   43 (74)
T 1neq_A           19 KKRKLSLSALSRQFGYAPTTLANAL   43 (74)
T ss_dssp             HTTSCCHHHHHHHHSSCHHHHHHTT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3579999999999999999999883

>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=97.01  E-value=0.00072  Score=40.17  Aligned_cols=33  Identities=12%  Similarity=0.299  Sum_probs=31.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |.+++|+.|+||.+||.+-++++.+.|-|...+
T Consensus        45 s~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           45 VASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            899999999999999999999999999998776

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

Probab=97.00  E-value=0.00096  Score=40.84  Aligned_cols=52  Identities=21%  Similarity=0.283  Sum_probs=36.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~   55 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++   -.+|+.-...
T Consensus        62 ~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~  116 (162)
T 2fa5_A           62 PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQV  116 (162)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHH
Confidence            569999999999999999999999999999997655433333   2355654443

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=97.00  E-value=0.00051  Score=38.11  Aligned_cols=56  Identities=13%  Similarity=0.116  Sum_probs=40.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDR   74 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~   74 (77)
                      +.|++..++|+.+|||+++|++|.+     |...|           +......|.+.....|+-...+|.+.
T Consensus        23 ~~gltq~~lA~~~gvs~~~is~~e~-----g~~~~-----------~~~~~~~ia~~l~v~~~~l~~~l~~~   78 (80)
T 3kz3_A           23 ELGLSYESVADKMGMGQSAVAALFN-----GINAL-----------NAYNAALLAKILKVSVEEFSPSIARE   78 (80)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHHT-----TSSCC-----------CHHHHHHHHHHHTSCGGGTCHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc-----CCCCC-----------CHHHHHHHHHHhCCCHHHHhHHHHhh
Confidence            4689999999999999999999964     43222           12356667777777776665555544

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

Probab=96.99  E-value=0.00094  Score=39.65  Aligned_cols=52  Identities=10%  Similarity=0.107  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        46 ~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~  100 (139)
T 3bja_A           46 GKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEET  100 (139)
T ss_dssp             CSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHH
Confidence            4689999999999999999999999999999976554444432   356654443

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

Probab=96.99  E-value=0.00094  Score=39.70  Aligned_cols=51  Identities=10%  Similarity=0.124  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~   54 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++   -.+|+.-..
T Consensus        51 ~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~  104 (140)
T 2nnn_A           51 GPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRA  104 (140)
T ss_dssp             SSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHH
Confidence            468999999999999999999999999999997655443333   245554333

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=96.98  E-value=0.00077  Score=39.02  Aligned_cols=49  Identities=16%  Similarity=0.189  Sum_probs=33.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFS   68 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl   68 (77)
                      +.|+|..++|+.+|||+++|++|     |+|...|.           .. ...|.+....+|+..+
T Consensus        41 ~~glsq~elA~~lgvs~~~is~~-----E~G~~~p~-----------~~-~~~l~~~l~~~~~~l~   89 (99)
T 2ppx_A           41 ALKLTQEEFSARYHIPLGTLRDW-----EQGRSEPD-----------QP-ARAYLKIIAVDPEGTA   89 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHH-----HTTSSCCC-----------HH-HHHHHHHHHHCHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHH-----HcCCCCCC-----------HH-HHHHHHHHCcCHHHHH
Confidence            36899999999999999999999     44543332           11 3446666666655443

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=96.98  E-value=0.00064  Score=39.44  Aligned_cols=33  Identities=15%  Similarity=0.152  Sum_probs=28.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||..|+||.+||...+++.++.=.+
T Consensus        42 ~~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           42 EKGFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            479999999999999999999999998765443

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

Probab=96.98  E-value=0.0015  Score=40.25  Aligned_cols=52  Identities=8%  Similarity=0.139  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|++-.+.
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~  120 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKK  120 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHH
Confidence            4689999999999999999999999999999977665555543   355544443

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

Probab=96.98  E-value=0.00065  Score=41.37  Aligned_cols=36  Identities=19%  Similarity=0.158  Sum_probs=32.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.||||.+||.+-+++..+.|-|...+..|
T Consensus        39 s~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   74 (125)
T 3neu_A           39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMG   74 (125)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCE
Confidence            689999999999999999999999999998876544

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=96.97  E-value=0.00062  Score=38.23  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        29 ~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           29 NSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            5799999999999999999999975

>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=96.97  E-value=0.0016  Score=39.48  Aligned_cols=51  Identities=12%  Similarity=0.147  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|+.-..
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~  103 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDI  103 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHH
Confidence            4589999999999999999999999999999976654434432   35554333

>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=96.96  E-value=0.0008  Score=38.68  Aligned_cols=53  Identities=11%  Similarity=0.065  Sum_probs=40.0

Q ss_pred             CCCCHHHH----HHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH
Q psy15513          4 AGVRPCVI----SRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~i----A~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i   56 (77)
                      .+++..++    |+.++||++||++.+++..+.|-+...+.+..+.-.+|+.-.+.+
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~   77 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFA   77 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHH
Confidence            56899999    999999999999999999999999766544222234666544433

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=96.96  E-value=0.00077  Score=38.66  Aligned_cols=54  Identities=15%  Similarity=0.046  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHhccCHHH-HHHHHHHHHHhcCCCccccCCCCC-CCCCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGC-VSKILNRYQETGSIRPGVIGGSKP-RVATPDVERRIEE   58 (77)
Q Consensus         5 G~s~~~iA~rf~VS~st-v~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~~~~~i~~   58 (77)
                      +++..++|+.++||++| |++.+++..+.|-|.+.+..+... -.+|+.-.+.+..
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~~   85 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAEC   85 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHHH
Confidence            69999999999999999 999999999999998333221111 2456654443333

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=96.96  E-value=0.0011  Score=39.94  Aligned_cols=30  Identities=17%  Similarity=0.133  Sum_probs=26.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..+|||.+||.+++.+.+..
T Consensus        39 ~~g~s~~EIA~~lgiS~~tV~~~l~ra~~k   68 (113)
T 1xsv_A           39 LEDYSLSEIADTFNVSRQAVYDNIRRTGDL   68 (113)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            479999999999999999999998886643

>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=96.96  E-value=0.00076  Score=38.48  Aligned_cols=37  Identities=27%  Similarity=0.416  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .+++..++|+.++||++||++.+++..+.|-|...+.
T Consensus        33 ~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee
Confidence            4689999999999999999999999999999976543

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

Probab=96.96  E-value=0.00047  Score=41.04  Aligned_cols=41  Identities=20%  Similarity=0.377  Sum_probs=35.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...++
T Consensus        42 ~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~~d~   82 (138)
T 3bpv_A           42 PGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENR   82 (138)
T ss_dssp             TTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCc
Confidence            56899999999999999999999999999999765544333

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

Probab=96.96  E-value=0.00071  Score=40.46  Aligned_cols=36  Identities=19%  Similarity=0.076  Sum_probs=32.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|++||||.+||.+-+++..+.|-+...+..|
T Consensus        35 s~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~~~G   70 (113)
T 3tqn_A           35 SIRKISTEYQINPLTVSKAYQSLLDDNVIEKRRGLG   70 (113)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            789999999999999999999999999998776444

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

Probab=96.95  E-value=0.0017  Score=39.15  Aligned_cols=36  Identities=17%  Similarity=0.339  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..++|++|+||++||++.+++..+.|-|.-.+
T Consensus        30 ~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            468999999999999999999999999999887554

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

Probab=96.95  E-value=0.00061  Score=41.46  Aligned_cols=42  Identities=14%  Similarity=0.211  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++
T Consensus        60 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R  101 (153)
T 2pex_A           60 DERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTRAASDER  101 (153)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC------
T ss_pred             CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCcccCC
Confidence            468999999999999999999999999999997665443433

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=96.95  E-value=0.0011  Score=40.18  Aligned_cols=29  Identities=14%  Similarity=0.161  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||.+||.+++.+.+.
T Consensus       122 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~  150 (164)
T 3mzy_A          122 IRGYSYREIATILSKNLKSIDNTIQRIRK  150 (164)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            47999999999999999999999888654

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

Probab=96.95  E-value=0.00091  Score=40.63  Aligned_cols=53  Identities=9%  Similarity=0.106  Sum_probs=39.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc--cccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p--k~~gg~~~~---~~~~~~~~~i   56 (77)
                      .++++.++|+.++||++||++.+++..+.|-|.-  .+...+++.   .+|+.-...+
T Consensus        54 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~  111 (154)
T 2qww_A           54 PGISVADLTKRLIITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLS  111 (154)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHH
Confidence            4589999999999999999999999999999977  555444442   4566544433

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=96.94  E-value=0.00074  Score=37.42  Aligned_cols=25  Identities=20%  Similarity=0.288  Sum_probs=22.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.| |..++|+++|||+++|++|.+-
T Consensus        10 ~~g-sq~~lA~~lgvs~~~is~~e~g   34 (79)
T 3bd1_A           10 KLG-SVSALAASLGVRQSAISNWRAR   34 (79)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhC-CHHHHHHHHCCCHHHHHHHHHC
Confidence            358 9999999999999999999763

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=96.94  E-value=0.00065  Score=41.84  Aligned_cols=32  Identities=16%  Similarity=0.302  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|..++|+.+|+|.+||.+.+++..+.|-+.
T Consensus        19 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   50 (144)
T 2cfx_A           19 RLSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (144)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            48999999999999999999999999999885

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=96.94  E-value=0.00067  Score=35.85  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        16 ~~g~s~~~lA~~~gis~~~i~~~e~   40 (68)
T 2r1j_L           16 KLKIRQAALGKMVGVSNVAISQWER   40 (68)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            3689999999999999999999963

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

Probab=96.92  E-value=0.0013  Score=40.42  Aligned_cols=50  Identities=14%  Similarity=0.110  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      ++++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~  103 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGRE  103 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHH
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHH
Confidence            489999999999999999999999999999987776666653   35664333

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=96.92  E-value=0.00059  Score=40.38  Aligned_cols=33  Identities=18%  Similarity=0.090  Sum_probs=29.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||..++||.+||..++.+.++.=.+
T Consensus        47 ~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           47 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            479999999999999999999999998875444

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=96.92  E-value=0.0011  Score=41.80  Aligned_cols=34  Identities=15%  Similarity=0.277  Sum_probs=31.0

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ++| +|..++|+++|+|.+||.+-+++..+.|-+.
T Consensus        14 ~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~   48 (162)
T 3i4p_A           14 EDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIR   48 (162)
T ss_dssp             TCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSC
T ss_pred             HCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            344 8999999999999999999999999999875

>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=96.91  E-value=0.00071  Score=42.30  Aligned_cols=42  Identities=7%  Similarity=0.245  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|++..++|+.++|++++|++.+++..+.|-|.-.+...+++
T Consensus        67 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~~DrR  108 (166)
T 3deu_A           67 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRR  108 (166)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-------
T ss_pred             CCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCCCCCC
Confidence            569999999999999999999999999999997665544444

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=96.91  E-value=0.0061  Score=38.19  Aligned_cols=65  Identities=9%  Similarity=-0.024  Sum_probs=43.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      -+++.++|+.+|||.+|+..|-    +.|-+.|-....+..+.=++.+...   |..+  .+-++++.||++.|
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye----~~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~l--r~~G~sL~eIk~~l   83 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYD----KQGLFPFLQRNEKGDRIFNEEALKYLEMILCL--KNTGMPIQKIKQFI   83 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHH----HTTCCTTCEECTTCCEEBCHHHHHHHHHHHHH--HTTTCCHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCeecCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence            4789999999999999998774    4588865333222223344444443   4444  44579999998765

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

Probab=96.90  E-value=0.0021  Score=39.93  Aligned_cols=51  Identities=12%  Similarity=0.081  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-..
T Consensus        58 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~  111 (168)
T 2nyx_A           58 GPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRD  111 (168)
T ss_dssp             CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHH
Confidence            4689999999999999999999999999999976655444442   45554333

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=96.90  E-value=0.0023  Score=40.51  Aligned_cols=65  Identities=11%  Similarity=0.024  Sum_probs=43.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc-CCCCC-CCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKP-RVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~-gg~~~-~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      -+++.++|+.+|||..|+..|-+    .|-+.|... +|.|. +...-....+|..+.+.  ++++.||++.|
T Consensus        11 ~~~i~e~A~~~gvs~~TLR~ye~----~Gll~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~--G~sl~eI~~~l   77 (154)
T 2zhg_A           11 LLTPGEVAKRSGVAVSALHFYES----KGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRI--GIPLATIGEAF   77 (154)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHH----TTSSCCEECTTSCEEBCTTHHHHHHHHHHHHHH--TCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH----cCCCCcccCCCCCEEeCHHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            48999999999999999987754    488877643 44332 22222223455555443  68888887655

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=96.90  E-value=0.00072  Score=41.75  Aligned_cols=32  Identities=13%  Similarity=0.217  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .++..++|+++|+|.+||++.+++..+.|-+.
T Consensus        21 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A           21 RATLSELATRAGLSVSAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999999999984

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=96.90  E-value=0.00069  Score=36.71  Aligned_cols=25  Identities=12%  Similarity=0.081  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||++++++|.+
T Consensus        21 ~~g~s~~~lA~~~gis~~~i~~~e~   45 (76)
T 3bs3_A           21 EKQRTNRWLAEQMGKSENTISRWCS   45 (76)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999974

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=96.90  E-value=0.0007  Score=36.42  Aligned_cols=25  Identities=12%  Similarity=0.124  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        24 ~~g~s~~~lA~~~gis~~~i~~~e~   48 (74)
T 1y7y_A           24 AKGLSQETLAFLSGLDRSYVGGVER   48 (74)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4799999999999999999999863

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=96.89  E-value=0.00077  Score=41.71  Aligned_cols=62  Identities=11%  Similarity=0.098  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-------ccccCCCCC---CCC--CHHHHHHHHHHHHhCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR-------PGVIGGSKP---RVA--TPDVERRIEEYKGENPAM   66 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-------pk~~gg~~~---~~~--~~~~~~~i~~~v~~~pd~   66 (77)
                      .+|..++|+.+|+|.+||.+.+++..+.|-+.       |.+.|-+-.   ...  .....+.+.+.+.+.|.+
T Consensus        22 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~~~~~~~~~~~~~l~~~peV   95 (152)
T 2cg4_A           22 RTAYAELAKQFGVSPETIHVRVEKMKQAGIITGARIDVSPKQLGYDVGCFIGIILKSAKDYPSALAKLESLDEV   95 (152)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEEEEEECTTTTTCCEEEEEEEEESSGGGHHHHHHHHHTCTTE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceEEEecCHHHcCCeEEEEEEEEECCCCCHHHHHHHHhCCcCe
Confidence            48999999999999999999999999999885       343342200   111  111245567777777764

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

Probab=96.89  E-value=0.00074  Score=42.26  Aligned_cols=32  Identities=16%  Similarity=0.295  Sum_probs=30.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|..++|+.+|+|.+||.+.+++..+.|-+.
T Consensus        24 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   55 (162)
T 2p5v_A           24 RLTNVELSERVALSPSPCLRRLKQLEDAGIVR   55 (162)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            38999999999999999999999999999885

>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=96.88  E-value=0.00083  Score=38.66  Aligned_cols=30  Identities=20%  Similarity=0.326  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +++.++|+.++|+++||++++++..+.|-|
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCc
Confidence            899999999999999999999999999999

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=96.88  E-value=0.00057  Score=37.09  Aligned_cols=28  Identities=0%  Similarity=-0.013  Sum_probs=24.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..|....++|+.||||.+|+++++++|.
T Consensus        30 ~~~gn~~~aA~~LGisr~tL~rklkk~g   57 (63)
T 3e7l_A           30 EYDYDLKRTAEEIGIDLSNLYRKIKSLN   57 (63)
T ss_dssp             HTTTCHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             HhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            3456788999999999999999999873

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

Probab=96.88  E-value=0.00075  Score=40.89  Aligned_cols=33  Identities=12%  Similarity=0.310  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..+||+.+++|.+||+|.++++.+.|-|...
T Consensus        43 ~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           43 IDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             EEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            799999999999999999999999999999654

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=96.87  E-value=0.00074  Score=36.68  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        21 ~~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           21 QKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            4699999999999999999999974

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=96.87  E-value=0.00078  Score=36.58  Aligned_cols=25  Identities=20%  Similarity=0.161  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++|+++|.+
T Consensus        19 ~~glsq~~lA~~~gis~~~is~~e~   43 (73)
T 3omt_A           19 EKGKTNLWLTETLDKNKTTVSKWCT   43 (73)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4689999999999999999999975

>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=96.87  E-value=0.0011  Score=40.17  Aligned_cols=36  Identities=17%  Similarity=0.169  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..++|+.|+||++||++.+++..+.|-|.-.+
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~   56 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK   56 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEee
Confidence            569999999999999999999999999999997653

>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}

Probab=96.84  E-value=0.00045  Score=45.03  Aligned_cols=28  Identities=14%  Similarity=0.240  Sum_probs=25.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.+|+|..+||+.||||.+||+||++..
T Consensus       172 ~~~G~s~~~Ia~~l~is~~tv~r~l~~~  199 (209)
T 2r0q_C          172 LEEGQAISKIAKEVNITRQTVYRIKHDN  199 (209)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHTTC
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence            3579999999999999999999998753

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

Probab=96.83  E-value=0.0013  Score=39.72  Aligned_cols=35  Identities=9%  Similarity=0.134  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .++..+||++++||+++|.++++..++.|=|...+
T Consensus        26 ~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~   60 (129)
T 2y75_A           26 PTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIR   60 (129)
T ss_dssp             CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             cCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecC
Confidence            38999999999999999999999999999987653

>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=96.83  E-value=0.0019  Score=39.18  Aligned_cols=35  Identities=11%  Similarity=0.177  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ..|+++.++|+.++||+++|++.+++..+.|-|.-
T Consensus        49 ~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           49 IEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            35799999999999999999999999999999975

>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=96.82  E-value=0.00059  Score=40.18  Aligned_cols=50  Identities=18%  Similarity=0.115  Sum_probs=39.4

Q ss_pred             ccCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHH
Q psy15513          2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPD   51 (77)
Q Consensus         2 ~~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~   51 (77)
                      .+.+++..++|+.+ |||++++++.+++..+.|-|.-.+...+++   -.+|+.
T Consensus        35 ~~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~   88 (107)
T 2fsw_A           35 NRRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPL   88 (107)
T ss_dssp             TTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHH
T ss_pred             HhCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECcc
Confidence            34458999999999 599999999999999999997665544444   255664

>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=96.82  E-value=0.0016  Score=39.02  Aligned_cols=53  Identities=23%  Similarity=0.233  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~i   56 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++   -.+|+.-...+
T Consensus        46 ~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~  101 (145)
T 2a61_A           46 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVI  101 (145)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHH
Confidence            468999999999999999999999999999997665433333   24566544433

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=96.81  E-value=0.0011  Score=36.87  Aligned_cols=25  Identities=12%  Similarity=0.318  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||+++|++|.+
T Consensus        23 ~~glsq~~lA~~~gis~~~i~~~e~   47 (88)
T 2wiu_B           23 QNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4699999999999999999999976

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=96.81  E-value=0.00097  Score=38.10  Aligned_cols=25  Identities=12%  Similarity=0.080  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||.++|++|.+
T Consensus        20 ~~glsq~~lA~~~gis~~~is~~e~   44 (94)
T 2kpj_A           20 KSEKTQLEIAKSIGVSPQTFNTWCK   44 (94)
T ss_dssp             TSSSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            4799999999999999999999964

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=96.80  E-value=0.00099  Score=35.99  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        16 ~~gls~~~lA~~~gis~~~i~~~e~   40 (76)
T 1adr_A           16 KLKIRQAALGKMVGVSNVAISQWER   40 (76)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4689999999999999999999964

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=96.78  E-value=0.0012  Score=35.93  Aligned_cols=25  Identities=4%  Similarity=0.116  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        18 ~~g~sq~~lA~~~gis~~~i~~~e~   42 (78)
T 3b7h_A           18 QQNLTINRVATLAGLNQSTVNAMFE   42 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999974

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=96.78  E-value=0.00079  Score=41.66  Aligned_cols=31  Identities=16%  Similarity=0.198  Sum_probs=25.2

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ...|+|.++||+.+|||.+||+|.-+ .-..|
T Consensus        72 L~~G~syreIA~~~g~S~aTIsRv~r-~L~~g  102 (119)
T 3kor_A           72 IKQGYTYATIEQESGASTATISRVKR-SLQWG  102 (119)
T ss_dssp             HHHTCCHHHHHHHHCCCHHHHHHHHH-HHHSS
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHH-HHhcC
Confidence            35789999999999999999999544 44444

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

Probab=96.78  E-value=0.0012  Score=39.34  Aligned_cols=53  Identities=11%  Similarity=0.120  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~i   56 (77)
                      .+++..++|+.++||+++|++.+++..+.|-|.-.+...+++   -.+|+.-.+.+
T Consensus        49 ~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~  104 (142)
T 2fbi_A           49 GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCF  104 (142)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHH
Confidence            468999999999999999999999999999997655433333   24566544433

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=96.78  E-value=0.00048  Score=42.89  Aligned_cols=28  Identities=11%  Similarity=0.184  Sum_probs=25.7

Q ss_pred             cCCCCHHHHHHHhcc-CHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRV-SHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~V-S~stv~r~~~r~r   30 (77)
                      ..|+|.++||+.+|| |.+|+++|+++.-
T Consensus        26 ~~G~sl~~i~~~~~~ps~~T~~~W~~~~~   54 (140)
T 4dyq_A           26 SSGESLLKVCKRPGMPDKSTVFRWLAKHE   54 (140)
T ss_dssp             HTTCCHHHHHTSTTCCCHHHHHHHHHHCH
T ss_pred             HCCCcHHHHHhcCCCCCHHHHHHHHHcCH
Confidence            479999999999999 9999999999854

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=96.77  E-value=0.00097  Score=37.10  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||.++|++|.+
T Consensus        21 ~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           21 EKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999864

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

Probab=96.77  E-value=0.0012  Score=40.33  Aligned_cols=36  Identities=17%  Similarity=0.084  Sum_probs=32.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|++||||.+||.+-+++....|-|...+..|
T Consensus        37 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   72 (126)
T 3by6_A           37 SVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKG   72 (126)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            889999999999999999999999999998776544

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

Probab=96.76  E-value=0.0014  Score=40.28  Aligned_cols=36  Identities=28%  Similarity=0.303  Sum_probs=32.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+.+..++|+.|+||++||++.+++..+.|-|.-.+
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEec
Confidence            458999999999999999999999999999886553

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

Probab=96.75  E-value=0.006  Score=37.56  Aligned_cols=50  Identities=12%  Similarity=0.175  Sum_probs=33.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      ++++.++|++++|+++||++.+++..+.|-|.- +...+++.   .+|++-.+.
T Consensus        52 ~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~-~~~~DrR~~~v~LT~~G~~~  104 (148)
T 4fx0_A           52 DLTMSELAARIGVERTTLTRNLEVMRRDGLVRV-MAGADARCKRIELTAKGRAA  104 (148)
T ss_dssp             --CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC------------CCBCHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEe-eCCCCCCeeEEEECHHHHHH
Confidence            489999999999999999999999999998843 33445442   455654443

>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=96.74  E-value=0.00066  Score=40.74  Aligned_cols=51  Identities=20%  Similarity=0.202  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .+++..++|+.++||++||++.+++..+.|-|.-.+...+++.   .+|+.-..
T Consensus        50 ~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~  103 (142)
T 2bv6_A           50 SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSET  103 (142)
T ss_dssp             SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHH
Confidence            4589999999999999999999999999999976655434432   34554433

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=96.73  E-value=0.0012  Score=37.38  Aligned_cols=24  Identities=21%  Similarity=0.344  Sum_probs=22.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|+|..++|+++|||+++|++|-
T Consensus        25 ~~gltq~elA~~~gis~~~is~~E   48 (86)
T 3eus_A           25 DAGLTQADLAERLDKPQSFVAKVE   48 (86)
T ss_dssp             HTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHH
Confidence            479999999999999999999984

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=96.73  E-value=0.0014  Score=36.34  Aligned_cols=21  Identities=10%  Similarity=0.213  Sum_probs=20.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |..++|+.||||+++|++|++
T Consensus        15 s~t~aA~~L~vtQ~AVS~~ir   35 (66)
T 2ovg_A           15 GQTKTAKDLGVYPSSINQAIH   35 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            889999999999999999985

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=96.72  E-value=0.0011  Score=36.52  Aligned_cols=25  Identities=24%  Similarity=0.232  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||++++++|.+
T Consensus        21 ~~glsq~~lA~~~gis~~~i~~~e~   45 (84)
T 2ef8_A           21 EASLSQSELAIFLGLSQSDISKIES   45 (84)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4699999999999999999999864

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

Probab=96.69  E-value=0.0013  Score=40.12  Aligned_cols=52  Identities=21%  Similarity=0.264  Sum_probs=37.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|++..++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-...
T Consensus        61 ~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~  115 (160)
T 3boq_A           61 DGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTT  115 (160)
T ss_dssp             TCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHH
T ss_pred             CCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHH
Confidence            5789999999999999999999999999999976654444432   355554443

>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=96.69  E-value=0.0025  Score=39.66  Aligned_cols=37  Identities=14%  Similarity=0.243  Sum_probs=32.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc-cCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~-~gg   42 (77)
                      ++..+||++++||.+++.++++..++.|=|...+ .||
T Consensus        31 ~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG~GG   68 (149)
T 1ylf_A           31 CTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGPGG   68 (149)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---CC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccCCCc
Confidence            8999999999999999999999999999987654 344

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=96.69  E-value=0.0013  Score=36.10  Aligned_cols=25  Identities=8%  Similarity=0.161  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||.++|++|.+
T Consensus        13 ~~glsq~~lA~~~gis~~~i~~~e~   37 (77)
T 2k9q_A           13 RLSLTAKSVAEEMGISRQQLCNIEQ   37 (77)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4689999999999999999999863

>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=96.69  E-value=0.0015  Score=40.00  Aligned_cols=36  Identities=17%  Similarity=0.081  Sum_probs=32.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.||||.+||.+-+++....|-|..++..|
T Consensus        40 ser~La~~~gVSr~tVReAl~~L~~eGlv~~~~g~G   75 (134)
T 4ham_A           40 SIREFASRIGVNPNTVSKAYQELERQEVIITVKGKG   75 (134)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCcE
Confidence            779999999999999999999999999998776544

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=96.67  E-value=0.0049  Score=41.66  Aligned_cols=22  Identities=23%  Similarity=0.285  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||+++|||.+||||-++
T Consensus         1 ~ti~diA~~agVS~~TVSrvLn   22 (340)
T 1qpz_A            1 ATIKDVAKRANVSTTTVSHVIN   22 (340)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            3678999999999999999998

>3iuo_A ATP-dependent DNA helicase RECQ; C-terminal, GI PSI, MCSG, structural genomics, midwest center for structur genomics; 1.60A {Porphyromonas gingivalis}

Probab=96.67  E-value=0.0048  Score=37.66  Aligned_cols=72  Identities=17%  Similarity=0.006  Sum_probs=56.3

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC-CCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~-v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.|++..+||..-|++.+||..-+..+...|. +.--.-   -+....++..+.|.+.+.+.++..|..+.+.|
T Consensus        28 l~~~G~sleeIA~~R~L~~~TI~~Hl~~~v~~G~~l~i~~~---i~~~l~~~~~~~I~~~~~~~~~~~Lk~i~e~l  100 (122)
T 3iuo_A           28 QIDRKVALDDIAVSHGLDFPELLSEVETIVYSGTRINIDYF---INEVMDEDHLEDIFEYFKESTTDSLEEAMQEL  100 (122)
T ss_dssp             HHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHTTCCCCCHHH---HHHHSCHHHHHHHHHHHHHCSCCCHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHcCCccCHHHH---cccccCHHHHHHHHHHHHHcCcccHHHHHHHc
Confidence            4679999999999999999999999999999995 432210   01133356677888988888888888888776

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=96.66  E-value=0.00081  Score=38.98  Aligned_cols=27  Identities=11%  Similarity=0.008  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .|....++|+.||||.+|+++++++|.
T Consensus        63 ~~gn~~~aA~~LGIsr~tL~rklkk~~   89 (91)
T 1ntc_A           63 TQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             TTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            455777899999999999999999984

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=96.65  E-value=0.00034  Score=40.90  Aligned_cols=36  Identities=22%  Similarity=0.190  Sum_probs=32.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.|+||.+||.+-++++.+.|-|...+..|
T Consensus        37 s~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~g~G   72 (102)
T 1v4r_A           37 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGALG   72 (102)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            899999999999999999999999999997765443

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=96.65  E-value=0.0018  Score=36.81  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        19 ~~gltq~~lA~~~gis~~~is~~e~   43 (94)
T 2ict_A           19 ELNVSLREFARAMEIAPSTASRLLT   43 (94)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4689999999999999999999986

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

Probab=96.65  E-value=0.003  Score=41.49  Aligned_cols=52  Identities=10%  Similarity=0.072  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEE   58 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~   58 (77)
                      .+++..++|++|+||++||++.+++..+.|-|.-.+.+   .=.+|+.-.+...+
T Consensus        19 ~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~~---~i~LT~~G~~~~~~   70 (214)
T 3hrs_A           19 NKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKKA---GYLLTDLGLKLVSD   70 (214)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTT---EEEECHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecCC---CeEECHHHHHHHHH
Confidence            45999999999999999999999999999999766532   22455544443333

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

Probab=96.65  E-value=0.0014  Score=41.78  Aligned_cols=32  Identities=22%  Similarity=0.310  Sum_probs=30.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|..++|+.+|||.+||.+.+++..+.|-+.
T Consensus        31 ~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~   62 (171)
T 2ia0_A           31 RLTISELSEQLKKPESTIHFRIKKLQERGVIE   62 (171)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            48999999999999999999999999999884

>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=96.64  E-value=0.0034  Score=38.02  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .+|..++|+.||||.+||.+.+++..+.|-+.
T Consensus        18 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A           18 RTPFTEIAKKLGISETAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            48999999999999999999999999999885

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

Probab=96.64  E-value=0.0026  Score=39.13  Aligned_cols=62  Identities=10%  Similarity=0.121  Sum_probs=45.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-------ccccCCCCC---C-CCCHHHHHHHHHHHHhCCCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR-------PGVIGGSKP---R-VATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-------pk~~gg~~~---~-~~~~~~~~~i~~~v~~~pd~   66 (77)
                      .+|..++|+.+|+|.+||.+.+++..+.|-+.       |.+.|-+-.   . ...+...+.+.+.+.+.|.+
T Consensus        23 ~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~~~~~~~~~~~~l~~~peV   95 (151)
T 2dbb_A           23 RLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGYMYAIVLIKSKVPSDADKVISEISDIEYV   95 (151)
T ss_dssp             TCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEEEEEECTGGGTEEEEEEEEEESSHHHHHHHHHHHTTCTTE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEecCChHHhCCCEEEEEEEEeCCCCHHHHHHHHHcCCCe
Confidence            48999999999999999999999999999885       443332100   0 12344456677777777764

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

Probab=96.64  E-value=0.0015  Score=40.12  Aligned_cols=36  Identities=14%  Similarity=0.035  Sum_probs=32.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|++||||.+||.+-+++....|-|...+..|
T Consensus        30 se~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g~G   65 (129)
T 2ek5_A           30 STNELAAFHRINPATARNGLTLLVEAGILYKKRGIG   65 (129)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCE
Confidence            789999999999999999999999999998776443

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=96.63  E-value=0.0017  Score=35.94  Aligned_cols=25  Identities=32%  Similarity=0.343  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        25 ~~gltq~elA~~~gis~~~is~~e~   49 (83)
T 3f6w_A           25 AAGITQKELAARLGRPQSFVSKTEN   49 (83)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3689999999999999999999953

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=96.62  E-value=0.0025  Score=37.30  Aligned_cols=36  Identities=14%  Similarity=0.160  Sum_probs=33.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .|++++++|++++++++||.++++++.+.|-|...+
T Consensus        35 ~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~~   70 (91)
T 2dk5_A           35 KGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVK   70 (91)
T ss_dssp             TCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            589999999999999999999999999999997444

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=96.61  E-value=0.0018  Score=38.04  Aligned_cols=26  Identities=19%  Similarity=0.304  Sum_probs=23.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ...|+|..++|+.+|||+++|++|.+
T Consensus        21 ~~~glsq~~lA~~~gis~~~is~~e~   46 (113)
T 2eby_A           21 EPLDLKINELAELLHVHRNSVSALIN   46 (113)
T ss_dssp             TTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35799999999999999999999965

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

Probab=96.61  E-value=0.0013  Score=40.48  Aligned_cols=50  Identities=18%  Similarity=0.151  Sum_probs=39.9

Q ss_pred             ccCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHH
Q psy15513          2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPD   51 (77)
Q Consensus         2 ~~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~   51 (77)
                      ...+++..++|+.+ |||++++++.+++..+.|=|.-.+...+++   -.+|+.
T Consensus        45 ~~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~   98 (131)
T 1yyv_A           45 RDGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPL   98 (131)
T ss_dssp             GGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHH
T ss_pred             HcCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECcc
Confidence            44458999999999 799999999999999999998666544444   256664

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

Probab=96.59  E-value=0.0019  Score=38.77  Aligned_cols=50  Identities=10%  Similarity=0.171  Sum_probs=39.1

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      ++.++|+.++||+++|++.+++..+.|-|.-.+...+++.   .+|++-...+
T Consensus        52 ~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~  104 (144)
T 3f3x_A           52 SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVL  104 (144)
T ss_dssp             EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHH
Confidence            8999999999999999999999999999976665544432   4556544433

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=96.58  E-value=0.0018  Score=35.80  Aligned_cols=25  Identities=12%  Similarity=0.139  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||++++++|.+
T Consensus        22 ~~glsq~~lA~~~gis~~~i~~~e~   46 (82)
T 3s8q_A           22 EKGMTQEDLAYKSNLDRTYISGIER   46 (82)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            4799999999999999999999853

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

Probab=96.57  E-value=0.0032  Score=42.56  Aligned_cols=35  Identities=11%  Similarity=0.164  Sum_probs=32.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..++|+.+++|++||+|.+++..+.|-+.-.
T Consensus       165 ~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          165 KGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            57999999999999999999999999999999765

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=96.56  E-value=0.0029  Score=39.56  Aligned_cols=29  Identities=21%  Similarity=0.192  Sum_probs=26.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.+||.+++.+-+.
T Consensus       154 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~  182 (194)
T 1or7_A          154 LDGLSYEEIAAIMDCPVGTVRSRIFRARE  182 (194)
T ss_dssp             TTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            37999999999999999999999998765

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=96.56  E-value=0.0018  Score=39.41  Aligned_cols=30  Identities=13%  Similarity=0.028  Sum_probs=26.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ...|+|.++||+..|+|.+||+|.-+-+..
T Consensus        55 L~~G~SyreIa~~tG~StaTIsRv~r~L~~   84 (107)
T 3frw_A           55 LTDKRTYLDISEKTGASTATISRVNRSLNY   84 (107)
T ss_dssp             HHTTCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCccHHHHHHHHHHHHc
Confidence            457999999999999999999998776553

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=96.56  E-value=0.0023  Score=34.16  Aligned_cols=25  Identities=8%  Similarity=-0.003  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhc--cCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLR--VSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~--VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|  ||++++++|.+
T Consensus        19 ~~glsq~~lA~~~g~~is~~~i~~~e~   45 (71)
T 2ewt_A           19 QQGLSLHGVEEKSQGRWKAVVVGSYER   45 (71)
T ss_dssp             HTTCCHHHHHHHTTTSSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCcCCHHHHHHHHC
Confidence            46999999999999  99999999875

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=96.53  E-value=0.0048  Score=41.02  Aligned_cols=59  Identities=15%  Similarity=0.111  Sum_probs=46.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~   66 (77)
                      ..++.+++|++++||.+||+..+++..+.|-|.-.+ +   .-.+|++=.+...++...+.++
T Consensus        29 ~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~-~---Gv~LTe~G~~~A~~i~~rhr~~   87 (200)
T 2p8t_A           29 EPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ-R---GHFLTLKGKEIRDKLLSMFSEP   87 (200)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC------CEEECHHHHHHHHHHHTTBCCC
T ss_pred             CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC-C---CeEECHHHHHHHHHHHHHHHHh
Confidence            458899999999999999999999999999997776 3   2457777666666777666544

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=96.52  E-value=0.002  Score=45.44  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ..+|..++|+.+++|++||+++++++.+.|-+..
T Consensus        29 ~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           29 GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            3489999999999999999999999999998855

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=96.51  E-value=0.0019  Score=36.32  Aligned_cols=54  Identities=13%  Similarity=0.119  Sum_probs=37.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR   72 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~   72 (77)
                      +.|+|..++|+.+|||++++++|.+     |..        .|   +......|.+.....++..+.+.-
T Consensus        28 ~~glsq~~lA~~~gis~~~is~~e~-----g~~--------~~---~~~~l~~ia~~l~v~~~~l~~~~~   81 (92)
T 1lmb_3           28 ELGLSQESVADKMGMGQSGVGALFN-----GIN--------AL---NAYNAALLAKILKVSVEEFSPSIA   81 (92)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT-----TSS--------CC---CHHHHHHHHHHHTSCGGGTCHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc-----CCC--------CC---CHHHHHHHHHHHCCCHHHHhhhhh
Confidence            4699999999999999999999975     321        11   233455566777666666655443

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=96.50  E-value=0.0031  Score=39.03  Aligned_cols=30  Identities=13%  Similarity=0.156  Sum_probs=26.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..+|||.+||...+.|-+..
T Consensus       107 ~~g~s~~EIA~~lgis~~tV~~~l~rar~~  136 (157)
T 2lfw_A          107 MEGFSPEDAAYLIEVDTSEVETLVTEALAE  136 (157)
T ss_dssp             SSCCCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            479999999999999999999999887654

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

Probab=96.49  E-value=0.002  Score=40.56  Aligned_cols=51  Identities=24%  Similarity=0.206  Sum_probs=37.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERR   55 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~   55 (77)
                      |+++.++|+.++||++||++.+++..+.|-|.-.+...+++   -.+|+.-...
T Consensus        86 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~  139 (181)
T 2fbk_A           86 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  139 (181)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHH
Confidence            48999999999999999999999999999997665443443   2355654443

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=96.49  E-value=0.0029  Score=35.69  Aligned_cols=25  Identities=4%  Similarity=0.129  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||+++|++|.+
T Consensus        24 ~~glsq~~lA~~~gis~~~is~~e~   48 (91)
T 1x57_A           24 SKGLTQKDLATKINEKPQVIADYES   48 (91)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999975

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

Probab=96.49  E-value=0.0049  Score=40.03  Aligned_cols=60  Identities=13%  Similarity=0.007  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHHHhC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYKGEN   63 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v~~~   63 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-...+..+....
T Consensus        61 ~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  123 (207)
T 2fxa_A           61 NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  123 (207)
T ss_dssp             TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHHHHHHH
Confidence            5689999999999999999999999999999977665555542   46676555555555443

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=96.47  E-value=0.0022  Score=37.98  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        25 ~~gltq~eLA~~lGis~~~is~ie~   49 (104)
T 3trb_A           25 LDKMSANQLAKHLAIPTNRVTAILN   49 (104)
T ss_dssp             TTSCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            5799999999999999999999974

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=96.47  E-value=0.0019  Score=37.38  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|+|..++|+.+|||++++++|.+
T Consensus        12 ~~gltq~~lA~~~gis~~~i~~~e~   36 (111)
T 1b0n_A           12 EKGYSLSELAEKAGVAKSYLSSIER   36 (111)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999975

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.46  E-value=0.00046  Score=43.21  Aligned_cols=30  Identities=17%  Similarity=0.273  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      +.|+|..++|+++|||++||++|     ++|...|
T Consensus        12 ~~gltq~elA~~lgis~~~vs~~-----e~G~~~~   41 (158)
T 2p5t_A           12 THDLTQLEFARIVGISRNSLSRY-----ENGTSSV   41 (158)
T ss_dssp             -----------------------------------
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHH-----HCCCCCC
Confidence            47899999999999999999999     5565543

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

Probab=96.46  E-value=0.0015  Score=40.56  Aligned_cols=54  Identities=11%  Similarity=0.159  Sum_probs=39.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIE   57 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~   57 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.
T Consensus        61 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  117 (168)
T 3u2r_A           61 EGMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLK  117 (168)
T ss_dssp             SCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHH
Confidence            4799999999999999999999999999999987665555542   45565444333

>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=96.44  E-value=0.002  Score=41.05  Aligned_cols=34  Identities=18%  Similarity=0.270  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +|..+||++++||++++.|++++.++.|=|...+
T Consensus        29 ~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~r   62 (162)
T 3k69_A           29 VASRELAQSLHLNPVMIRNILSVLHKHGYLTGTV   62 (162)
T ss_dssp             BCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEEC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            7899999999999999999999999999996654

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=96.43  E-value=0.0028  Score=39.38  Aligned_cols=49  Identities=12%  Similarity=0.045  Sum_probs=38.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC--CCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~--~~~~~~   51 (77)
                      ..+++..++++.++||++++++.+++..+.|-|.-.+...++.  -.+|+.
T Consensus        35 ~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~   85 (146)
T 2f2e_A           35 EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDK   85 (146)
T ss_dssp             TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHH
T ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECch
Confidence            3459999999999999999999999999999997665433221  245654

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=96.42  E-value=0.0024  Score=36.37  Aligned_cols=25  Identities=12%  Similarity=0.011  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+++|||+++|++|.+
T Consensus        15 ~~gltq~~lA~~~gis~~~is~~e~   39 (99)
T 2l49_A           15 SEYLSRQQLADLTGVPYGTLSYYES   39 (99)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4699999999999999999999864

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=96.42  E-value=0.0055  Score=41.20  Aligned_cols=23  Identities=30%  Similarity=0.388  Sum_probs=21.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+++|||.+||||-++.
T Consensus         3 ~ti~dvA~~agVS~~TVSrvln~   25 (332)
T 2hsg_A            3 VTIYDVAREASVSMATVSRVVNG   25 (332)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            57899999999999999999974

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=96.40  E-value=0.0024  Score=36.99  Aligned_cols=25  Identities=16%  Similarity=0.315  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        29 ~~gltq~~lA~~~gis~~~is~~e~   53 (104)
T 3cec_A           29 DLDINTANFAEILGVSNQTIQEVIN   53 (104)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4689999999999999999999974

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=96.40  E-value=0.0046  Score=32.68  Aligned_cols=29  Identities=17%  Similarity=0.133  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCC
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..++..+++..|     +||.+||+|.++   +-|-+
T Consensus        18 ~~~t~~el~~~l~~~~~~vs~~Tv~R~L~---~lg~v   51 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYKVTQATVSRDIK---ELHLV   51 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCCCCHHHHHHHHH---HHTCE
T ss_pred             CCCCHHHHHHHHHHhCCCcCHHHHHHHHH---HcCCE
Confidence            348999999999     999999999999   55655

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=96.40  E-value=0.002  Score=40.06  Aligned_cols=34  Identities=15%  Similarity=0.195  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +|..+||++++||++++.+++++.++.|=|...+
T Consensus        29 ~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~r   62 (143)
T 3t8r_A           29 ISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVR   62 (143)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECS
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecC
Confidence            7899999999999999999999999999996554

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=96.39  E-value=0.002  Score=41.57  Aligned_cols=33  Identities=18%  Similarity=0.154  Sum_probs=30.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .|.+++|+.||+|.+||.+++++..+.|-+.-.
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEec
Confidence            799999999999999999999999999999654

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=96.38  E-value=0.0046  Score=35.38  Aligned_cols=33  Identities=12%  Similarity=0.270  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+..+||++||+|...|.|.+-.+.+.|.|.--
T Consensus        30 ~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~   62 (75)
T 1sfu_A           30 TTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   62 (75)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecC
Confidence            788999999999999999999999999999543

>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=96.36  E-value=0.0024  Score=35.65  Aligned_cols=38  Identities=16%  Similarity=0.258  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHhc----cCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~----VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..+||+.|+    +|++||++.+++..+.|-|.-.+.|
T Consensus        22 ~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~g   63 (82)
T 1p6r_A           22 SSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKEG   63 (82)
T ss_dssp             SSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEecC
Confidence            4589999999997    7999999999999999999766544

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=96.36  E-value=0.0027  Score=37.66  Aligned_cols=23  Identities=4%  Similarity=0.057  Sum_probs=21.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +.|+|+.++|++.|||++++++|
T Consensus        47 ~~glTQ~eLA~~~gvs~~~is~~   69 (101)
T 4ghj_A           47 NRDLTQSEVAEIAGIARKTVLNA   69 (101)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HcCCCHHHHHHHcCCCHHHHHHH
Confidence            37999999999999999999998

>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=96.36  E-value=0.0031  Score=41.48  Aligned_cols=52  Identities=17%  Similarity=0.114  Sum_probs=38.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~   55 (77)
                      .|++..++|++++||+++|++.+++..+.|=+.-.+.++.+.-.+|++-...
T Consensus        26 ~~~s~s~aA~~L~isq~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G~~l   77 (230)
T 3cta_A           26 AYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDV   77 (230)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHHHHH
Confidence            4688999999999999999999999999887755443311223566654443

>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=96.35  E-value=0.0058  Score=37.83  Aligned_cols=37  Identities=8%  Similarity=0.242  Sum_probs=32.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc-cCCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~-~gg~   43 (77)
                      +..+||++++||.+++.+++.+.++.|=|...+ .||.
T Consensus        25 s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG~GGy   62 (145)
T 1xd7_A           25 SSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGA   62 (145)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecCCCCc
Confidence            899999999999999999999999999987654 3443

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=96.34  E-value=0.0032  Score=40.50  Aligned_cols=34  Identities=18%  Similarity=0.303  Sum_probs=29.8

Q ss_pred             cCCC--CHHHHHHHhccC-HHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGV--RPCVISRQLRVS-HGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~--s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~   36 (77)
                      +.|+  |..++|+.+||| ++||++|++...+.|-+.
T Consensus        21 ~~g~~ps~~elA~~lgiss~~tv~~~~~~l~~~~~l~   57 (202)
T 1jhf_A           21 QTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIE   57 (202)
T ss_dssp             HHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEE
T ss_pred             HhCCCccHHHHHHHhCCCChHHHHHHHHHHHHCCCce
Confidence            3588  999999999999 999999999988877654

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=96.33  E-value=0.0036  Score=43.89  Aligned_cols=34  Identities=18%  Similarity=0.296  Sum_probs=31.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ..+|..++|+.+|+|++||+++++++.+.|-+..
T Consensus        32 ~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~   65 (380)
T 2hoe_A           32 SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVE   65 (380)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            3489999999999999999999999999998854

>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=96.31  E-value=0.01  Score=40.05  Aligned_cols=55  Identities=9%  Similarity=0.002  Sum_probs=44.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEY   59 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~   59 (77)
                      ++++.++|+.++|+++||++.+++..+.|=|.-.+...+++.   .+|++-.+.+.++
T Consensus       174 ~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~  231 (250)
T 1p4x_A          174 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQL  231 (250)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHHH
Confidence            389999999999999999999999999999987777667764   4566544444433

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=96.30  E-value=0.0094  Score=40.33  Aligned_cols=22  Identities=27%  Similarity=0.218  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++..+||+.+|||.+||||-++
T Consensus        11 ~ti~diA~~agVS~~TVSr~Ln   32 (344)
T 3kjx_A           11 LTLRDVSEASGVSEMTVSRVLR   32 (344)
T ss_dssp             CCHHHHHHHHCCCSHHHHHHHT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            6899999999999999999885

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=96.29  E-value=0.0048  Score=39.28  Aligned_cols=34  Identities=9%  Similarity=0.215  Sum_probs=31.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      ++..+||++++||++++.+++++.++.|=|...+
T Consensus        45 ~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~r   78 (159)
T 3lwf_A           45 ISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIR   78 (159)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEec
Confidence            7999999999999999999999999999997654

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=96.28  E-value=0.0055  Score=40.92  Aligned_cols=67  Identities=10%  Similarity=-0.071  Sum_probs=46.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc---CCCCC-CCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI---GGSKP-RVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~---gg~~~-~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +.-+++.++|+.+|||.+|+..|-    +.|-+.|...   +|.|. +...-.....|..+.+.  +++|.|+++.|
T Consensus         3 ~~~~~i~e~a~~~gvs~~tlr~y~----~~gll~p~~~d~~~g~R~y~~~~~~~l~~i~~l~~~--g~~l~~i~~~~   73 (278)
T 1r8e_A            3 ESYYSIGEVSKLANVSIKALRYYD----KIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYI--GTPLEEMKKAQ   73 (278)
T ss_dssp             CCEEEHHHHHHHHTCCHHHHHHHH----HTTSSCCSEECTTTCCEEEETGGGGHHHHHHHHHHT--TCCHHHHHHHT
T ss_pred             CCcEeHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCccccCHHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            345789999999999999998764    4599988643   55443 33333345567676443  79999998865

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=96.28  E-value=0.018  Score=38.89  Aligned_cols=66  Identities=14%  Similarity=0.030  Sum_probs=45.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L   75 (77)
                      +.+++.++|+.+|||..|+.-|-+    .|-+.|.....+..+.=++.+...   |..+.  .-+++|.||.+.|
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~----~GLL~p~~~~~~GyR~Y~~~dl~~L~~I~~lr--~~G~sL~eIk~~l   70 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDK----IGLLVPQKDDWNGYRIYSEKDVDKLQQILFFK--ELDFPLKKIQQIL   70 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHH----TTSSCCEECTTTCCEEBCHHHHHHHHHHHHHH--HTTCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH----CCCCCCceECCCCCeeeCHHHHHHHHHHHHHH--HCCCCHHHHHHHh
Confidence            468999999999999999987654    699988763222233344444443   44443  3468999988765

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=96.28  E-value=0.0052  Score=39.31  Aligned_cols=29  Identities=17%  Similarity=0.132  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||.++|.+++.+-+.
T Consensus       201 ~~g~s~~EIA~~lgis~~~V~~~~~ra~~  229 (239)
T 1rp3_A          201 YEELPAKEVAKILETSVSRVSQLKAKALE  229 (239)
T ss_dssp             TSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            47999999999999999999999988664

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=96.28  E-value=0.004  Score=36.52  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|-+
T Consensus        20 ~~glsq~~lA~~~gis~~~i~~~e~   44 (114)
T 3op9_A           20 EHGLKNHQIAELLNVQTRTVAYYMS   44 (114)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3699999999999999999999965

>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=96.25  E-value=0.0038  Score=40.66  Aligned_cols=36  Identities=11%  Similarity=0.154  Sum_probs=32.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.+++..++|+.+|||++||++-+++..+.|-+...
T Consensus        31 ~~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           31 NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            345899999999999999999999999999999655

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=96.23  E-value=0.0038  Score=38.73  Aligned_cols=25  Identities=16%  Similarity=0.242  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||+++|++|.+
T Consensus        79 ~~glTq~elA~~lGis~s~is~~E~  103 (141)
T 3kxa_A           79 KKGFTQSELATAAGLPQPYLSRIEN  103 (141)
T ss_dssp             HTTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999975

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

Probab=96.21  E-value=0.0031  Score=38.19  Aligned_cols=50  Identities=20%  Similarity=0.226  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHh--ccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHH
Q psy15513          5 GVRPCVISRQL--RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIE   57 (77)
Q Consensus         5 G~s~~~iA~rf--~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~   57 (77)
                      .+++.++|+.|  +||.++|++-+++..+.|-|...+.   .--.+++.-.+++.
T Consensus        27 ~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~~r---g~Y~LT~~G~~~l~   78 (111)
T 3b73_A           27 NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLAN---GVYVITEEGEAYLN   78 (111)
T ss_dssp             CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEECST---TCEEECHHHHHHHT
T ss_pred             CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEecCC---ceEEECchHHHHHH
Confidence            48999999999  9999999999999999999986421   13456665555443

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=96.18  E-value=0.0028  Score=37.59  Aligned_cols=27  Identities=15%  Similarity=0.198  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..|-...++|+.||||.+|+++++++|
T Consensus        69 ~~~gn~~~AA~~LGIsR~TL~rkLkk~   95 (98)
T 1eto_A           69 YTLGNQTRAALMMGINRGTLRKKLKKY   95 (98)
T ss_dssp             HTTTCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            345678899999999999999999987

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=96.15  E-value=0.0048  Score=36.60  Aligned_cols=25  Identities=12%  Similarity=0.206  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|-+
T Consensus        34 ~~gltq~elA~~~gis~~~is~~E~   58 (111)
T 3mlf_A           34 DYGLTQKELGDLFKVSSRTIQNMEK   58 (111)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4799999999999999999999975

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=96.14  E-value=0.0024  Score=45.50  Aligned_cols=35  Identities=11%  Similarity=0.184  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ..+|..++|+.+++|++||+++++++.+.|-+...
T Consensus        52 ~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~~   86 (429)
T 1z05_A           52 GPISRIDLSKESELAPASITKITRELIDAHLIHET   86 (429)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            34899999999999999999999999999988654

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=96.13  E-value=0.003  Score=34.08  Aligned_cols=23  Identities=26%  Similarity=0.492  Sum_probs=21.3

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ...++|+.||||++|+++++++|
T Consensus        35 n~~~aA~~LGIsr~tL~rklkk~   57 (61)
T 1g2h_A           35 STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHh
Confidence            67889999999999999999986

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=96.11  E-value=0.0052  Score=36.15  Aligned_cols=25  Identities=4%  Similarity=0.117  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||+++|++|.+
T Consensus        47 ~~glsq~elA~~~gis~~~is~~E~   71 (107)
T 2jvl_A           47 EPTMTQAELGKEIGETAATVASYER   71 (107)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            6799999999999999999999854

>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=96.11  E-value=0.0099  Score=38.56  Aligned_cols=45  Identities=16%  Similarity=0.039  Sum_probs=37.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      .+-+++|++||||.++|..-+++....|=|...|..|-.-...+.
T Consensus        36 L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~   80 (218)
T 3sxy_A           36 LNVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDE   80 (218)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEETTTEEEECCCCH
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCH
Confidence            577899999999999999999999999999888765544344444

>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=96.10  E-value=0.007  Score=40.19  Aligned_cols=38  Identities=18%  Similarity=0.207  Sum_probs=34.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      .+..++|++||||.+||..-+++....|-|...|.+|-
T Consensus        50 L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~~~G~   87 (237)
T 3c7j_A           50 LRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGA   87 (237)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCce
Confidence            68899999999999999999999999999998876653

>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=96.10  E-value=0.014  Score=38.74  Aligned_cols=34  Identities=18%  Similarity=0.167  Sum_probs=31.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +++..+||+++|++++||+|+++.+.+.|-+...
T Consensus        23 ~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           23 DVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            5999999999999999999999999999998754

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=96.09  E-value=0.0045  Score=36.55  Aligned_cols=24  Identities=21%  Similarity=0.191  Sum_probs=22.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|+|..++|+++|||++++++|.
T Consensus        32 ~~gltq~elA~~~gis~~~is~~E   55 (114)
T 3vk0_A           32 NKGWSQEELARQCGLDRTYVSAVE   55 (114)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999999995

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=96.09  E-value=0.0049  Score=40.66  Aligned_cols=52  Identities=23%  Similarity=0.212  Sum_probs=39.7

Q ss_pred             CCCCH--HHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHH
Q psy15513          4 AGVRP--CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEE   58 (77)
Q Consensus         4 ~G~s~--~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~   58 (77)
                      .|+++  .++|++|+||++||++.+++..+.|-|.-.+.   +.-.+|+.-.+.+.+
T Consensus        21 ~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~   74 (230)
T 1fx7_A           21 EGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD---RHLELTEKGRALAIA   74 (230)
T ss_dssp             HTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SCEEECHHHHHHHHH
T ss_pred             cCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC---ccEEECHHHHHHHHH
Confidence            47777  99999999999999999999999999976653   333456654444333

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=96.05  E-value=0.0056  Score=36.54  Aligned_cols=25  Identities=12%  Similarity=0.234  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|-+
T Consensus        23 ~~glsq~~lA~~~gis~~~is~~E~   47 (126)
T 3ivp_A           23 KQGLTREQVGAMIEIDPRYLTNIEN   47 (126)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            4799999999999999999999964

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=96.01  E-value=0.025  Score=37.12  Aligned_cols=37  Identities=24%  Similarity=0.349  Sum_probs=32.9

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCc--ccc--CCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVI--GGS   43 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p--k~~--gg~   43 (77)
                      +-+++|++||||.++|..-+++....|=|..  .|.  +|-
T Consensus        30 sE~~La~~lgVSRtpVREAL~~L~~~GlV~~~~~~~~~~G~   70 (239)
T 2di3_A           30 SERALSETLGVSRSSLREALRVLEALGTISTATGSGPRSGT   70 (239)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHTSEECCSTTSGGGCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeecccCCCCCc
Confidence            5679999999999999999999999999988  765  553

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=96.01  E-value=0.005  Score=37.31  Aligned_cols=25  Identities=20%  Similarity=0.234  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+++.++|+++|||+++|++|.+
T Consensus        51 ~~glTQ~eLA~~lGis~~~Is~iE~   75 (120)
T 2o38_A           51 RARLSQAAAAARLGINQPKVSALRN   75 (120)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4699999999999999999999864

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=96.01  E-value=0.0078  Score=40.40  Aligned_cols=36  Identities=3%  Similarity=0.018  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+++|+++|||+|+++.+.+.|-+...+
T Consensus        37 ~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~   72 (260)
T 2o0y_A           37 PTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRA   72 (260)
T ss_dssp             SSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            579999999999999999999999999999987654

>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=96.00  E-value=0.0077  Score=42.85  Aligned_cols=56  Identities=9%  Similarity=0.050  Sum_probs=44.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~   59 (77)
                      .|++..++|++++++.+||.+.+++..+.|=|.-.+...+++.   .+|+.-.+.+.++
T Consensus       419 ~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~~~  477 (487)
T 1hsj_A          419 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKL  477 (487)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHHHH
Confidence            4699999999999999999999999999999988777667764   3455444444333

>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=95.95  E-value=0.014  Score=37.86  Aligned_cols=47  Identities=15%  Similarity=0.138  Sum_probs=38.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV   52 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~   52 (77)
                      .+-+++|++||||.++|.--+++....|=|...|..|-.-...+...
T Consensus        40 L~E~~La~~lgVSRtpVREAl~~L~~eGlv~~~~~~G~~V~~~~~~~   86 (222)
T 3ihu_A           40 LVETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGAVIRRLSLQE   86 (222)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECSTTCEEECCCCHHH
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHH
Confidence            45788999999999999999999999999988876654444444433

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=95.93  E-value=0.0084  Score=38.45  Aligned_cols=32  Identities=19%  Similarity=0.246  Sum_probs=29.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcC-CCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGS-IRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~-v~p   37 (77)
                      +|..++|++|+||.+||++-++..++.|- +..
T Consensus        37 ~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           37 VSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            89999999999999999999999999997 543

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=95.91  E-value=0.0038  Score=40.67  Aligned_cols=27  Identities=11%  Similarity=0.277  Sum_probs=24.2

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .+.|+|..++|+++|||++||++|.+.
T Consensus        27 ~~~g~t~~~lA~~~gis~~~i~~~~~g   53 (236)
T 3bdn_A           27 NELGLSQESVADKMGMGQSGVGALFNG   53 (236)
T ss_dssp             TTTTCCSHHHHHHHTSCHHHHHHHTTT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            357999999999999999999999753

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=95.90  E-value=0.0063  Score=39.97  Aligned_cols=33  Identities=12%  Similarity=0.153  Sum_probs=29.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||+.++||.+||...+++.++.=.+
T Consensus       188 ~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          188 SKGKTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            479999999999999999999999998875444

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=95.87  E-value=0.009  Score=35.71  Aligned_cols=26  Identities=15%  Similarity=0.239  Sum_probs=23.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .+|..++|+..+||.+||.|..++.=
T Consensus        35 ~~si~elA~~~~vS~aTv~Rf~kkLG   60 (107)
T 3iwf_A           35 NMTSQEIANQLETSSTSIIRLSKKVT   60 (107)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHS
T ss_pred             HCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence            48999999999999999999998753

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=95.85  E-value=0.004  Score=40.09  Aligned_cols=39  Identities=8%  Similarity=0.113  Sum_probs=33.8

Q ss_pred             CccCCCCHHHHHHHhc-cCHHHHHHHHHHHHHhcCCCccc
Q psy15513          1 MAAAGVRPCVISRQLR-VSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~-VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      |.+.+++.+++|..|+ +|++||++-++..++.|=|...+
T Consensus        32 L~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv~~~~   71 (182)
T 4g6q_A           32 LIGRSLTTRELAELLPDVATTTLYRQVGILVKAGVLMVTA   71 (182)
T ss_dssp             TTTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCeEEEE
Confidence            4556799999999996 99999999999999999986443

>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=95.84  E-value=0.0064  Score=35.78  Aligned_cols=37  Identities=14%  Similarity=0.099  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHhc----cCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf~----VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .++++.+||+.++    ||++||++.+++..+.|-|.-.+.
T Consensus        23 ~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~   63 (123)
T 1okr_A           23 KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD   63 (123)
T ss_dssp             SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             CCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec
Confidence            4689999999999    899999999999999999977655

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=95.84  E-value=0.0096  Score=39.84  Aligned_cols=35  Identities=17%  Similarity=0.202  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..+||+++|++++||+|+++.+.+.|-+...
T Consensus        28 ~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           28 PNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             SSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            46999999999999999999999999999988653

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=95.83  E-value=0.007  Score=35.58  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=22.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||++++++|-+
T Consensus        39 ~~glsq~~lA~~~gis~~~is~~E~   63 (117)
T 3f52_A           39 DKGVTLRELAEASRVSPGYLSELER   63 (117)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3689999999999999999999953

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=95.83  E-value=0.0069  Score=35.25  Aligned_cols=25  Identities=12%  Similarity=0.139  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+++|||++++++|-+
T Consensus        39 ~~gltq~elA~~~gis~~~is~iE~   63 (99)
T 3g5g_A           39 EKGMTQEDLAYKSNLDRTYISGIER   63 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4799999999999999999999853

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=95.82  E-value=0.01  Score=39.60  Aligned_cols=36  Identities=17%  Similarity=0.091  Sum_probs=32.0

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |-+++|++||||..||.+-++...+.|-+...+..|
T Consensus        36 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   71 (243)
T 2wv0_A           36 SEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRG   71 (243)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTTSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEeCCCe
Confidence            679999999999999999999999999998665433

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=95.82  E-value=0.0077  Score=36.05  Aligned_cols=25  Identities=16%  Similarity=0.046  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+|..++|+..+||.+||.|..+..
T Consensus        39 ~~si~elA~~~~vS~aTv~Rf~kkl   63 (111)
T 2o3f_A           39 ESTVNEISALANSSDAAVIRLCXSL   63 (111)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             hcCHHHHHHHHCCCHHHHHHHHHHc
Confidence            5899999999999999999998753

>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=95.77  E-value=0.0065  Score=40.39  Aligned_cols=35  Identities=17%  Similarity=0.243  Sum_probs=32.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +++..+||+++|++++||+|+++.+.+.|-|.-.+
T Consensus        21 ~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~   55 (241)
T 2xrn_A           21 GLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALG   55 (241)
T ss_dssp             CEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECG
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            58999999999999999999999999999997654

>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=95.77  E-value=0.016  Score=38.38  Aligned_cols=45  Identities=22%  Similarity=0.158  Sum_probs=37.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP   50 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~   50 (77)
                      .+-.++|++||||.++|..-+++....|-|...|..|-.-...+.
T Consensus        52 L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~   96 (239)
T 2hs5_A           52 LSEPDICAALDVSRNTVREAFQILIEDRLVAHELNRGVFVRVPTA   96 (239)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEEEECCCCH
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEEeCCCH
Confidence            578899999999999999999999999999888765544333443

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=95.76  E-value=0.0074  Score=39.78  Aligned_cols=36  Identities=28%  Similarity=0.394  Sum_probs=31.9

Q ss_pred             CCCCH--HHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRP--CVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~--~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .|.++  .++|++|+||++||++.+++..+.|-|.-.+
T Consensus        21 ~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~   58 (226)
T 2qq9_A           21 EGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS   58 (226)
T ss_dssp             HTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             cCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            46665  9999999999999999999999999987654

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

Probab=95.74  E-value=0.0017  Score=45.43  Aligned_cols=39  Identities=10%  Similarity=0.175  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ..|++..++|++|+||.+||.|.+++..+.|-|.-+..|
T Consensus        32 ~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~~~~g   70 (345)
T 2o0m_A           32 MQPIGRRSLSETMGITERVLRTETDVLKQLNLIEPSKSG   70 (345)
T ss_dssp             ---------------------------------------
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecc
Confidence            367999999999999999999999999999999755443

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=95.73  E-value=0.0017  Score=43.84  Aligned_cols=28  Identities=21%  Similarity=0.216  Sum_probs=0.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+.-++..+||+++|||.+||||-++..
T Consensus         2 ~~~~~ti~diA~~agVS~~TVSrvln~~   29 (332)
T 2o20_A            2 VESTTTIYDVARVAGVSMATVSRVVNGN   29 (332)
T ss_dssp             ----------------------------
T ss_pred             CCCCCcHHHHHHHHCCCHHHHHHHHcCC
Confidence            3444788999999999999999999863

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=95.71  E-value=0.0056  Score=41.80  Aligned_cols=22  Identities=27%  Similarity=0.250  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+..+||+.+|||.+||||-++
T Consensus        10 ~Ti~diA~~aGVS~~TVSrvLn   31 (366)
T 3h5t_A           10 GTLASIAAKLGISRTTVSNAYN   31 (366)
T ss_dssp             THHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHhCCCHHHHHHHHC
Confidence            5689999999999999999996

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=95.70  E-value=0.0058  Score=40.18  Aligned_cols=38  Identities=26%  Similarity=0.225  Sum_probs=33.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      +.+++..++|+.++||++||++-+++..+.|-|...+.
T Consensus        26 ~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~   63 (202)
T 2p4w_A           26 KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (202)
T ss_dssp             HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEee
Confidence            35689999999999999999999999999999965443

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=95.69  E-value=0.011  Score=35.26  Aligned_cols=26  Identities=15%  Similarity=0.212  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhc--cCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLR--VSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G~s~~~iA~rf~--VS~stv~r~~~r~   29 (77)
                      .+.|+.+|+..||  ||.+||++|+++.
T Consensus        76 ~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           76 SCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             CCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            3489999999999  8999999999863

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=95.68  E-value=0.016  Score=34.21  Aligned_cols=28  Identities=11%  Similarity=0.120  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .|+|..+||..+|||.+||..++.+-..
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlk   65 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALR   65 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6899999999999999999998876543

>1rr7_A Middle operon regulator; MOR, transcription; 2.20A {Enterobacteria phage MU} SCOP: a.4.1.14

Probab=95.65  E-value=0.015  Score=35.92  Aligned_cols=29  Identities=17%  Similarity=0.259  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +|.+..++|+++|+|..+|++++++.+..
T Consensus        91 ~G~n~~eLArkYgLSer~I~~Ii~~~r~~  119 (129)
T 1rr7_A           91 NGRNVSELTTRYGVTFNTVYKAIRRMRRL  119 (129)
T ss_dssp             CSSCHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            49999999999999999999999988764

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=95.65  E-value=0.012  Score=36.75  Aligned_cols=33  Identities=18%  Similarity=0.234  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       168 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~~  200 (210)
T 3ryp_A          168 ITRQEIGQIVGCSRETVGRILKMLEDQNLISAH  200 (210)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEeC
Confidence            688999999999999999999999999988643

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=95.64  E-value=0.012  Score=36.64  Aligned_cols=33  Identities=21%  Similarity=0.321  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       165 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  197 (207)
T 2oz6_A          165 ITRQEIGRIVGCSREMVGRVLKSLEEQGLVHVK  197 (207)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            688999999999999999999999999988643

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=95.63  E-value=0.0091  Score=39.45  Aligned_cols=33  Identities=15%  Similarity=-0.013  Sum_probs=29.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||+.++||.+||...+++.++.=.+
T Consensus       188 ~~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (237)
T 3szt_A          188 AVGKTYGEIGLILSIDQRTVKFHIVNAMRKLNS  220 (237)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            479999999999999999999999998876444

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

Probab=95.61  E-value=0.0088  Score=36.99  Aligned_cols=44  Identities=14%  Similarity=0.141  Sum_probs=36.8

Q ss_pred             ccCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          2 AAAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         2 ~~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      +...++..++++.+ +||.+++++-+++..+.|=|.-.+...+++
T Consensus        36 ~~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r   80 (131)
T 4a5n_A           36 IDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPP   80 (131)
T ss_dssp             TTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             hcCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCC
Confidence            34458999999999 999999999999999999997665544444

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=95.61  E-value=0.012  Score=37.63  Aligned_cols=54  Identities=15%  Similarity=0.303  Sum_probs=37.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM   66 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~   66 (77)
                      ++..+||..+|+|+.||+|.++++++.| +. .  .+++-.+.+   .+.+.++....|..
T Consensus       179 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g-i~-~--~~~~i~I~d---~~~L~~~~~~~~~~  232 (237)
T 3fx3_A          179 YDKMLIAGRLGMKPESLSRAFSRLKAAG-VT-V--KRNHAEIED---IALLRDYAESDPAD  232 (237)
T ss_dssp             SCTHHHHHHTTCCHHHHHHHHHHHGGGT-EE-C--CTTEEEESC---HHHHHHHHCC----
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCC-eE-e--eCCEEEEcC---HHHHHHHhcCCccc
Confidence            5688999999999999999999999999 73 2  222324444   45577777666644

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=95.57  E-value=0.011  Score=38.67  Aligned_cols=33  Identities=18%  Similarity=0.018  Sum_probs=29.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||..++||.+||...+++.++.=.+
T Consensus       186 ~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  218 (234)
T 1l3l_A          186 AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            479999999999999999999999998875444

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

Probab=95.55  E-value=0.001  Score=40.60  Aligned_cols=36  Identities=14%  Similarity=-0.028  Sum_probs=31.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.||||.+||.+-+++..+.|-|...+..|
T Consensus        37 s~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~~~G   72 (126)
T 3ic7_A           37 SVREYASIVEVNANTVMRSYEYLQSQEVIYNKRGIG   72 (126)
T ss_dssp             CTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEcCCc
Confidence            778999999999999999999999999998876444

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=95.55  E-value=0.036  Score=35.28  Aligned_cols=51  Identities=6%  Similarity=-0.045  Sum_probs=39.2

Q ss_pred             CCHHHHHHHhc-cCHHHHHHHHHHHHHhcCCCccc-----cCCCCC---CCCCHHHHHHH
Q psy15513          6 VRPCVISRQLR-VSHGCVSKILNRYQETGSIRPGV-----IGGSKP---RVATPDVERRI   56 (77)
Q Consensus         6 ~s~~~iA~rf~-VS~stv~r~~~r~r~tG~v~pk~-----~gg~~~---~~~~~~~~~~i   56 (77)
                      ++..+++..++ ||++||++-|+.+.+.|-|....     .++++|   -.++++-.+.+
T Consensus        46 ~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l  105 (151)
T 3u1d_A           46 LSVEELLYRNPDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALL  105 (151)
T ss_dssp             BCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHH
T ss_pred             CCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHH
Confidence            78999999999 99999999999999999997432     122333   36777655554

>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=95.55  E-value=0.011  Score=39.34  Aligned_cols=36  Identities=11%  Similarity=0.092  Sum_probs=32.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |-+++|++||||..||.+-++...+.|-+...+..|
T Consensus        35 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   70 (236)
T 3edp_A           35 NETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVG   70 (236)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEECCce
Confidence            788999999999999999999999999998776443

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=95.53  E-value=0.016  Score=36.49  Aligned_cols=33  Identities=15%  Similarity=0.325  Sum_probs=30.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            468899999999999999999999999999864

>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=95.52  E-value=0.019  Score=38.73  Aligned_cols=54  Identities=7%  Similarity=-0.039  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIE   57 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~   57 (77)
                      +|+++.++|++++++.+|+.+.+++..+.|=|.-.+...+++.   .+|+.-.+.+.
T Consensus        49 ~~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~~  105 (250)
T 1p4x_A           49 NTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIA  105 (250)
T ss_dssp             SEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHHH
Confidence            4799999999999999999999999999999987777777775   35665444333

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=95.52  E-value=0.016  Score=36.36  Aligned_cols=32  Identities=25%  Similarity=0.365  Sum_probs=30.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus       164 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          164 IRHHELAALAGTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            68899999999999999999999999999974

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=95.51  E-value=0.011  Score=35.35  Aligned_cols=30  Identities=13%  Similarity=0.155  Sum_probs=25.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      +.|+|..++|+++|||+++|++|     |.|...|
T Consensus        18 ~~glSq~eLA~~~gis~~~is~i-----E~G~~~~   47 (112)
T 2wus_R           18 ERRITLLDASLFTNINPSKLKRI-----EEGDLKG   47 (112)
T ss_dssp             TTTCCHHHHHHHSSCCHHHHHHH-----HHTCCTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHH-----HCCCCCC
Confidence            47999999999999999999986     5676544

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=95.50  E-value=0.011  Score=39.70  Aligned_cols=35  Identities=11%  Similarity=0.146  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+++..+||+++|+++|||+|+++.+.+.|-+...
T Consensus        35 ~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~   69 (265)
T 2ia2_A           35 QRRTLSDVARATDLTRATARRFLLTLVELGYVATD   69 (265)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            56899999999999999999999999999988653

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=95.50  E-value=0.025  Score=34.98  Aligned_cols=39  Identities=23%  Similarity=0.248  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..++
T Consensus        36 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~   79 (145)
T 2fe3_A           36 AHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGD   79 (145)
T ss_dssp             SCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTT
T ss_pred             CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCC
Confidence            358999999999     899999999999999999997655543

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=95.48  E-value=0.014  Score=36.86  Aligned_cols=34  Identities=21%  Similarity=0.350  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       178 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  211 (227)
T 3dkw_A          178 PVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHLD  211 (227)
T ss_dssp             CSCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEES
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEec
Confidence            3678999999999999999999999999988643

>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=95.48  E-value=0.011  Score=39.76  Aligned_cols=36  Identities=14%  Similarity=0.208  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..|||+++|+++|||+|+++-+.+.|=+.--+
T Consensus        20 ~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~   55 (260)
T 3r4k_A           20 LEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVE   55 (260)
T ss_dssp             SEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            468999999999999999999999999999997544

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=95.47  E-value=0.015  Score=36.39  Aligned_cols=53  Identities=15%  Similarity=0.216  Sum_probs=39.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP   64 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p   64 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.   +++-...++   +.+.++....+
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~---~~~i~i~d~---~~L~~~~~~~~  199 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRSG---YGKIQLLDL---KGLKELAESRG  199 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE---TTEEEESCH---HHHHHHHTSCC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeC---CCEEEEeCH---HHHHHHhcccc
Confidence            688999999999999999999999999998743   223234443   34666554443

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=95.47  E-value=0.015  Score=36.82  Aligned_cols=33  Identities=18%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~  220 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLHAR  220 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEEC
Confidence            688999999999999999999999999988643

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=95.46  E-value=0.015  Score=33.25  Aligned_cols=24  Identities=8%  Similarity=0.126  Sum_probs=21.1

Q ss_pred             cCCCCHHHHHHHhccCHHH----HHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGC----VSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~st----v~r~~   26 (77)
                      +.|+|..++|+.+|||+++    +++|-
T Consensus        12 ~~glsq~~lA~~~gis~~~~~~~is~~E   39 (98)
T 3lfp_A           12 RAGISQEKLGVLAGIDEASASARMNQYE   39 (98)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCcchhhhHHHHHH
Confidence            4699999999999999999    77764

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=95.45  E-value=0.014  Score=39.60  Aligned_cols=36  Identities=14%  Similarity=0.083  Sum_probs=31.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |-+++|++||||..||.+-+++..+.|-|...+..|
T Consensus        55 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   90 (272)
T 3eet_A           55 SQARIREEYGVSDTVALEARKVLMAEGLVEGRSGSG   90 (272)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCC--
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            789999999999999999999999999997766433

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=95.44  E-value=0.0069  Score=39.37  Aligned_cols=27  Identities=15%  Similarity=0.230  Sum_probs=24.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|++..+||++||+|.++|++.++-.
T Consensus        50 ~~G~t~eeiA~~lG~s~s~V~~~LrLl   76 (178)
T 1r71_A           50 AKGKKKGDIAKEIGKSPAFITQHVTLL   76 (178)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            469999999999999999999988764

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=95.42  E-value=0.019  Score=38.25  Aligned_cols=31  Identities=19%  Similarity=0.146  Sum_probs=27.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      -.|+|..+||..+|||.+||...+.|.++.=
T Consensus       210 ~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          210 RKGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3799999999999999999999999987643

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=95.40  E-value=0.016  Score=36.22  Aligned_cols=54  Identities=19%  Similarity=0.138  Sum_probs=40.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA   65 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd   65 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.   +++-...+   .+.+.++....++
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~---~~~i~i~d---~~~L~~~~~~~~e  193 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRREGLIATA---YRRVYLLD---LAALEREAGSALE  193 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEEE---TTEEEECC---HHHHHHHHCSCCC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec---CCEEEEeC---HHHHHHHhccccc
Confidence            688999999999999999999999999988654   22223444   3446666655544

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=95.39  E-value=0.0027  Score=43.13  Aligned_cols=23  Identities=13%  Similarity=0.036  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+++|||.+||||-++.
T Consensus         7 ~ti~diA~~agVS~~TVSr~Ln~   29 (333)
T 3jvd_A            7 SSLKEVAELAGVGYATASRALSG   29 (333)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            67899999999999999999984

>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=95.38  E-value=0.022  Score=33.69  Aligned_cols=46  Identities=13%  Similarity=0.094  Sum_probs=36.4

Q ss_pred             CCC--HHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHH
Q psy15513          5 GVR--PCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         5 G~s--~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~   51 (77)
                      .++  ..++++.+ |||++++++-+++..+.|=|...+. ....-.+|+.
T Consensus        40 ~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~-r~~~y~LT~~   88 (111)
T 3df8_A           40 STRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG-QITTYALTEK   88 (111)
T ss_dssp             SSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES-SSEEEEECHH
T ss_pred             CCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec-CcEEEEECcc
Confidence            356  99999999 9999999999999999999986654 1112356664

>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=95.37  E-value=0.015  Score=33.25  Aligned_cols=35  Identities=6%  Similarity=0.220  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHhccCHH-HHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHG-CVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~s-tv~r~~~r~r~tG~v~pk   38 (77)
                      .+.++.+||+.|||+.. .|.+-+....+.|-|.-.
T Consensus        24 g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           24 SDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             CCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            45889999999999999 999999999999999844

>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=95.36  E-value=0.012  Score=38.45  Aligned_cols=36  Identities=14%  Similarity=0.122  Sum_probs=32.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |-+++|++||||.+||..-+++....|-|...+..|
T Consensus        33 sE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~g~G   68 (239)
T 1hw1_A           33 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   68 (239)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTEE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            678999999999999999999999999998776443

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=95.35  E-value=0.017  Score=36.61  Aligned_cols=32  Identities=25%  Similarity=0.301  Sum_probs=30.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus       178 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          178 LTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            68999999999999999999999999998865

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=95.34  E-value=0.02  Score=36.74  Aligned_cols=33  Identities=30%  Similarity=0.281  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       187 ~t~~~lA~~lG~sr~tvsR~l~~l~~~glI~~~  219 (232)
T 1zyb_A          187 VKMDDLARCLDDTRLNISKTLNELQDNGLIELH  219 (232)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEEE
T ss_pred             CCHHHHHHHhCCChhHHHHHHHHHHHCCCEEec
Confidence            689999999999999999999999999988643

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=95.33  E-value=0.018  Score=36.65  Aligned_cols=33  Identities=18%  Similarity=0.212  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       176 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~~  208 (231)
T 3e97_A          176 LGTQDIMARTSSSRETVSRVLKRLEAHNILEVS  208 (231)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEec
Confidence            688999999999999999999999999998753

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=95.32  E-value=0.011  Score=37.36  Aligned_cols=25  Identities=16%  Similarity=0.167  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||++++++|.+
T Consensus        22 ~~gltq~~lA~~~gis~~~is~~e~   46 (192)
T 1y9q_A           22 SRGLSLDATAQLTGVSKAMLGQIER   46 (192)
T ss_dssp             HTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999964

>3hhg_A Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B}

Probab=95.32  E-value=0.013  Score=38.20  Aligned_cols=46  Identities=22%  Similarity=0.283  Sum_probs=33.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++-+++..+. |.----+.  +++-.+|++
T Consensus        16 ~~g-s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~--~~~~~lT~~   62 (306)
T 3hhg_A           16 ESG-SFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNRT--TRQLSLTEE   62 (306)
T ss_dssp             HSS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEETT--SSSCEECHH
T ss_pred             HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEeec--CCCeeECHh
Confidence            445 88999999999999999999999854 54433322  244456664

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=95.31  E-value=0.018  Score=36.47  Aligned_cols=33  Identities=24%  Similarity=0.384  Sum_probs=30.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      .++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus       167 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          167 GLNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             SSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            478999999999999999999999999998864

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=95.31  E-value=0.024  Score=34.98  Aligned_cols=37  Identities=14%  Similarity=0.026  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHh----------ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL----------RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf----------~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .+++..+|+..|          .||.+||++|++++...|.=.|-+.
T Consensus       100 ~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~~~~~~~~  146 (159)
T 2k27_A          100 PTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMDS  146 (159)
T ss_dssp             SSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCCSCCCCCC
T ss_pred             ccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCCccCcccC
Confidence            357899999887          4899999999999999887766553

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=95.26  E-value=0.015  Score=38.56  Aligned_cols=34  Identities=21%  Similarity=0.153  Sum_probs=31.1

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|++||||..||.+-++...+.|-+...+.
T Consensus        31 se~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~g   64 (239)
T 3bwg_A           31 VLETLMAQFEVSKSTITKSLELLEQKGAIFQVRG   64 (239)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeCC
Confidence            7889999999999999999999999999976654

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=95.24  E-value=0.011  Score=39.07  Aligned_cols=26  Identities=12%  Similarity=0.139  Sum_probs=23.6

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|++..++|+.+|||+++|++|++
T Consensus        40 ~~~gitQ~~lA~~~GiSqs~ISr~l~   65 (194)
T 1ic8_A           40 QQHNIPQREVVDTTGLNQSHLSQHLN   65 (194)
T ss_dssp             HHTTCCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCCChHHHHHHHh
Confidence            35799999999999999999999975

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=95.23  E-value=0.017  Score=35.07  Aligned_cols=38  Identities=11%  Similarity=0.059  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..+
T Consensus        25 ~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~   67 (131)
T 2o03_A           25 DFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTD   67 (131)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECT
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeC
Confidence            347899999999     99999999999999999998655443

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=95.23  E-value=0.027  Score=35.72  Aligned_cols=33  Identities=21%  Similarity=0.143  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~~  196 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ  196 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEEc
Confidence            789999999999999999999999999988653

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

Probab=95.22  E-value=0.013  Score=34.61  Aligned_cols=38  Identities=21%  Similarity=0.165  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHhc----cCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~----VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..+|++.++    ++.+||++.+.+..+.|-|.-.+.|
T Consensus        48 ~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~g   89 (99)
T 2k4b_A           48 GEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEG   89 (99)
T ss_dssp             SCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEET
T ss_pred             CCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeCC
Confidence            4689999999997    5799999999999999999766544

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=95.21  E-value=0.032  Score=31.46  Aligned_cols=28  Identities=7%  Similarity=0.099  Sum_probs=23.2

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      .+| ||+..+|+.|||.++|...=++-..
T Consensus        27 r~g~mS~~~Aak~yGVP~sTL~~RVk~~~   55 (70)
T 2cob_A           27 MSGKMSVSKAQSIYGIPHSTLEYKVKERL   55 (70)
T ss_dssp             HTTSSCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HcCCccHHHHHHHhCCChHHHHHHHHhhc
Confidence            357 9999999999999999987665543

>2og0_A Excisionase; protein-DNA complex, DNA architectural protein, 'winged'HELI protein, phage excision; 1.90A {Enterobacteria phage lambda} SCOP: a.6.1.7 PDB: 1lx8_A 1rh6_A 2ief_A

Probab=95.15  E-value=0.0098  Score=31.61  Aligned_cols=32  Identities=16%  Similarity=0.023  Sum_probs=25.4

Q ss_pred             CHHHHHHHh--ccCHHHHHHHHHHHHHhcCC--CccccCC
Q psy15513          7 RPCVISRQL--RVSHGCVSKILNRYQETGSI--RPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf--~VS~stv~r~~~r~r~tG~v--~pk~~gg   42 (77)
                      +..|.|+.+  .+|.+||+||.+.    |.+  .|.+.|+
T Consensus         4 tl~EwA~~~~~~~s~~Tl~r~ar~----G~I~Pp~~KvGr   39 (52)
T 2og0_A            4 TLQEWNARQRRPRSLETVRRWVRE----SRIFPPPVKDGR   39 (52)
T ss_dssp             EHHHHHHTSSSCCCHHHHHHHHHT----TCEESCCEEETT
T ss_pred             eHHHHHHHhcCCCCHHHHHHHHHC----CCCCCcccccCC
Confidence            457888887  7999999999765    999  6666674

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=95.14  E-value=0.0036  Score=40.04  Aligned_cols=29  Identities=10%  Similarity=0.146  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||+.||||.+||.+++.+-++
T Consensus       212 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~  240 (243)
T 1l0o_C          212 YKDQTQSEVASRLGISQVQMSRLEKKILQ  240 (243)
T ss_dssp             -----------------------------
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47999999999999999999999988654

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=95.13  E-value=0.016  Score=35.25  Aligned_cols=31  Identities=10%  Similarity=0.147  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.|+|..++|++.|||++++++|     |.|...|.
T Consensus        14 ~~gltq~elA~~~gis~~~is~i-----E~g~~~~~   44 (130)
T 3fym_A           14 RLGMTLTELEQRTGIKREMLVHI-----ENNEFDQL   44 (130)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHH-----HTTCGGGS
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHH-----HCCCCCCC
Confidence            47999999999999999999987     56766554

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=95.12  E-value=0.016  Score=33.69  Aligned_cols=23  Identities=17%  Similarity=0.385  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |+++.++|+..|||++|++.+.+
T Consensus        32 GikQ~eLAK~iGIsqsTLSaIen   54 (83)
T 2l1p_A           32 DMNQSSLAKECPLSQSMISSIVN   54 (83)
T ss_dssp             TSCHHHHHHHSSSCHHHHHHHHT
T ss_pred             hcCHHHHHHHcCCCHHHHHHHHc
Confidence            99999999999999999998753

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

Probab=95.09  E-value=0.02  Score=34.79  Aligned_cols=38  Identities=11%  Similarity=0.013  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHHhc----cCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~----VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..+|+++|+    |+.+||++.+++..+.|-|.-.+.+
T Consensus        23 ~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~   64 (138)
T 2g9w_A           23 EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDD   64 (138)
T ss_dssp             SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecC
Confidence            5699999999998    8999999999999999999776543

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=95.08  E-value=0.016  Score=36.69  Aligned_cols=25  Identities=12%  Similarity=0.072  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||++++++|-+
T Consensus        21 ~~g~s~~~la~~~gis~~~ls~~e~   45 (198)
T 2bnm_A           21 QVKMDHAALASLLGETPETVAAWEN   45 (198)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999865

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=95.06  E-value=0.024  Score=36.08  Aligned_cols=34  Identities=3%  Similarity=-0.015  Sum_probs=31.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       180 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  213 (232)
T 2gau_A          180 YLSREELATLSNMTVSNAIRTLSTFVSERMLALD  213 (232)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeC
Confidence            4688999999999999999999999999988644

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=95.05  E-value=0.024  Score=36.72  Aligned_cols=57  Identities=14%  Similarity=0.093  Sum_probs=43.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMF   67 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~t   67 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-.   +++-.+.+   .+.+.++.+..|...
T Consensus       177 ~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~~---~~~i~i~d---~~~L~~~a~~~~~~~  233 (250)
T 3e6c_C          177 PLSQKSIGEITGVHHVTVSRVLASLKRENILDKK---KNKIIVYN---LGELKHLSEQTSYYS  233 (250)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---SSEEEESC---HHHHHHHHTSSCCCC
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEeC---CCEEEEec---HHHHHHHHccCcccc
Confidence            4689999999999999999999999999988754   22223343   456778777766543

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=95.04  E-value=0.024  Score=36.69  Aligned_cols=34  Identities=15%  Similarity=0.183  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       193 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~~  226 (243)
T 3la7_A          193 KLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIH  226 (243)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEEc
Confidence            3688999999999999999999999999988743

>1zs4_A Regulatory protein CII; helix-turn-helix, transcription activator, transcription-DNA; HET: DNA; 1.70A {Enterobacteria phage lambda} SCOP: a.35.1.9

Probab=95.04  E-value=0.013  Score=34.04  Aligned_cols=23  Identities=9%  Similarity=0.065  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +....+|+..||+.|||+||-.-
T Consensus        25 ~gQ~~vAe~~GvdeStISR~k~~   47 (83)
T 1zs4_A           25 LGTEKTAEAVGVDKSQISRWKRD   47 (83)
T ss_dssp             HCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HhhHHHHHHhCCCHHHHhhhhhh
Confidence            45788999999999999999763

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=95.00  E-value=0.019  Score=38.72  Aligned_cols=33  Identities=15%  Similarity=0.062  Sum_probs=29.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|++..+||+.++||.+||...+++.++.=.+
T Consensus       210 ~~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~  242 (265)
T 3qp6_A          210 SRGKTNWEIATILNISERTVKFHVANVIRKLNA  242 (265)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            479999999999999999999999998876444

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=94.99  E-value=0.0042  Score=42.02  Aligned_cols=23  Identities=30%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+.+|||.+||||-++.
T Consensus         5 ~ti~diA~~agVS~~TVSr~Ln~   27 (339)
T 3h5o_A            5 VTMHDVAKAAGVSAITVSRVLNQ   27 (339)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            67899999999999999999975

>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domai binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A

Probab=94.99  E-value=0.026  Score=36.50  Aligned_cols=46  Identities=15%  Similarity=0.208  Sum_probs=31.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++-+++..+. |.---.+ . +++-.+|++
T Consensus        14 ~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R-~-~~~~~lT~~   60 (294)
T 1ixc_A           14 EAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLER-S-HRGIELTAA   60 (294)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC-------CCBCHH
T ss_pred             HcC-CHHHHHHHhCCCcchHHHHHHHHHHHHCCEEEEe-C-CCCeeECHh
Confidence            345 88999999999999999999999854 4333332 2 233456664

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=94.97  E-value=0.025  Score=37.08  Aligned_cols=33  Identities=18%  Similarity=0.234  Sum_probs=30.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++..+||..+|+|+.||+|.++++++.|-+.-.
T Consensus       218 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~~  250 (260)
T 3kcc_A          218 ITRQEIGQIVGCSRETVGRILKMLEDQNLISAH  250 (260)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEc
Confidence            678999999999999999999999999988643

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=94.96  E-value=0.041  Score=33.57  Aligned_cols=37  Identities=14%  Similarity=0.235  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..
T Consensus        33 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~   74 (136)
T 1mzb_A           33 RHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNF   74 (136)
T ss_dssp             CSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            348999999999     8999999999999999999965554

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=94.95  E-value=0.018  Score=37.35  Aligned_cols=25  Identities=16%  Similarity=0.094  Sum_probs=22.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|+.++|+.+|||++|+++|-+
T Consensus       101 ~~glTQ~elA~~LGvsr~tis~yE~  125 (170)
T 2auw_A          101 RNNLSLTTAAEALGISRRMVSYYRT  125 (170)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4799999999999999999998744

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=94.89  E-value=0.0046  Score=41.70  Aligned_cols=23  Identities=22%  Similarity=0.316  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .+..+||+.+|||.+||||-++.
T Consensus         4 ~ti~diA~~agVS~~TVSrvln~   26 (338)
T 3dbi_A            4 TTMLEVAKRAGVSKATVSRVLSG   26 (338)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCC
Confidence            46789999999999999999975

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

Probab=94.88  E-value=0.037  Score=33.57  Aligned_cols=35  Identities=17%  Similarity=0.214  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +.|+.+||+++++|.++|.+.+++..+.|=+.-..
T Consensus        51 ~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~   85 (128)
T 2vn2_A           51 FPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEE   85 (128)
T ss_dssp             SCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            48999999999999999999999999999986543

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=94.85  E-value=0.022  Score=38.07  Aligned_cols=33  Identities=18%  Similarity=0.164  Sum_probs=30.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      |-+++|++||||..||.+-+++..+.|-+.. +.
T Consensus        38 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~-~g   70 (248)
T 3f8m_A           38 AEREIAEQFEVARETVRQALRELLIDGRVER-RG   70 (248)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE-ET
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe-CC
Confidence            7799999999999999999999999999987 54

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=94.83  E-value=0.0049  Score=42.06  Aligned_cols=23  Identities=26%  Similarity=0.153  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+++|||.+||||-++.
T Consensus         9 ~ti~dvA~~aGVS~~TVSrvLn~   31 (348)
T 3bil_A            9 PTLKDVARQAGVSIATASRALAD   31 (348)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
Confidence            47899999999999999999986

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=94.83  E-value=0.0049  Score=42.00  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+.+|||.+||||-++.
T Consensus        13 ~ti~diA~~agVS~~TVSr~Ln~   35 (355)
T 3e3m_A           13 VTMRDVAKAAGVSRMTVSRALKK   35 (355)
T ss_dssp             -----------------------
T ss_pred             CcHHHHHHHhCCCHHHHHHHHCC
Confidence            57889999999999999999974

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=94.81  E-value=0.025  Score=36.43  Aligned_cols=34  Identities=15%  Similarity=0.221  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHhccCHH-HHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHG-CVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~s-tv~r~~~r~r~tG~v~pk   38 (77)
                      .++..++|..+|+|++ ||+|.++++++.|-+.-.
T Consensus       169 ~~t~~~lA~~lG~sr~etvsR~l~~l~~~glI~~~  203 (238)
T 2bgc_A          169 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYK  203 (238)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhCCChHHHHHHHHHHHHHCCCEEec
Confidence            5788999999999995 999999999999988654

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=94.80  E-value=0.005  Score=41.47  Aligned_cols=23  Identities=26%  Similarity=0.264  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..+||+.+|||.+||+|-++.
T Consensus         3 ~ti~diA~~agVS~~TVSrvln~   25 (330)
T 3ctp_A            3 ANIREIAKRAGISIATVSRHLNN   25 (330)
T ss_dssp             -----------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC
Confidence            46789999999999999999986

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=94.78  E-value=0.0051  Score=41.89  Aligned_cols=24  Identities=25%  Similarity=0.229  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ++..+||+++|||.+||||-++..
T Consensus         4 ~ti~diA~~aGVS~~TVSrvLn~~   27 (349)
T 1jye_A            4 VTLYDVAEYAGVSYQTVSRVVNQA   27 (349)
T ss_dssp             ------------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Confidence            578899999999999999999864

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B

Probab=94.77  E-value=0.032  Score=35.73  Aligned_cols=43  Identities=5%  Similarity=-0.006  Sum_probs=31.2

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHH-hcCCCccccCCCCCCCCCHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQE-TGSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk~~gg~~~~~~~~~   51 (77)
                      |...+|++++||+++|++-+++..+ -|.---.+.+  ++-.+|++
T Consensus        17 s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~~   60 (291)
T 3szp_A           17 SYTSTSKKTMIPVATITRRIQALEDSLNLRLLNRHA--RKLTLTEA   60 (291)
T ss_dssp             SHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCEEEET--TEEEECHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEeecC--CCcccCHh
Confidence            7889999999999999999999884 4544333222  33446664

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=94.76  E-value=0.027  Score=39.01  Aligned_cols=32  Identities=13%  Similarity=0.093  Sum_probs=29.8

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      +|..++|++|+||.+||.|-++..++.|-+.-
T Consensus        20 ~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~   51 (321)
T 1bia_A           20 HSGEQLGETLGMSRAAINKHIQTLRDWGVDVF   51 (321)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEE
Confidence            89999999999999999999999999997753

>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1

Probab=94.74  E-value=0.032  Score=36.47  Aligned_cols=46  Identities=15%  Similarity=0.053  Sum_probs=32.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++-+++..+ -|.---.+.+  ++-.+|++
T Consensus        23 ~~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~--~~~~lT~~   69 (310)
T 2esn_A           23 RHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQG--NRMQPTQR   69 (310)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEEET--TEEEECHH
T ss_pred             HcC-CHHHHHHHhCCChHHHHHHHHHHHHhhCCcceeecC--CCccccHH
Confidence            344 8889999999999999999999985 4443333222  33345554

>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- transcription, transcription regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A 3n6t_A 3n6u_A*

Probab=94.72  E-value=0.033  Score=36.51  Aligned_cols=46  Identities=11%  Similarity=0.042  Sum_probs=33.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++-+++..+. |.---.+.  +++-.+|++
T Consensus        15 ~~g-s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~--~r~~~lT~~   61 (305)
T 3fxq_A           15 EVG-SLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRT--KRGVSLTSF   61 (305)
T ss_dssp             HHS-CHHHHHHHTTCCHHHHHHHHHHHHHHHTSCSEEEC--SSSEEECHH
T ss_pred             HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEEec--CCCccCCHh
Confidence            344 88999999999999999999999855 54433322  244456664

>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=94.67  E-value=0.086  Score=31.08  Aligned_cols=54  Identities=11%  Similarity=0.113  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC-CCCCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP-RVATPDVERRIEE   58 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~~~~~i~~   58 (77)
                      ..|..++|++++++.|+++|.+.+..+.|-|.-.+...+|. -.+|++=.+.+.+
T Consensus        36 ~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~~~D~R~~v~LT~~G~~~l~~   90 (96)
T 2obp_A           36 PWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALAAQ   90 (96)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHHHHHHHH
Confidence            38999999999999999999999999999997655422232 3566654444433

>1al3_A Cys regulon transcriptional activator CYSB; LYSR family, cysteine biosynthesis, transcription regulation; 1.80A {Klebsiella aerogenes} SCOP: c.94.1.1

Probab=94.60  E-value=0.006  Score=40.73  Aligned_cols=31  Identities=13%  Similarity=0.131  Sum_probs=0.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ++.|.|...+|++++||+++|++-+++..+.
T Consensus        13 ~~~gls~s~AA~~L~isq~avS~~I~~LE~~   43 (324)
T 1al3_A           13 VNHNLNVSSTAEGLYTSQPGISKQVRMLEDE   43 (324)
T ss_dssp             -------------------------------
T ss_pred             HHcccCHHHHHHHhCCCchHHHHHHHHHHHH
Confidence            4556789999999999999999999998753

>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped structure, DNA binding domain, regulatory domain, DNA-binding; 2.70A {Mycobacterium tuberculosis}

Probab=94.56  E-value=0.03  Score=36.61  Aligned_cols=31  Identities=16%  Similarity=0.236  Sum_probs=26.4

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHh-cCCCc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQET-GSIRP   37 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~p   37 (77)
                      |...+|++++||+++|++-+++..+. |.---
T Consensus        22 s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf   53 (303)
T 3isp_A           22 SFDAAAERLHVTPSAVSQRIKSLEQQVGQVLV   53 (303)
T ss_dssp             CHHHHHTTTTCCHHHHHHHHHHHHHHHTSCCE
T ss_pred             CHHHHHHHhCCChHHHHHHHHHHHHHhCCeeE
Confidence            78899999999999999999999855 54433

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=94.55  E-value=0.013  Score=39.55  Aligned_cols=25  Identities=12%  Similarity=0.128  Sum_probs=23.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|...|||+|+|++|++
T Consensus        42 ~~gltQ~evA~~tGISqS~ISq~e~   66 (221)
T 2h8r_A           42 QHNIPQREVVDVTGLNQSHLSQHLN   66 (221)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4699999999999999999999986

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=94.55  E-value=0.043  Score=34.09  Aligned_cols=48  Identities=10%  Similarity=-0.064  Sum_probs=31.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCC-C-ccccCC--CCCCCCCHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSI-R-PGVIGG--SKPRVATPDVER   54 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~-pk~~gg--~~~~~~~~~~~~   54 (77)
                      |...+|+.++||+++|++.+++..+.=.+ - -+..||  +++-.+|++-..
T Consensus        40 S~s~AA~~L~iSqsavS~~I~~LE~~lG~~Lf~R~~~G~~grg~~LT~~G~~   91 (135)
T 2ijl_A           40 SISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAE   91 (135)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHHBSSCSEEECCC------EEECHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHHHCCeeEEecCCCCCCCceeECHHHHH
Confidence            88899999999999999999999866333 2 222121  234567765333

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=94.55  E-value=0.028  Score=35.36  Aligned_cols=21  Identities=5%  Similarity=0.205  Sum_probs=20.2

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |+.++|+.+|||++|+++|.+
T Consensus        22 tq~elA~~~Gis~~~i~~~e~   42 (189)
T 2fjr_A           22 QKIQLANHFDIASSSLSNRYT   42 (189)
T ss_dssp             SHHHHHHHTTCCHHHHHHHHH
T ss_pred             CHHHHHHHhCcCHHHHHHHHh
Confidence            899999999999999999987

>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=94.53  E-value=0.025  Score=33.30  Aligned_cols=38  Identities=16%  Similarity=0.173  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHHhc----cCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          4 AGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         4 ~G~s~~~iA~rf~----VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      .+++..+||+.|+    ++.+||++.+++..+.|-|.-.+.|
T Consensus        23 ~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~   64 (126)
T 1sd4_A           23 KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSE   64 (126)
T ss_dssp             SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCC
Confidence            4689999999998    5999999999999999999776653

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=94.35  E-value=0.021  Score=38.68  Aligned_cols=36  Identities=11%  Similarity=0.174  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+++|+++|||+|+++-+.+.|=|..-+
T Consensus        44 ~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~   79 (275)
T 3mq0_A           44 RDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA   79 (275)
T ss_dssp             SCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            468999999999999999999999999999997543

>1pm6_A Excisionase; antiparallel beta-sheet, winged-helix, CIS-trans-trans triproline, gene regulation; NMR {Enterobacteria phage HK022} SCOP: a.6.1.7

Probab=94.27  E-value=0.035  Score=31.30  Aligned_cols=32  Identities=16%  Similarity=0.023  Sum_probs=25.6

Q ss_pred             CHHHHHHHh--ccCHHHHHHHHHHHHHhcCC--CccccCC
Q psy15513          7 RPCVISRQL--RVSHGCVSKILNRYQETGSI--RPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf--~VS~stv~r~~~r~r~tG~v--~pk~~gg   42 (77)
                      +..|.|+.+  .+|.+||++|.+.    |.+  .|.+.|+
T Consensus         4 Tl~EwA~~~~~~~s~~Tl~r~ar~----G~I~Pp~~KvGr   39 (72)
T 1pm6_A            4 TLQEWNARQRRPRSLETVRRWVRE----SRIFPPPVKDGR   39 (72)
T ss_dssp             EHHHHHHHSSSCCCHHHHHHHHHH----TCEESCCEECSS
T ss_pred             eHHHHHHHhcCCCCHHHHHHHHHC----CCCCCchhhcCC
Confidence            456888887  7999999999775    999  6666675

>3fzv_A Probable transcriptional regulator; LYSR, structural genomics, PSI-2, structure initiative; 2.71A {Pseudomonas aeruginosa PA01}

Probab=94.23  E-value=0.096  Score=33.95  Aligned_cols=47  Identities=19%  Similarity=0.176  Sum_probs=28.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++|+||+++|++-+++..+. |.---.+.+ +++-.+|++
T Consensus        17 ~~~-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~-~~~~~lT~~   64 (306)
T 3fzv_A           17 ECG-SVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHH-AQGVSLTPA   64 (306)
T ss_dssp             HSS-SHHHHHHHHTCCC-CHHHHHHHHHHHC-CCCC----------CCHH
T ss_pred             HhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCeeEeecC-CCCceECHh
Confidence            445 88999999999999999999999865 433333211 243456664

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=94.16  E-value=0.061  Score=33.44  Aligned_cols=37  Identities=22%  Similarity=0.197  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..
T Consensus        41 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~   82 (150)
T 2xig_A           41 THLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLET   82 (150)
T ss_dssp             SCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEe
Confidence            358999999988     8999999999999999999865544

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=94.13  E-value=0.04  Score=30.37  Aligned_cols=21  Identities=14%  Similarity=0.091  Sum_probs=19.2

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +..++|+++|||++++++|-+
T Consensus        29 sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           29 SMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHT
T ss_pred             CHHHHHHHhCCCHHHHHHHHc
Confidence            788999999999999999854

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

Probab=94.11  E-value=0.059  Score=33.31  Aligned_cols=58  Identities=12%  Similarity=0.067  Sum_probs=41.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc--cCCCCC--C-CCCHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKP--R-VATPDVERRIEEYKGE   62 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~--~gg~~~--~-~~~~~~~~~i~~~v~~   62 (77)
                      .+.|+.++|+++++|.++|.+++++.-+.|=+.-..  ...++.  . -++| -.+.|..++++
T Consensus        50 ~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~p-L~ekL~~~~~~  112 (135)
T 2v79_A           50 YFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQP-LWGKLYEYIQL  112 (135)
T ss_dssp             CSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHH-HHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHH-HHHHHHHHHHH
Confidence            457999999999999999999999999999886532  222222  1 3334 45666666644

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=94.10  E-value=0.018  Score=34.22  Aligned_cols=25  Identities=8%  Similarity=0.068  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +++.+.+|+.+||+.|||+||-.-+
T Consensus        23 ~~gq~~vA~~iGV~~StISR~k~~~   47 (97)
T 1xwr_A           23 MLGTEKTAEAVGVDKSQISRWKRDW   47 (97)
T ss_dssp             HHCHHHHHHHHTCCTTTHHHHHHHH
T ss_pred             HHhHHHHHHHhCCCHHHHHHHHhhh
Confidence            4678899999999999999997754

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=93.98  E-value=0.0017  Score=39.23  Aligned_cols=28  Identities=25%  Similarity=0.271  Sum_probs=24.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      -+.|+|+.++|+++|||+++|++|-+--
T Consensus         2 R~~glTQ~eLA~~~Gvs~~~is~~E~G~   29 (122)
T 1nr3_A            2 RERGWSQKKIARELKTTRQNVSAIERKA   29 (122)
T ss_dssp             CCCSCSSCSTHHHHHHCCSSSCCHHHHH
T ss_pred             cccCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence            4579999999999999999999997753

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=93.98  E-value=0.0098  Score=40.00  Aligned_cols=26  Identities=15%  Similarity=0.083  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.|+|..++|+++|||++|+++|.+-
T Consensus        41 ~~g~t~~~la~~~g~s~~~is~~e~g   66 (311)
T 4ich_A           41 SRPGAQREFAAAIGLDESKLSKSLNG   66 (311)
T ss_dssp             --------------------------
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            47999999999999999999999764

>3mz1_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative, MI center for STR uctural genomics, MCSG; 1.88A {Sinorhizobium meliloti}

Probab=93.87  E-value=0.01  Score=38.15  Aligned_cols=29  Identities=14%  Similarity=0.249  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +.| |...+|++++||+++|++-+++..+.
T Consensus        11 ~~~-s~s~AA~~L~isq~avS~~i~~LE~~   39 (300)
T 3mz1_A           11 ETG-NFTRASASLNMPKATVTNLIQGLEAH   39 (300)
T ss_dssp             ------------------------------
T ss_pred             hcC-CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            445 88899999999999999999998854

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=93.82  E-value=0.054  Score=36.14  Aligned_cols=26  Identities=15%  Similarity=0.259  Sum_probs=23.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      +.|++..+||++||+|.++|+++++-
T Consensus       132 ~~g~t~~~iA~~lG~s~~~V~~~l~l  157 (230)
T 1vz0_A          132 EMGLTQEEVARRVGKARSTVANALRL  157 (230)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46899999999999999999998765

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=93.78  E-value=0.077  Score=32.56  Aligned_cols=37  Identities=14%  Similarity=0.053  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..
T Consensus        28 ~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~   69 (139)
T 3mwm_A           28 EFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRT   69 (139)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEEC
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            347899998888     7999999999999999999865544

>2h9b_A HTH-type transcriptional regulator BENM; LTTR, transcriptional activator, LYSR-type transcripti regulator; 1.80A {Acinetobacter SP} PDB: 2h99_A 3k1m_A 3k1n_A 3k1p_A 2f7a_A* 2f6p_A 2f78_A 2f6g_A* 2f8d_A 2f97_A*

Probab=93.75  E-value=0.011  Score=39.06  Aligned_cols=30  Identities=10%  Similarity=0.121  Sum_probs=0.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ++.| |...+|++++||+++|++-+++..+.
T Consensus        13 a~~g-s~s~AA~~L~isq~avS~~I~~LE~~   42 (312)
T 2h9b_A           13 VEEQ-SFTKAADKLCIAQPPLSRQIQNLEEE   42 (312)
T ss_dssp             -------------------------------
T ss_pred             HHhC-CHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            3455 88899999999999999999998754

>2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding, phosphorylation, DNA-binding protein; NMR {Mycobacterium tuberculosis}

Probab=93.74  E-value=0.038  Score=35.20  Aligned_cols=33  Identities=18%  Similarity=0.126  Sum_probs=27.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ++..|+|+.||||.++|++|++.    |.+.+-+.|+
T Consensus        32 LTv~EVAe~LgVs~srV~~LIr~----G~L~AVr~Gr   64 (148)
T 2kfs_A           32 YDLPRVAELLGVPVSKVAQQLRE----GHLVAVRRAG   64 (148)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHT----TSCCCEEETT
T ss_pred             EcHHHHHHHhCCCHHHHHHHHHC----CCceEEEECC
Confidence            57789999999999999999765    8887766654

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=93.67  E-value=0.2  Score=29.41  Aligned_cols=60  Identities=12%  Similarity=-0.060  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...+..++|+.+|||.++.++.+++   +| +.|..-       ....-......++ .+++.++.||+..+
T Consensus        22 ~~~~~~~lA~~~~~S~~~l~r~fk~---~G-~s~~~~-------~~~~Rl~~A~~lL-~~~~~si~eIA~~~   81 (120)
T 3mkl_A           22 HEWTLARIASELLMSPSLLKKKLRE---EE-TSYSQL-------LTECRMQRALQLI-VIHGFSIKRVAVSC   81 (120)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHH---TT-CCHHHH-------HHHHHHHHHHHHH-TSTTCCHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH---cC-CCHHHH-------HHHHHHHHHHHHH-HcCCCCHHHHHHHH
Confidence            3578999999999999999998765   34 444421       1111122233444 56899999998764

>2ra5_A Putative transcriptional regulator; beta structure, UTRA domain, structural genomics, PSI-2, protein structure initiative; HET: SRT; 2.40A {Streptomyces coelicolor A3} SCOP: d.190.1.2

Probab=93.49  E-value=0.01  Score=39.64  Aligned_cols=35  Identities=11%  Similarity=0.090  Sum_probs=5.5

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      |-+++|++||||..||.+-++...+.|-+...+..
T Consensus        42 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~   76 (247)
T 2ra5_A           42 NEIELAARLGLSRPTVRQAIQSLVDKGLLVRRRGV   76 (247)
T ss_dssp             --------------------------CEEEEEC--
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc
Confidence            67889999999999999999999999999766543

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

Probab=93.48  E-value=0.09  Score=33.23  Aligned_cols=35  Identities=11%  Similarity=0.068  Sum_probs=30.9

Q ss_pred             HHHHHHHhc--------------cCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          8 PCVISRQLR--------------VSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         8 ~~~iA~rf~--------------VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      .+++|+.||              ||.++|.+-++++...|-|...+.+|
T Consensus        70 ~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~~~G  118 (150)
T 2v7f_A           70 IERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKG  118 (150)
T ss_dssp             HHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEeCCCc
Confidence            388999999              99999999999999999998775433

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=93.48  E-value=0.067  Score=33.55  Aligned_cols=33  Identities=18%  Similarity=0.297  Sum_probs=28.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|.|..+||+.+++|.+||...+++.++.=.+
T Consensus       167 ~~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~  199 (215)
T 1a04_A          167 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKL  199 (215)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            468999999999999999999999998875433

>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=93.42  E-value=0.073  Score=33.12  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||++.|||++|+|++.+
T Consensus        27 ~~~s~~~IA~~aGvs~~tiY~~F~   50 (202)
T 2d6y_A           27 AGARIDRIAAEARANKQLIYAYYG   50 (202)
T ss_dssp             TSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcC
Confidence            358999999999999999998753

>2zcm_A Biofilm operon icaabcd HTH-type negative transcri regulator ICAR; helix-turn-helix, TETR family, repressor; 1.33A {Staphylococcus epidermidis} PDB: 2zcn_A

Probab=93.37  E-value=0.069  Score=32.60  Aligned_cols=23  Identities=13%  Similarity=0.131  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|.++||++-|||++|+++..
T Consensus        26 ~~~t~~~IA~~agvs~~tlY~~F   48 (192)
T 2zcm_A           26 DGTTLDDISKSVNIKKASLYYHY   48 (192)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHT
T ss_pred             ccCCHHHHHHHhCCChHHHHHHC
Confidence            35899999999999999999753

>3vpr_A Transcriptional regulator, TETR family; all alpha, helix-turn-helix, transcriptional repressor, DNA protein; 2.27A {Thermus thermophilus}

Probab=93.36  E-value=0.076  Score=32.42  Aligned_cols=24  Identities=8%  Similarity=0.109  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|..+||++-|||++|+|+..+
T Consensus        22 ~~~s~~~IA~~agvsk~t~Y~~F~   45 (190)
T 3vpr_A           22 EATSVQDLAQALGLSKAALYHHFG   45 (190)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcC
Confidence            458999999999999999998754

>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A {Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A* 3m1e_A

Probab=93.34  E-value=0.015  Score=38.86  Aligned_cols=30  Identities=10%  Similarity=0.175  Sum_probs=0.0

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ++.| |...+|++++||+++|++-+++..+.
T Consensus        13 ae~g-S~s~AA~~L~isq~avS~~I~~LE~~   42 (313)
T 2h98_A           13 VEEQ-SISKAAEKLCIAQPPLSRQIQKLEEE   42 (313)
T ss_dssp             -------------------------------
T ss_pred             HHhC-CHHHHHHHhCCCccHHHHHHHHHHHH
Confidence            3455 88899999999999999999997743

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=93.23  E-value=0.057  Score=31.21  Aligned_cols=25  Identities=20%  Similarity=0.276  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHh---c-------cCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQL---R-------VSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf---~-------VS~stv~r~~~r~   29 (77)
                      ..+..+|+..|   |       ||.+||++|+++.
T Consensus        93 ~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~~~  127 (128)
T 1pdn_C           93 GMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGR  127 (128)
T ss_dssp             TCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC---
T ss_pred             chHHHHHHHHHHHcCCccccCCcCHHHHHHHHHhc
Confidence            48999999999   7       5999999999863

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=93.23  E-value=0.047  Score=33.13  Aligned_cols=27  Identities=15%  Similarity=0.175  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHh--------c--cCHHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQL--------R--VSHGCVSKILNRYQE   31 (77)
Q Consensus         5 G~s~~~iA~rf--------~--VS~stv~r~~~r~r~   31 (77)
                      +.+..+|+..|        |  ||.+||++|+++...
T Consensus       108 ~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~~~  144 (149)
T 1k78_A          108 TMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQ  144 (149)
T ss_dssp             TCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC--
T ss_pred             chhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHHhc
Confidence            47889999988        6  899999999987654

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

Probab=93.23  E-value=0.013  Score=39.49  Aligned_cols=35  Identities=20%  Similarity=0.268  Sum_probs=32.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ...++..++|+.||+|++||++-++...+.|-|..
T Consensus        23 ~g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A           23 CMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             TTTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            34588999999999999999999999999999976

>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, bacillu structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus} SCOP: a.4.1.9 a.121.1.1

Probab=93.16  E-value=0.078  Score=32.58  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|..+||++-|||++|+|++.+
T Consensus        31 ~~~t~~~IA~~agvsk~tlY~~F~   54 (192)
T 2fq4_A           31 KAVTVDKIAERAKVSKATIYKWWP   54 (192)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccccHHHHHHHcCCCHHHHHHHCC
Confidence            358999999999999999999753

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=93.14  E-value=0.079  Score=33.78  Aligned_cols=33  Identities=12%  Similarity=0.201  Sum_probs=28.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||+.+++|.+||...+++.++.=.+
T Consensus       162 ~~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~~  194 (225)
T 3c3w_A          162 SEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM  194 (225)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            468999999999999999999999998875433

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=93.02  E-value=0.094  Score=36.54  Aligned_cols=39  Identities=21%  Similarity=0.296  Sum_probs=32.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcC-CCccccCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSK   44 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~-v~pk~~gg~~   44 (77)
                      +|-.++|++||||.++|.|-++..++.|- +...+..|.+
T Consensus        20 ~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~~~~~~GY~   59 (323)
T 3rkx_A           20 ISGQSIAESLNISRTAVKKVIDQLKLEGCKIDSVNHKGHL   59 (323)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEEETTTEEE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEEEeCCCeEE
Confidence            89999999999999999999999999997 4433333443

>3egq_A TETR family transcriptional regulator; DNA-binding, transcription regulation, bacterial regulatory DNA/RNA-binding 3-helical bundle fold; HET: MSE PE8; 2.55A {Archaeoglobus fulgidus}

Probab=93.02  E-value=0.075  Score=31.80  Aligned_cols=22  Identities=23%  Similarity=0.169  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|..+||++.|||++|+++..
T Consensus        24 ~~t~~~Ia~~agvs~~t~Y~~F   45 (170)
T 3egq_A           24 EVSIEEIAREAKVSKSLIFYHF   45 (170)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHC
T ss_pred             cCcHHHHHHHhCCCchhHHHHc
Confidence            4899999999999999999864

>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=92.97  E-value=0.14  Score=29.57  Aligned_cols=49  Identities=14%  Similarity=0.064  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i   56 (77)
                      .|++++++|..+++|.+++.+.+....+.|=|.-.. ++   -.+|+.-.+.+
T Consensus        19 ~~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~-~~---~~LT~kG~~~l   67 (95)
T 1r7j_A           19 SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG-KQ---YMLTKKGEELL   67 (95)
T ss_dssp             TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TE---EEECHHHHHHH
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC-Ce---eEEChhHHHHH
Confidence            358999999999999999999999999999997663 22   45666544433

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=92.95  E-value=0.072  Score=33.09  Aligned_cols=37  Identities=14%  Similarity=0.345  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+|+.+|...+     +||.+||||-++.+.+.|-|..-..
T Consensus        32 ~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~   73 (150)
T 2w57_A           32 QHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHF   73 (150)
T ss_dssp             SSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            347899999988     8999999999999999999865543

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=92.93  E-value=0.089  Score=32.10  Aligned_cols=23  Identities=13%  Similarity=-0.019  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        31 ~~~t~~~Ia~~agvs~~t~Y~~F   53 (202)
T 3lwj_A           31 YNTSIRDIIALSEVGTGTFYNYF   53 (202)
T ss_dssp             TTCCHHHHHHHHCSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCchhHHHHc
Confidence            35899999999999999999853

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=92.91  E-value=0.089  Score=31.69  Aligned_cols=23  Identities=22%  Similarity=0.367  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++|+++..
T Consensus        28 ~~~tv~~Ia~~agvs~~t~Y~~F   50 (195)
T 3ppb_A           28 HGTSTATIAREAGVATGTLFHHF   50 (195)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChhHHHHHc
Confidence            35899999999999999999853

>1uth_A LYSR-type regulatory protein; transcription regulation, transcriptional regulator; 2.2A {Burkholderia SP} SCOP: c.94.1.1 PDB: 1utb_A 1utb_B 1uth_B 2uyf_A 2uye_A

Probab=92.87  E-value=0.019  Score=38.10  Aligned_cols=29  Identities=17%  Similarity=0.227  Sum_probs=0.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      +.| |...+|++|+||+++|++-+++..+.
T Consensus        27 ~~g-s~t~AA~~L~isq~avS~~I~~LE~~   55 (315)
T 1uth_A           27 LDR-SVSTAGEKLGLTQPAVSNSLKRLRTA   55 (315)
T ss_dssp             ------------------------------
T ss_pred             HcC-CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            445 78899999999999999999998754

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=92.84  E-value=0.019  Score=36.35  Aligned_cols=34  Identities=18%  Similarity=0.257  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      -++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~G~I~~~  197 (213)
T 1o5l_A          164 PVTLEELSRLFGCARPALSRVFQELEREGYIEKH  197 (213)
T ss_dssp             ----------------------------------
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEc
Confidence            3678899999999999999999999999988643

>2v57_A TETR family transcriptional repressor LFRR; DNA-binding, transcription regulation; HET: PRL; 1.90A {Mycobacterium smegmatis} PDB: 2wgb_A

Probab=92.84  E-value=0.094  Score=31.76  Aligned_cols=23  Identities=13%  Similarity=0.047  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|..+||++.|||++|+|+..
T Consensus        31 ~~~t~~~Ia~~agvs~~t~Y~~F   53 (190)
T 2v57_A           31 PTAALGDIAAAAGVGRSTVHRYY   53 (190)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHc
Confidence            57899999999999999999864

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=92.83  E-value=0.081  Score=32.05  Aligned_cols=24  Identities=17%  Similarity=0.098  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||++-|||++|++++..
T Consensus        27 ~~~t~~~Ia~~agvs~~t~Y~~F~   50 (206)
T 3dew_A           27 YGVSIRELAQAAGASISMISYHFG   50 (206)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             ccCcHHHHHHHhCCCHHHHHHHcC
Confidence            358999999999999999998743

>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp}

Probab=92.83  E-value=0.082  Score=31.82  Aligned_cols=23  Identities=4%  Similarity=0.039  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|.++||++-|||++|+++..
T Consensus        29 ~~~t~~~IA~~agvs~~t~Y~~F   51 (191)
T 3on4_A           29 NAFSFKDIATAINIKTASIHYHF   51 (191)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCcchhhhcC
Confidence            35899999999999999999753

>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A

Probab=92.79  E-value=0.095  Score=32.08  Aligned_cols=23  Identities=13%  Similarity=0.159  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|.++||++-|||++|++++.
T Consensus        33 ~~~ti~~Ia~~agvs~~t~Y~~F   55 (220)
T 3lhq_A           33 SATSLAEIANAAGVTRGAIYWHF   55 (220)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCceeehhhc
Confidence            35899999999999999999863

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=92.77  E-value=0.097  Score=31.80  Aligned_cols=23  Identities=22%  Similarity=0.108  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|+|.++||++-|||++|+++..
T Consensus        27 ~~~t~~~IA~~Agvs~~tly~~F   49 (194)
T 3dpj_A           27 AQTSFVDISAAVGISRGNFYYHF   49 (194)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCCChHHHHHHc
Confidence            46899999999999999999864

>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4}

Probab=92.75  E-value=0.095  Score=32.36  Aligned_cols=22  Identities=14%  Similarity=0.051  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|.++||++-|||++|++++.
T Consensus        37 ~~t~~~IA~~agvs~~t~Y~~F   58 (218)
T 3gzi_A           37 QVSIREIASLAGTDPGLIRYYF   58 (218)
T ss_dssp             CCCHHHHHHHHTSCTHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHc
Confidence            5899999999999999999875

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=92.73  E-value=0.1  Score=31.33  Aligned_cols=23  Identities=9%  Similarity=0.180  Sum_probs=20.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        27 ~~~ti~~Ia~~agvs~~t~Y~~F   49 (188)
T 3qkx_A           27 NQLSMLKLAKEANVAAGTIYLYF   49 (188)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             ccCCHHHHHHHhCCCcchHHHHc
Confidence            35899999999999999999753

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=92.71  E-value=0.1  Score=31.68  Aligned_cols=23  Identities=17%  Similarity=0.030  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++|+++..
T Consensus        36 ~~~s~~~Ia~~agvs~~t~Y~~F   58 (206)
T 3kz9_A           36 GRGGHADIAEIAQVSVATVFNYF   58 (206)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccccHHHHHHHhCCCHHHHHHHc
Confidence            35899999999999999999863

>3loc_A HTH-type transcriptional regulator RUTR; helix-turn-helix, putative transcriptional regulator, dimer, structural genomics, PSI; HET: MSE; 2.50A {Escherichia coli}

Probab=92.67  E-value=0.06  Score=32.98  Aligned_cols=22  Identities=23%  Similarity=0.129  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      |.|.++||++-|||++|++++.
T Consensus        38 ~~s~~~IA~~aGvs~~tlY~~F   59 (212)
T 3loc_A           38 GTRLEQIAELAGVSKTNLLYYF   59 (212)
T ss_dssp             HCCHHHHHHHHTSCHHHHHHHS
T ss_pred             cCCHHHHHHHHCcCHHHHhhhC
Confidence            5899999999999999999865

>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=92.67  E-value=0.26  Score=34.57  Aligned_cols=37  Identities=11%  Similarity=0.054  Sum_probs=33.2

Q ss_pred             CCHHHHHHHh--ccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          6 VRPCVISRQL--RVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         6 ~s~~~iA~rf--~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      ++.+++|++|  +||.+||.+=++...+.|-+. +++||.
T Consensus        37 V~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~-r~HgsA   75 (338)
T 1stz_A           37 VSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIY-QPHTSA   75 (338)
T ss_dssp             BCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEE-CCSSCS
T ss_pred             ccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEE-EccCcc
Confidence            7889999999  999999999999999999887 477764

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=92.64  E-value=0.12  Score=32.09  Aligned_cols=31  Identities=13%  Similarity=0.049  Sum_probs=27.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ..|.+..+||..+++|.+||...+++.++.=
T Consensus       155 ~~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl  185 (208)
T 1yio_A          155 IRGLMNKQIAGELGIAEVTVKVHRHNIMQKL  185 (208)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HcCCcHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999888754

>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin repressor-like, C-terminal D homeodomain-like, DNA/RNA-binding 3-helical bundle; 1.55A {Aquifex aeolicus}

Probab=92.58  E-value=0.11  Score=31.51  Aligned_cols=23  Identities=17%  Similarity=0.179  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|..+||++-|||++|+++..
T Consensus        21 ~~~s~~~Ia~~agvskgtlY~~F   43 (179)
T 2eh3_A           21 QGTSVEEIVKRANLSKGAFYFHF   43 (179)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCcHHHHHHc
Confidence            35899999999999999998753

>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=92.53  E-value=0.43  Score=27.90  Aligned_cols=52  Identities=13%  Similarity=0.195  Sum_probs=39.5

Q ss_pred             HHHHHHh--ccCHHHHHHHHHHHHHhcCCCccccCCCCC-CCCCHHHHHHHHHHHH
Q psy15513          9 CVISRQL--RVSHGCVSKILNRYQETGSIRPGVIGGSKP-RVATPDVERRIEEYKG   61 (77)
Q Consensus         9 ~~iA~rf--~VS~stv~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~~~~~i~~~v~   61 (77)
                      .+++++|  .+|.++++..+++..+.|-|.... |+++. -.+|++=.+.+.++.+
T Consensus        32 ~ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~-~~~rk~Y~iT~~Gr~~l~~~~~   86 (99)
T 2co5_A           32 SEILKRFDIDISDGVLYPLIDSLIDDKILREEE-APDGKVLFLTEKGMKEFEELHE   86 (99)
T ss_dssp             HHHHHHHCCBCCHHHHHHHHHHHHHTTSEEEEC-CTTSCEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCcHHHHHHHHHHCCCEEEee-CCCcEEEEECHHHHHHHHHHHH
Confidence            5677887  599999999999999999998766 43333 4677776666666654

>4aci_A HTH-type transcriptional repressor ACNR; aconitase, citrate, TETR superfamily; HET: CIT; 1.65A {Corynebacterium glutamicum} PDB: 4ac6_A*

Probab=92.53  E-value=0.071  Score=32.35  Aligned_cols=23  Identities=13%  Similarity=0.157  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|..+||++-|||++|++++..
T Consensus        34 ~~t~~~IA~~agvs~~t~Y~~F~   56 (191)
T 4aci_A           34 GATVRRLEEATGKSRGAIFHHFG   56 (191)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             cCCHHHHHHHHCCCchHHHHHCC
Confidence            48999999999999999998753

>2g7s_A Transcriptional regulator, TETR family; APC5906, PSI, protein structure initiat midwest center for structural genomics, MCSG; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: a.4.1.9 a.121.1.1

Probab=92.52  E-value=0.096  Score=31.49  Aligned_cols=23  Identities=9%  Similarity=0.140  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++-|||++|+++..
T Consensus        27 ~~~ti~~Ia~~agvs~~t~Y~~F   49 (194)
T 2g7s_A           27 NSFSYADISQVVGIRNASIHHHF   49 (194)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCchHHHHHc
Confidence            35899999999999999999863

>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A*

Probab=92.51  E-value=0.11  Score=31.84  Aligned_cols=23  Identities=4%  Similarity=-0.060  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||++|++++.
T Consensus        23 ~~~t~~~Ia~~agvs~~t~Y~~F   45 (185)
T 2yve_A           23 ETLSYDSLAEATGLSKSGLIYHF   45 (185)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHC
T ss_pred             hhccHHHHHHHhCCChHHHHHhC
Confidence            35899999999999999999864

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=92.50  E-value=0.11  Score=33.53  Aligned_cols=41  Identities=20%  Similarity=0.388  Sum_probs=36.2

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK   44 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~   44 (77)
                      +| +|..++|+.+|+|+|-|.-.+......|-|..-+.|..+
T Consensus        22 ~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~a   63 (165)
T 2vxz_A           22 DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVA   63 (165)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEE
T ss_pred             hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEE
Confidence            45 889999999999999999999999999999888777433

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=92.49  E-value=0.04  Score=34.09  Aligned_cols=28  Identities=11%  Similarity=0.148  Sum_probs=23.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..|.+..++|+.|++|..||+++++++.
T Consensus       154 ~~~~~~~~ia~~l~is~~tv~~~l~~~~  181 (184)
T 3rqi_A          154 ENNNNISATARALNMHRRTLQRKLAKKP  181 (184)
T ss_dssp             HTTSCHHHHHHHHTSCHHHHHHHHCC--
T ss_pred             hccccHHHHHHHcCCcHHHHHHHHHhcC
Confidence            3588999999999999999999988754

>2qtq_A Transcriptional regulator, TETR family; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: MSE; 1.85A {Novosphingobium aromaticivorans} PDB: 2rha_A*

Probab=92.46  E-value=0.12  Score=31.54  Aligned_cols=23  Identities=9%  Similarity=0.066  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++|+++..
T Consensus        35 ~~~t~~~Ia~~agvs~~t~Y~~F   57 (213)
T 2qtq_A           35 VDISLSELSLRSGLNSALVKYYF   57 (213)
T ss_dssp             SCCCHHHHHHHHCCCHHHHHHHH
T ss_pred             ccccHHHHHHHhCCChhhHhHhc
Confidence            35899999999999999999865

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=92.44  E-value=0.11  Score=31.51  Aligned_cols=22  Identities=9%  Similarity=-0.022  Sum_probs=20.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +++|.++||++-|||++|+++.
T Consensus        33 ~~~ti~~Ia~~agvs~~t~Y~~   54 (203)
T 3f1b_A           33 HETSMDAIAAKAEISKPMLYLY   54 (203)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHH
T ss_pred             ccccHHHHHHHhCCchHHHHHH
Confidence            3589999999999999999986

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=92.43  E-value=0.096  Score=31.99  Aligned_cols=23  Identities=9%  Similarity=0.080  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|.++||++.|||++|+++...
T Consensus        27 ~~t~~~Ia~~agvs~~t~Y~~F~   49 (195)
T 2dg7_A           27 NVTVTDIAERAGLTRRSYFRYFP   49 (195)
T ss_dssp             GCCHHHHHHHTTCCHHHHHHHCS
T ss_pred             ccCHHHHHHHhCCCHHHHHHHcC
Confidence            58999999999999999998754

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=92.42  E-value=0.11  Score=31.81  Aligned_cols=23  Identities=22%  Similarity=0.112  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++-|||++|+++..
T Consensus        37 ~~~s~~~Ia~~agvs~~t~Y~~F   59 (212)
T 1pb6_A           37 HGTRLEQIAELAGVSKTNLLYYF   59 (212)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             chhhHHHHHHHHCCChhHHHHhC
Confidence            35899999999999999999863

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=92.42  E-value=0.17  Score=33.95  Aligned_cols=68  Identities=13%  Similarity=0.014  Sum_probs=50.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ..++++..+++....+..+++...+.|.+..-..+=.=.+-......+.|.++. +++.+|+.|.++.+
T Consensus       159 ~~~dl~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~~~~~~~~~~~~~~~l~~~~-~~~~it~a~~Rd~l  226 (258)
T 1lva_A          159 SFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLA-STGPFGLAEARDAL  226 (258)
T ss_dssp             BHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBEEEHHHHHHHHHHHHHHH-TTSCBCHHHHHHHH
T ss_pred             CHHHHHhHhCCCHHHHHHHHHHHHHCCCEEEecCCeEEcHHHHHHHHHHHHHHH-hcCCcCHHHHHHHh
Confidence            468999999999999999999999999998764221111222233455566777 79999999999986

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=92.40  E-value=0.1  Score=31.78  Aligned_cols=23  Identities=4%  Similarity=0.070  Sum_probs=20.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|.++||++.|||++|+++..
T Consensus        36 ~~~ti~~Ia~~agvs~~t~Y~~F   58 (208)
T 3cwr_A           36 AAMTMEGVASEAGIAKKTLYRFA   58 (208)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HhccHHHHHHHhCCCHHHHHHHc
Confidence            45899999999999999999874

>3vib_A MTRR; helix-turn-helix motif, DNA binding, DNA binding protein; HET: CXS; 2.40A {Neisseria gonorrhoeae}

Probab=92.38  E-value=0.11  Score=32.11  Aligned_cols=23  Identities=13%  Similarity=0.027  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|..+||++-|||++|+|++.
T Consensus        29 ~~~s~~~IA~~aGvs~~t~Y~~F   51 (210)
T 3vib_A           29 ARTSLNEIAQAAGVTRDALYWHF   51 (210)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            45899999999999999999863

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=92.33  E-value=0.12  Score=31.70  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++|+++..
T Consensus        33 ~~~ti~~IA~~agvs~~t~Y~~F   55 (212)
T 3knw_A           33 VGVGLQEILKTSGVPKGSFYHYF   55 (212)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChHHHHHHC
Confidence            35899999999999999999854

>3c2b_A Transcriptional regulator, TETR family; structural genomics, APC5923, PSI-2, PR structure initiative; 2.10A {Agrobacterium tumefaciens str}

Probab=92.33  E-value=0.11  Score=32.21  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||++-|||++|+|+...
T Consensus        34 ~~~s~~~IA~~agvs~~t~Y~~F~   57 (221)
T 3c2b_A           34 KALTTSGLARAANCSKESLYKWFG   57 (221)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             ccCCHHHHHHHhCCCHHHHHHhCC
Confidence            358999999999999999999764

>3bqz_B HTH-type transcriptional regulator QACR; multidrug resistance, TETR, malachite green, DNA- binding, plasmid, repressor; HET: MGR; 2.17A {Staphylococcus aureus} PDB: 3br1_B* 3br3_B* 3pm1_B* 1rkw_B* 1jt0_A* 1jty_B* 1jum_B* 1jup_B* 1jtx_B* 1jus_B* 2dtz_B 2gby_B* 2hq5_B 3br2_B* 3br5_B* 1qvt_B* 1qvu_B* 3br0_B* 3br6_B* 1jt6_B* ...

Probab=92.32  E-value=0.12  Score=31.23  Aligned_cols=22  Identities=14%  Similarity=0.015  Sum_probs=19.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +++|.++||++-|||++|+++.
T Consensus        21 ~~~ti~~Ia~~agvs~~t~Y~~   42 (194)
T 3bqz_B           21 NATTTGEIVKLSESSKGNLYYH   42 (194)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHH
T ss_pred             ccCCHHHHHHHhCCCchhHHHh
Confidence            3589999999999999999976

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

Probab=92.28  E-value=0.26  Score=31.13  Aligned_cols=61  Identities=18%  Similarity=0.217  Sum_probs=44.7

Q ss_pred             cCCCCHHHHHHHh--------ccCHHHHHHHHHHHHHhcCCCcccc--CC-C-CC-CCCCHHHHHHHHHHHHhC
Q psy15513          3 AAGVRPCVISRQL--------RVSHGCVSKILNRYQETGSIRPGVI--GG-S-KP-RVATPDVERRIEEYKGEN   63 (77)
Q Consensus         3 ~~G~s~~~iA~rf--------~VS~stv~r~~~r~r~tG~v~pk~~--gg-~-~~-~~~~~~~~~~i~~~v~~~   63 (77)
                      +..++.-++++.|        ++|+++++.-+++..+.|-|.....  +| + +. -.+|+.-.+.+.+++.+.
T Consensus        13 ~~~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l~~~~~~~   86 (179)
T 1yg2_A           13 TRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWFDQP   86 (179)
T ss_dssp             HCCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHHHHSC
T ss_pred             cCCCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHHHHHHhCc
Confidence            3447888999999        7999999999999999999976542  22 2 22 467777777777777654

>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription regulation, TETR, DNA-binding transcription; 2.90A {Pseudomonas aeruginosa}

Probab=92.26  E-value=0.12  Score=32.16  Aligned_cols=24  Identities=17%  Similarity=0.106  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .|.|..+||++-|||++|+|+..+
T Consensus        30 ~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2wui_A           30 GTTAMADLADAAGVSRGAVYGHYK   53 (210)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             cccCHHHHHHHhCCCHHHHHHHcC
Confidence            358999999999999999998754

>3ljl_A Transcriptional regulator LUXT; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MES; 3.20A {Vibrio parahaemolyticus}

Probab=92.24  E-value=0.075  Score=31.93  Aligned_cols=22  Identities=23%  Similarity=0.190  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      |.|.++||++-|||++|++++.
T Consensus        34 ~~ti~~Ia~~agvs~~t~Y~~F   55 (156)
T 3ljl_A           34 KMSYTTLSQQTGVSRTGISHHF   55 (156)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hcCHHHHHHHHCCCHHHHHHHC
Confidence            4899999999999999999864

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=92.23  E-value=0.12  Score=31.67  Aligned_cols=22  Identities=5%  Similarity=0.025  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++|..+||++-|||++|+|++.
T Consensus        51 ~~tv~~Ia~~agvs~~t~Y~~F   72 (218)
T 3dcf_A           51 ATSLDDIADRIGFTKPAIYYYF   72 (218)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cCcHHHHHHHhCCCHHHHHHHc
Confidence            5899999999999999999754

>2jj7_A Hemolysin II regulatory protein; DNA-binding protein, transcription regulation, DNA-binding, family, transcription, transcriptional regulator; 2.10A {Bacillus cereus} PDB: 2wv1_A 2jk3_A 2fx0_A

Probab=92.14  E-value=0.084  Score=31.94  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++|.++||++.|||++|+++..+
T Consensus        27 ~~t~~~IA~~agvs~~tlY~~F~   49 (186)
T 2jj7_A           27 GTSIQEIAKEAKVNVAMASYYFN   49 (186)
T ss_dssp             HCCHHHHHHHHTSCHHHHHHHHS
T ss_pred             cCCHHHHHHHhCCChhhhhhhcC
Confidence            48999999999999999999654

>2oer_A Probable transcriptional regulator; helix-turn-helix, alpha-beta, structural genomics, PSI-2, protein structure initiative; 2.00A {Pseudomonas aeruginosa}

Probab=92.14  E-value=0.13  Score=32.21  Aligned_cols=23  Identities=13%  Similarity=0.205  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|..+||++-|||++|+|+..
T Consensus        43 ~~~s~~~IA~~aGvskgtlY~yF   65 (214)
T 2oer_A           43 QRFTTARVAERAGVSIGSLYQYF   65 (214)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccccHHHHHHHhCCCCchHHHhC
Confidence            35899999999999999999864

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=92.13  E-value=0.078  Score=32.32  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=19.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++.|.++||++.|||++|+++.
T Consensus        30 ~~~s~~~Ia~~agvs~~t~Y~~   51 (203)
T 3b81_A           30 ENTTLAFIINKLGISKGALYHY   51 (203)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHTT
T ss_pred             ccCcHHHHHHHhCCCchhHHHH
Confidence            3589999999999999999874

>3bqy_A Putative TETR family transcriptional regulator; structural genomics, strept coelicolor, PSI-2, protein structure initiative; 1.95A {Streptomyces coelicolor A3}

Probab=92.06  E-value=0.11  Score=33.10  Aligned_cols=23  Identities=9%  Similarity=0.220  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++|+|+..
T Consensus        21 ~~~s~~~IA~~aGvs~~tlY~hf   43 (209)
T 3bqy_A           21 DTLTMRRLAQAMDVQAGALYRYF   43 (209)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCcchHHhhc
Confidence            35899999999999999999864

>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD, structural genomics, protein structure initiative; 2.96A {Cytophaga hutchinsonii}

Probab=92.04  E-value=0.14  Score=31.57  Aligned_cols=23  Identities=4%  Similarity=0.031  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++-|||++|+++..
T Consensus        30 ~~~ti~~Ia~~agvs~~t~Y~~F   52 (216)
T 3f0c_A           30 CKTTMNEIASDVGMGKASLYYYF   52 (216)
T ss_dssp             SSCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHc
Confidence            35899999999999999999864

>2i10_A Putative TETR transcriptional regulator; structural genomics, APC5890, TETR family, PSI-2, protein ST initiative; HET: MSE NPO PGE; 2.05A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=92.04  E-value=0.14  Score=31.73  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +|.|..+||++-|||++|+|+..+
T Consensus        30 ~~ts~~~IA~~aGvsk~tlY~~F~   53 (202)
T 2i10_A           30 EGTSITDLTKALGINPPSLYAAFG   53 (202)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChHHHHHHhC
Confidence            468999999999999999998764

>3rh2_A Hypothetical TETR-like transcriptional regulator; DNA/RNA-binding 3-helical bundle, structural genomics, joint for structural genomics; 2.42A {Shewanella amazonensis}

Probab=92.00  E-value=0.12  Score=32.02  Aligned_cols=23  Identities=17%  Similarity=0.197  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|.++||++-|||++|+++..
T Consensus        22 ~~~s~~~IA~~Agvs~~t~Y~~F   44 (212)
T 3rh2_A           22 RTITTNHIAAHLDISPGNLYYHF   44 (212)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHC
Confidence            35899999999999999999863

>2hku_A A putative transcriptional regulator; structural genomics, APC6040, TET rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=92.00  E-value=0.14  Score=31.77  Aligned_cols=24  Identities=17%  Similarity=0.070  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||++-|||++|+|++..
T Consensus        38 ~~~s~~~IA~~aGvs~~tlY~~F~   61 (215)
T 2hku_A           38 EGVPITQICAAAGAHPNQVTYYYG   61 (215)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHcC
Confidence            368999999999999999998643

>3bhq_A Transcriptional regulator; bacterial RE proteins, structural genomics, joint center for structural JCSG, protein structure initiative, PSI-2; HET: MSE; 1.54A {Mesorhizobium loti}

Probab=91.99  E-value=0.15  Score=31.69  Aligned_cols=23  Identities=22%  Similarity=0.131  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+|+..
T Consensus        31 ~~ts~~~IA~~aGvsk~tlY~~F   53 (211)
T 3bhq_A           31 DGTSMEEIATKAGASKQTVYKHF   53 (211)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHc
Confidence            46899999999999999999865

>2o7t_A Transcriptional regulator; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1

Probab=91.93  E-value=0.12  Score=31.71  Aligned_cols=22  Identities=14%  Similarity=0.063  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|..+||++-|||++|+|++.
T Consensus        28 ~~t~~~IA~~agvs~~tlY~~F   49 (199)
T 2o7t_A           28 SLTMENIAEQAGVGVATLYRNF   49 (199)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cCCHHHHHHHhCCCHHHHHHHc
Confidence            5899999999999999999864

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=91.90  E-value=0.12  Score=32.80  Aligned_cols=31  Identities=23%  Similarity=0.187  Sum_probs=27.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ..|.+..+||+.+++|..||...+++.++.=
T Consensus       172 ~~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL  202 (225)
T 3klo_A          172 GSGASNIEIADKLFVSENTVKTHLHNVFKKI  202 (225)
T ss_dssp             TTTCCHHHHHHHTTCCHHHHHHHHHHHTTTS
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999988643

>2opt_A Actii protein; helical protein, TETR family, APO-protein, transcriptional R transcription; 2.05A {Streptomyces coelicolor} PDB: 3b6a_A* 3b6c_A*

Probab=91.89  E-value=0.13  Score=33.68  Aligned_cols=24  Identities=8%  Similarity=0.217  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||+++|||++|+|+...
T Consensus        25 ~~~S~r~IA~~aGvs~~tlY~hF~   48 (234)
T 2opt_A           25 DALSMRRLAQELKTGHASLYAHVG   48 (234)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             cccCHHHHHHHHCCChhHHHHHcC
Confidence            358999999999999999999753

>2ibd_A Possible transcriptional regulator; probable transcriptional regulatory protein, rhodococcus SP. structural genomics, PSI-2; 1.50A {Rhodococcus SP}

Probab=91.88  E-value=0.14  Score=31.62  Aligned_cols=23  Identities=9%  Similarity=0.046  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        33 ~~~s~~~IA~~agvs~~tlY~~F   55 (204)
T 2ibd_A           33 RATTVRDIADAAGILSGSLYHHF   55 (204)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHC
T ss_pred             hhcCHHHHHHHhCCCchhHHHhc
Confidence            46899999999999999999863

>3bjb_A Probable transcriptional regulator, TETR family P; APC7331, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.50A {Rhodococcus SP}

Probab=91.83  E-value=0.12  Score=32.22  Aligned_cols=23  Identities=13%  Similarity=0.232  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|..+||++-|||++|+|++..
T Consensus        42 ~~s~~~IA~~AGVsk~tlY~~F~   64 (207)
T 3bjb_A           42 RVQMHEVAKRAGVAIGTLYRYFP   64 (207)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cCCHHHHHHHhCCCHHHHHHHCC
Confidence            48999999999999999998753

>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structur initiative; 2.30A {Rhodobacter sphaeroides 2}

Probab=91.80  E-value=0.15  Score=31.57  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++-|||++|++++.
T Consensus        49 ~~~t~~~IA~~aGvs~~t~Y~~F   71 (222)
T 3bru_A           49 SSVGVDEILKAARVPKGSFYHYF   71 (222)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CcCcHHHHHHHhCCCcchhhhhC
Confidence            35899999999999999999864

>3frq_A Repressor protein MPHR(A); macrolide antibiotic. repressor, biosensor, erythromycin, STRPTOMYCES, natural products, biosynthesis, DNA-binding; HET: ERY; 1.76A {Escherichia coli} PDB: 3g56_A

Probab=91.80  E-value=0.097  Score=31.99  Aligned_cols=23  Identities=4%  Similarity=0.150  Sum_probs=20.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|.++||++-|||++|+++...
T Consensus        28 ~~t~~~IA~~agvs~~t~Y~~F~   50 (195)
T 3frq_A           28 EFTLSGVAKEVGLSRAALIQRFT   50 (195)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcC
Confidence            57999999999999999998653

>2np5_A Transcriptional regulator; TETR family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE LMT NDS; 1.80A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.77  E-value=0.13  Score=31.91  Aligned_cols=23  Identities=22%  Similarity=0.310  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|..+||++-|||++|+++..
T Consensus        28 ~~~s~~~IA~~AGvs~gtlY~~F   50 (203)
T 2np5_A           28 EGASVREVAKRAGVSIGAVQHHF   50 (203)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hhccHHHHHHHhCCCHHHHHHHc
Confidence            35899999999999999999864

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=91.75  E-value=0.15  Score=31.40  Aligned_cols=23  Identities=17%  Similarity=0.196  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+|+..
T Consensus        28 ~~~t~~~Ia~~Agvs~gt~Y~yF   50 (204)
T 3anp_C           28 QETTATEIAKAAHVSRGTFFNYY   50 (204)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccccHHHHHHHcCCchHHHHHHc
Confidence            35899999999999999999864

>2xdn_A HTH-type transcriptional regulator TTGR; transcription regulation, TETR family; 2.20A {Pseudomonas putida} PDB: 2uxu_A* 2uxi_A* 2uxo_A* 2uxp_A* 2uxh_A*

Probab=91.73  E-value=0.12  Score=32.08  Aligned_cols=23  Identities=17%  Similarity=0.123  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|..+||++-|||++|+|++.
T Consensus        30 ~~~s~~~IA~~aGvskgtlY~~F   52 (210)
T 2xdn_A           30 ARTTLADIAELAGVTRGAIYWHF   52 (210)
T ss_dssp             TTCCHHHHHHHHTCCTTHHHHHC
T ss_pred             ccCcHHHHHHHHCCChHHHHHHh
Confidence            46899999999999999999864

>3s5r_A Transcriptional regulator TETR family; DNA/RNA-binding 3-helical bundle, tetracyclin repressor-like structural genomics; 2.60A {Syntrophus aciditrophicus}

Probab=91.71  E-value=0.14  Score=31.51  Aligned_cols=23  Identities=13%  Similarity=0.137  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+|+..
T Consensus        29 ~~~ti~~Ia~~agvs~~t~Y~~F   51 (216)
T 3s5r_A           29 AATTMAEIAASVGVNPAMIHYYF   51 (216)
T ss_dssp             TTCCHHHHHHTTTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHc
Confidence            45899999999999999999863

>3v6g_A Probable transcriptional regulatory protein (PROB family); helix-turn-helix DNA binding domain; 1.82A {Mycobacterium tuberculosis}

Probab=91.71  E-value=0.15  Score=32.15  Aligned_cols=23  Identities=13%  Similarity=0.248  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|.++||++-|||++++|++.
T Consensus        33 ~~~s~~~IA~~AGvs~~tlY~~F   55 (208)
T 3v6g_A           33 GGLSHRRVAAEANVPVGSTTYYF   55 (208)
T ss_dssp             TCCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCchhHHHHc
Confidence            46899999999999999999864

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=91.69  E-value=0.12  Score=31.64  Aligned_cols=22  Identities=23%  Similarity=0.193  Sum_probs=19.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +|.|.++||++-|||++|+++.
T Consensus        28 ~~~ti~~IA~~agvs~~t~Y~~   49 (193)
T 2dg8_A           28 ARVSHRRIAQRAGVPLGSMTYH   49 (193)
T ss_dssp             GGCCHHHHHHHHTSCTHHHHHH
T ss_pred             hhccHHHHHHHhCCCchhhhee
Confidence            3589999999999999999975

>1vi0_A Transcriptional regulator; structural genomics; HET: MSE DCC; 1.65A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=91.68  E-value=0.13  Score=32.00  Aligned_cols=23  Identities=17%  Similarity=0.219  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|++++.
T Consensus        27 ~~~s~~~IA~~AGvs~gt~Y~yF   49 (206)
T 1vi0_A           27 HQSQVSKIAKQAGVADGTIYLYF   49 (206)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChhHHHHHc
Confidence            35899999999999999999863

>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}

Probab=91.64  E-value=0.096  Score=31.72  Aligned_cols=22  Identities=18%  Similarity=0.175  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++.|.++||++-|||++|+++.
T Consensus        26 ~~~t~~~IA~~agvs~~t~Y~~   47 (199)
T 3qbm_A           26 AGTAISDIMAATGLEKGGIYRH   47 (199)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHTT
T ss_pred             CcCCHHHHHHHhCCCccHHHHh
Confidence            4689999999999999999874

>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp}

Probab=91.63  E-value=0.16  Score=31.36  Aligned_cols=23  Identities=9%  Similarity=0.059  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        29 ~~~s~~~Ia~~Agvskgt~Y~yF   51 (197)
T 2f07_A           29 DKASISDIVKKAGTAQGTFYLYF   51 (197)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCchHHHHhC
Confidence            35899999999999999999864

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

Probab=91.63  E-value=0.13  Score=30.17  Aligned_cols=57  Identities=16%  Similarity=0.158  Sum_probs=38.9

Q ss_pred             CCHHHHHHH----hccCHHHHHHHHHHHHHhcCCCcccc--CCCCC--CCCCHHHHHHHHHHHHh
Q psy15513          6 VRPCVISRQ----LRVSHGCVSKILNRYQETGSIRPGVI--GGSKP--RVATPDVERRIEEYKGE   62 (77)
Q Consensus         6 ~s~~~iA~r----f~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~--~~~~~~~~~~i~~~v~~   62 (77)
                      +.--++++.    ++||.+|++..+++..+.|-|.....  +|++.  -.+|+.-.+.+.++.++
T Consensus        23 ~~gyel~~~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l~~~~~~   87 (108)
T 3l7w_A           23 SYGYDISQTIKLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHLVYLTKE   87 (108)
T ss_dssp             EEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHHHHHHHH
Confidence            334455555    69999999999999999999976653  33222  24777666666555433

>2hxi_A Putative transcriptional regulator; structural genomics, APC6293, TET streptomyces coelicolor A3(2), PSI-2; 1.70A {Streptomyces coelicolor}

Probab=91.62  E-value=0.12  Score=33.68  Aligned_cols=22  Identities=5%  Similarity=0.045  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++|.++||++.|||++|+|+..
T Consensus        49 ~~s~~~IA~~aGvs~~tlY~hF   70 (241)
T 2hxi_A           49 TFSVRKLAASLGTDSSSLYRHF   70 (241)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHT
T ss_pred             cCCHHHHHHHhCcCHHHHHHHc
Confidence            4899999999999999999854

>3cjd_A Transcriptional regulator, TETR family; YP_510936.1, putative TETR transcriptional regulator, struct genomics; HET: STE; 1.79A {Jannaschia SP}

Probab=91.62  E-value=0.14  Score=31.81  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|.++||++-|||++|+|+..+
T Consensus        31 ~~~s~~~IA~~agvs~~t~Y~hF~   54 (198)
T 3cjd_A           31 ASLRARELARQADCAVGAIYTHFQ   54 (198)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hhcCHHHHHHHhCCCccHHHHHhC
Confidence            358999999999999999998643

>2gen_A Probable transcriptional regulator; APC6095, TETR family, structural genomics, PSI, protein structure initiative; 1.70A {Pseudomonas aeruginosa PAO1} SCOP: a.4.1.9 a.121.1.1

Probab=91.61  E-value=0.16  Score=31.32  Aligned_cols=23  Identities=13%  Similarity=0.075  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        26 ~~ts~~~IA~~aGvs~gtlY~~F   48 (197)
T 2gen_A           26 DATTIEMIRDRSGASIGSLYHHF   48 (197)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHT
T ss_pred             ccCCHHHHHHHHCCChHHHHHHC
Confidence            35899999999999999999864

>2nx4_A Transcriptional regulator, TETR family protein; HTH DNA binding motif, structural genomics, PSI-2, Pro structure initiative; 1.70A {Rhodococcus SP}

Probab=91.60  E-value=0.16  Score=31.25  Aligned_cols=23  Identities=13%  Similarity=0.182  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .|.|.++||++-|||++|++...
T Consensus        29 ~~~s~~~IA~~aGvs~gtlY~yF   51 (194)
T 2nx4_A           29 EAANMRDIATEAGYTNGALSHYF   51 (194)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCcchHHHhC
Confidence            46899999999999999999864

>1i3j_A I-TEVI, intron-associated endonuclease 1; protein-DNA complex, extended structure, Zn-finger, minor groove helix, helix-turn-helix; 2.20A {Enterobacteria phage T4} SCOP: d.285.1.1 PDB: 1t2t_A

Probab=91.59  E-value=0.16  Score=30.96  Aligned_cols=23  Identities=17%  Similarity=0.244  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      -|+.++|+.|++|.+||.+|++.
T Consensus        84 ~S~~eAar~lg~s~~ti~~~~~~  106 (116)
T 1i3j_A           84 DCAADAARHFKISSGLVTYRVKS  106 (116)
T ss_dssp             SSHHHHHHHHTCCHHHHHHHHHC
T ss_pred             cCHHHHHHHHCCCchhHHHHHhc
Confidence            37899999999999999999953

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=91.55  E-value=0.24  Score=33.35  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=26.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -+|+|..+||..+|+|.+||..++.+-+..
T Consensus       125 ~eg~s~~EIA~~lgis~~tVks~l~rA~~~  154 (286)
T 3n0r_A          125 LEGFTPTEAAQILDCDFGEVERLIGDAQAE  154 (286)
T ss_dssp             TTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHhCcCHHHHHHHHHHHHhh
Confidence            379999999999999999999999887754

>3col_A Putative transcription regulator; structural genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Lactobacillus plantarum WCFS1}

Probab=91.55  E-value=0.086  Score=31.78  Aligned_cols=21  Identities=14%  Similarity=0.313  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +.|.++||++.|||++|+++.
T Consensus        30 ~~ti~~Ia~~agvs~~t~Y~~   50 (196)
T 3col_A           30 GVSTTKVAKRVGIAQSNVYLY   50 (196)
T ss_dssp             GCCHHHHHHHHTSCHHHHHTT
T ss_pred             cCCHHHHHHHhCCcHHHHHHH
Confidence            589999999999999999874

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=91.54  E-value=0.16  Score=31.21  Aligned_cols=22  Identities=14%  Similarity=0.224  Sum_probs=19.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++.|.++||++.|||++|+++.
T Consensus        31 ~~~ti~~Ia~~agvs~~t~Y~~   52 (189)
T 3vp5_A           31 HEAKIMHIVKALDIPRGSFYQY   52 (189)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHH
T ss_pred             ccccHHHHHHHhCCChHHHHHH
Confidence            3579999999999999999874

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=91.52  E-value=0.14  Score=31.66  Aligned_cols=23  Identities=22%  Similarity=0.056  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||++|+++..
T Consensus        42 ~~~t~~~IA~~agvs~~t~Y~~F   64 (214)
T 2zb9_A           42 AQLTFERVARVSGVSKTTLYKWW   64 (214)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHC
Confidence            35899999999999999999863

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

Probab=91.50  E-value=0.071  Score=35.77  Aligned_cols=36  Identities=8%  Similarity=0.044  Sum_probs=32.5

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ...+++..++|.++++|+++|+..+++..+.|-|.-
T Consensus       175 ~~~~~t~~~la~~~~l~~~~V~~~l~~L~~~~~v~~  210 (232)
T 2qlz_A          175 LNGRATVEELSDRLNLKEREVREKISEMARFVPVKI  210 (232)
T ss_dssp             HSSEEEHHHHHHHHTCCHHHHHHHHHHHTTTSCEEE
T ss_pred             hcCCCCHHHHHHHhCcCHHHHHHHHHHHHhcCCeEE
Confidence            345689999999999999999999999999998873

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=91.48  E-value=0.31  Score=27.69  Aligned_cols=60  Identities=17%  Similarity=0.188  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ..+..++|+.+|+|.++.++.+++..  | +.|..       -....-......++. +++.++.|++..+
T Consensus        19 ~~~~~~lA~~~~~S~~~l~r~fk~~~--g-~s~~~-------~~~~~Rl~~A~~lL~-~~~~si~~iA~~~   78 (103)
T 3lsg_A           19 QFTLSVLSEKLDLSSGYLSIMFKKNF--G-IPFQD-------YLLQKRMEKAKLLLL-TTELKNYEIAEQV   78 (103)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHHH--S-SCHHH-------HHHHHHHHHHHHHHH-HCCCCHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH--C-cCHHH-------HHHHHHHHHHHHHHH-CCCCCHHHHHHHh
Confidence            57999999999999999999988743  3 23331       111111222334443 4789999998754

>3mnl_A KSTR, transcriptional regulatory protein (probably TETR; TETR family of transcriptional regulator, all-helical; 1.80A {Mycobacterium tuberculosis}

Probab=91.46  E-value=0.1  Score=31.77  Aligned_cols=21  Identities=14%  Similarity=0.244  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +.|.++||++.|||++|+++.
T Consensus        40 ~~t~~~Ia~~agvs~~t~Y~~   60 (203)
T 3mnl_A           40 AVQMRAVADRADVAVGTLYRY   60 (203)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHcCCChhHHHHH
Confidence            489999999999999999985

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=91.41  E-value=0.1  Score=31.35  Aligned_cols=22  Identities=9%  Similarity=0.006  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|.++||++-|||++|++++.
T Consensus        28 ~~t~~~Ia~~agvs~~t~Y~~F   49 (195)
T 3pas_A           28 ATSVGKIAKAAGLSPATLYIYY   49 (195)
T ss_dssp             HCCHHHHHHHHTSCHHHHHHHC
T ss_pred             hcCHHHHHHHhCCCchHHHHHc
Confidence            4899999999999999999863

>2hyt_A TETR-family transcriptional regulator; structural genomics, center for structural genomics, JCSG, protein structure INI PSI-2; HET: MSE; 1.64A {Pectobacterium atrosepticum}

Probab=91.39  E-value=0.14  Score=31.45  Aligned_cols=23  Identities=13%  Similarity=0.148  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|..+||++-|||++|+|+..
T Consensus        31 ~~~s~~~IA~~aGvs~~tlY~~F   53 (197)
T 2hyt_A           31 ADTSMDDLTAQASLTRGALYHHF   53 (197)
T ss_dssp             TTCCHHHHHHHHTCCTTHHHHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHc
Confidence            35899999999999999999864

>2rae_A Transcriptional regulator, ACRR family protein; TETR/ACRR family transcriptional regulator, structural genom 2, RHA08332, MCSG; 2.20A {Rhodococcus SP}

Probab=91.33  E-value=0.17  Score=30.99  Aligned_cols=23  Identities=0%  Similarity=0.013  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        36 ~~~ti~~Ia~~agvs~~t~Y~~F   58 (207)
T 2rae_A           36 DATSVDEVAEASGIARRTLFRYF   58 (207)
T ss_dssp             TTSCHHHHHHHTTSCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCcchHhhhC
Confidence            35899999999999999999853

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=91.28  E-value=0.31  Score=27.90  Aligned_cols=62  Identities=10%  Similarity=-0.010  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC-CcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA-MFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd-~tl~El~~~L   75 (77)
                      ...+..++|+.+|+|.++.++.+++.  +| +.|..       -....-.+....++...++ +++.|++..+
T Consensus        17 ~~~~~~~lA~~~~~s~~~l~r~fk~~--~G-~s~~~-------~~~~~Rl~~A~~lL~~~~~~~si~~IA~~~   79 (108)
T 3mn2_A           17 RPITIEKLTALTGISSRGIFKAFQRS--RG-YSPMA-------FAKRVRLQHAHNLLSDGATPTTVTAAALSC   79 (108)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHH--TS-SCHHH-------HHHHHHHHHHHHHHHSSSSCCCHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH--hC-cCHHH-------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHh
Confidence            34789999999999999999998863  33 22321       1111122334455555543 8999998754

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=91.28  E-value=0.18  Score=34.09  Aligned_cols=25  Identities=28%  Similarity=0.275  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ..+.+++|..|+||.+||.|++++.
T Consensus        86 ~~t~~~ia~~l~vs~~tV~r~L~~~  110 (345)
T 3hot_A           86 AQTQKQLAEQLEVSQQAVSNRLREM  110 (345)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHT
T ss_pred             cchHHHHHHHHCCCHHHHHHHHHHh
Confidence            3788999999999999999999873

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=91.27  E-value=0.31  Score=27.95  Aligned_cols=61  Identities=7%  Similarity=-0.060  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...+..++|+.+|+|.++.++.+++.  +| +.|..       -....-.+....++. +++.++.|++..+
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~fk~~--~G-~s~~~-------~~~~~Rl~~A~~lL~-~~~~si~~IA~~~   80 (108)
T 3oou_A           20 EGMSLKTLGNDFHINAVYLGQLFQKE--MG-EHFTD-------YLNRYRVNYAKEELL-QTKDNLTIIAGKS   80 (108)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHH--HS-SCHHH-------HHHHHHHHHHHHHHH-HCCCCHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH--HC-cCHHH-------HHHHHHHHHHHHHHH-cCCCCHHHHHHHc
Confidence            35789999999999999999999864  34 22331       111111222334443 5788999998764

>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3}

Probab=91.25  E-value=0.18  Score=31.93  Aligned_cols=23  Identities=13%  Similarity=0.252  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|..+||++.|||.+|++++.
T Consensus        62 ~~~tv~~IA~~AGvs~~t~Y~~F   84 (229)
T 3bni_A           62 DALSTRAVALRADVPIGSVYRFF   84 (229)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hhccHHHHHHHHCCCchhHHHHc
Confidence            35899999999999999999853

>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1}

Probab=91.23  E-value=0.17  Score=31.20  Aligned_cols=22  Identities=32%  Similarity=0.362  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|.++||++.|||++|+|++.
T Consensus        32 ~~t~~~IA~~agvs~~tlY~~F   53 (196)
T 2qwt_A           32 GVPMDEIARRAGVGAGTVYRHF   53 (196)
T ss_dssp             TSCHHHHHHHTTSCHHHHHHHC
T ss_pred             CCCHHHHHHHhCCCHHHHHHHC
Confidence            4899999999999999999863

>1t33_A Putative transcriptional repressor (TETR/ACRR FAM; structural genomics, TETR/CCRR FA helix turn helix DNA binding domain, PSI; 2.20A {Salmonella typhimurium} SCOP: a.4.1.9 a.121.1.1

Probab=91.14  E-value=0.18  Score=31.29  Aligned_cols=22  Identities=5%  Similarity=-0.028  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .|.++||++-|||++|++++..
T Consensus        32 ~s~~~IA~~agvs~~tiY~~F~   53 (224)
T 1t33_A           32 ATTRDIAALAGQNIAAITYYFG   53 (224)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHS
T ss_pred             ccHHHHHHHhCCCHHHHHHhcC
Confidence            7999999999999999998764

>2zcx_A SCO7815, TETR-family transcriptional regulator; helix-turn-helix, DNA-binding, transcription regulation; 2.22A {Streptomyces coelicolor}

Probab=91.14  E-value=0.18  Score=32.25  Aligned_cols=22  Identities=5%  Similarity=0.089  Sum_probs=19.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +|.|.++||++.|||++|+++.
T Consensus        42 ~~~s~~~IA~~agvs~~tlY~~   63 (231)
T 2zcx_A           42 REITLTDIAATVGMHKSALLRY   63 (231)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHh
Confidence            3689999999999999999975

>3g7r_A Putative transcriptional regulator; TETR, all-helical, structural genomics, PSI-2, protein structure initiative; 1.38A {Streptomyces coelicolor A3}

Probab=91.11  E-value=0.18  Score=31.62  Aligned_cols=23  Identities=13%  Similarity=0.133  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|.++||++-|||+++++++.
T Consensus        54 ~~~t~~~IA~~AGvs~~tlY~~F   76 (221)
T 3g7r_A           54 HSVGIDRITAEAQVTRATLYRHF   76 (221)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHC
Confidence            35899999999999999999854

>2xpw_A Tetracycline repressor protein class D; transcription, transcription regulator, helix-turn-helix, ME coordination; HET: OTC MES; 1.44A {Escherichia coli} PDB: 1bjy_A* 1bj0_A 1du7_A* 1ork_A* 2fj1_A* 1bjz_A* 2o7o_A* 2x6o_A* 2x9d_A* 2xps_A* 2xpt_A* 2vke_A* 2xpu_A* 2xpv_A* 2tct_A* 2xb5_A* 2trt_A* 2xrl_A* 1qpi_A* 1a6i_A ...

Probab=91.09  E-value=0.11  Score=33.01  Aligned_cols=22  Identities=9%  Similarity=0.194  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|.++||+++|||++|+|+..
T Consensus        23 ~~s~~~IA~~~Gvs~~slY~hF   44 (207)
T 2xpw_A           23 GLTTRKLAQKLGIEQPTLYWHV   44 (207)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cCCHHHHHHHhCCCcchHHHhc
Confidence            5899999999999999999853

>2rek_A Putative TETR-family transcriptional regulator; sulfur, SAD, structural genomics, PSI-2, protein structure initiative; 1.86A {Streptomyces coelicolor A3}

Probab=91.09  E-value=0.17  Score=30.96  Aligned_cols=22  Identities=14%  Similarity=0.148  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|..+||++.|||++|+++..
T Consensus        35 ~~s~~~Ia~~agvs~~t~Y~~F   56 (199)
T 2rek_A           35 DASLEEIARRAGVGSATLHRHF   56 (199)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CCCHHHHHHHhCCchHHHHHHC
Confidence            4799999999999999999754

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=91.07  E-value=0.11  Score=31.08  Aligned_cols=21  Identities=5%  Similarity=-0.110  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +.|.++||++.|||++|+++.
T Consensus        32 ~~tv~~Ia~~agvs~~t~Y~~   52 (177)
T 3kkc_A           32 KITVQDVIGLANVGRSTFYSH   52 (177)
T ss_dssp             TCCHHHHHHHHCCCHHHHTTT
T ss_pred             HhhHHHHHHHhCCcHhhHHHH
Confidence            479999999999999999874

>1zk8_A Transcriptional regulator, TETR family; TETR member,transcriptional regulator, STRU genomics, PSI, protein structure initiative; 2.15A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1

Probab=91.06  E-value=0.079  Score=31.99  Aligned_cols=21  Identities=14%  Similarity=0.129  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~   25 (77)
                      +.|.++||++.|||++|+++.
T Consensus        28 ~~t~~~Ia~~agvs~~t~Y~~   48 (183)
T 1zk8_A           28 EVTLASLAQTLGVRSPSLYNH   48 (183)
T ss_dssp             GCCHHHHHHHHTSCHHHHTTT
T ss_pred             ccCHHHHHHHcCCCchHHHHH
Confidence            589999999999999999864

>1ui5_A A-factor receptor homolog; helix-turn-helix, alpha-helix-bundle, antibiotic; 2.40A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 PDB: 1ui6_A

Probab=91.04  E-value=0.19  Score=31.51  Aligned_cols=23  Identities=13%  Similarity=0.096  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++-|||++|+++..
T Consensus        28 ~~ts~~~IA~~AGvskgtlY~~F   50 (215)
T 1ui5_A           28 ESTTLSEIVAHAGVTKGALYFHF   50 (215)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCCchhhHhhC
Confidence            46899999999999999999754

>3crj_A Transcription regulator; APC88200, TETR, structura genomics, PSI-2, protein structure initiative; HET: MSE; 2.60A {Haloarcula marismortui atcc 43049}

Probab=91.02  E-value=0.12  Score=32.06  Aligned_cols=22  Identities=18%  Similarity=0.066  Sum_probs=19.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      .|.|.++||++-|||++|+++.
T Consensus        33 ~~~s~~~IA~~agvsk~tlY~y   54 (199)
T 3crj_A           33 ADLTIQRIADEYGKSTAAVHYY   54 (199)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTT
T ss_pred             ccCCHHHHHHHhCCChhHHhhh
Confidence            3589999999999999999864

>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}

Probab=90.98  E-value=0.11  Score=31.90  Aligned_cols=21  Identities=10%  Similarity=0.200  Sum_probs=18.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++|.++||++-|||++|++++
T Consensus        45 ~~t~~~Ia~~agvs~~t~Y~~   65 (212)
T 3nxc_A           45 RITTAKLAASVGVSEAALYRH   65 (212)
T ss_dssp             -CCHHHHHHHTTSCHHHHHTT
T ss_pred             hcCHHHHHHHhCCChhHHHHH
Confidence            589999999999999999875

>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans}

Probab=90.92  E-value=0.18  Score=30.90  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|+|.++||++-|||++|+++..
T Consensus        45 ~~~t~~~Ia~~agvs~~t~Y~~F   67 (217)
T 3mvp_A           45 FNVTTNEIAKKADVSVGTLYAYF   67 (217)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             cccCHHHHHHHhCCChhHHHHHc
Confidence            35899999999999999999853

>2guh_A Putative TETR-family transcriptional regulator; helix-turn-helix, TETR fold, structural genomics, PSI, prote structure initiative; HET: MSE; 1.52A {Rhodococcus SP}

Probab=90.92  E-value=0.19  Score=31.74  Aligned_cols=23  Identities=17%  Similarity=0.092  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|.++||++-|||++|+++...
T Consensus        59 ~~tv~~IA~~AGvs~~tlY~~F~   81 (214)
T 2guh_A           59 EITLKDIAEDAGVSAPLIIKYFG   81 (214)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHHS
T ss_pred             hcCHHHHHHHhCCCHHHHHHHcC
Confidence            48999999999999999999764

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

Probab=90.91  E-value=0.32  Score=26.37  Aligned_cols=31  Identities=23%  Similarity=0.223  Sum_probs=27.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .....+|+.||||.-.|...+++..+.|-+.
T Consensus        26 ldI~~~a~kygV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           26 LDIEHFSKVYGVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             EEHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             EeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence            5678899999999999999999999999763

>1rkt_A Protein YFIR; transcription regulator, structural genomics, PSI, protein S initiative, midwest center for structural genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=90.91  E-value=0.12  Score=31.91  Aligned_cols=22  Identities=14%  Similarity=-0.079  Sum_probs=19.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      .|.|..+||++-|||++|+|++
T Consensus        31 ~~ts~~~IA~~agvs~gtlY~y   52 (205)
T 1rkt_A           31 ELTTMKDVVEESGFSRGGVYLY   52 (205)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTT
T ss_pred             ccCCHHHHHHHHCCCcchhhhh
Confidence            4689999999999999999974

>2id3_A Putative transcriptional regulator; structural genomics, PSI-2, prote structure initiative; 1.70A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=90.89  E-value=0.19  Score=31.69  Aligned_cols=24  Identities=17%  Similarity=0.126  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|..+||++.|||++|+++...
T Consensus        59 ~~~t~~~IA~~Agvs~~t~Y~~F~   82 (225)
T 2id3_A           59 DALDLGEIARRAGVGKTTVYRRWG   82 (225)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHCC
Confidence            358999999999999999998753

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=90.85  E-value=0.13  Score=36.52  Aligned_cols=34  Identities=12%  Similarity=0.022  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+..++++.++||..|+.+.++...+.|-+....
T Consensus       312 ~t~~~~~~~~~~S~~TA~r~L~~L~e~GiL~~~~  345 (373)
T 3eqx_A          312 CRIQNLVESGLAKRQTASVYLKQLCDIGVLEEVQ  345 (373)
T ss_dssp             EEHHHHHHTSSSCHHHHHHHHHHHHHTTSCEEC-
T ss_pred             ccHHHHHHHhCcCHHHHHHHHHHHHHCCcEEEeC
Confidence            5678899999999999999999999999998653

>2ras_A Transcriptional regulator, TETR family; bacterial regulatory proteins, DNA-binding, DNA binding 3-helical bundle fold; 1.80A {Novosphingobium aromaticivorans}

Probab=90.85  E-value=0.099  Score=32.29  Aligned_cols=23  Identities=17%  Similarity=0.325  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||++|++++.
T Consensus        30 ~~~s~~~IA~~agvs~~t~Y~~F   52 (212)
T 2ras_A           30 AGLTLSELAARAGISQANLSRYF   52 (212)
T ss_dssp             SCCCHHHHHHHHTSCHHHHTTTC
T ss_pred             ccCcHHHHHHHhCCCHHHHHHHc
Confidence            45899999999999999998754

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.81  E-value=0.067  Score=36.44  Aligned_cols=25  Identities=20%  Similarity=0.231  Sum_probs=21.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|....++|+.||||.+|+++.++
T Consensus       279 ~~~gn~~~aA~~Lgi~r~tl~~kl~  303 (304)
T 1ojl_A          279 KTGGNKTEAARQLGITRKTLLAKLS  303 (304)
T ss_dssp             TTTTCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            4566889999999999999999875

>3cdl_A Transcriptional regulator AEFR; APC88582, TETR, pseudomonas syringae PV. tomato STR. DC3000, structural genomics, PSI-2; HET: MSE; 2.36A {Pseudomonas syringae PV}

Probab=90.78  E-value=0.13  Score=31.87  Aligned_cols=22  Identities=18%  Similarity=-0.032  Sum_probs=19.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      .+.|..+||++-|||++|+++.
T Consensus        28 ~~~s~~~IA~~aGvsk~tlY~~   49 (203)
T 3cdl_A           28 EITSMDRIAARAEVSKRTVYNH   49 (203)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHTT
T ss_pred             hhcCHHHHHHHhCCCHHHHHHH
Confidence            3589999999999999999975

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=90.74  E-value=0.37  Score=27.83  Aligned_cols=61  Identities=13%  Similarity=0.052  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ...+..++|+.+|||.++.++.+++.  +| +.|..       -+...-.+....++. +++.++.||+..+
T Consensus        22 ~~~~~~~lA~~~~~S~~~l~r~fk~~--~G-~s~~~-------~~~~~Rl~~A~~lL~-~~~~~i~eIA~~~   82 (113)
T 3oio_A           22 EPLSTDDIAYYVGVSRRQLERLFKQY--LG-TVPSK-------YYLELRLNRARQLLQ-QTSKSIVQIGLAC   82 (113)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHH--TS-SCHHH-------HHHHHHHHHHHHHHH-HCCCCHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH--HC-cCHHH-------HHHHHHHHHHHHHHH-cCCCCHHHHHHHH
Confidence            34889999999999999999998864  23 22321       111111222334444 4789999998764

>3npi_A TETR family regulatory protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; 2.96A {Corynebacterium diphtheriae}

Probab=90.71  E-value=0.14  Score=32.79  Aligned_cols=23  Identities=9%  Similarity=0.109  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++|.++||++.|||++|+++...
T Consensus        38 ~~t~~~IA~~aGvs~~tlY~~F~   60 (251)
T 3npi_A           38 DAKLEAIAKKSGMSKRMIHYHFG   60 (251)
T ss_dssp             HCCHHHHHHHHCCCHHHHHHHHC
T ss_pred             ccCHHHHHHHHCCCHHHHHHHcC
Confidence            58999999999999999998753

>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei}

Probab=90.71  E-value=0.19  Score=31.50  Aligned_cols=23  Identities=17%  Similarity=0.215  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++-|||++|+++..
T Consensus        24 ~~~t~~~IA~~Agvs~~t~Y~~F   46 (228)
T 3nnr_A           24 RNITTNHIAAHLAISPGNLYYHF   46 (228)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hhcCHHHHHHHhCCCCccchhcC
Confidence            35899999999999999999853

>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A

Probab=90.69  E-value=0.35  Score=28.83  Aligned_cols=26  Identities=12%  Similarity=0.106  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      ...+..++|..+|+|.++.+|+.+++
T Consensus        92 ~~~sl~~lA~~~g~S~~~f~r~Fk~~  117 (133)
T 1u8b_A           92 TPVTLEALADQVAMSPFHLHRLFKAT  117 (133)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46899999999999999999998874

>2gfn_A HTH-type transcriptional regulator PKSA related P; transcriptional regulato PSI-2, regulatory protein, structural genomics, protein STR initiative; 1.90A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=90.65  E-value=0.19  Score=31.37  Aligned_cols=23  Identities=13%  Similarity=0.241  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|.|.++||++-|||++|++.+.
T Consensus        28 ~~~s~~~IA~~aGvs~gtlY~yF   50 (209)
T 2gfn_A           28 SAVTTRAVAEESGWSTGVLNHYF   50 (209)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHT
T ss_pred             ccCCHHHHHHHHCCCcchHHhcC
Confidence            35899999999999999999864

>3rd3_A Probable transcriptional regulator; 2.40A {Pseudomonas aeruginosa}

Probab=90.65  E-value=0.11  Score=31.47  Aligned_cols=22  Identities=23%  Similarity=0.224  Sum_probs=19.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++.|.++||++-|||++|+++.
T Consensus        29 ~~~t~~~IA~~agvs~~tlY~~   50 (197)
T 3rd3_A           29 SGVGLNEILQSAGVPKGSFYHY   50 (197)
T ss_dssp             TTCCHHHHHHHHTCCHHHHTTT
T ss_pred             ccCCHHHHHHHhCCChhhHHHH
Confidence            3579999999999999999874

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=90.63  E-value=0.24  Score=30.52  Aligned_cols=36  Identities=17%  Similarity=0.215  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          5 GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         5 G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..|+.+|...+     .||.+||||-+..+.+.|-|..-..
T Consensus        33 h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~   73 (145)
T 3eyy_A           33 HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHL   73 (145)
T ss_dssp             SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEe
Confidence            46788888777     7999999999999999998855443

>2oi8_A Putative regulatory protein SCO4313; TETR, structural genomics, PSI-2, P structure initiative; 2.50A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=90.59  E-value=0.13  Score=32.55  Aligned_cols=22  Identities=9%  Similarity=0.206  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKI   25 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~   25 (77)
                      ++.|.++||++.|||++|+|+.
T Consensus        35 ~~~s~~~IA~~agvs~~t~Y~~   56 (216)
T 2oi8_A           35 SALSLNAIAKRMGMSGPALYRY   56 (216)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTT
T ss_pred             ccCCHHHHHHHhCCCHHHHHHH
Confidence            4589999999999999999874

>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2

Probab=90.58  E-value=0.4  Score=27.80  Aligned_cols=28  Identities=11%  Similarity=0.057  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHh-ccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQL-RVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf-~VS~stv~r~~~r~r~   31 (77)
                      .|+|-.+|++.| |..++||..-+++..+
T Consensus        45 t~~Sl~~IG~~fggrdHsTV~ha~~ki~~   73 (94)
T 1j1v_A           45 TNHSLPEIGDAFGGRDHTTVLHACRKIEQ   73 (94)
T ss_dssp             SCCCHHHHHHHTTSCCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            589999999999 8999999999888765

---

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	77
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	3e-23
d1k78a2	61	a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta	5e-20
d6paxa2	65	a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta	2e-18
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	2e-12

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 83.0 bits (205), Expect = 3e-23
 Identities = 63/76 (82%), Positives = 71/76 (93%)

Query: 1   MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60
           MAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK
Sbjct: 28  MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYK 87

Query: 61  GENPAMFSWEIRDRLV 76
             +P MFSWEIR++L+
Sbjct: 88  RSSPGMFSWEIREKLI 103

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.1 bits (180), Expect = 5e-20
 Identities = 27/38 (71%), Positives = 32/38 (84%)

Query: 39 VIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76
          VIGGSKP+VATP V  +I EYK +NP MF+WEIRDRL+
Sbjct: 1  VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLL 38

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.9 bits (169), Expect = 2e-18
 Identities = 24/36 (66%), Positives = 31/36 (86%)

Query: 41 GGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76
          GGSKPRVATP+V  +I +YK E P++F+WEIRDRL+
Sbjct: 1  GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLL 36

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (131), Expect = 2e-12
 Identities = 31/38 (81%), Positives = 33/38 (86%)

Query: 1  MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38
          +A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI+PG
Sbjct: 26 LAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG 63

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	77
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.94
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.11
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.07
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	98.68
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	98.52
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	98.3
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	98.09
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.93
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	97.87
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	97.72
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	97.62
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	97.62
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	97.55
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	97.54
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	97.5
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	97.48
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.45
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	97.44
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.42
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	97.42
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	97.29
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.25
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	97.24
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.2
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.18
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	97.17
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	97.16
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.15
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	97.14
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.13
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.11
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	97.11
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	97.1
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	97.1
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	97.09
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	97.09
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	97.08
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	97.07
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	97.07
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	97.07
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	97.01
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	97.0
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.0
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	96.98
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	96.96
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.95
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	96.95
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	96.93
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.93
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.91
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	96.91
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	96.9
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.9
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.9
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	96.9
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	96.89
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	96.89
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.88
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	96.87
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.87
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.85
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	96.85
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	96.84
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	96.81
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	96.81
d1y7ya1	69	Restriction-modification controller protein C.AhdI	96.8
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	96.8
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	96.77
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	96.71
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	96.7
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	96.69
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	96.66
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	96.64
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	96.63
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.62
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	96.61
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	96.55
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	96.55
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	96.53
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	96.52
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	96.46
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	96.46
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	96.45
d1zyba1	73	Probable transcription regulator BT4300, C-termina	96.44
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	96.42
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	96.38
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	96.37
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	96.37
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	96.31
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	96.27
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	96.22
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	96.18
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	96.13
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	96.08
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	96.0
d2esna1	89	Probable LysR-type transcriptional regulator PA047	95.96
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	95.94
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	95.88
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.86
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	95.7
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	95.47
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.3
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	95.16
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	95.11
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	94.95
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	94.93
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	94.86
d2ezla_	99	Ibeta subdomain of the mu end DNA-binding domain o	94.72
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	94.7
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	94.54
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	94.5
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	94.41
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	94.4
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	94.38
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	94.23
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	94.14
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	94.1
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	94.1
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	94.09
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	94.05
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	94.05
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	93.99
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	93.97
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	93.96
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	93.84
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	93.81
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	93.62
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	93.56
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	93.43
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	93.36
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	93.3
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	93.3
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	93.27
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	93.26
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	92.99
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	92.84
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	92.62
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	92.1
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	92.09
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	91.88
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	91.85
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	91.6
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	91.56
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	91.48
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	91.43
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	91.09
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	90.66
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	90.6
d1okra_	120	Methicillin resistance regulatory protein MecI {St	90.53
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	90.51
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	90.14
d1e0ga_	48	Membrane-bound lytic murein transclycosylase D, Ml	89.86
d2np3a1	65	Putative transcriptional regulator SCO0857 {Strept	89.79
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	89.63
d2b0la1	91	GTP-sensing transcriptional pleiotropic repressor	88.97
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	88.92
d1i3ja_	96	DNA-binding domain of intron endonuclease I-TevI {	88.39
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	87.85
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	87.57
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	87.49
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	86.86
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	86.73
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	86.54
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	86.14
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	85.52
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	85.01
d1aisb2	95	Transcription factor IIB (TFIIB), core domain {Arc	84.96
d1vola2	109	Transcription factor IIB (TFIIB), core domain {Hum	84.92
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	84.68
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	84.54
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	84.38
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.4
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	82.22
d1tc3c_	51	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	81.92
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	81.9
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	81.58
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	81.56
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	81.49
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	81.06
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	80.39
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	80.36
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	80.34

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.94  E-value=4.1e-28  Score=150.58  Aligned_cols=76  Identities=83%  Similarity=1.412  Sum_probs=72.6

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      |+++|+|+|+||++|+||++||+||+++|++||+++|+++||++|+..+++++++|.+++++|||+|++||+++|.
T Consensus        28 ~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~~I~~~~~~~P~~t~~El~~~L~  103 (123)
T d1pdnc_          28 MAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLI  103 (123)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTTCCHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCccHHHHHHHHH
Confidence            3578999999999999999999999999999999999999999999999999999999999999999999999984

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.5e-18  Score=96.48  Aligned_cols=37  Identities=84%  Similarity=1.332  Sum_probs=35.1

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .++|+|+|+||++|+||++||+||+++|+|||+++|.
T Consensus        27 ~~~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~PG   63 (63)
T d1k78a1          27 AHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG   63 (63)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCC
Confidence            4689999999999999999999999999999999984

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=7.2e-11  Score=64.25  Aligned_cols=37  Identities=70%  Similarity=1.253  Sum_probs=35.3

Q ss_pred             cCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513         40 IGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus        40 ~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      .||.+|++.+|+++..|.++..+||++|.|||+++|+
T Consensus         2 IGGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li   38 (61)
T d1k78a2           2 IGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLL   38 (61)
T ss_dssp             CCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCcccHHHHHHHHH
Confidence            5899999999999999999999999999999999985

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=1.2e-10  Score=64.00  Aligned_cols=36  Identities=67%  Similarity=1.221  Sum_probs=34.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513         41 GGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV   76 (77)
Q Consensus        41 gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~   76 (77)
                      ||.+|++.+|+++..|.++..+||+||.|||+++|+
T Consensus         1 GGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li   36 (65)
T d6paxa2           1 GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLL   36 (65)
T ss_dssp             SCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHH
T ss_pred             CCCCcCcCCHHHHHHHHHHHHhCCccchHHHHHHHH
Confidence            688999999999999999999999999999999985

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=98.68  E-value=8.4e-09  Score=59.09  Aligned_cols=55  Identities=18%  Similarity=0.288  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP   64 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p   64 (77)
                      .|.|..+||+.||||.+|+++|+++|+..|.....     .+... ....+.|.+|-.+|-
T Consensus        22 ~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~~~~~-----~~~~~-~~~~~ei~~L~~En~   76 (89)
T d2jn6a1          22 DGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGT-----TPSAA-VSEAEQIRQLKKENA   76 (89)
T ss_dssp             GGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTCSC-----CCCHH-HHTHHHHHHHHHCGG
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHhhcccccCC-----CCCcc-hhHHHHHHHHHHHHH
Confidence            58999999999999999999999999876644332     11222 223556777777664

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=98.52  E-value=1.5e-08  Score=52.52  Aligned_cols=26  Identities=4%  Similarity=0.079  Sum_probs=23.9

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      |.++|+|..+||+.||||.+|++||+
T Consensus        17 l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_          17 LLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            35689999999999999999999996

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=98.30  E-value=1.8e-07  Score=47.39  Aligned_cols=27  Identities=26%  Similarity=0.460  Sum_probs=25.1

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      |.++|+++.+||+.+|||.+||||+++
T Consensus        14 L~~~G~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1          14 MWQQGLGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHh
Confidence            467899999999999999999999986

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=98.09  E-value=1.5e-06  Score=46.44  Aligned_cols=52  Identities=13%  Similarity=0.146  Sum_probs=39.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEI   71 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El   71 (77)
                      +.|+|..++|+.+|||++||++|     |+|...|.           +... .++..+..+|+..+..|
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~-----E~G~~~P~-----------~~~~-~ll~~l~~~Pe~v~~al   61 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDW-----EQGRSEPD-----------QPAR-AYLKIIAVDPEGTAAAL   61 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHH-----HTTSSCCC-----------HHHH-HHHHHHHHCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHH-----HCCCCCCC-----------HHHH-HHHHHHhcCHHHHHHHh
Confidence            47999999999999999999998     55655543           2222 45678889997766554

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=2.8e-06  Score=46.48  Aligned_cols=27  Identities=22%  Similarity=0.364  Sum_probs=23.9

Q ss_pred             cCC--CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          3 AAG--VRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         3 ~~G--~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      +.|  +|..+||+.|||+.|||+.|+++.
T Consensus        21 e~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1          21 EENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             HHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             HcCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            455  789999999999999999999874

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=97.87  E-value=8.9e-06  Score=43.53  Aligned_cols=38  Identities=18%  Similarity=0.198  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      .++..+||+.||||++||+..+++..+.|-|.-.|-+|
T Consensus        21 ~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~~Y~~   58 (61)
T d2ev0a1          21 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRG   58 (61)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----C
T ss_pred             CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEccCCC
Confidence            48899999999999999999999999999987766543

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.72  E-value=2.7e-05  Score=41.89  Aligned_cols=35  Identities=23%  Similarity=0.201  Sum_probs=32.1

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      .+..+||+.||||++||+..+++..+.|-|.-.+.
T Consensus        24 v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~~~y   58 (63)
T d2isya1          24 PLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD   58 (63)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             CcHHHHHHHhCCCchhHHHHHHHHHHCCCEEEcCC
Confidence            88999999999999999999999999999876553

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=97.62  E-value=3e-05  Score=44.59  Aligned_cols=57  Identities=12%  Similarity=0.083  Sum_probs=43.8

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC-CCCCHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP-RVATPDVERRIEE   58 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~~~~~i~~   58 (77)
                      .+..++.+++|+.||+|++||+.-++..++.|=|...+.|.... +...+...+.+..
T Consensus        33 ~~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~G~~~~Y~l~~~~i~~l~~~   90 (98)
T d1r1ta_          33 ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQN   90 (98)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEECCEEEEEEChHHHHHHHHH
Confidence            34558999999999999999999999999999999988775443 4444443333333

>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=97.62  E-value=2.6e-05  Score=43.81  Aligned_cols=56  Identities=16%  Similarity=0.090  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~   59 (77)
                      .++++.++|+++++|+++|+++++++.+.|-|.-.+.|....-.+|+.-.+.+.+.
T Consensus        20 ~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D~R~~~i~LT~~G~~~l~~~   75 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTE   75 (85)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeecccccccceECHHHHHHHHHH
Confidence            46999999999999999999999999999999764444222234666555544443

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.55  E-value=4e-05  Score=41.53  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=31.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ..+|..++|+.+|+|.+||++++..+-+.|-|..
T Consensus        18 g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1          18 GPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             CSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            4499999999999999999999999999998854

>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=97.54  E-value=4.1e-05  Score=40.84  Aligned_cols=30  Identities=13%  Similarity=0.163  Sum_probs=28.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      +|..++|+.||||.+||.+.++..++.|-.
T Consensus        20 ~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1          20 HSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            799999999999999999999999999963

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=97.50  E-value=4.5e-05  Score=40.60  Aligned_cols=36  Identities=17%  Similarity=0.268  Sum_probs=32.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +..+|..|+|+.+|+|.+||++.++.+.+.|-|...
T Consensus        10 ~~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~   45 (62)
T d2hoea1          10 KSPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEE   45 (62)
T ss_dssp             HSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            345899999999999999999999999999999443

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.48  E-value=2.6e-05  Score=45.65  Aligned_cols=48  Identities=17%  Similarity=0.143  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC-CCCCHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP-RVATPD   51 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~   51 (77)
                      .+++++++|+.|++|+++|+.-++..++.|=|...+.|.... +...+.
T Consensus        44 ~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~G~~~~Y~l~~~~   92 (108)
T d1u2wa1          44 EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEH   92 (108)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEESCHH
T ss_pred             CCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEEECCEEEEEECHHH
Confidence            348999999999999999999999999999999998876554 444443

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.45  E-value=5e-05  Score=43.05  Aligned_cols=57  Identities=12%  Similarity=0.151  Sum_probs=44.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYK   60 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v   60 (77)
                      ..++..++|+.|++|+++|++.+++..+.|=|...+..++++.   .+|+.-.+.+.+++
T Consensus        29 ~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~   88 (100)
T d1ub9a_          29 RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             CCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHHHHH
Confidence            3489999999999999999999999999999987765555552   46676555555554

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.44  E-value=0.00015  Score=42.25  Aligned_cols=56  Identities=11%  Similarity=0.024  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYK   60 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v   60 (77)
                      +++..++|+.++|++++|++.+++..+.|-+...+...+++.   .+|+.-.+.+.++.
T Consensus        49 ~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~  107 (115)
T d2frha1          49 EYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLL  107 (115)
T ss_dssp             EEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHHHHH
Confidence            389999999999999999999999999999988877666653   46676666665544

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.42  E-value=0.00021  Score=42.54  Aligned_cols=51  Identities=10%  Similarity=0.102  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|++..++|+.+++++++|++.+++..+.|=|.-.+..+++++   .+|+.-.+
T Consensus        49 ~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~  102 (141)
T d1lnwa_          49 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLA  102 (141)
T ss_dssp             TTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHH
Confidence            5799999999999999999999999999999977766666654   45665444

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.42  E-value=0.00022  Score=42.20  Aligned_cols=57  Identities=9%  Similarity=-0.012  Sum_probs=46.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYK   60 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v   60 (77)
                      .|++..+||+.+++++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.++.
T Consensus        48 ~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~  107 (125)
T d1p4xa2          48 NIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLL  107 (125)
T ss_dssp             CCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHHH
Confidence            4689999999999999999999999999999987777777764   46676666555554

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.29  E-value=0.00018  Score=38.18  Aligned_cols=30  Identities=17%  Similarity=0.125  Sum_probs=26.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..||||.+||...+.+-+.+
T Consensus        35 ~~~~s~~eIA~~lgis~~tv~~~~~ra~~~   64 (71)
T d1rp3a2          35 YEELPAKEVAKILETSVSRVSQLKAKALER   64 (71)
T ss_dssp             TSCCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             hHhCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            379999999999999999999999887653

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.25  E-value=0.00011  Score=43.78  Aligned_cols=42  Identities=29%  Similarity=0.375  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .+++..+||+.+|||+++|++.+++..+.|-|.-.+.+++++
T Consensus        40 ~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~drr   81 (151)
T d1ku9a_          40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERK   81 (151)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSS
T ss_pred             CCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCCc
Confidence            458999999999999999999999999999997666666665

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.24  E-value=0.00013  Score=41.63  Aligned_cols=57  Identities=19%  Similarity=0.142  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC-CCCCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP-RVATPDVERRIEEYK   60 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~-~~~~~~~~~~i~~~v   60 (77)
                      .-++.+++|..||+|+++|++-++..++-|=|...+.|.... +...+.....+.+++
T Consensus        30 ~~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~G~~~~Y~l~~~~v~~ll~~~l   87 (94)
T d1r1ua_          30 SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAI   87 (94)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECcHHHHHHHHHHH
Confidence            348999999999999999999999999999999888775443 444454444333333

>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=97.20  E-value=0.00019  Score=38.53  Aligned_cols=33  Identities=12%  Similarity=0.211  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      .++|..++|+.+|+|.+||++.++.+.+.|-|.
T Consensus        19 g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1          19 GPISRIDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            459999999999999999999999999999885

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.18  E-value=0.00019  Score=38.22  Aligned_cols=34  Identities=12%  Similarity=0.074  Sum_probs=29.4

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      .-.|+|..+||..++||.+||...+++.++.=.+
T Consensus        16 ~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_          16 LVQDKTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            3589999999999999999999999998765433

>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=97.17  E-value=0.00051  Score=40.77  Aligned_cols=52  Identities=15%  Similarity=0.215  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      ++++.++|++++|++++|++.+++..+.|-|.-.+...++++   .+|+.-.+.+
T Consensus        49 ~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~  103 (145)
T d2hr3a1          49 DVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNL  103 (145)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHH
Confidence            489999999999999999999999999999987776666654   4455544433

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=97.16  E-value=0.001  Score=39.05  Aligned_cols=64  Identities=8%  Similarity=0.042  Sum_probs=42.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      |++.++|+.+|||.+|+.-|-+.    |-+.|.+...+..+.=++.+..   .|..+..  =++++.||.+.+
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~~----GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~--~G~sl~eI~~~l   67 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEEK----GLVTPPMRSENGYRTYTQQHLNELTLLRQARQ--VGFNLEESGELV   67 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHT----TCSCCCEECTTSCEECCHHHHHHHHHHHHHHH--TTCCHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCccCCcCcccchHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            68899999999999999776544    9888754322222334444444   3445443  368888887654

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.15  E-value=0.00047  Score=41.09  Aligned_cols=51  Identities=20%  Similarity=0.225  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-.+
T Consensus        42 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~   95 (144)
T d1lj9a_          42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKN   95 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHH
T ss_pred             CCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHH
Confidence            5799999999999999999999999999999988777777653   34554333

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=97.14  E-value=0.001  Score=38.02  Aligned_cols=64  Identities=14%  Similarity=0.058  Sum_probs=44.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||.+|+.-|-    +.|-+.|.+...+..+.=++.+..   .|..+.+  =++++.|+.+.|
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~lr~--~G~sl~eI~~~l   69 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYD----NIELLNPSALTDAGYRLYSDADLERLQQILFFKE--IGFRLDEIKEML   69 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHH----HTTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHH--TTCCHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HcCCcCCcccCCcccccccHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            688999999999999998775    449998765432223344454444   3444443  369999998765

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=97.13  E-value=0.00013  Score=41.84  Aligned_cols=35  Identities=14%  Similarity=0.179  Sum_probs=31.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      +++..++|+++++|++||++.+++..+.|=|.-.+
T Consensus        36 ~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          36 PITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEee
Confidence            38999999999999999999999999999885444

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=97.11  E-value=0.00071  Score=39.83  Aligned_cols=53  Identities=11%  Similarity=0.103  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .++++.++|+.++||+++|++.+++..+.|-|...+...+++.   .+|+.-.+.+
T Consensus        45 ~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~  100 (140)
T d2etha1          45 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIF  100 (140)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHH
Confidence            4589999999999999999999999999999987777666653   4455444433

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=97.11  E-value=0.00036  Score=36.99  Aligned_cols=29  Identities=21%  Similarity=0.192  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      -.|+|..+||..+|||.+||...+.+-+.
T Consensus        32 ~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1          32 LDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             TTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            37999999999999999999999988764

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=97.10  E-value=0.00019  Score=37.86  Aligned_cols=25  Identities=12%  Similarity=0.106  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||++||++|-+
T Consensus        14 ~~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_          14 ALKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHhHHHHHHC
Confidence            4799999999999999999999943

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=97.10  E-value=0.00022  Score=38.07  Aligned_cols=33  Identities=18%  Similarity=0.297  Sum_probs=29.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..|+|..+||+.++||.+||...+++..+.=.+
T Consensus        19 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1          19 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            479999999999999999999999998875544

>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=97.09  E-value=0.00023  Score=38.95  Aligned_cols=36  Identities=22%  Similarity=0.209  Sum_probs=32.9

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.|+||.+||.+-+++....|-+...+..|
T Consensus        24 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   59 (78)
T d3bwga1          24 VLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSG   59 (78)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCcE
Confidence            789999999999999999999999999998886544

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.09  E-value=0.00034  Score=40.66  Aligned_cols=56  Identities=9%  Similarity=0.050  Sum_probs=43.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~   59 (77)
                      .|+++.+||+.+++++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.++
T Consensus        47 ~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~  105 (115)
T d1hsja1          47 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKL  105 (115)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHHHHH
Confidence            4699999999999999999999999999999987776666653   3455444444443

>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=97.08  E-value=0.00074  Score=39.68  Aligned_cols=37  Identities=5%  Similarity=0.109  Sum_probs=33.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ..+|..+||+.+++|+++|.|+++..+..|=|...+.
T Consensus        17 ~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG   53 (127)
T d1xd7a_          17 EKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAG   53 (127)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCC
Confidence            3589999999999999999999999999998876653

>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=97.07  E-value=0.0004  Score=36.81  Aligned_cols=34  Identities=18%  Similarity=0.206  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcC-CCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~-v~pk   38 (77)
                      .++..++|+.|+||..||.|-++...+.|- +...
T Consensus        22 ~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~~~   56 (65)
T d1j5ya1          22 PVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVAT   56 (65)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEE
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEEe
Confidence            379999999999999999999999999996 5443

>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=97.07  E-value=0.00039  Score=37.83  Aligned_cols=36  Identities=17%  Similarity=0.146  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+.+|+++||++|+++-..+.|-+...+
T Consensus        19 ~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~   54 (75)
T d1mkma1          19 GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK   54 (75)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            569999999999999999999999999999998654

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=97.07  E-value=0.00081  Score=37.39  Aligned_cols=56  Identities=11%  Similarity=0.060  Sum_probs=41.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDR   74 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~   74 (77)
                      +.|++..++|+++|||.+++++|     |+|.-.|.           ......|-+...-.|+.+..++.+.
T Consensus        23 ~~gltq~~lA~~lgis~~~is~~-----E~g~~~~s-----------~~~l~~ia~~l~v~~~~~~~~~~~~   78 (87)
T d1lmb3_          23 ELGLSQESVADKMGMGQSGVGAL-----FNGINALN-----------AYNAALLAKILKVSVEEFSPSIARE   78 (87)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHH-----HTTSSCCC-----------HHHHHHHHHHHTSCGGGTCHHHHHH
T ss_pred             HcCCCHHHHHHHhCccHHHHHHH-----HhccCCCc-----------HHHHHHHHHHHCCCHHHHChhHHHH
Confidence            46999999999999999999998     55643322           3356667788888887776665544

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.01  E-value=0.00032  Score=36.87  Aligned_cols=40  Identities=18%  Similarity=0.169  Sum_probs=29.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      +..|||+..|||.+||+|.+..   .+.             ..++.++.|++.+++
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~---~~~-------------vs~~tr~rV~~~a~~   41 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK---TRF-------------VAEETRNAVWAAIKE   41 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT---CSC-------------CCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC---CCc-------------cCHHHHHHHHHHHHH
Confidence            5789999999999999999963   111             335567777777665

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=97.00  E-value=0.00031  Score=37.18  Aligned_cols=31  Identities=16%  Similarity=0.323  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      +|.+++|+.+|+|.+||.+=++++.+.|-+.
T Consensus        20 ~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1          20 LSMRELGRKIKLSPPSVTERVRQLESFGIIK   50 (63)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            8999999999999999999999999999774

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.00  E-value=0.00036  Score=36.95  Aligned_cols=34  Identities=18%  Similarity=0.009  Sum_probs=29.1

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ...|+|..+||.+++||.+||...+++.++.=.+
T Consensus        16 ~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   49 (65)
T d1l3la1          16 IAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV   49 (65)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            3579999999999999999999999988765433

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=96.98  E-value=0.00028  Score=37.31  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=22.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|+|..++|+++|||.+++++|-
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e   35 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIE   35 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHH
Confidence            479999999999999999999986

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=96.96  E-value=0.0003  Score=38.09  Aligned_cols=27  Identities=19%  Similarity=0.148  Sum_probs=24.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      +.|+|..++|+.||||..||++|     |+|.
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~y-----E~G~   38 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYY-----RTAH   38 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHH-----HTTS
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHH-----HcCC
Confidence            47999999999999999999998     6664

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.95  E-value=0.00059  Score=39.98  Aligned_cols=42  Identities=10%  Similarity=0.224  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|+++.++|+.+++++++|++.+++..+.|-|.-.+...+++
T Consensus        42 ~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~D~R   83 (137)
T d2fbha1          42 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRR   83 (137)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTTBC
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCCCCC
Confidence            478999999999999999999999999999998776666655

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.95  E-value=0.00035  Score=41.24  Aligned_cols=44  Identities=16%  Similarity=0.223  Sum_probs=38.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~   46 (77)
                      ..|+++.++|+.++|++++|++.+++..+.|=|.-.+...+++.
T Consensus        45 ~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~D~R~   88 (137)
T d1z91a1          45 HETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERS   88 (137)
T ss_dssp             HSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSSCTTS
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecCCCCCe
Confidence            36799999999999999999999999999999987776666653

>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=96.93  E-value=0.00033  Score=38.22  Aligned_cols=35  Identities=14%  Similarity=0.140  Sum_probs=31.8

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG   41 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g   41 (77)
                      |.+++|+.|+||.+||.+-+++..+.|-+.-.+..
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~g~   63 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGK   63 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEeCc
Confidence            78999999999999999999999999999877543

>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=96.93  E-value=0.00091  Score=39.05  Aligned_cols=50  Identities=12%  Similarity=0.153  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER   54 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~   54 (77)
                      ++++.++|+.+++++++|++++++..+.|=|...+...+++.   .+|+.-.+
T Consensus        45 ~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~   97 (135)
T d3broa1          45 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANK   97 (135)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHT
T ss_pred             CCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHH
Confidence            389999999999999999999999999999977766555543   45554443

>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=96.91  E-value=6.6e-05  Score=43.41  Aligned_cols=36  Identities=28%  Similarity=0.398  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .+++..+||+.+||++++|++.+++..+.|=|.-.+
T Consensus        33 g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~   68 (109)
T d1sfxa_          33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEe
Confidence            458999999999999999999999999999996543

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=96.91  E-value=0.00049  Score=40.67  Aligned_cols=42  Identities=21%  Similarity=0.315  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|++..++|+.+++++++|++++++..+.|-|.-.+...+++
T Consensus        47 ~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~D~R   88 (138)
T d1jgsa_          47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKR   88 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSS
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccCCCC
Confidence            579999999999999999999999999999997666655554

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=96.90  E-value=0.00041  Score=37.03  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|+.++|+.+|||+++|++|..
T Consensus        17 ~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          17 NSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            5799999999999999999999964

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.90  E-value=0.00056  Score=35.80  Aligned_cols=34  Identities=24%  Similarity=0.303  Sum_probs=30.8

Q ss_pred             cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ++| +|..++|+++|+|.++|.+=+++..+.|-+.
T Consensus        14 ~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1          14 KDARTPFTEIAKKLGISETAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             HCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            345 7999999999999999999999999999774

>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=96.90  E-value=0.00092  Score=39.45  Aligned_cols=52  Identities=12%  Similarity=0.161  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|++..++|+.+++++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        48 ~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~  102 (143)
T d1s3ja_          48 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIK  102 (143)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHH
Confidence            4689999999999999999999999999999987776666653   455554443

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=96.90  E-value=0.00031  Score=39.39  Aligned_cols=25  Identities=20%  Similarity=0.234  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+++|||+++|++|.+
T Consensus        22 ~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          22 RARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            4799999999999999999999975

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.89  E-value=0.00033  Score=36.96  Aligned_cols=23  Identities=26%  Similarity=0.239  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ++..|||+..|||.+||++.+.-
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~   23 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVING   23 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            46789999999999999999974

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=96.89  E-value=0.0005  Score=36.96  Aligned_cols=34  Identities=15%  Similarity=0.130  Sum_probs=29.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      -.|++..+||..++||.+||...+.+.++.=.+.
T Consensus        25 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   58 (70)
T d1yioa1          25 IRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVR   58 (70)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            4799999999999999999999999988754443

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.88  E-value=0.00046  Score=36.39  Aligned_cols=31  Identities=16%  Similarity=0.268  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      +|..++|+.+|+|.++|.+=++++.+.|-+.
T Consensus        20 ~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1          20 TAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            8999999999999999999999999999774

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=96.87  E-value=0.00035  Score=36.66  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=30.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE   62 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~   62 (77)
                      ++..|||+..|||.+||+|.+..   .+.             ..++.++.|.+.+++
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~---~~~-------------Vs~~tr~rV~~aa~~   42 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNG---NPN-------------VKPSTRKKVLETIER   42 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT---CTT-------------SCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCC---CCc-------------CCHHHHHHHHHHHHH
Confidence            46789999999999999999863   111             345566777766665

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=96.87  E-value=0.00061  Score=40.16  Aligned_cols=52  Identities=21%  Similarity=0.222  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|.++.+||++++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        43 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~   97 (139)
T d2a61a1          43 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEV   97 (139)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHH
T ss_pred             CCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHH
Confidence            4799999999999999999999999999999976665555542   455544443

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.85  E-value=0.00066  Score=35.40  Aligned_cols=31  Identities=16%  Similarity=0.293  Sum_probs=29.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      +|..++|+++|+|.++|.+=+++..+.|-+.
T Consensus        18 ~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1          18 APLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            7999999999999999999999999999775

>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=96.85  E-value=0.00042  Score=40.80  Aligned_cols=42  Identities=7%  Similarity=0.245  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP   45 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~   45 (77)
                      .|+++.++|..++|++++|++.+++..+.|-|.-.+.+.+++
T Consensus        45 ~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~D~R   86 (140)
T d3deua1          45 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRR   86 (140)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-------
T ss_pred             CCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCCCCC
Confidence            468999999999999999999999999999998776665554

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=96.84  E-value=0.0005  Score=38.34  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|.+
T Consensus        12 ~~glsq~~LA~~lGvs~~~is~ie~   36 (87)
T d2icta1          12 ELNVSLREFARAMEIAPSTASRLLT   36 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHhhcHHHHHHHHH
Confidence            3699999999999999999999975

>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=96.81  E-value=0.00058  Score=36.55  Aligned_cols=37  Identities=19%  Similarity=0.145  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      ++.+++|+.||||.+||.+-+++..+.|-+...+..|
T Consensus        26 l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~~G   62 (69)
T d2hs5a1          26 LSEPDICAALDVSRNTVREAFQILIEDRLVAHELNRG   62 (69)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCCE
Confidence            5789999999999999999999999999998776543

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=96.81  E-value=0.00044  Score=37.63  Aligned_cols=27  Identities=7%  Similarity=-0.021  Sum_probs=21.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ...++|+.||||..||..|+++    |-...
T Consensus         4 nk~~lA~iFGVS~~TI~~W~~~----G~Pv~   30 (68)
T d1j9ia_           4 NKKQLADIFGASIRTIQNWQEQ----GMPVL   30 (68)
T ss_dssp             EHHHHHHHTTCCHHHHHHHTTT----TCCCS
T ss_pred             CHHHHHHHhCCCHHHHHHHHHC----CCCee
Confidence            3568999999999999999754    65443

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=96.80  E-value=0.00048  Score=36.58  Aligned_cols=24  Identities=13%  Similarity=0.124  Sum_probs=22.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|+|+.++|+++|||.+++++|-
T Consensus        20 ~~gltq~~lA~~~gis~~~i~~~E   43 (69)
T d1y7ya1          20 AKGLSQETLAFLSGLDRSYVGGVE   43 (69)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHhHhCCCHHHHHHHH
Confidence            479999999999999999999994

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.80  E-value=0.00083  Score=39.10  Aligned_cols=30  Identities=20%  Similarity=0.205  Sum_probs=26.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..+|||.+||...+.|-+..
T Consensus        30 ~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~   59 (106)
T d1s7oa_          30 ADDYSLAEIADEFGVSRQAVYDNIKRTEKI   59 (106)
T ss_dssp             HTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            379999999999999999999888776543

>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=96.77  E-value=0.001  Score=38.98  Aligned_cols=56  Identities=9%  Similarity=-0.035  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYK   60 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v   60 (77)
                      +++..+||+.+++++++|++.+++..+.|=|.-.+...+++.   .+|+.-.+.+.+++
T Consensus        50 ~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~  108 (125)
T d1p4xa1          50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERV  108 (125)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHHHHHH
Confidence            489999999999999999999999999999977766666664   46676666655554

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.71  E-value=0.00061  Score=35.97  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|++.|||++++++|-+
T Consensus        12 ~~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2          12 EKGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4799999999999999999999965

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=96.70  E-value=0.00064  Score=35.32  Aligned_cols=25  Identities=8%  Similarity=0.319  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|-+
T Consensus        12 ~~g~sq~elA~~~gvs~~~is~~E~   36 (63)
T d1r69a_          12 QLGLNQAELAQKVGTTQQSIEQLEN   36 (63)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCcHHHHHHHhCcCHHHHHHHHC
Confidence            4799999999999999999999853

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.69  E-value=0.00072  Score=36.89  Aligned_cols=24  Identities=4%  Similarity=0.122  Sum_probs=22.2

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ..|+|..++|+.+|||.+++++|-
T Consensus        17 ~~gltq~~lA~~~gis~~~is~~E   40 (78)
T d1x57a1          17 SKGLTQKDLATKINEKPQVIADYE   40 (78)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCChhHHHHcCCCCHHHHHHHH
Confidence            479999999999999999999984

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=96.66  E-value=0.0015  Score=40.07  Aligned_cols=60  Identities=13%  Similarity=0.007  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHHHHHHhC
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIEEYKGEN   63 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~~~v~~~   63 (77)
                      .|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.   .+|+.-.+.+.+..+..
T Consensus        54 ~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  116 (162)
T d2fxaa1          54 NGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  116 (162)
T ss_dssp             TSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             CCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHHHHHHH
Confidence            5789999999999999999999999999999987766666653   45676566565555543

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.64  E-value=0.0011  Score=35.72  Aligned_cols=34  Identities=18%  Similarity=0.157  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhcc-CHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~V-S~stv~r~~~r~r~tG~v~pk~   39 (77)
                      -|.++||+.||+ |++||.+.++++.+.|-+.-.+
T Consensus        25 Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          25 PTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             CCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCC
Confidence            467899999999 8999999999999999997653

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.63  E-value=0.0013  Score=34.84  Aligned_cols=32  Identities=19%  Similarity=0.256  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..++|..+|+|..||+|.++++++.|-+.-
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~~   61 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLISA   61 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            78999999999999999999999999998764

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.62  E-value=0.00042  Score=40.84  Aligned_cols=44  Identities=18%  Similarity=0.222  Sum_probs=38.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR   46 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~   46 (77)
                      ..|+++.++|..++|+++++++.+++..+.|-|.-.+...+++.
T Consensus        46 ~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~D~R~   89 (136)
T d2bv6a1          46 ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQRE   89 (136)
T ss_dssp             SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTC
T ss_pred             CCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCCcccc
Confidence            35789999999999999999999999999999987776666653

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=96.61  E-value=0.0016  Score=35.30  Aligned_cols=34  Identities=21%  Similarity=0.140  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      .++..++|.-+|||..||+|.++.+++.|-+.-.
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Confidence            4789999999999999999999999999998754

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=96.55  E-value=0.00043  Score=36.41  Aligned_cols=28  Identities=14%  Similarity=0.235  Sum_probs=24.4

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +.|-...++|+.||||.+|.++.+++|.
T Consensus        31 ~~~gn~~~aA~~LGIsR~TL~rkmkky~   58 (60)
T d1umqa_          31 MCDRNVSETARRLNMHRRTLQRILAKRS   58 (60)
T ss_dssp             HTTSCHHHHHHHHTSCHHHHHHHHHTSS
T ss_pred             HhcCcHHHHHHHHCCCHHHHHHHHHHcC
Confidence            4566788999999999999999999873

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=96.55  E-value=0.0022  Score=36.98  Aligned_cols=64  Identities=11%  Similarity=-0.097  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc---cCCCCC-CCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV---IGGSKP-RVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~---~gg~~~-~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +++.++|+.+|||..|+.-|-+    .|-+.|..   .+|.|- +...-.....|..+.+  =++++.||.+.+
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~----~GLl~P~~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~g~sl~eIk~~l   71 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDK----IDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKY--IGTPLEEMKKAQ   71 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHH----TTSSCCSEECTTTCCEEEETGGGGHHHHHHHHHH--TTCCHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----cCCcccccccCCCCcccccHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            5788999999999999977653    49898843   345443 3333334556666654  369999987654

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.53  E-value=0.00077  Score=35.56  Aligned_cols=42  Identities=19%  Similarity=0.220  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN   63 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~   63 (77)
                      .+..|||+..|||++||++.+...   +            . ..++.++.|.+.+++.
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~~~---~------------~-vs~~tr~rI~~~a~~l   44 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVNQA---S------------H-VSAKTREKVEAAMAEL   44 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHTTC---S------------S-CCTHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCC---C------------c-CCHHHHHHHHHHHHHH
Confidence            578899999999999999998531   1            1 2345677788777664

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=96.52  E-value=0.0019  Score=38.30  Aligned_cols=35  Identities=9%  Similarity=0.114  Sum_probs=31.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      ++..+||++++||+.++.|+++..++.|=|...+.
T Consensus        24 vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG   58 (138)
T d1ylfa1          24 CTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG   58 (138)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecC
Confidence            78999999999999999999999999999866543

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=96.46  E-value=0.0011  Score=34.72  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|++..++|+.+|||++++++|.+
T Consensus        14 ~~g~tq~~lA~~~gvs~~~i~~~e~   38 (66)
T d2r1jl1          14 KLKIRQAALGKMVGVSNVAISQWER   38 (66)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4699999999999999999999964

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=96.46  E-value=0.0017  Score=35.15  Aligned_cols=32  Identities=3%  Similarity=0.024  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ++..++|..+|+|..||+|.++++++.|-+.-
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            68899999999999999999999999998874

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=96.45  E-value=0.002  Score=37.45  Aligned_cols=30  Identities=17%  Similarity=0.133  Sum_probs=26.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      -.|+|..+||..+|||.++|...+.|-+..
T Consensus        32 ~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~   61 (106)
T d1xsva_          32 LEDYSLSEIADTFNVSRQAVYDNIRRTGDL   61 (106)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HhCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            379999999999999999999988876643

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=96.44  E-value=0.0021  Score=34.69  Aligned_cols=31  Identities=32%  Similarity=0.339  Sum_probs=29.6

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR   36 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~   36 (77)
                      ++..++|..+|+|..||+|.++.+++.|-+.
T Consensus        28 lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6889999999999999999999999999886

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=96.42  E-value=0.0012  Score=35.50  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=22.7

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.|+|..++|+.+|||++++++|-+
T Consensus        21 ~~gltq~~lA~~~gis~~~i~~~e~   45 (77)
T d2b5aa1          21 QKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4699999999999999999999854

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=96.38  E-value=0.0022  Score=34.69  Aligned_cols=33  Identities=18%  Similarity=0.196  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      -++..++|..+|+|..||+|.++++++.|-+.-
T Consensus        30 ~lt~~elA~~~g~sretvsr~l~~l~~~glI~~   62 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRVLASLKRENILDK   62 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            468899999999999999999999999998764

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.37  E-value=0.00056  Score=42.06  Aligned_cols=52  Identities=23%  Similarity=0.216  Sum_probs=37.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERR   55 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~   55 (77)
                      .|+++.++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|+.-.+.
T Consensus        78 ~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l  132 (172)
T d2fbka1          78 EGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRAL  132 (172)
T ss_dssp             SCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHH
Confidence            4689999999999999999999999999999987776555543   345543333

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.00078  Score=39.03  Aligned_cols=28  Identities=14%  Similarity=0.208  Sum_probs=24.7

Q ss_pred             ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          2 AAAGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+.|.|..+||++||+|.++|++.++-.
T Consensus        27 ~~~g~s~~eiA~~~G~s~~~V~~~l~L~   54 (114)
T d1r71a_          27 LAKGKKKGDIAKEIGKSPAFITQHVTLL   54 (114)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             HHhCCCHHHHHHHHCCcHHHHHHHHHHh
Confidence            3569999999999999999999998754

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=96.31  E-value=0.0013  Score=36.59  Aligned_cols=31  Identities=19%  Similarity=0.058  Sum_probs=27.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG   33 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG   33 (77)
                      ..|++..+||..|+||.+||...+++.++.=
T Consensus        35 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   65 (87)
T d1p4wa_          35 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKL   65 (87)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence            4799999999999999999999999888653

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=96.27  E-value=0.0016  Score=35.08  Aligned_cols=25  Identities=16%  Similarity=0.167  Sum_probs=22.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ..|+|..++|+++|||++++++|-+
T Consensus        19 ~~g~sq~~lA~~~gis~~~i~~~E~   43 (79)
T d1y9qa1          19 SRGLSLDATAQLTGVSKAMLGQIER   43 (79)
T ss_dssp             HTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcchhHHHHHHc
Confidence            4799999999999999999999853

>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=96.22  E-value=0.0018  Score=37.88  Aligned_cols=53  Identities=13%  Similarity=0.162  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRI   56 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i   56 (77)
                      .|++..++|+.++|++++|++.+++..+.|-|.-.+...+++.   .+|++-.+.+
T Consensus        43 ~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~   98 (136)
T d2fbia1          43 GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCF   98 (136)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHH
Confidence            4689999999999999999999999999999977766666543   4555544433

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=96.18  E-value=0.002  Score=35.72  Aligned_cols=25  Identities=16%  Similarity=0.061  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      -+|..++|+..+||++||.|..+.+
T Consensus        36 ~~si~~lA~~~~vS~sTi~Rf~kkl   60 (83)
T d2o3fa1          36 ESTVNEISALANSSDAAVIRLCKSL   60 (83)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HccHHHHHHHHCCCHHHHHHHHHHh
Confidence            4789999999999999999999874

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=96.08  E-value=0.004  Score=35.33  Aligned_cols=28  Identities=18%  Similarity=0.284  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      +|.+..++|++|++|..+|++++++.+.
T Consensus        65 ~G~n~~eLA~kY~lS~~~I~~Ii~~~rk   92 (94)
T d1rr7a_          65 NGRNVSELTTRYGVTFNTVYKAIRRMRR   92 (94)
T ss_dssp             CSSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            6999999999999999999999999875

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=96.00  E-value=0.002  Score=36.55  Aligned_cols=28  Identities=18%  Similarity=0.273  Sum_probs=24.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +-|++..+||++||.|+++|++.++-..
T Consensus        17 e~g~t~~~iA~~~Gks~~~V~~~LrLl~   44 (93)
T d1vz0a1          17 EMGLTQEEVARRVGKARSTVANALRLLQ   44 (93)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHGGG
T ss_pred             HcCCCHHHHHHHHccchHHHHHHHHHHH
Confidence            4689999999999999999999887543

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.96  E-value=0.0043  Score=34.36  Aligned_cols=46  Identities=15%  Similarity=0.055  Sum_probs=32.1

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|++++||+++|++.++++.+. |.---...|  ++-..|++
T Consensus        19 ~~g-s~t~AA~~l~isq~avs~~l~~lE~~~g~~Lf~R~~--~~~~lT~~   65 (89)
T d2esna1          19 RHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQG--NRMQPTQR   65 (89)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEEET--TEEEECHH
T ss_pred             HhC-CHHHHHHHHCCCCcHhhHHHHHHHhcCCceeEEECC--CceeECHH
Confidence            344 78899999999999999999999854 443333222  33345554

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=95.94  E-value=0.0013  Score=34.61  Aligned_cols=25  Identities=24%  Similarity=0.402  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .| +.+++|+.||||.+|+++-+++|
T Consensus        33 ~g-n~~~aA~~Lgisr~tL~rKlkk~   57 (61)
T d1g2ha_          33 YP-STRKLAQRLGVSHTAIANKLKQY   57 (61)
T ss_dssp             SC-SHHHHHHHTTSCTHHHHHHHHTT
T ss_pred             CC-CHHHHHHHHCCCHHHHHHHHHHh
Confidence            45 67899999999999999999886

>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=95.88  E-value=0.00075  Score=38.55  Aligned_cols=36  Identities=22%  Similarity=0.190  Sum_probs=32.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      |.+++|+.|+||.+||.+-+++..+.|-|...+..|
T Consensus        35 s~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   70 (100)
T d1v4ra1          35 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGALG   70 (100)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETTTE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCCE
Confidence            789999999999999999999999999998776543

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.86  E-value=0.0021  Score=40.06  Aligned_cols=36  Identities=25%  Similarity=0.230  Sum_probs=32.0

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +.-++..++|..||||+++|++-++...+.|-|...
T Consensus        26 ~~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~   61 (194)
T d2p4wa1          26 KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESR   61 (194)
T ss_dssp             HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            344899999999999999999999999999999643

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=95.70  E-value=0.0029  Score=35.51  Aligned_cols=26  Identities=15%  Similarity=0.284  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .+-...++|+.||||.+|.++.+++|
T Consensus        61 ~~gn~~~aA~~LGisR~tL~~klk~~   86 (89)
T d1etxa_          61 TRGNATRAALMMGINRGTLRKKLKKY   86 (89)
T ss_dssp             TTTCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             cCCcHHHHHHHHCCCHHHHHHHHHHh
Confidence            45578899999999999999999987

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=95.47  E-value=0.0046  Score=32.75  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=21.6

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +...+|+-||||++.|+.|       |.+-|.
T Consensus        12 ~~~k~A~algis~~AVsqW-------Ge~VPe   36 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW-------KEVIPE   36 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC-------CSBCCH
T ss_pred             CHHHHHHHhCCCHHHHHHH-------hccCcH
Confidence            5678999999999999999       776665

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.30  E-value=0.0052  Score=37.76  Aligned_cols=36  Identities=11%  Similarity=0.154  Sum_probs=32.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      +..++..+||+.+|+|+++|++-++...+.|-|...
T Consensus        30 ~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~   65 (190)
T d1ulya_          30 NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   65 (190)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            345899999999999999999999999999998543

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=95.16  E-value=0.0072  Score=34.88  Aligned_cols=26  Identities=12%  Similarity=0.176  Sum_probs=22.3

Q ss_pred             CC-CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513          4 AG-VRPCVISRQLRVSHGCVSKILNRY   29 (77)
Q Consensus         4 ~G-~s~~~iA~rf~VS~stv~r~~~r~   29 (77)
                      .| +|.++||+.+|||.+||.|--+-.
T Consensus        56 ~G~~s~reI~~~~gvs~aTItR~s~~L   82 (101)
T d1jhga_          56 RGEMSQRELKNELGAGIATITRGSNSL   82 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCChHHHHHHHHHH
Confidence            57 899999999999999999865543

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=95.11  E-value=0.011  Score=32.06  Aligned_cols=35  Identities=11%  Similarity=0.214  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk   38 (77)
                      ++.++.+||+.|||+.+.|.|-+=.+.+.|.|.--
T Consensus        23 ~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~   57 (70)
T d1sfua_          23 DYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   57 (70)
T ss_dssp             CEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecC
Confidence            45889999999999999999999999999999644

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.95  E-value=0.0058  Score=33.88  Aligned_cols=26  Identities=12%  Similarity=0.000  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +-...++|+.||||.+|+++-+++|-
T Consensus        64 ~Gn~~~AA~~LGI~R~TL~~Klk~~g   89 (91)
T d1ntca_          64 QGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             TTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHC
Confidence            44667899999999999999999984

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=94.93  E-value=0.015  Score=33.08  Aligned_cols=34  Identities=12%  Similarity=0.161  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHhccC-HHHHHHHHHHHHHhcCCCcc
Q psy15513          5 GVRPCVISRQLRVS-HGCVSKILNRYQETGSIRPG   38 (77)
Q Consensus         5 G~s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~pk   38 (77)
                      .+|..++|..+|+| ..||+|.++.+++.|-+.-.
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~~   65 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYK   65 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEEc
Confidence            47899999999997 79999999999999988854

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=94.86  E-value=0.014  Score=30.46  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .++|..+||++.|||++++++..+
T Consensus        19 ~~~ti~~Ia~~agvs~~~~Y~~F~   42 (69)
T d2i10a1          19 EGTSITDLTKALGINPPSLYAAFG   42 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChhHHHHHCc
Confidence            468999999999999999998764

>d2ezla_ a.4.1.2 (A:) Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=94.72  E-value=0.012  Score=33.85  Aligned_cols=29  Identities=14%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             ccCCCCHHH----HHHHhccCHHHHHHHHHHHH
Q psy15513          2 AAAGVRPCV----ISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         2 ~~~G~s~~~----iA~rf~VS~stv~r~~~r~r   30 (77)
                      .++|++...    +|..|+||.+|+.+|..+..
T Consensus        46 ~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~~V~   78 (99)
T d2ezla_          46 LNQGISTKTAFATVAGHYQVSASTLRDKYYQVQ   78 (99)
T ss_dssp             HHTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHcCCcHHHHHHHHHHHhCCCHHHHHHHHHHHC
Confidence            346766654    68999999999999998643

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.70  E-value=0.013  Score=30.74  Aligned_cols=24  Identities=8%  Similarity=0.002  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|.++||++.|||++|+++...
T Consensus        22 ~~~t~~~Ia~~agvs~~t~Y~~F~   45 (73)
T d1t56a1          22 ADISVDDLAKGAGISRPTFYFYFP   45 (73)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCc
Confidence            458999999999999999998753

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=94.54  E-value=0.0098  Score=30.58  Aligned_cols=24  Identities=13%  Similarity=0.194  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|.++||++.|||+++++++..
T Consensus        18 ~~~s~~~Ia~~agvs~~tiy~~F~   41 (62)
T d2vkva1          18 EGLTTRKLAQKLGVEQPTLYWHVK   41 (62)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHSC
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCC
Confidence            358999999999999999998754

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.50  E-value=0.019  Score=29.98  Aligned_cols=24  Identities=13%  Similarity=0.052  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|.++||+..|||++++++...
T Consensus        20 ~~~s~~~Ia~~agvs~~~~y~~F~   43 (71)
T d1jt6a1          20 NATTTGEIVKLSESSKGNLYYHFK   43 (71)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHHS
T ss_pred             cccCHHHHHHHHCcCHhHHHHHCc
Confidence            468999999999999999998764

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.41  E-value=0.018  Score=31.55  Aligned_cols=23  Identities=13%  Similarity=0.108  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .|++..++|++.|||++++++|=
T Consensus        24 ~~~t~~eLA~~~Gvs~~~ls~iE   46 (82)
T d2ofya1          24 GDMSMVTVAFDAGISVETLRKIE   46 (82)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCHHHHHHHHcCCHHHHHHHH
Confidence            57899999999999999999983

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.40  E-value=0.019  Score=30.53  Aligned_cols=24  Identities=17%  Similarity=0.128  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +|+|.++||++.|||.+++++...
T Consensus        23 ~~~ti~~Ia~~agvs~~s~y~~F~   46 (79)
T d2fbqa1          23 AETSLRLITSKAGVNLAAVNYHFG   46 (79)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHTC
T ss_pred             ccccHHHHHHHHCcChhHHHHHCc
Confidence            569999999999999999998764

>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=94.38  E-value=0.026  Score=31.01  Aligned_cols=46  Identities=15%  Similarity=0.192  Sum_probs=30.5

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD   51 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~   51 (77)
                      +.| |...+|+.++||+++|++-+++..+. |.----+.  ++.-..|++
T Consensus        14 e~g-s~~~AA~~L~isq~avs~~i~~LE~~lg~~Lf~R~--~~~~~lT~~   60 (89)
T d1ixca1          14 EAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLERS--HRGIELTAA   60 (89)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC-------CCBCHH
T ss_pred             HhC-CHHHHHHHhCCChHHHHHHHHHHHhcCCceeeEec--CCccCccHh
Confidence            344 78899999999999999999998854 44333322  233345654

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=94.23  E-value=0.013  Score=30.65  Aligned_cols=23  Identities=13%  Similarity=0.112  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +|+|.++||++.|||++++++..
T Consensus        22 ~~~t~~~Ia~~agvs~~~iy~hF   44 (68)
T d1z0xa1          22 EQLSMRKVAKQLGVQAPAIYWYF   44 (68)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHTTC
T ss_pred             cccCHHHHHHHHCcchhHHHHhc
Confidence            35899999999999999999754

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.14  E-value=0.024  Score=29.40  Aligned_cols=24  Identities=13%  Similarity=0.077  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|.++||+..|||++|++++..
T Consensus        19 ~~~si~~Ia~~agvs~~t~Y~~F~   42 (70)
T d2gena1          19 DATTIEMIRDRSGASIGSLYHHFG   42 (70)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHTC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCC
Confidence            468999999999999999998754

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.10  E-value=0.024  Score=29.70  Aligned_cols=22  Identities=18%  Similarity=0.071  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      |.|..+||++.|||+++++++.
T Consensus        20 ~~t~~~Ia~~agvs~~~~Y~~F   41 (70)
T d2hkua1          20 GVPITQICAAAGAHPNQVTYYY   41 (70)
T ss_dssp             TSCHHHHHHHHTCCHHHHHHHH
T ss_pred             CchHHHHHHHHCCChhhHHhcC
Confidence            5899999999999999999987

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=94.10  E-value=0.02  Score=30.53  Aligned_cols=24  Identities=13%  Similarity=0.041  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|..+||++.|||.+|++++..
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~F~   49 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRNFP   49 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCc
Confidence            468999999999999999998753

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=94.09  E-value=0.024  Score=29.56  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|..+||++.|||++++++...
T Consensus        23 ~~~t~~~Ia~~agvs~~~~y~~F~   46 (69)
T d2fq4a1          23 KAVTVDKIAERAKVSKATIYKWWP   46 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCC
Confidence            468999999999999999998753

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=94.05  E-value=0.024  Score=29.71  Aligned_cols=24  Identities=21%  Similarity=0.095  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|.++||+..|||++|+++...
T Consensus        23 ~~~ti~~Ia~~agvs~~t~y~~F~   46 (72)
T d1pb6a1          23 HGTRLEQIAELAGVSKTNLLYYFP   46 (72)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHSS
T ss_pred             cccCHHHHHHHhCCChHHHHHHCc
Confidence            468999999999999999998753

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=94.05  E-value=0.021  Score=30.21  Aligned_cols=24  Identities=13%  Similarity=0.236  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .++|.++||++.|||.+++++...
T Consensus        25 ~~~s~~~Ia~~agvs~~~lY~~F~   48 (77)
T d2gfna1          25 SAVTTRAVAEESGWSTGVLNHYFG   48 (77)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHTS
T ss_pred             cccCHHHHHHHHCCCHHHHHHHCc
Confidence            458999999999999999998753

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=93.99  E-value=0.023  Score=30.01  Aligned_cols=24  Identities=21%  Similarity=0.247  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|.++||++.|||++++++..+
T Consensus        23 ~~~si~~Ia~~agvs~~~~Y~~F~   46 (73)
T d2fx0a1          23 EGTSIQEIAKEAKVNVAMASYYFN   46 (73)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             ccCcHHHHHHHHCcChhHHHHHCc
Confidence            468999999999999999998765

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.97  E-value=0.026  Score=29.49  Aligned_cols=24  Identities=13%  Similarity=0.088  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|.++||+..|||+++++.+..
T Consensus        24 ~~~si~~Ia~~agvs~~~~y~~F~   47 (71)
T d1ui5a1          24 ESTTLSEIVAHAGVTKGALYFHFA   47 (71)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cccCHHHHHHHHCcCHhHHHHHCc
Confidence            468999999999999999998753

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=93.96  E-value=0.027  Score=29.56  Aligned_cols=24  Identities=4%  Similarity=-0.069  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .|.|.++||+..|||++|+++...
T Consensus        23 ~~~s~~~Ia~~agvs~~t~Y~~F~   46 (74)
T d1v7ba1          23 ETLSYDSLAEATGLSKSGLIYHFP   46 (74)
T ss_dssp             TTCCHHHHHHHHCSCHHHHHHHCS
T ss_pred             cccCHHHHHHHhCcCcchHhhhCC
Confidence            468999999999999999998653

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.84  E-value=0.025  Score=29.75  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +|+|.++||+..|||++++++...
T Consensus        23 ~~~s~~~Ia~~agvs~~~iY~~F~   46 (74)
T d2g7sa1          23 NSFSYADISQVVGIRNASIHHHFP   46 (74)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             cccCHHHHHHHHCcCcchHHHHCc
Confidence            468999999999999999998753

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.62  E-value=0.033  Score=29.09  Aligned_cols=24  Identities=17%  Similarity=0.080  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .++|..+||++.|||++++++...
T Consensus        24 ~~~t~~~Ia~~agvs~~~~y~~F~   47 (75)
T d3c07a1          24 DRTTMRAIAQEAGVSVGNAYYYFA   47 (75)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCc
Confidence            458999999999999999998753

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=93.56  E-value=0.03  Score=28.90  Aligned_cols=23  Identities=22%  Similarity=0.310  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|.++||+..|||++++++..
T Consensus        20 ~~~ti~~Ia~~agvs~~~iy~~F   42 (69)
T d2np5a1          20 EGASVREVAKRAGVSIGAVQHHF   42 (69)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cccCHHHHHHHhCCCHHHHHHHC
Confidence            46899999999999999999865

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=93.43  E-value=0.023  Score=29.76  Aligned_cols=24  Identities=21%  Similarity=0.209  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .+.|.++||++.|||.++++++..
T Consensus        21 ~~~ti~~Ia~~agvs~~~ly~~F~   44 (72)
T d2g3ba1          21 RGLRVNDVAEVAGVSPGLLYYHFK   44 (72)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHHC
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHCc
Confidence            358999999999999999998764

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=93.36  E-value=0.021  Score=30.09  Aligned_cols=24  Identities=13%  Similarity=0.163  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +++|..+||+..|||++++++...
T Consensus        22 ~~~ti~~Ia~~agvs~~~iY~~F~   45 (75)
T d2id6a1          22 DRATTDEIAEKAGVAKGLIFHYFK   45 (75)
T ss_dssp             HHCCHHHHHHHHTCCTHHHHHHHS
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCC
Confidence            358999999999999999998764

>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=93.30  E-value=0.15  Score=28.12  Aligned_cols=56  Identities=16%  Similarity=0.132  Sum_probs=37.7

Q ss_pred             CCHHHHHHHhc--cCHHHHHHHHHHHHHhcCCCc-cccCCCCCCCCC-HHHHHHHHHHHHhCC
Q psy15513          6 VRPCVISRQLR--VSHGCVSKILNRYQETGSIRP-GVIGGSKPRVAT-PDVERRIEEYKGENP   64 (77)
Q Consensus         6 ~s~~~iA~rf~--VS~stv~r~~~r~r~tG~v~p-k~~gg~~~~~~~-~~~~~~i~~~v~~~p   64 (77)
                      .+-++||+.++  +|.+||...++.+.+.|-+.- -..+|   ++-| ...+-++..+++.++
T Consensus        24 v~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~h~s~G---riPT~~g~r~yv~~ll~~~~   83 (87)
T d1stza1          24 VSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHTSAG---RIPTDKGLRFYYEEMLKISK   83 (87)
T ss_dssp             BCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSSCSC---BEECHHHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCCCCCCC---CcccHHHHHHHHHHHcccCC
Confidence            57789999955  689999999999999999853 22233   2223 223445555555544

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.30  E-value=0.038  Score=28.57  Aligned_cols=24  Identities=17%  Similarity=0.126  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++.|..+||++.|||++++++...
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F~   48 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRWG   48 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCc
Confidence            358999999999999999998753

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=93.27  E-value=0.027  Score=29.23  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=20.4

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      ++|.++||++.|||++++++..+
T Consensus        19 ~~ti~~Ia~~agvs~~~iY~~F~   41 (65)
T d2g7ga1          19 DFRMPDLARHLNVQVSSIYHHAK   41 (65)
T ss_dssp             SCCHHHHHHHTTSCHHHHHTTSC
T ss_pred             CCCHHHHHHHhCccccchhhcCC
Confidence            68999999999999999987543

>d2oi8a1 a.4.1.9 (A:8-86) Putative regulatory protein Sco4313 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulatory protein Sco4313
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.26  E-value=0.028  Score=29.86  Aligned_cols=23  Identities=9%  Similarity=0.226  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +++|.++||++.|||++++++..
T Consensus        28 ~~~t~~~Ia~~agvs~~~~Y~~F   50 (79)
T d2oi8a1          28 SALSLNAIAKRMGMSGPALYRYF   50 (79)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTTC
T ss_pred             cccCHHHHHHHhCCCCCchhhhc
Confidence            46899999999999999998753

>d2d6ya1 a.4.1.9 (A:7-74) Putative regulator SCO4008 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulator SCO4008
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.99  E-value=0.054  Score=28.05  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      .++|..+||++-|||++++++...
T Consensus        21 ~~~ti~~Ia~~agvs~~~~Y~~F~   44 (68)
T d2d6ya1          21 AGARIDRIAAEARANKQLIYAYYG   44 (68)
T ss_dssp             TSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             cccCHHHHHHHHCcchhHHHHHCc
Confidence            468999999999999999998764

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=92.84  E-value=0.064  Score=26.44  Aligned_cols=27  Identities=7%  Similarity=0.059  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      +..+..++|+.+|+|.++.+|+.++.-
T Consensus        18 ~~~tl~~lA~~~~~s~~~l~r~Fk~~~   44 (54)
T d1bl0a1          18 SPLSLEKVSERSGYSKWHLQRMFKKET   44 (54)
T ss_dssp             SCCCCHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            457888999999999999999998753

>d1vi0a1 a.4.1.9 (A:6-77) Hypothetical transcriptional regulator YsiA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YsiA
species: Bacillus subtilis [TaxId: 1423]

Probab=92.62  E-value=0.049  Score=28.24  Aligned_cols=23  Identities=17%  Similarity=0.219  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||++++++..
T Consensus        20 ~~~ti~~Ia~~agvs~~~~y~~F   42 (72)
T d1vi0a1          20 HQSQVSKIAKQAGVADGTIYLYF   42 (72)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             ccccHHHHHHHHCcCHHHHHHHC
Confidence            45899999999999999999864

>d2hyja1 a.4.1.9 (A:8-82) Putative transcriptional regulator SCO4940 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4940
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.10  E-value=0.035  Score=29.23  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .++|..+||++.|||++++++..
T Consensus        24 ~~~t~~~Ia~~agvs~~~~Y~~F   46 (75)
T d2hyja1          24 DGITIGRLAEELEMSKSGVHKHF   46 (75)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHTTC
T ss_pred             ccCcHHHHHHHHCcCHHHHHHHC
Confidence            46899999999999999998754

>d1rkta1 a.4.1.9 (A:2-82) Hypothetical transcriptional regulator YfiR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YfiR
species: Bacillus subtilis [TaxId: 1423]

Probab=92.09  E-value=0.041  Score=29.28  Aligned_cols=23  Identities=13%  Similarity=-0.047  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++++..+||++.|||++|++++.
T Consensus        30 ~~~ti~~Ia~~agvs~~t~Y~~F   52 (81)
T d1rkta1          30 ELTTMKDVVEESGFSRGGVYLYF   52 (81)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHC
Confidence            46899999999999999999764

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=91.88  E-value=0.045  Score=28.53  Aligned_cols=23  Identities=9%  Similarity=0.128  Sum_probs=20.7

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      .+.|.++||+..|||++++++..
T Consensus        21 ~~~si~~Ia~~agvs~~~iy~~F   43 (73)
T d1sgma1          21 HATGLNQIVKESGAPKGSLYHFF   43 (73)
T ss_dssp             TTCCHHHHHHHHCCCSCHHHHST
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHc
Confidence            46899999999999999999865

>d1zk8a1 a.4.1.9 (A:6-77) Transcriptional regulator BC5000 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC5000
species: Bacillus cereus [TaxId: 1396]

Probab=91.85  E-value=0.036  Score=28.92  Aligned_cols=23  Identities=13%  Similarity=0.141  Sum_probs=20.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||.+++++..
T Consensus        22 ~~~t~~~Ia~~agvs~~slY~yF   44 (72)
T d1zk8a1          22 QEVTLASLAQTLGVRSPSLYNHV   44 (72)
T ss_dssp             GGCCHHHHHHHHTSCHHHHTTTC
T ss_pred             CcccHHHHHHHhCCCHHHHHHHC
Confidence            46899999999999999998653

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=91.60  E-value=0.18  Score=25.90  Aligned_cols=27  Identities=11%  Similarity=0.030  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..++..+||+.||||...|..+..+.-
T Consensus        27 ~~~tl~eIa~~lgiS~erVrqi~~~al   53 (61)
T d1ku3a_          27 REHTLEEVGAYFGVTRERIRQIENKAL   53 (61)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            558999999999999999998876643

>d2g7la1 a.4.1.9 (A:16-83) Putative transcriptional regulator SCO7704 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO7704
species: Streptomyces coelicolor [TaxId: 1902]

Probab=91.56  E-value=0.048  Score=28.26  Aligned_cols=23  Identities=9%  Similarity=0.082  Sum_probs=20.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|.++||++.|||++++++..
T Consensus        23 ~~~si~~ia~~~gvs~~~~y~hF   45 (68)
T d2g7la1          23 EKVTMRRLAQELDTGPASLYVYV   45 (68)
T ss_dssp             SSCCHHHHHHHTTSCHHHHTTTC
T ss_pred             ccCCHHHHHHHHCcCHhHhhHHC
Confidence            46899999999999999998643

>d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: SPO1678-like
domain: Uncharacterized protein SPO1678
species: Silicibacter pomeroyi [TaxId: 89184]

Probab=91.48  E-value=0.11  Score=29.37  Aligned_cols=29  Identities=10%  Similarity=0.126  Sum_probs=27.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGS   34 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~   34 (77)
                      .|..|+++++++|.+-.+.|.+.+-+.|.
T Consensus        51 ~S~~EAcrrY~LS~eEf~~W~~a~~~hGe   79 (93)
T d2oa4a1          51 ITLAEAKQTYGLSDEEFNSWVSALAEHGK   79 (93)
T ss_dssp             CCHHHHHHTTCSSHHHHHHHHHHHHCCCS
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHhH
Confidence            79999999999999999999999998774

>d2iu5a1 a.4.1.9 (A:1-71) Transcriptional activator DhaS {Lactococcus lactis [TaxId: 1358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional activator DhaS
species: Lactococcus lactis [TaxId: 1358]

Probab=91.43  E-value=0.022  Score=29.82  Aligned_cols=23  Identities=4%  Similarity=0.066  Sum_probs=20.1

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||++++++..
T Consensus        25 ~~~sv~~Ia~~agvs~~t~Y~~F   47 (71)
T d2iu5a1          25 HQISVSDIMQTAKIRRQTFYNYF   47 (71)
T ss_dssp             GGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             ccCCHHHHHHHhCccccHHHHHc
Confidence            35899999999999999998764

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.09  E-value=0.11  Score=25.60  Aligned_cols=26  Identities=4%  Similarity=0.005  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      -.+..++|+.+|+|+++..|..++.-
T Consensus        19 ~itl~~lA~~~~~S~~~l~r~Fk~~~   44 (54)
T d1d5ya1          19 PLSLDNVAAKAGYSKWHLQRMFKDVT   44 (54)
T ss_dssp             SCCCHHHHTTTSSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            37888999999999999999998753

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=90.66  E-value=0.094  Score=30.53  Aligned_cols=21  Identities=5%  Similarity=-0.001  Sum_probs=19.3

Q ss_pred             CCHHHHHHHhccCHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~   26 (77)
                      -...++|.-+|||+.|.+||-
T Consensus        37 ktqeqiAeelGisr~tLyrWr   57 (120)
T d2ao9a1          37 RTQDEMANELGINRTTLWEWR   57 (120)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH
T ss_pred             hhHHHHHHHhChhHHHHHHHh
Confidence            467899999999999999998

>d2fd5a1 a.4.1.9 (A:1-76) Probable transcriptional regulator PA3133 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA3133
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.60  E-value=0.034  Score=29.19  Aligned_cols=23  Identities=4%  Similarity=-0.093  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++.|..+||++.|||.+|++++.
T Consensus        26 ~~~si~~Ia~~agvs~~t~Y~~F   48 (76)
T d2fd5a1          26 VEPSVGEVMGAAGLTVGGFYAHF   48 (76)
T ss_dssp             TSCCHHHHHHHTTCCGGGGGGTC
T ss_pred             ccccHHHHHHHhCCCccchhhcC
Confidence            46899999999999999998754

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.53  E-value=0.099  Score=29.66  Aligned_cols=39  Identities=13%  Similarity=0.072  Sum_probs=33.1

Q ss_pred             CCCCHHHHHHHh----ccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513          4 AGVRPCVISRQL----RVSHGCVSKILNRYQETGSIRPGVIGG   42 (77)
Q Consensus         4 ~G~s~~~iA~rf----~VS~stv~r~~~r~r~tG~v~pk~~gg   42 (77)
                      .++++.+|...+    +++.+||...+++..+.|-|.-.+.|.
T Consensus        20 ~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~gr   62 (120)
T d1okra_          20 KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNK   62 (120)
T ss_dssp             SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETT
T ss_pred             CCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEecCC
Confidence            457888888777    799999999999999999998766553

>d1t33a1 a.4.1.9 (A:1-88) Putative transcriptional repressor YbiH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional repressor YbiH
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.51  E-value=0.12  Score=27.73  Aligned_cols=21  Identities=5%  Similarity=-0.031  Sum_probs=19.1

Q ss_pred             CHHHHHHHhccCHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~   27 (77)
                      +.++||++.|||++++++...
T Consensus        33 t~~~Ia~~agvs~~~~Y~~F~   53 (88)
T d1t33a1          33 TTRDIAALAGQNIAAITYYFG   53 (88)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHS
T ss_pred             CHHHHHHHhCCChhhhhccCC
Confidence            788999999999999998764

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=90.14  E-value=0.39  Score=23.43  Aligned_cols=31  Identities=10%  Similarity=0.129  Sum_probs=26.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513         43 SKPRVATPDVERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus        43 ~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      +||+.+++++.+.+.++++.  +.+..+++..+
T Consensus         1 GR~~~lt~~q~~~a~~l~~~--G~s~~~iA~~~   31 (47)
T d1ijwc_           1 GRPRAINKHEQEQISRLLEK--GHPRQQLAIIF   31 (47)
T ss_dssp             CCCCSSCHHHHHHHHHHHHT--TCCHHHHHHHH
T ss_pred             CCCCcCCHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence            37788999999999999964  47999998875

>d1e0ga_ d.7.1.1 (A:) Membrane-bound lytic murein transclycosylase D, MltD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: LysM domain
superfamily: LysM domain
family: LysM domain
domain: Membrane-bound lytic murein transclycosylase D, MltD
species: Escherichia coli [TaxId: 562]

Probab=89.86  E-value=0.19  Score=24.62  Aligned_cols=24  Identities=17%  Similarity=0.050  Sum_probs=20.6

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      +.|=+-..||++|+||...+.+|=
T Consensus         8 ~~GDTl~~IA~~y~vs~~~i~~~N   31 (48)
T d1e0ga_           8 RKGDSLSSIAKRHGVNIKDVMRWN   31 (48)
T ss_dssp             CTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHc
Confidence            467888999999999999888774

>d2np3a1 a.4.1.9 (A:35-99) Putative transcriptional regulator SCO0857 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO0857
species: Streptomyces coelicolor [TaxId: 1902]

Probab=89.79  E-value=0.029  Score=29.02  Aligned_cols=22  Identities=14%  Similarity=0.092  Sum_probs=0.5

Q ss_pred             CCCHHHHHHHhccCHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKIL   26 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~   26 (77)
                      ++|.++||+..|||++++++..
T Consensus        16 ~~s~~~IA~~agvs~~~ly~~F   37 (65)
T d2np3a1          16 ATSLRRIAETAGVDQSLVHHFY   37 (65)
T ss_dssp             ---------------------C
T ss_pred             cCCHHHHHHHHCcCHHHHHHHC
Confidence            5899999999999999999764

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.63  E-value=0.12  Score=29.22  Aligned_cols=26  Identities=12%  Similarity=0.176  Sum_probs=23.3

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      ....|.+.||.--|||+|.+|.|+.+
T Consensus        39 ~h~I~Q~~Va~~TGlsQS~iSq~L~~   64 (94)
T d1ic8a2          39 QHNIPQREVVDTTGLNQSHLSQHLNK   64 (94)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHHHS
T ss_pred             HcCCcHHHHHHHHcccHHHHHHHHhC
Confidence            45789999999999999999999973

>d2b0la1 a.4.5.66 (A:167-257) GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CodY HTH domain
domain: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=88.97  E-value=0.42  Score=26.38  Aligned_cols=47  Identities=13%  Similarity=0.294  Sum_probs=37.2

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC--CCCCHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPDV   52 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~--~~~~~~~   52 (77)
                      .-...||.+.||+.|.+.+-++.+...|-++.+.-|=...  +++++..
T Consensus        35 lvASkiADrvgiTRSVIVNALRK~ESAGvIEsrSlGMKGTyikvln~~~   83 (91)
T d2b0la1          35 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKF   83 (91)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSCEEEEECCHHH
T ss_pred             EeehhhhhhhCchHHHHHHHHHHhhhcceeeeccCCCCeeeeeeecHHH
Confidence            4567899999999999999999999999999887653222  4565543

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.92  E-value=0.2  Score=26.52  Aligned_cols=33  Identities=18%  Similarity=0.292  Sum_probs=30.3

Q ss_pred             cCCCCHHHHHHHh-ccCHHHHHHHHHHHHHhcCC
Q psy15513          3 AAGVRPCVISRQL-RVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         3 ~~G~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v   35 (77)
                      +.|++..+|+.+| ++|.+.|...+.-.-..|.+
T Consensus        21 ~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~I   54 (69)
T d1dpua_          21 PEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHI   54 (69)
T ss_dssp             TTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSE
T ss_pred             ccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCce
Confidence            5799999999999 79999999999998888876

>d1i3ja_ d.285.1.1 (A:) DNA-binding domain of intron endonuclease I-TevI {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding domain of intron-encoded endonucleases
superfamily: DNA-binding domain of intron-encoded endonucleases
family: DNA-binding domain of intron-encoded endonucleases
domain: DNA-binding domain of intron endonuclease I-TevI
species: Bacteriophage T4 [TaxId: 10665]

Probab=88.39  E-value=0.21  Score=28.17  Aligned_cols=22  Identities=18%  Similarity=0.258  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhccCHHHHHHHHH
Q psy15513          6 VRPCVISRQLRVSHGCVSKILN   27 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~   27 (77)
                      -|..|||+.|||+.+||...++
T Consensus        65 ~S~~EAar~lgi~~~tI~~R~k   86 (96)
T d1i3ja_          65 DCAADAARHFKISSGLVTYRVK   86 (96)
T ss_dssp             SSHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccHHHHHHHhCCChHHHHHHHc
Confidence            4789999999999999998876

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.85  E-value=0.83  Score=23.97  Aligned_cols=31  Identities=3%  Similarity=-0.030  Sum_probs=25.0

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHH---HhcCCCcc
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQ---ETGSIRPG   38 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r---~tG~v~pk   38 (77)
                      ..++|..+|++...|..|.+..|   ..+.+...
T Consensus        33 ~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~~~~   66 (76)
T d2ecca1          33 YQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWF   66 (76)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSST
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHhchHHhh
Confidence            45689999999999999999888   45665443

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.57  E-value=0.38  Score=24.36  Aligned_cols=25  Identities=16%  Similarity=0.025  Sum_probs=21.6

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..++|+.+|+|...|..|.+..|..
T Consensus        32 ~~~LA~~lgls~~qV~~WFqNrR~k   56 (59)
T d2cqxa1          32 LKGLSKQLDWSVRKIQCWFRHRRNQ   56 (59)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            4568999999999999999987754

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=87.49  E-value=0.57  Score=24.45  Aligned_cols=27  Identities=11%  Similarity=0.117  Sum_probs=23.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      .++..+||..||||...|..+-++.-.
T Consensus        25 ~~tl~eI~~~lgiSrerVrqie~~al~   51 (68)
T d2p7vb1          25 DYTLEEVGKQFDVTRERIRQIEAKALR   51 (68)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            389999999999999999998877654

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.86  E-value=0.46  Score=23.42  Aligned_cols=24  Identities=4%  Similarity=-0.085  Sum_probs=21.0

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..++|+.+|+|...|..|.+..|.
T Consensus        27 ~~~LA~~lgl~~~qV~~WFqNrR~   50 (53)
T d1le8a_          27 KEEVAKKCGITPLQVRVWFINKRM   50 (53)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHhhhh
Confidence            457899999999999999988764

>d2ve8a1 a.4.5.67 (A:745-811) DNA translocase FtsK {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=86.73  E-value=1.1  Score=23.48  Aligned_cols=43  Identities=12%  Similarity=0.278  Sum_probs=35.7

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCC
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVAT   49 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~   49 (77)
                      .|..-+=++|+|.-+-+.+++-+..+.|-|.|.. |.+++.++.
T Consensus        19 aS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~-g~~~ReVL~   61 (67)
T d2ve8a1          19 ASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMN-TNGSREVIA   61 (67)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCC-TTSCCCBCS
T ss_pred             ccHHHHHHHHhcchHHHHHHHHHHHHCcCCCCCC-CCCCCeEeC
Confidence            7889999999999999999999999999999874 333444544

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.54  E-value=0.51  Score=23.27  Aligned_cols=25  Identities=12%  Similarity=0.123  Sum_probs=21.9

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..++|+.+|+|...|..|.+..|..
T Consensus        24 ~~~LA~~~~ls~~qV~~WFqNrR~k   48 (52)
T d1x2ma1          24 LEGLSKQLDWDVRSIQRWFRQRRNQ   48 (52)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            4679999999999999999987754

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=86.14  E-value=0.77  Score=24.80  Aligned_cols=35  Identities=11%  Similarity=0.012  Sum_probs=30.6

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      ..+..|||..++||..|+.|-.+...+.=.+.|+.
T Consensus        62 ~~t~~eIa~~~~is~~ti~k~yk~i~~~L~l~~~~   96 (98)
T d1aisb1          62 PRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKK   96 (98)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCTTT
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCccc
Confidence            36789999999999999999999998887777764

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.52  E-value=0.22  Score=26.81  Aligned_cols=32  Identities=6%  Similarity=0.249  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhccCHHH-HHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGC-VSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~st-v~r~~~r~r~tG~v~p   37 (77)
                      .++.+||+.||++.+. |.+.+-.....|.|.-
T Consensus        20 ~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k   52 (73)
T d1xmka1          20 SSALNLAKNIGLTKARDINAVLIDMERQGDVYR   52 (73)
T ss_dssp             EEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEE
T ss_pred             chHHHHHHHhCCCcHHHHhHHHHHHHHCCCeec
Confidence            6788999999999987 9999999999999964

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=85.01  E-value=0.83  Score=24.89  Aligned_cols=29  Identities=7%  Similarity=0.000  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..++..+||+.||||..-|..+-++.-..
T Consensus        37 ~~~tl~eI~~~lgiSrERVRQie~~al~k   65 (87)
T d1ttya_          37 KPKTLEEVGQYFNVTRERIRQIEVKALRK   65 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            44899999999999999999888776543

>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=84.96  E-value=0.59  Score=25.22  Aligned_cols=31  Identities=16%  Similarity=0.058  Sum_probs=26.0

Q ss_pred             CCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513          5 GVRPCVISRQLRVSHGCVSKILNRYQETGSI   35 (77)
Q Consensus         5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v   35 (77)
                      ..+..+||..+|||..|+.+..+.+.+.=++
T Consensus        60 ~~t~~eIa~~~~vs~~tI~~~yk~l~~~l~~   90 (95)
T d1aisb2          60 KRTQREVAEVARVTEVTVRNRYKELVEKLKI   90 (95)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            4678999999999999999999987765443

>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.92  E-value=0.79  Score=25.37  Aligned_cols=37  Identities=11%  Similarity=-0.042  Sum_probs=28.8

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccc
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGV   39 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~   39 (77)
                      ....+..+||..+|||..|+.+..+...+. +.+-|..
T Consensus        59 ~~~~t~~eIa~~~~vs~~tI~k~yk~l~~~~~~lip~~   96 (109)
T d1vola2          59 AEKRTQKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTD   96 (109)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHHGGGHHHHSCSS
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCChh
Confidence            345789999999999999999999887655 3345543

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=84.68  E-value=0.16  Score=27.50  Aligned_cols=28  Identities=18%  Similarity=0.275  Sum_probs=24.2

Q ss_pred             CccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          1 MAAAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         1 l~~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      |.+.|+|-+++++.-|+|.+|+..-+.+
T Consensus        18 L~krG~sLa~lsr~~gls~stl~naL~r   45 (74)
T d1nera_          18 LKKRKLSLSALSRQFGYAPTTLANALER   45 (74)
T ss_dssp             HTTSSCCHHHHHHHHSCCHHHHHHTTTS
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            4578999999999999999999876654

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.54  E-value=0.74  Score=23.63  Aligned_cols=32  Identities=13%  Similarity=0.262  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP   37 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p   37 (77)
                      ...+++|++|+|...-|.|.+=.+...|.+.-
T Consensus        17 ~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~k   48 (59)
T d2gxba1          17 TTAHDLSGKLGTPKKEINRVLYSLAKKGKLQK   48 (59)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hhHHHHHHHhCCcHHHHHHHHHHHHHccchhh
Confidence            67899999999999999999999999998863

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.38  E-value=0.51  Score=26.79  Aligned_cols=38  Identities=11%  Similarity=0.027  Sum_probs=31.3

Q ss_pred             CCHHHHHHHh----ccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513          6 VRPCVISRQL----RVSHGCVSKILNRYQETGSIRPGVIGGS   43 (77)
Q Consensus         6 ~s~~~iA~rf----~VS~stv~r~~~r~r~tG~v~pk~~gg~   43 (77)
                      ++.++|...|    +.+.+||...+++..+.|-|.-.+.|..
T Consensus        23 ~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~gr~   64 (122)
T d2g9wa1          23 QTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRA   64 (122)
T ss_dssp             EEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---C
T ss_pred             ccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeecCCe
Confidence            6889999888    5789999999999999999988776643

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=82.40  E-value=0.88  Score=22.74  Aligned_cols=24  Identities=21%  Similarity=0.124  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513         52 VERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus        52 ~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ....|+..+++||.++..||++.+
T Consensus         4 ~D~kIl~~L~~n~r~s~~~lA~~~   27 (60)
T d1i1ga1           4 RDKIILEILEKDARTPFTEIAKKL   27 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHH
Confidence            356799999999999999999876

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=82.22  E-value=1.1  Score=22.50  Aligned_cols=24  Identities=21%  Similarity=0.131  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513         52 VERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus        52 ~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ....|+..+++||.++..||++.+
T Consensus         6 ~D~~IL~~L~~~~r~s~~eiA~~l   29 (63)
T d2cg4a1           6 LDRGILEALMGNARTAYAELAKQF   29 (63)
T ss_dssp             HHHHHHHHHHHCTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHH
Confidence            466799999999999999999886

>d1tc3c_ a.4.1.2 (C:) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase tc3a1-65
species: Caenorhabditis elegans [TaxId: 6239]

Probab=81.92  E-value=0.59  Score=23.18  Aligned_cols=26  Identities=23%  Similarity=0.323  Sum_probs=21.9

Q ss_pred             cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513          3 AAGVRPCVISRQLRVSHGCVSKILNR   28 (77)
Q Consensus         3 ~~G~s~~~iA~rf~VS~stv~r~~~r   28 (77)
                      .-|.|-.++|+.+.=|.-||.++++-
T Consensus        19 ~L~~slhemaR~i~rSR~~ir~Yl~~   44 (51)
T d1tc3c_          19 LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HhCCcHHHHHHHHHHhHHHHHHHhcC
Confidence            45788899999999999999998864

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.90  E-value=1  Score=22.42  Aligned_cols=24  Identities=13%  Similarity=0.102  Sum_probs=21.0

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ..++|..+|+|...|.-|.+-.|.
T Consensus        30 r~~LA~~l~l~~~~V~~WFqNrR~   53 (58)
T d1ig7a_          30 RAEFSSSLSLTETQVKIWFQNRRA   53 (58)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCChhheeecCcchHh
Confidence            467999999999999999987664

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=81.58  E-value=1.1  Score=21.88  Aligned_cols=23  Identities=9%  Similarity=0.111  Sum_probs=20.3

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHH
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQ   30 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r   30 (77)
                      ..++|..+|+|...|.-|.+-.|
T Consensus        29 r~~LA~~lgL~~~qV~vWFqNrR   51 (53)
T d1p7ia_          29 RQQLSSELGLNEAQIKIWFQNAR   51 (53)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCChHHhhhcccccC
Confidence            56799999999999999998755

>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=81.56  E-value=1.9  Score=22.54  Aligned_cols=52  Identities=19%  Similarity=0.225  Sum_probs=40.0

Q ss_pred             CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHH
Q psy15513          4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEY   59 (77)
Q Consensus         4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~   59 (77)
                      +-+..+.+|..+++|-..|.-.+...++.|-+...+.|    -..|++-.+++.++
T Consensus        16 qPiGRr~La~~L~l~Er~vRte~~~Lk~~gLI~~~~~G----m~lTe~G~~~l~~L   67 (69)
T d2p8ta1          16 EPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQRG----HFLTLKGKEIRDKL   67 (69)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC--C----EEECHHHHHHHHHH
T ss_pred             CCccHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeeCCC----CEECHhHHHHHHHH
Confidence            45778999999999999999999999999999988644    34666545544443

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=81.49  E-value=1.1  Score=25.40  Aligned_cols=36  Identities=14%  Similarity=0.247  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513          5 GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI   40 (77)
Q Consensus         5 G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~   40 (77)
                      -+|+.+|-..+     .||.+||||-+..+.+.|-|..-..
T Consensus        32 h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~   72 (134)
T d1mzba_          32 HMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNF   72 (134)
T ss_dssp             SBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             CCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEee
Confidence            37888886665     5999999999999999999864443

>d2j5pa1 a.4.5.67 (A:1261-1329) DNA translocase FtsK {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Escherichia coli [TaxId: 562]

Probab=81.06  E-value=1.1  Score=23.59  Aligned_cols=34  Identities=15%  Similarity=0.281  Sum_probs=31.5

Q ss_pred             CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513          6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV   39 (77)
Q Consensus         6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~   39 (77)
                      .|..-+=++|+|.-+-+.|++-+..+.|-|.|..
T Consensus        22 aS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~   55 (69)
T d2j5pa1          22 ASISGVQRQFRIGYNRAARIIEQMEAQGIVSEQG   55 (69)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHHTSBCCCC
T ss_pred             ccHHHHHHHHhccchHHHHHHHHHHHCCcCCCCC
Confidence            6788899999999999999999999999999874

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=80.39  E-value=1.2  Score=22.70  Aligned_cols=25  Identities=0%  Similarity=0.061  Sum_probs=21.7

Q ss_pred             CHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513          7 RPCVISRQLRVSHGCVSKILNRYQE   31 (77)
Q Consensus         7 s~~~iA~rf~VS~stv~r~~~r~r~   31 (77)
                      ...++|..+|+|...|.-|.+..|.
T Consensus        31 ~r~~LA~~lgl~~~~V~~WFqNrR~   55 (65)
T d1fjla_          31 TREELAQRTNLTEARIQVWFQNRRA   55 (65)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhhhhHHH
Confidence            3567999999999999999988764

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.36  E-value=1.3  Score=22.05  Aligned_cols=25  Identities=12%  Similarity=0.227  Sum_probs=21.6

Q ss_pred             HHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513          8 PCVISRQLRVSHGCVSKILNRYQET   32 (77)
Q Consensus         8 ~~~iA~rf~VS~stv~r~~~r~r~t   32 (77)
                      ..++|..+|++...|.-|.+..|..
T Consensus        28 ~~~LA~~lgL~~~qV~~WFqNrR~k   52 (57)
T d1e3oc1          28 ITLIAEQLNMEKEVIRVWFSNRRQK   52 (57)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            4578999999999999999987753

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=80.34  E-value=1.4  Score=21.80  Aligned_cols=24  Identities=13%  Similarity=0.100  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513         52 VERRIEEYKGENPAMFSWEIRDRL   75 (77)
Q Consensus        52 ~~~~i~~~v~~~pd~tl~El~~~L   75 (77)
                      ....|+..+++||.++..||++++
T Consensus         4 ~D~~Il~~L~~n~r~s~~eiA~~l   27 (60)
T d2cyya1           4 IDKKIIKILQNDGKAPLREISKIT   27 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHH
Confidence            456799999999999999999886