Psyllid ID: psy1898

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230
Protein Sequence
MGQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRKNHSIDGILEQSN
Secondary Structure (PSIPRED)
cccccccccccEEccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccccccccHHHHHccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEcccccEEEccccccHHHHHHHHHHHHccccccccEEEcccccEEEccccccHHHHHHHHHHHHccccHHHHHHHHcccHcEcccccEccccccccHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
mgqgrmnqlggvfingrplpnhIRLKIVEMAAagrgsscqgrmnqlggvfingrplpnhIRLKIVEMAAAgvrpcvisrqlrvshgvnqlggvfingrplpnhIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYqetgsirpgviggskprvatpdVEKRIEEYkktnpgifswEIRDRLVkqdgicdknsapsvsSISRLlrggrrddcdrknhsidgileqsn
Flexible Loop (DISEMBL)
mgqgrmnqlggvfingrplpNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNryqetgsirpgviggskprvatpdvEKRIeeykktnpgifsweIRDRLVKQdgicdknsapsvssisrllrggrrddcdrknhsidgileqsn
Low Complexity Region (SEG)
MGQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISrllrggrrddcdrKNHSIDGILEQSN
Disordered region (IsUnstruct)
********LGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG**************IEEYKKTNPGIFSWEIRDRLVKQDGIC**************************************
Disordered Region (DISOPRED)
********LGGVFINGRPLPNHIRLK*************************************************************NQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY**********************VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSI***************************
Disordered Region (DISEMBL)
MGQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRKNHSIDGILEQSN
Disordered Region (DISPRO)
*GQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR******************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRKNHSIDGILEQSN
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	230	2.2.26 [Sep-21-2011]
Q0IH87	483	Paired box protein Pax-3-	N/A	N/A	0.613	0.291	0.707	2e-57
P06601	613	Segmentation protein pair	yes	N/A	0.639	0.239	0.699	3e-57
P09082	427	Protein gooseberry OS=Dro	no	N/A	0.591	0.318	0.792	7e-57
P47239	503	Paired box protein Pax-7	yes	N/A	0.604	0.276	0.740	1e-56
P23760	479	Paired box protein Pax-3	yes	N/A	0.613	0.294	0.696	3e-56
P24610	479	Paired box protein Pax-3	no	N/A	0.613	0.294	0.696	3e-56
P09083	449	Protein gooseberry-neuro	no	N/A	0.686	0.351	0.676	6e-56
Q645N4	484	Paired box protein Pax-3-	N/A	N/A	0.613	0.291	0.702	8e-56
P23759	520	Paired box protein Pax-7	no	N/A	0.604	0.267	0.717	6e-53
P09084	446	Paired box protein Pax-1	no	N/A	0.6	0.309	0.685	1e-48

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

 Score =  221 bits (564), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 111/157 (70%), Positives = 127/157 (80%), Gaps = 16/157 (10%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PG IGGSKP+V TP+VEK+IEE+K+ NPG+FSWEIRD+L+K DG+CD+N+ PSVSSISR+
Sbjct: 98  PGAIGGSKPKVTTPEVEKKIEEFKRDNPGMFSWEIRDKLLK-DGVCDRNTVPSVSSISRI 156

Query: 207 LRG--GRRDDCD-------------RKNHSIDGILEQ 228
           LR   G+ D+ D             R  HSIDGIL +
Sbjct: 157 LRSKFGKGDEEDMELDRKEQEESEKRAKHSIDGILRE 193

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

 Score =  221 bits (563), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 107/153 (69%), Positives = 131/153 (85%), Gaps = 6/153 (3%)

Query: 62  LKIVEMAAAGVRPCV--ISRQLRVSHG---VNQLGGVFINGRPLPNHIRLKIVEMAAAGV 116
           + +   AAA  RP     S    ++ G   VNQLGGVFINGRPLPN+IRLKIVEMAA G+
Sbjct: 1   MTVTAFAAAMHRPFFNGYSTMQDMNSGQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGI 60

Query: 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI 176
           RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR+ATP++E RIEEYK+++PG+
Sbjct: 61  RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGM 120

Query: 177 FSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209
           FSWEIR++L++ +G+CD+++APSVS+ISRL+RG
Sbjct: 121 FSWEIREKLIR-EGVCDRSTAPSVSAISRLVRG 152

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 =  220 bits (560), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 111/140 (79%), Positives = 122/140 (87%), Gaps = 4/140 (2%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR +IVEMAAAGVRPCVISRQLRVSHGCVSKILNR+QETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRRQIVEMAAAGVRPCVISRQLRVSHGCVSKILNRFQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATPD+E RIEE K++ PGIFSWEIR +L+ + G+CDK +APSVSSISRL
Sbjct: 83  PGVIGGSKPRVATPDIESRIEELKQSQPGIFSWEIRAKLI-EAGVCDKQNAPSVSSISRL 141

Query: 207 LRGGRRDDCDRKNHSIDGIL 226
           L   R       +HSIDGIL
Sbjct: 142 L---RGSSGSGTSHSIDGIL 158

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 =  219 bits (558), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 114/154 (74%), Positives = 126/154 (81%), Gaps = 15/154 (9%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           PG IGGSKPR VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PSVSSISR
Sbjct: 98  PGAIGGSKPRQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSVSSISR 156

Query: 206 LLR---GGRRDDCD----------RKNHSIDGIL 226
           +LR   G + DD +          +  HSIDGIL
Sbjct: 157 VLRIKFGKKEDDEEGDKKEEDGEKKAKHSIDGIL 190

Probable transcription factor. May have a role in myogenesis.

Mus musculus (taxid: 10090)

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

 Score =  218 bits (555), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/158 (69%), Positives = 125/158 (79%), Gaps = 17/158 (10%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           PG IGGSKP+ V TPDVEK+IEEYK+ NPG+FSWEIRD+L+K D +CD+N+ PSVSSISR
Sbjct: 98  PGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLK-DAVCDRNTVPSVSSISR 156

Query: 206 LLRG----GRRDDCD-----------RKNHSIDGILEQ 228
           +LR     G  ++ D           +  HSIDGIL +
Sbjct: 157 ILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSE 194

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 =  218 bits (555), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/158 (69%), Positives = 125/158 (79%), Gaps = 17/158 (10%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           PG IGGSKP+ V TPDVEK+IEEYK+ NPG+FSWEIRD+L+K D +CD+N+ PSVSSISR
Sbjct: 98  PGAIGGSKPKQVTTPDVEKKIEEYKRENPGMFSWEIRDKLLK-DAVCDRNTVPSVSSISR 156

Query: 206 LLRG----GRRDDCD-----------RKNHSIDGILEQ 228
           +LR     G  ++ D           +  HSIDGIL +
Sbjct: 157 ILRSKFGKGEEEEADLERKEAEESEKKAKHSIDGILSE 194

Probable transcription factor associated with development of alveolar rhabdomyosarcoma.

Mus musculus (taxid: 10090)

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

 Score =  217 bits (552), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 111/164 (67%), Positives = 132/164 (80%), Gaps = 6/164 (3%)

Query: 65  VEMAAA-GVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISR 123
           ++M++A  +RP       +    VNQLGGVFINGRPLPNHIRLKIVEMAA+GVRPCVISR
Sbjct: 1   MDMSSANSLRPLFAGYPFQGQGRVNQLGGVFINGRPLPNHIRLKIVEMAASGVRPCVISR 60

Query: 124 QLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRD 183
           QLRVSHGCVSKILNRYQETGSIRPGVIGGSKP+V +P++E RI+E +K NP IFSWEIR+
Sbjct: 61  QLRVSHGCVSKILNRYQETGSIRPGVIGGSKPKVTSPEIETRIDELRKENPSIFSWEIRE 120

Query: 184 RLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD-RKNHSIDGIL 226
           +L+K+ G  D    PS SSISRLLRG  R   D RK+++I+GIL
Sbjct: 121 KLIKE-GFADP---PSTSSISRLLRGSDRGSEDGRKDYTINGIL 160

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

Drosophila melanogaster (taxid: 7227)

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

 Score =  216 bits (551), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 127/158 (80%), Gaps = 17/158 (10%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  GVRPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGVRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           PG IGGSKP+ V TP+VEK++EE+K+ NPG+FSWEIRD+L+K DG+CD+N+ PSVSSISR
Sbjct: 98  PGAIGGSKPKQVTTPEVEKKMEEFKRDNPGMFSWEIRDKLLK-DGVCDRNTVPSVSSISR 156

Query: 206 LLRG--GRRDDCD-------------RKNHSIDGILEQ 228
           +LR   G+ D+ D             R  HSIDGIL +
Sbjct: 157 ILRSKFGKGDEEDMELDRKEQEESEKRAKHSIDGILRE 194

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

 Score =  207 bits (526), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 112/156 (71%), Positives = 122/156 (78%), Gaps = 17/156 (10%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct: 38  VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query: 147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS--VSSI 203
           PG IGGSKPR VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PS  VSSI
Sbjct: 98  PGAIGGSKPRQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSGLVSSI 156

Query: 204 SRLLR-------------GGRRDDCDRKNHSIDGIL 226
           SR+LR                 D   +  HSIDGIL
Sbjct: 157 SRVLRIKFGKKEEEDEADKKEDDGEKKAKHSIDGIL 192

Probable transcription factor. May have a role in myogenesis.

Homo sapiens (taxid: 9606)

>sp|P09084|PAX1_MOUSE Paired box protein Pax-1 OS=Mus musculus GN=Pax1 PE=1 SV=4

 Score =  192 bits (488), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 96/140 (68%), Positives = 113/140 (80%), Gaps = 2/140 (1%)

Query: 70  AGVRPCVISRQLRVSHG-VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVS 128
           +G R     R +  ++G VNQLGGVF+NGRPLPN IRL+IVE+A  G+RPC ISRQLRVS
Sbjct: 75  SGARQLAGPRAMEQTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVS 134

Query: 129 HGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQ 188
           HGCVSKIL RY ETGSI PG IGGSKPRV TP+V K I +YK+ +PGIF+WEIRDRL+  
Sbjct: 135 HGCVSKILARYNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRDRLLA- 193

Query: 189 DGICDKNSAPSVSSISRLLR 208
           DG+CDK + PSVSSISR+LR
Sbjct: 194 DGVCDKYNVPSVSSISRILR 213

This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column.

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	230
328713660	440	PREDICTED: protein gooseberry-like [Acyr	0.6	0.313	0.921	7e-70
242015336	390	protein gooseberry, putative [Pediculus	0.604	0.356	0.886	4e-68
357608260	471	gooseberry [Danaus plexippus]	0.604	0.295	0.879	1e-66
189240573	410	PREDICTED: similar to AGAP010358-PA [Tri	0.604	0.339	0.885	5e-66
270012821	406	gooseberry [Tribolium castaneum]	0.604	0.342	0.885	7e-66
307212050	438	Protein gooseberry-neuro [Harpegnathos s	0.626	0.328	0.843	8e-65
158290000	314	AGAP010358-PA [Anopheles gambiae str. PE	0.621	0.455	0.848	1e-64
380027472	405	PREDICTED: protein gooseberry-like [Apis	0.608	0.345	0.861	2e-64
307189638	574	Protein gooseberry [Camponotus floridanu	0.626	0.250	0.817	4e-64
312381651	550	hypothetical protein AND_05994 [Anophele	0.604	0.252	0.858	1e-63

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

 Score =  269 bits (687), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 129/140 (92%), Positives = 135/140 (96%), Gaps = 2/140 (1%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           +NQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  MNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATPDVE+RIEEYKK NP +FSWEIRD+LVKQDGICDKNSAPS+SSISRL
Sbjct: 83  PGVIGGSKPRVATPDVERRIEEYKKANPAMFSWEIRDKLVKQDGICDKNSAPSISSISRL 142

Query: 207 LRGGRRDDCDRKNHSIDGIL 226
           LRGGRRD+   KNHSIDGIL
Sbjct: 143 LRGGRRDEL--KNHSIDGIL 160

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242015336|ref|XP_002428315.1| protein gooseberry, putative [Pediculus humanus corporis] gi|212512911|gb|EEB15577.1| protein gooseberry, putative [Pediculus humanus corporis]

 Score =  263 bits (672), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 125/141 (88%), Positives = 137/141 (97%), Gaps = 2/141 (1%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNH+RLKIV+MA+AG+RPC ISRQLRVSHGCVSKILNRYQETGS+R
Sbjct: 25  VNQLGGVFINGRPLPNHVRLKIVQMASAGIRPCAISRQLRVSHGCVSKILNRYQETGSVR 84

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATP+VEKRIE+YKK+NPGIFSWEIRD+L+K +GICDKNSAPSVSSISRL
Sbjct: 85  PGVIGGSKPRVATPEVEKRIEDYKKSNPGIFSWEIRDKLIK-EGICDKNSAPSVSSISRL 143

Query: 207 LRGGRRDDCD-RKNHSIDGIL 226
           LRGGRRD+ D RKNHSIDGIL
Sbjct: 144 LRGGRRDENDPRKNHSIDGIL 164

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608260|gb|EHJ65894.1| gooseberry [Danaus plexippus]

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 124/141 (87%), Positives = 135/141 (95%), Gaps = 2/141 (1%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           +NQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  MNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATP+VE RIEE K+ NPGIFSWEIRD+L+K +GICDKN+APSVSSISRL
Sbjct: 83  PGVIGGSKPRVATPEVENRIEELKRQNPGIFSWEIRDKLIK-EGICDKNTAPSVSSISRL 141

Query: 207 LRGGRRDDCD-RKNHSIDGIL 226
           +RGG+RD+ D R+NHSIDGIL
Sbjct: 142 IRGGKRDESDPRRNHSIDGIL 162

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189240573|ref|XP_974212.2| PREDICTED: similar to AGAP010358-PA [Tribolium castaneum]

 Score =  256 bits (654), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 124/140 (88%), Positives = 132/140 (94%), Gaps = 1/140 (0%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRLKIVEMAAAG+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRLKIVEMAAAGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVAT +VE RIE+ KK  P IFSWEIRDRL+K +GICDKNSAPSVSSISRL
Sbjct: 83  PGVIGGSKPRVATLEVEARIEQLKKEEPQIFSWEIRDRLIK-EGICDKNSAPSVSSISRL 141

Query: 207 LRGGRRDDCDRKNHSIDGIL 226
           LRGGR++D DRKNHSI+GIL
Sbjct: 142 LRGGRKEDPDRKNHSIEGIL 161

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270012821|gb|EFA09269.1| gooseberry [Tribolium castaneum]

 Score =  256 bits (653), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 124/140 (88%), Positives = 132/140 (94%), Gaps = 1/140 (0%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRLKIVEMAAAG+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRLKIVEMAAAGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVAT +VE RIE+ KK  P IFSWEIRDRL+K +GICDKNSAPSVSSISRL
Sbjct: 83  PGVIGGSKPRVATLEVEARIEQLKKEEPQIFSWEIRDRLIK-EGICDKNSAPSVSSISRL 141

Query: 207 LRGGRRDDCDRKNHSIDGIL 226
           LRGGR++D DRKNHSI+GIL
Sbjct: 142 LRGGRKEDPDRKNHSIEGIL 161

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212050|gb|EFN87933.1| Protein gooseberry-neuro [Harpegnathos saltator]

 Score =  252 bits (644), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 124/147 (84%), Positives = 133/147 (90%), Gaps = 3/147 (2%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRLKIVEMAAAG+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 1   VNQLGGVFINGRPLPNHIRLKIVEMAAAGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 60

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATP+VE RIE+ K+ NPGIFSWEIRD+L+KQDG+CDK SAPSVSSISRL
Sbjct: 61  PGVIGGSKPRVATPEVEARIEDLKRQNPGIFSWEIRDKLIKQDGVCDKASAPSVSSISRL 120

Query: 207 LRG---GRRDDCDRKNHSIDGILEQSN 230
           LRG     R D  R+NHSIDGIL  S+
Sbjct: 121 LRGPANQTRPDDPRRNHSIDGILAGSS 147

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158290000|ref|XP_559100.2| AGAP010358-PA [Anopheles gambiae str. PEST] gi|157018429|gb|EAL41046.2| AGAP010358-PA [Anopheles gambiae str. PEST]

 Score =  252 bits (643), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 123/145 (84%), Positives = 136/145 (93%), Gaps = 2/145 (1%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRL+IVEMAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRLRIVEMAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRV+TP++E RIEE +K NPGIFSWEIRD+L+K DG+CDK SAPSVSSISRL
Sbjct: 83  PGVIGGSKPRVSTPEIEARIEELRKANPGIFSWEIRDKLIK-DGLCDKTSAPSVSSISRL 141

Query: 207 LRGGRRDDCD-RKNHSIDGILEQSN 230
           LRGGRR+D D R NHSI+GIL +S+
Sbjct: 142 LRGGRREDVDLRGNHSINGILGESS 166

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380027472|ref|XP_003697447.1| PREDICTED: protein gooseberry-like [Apis florea]

 Score =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 124/144 (86%), Positives = 131/144 (90%), Gaps = 4/144 (2%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATP+VE RIE+ K+ NPGIFSWEIR++L+KQDGICDK SAPSVSSISRL
Sbjct: 83  PGVIGGSKPRVATPEVEARIEDMKRQNPGIFSWEIREKLIKQDGICDKASAPSVSSISRL 142

Query: 207 LRG----GRRDDCDRKNHSIDGIL 226
           LRG     R  D  R+NHSIDGIL
Sbjct: 143 LRGPTNQTRPGDDPRRNHSIDGIL 166

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189638|gb|EFN73976.1| Protein gooseberry [Camponotus floridanus]

 Score =  249 bits (637), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 121/148 (81%), Positives = 135/148 (91%), Gaps = 4/148 (2%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRLKIVEMAAAG+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 23  VNQLGGVFINGRPLPNHIRLKIVEMAAAGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 82

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRVATP+VE +IE++K+ NPGIFSWEIR++L+KQDG+CDK SAPSVSSI+RL
Sbjct: 83  PGVIGGSKPRVATPEVEAKIEDFKRQNPGIFSWEIREKLIKQDGVCDKASAPSVSSITRL 142

Query: 207 LRGG----RRDDCDRKNHSIDGILEQSN 230
           LRG     R +D  R+NHSIDGIL  S+
Sbjct: 143 LRGPANQIRPNDDPRRNHSIDGILAGSS 170

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312381651|gb|EFR27354.1| hypothetical protein AND_05994 [Anopheles darlingi]

 Score =  248 bits (634), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 121/141 (85%), Positives = 131/141 (92%), Gaps = 2/141 (1%)

Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPNHIRL+IVEMAA+GVRPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 50  VNQLGGVFINGRPLPNHIRLRIVEMAASGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 109

Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRL 206
           PGVIGGSKPRV+TP++E RIEE +K NPGIFSWEIRDRL+K DG+CDK +APSVSSISRL
Sbjct: 110 PGVIGGSKPRVSTPEIEGRIEELRKANPGIFSWEIRDRLIK-DGLCDKTTAPSVSSISRL 168

Query: 207 LRGGRRDDCDRK-NHSIDGIL 226
           LRGGRR+D D   NHSI GIL
Sbjct: 169 LRGGRREDGDTHGNHSISGIL 189

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
FB|FBgn0001148	427	gsb "gooseberry" [Drosophila m	0.591	0.318	0.764	5.6e-52
ZFIN|ZDB-GENE-980526-52	509	pax3a "paired box gene 3a" [Da	0.508	0.229	0.831	4.2e-51
FB|FBgn0003145	613	prd "paired" [Drosophila melan	0.508	0.190	0.813	1.1e-50
ZFIN|ZDB-GENE-990415-201	507	pax7a "paired box gene 7a" [Da	0.508	0.230	0.818	2.9e-50
UNIPROTKB|Q0IH87	483	pax3-b "Paired box protein Pax	0.508	0.242	0.822	1.2e-49
ZFIN|ZDB-GENE-080917-54	510	pax7b "paired box gene 7b" [Da	0.508	0.229	0.792	1.6e-49
UNIPROTKB|O42349	524	Pax-7 "PAX7 protein" [Gallus g	0.508	0.223	0.848	2e-49
MGI|MGI:97491	503	Pax7 "paired box gene 7" [Mus	0.508	0.232	0.848	2e-49
RGD|1564360	503	Pax7 "paired box 7" [Rattus no	0.508	0.232	0.848	2e-49
UNIPROTKB|F1NYC8	503	PAX7 "Uncharacterized protein"	0.508	0.232	0.841	3.2e-49

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

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 107/140 (76%), Positives = 118/140 (84%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR +IVEMAAAGVRPCVISRQLRVSHGCVSKILNR+QETGSIR
Sbjct:    23 VNQLGGVFINGRPLPNHIRRQIVEMAAAGVRPCVISRQLRVSHGCVSKILNRFQETGSIR 82

Query:   147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISXX 206
             PGVIGGSKPRVATPD+E RIEE K++ PGIFSWEIR +L++  G+CDK +APSVSSIS  
Sbjct:    83 PGVIGGSKPRVATPDIESRIEELKQSQPGIFSWEIRAKLIEA-GVCDKQNAPSVSSISRL 141

Query:   207 XXXXXXXXXXXKNHSIDGIL 226
                         +HSIDGIL
Sbjct:   142 LRGSSGSGT---SHSIDGIL 158

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

ZFIN|ZDB-GENE-980526-52 pax3a "paired box gene 3a" [Danio rerio (taxid:7955)]

 Score = 512 (185.3 bits), Expect = 4.2e-51, Sum P(2) = 4.2e-51
 Identities = 99/119 (83%), Positives = 109/119 (91%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPRVAT-PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKP+ +T PDVEK+IEEYK+ NPG+FSWEIRD+L+K DGICD+N+ PSVSSIS
Sbjct:    98 PGAIGGSKPKQSTTPDVEKKIEEYKRENPGMFSWEIRDKLLK-DGICDRNNVPSVSSIS 155

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:0001755 "neural crest cell migration" evidence=IMP

GO:0048066 "developmental pigmentation" evidence=IMP

GO:0050936 "xanthophore differentiation" evidence=IMP

GO:0048484 "enteric nervous system development" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 96/118 (81%), Positives = 115/118 (97%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPN+IRLKIVEMAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct:    31 VNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 90

Query:   147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PGVIGGSKPR+ATP++E RIEEYK+++PG+FSWEIR++L+++ G+CD+++APSVS+IS
Sbjct:    91 PGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIRE-GVCDRSTAPSVSAIS 147

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

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

 Score = 504 (182.5 bits), Expect = 2.9e-50, Sum P(2) = 2.9e-50
 Identities = 99/121 (81%), Positives = 108/121 (89%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS--VSSI 203
             PG IGGSKPR VATPDVEKRIEEYK+ NPG+FSWEIRD+L+K DG+CD+ + PS   SS+
Sbjct:    98 PGAIGGSKPRQVATPDVEKRIEEYKRENPGMFSWEIRDKLLK-DGVCDRGTVPSGEASSV 156

Query:   204 S 204
             S
Sbjct:   157 S 157

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

UNIPROTKB|Q0IH87 pax3-b "Paired box protein Pax-3-B" [Xenopus laevis (taxid:8355)]

 Score = 517 (187.1 bits), Expect = 1.2e-49, P = 1.2e-49
 Identities = 97/118 (82%), Positives = 109/118 (92%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKP+V TP+VEK+IEE+K+ NPG+FSWEIRD+L+K DG+CD+N+ PSVSSIS
Sbjct:    98 PGAIGGSKPKVTTPEVEKKIEEFKRDNPGMFSWEIRDKLLK-DGVCDRNTVPSVSSIS 154

GO:0005634 "nucleus" evidence=ISS

GO:0008543 "fibroblast growth factor receptor signaling pathway" evidence=IGI

GO:0014029 "neural crest formation" evidence=IGI;IMP

GO:0014034 "neural crest cell fate commitment" evidence=IMP

GO:0016055 "Wnt receptor signaling pathway" evidence=IGI

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0048785 "hatching gland development" evidence=IMP

ZFIN|ZDB-GENE-080917-54 pax7b "paired box gene 7b" [Danio rerio (taxid:7955)]

 Score = 497 (180.0 bits), Expect = 1.6e-49, Sum P(2) = 1.6e-49
 Identities = 99/125 (79%), Positives = 109/125 (87%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR-----VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS-- 199
             PG IGGSKPR     VATPDVEKRIEEYK+ NPG+FSWEIRD+L+K DG+CD+++ PS  
Sbjct:    98 PGAIGGSKPRQTQKQVATPDVEKRIEEYKRENPGMFSWEIRDKLLK-DGVCDRSTVPSGE 156

Query:   200 VSSIS 204
              SS+S
Sbjct:   157 ASSVS 161

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 101/119 (84%), Positives = 109/119 (91%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKPR VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PSVSSIS
Sbjct:    98 PGAIGGSKPRQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSVSSIS 155

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

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

 Score = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 101/119 (84%), Positives = 109/119 (91%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKPR VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PSVSSIS
Sbjct:    98 PGAIGGSKPRQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSVSSIS 155

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 = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 101/119 (84%), Positives = 109/119 (91%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKPR VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PSVSSIS
Sbjct:    98 PGAIGGSKPRQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSVSSIS 155

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|F1NYC8 PAX7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 513 (185.6 bits), Expect = 3.2e-49, P = 3.2e-49
 Identities = 101/120 (84%), Positives = 109/120 (90%)

Query:    87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
             VNQLGGVFINGRPLPNHIR KIVEMA  G+RPCVISRQLRVSHGCVSKIL RYQETGSIR
Sbjct:    38 VNQLGGVFINGRPLPNHIRHKIVEMAHHGIRPCVISRQLRVSHGCVSKILCRYQETGSIR 97

Query:   147 PGVIGGSKPR--VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
             PG IGGSKPR  VATPDVEK+IEEYK+ NPG+FSWEIRDRL+K DG CD+++ PSVSSIS
Sbjct:    98 PGAIGGSKPRKQVATPDVEKKIEEYKRENPGMFSWEIRDRLLK-DGHCDRSTVPSVSSIS 156

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

---

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	0.7402	0.6043	0.2763	yes	N/A
P06601	PRD_DROME	No assigned EC number	0.6993	0.6391	0.2398	yes	N/A
P23760	PAX3_HUMAN	No assigned EC number	0.6962	0.6130	0.2943	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	230
pfam00292	125	pfam00292, PAX, 'Paired box' domain	8e-77
cd00131	128	cd00131, PAX, Paired Box domain	3e-74
smart00351	125	smart00351, PAX, Paired Box domain	1e-71
pfam13551	109	pfam13551, HTH_29, Winged helix-turn helix	8e-05
pfam13384	50	pfam13384, HTH_23, Homeodomain-like domain	1e-04
pfam13565	74	pfam13565, HTH_32, Homeodomain-like domain	2e-04

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

 Score =  227 bits (579), Expect = 8e-77
 Identities = 97/123 (78%), Positives = 111/123 (90%), Gaps = 1/123 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
            VNQLGGVF+NGRPLPNHIR KIVE+A +GVRPC ISRQLRVSHGCVSKIL RYQETGSI
Sbjct: 4   RVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQETGSI 63

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPGVIGGSKP+VATP+V K+I EYK+ NPGIF+WEIRDRL+  +G+CD ++ PSVSSISR
Sbjct: 64  RPGVIGGSKPKVATPEVVKKIAEYKRENPGIFAWEIRDRLLA-EGVCDNDNVPSVSSISR 122

Query: 206 LLR 208
           +LR
Sbjct: 123 ILR 125

Length = 125

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

 Score =  220 bits (563), Expect = 3e-74
 Identities = 94/124 (75%), Positives = 112/124 (90%), Gaps = 1/124 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
           GVNQLGGVF+NGRPLP+ IR +IVE+A +G+RPC ISRQLRVSHGCVSKILNRY ETGSI
Sbjct: 4   GVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSI 63

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPG IGGSKPRVATP+V K+IE YK+ NPG+F+WEIRDRL+ Q+G+CDK++ PSVSSI+R
Sbjct: 64  RPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLL-QEGVCDKSNVPSVSSINR 122

Query: 206 LLRG 209
           +LR 
Sbjct: 123 ILRN 126

Length = 128

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

 Score =  213 bits (545), Expect = 1e-71
 Identities = 90/123 (73%), Positives = 106/123 (86%), Gaps = 1/123 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
           GVNQLGGVF+NGRPLP+  R +IVE+A  GVRPC ISRQL VSHGCVSKIL RY ETGSI
Sbjct: 4   GVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSI 63

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPG IGGSKP+VATP V K+I +YK+ NPGIF+WEIRDRL+  +G+CDK++ PSVSSI+R
Sbjct: 64  RPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLL-SEGVCDKDNVPSVSSINR 122

Query: 206 LLR 208
           +LR
Sbjct: 123 ILR 125

Length = 125

>gnl|CDD|222216 pfam13551, HTH_29, Winged helix-turn helix

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 26/111 (23%), Positives = 48/111 (43%), Gaps = 12/111 (10%)

Query: 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRVATPDV 162
           R + + + A GV    I+R L +S   V + L R+ E G  +++     G      +P+ 
Sbjct: 1   RAQALLLLAEGVSVAQIARLLGLSRRTVYRWLKRFNEGGLAALKDRPRSGRPRNRLSPEQ 60

Query: 163 EKRIEEYKKTNP--GIFSWE---IRDRLVKQDGICDKNSAPSVSSISRLLR 208
           E  +    +  P  G   W    + + L ++ G+       S S++ RLL+
Sbjct: 61  EAALVALAREKPPEGFARWTLELLAELLERRFGV-----TVSRSTVRRLLK 106

This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. Length = 109

>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143
            R +I+ + A G+    I+  L VS   V + L RY+E G
Sbjct: 6   RRAEILLLLAEGLSVKEIAELLGVSRRTVYRWLKRYREGG 45

Length = 50

>gnl|CDD|222226 pfam13565, HTH_32, Homeodomain-like domain

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 7/78 (8%)

Query: 132 VSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIF--SWEIRDRLVKQD 189
           V + L RY+E G+       G       P+  + I       P          ++L +  
Sbjct: 2   VYRWLKRYREEGAAGLVHRPGRPSNHRYPEELRAIVLTLIREPYADFGPTLAAEKLAELH 61

Query: 190 GICDKNSAPSVSSISRLL 207
           G+       S  ++ R L
Sbjct: 62  GLK-----ISRETLRRWL 74

Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	100.0
KOG3517|consensus	334		100.0
KOG3862|consensus	327		99.96
cd00131	128	PAX Paired Box domain	99.95
smart00351	125	PAX Paired Box domain.	99.94
KOG0849|consensus	354		99.74
COG3415	138	Transposase and inactivated derivatives [DNA repli	99.73
PF13551	112	HTH_29: Winged helix-turn helix	99.72
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	99.68
PF13565	77	HTH_32: Homeodomain-like domain	99.32
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	99.29
cd00131	128	PAX Paired Box domain	99.22
KOG3862|consensus	327		99.12
smart00351	125	PAX Paired Box domain.	99.11
KOG3517|consensus	334		99.01
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	98.96
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	98.93
PF13518	52	HTH_28: Helix-turn-helix domain	98.79
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	98.45
PRK09413	121	IS2 repressor TnpA; Reviewed	98.44
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	98.38
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	98.2
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	98.18
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	98.14
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	98.12
KOG0849|consensus	354		98.05
PRK09409	301	IS2 transposase TnpB; Reviewed	97.94
COG2963	116	Transposase and inactivated derivatives [DNA repli	97.89
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	97.67
PHA02517	277	putative transposase OrfB; Reviewed	97.54
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.37
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	97.24
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	97.22
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	97.22
PHA02535	581	P terminase ATPase subunit; Provisional	97.13
PF01498	72	HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Tr	97.13
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	97.12
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	97.1
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	97.04
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	96.97
PRK00118	104	putative DNA-binding protein; Validated	96.92
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	96.91
PF13592	60	HTH_33: Winged helix-turn helix	96.89
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	96.87
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	96.83
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.7
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	96.7
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	96.7
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.66
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.5
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	96.49
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	96.48
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	96.47
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	96.44
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	96.4
PRK04217	110	hypothetical protein; Provisional	96.31
PF14493	91	HTH_40: Helix-turn-helix domain	96.3
TIGR01529	146	argR_whole arginine repressor. This model includes	96.29
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	96.28
PF13551	112	HTH_29: Winged helix-turn helix	96.28
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.26
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	96.23
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	96.18
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	96.08
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	96.06
PRK13413	200	mpi multiple promoter invertase; Provisional	96.06
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	96.05
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	96.0
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	95.95
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	95.86
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	95.84
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	95.81
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	95.75
PF13309	64	HTH_22: HTH domain	95.7
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	95.67
PRK06759	154	RNA polymerase factor sigma-70; Validated	95.64
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.64
PF01316	70	Arg_repressor: Arginine repressor, DNA binding dom	95.63
PRK12537	182	RNA polymerase sigma factor; Provisional	95.58
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	95.54
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	95.52
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	95.52
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	95.47
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	95.47
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	95.45
COG1725	125	Predicted transcriptional regulators [Transcriptio	95.43
TIGR02844	80	spore_III_D sporulation transcriptional regulator	95.43
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.43
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	95.41
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	95.39
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	95.39
PHA00675	78	hypothetical protein	95.39
PRK03975	141	tfx putative transcriptional regulator; Provisiona	95.37
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	95.35
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	95.34
PF11198	180	DUF2857: Protein of unknown function (DUF2857); In	95.33
PRK09047	161	RNA polymerase factor sigma-70; Validated	95.3
PHA02591	83	hypothetical protein; Provisional	95.28
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	95.28
PRK11924	179	RNA polymerase sigma factor; Provisional	95.27
PRK01381	99	Trp operon repressor; Provisional	95.2
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	95.2
PRK12514	179	RNA polymerase sigma factor; Provisional	95.19
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	95.13
PRK12528	161	RNA polymerase sigma factor; Provisional	95.12
PRK13919	186	putative RNA polymerase sigma E protein; Provision	95.1
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	95.09
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	95.08
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	95.07
PRK11050	152	manganese transport regulator MntR; Provisional	95.06
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	95.05
PRK15418	318	transcriptional regulator LsrR; Provisional	95.05
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	95.03
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	95.03
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	95.0
PRK12469	481	RNA polymerase factor sigma-54; Provisional	94.99
PHA00738	108	putative HTH transcription regulator	94.97
PRK15201	198	fimbriae regulatory protein FimW; Provisional	94.94
PF07638	185	Sigma70_ECF: ECF sigma factor	94.94
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	94.93
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	94.9
PRK12547	164	RNA polymerase sigma factor; Provisional	94.89
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.86
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	94.84
PRK12530	189	RNA polymerase sigma factor; Provisional	94.83
PF13276	60	HTH_21: HTH-like domain	94.77
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	94.77
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	94.77
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	94.76
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	94.76
PF12728	51	HTH_17: Helix-turn-helix domain	94.75
PF12298	172	Bot1p: Eukaryotic mitochondrial regulator protein	94.75
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	94.75
COG5484	279	Uncharacterized conserved protein [Function unknow	94.75
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	94.69
PRK12529	178	RNA polymerase sigma factor; Provisional	94.68
PRK04280	148	arginine repressor; Provisional	94.67
PRK12525	168	RNA polymerase sigma factor; Provisional	94.67
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	94.67
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	94.66
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	94.65
PRK08241	339	RNA polymerase factor sigma-70; Validated	94.63
PRK12519	194	RNA polymerase sigma factor; Provisional	94.61
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	94.61
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.61
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	94.6
COG1438	150	ArgR Arginine repressor [Transcription]	94.6
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	94.58
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	94.56
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	94.53
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	94.51
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	94.51
PRK12511	182	RNA polymerase sigma factor; Provisional	94.51
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	94.51
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	94.49
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	94.46
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	94.46
PRK12516	187	RNA polymerase sigma factor; Provisional	94.45
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	94.4
PRK09415	179	RNA polymerase factor sigma C; Reviewed	94.4
PRK13749	121	transcriptional regulator MerD; Provisional	94.37
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	94.37
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	94.36
PRK12523	172	RNA polymerase sigma factor; Reviewed	94.35
PRK12522	173	RNA polymerase sigma factor; Provisional	94.34
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	94.33
PRK12532	195	RNA polymerase sigma factor; Provisional	94.3
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	94.29
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	94.29
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	94.25
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	94.25
PHA00542	82	putative Cro-like protein	94.25
PRK06930	170	positive control sigma-like factor; Validated	94.24
PRK03341	168	arginine repressor; Provisional	94.23
TIGR01764	49	excise DNA binding domain, excisionase family. An	94.22
PRK12517	188	RNA polymerase sigma factor; Provisional	94.22
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	94.2
PRK05066	156	arginine repressor; Provisional	94.2
PRK06811	189	RNA polymerase factor sigma-70; Validated	94.18
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	94.18
PRK12520	191	RNA polymerase sigma factor; Provisional	94.15
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.15
PRK12524	196	RNA polymerase sigma factor; Provisional	94.1
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	94.1
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	94.09
PRK08301	234	sporulation sigma factor SigE; Reviewed	94.07
PRK12534	187	RNA polymerase sigma factor; Provisional	94.06
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	94.05
PRK05602	186	RNA polymerase sigma factor; Reviewed	94.04
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	94.03
PRK12540	182	RNA polymerase sigma factor; Provisional	94.02
PRK12542	185	RNA polymerase sigma factor; Provisional	94.01
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	93.99
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	93.99
PRK12536	181	RNA polymerase sigma factor; Provisional	93.99
PRK12533	216	RNA polymerase sigma factor; Provisional	93.98
PRK12512	184	RNA polymerase sigma factor; Provisional	93.98
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	93.96
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	93.94
PRK12526	206	RNA polymerase sigma factor; Provisional	93.92
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	93.92
TIGR02054	120	MerD mercuric resistence transcriptional repressor	93.89
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	93.88
PRK08583	257	RNA polymerase sigma factor SigB; Validated	93.88
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	93.87
PRK12543	179	RNA polymerase sigma factor; Provisional	93.84
PRK12539	184	RNA polymerase sigma factor; Provisional	93.83
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	93.83
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	93.81
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.8
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	93.8
PRK12545	201	RNA polymerase sigma factor; Provisional	93.72
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	93.7
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	93.69
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.68
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	93.67
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	93.65
PRK12541	161	RNA polymerase sigma factor; Provisional	93.64
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	93.64
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	93.62
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	93.61
PRK12544	206	RNA polymerase sigma factor; Provisional	93.59
PRK00441	149	argR arginine repressor; Provisional	93.58
COG1508	444	RpoN DNA-directed RNA polymerase specialized sigma	93.55
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	93.51
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	93.5
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	93.5
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	93.5
PRK12527	159	RNA polymerase sigma factor; Reviewed	93.47
PRK12535	196	RNA polymerase sigma factor; Provisional	93.47
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	93.46
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	93.45
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	93.45
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.4
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	93.38
PRK12546	188	RNA polymerase sigma factor; Provisional	93.36
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	93.34
PRK12531	194	RNA polymerase sigma factor; Provisional	93.33
PRK12515	189	RNA polymerase sigma factor; Provisional	93.31
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	93.24
COG3355	126	Predicted transcriptional regulator [Transcription	93.18
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	93.16
PHA01976	67	helix-turn-helix protein	93.15
PF08765	108	Mor: Mor transcription activator family; InterPro:	93.13
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	93.12
PRK12513	194	RNA polymerase sigma factor; Provisional	93.11
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	93.08
PRK12538	233	RNA polymerase sigma factor; Provisional	93.05
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	93.02
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	92.98
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	92.95
COG2197	211	CitB Response regulator containing a CheY-like rec	92.93
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	92.92
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	92.9
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	92.9
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	92.89
PRK06704	228	RNA polymerase factor sigma-70; Validated	92.85
PRK10840	216	transcriptional regulator RcsB; Provisional	92.79
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	92.78
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	92.76
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	92.69
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	92.62
PRK10046	225	dpiA two-component response regulator DpiA; Provis	92.61
PRK13182	175	racA polar chromosome segregation protein; Reviewe	92.5
PRK05803	233	sporulation sigma factor SigK; Reviewed	92.48
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	92.43
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	92.43
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	92.37
PRK05572	252	sporulation sigma factor SigF; Validated	92.26
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	92.22
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	92.2
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	92.2
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	92.19
COG1710	139	Uncharacterized protein conserved in archaea [Func	92.13
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	92.12
PF13730	55	HTH_36: Helix-turn-helix domain	92.07
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	92.06
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	92.06
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	92.01
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	92.0
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	91.96
PRK08295	208	RNA polymerase factor sigma-70; Validated	91.86
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	91.81
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.8
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	91.77
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	91.75
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	91.72
PRK13509	251	transcriptional repressor UlaR; Provisional	91.62
PRK07670	251	RNA polymerase sigma factor SigD; Validated	91.6
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	91.57
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	91.56
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	91.54
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	91.53
COG2522	119	Predicted transcriptional regulator [General funct	91.5
PRK09191	261	two-component response regulator; Provisional	91.48
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	91.42
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	91.38
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	91.36
COG4496	100	Uncharacterized protein conserved in bacteria [Fun	91.32
PRK12518	175	RNA polymerase sigma factor; Provisional	91.26
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	91.22
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	91.14
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	91.14
PF10654	126	DUF2481: Protein of unknown function (DUF2481) ; I	91.14
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	91.14
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	91.11
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	91.1
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.06
TIGR03338	212	phnR_burk phosphonate utilization associated trans	91.05
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	91.04
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	91.02
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	90.95
PRK01905	77	DNA-binding protein Fis; Provisional	90.95
TIGR02607	78	antidote_HigA addiction module antidote protein, H	90.9
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	90.87
COG2345	218	Predicted transcriptional regulator [Transcription	90.81
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	90.8
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	90.74
PRK11169	164	leucine-responsive transcriptional regulator; Prov	90.74
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	90.73
COG2944	104	Predicted transcriptional regulator [Transcription	90.73
PRK06474	178	hypothetical protein; Provisional	90.67
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	90.6
PRK09954	362	putative kinase; Provisional	90.58
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.5
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	90.49
PRK11608	326	pspF phage shock protein operon transcriptional ac	90.43
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	90.41
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	90.41
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	90.4
PF06413	225	Neugrin: Neugrin; InterPro: IPR010487 This family	90.35
PRK08215	258	sporulation sigma factor SigG; Reviewed	90.33
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	90.3
PRK09492	315	treR trehalose repressor; Provisional	90.27
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	90.25
PRK10072	96	putative transcriptional regulator; Provisional	90.23
PF13565	77	HTH_32: Homeodomain-like domain	90.23
PRK09863	584	putative frv operon regulatory protein; Provisiona	90.23
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.21
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	90.15
PRK13752	144	putative transcriptional regulator MerR; Provision	90.1
PRK15043	243	transcriptional regulator MirA; Provisional	90.07
PRK15320	251	transcriptional activator SprB; Provisional	90.06
COG2964	220	Uncharacterized protein conserved in bacteria [Fun	89.88
PF07141	174	Phage_term_sma: Putative bacteriophage terminase s	89.87
PRK09462	148	fur ferric uptake regulator; Provisional	89.85
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	89.79
PRK00430	95	fis global DNA-binding transcriptional dual regula	89.77
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	89.74
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	89.68
PRK11922	231	RNA polymerase sigma factor; Provisional	89.62
PRK09483	217	response regulator; Provisional	89.61
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	89.59
COG3415	138	Transposase and inactivated derivatives [DNA repli	89.54
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	89.49
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	89.43
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	89.34
PRK10651	216	transcriptional regulator NarL; Provisional	89.32
PRK09726	88	antitoxin HipB; Provisional	89.28
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	89.28
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	89.26
PRK09526	342	lacI lac repressor; Reviewed	89.18
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	89.11
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	89.08
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	88.91
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	88.88
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	88.87
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	88.86
COG1522	154	Lrp Transcriptional regulators [Transcription]	88.84
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	88.71
PRK14987	331	gluconate operon transcriptional regulator; Provis	88.68
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	88.67
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	88.65
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	88.63
PRK11639	169	zinc uptake transcriptional repressor; Provisional	88.62
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	88.61
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	88.36
PRK14702	262	insertion element IS2 transposase InsD; Provisiona	88.35
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	88.31
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	88.3
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	88.15
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	88.14
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	88.04
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	87.99
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	87.98
PF13518	52	HTH_28: Helix-turn-helix domain	87.95
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	87.93
PRK15369	211	two component system sensor kinase SsrB; Provision	87.81
COG1802	230	GntR Transcriptional regulators [Transcription]	87.77
COG2512	258	Predicted membrane-associated trancriptional regul	87.77
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	87.6
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	87.59
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	87.5
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	87.46
PRK09706	135	transcriptional repressor DicA; Reviewed	87.46
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	87.42
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	87.36
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	87.14
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	87.11
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	87.08
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	87.07
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	87.0
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	86.83
COG3355	126	Predicted transcriptional regulator [Transcription	86.82
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	86.64
PRK11014	141	transcriptional repressor NsrR; Provisional	86.63
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	86.5
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	86.41
COG3413	215	Predicted DNA binding protein [General function pr	86.28
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	86.27
COG1609	333	PurR Transcriptional regulators [Transcription]	86.26
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	86.23
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	86.13
COG2973	103	TrpR Trp operon repressor [Transcription]	86.09
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	85.99
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	85.89
COG1476	68	Predicted transcriptional regulators [Transcriptio	85.89
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	85.78
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	85.74
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	85.57
COG1654	79	BirA Biotin operon repressor [Transcription]	85.56
PRK09480	194	slmA division inhibitor protein; Provisional	85.52
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	85.51
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	85.34
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	85.32
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	85.25
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	85.24
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	85.21
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	85.04
PF13309	64	HTH_22: HTH domain	84.98
TIGR01453	214	grpIintron_endo group I intron endonuclease. This	84.96
COG5352	169	Uncharacterized protein conserved in bacteria [Fun	84.95
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	84.85
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	84.63
PRK15424	538	propionate catabolism operon regulatory protein Pr	84.6
PRK10423	327	transcriptional repressor RbsR; Provisional	84.57
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	84.53
PRK13890	120	conjugal transfer protein TrbA; Provisional	84.51
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	84.5
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	84.32
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	84.27
PRK00215	205	LexA repressor; Validated	84.23
PF11985	180	DUF3486: Protein of unknown function (DUF3486); In	84.21
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	84.12
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	84.03
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	83.98
TIGR02844	80	spore_III_D sporulation transcriptional regulator	83.96
PRK11169	164	leucine-responsive transcriptional regulator; Prov	83.94
COG3398	240	Uncharacterized protein conserved in archaea [Func	83.68
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	83.52
cd00283	113	GIY-YIG_Cterm GIYX(10-11)YIG family of class I hom	83.3
TIGR00647	279	MG103 conserved hypothetical protein.	83.22
PRK10403	215	transcriptional regulator NarP; Provisional	83.22
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	83.21
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	83.13
PRK06424	144	transcription factor; Provisional	83.11
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	83.0
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	82.85
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	82.53
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	82.48
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	82.29
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	82.29
PRK13870	234	transcriptional regulator TraR; Provisional	82.28
PRK04984	239	fatty acid metabolism regulator; Provisional	82.22
PRK12682	309	transcriptional regulator CysB-like protein; Revie	82.17
PRK14165	217	winged helix-turn-helix domain-containing protein/	82.09
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	82.03
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	81.87
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	81.86
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	81.85
PRK11569	274	transcriptional repressor IclR; Provisional	81.7
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	81.67
PRK03902	142	manganese transport transcriptional regulator; Pro	81.58
PRK15115	444	response regulator GlrR; Provisional	81.53
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	81.49
COG1961	222	PinR Site-specific recombinases, DNA invertase Pin	81.45
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	81.37
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	81.25
COG5566	137	Uncharacterized conserved protein [Function unknow	81.23
PRK09935	210	transcriptional regulator FimZ; Provisional	81.2
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	81.15
PRK14999	241	histidine utilization repressor; Provisional	81.01
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	80.98
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	80.97
PRK04841	903	transcriptional regulator MalT; Provisional	80.79
PF04645	181	DUF603: Protein of unknown function, DUF603; Inter	80.73
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	80.67
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	80.55
PRK12423	202	LexA repressor; Provisional	80.42
COG1356	143	tfx Transcriptional regulator [DNA replication, re	80.41
PF08069	60	Ribosomal_S13_N: Ribosomal S13/S15 N-terminal doma	80.4
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	80.38
PRK03837	241	transcriptional regulator NanR; Provisional	80.29
PRK09906	296	DNA-binding transcriptional regulator HcaR; Provis	80.13
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	80.03

>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=100.00  E-value=2.7e-35  Score=230.73  Aligned_cols=125  Identities=74%  Similarity=1.263  Sum_probs=95.1

Q ss_pred             CCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCH
Q psy1898          39 CQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRP  118 (230)
Q Consensus        39 ~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~  118 (230)
                      ||+++|||||+|+||+|||.++|.+||||+.+|++||+||++|+|+|||                               
T Consensus         1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gc-------------------------------   49 (125)
T PF00292_consen    1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGC-------------------------------   49 (125)
T ss_dssp             S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHH-------------------------------
T ss_pred             CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhH-------------------------------
Confidence            5788999999999999999999999999998888888888888877777                               


Q ss_pred             HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCC
Q psy1898         119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAP  198 (230)
Q Consensus       119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~v  198 (230)
                                   |+||++||++||++.|...+|.+|++.++++.++|.++..++|.+++|||++.|.+ .|+|+..++|
T Consensus        50 -------------VsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~-~gvc~~~~~P  115 (125)
T PF00292_consen   50 -------------VSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIA-DGVCDRSNVP  115 (125)
T ss_dssp             -------------HHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHH-TTSS-TTTS-
T ss_pred             -------------HHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHH-cCCCCCCCCC
Confidence                         67999999999999999998889999999999999999999999999999999998 9999999999


Q ss_pred             CHhHHHHHHH
Q psy1898         199 SVSSISRLLR  208 (230)
Q Consensus       199 S~sTV~R~Lr  208 (230)
                      |.|+|+|+|+
T Consensus       116 svssInRilr  125 (125)
T PF00292_consen  116 SVSSINRILR  125 (125)
T ss_dssp             -HHHHHHHHH
T ss_pred             CHHHHHHhhC
Confidence            9999999996

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.

>KOG3517|consensus

Probab=100.00  E-value=9e-34  Score=242.06  Aligned_cols=126  Identities=72%  Similarity=1.185  Sum_probs=121.4

Q ss_pred             CCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHH
Q psy1898          40 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPC  119 (230)
Q Consensus        40 ~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~  119 (230)
                      .+.||||||+||||||||.++|++|||++..|.+||||||||||||||                                
T Consensus         5 ~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGC--------------------------------   52 (334)
T KOG3517|consen    5 YGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGC--------------------------------   52 (334)
T ss_pred             ccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccch--------------------------------
Confidence            368999999999999999999999999999999999999999999999                                


Q ss_pred             HHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCC
Q psy1898         120 VISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS  199 (230)
Q Consensus       120 ~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS  199 (230)
                                  |+|++.||.|+|++-|.-++|.+|+++|+.+.++|+.+.+.+|.+++|||+++|.. .|||+...++|
T Consensus        53 ------------VSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLls-dgiCDk~NvPS  119 (334)
T KOG3517|consen   53 ------------VSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLS-DGICDKYNVPS  119 (334)
T ss_pred             ------------HHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhh-cccccccCCcc
Confidence                        46888999999999999999999999999999999999999999999999999999 99999999999


Q ss_pred             HhHHHHHHHcC
Q psy1898         200 VSSISRLLRGG  210 (230)
Q Consensus       200 ~sTV~R~Lr~~  210 (230)
                      +|+|.|+|+++
T Consensus       120 VSSISRILRNK  130 (334)
T KOG3517|consen  120 VSSISRILRNK  130 (334)
T ss_pred             hHHHHHHHHhh
Confidence            99999999987

>KOG3862|consensus

Probab=99.96  E-value=9.2e-29  Score=213.31  Aligned_cols=132  Identities=65%  Similarity=1.099  Sum_probs=124.4

Q ss_pred             CCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCC
Q psy1898          38 SCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVR  117 (230)
Q Consensus        38 ~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s  117 (230)
                      .|+++||||||+||||||||+.+|+.|+||+++|++||+|+||++|||||+                             
T Consensus         8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcv-----------------------------   58 (327)
T KOG3862|consen    8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCV-----------------------------   58 (327)
T ss_pred             CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCc-----------------------------
Confidence            478999999999999999999999999999999999999999999999995                             


Q ss_pred             HHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCC
Q psy1898         118 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSA  197 (230)
Q Consensus       118 ~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~  197 (230)
                                     ++++-||-|+|+++++.+++..|+..++.+.+.|..+.+++|.+++|||++.|.. .++|+.+++
T Consensus        59 ---------------Skil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~-~~ic~~d~v  122 (327)
T KOG3862|consen   59 ---------------SKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLA-EPICDNDTV  122 (327)
T ss_pred             ---------------hhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhc-ccccCCCCC
Confidence                           4667899999999999999999999999999999999999999999999999988 899999999


Q ss_pred             CCHhHHHHHHHcCCCCC
Q psy1898         198 PSVSSISRLLRGGRRDD  214 (230)
Q Consensus       198 vS~sTV~R~Lr~~g~~~  214 (230)
                      +|++.|.|+++...+.+
T Consensus       123 psVssinri~r~~~~~~  139 (327)
T KOG3862|consen  123 PSVSSINRIIRTKVQQK  139 (327)
T ss_pred             chHHHHHHHHHHhhhhc
Confidence            99999999999886553

>cd00131 PAX Paired Box domain

Probab=99.95  E-value=1.6e-27  Score=189.07  Aligned_cols=125  Identities=74%  Similarity=1.285  Sum_probs=115.8

Q ss_pred             ccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHH
Q psy1898          85 HGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEK  164 (230)
Q Consensus        85 hg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~  164 (230)
                      .++|+||+.|.++++||.+.|.+||+++++|+|.++||++|+||++||++|+++|+++|++.|++.+|.+|++++++..+
T Consensus         3 ~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~   82 (128)
T cd00131           3 GGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVK   82 (128)
T ss_pred             ccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHH
Confidence            35889999999999999999999999999999999999999999999999999999999999988877678988998888


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         165 RIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       165 ~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +|..+++++|++|++||+++|.. .|++..+..||.|||+|+|+++
T Consensus        83 ~i~~~v~~~p~~Tl~El~~~L~~-~gv~~~~~~~s~stI~R~L~~~  127 (128)
T cd00131          83 KIEIYKQENPGMFAWEIRDRLLQ-EGVCDKSNVPSVSSINRILRNK  127 (128)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHH-cCCcccCCCCCHHHHHHHHHhc
Confidence            99999999999999999999876 7887666678999999999875

>smart00351 PAX Paired Box domain

Probab=99.94  E-value=2.9e-26  Score=181.10  Aligned_cols=124  Identities=73%  Similarity=1.247  Sum_probs=116.3

Q ss_pred             cccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHH
Q psy1898          84 SHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE  163 (230)
Q Consensus        84 shg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~  163 (230)
                      +.|+|++|+-|.++++||.++|.+||.++++|.+.++||++|+||++||++|+++|+++|.+.|++.++.+|+++++++.
T Consensus         2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~   81 (125)
T smart00351        2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV   81 (125)
T ss_pred             CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999998887778999999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH
Q psy1898         164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR  208 (230)
Q Consensus       164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr  208 (230)
                      ++|.++++++|++|++||+++|.+ .|++.....||.|||+++|+
T Consensus        82 ~~I~~~~~~~p~~t~~el~~~L~~-~gv~~~~~~Ps~sti~~~l~  125 (125)
T smart00351       82 KKIADYKQENPGIFAWEIRDRLLS-EGVCDKDNVPSVSSINRILR  125 (125)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHH-cCCCcCCCCCChhhHHHhhC
Confidence            999999999999999999999986 89887778899999999985

>KOG0849|consensus

Probab=99.74  E-value=1.6e-18  Score=158.49  Aligned_cols=143  Identities=68%  Similarity=1.135  Sum_probs=120.7

Q ss_pred             CCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHH
Q psy1898          41 GRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCV  120 (230)
Q Consensus        41 ~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~  120 (230)
                      +++||+||+|+||+|+|.++|..|++|+..|.++|.|++++.|+|||                                 
T Consensus         1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~---------------------------------   47 (354)
T KOG0849|consen    1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGC---------------------------------   47 (354)
T ss_pred             CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHH---------------------------------
Confidence            35677777777777777777778888888888889999999866666                                 


Q ss_pred             HhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCC-CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCC
Q psy1898         121 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS  199 (230)
Q Consensus       121 IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr-~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS  199 (230)
                                 |.+++++|.++|++.|.-.++.+|+ +.+++++.+|..+..++|.+++|+|.+.|.. .++|+..+.+|
T Consensus        48 -----------~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~-~~~~~~~t~Ps  115 (354)
T KOG0849|consen   48 -----------VSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLH-EGLCTQATLPS  115 (354)
T ss_pred             -----------HHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccC-cccccCCCCCC
Confidence                       5678899999999999888777777 8889999999999999999999999999988 89998888999


Q ss_pred             HhHHHHHHHcCCCCCCC---------CCCcCccccccc
Q psy1898         200 VSSISRLLRGGRRDDCD---------RKNHSIDGILEQ  228 (230)
Q Consensus       200 ~sTV~R~Lr~~g~~~~~---------~~~~s~~~~~~~  228 (230)
                      .+++.|.|+...+....         .+.+++++++|.
T Consensus       116 ~ssi~r~~r~~~~~~d~~~~~~~~~~~~~~~~~~~~gs  153 (354)
T KOG0849|consen  116 VSSINRVLRNGALGKDQGLPSQQVTKEKSPSISGALGS  153 (354)
T ss_pred             hhhhhHHhhccccccccccccccccccccCCcccccCC
Confidence            99999999976654432         367899999986

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

Probab=99.73  E-value=3.2e-17  Score=131.15  Aligned_cols=117  Identities=21%  Similarity=0.239  Sum_probs=103.4

Q ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy1898          97 GRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPG  175 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~  175 (230)
                      .++++.++|..++..+ .+|+|.++||++||||.+||++|++||+++|...+...++++|++++++..+.|...+++.. 
T Consensus         2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-   80 (138)
T COG3415           2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-   80 (138)
T ss_pred             CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-
Confidence            5788999999999877 57999999999999999999999999999998855555677999999999999988887665 


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCCC
Q psy1898         176 IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRKN  219 (230)
Q Consensus       176 ~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~~  219 (230)
                      +|+.++...|..++|+.     .+.++|+++|++.|++...+..
T Consensus        81 wTl~~~~~~l~~e~gv~-----y~~~~v~~~l~~~GlsykK~~~  119 (138)
T COG3415          81 WTLKELVEELGLEFGVW-----YHASAVRRLLHELGLSYKKPRW  119 (138)
T ss_pred             chHHHHHHHHhhhcCeE-----EeHHHHHHHHHHcCCCcCCCCC
Confidence            99999999998889995     8999999999999999776443

>PF13551 HTH_29: Winged helix-turn helix

Probab=99.72  E-value=4.9e-17  Score=123.83  Aligned_cols=101  Identities=31%  Similarity=0.432  Sum_probs=87.3

Q ss_pred             HHHHHHHHHcCCC-HHHHhhhhccccchhhhHHHHHhhhC--CCCc-CCCCCCCCCC-CCHHHHHHHHHHHHhCC-----
Q psy1898         105 RLKIVEMAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRP-GVIGGSKPRV-ATPDVEKRIEEYKKTNP-----  174 (230)
Q Consensus       105 R~rIV~l~~~G~s-~~~IAr~lgVS~sTV~kwikRy~e~G--~v~p-~~~gg~rpr~-lt~~~~~~I~~l~~~~P-----  174 (230)
                      |.+|+.++.+|.+ ..+||+.+|||+.||++|+++|+++|  .+.+ .++ +++|+. +++++.+.|.+++.++|     
T Consensus         1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~-~g~~~~~l~~~~~~~l~~~~~~~p~~g~~   79 (112)
T PF13551_consen    1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPR-GGRPRKRLSEEQRAQLIELLRENPPEGRS   79 (112)
T ss_pred             CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhcccc-CCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Confidence            5789999999995 99999999999999999999999999  4445 333 346665 89999999999999988     


Q ss_pred             CCCHHHHHHHH-HHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         175 GIFSWEIRDRL-VKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       175 ~~t~~eI~~~L-~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      .++..+++++| ++.+|+.     +|.+||+|+|+++|
T Consensus        80 ~~t~~~l~~~l~~~~~~~~-----~s~~ti~r~L~~~G  112 (112)
T PF13551_consen   80 RWTLEELAEWLIEEEFGID-----VSPSTIRRILKRAG  112 (112)
T ss_pred             cccHHHHHHHHHHhccCcc-----CCHHHHHHHHHHCc
Confidence            58899999987 6667775     89999999999987

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

Probab=99.68  E-value=2.5e-16  Score=123.35  Aligned_cols=100  Identities=22%  Similarity=0.278  Sum_probs=86.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS  178 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~  178 (230)
                      .||.|+|.+||..++.|.|.+++|+.|+||.+||++|++ ..++|.+.+.++++  + +++   .+.|..++.++|+.|+
T Consensus         2 aYS~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~--~-Kid---~~~L~~~v~~~pd~tl   74 (119)
T PF01710_consen    2 AYSLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGR--K-KID---RDELKALVEENPDATL   74 (119)
T ss_pred             CCCHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hccccccccccccc--c-ccc---HHHHHHHHHHCCCcCH
Confidence            599999999999999999999999999999999999999 67789888776533  2 553   4678999999999999


Q ss_pred             HHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         179 WEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       179 ~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      .|+++.|    |       ||.+||+++|++.|+.-..
T Consensus        75 ~Ela~~l----~-------Vs~~ti~~~Lkrlg~t~KK  101 (119)
T PF01710_consen   75 RELAERL----G-------VSPSTIWRALKRLGITRKK  101 (119)
T ss_pred             HHHHHHc----C-------CCHHHHHHHHHHcCchhcc
Confidence            9998754    4       4999999999999998554

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 [].

>PF13565 HTH_32: Homeodomain-like domain

Probab=99.32  E-value=8e-12  Score=89.70  Aligned_cols=72  Identities=29%  Similarity=0.399  Sum_probs=59.7

Q ss_pred             hhhhHHHHHhhhC-----CCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHH
Q psy1898         131 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR  205 (230)
Q Consensus       131 TV~kwikRy~e~G-----~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R  205 (230)
                      ||++|+++|++.|     ...+++++ ++|++ ++++.+.|.+++.++|.++..+|++.|..++|+..   .||.+||+|
T Consensus         1 Tv~rw~~ry~~~G~~gL~~~~~~~~~-Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R   75 (77)
T PF13565_consen    1 TVYRWLKRYREEGLEGLKDRKRRPRP-GRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYR   75 (77)
T ss_pred             CHHHHHHHHHhhCchhhhcccccCCC-CCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHH
Confidence            8999999999999     32233443 46777 88888999999999999999999999999888740   259999999


Q ss_pred             HH
Q psy1898         206 LL  207 (230)
Q Consensus       206 ~L  207 (230)
                      +|
T Consensus        76 ~L   77 (77)
T PF13565_consen   76 IL   77 (77)
T ss_pred             hC
Confidence            86

>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=99.29  E-value=1.3e-12  Score=102.69  Aligned_cols=35  Identities=71%  Similarity=1.206  Sum_probs=27.8

Q ss_pred             CCcccccccceeecCccCChhHHHHHHHHHhcCCC
Q psy1898           2 GQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRG   36 (230)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   36 (230)
                      |||++|||||||+||||||+++|++|+|||..|-.
T Consensus         1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~r   35 (125)
T PF00292_consen    1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVR   35 (125)
T ss_dssp             S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--
T ss_pred             CCccccccCceeeCCccCcHHHHHHHHHHhhhcCC
Confidence            89999999999999999999999999999986543

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=99.22  E-value=7.6e-11  Score=93.52  Aligned_cols=100  Identities=46%  Similarity=0.686  Sum_probs=74.9

Q ss_pred             CCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccc--cCCc-----cc---C----CCcCCHHH
Q psy1898          39 CQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQ--LGGV-----FI---N----GRPLPNHI  104 (230)
Q Consensus        39 ~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~--l~~~-----~~---~----g~~~s~~~  104 (230)
                      ||+.+||+||+|.+++|++.+.|..|++++.+|.+..+|+++|+|++.++.  +.++     +.   .    .+..+.+.
T Consensus         1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~   80 (128)
T cd00131           1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEV   80 (128)
T ss_pred             CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHH
Confidence            578899999999999999999999999999999999999999999888751  1111     11   0    11233444


Q ss_pred             HHHHHHHHHc--CCCHHHHhhhh---cc-------ccchhhhHHHH
Q psy1898         105 RLKIVEMAAA--GVRPCVISRQL---RV-------SHGCVSKILNR  138 (230)
Q Consensus       105 R~rIV~l~~~--G~s~~~IAr~l---gV-------S~sTV~kwikR  138 (230)
                      ...|+.+..+  ..+..++++.|   +|       |.+||.+|+++
T Consensus        81 ~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          81 VKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence            4455554444  48999999886   55       99999999875

>KOG3862|consensus

Probab=99.12  E-value=6.1e-11  Score=103.26  Aligned_cols=122  Identities=34%  Similarity=0.439  Sum_probs=73.6

Q ss_pred             CCcccccccceeecCccCChhHHHHHHHHHhcCCCCCCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhh
Q psy1898           2 GQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQL   81 (230)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~l   81 (230)
                      |+|-|||||||||||||||+.+|+-|||||--|---..-+.  ||-  .-+|-+  .    +|.-.|.     +..|...
T Consensus         9 ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisr--Ql~--vShGcv--S----kil~r~y-----EtgS~~p   73 (327)
T KOG3862|consen    9 GHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISR--QLR--VSHGCV--S----KILGRYY-----ETGSIRP   73 (327)
T ss_pred             CccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHH--HHh--hccCCc--h----hHHHHHH-----HhcCccc
Confidence            78999999999999999999999999999987743111000  110  011111  0    0111110     1111111


Q ss_pred             cc--------cccc----------------cccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898          82 RV--------SHGV----------------NQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        82 rv--------shg~----------------~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++        ..-|                +--.+.+..++++-...++.+|..++.++....++++++++.++|.+-+.
T Consensus        74 g~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~~~s~vsk~l~  153 (327)
T KOG3862|consen   74 GVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGITHSCVTKVLA  153 (327)
T ss_pred             CCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccCCccchhhcccc
Confidence            11        0001                01112233355555566777888899999999999999999999998877


Q ss_pred             H
Q psy1898         138 R  138 (230)
Q Consensus       138 R  138 (230)
                      +
T Consensus       154 ~  154 (327)
T KOG3862|consen  154 R  154 (327)
T ss_pred             C
Confidence            5

>smart00351 PAX Paired Box domain

Probab=99.11  E-value=3e-10  Score=89.65  Aligned_cols=98  Identities=44%  Similarity=0.678  Sum_probs=75.3

Q ss_pred             CCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCCc-----cc-------CCCcCCHHHH
Q psy1898          40 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGGV-----FI-------NGRPLPNHIR  105 (230)
Q Consensus        40 ~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~~-----~~-------~g~~~s~~~R  105 (230)
                      +.++||+||+|++++|++.+.|.+|+.++.+|.+..+|+++|+|++.++  .+.++     ..       ..+..+....
T Consensus         2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~   81 (125)
T smart00351        2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV   81 (125)
T ss_pred             CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence            5789999999999999999999999999999999999999999988876  11111     11       1222444555


Q ss_pred             HHHHHHHHc--CCCHHHHhhhhc-----c-----ccchhhhHHH
Q psy1898         106 LKIVEMAAA--GVRPCVISRQLR-----V-----SHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~~~--G~s~~~IAr~lg-----V-----S~sTV~kwik  137 (230)
                      ..|+.+..+  .++..+|+..|.     +     |.+||.+|++
T Consensus        82 ~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~  125 (125)
T smart00351       82 KKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR  125 (125)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence            666766554  499999998773     3     8899998863

>KOG3517|consensus

Probab=99.01  E-value=1.3e-10  Score=100.36  Aligned_cols=33  Identities=70%  Similarity=1.164  Sum_probs=30.7

Q ss_pred             CcccccccceeecCccCChhHHHHHHHHHhcCC
Q psy1898           3 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGR   35 (230)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   35 (230)
                      -|.|||||||||||||||+.+|.+|||||--|-
T Consensus         5 ~GEVNQLGGVFVNGRPLPna~RlrIVELarlGi   37 (334)
T KOG3517|consen    5 YGEVNQLGGVFVNGRPLPNAIRLRIVELARLGI   37 (334)
T ss_pred             ccchhhccceeEcCccCcchhhhhHHHHHHcCC
Confidence            478999999999999999999999999998774

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=98.96  E-value=3.7e-09  Score=77.85  Aligned_cols=74  Identities=27%  Similarity=0.373  Sum_probs=60.3

Q ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCC--Cc-CCCCCCCCCCCCHHHHHHHHHHH
Q psy1898          97 GRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI--RP-GVIGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v--~p-~~~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      ..+++..-|..++..+ .+|++..++|+.||||+.|++||+.||++.|..  .+ .+++...|..+++++++.|.++.
T Consensus         6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~lR   83 (85)
T PF13011_consen    6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIELR   83 (85)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHHh
Confidence            3467888999999866 568999999999999999999999999998743  22 23445578888888888888765

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

Probab=98.93  E-value=4.2e-10  Score=74.36  Aligned_cols=44  Identities=27%  Similarity=0.428  Sum_probs=26.7

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         101 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       101 s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +.+.|.+|+.++.+|.|.++||+.||||++||++|+++|++.|.
T Consensus         3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen    3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEGL   46 (50)
T ss_dssp             -------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred             chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence            45789999999999999999999999999999999999999884

>PF13518 HTH_28: Helix-turn-helix domain

Probab=98.79  E-value=5.5e-09  Score=69.17  Aligned_cols=41  Identities=34%  Similarity=0.536  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +|.+||.++.+|.|..+||++||||++||++|+++|++.|.
T Consensus         1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen    1 FRLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGGI   41 (52)
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence            37889999999999999999999999999999999999884

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

Probab=98.45  E-value=9.8e-08  Score=61.92  Aligned_cols=42  Identities=26%  Similarity=0.276  Sum_probs=26.2

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+.++.+.|..|..++.+|+|.++||+.||+|++||+++++|
T Consensus         2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ----------HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            467889999999999999999999999999999999999987

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=98.44  E-value=7.5e-07  Score=69.79  Aligned_cols=49  Identities=20%  Similarity=0.242  Sum_probs=44.1

Q ss_pred             CCcCCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898          97 GRPLPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        97 g~~~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .+.||.+++..+|.. +..|.+..+||+.||||.+|+++|+++|++.+..
T Consensus        10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~   59 (121)
T PRK09413         10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLT   59 (121)
T ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccc
Confidence            578999999999986 5678999999999999999999999999987754

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

Probab=98.38  E-value=3.9e-07  Score=64.92  Aligned_cols=46  Identities=15%  Similarity=0.242  Sum_probs=37.9

Q ss_pred             cCCCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          95 INGRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        95 ~~g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...+.||.+++.++|..+ ..|.|..++|+.+||+++|+++|++.|.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            346789999999999988 7899999999999999999999999998

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.

>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=98.20  E-value=1.1e-06  Score=57.17  Aligned_cols=40  Identities=30%  Similarity=0.335  Sum_probs=32.7

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.++.+....|+.|+.+|+|..+||+.||||++|||++++
T Consensus         4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    4 PKLSKEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSHCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3466667789999999999999999999999999999975

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 ....

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

Probab=98.18  E-value=1.1e-05  Score=72.04  Aligned_cols=105  Identities=23%  Similarity=0.205  Sum_probs=82.7

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC---------CCCcCCCCCCCCCCCCHHHHHHHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG---------SIRPGVIGGSKPRVATPDVEKRIEE  168 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G---------~v~p~~~gg~rpr~lt~~~~~~I~~  168 (230)
                      +-++.+.|..|-.+.++|+|.++||++||.+++||++=++|=....         ..+...+...++.+.+++.++.|.+
T Consensus         6 ~hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e   85 (318)
T COG2826           6 KHLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLE   85 (318)
T ss_pred             hhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHH
Confidence            3688899999999999999999999999999999999888732222         1111122234677889999999999


Q ss_pred             HHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898         169 YKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR  212 (230)
Q Consensus       169 l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~  212 (230)
                      .++..  ++..+|..+|.. ..       +|.+||+++|.....
T Consensus        86 ~L~~~--wSPEQI~g~l~~-~~-------i~~eTIYr~ly~~~~  119 (318)
T COG2826          86 KLKSK--WSPEQIIGRLKK-SK-------ISFETIYRWLYQGKS  119 (318)
T ss_pred             HHHhh--CCHHHHHHHHHh-cc-------cCHHHHHHHHhhccc
Confidence            98775  999999999986 22       699999999876543

>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=98.14  E-value=3.8e-06  Score=56.62  Aligned_cols=42  Identities=29%  Similarity=0.370  Sum_probs=34.7

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      -+.++.+.+..||.++++|.+..+||+.|||+.+||+.|++.
T Consensus         4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            457899999999999999999999999999999999999985

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.

>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=98.12  E-value=2.6e-06  Score=58.57  Aligned_cols=41  Identities=17%  Similarity=0.175  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      |.|.++..|+-.|+++++||+.|||+.+||+.|.++|.-.+
T Consensus         1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~   41 (58)
T PF06056_consen    1 EVKEQARSLYLQGWSIKEIAEELGVPRSTVYSWKDRYKWDE   41 (58)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence            46788899999999999999999999999999999988544

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

>KOG0849|consensus

Probab=98.05  E-value=1.1e-06  Score=80.71  Aligned_cols=35  Identities=74%  Similarity=1.151  Sum_probs=32.7

Q ss_pred             cccccccceeecCccCChhHHHHHHHHHhcCCCCC
Q psy1898           4 GRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSS   38 (230)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   38 (230)
                      |++||+||||+||||||+++|++|+|+|..|+...
T Consensus         1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~   35 (354)
T KOG0849|consen    1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPC   35 (354)
T ss_pred             CCcccCCcccccCCCCCCchhhccccccccccCcc
Confidence            68999999999999999999999999999998744

>PRK09409 IS2 transposase TnpB; Reviewed

Probab=97.94  E-value=4.6e-05  Score=68.57  Aligned_cols=97  Identities=24%  Similarity=0.185  Sum_probs=72.0

Q ss_pred             HHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhh
Q psy1898         110 EMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQD  189 (230)
Q Consensus       110 ~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~  189 (230)
                      .|++.+.+...+|+.|+||++|.|+|++++..--   ..+.   .+.....+....|.++..++|...+..|..+|..+.
T Consensus         6 ~~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~~---~~~~---~~~~~~~~l~~~I~~i~~~~~~yG~Rri~~~L~~~g   79 (301)
T PRK09409          6 ALIARGWGVSLVSRCLRVSRAQLHVILRRTDDWM---DGRR---SRHTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQA   79 (301)
T ss_pred             HHHhcCCcHHHHHHhcCcChHHhhhhcccccccc---cccc---ccCcchHHHHHHHHHHHHhCccCCHHHHHHHHHhhh
Confidence            4677889999999999999999999999854211   1111   122234456777777777789999999999997631


Q ss_pred             ---CCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         190 ---GICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       190 ---Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                         |+.    .++..||+|+|++.||...+
T Consensus        80 ~~~g~~----~v~~k~V~RlMr~~Gl~~~~  105 (301)
T PRK09409         80 ELDGMP----AINAKRVYRIMRQNALLLER  105 (301)
T ss_pred             cccCcc----ccCHHHHHHHHHHcCCcccc
Confidence               441    27999999999999998543

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

Probab=97.89  E-value=6.2e-05  Score=58.09  Aligned_cols=51  Identities=16%  Similarity=0.197  Sum_probs=45.2

Q ss_pred             CCcCCHHHHHHHHHHHHc-CCCHHHHhhhhcc-ccchhhhHHHHHhhhCCCCc
Q psy1898          97 GRPLPNHIRLKIVEMAAA-GVRPCVISRQLRV-SHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~-G~s~~~IAr~lgV-S~sTV~kwikRy~e~G~v~p  147 (230)
                      -+.||.+++.+||.++.+ |.+.++||+.||| +.+++++|+++|.+.+...+
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~   57 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAF   57 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccc
Confidence            367999999999998874 7999999999996 99999999999999876543

>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=97.67  E-value=6.3e-05  Score=44.31  Aligned_cols=39  Identities=26%  Similarity=0.239  Sum_probs=34.9

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.++.+.+..|++++.++.+..+||+.++++++||++|+
T Consensus         4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            446778888898999999999999999999999999994

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

>PHA02517 putative transposase OrfB; Reviewed

Probab=97.54  E-value=0.00019  Score=63.16  Aligned_cols=77  Identities=10%  Similarity=0.077  Sum_probs=56.8

Q ss_pred             hccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHH
Q psy1898         125 LRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSI  203 (230)
Q Consensus       125 lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV  203 (230)
                      |+||++|.|+|+++...     |..+  ..+.....+..+.|.++..+ +|...+..|.+.|.. .|+.     +|.+||
T Consensus         1 l~vsrs~yY~~~~~~~~-----p~~~--~~~~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~-~g~~-----vs~~tV   67 (277)
T PHA02517          1 LGIAPSTYYRCQQQRHH-----PDKR--RARAQHDDWLKSEILRVYDENHQVYGVRKVWRQLNR-EGIR-----VARCTV   67 (277)
T ss_pred             CCCChHHHHHHHhccCC-----cchh--hhhhhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCcc-----cCHHHH
Confidence            68999999999876321     1111  01112345667788877655 678899999999987 6885     899999


Q ss_pred             HHHHHcCCCCC
Q psy1898         204 SRLLRGGRRDD  214 (230)
Q Consensus       204 ~R~Lr~~g~~~  214 (230)
                      +|+|+++|+..
T Consensus        68 ~Rim~~~gl~~   78 (277)
T PHA02517         68 GRLMKELGLAG   78 (277)
T ss_pred             HHHHHHcCCce
Confidence            99999999963

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.37  E-value=0.00039  Score=45.57  Aligned_cols=41  Identities=22%  Similarity=0.280  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++.+.+. ++.++..|++..+||+.++||++||++|+++..+
T Consensus         4 l~~~e~~-i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~   44 (58)
T smart00421        4 LTPRERE-VLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5666665 7788889999999999999999999999998643

lux regulon (activates the bioluminescence operon

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

Probab=97.24  E-value=0.00058  Score=45.03  Aligned_cols=45  Identities=20%  Similarity=0.259  Sum_probs=40.7

Q ss_pred             cCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898          95 INGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus        95 ~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ..+..++..++..|+.++.+..|.++||+.+|||.+||.++.++|
T Consensus         7 ~~~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen    7 DRYCRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             CcCCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            446678889999999999888999999999999999999999886

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

Probab=97.22  E-value=0.0012  Score=45.71  Aligned_cols=66  Identities=17%  Similarity=0.137  Sum_probs=44.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL  185 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L  185 (230)
                      .+..++|+.+|||.+|+++|.+++   |...+.... +..+..++++...+..... .....+..+|++.|
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---GLPAPQRTD-GGHRLYSEADVARLRLIRRLTSEGVRISQAAALA   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence            378899999999999999998764   444332222 2346677776666554433 23467888887765

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=97.22  E-value=0.00038  Score=51.79  Aligned_cols=35  Identities=20%  Similarity=0.264  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|..|..+..+|.|.++||+.+|||++||++|.+
T Consensus        38 s~R~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        38 AQRLQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             hHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45688889999999999999999999999999764

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.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=97.13  E-value=0.00096  Score=64.94  Aligned_cols=68  Identities=10%  Similarity=0.041  Sum_probs=51.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh--hhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ--ETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI  176 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~--e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~  176 (230)
                      .|+.++|..++.++.+|.|+.+||+.|||+.+||++|.++|+  +...+          ..+...+..+|..++.. +..
T Consensus         2 ~yt~EfK~~Av~Ly~~G~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~~~~----------~~v~~~~~~r~~~l~~k-~~k   70 (581)
T PHA02535          2 AYDDDVRRAAKFLYWQGWTVAEIAEELGLKSRTIYSWKERDGWRDLLPE----------ERIEESIEARLIQLIEK-ENK   70 (581)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHhccccccccCCc----------ccHHHHHHHHHHHHHcc-CCC
Confidence            589999999999999999999999999999999999999876  22211          11233456666666654 544


Q ss_pred             C
Q psy1898         177 F  177 (230)
Q Consensus       177 t  177 (230)
                      +
T Consensus        71 ~   71 (581)
T PHA02535         71 T   71 (581)
T ss_pred             C
Confidence            4

>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition

Probab=97.13  E-value=0.00029  Score=49.75  Aligned_cols=45  Identities=36%  Similarity=0.438  Sum_probs=22.2

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCC
Q psy1898         164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDD  214 (230)
Q Consensus       164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~  214 (230)
                      +.|...+..+|..|+.+|+..|... |+.     ||.+||+|+|++.|+..
T Consensus         2 r~I~~~v~~~p~~s~~~i~~~l~~~-~~~-----vS~~TI~r~L~~~g~~~   46 (72)
T PF01498_consen    2 RRIVRMVRRNPRISAREIAQELQEA-GIS-----VSKSTIRRRLREAGLKK   46 (72)
T ss_dssp             --------------HHHHHHHT----T-------S-HHHHHHHHHHT-EEE
T ss_pred             cHHHHHHHHCCCCCHHHHHHHHHHc-cCC-----cCHHHHHHHHHHcCccc
Confidence            4677888999999999999999874 875     89999999999999863

This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.

>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=97.12  E-value=0.00067  Score=45.05  Aligned_cols=43  Identities=23%  Similarity=0.261  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+.+|+|..+||+.+|+|.+||..|+.+-+.
T Consensus        10 ~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   10 QLPERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             CS-HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            3667777777777889999999999999999999999988653

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.

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=97.10  E-value=0.00073  Score=45.02  Aligned_cols=42  Identities=26%  Similarity=0.411  Sum_probs=32.0

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      |+.++..++.+|..|+..|+|..+||++++-|+.+|.++++.
T Consensus         2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~d   43 (50)
T PF11427_consen    2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKD   43 (50)
T ss_dssp             S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence            678999999999999999999999999999999999998864

>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=97.04  E-value=0.0013  Score=42.25  Aligned_cols=42  Identities=26%  Similarity=0.258  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++.+.+.-+...+.+|++..+||..++++.+||++|+.+.++
T Consensus        11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            566666666666679999999999999999999999998754

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

>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=96.97  E-value=0.0012  Score=43.28  Aligned_cols=42  Identities=29%  Similarity=0.271  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-|...+.+++|..+||+.+|+|.+||.++.++..
T Consensus         4 ~L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             TS-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            467788888888888999999999999999999999988753

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 ....

>PRK00118 putative DNA-binding protein; Validated

Probab=96.92  E-value=0.0016  Score=49.89  Aligned_cols=44  Identities=18%  Similarity=0.126  Sum_probs=39.3

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++.++...|.-+...+.+|+|..+||+.+|||++||++|+.|-+
T Consensus        15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RAr   58 (104)
T PRK00118         15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTE   58 (104)
T ss_pred             hccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            66788888888888888999999999999999999999998754

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

Probab=96.91  E-value=0.0029  Score=49.33  Aligned_cols=83  Identities=14%  Similarity=0.151  Sum_probs=57.5

Q ss_pred             hhHHHHHHHHHhcCCChhhhhhhhccccccc-------ccCCcccCCCcCCHHHHHHHHHHHHc--CCCHHHHhhhhccc
Q psy1898          58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVN-------QLGGVFINGRPLPNHIRLKIVEMAAA--GVRPCVISRQLRVS  128 (230)
Q Consensus        58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~-------~l~~~~~~g~~~s~~~R~rIV~l~~~--G~s~~~IAr~lgVS  128 (230)
                      -++|..|+..+..|.+..++++.|.||-.++       ..|..-...+.-..-....+..++++  ..+..|+|+.|+||
T Consensus         5 ~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~~~L~~~v~~~pd~tl~Ela~~l~Vs   84 (119)
T PF01710_consen    5 LDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDRDELKALVEENPDATLRELAERLGVS   84 (119)
T ss_pred             HHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccHHHHHHHHHHCCCcCHHHHHHHcCCC
Confidence            7899999999999999999999999866543       11111111111001112334445444  59999999999999


Q ss_pred             cchhhhHHHHHh
Q psy1898         129 HGCVSKILNRYQ  140 (230)
Q Consensus       129 ~sTV~kwikRy~  140 (230)
                      .+||++.+++..
T Consensus        85 ~~ti~~~Lkrlg   96 (119)
T PF01710_consen   85 PSTIWRALKRLG   96 (119)
T ss_pred             HHHHHHHHHHcC
Confidence            999999998754

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 [].

>PF13592 HTH_33: Winged helix-turn helix

Probab=96.89  E-value=0.0019  Score=44.36  Aligned_cols=41  Identities=20%  Similarity=0.033  Sum_probs=36.5

Q ss_pred             CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCC
Q psy1898         173 NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRK  218 (230)
Q Consensus       173 ~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~  218 (230)
                      +..+|..+|++.+.+++|+.     .|.++|+++|+++|++...+.
T Consensus         2 ~~~wt~~~i~~~I~~~fgv~-----ys~~~v~~lL~r~G~s~~kp~   42 (60)
T PF13592_consen    2 GGRWTLKEIAAYIEEEFGVK-----YSPSGVYRLLKRLGFSYQKPR   42 (60)
T ss_pred             CCcccHHHHHHHHHHHHCCE-----EcHHHHHHHHHHcCCccccCC
Confidence            46789999999999999996     799999999999999977643

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

Probab=96.87  E-value=0.0022  Score=42.09  Aligned_cols=39  Identities=21%  Similarity=0.190  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ...+. ++.++.+|++..+||+.+++|++||++|+++..+
T Consensus         3 ~~e~~-i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170           3 PRERE-VLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             HHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33444 6777889999999999999999999999998653

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

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=96.83  E-value=0.0013  Score=51.46  Aligned_cols=73  Identities=19%  Similarity=0.206  Sum_probs=55.1

Q ss_pred             CcCCHHHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH
Q psy1898          98 RPLPNHIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      +.++...|.+|+.++..  ..+..+||+.|+++++||++-++..++.|.+...+.|...--.+.+++.+++....
T Consensus        11 kaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~   85 (117)
T PRK10141         11 KILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKII   85 (117)
T ss_pred             HHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHH
Confidence            35667899999997753  48999999999999999999999999999886555543333445555555555533

>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=96.70  E-value=0.0017  Score=42.24  Aligned_cols=43  Identities=26%  Similarity=0.488  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.|.+|+.++.+| .+.++||+.+++|++||++-++..++.|-+
T Consensus         2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV   45 (47)
T PF01022_consen    2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV   45 (47)
T ss_dssp             HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence            5789999988776 999999999999999999999999998865

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 ....

>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=96.70  E-value=0.0016  Score=42.46  Aligned_cols=40  Identities=30%  Similarity=0.290  Sum_probs=35.9

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+.+.++.+|++|..+|...+++|+.|+|+..||-+-++
T Consensus         4 ~A~kpgikeqIvema~nG~GiRdtaRvL~I~~nTVlrtLK   43 (46)
T PF12759_consen    4 EARKPGIKEQIVEMAFNGSGIRDTARVLKISINTVLRTLK   43 (46)
T ss_pred             cccCccHHHHHHHHHhcCCcchhhHhHhcchHHHHHHHHh
Confidence            4555688999999999999999999999999999988765

>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data

Probab=96.70  E-value=0.0021  Score=52.96  Aligned_cols=96  Identities=16%  Similarity=0.176  Sum_probs=34.4

Q ss_pred             CCCHHHHhhhhccccchhhhHHH-HHhhhC--CC-----CcCCCCCCCCCCC-CHHHHHHHHHHHHh-CC--CCCHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILN-RYQETG--SI-----RPGVIGGSKPRVA-TPDVEKRIEEYKKT-NP--GIFSWEIR  182 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwik-Ry~e~G--~v-----~p~~~gg~rpr~l-t~~~~~~I~~l~~~-~P--~~t~~eI~  182 (230)
                      -++.++||..+|++.+||++.++ +|-++.  .+     -+..........+ ...+...|.+++.+ +|  ..+=.+|.
T Consensus        49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~  128 (160)
T PF04552_consen   49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIA  128 (160)
T ss_dssp             ------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHH
T ss_pred             CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence            47899999999999999999665 465554  21     1111111111112 23467788888875 34  46677899


Q ss_pred             HHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         183 DRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       183 ~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      +.|.+ .|+.     +|+.||..+=..+||.++.
T Consensus       129 ~~L~~-~gi~-----isRRTVaKYR~~L~Ip~s~  156 (160)
T PF04552_consen  129 ELLKE-EGIK-----ISRRTVAKYREELGIPSSS  156 (160)
T ss_dssp             HHHTT-TTS--------HHHHHHHHHHHT-S-SH
T ss_pred             HHHHH-cCCC-----ccHHHHHHHHHHcCCCChh
Confidence            99987 8885     8999999999999988764

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.

>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=96.66  E-value=0.0033  Score=40.60  Aligned_cols=44  Identities=23%  Similarity=0.274  Sum_probs=33.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         153 SKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       153 ~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      +||++++++..+.+.++..+.  .+..+|++.    +|+       |.+||+|+|+.
T Consensus         1 GRp~~~~~~~~~~i~~l~~~G--~si~~IA~~----~gv-------sr~TvyR~l~~   44 (45)
T PF02796_consen    1 GRPPKLSKEQIEEIKELYAEG--MSIAEIAKQ----FGV-------SRSTVYRYLNK   44 (45)
T ss_dssp             SSSSSSSHCCHHHHHHHHHTT----HHHHHHH----TTS--------HHHHHHHHCC
T ss_pred             CcCCCCCHHHHHHHHHHHHCC--CCHHHHHHH----HCc-------CHHHHHHHHhc
Confidence            478899998888888888665  788887764    554       99999999975

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 ....

>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=96.50  E-value=0.0029  Score=43.71  Aligned_cols=37  Identities=24%  Similarity=0.209  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .|.++.+++.+   .+...+||.+||||.+||.+|..+.+
T Consensus         8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dk   47 (60)
T PF10668_consen    8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDK   47 (60)
T ss_pred             CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcc
Confidence            56777777764   39999999999999999999988743

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 [].

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

Probab=96.49  E-value=0.023  Score=41.90  Aligned_cols=68  Identities=16%  Similarity=0.076  Sum_probs=48.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||.+|+..|.+    .|.+.|....++..+..++++...|..... .....+..+|++.+..
T Consensus         2 ~ti~evA~~~gvs~~tLR~ye~----~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~   70 (88)
T cd01105           2 IGIGEVSKLTGVSPRQLRYWEE----KGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRR   70 (88)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            5789999999999999999944    476665443322456677776665543322 2357899999998876

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=96.48  E-value=0.0029  Score=43.90  Aligned_cols=66  Identities=20%  Similarity=0.170  Sum_probs=42.6

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      +..++|+.+|||++||..|.++    |.+.|....+ ..+..+.++...|..... .+-..+..+|++.|.+
T Consensus         2 ti~eva~~~gvs~~tlr~y~~~----gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~   68 (69)
T PF13411_consen    2 TIKEVAKLLGVSPSTLRYYERE----GLLPPPRDEN-GYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ   68 (69)
T ss_dssp             EHHHHHHHTTTTHHHHHHHHHT----TSSTTBESTT-SSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred             cHHHHHHHHCcCHHHHHHHHHh----cCcccccccC-ceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence            6789999999999999999774    4455444323 347788887766643332 1245677777776643

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

Probab=96.47  E-value=0.0033  Score=43.07  Aligned_cols=43  Identities=26%  Similarity=0.288  Sum_probs=31.0

Q ss_pred             CCcCCHHHHHHHHHHHHc-CC---CHHHHhhhhccccchhhhHHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAA-GV---RPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~-G~---s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      -+.|+..++.+||+.+.. +.   +.+++|+.|+|++.+|.+|++.-
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kqe   49 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQE   49 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred             ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHHH
Confidence            357899999999998754 44   45889999999999999998753

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.

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

Probab=96.44  E-value=0.006  Score=40.74  Aligned_cols=42  Identities=17%  Similarity=0.194  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|.+.+.-++.+ ++.+.+..++|..||||++||++|.+.+.+
T Consensus         3 Ls~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~   45 (53)
T PF13613_consen    3 LSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP   45 (53)
T ss_pred             CCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence            466666666664 467999999999999999999999998764

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

Probab=96.40  E-value=0.015  Score=40.47  Aligned_cols=66  Identities=15%  Similarity=0.188  Sum_probs=42.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL  185 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L  185 (230)
                      .+..++|+.+|||.+|+..|.+.+   |.+.|....+ ..+..+.++...+..... .+...+..+|+..|
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---GLLKPQRSDG-GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence            367899999999999999985533   5554433222 345677776655543322 22567777776654

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

>PRK04217 hypothetical protein; Provisional

Probab=96.31  E-value=0.0083  Score=46.45  Aligned_cols=44  Identities=14%  Similarity=0.068  Sum_probs=34.9

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...++.+.+.-+.....+|+|..+||+.++||.+||++.+.+..
T Consensus        40 ~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr   83 (110)
T PRK04217         40 PIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR   83 (110)
T ss_pred             cccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            44567788744444555899999999999999999999998754

>PF14493 HTH_40: Helix-turn-helix domain

Probab=96.30  E-value=0.029  Score=41.51  Aligned_cols=83  Identities=16%  Similarity=0.048  Sum_probs=65.0

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLV  186 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~  186 (230)
                      .-+.++.+|+|..+||+.-+++.+||+.-+-.|...|...+-      ...++.+..+.|.....+.+...+..+.+.|.
T Consensus         5 ~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~------~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l~   78 (91)
T PF14493_consen    5 ITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDI------EELLSEEEIKQIEDAIEKLGSEKLKPIKEALP   78 (91)
T ss_pred             HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH------HHhCCHHHHHHHHHHHHHcCcccHHHHHHHCC
Confidence            456789999999999999999999999999999999873221      23467888888888888877777888887664


Q ss_pred             HhhCCCCCCCCCCHhHHH
Q psy1898         187 KQDGICDKNSAPSVSSIS  204 (230)
Q Consensus       187 ~~~Gi~~~~~~vS~sTV~  204 (230)
                      .         .+|+..++
T Consensus        79 ~---------~~sy~~iR   87 (91)
T PF14493_consen   79 G---------DYSYFEIR   87 (91)
T ss_pred             C---------CCCHHHHH
Confidence            2         25776665

>TIGR01529 argR_whole arginine repressor

Probab=96.29  E-value=0.011  Score=47.89  Aligned_cols=45  Identities=24%  Similarity=0.159  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+.|..++.+++..|++||.+.|.+ .|+.     +|.+||+|.|++.|+.
T Consensus         4 ~~~i~~Li~~~~i~tqeeL~~~L~~-~G~~-----vsqaTIsRdL~elglv   48 (146)
T TIGR01529         4 QERIKEIITEEKISTQEELVALLKA-EGIE-----VTQATVSRDLRELGAV   48 (146)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHH-hCCC-----cCHHHHHHHHHHcCCE
Confidence            3457788889999999999999977 8985     8999999999999984

This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.

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

Probab=96.28  E-value=0.011  Score=53.04  Aligned_cols=84  Identities=20%  Similarity=0.224  Sum_probs=67.3

Q ss_pred             CCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCC-----ccc----------------CCCcCCHHHHHHHHHH
Q psy1898          55 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGG-----VFI----------------NGRPLPNHIRLKIVEM  111 (230)
Q Consensus        55 plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~-----~~~----------------~g~~~s~~~R~rIV~l  111 (230)
                      -|+...|.+|-.+..+|++..+|+++|+.+|++.  .+.+     .|.                ..-..+.+++..|++.
T Consensus         7 hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~   86 (318)
T COG2826           7 HLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEK   86 (318)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHH
Confidence            4778899999999999999999999999988885  1222     111                1112557899999999


Q ss_pred             HHcCCCHHHHhhhhc---cccchhhhHHHH
Q psy1898         112 AAAGVRPCVISRQLR---VSHGCVSKILNR  138 (230)
Q Consensus       112 ~~~G~s~~~IAr~lg---VS~sTV~kwikR  138 (230)
                      +++-+|+.+|+..+.   |+..|+|+|+-.
T Consensus        87 L~~~wSPEQI~g~l~~~~i~~eTIYr~ly~  116 (318)
T COG2826          87 LKSKWSPEQIIGRLKKSKISFETIYRWLYQ  116 (318)
T ss_pred             HHhhCCHHHHHHHHHhcccCHHHHHHHHhh
Confidence            999999999998765   789999999864

>PF13551 HTH_29: Winged helix-turn helix

Probab=96.28  E-value=0.015  Score=43.58  Aligned_cols=78  Identities=26%  Similarity=0.280  Sum_probs=57.2

Q ss_pred             HHHHHHHHhcCC-Chhhhhhhhccccccc-------------ccCC-ccc--CCCc-CCHHHHHHHHHHHHcC-------
Q psy1898          61 RLKIVEMAAAGV-RPCVISRQLRVSHGVN-------------QLGG-VFI--NGRP-LPNHIRLKIVEMAAAG-------  115 (230)
Q Consensus        61 r~~I~e~~~~g~-~~~~isr~lrvshg~~-------------~l~~-~~~--~g~~-~s~~~R~rIV~l~~~G-------  115 (230)
                      |..|+.++.+|. +..++++.+++|..++             .+-. ...  .++. ++.+.+..|++++.+.       
T Consensus         1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~   80 (112)
T PF13551_consen    1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSR   80 (112)
T ss_pred             CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCc
Confidence            568899999999 5999999999854432             1111 111  1222 7899999999988762       


Q ss_pred             CCHHHHhhhh-------ccccchhhhHHHH
Q psy1898         116 VRPCVISRQL-------RVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~l-------gVS~sTV~kwikR  138 (230)
                      ++..+|+..+       .+|.+||++|+++
T Consensus        81 ~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~  110 (112)
T PF13551_consen   81 WTLEELAEWLIEEEFGIDVSPSTIRRILKR  110 (112)
T ss_pred             ccHHHHHHHHHHhccCccCCHHHHHHHHHH
Confidence            6788888855       5799999999986

>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=96.26  E-value=0.0085  Score=38.78  Aligned_cols=43  Identities=21%  Similarity=0.360  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.+.+|+....+  +.|.++||+.+++|.+||++.+++..+.|-+
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            456677775543  4999999999999999999999999988854

...

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

Probab=96.23  E-value=0.0053  Score=47.93  Aligned_cols=55  Identities=16%  Similarity=0.221  Sum_probs=38.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      +++.|+|..+|+|+.||.||++++.=.-+..|...+| .|--.++.+++++|...-
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            5789999999999999999998754221223444443 133466778888887554

The function of this family is unknown.

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

Probab=96.18  E-value=0.021  Score=39.49  Aligned_cols=65  Identities=15%  Similarity=0.105  Sum_probs=41.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL  185 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L  185 (230)
                      ++..++|+.+|||++|+..|.+++.   ...++..  +..+..+.++...+..... .+...+..+|++.|
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 YTIKEVSEIIGVKPHTLRYYEKEFN---LYIPRTE--NGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL   66 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcC---CCCCCCC--CCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence            3678999999999999999976533   2223222  2346677776665543332 22567777777654

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.

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=96.08  E-value=0.032  Score=38.54  Aligned_cols=50  Identities=12%  Similarity=0.050  Sum_probs=33.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      ++..++|+.+|||++|+..|.+    .|.+.|..+..+..+..+.++...+...
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~g~r~y~~~dl~~l~~i   50 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEGGYRLYSDEDLERLRFI   50 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCEecCHHHHHHHHHH
Confidence            4788999999999999999965    6777654121123456677666555433

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

Probab=96.06  E-value=0.008  Score=38.03  Aligned_cols=23  Identities=13%  Similarity=0.133  Sum_probs=20.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      ++..++|+.|+||++||++|.+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~   23 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            46789999999999999999884

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.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=96.06  E-value=0.0065  Score=51.18  Aligned_cols=36  Identities=25%  Similarity=0.329  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      .+..|..++.+|.|..+||+.||||++||+++++.+
T Consensus       161 ~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~  196 (200)
T PRK13413        161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTR  196 (200)
T ss_pred             hHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence            345777888999999999999999999999999853

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=96.05  E-value=0.0086  Score=45.04  Aligned_cols=35  Identities=23%  Similarity=0.241  Sum_probs=29.7

Q ss_pred             HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|..|+..+ +.++|.++||+.+|||++||+||-+
T Consensus        42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn   77 (94)
T TIGR01321        42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN   77 (94)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence            5677777644 5679999999999999999999965

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.

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

Probab=96.00  E-value=0.058  Score=40.72  Aligned_cols=68  Identities=10%  Similarity=0.004  Sum_probs=49.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      .+..++|+.+|||.+|+..|.+.   .|.+.|...+ +.-+..+.++...|.....  ..-.++..++++.|..
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~-~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~   70 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRA-GGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE   70 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCC-CCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            36789999999999999999654   3444443322 2466788888777766553  5667999999999876

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.

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

Probab=95.95  E-value=0.015  Score=37.97  Aligned_cols=40  Identities=30%  Similarity=0.361  Sum_probs=32.0

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||.+||++.++.                +..++++.+++|.+..++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~----------------~~~vs~~tr~rI~~~a~~   40 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG----------------PPRVSEETRERILEAAEE   40 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT----------------CSSSTHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC----------------CCCCCHHHHHHHHHHHHH
Confidence            4689999999999999999851                235688888888877654

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 ....

>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=95.86  E-value=0.015  Score=37.69  Aligned_cols=35  Identities=14%  Similarity=0.155  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.=+.+|..+..| +|.+++|+.|||+++|+++.++
T Consensus         3 e~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~   38 (45)
T PF05225_consen    3 EDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR   38 (45)
T ss_dssp             HHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3446677888888 9999999999999999997665

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.

>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=95.84  E-value=0.016  Score=43.02  Aligned_cols=39  Identities=13%  Similarity=0.166  Sum_probs=34.3

Q ss_pred             HHHHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         102 NHIRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       102 ~~~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...|.+|+. |+.+|+|.++||+.+|+|..||+|.-+-.+
T Consensus        35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk   74 (87)
T PF01371_consen   35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLK   74 (87)
T ss_dssp             HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            367999998 999999999999999999999999865443

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 ....

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=95.81  E-value=0.036  Score=52.42  Aligned_cols=95  Identities=13%  Similarity=0.160  Sum_probs=68.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----CcCCCCCCC--CCCCCHHHHHHHHHHHHhC-C--CCCHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RPGVIGGSK--PRVATPDVEKRIEEYKKTN-P--GIFSWEIR  182 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p~~~gg~r--pr~lt~~~~~~I~~l~~~~-P--~~t~~eI~  182 (230)
                      ++.++||..+|++.|||+|.++. |-++.  .+     .........  .-.-+..+...|.+++... +  ..+=.+|.
T Consensus       319 LtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI~~E~~~~PlSD~~I~  398 (429)
T TIGR02395       319 LTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKELIAAEDKRKPLSDQKIA  398 (429)
T ss_pred             CcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence            78999999999999999999864 55553  21     111100000  1133556788888888753 3  36677899


Q ss_pred             HHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         183 DRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       183 ~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      +.|.+ .|+.     +|+.||..+=...|+.++.
T Consensus       399 ~~L~~-~Gi~-----IaRRTVaKYRe~L~Ip~s~  426 (429)
T TIGR02395       399 ELLKE-KGIK-----IARRTVAKYREELGIPSSS  426 (429)
T ss_pred             HHHHh-cCCC-----eehHHHHHHHHHcCCCccc
Confidence            99988 6995     9999999999999998875

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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=95.75  E-value=0.013  Score=42.12  Aligned_cols=44  Identities=16%  Similarity=0.149  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898         100 LPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus       100 ~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      ++...|+-+... +.+|+|..+||+.++||.+||..|+.+-...|
T Consensus        16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~   60 (73)
T TIGR03879        16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAG   60 (73)
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence            444555444443 35899999999999999999999998633333

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.

>PF13309 HTH_22: HTH domain

Probab=95.70  E-value=0.009  Score=41.66  Aligned_cols=41  Identities=20%  Similarity=0.220  Sum_probs=33.2

Q ss_pred             CCcCCHHHHHHHHHHH-HcC-----CCHHHHhhhhccccchhhhHHH
Q psy1898          97 GRPLPNHIRLKIVEMA-AAG-----VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~~G-----~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ...++.+.|..||..+ +.|     -+...+|+.|+||+.|||+.++
T Consensus        18 ~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   18 PSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             hhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence            4556778899999754 567     5788899999999999999863

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=95.67  E-value=0.039  Score=52.59  Aligned_cols=93  Identities=14%  Similarity=0.181  Sum_probs=68.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----CcC---CCCCCCCCCCCHHHHHHHHHHHHhC-C--CCCHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RPG---VIGGSKPRVATPDVEKRIEEYKKTN-P--GIFSWEI  181 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p~---~~gg~rpr~lt~~~~~~I~~l~~~~-P--~~t~~eI  181 (230)
                      ++.++||..+|++.|||+|.++- |-++.  .+     ...   ...|  ...-+..+...|.+++... |  ..+=.+|
T Consensus       344 LtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g--~~~S~~~Ik~~Ik~lI~~Ed~~~PlSD~~I  421 (455)
T PRK05932        344 LVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGG--GEASSTAIRALIKKLIAAENPKKPLSDSKI  421 (455)
T ss_pred             ccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            78999999999999999998864 54443  21     111   0111  1133455788899998754 3  3667789


Q ss_pred             HHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         182 RDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      .+.|.+ .|+.     +|+.||..+=...||.++.
T Consensus       422 ~~~L~~-~Gi~-----IaRRTVaKYRe~L~Ip~s~  450 (455)
T PRK05932        422 AELLKE-QGID-----VARRTVAKYREALNIPSSS  450 (455)
T ss_pred             HHHHHH-cCCC-----eehHHHHHHHHHcCCCChH
Confidence            999988 6995     9999999999999999875

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=95.64  E-value=0.02  Score=45.39  Aligned_cols=42  Identities=17%  Similarity=0.008  Sum_probs=36.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|+|..+||..+|+|.+||..++.|-.
T Consensus       106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~  147 (154)
T PRK06759        106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQAL  147 (154)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            356677777777788999999999999999999999998754

>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=95.64  E-value=0.0085  Score=40.92  Aligned_cols=48  Identities=25%  Similarity=0.412  Sum_probs=40.9

Q ss_pred             CCHHHHHHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         100 LPNHIRLKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       100 ~s~~~R~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++...|.+|+.++ . .+++..+||+.++++.+||+.-++...+.|.+..
T Consensus         7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~   56 (61)
T PF12840_consen    7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV   56 (61)
T ss_dssp             HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            4557899999988 4 4599999999999999999999999999997743

...

>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []

Probab=95.63  E-value=0.032  Score=39.73  Aligned_cols=46  Identities=22%  Similarity=0.119  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         162 VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       162 ~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      -.+.|..++.+++-.+..||.+.|.. .|+.     ++.+||+|-|+..++.
T Consensus         6 R~~~I~~li~~~~i~sQ~eL~~~L~~-~Gi~-----vTQaTiSRDLkeL~~v   51 (70)
T PF01316_consen    6 RQELIKELISEHEISSQEELVELLEE-EGIE-----VTQATISRDLKELGAV   51 (70)
T ss_dssp             HHHHHHHHHHHS---SHHHHHHHHHH-TT-T-------HHHHHHHHHHHT-E
T ss_pred             HHHHHHHHHHHCCcCCHHHHHHHHHH-cCCC-----cchhHHHHHHHHcCcE
Confidence            35678889999999999999999988 8995     8999999999999875

The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=95.58  E-value=0.022  Score=46.78  Aligned_cols=42  Identities=21%  Similarity=0.227  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|.+.|.-++..+.+|++..+||+.+|||.+||..++.|-.+
T Consensus       134 L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~  175 (182)
T PRK12537        134 LEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK  175 (182)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence            566777666666779999999999999999999999988653

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=95.54  E-value=0.02  Score=46.03  Aligned_cols=42  Identities=26%  Similarity=0.388  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .++ +...+|+.++.+|+|..+||+.+|+|++||.++.++..+
T Consensus         6 ~Lt-e~qr~VL~Lr~~GlTq~EIAe~LgiS~stV~~~e~ra~k   47 (137)
T TIGR00721         6 FLT-ERQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAME   47 (137)
T ss_pred             CCC-HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence            344 444567777889999999999999999999999988553

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

>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=95.52  E-value=0.018  Score=38.82  Aligned_cols=35  Identities=23%  Similarity=0.321  Sum_probs=30.4

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..|+.++..|.+..+||..++||..||+.++++-.
T Consensus         9 ~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~   43 (58)
T PF00196_consen    9 LEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIM   43 (58)
T ss_dssp             HHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHH
Confidence            45888999999999999999999999999988744

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 ....

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

Probab=95.52  E-value=0.062  Score=40.52  Aligned_cols=68  Identities=16%  Similarity=0.112  Sum_probs=46.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||+.|+..|.+    .|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~   69 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKD   69 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence            4688999999999999998765    577655333222346678877665532221 2347888888887754

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

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=95.47  E-value=0.025  Score=45.28  Aligned_cols=42  Identities=19%  Similarity=0.123  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+.+|+|..+||+.+|+|.+||...+.|.+.
T Consensus       107 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  148 (160)
T PRK09642        107 LPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK  148 (160)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            677777777777889999999999999999999999887553

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

Probab=95.47  E-value=0.13  Score=38.48  Aligned_cols=68  Identities=16%  Similarity=0.138  Sum_probs=46.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..++.+.-+..+.++...|..... ..-..+..+|++.+..
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~   69 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN   69 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            3678999999999999887744    688877543223456677776655543332 3346888888887743

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.

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

Probab=95.45  E-value=0.062  Score=41.10  Aligned_cols=68  Identities=13%  Similarity=0.088  Sum_probs=47.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||+.|+..|.+    .|.+.|.....+.-+..++++...+..... ..-..+..+|++.|..
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~   69 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ   69 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            4789999999999999998854    587766443323456678877666654332 2335788888888764

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=95.43  E-value=0.048  Score=43.17  Aligned_cols=55  Identities=20%  Similarity=0.330  Sum_probs=44.4

Q ss_pred             ccCCCcCCHHHHHHHHHHHHcC--------CCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898          94 FINGRPLPNHIRLKIVEMAAAG--------VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus        94 ~~~g~~~s~~~R~rIV~l~~~G--------~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      +.+.+|...++..+|......|        -|.+++|..++|++.||.|-.+...+.|.+...
T Consensus         6 f~s~~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~   68 (125)
T COG1725           6 FDSSKPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK   68 (125)
T ss_pred             cCCCCCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3456677777777777766554        589999999999999999999999999987544

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=95.43  E-value=0.056  Score=39.49  Aligned_cols=55  Identities=15%  Similarity=0.160  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH
Q psy1898         102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK  171 (230)
Q Consensus       102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~  171 (230)
                      .+.+..|++++..| .+..+||+.+|||.+||++-+.               ..+..++++.++.|.+..+
T Consensus         5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~---------------~~~~~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844         5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT---------------ERLPEINPELAEEVKEVLD   60 (80)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc---------------CCCCCCCHHHHHHHHHHHc
Confidence            45567777776657 8999999999999999999652               1112368888999888886

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.

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

Probab=95.43  E-value=0.013  Score=35.45  Aligned_cols=29  Identities=24%  Similarity=0.350  Sum_probs=24.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      ++..+||..+|+++-||+|.++++++.|.
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            57889999999999999999999998874

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 ....

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

Probab=95.41  E-value=0.028  Score=36.00  Aligned_cols=47  Identities=15%  Similarity=0.126  Sum_probs=32.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE  167 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~  167 (230)
                      ++..++|+.+||+++||..|.+    .|.+.+....+ ..+..+.++...+.
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~----~g~l~~~~~~~-~~~~y~~~~v~~l~   47 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYER----IGLLSPARTEG-GYRLYSDADLERLR   47 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCEEeCHHHHHHhh
Confidence            4788999999999999999965    45554332222 45566776665543

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.

>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=95.39  E-value=0.022  Score=36.15  Aligned_cols=36  Identities=19%  Similarity=0.237  Sum_probs=27.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ++.-|...++ .+....++|+.||||++|+++-+++|
T Consensus         6 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen    6 EKQLIRQALERCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            4455555554 57899999999999999999999886

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 ....

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

Probab=95.39  E-value=0.086  Score=40.42  Aligned_cols=68  Identities=15%  Similarity=0.041  Sum_probs=48.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||+.|+..|.+    .|.+.|..+.....+..++++.+.|..... ..-+.++.+|++.|..
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL   69 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4688999999999999988854    577754433333467788887766643332 3457899999988864

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.

>PHA00675 hypothetical protein

Probab=95.39  E-value=0.02  Score=41.34  Aligned_cols=39  Identities=23%  Similarity=0.362  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         100 LPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       100 ~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      +....=..|..++ ..|.|..+||+.||||++||+.+.+.
T Consensus        23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHcc
Confidence            4555556677777 78999999999999999999999653

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=95.37  E-value=0.025  Score=45.67  Aligned_cols=42  Identities=24%  Similarity=0.297  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|... .+|+.++..|+|..+||+.||+|++||..|.++..+
T Consensus         6 ~Lt~rq-reVL~lr~~GlTq~EIAe~LGiS~~tVs~ie~ra~k   47 (141)
T PRK03975          6 FLTERQ-IEVLRLRERGLTQQEIADILGTSRANVSSIEKRARE   47 (141)
T ss_pred             CCCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345444 456677889999999999999999999999987543

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

Probab=95.35  E-value=0.028  Score=44.65  Aligned_cols=43  Identities=26%  Similarity=0.256  Sum_probs=36.1

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+-+|++.++||+.+|+|.+||+.++.|-+.
T Consensus       111 ~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~  153 (159)
T TIGR02989       111 KLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRV  153 (159)
T ss_pred             HCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4666777666666889999999999999999999999988653

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).

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=95.34  E-value=0.027  Score=45.39  Aligned_cols=41  Identities=22%  Similarity=0.261  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+..|+|.++||+.||+|.+||+.++.|-+
T Consensus       129 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~  169 (182)
T PRK09652        129 LPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAR  169 (182)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56677766666678999999999999999999999988744

>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins

Probab=95.33  E-value=0.25  Score=41.35  Aligned_cols=92  Identities=18%  Similarity=0.140  Sum_probs=62.5

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh---CCC------
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT---NPG------  175 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~---~P~------  175 (230)
                      .+.|-.++.-|.|..-+.+.||.|..-|..|.+--   |.  +. + .+||+.+++++...|-..-++   .+.      
T Consensus        77 ~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~ll---gi--~~-~-~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~  149 (180)
T PF11198_consen   77 QQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLL---GI--PV-R-KGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDS  149 (180)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh---CC--CC-C-CCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccc
Confidence            45555688899999999999999999999986531   22  22 2 348888899888887544432   222      


Q ss_pred             CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         176 IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       176 ~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ...-++.-.+.++.++       |.++||..++.+
T Consensus       150 ~~~Le~~m~~Ae~~~i-------sL~~iW~~i~~w  177 (180)
T PF11198_consen  150 PDALELMMLLAEETNI-------SLTVIWSLIQEW  177 (180)
T ss_pred             hHHHHHHHHHHHHhCC-------CHHHHHHHHHHH
Confidence            2244444444454554       999999998764

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=95.30  E-value=0.031  Score=44.56  Aligned_cols=42  Identities=17%  Similarity=0.127  Sum_probs=35.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|+|..+||..+|||.+||...+.|-+
T Consensus       106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  147 (161)
T PRK09047        106 KLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT  147 (161)
T ss_pred             hCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            366677777777788999999999999999999999988754

>PHA02591 hypothetical protein; Provisional

Probab=95.28  E-value=0.023  Score=41.12  Aligned_cols=36  Identities=25%  Similarity=0.193  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .|.+.-+-+|++.|+|..+||+.|||+..+|+++++
T Consensus        46 dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         46 DDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             chHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            467777778999999999999999999999999875

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

Probab=95.28  E-value=0.034  Score=37.81  Aligned_cols=48  Identities=23%  Similarity=0.425  Sum_probs=38.7

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         100 LPNHIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++.+.+..|+..+.. +.+..+||+.++++.+||++++++..+.|-+..
T Consensus         4 ~~~~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~   52 (78)
T cd00090           4 LSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVES   52 (78)
T ss_pred             ccChHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence            334566677775544 499999999999999999999999999987643

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.

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=95.27  E-value=0.029  Score=45.13  Aligned_cols=41  Identities=27%  Similarity=0.242  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+..|++..+||+.+|+|++||++|+.+.+
T Consensus       126 L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~  166 (179)
T PRK11924        126 LPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR  166 (179)
T ss_pred             CCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666666666677899999999999999999999998854

>PRK01381 Trp operon repressor; Provisional

Probab=95.20  E-value=0.022  Score=43.17  Aligned_cols=35  Identities=26%  Similarity=0.321  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|.+|+.++..| +|.++||..+|||.+||+|--+
T Consensus        42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn   77 (99)
T PRK01381         42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSN   77 (99)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence            5688889877775 9999999999999999998855

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=95.20  E-value=0.027  Score=46.37  Aligned_cols=43  Identities=26%  Similarity=0.255  Sum_probs=38.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|.+.|.-++..+-+|.|..+||..+|||.+||..++.|-+.
T Consensus       127 ~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~  169 (182)
T COG1595         127 RLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK  169 (182)
T ss_pred             hCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4778889888888899999999999999999999999988653

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=95.19  E-value=0.037  Score=45.17  Aligned_cols=42  Identities=12%  Similarity=0.048  Sum_probs=36.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||..||+|.+||..++.|.+.
T Consensus       130 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  171 (179)
T PRK12514        130 LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL  171 (179)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence            566777777777789999999999999999999999988653

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=95.13  E-value=0.1  Score=46.65  Aligned_cols=89  Identities=18%  Similarity=0.177  Sum_probs=54.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC-CCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCC
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIF  177 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~-v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t  177 (230)
                      .+|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+..=. .-...+....+...+.+..+.+..+...--...
T Consensus       142 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD  221 (324)
T TIGR02960       142 YLPPRQRAVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYD  221 (324)
T ss_pred             hCCHHHhhHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCC
Confidence            3566777777777789999999999999999999999988764321 111111111122334444444554444322334


Q ss_pred             HHHHHHHHHH
Q psy1898         178 SWEIRDRLVK  187 (230)
Q Consensus       178 ~~eI~~~L~~  187 (230)
                      ...+.+.|..
T Consensus       222 ~~~l~~Lla~  231 (324)
T TIGR02960       222 LDALTALLHE  231 (324)
T ss_pred             HHHHHHHhcC
Confidence            5556666654

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.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=95.12  E-value=0.038  Score=44.31  Aligned_cols=42  Identities=21%  Similarity=0.286  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|.+.|.-++..+-+|+|..+||+.+|+|.+||..++.|..+
T Consensus       114 L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528        114 LPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            566666666666779999999999999999999999988653

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=95.10  E-value=0.037  Score=45.34  Aligned_cols=42  Identities=17%  Similarity=0.081  Sum_probs=35.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|++..+||..+|+|.+||.+++.|.++
T Consensus       136 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~  177 (186)
T PRK13919        136 LSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS  177 (186)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            566666666666789999999999999999999999988653

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=95.09  E-value=0.043  Score=45.37  Aligned_cols=47  Identities=11%  Similarity=0.025  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898          99 PLPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .++.+.|..+-.+|- ++++...+|..+|||.+|+.+|.++-++.|.-
T Consensus         2 Ah~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDD   49 (165)
T PF08822_consen    2 AHPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGDD   49 (165)
T ss_pred             CCcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence            357799999998876 78999999999999999999999999999954

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=95.08  E-value=0.22  Score=39.09  Aligned_cols=68  Identities=18%  Similarity=0.111  Sum_probs=47.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+..+.-+..+.++.+.+..... .+-..++.+|++.+..
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~   69 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYE----EIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL   69 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            478899999999999987664    4687765433223467778877666654332 3557899999988754

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

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=95.07  E-value=0.036  Score=44.42  Aligned_cols=40  Identities=18%  Similarity=0.186  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+ +|++..+||..||+|.+||.+++.|-+
T Consensus       113 L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~  152 (166)
T PRK09639        113 MTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAK  152 (166)
T ss_pred             CCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            5667777777777 999999999999999999999998754

>PRK11050 manganese transport regulator MntR; Provisional

Probab=95.06  E-value=0.17  Score=41.01  Aligned_cols=34  Identities=29%  Similarity=0.399  Sum_probs=31.0

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++.+..+||+.|+|+++||++++++..+.|.+..
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r   83 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEM   83 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3589999999999999999999999999997754

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

Probab=95.05  E-value=0.1  Score=38.96  Aligned_cols=68  Identities=15%  Similarity=0.094  Sum_probs=46.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..++++...|..... .+-..+..+|++.+..
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~   69 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDG   69 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhC
Confidence            4688999999999999988854    687766433223456777777655543322 2346889999887753

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.

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=95.05  E-value=0.019  Score=52.22  Aligned_cols=41  Identities=22%  Similarity=0.311  Sum_probs=35.7

Q ss_pred             HHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         105 RLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       105 R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      -.++-.+ |.+|++..|||++||||+++|+|.+++.++.|.+
T Consensus        18 ~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV   59 (318)
T PRK15418         18 VARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGII   59 (318)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcE
Confidence            4455554 4689999999999999999999999999999976

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=95.03  E-value=0.026  Score=44.39  Aligned_cols=36  Identities=25%  Similarity=0.265  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSK  134 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~k  134 (230)
                      .+|.+.|.-++..+-+|+|..+||..+|+|.+||++
T Consensus       107 ~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~~  142 (142)
T TIGR03209       107 ILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVYK  142 (142)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence            366677777777778999999999999999999975

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=95.03  E-value=0.039  Score=45.03  Aligned_cols=42  Identities=17%  Similarity=-0.021  Sum_probs=36.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus       135 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~  176 (183)
T TIGR02999       135 VDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARA  176 (183)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            677777777777789999999999999999999999988653

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.

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

Probab=95.00  E-value=0.11  Score=39.69  Aligned_cols=68  Identities=15%  Similarity=-0.001  Sum_probs=49.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      .+..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~----~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~   69 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLL----RGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA   69 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            3678999999999999877754    588876544333467778887777765443 4457889999888865

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,

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=94.99  E-value=0.073  Score=51.10  Aligned_cols=95  Identities=11%  Similarity=0.167  Sum_probs=68.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHH-HhhhC--CC------CcCCCCCCCCCCCCHHHHHHHHHHHHh-CCC--CCHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI------RPGVIGGSKPRVATPDVEKRIEEYKKT-NPG--IFSWEIRD  183 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v------~p~~~gg~rpr~lt~~~~~~I~~l~~~-~P~--~t~~eI~~  183 (230)
                      ++.++||..+|++.|||+|..+. |..|.  .+      ............-+..++..|++++.. +|.  .+=.+|.+
T Consensus       370 LtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~lI~~Ed~~kPLSD~~I~~  449 (481)
T PRK12469        370 LVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEMIAAEQAGDPLSDVALAE  449 (481)
T ss_pred             CcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence            78899999999999999998764 55553  21      111110000112355688889998875 443  66778999


Q ss_pred             HHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         184 RLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       184 ~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      .|.+ .||.     ||+.||-.+=...||.++.
T Consensus       450 ~L~~-~GI~-----IARRTVAKYRe~L~IpsS~  476 (481)
T PRK12469        450 MLAG-RGVL-----IARRTVAKYREAMKIPPAE  476 (481)
T ss_pred             HHHh-cCCC-----eechhHHHHHHHcCCCChh
Confidence            9988 7995     9999999999999998875

>PHA00738 putative HTH transcription regulator

Probab=94.97  E-value=0.033  Score=42.84  Aligned_cols=50  Identities=30%  Similarity=0.317  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCC
Q psy1898         102 NHIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG  151 (230)
Q Consensus       102 ~~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~g  151 (230)
                      ...|.+|+.++..+  .+.++|+..|++|++||++-++--++.|.+...+.|
T Consensus        11 dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G   62 (108)
T PHA00738         11 KILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG   62 (108)
T ss_pred             CHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence            47899999977764  899999999999999999999999999988665543

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=94.94  E-value=0.052  Score=45.58  Aligned_cols=48  Identities=13%  Similarity=0.167  Sum_probs=39.8

Q ss_pred             cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|.+...+|..++ +|+.++.+|++.++||+.|++|.+||...+.+-.+
T Consensus       127 ~~~~~~~LSpREr-EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImk  174 (198)
T PRK15201        127 HYCTTRHFSVTER-HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMR  174 (198)
T ss_pred             cccCCCCCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3455677886655 78889999999999999999999999998887543

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=94.94  E-value=0.041  Score=45.75  Aligned_cols=36  Identities=25%  Similarity=0.310  Sum_probs=29.7

Q ss_pred             HHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         105 RLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       105 R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..++|. .+-+|+|..+||+.+|||..||++.++..+
T Consensus       140 ~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR  176 (185)
T PF07638_consen  140 QRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR  176 (185)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            344554 556999999999999999999999988755

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

Probab=94.93  E-value=0.043  Score=42.18  Aligned_cols=41  Identities=29%  Similarity=0.310  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...+.-+...+..|.+..+||+.+|||++||++++++-.
T Consensus       111 L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~  151 (158)
T TIGR02937       111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR  151 (158)
T ss_pred             CCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45566655555557899999999999999999999998854

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.

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=94.90  E-value=0.041  Score=44.33  Aligned_cols=43  Identities=14%  Similarity=-0.003  Sum_probs=36.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|.+.|.-++..+-+|++..+||..||+|.+||+.++.|-++
T Consensus       108 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~  150 (165)
T PRK09644        108 TLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK  150 (165)
T ss_pred             hCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3566777766667789999999999999999999999988653

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=94.89  E-value=0.046  Score=44.12  Aligned_cols=42  Identities=17%  Similarity=0.172  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||+.+|||.+||..++.|-+.
T Consensus       113 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  154 (164)
T PRK12547        113 LSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN  154 (164)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            566777666666789999999999999999999999988653

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

Probab=94.86  E-value=0.055  Score=37.99  Aligned_cols=46  Identities=15%  Similarity=0.312  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHc--C--CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         102 NHIRLKIVEMAAA--G--VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       102 ~~~R~rIV~l~~~--G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ...+.+|+.++..  +  .+..+||+.+|+++.+|++.+.+..+.|.+..
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~   54 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK   54 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            3567788886654  4  89999999999999999999999999998853

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

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

Probab=94.84  E-value=0.051  Score=42.79  Aligned_cols=41  Identities=20%  Similarity=0.171  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+.+|.+..+||+.+|+|.+||+.++.|-+
T Consensus       114 L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~  154 (161)
T TIGR02985       114 LPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKAL  154 (161)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555555555577899999999999999999999998754

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.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=94.83  E-value=0.046  Score=45.35  Aligned_cols=41  Identities=15%  Similarity=0.138  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||..++.|.+
T Consensus       135 Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr  175 (189)
T PRK12530        135 LPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR  175 (189)
T ss_pred             CCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56677766666777899999999999999999999988755

>PF13276 HTH_21: HTH-like domain

Probab=94.77  E-value=0.13  Score=34.83  Aligned_cols=54  Identities=24%  Similarity=0.239  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCC
Q psy1898         160 PDVEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRK  218 (230)
Q Consensus       160 ~~~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~  218 (230)
                      .+..+.|.+...++ +...+..|...|..+.|+.     +|..+|+|+++..||....++
T Consensus         4 ~~l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~-----v~~krV~RlM~~~gL~~~~rr   58 (60)
T PF13276_consen    4 EALRELIKEIFKESKPTYGYRRIWAELRREGGIR-----VSRKRVRRLMREMGLRSKRRR   58 (60)
T ss_pred             HHHHHHHHHHHHHcCCCeehhHHHHHHhccCccc-----ccHHHHHHHHHHcCCcccCCC
Confidence            44566677777666 6788999999998854674     899999999999999876544

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=94.77  E-value=0.053  Score=43.38  Aligned_cols=41  Identities=24%  Similarity=0.225  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-.
T Consensus       110 L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~  150 (163)
T PRK07037        110 LPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDAL  150 (163)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45566665555677899999999999999999999987654

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=94.77  E-value=0.052  Score=43.55  Aligned_cols=43  Identities=16%  Similarity=0.085  Sum_probs=35.8

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+-+|+|..+||+.||||.+||...+.|-++
T Consensus       122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~  164 (170)
T TIGR02952       122 ILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIK  164 (170)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666777666666789999999999999999999999987653

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.

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

Probab=94.76  E-value=0.15  Score=39.97  Aligned_cols=68  Identities=16%  Similarity=0.105  Sum_probs=46.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+    +.|.+.|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus         1 m~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (126)
T cd04783           1 LTIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL   69 (126)
T ss_pred             CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            46889999999999999    44566788864333223467778877666543322 3446888888887754

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.

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=94.76  E-value=0.048  Score=43.62  Aligned_cols=42  Identities=24%  Similarity=0.267  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|++..+||..+|+|.+||..++.|-++
T Consensus       111 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~  152 (162)
T TIGR02983       111 LPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA  152 (162)
T ss_pred             CCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            455666666666788999999999999999999999988653

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.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=94.75  E-value=0.017  Score=37.74  Aligned_cols=23  Identities=13%  Similarity=0.147  Sum_probs=20.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      +|..|+|+.|+||++||++|+++
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            47899999999999999999963

>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes

Probab=94.75  E-value=0.071  Score=44.45  Aligned_cols=56  Identities=18%  Similarity=0.146  Sum_probs=48.4

Q ss_pred             cCCcccCCCcCCHHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898          90 LGGVFINGRPLPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        90 l~~~~~~g~~~s~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.++|.+..++|.+.|..|+..+. .|+|.+++|..|||+...|.-+++-+.-.+..
T Consensus         7 ~Np~f~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~   63 (172)
T PF12298_consen    7 LNPSFRSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIEKRW   63 (172)
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            456778899999999999999885 57999999999999999999999887755544

This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].

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

Probab=94.75  E-value=0.1  Score=39.26  Aligned_cols=67  Identities=10%  Similarity=0.070  Sum_probs=48.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||.+|+..|.+    .|.+.|.... +..+..+..+...+.....  ++-.++..+|...|.-
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~----~Gli~p~r~~-~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l   70 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR----LGLVSPARTN-GGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIEL   70 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCC-CCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            4688999999999999998854    6777663222 2456678887777765442  3367888888877754

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.

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=94.75  E-value=0.028  Score=49.36  Aligned_cols=37  Identities=19%  Similarity=0.120  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      -|..+-.++-+|+...+||..||||+.||.+|.+|+.
T Consensus         8 ~r~~Akk~yl~gmk~~dIAeklGvspntiksWKrr~g   44 (279)
T COG5484           8 KRIIAKKDYLKGMKLKDIAEKLGVSPNTIKSWKRRDG   44 (279)
T ss_pred             hHHHHHHHHHhhccHHHHHHHhCCChHHHHHHHHhcC
Confidence            3555566899999999999999999999999999863

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=94.69  E-value=0.31  Score=38.16  Aligned_cols=68  Identities=15%  Similarity=0.109  Sum_probs=47.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|    .+.|.+.|..+..+.-+..+.++...+..... ..-.+++.+|++.+..
T Consensus         1 m~I~e~a~~~gvs~~tlRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYY----EEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNL   69 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            47889999999999998755    45788866444223467778877666653332 3457889999888753

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=94.68  E-value=0.049  Score=44.70  Aligned_cols=42  Identities=14%  Similarity=0.230  Sum_probs=35.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|.+.|.-++..+-+|+|..+||+.+|||.+||...+.|-.
T Consensus       127 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl  168 (178)
T PRK12529        127 TLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAY  168 (178)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            367777777777778999999999999999999999987643

>PRK04280 arginine repressor; Provisional

Probab=94.67  E-value=0.078  Score=43.08  Aligned_cols=45  Identities=22%  Similarity=0.178  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+.|.+++.+++-.+..|+.+.|.+ .|+.     ++.+||+|-|++.++.
T Consensus         6 ~~~I~~iI~~~~I~tQeeL~~~L~~-~Gi~-----vTQATiSRDikeL~lv   50 (148)
T PRK04280          6 HIKIREIITNNEIETQDELVDRLRE-EGFN-----VTQATVSRDIKELHLV   50 (148)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHH-cCCC-----eehHHHHHHHHHcCCE
Confidence            5678899999999999999999988 8995     8999999999999976

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=94.67  E-value=0.06  Score=43.64  Aligned_cols=41  Identities=17%  Similarity=0.165  Sum_probs=35.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..||+|.+||..++.+-.
T Consensus       119 L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~  159 (168)
T PRK12525        119 LSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF  159 (168)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66677776666678999999999999999999999998754

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

Probab=94.67  E-value=0.17  Score=37.81  Aligned_cols=68  Identities=15%  Similarity=0.055  Sum_probs=47.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      .+..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..+.++...|..... .+-.++..+|++.+..
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~----~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~   69 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDD----IGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT   69 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            3678999999999999987765    588877544223456777776666543332 3446889999887753

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.

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

Probab=94.66  E-value=0.19  Score=39.00  Aligned_cols=68  Identities=18%  Similarity=0.179  Sum_probs=48.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-    |.+.|.+.|..+..+.-+..++++...+..... .+-+.+..+|++.+..
T Consensus         1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~   69 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSL   69 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            4788999999999999854    566788876444333467778877666543322 4557889999888764

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.

>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=94.65  E-value=0.03  Score=42.69  Aligned_cols=44  Identities=18%  Similarity=0.192  Sum_probs=29.5

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      |.-++...|.-+-..+.+.+|..+||..++||+..|+.|++|-.
T Consensus        15 g~LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~   58 (101)
T PF04297_consen   15 GELLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE   58 (101)
T ss_dssp             GGGS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34455555544444556789999999999999999999999854

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=94.63  E-value=0.18  Score=45.58  Aligned_cols=109  Identities=17%  Similarity=0.134  Sum_probs=61.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC-CcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS  178 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v-~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~  178 (230)
                      +|...|.-++..+-+|+|..+||..||+|.+||...+.|-++.=.. .+.-. ...+.....+..+.+.++...--....
T Consensus       154 Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~-~~~~~~~~~~~~~~v~~~~~A~~~gD~  232 (339)
T PRK08241        154 LPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAA-DTLREPDDPEERALLARYVAAFEAYDV  232 (339)
T ss_pred             CCHHHhhhhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcc-cccCCCCChHHHHHHHHHHHHHhcCCH
Confidence            5667777666677899999999999999999999999887643211 11101 112333334444444444443222334


Q ss_pred             HHHHHHHHHhhCCC----CCCCCCCHhHHHHHHHcC
Q psy1898         179 WEIRDRLVKQDGIC----DKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       179 ~eI~~~L~~~~Gi~----~~~~~vS~sTV~R~Lr~~  210 (230)
                      ..+.+.|.. ..+.    ......-..-|..++...
T Consensus       233 ~~l~~lla~-Dv~~~~p~~~~~~~G~~~v~~~~~~~  267 (339)
T PRK08241        233 DALVALLTE-DATWSMPPFPLWYRGRDAIAAFLAGQ  267 (339)
T ss_pred             HHHHHHhcC-CEEEEcCCCCCcccCHHHHHHHHHhh
Confidence            555565544 2211    001133455566666663

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=94.61  E-value=0.044  Score=45.27  Aligned_cols=41  Identities=20%  Similarity=0.219  Sum_probs=33.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|.+.|.-++..+-+|++.++||..+|+|.+||..++.|.+
T Consensus       142 L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  182 (194)
T PRK12519        142 LPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL  182 (194)
T ss_pred             CCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            45555555555567899999999999999999999998755

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

Probab=94.61  E-value=0.11  Score=38.91  Aligned_cols=67  Identities=15%  Similarity=0.179  Sum_probs=48.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||.+|+..|.+    .|.+.|... .+..+..++.+...+.....  +.-..+..+++..+..
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~-~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~   69 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERS-EGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLER   69 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcC-CCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            3678999999999999999954    477765433 23567788887776654432  3257888888887754

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.

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

Probab=94.61  E-value=0.028  Score=37.16  Aligned_cols=41  Identities=27%  Similarity=0.417  Sum_probs=33.3

Q ss_pred             HHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|++.+.+   +++..+||+.+|++++||++.++...+.|-+.
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~   49 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE   49 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence            456665543   37899999999999999999999999998764

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.

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

Probab=94.60  E-value=0.15  Score=38.49  Aligned_cols=66  Identities=20%  Similarity=0.112  Sum_probs=44.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      .+..++|+.+|||++|+.-|.+    .|.+.|. +..+.-+..++++...|..... .+...+..+|+..+.
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~-r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~   68 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSA-RSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA   68 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCC-CCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence            4789999999999999966654    5877433 3222346677776665543332 345788999887664

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

>COG1438 ArgR Arginine repressor [Transcription]

Probab=94.60  E-value=0.087  Score=42.93  Aligned_cols=47  Identities=19%  Similarity=0.085  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +-.+.|++++.++.-.|..||.+.|++ .|+.     ++.+||+|-|++.|+.
T Consensus         6 ~R~~~Ik~iI~~~~i~TQ~Elv~~L~~-~Gi~-----vTQaTvSRDlkelglv   52 (150)
T COG1438           6 ERLELIKEIITEEKISTQEELVELLQE-EGIE-----VTQATVSRDLKELGLV   52 (150)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCe-----EehHHHHHHHHHcCCE
Confidence            346788999999999999999999988 9995     8999999999999986

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

Probab=94.58  E-value=0.15  Score=38.23  Aligned_cols=68  Identities=16%  Similarity=0.155  Sum_probs=48.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+...--+..++++.+.|.....  ++-..+..+|++.+..
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~   70 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA   70 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4678999999999999877765    687766433222346788888777765443  3357889999988864

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.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=94.56  E-value=0.065  Score=43.36  Aligned_cols=41  Identities=22%  Similarity=0.212  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus       119 L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  159 (173)
T PRK09645        119 LSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAL  159 (173)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56677776666678999999999999999999998887754

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=94.53  E-value=0.19  Score=44.53  Aligned_cols=84  Identities=11%  Similarity=-0.001  Sum_probs=55.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS  178 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~  178 (230)
                      .+|...|.-++.....|+|..+||+.+|+|.+||...+.|-+..=  ....   .++...+++..+.+..++..--.-..
T Consensus       108 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L--r~~~---~~~~~~~~~~~~~~~~f~~a~~~gD~  182 (281)
T TIGR02957       108 RLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL--DARR---PRFEVSREESRQLLERFVEAAQTGDL  182 (281)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH--HhhC---CCCCCChHHHHHHHHHHHHHHHhCCH
Confidence            356677777777778999999999999999999999999877542  1111   01222234455555555544333456


Q ss_pred             HHHHHHHHH
Q psy1898         179 WEIRDRLVK  187 (230)
Q Consensus       179 ~eI~~~L~~  187 (230)
                      ..+.+.|..
T Consensus       183 ~~l~~lL~~  191 (281)
T TIGR02957       183 DGLLELLAE  191 (281)
T ss_pred             HHHHHHHhh
Confidence            667777765

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.

>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=94.51  E-value=0.034  Score=40.49  Aligned_cols=26  Identities=15%  Similarity=0.112  Sum_probs=19.2

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .++...+.+++|+.||||.|||++=+
T Consensus        15 Ii~~~aTVR~~Ak~FGvSKSTVHkDv   40 (82)
T PF12116_consen   15 IIETKATVRQAAKVFGVSKSTVHKDV   40 (82)
T ss_dssp             HHHH---HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHcccHHHHHHHHHCCcHHHHHHHH
Confidence            44668999999999999999999876

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.

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

Probab=94.51  E-value=0.41  Score=37.61  Aligned_cols=68  Identities=18%  Similarity=0.113  Sum_probs=46.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..+.++...+..... ..-.+++.+|++.|..
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~   69 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY   69 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4688999999999999877654    687764333223456777777555543332 3446889999888753

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.

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=94.51  E-value=0.063  Score=44.48  Aligned_cols=42  Identities=19%  Similarity=0.234  Sum_probs=35.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|+|..+||..||||.+||..++.|-+
T Consensus       111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar  152 (182)
T PRK12511        111 DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRAR  152 (182)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            366777777777788999999999999999999999987754

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

Probab=94.51  E-value=0.21  Score=37.55  Aligned_cols=67  Identities=18%  Similarity=0.166  Sum_probs=45.3

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVK  187 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~  187 (230)
                      +..++|+.+|||..|+..|.    +.|.+.|..+....-+..++++...+.....-....+..++++.+..
T Consensus         2 ~i~e~A~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~~~~   68 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNYE----SLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRIMRA   68 (99)
T ss_pred             CHHHHHHHHCcCHHHHHHHH----HcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            67899999999999998774    47877654332234566788877766544332246777777665544

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=94.49  E-value=0.06  Score=44.51  Aligned_cols=43  Identities=12%  Similarity=0.112  Sum_probs=36.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|.+.|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus       130 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~  172 (185)
T PRK09649        130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD  172 (185)
T ss_pred             hCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3567777777777889999999999999999999999988654

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=94.46  E-value=0.066  Score=43.22  Aligned_cols=42  Identities=17%  Similarity=0.155  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||+.+|||.+||+..+.|-+.
T Consensus       120 L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~  161 (169)
T TIGR02954       120 LNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK  161 (169)
T ss_pred             CCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            566666666666778999999999999999999999988653

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.

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

Probab=94.46  E-value=0.093  Score=41.22  Aligned_cols=66  Identities=18%  Similarity=0.179  Sum_probs=48.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||++|+..|.+    .|.+.|...  +..+..++++.+.|.....  ++..++..+|+..|..
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~----~GLl~p~r~--~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l   69 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWER----HGLIKPARR--NGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSM   69 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCC--CCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4788999999999999998866    377766543  2457778887766654432  3467888888887754

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

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=94.45  E-value=0.066  Score=44.48  Aligned_cols=41  Identities=22%  Similarity=0.276  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus       117 Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar  157 (187)
T PRK12516        117 LPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR  157 (187)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56677766666678999999999999999999999988754

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=94.40  E-value=0.069  Score=43.98  Aligned_cols=41  Identities=17%  Similarity=0.209  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|||.+||..++.|.+
T Consensus       140 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  180 (189)
T PRK09648        140 LPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRAL  180 (189)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55666666666678899999999999999999999998754

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=94.40  E-value=0.059  Score=44.18  Aligned_cols=42  Identities=21%  Similarity=0.142  Sum_probs=35.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||+.+|||.+||..++.|.++
T Consensus       128 L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~  169 (179)
T PRK09415        128 LPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE  169 (179)
T ss_pred             CCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            566667666677789999999999999999999999988654

>PRK13749 transcriptional regulator MerD; Provisional

Probab=94.37  E-value=0.22  Score=39.14  Aligned_cols=68  Identities=15%  Similarity=0.021  Sum_probs=52.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..||.-    |.+.|.+.|..+..+.-+..++++.+.+..... ..-++++.+|++.|.-
T Consensus         4 ~tIgelA~~~gvS~~tiR~----YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l   72 (121)
T PRK13749          4 YTVSRLALDAGVSVHIVRD----YLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA   72 (121)
T ss_pred             CcHHHHHHHHCCCHHHHHH----HHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence            6899999999999998754    556788876545334567888888887765554 5668999999998875

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=94.37  E-value=0.29  Score=42.22  Aligned_cols=88  Identities=19%  Similarity=0.131  Sum_probs=57.7

Q ss_pred             HHHcC--CCHHHHhhhhccccchhhhHHHHHhhh-CCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898         111 MAAAG--VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVK  187 (230)
Q Consensus       111 l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~-G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~  187 (230)
                      ++++|  ++..++|-.|++|..||++-++.|++. |.+.|... --+-.--+-.+...|.++-.+.  .+..||+.+.. 
T Consensus        99 Ay~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG-~i~DiGp~~tHK~~ii~~~l~g--~~~~eiar~t~-  174 (220)
T PF07900_consen   99 AYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRG-TIHDIGPGVTHKKIIIRLYLKG--KPTPEIARRTN-  174 (220)
T ss_pred             HHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCC-cccccCCcchHHHHHHHHHHcC--CCHHHHHHHhc-
Confidence            55666  999999999999999999999999977 87765421 0010000112334444433333  56777776542 


Q ss_pred             hhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898         188 QDGICDKNSAPSVSSISRLLRGGRR  212 (230)
Q Consensus       188 ~~Gi~~~~~~vS~sTV~R~Lr~~g~  212 (230)
                                -|..+|-|.++....
T Consensus       175 ----------HS~~av~rYi~~F~r  189 (220)
T PF07900_consen  175 ----------HSPEAVDRYIKDFKR  189 (220)
T ss_pred             ----------cCHHHHHHHHHhhHH
Confidence                      388899998887643

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

Probab=94.36  E-value=0.18  Score=39.87  Aligned_cols=68  Identities=16%  Similarity=0.135  Sum_probs=47.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-    |.+.|.+.|.....+.-+..++++...+..... .+-..++.||++.+..
T Consensus         1 m~IgE~A~~~gvs~~TLRy----YE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~   69 (133)
T cd04787           1 MKVKELANAAGVTPDTVRF----YTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSH   69 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence            4688999999999999844    466798877543323356778877666543322 3456889999988864

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

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=94.35  E-value=0.075  Score=43.17  Aligned_cols=41  Identities=22%  Similarity=0.198  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|.+.|.-++..+-+|++..+||+.+|+|.+||..++.|-.
T Consensus       120 Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  160 (172)
T PRK12523        120 LSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL  160 (172)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666666666677999999999999999999999998754

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=94.34  E-value=0.071  Score=43.27  Aligned_cols=42  Identities=19%  Similarity=0.103  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus       120 L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (173)
T PRK12522        120 LNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK  161 (173)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            555667666666679999999999999999999999987653

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

Probab=94.33  E-value=0.19  Score=38.03  Aligned_cols=65  Identities=12%  Similarity=0.005  Sum_probs=45.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL  185 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L  185 (230)
                      ++..++|+.+|||++|+.-|.+    .|.+.|... ...-+..++++.+.+..... .+..++..+|++.+
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----LGLITGTRN-ANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL   67 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcC-CCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            4788999999999999986654    588766332 23456777777666653322 34568888888766

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.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=94.30  E-value=0.068  Score=44.32  Aligned_cols=41  Identities=17%  Similarity=0.179  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus       137 L~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  177 (195)
T PRK12532        137 LPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR  177 (195)
T ss_pred             CCHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666666666678999999999999999999999988754

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=94.29  E-value=0.071  Score=46.55  Aligned_cols=43  Identities=19%  Similarity=0.152  Sum_probs=37.0

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+.+|+|.++||..+|||.+||..++.|-+.
T Consensus       161 ~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~  203 (244)
T TIGR03001       161 ALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARE  203 (244)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3666778777777889999999999999999999999988553

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.

>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=94.29  E-value=0.061  Score=35.55  Aligned_cols=38  Identities=16%  Similarity=0.304  Sum_probs=30.9

Q ss_pred             HHHHHHH-Hc-C-CCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898         106 LKIVEMA-AA-G-VRPCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus       106 ~rIV~l~-~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      .+|+.++ .. + +|..++|..|+||+.||++-++.-++.|
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            3566655 33 3 8999999999999999999999999888

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 ....

>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=94.25  E-value=0.043  Score=37.71  Aligned_cols=32  Identities=34%  Similarity=0.448  Sum_probs=28.9

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..+||+.|+||++||+.-+++..+.|.+.
T Consensus        22 ~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~   53 (60)
T PF01325_consen   22 PVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE   53 (60)
T ss_dssp             SBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence            38999999999999999999999999999774

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 ....

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=94.25  E-value=0.036  Score=45.95  Aligned_cols=41  Identities=22%  Similarity=0.246  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||..++.|-+
T Consensus       132 Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  172 (193)
T TIGR02947       132 LPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGR  172 (193)
T ss_pred             CCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666766666778999999999999999999999988754

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.

>PHA00542 putative Cro-like protein

Probab=94.25  E-value=0.05  Score=39.62  Aligned_cols=27  Identities=22%  Similarity=0.266  Sum_probs=24.3

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +...|++..++|+.+|||++||++|.+
T Consensus        27 l~~~glTq~elA~~lgIs~~tIsr~e~   53 (82)
T PHA00542         27 LIRAGWSQEQIADATDVSQPTICRIYS   53 (82)
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            446689999999999999999999974

>PRK06930 positive control sigma-like factor; Validated

Probab=94.24  E-value=0.08  Score=43.90  Aligned_cols=42  Identities=14%  Similarity=0.187  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+.+|++..+||+.||+|.+||..++.|..
T Consensus       114 ~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~  155 (170)
T PRK06930        114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE  155 (170)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366676766666678999999999999999999999988754

>PRK03341 arginine repressor; Provisional

Probab=94.23  E-value=0.13  Score=42.76  Aligned_cols=48  Identities=19%  Similarity=0.079  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+-.+.|.+++.+++-.+..|+.+.|.+ .|+.     +|.+||+|-|+..++.
T Consensus        14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~-~Gi~-----vTQaTiSRDl~eL~~~   61 (168)
T PRK03341         14 AARQARIVAILSRQSVRSQAELAALLAD-EGIE-----VTQATLSRDLDELGAV   61 (168)
T ss_pred             HHHHHHHHHHHHHCCCccHHHHHHHHHH-cCCc-----ccHHHHHHHHHHhcCE
Confidence            3456788899999999999999999988 8996     8999999999999876

>TIGR01764 excise DNA binding domain, excisionase family

Probab=94.22  E-value=0.028  Score=35.63  Aligned_cols=22  Identities=18%  Similarity=0.209  Sum_probs=20.3

Q ss_pred             CCHHHHhhhhccccchhhhHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++..++|+.||||++||++|++
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~   23 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIH   23 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Confidence            4789999999999999999986

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).

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=94.22  E-value=0.079  Score=44.00  Aligned_cols=43  Identities=19%  Similarity=0.152  Sum_probs=36.1

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+.+|++..+||..+|||.+||..++.|.+.
T Consensus       128 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (188)
T PRK12517        128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN  170 (188)
T ss_pred             hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3666777766666789999999999999999999999988653

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=94.20  E-value=0.08  Score=44.69  Aligned_cols=41  Identities=27%  Similarity=0.322  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|++..+||..||+|.+||+.++.|-+
T Consensus       139 L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr  179 (203)
T PRK09647        139 LPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR  179 (203)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55566666666778999999999999999999999998865

>PRK05066 arginine repressor; Provisional

Probab=94.20  E-value=0.15  Score=41.86  Aligned_cols=48  Identities=21%  Similarity=0.079  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +..+.|.+++.+++-.|..|+.+.|++ .|+.    .++.+||+|-|++.|+.
T Consensus         9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~-~Gi~----~vTQATiSRDikeL~lv   56 (156)
T PRK05066          9 ELVKAFKALLKEEKFGSQGEIVTALQE-QGFD----NINQSKVSRMLTKFGAV   56 (156)
T ss_pred             HHHHHHHHHHhhCCCCCHHHHHHHHHH-CCCC----eecHHHHHHHHHHcCCE
Confidence            445788999999999999999999988 8993    27999999999999986

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=94.18  E-value=0.084  Score=43.65  Aligned_cols=43  Identities=16%  Similarity=0.182  Sum_probs=35.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|.+.|.-++..+-+|+|..+||+.+|+|.+||...+.|-+.
T Consensus       131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~  173 (189)
T PRK06811        131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRK  173 (189)
T ss_pred             hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666766666656778999999999999999999999988654

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=94.18  E-value=0.086  Score=42.90  Aligned_cols=42  Identities=21%  Similarity=0.230  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||+.+|+|.+||..++.|-+
T Consensus       100 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar  141 (170)
T TIGR02959       100 ELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGR  141 (170)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            356666666666678999999999999999999999988744

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).

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=94.15  E-value=0.083  Score=43.66  Aligned_cols=41  Identities=15%  Similarity=0.122  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus       132 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar  172 (191)
T PRK12520        132 LPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRAR  172 (191)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66677777777778999999999999999999999988754

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.15  E-value=0.043  Score=36.19  Aligned_cols=45  Identities=27%  Similarity=0.361  Sum_probs=34.5

Q ss_pred             HHHHHHHHH-HHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEM-AAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l-~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .++..++.. +..|  + |..++|+.|+||++||.+.+++..+.|.+..
T Consensus         4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~   52 (60)
T smart00345        4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQR   52 (60)
T ss_pred             HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            344555443 2223  4 8999999999999999999999999998743

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=94.10  E-value=0.085  Score=43.87  Aligned_cols=41  Identities=20%  Similarity=0.263  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|.+..+||+.||||.+||..++.|-+
T Consensus       137 L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~  177 (196)
T PRK12524        137 LPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK  177 (196)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56566666666677999999999999999999999998854

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=94.10  E-value=0.24  Score=39.13  Aligned_cols=68  Identities=21%  Similarity=0.160  Sum_probs=48.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+....-+..++++...+..... .+-..+..+|++.+..
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~   70 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEK----NGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI   70 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5789999999999999877754    588876544233456777777666643332 3457889999988864

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.

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

Probab=94.09  E-value=0.41  Score=36.46  Aligned_cols=68  Identities=15%  Similarity=0.144  Sum_probs=47.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCC-CCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG-GSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~g-g~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||++|+.-|.+    .|.+.|..+. ....+..++++...|..... .+-+.+..+|...+..
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~----~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~   70 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDK----IGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDA   70 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----cCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            3678999999999999987765    5888664432 13467778887766654332 2346888888877643

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.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=94.07  E-value=0.068  Score=45.81  Aligned_cols=41  Identities=12%  Similarity=0.111  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+    .+|+|..+||+.+|||.+||.+++.|-.
T Consensus       179 Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~  223 (234)
T PRK08301        179 LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRII  223 (234)
T ss_pred             CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            5556555555544    4899999999999999999999987754

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=94.06  E-value=0.1  Score=42.88  Aligned_cols=42  Identities=14%  Similarity=0.031  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+.+|++..+||..||+|.+||+..+.|-+.
T Consensus       138 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~  179 (187)
T PRK12534        138 LEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA  179 (187)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence            566677666667789999999999999999999999988653

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=94.05  E-value=0.15  Score=41.14  Aligned_cols=76  Identities=14%  Similarity=0.073  Sum_probs=40.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKN  195 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~  195 (230)
                      .|..+||..+||+++|+|+|.+.-+.                    -.++...+..+.-.-...++...|....-..   
T Consensus        35 ~T~~eiAee~Gis~~tLYrWr~~~~~--------------------Fiey~n~la~~~~~~~~~eVy~~L~~~i~~~---   91 (142)
T PF13022_consen   35 RTQAEIAEEVGISRSTLYRWRQQNKA--------------------FIEYKNELADRFLSSHREEVYTQLMKKIRGG---   91 (142)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHH-HH--------------------HHHHHHHHHHHHHHTTHHHHHHHHHHHHHSS---
T ss_pred             chHHHHHHHhCCCHHHHHHHHhcCHH--------------------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhCC---
Confidence            78999999999999999999863111                    1111111121111223344433333322222   


Q ss_pred             CCCCHhHHHHHHHcCCCCCC
Q psy1898         196 SAPSVSSISRLLRGGRRDDC  215 (230)
Q Consensus       196 ~~vS~sTV~R~Lr~~g~~~~  215 (230)
                       .+|+..|-=+|+++|+-.+
T Consensus        92 -~~svKaieLflk~~GLLtD  110 (142)
T PF13022_consen   92 -QPSVKAIELFLKRHGLLTD  110 (142)
T ss_dssp             -S--HHHHHHHHHHTT--EE
T ss_pred             -CccHHHHHHHHHHcCcccc
Confidence             2688899999999998755

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=94.04  E-value=0.082  Score=43.42  Aligned_cols=41  Identities=22%  Similarity=0.257  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|++..+||+.+|+|.+||..++.|-+
T Consensus       129 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar  169 (186)
T PRK05602        129 LPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGR  169 (186)
T ss_pred             CCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            56676766666678999999999999999999999988755

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

Probab=94.03  E-value=0.51  Score=36.86  Aligned_cols=68  Identities=12%  Similarity=0.088  Sum_probs=47.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|    .+.|.+.|..+....-+..++++...+..... ..-.+++.||++.+..
T Consensus         1 m~IgevA~~~gvs~~tLRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYY----EKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL   69 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            46889999999999997655    45788765444223467778887765543322 3446889999988754

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.

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=94.02  E-value=0.089  Score=43.50  Aligned_cols=42  Identities=19%  Similarity=0.237  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+.+|+|..+||+.||+|.+||...+.|.++
T Consensus       112 Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~  153 (182)
T PRK12540        112 LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS  153 (182)
T ss_pred             CCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            466777777777789999999999999999999999887553

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=94.01  E-value=0.09  Score=43.19  Aligned_cols=41  Identities=17%  Similarity=0.077  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus       123 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  163 (185)
T PRK12542        123 LNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR  163 (185)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666666666678999999999999999999999988754

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

Probab=93.99  E-value=0.27  Score=37.75  Aligned_cols=67  Identities=18%  Similarity=0.152  Sum_probs=47.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|... .+.-+..++++...|..... ..-..+..+|++.+..
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~-~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~   68 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERS-ANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC   68 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4688999999999999987755    588876432 23457778877666654332 3457889999987764

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.

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

Probab=93.99  E-value=0.57  Score=36.65  Aligned_cols=68  Identities=15%  Similarity=0.088  Sum_probs=47.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+..+.-+..++++...+..... ..-.+++.+|++.+..
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAL   69 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence            468899999999999987554    4687765433223456778877666654332 3446889999888754

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.

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=93.99  E-value=0.094  Score=42.99  Aligned_cols=41  Identities=24%  Similarity=0.304  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+
T Consensus       130 L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar  170 (181)
T PRK12536        130 LPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGL  170 (181)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45566665556668999999999999999999999988754

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=93.98  E-value=0.078  Score=45.36  Aligned_cols=41  Identities=24%  Similarity=0.169  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.||||.+||..++.|-+
T Consensus       135 Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr  175 (216)
T PRK12533        135 LPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARAR  175 (216)
T ss_pred             CCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55566666666677999999999999999999999998754

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=93.98  E-value=0.097  Score=42.85  Aligned_cols=42  Identities=24%  Similarity=0.277  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus       131 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~  172 (184)
T PRK12512        131 TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGL  172 (184)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            356666666666667899999999999999999999988754

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=93.96  E-value=0.24  Score=39.65  Aligned_cols=68  Identities=19%  Similarity=0.159  Sum_probs=48.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+....-+..++++...|..... ..-..++.+|++.+..
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   70 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI   70 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4788999999999999988754    587776444233457778877666643322 3457889998887753

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=93.94  E-value=0.1  Score=43.32  Aligned_cols=41  Identities=17%  Similarity=0.154  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|++..+||+.+|+|.+||..++.|-+
T Consensus       143 L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~  183 (194)
T PRK09646        143 LTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGL  183 (194)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHH
Confidence            56666665555578999999999999999999999998754

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=93.92  E-value=0.098  Score=44.02  Aligned_cols=42  Identities=19%  Similarity=0.170  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+-+|+|..+||..+|||.+||..++.|-+
T Consensus       153 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  194 (206)
T PRK12526        153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLAL  194 (206)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            356666666666678999999999999999999999987754

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

Probab=93.92  E-value=0.2  Score=40.04  Aligned_cols=66  Identities=20%  Similarity=0.136  Sum_probs=47.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|.... +.-+..++++.+.|..... .+-..+..+|++.|.
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~----~GLl~p~r~~-~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQ----KGLIASWRNA-GNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA   68 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCC-CCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5789999999999999887765    4877664332 3456778877666654332 345688888888775

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.

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=93.89  E-value=0.27  Score=38.53  Aligned_cols=69  Identities=16%  Similarity=0.035  Sum_probs=50.8

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      .++..++|+.+|||..||.-|.+    .|.+.|..+..+.-+..++++.+.|..... ..-..+..+|++.+..
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~   72 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRA   72 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            36899999999999999876644    588877655334567778887777765544 4457889999887754

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.

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=93.88  E-value=0.098  Score=43.15  Aligned_cols=42  Identities=17%  Similarity=0.173  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||..+|+|.+||.+.+.|-+
T Consensus       106 ~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar  147 (181)
T PRK09637        106 ALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGR  147 (181)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            356677766666678999999999999999999999988754

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=93.88  E-value=0.094  Score=45.68  Aligned_cols=41  Identities=15%  Similarity=0.080  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+-.|+|..+||+.||||.+||++|+.+..
T Consensus       206 L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~  246 (257)
T PRK08583        206 LSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAI  246 (257)
T ss_pred             CCHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56677766666678999999999999999999999988754

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=93.87  E-value=0.097  Score=44.57  Aligned_cols=42  Identities=24%  Similarity=0.246  Sum_probs=35.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+.+|+|.++||+.+|+|.+||++++++-.
T Consensus       178 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ra~  219 (227)
T TIGR02980       178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRAL  219 (227)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366677776666677899999999999999999999998754

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=93.84  E-value=0.11  Score=42.62  Aligned_cols=41  Identities=20%  Similarity=0.212  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|||.+||...+.|-+
T Consensus       118 Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~  158 (179)
T PRK12543        118 LPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL  158 (179)
T ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56666766666677999999999999999999999988754

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=93.83  E-value=0.1  Score=42.96  Aligned_cols=42  Identities=21%  Similarity=0.289  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||+.+|||.+||..++.|-+
T Consensus       131 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~  172 (184)
T PRK12539        131 RLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGL  172 (184)
T ss_pred             hCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356666666666677899999999999999999999998754

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=93.83  E-value=0.091  Score=42.84  Aligned_cols=42  Identities=29%  Similarity=0.296  Sum_probs=33.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-+...+-+|+|..+||+.+|+|.+||+.++.|-+.
T Consensus       137 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~  178 (187)
T TIGR02948       137 LPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             CCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            455555555555778999999999999999999999988653

This sigma factor is restricted to certain lineages of the order Bacillales.

>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=93.81  E-value=0.057  Score=37.45  Aligned_cols=37  Identities=19%  Similarity=0.282  Sum_probs=32.5

Q ss_pred             HHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         111 MAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       111 l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++.. +.+..+||+.++++++||++.+++..+.|-+..
T Consensus        17 Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~   54 (68)
T PF01978_consen   17 LLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVER   54 (68)
T ss_dssp             HHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4444 499999999999999999999999999998754

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.80  E-value=0.34  Score=34.95  Aligned_cols=67  Identities=19%  Similarity=0.245  Sum_probs=45.3

Q ss_pred             HHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898         105 RLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN  173 (230)
Q Consensus       105 R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~  173 (230)
                      -..|++++..   +.+..+||+.++++++||++.++...+.|-+...+.+  ....+.+...+.-..+....
T Consensus         7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~--~~y~l~~~~~~~~~~~~~~~   76 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQN--GRYRLGPKVLELGQSYLSSL   76 (91)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCC--CceeecHHHHHHHHHHHhcC
Confidence            3456665542   4999999999999999999999999999987543221  22344555444444444333

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

Probab=93.80  E-value=0.21  Score=36.83  Aligned_cols=66  Identities=12%  Similarity=0.095  Sum_probs=46.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~  186 (230)
                      .+..++|+.+|||+.|+..|.+    .|.+.|....+ ..+..++.+...+.....  ++-.++..+++..+.
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~   69 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE   69 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4688999999999999999964    58887643322 456778887766654442  335677777765553

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.

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=93.72  E-value=0.11  Score=43.54  Aligned_cols=41  Identities=20%  Similarity=0.173  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|.++||..+|+|.+||...+.|-+
T Consensus       140 Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr  180 (201)
T PRK12545        140 LPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRAR  180 (201)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56677777777778999999999999999999998887643

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

Probab=93.70  E-value=0.5  Score=37.46  Aligned_cols=68  Identities=13%  Similarity=0.069  Sum_probs=46.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+....-+..++.+...+..... ..-..++.+|++.|..
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~   69 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA   69 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            468899999999999986664    4687766433233456777776655543322 3346889999988864

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

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=93.69  E-value=0.11  Score=36.23  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=33.0

Q ss_pred             HHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         107 KIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       107 rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +|+.+..++ .+..++|+.|+||++||++-+++.++.|-.
T Consensus         4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~   43 (69)
T TIGR00122         4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGVD   43 (69)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence            456656555 789999999999999999999999988863

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.68  E-value=0.19  Score=33.85  Aligned_cols=38  Identities=21%  Similarity=0.227  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHcC-------CCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAAAG-------VRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~~G-------~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+.-+..+++.|       .+..++|+.||||++|++.-+++-.
T Consensus         4 ~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae   48 (53)
T PF04967_consen    4 RQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE   48 (53)
T ss_pred             HHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3444444455555       7889999999999999999888754

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=93.67  E-value=0.097  Score=44.98  Aligned_cols=41  Identities=24%  Similarity=0.180  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|+|..+||+.+|||.+||.+++.+-.
T Consensus       185 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  225 (236)
T PRK06986        185 LPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAI  225 (236)
T ss_pred             CCHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56677766667778999999999999999999999988754

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=93.65  E-value=0.34  Score=43.03  Aligned_cols=43  Identities=19%  Similarity=0.119  Sum_probs=37.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      +|...|.-++..+..|+|..+||+.+|+|.+||.+.+.|-+..
T Consensus       116 L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~  158 (293)
T PRK09636        116 LSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH  158 (293)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            6777777777777899999999999999999999999987654

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=93.64  E-value=0.11  Score=41.58  Aligned_cols=43  Identities=21%  Similarity=0.083  Sum_probs=35.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+-+|++..+||..+|+|.+||..++.|-+.
T Consensus       112 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~  154 (161)
T PRK12541        112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK  154 (161)
T ss_pred             HCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3566667666666779999999999999999999999988653

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

Probab=93.64  E-value=0.056  Score=34.68  Aligned_cols=41  Identities=37%  Similarity=0.500  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         156 RVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       156 r~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      +.++++++..|..+..+  ..+..+|++.|    |       +|.+||+|.|++
T Consensus         3 ~~Lt~~eR~~I~~l~~~--G~s~~~IA~~l----g-------~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALLEQ--GMSIREIAKRL----G-------RSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHHCS-----HHHHHHHT----T---------HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHHc--CCCHHHHHHHH----C-------cCcHHHHHHHhc
Confidence            35688888888888644  48888888765    4       399999999986

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=93.62  E-value=0.054  Score=43.92  Aligned_cols=42  Identities=17%  Similarity=0.176  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-.|+|..+||+.||+|.+||..++.|.++
T Consensus       127 L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~  168 (176)
T PRK09638        127 LDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK  168 (176)
T ss_pred             CCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            566666666666778999999999999999999999987654

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=93.61  E-value=0.12  Score=32.99  Aligned_cols=34  Identities=24%  Similarity=0.270  Sum_probs=30.6

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+.+..+||+.|+++++||++.++.+.+.|.+..
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~   46 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR   46 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3599999999999999999999999999987753

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=93.59  E-value=0.12  Score=43.69  Aligned_cols=42  Identities=14%  Similarity=0.127  Sum_probs=36.1

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||+.+|+|.+||...+.|-+
T Consensus       148 ~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr  189 (206)
T PRK12544        148 GLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRAR  189 (206)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            466777877777788999999999999999999999988754

>PRK00441 argR arginine repressor; Provisional

Probab=93.58  E-value=0.23  Score=40.42  Aligned_cols=46  Identities=17%  Similarity=0.085  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         162 VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       162 ~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      -.+.|.+++.++...+..|+.+.|++ .|+.     ||.+||+|-|+..++.
T Consensus         5 R~~~I~~ll~~~~~~~q~eL~~~L~~-~G~~-----vSqaTisRDl~~L~lv   50 (149)
T PRK00441          5 RHAKILEIINSKEIETQEELAEELKK-MGFD-----VTQATVSRDIKELKLI   50 (149)
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHh-cCCC-----cCHHHHHHHHHHcCcE
Confidence            35678889999999999999999988 7995     8999999999999976

>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]

Probab=93.55  E-value=0.26  Score=46.81  Aligned_cols=94  Identities=11%  Similarity=0.144  Sum_probs=68.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----Cc---CCCCCCCCCCCCHHHHHHHHHHHHh-CC--CCCHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RP---GVIGGSKPRVATPDVEKRIEEYKKT-NP--GIFSWEI  181 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p---~~~gg~rpr~lt~~~~~~I~~l~~~-~P--~~t~~eI  181 (230)
                      ++.++||..+|++.|||+|.+.. |..+.  .+     ..   ...+|+. ..-+..++..|.+++.. +|  ..+=.+|
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~-~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kI  409 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGE-ASSTEAIKALIKKLIEAEDKKKPLSDSKI  409 (444)
T ss_pred             ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCc-cccHHHHHHHHHHHHhhccCCCCCCHHHH
Confidence            77899999999999999998764 66554  21     00   1111111 22245788999999864 55  4567789


Q ss_pred             HHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         182 RDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      .+.|++ .||.     |++.||-.+=...++.++.
T Consensus       410 a~lLke-kGi~-----iARRTVAKYRe~L~I~sS~  438 (444)
T COG1508         410 AELLKE-KGID-----VARRTVAKYREELNIPSSS  438 (444)
T ss_pred             HHHHHH-cCCc-----hhHHhHHHHHHHcCCCchh
Confidence            999987 8885     9999999999999988775

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=93.51  E-value=0.1  Score=42.54  Aligned_cols=41  Identities=22%  Similarity=0.225  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|.+.|.-++..+-+|+|..+||+.+|+|.+||..++.|-.
T Consensus       120 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  160 (172)
T PRK09651        120 LNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT  160 (172)
T ss_pred             CCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            45566655555567899999999999999999999998754

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=93.50  E-value=0.12  Score=42.70  Aligned_cols=41  Identities=20%  Similarity=0.249  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+-+|++..+||+.||+|..||+..+.|-+
T Consensus       139 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar  179 (193)
T PRK11923        139 LPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR  179 (193)
T ss_pred             CCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55566666666688999999999999999999999987754

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=93.50  E-value=0.32  Score=43.51  Aligned_cols=107  Identities=10%  Similarity=0.002  Sum_probs=66.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS  178 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~  178 (230)
                      .+|...|.-++...-.|+|..+||+.+|+|.+||...+.|-+..  +.....   +....+.+..+.+..++..--.-..
T Consensus       118 ~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~--Lr~~~~---~~~~~~~~~~~~~~~f~~a~~~gd~  192 (290)
T PRK09635        118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK--INESRI---AASVEPAQHRVVTRAFIEACSNGDL  192 (290)
T ss_pred             hCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHH--HHhhCC---CCCCChHHHHHHHHHHHHHHHhCCH
Confidence            36677787777777889999999999999999999999987753  211100   1122233445555555554334456


Q ss_pred             HHHHHHHHHhhC--CC--CCCCCCCHhHHHHHHHcC
Q psy1898         179 WEIRDRLVKQDG--IC--DKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       179 ~eI~~~L~~~~G--i~--~~~~~vS~sTV~R~Lr~~  210 (230)
                      ..+.+.|....+  ..  ..........|.+++...
T Consensus       193 ~~l~~ll~~d~~~~~~~~~~~~~~G~~~v~~~~~~~  228 (290)
T PRK09635        193 DTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRH  228 (290)
T ss_pred             HHHHHHhhhhhcCCCcCCCCccccCHHHHHHHHHHh
Confidence            667777754322  11  011224667788887654

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

Probab=93.50  E-value=0.062  Score=37.34  Aligned_cols=43  Identities=19%  Similarity=0.219  Sum_probs=33.8

Q ss_pred             HHHHHHHH---cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         106 LKIVEMAA---AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       106 ~rIV~l~~---~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      .+|++.++   .+.+.++||..+++|+.+|.+|+..-...|.+...
T Consensus         3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~   48 (62)
T PF04703_consen    3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS   48 (62)
T ss_dssp             HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34555443   45999999999999999999999999999988643

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=93.47  E-value=0.14  Score=40.85  Aligned_cols=41  Identities=22%  Similarity=0.216  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|.+.|.-++..+-+|+|..+||..+|+|.+||...+.|-.
T Consensus       106 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~  146 (159)
T PRK12527        106 LPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM  146 (159)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            56666665555667999999999999999999999988754

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=93.47  E-value=0.12  Score=43.34  Aligned_cols=42  Identities=17%  Similarity=0.174  Sum_probs=35.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+-+|++..+||..+|+|.+||..++.|.+.
T Consensus       134 Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~  175 (196)
T PRK12535        134 LPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA  175 (196)
T ss_pred             CCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            566777777777789999999999999999999999887553

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=93.46  E-value=0.12  Score=43.93  Aligned_cols=41  Identities=17%  Similarity=0.097  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+.+|+|.++||..+|+|.+||.+++.+-.
T Consensus       176 L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~  216 (224)
T TIGR02479       176 LSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQAL  216 (224)
T ss_pred             CCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            56677777777788999999999999999999999988754

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.

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=93.45  E-value=0.043  Score=43.37  Aligned_cols=41  Identities=22%  Similarity=0.152  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|++..+||+.||+|.+||..++.|.+
T Consensus       106 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~  146 (154)
T TIGR02950       106 LPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRAR  146 (154)
T ss_pred             CCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555655555667899999999999999999999998865

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.

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=93.45  E-value=0.28  Score=38.31  Aligned_cols=67  Identities=15%  Similarity=0.037  Sum_probs=45.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      +..++|+.+|||..|+.-|    .+.|.+.|..+..+.-+..++++.+.|..... ..-..+..+|++.+..
T Consensus         1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~   68 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL   68 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhc
Confidence            4679999999999999555    55687764333223456667777666653332 3456889998887754

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.

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=93.40  E-value=0.13  Score=40.79  Aligned_cols=45  Identities=22%  Similarity=0.231  Sum_probs=40.5

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         101 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       101 s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ..+.+..++.++..|.+..++|+.++|+.+||.+|.+++.+....
T Consensus        75 ~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~  119 (129)
T COG3677          75 LYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG  119 (129)
T ss_pred             chHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence            368899999999999999999999999999999999998876543

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=93.38  E-value=0.39  Score=38.26  Aligned_cols=68  Identities=10%  Similarity=0.084  Sum_probs=48.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|    .+.|.+.|..+....-+..++++...|..... ..-..++.+|++.+..
T Consensus         1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~   69 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL   69 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            46889999999999998655    45787766444223467778887777654443 3457888998887753

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=93.36  E-value=0.12  Score=42.97  Aligned_cols=42  Identities=24%  Similarity=0.275  Sum_probs=36.0

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+.+|+|..+||..||||.+||..++.|-+
T Consensus       113 ~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar  154 (188)
T PRK12546        113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRAR  154 (188)
T ss_pred             hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            356677777777778999999999999999999999998855

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=93.34  E-value=0.11  Score=42.59  Aligned_cols=42  Identities=26%  Similarity=0.313  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++...|.-+...+-+|.+..+||..+|+|.+||..++.|-++
T Consensus       139 L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       139 LPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             CCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            445556555555678999999999999999999999987553

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.

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=93.33  E-value=0.15  Score=42.35  Aligned_cols=42  Identities=14%  Similarity=0.121  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||..+|||.+||..-+.|.+
T Consensus       141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~  182 (194)
T PRK12531        141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV  182 (194)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            356667766666678999999999999999999988877654

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=93.31  E-value=0.15  Score=42.02  Aligned_cols=42  Identities=10%  Similarity=-0.077  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-+|++..+||+.||+|.+||.+.+.|-+
T Consensus       131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar  172 (189)
T PRK12515        131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR  172 (189)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356676666666678999999999999999999998887744

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=93.24  E-value=0.15  Score=42.26  Aligned_cols=41  Identities=20%  Similarity=0.259  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-++..+-+|++..+||..+|+|.+||...+.|-+
T Consensus       132 L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar  172 (188)
T TIGR02943       132 LPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRAR  172 (188)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            55667776666678999999999999999999999887644

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=93.18  E-value=0.21  Score=39.60  Aligned_cols=74  Identities=12%  Similarity=0.078  Sum_probs=46.0

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGSKPRVAT-PDVEKRIEEYKKTNPGIFSWEIRDRLVK  187 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~rpr~lt-~~~~~~I~~l~~~~P~~t~~eI~~~L~~  187 (230)
                      ...+.-+||..++++++||+|-+++-.+.|.+...  +..+++|.-+= +...+.+...+..+-+--+..+.+++.+
T Consensus        41 ~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~~~~i~~  117 (126)
T COG3355          41 GPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKMKQLIEE  117 (126)
T ss_pred             CCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35999999999999999999999999999977321  11233443222 3333333333333322245556666655

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=93.16  E-value=0.051  Score=44.85  Aligned_cols=41  Identities=12%  Similarity=-0.044  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|+|..+||..+|||.+||..++.|-+
T Consensus       135 L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  175 (188)
T PRK09640        135 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRAL  175 (188)
T ss_pred             cChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44455554445567899999999999999999999998754

>PHA01976 helix-turn-helix protein

Probab=93.15  E-value=0.083  Score=36.24  Aligned_cols=31  Identities=16%  Similarity=0.204  Sum_probs=25.1

Q ss_pred             HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus         6 rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~   37 (67)
T PHA01976          6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEA   37 (67)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            333433 4589999999999999999999964

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=93.13  E-value=0.074  Score=40.69  Aligned_cols=50  Identities=14%  Similarity=0.197  Sum_probs=32.1

Q ss_pred             cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      |++.+..+....|.+-|..-.+|.+..++|+.||+|..+|++++++.+..
T Consensus        50 yiP~~~~~~~~~R~~~I~~~f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~   99 (108)
T PF08765_consen   50 YIPKCDRLLRALRNREIRREFNGMNVRELARKYGLSERQIYRIIKRVRRR   99 (108)
T ss_dssp             ----SHHHHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred             EeeCccHHHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            44455555567776555544459999999999999999999999998753

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.

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

Probab=93.12  E-value=0.48  Score=35.85  Aligned_cols=66  Identities=15%  Similarity=0.204  Sum_probs=45.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.    -|.+.|.+.|...+|.  +..++++.+.+..... .+-+.++.||++.+..
T Consensus         1 m~Ige~a~~~gvs~~tlR----yYe~~GLl~p~~~~g~--r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~   67 (107)
T cd04777           1 MKIGKFAKKNNITIDTVR----HYIDLGLLIPEKKGGQ--YFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY   67 (107)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHCCCcCCccCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            467899999999999874    4566898877543332  3456666555543332 3447999999998854

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.

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=93.11  E-value=0.067  Score=44.27  Aligned_cols=41  Identities=17%  Similarity=0.084  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||..++.|.+
T Consensus       140 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  180 (194)
T PRK12513        140 LPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYAL  180 (194)
T ss_pred             CCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555655555567899999999999999999998887654

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=93.08  E-value=0.1  Score=44.22  Aligned_cols=40  Identities=23%  Similarity=0.216  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|..++ +|+.++.+|+|.++||++++||..||..-+++-.
T Consensus       138 LT~RE~-eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~  177 (207)
T PRK15411        138 LSRTES-SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK  177 (207)
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence            665544 7899999999999999999999999999887743

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=93.05  E-value=0.13  Score=44.46  Aligned_cols=41  Identities=17%  Similarity=0.289  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+
T Consensus       172 Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr  212 (233)
T PRK12538        172 LPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGR  212 (233)
T ss_pred             CCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666766666678999999999999999999999988744

>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=93.02  E-value=0.13  Score=34.78  Aligned_cols=41  Identities=24%  Similarity=0.401  Sum_probs=34.8

Q ss_pred             HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|++++.+ | .+..++|..|+||..||.+=++...+.|.+.
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~   45 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK   45 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            567776654 4 9999999999999999999999998888763

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

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=92.98  E-value=0.15  Score=43.90  Aligned_cols=41  Identities=12%  Similarity=0.104  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.    +|+|..+||+.+|||.+||.+++.|-.
T Consensus       179 Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~  223 (234)
T TIGR02835       179 LNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRIL  223 (234)
T ss_pred             CCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55566665555442    789999999999999999999987643

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.

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=92.95  E-value=0.18  Score=41.11  Aligned_cols=42  Identities=24%  Similarity=0.268  Sum_probs=35.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+-.|++..+||..+|||.+||++-+.|.+
T Consensus       140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~  181 (189)
T TIGR02984       140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGL  181 (189)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            367777777766678999999999999999999999887754

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).

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=92.93  E-value=0.41  Score=40.74  Aligned_cols=86  Identities=17%  Similarity=0.178  Sum_probs=53.3

Q ss_pred             ccCCCCCChhHHHHHHHHHhcCCC--hhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898          50 FINGRPLPNHIRLKIVEMAAAGVR--PCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV  127 (230)
Q Consensus        50 ~~~g~plp~~~r~~I~e~~~~g~~--~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV  127 (230)
                      |+.+. .+.+.-.+.++.+..|.+  +.++.+.+.-...-.. .... ....+| +....|+.++..|+|.++||.+|++
T Consensus       100 yl~K~-~~~~~l~~ai~~v~~G~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~LT-~RE~eVL~lla~G~snkeIA~~L~i  175 (211)
T COG2197         100 YLLKD-ASPEELVEAIRAVAAGGTYLPPDIARKLAGLLPSSS-AEAP-LAELLT-PRELEVLRLLAEGLSNKEIAEELNL  175 (211)
T ss_pred             EEeCC-CCHHHHHHHHHHHHCCCeEeCHHHHHHHHhhccccc-cccc-ccCCCC-HHHHHHHHHHHCCCCHHHHHHHHCC
Confidence            44444 456667788888888863  4445554432111100 0000 001233 3344666899999999999999999


Q ss_pred             ccchhhhHHHHH
Q psy1898         128 SHGCVSKILNRY  139 (230)
Q Consensus       128 S~sTV~kwikRy  139 (230)
                      |..||..-+.+-
T Consensus       176 S~~TVk~h~~~i  187 (211)
T COG2197         176 SEKTVKTHVSNI  187 (211)
T ss_pred             CHhHHHHHHHHH
Confidence            999998887763

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

Probab=92.92  E-value=0.45  Score=35.28  Aligned_cols=67  Identities=18%  Similarity=0.154  Sum_probs=45.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+||+++||..|.+    .|.+.|...++ .-+..+.++...+..... .....+..++...+..
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~   68 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSEN-GYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDA   68 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            4688999999999999999965    47665433222 445677776665544332 2267888888877754

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.

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=92.90  E-value=0.5  Score=36.24  Aligned_cols=68  Identities=18%  Similarity=0.085  Sum_probs=47.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+..+.-+..++++.+.+..... .+-..+..+|++.|..
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE----~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~   69 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYE----RKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDL   69 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHH----HcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            468899999999999986664    5687876655423466778877655543332 2457889999988865

>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=92.90  E-value=0.075  Score=34.90  Aligned_cols=25  Identities=24%  Similarity=0.408  Sum_probs=21.4

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++||++|.+
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~~   31 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIEN   31 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHhc
Confidence            5699999999999999999999975

; 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 ....

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=92.89  E-value=0.14  Score=42.24  Aligned_cols=38  Identities=16%  Similarity=0.188  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +.+..++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus       153 ~~~~~i~~~~~~~~s~~eIA~~l~~s~~tV~~~l~r~r  190 (198)
T TIGR02859       153 DLEWKVLQSYLDGKSYQEIACDLNRHVKSIDNALQRVK  190 (198)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55666777788999999999999999999998887755

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.

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=92.85  E-value=0.15  Score=44.27  Aligned_cols=75  Identities=17%  Similarity=0.121  Sum_probs=48.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC-CCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI  176 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~-v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~  176 (230)
                      .+|...|.-++..+.+|+|.++||+.+|+|.+||..++.|-++.=. ...  .++ .+.-.+......+..+..++|..
T Consensus       116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~--~~~-~~~~~~~~~~~~~~~~~~~~~~~  191 (228)
T PRK06704        116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE--EGI-EIVEFTDDMEVVVTSIREERPEL  191 (228)
T ss_pred             hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH--hcC-CCCCccccHHHHHHHHHhcCHHH
Confidence            3566667666666778999999999999999999999888654211 111  111 12222334555566666677654

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=92.79  E-value=0.17  Score=42.26  Aligned_cols=41  Identities=17%  Similarity=0.185  Sum_probs=35.2

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ..+|..++ +|+.++.+|.|.++||+.++||..||..-+++-
T Consensus       149 ~~Lt~rE~-evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i  189 (216)
T PRK10840        149 KRLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSA  189 (216)
T ss_pred             ccCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34776664 888899999999999999999999999888763

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=92.78  E-value=0.43  Score=38.42  Aligned_cols=47  Identities=19%  Similarity=0.127  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         157 VATPDVEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       157 ~lt~~~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++|+.-. .|.+++.+. ...++.+|.++|.+ .+..     +|.+||||.|+.+
T Consensus        18 r~T~qR~-~vl~~L~~~~~~~sAeei~~~l~~-~~p~-----islaTVYr~L~~l   65 (145)
T COG0735          18 RLTPQRL-AVLELLLEADGHLSAEELYEELRE-EGPG-----ISLATVYRTLKLL   65 (145)
T ss_pred             CcCHHHH-HHHHHHHhcCCCCCHHHHHHHHHH-hCCC-----CCHhHHHHHHHHH
Confidence            3455434 455555543 34999999999987 5553     7999999998764

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=92.76  E-value=0.18  Score=41.13  Aligned_cols=41  Identities=27%  Similarity=0.254  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-.|.+..+||..||||.+||...+.|-+
T Consensus       137 L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar  177 (187)
T PRK09641        137 LPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGR  177 (187)
T ss_pred             CCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555655555567899999999999999999999988755

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=92.69  E-value=0.27  Score=38.89  Aligned_cols=51  Identities=18%  Similarity=0.307  Sum_probs=42.4

Q ss_pred             CCcCCHH----HHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898          97 GRPLPNH----IRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus        97 g~~~s~~----~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +++++.+    +..+||+++.+ | ++..+++..+|+|+.||.+..+...++|.+-.
T Consensus         2 a~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~   58 (127)
T PF06163_consen    2 ARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR   58 (127)
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence            4566654    45678887764 6 99999999999999999999999999998854

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

Probab=92.62  E-value=0.22  Score=38.35  Aligned_cols=42  Identities=17%  Similarity=0.105  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++.|+-.-|-+...+|++..+.|++.|||++|+++++...+
T Consensus        41 ~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~AR   82 (106)
T PF02001_consen   41 VLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESAR   82 (106)
T ss_pred             EeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHH
Confidence            356676666666667899999999999999999999998654

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=92.61  E-value=0.24  Score=41.81  Aligned_cols=41  Identities=10%  Similarity=0.071  Sum_probs=36.2

Q ss_pred             HHHHHHHHcC---CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAAG---VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~G---~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|+.++.+|   .+.++||+.++||+.||.+.+..-.+.|.+.
T Consensus       165 r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~  208 (225)
T PRK10046        165 NAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLII  208 (225)
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEE
Confidence            3788888885   8999999999999999999999888888663

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=92.50  E-value=0.38  Score=40.18  Aligned_cols=63  Identities=13%  Similarity=0.109  Sum_probs=43.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRD  183 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~  183 (230)
                      ++..++|+.+|||..||.+|.+++    .+.+ .+..+..+..++++.+.|..... .+-+++..+|+.
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 MKTPFVAKKLGVSPKTVQRWVKQL----NLPC-EKNEYGHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK   64 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC----CCCC-CcCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            468899999999999999998854    3322 22222356777877766655543 344678888865

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=92.48  E-value=0.17  Score=43.49  Aligned_cols=42  Identities=21%  Similarity=0.118  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+    .+|.|.++||..+|||.+||++++.|..
T Consensus       175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~  220 (233)
T PRK05803        175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRAL  220 (233)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35556665555545    4889999999999999999999977643

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=92.43  E-value=0.36  Score=38.45  Aligned_cols=105  Identities=17%  Similarity=0.191  Sum_probs=64.4

Q ss_pred             CChhHHHHHHHHHhcCCCCCCCCCccccCccccCCCCCChhHHHHH--HHHHhcCCChhhhhhhhcccccccccCCcccC
Q psy1898          19 LPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKI--VEMAAAGVRPCVISRQLRVSHGVNQLGGVFIN   96 (230)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~plp~~~r~~I--~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~   96 (230)
                      |-..+++..-|+-.+  .    ...|+=||.=-|+..-|.+.-+.+  +|+-      ..|.+..+.-+-..   ..   
T Consensus        17 l~~~I~~R~~el~~~--~----~~DNiGGgra~n~~s~p~e~~li~e~~e~D------~~L~~L~~~k~~id---~~---   78 (130)
T PF05263_consen   17 LDAKIKLRKLELQYR--E----NDDNIGGGRAQNKSSRPEENVLIKERLESD------EELQSLKRQKEAID---RW---   78 (130)
T ss_pred             HHHHHHHHHHHhhcC--C----CCCCcccccccCCCCcHHHHHHHHHHHHhh------HHHHHHHHHHHHHH---HH---
Confidence            344555555566653  2    223887887668888666665554  3444      44444333222121   11   


Q ss_pred             CCcCCHHHHHHHHHHH-Hc--CCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          97 GRPLPNHIRLKIVEMA-AA--GVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      -.++..+ ..+||.+. ..  +.|.-+||..++|+.+|+++|...|+++
T Consensus        79 ~~~l~de-~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~  126 (130)
T PF05263_consen   79 LETLIDE-EKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKND  126 (130)
T ss_pred             HHhhCHH-HHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence            1234444 45555544 33  4999999999999999999999999864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=92.43  E-value=0.57  Score=36.07  Aligned_cols=67  Identities=15%  Similarity=0.094  Sum_probs=47.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+.+ .-+..++.+...|..... .+-..+..+|++.+..
T Consensus         1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~   68 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG   68 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            478899999999999987664    468887755543 456677777666543322 3346889999988765

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.

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

Probab=92.37  E-value=0.12  Score=34.76  Aligned_cols=31  Identities=23%  Similarity=0.483  Sum_probs=28.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||+.++++++||++.+++..+.|-+.
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~   52 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVE   52 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            7999999999999999999999999999773

...

>PRK05572 sporulation sigma factor SigF; Validated

Probab=92.26  E-value=0.19  Score=43.67  Aligned_cols=41  Identities=17%  Similarity=0.158  Sum_probs=33.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+.+|+|..+||+.+|||.+||+++.++-.
T Consensus       203 L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral  243 (252)
T PRK05572        203 LDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKIL  243 (252)
T ss_pred             CCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56566655555666899999999999999999999988743

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=92.22  E-value=0.18  Score=32.92  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|++..++|+.+|||++||++|.+
T Consensus        13 ~~gltq~~lA~~~gvs~~~vs~~e~   37 (58)
T TIGR03070        13 ALGLTQADLADLAGVGLRFIRDVEN   37 (58)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4589999999999999999999973

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=92.20  E-value=0.21  Score=43.38  Aligned_cols=42  Identities=14%  Similarity=0.049  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+.+|+|..+||..+|||.+||.+++.+..
T Consensus       205 ~L~~~~r~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~  246 (255)
T TIGR02941       205 ILSEREKSIIHCTFEENLSQKETGERLGISQMHVSRLQRQAI  246 (255)
T ss_pred             cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356677766666667899999999999999999999987644

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

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

Probab=92.20  E-value=0.13  Score=46.97  Aligned_cols=35  Identities=26%  Similarity=0.458  Sum_probs=32.7

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .|.+|++..+||++||||+.||++.+++.++.|.+
T Consensus        22 YY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV   56 (321)
T COG2390          22 YYVEGLTQSEIAERLGISRATVSRLLAKAREEGIV   56 (321)
T ss_pred             HHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeE
Confidence            45689999999999999999999999999999976

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=92.19  E-value=0.24  Score=42.28  Aligned_cols=42  Identities=17%  Similarity=0.087  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++...+.-+...+.+|++..+||+.||||+.+|+++.++..
T Consensus       183 ~L~~~e~~i~~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al  224 (231)
T TIGR02885       183 KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVL  224 (231)
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            355556555555566899999999999999999999988754

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.

>COG1710 Uncharacterized protein conserved in archaea [Function unknown]

Probab=92.13  E-value=0.3  Score=38.29  Aligned_cols=44  Identities=27%  Similarity=0.357  Sum_probs=39.0

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+.|+...+..|-+|+..|+++++||+.+||.-.|||=.++..+
T Consensus        91 prkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k  134 (139)
T COG1710          91 PRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLK  134 (139)
T ss_pred             CcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHHHHHHh
Confidence            56688888999999999999999999999999999998877544

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=92.12  E-value=0.27  Score=34.42  Aligned_cols=41  Identities=20%  Similarity=0.235  Sum_probs=30.8

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN  173 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~  173 (230)
                      +..+||+..|||.+||+++++              + ++ .++++..+.|.+..++-
T Consensus         2 t~~~iA~~~gvS~~TVSr~ln--------------~-~~-~v~~~t~~~i~~~~~~~   42 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLN--------------G-NG-RVSEETREKVLAAMEEL   42 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHC--------------C-CC-CCCHHHHHHHHHHHHHh
Confidence            578999999999999999873              1 12 23777787777777653

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.07  E-value=0.14  Score=33.75  Aligned_cols=28  Identities=21%  Similarity=0.373  Sum_probs=25.9

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      |...||+.+|+|++||.++++.-.+.|-
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            8899999999999999999999888774

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=92.06  E-value=0.25  Score=32.38  Aligned_cols=34  Identities=24%  Similarity=0.421  Sum_probs=30.6

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+..+|++.+++|++||++.+++..+.|-+.
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~   41 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE   41 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence            3458999999999999999999999999999775

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=92.06  E-value=0.25  Score=43.28  Aligned_cols=41  Identities=15%  Similarity=0.058  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+.+|+|..+||..+|||.+||++++.+-.
T Consensus       204 L~~~~r~vl~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~  244 (256)
T PRK07408        204 LEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGL  244 (256)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55566666666778899999999999999999999988754

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

Probab=92.01  E-value=0.71  Score=38.24  Aligned_cols=67  Identities=19%  Similarity=0.206  Sum_probs=45.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      ++..++|+.+|||+.|+.-|.    +.|.+.|..+....-+..++++...+..... ..-..+..+|+..|.
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~   69 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYE----RIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ   69 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            478999999999999986664    4688877544223456677776555543322 334677888777664

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

>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=92.00  E-value=0.19  Score=41.45  Aligned_cols=39  Identities=26%  Similarity=0.297  Sum_probs=32.6

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHhhhhc-cccchhhhHHHHH
Q psy1898         101 PNHIRLKIVEMAAAGVRPCVISRQLR-VSHGCVSKILNRY  139 (230)
Q Consensus       101 s~~~R~rIV~l~~~G~s~~~IAr~lg-VS~sTV~kwikRy  139 (230)
                      +.+.-.++-+|+.+|+|..+||++|| ||++.|.--+.|.
T Consensus         4 tde~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl   43 (162)
T PF07750_consen    4 TDERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL   43 (162)
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence            34555566679999999999999999 9999998887775

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 [].

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

Probab=91.96  E-value=0.2  Score=35.08  Aligned_cols=36  Identities=8%  Similarity=0.233  Sum_probs=30.6

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      .+|.++-.-.|..++|+++|++..||.+|+..|++-
T Consensus         5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~w   40 (65)
T PF05344_consen    5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQW   40 (65)
T ss_pred             HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            345566667899999999999999999999999753

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=91.86  E-value=0.27  Score=40.87  Aligned_cols=40  Identities=15%  Similarity=0.088  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++. +-+|+|..+||..+|+|.+||...+.|-+
T Consensus       156 L~~~~r~vl~l-~~e~~s~~EIA~~lgis~~tV~~~l~rar  195 (208)
T PRK08295        156 LSELEKEVLEL-YLDGKSYQEIAEELNRHVKSIDNALQRVK  195 (208)
T ss_pred             CCHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45566666655 88999999999999999999998887654

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

Probab=91.81  E-value=0.8  Score=35.51  Aligned_cols=66  Identities=20%  Similarity=0.208  Sum_probs=48.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|-+    .|.+.|...+  .-+..++++.+.|..... .+-..++.+|++.+..
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~----~GLl~p~r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~   67 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYED----KGLLSPERRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL   67 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            3678999999999999876654    5888775433  467888887777653332 3457889999888864

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.

>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=91.80  E-value=0.26  Score=31.38  Aligned_cols=34  Identities=21%  Similarity=0.326  Sum_probs=25.1

Q ss_pred             HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHH
Q psy1898         106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      .+|+..+.. + .|..+||+.+|+|.+||.+=+++.
T Consensus         6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen    6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            456665543 4 999999999999999998876654

...

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=91.77  E-value=0.63  Score=38.01  Aligned_cols=67  Identities=18%  Similarity=0.128  Sum_probs=47.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK-KTNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~-~~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|....+ .-+..++.+.+.+.-.. ...-.+++.+|++.+..
T Consensus        12 ~~IgevAk~~gvs~~TlRyYE----~~GLi~~~r~~~-g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~   79 (154)
T PRK15002         12 LTPGEVAKRSGVAVSALHFYE----SKGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV   79 (154)
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            789999999999999986664    578887643333 34677777766654332 23456889999888753

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

Probab=91.75  E-value=0.079  Score=34.98  Aligned_cols=22  Identities=18%  Similarity=0.329  Sum_probs=18.5

Q ss_pred             CCHHHHhhhhccccchhhhHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++..++++.+|+|++|+++|++
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k   25 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIK   25 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHH
T ss_pred             ccHHHHHHHHCCCHHHHHHHHh
Confidence            3678999999999999999988

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.

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=91.72  E-value=0.63  Score=37.41  Aligned_cols=67  Identities=19%  Similarity=0.150  Sum_probs=46.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|....+ .-+..++++...|..... ..-..++.+|++.+..
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~----~GLl~~~r~~~-g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~   69 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV   69 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5789999999999999877654    58886633323 346777776655543322 3346889998888753

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.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=91.62  E-value=0.25  Score=43.20  Aligned_cols=43  Identities=21%  Similarity=0.350  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.+.+|++.+.+ | .+..++|+.|+||..||+|.++...+.|.+
T Consensus         5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i   49 (251)
T PRK13509          5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKL   49 (251)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            556777776654 4 999999999999999999999999988866

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=91.60  E-value=0.29  Score=42.53  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+.+|+|..+||..+|+|.+||..++.|..
T Consensus       202 L~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~  242 (251)
T PRK07670        202 LSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKAL  242 (251)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666766666778999999999999999999999987754

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

Probab=91.57  E-value=0.12  Score=34.94  Aligned_cols=27  Identities=33%  Similarity=0.517  Sum_probs=20.7

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      |.+.|++..++|+..||+++|+++|.+
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            556799999999999999999999985

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=91.56  E-value=0.28  Score=41.37  Aligned_cols=43  Identities=16%  Similarity=0.254  Sum_probs=36.9

Q ss_pred             HHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .|.+|+.++. . +.|..+||+.++|+++||++.+++..+.|.+.
T Consensus         2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~   46 (203)
T TIGR02702         2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIE   46 (203)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            4677887553 3 59999999999999999999999999999774

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=91.54  E-value=0.31  Score=42.74  Aligned_cols=41  Identities=22%  Similarity=0.098  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+.+++|..+||..||||.+||.++..+..
T Consensus       206 L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral  246 (257)
T PRK05911        206 LEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKAL  246 (257)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666665556667899999999999999999999988754

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=91.53  E-value=0.17  Score=31.89  Aligned_cols=32  Identities=25%  Similarity=0.341  Sum_probs=29.4

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..+||+.+++|++||++.++++.+.|.+.
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~   39 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS   39 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            36889999999999999999999999999874

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=91.50  E-value=0.2  Score=39.27  Aligned_cols=36  Identities=22%  Similarity=0.383  Sum_probs=30.9

Q ss_pred             HHHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         103 HIRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       103 ~~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+|..+.. |..+|+|..+||+.||+|++.|+++++-
T Consensus         9 aiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~   45 (119)
T COG2522           9 AIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG   45 (119)
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHcc
Confidence            56766664 7788999999999999999999999863

>PRK09191 two-component response regulator; Provisional

Probab=91.48  E-value=0.32  Score=41.41  Aligned_cols=44  Identities=16%  Similarity=0.079  Sum_probs=36.9

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      .+|...|.-++..+.+|+|..+||+.+|+|.+||...+.+..+.
T Consensus        88 ~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~  131 (261)
T PRK09191         88 GLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE  131 (261)
T ss_pred             hCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            36667777666677899999999999999999999999887643

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

Probab=91.42  E-value=0.79  Score=36.56  Aligned_cols=67  Identities=16%  Similarity=0.151  Sum_probs=46.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||+.|+..|.    +.|.+.|....+ .-+..+.++.+.|..... .+-..+..+|++.+..
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~-g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   68 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDS-NYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEE   68 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            367899999999999998885    468887654322 345667766555543322 3456889999988865

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.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=91.38  E-value=0.34  Score=36.30  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=34.6

Q ss_pred             HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|+.++.. + .+..+||+.+|+|++||++.+++..+.|-+.
T Consensus         6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            466665543 3 8999999999999999999999999999663

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

>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=91.36  E-value=0.75  Score=33.45  Aligned_cols=52  Identities=25%  Similarity=0.366  Sum_probs=39.9

Q ss_pred             HHHHHHHHHc-C--CCHHHHhhhhccccchhhhHHHHHhhhCCCC--cCCCCCCCCC
Q psy1898         105 RLKIVEMAAA-G--VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR  156 (230)
Q Consensus       105 R~rIV~l~~~-G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~--p~~~gg~rpr  156 (230)
                      -..+|+.+.+ |  +.-++||+.+++|..||.+-....++-|.+.  |.+.+|..|.
T Consensus        10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT   66 (78)
T PF03444_consen   10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT   66 (78)
T ss_pred             HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence            3445566643 4  8889999999999999999999999999885  5555554444

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

>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.32  E-value=0.22  Score=37.10  Aligned_cols=43  Identities=21%  Similarity=0.227  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      .|...|.+|+.|+++|.+..+|....|.|..|+++.. |--+.|
T Consensus        41 qslaqRlqVa~mL~eg~tY~~I~~eTGaStaTIsRVk-Rcl~yG   83 (100)
T COG4496          41 QSLAQRLQVAKMLKEGRTYRDIEDETGASTATISRVK-RCLNYG   83 (100)
T ss_pred             HHHHHHHHHHHHHHcCCCcchhhhccCcchhhHHHHH-HHHHcC
Confidence            4568899999999999999999999999999999984 444444

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=91.26  E-value=0.14  Score=41.37  Aligned_cols=41  Identities=20%  Similarity=0.110  Sum_probs=32.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus       121 L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar  161 (175)
T PRK12518        121 LSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR  161 (175)
T ss_pred             CCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44455544444467999999999999999999999988754

>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=91.22  E-value=0.67  Score=29.68  Aligned_cols=39  Identities=31%  Similarity=0.532  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +....|..++.++|.++..++++.+    |       +|.+||++.|++.
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~----~-------is~~tv~~~l~~L   41 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKL----G-------ISRSTVNRYLKKL   41 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHH----T-------S-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHh----C-------CCHHHHHHHHHHH
Confidence            3456778888899999999998865    4       4999999998753

...

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=91.14  E-value=0.19  Score=34.01  Aligned_cols=33  Identities=24%  Similarity=0.294  Sum_probs=30.3

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .++..+||+.+++|++||++.++++.+.|-+..
T Consensus        25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~   57 (67)
T cd00092          25 PLTRQEIADYLGLTRETVSRTLKELEEEGLISR   57 (67)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            489999999999999999999999999998753

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=91.14  E-value=0.51  Score=38.03  Aligned_cols=42  Identities=19%  Similarity=0.305  Sum_probs=35.4

Q ss_pred             HHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         104 IRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       104 ~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +=.+|+.++. +| .|.++||+++|+|++||.+=+++..+.|.+
T Consensus        10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI   53 (153)
T PRK11179         10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGII   53 (153)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            4456666554 45 999999999999999999999999999965

>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59

Probab=91.14  E-value=0.21  Score=38.78  Aligned_cols=36  Identities=17%  Similarity=0.300  Sum_probs=31.3

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ...+++..+|+|..+||..|+||++||.....++++
T Consensus        71 ~Efi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~  106 (126)
T PF10654_consen   71 REFIELRHAGLTCYAIADYFKISKSTVFNFTQNNKK  106 (126)
T ss_pred             HHHHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHH
Confidence            456778899999999999999999999999876553

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=91.14  E-value=0.31  Score=42.95  Aligned_cols=41  Identities=22%  Similarity=0.264  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+.+|++..+||..||||..||++++++..
T Consensus       216 L~~rer~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral  256 (264)
T PRK07122        216 LPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTL  256 (264)
T ss_pred             CCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45555555555567899999999999999999999988754

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=91.11  E-value=0.33  Score=41.53  Aligned_cols=41  Identities=24%  Similarity=0.137  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-    +|+|..+||+.+|+|.+||.+++.+-.
T Consensus       175 L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl  219 (227)
T TIGR02846       175 LDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL  219 (227)
T ss_pred             CCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555544444342    789999999999999999999887644

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=91.10  E-value=0.36  Score=42.36  Aligned_cols=41  Identities=15%  Similarity=0.179  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+.+|+|..+||..+|+|.+||.+++.+..
T Consensus       213 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~ra~  253 (268)
T PRK06288        213 LPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAV  253 (268)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            66677766666778899999999999999999998876543

>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=91.06  E-value=0.87  Score=28.94  Aligned_cols=38  Identities=21%  Similarity=0.313  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      +....|...+++++..++.+|.+.+    |       +|.+||++.+++
T Consensus         3 ~~D~~Il~~Lq~d~r~s~~~la~~l----g-------lS~~~v~~Ri~r   40 (42)
T PF13404_consen    3 ELDRKILRLLQEDGRRSYAELAEEL----G-------LSESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHHHHH-TTS-HHHHHHHH----T-------S-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHH----C-------cCHHHHHHHHHH
Confidence            4567888888999999999998865    4       499999999875

...

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=91.05  E-value=0.71  Score=38.68  Aligned_cols=60  Identities=23%  Similarity=0.254  Sum_probs=42.0

Q ss_pred             HHHHHHHH-HHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH
Q psy1898         103 HIRLKIVE-MAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV  162 (230)
Q Consensus       103 ~~R~rIV~-l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~  162 (230)
                      .++.+|+. .+..|  ++..++|+.||||+++|..-+++....|.+...+..|..-..++.+.
T Consensus        19 ~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~~   81 (212)
T TIGR03338        19 EIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISLAE   81 (212)
T ss_pred             HHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHH
Confidence            44445544 23334  67789999999999999999999999998865554443333445443

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.

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=91.04  E-value=0.45  Score=35.86  Aligned_cols=38  Identities=16%  Similarity=0.059  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +.|.-+...+-.+++..+||..+++|++|+|+|.++.-
T Consensus        59 ~~r~iL~~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al   96 (100)
T PF07374_consen   59 DERLILRMRYINKLTWEQIAEELNISRRTYYRIHKKAL   96 (100)
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55655556777899999999999999999999988754

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

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

Probab=91.02  E-value=0.21  Score=34.23  Aligned_cols=32  Identities=22%  Similarity=0.270  Sum_probs=27.4

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      +..++|+.|+||++||.+-+++..+.|.+...
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~   57 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAEGLIERR   57 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence            88999999999999999999999999987544

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 ....

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=90.95  E-value=0.25  Score=42.26  Aligned_cols=88  Identities=14%  Similarity=0.063  Sum_probs=52.2

Q ss_pred             ccCCCCCChhHHHHHHHHHhcCCC--hhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898          50 FINGRPLPNHIRLKIVEMAAAGVR--PCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV  127 (230)
Q Consensus        50 ~~~g~plp~~~r~~I~e~~~~g~~--~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV  127 (230)
                      |+.+.- +.+.-.+.++.+..|..  +.++...+--.+.... ... .....+|. .-.+|+.++..|+|.++||+.|++
T Consensus       107 ~l~K~~-~~~~L~~aI~~v~~G~~~~~~~~~~~l~~~~~~~~-~~~-~~~~~Lt~-rE~~Vl~l~~~G~s~~eIA~~L~i  182 (216)
T PRK10100        107 VFYAME-DQERVVNGLQGVLRGECYFTQKLASYLITHSGNYR-YNS-TESALLTH-REKEILNKLRIGASNNEIARSLFI  182 (216)
T ss_pred             EEECCC-CHHHHHHHHHHHHcCCcccCHHHHHHHHHhhcccc-cCC-CccCCCCH-HHHHHHHHHHcCCCHHHHHHHhCC
Confidence            445533 35555666677777763  2233322211111000 000 00123664 445788888889999999999999


Q ss_pred             ccchhhhHHHHHhh
Q psy1898         128 SHGCVSKILNRYQE  141 (230)
Q Consensus       128 S~sTV~kwikRy~e  141 (230)
                      |..||..++.+-..
T Consensus       183 S~~TVk~~~~~i~~  196 (216)
T PRK10100        183 SENTVKTHLYNLFK  196 (216)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999987543

>PRK01905 DNA-binding protein Fis; Provisional

Probab=90.95  E-value=0.36  Score=34.63  Aligned_cols=37  Identities=14%  Similarity=0.141  Sum_probs=29.5

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+.-+..+++ .+.+..++|+.+|||++|+++.+++|.
T Consensus        38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~g   75 (77)
T PRK01905         38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG   75 (77)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence            3444555554 467899999999999999999999873

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=90.90  E-value=0.37  Score=33.85  Aligned_cols=27  Identities=26%  Similarity=0.460  Sum_probs=24.0

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-+.|++..++|+.+|||++||++|.+
T Consensus        14 ~~~~~~t~~~lA~~~gis~~tis~~~~   40 (78)
T TIGR02607        14 LEPLGLSIRALAKALGVSRSTLSRIVN   40 (78)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            445689999999999999999999964

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.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=90.87  E-value=0.26  Score=41.92  Aligned_cols=78  Identities=17%  Similarity=0.094  Sum_probs=50.9

Q ss_pred             ccCCCCCChhHHHHHHHHHhcCCCh--hhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898          50 FINGRPLPNHIRLKIVEMAAAGVRP--CVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV  127 (230)
Q Consensus        50 ~~~g~plp~~~r~~I~e~~~~g~~~--~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV  127 (230)
                      |+.+ |.+.+.-.+.++.+.+|..+  ..+.....        ...   -..+|..++ +|+.++.+|++.++||+.|+|
T Consensus        95 yl~K-~~~~~eL~~aI~~v~~G~~~~~~~~~~~~~--------~~~---~~~LT~RE~-eVL~ll~~G~snkeIA~~L~i  161 (207)
T PRK11475         95 VLSK-ASTLEILQQELFLSLNGVRQATDRLNNQWY--------INQ---SRMLSPTER-EILRFMSRGYSMPQIAEQLER  161 (207)
T ss_pred             EEec-CCCHHHHHHHHHHHHCCCcccCHHHHHHhh--------ccC---cCCCCHHHH-HHHHHHHCCCCHHHHHHHHCC
Confidence            6666 34455566666666666532  22222110        000   123665554 788999999999999999999


Q ss_pred             ccchhhhHHHHHh
Q psy1898         128 SHGCVSKILNRYQ  140 (230)
Q Consensus       128 S~sTV~kwikRy~  140 (230)
                      |..||..-+.+-.
T Consensus       162 S~~TV~~h~~~I~  174 (207)
T PRK11475        162 NIKTIRAHKFNVM  174 (207)
T ss_pred             CHHHHHHHHHHHH
Confidence            9999998887743

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=90.81  E-value=0.39  Score=41.52  Aligned_cols=56  Identities=20%  Similarity=0.296  Sum_probs=44.1

Q ss_pred             CHHHHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCCCCCCC
Q psy1898         101 PNHIRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSKPR  156 (230)
Q Consensus       101 s~~~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~gg~rpr  156 (230)
                      +...|.+|+.+.+ . ++|..+||+.||||..+|.+-+....+.|.+..  .+.+.+||.
T Consensus         9 ~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~   68 (218)
T COG2345           9 SGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPA   68 (218)
T ss_pred             CccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCc
Confidence            4578889998776 3 499999999999999999999999999996532  222335665

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=90.80  E-value=0.43  Score=39.60  Aligned_cols=41  Identities=27%  Similarity=0.313  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|++..+||..+|+|.+||..=+.|-+
T Consensus       135 Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar  175 (192)
T PRK09643        135 LPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR  175 (192)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666655555577999999999999999999987766543

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

Probab=90.74  E-value=0.34  Score=31.33  Aligned_cols=38  Identities=32%  Similarity=0.429  Sum_probs=26.7

Q ss_pred             HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +++|+.+|||++||++|++     |          ++ ..+++....|.+...+
T Consensus         1 ~~lA~~~gvs~~tvs~~l~-----g----------~~-~vs~~~~~~i~~~~~~   38 (52)
T cd01392           1 KDIARAAGVSVATVSRVLN-----G----------KP-RVSEETRERVLAAAEE   38 (52)
T ss_pred             CcHHHHHCcCHHHHHHHHc-----C----------CC-CCCHHHHHHHHHHHHH
Confidence            3789999999999999984     1          11 3456666666666544

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

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=90.74  E-value=0.38  Score=39.28  Aligned_cols=43  Identities=19%  Similarity=0.271  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ++=.+|+.++. +| .|.++||+.+|+|++||++=+++..+.|.+
T Consensus        14 ~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI   58 (164)
T PRK11169         14 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI   58 (164)
T ss_pred             HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            44567777664 44 999999999999999999999999999965

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=90.73  E-value=0.43  Score=35.20  Aligned_cols=41  Identities=24%  Similarity=0.282  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      ++....+..+..++|++++.|+.+.+..         .+|.|+|+.+|++
T Consensus        39 ~~~l~~~a~lRl~~Pd~SL~EL~~~~~~---------~iSKSgvnhrlrK   79 (85)
T PF02650_consen   39 PEKLREFAELRLENPDASLKELGELLEP---------PISKSGVNHRLRK   79 (85)
T ss_dssp             -HHHHHHHHHHHH-TTS-HHHHHHTT-----------T--HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCccccHHHHHHHHcC---------cCcHHHHHHHHHH
Confidence            3445567777889999999999998854         2799999999986

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=90.73  E-value=0.63  Score=35.67  Aligned_cols=24  Identities=33%  Similarity=0.296  Sum_probs=22.1

Q ss_pred             cCCCHHHHhhhhccccchhhhHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++|..+-|+.||||.+||.+|.+
T Consensus        56 ~~lSQ~vFA~~L~vs~~Tv~~WEq   79 (104)
T COG2944          56 LGLSQPVFARYLGVSVSTVRKWEQ   79 (104)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHc
Confidence            489999999999999999999954

>PRK06474 hypothetical protein; Provisional

Probab=90.67  E-value=0.34  Score=40.34  Aligned_cols=50  Identities=18%  Similarity=0.336  Sum_probs=42.6

Q ss_pred             CCcCCHHHHHHHHHHHHc-C--CCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898          97 GRPLPNHIRLKIVEMAAA-G--VRPCVISRQL-RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~-G--~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ...++...|.+|+..+.. +  .+..+|+..+ +|+.+|||+-++.+.+.|.+.
T Consensus         5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~   58 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILH   58 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence            345677899999986654 3  8999999999 799999999999999999763

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

Probab=90.60  E-value=0.23  Score=33.25  Aligned_cols=30  Identities=20%  Similarity=0.298  Sum_probs=27.9

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +..+||..+++|+.||++.+++..+.|.+.
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~   56 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVE   56 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            488999999999999999999999999774

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

>PRK09954 putative kinase; Provisional

Probab=90.58  E-value=0.36  Score=43.96  Aligned_cols=43  Identities=16%  Similarity=0.234  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+..+++.  .|..+||+.|+||++||++++++.++.|.+
T Consensus         3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954          3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            4456788877654  999999999999999999999999998844

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=90.50  E-value=0.77  Score=34.79  Aligned_cols=42  Identities=26%  Similarity=0.176  Sum_probs=30.6

Q ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         163 EKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       163 ~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +..|.+.+.+ +...++.+|.+.|.+ .+.     .+|.+||+|.|..+
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~-~~~-----~i~~~TVYR~L~~L   45 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRK-KGP-----SISLATVYRTLELL   45 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHh-cCC-----CCCHHHHHHHHHHH
Confidence            4456666655 446899999999987 454     37999999977543

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.

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

Probab=90.49  E-value=1.2  Score=34.45  Aligned_cols=67  Identities=19%  Similarity=0.127  Sum_probs=46.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+.+ .-+..++++...|..... ..-+.+..+|++.+..
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~----~GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~   68 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEE----KGLIASIGRRG-LRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSH   68 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            4788999999999999876654    58776644433 566778877666653221 2346888888887754

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

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=90.43  E-value=0.3  Score=44.32  Aligned_cols=37  Identities=11%  Similarity=0.021  Sum_probs=31.0

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .|..|..+++ .+....++|+.||||++|+|+++++|.
T Consensus       287 Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~g  324 (326)
T PRK11608        287 EKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKHQ  324 (326)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence            4555666665 478999999999999999999999873

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=90.41  E-value=0.47  Score=40.96  Aligned_cols=42  Identities=10%  Similarity=0.078  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++...|.-+...+.+|+|..+||+.+|||.++|+++.++..+
T Consensus       184 L~~~er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~  225 (231)
T PRK12427        184 LDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ  225 (231)
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            455666666666778999999999999999999999887653

>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=90.41  E-value=0.24  Score=34.57  Aligned_cols=32  Identities=34%  Similarity=0.435  Sum_probs=29.7

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..+||..+|+|+.||.+.++++++.|-+.
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            36899999999999999999999999999775

...

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=90.40  E-value=0.33  Score=42.59  Aligned_cols=44  Identities=23%  Similarity=0.296  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .+.+.+|++++++ + .+..++|+.|+||..||+|.+....+.|.+
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l   49 (252)
T PRK10906          4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI   49 (252)
T ss_pred             HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence            3567788887765 4 899999999999999999999999999976

>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins

Probab=90.35  E-value=0.62  Score=40.44  Aligned_cols=52  Identities=17%  Similarity=0.223  Sum_probs=41.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCC-CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCC
Q psy1898         152 GSKPRVATPDVEKRIEEYKKTNPG-IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDC  215 (230)
Q Consensus       152 g~rpr~lt~~~~~~I~~l~~~~P~-~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~  215 (230)
                      |.++++++++..+.|..+-..+|. +|...|++.    +.       ||..+|.|||+.. +.|.
T Consensus         5 ~~p~k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~----F~-------vspe~irrILksk-w~p~   57 (225)
T PF06413_consen    5 GNPPKKLSREAMEQIRYLHKEDPEEWTVERLAES----FK-------VSPEAIRRILKSK-WVPT   57 (225)
T ss_pred             CCCCCCCCHHHHHHHHHHHHhCccccCHHHHHhh----CC-------CCHHHHHHHHhcC-CCCC
Confidence            568899999999999999999996 777666652    43       5999999999973 4443

Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=90.33  E-value=0.4  Score=41.84  Aligned_cols=40  Identities=15%  Similarity=0.167  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ++...|.-+...+.+|+|..+||+.+|||.+||+++.++-
T Consensus       210 L~~~er~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~~a  249 (258)
T PRK08215        210 LNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAA  249 (258)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5556655444455689999999999999999999998764

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=90.30  E-value=0.36  Score=41.68  Aligned_cols=43  Identities=9%  Similarity=0.138  Sum_probs=35.3

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      -.++|.. -..|+.++.+|++.++||+.+++|.+||.+-+.+-.
T Consensus       141 ~~~LS~R-E~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~  183 (217)
T PRK13719        141 KNKVTKY-QNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL  183 (217)
T ss_pred             cCCCCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3445543 357888999999999999999999999999988754

>PRK09492 treR trehalose repressor; Provisional

Probab=90.27  E-value=0.37  Score=42.21  Aligned_cols=41  Identities=22%  Similarity=0.281  Sum_probs=31.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+.+|||++||++.++.               + ..++++.+++|.+..++
T Consensus         5 ~ti~dIA~~agVS~~TVSrvLn~---------------~-~~vs~~tr~rV~~~a~e   45 (315)
T PRK09492          5 LTIKDIARLSGVGKSTVSRVLNN---------------E-SGVSEETRERVEAVINQ   45 (315)
T ss_pred             CcHHHHHHHhCCCHHHHhHHhCC---------------C-CCCCHHHHHHHHHHHHH
Confidence            58899999999999999999852               1 12467777777766655

>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=90.25  E-value=0.45  Score=31.60  Aligned_cols=34  Identities=24%  Similarity=0.531  Sum_probs=29.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+.+..+||+.++++++|+.+++++-.+.|-+.
T Consensus        15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~   48 (59)
T PF01047_consen   15 NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE   48 (59)
T ss_dssp             HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence            4569999999999999999999999999999773

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 ....

>PRK10072 putative transcriptional regulator; Provisional

Probab=90.23  E-value=0.23  Score=37.42  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=23.5

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ...|++..++|+.+|||.+||++|.+
T Consensus        43 ~~~glTQ~elA~~lGvS~~TVs~WE~   68 (96)
T PRK10072         43 KGTGLKIDDFARVLGVSVAMVKEWES   68 (96)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            34699999999999999999999974

>PF13565 HTH_32: Homeodomain-like domain

Probab=90.23  E-value=0.47  Score=33.28  Aligned_cols=40  Identities=33%  Similarity=0.432  Sum_probs=31.5

Q ss_pred             CCcC-CHHHHHHHHHHHHcC--CCHHHHhhhh----c--c--ccchhhhHH
Q psy1898          97 GRPL-PNHIRLKIVEMAAAG--VRPCVISRQL----R--V--SHGCVSKIL  136 (230)
Q Consensus        97 g~~~-s~~~R~rIV~l~~~G--~s~~~IAr~l----g--V--S~sTV~kwi  136 (230)
                      |++. +.+.+..|++++.+.  ++..+|+..+    |  +  |.+||++|+
T Consensus        27 Grp~~~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L   77 (77)
T PF13565_consen   27 GRPRKDPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL   77 (77)
T ss_pred             CCCCCcHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence            4444 478889999998765  9999999865    3  4  999999984

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=90.23  E-value=1.7  Score=42.40  Aligned_cols=94  Identities=15%  Similarity=0.017  Sum_probs=58.2

Q ss_pred             HHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhh----hCCC-CcCCCCCCCC-----C-------CCCHHHHHHH
Q psy1898         105 RLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQE----TGSI-RPGVIGGSKP-----R-------VATPDVEKRI  166 (230)
Q Consensus       105 R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e----~G~v-~p~~~gg~rp-----r-------~lt~~~~~~I  166 (230)
                      ..+|+.++. +..+..++|+.|+||..||++=++.-.+    .|.. ..... |-+-     .       ..+++....+
T Consensus         6 ~~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~~-Gy~l~~~~~~~~~~~~~~~~~e~~~il   84 (584)
T PRK09863          6 ELKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGSA-KYHLEILNRRSLFQLLQKSDNEDRLLL   84 (584)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecCC-ceEEEeCCHHHHHHHHhcCCHHHHHHH
Confidence            355666554 4599999999999999999998886533    3321 11111 1110     0       1122333333


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      ..++. +...+..++++.|.           ||.+||.+.|++..
T Consensus        85 ~~Ll~-~~~~~~~~La~~l~-----------vS~sTi~~dl~~v~  117 (584)
T PRK09863         85 LRLLL-NTFTPMAQLASALN-----------LSRTWVAERLPRLN  117 (584)
T ss_pred             HHHHH-cCCccHHHHHHHhC-----------CCHHHHHHHHHHHH
Confidence            44554 55677888887762           69999999987764

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=90.21  E-value=0.48  Score=35.92  Aligned_cols=43  Identities=28%  Similarity=0.360  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~  146 (230)
                      .|..|++.+.+   ..|..+|...+     .++++|||+.++.+.+.|.+.
T Consensus         2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~   52 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR   52 (116)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence            47777776543   38999999988     699999999999999999764

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.

>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=90.15  E-value=0.35  Score=32.27  Aligned_cols=35  Identities=23%  Similarity=0.296  Sum_probs=27.3

Q ss_pred             CCCChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          54 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        54 ~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      ..|+...+.+|++++..|.+..+|+++|+|+...+
T Consensus         5 ~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv   39 (53)
T PF04218_consen    5 KSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTV   39 (53)
T ss_dssp             SS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHH
T ss_pred             ccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHH
Confidence            46789999999999999999999999999877665

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.

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=90.10  E-value=1.2  Score=35.87  Aligned_cols=67  Identities=15%  Similarity=-0.004  Sum_probs=46.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      ++..++|+.+|||..|+.-|.    +.|.+.|..+..+.-+..++++.+.|..... ..-..++.+|++.+.
T Consensus         8 ~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~   75 (144)
T PRK13752          8 LTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLR   75 (144)
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            789999999999999976554    4687765433223457778877666653332 234578888887774

>PRK15043 transcriptional regulator MirA; Provisional

Probab=90.07  E-value=1  Score=39.55  Aligned_cols=68  Identities=18%  Similarity=0.220  Sum_probs=48.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+..|.++|   |.+.|....+ .-+..++++.+.|..... .+-..+..+|++.+..
T Consensus         4 ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~-G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~   72 (243)
T PRK15043          4 YTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDG-GHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN   72 (243)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            578999999999999999997654   5666643322 456778877666653332 2346888888887764

>PRK15320 transcriptional activator SprB; Provisional

Probab=90.06  E-value=0.5  Score=40.55  Aligned_cols=40  Identities=8%  Similarity=0.115  Sum_probs=34.2

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      -..|+.++.+|.|.++||..|++|.+||++...+-.+-=.
T Consensus       169 EIEVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg  208 (251)
T PRK15320        169 KYALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG  208 (251)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence            3467778899999999999999999999999998775433

>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.88  E-value=0.4  Score=41.38  Aligned_cols=41  Identities=20%  Similarity=0.343  Sum_probs=31.8

Q ss_pred             HHHHHHHH-HHHcC-----CCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898         103 HIRLKIVE-MAAAG-----VRPCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus       103 ~~R~rIV~-l~~~G-----~s~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      +.+.+||. +++.|     -....+|..|++|+.|||++++.+++.|
T Consensus       173 ~~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k~~~  219 (220)
T COG2964         173 AKNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFKAGG  219 (220)
T ss_pred             HHHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHhhcCC
Confidence            55555665 66778     3455689999999999999999988765

>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins

Probab=89.87  E-value=0.39  Score=38.43  Aligned_cols=44  Identities=9%  Similarity=0.078  Sum_probs=38.4

Q ss_pred             CCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898          96 NGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus        96 ~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      -++-|...+-.+||...+++.+.++|+..|.||+-|.+.|.+.-
T Consensus        12 lpkmYtE~Lve~II~~IE~dt~~sEIc~~L~isrKtFyeWrdtk   55 (174)
T PF07141_consen   12 LPKMYTEPLVEQIIDKIESDTNDSEICTSLHISRKTFYEWRDTK   55 (174)
T ss_pred             cHHhhhhHHHHHHHHHHHcCCcHHHHHHHHhccHHHHHHHHhhh
Confidence            34557778889999999999999999999999999999998653

This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.

>PRK09462 fur ferric uptake regulator; Provisional

Probab=89.85  E-value=1.2  Score=35.70  Aligned_cols=45  Identities=18%  Similarity=0.147  Sum_probs=32.3

Q ss_pred             CHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+...  ...++.||.+.|.+ .+..     +|.+||||.|..+
T Consensus        16 T~q-R~~Il~~l~~~~~~h~sa~eI~~~l~~-~~~~-----i~~aTVYR~L~~L   62 (148)
T PRK09462         16 TLP-RLKILEVLQEPDNHHVSAEDLYKRLID-MGEE-----IGLATVYRVLNQF   62 (148)
T ss_pred             CHH-HHHHHHHHHhCCCCCCCHHHHHHHHHh-hCCC-----CCHHHHHHHHHHH
Confidence            444 44555555542  37899999999987 5553     7999999998654

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=89.79  E-value=0.46  Score=41.88  Aligned_cols=42  Identities=17%  Similarity=0.164  Sum_probs=32.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCC--CCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rp--r~lt~~~~~~I~~l~~~  172 (230)
                      ++.++||+..|||.+||++.++.               ++  ...+++.+++|.+..++
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~~~~~Vs~~tr~rV~~~a~e   44 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVING---------------KAKQYRVSDKTVEKVMAVVRE   44 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC---------------CCCCCCcCHHHHHHHHHHHHH
Confidence            47899999999999999999851               11  13577888888777665

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=89.77  E-value=0.5  Score=35.51  Aligned_cols=37  Identities=14%  Similarity=0.116  Sum_probs=29.2

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+.-+..+++ .+....++|+.+|||++|+++.+++|.
T Consensus        56 Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~g   93 (95)
T PRK00430         56 EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG   93 (95)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            3444445444 577899999999999999999999874

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=89.74  E-value=0.81  Score=38.75  Aligned_cols=46  Identities=13%  Similarity=0.024  Sum_probs=35.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD  161 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~  161 (230)
                      ++..++|+.||||+++|..=+++-...|.+.-.+..|-.-..++.+
T Consensus        35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~   80 (221)
T PRK11414         35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR   80 (221)
T ss_pred             cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCHH
Confidence            6788999999999999999999999999875444433333334443

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=89.68  E-value=0.49  Score=36.33  Aligned_cols=43  Identities=30%  Similarity=0.240  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         162 VEKRIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       162 ~~~~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+..|..++.+.+ ..|+.+|.+.|.+ .+..     +|.+||+|.|..+
T Consensus         9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~-~~~~-----is~~TVYR~L~~L   52 (120)
T PF01475_consen    9 QRLAILELLKESPEHLTAEEIYDKLRK-KGPR-----ISLATVYRTLDLL   52 (120)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHH-TTTT-------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHhhh-ccCC-----cCHHHHHHHHHHH
Confidence            3455666665544 7889999999987 6653     8999999998754

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=89.62  E-value=0.3  Score=41.85  Aligned_cols=41  Identities=20%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+-+|++..+||+.||+|.+||...+.|.+
T Consensus       150 L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar  190 (231)
T PRK11922        150 LPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR  190 (231)
T ss_pred             CCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            44455544444467899999999999999999999887654

>PRK09483 response regulator; Provisional

Probab=89.61  E-value=0.45  Score=38.87  Aligned_cols=41  Identities=27%  Similarity=0.234  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++..++ +|+.++..|.+.++||..+++|..||...+++-.
T Consensus       148 ~Lt~rE~-~vl~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~  188 (217)
T PRK09483        148 SLSEREL-QIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMF  188 (217)
T ss_pred             ccCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3665554 5567889999999999999999999998887744

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=89.59  E-value=0.7  Score=39.30  Aligned_cols=46  Identities=9%  Similarity=0.024  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ++..+...++.+..    .|++.++||+.+++|..||.+.+++-...|.+
T Consensus       159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~  208 (239)
T PRK10430        159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHIL  208 (239)
T ss_pred             CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence            55555555555554    79999999999999999999999988888855

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

Probab=89.54  E-value=2  Score=34.54  Aligned_cols=84  Identities=18%  Similarity=0.209  Sum_probs=58.3

Q ss_pred             CCChhHHHHHHHHH-hcCCChhhhhhhhccccccc--c----------cCCcccCCC--cCCHHHHHHHHHHHHcC-CCH
Q psy1898          55 PLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGVN--Q----------LGGVFINGR--PLPNHIRLKIVEMAAAG-VRP  118 (230)
Q Consensus        55 plp~~~r~~I~e~~-~~g~~~~~isr~lrvshg~~--~----------l~~~~~~g~--~~s~~~R~rIV~l~~~G-~s~  118 (230)
                      |-....|..++..+ ..|.+..+++..|+||-++.  -          |-..+..|+  -++.+....+++...+. ++.
T Consensus         4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~wTl   83 (138)
T COG3415           4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDWTL   83 (138)
T ss_pred             hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccchH
Confidence            44577888888887 59999999999999865553  0          223333333  37778888888877654 777


Q ss_pred             HHH----hhhhcc--ccchhhhHHHH
Q psy1898         119 CVI----SRQLRV--SHGCVSKILNR  138 (230)
Q Consensus       119 ~~I----Ar~lgV--S~sTV~kwikR  138 (230)
                      +++    ...|||  +.++|++++++
T Consensus        84 ~~~~~~l~~e~gv~y~~~~v~~~l~~  109 (138)
T COG3415          84 KELVEELGLEFGVWYHASAVRRLLHE  109 (138)
T ss_pred             HHHHHHHhhhcCeEEeHHHHHHHHHH
Confidence            777    446777  55578888765

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=89.49  E-value=0.46  Score=41.81  Aligned_cols=41  Identities=22%  Similarity=0.284  Sum_probs=30.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+.+|||++||++.++.                ....+++.+++|.+..++
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~----------------~~~vs~~tr~rV~~~a~~   42 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNN----------------EPKVSIETRERVEQVIQQ   42 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC----------------CCCCCHHHHHHHHHHHHH
Confidence            47899999999999999999852                112466777777666655

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

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=89.43  E-value=0.46  Score=42.15  Aligned_cols=41  Identities=10%  Similarity=-0.001  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+    .+|+|.++||..||||.+||..++.+..
T Consensus       223 Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAl  267 (285)
T TIGR02394       223 LNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEAL  267 (285)
T ss_pred             CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555554444333    6899999999999999999999988754

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).

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=89.34  E-value=0.55  Score=31.36  Aligned_cols=33  Identities=27%  Similarity=0.327  Sum_probs=28.6

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      .++.+..+|.+..+||..+++|..||..-+.+-
T Consensus        11 ~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i   43 (65)
T COG2771          11 EILRLVAQGKSNKEIARILGISEETVKTHLRNI   43 (65)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            455688899999999999999999999887764

>PRK10651 transcriptional regulator NarL; Provisional

Probab=89.32  E-value=0.65  Score=37.43  Aligned_cols=41  Identities=20%  Similarity=0.311  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++... .+|+.++.+|.+.++||+.+++|..||...+++-..
T Consensus       156 Lt~rE-~~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~  196 (216)
T PRK10651        156 LTPRE-RDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK  196 (216)
T ss_pred             CCHHH-HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            66555 488889999999999999999999999999987543

>PRK09726 antitoxin HipB; Provisional

Probab=89.28  E-value=0.42  Score=34.99  Aligned_cols=25  Identities=12%  Similarity=0.318  Sum_probs=23.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|++..++|+.+|||++||++|.+
T Consensus        23 ~~gltq~elA~~~gvs~~tis~~e~   47 (88)
T PRK09726         23 QNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4589999999999999999999975

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=89.28  E-value=1.1  Score=39.42  Aligned_cols=45  Identities=16%  Similarity=0.285  Sum_probs=37.8

Q ss_pred             HHHHHHHHHc--C-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         105 RLKIVEMAAA--G-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       105 R~rIV~l~~~--G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      =.+|+..+..  | .+..++|+++|||+++|..=+++..+.|.+..++
T Consensus       185 v~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       185 VEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            3556666554  4 8999999999999999999999999999887655

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.

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

Probab=89.26  E-value=0.21  Score=34.49  Aligned_cols=19  Identities=26%  Similarity=0.281  Sum_probs=17.3

Q ss_pred             CHHHHhhhhccccchhhhH
Q psy1898         117 RPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kw  135 (230)
                      +...+|+.||||+++|+.|
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            7889999999999999999

>PRK09526 lacI lac repressor; Reviewed

Probab=89.18  E-value=0.51  Score=41.88  Aligned_cols=41  Identities=22%  Similarity=0.265  Sum_probs=30.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||++.|||++||++.++.               ++ ..+++.+++|.+..++
T Consensus         6 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~e   46 (342)
T PRK09526          6 VTLYDVARYAGVSYQTVSRVLNQ---------------AS-HVSAKTREKVEAAMAE   46 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhcC---------------CC-CCCHHHHHHHHHHHHH
Confidence            58999999999999999999852               11 2466777777666554

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=89.11  E-value=2.7  Score=30.80  Aligned_cols=39  Identities=21%  Similarity=0.235  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHH--cCCCHHHHhhhhc-cccchhhhHHHHHhh
Q psy1898         103 HIRLKIVEMAA--AGVRPCVISRQLR-VSHGCVSKILNRYQE  141 (230)
Q Consensus       103 ~~R~rIV~l~~--~G~s~~~IAr~lg-VS~sTV~kwikRy~e  141 (230)
                      .-|+-+..+..  .|+|..+|++.|| .+++||..-+++.++
T Consensus        30 ~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~   71 (90)
T cd06571          30 LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEE   71 (90)
T ss_pred             hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence            44555555444  3899999999999 999999999888764

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.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=89.08  E-value=0.66  Score=36.77  Aligned_cols=41  Identities=17%  Similarity=0.154  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHcCC--CHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGV--RPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~--s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++.+.|.-|-..+-.+.  +..+||..|++|.+||+++.+++-
T Consensus        83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l  125 (134)
T TIGR01636        83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHII  125 (134)
T ss_pred             CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            55677765556665554  999999999999999999988764

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=88.91  E-value=0.66  Score=40.07  Aligned_cols=68  Identities=15%  Similarity=0.122  Sum_probs=50.0

Q ss_pred             hhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhH
Q psy1898          58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus        58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kw  135 (230)
                      ..-|..|+++++.|..+.+|+|...  |...+..+|..        .=.+|..++..|++..+||..+|+|.+-|.-.
T Consensus       150 ~tHK~~ii~~~l~g~~~~eiar~t~--HS~~av~rYi~--------~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~eY  217 (220)
T PF07900_consen  150 VTHKKIIIRLYLKGKPTPEIARRTN--HSPEAVDRYIK--------DFKRVLMLYEKGMSPEEIAFITGMSERLVKEY  217 (220)
T ss_pred             chHHHHHHHHHHcCCCHHHHHHHhc--cCHHHHHHHHH--------hhHHhHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            4567888999999998889988765  66665555542        22466667888899999999999987766544

>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=88.88  E-value=0.57  Score=31.65  Aligned_cols=36  Identities=17%  Similarity=0.220  Sum_probs=28.7

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      +++..+.+-.+...+|+.++||+++|++.+++.++.
T Consensus         5 ~~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~LE~~   40 (60)
T PF00126_consen    5 RYFLAVAETGSISAAAEELGISQSAVSRQIKQLEEE   40 (60)
T ss_dssp             HHHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHhhccchHHHHHHHHHHHH
Confidence            344444443499999999999999999999998854

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 ....

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=88.87  E-value=0.56  Score=41.64  Aligned_cols=41  Identities=15%  Similarity=0.169  Sum_probs=31.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||++.|||++||++.++.               ++ .++++.+++|.+..++
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn~---------------~~-~vs~~tr~~V~~~a~e   42 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVINK---------------TR-FVAEETRNAVWAAIKE   42 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence            37899999999999999999852               11 2467777777776655

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=88.86  E-value=0.62  Score=40.99  Aligned_cols=42  Identities=24%  Similarity=0.299  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +++.-.|.-+...+.++++.++||+.+|||.+.|+++.++.-
T Consensus       196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai  237 (247)
T COG1191         196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAI  237 (247)
T ss_pred             ccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence            344455555555677899999999999999999999988753

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=88.84  E-value=0.63  Score=36.87  Aligned_cols=43  Identities=19%  Similarity=0.369  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.-.+|+..+.. + .|.++||+.+|+|.+||.+-+++..+.|.+
T Consensus         8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522           8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            445567776654 3 999999999999999999999999999954

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=88.71  E-value=9.1  Score=31.18  Aligned_cols=98  Identities=20%  Similarity=0.149  Sum_probs=59.2

Q ss_pred             HHHHH-HHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH----------HHHHHHh
Q psy1898         106 LKIVE-MAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR----------IEEYKKT  172 (230)
Q Consensus       106 ~rIV~-l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~----------I~~l~~~  172 (230)
                      .++|. +.. .| ....+||+.|+|+++||..-+++-.+.|-+.-.+.+   .-.+|+.-.+.          +..++.+
T Consensus        12 L~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~---gi~LT~~G~~~a~~~~r~hrlle~fL~~   88 (154)
T COG1321          12 LETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYG---GVTLTEKGREKAKELLRKHRLLERFLVD   88 (154)
T ss_pred             HHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCC---CeEEChhhHHHHHHHHHHHHHHHHHHHH
Confidence            34444 443 34 899999999999999999999999999987543332   23344332211          1222222


Q ss_pred             CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898         173 NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR  212 (230)
Q Consensus       173 ~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~  212 (230)
                      --.....+..+.... ...     .+|..++.|+.+-.+.
T Consensus        89 ~lg~~~~~~~~ea~~-leh-----~~s~~~~~rl~~~l~~  122 (154)
T COG1321          89 VLGLDWEEAHEEAEG-LEH-----ALSDETAERLDELLGF  122 (154)
T ss_pred             HhCCCHHHHHHHHHH-Hhh-----cCCHHHHHHHHHHhCC
Confidence            223344444322222 222     2699999999888874

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=88.68  E-value=0.53  Score=41.66  Aligned_cols=41  Identities=12%  Similarity=0.099  Sum_probs=31.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||++||++.++.               . ...+++.+++|.+..++
T Consensus         6 ~ti~dIA~~agVS~~TVSrvLn~---------------~-~~vs~~tr~rV~~~a~e   46 (331)
T PRK14987          6 PVLQDVADRVGVTKMTVSRFLRN---------------P-EQVSVALRGKIAAALDE   46 (331)
T ss_pred             CcHHHHHHHhCCCHHHhhhhhCC---------------C-CCCCHHHHHHHHHHHHH
Confidence            58899999999999999999841               1 12467777777766655

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=88.67  E-value=0.85  Score=38.64  Aligned_cols=59  Identities=8%  Similarity=0.117  Sum_probs=40.7

Q ss_pred             HHHHHHHHH-HHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHH
Q psy1898         103 HIRLKIVEM-AAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD  161 (230)
Q Consensus       103 ~~R~rIV~l-~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~  161 (230)
                      .+|..|+.. +..|  ++..++|++||||+++|.-=+++-...|.+...+..|-.-..++.+
T Consensus        15 ~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~   76 (224)
T PRK11534         15 WLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQ   76 (224)
T ss_pred             HHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHH
Confidence            344445442 2334  6788999999999999999999999999876544434333334444

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=88.65  E-value=0.57  Score=41.54  Aligned_cols=41  Identities=17%  Similarity=0.144  Sum_probs=30.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .|.++||+.+|||++||++.++.               ++ .++++.+++|.+..++
T Consensus         7 ~Ti~dIA~~agVS~~TVSr~Ln~---------------~~-~vs~~tr~~V~~~a~e   47 (342)
T PRK10014          7 ITIHDVALAAGVSVSTVSLVLSG---------------KG-RISTATGERVNQAIEE   47 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            68999999999999999999852               11 2466667776665544

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=88.63  E-value=0.55  Score=41.28  Aligned_cols=42  Identities=17%  Similarity=0.099  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|..+ ..|+.+..+|+|..+||+.|+||..||...+++-.+
T Consensus       190 ~LT~RE-~evl~l~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~  231 (247)
T TIGR03020       190 LITARE-AEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFK  231 (247)
T ss_pred             CCCHHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            566644 456667889999999999999999999999987543

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.

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=88.62  E-value=1.3  Score=36.48  Aligned_cols=42  Identities=14%  Similarity=0.115  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         163 EKRIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       163 ~~~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +..|.+++...+ ..++.+|.+.|.+ .+..     +|.+||||.|..+
T Consensus        28 R~~IL~~l~~~~~hlSa~eI~~~L~~-~~~~-----is~aTVYRtL~~L   70 (169)
T PRK11639         28 RLEVLRLMSLQPGAISAYDLLDLLRE-AEPQ-----AKPPTVYRALDFL   70 (169)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHh-hCCC-----CCcchHHHHHHHH
Confidence            345555555444 6899999999987 5553     8999999999654

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=88.61  E-value=5.2  Score=31.11  Aligned_cols=79  Identities=16%  Similarity=0.024  Sum_probs=49.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHH
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSW  179 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~  179 (230)
                      ++.+...=|...+...-+.+++++.||||.+||..=+.+--+.=...+      .+.......+..|...+. +-.+++.
T Consensus        34 L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~------~~~~~~~~~~~~IL~~L~-~GeIs~e  106 (113)
T PF09862_consen   34 LSPEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGYEE------DEEEEEEDERKEILDKLE-KGEISVE  106 (113)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC------CcccccchhHHHHHHHHH-cCCCCHH
Confidence            555555555556667779999999999999999988877543311111      111223344556666663 5577777


Q ss_pred             HHHHHH
Q psy1898         180 EIRDRL  185 (230)
Q Consensus       180 eI~~~L  185 (230)
                      |-.+.|
T Consensus       107 eA~~~L  112 (113)
T PF09862_consen  107 EALEIL  112 (113)
T ss_pred             HHHHHh
Confidence            655544

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=88.36  E-value=0.61  Score=41.57  Aligned_cols=40  Identities=20%  Similarity=0.228  Sum_probs=31.7

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||.+||++.++.               ++ ..+++.+++|.+..++
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn~---------------~~-~Vs~~tr~rV~~~a~e   42 (343)
T PRK10727          3 TIKDVARLAGVSVATVSRVINN---------------SP-KASEASRLAVHSAMES   42 (343)
T ss_pred             CHHHHHHHhCCCHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            7899999999999999999851               11 2578888888777765

>PRK14702 insertion element IS2 transposase InsD; Provisional

Probab=88.35  E-value=2.2  Score=37.53  Aligned_cols=53  Identities=25%  Similarity=0.151  Sum_probs=41.3

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHh---hCCCCCCCCCCHhHHHHHHHcCCCCCC
Q psy1898         159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQ---DGICDKNSAPSVSSISRLLRGGRRDDC  215 (230)
Q Consensus       159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~---~Gi~~~~~~vS~sTV~R~Lr~~g~~~~  215 (230)
                      ..+..+.|.++..++|...+..|...|..+   .|+.    .++..||+|+|++.||...
T Consensus        10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~----~v~~krV~rlmr~~gL~~~   65 (262)
T PRK14702         10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMP----AINAKRVYRLMRQNALLLE   65 (262)
T ss_pred             hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCcc----ccCHHHHHHHHHHhCCccc
Confidence            455677777776788999999999999762   1441    2799999999999999844

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=88.31  E-value=0.72  Score=40.15  Aligned_cols=41  Identities=12%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+.+|++..+||..+|||..+|+++.++..
T Consensus       207 L~~rer~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ral  247 (254)
T TIGR02850       207 LNEREKMILNMRFFEGKTQMEVAEEIGISQAQVSRLEKAAL  247 (254)
T ss_pred             CCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55555544444555799999999999999999999988754

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.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=88.30  E-value=1.7  Score=29.82  Aligned_cols=79  Identities=16%  Similarity=0.146  Sum_probs=51.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKN  195 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~  195 (230)
                      .+..++|+.+++|..++++..+++.  |. .+..       .+.....+.+..++..+ .++..++++.    .|+.   
T Consensus         2 ~~~~~la~~~~~s~~~l~~~f~~~~--~~-s~~~-------~~~~~r~~~a~~~l~~~-~~~~~~ia~~----~g~~---   63 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKET--GT-TPKQ-------YLRDRRLERARRLLRDT-DLSVTEIALR----VGFS---   63 (84)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHh--Cc-CHHH-------HHHHHHHHHHHHHHHcC-CCCHHHHHHH----hCCC---
Confidence            5788999999999999988877542  21 1110       11222344455666555 6788777763    5763   


Q ss_pred             CCCCHhHHHHHHHcC-CCCCC
Q psy1898         196 SAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       196 ~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                         |.++.+|.+++. |.+|.
T Consensus        64 ---s~~~f~r~Fk~~~g~sp~   81 (84)
T smart00342       64 ---SQSYFSRAFKKLFGVTPS   81 (84)
T ss_pred             ---ChHHHHHHHHHHHCcChh
Confidence               899999998654 55543

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=88.15  E-value=0.57  Score=41.25  Aligned_cols=40  Identities=15%  Similarity=0.024  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHH--HcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         100 LPNHIRLKIVEMA--AAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       100 ~s~~~R~rIV~l~--~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      +|...|.-+...+  ..++|.++||+.||||..+|+++.++.
T Consensus       219 L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~A  260 (270)
T TIGR02392       219 LDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNA  260 (270)
T ss_pred             CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            5555555444444  247999999999999999999988764

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.

>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=88.14  E-value=0.38  Score=31.40  Aligned_cols=31  Identities=32%  Similarity=0.290  Sum_probs=27.6

Q ss_pred             hhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      +.++.+|+||+.+|....+.+|-|+|+...+
T Consensus         8 pgikeqIvema~nG~GiRdtaRvL~I~~nTV   38 (46)
T PF12759_consen    8 PGIKEQIVEMAFNGSGIRDTARVLKISINTV   38 (46)
T ss_pred             ccHHHHHHHHHhcCCcchhhHhHhcchHHHH
Confidence            5688999999999999999999999887665

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=88.04  E-value=0.59  Score=40.23  Aligned_cols=41  Identities=10%  Similarity=0.049  Sum_probs=31.9

Q ss_pred             CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+    .+++|..+||..+|||..+|.++.++-.
T Consensus       177 L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al  221 (238)
T TIGR02393       177 LTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKAL  221 (238)
T ss_pred             CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555555554445    4789999999999999999999987644

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.

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

Probab=87.99  E-value=1.7  Score=30.35  Aligned_cols=46  Identities=15%  Similarity=0.265  Sum_probs=34.3

Q ss_pred             CHHHHHHHHHHHHhCCC--CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc---CCCCCC
Q psy1898         159 TPDVEKRIEEYKKTNPG--IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG---GRRDDC  215 (230)
Q Consensus       159 t~~~~~~I~~l~~~~P~--~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~---~g~~~~  215 (230)
                      ..+.++.|..++.+++.  +++.+|.+.|    |+       +.++|+|.|..   .|+-.+
T Consensus         4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~l----gl-------~~~~v~r~L~~L~~~G~V~~   54 (68)
T smart00550        4 QDSLEEKILEFLENSGDETSTALQLAKNL----GL-------PKKEVNRVLYSLEKKGKVCK   54 (68)
T ss_pred             chHHHHHHHHHHHHCCCCCcCHHHHHHHH----CC-------CHHHHHHHHHHHHHCCCEEe
Confidence            34567888888888766  9999988865    44       88899999864   465543

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

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

Probab=87.98  E-value=3.8  Score=29.73  Aligned_cols=31  Identities=23%  Similarity=0.382  Sum_probs=27.6

Q ss_pred             HHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         118 PCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       118 ~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ..++|+.++|+++||++.+++..+.|-+...
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~   32 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYE   32 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence            5789999999999999999999999977543

iron dependent repressor

>PF13518 HTH_28: Helix-turn-helix domain

Probab=87.95  E-value=0.4  Score=30.88  Aligned_cols=29  Identities=31%  Similarity=0.424  Sum_probs=25.8

Q ss_pred             HHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          60 IRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        60 ~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      +|.+||+++.+|.+..+++++++|++..+
T Consensus         1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv   29 (52)
T PF13518_consen    1 FRLQIVELYLEGESVREIAREFGISRSTV   29 (52)
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCCCHhHH
Confidence            48899999999999999999999877664

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=87.93  E-value=1.7  Score=38.04  Aligned_cols=45  Identities=24%  Similarity=0.304  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.+++|++++.+ | .+..++|+.|+||..||+|=++...+.|.+.
T Consensus         4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~   50 (253)
T COG1349           4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL   50 (253)
T ss_pred             HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence            4567888887765 6 9999999999999999999999999999764

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=87.81  E-value=0.87  Score=36.17  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++.. ..+|+.++.+|.+.++||+.+++|..||..++.+-..
T Consensus       150 lt~~-e~~vl~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~  190 (211)
T PRK15369        150 LTPR-ERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMR  190 (211)
T ss_pred             CCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            5544 4566778899999999999999999999999988553

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=87.77  E-value=1.4  Score=37.48  Aligned_cols=63  Identities=19%  Similarity=0.192  Sum_probs=45.9

Q ss_pred             HHHHHHHHHH-HcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH
Q psy1898         103 HIRLKIVEMA-AAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR  165 (230)
Q Consensus       103 ~~R~rIV~l~-~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~  165 (230)
                      .+|..|+... .-|  ++..+||++||||+..|..-+.+....|.+.-.+..|-.-..++.+..+.
T Consensus        24 ~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~e   89 (230)
T COG1802          24 ELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEARE   89 (230)
T ss_pred             HHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHH
Confidence            5666666532 334  88999999999999999999999999998865555454444555554333

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=87.77  E-value=0.74  Score=40.79  Aligned_cols=53  Identities=23%  Similarity=0.279  Sum_probs=43.2

Q ss_pred             CcCCHHHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898          98 RPLPNHIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      .+++.+.+.-+......|  ...+++.+.+|.|++||+|.+++-.+.|-++--+.
T Consensus       191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence            467777776666665554  89999999999999999999999999998865444

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=87.60  E-value=0.73  Score=41.11  Aligned_cols=41  Identities=22%  Similarity=0.293  Sum_probs=31.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||++||++.++.               ++ .++++.+++|.+..++
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~-~Vs~~tr~kV~~~a~e   42 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNN---------------SA-LVSADTREAVMKAVSE   42 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            47899999999999999999852               11 2467777777776655

>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=87.59  E-value=0.31  Score=30.37  Aligned_cols=25  Identities=16%  Similarity=0.110  Sum_probs=19.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +..++|+.+|||..|+..|.+    .|.+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~----~Gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYER----EGLL   25 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHH----TTSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHH----CCCC
Confidence            467999999999999988755    4766

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 ....

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=87.50  E-value=2.3  Score=32.37  Aligned_cols=56  Identities=13%  Similarity=0.068  Sum_probs=40.0

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+...
T Consensus        41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~   99 (118)
T TIGR02337        41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL   99 (118)
T ss_pred             CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence            45999999999999999999999999999976422  1111 12235666666554444

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.

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=87.46  E-value=0.95  Score=32.66  Aligned_cols=33  Identities=9%  Similarity=0.085  Sum_probs=25.9

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhc------cccchhhhHHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLR------VSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lg------VS~sTV~kwik  137 (230)
                      -.++..+. +.|+|..++|+.+|      +|++||++|.+
T Consensus        13 ~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es   52 (75)
T smart00352       13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA   52 (75)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence            34444444 45999999999999      59999999975

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=87.46  E-value=0.68  Score=36.47  Aligned_cols=33  Identities=15%  Similarity=0.157  Sum_probs=26.5

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+|-.+. ..|+|..++|..+|||++||++|.+.
T Consensus         8 ~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g   41 (135)
T PRK09706          8 QRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERD   41 (135)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            4444444 45899999999999999999999754

>TIGR01481 ccpA catabolite control protein A

Probab=87.42  E-value=0.77  Score=40.48  Aligned_cols=41  Identities=29%  Similarity=0.404  Sum_probs=31.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||.+||++.++.               ++ .++++.+++|.+..++
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~~   42 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNG---------------NP-NVKPATRKKVLEVIKR   42 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            47889999999999999999851               11 2567777777766654

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.

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

Probab=87.36  E-value=0.75  Score=31.30  Aligned_cols=24  Identities=33%  Similarity=0.473  Sum_probs=20.2

Q ss_pred             cCCCHHHHhhhhccccchhhhHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .|+|..++|+.+|+|.+||++|.+
T Consensus        13 ~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen   13 AGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHC
Confidence            489999999999999999999964

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=87.14  E-value=0.91  Score=39.50  Aligned_cols=44  Identities=25%  Similarity=0.316  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+.+|++.+.+ + .+..++|+.|+||..||+|.++...+.|.+.
T Consensus         4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~   49 (240)
T PRK10411          4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL   49 (240)
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            344566666543 3 9999999999999999999999998887663

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=87.11  E-value=0.94  Score=39.00  Aligned_cols=42  Identities=21%  Similarity=0.218  Sum_probs=34.3

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|... ..++.+..+|+|..+||..|+||.+||..++++-.
T Consensus       170 ~~Lt~re-~evl~~~a~G~t~~eIa~~l~is~~Tv~~~l~~~~  211 (232)
T TIGR03541       170 GVLSERE-REVLAWTALGRRQADIAAILGISERTVENHLRSAR  211 (232)
T ss_pred             ccCCHHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3466544 45666678999999999999999999999998865

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.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=87.08  E-value=0.7  Score=43.14  Aligned_cols=38  Identities=16%  Similarity=0.087  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|..|..+++ .+....++|+.||||++|+|+.+++|.
T Consensus       417 ~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~~  455 (457)
T PRK11361        417 VEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYG  455 (457)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence            35666666665 478999999999999999999999884

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=87.07  E-value=0.82  Score=40.46  Aligned_cols=42  Identities=26%  Similarity=0.290  Sum_probs=32.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCC-CCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr-~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||++||++.++.               ++. ..+++.+++|.+..++
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~---------------~~~~~vs~~tr~rV~~~a~~   44 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLND---------------DPTLNVKEETKHRILEIAEK   44 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcC---------------CCCCCcCHHHHHHHHHHHHH
Confidence            37899999999999999999851               121 2578888888877765

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=87.00  E-value=2.5  Score=36.51  Aligned_cols=67  Identities=15%  Similarity=0.110  Sum_probs=48.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+..|||..||.-|.+    .|.+.|..+.+ .-+..++++.+.|..... .....++.+|++.|..
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~----~GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~   69 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQD----RGLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA   69 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            5788999999999999877654    58876644432 356888988777765554 3456789999888765

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.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=86.83  E-value=4.9  Score=28.72  Aligned_cols=42  Identities=21%  Similarity=0.442  Sum_probs=34.3

Q ss_pred             HHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ...|+..+. . +++..+||+.++++++||++-+++..+.|-+.
T Consensus        12 ~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~   55 (101)
T smart00347       12 QFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR   55 (101)
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence            344555443 3 48999999999999999999999999999774

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=86.82  E-value=1.2  Score=35.20  Aligned_cols=42  Identities=17%  Similarity=0.010  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         158 ATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       158 lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++..+.+.+..+++.+...|..+|++.|.           .+.|||+|.|+++
T Consensus        25 Ls~~Dv~v~~~LL~~~~~~tvdelae~ln-----------r~rStv~rsl~~L   66 (126)
T COG3355          25 LSELDVEVYKALLEENGPLTVDELAEILN-----------RSRSTVYRSLQNL   66 (126)
T ss_pred             CcHHHHHHHHHHHhhcCCcCHHHHHHHHC-----------ccHHHHHHHHHHH
Confidence            56677778888887888899999999884           3999999999875

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

Probab=86.64  E-value=1.4  Score=32.83  Aligned_cols=33  Identities=21%  Similarity=0.160  Sum_probs=30.8

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ...|..+||..+|+++.||++.+++..+.|-+.
T Consensus        46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~   78 (95)
T TIGR01610        46 DRVTATVIAELTGLSRTHVSDAIKSLARRRIIF   78 (95)
T ss_pred             CccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            468999999999999999999999999999885

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

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=86.63  E-value=1  Score=35.73  Aligned_cols=47  Identities=19%  Similarity=0.232  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHH-cC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         103 HIRLKIVEMAA-AG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       103 ~~R~rIV~l~~-~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      .+|..|..... .|  .+..+||+.++||+.+|.+.+++....|-+...+
T Consensus        10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~   59 (141)
T PRK11014         10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR   59 (141)
T ss_pred             HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence            56666665532 34  6789999999999999999999999999875443

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=86.50  E-value=3.9  Score=31.83  Aligned_cols=82  Identities=10%  Similarity=0.026  Sum_probs=51.2

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHHhhC
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV-EKRIEEYKKTNPGIFSWEIRDRLVKQDG  190 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~-~~~I~~l~~~~P~~t~~eI~~~L~~~~G  190 (230)
                      +.+..+..++|+.+|+|+.++.++.+++-  |..         |...-... .+....++ .+.+.+..+|+..    .|
T Consensus        22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~--G~s---------~~~~l~~~Rl~~A~~~L-~~t~~~i~eIA~~----~G   85 (127)
T PRK11511         22 LESPLSLEKVSERSGYSKWHLQRMFKKET--GHS---------LGQYIRSRKMTEIAQKL-KESNEPILYLAER----YG   85 (127)
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHH--CcC---------HHHHHHHHHHHHHHHHH-HcCCCCHHHHHHH----hC
Confidence            33458999999999999999999987643  221         11111111 11122333 2446677666653    68


Q ss_pred             CCCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898         191 ICDKNSAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       191 i~~~~~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                      ..      +.++..|.+++. |..|.
T Consensus        86 f~------s~s~F~r~Fkk~~G~tP~  105 (127)
T PRK11511         86 FE------SQQTLTRTFKNYFDVPPH  105 (127)
T ss_pred             CC------CHHHHHHHHHHHHCcCHH
Confidence            74      899999988665 66665

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=86.41  E-value=1.2  Score=31.72  Aligned_cols=23  Identities=9%  Similarity=0.226  Sum_probs=20.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      +...|++..+|+|++|+|++++.
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~   36 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKD   36 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHcc
Confidence            56789999999999999999874

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=86.28  E-value=1.3  Score=37.59  Aligned_cols=42  Identities=19%  Similarity=0.177  Sum_probs=36.5

Q ss_pred             cCCHHHHHHHHHHHHcC-------CCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAG-------VRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-------~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++..++.-+..+++.|       .+.++||+.||||++|++.-+++..
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe  203 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE  203 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            68888887777788888       7899999999999999999988754

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=86.27  E-value=0.63  Score=28.64  Aligned_cols=26  Identities=27%  Similarity=0.377  Sum_probs=22.8

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ...++|..++|+.++++..||++|..
T Consensus         7 ~~~~~s~~~la~~~~i~~~~i~~~~~   32 (56)
T smart00530        7 EEKGLTQEELAEKLGVSRSTLSRIEN   32 (56)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            34589999999999999999999963

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=86.26  E-value=1.1  Score=40.55  Aligned_cols=40  Identities=18%  Similarity=0.207  Sum_probs=33.3

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||++||++.++.                +...+++.+++|.+..++
T Consensus         2 TikDVA~~AGVS~sTVSrvln~----------------~~~Vs~eTr~kV~~a~~e   41 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLNG----------------SPYVSEETREKVLAAIKE   41 (333)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcC----------------CCCCCHHHHHHHHHHHHH
Confidence            6789999999999999999851                225688999999888876

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=86.23  E-value=0.64  Score=28.87  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=22.6

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+++..++|+.+++++.+|++|.+
T Consensus        10 ~~~~s~~~~a~~~~~~~~~v~~~~~   34 (58)
T cd00093          10 EKGLTQEELAEKLGVSRSTISRIEN   34 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4589999999999999999999964

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>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=86.13  E-value=2.6  Score=23.51  Aligned_cols=41  Identities=29%  Similarity=0.342  Sum_probs=27.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHH
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLL  207 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~L  207 (230)
                      +|..++++....+......  ..+..++.+.    +++       |.+||++++
T Consensus         2 r~~~~~~~~~~~i~~~~~~--~~s~~~ia~~----~~i-------s~~tv~~~~   42 (42)
T cd00569           2 RPPKLTPEQIEEARRLLAA--GESVAEIARR----LGV-------SRSTLYRYL   42 (42)
T ss_pred             CCCcCCHHHHHHHHHHHHc--CCCHHHHHHH----HCC-------CHHHHHHhC
Confidence            5666777777677666543  3477777653    454       999999864

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

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=86.09  E-value=0.8  Score=34.67  Aligned_cols=33  Identities=24%  Similarity=0.274  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHc-CCCHHHHhhhhccccchhhhH
Q psy1898         103 HIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       103 ~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kw  135 (230)
                      -.|.+||..+-. .+|.++|+..||+|..||.|=
T Consensus        47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG   80 (103)
T COG2973          47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRG   80 (103)
T ss_pred             HHHHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence            457888875555 599999999999999998753

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=85.99  E-value=1  Score=39.72  Aligned_cols=41  Identities=17%  Similarity=0.165  Sum_probs=31.8

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCC--CCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rp--r~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||.+||++.++.               ++  ..++++.+++|.+..++
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            4689999999999999999851               11  13578888888877766

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.

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

Probab=85.89  E-value=0.92  Score=32.79  Aligned_cols=67  Identities=24%  Similarity=0.396  Sum_probs=45.8

Q ss_pred             HHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC-CCCCCCC---CCCHHHHHHHHHHH
Q psy1898         104 IRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGSKPR---VATPDVEKRIEEYK  170 (230)
Q Consensus       104 ~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~-~gg~rpr---~lt~~~~~~I~~l~  170 (230)
                      +|..|+.++.  +.++..+|.+.++++.+++++-++.-.+.|-+.-.+ ..+++|+   .+|+.-++.+..++
T Consensus         1 vRl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~   73 (80)
T PF13601_consen    1 VRLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV   73 (80)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred             CHHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence            4677777543  459999999999999999999999999999774322 2234565   67777777766554

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=85.89  E-value=0.87  Score=32.23  Aligned_cols=31  Identities=23%  Similarity=0.300  Sum_probs=25.3

Q ss_pred             HHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         107 KIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       107 rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++-.+.. .|+|..++|+.+|||+.|+..|.+
T Consensus         5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk   36 (68)
T COG1476           5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEK   36 (68)
T ss_pred             HHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence            4444443 489999999999999999999964

>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=85.78  E-value=0.74  Score=31.07  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=19.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|..++++++++++|.+
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            3589999999999999999999974

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=85.74  E-value=0.94  Score=39.75  Aligned_cols=44  Identities=14%  Similarity=0.196  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .+.+.+|++++.+ | .+..++|+.|+||..||+|=++...+.|.+
T Consensus         4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l   49 (256)
T PRK10434          4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV   49 (256)
T ss_pred             HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            3566778887765 5 999999999999999999999999888865

>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=85.57  E-value=1.2  Score=29.96  Aligned_cols=36  Identities=25%  Similarity=0.207  Sum_probs=30.0

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ..|.+++.+++..+..++++.+    +       ||.+||+|-|..+
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~----~-------VS~~TiRRDl~~L   38 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEF----G-------VSEMTIRRDLNKL   38 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            5678888899999999998865    3       5999999988764

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

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=85.56  E-value=1.6  Score=31.77  Aligned_cols=29  Identities=24%  Similarity=0.322  Sum_probs=27.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      .|-.+||+.||+|+.+|.+-++.-++.|-
T Consensus        20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~   48 (79)
T COG1654          20 VSGEKLAEELGISRTAVWKHIQQLREEGV   48 (79)
T ss_pred             ccHHHHHHHHCccHHHHHHHHHHHHHhCC
Confidence            89999999999999999999999999994

>PRK09480 slmA division inhibitor protein; Provisional

Probab=85.52  E-value=1.3  Score=36.04  Aligned_cols=44  Identities=14%  Similarity=0.221  Sum_probs=34.3

Q ss_pred             cCCCcCCHHHHHHHHHH----H-Hc---CCCHHHHhhhhccccchhhhHHHH
Q psy1898          95 INGRPLPNHIRLKIVEM----A-AA---GVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        95 ~~g~~~s~~~R~rIV~l----~-~~---G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      ++.++-+.+.|.+|++.    + +.   +.|..+||++.|||++|+|.+-.-
T Consensus         2 ~~~~~~~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~   53 (194)
T PRK09480          2 AMKRPKKGERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS   53 (194)
T ss_pred             CCcCCCchhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence            45666677888888873    2 33   489999999999999999987543

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

Probab=85.51  E-value=0.39  Score=30.93  Aligned_cols=32  Identities=22%  Similarity=0.279  Sum_probs=20.5

Q ss_pred             ChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      ....|.+|++++.+|.+..+|++.++||+.++
T Consensus         3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv   34 (50)
T PF13384_consen    3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTV   34 (50)
T ss_dssp             -------HHHHHHHT--HHHHHHHHTS-HHHH
T ss_pred             chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHH
Confidence            36789999999999999999999999888775

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=85.34  E-value=0.96  Score=42.20  Aligned_cols=37  Identities=8%  Similarity=0.062  Sum_probs=30.2

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|..|...+. .+....++|+.||||++|+|+.+++|.
T Consensus       406 E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~  443 (445)
T TIGR02915       406 EREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHG  443 (445)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            4555666554 478999999999999999999999884

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).

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=85.32  E-value=1.1  Score=39.98  Aligned_cols=41  Identities=20%  Similarity=0.118  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+    .+++|..+||+.||||+.||..+..+..
T Consensus       250 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl  294 (298)
T TIGR02997       250 LTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKAL  294 (298)
T ss_pred             CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5556655555444    3689999999999999999999988754

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=85.25  E-value=5.4  Score=29.66  Aligned_cols=81  Identities=12%  Similarity=0.018  Sum_probs=51.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVA-TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGI  191 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~l-t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi  191 (230)
                      .+..+..++|+.+++|+.++.+..+++  +|..         |... ...-.+....++ .+++.+..+|+..    .|.
T Consensus        19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~--~g~s---------~~~~i~~~Rl~~a~~~L-~~~~~~i~~iA~~----~Gf   82 (107)
T PRK10219         19 DQPLNIDVVAKKSGYSKWYLQRMFRTV--THQT---------LGDYIRQRRLLLAAVEL-RTTERPIFDIAMD----LGY   82 (107)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH--HCcC---------HHHHHHHHHHHHHHHHH-HccCCCHHHHHHH----HCC
Confidence            345899999999999999999888765  2321         1111 111112223333 3456777766653    687


Q ss_pred             CCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898         192 CDKNSAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       192 ~~~~~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                      .      +.+...+.+++. |..|.
T Consensus        83 ~------~~s~f~~~Fk~~~G~tP~  101 (107)
T PRK10219         83 V------SQQTFSRVFRRQFDRTPS  101 (107)
T ss_pred             C------CHHHHHHHHHHHHCcCHH
Confidence            4      899999999776 66654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=85.24  E-value=1.3  Score=39.62  Aligned_cols=41  Identities=22%  Similarity=0.134  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-+...+-  +|+|..+||+.||||..||.++..+..
T Consensus       228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al  270 (289)
T PRK07500        228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARAL  270 (289)
T ss_pred             CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44444443333333  689999999999999999999988744

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=85.21  E-value=0.61  Score=33.28  Aligned_cols=40  Identities=30%  Similarity=0.351  Sum_probs=26.0

Q ss_pred             HHHHHHHHHhCC----CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNP----GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P----~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      ++.|.+++.++|    ..+..||++.    .+       ||.+||.|+.++.|++
T Consensus        18 e~~Ia~yil~~~~~~~~~si~elA~~----~~-------vS~sti~Rf~kkLG~~   61 (77)
T PF01418_consen   18 EKKIADYILENPDEIAFMSISELAEK----AG-------VSPSTIVRFCKKLGFS   61 (77)
T ss_dssp             HHHHHHHHHH-HHHHCT--HHHHHHH----CT-------S-HHHHHHHHHHCTTT
T ss_pred             HHHHHHHHHhCHHHHHHccHHHHHHH----cC-------CCHHHHHHHHHHhCCC
Confidence            345666666666    4666666653    44       5999999999999986

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=85.04  E-value=1.2  Score=40.60  Aligned_cols=41  Identities=12%  Similarity=0.092  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHH----HHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEM----AAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l----~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...    +.+|+|..+||+.+|||.+||..++.+..
T Consensus       263 L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl  307 (325)
T PRK05657        263 LNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEAL  307 (325)
T ss_pred             CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            555566555432    25789999999999999999999988744

>PF13309 HTH_22: HTH domain

Probab=84.98  E-value=2.2  Score=29.49  Aligned_cols=48  Identities=19%  Similarity=0.173  Sum_probs=30.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR  208 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr  208 (230)
                      .+..++.+++..|.+.+.++--.-...-.+.+.+..|+       |..||++.|+
T Consensus        17 ~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~i-------S~~TVY~YLr   64 (64)
T PF13309_consen   17 PPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGI-------SRATVYRYLR   64 (64)
T ss_pred             ChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCC-------CHHHHHHHcC
Confidence            45566788888888888665433333333333343565       9999999985

>TIGR01453 grpIintron_endo group I intron endonuclease

Probab=84.96  E-value=5  Score=34.29  Aligned_cols=41  Identities=24%  Similarity=0.351  Sum_probs=31.3

Q ss_pred             CCcCCHHHHHHHHHHHHcC----------------CCHHHHhhhhccccchhhhHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAG----------------VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G----------------~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      |+..+.+.+.++-...+.+                -|..++|+.|+|++.||.++++
T Consensus       145 gk~~s~e~k~k~s~~~k~~~~v~vyd~~~~~~~~F~S~~eAa~~l~i~~~tI~~~l~  201 (214)
T TIGR01453       145 GKKHSEETKKKISEKEKGAKKVNVYDKNNGLLIIFDSIAEAARHLGISRGTISKYIK  201 (214)
T ss_pred             cccCCHHHHHHHHHhhcCCceeEEEECCCCcEEEecCHHHHHHHhCCCHHHHHHHHc
Confidence            7778888888875433221                4789999999999999887764

This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.

>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.95  E-value=0.92  Score=36.61  Aligned_cols=43  Identities=23%  Similarity=0.326  Sum_probs=33.4

Q ss_pred             HHHHHHH-HHHHcCCCHHHHhhhhc-cccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIV-EMAAAGVRPCVISRQLR-VSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV-~l~~~G~s~~~IAr~lg-VS~sTV~kwikRy~e~G~v  145 (230)
                      |+|...+ +++.+|+|.++||++|| ||++.|---+.|..-.|.-
T Consensus         5 dERve~LkKLWseGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR~   49 (169)
T COG5352           5 DERVETLKKLWSEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGRA   49 (169)
T ss_pred             HHHHHHHHHHHHcccCHHHHHHHhcCcchhhhheeeeeccccccC
Confidence            5665555 48899999999999998 8999887777776655543

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

Probab=84.85  E-value=0.86  Score=32.74  Aligned_cols=30  Identities=27%  Similarity=0.417  Sum_probs=21.8

Q ss_pred             HHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         108 IVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       108 IV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      |....+ .|+|..++|+.+||++++|++..+
T Consensus        23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   23 IRELREERGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence            334444 489999999999999999999874

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=84.63  E-value=3.9  Score=35.55  Aligned_cols=45  Identities=13%  Similarity=0.197  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +.=.+|++++..  +++.++||+++|++++||++.++-..+.|-+..
T Consensus        14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~   60 (257)
T PRK15090         14 LKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ   60 (257)
T ss_pred             HHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            333566766643  489999999999999999999999999998753

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=84.60  E-value=1.2  Score=43.58  Aligned_cols=40  Identities=8%  Similarity=0.016  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ...|..|...++ .+....++|+.||||++|+|+++++|..
T Consensus       496 ~~Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~  536 (538)
T PRK15424        496 RLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEAK  536 (538)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            345666666554 5788999999999999999999998853

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=84.57  E-value=1.1  Score=39.37  Aligned_cols=38  Identities=21%  Similarity=0.304  Sum_probs=28.1

Q ss_pred             HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      ++||+..|||.+||++.++.               ++ ..+++.+++|.+..++
T Consensus         2 ~dIA~~agVS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~~   39 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINK---------------DR-FVSEAITAKVEAAIKE   39 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            68999999999999999851               11 2467777777666654

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=84.53  E-value=3.1  Score=36.42  Aligned_cols=45  Identities=18%  Similarity=0.269  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         102 NHIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       102 ~~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.-..|++.+.+   +.+..+||+.++++++||++.++...+.|-+.
T Consensus        10 l~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~   57 (263)
T PRK09834         10 LSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR   57 (263)
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3444667776643   38999999999999999999999999999875

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=84.51  E-value=1.1  Score=35.01  Aligned_cols=31  Identities=13%  Similarity=0.164  Sum_probs=25.4

Q ss_pred             HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++..+. +.|+|..++|+..|||++|+++|.+
T Consensus         9 ~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~   40 (120)
T PRK13890          9 NVLRLLDERHMTKKELSERSGVSISFLSDLTT   40 (120)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            344433 5699999999999999999999974

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=84.50  E-value=1.4  Score=35.34  Aligned_cols=42  Identities=24%  Similarity=0.219  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .++..+ ..++.++.+|.+.++||+.+++|.+||...+.+.++
T Consensus       137 ~Lt~~E-~~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~  178 (196)
T PRK10360        137 PLTKRE-RQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLME  178 (196)
T ss_pred             CCCHHH-HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            344433 367778888999999999999999999999888654

>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=84.32  E-value=0.74  Score=31.91  Aligned_cols=22  Identities=14%  Similarity=0.139  Sum_probs=17.7

Q ss_pred             CCHHHHhhhhccccchhh-hHHH
Q psy1898         116 VRPCVISRQLRVSHGCVS-KILN  137 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~-kwik  137 (230)
                      .+..++|+.+|||++||+ .|.+
T Consensus        13 ~~~~~lA~~lgis~st~s~~~~~   35 (66)
T PF07022_consen   13 KSDKELAERLGISKSTLSNNWKK   35 (66)
T ss_dssp             SSCHHHHCCTT--HHHHH-HHHH
T ss_pred             CCHHHHHHHhCcCHHHhhHHHHh
Confidence            567799999999999999 8876

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=84.27  E-value=1.1  Score=40.85  Aligned_cols=35  Identities=11%  Similarity=0.016  Sum_probs=28.2

Q ss_pred             HHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         105 RLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       105 R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      |.-|...++ .+....++|+.||||++|+|+++++|
T Consensus       294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~  329 (329)
T TIGR02974       294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLRKH  329 (329)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            444444444 47899999999999999999999876

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

>PRK00215 LexA repressor; Validated

Probab=84.23  E-value=1.7  Score=36.44  Aligned_cols=32  Identities=25%  Similarity=0.258  Sum_probs=29.4

Q ss_pred             CCHHHHhhhhcc-ccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRV-SHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgV-S~sTV~kwikRy~e~G~v~p  147 (230)
                      .+.++||+.+++ +++||++++++..+.|.+..
T Consensus        24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~   56 (205)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERKGFIRR   56 (205)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence            588899999999 99999999999999998743

>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27

Probab=84.21  E-value=3.1  Score=34.48  Aligned_cols=48  Identities=17%  Similarity=0.297  Sum_probs=33.8

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhh---CCCCCCCCCCHhHHHHHHHcC
Q psy1898         157 VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQD---GICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       157 ~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~---Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+++++++.+...+.++ ..|..++.+.|.+..   |..     ||+|+|||+-.+.
T Consensus         9 ~LP~eir~~l~~~L~~~-~~t~~ei~~~~~~~~~~~g~~-----iSrSav~RY~~~~   59 (180)
T PF11985_consen    9 LLPPEIREWLDQMLRDG-GFTQYEILAEWLEELAEEGYD-----ISRSAVHRYAQRF   59 (180)
T ss_pred             hCCHHHHHHHHHHHHhC-CCChHHHHHHHHHhhhccCCC-----cCHHHHHHHHHHH
Confidence            56788999998877555 455555555554535   664     8999999987654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=84.12  E-value=1.3  Score=38.32  Aligned_cols=42  Identities=14%  Similarity=0.216  Sum_probs=36.0

Q ss_pred             HHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      =..|++++..   +++.++||+.+|++++||++.++-..+.|-+.
T Consensus        11 al~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~   55 (248)
T TIGR02431        11 GLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT   55 (248)
T ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3566776653   59999999999999999999999999999875

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=84.03  E-value=3.7  Score=32.43  Aligned_cols=55  Identities=20%  Similarity=0.182  Sum_probs=39.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCC-CCCCCCHHHHHHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGS-KPRVATPDVEKRIE  167 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~-rpr~lt~~~~~~I~  167 (230)
                      ..+.+..+||+.++++++||++.+++..+.|-+...  +..++ .--.+|++-.+.+.
T Consensus        52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~  109 (144)
T PRK11512         52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE  109 (144)
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence            346999999999999999999999999999977322  22221 22355665554443

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=83.98  E-value=1.1  Score=38.32  Aligned_cols=33  Identities=27%  Similarity=0.199  Sum_probs=29.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |-.++|++||||+.||.+=++.-.+.|.+....
T Consensus        26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   58 (233)
T TIGR02404        26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQ   58 (233)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            788999999999999999999999999875443

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.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=83.96  E-value=1.8  Score=31.53  Aligned_cols=68  Identities=12%  Similarity=0.041  Sum_probs=47.6

Q ss_pred             HHHHHHHHhcCC-ChhhhhhhhcccccccccCCcccCC-CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhh
Q psy1898          61 RLKIVEMAAAGV-RPCVISRQLRVSHGVNQLGGVFING-RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSK  134 (230)
Q Consensus        61 r~~I~e~~~~g~-~~~~isr~lrvshg~~~l~~~~~~g-~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~k  134 (230)
                      +.+|+|++..|. +..++++.++||-..+..  ....+ ...+.+.|.+|..+++    +...|+.+....+|-.+
T Consensus         8 ~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr--~L~~~~~~Vs~~Tr~rV~~aa~----~n~~Ar~l~~~~~~~~~   77 (80)
T TIGR02844         8 VLEIGKYIVETKATVRETAKVFGVSKSTVHK--DVTERLPEINPELAEEVKEVLD----LNKAERHIRGGKATKLK   77 (80)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH--HhcCCCCCCCHHHHHHHHHHHc----cCHHHHHhhccchHHHH
Confidence            567888887765 788899999987777632  11112 3588999999999888    35667766665555433

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=83.94  E-value=1.9  Score=35.12  Aligned_cols=41  Identities=17%  Similarity=0.168  Sum_probs=34.6

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      -++.+.+|...+++|+.++..+|++.+    |       +|.+||++.++++
T Consensus        12 lD~~D~~IL~~Lq~d~R~s~~eiA~~l----g-------lS~~tv~~Ri~rL   52 (164)
T PRK11169         12 LDRIDRNILNELQKDGRISNVELSKRV----G-------LSPTPCLERVRRL   52 (164)
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            456788888999999999999998865    4       4999999998876

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=83.68  E-value=8.3  Score=33.56  Aligned_cols=104  Identities=19%  Similarity=0.136  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCC---C----------CCCCHHHHHHH
Q psy1898         102 NHIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK---P----------RVATPDVEKRI  166 (230)
Q Consensus       102 ~~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~r---p----------r~lt~~~~~~I  166 (230)
                      ...|.+|....+.  |.+..|+.+.+++.++|..=-++.....+.++...-+|..   |          ..+..+..+.|
T Consensus       100 ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k~I  179 (240)
T COG3398         100 NSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSKAI  179 (240)
T ss_pred             hhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHHHH
Confidence            3678999988764  7999999999999999987777776666655433322210   1          12223345677


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH---cCCCCCCC
Q psy1898         167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR---GGRRDDCD  216 (230)
Q Consensus       167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr---~~g~~~~~  216 (230)
                      ...+++++..+..+|+..+    +       +|..||.=.++   ..|+.+..
T Consensus       180 ~~eiq~~~~~t~~~ia~~l----~-------ls~aTV~~~lk~l~~~Gii~~~  221 (240)
T COG3398         180 IYEIQENKCNTNLLIAYEL----N-------LSVATVAYHLKKLEELGIIPED  221 (240)
T ss_pred             HHHHhcCCcchHHHHHHHc----C-------ccHHHHHHHHHHHHHcCCCccc
Confidence            7888889999998888755    3       49999986655   45777764

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=83.52  E-value=1.2  Score=43.09  Aligned_cols=37  Identities=19%  Similarity=0.252  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|.-+..++....+.+++|+.||||++|+|+.+++|.
T Consensus       475 E~~~i~~~l~~~~~~~~aA~~LGisr~tL~rkl~~~g  511 (520)
T PRK10820        475 ERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYG  511 (520)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence            4444555666555899999999999999999999885

>cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm)

Probab=83.30  E-value=4.7  Score=31.24  Aligned_cols=67  Identities=22%  Similarity=0.341  Sum_probs=46.2

Q ss_pred             cCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHc----------------
Q psy1898          51 INGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAA----------------  114 (230)
Q Consensus        51 ~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~----------------  114 (230)
                      +=|+..++++|..|.+.- .|.                 ...+|  |+..|.+.+.+|-+....                
T Consensus        17 ~~Gk~hseetk~kms~~~-~G~-----------------~n~~y--Gk~~s~Etk~k~s~~~~g~kn~~~k~~~~~~ng~   76 (113)
T cd00283          17 MFGKTHSEETKAKISKNR-SGE-----------------NNPMF--GKKHSDETKAKISAKKKGRKNLNAKKKQSDTDGY   76 (113)
T ss_pred             ccCccCCHHHHHHHHHHh-cCC-----------------CCccc--CccCCHHHHHHHHHHHcCCCCCCcceEEEeCCCC
Confidence            557888899888877553 221                 11222  666777777777665421                


Q ss_pred             -C--CCHHHHhhhhccccchhhhHHH
Q psy1898         115 -G--VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       115 -G--~s~~~IAr~lgVS~sTV~kwik  137 (230)
                       .  -|..++|+.|+++.+||.+++.
T Consensus        77 i~~F~S~~EAar~lgi~~~tIs~~~~  102 (113)
T cd00283          77 IGIFDSTTEAARFLKVHSGTISKNIK  102 (113)
T ss_pred             eEEeCCHHHHHHHHCCCcchhHHHHC
Confidence             1  4889999999999999999853

Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit

>TIGR00647 MG103 conserved hypothetical protein

Probab=83.22  E-value=2  Score=38.47  Aligned_cols=46  Identities=24%  Similarity=0.086  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+..+.+..++.++|++++.|+.+.|...++..     +|.|+|+.+|++.
T Consensus       229 p~~L~~~a~lRl~~Pd~SL~ELgell~~~~~~~-----isKSgvnhRlrKl  274 (279)
T TIGR00647       229 PLNFQRICLLKIDHPDWSLEQIAEFFASKYKVK-----ISRSGIQHRLRKL  274 (279)
T ss_pred             CHHHHHHHHHHHhCcccCHHHHHHHhccCCCCC-----cCHHHHHHHHHHH
Confidence            344567777888999999999999985323343     7999999999874

>PRK10403 transcriptional regulator NarP; Provisional

Probab=83.22  E-value=1.6  Score=34.99  Aligned_cols=40  Identities=18%  Similarity=0.184  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++.... .|+.++..|.+.++||+.+++|..||...+++-.
T Consensus       154 Lt~~e~-~vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~  193 (215)
T PRK10403        154 LTEREL-DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLL  193 (215)
T ss_pred             CCHHHH-HHHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence            554444 5778888999999999999999999999888754

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=83.21  E-value=1.5  Score=38.03  Aligned_cols=41  Identities=20%  Similarity=0.195  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|..+ ..|+.+..+|+|..+||..|+||..||..-++.-.
T Consensus       179 ~LT~rE-~evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~  219 (240)
T PRK10188        179 NFSKRE-KEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ  219 (240)
T ss_pred             CCCHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            455444 46777889999999999999999999998887754

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=83.13  E-value=1  Score=29.97  Aligned_cols=36  Identities=25%  Similarity=0.261  Sum_probs=26.5

Q ss_pred             CCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          53 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        53 g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      |.+|+++.+-+|.-|.+.|++..+|+++++.|+.|.
T Consensus         2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~I   37 (50)
T PF11427_consen    2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCI   37 (50)
T ss_dssp             S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHH
T ss_pred             CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHH
Confidence            678999999999999999999999999999999886

>PRK06424 transcription factor; Provisional

Probab=83.11  E-value=1.5  Score=35.51  Aligned_cols=31  Identities=3%  Similarity=0.060  Sum_probs=25.1

Q ss_pred             HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +|-.+. +.|+|..++|+.+|++.+||++|.+
T Consensus        88 ~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~  119 (144)
T PRK06424         88 LVKNARERLSMSQADLAAKIFERKNVIASIER  119 (144)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            333333 3599999999999999999999964

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=83.00  E-value=5.2  Score=30.04  Aligned_cols=62  Identities=15%  Similarity=0.104  Sum_probs=43.0

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh-CCC-CcCCCC--CCCCCCCCHHHHHHH
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI-RPGVIG--GSKPRVATPDVEKRI  166 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~-G~v-~p~~~g--g~rpr~lt~~~~~~I  166 (230)
                      ..+++..+.+-.|.+..|+.++||++||++-+++.++. |.. -.+..+  +++...+|+.-++.+
T Consensus         6 ~l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~   71 (99)
T TIGR00637         6 RVALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI   71 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence            34566666666799999999999999999999998854 432 222211  134667777766554

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.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=82.85  E-value=0.97  Score=36.76  Aligned_cols=32  Identities=9%  Similarity=0.185  Sum_probs=29.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++..+||..+|+++.||++.++++++.|.+.-
T Consensus       144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~  175 (193)
T TIGR03697       144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI  175 (193)
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            68999999999999999999999999998753

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.

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=82.53  E-value=1.2  Score=30.99  Aligned_cols=39  Identities=26%  Similarity=0.407  Sum_probs=30.2

Q ss_pred             HHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         108 IVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       108 IV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      |.+.++ .| .|..+||++|++++.+|..-+..+..-|.++
T Consensus         5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~   45 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR   45 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            444343 34 8999999999999999999999999999773

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=82.48  E-value=1.4  Score=43.55  Aligned_cols=39  Identities=13%  Similarity=0.129  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|..|..+++ .+....++|+.||||++|+|+-+++|.
T Consensus       590 ~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~  629 (638)
T PRK11388        590 ELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHG  629 (638)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcC
Confidence            445666777665 578899999999999999999999886

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=82.29  E-value=2.2  Score=36.76  Aligned_cols=50  Identities=20%  Similarity=0.333  Sum_probs=37.2

Q ss_pred             HHHHHHHHH-HHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC
Q psy1898         103 HIRLKIVEM-AAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG  152 (230)
Q Consensus       103 ~~R~rIV~l-~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg  152 (230)
                      .++..|+.. +..|  + +-.++|++||||+++|.--+++....|.+...+..|
T Consensus        18 ~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G   71 (254)
T PRK09464         18 QLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGG   71 (254)
T ss_pred             HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            445555542 3335  4 678999999999999999999999999876554433

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.29  E-value=1.9  Score=32.91  Aligned_cols=40  Identities=13%  Similarity=0.115  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ++...+.=+-..+....|..+||..|+||++.||.-++|-
T Consensus        18 LT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~   57 (105)
T COG2739          18 LTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRT   57 (105)
T ss_pred             HhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHH
Confidence            3334444444456778999999999999999999999873

>PRK13870 transcriptional regulator TraR; Provisional

Probab=82.28  E-value=1.7  Score=37.55  Aligned_cols=41  Identities=17%  Similarity=-0.030  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++|.-+ ..++.+..+|+|..|||..|+||..||..-++.-+
T Consensus       173 ~LT~RE-~E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~  213 (234)
T PRK13870        173 WLDPKE-ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM  213 (234)
T ss_pred             CCCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455443 46777888999999999999999999998887654

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=82.22  E-value=2.3  Score=36.25  Aligned_cols=35  Identities=14%  Similarity=0.168  Sum_probs=30.5

Q ss_pred             C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         116 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       116 ~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      + |-.++|++||||++||..=+++-...|.+...+.
T Consensus        31 LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g   66 (239)
T PRK04984         31 LPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG   66 (239)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            5 6889999999999999999999999998754443

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=82.17  E-value=3.7  Score=36.08  Aligned_cols=36  Identities=22%  Similarity=0.256  Sum_probs=30.4

Q ss_pred             HHH-HHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         107 KIV-EMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       107 rIV-~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      ++. ..++.|.|.+.+|+.++||+++|++.+++.++.
T Consensus         7 ~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~   43 (309)
T PRK12682          7 RFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEE   43 (309)
T ss_pred             HHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHH
Confidence            344 455667899999999999999999999999855

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

Probab=82.09  E-value=1.7  Score=37.61  Aligned_cols=52  Identities=12%  Similarity=0.161  Sum_probs=37.4

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI  166 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I  166 (230)
                      +.|..++|+.+++|++||++++++..+.|-+.....+...--.+|+.-.+.+
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            3789999999999999999999999999987432211123334555544443

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=82.03  E-value=6.6  Score=34.54  Aligned_cols=44  Identities=14%  Similarity=0.121  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.=..|++++..   +++..+||+.++++++||++.++-..+.|-+.
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~   71 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY   71 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            444667777653   48999999999999999999999999999874

>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family

Probab=81.87  E-value=6.5  Score=31.05  Aligned_cols=24  Identities=4%  Similarity=0.043  Sum_probs=21.5

Q ss_pred             cCCCHHHHhhhhccccchhhhHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      -|.+..+++..++||++|+++|.+
T Consensus        35 l~ls~~el~~~lgis~~Tl~R~~~   58 (133)
T TIGR02293        35 LAIGKAEIFKATGIPKATLQRRKM   58 (133)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHhh
Confidence            378999999999999999999975

Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.

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

Probab=81.86  E-value=1.1  Score=34.44  Aligned_cols=25  Identities=12%  Similarity=0.032  Sum_probs=22.6

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|++..++|+.+|++++||++|.+
T Consensus        76 ~~gltq~~lA~~lg~~~~tis~~e~  100 (127)
T TIGR03830        76 KLGLSQREAAELLGGGVNAFSRYER  100 (127)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4599999999999999999999953

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.

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=81.85  E-value=1.9  Score=42.06  Aligned_cols=38  Identities=18%  Similarity=0.220  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++..|..+++ .+-+...+|+.||||++|+|+|+++|.
T Consensus       520 ~Ek~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk~~  558 (560)
T COG3829         520 YEKHLIREALERHGGNKSKAAKELGISRTTLYRKLKKYG  558 (560)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhc
Confidence            34444445554 467999999999999999999999985

>PRK11569 transcriptional repressor IclR; Provisional

Probab=81.70  E-value=2.1  Score=37.77  Aligned_cols=44  Identities=23%  Similarity=0.345  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.=..|++++.+   +++.++||+.+|++++||++.+.-..+.|-+.
T Consensus        28 ~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~   74 (274)
T PRK11569         28 TRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR   74 (274)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            444567776653   48999999999999999999999999999874

>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=81.67  E-value=1.5  Score=30.61  Aligned_cols=34  Identities=24%  Similarity=0.316  Sum_probs=28.3

Q ss_pred             HcC--CCHHHHhhhhccc-cchhhhHHHHHhhhCCCC
Q psy1898         113 AAG--VRPCVISRQLRVS-HGCVSKILNRYQETGSIR  146 (230)
Q Consensus       113 ~~G--~s~~~IAr~lgVS-~sTV~kwikRy~e~G~v~  146 (230)
                      +.|  -|.+|||+.||++ ++||+.-++.-.+-|.+.
T Consensus        21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen   21 ENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             HHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred             HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence            346  5778999999995 999999999999999875

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.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=81.58  E-value=2.9  Score=33.08  Aligned_cols=31  Identities=19%  Similarity=0.297  Sum_probs=29.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.++||+.++||++||++.+++..+.|.+.
T Consensus        23 ~~~~ela~~l~vs~~svs~~l~~L~~~Gli~   53 (142)
T PRK03902         23 ARVSDIAEALSVHPSSVTKMVQKLDKDEYLI   53 (142)
T ss_pred             cCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence            8899999999999999999999999999774

>PRK15115 response regulator GlrR; Provisional

Probab=81.53  E-value=1.7  Score=40.51  Aligned_cols=37  Identities=11%  Similarity=-0.033  Sum_probs=30.6

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|..|..+++ .+....++|+.||||++|+|+-+++|.
T Consensus       399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~  436 (444)
T PRK15115        399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHE  436 (444)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            4555666554 478999999999999999999999985

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=81.49  E-value=3.1  Score=28.94  Aligned_cols=40  Identities=18%  Similarity=0.051  Sum_probs=30.9

Q ss_pred             HHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         165 RIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       165 ~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +|...+.+.. .++.++|++.|.. .|..     +|..||.|.|+..
T Consensus         2 ~IL~~L~~~~~P~g~~~l~~~L~~-~g~~-----~se~avRrrLr~m   42 (66)
T PF08461_consen    2 FILRILAESDKPLGRKQLAEELKL-RGEE-----LSEEAVRRRLRAM   42 (66)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHh-cChh-----hhHHHHHHHHHHH
Confidence            4555555544 5899999999987 6874     8999999988764

>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]

Probab=81.45  E-value=1.7  Score=36.88  Aligned_cols=47  Identities=26%  Similarity=0.352  Sum_probs=40.2

Q ss_pred             CcCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898          98 RPLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      .+...+....|..++..+ .+..++|+.++++..||++|.+.....+.
T Consensus       159 ~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~  206 (222)
T COG1961         159 RKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG  206 (222)
T ss_pred             ccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhhhcccc
Confidence            556667788888899999 79999999999999999999988765554

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=81.37  E-value=3.2  Score=35.72  Aligned_cols=37  Identities=16%  Similarity=0.175  Sum_probs=31.5

Q ss_pred             C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC
Q psy1898         116 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG  152 (230)
Q Consensus       116 ~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg  152 (230)
                      + +-.++|+.||||+++|.-=+++-...|.+.-.+..|
T Consensus        31 LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G   68 (251)
T PRK09990         31 LPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRG   68 (251)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            6 678999999999999999999999999875544433

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=81.25  E-value=2.1  Score=36.35  Aligned_cols=33  Identities=15%  Similarity=0.256  Sum_probs=29.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |-.++|++|+||+.||.+=++.-.+.|.+....
T Consensus        34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   66 (238)
T TIGR02325        34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ   66 (238)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            788999999999999999999999999875443

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.

>COG5566 Uncharacterized conserved protein [Function unknown]

Probab=81.23  E-value=2  Score=34.13  Aligned_cols=50  Identities=14%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      |++.|-..-..+|..-+..--+|.+..++|+.+.+|..+||++++|+...
T Consensus        80 YlP~G~s~r~t~Rn~~ifsd~dG~n~~eLaKkYrlS~~~Iy~VIrr~~t~  129 (137)
T COG5566          80 YLPKGDSIRATLRNKQIFSDFDGSNYVELAKKYRLSENHIYRVIRRTHTS  129 (137)
T ss_pred             EeeCchHHHHHHHHHHHHHhcCCccHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            33334333445665555555569999999999999999999999986643

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=81.20  E-value=2.1  Score=34.33  Aligned_cols=34  Identities=24%  Similarity=0.211  Sum_probs=29.4

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++.++.+|++..+||+.+++|..||..++.+-+
T Consensus       156 ~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~  189 (210)
T PRK09935        156 TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIY  189 (210)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4455677899999999999999999999998855

>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=81.15  E-value=1.3  Score=30.15  Aligned_cols=30  Identities=13%  Similarity=0.122  Sum_probs=26.2

Q ss_pred             hHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          59 HIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        59 ~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      +.|.++..|+..|+++.+|+..|+++..++
T Consensus         1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV   30 (58)
T PF06056_consen    1 EVKEQARSLYLQGWSIKEIAEELGVPRSTV   30 (58)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHCCChHHH
Confidence            368889999999999999999999876655

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

>PRK14999 histidine utilization repressor; Provisional

Probab=81.01  E-value=2.3  Score=36.55  Aligned_cols=33  Identities=12%  Similarity=0.105  Sum_probs=29.7

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |-.++|++||||+.||.+=+..-.+.|.+...+
T Consensus        38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   70 (241)
T PRK14999         38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ   70 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            789999999999999999999999999875443

>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=80.98  E-value=2.7  Score=27.44  Aligned_cols=35  Identities=23%  Similarity=0.255  Sum_probs=24.3

Q ss_pred             HHHHHH-HhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         165 RIEEYK-KTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       165 ~I~~l~-~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .|..++ +.++.++..+|++.|    +       ||..||++.|+..
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l----~-------vS~rTi~~~i~~L   39 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEEL----G-------VSRRTIRRDIKEL   39 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHC----T-------S-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHh----C-------CCHHHHHHHHHHH
Confidence            344444 555569999998865    3       5999999988764

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 ....

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=80.97  E-value=1.9  Score=40.62  Aligned_cols=37  Identities=11%  Similarity=0.035  Sum_probs=30.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .|.-|..+++ .+....++|+.||||++|+|+.+++|.
T Consensus       430 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~~  467 (469)
T PRK10923        430 ERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELG  467 (469)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            4555666554 478999999999999999999999884

>PRK04841 transcriptional regulator MalT; Provisional

Probab=80.79  E-value=1.9  Score=43.73  Aligned_cols=44  Identities=20%  Similarity=0.397  Sum_probs=36.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH-HhhhC
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR-YQETG  143 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR-y~e~G  143 (230)
                      ++|.. -.+|+.++.+|+|.++||..++||.+||...+++ |..-|
T Consensus       838 ~lt~~-e~~v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~  882 (903)
T PRK04841        838 PLTQR-EWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG  882 (903)
T ss_pred             CCCHH-HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            45533 3578888999999999999999999999999888 66665

>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species

Probab=80.73  E-value=1.8  Score=36.04  Aligned_cols=36  Identities=19%  Similarity=0.281  Sum_probs=31.9

Q ss_pred             HHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         109 VEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       109 V~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      |.++.+| ++-.+||..+|||+..|.+..++|.....
T Consensus        12 i~yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~   48 (181)
T PF04645_consen   12 IFYFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSED   48 (181)
T ss_pred             HHHHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCC
Confidence            4567788 99999999999999999999999987664

>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=80.67  E-value=1.2  Score=33.32  Aligned_cols=26  Identities=15%  Similarity=0.249  Sum_probs=22.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+.+.+|+..||+.+||+||..-|.
T Consensus        23 ~~gq~~vA~~~Gv~eStISR~k~~~~   48 (91)
T PF05269_consen   23 SVGQKKVAEAMGVDESTISRWKNDFI   48 (91)
T ss_dssp             HHHHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred             HHhhHHHHHHhCCCHHHHHHHHhhHH
Confidence            35788999999999999999976543

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=80.55  E-value=3.3  Score=33.24  Aligned_cols=40  Identities=18%  Similarity=0.119  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++.+..|...+++|+..+..+|++.|    |       +|.+||++.++++
T Consensus         8 D~~D~~Il~~Lq~d~R~s~~eiA~~l----g-------lS~~tV~~Ri~rL   47 (153)
T PRK11179          8 DNLDRGILEALMENARTPYAELAKQF----G-------VSPGTIHVRVEKM   47 (153)
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            34677888888899999999999876    4       4999999998876

>PRK12423 LexA repressor; Provisional

Probab=80.42  E-value=2.8  Score=35.34  Aligned_cols=45  Identities=22%  Similarity=0.254  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHH-----cCC--CHHHHhhhhc-cccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAA-----AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~-----~G~--s~~~IAr~lg-VS~sTV~kwikRy~e~G~v~p  147 (230)
                      ..|..|++.+.     .|.  |.++||++|| +|++||++.+++..+.|.+..
T Consensus         6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~   58 (202)
T PRK12423          6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV   58 (202)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence            34555555332     344  9999999999 599999999999999997743

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=80.41  E-value=0.97  Score=35.88  Aligned_cols=40  Identities=25%  Similarity=0.373  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      +..-+++.|.+.|++..+||+.|+-++.-|+-+.++.+++
T Consensus        11 e~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA~en   50 (143)
T COG1356          11 EQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRALEN   50 (143)
T ss_pred             hhheeeeehhhccccHHHHHHHHccchhhHHHHHHHHHHH
Confidence            4455677789999999999999999999999999987654

>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=80.40  E-value=0.79  Score=31.64  Aligned_cols=31  Identities=32%  Similarity=0.527  Sum_probs=28.4

Q ss_pred             ChhHHHHHHHHHhcCCChhhhhhhhcccccc
Q psy1898          57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGV   87 (230)
Q Consensus        57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~   87 (230)
                      |+++...|++++..|++|++|--.||-+||+
T Consensus        30 ~~eVe~~I~klakkG~tpSqIG~iLRD~~GI   60 (60)
T PF08069_consen   30 PEEVEELIVKLAKKGLTPSQIGVILRDQYGI   60 (60)
T ss_dssp             HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence            4888899999999999999999999988884

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=80.38  E-value=7.3  Score=29.35  Aligned_cols=33  Identities=12%  Similarity=0.300  Sum_probs=30.3

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ++.+..+||..++++++||++.+++..+.|-+.
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~   74 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS   74 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence            359999999999999999999999999999763

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.

>PRK03837 transcriptional regulator NanR; Provisional

Probab=80.29  E-value=1.6  Score=37.29  Aligned_cols=34  Identities=12%  Similarity=0.079  Sum_probs=30.1

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      +..++|++||||++||..-+.+....|-+.-.+.
T Consensus        39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~   72 (241)
T PRK03837         39 SERELMAFFGVGRPAVREALQALKRKGLVQISHG   72 (241)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            7889999999999999999999999998754443

>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional

Probab=80.13  E-value=4.9  Score=34.86  Aligned_cols=36  Identities=8%  Similarity=0.131  Sum_probs=29.5

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      +++..+.+-.|.+.+|+.+++|+++|++++++.++.
T Consensus         7 ~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~   42 (296)
T PRK09906          7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENC   42 (296)
T ss_pred             HHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence            444444444599999999999999999999999855

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=80.03  E-value=2.1  Score=35.38  Aligned_cols=25  Identities=16%  Similarity=0.227  Sum_probs=23.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++||++|.+
T Consensus        18 ~~glt~~elA~~~gis~~~is~~E~   42 (185)
T PRK09943         18 QQGLSQRRAAELSGLTHSAISTIEQ   42 (185)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4589999999999999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	230
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		1e-53
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		6e-45
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		8e-44
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		8e-40

>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 =  206 bits (524), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 96/118 (81%), Positives = 115/118 (97%), Gaps = 1/118 (0%)
Query: 87  VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146
           VNQLGGVFINGRPLPN+IRLKIVEMAA G+RPCVISRQLRVSHGCVSKILNRYQETGSIR
Sbjct: 5   VNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIR 64
Query: 147 PGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSIS 204
           PGVIGGSKPR+ATP++E RIEEYK+++PG+FSWEIR++L++ +G+CD+++APSVS+IS
Sbjct: 65  PGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAIS 121

>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149

Iteration: 1
 Score =  177 bits (448), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 87/127 (68%), Positives = 105/127 (82%), Gaps = 2/127 (1%)
Query: 79  RQLRVSHG-VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137
           R  R  HG VNQLGGVF+NGRPLP+ +R +IVE+A  GVRPC ISRQLRVSHGCVSKIL 
Sbjct: 11  RTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILG 70
Query: 138 RYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSA 197
           RY ETGSI+PGVIGGSKP+VATP V ++I EYK+ NP +F+WEIRDRL+ +  +CD ++ 
Sbjct: 71  RYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAER-VCDNDTV 129
Query: 198 PSVSSIS 204
           PSVSSI+
Sbjct: 130 PSVSSIN 136

>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159

Iteration: 1
 Score =  173 bits (438), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 84/125 (67%), Positives = 104/125 (83%), Gaps = 2/125 (1%)
Query: 81  LRVSHG-VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139
           +R  HG +NQLGG F+NGRPLP  +R +IV++A  GVRPC ISRQLRVSHGCVSKIL RY
Sbjct: 6   IRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRY 65
Query: 140 QETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS 199
            ETGSIRPGVIGGSKP+VATP V ++I +YK+ NP +F+WEIRDRL+ + G+CD ++ PS
Sbjct: 66  YETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAE-GVCDNDTVPS 124
Query: 200 VSSIS 204
           VSSI+
Sbjct: 125 VSSIN 129

>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 =  160 bits (404), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 78/118 (66%), Positives = 95/118 (80%), Gaps = 1/118 (0%)
Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
           GVNQLGGVF+NGRPLP+  R +IVE+A +G RPC ISR L+VS+GCVSKIL RY  TGSI
Sbjct: 4   GVNQLGGVFVNGRPLPDSTRQRIVELAHSGARPCDISRILQVSNGCVSKILGRYYATGSI 63
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSI 203
           RP  IGGSKPRVATP+V  +I +YK+  P IF+WEIRDRL+  +G+C  ++ PSVSSI
Sbjct: 64  RPRAIGGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLS-EGVCTNDNIPSVSSI 120

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	230
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	1e-53
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	2e-52
2k27_A	159	Paired box protein PAX-8; paired domain, solution	2e-51
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	3e-15
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	4e-10
1u78_A	141	TC3 transposase, transposable element TC3 transpos	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-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 =  167 bits (425), Expect = 1e-53
 Identities = 100/124 (80%), Positives = 120/124 (96%), Gaps = 1/124 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
            VNQLGGVFINGRPLPN+IRLKIVEMAA G+RPCVISRQLRVSHGCVSKILNRYQETGSI
Sbjct: 4   RVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSI 63

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPGVIGGSKPR+ATP++E RIEEYK+++PG+FSWEIR++L++ +G+CD+++APSVS+ISR
Sbjct: 64  RPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAISR 122

Query: 206 LLRG 209
           L+RG
Sbjct: 123 LVRG 126

>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 =  165 bits (418), Expect = 2e-52
 Identities = 86/126 (68%), Positives = 106/126 (84%), Gaps = 1/126 (0%)

Query: 84  SHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143
             GVNQLGGVF+NGRPLP+ +R +IVE+A  GVRPC ISRQLRVSHGCVSKIL RY ETG
Sbjct: 17  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 76

Query: 144 SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSI 203
           SI+PGVIGGSKP+VATP V ++I EYK+ NP +F+WEIRDRL+  + +CD ++ PSVSSI
Sbjct: 77  SIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA-ERVCDNDTVPSVSSI 135

Query: 204 SRLLRG 209
           +R++R 
Sbjct: 136 NRIIRT 141

>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 =  163 bits (412), Expect = 2e-51
 Identities = 84/124 (67%), Positives = 105/124 (84%), Gaps = 1/124 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
           G+NQLGG F+NGRPLP  +R +IV++A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI
Sbjct: 12  GLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSI 71

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPGVIGGSKP+VATP V ++I +YK+ NP +F+WEIRDRL+  +G+CD ++ PSVSSI+R
Sbjct: 72  RPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLA-EGVCDNDTVPSVSSINR 130

Query: 206 LLRG 209
           ++R 
Sbjct: 131 IIRT 134

>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 = 70.3 bits (171), Expect = 3e-15
 Identities = 7/63 (11%), Positives = 21/63 (33%), Gaps = 3/63 (4%)

Query: 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQ---DGICDKNSAPSVSSISRLLRGGRRDDCD 216
              +  +E   + +P   +  ++  L +           +  + S +S+ L  G      
Sbjct: 14  AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQ 73

Query: 217 RKN 219
           ++ 
Sbjct: 74  KRA 76

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 56.9 bits (136), Expect = 4e-10
 Identities = 6/55 (10%), Positives = 18/55 (32%), Gaps = 3/55 (5%)

Query: 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVK---QDGICDKNSAPSVSSISRLLRGGR 211
            +    ++     +P   +  I+  + +           +  + S +S+ L  G 
Sbjct: 15  AEQRAEVDRMLSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGT 69

>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 Length = 141

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 17/112 (15%), Positives = 39/112 (34%), Gaps = 14/112 (12%)

Query: 97  GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR 156
           G  L +  R ++  M    V    +SR++  S  C+   L      G+ +       + +
Sbjct: 4   GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRK 59

Query: 157 VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR 208
             +   E+ +      +      +IR+ L           + S  +I  +++
Sbjct: 60  ALSVRDERNVIRAASNSCKTAR-DIRNEL---------QLSASKRTILNVIK 101

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

 Score = 40.2 bits (93), Expect = 3e-04
 Identities = 33/263 (12%), Positives = 78/263 (29%), Gaps = 82/263 (31%)

Query: 5   RMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSC-----------QGRMNQLGGVF-IN 52
            +     V I+G             +   G G +            Q +M+    +F +N
Sbjct: 146 ELRPAKNVLIDG-------------VL--GSGKTWVALDVCLSYKVQCKMD--FKIFWLN 188

Query: 53  -GRPLPNHIRLKIVEMAAAGVRPCVISRQ---LRVSHGVNQLGGV---FINGRPLPN--- 102
                     L++++     + P   SR      +   ++ +       +  +P  N   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248

Query: 103 ---HIR-LKIVEMAAAGVRPCVISRQLRVSHGCVSKIL--NRYQETGSIRPGVIGGSKPR 156
              +++  K                    +  C  KIL   R++    +   +   +   
Sbjct: 249 VLLNVQNAKAWNA---------------FNLSC--KILLTTRFK---QVTDFLSAATTTH 288

Query: 157 VATPDVEKRIEEYKKTNPGIFS-W-EIR-DRLVKQDGICDKNSAP-SVSSISRLLRGG-- 210
           ++       +   +     +   + + R   L ++  +   N  P  +S I+  +R G  
Sbjct: 289 ISLDHHSMTLTPDEVK--SLLLKYLDCRPQDLPRE--VLTTN--PRRLSIIAESIRDGLA 342

Query: 211 -----RRDDCDRKNHSIDGILEQ 228
                +  +CD+    I+  L  
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNV 365

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	230
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.84
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.82
2k27_A	159	Paired box protein PAX-8; paired domain, solution	99.77
1u78_A	141	TC3 transposase, transposable element TC3 transpos	99.65
3hot_A	345	Transposable element mariner, complete CDS; protei	99.37
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.14
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.09
2k27_A	159	Paired box protein PAX-8; paired domain, solution	98.9
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.81
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	98.63
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	98.54
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	98.49
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	98.45
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	98.28
1u78_A	141	TC3 transposase, transposable element TC3 transpos	98.23
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	98.11
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	97.99
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	97.67
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	97.57
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	97.55
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	97.38
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	97.04
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	96.96
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	96.96
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	96.91
3jth_A	98	Transcription activator HLYU; transcription factor	96.84
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.82
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	96.76
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	96.71
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	96.68
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	96.63
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	96.62
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.58
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.57
2kko_A	108	Possible transcriptional regulatory protein (possi	96.56
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	96.55
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.53
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.47
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	96.44
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	96.43
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	96.42
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	96.4
3frw_A	107	Putative Trp repressor protein; structural genomic	96.35
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.22
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.22
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.22
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	96.2
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	96.18
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	96.18
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.16
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	96.16
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.13
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.1
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.07
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	96.05
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	96.0
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	95.96
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.95
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.89
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	95.88
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	95.84
3c57_A	95	Two component transcriptional regulatory protein;	95.76
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	95.74
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.7
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	95.7
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	95.64
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	95.61
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	95.6
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	95.55
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	95.48
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.43
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	95.42
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	95.41
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.34
1q06_A	135	Transcriptional regulator CUER; MERR family transc	95.28
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	95.24
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	95.2
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	95.14
2jml_A	81	DNA binding domain/transcriptional regulator; anti	95.12
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	95.12
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	95.04
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	95.02
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.0
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	94.97
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	94.95
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	94.93
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	94.81
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.8
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.78
3gp4_A	142	Transcriptional regulator, MERR family; structural	94.77
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	94.7
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	94.69
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.46
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	94.41
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	94.36
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.31
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	94.29
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	94.26
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	94.2
3hot_A	345	Transposable element mariner, complete CDS; protei	94.11
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	94.07
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	94.06
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.06
2hin_A	71	GP39, repressor protein; transcription factor, dim	94.05
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.98
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	93.97
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	93.92
3v4g_A	180	Arginine repressor; vibrio vulnificus CMCP6, virul	93.89
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	93.82
3lap_A	170	Arginine repressor; arginine repressor, DNA bindin	93.79
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	93.76
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	93.75
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	93.7
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	93.67
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	93.66
1eto_A	98	FIS, factor for inversion stimulation; transcripti	93.62
3gpv_A	148	Transcriptional regulator, MERR family; protein st	93.62
3hh0_A	146	Transcriptional regulator, MERR family; protein st	93.4
3iuo_A	122	ATP-dependent DNA helicase RECQ; C-terminal, GI PS	93.34
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	93.33
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	93.32
2dg6_A	222	Putative transcriptional regulator; winged-helix m	93.26
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	93.24
2w25_A	150	Probable transcriptional regulatory protein; trans	93.23
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.23
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.22
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	93.21
2q0o_A	236	Probable transcriptional activator protein TRAR; h	93.2
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	93.09
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	93.08
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	93.07
1rr7_A	129	Middle operon regulator; MOR, transcription; 2.20A	93.03
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	93.02
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	93.02
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	92.96
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	92.94
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	92.93
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	92.93
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	92.87
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	92.78
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	92.68
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	92.66
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	92.65
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	92.62
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	92.6
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	92.53
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	92.51
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	92.48
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	92.47
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	92.45
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	92.45
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	92.44
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	92.38
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	92.36
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	92.36
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	92.32
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	92.24
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	92.09
3by6_A	126	Predicted transcriptional regulator; structural ge	92.07
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	92.07
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	92.02
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	92.02
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	91.99
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	91.97
1sfx_A	109	Conserved hypothetical protein AF2008; structural	91.93
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.84
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	91.76
3t76_A	88	VANU, transcriptional regulator vanug; structural	91.74
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	91.73
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	91.73
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	91.63
3r0a_A	123	Putative transcriptional regulator; structural gen	91.57
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	91.55
4g6q_A	182	Putative uncharacterized protein; structural genom	91.51
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	91.47
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	91.39
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	91.38
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	91.38
1mkm_A	249	ICLR transcriptional regulator; structural genomic	91.33
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	91.21
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	91.18
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	91.15
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	91.14
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	91.11
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	91.04
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	91.01
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	91.0
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	90.98
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	90.95
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	90.9
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	90.89
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	90.88
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	90.84
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	90.8
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	90.79
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	90.78
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	90.74
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	90.71
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	90.67
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	90.65
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	90.65
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	90.56
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	90.55
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	90.47
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	90.28
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	90.07
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	90.0
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	89.94
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	89.93
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	89.92
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	89.83
2pg4_A	95	Uncharacterized protein; structural genomics, join	89.81
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	89.62
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	89.61
4ghj_A	101	Probable transcriptional regulator; structural gen	89.59
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	89.58
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	89.42
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	89.42
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	89.39
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	89.19
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	89.18
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	89.15
1z05_A	429	Transcriptional regulator, ROK family; structural	89.12
4ets_A	162	Ferric uptake regulation protein; metal binding pr	89.1
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	89.1
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	88.98
3vib_A	210	MTRR; helix-turn-helix motif, DNA binding, DNA bin	88.83
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	88.8
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	88.57
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	88.53
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	88.5
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	88.5
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	88.48
3c7j_A	237	Transcriptional regulator, GNTR family; structural	88.45
2w57_A	150	Ferric uptake regulation protein; gene regulation,	88.44
3ivp_A	126	Putative transposon-related DNA-binding protein; A	88.41
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	88.35
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	88.34
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	88.32
1b0n_A	111	Protein (SINR protein); transcription regulator, a	88.23
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	88.2
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	88.17
3bja_A	139	Transcriptional regulator, MARR family, putative;	88.17
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	88.13
2eth_A	154	Transcriptional regulator, putative, MAR family; M	88.09
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	88.06
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	87.93
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	87.84
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	87.81
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	87.81
3df8_A	111	Possible HXLR family transcriptional factor; APC89	87.81
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	87.8
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	87.75
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	87.7
3trb_A	104	Virulence-associated protein I; mobIle and extrach	87.63
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	87.6
3bhq_A	211	Transcriptional regulator; bacterial RE proteins,	87.44
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	87.38
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	87.28
2h09_A	155	Transcriptional regulator MNTR; transcription regu	87.26
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	87.25
2nnn_A	140	Probable transcriptional regulator; structural gen	87.15
3lsg_A	103	Two-component response regulator YESN; structural	87.11
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.05
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	86.96
3cec_A	104	Putative antidote protein of plasmid maintenance;	86.95
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	86.94
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	86.83
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	86.82
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	86.72
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	86.7
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	86.68
1yyv_A	131	Putative transcriptional regulator; reductive meth	86.65
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	86.56
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	86.48
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	86.45
2w57_A	150	Ferric uptake regulation protein; gene regulation,	86.37
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	86.35
1ku9_A	152	Hypothetical protein MJ223; putative transcription	86.33
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	86.32
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	86.28
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	86.25
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	86.24
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	86.12
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	86.12
2gxg_A	146	146AA long hypothetical transcriptional regulator;	86.07
3geu_A	189	Intercellular adhesion protein R; TETR family, int	86.01
3mlf_A	111	Transcriptional regulator; structural genomics, he	85.98
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	85.97
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	85.97
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	85.95
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	85.91
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	85.85
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	85.74
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	85.71
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	85.56
3u5c_N	151	S27A, YS15, 40S ribosomal protein S13; translation	85.41
2zb9_A	214	Putative transcriptional regulator; transcription	85.38
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	85.29
1z91_A	147	Organic hydroperoxide resistance transcriptional;	85.26
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	85.15
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	85.14
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	85.07
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	84.95
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	84.94
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	84.94
3s2w_A	159	Transcriptional regulator, MARR family; structural	84.9
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	84.85
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	84.66
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	84.65
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	84.58
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	84.53
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	84.51
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	84.5
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	84.47
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	84.43
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	84.38
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	84.38
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	84.34
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	84.31
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	84.25
1p6r_A	82	Penicillinase repressor; transcription regulation,	84.17
3nrg_A	217	TETR family transcriptional regulator; structural	84.11
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	84.06
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	83.99
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	83.93
2pex_A	153	Transcriptional regulator OHRR; transcription regu	83.9
3mn2_A	108	Probable ARAC family transcriptional regulator; st	83.81
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	83.8
2g7u_A	257	Transcriptional regulator; ICLR family, structural	83.53
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	83.5
3nqo_A	189	MARR-family transcriptional regulator; structural	83.49
3hta_A	217	EBRA repressor; TETR family, DNA binding protein,	83.39
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	83.34
3eet_A	272	Putative GNTR-family transcriptional regulator; st	83.15
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	83.06
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	83.06
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	83.04
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	82.94
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	82.94
4fx0_A	148	Probable transcriptional repressor protein; helix-	82.92
3q0w_A	236	HTH-type transcriptional regulator EThr; TETR fami	82.87
2iu5_A	195	DHAS, YCEG, HTH-type dhaklm operon transcriptional	82.85
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	82.75
2ahq_A	76	Sigma-54, RNA polymerase sigma factor RPON; sigma-	82.74
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	82.71
3c3w_A	225	Two component transcriptional regulatory protein;	82.66
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	82.61
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	82.58
2xzm_O	153	RPS13E; ribosome, translation; 3.93A {Tetrahymena	82.52
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	82.49
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	82.33
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	82.3
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	82.21
3iwf_A	107	Transcription regulator RPIR family; transcription	82.21
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	82.21
2wus_R	112	RODZ, putative uncharacterized protein; structural	82.17
3f3x_A	144	Transcriptional regulator, MARR family, putative;	82.07
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	81.94
3cdl_A	203	Transcriptional regulator AEFR; APC88582, TETR, ps	81.94
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	81.93
3bqz_B	194	HTH-type transcriptional regulator QACR; multidrug	81.74
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	81.72
2wui_A	210	MEXZ, transcriptional regulator; gene regulation,	81.61
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	81.61
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	81.57
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	81.56
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	81.56
3b02_A	195	Transcriptional regulator, CRP family; structural	81.42
2eh3_A	179	Transcriptional regulator; all alpha proteins, tet	81.36
1okr_A	123	MECI, methicillin resistance regulatory protein ME	81.14
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	81.07
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	81.07
3lwj_A	202	Putative TETR-family transcriptional regulator; st	81.04
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	81.03
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	80.99
2o7t_A	199	Transcriptional regulator; transcription regulator	80.96
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	80.9
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	80.88
3k69_A	162	Putative transcription regulator; putative transcr	80.82
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	80.75
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	80.73
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	80.63
3egq_A	170	TETR family transcriptional regulator; DNA-binding	80.62
2np5_A	203	Transcriptional regulator; TETR family, structural	80.57
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	80.56
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	80.54
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	80.54
3anp_C	204	Transcriptional repressor, TETR family; all alpha	80.5
3bjb_A	207	Probable transcriptional regulator, TETR family P;	80.5
3pas_A	195	TETR family transcription regulator; structural ge	80.45
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	80.43
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	80.36
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	80.36
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	80.3
3dew_A	206	Transcriptional regulator, TETR family; S genomics	80.2
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	80.12
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	80.1
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	80.04
1ft9_A	222	Carbon monoxide oxidation system transcription reg	80.02

>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=99.84  E-value=8.1e-21  Score=145.32  Aligned_cols=124  Identities=81%  Similarity=1.401  Sum_probs=104.6

Q ss_pred             ccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHH
Q psy1898          87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI  166 (230)
Q Consensus        87 ~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I  166 (230)
                      ++.+|+.|.+++.|+.++|.+|+.++.+|.|..+||+.|+||++||++|+++|++.|...+.++++.+|++++++..+.|
T Consensus         5 ~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~~i   84 (128)
T 1pdn_C            5 VNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRI   84 (128)
T ss_dssp             ECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHH
T ss_pred             HhhhcccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHHHH
Confidence            67889988889999999999999999999999999999999999999999999999987766654447788899889999


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      .+++.++|.++.++|+++|.+ .|+......+|.+||+|+|+++|
T Consensus        85 ~~~~~~~~~~s~~~i~~~l~~-~g~~~~~~~~s~~tv~r~l~~~~  128 (128)
T 1pdn_C           85 EEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAISRLVRGRD  128 (128)
T ss_dssp             HHTTTTCTTCCHHHHHHHHHH-TSSSCSTTCCCHHHHHHHC----
T ss_pred             HHHHHhCcchHHHHHHHHHHH-cCCccccCCcCHHHHHHHHHhcC
Confidence            999988999999999999986 47621112379999999999875

>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=99.82  E-value=4.2e-19  Score=141.15  Aligned_cols=123  Identities=68%  Similarity=1.166  Sum_probs=107.0

Q ss_pred             cccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH
Q psy1898          86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR  165 (230)
Q Consensus        86 g~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~  165 (230)
                      +.+.+++.|.+++.|+.++|.+|+.++.+|.|..+||+.||||++||++|+++|++.|.+.++++++.+|++++++..+.
T Consensus        19 ~~~~~gg~~~~~~~~s~e~r~~iv~~~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~~~~~~~   98 (149)
T 1k78_A           19 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEK   98 (149)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSCHHHHHH
T ss_pred             CccCCCceecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCCHHHHHH
Confidence            46788998888999999999999999999999999999999999999999999999998877666554478889999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhh----CCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         166 IEEYKKTNPGIFSWEIRDRLVKQD----GICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       166 I~~l~~~~P~~t~~eI~~~L~~~~----Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      |.+++.++|.++.++|+++|..+.    |+     .+|.+||+|+|++..-.
T Consensus        99 I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~-----~~S~sTV~r~L~~~~~~  145 (149)
T 1k78_A           99 IAEYKRQNPTMFAWEIRDRLLAERVCDNDT-----VPSVSSINRIIRTKVQQ  145 (149)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHHHTTSSCTTT-----SCCHHHHHHHHHCC---
T ss_pred             HHHHHHhCcchhHHHHHHHHHHhcccccCC-----CcCHHHHHHHHHHHhcC
Confidence            999999999999999999997633    55     38999999999987543

>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=99.77  E-value=3e-18  Score=137.90  Aligned_cols=126  Identities=66%  Similarity=1.188  Sum_probs=106.5

Q ss_pred             ccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHH
Q psy1898          87 VNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI  166 (230)
Q Consensus        87 ~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I  166 (230)
                      .+.+|+.+.+++.|+.++|.+|+.++.+|.|.++||+.|+||++||++|+++|++.|.+.++++++.+|++++++..+.|
T Consensus        13 ~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~~~~~I   92 (159)
T 2k27_A           13 LNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVEKI   92 (159)
T ss_dssp             CCCCCCTTSSSCSSCHHHHHHHHHHHHHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTTHHHHH
T ss_pred             hhhcCCcCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHHHHHHH
Confidence            45788888788899999999999999999999999999999999999999999999987776655544778899899999


Q ss_pred             HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+++.++|.++.++|+++|.+ .+++..+..+|.+||+|+|++..-.
T Consensus        93 ~~~~~~~~~~s~~~i~~~l~~-~~~~~~~~~~S~sTV~r~L~~~~~~  138 (159)
T 2k27_A           93 GDYKRQNPTMFAWEIRDRLLA-EGVCDNDTVPSVSSINRIIRTKVQQ  138 (159)
T ss_dssp             HHHHHHCSSSCHHHHHHHHHH-HTCSCTTTSCCHHHHHHHHHHHSCC
T ss_pred             HHHHHHCccchHHHHHHHHHH-hcccccCCccCHHHHHHHHHHHhCC
Confidence            999999999999999999976 4421111248999999999986443

>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=99.65  E-value=9.9e-16  Score=119.40  Aligned_cols=102  Identities=18%  Similarity=0.252  Sum_probs=88.8

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI  176 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~  176 (230)
                      ++.|+.++|.+|+.++.+|.|.++||+.||||++||++|+++|.+.|....    .++|++++++..+.|..+ ..+|.+
T Consensus         4 ~~~~s~~~r~~i~~~~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~----~gr~~~l~~~~~~~i~~~-~~~~~~   78 (141)
T 1u78_A            4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRKALSVRDERNVIRA-ASNSCK   78 (141)
T ss_dssp             SCCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCC----CCCCCSSCHHHHHHHHHH-HHHCCC
T ss_pred             cccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCC----CCCCCcCCHHHHHHHHHH-HhCCCC
Confidence            567999999999999999999999999999999999999999998886532    247788999988888887 678899


Q ss_pred             CHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898         177 FSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR  212 (230)
Q Consensus       177 t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~  212 (230)
                      ++.+|.++|    |+.     +|.+||+|+|++.|+
T Consensus        79 s~~~i~~~l----g~~-----~s~~tV~r~l~~~g~  105 (141)
T 1u78_A           79 TARDIRNEL----QLS-----ASKRTILNVIKRSGV  105 (141)
T ss_dssp             CHHHHHHHT----TCC-----SCHHHHHHHHHHTC-
T ss_pred             CHHHHHHHH----CCC-----ccHHHHHHHHHHCCC
Confidence            999988766    653     799999999999998

>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=99.37  E-value=2.3e-12  Score=114.23  Aligned_cols=101  Identities=13%  Similarity=0.143  Sum_probs=86.3

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhc-------cccchhhhHHHHHhhhC--CCCcCCCCCCCCCCCCHHHHHHHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLR-------VSHGCVSKILNRYQETG--SIRPGVIGGSKPRVATPDVEKRIEE  168 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lg-------VS~sTV~kwikRy~e~G--~v~p~~~gg~rpr~lt~~~~~~I~~  168 (230)
                      .+...++|..|+.++++|.+..+||+.|+       ||++||++|+++|++ |  .+.+.+++| +|+.+++   +.|.+
T Consensus         5 ~~~~~~~R~~i~~~~~~G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~-g~~~l~~~~r~g-rp~~~~~---~~i~~   79 (345)
T 3hot_A            5 VPNKEQTRTVLIFCFHLKKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKS-GDFDVDDKEHGK-PPKRYED---AELQA   79 (345)
T ss_dssp             CCCHHHHHHHHHHHHHTTCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTT-CCCCCSCCCCCC-CCCSSCH---HHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhC-CCccccCCCCCC-CCCcccH---HHHHH
Confidence            45667999999999999999999999977       999999999999997 5  356666654 7888776   55667


Q ss_pred             HHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCC
Q psy1898         169 YKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDD  214 (230)
Q Consensus       169 l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~  214 (230)
                      +++.+|..++.+|++.|    +       +|.+||+|+|+++|+..
T Consensus        80 ~v~~~~~~t~~~ia~~l----~-------vs~~tV~r~L~~~g~~~  114 (345)
T 3hot_A           80 LLDEDDAQTQKQLAEQL----E-------VSQQAVSNRLREMGKIQ  114 (345)
T ss_dssp             HHHHCSCCCHHHHHHHT----T-------SCHHHHHHHHHHTTCEE
T ss_pred             HHHhCccchHHHHHHHH----C-------CCHHHHHHHHHHhCCee
Confidence            78899999999999876    3       59999999999999974

>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=99.14  E-value=2.7e-11  Score=91.88  Aligned_cols=101  Identities=53%  Similarity=0.802  Sum_probs=69.8

Q ss_pred             CCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--------ccCCcc---c---CCCcCCHHH
Q psy1898          39 CQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--------QLGGVF---I---NGRPLPNHI  104 (230)
Q Consensus        39 ~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--------~l~~~~---~---~g~~~s~~~  104 (230)
                      ||+.+|++||+|+.+++++.++|.+|++++.+|.+..+|++.+++++.++        ..|...   .   ....++.+.
T Consensus         1 ~~~~~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~   80 (128)
T 1pdn_C            1 GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEI   80 (128)
T ss_dssp             -CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTH
T ss_pred             CCchHhhhcccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHH
Confidence            46677777777777777777788888887777777788888887765443        001110   0   123467778


Q ss_pred             HHHHHHHHHc--CCCHHHHhhhh---c-------cccchhhhHHHHH
Q psy1898         105 RLKIVEMAAA--GVRPCVISRQL---R-------VSHGCVSKILNRY  139 (230)
Q Consensus       105 R~rIV~l~~~--G~s~~~IAr~l---g-------VS~sTV~kwikRy  139 (230)
                      +..|+.++.+  .++..+|+..|   |       +|.+||++|+++.
T Consensus        81 ~~~i~~~~~~~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~~~  127 (128)
T 1pdn_C           81 ENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGR  127 (128)
T ss_dssp             HHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC---
T ss_pred             HHHHHHHHHhCcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHHhc
Confidence            8888887754  48999999999   7       5999999998763

>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=99.09  E-value=1.9e-10  Score=90.78  Aligned_cols=106  Identities=41%  Similarity=0.643  Sum_probs=80.9

Q ss_pred             CCCCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--------ccCCcc---cC---CCcCC
Q psy1898          36 GSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--------QLGGVF---IN---GRPLP  101 (230)
Q Consensus        36 ~~~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--------~l~~~~---~~---g~~~s  101 (230)
                      +-.|++++|++||+|+.++.++.++|.+|++++.+|.+..+|++.+++++.++        ..|...   ..   ...++
T Consensus        13 ~~~~~~~~~~~gg~~~~~~~~s~e~r~~iv~~~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~   92 (149)
T 1k78_A           13 SRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVAT   92 (149)
T ss_dssp             ------CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSC
T ss_pred             ccCCCCCccCCCceecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCC
Confidence            34577899999999999999999999999999999999999999999977654        011111   11   33578


Q ss_pred             HHHHHHHHHHHHc--CCCHHHHhhhh--------c--cccchhhhHHHHHhh
Q psy1898         102 NHIRLKIVEMAAA--GVRPCVISRQL--------R--VSHGCVSKILNRYQE  141 (230)
Q Consensus       102 ~~~R~rIV~l~~~--G~s~~~IAr~l--------g--VS~sTV~kwikRy~e  141 (230)
                      .+....|+.++.+  ..+..+|+..|        +  +|.+||++|++++.+
T Consensus        93 ~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~~~  144 (149)
T 1k78_A           93 PKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQ  144 (149)
T ss_dssp             HHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC--
T ss_pred             HHHHHHHHHHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHHhc
Confidence            8899999988765  48999999988        6  799999999987553

>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=98.90  E-value=5e-09  Score=83.62  Aligned_cols=108  Identities=39%  Similarity=0.584  Sum_probs=87.7

Q ss_pred             CCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccC-----Cccc----C---CCcCCHH
Q psy1898          38 SCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLG-----GVFI----N---GRPLPNH  103 (230)
Q Consensus        38 ~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~-----~~~~----~---g~~~s~~  103 (230)
                      .|..+.+++|+.|+.++.++.++|.+|++++.+|.+..+|+++|+++..++  -+.     +.+.    .   ...++.+
T Consensus         8 ~~~~~~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~   87 (159)
T 2k27_A            8 SGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPK   87 (159)
T ss_dssp             CSCSSCCCCCCTTSSSCSSCHHHHHHHHHHHHHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTT
T ss_pred             hcchhhhhcCCcCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHH
Confidence            456789999999999999999999999999999999999999999987664  111     1111    1   2347778


Q ss_pred             HHHHHHHHHHc--CCCHHHHhhhh----------ccccchhhhHHHHHhhhCCC
Q psy1898         104 IRLKIVEMAAA--GVRPCVISRQL----------RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       104 ~R~rIV~l~~~--G~s~~~IAr~l----------gVS~sTV~kwikRy~e~G~v  145 (230)
                      ....|+.++.+  .++..+|+..|          .+|.+||++|+++|...|.-
T Consensus        88 ~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~~~  141 (159)
T 2k27_A           88 VVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFN  141 (159)
T ss_dssp             HHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCCSC
T ss_pred             HHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCCcc
Confidence            88889888764  49999999987          47999999999999988854

>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=98.81  E-value=3.5e-09  Score=67.23  Aligned_cols=47  Identities=21%  Similarity=0.268  Sum_probs=43.5

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +.++.+.+..|+.++.+|++..+||+.|+||++||++|+++|++.|.
T Consensus         4 ~~l~~~~~~~i~~~~~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g~   50 (51)
T 1tc3_C            4 SALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT   50 (51)
T ss_dssp             CCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCSTTTTC
T ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhhHHhcCC
Confidence            46889999999999999999999999999999999999999988764

>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=98.63  E-value=5.8e-07  Score=69.06  Aligned_cols=111  Identities=14%  Similarity=0.091  Sum_probs=77.6

Q ss_pred             CCcCCHHHHHHHHHHH-HcCCCHH-HHhhhhccccchhhhHHHHHhh-------hCCCCcCCCCCCCCCCCCHHHHHHHH
Q psy1898          97 GRPLPNHIRLKIVEMA-AAGVRPC-VISRQLRVSHGCVSKILNRYQE-------TGSIRPGVIGGSKPRVATPDVEKRIE  167 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~~G~s~~-~IAr~lgVS~sTV~kwikRy~e-------~G~v~p~~~gg~rpr~lt~~~~~~I~  167 (230)
                      .+.|+.++|..||.++ +.|.+.. +||+.|||+++||++|++.+..       .+...+... + ......++.++.|.
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~~~~~~~~~~~~~k-r-~r~~~~~~~E~~L~   82 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRK-T-NKLSPYDKLEGLLI   82 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHHHHHHHGGGGGTCC-C-CCCCTTHHHHHHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhhcchhhhccccchhhc-c-cCCCCCHHHHHHHH
Confidence            5679999999999998 6776655 9999999999999999998764       343222111 1 23445778888888


Q ss_pred             HHHHh----CCCCCHHH---HHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         168 EYKKT----NPGIFSWE---IRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       168 ~l~~~----~P~~t~~e---I~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      .++.+    +-..+...   .+..+....|+.  +-.+|..-++++.++||
T Consensus        83 ~Wi~~~~~~g~pvs~~~I~~kA~~i~~~~g~~--~f~~S~gWl~~F~~Rh~  131 (131)
T 1hlv_A           83 AWFQQIRAAGLPVKGIILKEKALRIAEELGMD--DFTASNGWLDRFRRRRS  131 (131)
T ss_dssp             HHHHHHGGGTCCCCHHHHHHHHHHHHHHHTCT--TCCCCHHHHHHHHHHTC
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHhCCC--CCCCCHHHHHHHHHhcC
Confidence            88754    22355443   344455445653  23579999999999885

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=98.54  E-value=7.7e-08  Score=70.69  Aligned_cols=47  Identities=11%  Similarity=0.227  Sum_probs=43.2

Q ss_pred             CcCCHHHHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898          98 RPLPNHIRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +.||.+++..+|.++. . |.|..+||+.||||++||++|+++|.+.|.
T Consensus         4 ~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~~~g~   52 (97)
T 2jn6_A            4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHN   52 (97)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCST
T ss_pred             CCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHhhcCc
Confidence            5799999999999885 5 899999999999999999999999998775

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=98.49  E-value=2.3e-07  Score=67.21  Aligned_cols=48  Identities=10%  Similarity=0.133  Sum_probs=43.8

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      .+.|+.+++..++.++.+|.+..+||+.||||++||++|+++|.+...
T Consensus        20 ~~~ys~e~k~~~v~~~~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~~~   67 (87)
T 2elh_A           20 LRSLTPRDKIHAIQRIHDGESKASVARDIGVPESTLRGWCKNEDKLRF   67 (87)
T ss_dssp             CSSCCHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHhccc
Confidence            458999999999999988999999999999999999999999987653

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=98.45  E-value=1.3e-07  Score=63.55  Aligned_cols=47  Identities=15%  Similarity=0.195  Sum_probs=42.5

Q ss_pred             CCcCCHHHHHHHHHHHHcCCC----HHHHhhhhccccchhhhHHHHHhhhC
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVR----PCVISRQLRVSHGCVSKILNRYQETG  143 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s----~~~IAr~lgVS~sTV~kwikRy~e~G  143 (230)
                      .+.||.+++.+|++++..|.|    ..+||+.|||+++||++|+++|++.+
T Consensus         3 r~~ys~efK~~~~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~~   53 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNLR   53 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            357999999999888888999    99999999999999999999998654

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=98.28  E-value=4e-07  Score=68.03  Aligned_cols=50  Identities=10%  Similarity=0.189  Sum_probs=43.9

Q ss_pred             CCCcCCHHHHHHHHHHHH-cC-------CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898          96 NGRPLPNHIRLKIVEMAA-AG-------VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        96 ~g~~~s~~~R~rIV~l~~-~G-------~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ..+.||.+++..+|.++. .|       .+..+||+.||||++||++|+++|.+.|..
T Consensus         3 ~~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~~~~~~~~   60 (108)
T 2rn7_A            3 KNTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQHERDTGG   60 (108)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHHHHhcccc
Confidence            456799999999999874 34       799999999999999999999999987753

>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=98.23  E-value=3.1e-06  Score=65.01  Aligned_cols=86  Identities=16%  Similarity=0.148  Sum_probs=67.3

Q ss_pred             CCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCCcc------cC--CCcCCHHHHHHHHHHHHc-CCCHHHHh
Q psy1898          54 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGGVF------IN--GRPLPNHIRLKIVEMAAA-GVRPCVIS  122 (230)
Q Consensus        54 ~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~~~------~~--g~~~s~~~R~rIV~l~~~-G~s~~~IA  122 (230)
                      ..++.+.|.+|+.++.+|.+..+|++.++++..++  -+..+-      ..  ...++.+....|+.+..+ .+|..+|+
T Consensus         5 ~~~s~~~r~~i~~~~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~   84 (141)
T 1u78_A            5 SALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRRKALSVRDERNVIRAASNSCKTARDIR   84 (141)
T ss_dssp             CCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCCCCCCCSSCHHHHHHHHHHHHHCCCCHHHHH
T ss_pred             ccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCCCCCCCcCCHHHHHHHHHHHhCCCCCHHHHH
Confidence            45779999999999999999999999999987664  111110      01  234788888888877554 49999999


Q ss_pred             hhhc--cccchhhhHHHHH
Q psy1898         123 RQLR--VSHGCVSKILNRY  139 (230)
Q Consensus       123 r~lg--VS~sTV~kwikRy  139 (230)
                      ..|+  +|.+||++|+++.
T Consensus        85 ~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           85 NELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             HHTTCCSCHHHHHHHHHHT
T ss_pred             HHHCCCccHHHHHHHHHHC
Confidence            9999  7999999999863

>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=98.11  E-value=9.2e-07  Score=56.43  Aligned_cols=42  Identities=7%  Similarity=0.103  Sum_probs=36.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++.+.+..|+.++.+|.+..+||+.||||++||++|++++.
T Consensus         5 ~~~~~~~~~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~~~   46 (52)
T 1jko_C            5 AINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASS   46 (52)
T ss_dssp             SSCTTHHHHHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCTTC
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHcc
Confidence            456677788888999999999999999999999999987543

>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=97.99  E-value=3e-05  Score=72.56  Aligned_cols=104  Identities=13%  Similarity=0.041  Sum_probs=65.6

Q ss_pred             HHHHHHHH----HHHcCCCH----HHHhhhhccccchhhhHHHHHhhhCC------CCcCCC---CCCCCCCCCHHHHHH
Q psy1898         103 HIRLKIVE----MAAAGVRP----CVISRQLRVSHGCVSKILNRYQETGS------IRPGVI---GGSKPRVATPDVEKR  165 (230)
Q Consensus       103 ~~R~rIV~----l~~~G~s~----~~IAr~lgVS~sTV~kwikRy~e~G~------v~p~~~---gg~rpr~lt~~~~~~  165 (230)
                      +.|..+|.    +...|.+.    .++|+.+|||.+|+++|+++|+..+.      +.|+..   .+.+...++++..+.
T Consensus        32 ~~r~~~i~~v~~l~~~g~~~~~a~~~~a~~~gvS~~Tl~rW~~~y~~~~~~~gl~~L~~~~~~~~~~~~~~~~~~~~~~~  111 (529)
T 4fcy_A           32 EKWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVDGRGASRRNVHKSEFDEDAWQF  111 (529)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTSCHHHHHHHHHHHHTSCGGGHHHHHC------------CCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCcccCceecccCCCCCCCCCCcCcCCHHHHHH
Confidence            34445554    44567764    45689999999999999999986542      233322   112344567888877


Q ss_pred             HHHHHHhCCCCCHH----HHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         166 IEEYKKTNPGIFSW----EIRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       166 I~~l~~~~P~~t~~----eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      |.......+..+..    ++...+.. .|+.    .||.+||+|+|++.+
T Consensus       112 i~~~yl~~~~~s~~~~~~~~~~~~~~-~g~~----~PS~~tv~r~l~~~~  156 (529)
T 4fcy_A          112 LIADYLRPEKPAFRKCYERLELAARE-HGWS----IPSRATAFRRIQQLD  156 (529)
T ss_dssp             HHHHHTSTTCCCHHHHHHHHHHHHHH-HTCC----CCCHHHHHHHHHHHC
T ss_pred             HHHHHhCcCCCCHHHHHHHHHHHHHH-cCCC----CCCHHHHHHHHHhcC
Confidence            77665555555544    45555544 6764    579999999998754

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=97.67  E-value=5.3e-05  Score=56.07  Aligned_cols=51  Identities=10%  Similarity=0.052  Sum_probs=45.2

Q ss_pred             CCCcCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898          96 NGRPLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus        96 ~g~~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +-+.++.+++..||.....| .|..++|++++||.+++++|.+.|.+.|...
T Consensus        29 ~~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~~   80 (95)
T 2jrt_A           29 DTRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVAAHGEKA   80 (95)
T ss_dssp             SCCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTTS
T ss_pred             hhhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHH
Confidence            45668899999999987765 8999999999999999999999999998653

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=97.57  E-value=4.2e-05  Score=49.90  Aligned_cols=37  Identities=24%  Similarity=0.222  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+....|+.++.+|.|..+||+.||||++||++|+++
T Consensus        18 ~~~~~~i~~l~~~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           18 DDLVSVAHELAKMGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            5666777778889999999999999999999999853

>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=97.55  E-value=0.0017  Score=50.85  Aligned_cols=116  Identities=11%  Similarity=0.024  Sum_probs=76.3

Q ss_pred             CCcCCHHHHHHHHHHH-H-c-CCCHHHHhh----hh--ccccchhhhHHHHHhhhCCC---CcCCCCCCCCCCCCHHHHH
Q psy1898          97 GRPLPNHIRLKIVEMA-A-A-GVRPCVISR----QL--RVSHGCVSKILNRYQETGSI---RPGVIGGSKPRVATPDVEK  164 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~-~-~-G~s~~~IAr----~l--gVS~sTV~kwikRy~e~G~v---~p~~~gg~rpr~lt~~~~~  164 (230)
                      -..|+.+.|..|++.+ + . +++..++|+    .|  +|+++||++|++...+--..   .+..... ......+++++
T Consensus         9 R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~~~~~~~~~kr-~r~~~~~~le~   87 (144)
T 1iuf_A            9 RRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDNTVEKPWDVKR-NRPPKYPLLEA   87 (144)
T ss_dssp             SSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTTSCSSSSSSSC-CCCCSCHHHHH
T ss_pred             CccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhhcccccccccC-CCCCCCHHHHH
Confidence            4678999999999999 3 3 489999999    99  89999999999985542211   1112211 23345788888


Q ss_pred             HHHHHHHh---CCCCCHHHHHHHHHH---hhCC--CCCCCCCCHhHHHHHHHcCCCC
Q psy1898         165 RIEEYKKT---NPGIFSWEIRDRLVK---QDGI--CDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       165 ~I~~l~~~---~P~~t~~eI~~~L~~---~~Gi--~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+..++.+   +..+|-..|++....   ....  ....-..|..-+.++-++|||.
T Consensus        88 ~L~~Wi~~~~~~~~it~~~I~~kA~~i~~~l~~~~~~~~f~~S~GWL~~Fk~Rh~i~  144 (144)
T 1iuf_A           88 ALFEWQVQQGDDATLSGETIKRAAAILWHKIPEYQDQPVPNFSNGWLEGFRKRHILH  144 (144)
T ss_dssp             HHHHHHHHTCTTCCCSSHHHHHHHHHHHHHCSSSSCCCCCSCCSHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhccCCCCCCCcCHHHHHHHHHHcCCC
Confidence            88887766   334664444433322   2210  1122356888999999999874

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=97.38  E-value=3.7e-05  Score=58.79  Aligned_cols=100  Identities=13%  Similarity=0.073  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHH
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEI  181 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI  181 (230)
                      +.+.+|+..+. ++.++.++|..|+++..++..|++...+.|.+.+...+.--.+..-.+..+.|..+..+++.+|..++
T Consensus         7 ~l~~~i~~~~~~~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~   86 (121)
T 2pjp_A            7 AIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADF   86 (121)
T ss_dssp             HHHHHHGGGCSSSCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceECHHHHHHHHHHHHHHHHHCCCccHHHH
Confidence            56777887775 56789999999999999999999999999988654332112233344556677778888999999999


Q ss_pred             HHHHHHhhCCCCCCCCCCHh---HHHHHHHcCCCC
Q psy1898         182 RDRLVKQDGICDKNSAPSVS---SISRLLRGGRRD  213 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~s---TV~R~Lr~~g~~  213 (230)
                      ++.|    |+       |+.   ++..+|.+.|+-
T Consensus        87 Rd~l----g~-------sRK~ai~lLE~~Dr~g~T  110 (121)
T 2pjp_A           87 RDRL----GV-------GRKLAIQILEYFDRIGFT  110 (121)
T ss_dssp             HHHH----TS-------CHHHHHHHHHHHHHHTSE
T ss_pred             HHHH----CC-------cHHHHHHHHHHHhhcCCe
Confidence            9987    43       888   999999888764

>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=97.04  E-value=0.00046  Score=51.53  Aligned_cols=44  Identities=11%  Similarity=0.126  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ...+..||....+| +|..++|+.|+||.++|.+|.+.|++.|.-
T Consensus        36 a~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~~   80 (101)
T 2oa4_A           36 ASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGKD   80 (101)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSS
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHH
Confidence            34578888877665 999999999999999999999999999864

>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=96.96  E-value=0.00054  Score=53.68  Aligned_cols=44  Identities=9%  Similarity=0.146  Sum_probs=39.9

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhcc-ccchhhhHHHHHhh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRV-SHGCVSKILNRYQE  141 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV-S~sTV~kwikRy~e  141 (230)
                      ..|+.++-.+|++++..|.|.++||+.++| |.+||++|++++.+
T Consensus        11 tk~t~e~~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~~~e   55 (140)
T 4dyq_A           11 SDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHED   55 (140)
T ss_dssp             CSCCTTHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHHCHH
T ss_pred             CCCCHHHHHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHcCHH
Confidence            458889999999999999999999999999 99999999998544

>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=96.96  E-value=0.00059  Score=54.75  Aligned_cols=42  Identities=5%  Similarity=-0.013  Sum_probs=35.6

Q ss_pred             CCcCCHHHHHHHHHHHH-c--------CCCHHHHhhhhccccchhhhHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAA-A--------GVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~-~--------G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      -+.|+.+++..++.+.. .        |.|..+||+.+|||++|+|+|.+.
T Consensus        21 ~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           21 KQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHHc
Confidence            35588899999987643 2        689999999999999999999984

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=96.91  E-value=0.0012  Score=44.47  Aligned_cols=43  Identities=12%  Similarity=0.112  Sum_probs=35.5

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+.+|.|..+||..+|+|.+||++++.+...
T Consensus        15 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~   57 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD   57 (70)
T ss_dssp             SSCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3666677555556789999999999999999999999988653

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.84  E-value=0.00042  Score=50.22  Aligned_cols=68  Identities=16%  Similarity=0.162  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      ...|.+|+.++.+| .+..+||+.+++|++||++-++...+.|.+.....+...--.++++..+.+...
T Consensus        22 ~~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~   90 (98)
T 3jth_A           22 NERRLQILCMLHNQELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKL   90 (98)
T ss_dssp             SHHHHHHHHHTTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHH
Confidence            37788999877655 899999999999999999999999999988544332222234444444444333

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

Probab=96.82  E-value=0.00076  Score=49.25  Aligned_cols=48  Identities=19%  Similarity=0.296  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      ...|.+|+..+.+| .+..+||+.+++|++||++-++...+.|.+...+
T Consensus        22 ~~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~   70 (102)
T 3pqk_A           22 HPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRR   70 (102)
T ss_dssp             SHHHHHHHHHHHTCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEEC
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            47889999987766 8999999999999999999999999999875433

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=96.76  E-value=0.00022  Score=58.35  Aligned_cols=45  Identities=11%  Similarity=0.000  Sum_probs=0.0

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      .+++.+...+|..++.+|.|..+||+.||||++|||+|++.+.+.
T Consensus       141 ~~~~~~~~~~i~~l~~~G~s~~~Ia~~l~vs~~Tvyr~l~~~~~~  185 (193)
T 3uj3_X          141 PKLTKAEWEQAGRLLAQGIPRKQVALIYDVALSTLYKKHPAKRAH  185 (193)
T ss_dssp             ---------------------------------------------
T ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHhhhc
Confidence            345666777888999999999999999999999999999876543

>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=96.71  E-value=0.0015  Score=48.79  Aligned_cols=37  Identities=14%  Similarity=0.212  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..|..|..++.+| +|.++||+.+|||++||+|. +++-
T Consensus        45 ~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L   82 (101)
T 1jhg_A           45 GTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSL   82 (101)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHH
Confidence            3457777777788 99999999999999999999 6654

>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=96.68  E-value=0.0026  Score=39.77  Aligned_cols=48  Identities=17%  Similarity=0.208  Sum_probs=34.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCC
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDD  214 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~  214 (230)
                      ||+.++++..+.+..+..+.  .+..+|++.    .|+       |.+||+++|++.++.+
T Consensus         2 Rp~~~~~~~~~~i~~l~~~g--~s~~~ia~~----lgv-------s~~Tv~r~l~~~~~~~   49 (52)
T 1jko_C            2 RPRAINKHEQEQISRLLEKG--HPRQQLAII----FGI-------GVSTLYRYFPASSIKK   49 (52)
T ss_dssp             CCCSSCTTHHHHHHHHHHTT--CCHHHHHHT----TSC-------CHHHHHHHSCTTC---
T ss_pred             CCCCCCHHHHHHHHHHHHcC--CCHHHHHHH----HCC-------CHHHHHHHHHHccccc
Confidence            67778888777787776543  788777764    454       9999999999988754

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=96.63  E-value=0.0021  Score=46.15  Aligned_cols=41  Identities=22%  Similarity=0.196  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-++..+.+|+|..+||+.+|||.+||..++.|.+
T Consensus        38 L~~~~r~vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~   78 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAV   78 (92)
T ss_dssp             SCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666766666678999999999999999999999988754

>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=96.62  E-value=0.0025  Score=48.16  Aligned_cols=42  Identities=19%  Similarity=0.086  Sum_probs=36.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+.+|+|..+||..+|||.+||++++.+..
T Consensus        22 ~L~~~~r~vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~ra~   63 (113)
T 1s7o_A           22 LLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTE   63 (113)
T ss_dssp             GSCHHHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            467777776666778999999999999999999999998865

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

Probab=96.58  E-value=0.00072  Score=48.48  Aligned_cols=67  Identities=18%  Similarity=0.117  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      ..|.+|+..+.++  .+..+||+.+++|++||++.+++..+.|.+.....++..--.++++....+...
T Consensus        24 ~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~   92 (99)
T 3cuo_A           24 PKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIAT   92 (99)
T ss_dssp             HHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHH
T ss_pred             hHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHH
Confidence            6678888877553  899999999999999999999999999987533222212223455444444433

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.57  E-value=0.0006  Score=51.41  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=52.9

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH
Q psy1898         100 LPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      ++...|.+|+.++.+| .+..+||+.+++|++||++-++...+.|.+...+.+...--.++++..+.+..++
T Consensus        15 l~~~~R~~Il~~L~~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~   86 (118)
T 3f6o_A           15 LADPTRRAVLGRLSRGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWL   86 (118)
T ss_dssp             HTSHHHHHHHHHHHTCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHH
Confidence            4457899999987765 8999999999999999999999999999885433322233455665555554444

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.56  E-value=0.00027  Score=52.62  Aligned_cols=46  Identities=20%  Similarity=0.223  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ..|.+|+.++.+| .+..+||+.+++|++||++.++...+.|.+...
T Consensus        25 ~~r~~IL~~L~~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~   71 (108)
T 2kko_A           25 GRRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVEAR   71 (108)
T ss_dssp             STTHHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4567788776654 899999999999999999999999999988543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=96.55  E-value=0.0021  Score=42.28  Aligned_cols=36  Identities=17%  Similarity=0.166  Sum_probs=31.6

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ..|+.++.+|++.++||+.+++|.+||..++.+..+
T Consensus         4 ~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~~~~~   39 (61)
T 2jpc_A            4 RQVLKLIDEGYTNHGISEKLHISIKTVETHRMNMMR   39 (61)
T ss_dssp             HHHHHHHHTSCCSHHHHHHTCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456777889999999999999999999999988653

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

Probab=96.53  E-value=0.0011  Score=48.83  Aligned_cols=68  Identities=18%  Similarity=0.164  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH
Q psy1898         103 HIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       103 ~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      ..|.+|+..+.. +.+..+||+.+++|++||++.+++..+.|.+.....++..--.+++...+.+...+
T Consensus        21 ~~r~~IL~~L~~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l~~~~~~~~~~~~   89 (114)
T 2oqg_A           21 ETRWEILTELGRADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKVGREIRYRALGAELNKTARTL   89 (114)
T ss_dssp             HHHHHHHHHHHHSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEechHHHHHHHHHH
Confidence            678888887655 49999999999999999999999999999885432221122345555544444443

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.47  E-value=0.0022  Score=43.81  Aligned_cols=45  Identities=13%  Similarity=0.299  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +.+.+|++++.+   .++..+||+.|+||++||++.++..++.|.+..
T Consensus        10 ~~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           10 NLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            467788887753   389999999999999999999999999998743

>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=96.44  E-value=0.0038  Score=42.79  Aligned_cols=42  Identities=10%  Similarity=0.025  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+-    +|+|..+||..+|+|.+||..++.+..
T Consensus        10 ~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~   55 (73)
T 1ku3_A           10 KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL   55 (73)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777766666665    899999999999999999999988754

>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=96.43  E-value=0.0084  Score=39.63  Aligned_cols=44  Identities=23%  Similarity=0.138  Sum_probs=36.1

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      ..|..++..++..++.||.+.|.+ .+..     ||.+||+|.|+..|+.
T Consensus         8 ~~i~~ll~~~~~~t~~el~~~l~~-~~~~-----vs~~Tv~R~L~~lg~v   51 (64)
T 2p5k_A            8 IKIREIITSNEIETQDELVDMLKQ-DGYK-----VTQATVSRDIKELHLV   51 (64)
T ss_dssp             HHHHHHHHHSCCCSHHHHHHHHHH-TTCC-----CCHHHHHHHHHHHTCE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHH-hCCC-----cCHHHHHHHHHHcCCE
Confidence            345667777889999999999977 6664     8999999999988764

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=96.42  E-value=0.0042  Score=42.09  Aligned_cols=42  Identities=17%  Similarity=0.173  Sum_probs=34.4

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..++...+ .|+.++.+|.+..+||+.+++|.+||+.++++-.
T Consensus        10 ~~L~~~e~-~il~~~~~g~s~~eIA~~l~is~~tV~~~~~~~~   51 (74)
T 1fse_A           10 PLLTKRER-EVFELLVQDKTTKEIASELFISEKTVRNHISNAM   51 (74)
T ss_dssp             CCCCHHHH-HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34665555 5666678899999999999999999999999854

>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=96.40  E-value=0.0032  Score=42.61  Aligned_cols=43  Identities=9%  Similarity=0.003  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+    .+|+|..+||+.+|||.+||..++.+-..
T Consensus         5 ~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~   51 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALR   51 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36666665555555    48999999999999999999999988654

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=96.35  E-value=0.0041  Score=46.76  Aligned_cols=39  Identities=15%  Similarity=0.143  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...|.+|+.++.+|.|.++|++.+|+|.+||+|+.+-.+
T Consensus        45 laqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv~r~L~   83 (107)
T 3frw_A           45 LSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLN   83 (107)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHHHHHHH
Confidence            477999999999999999999999999999999876554

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.22  E-value=0.0037  Score=44.88  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ...+.+|+.++. .|.+..+||+.||||+++|++-+.+..+.|.+...
T Consensus        16 ~~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            478899998765 57999999999999999999999999999988543

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.22  E-value=0.0055  Score=42.92  Aligned_cols=42  Identities=19%  Similarity=0.250  Sum_probs=36.6

Q ss_pred             HHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      |.+|+.++..  ..+..+||+.|+||++||++.++...+.|.+.
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~   45 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQ   45 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            5677776653  49999999999999999999999999999875

>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=96.22  E-value=0.0023  Score=47.15  Aligned_cols=46  Identities=24%  Similarity=0.311  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ...|.+|+.++..+ .+..+||+.+++|++||++.++...+.|.+..
T Consensus        25 ~~~r~~IL~~L~~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~   71 (106)
T 1r1u_A           25 DYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA   71 (106)
T ss_dssp             SHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            36788898876554 89999999999999999999999999998753

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=96.20  E-value=0.0058  Score=43.47  Aligned_cols=43  Identities=7%  Similarity=-0.020  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+-    +|+|..+||..+|||.+||..++.+-..
T Consensus        18 ~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~   64 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            366677766666565    8999999999999999999999988653

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=96.18  E-value=0.0065  Score=44.76  Aligned_cols=42  Identities=17%  Similarity=0.173  Sum_probs=35.1

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|...+ .|+.++.+|++.++||+.++||.+||..++.+-.
T Consensus        33 ~~Lt~re~-~Vl~l~~~G~s~~EIA~~L~iS~~TV~~~l~ri~   74 (99)
T 1p4w_A           33 KRLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM   74 (99)
T ss_dssp             SSCCHHHH-HHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            44666666 5667778999999999999999999999998754

>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=96.18  E-value=0.0053  Score=46.20  Aligned_cols=42  Identities=19%  Similarity=0.096  Sum_probs=35.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-+...+.+|+|..+||..+|||.+||++++.|-+
T Consensus        25 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~ra~   66 (113)
T 1xsv_A           25 LLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTG   66 (113)
T ss_dssp             GSCHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366677766666678999999999999999999999998854

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

Probab=96.16  E-value=0.00088  Score=53.14  Aligned_cols=72  Identities=15%  Similarity=0.206  Sum_probs=55.2

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH
Q psy1898         100 LPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK  171 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~  171 (230)
                      ++...|.+|+.++..| .+..+||+.++++++||++-++..++.|.+...+.+...--.++++..+.+..++.
T Consensus        55 L~~p~R~~IL~~L~~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~~~~~l~~~l~  127 (151)
T 3f6v_A           55 AAEPTRRRLVQLLTSGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLDPQGLAQLRALFD  127 (151)
T ss_dssp             HTSHHHHHHHHHGGGCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHH
Confidence            4458899999977654 99999999999999999999999999998854433222334567776666666554

>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=96.16  E-value=0.0049  Score=43.48  Aligned_cols=42  Identities=21%  Similarity=0.357  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .++...+ .|+.++.+|++.++||+.++||.+||..++.+-.+
T Consensus        21 ~Lt~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           21 QLTPRER-DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK   62 (82)
T ss_dssp             GSCHHHH-HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3555555 56666789999999999999999999999988654

>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=96.10  E-value=0.02  Score=34.94  Aligned_cols=45  Identities=11%  Similarity=0.127  Sum_probs=35.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      ||..++++....|..+..+  ..+..+|++.|    |       +|.+||++++++..
T Consensus         2 R~~~l~~~~~~~i~~~~~~--g~s~~~IA~~l----g-------is~~Tv~~~~~~~~   46 (51)
T 1tc3_C            2 RGSALSDTERAQLDVMKLL--NVSLHEMSRKI----S-------RSRHCIRVYLKDPV   46 (51)
T ss_dssp             CSCCCCHHHHHHHHHHHHT--TCCHHHHHHHH----T-------CCHHHHHHHHHCST
T ss_pred             CCCCCCHHHHHHHHHHHHc--CCCHHHHHHHH----C-------cCHHHHHHHHhhHH
Confidence            6778888888788777644  47888888755    4       49999999998753

>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=96.07  E-value=0.0024  Score=48.42  Aligned_cols=46  Identities=22%  Similarity=0.190  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         103 HIRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       103 ~~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ..|.+|+.++. . +.+..+||+.+++|++||++.++...+.|.+...
T Consensus        42 ~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~   89 (122)
T 1u2w_A           42 ENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR   89 (122)
T ss_dssp             HHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            67888998776 4 4899999999999999999999999999987543

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=96.05  E-value=0.014  Score=46.24  Aligned_cols=46  Identities=22%  Similarity=0.146  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         162 VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       162 ~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      -.+.|.+++.+++..+..|+.+.|.+ .|+.     ||.+||+|.|+++++.
T Consensus         6 R~~~I~~li~~~~~~tq~eL~~~L~~-~G~~-----VtqaTisRDL~eL~~v   51 (149)
T 1b4a_A            6 RHIKIREIIMSNDIETQDELVDRLRE-AGFN-----VTQATVSRDIKEMQLV   51 (149)
T ss_dssp             HHHHHHHHHHHSCCCSHHHHHHHHHH-TTCC-----CCHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHCCCccHHHHHHHHHH-cCCC-----cCHHHHHHHHHHcCCe
Confidence            45688999999999999999999988 8995     9999999999999875

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=96.00  E-value=0.0061  Score=46.66  Aligned_cols=71  Identities=10%  Similarity=0.044  Sum_probs=49.1

Q ss_pred             hhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcC-CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHH
Q psy1898          58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPL-PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~-s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ....-++.+..+.=....++.+-|.--  |        +...+ ....|.+|+.++.+|+|.++||+.+|+|..||.|..
T Consensus        27 ~~~~d~L~~AIl~l~~~ee~~~fl~dL--~--------T~~E~~aLs~R~eV~klL~~G~syreIA~~~g~S~aTIsRv~   96 (119)
T 3kor_A           27 GAALDELFDAILTLENREECYQFFDDL--C--------TVNEIQSLSQRLQVAKMIKQGYTYATIEQESGASTATISRVK   96 (119)
T ss_dssp             SHHHHHHHHHHHTCCSHHHHHHHHHHH--S--------CHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHCCCHHHHHHHH
T ss_pred             cccHHHHHHHHHHhCCHHHHHHHHHHh--C--------CchHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            555566666665555666655444200  0        11122 446789999999999999999999999999999975


Q ss_pred             HH
Q psy1898         137 NR  138 (230)
Q Consensus       137 kR  138 (230)
                      +-
T Consensus        97 r~   98 (119)
T 3kor_A           97 RS   98 (119)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

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

Probab=95.95  E-value=0.0039  Score=44.96  Aligned_cols=45  Identities=22%  Similarity=0.180  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ..|.+|+.++....+..+||+.++||++||++.++...+.|.+..
T Consensus        31 ~~r~~Il~~L~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~   75 (96)
T 1y0u_A           31 PVRRKILRMLDKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIER   75 (96)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            678889887744599999999999999999999999999998753

>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=95.89  E-value=0.0072  Score=43.08  Aligned_cols=46  Identities=13%  Similarity=0.263  Sum_probs=38.9

Q ss_pred             CHHHHHHHHHHHH-cC----CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         101 PNHIRLKIVEMAA-AG----VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       101 s~~~R~rIV~l~~-~G----~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+...+|+.++. .+    .+..+||+.||||++||.+.+.+.++.|.+.
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~   58 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   58 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3466777887664 34    7999999999999999999999999999874

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=95.88  E-value=0.0096  Score=49.24  Aligned_cols=48  Identities=17%  Similarity=0.191  Sum_probs=39.0

Q ss_pred             CCCcCCH-HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh-hhC
Q psy1898          96 NGRPLPN-HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ-ETG  143 (230)
Q Consensus        96 ~g~~~s~-~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~-e~G  143 (230)
                      +.+++|. +.-.++..++..|++..+||+.+|||+.||++|++..+ +.|
T Consensus         4 Take~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~   53 (192)
T 1zx4_A            4 TALQHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAASAPEE   53 (192)
T ss_dssp             -CCSSCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHH
T ss_pred             ccccccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHhccchh
Confidence            4566665 45567777888999999999999999999999999887 444

>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=95.84  E-value=0.0081  Score=46.07  Aligned_cols=41  Identities=10%  Similarity=0.097  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++ ++.+|+|..+||+.+|||.+||.+++.|.+
T Consensus       109 ~L~~~~r~v~~-~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  149 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLIRGYSYREIATILSKNLKSIDNTIQRIR  149 (164)
T ss_dssp             HSCHHHHHHHH-HHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            35667777666 788999999999999999999999988754

>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=95.76  E-value=0.013  Score=42.40  Aligned_cols=41  Identities=15%  Similarity=0.295  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++...| .|+.++.+|++.++||+.++||.+||..++.+-.+
T Consensus        28 Lt~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   68 (95)
T 3c57_A           28 LTDQER-TLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLA   68 (95)
T ss_dssp             CCHHHH-HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            555555 55555689999999999999999999999988653

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=95.74  E-value=0.0078  Score=43.07  Aligned_cols=41  Identities=15%  Similarity=0.131  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ++...| .|+.++.+|++..+||..++||.+||..++.+-.+
T Consensus        30 Lt~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   70 (91)
T 2rnj_A           30 LTEREM-EILLLIAKGYSNQEIASASHITIKTVKTHVSNILS   70 (91)
T ss_dssp             CCSHHH-HHHHHHHTTCCTTHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            454555 45556789999999999999999999999988654

>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=95.70  E-value=0.0058  Score=43.00  Aligned_cols=46  Identities=13%  Similarity=0.263  Sum_probs=38.0

Q ss_pred             CHHHHHHHHHHHH-cC----CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         101 PNHIRLKIVEMAA-AG----VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       101 s~~~R~rIV~l~~-~G----~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+...+|+.++. .+    .+..+||+.|+|+++||.+.+.+..+.|.+.
T Consensus        12 ~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~   62 (77)
T 1qgp_A           12 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   62 (77)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEE
T ss_pred             CHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3456677777554 34    7999999999999999999999999999874

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=95.70  E-value=0.011  Score=40.67  Aligned_cols=40  Identities=18%  Similarity=0.179  Sum_probs=32.3

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         101 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       101 s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      |...+ .|+.++.+|++..+||..+++|.+||+.++.+-.+
T Consensus        18 ~~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~   57 (79)
T 1x3u_A           18 SERER-QVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMA   57 (79)
T ss_dssp             CHHHH-HHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            43444 55566788999999999999999999999987654

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=95.64  E-value=0.0031  Score=46.01  Aligned_cols=67  Identities=19%  Similarity=0.189  Sum_probs=45.8

Q ss_pred             HHHHHHHH-HHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         102 NHIRLKIV-EMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       102 ~~~R~rIV-~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      ...|.+|+ .+... +.+.++||+.+++|++||++-++...+. .+...+.+...--.++++..+.+...
T Consensus        26 ~~~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~~gr~~~y~l~~~~~~~~~~~   94 (99)
T 2zkz_A           26 HPMRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNRQGLEIYYSINNPKVEGIIKL   94 (99)
T ss_dssp             SHHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEEETTEEEEECCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheEeCcEEEEEEChHHHHHHHHH
Confidence            47788998 45444 5999999999999999999999999988 66433332222233444444444433

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=95.61  E-value=0.011  Score=39.60  Aligned_cols=37  Identities=5%  Similarity=0.009  Sum_probs=29.9

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+.-|..++. .+....++|+.||||++|+++++++|.
T Consensus        20 E~~~i~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~g   57 (63)
T 3e7l_A           20 EKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLN   57 (63)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            4455555554 467899999999999999999999985

>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=95.60  E-value=0.014  Score=39.03  Aligned_cols=41  Identities=17%  Similarity=0.136  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +....|.-|..+++...+..++|+.||||++|+++++++|.
T Consensus        18 l~~~Er~~I~~aL~~~gn~~~aA~~LGIsr~tL~rklkk~g   58 (61)
T 1g2h_A           18 IGFYEAQVLKLFYAEYPSTRKLAQRLGVSHTAIANKLKQYG   58 (61)
T ss_dssp             CSHHHHHHHHHHHHHSCSHHHHHHHTTSCTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            44456666666665446889999999999999999999874

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=95.55  E-value=0.027  Score=41.75  Aligned_cols=68  Identities=12%  Similarity=0.002  Sum_probs=47.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      +++..++|+.+|||..|+..|.+    .|.+.|..+..+.-+..+.++...+..... .+-.++..+|++.+.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~----~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~   69 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDD----IGLLVPSERSHAGHRRYSDADLDRLQQILFYRELGFPLDEVAALLD   69 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHH----HTSSCCSEECSSCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            36889999999999999998865    487766442222356678877665543332 334688888888774

>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=95.48  E-value=0.016  Score=46.66  Aligned_cols=33  Identities=21%  Similarity=0.395  Sum_probs=29.9

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      ..|.+++.+|.|..+||+.|+||++||++|++.
T Consensus       149 ~~i~~~~~~G~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          149 DAVLNMWQQGLGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            367888899999999999999999999999864

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

Probab=95.43  E-value=0.048  Score=41.47  Aligned_cols=100  Identities=17%  Similarity=0.087  Sum_probs=57.8

Q ss_pred             CcCCHHHHHHHHHHHHcC-------C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898          98 RPLPNHIRLKIVEMAAAG-------V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G-------~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      .++...+-..+......|       + |.+++|+.|+||++||.+-+++..+.|.+...+..|  ..+ .+...+.+.+.
T Consensus        10 ~~~~~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~~~G--~~V-~~~~~~~~~~~   86 (126)
T 3ic7_A           10 RAIYLQIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNKRGIG--FFV-ASGAKMLIHSL   86 (126)
T ss_dssp             --CTTHHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEETTTE--EEE-CTTHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEcCCc--cEE-ccCcHHHHHHH
Confidence            344445555555555544       2 788999999999999999999999999886554322  222 22223333333


Q ss_pred             HHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH
Q psy1898         170 KKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR  208 (230)
Q Consensus       170 ~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr  208 (230)
                      .... -..........+.. .|+       +...+...+.
T Consensus        87 ~~~~~~~~~le~~~~~~~~-~~~-------~~~~l~~l~~  118 (126)
T 3ic7_A           87 RKEQFLKEEVGSFFRQLYT-LGI-------SIKEIEKMYY  118 (126)
T ss_dssp             HHTTCCCCCSHHHHHHHHH-TTC-------CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH-cCC-------CHHHHHHHHH
Confidence            3222 22334445555544 454       6666666554

>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=95.42  E-value=0.018  Score=41.48  Aligned_cols=41  Identities=17%  Similarity=0.122  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++...+ .|+.++.+|++.++||+.|+||..||...+.+-.
T Consensus        29 ~Lt~rE~-~Vl~l~~~G~s~~eIA~~L~iS~~TV~~~~~~i~   69 (90)
T 3ulq_B           29 VLTPREC-LILQEVEKGFTNQEIADALHLSKRSIEYSLTSIF   69 (90)
T ss_dssp             CCCHHHH-HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3554444 5677777999999999999999999999988754

>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=95.41  E-value=0.015  Score=46.15  Aligned_cols=42  Identities=24%  Similarity=0.309  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+.+|+|..+||+.+|||.+||.+++.|.+.
T Consensus       141 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  182 (194)
T 1or7_A          141 LPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRARE  182 (194)
T ss_dssp             SCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            566666666566778999999999999999999999988653

>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=95.34  E-value=0.0053  Score=46.63  Aligned_cols=45  Identities=18%  Similarity=0.208  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ..|.+|+.++.+ ..+..+||+.+++|++||++-++...+.|.+..
T Consensus        46 ~~rl~IL~~L~~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~   91 (122)
T 1r1t_A           46 PNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY   91 (122)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            678888887766 489999999999999999999999999997753

>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=95.28  E-value=0.074  Score=41.03  Aligned_cols=68  Identities=9%  Similarity=0.049  Sum_probs=47.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+..|.+    .|.+.|..+..+.-+..+.++...|..... .+-.+++.+|++.|..
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~----~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~   69 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE----KGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL   69 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----TTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            4788999999999999988754    577765433222356678877665543321 3347899999988864

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=95.24  E-value=0.026  Score=41.90  Aligned_cols=39  Identities=18%  Similarity=0.281  Sum_probs=32.5

Q ss_pred             HHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898         104 IRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus       104 ~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      .-.+|..+ +.+|++..+||+.||||+.||++.+++.++.
T Consensus        22 ~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~   61 (101)
T 2w7n_A           22 QTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAA   61 (101)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            33555554 5689999999999999999999999998765

>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=95.14  E-value=0.027  Score=38.24  Aligned_cols=44  Identities=18%  Similarity=0.205  Sum_probs=31.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      ++..+||+.+|||++||+++++     |..        ....++++.+++|.+..++
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLn-----g~~--------~~~~vs~et~~rI~~aa~~   44 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVIN-----GKA--------KQYRVSDKTVEKVMAVVRE   44 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHH-----TCT--------TTTTCTTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc-----CCC--------CCCCCCHHHHHHHHHHHHH
Confidence            3678999999999999999986     110        0013467777777776543

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=95.12  E-value=0.04  Score=38.62  Aligned_cols=69  Identities=17%  Similarity=0.175  Sum_probs=46.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-h-CCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-T-NPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~-~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+..|.+.   .|.+.|.....+.-+..+.++...|..... . +-..++.+|++.|..
T Consensus         6 ~~i~e~A~~~gvs~~tlR~ye~~---~gl~~p~r~~~~g~R~Y~~~dl~~l~~I~~l~~~~G~sl~ei~~~l~~   76 (81)
T 2jml_A            6 LRIRTIARMTGIREATLRAWERR---YGFPRPLRSEGNNYRVYSREEVEAVRRVARLIQEEGLSVSEAIAQVKT   76 (81)
T ss_dssp             EEHHHHHHTTSTTHHHHHHHHHH---TCCSCCBSSSCSSSCEECHHHHHHHHHHHHHHHHTSTHHHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHh---CCCCCCcCCCCCCeeecCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            57899999999999999988654   355555432202356677877665543321 2 446788888888765

>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=95.12  E-value=0.018  Score=41.51  Aligned_cols=37  Identities=11%  Similarity=-0.005  Sum_probs=30.0

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .|.-|..+++ .+.+..++|+.||||++|+++++++|.
T Consensus        52 E~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rklkk~~   89 (91)
T 1ntc_A           52 ERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            4555555554 467889999999999999999999985

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

Probab=95.02  E-value=0.086  Score=39.94  Aligned_cols=52  Identities=17%  Similarity=0.181  Sum_probs=39.5

Q ss_pred             cCCHHHHHHHHHHHHcC-------C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898          99 PLPNHIRLKIVEMAAAG-------V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-------~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      ++..++...|......|       + |..++|++|+||+.||.+-+++..+.|.+...+.
T Consensus        13 ~~~~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g   72 (125)
T 3neu_A           13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
T ss_dssp             CHHHHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecC
Confidence            34445555555555544       2 6899999999999999999999999998865443

>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=95.00  E-value=0.017  Score=41.10  Aligned_cols=69  Identities=13%  Similarity=0.084  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC---CCCCCCCCCCHHHHHHHHHHH
Q psy1898         102 NHIRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV---IGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       102 ~~~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~---~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      ...|.+|+..+.  .+.+..+||+.+++|++||++.+++..+.|-+....   .+....-.+++.-.+.+..+.
T Consensus        15 ~~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~~~~   88 (100)
T 1ub9_A           15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHHHHH
Confidence            366788887553  459999999999999999999999999999774211   111122345666554444433

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=94.97  E-value=0.017  Score=42.18  Aligned_cols=36  Identities=25%  Similarity=0.245  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.+.+|++++. .+.+..+||+.+|||.+||+++++
T Consensus         6 ~~R~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~   42 (93)
T 2l0k_A            6 KERTIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLT   42 (93)
T ss_dssp             HHHHHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            355566776554 579999999999999999999985

>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=94.95  E-value=0.0068  Score=41.21  Aligned_cols=23  Identities=9%  Similarity=0.049  Sum_probs=20.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      ++..++|+.||||++|+++|++.
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~   25 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ   25 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC
Confidence            36789999999999999999864

>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=94.93  E-value=0.017  Score=47.45  Aligned_cols=33  Identities=21%  Similarity=0.371  Sum_probs=29.9

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+|.+++.+|.|..+||+.||||++||++|++.
T Consensus       166 ~~i~~~~~~G~s~~~Ia~~l~is~~tv~r~l~~  198 (209)
T 2r0q_C          166 HRVVEMLEEGQAISKIAKEVNITRQTVYRIKHD  198 (209)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            467778889999999999999999999999874

>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=94.81  E-value=0.029  Score=45.68  Aligned_cols=42  Identities=19%  Similarity=0.180  Sum_probs=35.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|...|.-++..+.+|+|..+||+.+|||.+||.+++.+..
T Consensus       187 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~  228 (239)
T 1rp3_A          187 KLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKAL  228 (239)
T ss_dssp             TSCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            367777766666678899999999999999999999998754

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=94.80  E-value=0.027  Score=39.24  Aligned_cols=44  Identities=25%  Similarity=0.440  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHc----CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA----GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~----G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|..|++++.+    ..+..+|++.+     +||.+|||+.++.+.+.|.+.
T Consensus        17 ~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~   69 (83)
T 2fu4_A           17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT   69 (83)
T ss_dssp             HHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeE
Confidence            677888887743    48999999999     999999999999999999874

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.78  E-value=0.016  Score=43.07  Aligned_cols=44  Identities=16%  Similarity=0.185  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+.+|+.++.+ ..+..+||+.++++++||++.+++..+.|.+.
T Consensus        32 ~~~~~il~~L~~~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~   76 (119)
T 2lkp_A           32 PSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVV   76 (119)
T ss_dssp             HHHHHHHHHHHHCCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEE
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            557778876665 69999999999999999999999999999774

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=94.77  E-value=0.094  Score=40.90  Aligned_cols=68  Identities=18%  Similarity=0.029  Sum_probs=48.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||+.|+.-|.+    .|.+.|..+..+.-+..++++...|..... ..-..++.+|++.|..
T Consensus         3 ~~I~e~A~~~gvs~~tLR~Ye~----~GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~~   71 (142)
T 3gp4_A            3 LNIKEASEKSGVSADTIRYYER----IGLIPPIHRNESGVRKFGAEDLRWILFTRQMRRAGLSIEALIDYLAL   71 (142)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHH----HTSSCCCCBCTTSCBCBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            5789999999999999987754    488877444333457778877665543322 3457899999888754

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=94.70  E-value=0.03  Score=40.08  Aligned_cols=46  Identities=13%  Similarity=0.186  Sum_probs=36.4

Q ss_pred             CHHHHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         101 PNHIRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       101 s~~~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +...+..++.++.  .+.+..+||+.+++|++||++.++...+.|.+.
T Consensus        20 ~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~   67 (109)
T 2d1h_A           20 TDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVV   67 (109)
T ss_dssp             CHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3344444445554  359999999999999999999999999999773

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=94.69  E-value=0.067  Score=39.57  Aligned_cols=67  Identities=15%  Similarity=0.084  Sum_probs=46.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV  186 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~  186 (230)
                      ++..++|+.+|||+.|+..|.+    .|.+.|..+..+..+..++++...+..... .+-..+..+|++.+.
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~~I~~~l~   70 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDN----IELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLD   70 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH----TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----CCCCCCCeECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            5789999999999999998854    587766442222356678887666543332 233678888888775

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=94.46  E-value=0.025  Score=39.87  Aligned_cols=45  Identities=22%  Similarity=0.277  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHH-c-----C--CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAA-A-----G--VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~-~-----G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +...+|++.++ .     |  .|..+||+.||||..||.+-++...+.|.+..
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R   56 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEK   56 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            44566666543 2     3  67999999999999999999999999998743

>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=94.41  E-value=0.029  Score=41.16  Aligned_cols=46  Identities=22%  Similarity=0.254  Sum_probs=38.5

Q ss_pred             HHHHHHHHHH-HcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         103 HIRLKIVEMA-AAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       103 ~~R~rIV~l~-~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      +.+.+|+... ..|  .+..+||+.||||++||++-+++..+.|.+...
T Consensus        18 ~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             STTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3567788755 444  899999999999999999999999999987543

>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=94.36  E-value=0.033  Score=38.02  Aligned_cols=41  Identities=17%  Similarity=0.195  Sum_probs=32.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+..+||+..|||++||++|++              + ++ .++++.++.|.+..++
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln--------------~-~~-~vs~~t~~rV~~~a~~   50 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM--------------N-PD-KVSQATRNRVEKAARE   50 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT--------------C-CC-CSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc--------------C-CC-CCCHHHHHHHHHHHHH
Confidence            6899999999999999999973              1 12 2578888888777654

>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=94.31  E-value=0.055  Score=41.96  Aligned_cols=44  Identities=20%  Similarity=0.365  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +...+|+.++.. + .+.++||+.+|+|++||++.+++..+.|.+.
T Consensus         7 ~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~   52 (151)
T 2cyy_A            7 EIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIK   52 (151)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            455678876653 4 9999999999999999999999999999763

>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=94.29  E-value=0.047  Score=40.19  Aligned_cols=41  Identities=10%  Similarity=0.020  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+-    +++|..+||..+|||..||..+..+..
T Consensus        20 Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAl   64 (99)
T 3t72_q           20 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKAL   64 (99)
T ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55566655554443    689999999999999999999987643

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=94.26  E-value=0.11  Score=35.50  Aligned_cols=25  Identities=12%  Similarity=0.320  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++||++|.+
T Consensus        23 ~~gltq~~lA~~~gvs~~~is~~e~   47 (80)
T 3kz3_A           23 ELGLSYESVADKMGMGQSAVAALFN   47 (80)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            4599999999999999999999974

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=94.20  E-value=0.013  Score=45.72  Aligned_cols=43  Identities=14%  Similarity=0.139  Sum_probs=36.1

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-++..+.+|+|..+||+.+|||.+||...+.|-+.
T Consensus        93 ~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~  135 (157)
T 2lfw_A           93 RMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALA  135 (157)
T ss_dssp             TSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3677777666666788999999999999999999999988653

>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=94.11  E-value=0.11  Score=45.03  Aligned_cols=79  Identities=14%  Similarity=0.086  Sum_probs=53.8

Q ss_pred             ChhHHHHHHHHHhcCCChhhhhhhhc-------cccccc------------ccCCcccCCCc--CCHHHHHHHHHHHHc-
Q psy1898          57 PNHIRLKIVEMAAAGVRPCVISRQLR-------VSHGVN------------QLGGVFINGRP--LPNHIRLKIVEMAAA-  114 (230)
Q Consensus        57 p~~~r~~I~e~~~~g~~~~~isr~lr-------vshg~~------------~l~~~~~~g~~--~s~~~R~rIV~l~~~-  114 (230)
                      ..+.|..|+.++.+|.+..++++.+.       ++..++            .+...-..|++  ++.   ..+..++.. 
T Consensus         8 ~~~~R~~i~~~~~~G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~g~~~l~~~~r~grp~~~~~---~~i~~~v~~~   84 (345)
T 3hot_A            8 KEQTRTVLIFCFHLKKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKSGDFDVDDKEHGKPPKRYED---AELQALLDED   84 (345)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTTCCCCCSCCCCCCCCCSSCH---HHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhCCCccccCCCCCCCCCcccH---HHHHHHHHhC
Confidence            35678889999999999999999887       654333            11111112223  333   233333333 


Q ss_pred             -CCCHHHHhhhhccccchhhhHHHH
Q psy1898         115 -GVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       115 -G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                       ..+..+||+.|+||.+||++++++
T Consensus        85 ~~~t~~~ia~~l~vs~~tV~r~L~~  109 (345)
T 3hot_A           85 DAQTQKQLAEQLEVSQQAVSNRLRE  109 (345)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             ccchHHHHHHHHCCCHHHHHHHHHH
Confidence             499999999999999999999987

>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=94.07  E-value=0.054  Score=41.76  Aligned_cols=44  Identities=20%  Similarity=0.400  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+.+|+.++.. + .+.++||+.+|+|++||++.+++..+.|.+.
T Consensus         3 ~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   48 (150)
T 2pn6_A            3 EIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIK   48 (150)
T ss_dssp             HHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            456788887754 3 8999999999999999999999999999763

>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=94.06  E-value=0.015  Score=38.68  Aligned_cols=26  Identities=15%  Similarity=0.109  Sum_probs=22.5

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.+.+.+..++|+.+|||++||++|.
T Consensus         6 ~i~~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            6 VIDHFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHHHHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HHHHcCCHHHHHHHhCCCHHHHHHHH
Confidence            44555699999999999999999995

>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=94.06  E-value=0.055  Score=41.95  Aligned_cols=43  Identities=16%  Similarity=0.259  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .+..+||+.+|+|++||++.+++..+.|.+
T Consensus         8 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   52 (152)
T 2cg4_A            8 NLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGII   52 (152)
T ss_dssp             HHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence            445678876654 3 999999999999999999999999999966

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=94.05  E-value=0.022  Score=39.58  Aligned_cols=21  Identities=19%  Similarity=0.131  Sum_probs=19.8

Q ss_pred             CHHHHhhhhccccchhhhHHH
Q psy1898         117 RPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +..++|+.||||++||++|++
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            589999999999999999986

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=93.98  E-value=0.061  Score=41.60  Aligned_cols=43  Identities=9%  Similarity=0.308  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .|..+||+.+|+|++||++.+++..+.|.+
T Consensus         9 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   53 (151)
T 2dbb_A            9 RVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGII   53 (151)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            445577776654 3 999999999999999999999999999976

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=93.97  E-value=0.058  Score=42.33  Aligned_cols=43  Identities=16%  Similarity=0.346  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .+.++||+.+|+|++||++.+++..+.|.+
T Consensus        10 ~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   54 (162)
T 2p5v_A           10 KTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIV   54 (162)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            455677776653 3 999999999999999999999999999966

>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=93.92  E-value=0.062  Score=41.38  Aligned_cols=43  Identities=21%  Similarity=0.342  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .+..+||+.+|+|++||++.+++..+.|.+
T Consensus         5 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   49 (144)
T 2cfx_A            5 QIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGII   49 (144)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            345577776653 3 999999999999999999999999999966

>3v4g_A Arginine repressor; vibrio vulnificus CMCP6, virulence, type secretion system, center for structural genomics of infecti diseases, csgid; 1.60A {Vibrio vulnificus} PDB: 1aoy_A

Probab=93.89  E-value=0.15  Score=41.62  Aligned_cols=49  Identities=18%  Similarity=0.110  Sum_probs=43.6

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCC-CHhHHHHHHHcCCCC
Q psy1898         159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAP-SVSSISRLLRGGRRD  213 (230)
Q Consensus       159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~v-S~sTV~R~Lr~~g~~  213 (230)
                      .....+.|++++.+++-.|..|+.+.|++ .|+.     + +.+||+|-|++.|+.
T Consensus        31 ~~~r~~~I~eiI~~~~I~TQeEL~~~L~~-~Gi~-----viTQATvSRDIkELglv   80 (180)
T 3v4g_A           31 QDNLVRAFKALLKEERFGSQGEIVEALKQ-EGFE-----NINQSKVSRMLTKFGAV   80 (180)
T ss_dssp             HHHHHHHHHHHHHHTCCCSHHHHHHHHHH-TTCT-----TCCHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHhhCCcCCHHHHHHHHHH-CCCc-----ccCHHHHHHHHHHcCCE
Confidence            34567789999999999999999999988 8996     6 999999999999975

>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=93.82  E-value=0.044  Score=42.64  Aligned_cols=52  Identities=17%  Similarity=0.161  Sum_probs=44.1

Q ss_pred             CCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         154 KPRVATPDVEKRIEEYK-KTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~-~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ....+|.++...|..+. +++|.++..++++|...+++..     ||.+||+++|+..
T Consensus         8 ~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~-----is~stis~ilk~k   60 (144)
T 1iuf_A            8 KRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKD-----ISQPSVSQILSSK   60 (144)
T ss_dssp             SSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSC-----CSSSSTTHHHHHH
T ss_pred             cCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCC-----CcHHHHHHHHhhH
Confidence            34567888888888888 7899999999999999888653     6999999999875

>3lap_A Arginine repressor; arginine repressor, DNA binding, DNA-canavanine ternary complex; HET: GGB; 2.15A {Mycobacterium tuberculosis} PDB: 3fhz_A* 3ere_D* 3laj_A*

Probab=93.79  E-value=0.1  Score=42.25  Aligned_cols=47  Identities=19%  Similarity=0.081  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +-.+.|++++.+++--|..||.+.|.+ .|+.     |+.+||+|-|++.|+.
T Consensus        20 ~R~~~I~~iI~~~~I~tQeEL~~~L~~-~Gi~-----vTQATlSRDikEL~lv   66 (170)
T 3lap_A           20 GRQARIVAILSSAQVRSQNELAALLAA-EGIE-----VTQATLSRDLEELGAV   66 (170)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHH-TTCC-----CCHHHHHHHHHHHTCE
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCC-----cCchhHHHHHHHcCcE
Confidence            346688999999999999999999988 8995     8999999999999975

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=93.76  E-value=0.059  Score=37.97  Aligned_cols=41  Identities=17%  Similarity=0.391  Sum_probs=35.3

Q ss_pred             HHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|++++. .| .+..++|++|+||..||.+-+....+.|.+.
T Consensus         5 ~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~   47 (78)
T 1xn7_A            5 IQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV   47 (78)
T ss_dssp             HHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            35666665 45 9999999999999999999999999999774

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=93.70  E-value=0.068  Score=42.14  Aligned_cols=43  Identities=14%  Similarity=0.274  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .|..+||+.+|+|++||.+-+++..+.|.+
T Consensus         3 ~~d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i   47 (162)
T 3i4p_A            3 RLDRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVI   47 (162)
T ss_dssp             HHHHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            455678887754 4 999999999999999999999999999965

>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=93.67  E-value=0.015  Score=42.89  Aligned_cols=45  Identities=13%  Similarity=0.237  Sum_probs=37.1

Q ss_pred             HHHHHHHHHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         105 RLKIVEMAAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       105 R~rIV~l~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      +..|+..+..|  + +..++|+.|+||++||.+-+++..+.|.+...+
T Consensus        30 ~~~I~~~l~~g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           30 IEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             HHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHhhhcCCCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            66776545445  4 999999999999999999999999999886444

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=93.66  E-value=0.03  Score=44.58  Aligned_cols=68  Identities=10%  Similarity=0.105  Sum_probs=50.5

Q ss_pred             CCHHHHHHHHHHHHc---C-CCHHHHhhhhc-cccchhhhHHHHHhhhCCCCc-----CCCCCCCCC---CCCHHHHHHH
Q psy1898         100 LPNHIRLKIVEMAAA---G-VRPCVISRQLR-VSHGCVSKILNRYQETGSIRP-----GVIGGSKPR---VATPDVEKRI  166 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~---G-~s~~~IAr~lg-VS~sTV~kwikRy~e~G~v~p-----~~~gg~rpr---~lt~~~~~~I  166 (230)
                      +....|..|+..+..   + .+..+|+..++ ||.+|||+-++...+.|.+..     ...++++|.   .+|++-++.+
T Consensus        26 l~~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l  105 (151)
T 3u1d_A           26 VLHETRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALL  105 (151)
T ss_dssp             HCCHHHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHH
T ss_pred             hcchHHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHH
Confidence            344789999987654   3 68999999999 999999999999999997742     112234554   6777776655


Q ss_pred             H
Q psy1898         167 E  167 (230)
Q Consensus       167 ~  167 (230)
                      .
T Consensus       106 ~  106 (151)
T 3u1d_A          106 R  106 (151)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=93.62  E-value=0.061  Score=39.52  Aligned_cols=37  Identities=11%  Similarity=0.075  Sum_probs=29.5

Q ss_pred             HHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         104 IRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+.-|..++ ..+....++|+.||||++|+++++++|.
T Consensus        59 Er~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkLkk~g   96 (98)
T 1eto_A           59 EQPLLDMVMQYTLGNQTRAALMMGINRGTLRKKLKKYG   96 (98)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            444455544 4577899999999999999999999984

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=93.62  E-value=0.18  Score=39.51  Aligned_cols=69  Identities=10%  Similarity=-0.032  Sum_probs=49.5

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      -++..++|+.+|||..|+.-|.    +.|.+.|..+....-+..+.++...|..... ..-..++.+|++.|..
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye----~~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~~   85 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYD----KQGLFPFLQRNEKGDRIFNEEALKYLEMILCLKNTGMPIQKIKQFIDW   85 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHH----HTTCCTTCEECTTCCEEBCHHHHHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4789999999999999988775    4687765433223456778877666654332 4567999999988863

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=93.40  E-value=0.14  Score=40.09  Aligned_cols=69  Identities=12%  Similarity=0.050  Sum_probs=48.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      -++..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..++++...|..... ..-..+..+|++.+..
T Consensus         4 ~~tI~evA~~~Gvs~~tLR~ye~----~GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~~   73 (146)
T 3hh0_A            4 AWLISEFASVGDVTVRALRYYDK----INLLKPSDYTEGGHRLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQ   73 (146)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHH----TTSSCCSEECTTSCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHTS
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCeECCCCCEeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence            47899999999999999987754    588866533223456778887666643332 2346888888887743

>3iuo_A ATP-dependent DNA helicase RECQ; C-terminal, GI PSI, MCSG, structural genomics, midwest center for structur genomics; 1.60A {Porphyromonas gingivalis}

Probab=93.34  E-value=0.26  Score=37.35  Aligned_cols=92  Identities=18%  Similarity=0.064  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC-CCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHH
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEI  181 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~-v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI  181 (230)
                      ......+.++.+|++..+||..-+++.+||..-+..+...|. +.-..-   -+..++.+..+.|.....+.....+..+
T Consensus        20 ~t~~~t~~l~~~G~sleeIA~~R~L~~~TI~~Hl~~~v~~G~~l~i~~~---i~~~l~~~~~~~I~~~~~~~~~~~Lk~i   96 (122)
T 3iuo_A           20 KMKVSIVQQIDRKVALDDIAVSHGLDFPELLSEVETIVYSGTRINIDYF---INEVMDEDHLEDIFEYFKESTTDSLEEA   96 (122)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHTTCCCCCHHH---HHHHSCHHHHHHHHHHHHHCSCCCHHHH
T ss_pred             ccHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHcCCccCHHHH---cccccCHHHHHHHHHHHHHcCcccHHHH
Confidence            567788899999999999999999999999999999999996 321100   1113446777788888877777778888


Q ss_pred             HHHHHHhhCCCCCCCCCCHhHHHHH
Q psy1898         182 RDRLVKQDGICDKNSAPSVSSISRL  206 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~sTV~R~  206 (230)
                      .+.|..         .+|+-.|+=+
T Consensus        97 ~e~l~~---------~~sy~eIRlv  112 (122)
T 3iuo_A           97 MQELGK---------DYSEEEIRLV  112 (122)
T ss_dssp             HHHHTT---------TSCHHHHHHH
T ss_pred             HHHccC---------cCCHHHHHHH
Confidence            887743         2577666533

>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=93.33  E-value=0.043  Score=38.20  Aligned_cols=35  Identities=17%  Similarity=0.265  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+..++-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        18 ~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           18 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            44455555544 489999999999999999999975

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=93.32  E-value=0.056  Score=36.81  Aligned_cols=23  Identities=22%  Similarity=0.317  Sum_probs=21.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .+..++|+.||||++||++|++.
T Consensus        14 ~sq~~~A~~Lgvsq~aVS~~~~~   36 (65)
T 2cw1_A           14 KNQEYAARALGLSQKLIEEVLKR   36 (65)
T ss_dssp             SCHHHHHHHSSSCHHHHHHHHHT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHh
Confidence            49999999999999999999853

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=93.26  E-value=0.5  Score=39.58  Aligned_cols=68  Identities=18%  Similarity=0.159  Sum_probs=45.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..+.++.+.|.....  +....+..+|++.|..
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~----~GLl~p~~R~~~gyR~Y~~~dl~~L~~I~~lr~~~G~sL~eIk~~l~~   70 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLR----EGLLPPGRQVNATTAEYDEDHLRRLRLVRALIQVGKVPVATAREVLGH   70 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----HTSSCCC---------CCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCeeCCCCceeeCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence            4788999999999999987754    587766433223456778887766654432  3337999999998876

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=93.24  E-value=0.053  Score=37.58  Aligned_cols=32  Identities=16%  Similarity=0.215  Sum_probs=25.8

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhccccchhhhHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.+|..+. +.|+|..++|+.+|||++||++|.
T Consensus        11 ~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~   43 (74)
T 1neq_A           11 RADVIAGLKKRKLSLSALSRQFGYAPTTLANAL   43 (74)
T ss_dssp             HHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            34455433 568999999999999999999884

>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=93.23  E-value=0.094  Score=40.49  Aligned_cols=43  Identities=19%  Similarity=0.251  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++. +| .+..+||+.+|+|++||++.+++..+.|.+
T Consensus         7 ~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   51 (150)
T 2w25_A            7 DIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESRGVV   51 (150)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            44557777654 34 999999999999999999999999999976

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

Probab=93.23  E-value=0.88  Score=37.39  Aligned_cols=94  Identities=13%  Similarity=0.001  Sum_probs=60.0

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH----------HHHHhCCCCCHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE----------EYKKTNPGIFSWEIRDR  184 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~----------~l~~~~P~~t~~eI~~~  184 (230)
                      +.+..+||+.++||++||++.+++..+.|.+...+.   +.-.+|+.-++...          .++.+.-..+..++.+.
T Consensus        20 ~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~i~LT~~G~~~~~~~~~~h~~~e~~l~~~lg~~~~e~~~~   96 (214)
T 3hrs_A           20 KITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKK---AGYLLTDLGLKLVSDLYRKHRLIEVFLVHHLGYTTEEIHEE   96 (214)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT---TEEEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecC---CCeEECHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            489999999999999999999999999998743321   22345665443332          33333345555554443


Q ss_pred             HHHhhCCCCCCCCCCHhHHHHHHHcCCC---CCCCC
Q psy1898         185 LVKQDGICDKNSAPSVSSISRLLRGGRR---DDCDR  217 (230)
Q Consensus       185 L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~---~~~~~  217 (230)
                      ...-..+      +|..++.++-.-.+.   +||..
T Consensus        97 a~~lEh~------~s~~~~~~l~~~l~~p~~~Phg~  126 (214)
T 3hrs_A           97 AEVLEHT------VSDHFVERLDQLLDYPKACPHGG  126 (214)
T ss_dssp             HHHHHTT------SCHHHHHHHHHHTTCCSBCTTSC
T ss_pred             HHHHhcc------CCHHHHHHHHHHhCCCCCCcCcC
Confidence            3331223      688888887666654   45543

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=93.22  E-value=0.084  Score=40.09  Aligned_cols=43  Identities=23%  Similarity=0.272  Sum_probs=36.2

Q ss_pred             HHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ...+|+..+. .+ .+..+||+.+|+|++||++.+++..+.|.+.
T Consensus         5 ~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A            5 RDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEe
Confidence            3456777664 33 8999999999999999999999999999763

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

Probab=93.21  E-value=0.13  Score=38.68  Aligned_cols=62  Identities=21%  Similarity=0.243  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhh--ccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQL--RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE  167 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~l--gVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~  167 (230)
                      ....+|+.++.. | .++.+||+.+  ++|+++|++-+++-.+.|.+....+   .--.+|+.-.+++.
T Consensus        13 ~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~~r---g~Y~LT~~G~~~l~   78 (111)
T 3b73_A           13 IWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPLAN---GVYVITEEGEAYLN   78 (111)
T ss_dssp             HHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEECST---TCEEECHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEecCC---ceEEECchHHHHHH
Confidence            556788887753 5 9999999999  9999999999999999998864321   24567777666554

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=93.20  E-value=0.099  Score=43.42  Aligned_cols=42  Identities=17%  Similarity=0.180  Sum_probs=35.5

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|..++. |+.++.+|+|.++||+.++||.+||...+++-.
T Consensus       174 ~~Lt~~e~~-vl~~~~~g~s~~eIa~~l~is~~tV~~~~~~~~  215 (236)
T 2q0o_A          174 QMLSPREML-CLVWASKGKTASVTANLTGINARTVQHYLDKAR  215 (236)
T ss_dssp             GSCCHHHHH-HHHHHHTTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            457777764 667778999999999999999999999988755

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=93.09  E-value=0.035  Score=37.46  Aligned_cols=23  Identities=9%  Similarity=0.011  Sum_probs=21.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      ++..++|+.+|||++|+|+|++.
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~   33 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKS   33 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999985

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=93.08  E-value=0.067  Score=38.59  Aligned_cols=41  Identities=20%  Similarity=0.421  Sum_probs=35.1

Q ss_pred             HHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|++++. .| .+..++|+.|+||..||.+-+.++.+.|.+.
T Consensus         5 ~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~   47 (87)
T 2k02_A            5 MEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVV   47 (87)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            35666665 45 9999999999999999999999999999763

>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=93.07  E-value=0.073  Score=34.88  Aligned_cols=25  Identities=8%  Similarity=0.319  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999964

>1rr7_A Middle operon regulator; MOR, transcription; 2.20A {Enterobacteria phage MU} SCOP: a.4.1.14

Probab=93.03  E-value=0.05  Score=42.00  Aligned_cols=50  Identities=18%  Similarity=0.168  Sum_probs=38.4

Q ss_pred             cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898          93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET  142 (230)
Q Consensus        93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~  142 (230)
                      |++.+.......|.+-|..--.|.+..++|+.+++|..||++++++.+..
T Consensus        70 YIPk~~~~~~~~Rn~~I~~~f~G~n~~eLArkYgLSer~I~~Ii~~~r~~  119 (129)
T 1rr7_A           70 YIPRGQALDSLIRDLRIWNDFNGRNVSELTTRYGVTFNTVYKAIRRMRRL  119 (129)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHCCSSCHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             EeeCCchHHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            34444444446777777665569999999999999999999999987753

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=93.02  E-value=0.1  Score=41.68  Aligned_cols=43  Identities=19%  Similarity=0.305  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +...+|+.++.. + .|..+||+.+|+|++||++.+++..+.|.+
T Consensus        17 ~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I   61 (171)
T 2ia0_A           17 DLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQERGVI   61 (171)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            455577876653 4 899999999999999999999999999976

>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=93.02  E-value=0.076  Score=34.62  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999964

>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=92.96  E-value=0.077  Score=36.08  Aligned_cols=25  Identities=8%  Similarity=-0.068  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
T Consensus        22 ~~gltq~elA~~~gvs~~tis~~E~   46 (73)
T 3fmy_A           22 KLSLTQKEASEIFGGGVNAFSRYEK   46 (73)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            4599999999999999999999964

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=92.94  E-value=0.35  Score=36.78  Aligned_cols=33  Identities=15%  Similarity=0.078  Sum_probs=29.6

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |.+++|+.||||+.||.+-+++-...|.+...+
T Consensus        40 ser~La~~~gVSr~tVReAl~~L~~eGlv~~~~   72 (134)
T 4ham_A           40 SIREFASRIGVNPNTVSKAYQELERQEVIITVK   72 (134)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            788999999999999999999999999875444

>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=92.93  E-value=0.078  Score=34.94  Aligned_cols=25  Identities=12%  Similarity=0.106  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999974

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=92.93  E-value=0.037  Score=37.29  Aligned_cols=32  Identities=9%  Similarity=0.145  Sum_probs=25.6

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        13 ~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           13 RTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            3444433 4589999999999999999999974

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

Probab=92.87  E-value=0.1  Score=38.74  Aligned_cols=52  Identities=25%  Similarity=0.257  Sum_probs=38.9

Q ss_pred             cCCHHHHHHHHHHHHcC-------C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898          99 PLPNHIRLKIVEMAAAG-------V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-------~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      ++..++...+......|       + |..++|++|+||++||.+-+++..+.|.+...+.
T Consensus         9 ~~~~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~~   68 (113)
T 3tqn_A            9 PIYQQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRRG   68 (113)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence            33444555555555543       2 7889999999999999999999999998865443

>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=92.78  E-value=0.057  Score=35.04  Aligned_cols=25  Identities=16%  Similarity=0.198  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4689999999999999999999974

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=92.68  E-value=0.12  Score=36.19  Aligned_cols=38  Identities=5%  Similarity=0.054  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         100 LPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       100 ~s~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ....+-.++-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        10 ~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~   48 (91)
T 1x57_A           10 VTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYES   48 (91)
T ss_dssp             CCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34456666666555 489999999999999999999975

>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=92.66  E-value=0.15  Score=39.56  Aligned_cols=47  Identities=19%  Similarity=0.292  Sum_probs=36.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         152 GSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       152 g~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+||++++++..+.|..++...  .++.+++.   . .|+      ||.+||+++++++
T Consensus         7 ~GRPtk~t~e~~e~I~~~i~~G--~sl~~i~~---~-~~~------ps~~T~~~W~~~~   53 (140)
T 4dyq_A            7 AGRPSDYMPEVADDICSLLSSG--ESLLKVCK---R-PGM------PDKSTVFRWLAKH   53 (140)
T ss_dssp             ---CCSCCTTHHHHHHHHHHTT--CCHHHHHT---S-TTC------CCHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHCC--CcHHHHHh---c-CCC------CCHHHHHHHHHcC
Confidence            3589999999999999988764  78887775   2 566      6999999999875

>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=92.65  E-value=0.1  Score=35.79  Aligned_cols=32  Identities=28%  Similarity=0.277  Sum_probs=25.7

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        17 ~~l~~~R~~~gltq~elA~~~gis~~~is~~e~   49 (83)
T 3f6w_A           17 DLLLEARSAAGITQKELAARLGRPQSFVSKTEN   49 (83)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3444443 3599999999999999999999964

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=92.62  E-value=0.12  Score=34.72  Aligned_cols=35  Identities=6%  Similarity=0.184  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+..++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus         7 ~~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~   42 (78)
T 3b7h_A            7 FVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFE   42 (78)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3444555544 4589999999999999999999964

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=92.60  E-value=0.11  Score=34.55  Aligned_cols=32  Identities=13%  Similarity=0.177  Sum_probs=25.6

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        16 ~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~   48 (74)
T 1y7y_A           16 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   48 (74)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3444433 4589999999999999999999964

>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=92.53  E-value=0.13  Score=35.46  Aligned_cols=35  Identities=9%  Similarity=0.218  Sum_probs=27.5

Q ss_pred             HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++-.++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        12 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   47 (88)
T 2wiu_B           12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            3444444444 4589999999999999999999976

>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=92.51  E-value=0.12  Score=42.94  Aligned_cols=42  Identities=17%  Similarity=-0.029  Sum_probs=35.5

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|...+ .|+.++.+|+|.++||+.++||.+||...+++-.
T Consensus       172 ~~Lt~~e~-~vl~~~~~g~s~~eIa~~l~is~~tV~~~~~~~~  213 (234)
T 1l3l_A          172 AWLDPKEA-TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM  213 (234)
T ss_dssp             CCCCHHHH-HHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45777777 5666778999999999999999999999988754

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=92.48  E-value=0.13  Score=44.90  Aligned_cols=42  Identities=24%  Similarity=0.404  Sum_probs=36.1

Q ss_pred             HHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      -.+|..++. ++++..+||++|+||+.||+|-++..++.|.+.
T Consensus        10 ~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~   52 (315)
T 2w48_A           10 IVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVT   52 (315)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            345556655 569999999999999999999999999999885

>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=92.47  E-value=0.2  Score=34.68  Aligned_cols=41  Identities=10%  Similarity=0.135  Sum_probs=36.2

Q ss_pred             CCcCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.|+.+.=..+|+++.+| +|...+|+.|||..+|+..=++
T Consensus        11 yr~Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk   52 (70)
T 2cob_A           11 YRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVK   52 (70)
T ss_dssp             SCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHH
Confidence            4678999999999999999 9999999999999999875544

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

Probab=92.45  E-value=1.1  Score=33.46  Aligned_cols=33  Identities=18%  Similarity=0.400  Sum_probs=30.4

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +.+.++||+.++++++||++.+++..+.|.+..
T Consensus        31 ~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r   63 (139)
T 2x4h_A           31 GAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKK   63 (139)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEe
Confidence            589999999999999999999999999997753

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=92.45  E-value=0.087  Score=36.10  Aligned_cols=24  Identities=17%  Similarity=0.235  Sum_probs=22.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..| |..++|+.+|||++||++|.+
T Consensus        10 ~~g-sq~~lA~~lgvs~~~is~~e~   33 (79)
T 3bd1_A           10 KLG-SVSALAASLGVRQSAISNWRA   33 (79)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHH
T ss_pred             HhC-CHHHHHHHHCCCHHHHHHHHH
Confidence            348 999999999999999999986

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=92.44  E-value=0.023  Score=46.24  Aligned_cols=41  Identities=15%  Similarity=0.122  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+.+|+|..+||+.+|||.+||.+++.+-.
T Consensus       199 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  239 (243)
T 1l0o_C          199 LDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKIL  239 (243)
T ss_dssp             -----------------------------------------
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            56666655555577899999999999999999999988754

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=92.38  E-value=0.1  Score=34.87  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4599999999999999999999964

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=92.36  E-value=0.065  Score=35.96  Aligned_cols=25  Identities=20%  Similarity=0.161  Sum_probs=23.1

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4699999999999999999999974

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=92.36  E-value=0.15  Score=42.93  Aligned_cols=43  Identities=16%  Similarity=0.106  Sum_probs=35.8

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      ..+|...|.-+.. ..+|+|.++||+.+++|.+||...+.|-++
T Consensus       196 ~~L~~~erevl~L-~~~G~s~~EIA~~L~iS~~TVk~~l~ra~~  238 (258)
T 3clo_A          196 NILSEREKEILRC-IRKGLSSKEIAATLYISVNTVNRHRQNILE  238 (258)
T ss_dssp             TSSCHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4578777765555 479999999999999999999999988664

>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=92.32  E-value=0.11  Score=42.52  Aligned_cols=44  Identities=16%  Similarity=0.251  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+.+|+.++.+| .+..+||+.+++|++||++-+++..+.|.+.
T Consensus        20 ~~~~~IL~~L~~~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~   64 (192)
T 1uly_A           20 DTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVE   64 (192)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            6677888876654 9999999999999999999999999999764

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=92.24  E-value=0.095  Score=37.16  Aligned_cols=34  Identities=12%  Similarity=0.073  Sum_probs=26.5

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.++-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        10 ~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~   44 (94)
T 2kpj_A           10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCK   44 (94)
T ss_dssp             HHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3344444443 489999999999999999999964

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=92.09  E-value=0.088  Score=36.19  Aligned_cols=34  Identities=18%  Similarity=0.217  Sum_probs=26.7

Q ss_pred             HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +=.+|-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        11 ~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             ccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3344444443 589999999999999999999964

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

Probab=92.07  E-value=0.54  Score=35.52  Aligned_cols=34  Identities=15%  Similarity=0.035  Sum_probs=30.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      |..++|+.||||+.||.+-+++....|.+...+.
T Consensus        37 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   70 (126)
T 3by6_A           37 SVRETALQEKINPNTVAKAYKELEAQKVIRTIPG   70 (126)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence            8999999999999999999999999998865443

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=92.07  E-value=0.068  Score=36.35  Aligned_cols=25  Identities=8%  Similarity=0.161  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4599999999999999999999964

>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=92.02  E-value=1.3  Score=36.60  Aligned_cols=92  Identities=18%  Similarity=0.155  Sum_probs=58.5

Q ss_pred             HcCCCH--HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHH----------HHHhCCCCCHHH
Q psy1898         113 AAGVRP--CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE----------YKKTNPGIFSWE  180 (230)
Q Consensus       113 ~~G~s~--~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~----------l~~~~P~~t~~e  180 (230)
                      .+|.+.  .+||+.++++++||++.+++..+.|.+...+.   +.-.+|+.-++....          ++.+.-.++..+
T Consensus        20 ~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~~~~~~~~~e~~l~~~lgl~~ee   96 (226)
T 2qq9_A           20 EEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD---RSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINK   96 (226)
T ss_dssp             HHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SBEEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHH
T ss_pred             hcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC---CCeEECHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHH
Confidence            457766  99999999999999999999999998743221   233456654333322          222322455555


Q ss_pred             HHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         181 IRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       181 I~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +.+....-..+      +|..++.++....+-.
T Consensus        97 ~~~~a~~leh~------~s~~~~~~l~~~l~~~  123 (226)
T 2qq9_A           97 VHDEADRWEHV------MSDEVERRLVKVLKDV  123 (226)
T ss_dssp             HHHHHHHHTTT------CCHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHhh------CCHHHHHHHHHHhCCC
Confidence            55444331222      6888888887766644

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=92.02  E-value=0.1  Score=34.39  Aligned_cols=26  Identities=15%  Similarity=0.415  Sum_probs=22.9

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.+.| +..++|+.+|||++||++|++
T Consensus        10 ~~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A           10 LEEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HHHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            34557 999999999999999999984

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=91.99  E-value=0.14  Score=34.99  Aligned_cols=33  Identities=18%  Similarity=0.182  Sum_probs=26.1

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      -.++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        12 ~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (84)
T 2ef8_A           12 VQLLTKLRKEASLSQSELAIFLGLSQSDISKIES   45 (84)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            34444444 4589999999999999999999974

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

Probab=91.97  E-value=0.64  Score=34.88  Aligned_cols=57  Identities=16%  Similarity=0.055  Sum_probs=40.2

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCC-CCCCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIG-GSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~g-g~rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +.. +...-.+|+.-.+.+....
T Consensus        53 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~~~  112 (148)
T 3nrv_A           53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS  112 (148)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHHHH
Confidence            35999999999999999999999999999976322  111 1234466777665555443

>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=91.93  E-value=0.22  Score=35.28  Aligned_cols=44  Identities=25%  Similarity=0.352  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..|+..+.  .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        20 ~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~   65 (109)
T 1sfx_A           20 PSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            34556666443  469999999999999999999999999999774

>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=91.84  E-value=0.16  Score=35.89  Aligned_cols=44  Identities=11%  Similarity=0.258  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHc--CCCHHHHhhhhccccc-hhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA--GVRPCVISRQLRVSHG-CVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~--G~s~~~IAr~lgVS~s-TV~kwikRy~e~G~v~  146 (230)
                      +.+.+|+.+++.  +.+..+||+.|+|+.. +|.+-+..-.+.|.+.
T Consensus        11 ~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~   57 (79)
T 1xmk_A           11 EIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVY   57 (79)
T ss_dssp             HHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEE
Confidence            678889987653  4999999999999999 9999999999999886

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

Probab=91.76  E-value=0.53  Score=35.28  Aligned_cols=57  Identities=11%  Similarity=-0.016  Sum_probs=40.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      ..+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|++-.+.+...
T Consensus        43 ~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~  102 (145)
T 3g3z_A           43 EGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAAPL  102 (145)
T ss_dssp             HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHHHH
Confidence            446999999999999999999999999999977422  1111 12335677666555443

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=91.73  E-value=0.39  Score=37.11  Aligned_cols=45  Identities=24%  Similarity=0.085  Sum_probs=31.9

Q ss_pred             CHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+.+ +...++.+|.+.|.+ .+.     .+|.+||||.|..+
T Consensus        21 T~q-R~~Il~~L~~~~~~~sa~ei~~~l~~-~~~-----~is~aTVYR~L~~L   66 (145)
T 2fe3_A           21 TPQ-RHAILEYLVNSMAHPTADDIYKALEG-KFP-----NMSVATVYNNLRVF   66 (145)
T ss_dssp             CHH-HHHHHHHHHHCSSCCCHHHHHHHHGG-GCT-----TCCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhCCCCCCHHHHHHHHHH-hCC-----CCChhhHHHHHHHH
Confidence            554 3445555544 457999999999977 444     37999999998754

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=91.73  E-value=0.022  Score=41.44  Aligned_cols=46  Identities=26%  Similarity=0.298  Sum_probs=35.1

Q ss_pred             HHHHHHHH-HHHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         103 HIRLKIVE-MAAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       103 ~~R~rIV~-l~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      .++..|+. .+..|  + |.+++|+.|+||++||++-++...+.|.+...
T Consensus        19 ~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           19 HFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             HHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            44444444 23333  3 89999999999999999999999999987543

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=91.63  E-value=0.32  Score=33.51  Aligned_cols=45  Identities=18%  Similarity=0.147  Sum_probs=32.5

Q ss_pred             CHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++. +..|.+++.+.  ...++.||.+.+.+ .+..     +|.+||+|.|+.+
T Consensus        16 t~~-r~~IL~~l~~~~~~~~s~~el~~~l~~-~~~~-----is~~TVyR~L~~L   62 (83)
T 2fu4_A           16 TLP-RLKILEVLQEPDNHHVSAEDLYKRLID-MGEE-----IGLATVYRVLNQF   62 (83)
T ss_dssp             CHH-HHHHHHHHTSGGGSSBCHHHHHHHHHH-TTCC-----CCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhCCCCCCCHHHHHHHHHH-hCCC-----CCHhhHHHHHHHH
Confidence            444 34566666554  46899999999976 4442     7999999998764

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=91.57  E-value=0.21  Score=37.53  Aligned_cols=42  Identities=12%  Similarity=0.299  Sum_probs=34.5

Q ss_pred             HHHHHHHH-Hc-C--CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMA-AA-G--VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~-~~-G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+|+..+ .. +  .+..+||+.++++++||++.+++..+.|.+.
T Consensus        28 e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~   73 (123)
T 3r0a_A           28 DLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQ   73 (123)
T ss_dssp             HHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44555543 33 4  6999999999999999999999999999773

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

Probab=91.55  E-value=0.13  Score=39.31  Aligned_cols=34  Identities=12%  Similarity=0.016  Sum_probs=30.4

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      |.+++|+.|+||++||.+-+++....|.+...+.
T Consensus        30 se~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g   63 (129)
T 2ek5_A           30 STNELAAFHRINPATARNGLTLLVEAGILYKKRG   63 (129)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETT
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            8899999999999999999999999998865443

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=91.51  E-value=0.064  Score=43.39  Aligned_cols=47  Identities=13%  Similarity=0.224  Sum_probs=41.1

Q ss_pred             cCCHHHHHHHHHHHHcC-CCHHHHhhhhc-cccchhhhHHHHHhhhCCC
Q psy1898          99 PLPNHIRLKIVEMAAAG-VRPCVISRQLR-VSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-~s~~~IAr~lg-VS~sTV~kwikRy~e~G~v  145 (230)
                      .++...|.+|+.++.+| .+.++||+.|+ ++.+||+.-++..++.|.+
T Consensus        19 ~La~P~Rl~il~~L~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv   67 (182)
T 4g6q_A           19 LLHHPLRWRITQLLIGRSLTTRELAELLPDVATTTLYRQVGILVKAGVL   67 (182)
T ss_dssp             HTTSHHHHHHHHHTTTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSE
T ss_pred             HhCCHHHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCe
Confidence            35567899999987654 99999999996 9999999999999999976

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=91.47  E-value=0.24  Score=40.74  Aligned_cols=53  Identities=13%  Similarity=0.103  Sum_probs=35.5

Q ss_pred             ccccccCCcccCCCcCCHHHHHHHHH-HHHcC--CCHHHHhhhhccccchhhhHHHHHh
Q psy1898          85 HGVNQLGGVFINGRPLPNHIRLKIVE-MAAAG--VRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        85 hg~~~l~~~~~~g~~~s~~~R~rIV~-l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .|.+-+++.   .+++|.-+|-+-.. ++.+|  .+.+++|+.+|||+++|++.++-.+
T Consensus        12 ~~~~~~~N~---~rplS~yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~A~   67 (189)
T 3mky_B           12 SGLVPRGSH---YRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAK   67 (189)
T ss_dssp             --------------CCCHHHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             cCccccccc---CCCCCHHHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHHhc
Confidence            366667777   68999988866665 55566  8999999999999999999988765

>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=91.39  E-value=0.2  Score=40.33  Aligned_cols=42  Identities=17%  Similarity=0.182  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHc--C-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         103 HIRLKIVEMAAA--G-VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       103 ~~R~rIV~l~~~--G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +.+.+|+.++.+  + .|..++|+.|+||++||++-+++.++.|.
T Consensus        21 ~R~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~   65 (187)
T 1j5y_A           21 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   65 (187)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence            455677877753  3 89999999999999999999999999986

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=91.38  E-value=0.23  Score=32.66  Aligned_cols=32  Identities=9%  Similarity=0.047  Sum_probs=25.6

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhc--cccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLR--VSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lg--VS~sTV~kwik  137 (230)
                      .++-.+. ..|+|..++|+.+|  ||++||++|.+
T Consensus        11 ~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~   45 (71)
T 2ewt_A           11 AKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYER   45 (71)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHC
Confidence            3343433 45899999999999  99999999975

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=91.38  E-value=0.1  Score=34.94  Aligned_cols=25  Identities=12%  Similarity=0.081  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|++..++|+.+|||++||++|.+
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            4589999999999999999999974

>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=91.33  E-value=0.42  Score=40.04  Aligned_cols=70  Identities=13%  Similarity=0.045  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898         101 PNHIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN  173 (230)
Q Consensus       101 s~~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~  173 (230)
                      +.+.-.+|++++..   +++..+||+.++++++||++.++...+.|-+... ..  +.-.+.+...+.-..+....
T Consensus         6 sl~r~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~-~~--~~Y~lg~~~~~l~~~~~~~~   78 (249)
T 1mkm_A            6 TLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK-KD--KRYVPGYKLIEYGSFVLRRF   78 (249)
T ss_dssp             THHHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC-TT--SCEEECTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC-CC--CcEEECHHHHHHHHHHHhcC
Confidence            34555677776653   4899999999999999999999999999987533 21  23344555444444444333

>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=91.21  E-value=0.062  Score=39.38  Aligned_cols=44  Identities=16%  Similarity=0.327  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQL-RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..|+..+..| .+..+||+.+ ++|++||++-+++..+.|-+.
T Consensus        14 ~~~~~IL~~L~~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~   59 (107)
T 2hzt_A           14 KWKXVILXHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVIN   59 (107)
T ss_dssp             TTHHHHHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ccHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence            4566677655454 9999999999 999999999999999999874

>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=91.18  E-value=0.24  Score=32.22  Aligned_cols=40  Identities=15%  Similarity=0.146  Sum_probs=30.3

Q ss_pred             HHHHHHHH-HHHc-C-CCHHHHhhhh-----ccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVE-MAAA-G-VRPCVISRQL-----RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~-l~~~-G-~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|..++. ++.. + .+..+|++.|     +||.+||++.++   +-|.+
T Consensus         4 ~~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~---~lg~v   51 (64)
T 2p5k_A            4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIK---ELHLV   51 (64)
T ss_dssp             HHHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH---HHTCE
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH---HcCCE
Confidence            45666554 4443 3 8999999999     999999999998   44544

>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=91.15  E-value=0.12  Score=36.80  Aligned_cols=53  Identities=19%  Similarity=0.217  Sum_probs=38.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC-CCCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+..+||+.++++++||++.+++..+.|-+. .+..+ ..--.+|+.-.+.+...
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~-~~~d~R~~~v~LT~~G~~~~~~~   84 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLIIKKFEEAKMVE-CELEGRTKIIRLTDKGQKIAQQI   84 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHHHHHTTSEE-EEEETTEEEEEECHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCcc-CCCCCCeEEEEEChhHHHHHHHH
Confidence            8999999999999999999999999999882 22211 12345677665554443

>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=91.14  E-value=0.057  Score=48.21  Aligned_cols=40  Identities=18%  Similarity=0.312  Sum_probs=33.4

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .+|+.++ ....|..+||+.+++|++||++.+++..+.|.+
T Consensus        23 ~~il~~l~~~~~sr~~la~~~gls~~tv~~~v~~L~~~gli   63 (380)
T 2hoe_A           23 SRILKRIMKSPVSRVELAEELGLTKTTVGEIAKIFLEKGIV   63 (380)
T ss_dssp             CCSHHHHHHSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            3455533 344999999999999999999999999999976

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=91.11  E-value=0.26  Score=31.25  Aligned_cols=44  Identities=23%  Similarity=0.232  Sum_probs=31.8

Q ss_pred             CCCCCCC--HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         153 SKPRVAT--PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       153 ~rpr~lt--~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      ++|..++  ++..+.+..+..+  ..+..+|++.|    |       +|.+||++++++
T Consensus         9 g~~~~l~~~~~~~~~i~~l~~~--g~s~~eIA~~l----g-------is~~TV~~~l~~   54 (55)
T 2x48_A            9 GVRYYVESEDDLVSVAHELAKM--GYTVQQIANAL----G-------VSERKVRRYLES   54 (55)
T ss_dssp             TEEEEECSHHHHHHHHHHHHHT--TCCHHHHHHHH----T-------SCHHHHHHHHTC
T ss_pred             cHHHHHhcCHHHHHHHHHHHHc--CCCHHHHHHHH----C-------cCHHHHHHHHHh
Confidence            3555667  7777777766533  47898888765    4       499999999865

>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=91.04  E-value=0.11  Score=35.32  Aligned_cols=27  Identities=11%  Similarity=0.106  Sum_probs=23.1

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      +.+.+ +..++|+.|+||+++|++|++.
T Consensus        10 ~~~~~-s~t~aA~~L~vtQ~AVS~~ir~   36 (66)
T 2ovg_A           10 YAMRF-GQTKTAKDLGVYPSSINQAIHA   36 (66)
T ss_dssp             HHHHH-CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHC-CHHHHHHHhCCCHHHHHHHHHh
Confidence            34445 9999999999999999999964

>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=91.01  E-value=0.14  Score=37.73  Aligned_cols=43  Identities=14%  Similarity=0.288  Sum_probs=36.2

Q ss_pred             HHHHHHHHH-HcCCCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMA-AAGVRPCVISRQL-RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..|+..+ ..+.+..+||+.+ +++++||++-+++..+.|.+.
T Consensus        23 ~~~~IL~~L~~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~   67 (112)
T 1z7u_A           23 WKLSLMDELFQGTKRNGELMRALDGITQRVLTDRLREMEKDGLVH   67 (112)
T ss_dssp             THHHHHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             cHHHHHHHHHhCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEE
Confidence            455666544 4459999999999 999999999999999999874

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=91.00  E-value=0.16  Score=38.61  Aligned_cols=43  Identities=14%  Similarity=0.163  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|..|++++.+   -.|..+|.+.+     +||.+||||-++.+.+.|.+
T Consensus        11 ~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv   61 (131)
T 2o03_A           11 RQRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLV   61 (131)
T ss_dssp             HHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCE
Confidence            678888887753   38999999998     89999999999999999976

>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=90.98  E-value=0.2  Score=34.21  Aligned_cols=32  Identities=13%  Similarity=0.169  Sum_probs=25.4

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        14 ~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~   46 (82)
T 3s8q_A           14 FVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   46 (82)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            3333333 4589999999999999999999964

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=90.95  E-value=0.3  Score=35.65  Aligned_cols=90  Identities=16%  Similarity=0.118  Sum_probs=56.0

Q ss_pred             HHHHHHHHc----CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHH
Q psy1898         106 LKIVEMAAA----GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEI  181 (230)
Q Consensus       106 ~rIV~l~~~----G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI  181 (230)
                      .+++.++.+    ..+..++|+.+++|+.++++..+++-  |.. +..       -+...-.+....++ .+++.+..+|
T Consensus        10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~--G~s-~~~-------~~~~~Rl~~A~~lL-~~~~~~i~eI   78 (113)
T 3oio_A           10 TEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYL--GTV-PSK-------YYLELRLNRARQLL-QQTSKSIVQI   78 (113)
T ss_dssp             HHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHT--SSC-HHH-------HHHHHHHHHHHHHH-HHCCCCHHHH
T ss_pred             HHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHH--CcC-HHH-------HHHHHHHHHHHHHH-HcCCCCHHHH
Confidence            345554443    48999999999999999998877542  321 100       00111122223344 3467888887


Q ss_pred             HHHHHHhhCCCCCCCCCCHhHHHHHHHcC-CCCCCC
Q psy1898         182 RDRLVKQDGICDKNSAPSVSSISRLLRGG-RRDDCD  216 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~-g~~~~~  216 (230)
                      +..    .|..      +.+...|..++. |..|..
T Consensus        79 A~~----~Gf~------~~s~F~r~Fk~~~G~tP~~  104 (113)
T 3oio_A           79 GLA----CGFS------SGPHFSSTYRNHFNITPRE  104 (113)
T ss_dssp             HHH----TTCS------CHHHHHHHHHHHHSSCHHH
T ss_pred             HHH----HCCC------CHHHHHHHHHHHHCcCHHH
Confidence            763    6875      888999888775 666653

>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=90.90  E-value=0.2  Score=34.94  Aligned_cols=52  Identities=13%  Similarity=0.144  Sum_probs=35.5

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWE  180 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~e  180 (230)
                      ..|+|..++|+.+|||++||++|.+     |..           ..+.+....|...+.-.+......
T Consensus        28 ~~glsq~~lA~~~gis~~~is~~e~-----g~~-----------~~~~~~l~~ia~~l~v~~~~l~~~   79 (92)
T 1lmb_3           28 ELGLSQESVADKMGMGQSGVGALFN-----GIN-----------ALNAYNAALLAKILKVSVEEFSPS   79 (92)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT-----TSS-----------CCCHHHHHHHHHHHTSCGGGTCHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc-----CCC-----------CCCHHHHHHHHHHHCCCHHHHhhh
Confidence            4599999999999999999999974     221           124555556666665455444333

>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=90.89  E-value=0.54  Score=36.40  Aligned_cols=45  Identities=20%  Similarity=0.102  Sum_probs=31.5

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+.+.+..++.+|.+.|.+ .+.     .+|.+||||.|..+
T Consensus        18 T~q-R~~Il~~l~~~~h~ta~ei~~~l~~-~~~-----~is~~TVYR~L~~L   62 (145)
T 3eyy_A           18 TPQ-RQLVLEAVDTLEHATPDDILGEVRK-TAS-----GINISTVYRTLELL   62 (145)
T ss_dssp             CHH-HHHHHHHHHHHSSBCHHHHHHHHHT-TCT-----TCCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhcCCCCHHHHHHHHHh-hCC-----CCCHhHHHHHHHHH
Confidence            554 3444444444347899999999987 444     37999999998754

>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=90.88  E-value=0.16  Score=35.94  Aligned_cols=42  Identities=21%  Similarity=0.298  Sum_probs=33.9

Q ss_pred             CCHHHHHHHHHHHHhCC---CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         158 ATPDVEKRIEEYKKTNP---GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       158 lt~~~~~~I~~l~~~~P---~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +..+..+.|..++.+++   .+++.+|++.|    |       +|.+||++.|.++
T Consensus         7 ~~~~~~~~IL~~L~~~~pg~~~t~~eLA~~L----g-------vsr~tV~~~L~~L   51 (81)
T 1qbj_A            7 IYQDQEQRILKFLEELGEGKATTAHDLSGKL----G-------TPKKEINRVLYSL   51 (81)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCBCHHHHHHHH----T-------CCHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHcCCCCCcCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            34566778888888888   89999999876    3       4999999998765

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=90.84  E-value=0.21  Score=34.84  Aligned_cols=33  Identities=15%  Similarity=0.257  Sum_probs=26.2

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      -.++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        16 g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~   49 (86)
T 3eus_A           16 CQRLRQARLDAGLTQADLAERLDKPQSFVAKVET   49 (86)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            34444444 3599999999999999999999963

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=90.80  E-value=0.27  Score=38.05  Aligned_cols=44  Identities=23%  Similarity=0.248  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|..|++.+.+   ..|..+|...+     +||.+|||+-++.+.+.|.+.
T Consensus        22 ~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   73 (145)
T 2fe3_A           22 PQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVK   73 (145)
T ss_dssp             HHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEE
Confidence            678889987753   38999999998     899999999999999999764

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=90.79  E-value=0.43  Score=36.43  Aligned_cols=45  Identities=13%  Similarity=0.148  Sum_probs=32.8

Q ss_pred             CHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+.+.  ...++.||.+.|.+ .+.     .+|.+||||.|..+
T Consensus        17 T~q-R~~Il~~L~~~~~~~~sa~ei~~~l~~-~~~-----~is~aTVYR~L~~L   63 (136)
T 1mzb_A           17 TLP-RVKILQMLDSAEQRHMSAEDVYKALME-AGE-----DVGLATVYRVLTQF   63 (136)
T ss_dssp             CHH-HHHHHHHHHCC-CCSBCHHHHHHHHHH-TTC-----CCCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhCCCCCCCHHHHHHHHHh-hCC-----CCCHHHHHHHHHHH
Confidence            544 44566666554  36899999999987 444     37999999998764

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=90.78  E-value=0.14  Score=40.26  Aligned_cols=43  Identities=16%  Similarity=0.220  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +++.+|+..+..|  .+..++|+.||||++||..-+++..+.|.+
T Consensus        13 ~l~~~Il~~l~~~~~ls~~eLa~~lgvSr~~vr~al~~L~~~Gli   57 (163)
T 2gqq_A           13 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI   57 (163)
T ss_dssp             SHHHHHHHHHHHCSSCCTTGGGTSSSCCTTTSSSTHHHHHHHTSE
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcE
Confidence            5677888866655  899999999999999999999999999965

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=90.74  E-value=0.23  Score=37.74  Aligned_cols=43  Identities=19%  Similarity=0.179  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         162 VEKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       162 ~~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+..|.+.+.+ +...|+.||.+.|.+ .+.     .+|.+||||.|..+
T Consensus        12 qR~~Il~~l~~~~~~~sa~ei~~~l~~-~~~-----~is~~TVYR~L~~L   55 (131)
T 2o03_A           12 QRAAISTLLETLDDFRSAQELHDELRR-RGE-----NIGLTTVYRTLQSM   55 (131)
T ss_dssp             HHHHHHHHHHHCCSCEEHHHHHHHHHH-TTC-----CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHH-hCC-----CCCHhhHHHHHHHH
Confidence            34555555554 446899999999987 444     37999999998754

>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=90.71  E-value=0.25  Score=41.19  Aligned_cols=43  Identities=14%  Similarity=0.069  Sum_probs=35.5

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...+|..++ +|+.++.+|++.++||+.++||..||..-+++-.
T Consensus       173 ~~~Lt~re~-~vl~~~~~G~s~~eIa~~l~is~~tV~~~~~~~~  215 (237)
T 3szt_A          173 NVRLTARET-EMLKWTAVGKTYGEIGLILSIDQRTVKFHIVNAM  215 (237)
T ss_dssp             GCCCCHHHH-HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            345666555 6777888999999999999999999999988754

>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=90.67  E-value=0.36  Score=33.90  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=23.2

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999986

>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=90.65  E-value=0.14  Score=35.76  Aligned_cols=42  Identities=21%  Similarity=0.298  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHhCC---CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         158 ATPDVEKRIEEYKKTNP---GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       158 lt~~~~~~I~~l~~~~P---~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++++.+..|..++.+++   .+++.||++.|    |       +|.+||++.|.++
T Consensus        11 ~~~~~~~~IL~~L~~~~~~~~~t~~eLA~~L----g-------vs~~tV~~~L~~L   55 (77)
T 1qgp_A           11 IYQDQEQRILKFLEELGEGKATTAHDLSGKL----G-------TPKKEINRVLYSL   55 (77)
T ss_dssp             HHHHHHHHHHHHHHHHCSSSCEEHHHHHHHH----C-------CCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            45667788888999998   89999999876    3       4999999998875

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=90.65  E-value=0.27  Score=37.54  Aligned_cols=44  Identities=20%  Similarity=0.354  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHc----CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA----GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~----G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|..|++.+.+    -.|..+|.+.+     +||.+|||+-++.+.+.|.+.
T Consensus        18 ~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   70 (136)
T 1mzb_A           18 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVV   70 (136)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEE
Confidence            678889987753    37999999998     799999999999999999763

>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=90.56  E-value=0.22  Score=37.51  Aligned_cols=25  Identities=8%  Similarity=-0.068  Sum_probs=23.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++||++|.+
T Consensus        82 ~~glsq~~la~~~g~s~~~i~~~E~  106 (133)
T 3o9x_A           82 KLSLTQKEASEIFGGGVNAFSRYEK  106 (133)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            4599999999999999999999975

>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=90.55  E-value=0.16  Score=37.22  Aligned_cols=34  Identities=15%  Similarity=0.247  Sum_probs=27.0

Q ss_pred             HHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        10 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   44 (114)
T 3op9_A           10 FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMS   44 (114)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            334444444 3599999999999999999999975

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=90.47  E-value=0.45  Score=37.08  Aligned_cols=43  Identities=16%  Similarity=0.094  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         162 VEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       162 ~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+..|.+.+.+. ...++.||.+.|.+ .+..     +|.+||||.|..+
T Consensus        28 qR~~IL~~l~~~~~~~sa~ei~~~l~~-~~~~-----is~aTVYR~L~~L   71 (150)
T 2xig_A           28 QREEVVSVLYRSGTHLSPEEITHSIRQ-KDKN-----TSISSVYRILNFL   71 (150)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHHH-HSTT-----CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHH-hCCC-----CCHhhHHHHHHHH
Confidence            345566566553 46899999999987 4443     7999999998754

>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=90.28  E-value=0.23  Score=44.47  Aligned_cols=43  Identities=16%  Similarity=0.221  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      .-+.+|+.++.. | .|..+||+.+++|++||++.+++..+.|.+
T Consensus        16 ~n~~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i   60 (406)
T 1z6r_A           16 TNAGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLV   60 (406)
T ss_dssp             HHHHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSE
T ss_pred             hHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcE
Confidence            345567776654 4 999999999999999999999999999976

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

Probab=90.07  E-value=0.74  Score=34.74  Aligned_cols=65  Identities=11%  Similarity=0.164  Sum_probs=44.0

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCC-CCCC--CCCCCHHHHHHHHHHH
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVI-GGSK--PRVATPDVEKRIEEYK  170 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~-gg~r--pr~lt~~~~~~I~~l~  170 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+..  .+- ..+|  .-.+|+.-.+.+....
T Consensus        44 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~~~  115 (154)
T 2qww_A           44 LAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSKRST  115 (154)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHHHHH
Confidence            3444433 3 3589999999999999999999999999997743  221 1112  2356777665555443

>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=90.00  E-value=0.18  Score=36.12  Aligned_cols=25  Identities=12%  Similarity=0.098  Sum_probs=22.6

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
T Consensus        41 ~~glsq~elA~~lgvs~~~is~~E~   65 (99)
T 2ppx_A           41 ALKLTQEEFSARYHIPLGTLRDWEQ   65 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            3589999999999999999999953

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=89.94  E-value=0.58  Score=37.12  Aligned_cols=95  Identities=15%  Similarity=0.182  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHH
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEI  181 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI  181 (230)
                      +.+.+|++.+++| .|..+||+.+|+|.+-|.-.+.....+|-+..-.+|..+--.+...  +++. .+.+    ...|+
T Consensus        11 erk~~ILE~Lk~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~ayw~L~~s--~y~~-kV~d----ilrel   83 (165)
T 2vxz_A           11 VRLRDILALLADGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVALVCLSMD--QYRQ-LVDG----MIREV   83 (165)
T ss_dssp             HHHHHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEEEEESCHH--HHHH-HHHH----HHHHH
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEEEEEecHH--HHHH-HHHH----HHHHH
Confidence            6678888877787 9999999999999999999999889999875544432222233322  2222 2211    23444


Q ss_pred             HHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         182 RDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      ...|.+ .|+.    -++.+-.+|.+.+
T Consensus        84 ~~~l~s-~gvk----~i~p~~l~~li~~  106 (165)
T 2vxz_A           84 ERLVTT-NKLK----FISPPRLHDLIIK  106 (165)
T ss_dssp             HHHHHH-TTCS----EECHHHHHHHHHH
T ss_pred             HHHHHH-cCCe----eeCcHHHHHHHHh
Confidence            455544 6765    3677777776654

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=89.93  E-value=0.58  Score=39.75  Aligned_cols=69  Identities=10%  Similarity=-0.005  Sum_probs=48.9

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      .+++.++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..+.++...|..... ..-..++.+|++.|..
T Consensus         3 ~~tI~evA~~~gvs~~TLRyYe~----~GLL~p~~~~~~GyR~Y~~~dl~~L~~I~~lr~~G~sL~eIk~~l~~   72 (249)
T 3qao_A            3 AMQIKELAELTGVSVRTLHHYDK----IGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKIQQILDD   72 (249)
T ss_dssp             CBCHHHHHHHHCCCHHHHHHHHH----TTSSCCEECTTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH----CCCCCCceECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhcc
Confidence            47899999999999999887654    688877653233456778877666644332 3446888888887753

>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=89.92  E-value=0.095  Score=43.25  Aligned_cols=44  Identities=27%  Similarity=0.292  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         102 NHIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       102 ~~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ...|.+|+.++.. ..+..+||+.+++|.+||+.-+++..+.|.+
T Consensus        14 ~~~rl~IL~~L~~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV   58 (202)
T 2p4w_A           14 NETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEAGLI   58 (202)
T ss_dssp             SHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCce
Confidence            3678888887665 4999999999999999999999999999976

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

Probab=89.83  E-value=0.85  Score=34.15  Aligned_cols=56  Identities=13%  Similarity=0.119  Sum_probs=39.7

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        55 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  113 (150)
T 2rdp_A           55 GDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEEV  113 (150)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHHH
Confidence            46999999999999999999999999999977321  1111 12235677665555433

>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=89.81  E-value=0.29  Score=34.65  Aligned_cols=55  Identities=15%  Similarity=0.062  Sum_probs=39.8

Q ss_pred             CCCHHHHhhhhccccch-hhhHHHHHhhhCCCCcCCCCC-CCCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGC-VSKILNRYQETGSIRPGVIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sT-V~kwikRy~e~G~v~p~~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      +.+..+||+.++++++| |++.+++..+.|-+.+.+..+ ...-.+|+.-.+.+...
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~~~   86 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECL   86 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHHHH
Confidence            59999999999999999 999999999999886222211 12235677655554443

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

Probab=89.62  E-value=0.5  Score=35.31  Aligned_cols=69  Identities=19%  Similarity=0.178  Sum_probs=44.2

Q ss_pred             CCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC--CC-CCCCCCCCHHHHHHHHHH
Q psy1898         100 LPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IG-GSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       100 ~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~--~g-g~rpr~lt~~~~~~I~~l  169 (230)
                      ++.. ...|+..+ ..+.+.++||+.++++++||++.+++..+.|-+...+  .. +...-.+|+.-.+.+...
T Consensus        36 lt~~-~~~iL~~l~~~~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~~  108 (146)
T 3tgn_A           36 LTNT-QEHILMLLSEESLTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEH  108 (146)
T ss_dssp             CCHH-HHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHHH
T ss_pred             CCHH-HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHHH
Confidence            3433 34455543 4469999999999999999999999999999773221  11 123345566555444443

>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=89.61  E-value=0.31  Score=38.02  Aligned_cols=41  Identities=24%  Similarity=0.293  Sum_probs=31.1

Q ss_pred             CCcCCHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHHH
Q psy1898          97 GRPLPNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        97 g~~~s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +++-+.+.|.+|++.     .+.|   .|..+||+..|||++|+|+...
T Consensus         6 ~r~r~~~~r~~Il~aA~~lf~e~G~~~~t~~~IA~~agvsk~tlY~~F~   54 (192)
T 2fq4_A            6 GRPRNIETQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   54 (192)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             CCCCChHHHHHHHHHHHHHHHHcCcccccHHHHHHHcCCCHHHHHHHCC
Confidence            455667888888873     2345   8999999999999999998753

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=89.59  E-value=0.29  Score=35.88  Aligned_cols=34  Identities=6%  Similarity=0.039  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ++-.+|-.+.+ .|+|..++|+.+|||++||++|.
T Consensus        36 ~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E   70 (101)
T 4ghj_A           36 EIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAE   70 (101)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH
Confidence            44455555554 59999999999999999999995

>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=89.58  E-value=0.5  Score=38.57  Aligned_cols=47  Identities=15%  Similarity=0.042  Sum_probs=36.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV  162 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~  162 (230)
                      ++..++|+.||||+++|..-+++-...|.+...+..|..-..++.+.
T Consensus        36 L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~   82 (218)
T 3sxy_A           36 LNVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEKF   82 (218)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEETTTEEEECCCCHHH
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCHHH
Confidence            78899999999999999999999999998865544343333445543

>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=89.42  E-value=0.91  Score=33.85  Aligned_cols=57  Identities=11%  Similarity=0.029  Sum_probs=36.7

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+....
T Consensus        50 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~  109 (142)
T 3ech_A           50 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLHAE  109 (142)
T ss_dssp             TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHHHH
Confidence            46999999999999999999999999999977322  1111 123456776665554443

>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=89.42  E-value=0.19  Score=35.77  Aligned_cols=57  Identities=12%  Similarity=0.065  Sum_probs=40.7

Q ss_pred             cCCCHHHH----hhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVI----SRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~I----Ar~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+|    |+.++++++||++.+++..+.|-+.....++.+.-.+|+.-.+.+....
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~   81 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLK   81 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHH
Confidence            35899999    9999999999999999999999774322111233456776665554443

>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=89.39  E-value=0.36  Score=41.07  Aligned_cols=42  Identities=19%  Similarity=0.178  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|..++ .|+.++.+|++.++||+.++||..||...+++-.+
T Consensus       197 ~Lt~re~-~vl~~~~~G~s~~eIA~~l~is~~TV~~~~~~~~~  238 (265)
T 3qp6_A          197 PLSQREY-DIFHWMSRGKTNWEIATILNISERTVKFHVANVIR  238 (265)
T ss_dssp             CCCHHHH-HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4665544 56666789999999999999999999999887553

>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=89.19  E-value=0.41  Score=41.06  Aligned_cols=40  Identities=15%  Similarity=0.183  Sum_probs=30.9

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||++||++.++.               ++ .++++.+++|.+..++
T Consensus         2 ti~diA~~agVS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~~   41 (340)
T 1qpz_A            2 TIKDVAKRANVSTTTVSHVINK---------------TR-FVAEETRNAVWAAIKE   41 (340)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT---------------CS-CCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHcC---------------cC-CCCHHHHHHHHHHHHH
Confidence            6889999999999999999971               11 2477777777766654

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=89.18  E-value=0.44  Score=37.49  Aligned_cols=66  Identities=18%  Similarity=0.130  Sum_probs=44.4

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH---HHHHhCCCCCHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE---EYKKTNPGIFSWEIRDRLV  186 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~---~l~~~~P~~t~~eI~~~L~  186 (230)
                      .-++..++|+.+|||..|+..|.+    .|.+.|....+ .-+..+.++...|.   .+..  -..++.+|++.|.
T Consensus        10 ~~~~i~e~A~~~gvs~~TLR~ye~----~Gll~p~r~~~-g~R~Y~~~dl~~l~~I~~lr~--~G~sl~eI~~~l~   78 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQR--IGIPLATIGEAFG   78 (154)
T ss_dssp             CCBCHHHHHHHHTSCHHHHHHHHH----TTSSCCEECTT-SCEEBCTTHHHHHHHHHHHHH--HTCCHHHHHHHHC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH----cCCCCcccCCC-CCEEeCHHHHHHHHHHHHHHH--CCCCHHHHHHHHH
Confidence            358999999999999999987754    57776542222 34556666555443   3332  2588888888774

>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=89.15  E-value=0.99  Score=33.26  Aligned_cols=57  Identities=18%  Similarity=0.210  Sum_probs=41.2

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC-CCCCC--CCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKP--RVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~-gg~rp--r~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+..... ..+|.  -.+|+.-.+.+....
T Consensus        47 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~  106 (138)
T 1jgs_A           47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCH  106 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHHHHH
Confidence            4689999999999999999999999999997732211 11122  356777666555443

>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=89.12  E-value=0.12  Score=46.98  Aligned_cols=43  Identities=12%  Similarity=0.217  Sum_probs=35.9

Q ss_pred             HHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      -+.+|+.++. .| .|..+||+.+++|++||++.+++..+.|.+.
T Consensus        40 n~~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~   84 (429)
T 1z05_A           40 NAGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIH   84 (429)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            4456776553 34 9999999999999999999999999999763

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=89.10  E-value=0.55  Score=37.14  Aligned_cols=46  Identities=7%  Similarity=-0.003  Sum_probs=32.5

Q ss_pred             CHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhh-CCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTN-PGIFSWEIRDRLVKQD-GICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~-P~~t~~eI~~~L~~~~-Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+.+. ...|+.||.+.|.+.. +..     +|.+||||.|..+
T Consensus        32 T~q-R~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~-----is~aTVYRtL~~L   79 (162)
T 4ets_A           32 TKQ-REVLLKTLYHSDTHYTPESLYMEIKQAEPDLN-----VGIATVYRTLNLL   79 (162)
T ss_dssp             CHH-HHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGC-----CCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCC-----CCHHHHHHHHHHH
Confidence            444 45566666554 4689999999998731 443     7999999998754

>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=89.10  E-value=1.5  Score=32.81  Aligned_cols=56  Identities=14%  Similarity=0.216  Sum_probs=34.1

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|++-.+.+...
T Consensus        56 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~  114 (148)
T 3jw4_A           56 SGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEF  114 (148)
T ss_dssp             TCCCHHHHHHC------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHHHH
Confidence            46999999999999999999999999999977422  1111 12345777666555443

>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=88.98  E-value=0.46  Score=38.30  Aligned_cols=40  Identities=18%  Similarity=0.225  Sum_probs=31.3

Q ss_pred             HHHHHHH-HcCC--CHHHHhhhhccc-cchhhhHHHHHhhhCCC
Q psy1898         106 LKIVEMA-AAGV--RPCVISRQLRVS-HGCVSKILNRYQETGSI  145 (230)
Q Consensus       106 ~rIV~l~-~~G~--s~~~IAr~lgVS-~sTV~kwikRy~e~G~v  145 (230)
                      .++-.+. +.|+  |.+++|+.+|++ ++||++|+++..+.|.+
T Consensus        13 ~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~l~~~~~l   56 (202)
T 1jhf_A           13 DLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVI   56 (202)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHHHHHCCCc
Confidence            3444443 3488  999999999998 99999999988776644

>3vib_A MTRR; helix-turn-helix motif, DNA binding, DNA binding protein; HET: CXS; 2.40A {Neisseria gonorrhoeae}

Probab=88.83  E-value=0.36  Score=38.06  Aligned_cols=39  Identities=8%  Similarity=0.022  Sum_probs=29.5

Q ss_pred             CcCCHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898          98 RPLPNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        98 ~~~s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.-..+.|.+|++.    + +.|   .|..+||+..|||++|+|..-
T Consensus         5 ~~~~~~tR~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~t~Y~~F   51 (210)
T 3vib_A            5 KTEALKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRDALYWHF   51 (210)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             chhHHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            44456788999873    2 345   899999999999999999863

>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=88.80  E-value=0.79  Score=34.06  Aligned_cols=57  Identities=12%  Similarity=-0.004  Sum_probs=41.1

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCC-CCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGS-KPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~-rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..++ .--.+|+.-.+.+....
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~  111 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLL  111 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            45899999999999999999999999999977432  22111 22356777666555444

>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=88.57  E-value=4.2  Score=33.41  Aligned_cols=63  Identities=21%  Similarity=0.187  Sum_probs=44.5

Q ss_pred             HHHHHHHHH-HcCCCH--HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         104 IRLKIVEMA-AAGVRP--CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~--~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      .-.+++..+ ..|.+.  .+||+.++++++||++.+++..+.|.+...+.   +.-.+|+.-.+.+...
T Consensus        10 ~~L~~L~~l~~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~~   75 (230)
T 1fx7_A           10 MYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD---RHLELTEKGRALAIAV   75 (230)
T ss_dssp             HHHHHHHHHHHHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SCEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC---ccEEECHHHHHHHHHH
Confidence            334455433 458877  99999999999999999999999998753321   2345677655554433

>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=88.53  E-value=0.32  Score=42.94  Aligned_cols=43  Identities=14%  Similarity=0.275  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHH--cC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAA--AG--VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~--~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.|.+|++++.  .|  .|-.+||++|+||+.+|++-++..++.|..
T Consensus         3 ~~~~~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~   49 (323)
T 3rkx_A            3 KYSQDVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLEGCK   49 (323)
T ss_dssp             CHHHHHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCE
T ss_pred             hHHHHHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCe
Confidence            35778888773  34  899999999999999999999999999963

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=88.50  E-value=0.46  Score=36.98  Aligned_cols=43  Identities=23%  Similarity=0.281  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|..|++.+.+   ..|..+|...+     +||.+|||+-++.+.+.|.+
T Consensus        27 ~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv   77 (150)
T 2xig_A           27 KQREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFI   77 (150)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcE
Confidence            778889987753   38999999988     79999999999999999976

>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=88.50  E-value=0.42  Score=40.82  Aligned_cols=41  Identities=27%  Similarity=0.395  Sum_probs=31.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||++||++.++.               ++ ..+++.+++|.+..++
T Consensus         3 ~ti~dvA~~agVS~~TVSrvln~---------------~~-~vs~~tr~rV~~aa~~   43 (332)
T 2hsg_A            3 VTIYDVAREASVSMATVSRVVNG---------------NP-NVKPSTRKKVLETIER   43 (332)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT---------------CT-TSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence            47899999999999999999862               11 2467777777665554

>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=88.48  E-value=1.2  Score=33.46  Aligned_cols=57  Identities=14%  Similarity=0.111  Sum_probs=39.8

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc----CCCCC-CCCCCCCHHHHHHHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP----GVIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p----~~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      ...+.+..+||+.++++++||++.+++..+.|-+..    .+..+ ...-.+|+.-.+.+..
T Consensus        48 ~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~  109 (151)
T 3kp7_A           48 SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKE  109 (151)
T ss_dssp             HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHH
Confidence            445699999999999999999999999999997743    22211 1233567665555443

>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=88.45  E-value=0.21  Score=41.81  Aligned_cols=50  Identities=20%  Similarity=0.283  Sum_probs=38.6

Q ss_pred             HHHHHHHH-HHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC
Q psy1898         103 HIRLKIVE-MAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG  152 (230)
Q Consensus       103 ~~R~rIV~-l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg  152 (230)
                      .+|..|+. .+..|  ++..++|++||||++||..=+++....|.+...+.+|
T Consensus        34 ~L~~~I~~g~l~pG~~L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~~~G   86 (237)
T 3c7j_A           34 KLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKG   86 (237)
T ss_dssp             HHHHHHHTSSSCTTCBCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHhCCCCCcCeeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence            55555554 33334  8999999999999999999999999999886554433

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=88.44  E-value=0.5  Score=36.78  Aligned_cols=45  Identities=20%  Similarity=0.168  Sum_probs=32.0

Q ss_pred             CHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         159 TPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       159 t~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      |+. +..|.+.+.+.  ...|+.||.+.|.+ .+.     .+|.+||||.|..+
T Consensus        16 T~q-R~~Il~~L~~~~~~h~sa~ei~~~l~~-~~~-----~is~aTVYR~L~~L   62 (150)
T 2w57_A           16 TLP-RLKILEVLQQPECQHISAEELYKKLID-LGE-----EIGLATVYRVLNQF   62 (150)
T ss_dssp             CHH-HHHHHHHHTSGGGSSEEHHHHHHHHHH-TTC-----CCCHHHHHHHHHHH
T ss_pred             CHH-HHHHHHHHHhCCCCCCCHHHHHHHHHH-hCC-----CCCHHHHHHHHHHH
Confidence            444 44555555443  46899999999987 444     37999999998754

>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=88.41  E-value=0.64  Score=34.47  Aligned_cols=36  Identities=17%  Similarity=0.251  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+-.++-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        11 ~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~   47 (126)
T 3ivp_A           11 RALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIEN   47 (126)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            345555555554 599999999999999999999975

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=88.35  E-value=0.48  Score=34.53  Aligned_cols=40  Identities=5%  Similarity=0.101  Sum_probs=31.5

Q ss_pred             CcCCHHHHHHHHHHHH---cCCCHHHHhhhhccccchhhhHHH
Q psy1898          98 RPLPNHIRLKIVEMAA---AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~---~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+...+-.++-.+..   .|+|..++|+.+|||++||++|.+
T Consensus        29 ~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~   71 (107)
T 2jvl_A           29 KTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYER   71 (107)
T ss_dssp             CCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3445566666666555   489999999999999999999953

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=88.34  E-value=0.46  Score=40.81  Aligned_cols=41  Identities=20%  Similarity=0.161  Sum_probs=30.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .|.++||+.+|||++||++.++.               + ...+++.+++|.+..++
T Consensus        11 ~ti~diA~~agVS~~TVSr~Ln~---------------~-~~vs~~tr~rV~~~~~~   51 (344)
T 3kjx_A           11 LTLRDVSEASGVSEMTVSRVLRN---------------R-GDVSDATRARVLAAAKE   51 (344)
T ss_dssp             CCHHHHHHHHCCCSHHHHHHHTT---------------C-SCCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC---------------C-CCCCHHHHHHHHHHHHH
Confidence            68999999999999999999852               1 12466667776666553

>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=88.32  E-value=0.48  Score=36.64  Aligned_cols=43  Identities=21%  Similarity=0.232  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..|+..+..| .+..+|++.++||++||++-+++..+.|.+.
T Consensus        25 w~l~IL~~L~~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~   68 (146)
T 2f2e_A           25 WSMLIVRDAFEGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMV   68 (146)
T ss_dssp             SHHHHHHHHHTTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            355677655555 9999999999999999999999999999874

>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=88.23  E-value=0.3  Score=35.08  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=23.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999975

>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=88.20  E-value=1.2  Score=34.20  Aligned_cols=57  Identities=14%  Similarity=0.181  Sum_probs=40.6

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|+.-.+.+....
T Consensus        59 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~  118 (162)
T 3k0l_A           59 PNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQCN  118 (162)
T ss_dssp             TTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHHHH
Confidence            46999999999999999999999999999977322  1111 122356776655554433

>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=88.17  E-value=0.61  Score=38.14  Aligned_cols=47  Identities=15%  Similarity=0.138  Sum_probs=36.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV  162 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~  162 (230)
                      ++..++|++||||+++|..-+++-...|.+...+..|..-..++.+.
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            67889999999999999999999999998865554443334445544

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

Probab=88.17  E-value=1  Score=33.13  Aligned_cols=64  Identities=8%  Similarity=0.108  Sum_probs=43.1

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        36 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~~~  104 (139)
T 3bja_A           36 FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKKQV  104 (139)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHHHH
Confidence            3444443 3 35899999999999999999999999999977321  1111 11234677666555443

>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=88.13  E-value=1.5  Score=31.44  Aligned_cols=81  Identities=7%  Similarity=0.019  Sum_probs=51.1

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGIC  192 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~  192 (230)
                      .+..+..++|+.+++|++++++..+++-  |.. +..       -+...-.+....++ .+++.+..+|+..    .|..
T Consensus        19 ~~~~~~~~lA~~~~~S~~~l~r~fk~~~--G~s-~~~-------~~~~~Rl~~A~~lL-~~~~~si~~IA~~----~Gf~   83 (108)
T 3oou_A           19 SEGMSLKTLGNDFHINAVYLGQLFQKEM--GEH-FTD-------YLNRYRVNYAKEEL-LQTKDNLTIIAGK----SGYT   83 (108)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHH--SSC-HHH-------HHHHHHHHHHHHHH-HHCCCCHHHHHHH----TTCC
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHH--CcC-HHH-------HHHHHHHHHHHHHH-HcCCCCHHHHHHH----cCCC
Confidence            4469999999999999999999887543  421 100       00111122223333 3456788777763    6874


Q ss_pred             CCCCCCCHhHHHHHHHcC-CCCC
Q psy1898         193 DKNSAPSVSSISRLLRGG-RRDD  214 (230)
Q Consensus       193 ~~~~~vS~sTV~R~Lr~~-g~~~  214 (230)
                            +.+...|..++. |..|
T Consensus        84 ------~~s~F~r~Fk~~~G~tP  100 (108)
T 3oou_A           84 ------DMAYFYRQFKKHTGETP  100 (108)
T ss_dssp             ------CHHHHHHHHHHHHSSCH
T ss_pred             ------ChHHHHHHHHHHhCcCH
Confidence                  888988888765 4444

>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=88.09  E-value=1.3  Score=33.61  Aligned_cols=56  Identities=13%  Similarity=0.116  Sum_probs=40.0

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC-CCCCC--CCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKP--RVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~-gg~rp--r~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+..... ..+|.  -.+|+.-.+.+...
T Consensus        57 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~  115 (154)
T 2eth_A           57 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEI  115 (154)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHHHH
Confidence            4699999999999999999999999999997732211 11122  34677665555443

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=88.06  E-value=0.12  Score=43.69  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=40.8

Q ss_pred             CHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         101 PNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       101 s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ....|.+|+.++..| .+..+||+.+++|++||++-++...+.|.+..
T Consensus        10 ~~~~R~~IL~~L~~g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A           10 GNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             TSHHHHHHHHHHTTTTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            446788999877665 99999999999999999999999999997743

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

Probab=87.93  E-value=1.7  Score=33.02  Aligned_cols=63  Identities=17%  Similarity=0.216  Sum_probs=41.8

Q ss_pred             HHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC--CCC-CCCCCCCHHHHHHHHHH
Q psy1898         107 KIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       107 rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~--~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .|+..+ . .+.+..+||+.++++++||++.+++..+.|-+....  ..+ ...-.+|+.-.+.+...
T Consensus        53 ~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  120 (162)
T 2fa5_A           53 RVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYETV  120 (162)
T ss_dssp             HHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHHH
Confidence            344433 3 459999999999999999999999999999774221  111 12335677665555433

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=87.84  E-value=0.37  Score=40.31  Aligned_cols=54  Identities=15%  Similarity=0.143  Sum_probs=40.4

Q ss_pred             CCcCCHHHHHHHHHHHHcC-------C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898          97 GRPLPNHIRLKIVEMAAAG-------V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G-------~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      ..++..++...+......|       + |..++|++|+||+.||.+-++...+.|.+...+.
T Consensus         7 ~~~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g   68 (236)
T 3edp_A            7 KKPLFEVIASKIKDSINRDEYKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNG   68 (236)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCCHHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEECC
Confidence            3444445566666655543       3 7899999999999999999999999998855443

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=87.81  E-value=0.45  Score=34.29  Aligned_cols=34  Identities=12%  Similarity=0.187  Sum_probs=26.4

Q ss_pred             HHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.+|-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        29 ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~   63 (99)
T 3g5g_A           29 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   63 (99)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            334444444 3589999999999999999999964

>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=87.81  E-value=0.39  Score=34.17  Aligned_cols=31  Identities=13%  Similarity=0.304  Sum_probs=25.0

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .++..+.+ |++..++|+..|||++|++.+.+
T Consensus        24 ~kLK~il~-GikQ~eLAK~iGIsqsTLSaIen   54 (83)
T 2l1p_A           24 NALKDLLK-DMNQSSLAKECPLSQSMISSIVN   54 (83)
T ss_dssp             HHHHHHHT-TSCHHHHHHHSSSCHHHHHHHHT
T ss_pred             HHHHHHHH-hcCHHHHHHHcCCCHHHHHHHHc
Confidence            33333334 99999999999999999999974

>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=87.81  E-value=0.45  Score=35.05  Aligned_cols=60  Identities=13%  Similarity=0.123  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHcC-CC--HHHHhhhh-ccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHH
Q psy1898         103 HIRLKIVEMAAAG-VR--PCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE  163 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s--~~~IAr~l-gVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~  163 (230)
                      ..|..|+..+..| .+  ..+|++.+ +||++|+++-+++-.+.|.+..... ...--.+|+.-.
T Consensus        27 ~wrl~IL~~L~~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~-r~~~y~LT~~G~   90 (111)
T 3df8_A           27 KYTMLIISVLGNGSTRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG-QITTYALTEKGM   90 (111)
T ss_dssp             TTHHHHHHHHTSSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES-SSEEEEECHHHH
T ss_pred             ccHHHHHHHHhcCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec-CcEEEEECccHH
Confidence            4577888776666 66  99999999 9999999999999999998753322 112335666544

>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=87.80  E-value=1.4  Score=33.07  Aligned_cols=63  Identities=24%  Similarity=0.218  Sum_probs=42.4

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|+.-.+.+..
T Consensus        43 ~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  110 (152)
T 3bj6_A           43 RAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITA  110 (152)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHH
Confidence            3444433 3 35999999999999999999999999999977322  1111 1223467765554443

>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=87.75  E-value=0.32  Score=40.60  Aligned_cols=46  Identities=22%  Similarity=0.174  Sum_probs=35.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD  161 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~  161 (230)
                      ++..++|++||||++||..-+++-...|.+...+..|..-..++.+
T Consensus        52 L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~   97 (239)
T 2hs5_A           52 LSEPDICAALDVSRNTVREAFQILIEDRLVAHELNRGVFVRVPTAE   97 (239)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEEEECCCCHH
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEEeCCCHH
Confidence            7889999999999999999999999999886554433333333443

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=87.70  E-value=0.38  Score=33.93  Aligned_cols=25  Identities=12%  Similarity=0.011  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999964

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=87.63  E-value=0.47  Score=34.71  Aligned_cols=27  Identities=19%  Similarity=0.235  Sum_probs=23.8

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-..|+|..++|+.+|||++||++|.+
T Consensus        23 r~~~gltq~eLA~~lGis~~~is~ie~   49 (104)
T 3trb_A           23 GFLDKMSANQLAKHLAIPTNRVTAILN   49 (104)
T ss_dssp             HHTTSCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345699999999999999999999974

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=87.60  E-value=0.34  Score=37.28  Aligned_cols=43  Identities=16%  Similarity=0.093  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         162 VEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       162 ~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+..|.+.+.+. ...++.||.+.|.+ .+.     .+|.+||||.|..+
T Consensus        15 qR~~Il~~L~~~~~h~sa~eI~~~l~~-~~~-----~is~aTVYR~L~~L   58 (139)
T 3mwm_A           15 QRAAVSAALQEVEEFRSAQELHDMLKH-KGD-----AVGLTTVYRTLQSL   58 (139)
T ss_dssp             HHHHHHHHHTTCSSCEEHHHHHHHHHH-TTC-----CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHH-hCC-----CCCHHHHHHHHHHH
Confidence            355666666554 46889999999987 444     37999999988654

>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=87.44  E-value=0.34  Score=38.32  Aligned_cols=41  Identities=20%  Similarity=0.203  Sum_probs=31.5

Q ss_pred             CCCcCCHHHHHHHHHHH-----HcC---CCHHHHhhhhccccchhhhHH
Q psy1898          96 NGRPLPNHIRLKIVEMA-----AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        96 ~g~~~s~~~R~rIV~l~-----~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +++..+.+.|.+|++..     +.|   .|..+||+..|||++|+|+..
T Consensus         5 ~~~~r~~~~r~~Il~aA~~lf~~~G~~~ts~~~IA~~aGvsk~tlY~~F   53 (211)
T 3bhq_A            5 DGETRSARKDREIIQAATAAFISKGYDGTSMEEIATKAGASKQTVYKHF   53 (211)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCccHhHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHc
Confidence            45556678888888732     335   899999999999999999864

>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=87.38  E-value=0.47  Score=35.63  Aligned_cols=25  Identities=20%  Similarity=0.234  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4589999999999999999999964

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=87.28  E-value=0.5  Score=34.55  Aligned_cols=34  Identities=21%  Similarity=0.273  Sum_probs=26.6

Q ss_pred             HHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus        29 ~g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~   63 (117)
T 3f52_A           29 LGAALRSFRADKGVTLRELAEASRVSPGYLSELER   63 (117)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            334444444 3599999999999999999999964

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

Probab=87.26  E-value=0.84  Score=34.91  Aligned_cols=51  Identities=25%  Similarity=0.240  Sum_probs=37.8

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE  167 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~  167 (230)
                      .+.+..++|+.|+||++||++.+++..+.|.+...+.   +.-.+++.-.+.+.
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~~---~~~~lT~~g~~~~~  103 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPW---RGVFLTAEGEKLAQ  103 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEETT---TEEEECHHHHHHHH
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEecC---CceEEChhHHHHHH
Confidence            3599999999999999999999999999997743321   23345665444433

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

Probab=87.25  E-value=0.8  Score=33.73  Aligned_cols=41  Identities=20%  Similarity=0.393  Sum_probs=33.7

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        32 ~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~   74 (138)
T 3bpv_A           32 VACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIE   74 (138)
T ss_dssp             HHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            3444433 3 459999999999999999999999999999774

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

Probab=87.15  E-value=0.75  Score=33.90  Aligned_cols=64  Identities=11%  Similarity=0.109  Sum_probs=43.1

Q ss_pred             HHHHHHH--HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         106 LKIVEMA--AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       106 ~rIV~l~--~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      ..|+..+  ..+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        41 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  109 (140)
T 2nnn_A           41 WAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEAG  109 (140)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHHH
Confidence            3444433  346999999999999999999999999999977422  1111 12235677665554443

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=87.11  E-value=2  Score=30.46  Aligned_cols=83  Identities=13%  Similarity=0.097  Sum_probs=52.1

Q ss_pred             HHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhh
Q psy1898         111 MAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQD  189 (230)
Q Consensus       111 l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~  189 (230)
                      .+.+ ..+..++|+.+++|++++.+..+++-  |.. +..       -+...-.+....++ .+++.+..+|+..    .
T Consensus        14 ~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~--g~s-~~~-------~~~~~Rl~~A~~lL-~~~~~si~~iA~~----~   78 (103)
T 3lsg_A           14 SYTDSQFTLSVLSEKLDLSSGYLSIMFKKNF--GIP-FQD-------YLLQKRMEKAKLLL-LTTELKNYEIAEQ----V   78 (103)
T ss_dssp             HTTCTTCCHHHHHHHTTCCHHHHHHHHHHHH--SSC-HHH-------HHHHHHHHHHHHHH-HHCCCCHHHHHHH----T
T ss_pred             HccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--CcC-HHH-------HHHHHHHHHHHHHH-HCCCCCHHHHHHH----h
Confidence            3344 58999999999999999999877543  321 100       00111122223334 3467888877753    6


Q ss_pred             CCCCCCCCCCHhHHHHHHHcC-CCCC
Q psy1898         190 GICDKNSAPSVSSISRLLRGG-RRDD  214 (230)
Q Consensus       190 Gi~~~~~~vS~sTV~R~Lr~~-g~~~  214 (230)
                      |..      +.+...|..++. |..|
T Consensus        79 Gf~------~~s~F~r~Fk~~~G~tP   98 (103)
T 3lsg_A           79 GFE------DVNYFITKFKKYYQITP   98 (103)
T ss_dssp             TCS------CHHHHHHHHHHHHSSCH
T ss_pred             CCC------CHHHHHHHHHHHHCcCH
Confidence            885      899999988764 5544

>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=87.05  E-value=0.48  Score=41.53  Aligned_cols=43  Identities=19%  Similarity=0.310  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.+.+|+.++..+  .|..++|++|+||+.||++=++..++.|.+
T Consensus         5 ~r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~   49 (321)
T 1bia_A            5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (321)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             hHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCc
Confidence            5667788877654  899999999999999999999999999865

>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=86.96  E-value=1.3  Score=32.74  Aligned_cols=56  Identities=20%  Similarity=0.175  Sum_probs=40.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      +.+..+||+.++++++||++.+++..+.|-+..  .+..+ ...-.+|+.-.+.+....
T Consensus        47 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~~~  105 (139)
T 3eco_A           47 GLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFT  105 (139)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHHHH
Confidence            789999999999999999999999999997732  22211 122356776665555443

>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=86.95  E-value=0.3  Score=35.03  Aligned_cols=25  Identities=16%  Similarity=0.315  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4599999999999999999999974

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

Probab=86.94  E-value=1.2  Score=33.23  Aligned_cols=56  Identities=13%  Similarity=-0.012  Sum_probs=39.9

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|+.-.+.+...
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~  108 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTEL  108 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHHH
Confidence            56999999999999999999999999999977422  1111 12235677666555443

>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=86.83  E-value=0.26  Score=35.25  Aligned_cols=34  Identities=9%  Similarity=0.086  Sum_probs=25.6

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      ...|+..+. -.+.+.+|+.+||+.+||+||..-|
T Consensus        15 es~iL~~La-~~gQ~~vAe~~GvdeStISR~k~~~   48 (83)
T 1zs4_A           15 ESALLNKIA-MLGTEKTAEAVGVDKSQISRWKRDW   48 (83)
T ss_dssp             HHHHHHHHH-HHCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHHHH-HHhhHHHHHHhCCCHHHHhhhhhhH
Confidence            344444333 3679999999999999999997744

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

Probab=86.82  E-value=1.2  Score=33.92  Aligned_cols=63  Identities=17%  Similarity=0.188  Sum_probs=42.0

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|.+...  +..+ ...-.+|+.-.+.+..
T Consensus        55 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  122 (162)
T 3cjn_A           55 MRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDR  122 (162)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            3444433 3 35899999999999999999999999999977422  1111 1223567765554443

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=86.72  E-value=0.59  Score=34.20  Aligned_cols=34  Identities=15%  Similarity=0.132  Sum_probs=26.7

Q ss_pred             HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+-.++-.+. ..|+|..++|+.+|||++||++|.
T Consensus        21 ~~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E   55 (114)
T 3vk0_A           21 VLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVE   55 (114)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3444444444 358999999999999999999995

>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=86.70  E-value=0.28  Score=35.73  Aligned_cols=43  Identities=19%  Similarity=0.135  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHc-CCCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAA-GVRPCVISRQL-RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~-G~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..|+..+.. +.+..+|++.+ +++++||++-+++..+.|-+.
T Consensus        26 ~~~~IL~~L~~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~   70 (107)
T 2fsw_A           26 WTLLIIFQINRRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIK   70 (107)
T ss_dssp             SHHHHHHHHTTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHHhCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEE
Confidence            35566665544 49999999999 599999999999999999874

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=86.68  E-value=0.45  Score=41.30  Aligned_cols=41  Identities=22%  Similarity=0.270  Sum_probs=32.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .|.++||+.+|||++||++.++.               .+ .++++.+++|.+..++
T Consensus        10 ~Ti~diA~~aGVS~~TVSrvLn~---------------~~-~Vs~~tr~rV~~~a~~   50 (366)
T 3h5t_A           10 GTLASIAAKLGISRTTVSNAYNR---------------PE-QLSAELRQRILDTAED   50 (366)
T ss_dssp             THHHHHHHHHTSCHHHHHHHHHC---------------GG-GSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCC---------------CC-CCCHHHHHHHHHHHHH
Confidence            57899999999999999999862               11 2478888888877765

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

Probab=86.65  E-value=0.65  Score=35.32  Aligned_cols=63  Identities=19%  Similarity=0.154  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhh-ccccchhhhHHHHHhhhCCCCcCCCCCCCC---CCCCHHHHHH
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVEKR  165 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~p~~~gg~rp---r~lt~~~~~~  165 (230)
                      ..+..|+..+..| .+..+|++.+ +|+++|+++.+++..+.|.+.....+..++   -.+|+.-.+.
T Consensus        35 ~w~l~IL~~L~~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l  102 (131)
T 1yyv_A           35 RWGVLILVALRDGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQV  102 (131)
T ss_dssp             HHHHHHHHHGGGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHH
Confidence            5666777655454 8999999999 799999999999999999874322111122   3567665443

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=86.56  E-value=0.51  Score=36.25  Aligned_cols=44  Identities=14%  Similarity=0.125  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|..|++.+.+   -.|..+|...+     .||.+||||-++.+.+.|.+.
T Consensus        14 ~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   65 (139)
T 3mwm_A           14 RQRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVD   65 (139)
T ss_dssp             HHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEE
Confidence            678888887754   28899999888     699999999999999999763

>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=86.48  E-value=1.3  Score=33.04  Aligned_cols=57  Identities=12%  Similarity=0.193  Sum_probs=39.9

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+....
T Consensus        49 ~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~  108 (147)
T 2hr3_A           49 GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNR  108 (147)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHHHHH
Confidence            36999999999999999999999999999977322  1111 122356776665554443

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=86.45  E-value=0.36  Score=35.43  Aligned_cols=26  Identities=12%  Similarity=0.096  Sum_probs=23.2

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      .+.+.+.+|+.+||+.+||++|...+
T Consensus        22 a~~gq~~vA~~iGV~~StISR~k~~~   47 (97)
T 1xwr_A           22 AMLGTEKTAEAVGVDKSQISRWKRDW   47 (97)
T ss_dssp             HHHCHHHHHHHHTCCTTTHHHHHHHH
T ss_pred             HHHhHHHHHHHhCCCHHHHHHHHhhh
Confidence            35789999999999999999998765

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=86.37  E-value=0.45  Score=37.06  Aligned_cols=43  Identities=23%  Similarity=0.455  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHc----CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA----GVRPCVISRQL-----RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~----G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|..|++.+.+    -.|..+|...+     +||.+|||+-++.+.+.|.+
T Consensus        17 ~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv   68 (150)
T 2w57_A           17 LPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIV   68 (150)
T ss_dssp             HHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcE
Confidence            678888887743    37899999988     79999999999999999976

>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=86.35  E-value=0.68  Score=34.85  Aligned_cols=34  Identities=18%  Similarity=0.203  Sum_probs=31.1

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+.+.++||+.++||++||++.+++..+.|.+..
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r   54 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY   54 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            4699999999999999999999999999998743

>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=86.33  E-value=0.47  Score=35.34  Aligned_cols=33  Identities=30%  Similarity=0.423  Sum_probs=30.7

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        40 ~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~   72 (152)
T 1ku9_A           40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVR   72 (152)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            469999999999999999999999999999774

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=86.32  E-value=0.69  Score=35.72  Aligned_cols=40  Identities=23%  Similarity=0.388  Sum_probs=30.7

Q ss_pred             CCcC-C-HHHHHHHHHHH-----HcC---CCHHHHhhhhccccchhhhHH
Q psy1898          97 GRPL-P-NHIRLKIVEMA-----AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        97 g~~~-s-~~~R~rIV~l~-----~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +++- + .+.|.+|++..     +.|   .|..+||+..|||++|+|+..
T Consensus         9 ~r~r~~~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   58 (208)
T 3cwr_A            9 GRPAVPDAVVRESIVGAAQRLLSSGGAAAMTMEGVASEAGIAKKTLYRFA   58 (208)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CCCCcccHHHHHHHHHHHHHHHHHcCHHhccHHHHHHHhCCCHHHHHHHc
Confidence            4444 5 78888888732     344   899999999999999999874

>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=86.28  E-value=0.34  Score=38.68  Aligned_cols=35  Identities=9%  Similarity=0.010  Sum_probs=27.3

Q ss_pred             HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+-.++-.+. +.|+|..++|+.+|||++|+++|.+
T Consensus        10 ~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~   45 (198)
T 2bnm_A           10 GFAELLKDRREQVKMDHAALASLLGETPETVAAWEN   45 (198)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3444444444 4589999999999999999999974

>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=86.25  E-value=0.51  Score=33.96  Aligned_cols=32  Identities=16%  Similarity=0.233  Sum_probs=30.3

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      |.+.++||+.++++.+||.+++++..+-|.+.
T Consensus        36 gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIk   67 (91)
T 2dk5_A           36 GIWSRDVRYKSNLPLTEINKILKNLESKKLIK   67 (91)
T ss_dssp             CEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            79999999999999999999999999999774

>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=86.24  E-value=2.2  Score=34.96  Aligned_cols=26  Identities=12%  Similarity=0.139  Sum_probs=23.0

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.|++..++|+.+|||.+||++|++
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            35699999999999999999999975

>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=86.12  E-value=0.91  Score=33.73  Aligned_cols=62  Identities=16%  Similarity=0.161  Sum_probs=41.8

Q ss_pred             HHHHHHH-Hc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC-CCCCC--CCCCHHHHHHHH
Q psy1898         106 LKIVEMA-AA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKP--RVATPDVEKRIE  167 (230)
Q Consensus       106 ~rIV~l~-~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~-gg~rp--r~lt~~~~~~I~  167 (230)
                      ..|+..+ .. +.+..+||+.++++++||++.+++..+.|-+...+. ..+|.  -.+|+.-.+.+.
T Consensus        40 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  106 (142)
T 2bv6_A           40 FLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRP  106 (142)
T ss_dssp             HHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHH
Confidence            3444433 33 489999999999999999999999999997732211 11222  245666554443

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

Probab=86.12  E-value=0.88  Score=33.59  Aligned_cols=41  Identities=20%  Similarity=0.357  Sum_probs=33.9

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        34 ~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~   76 (142)
T 3bdd_A           34 YSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEESGYII   76 (142)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            3455433 3 469999999999999999999999999999763

>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=86.07  E-value=1.2  Score=33.03  Aligned_cols=56  Identities=7%  Similarity=0.026  Sum_probs=40.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      ..+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+..
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  106 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNK  106 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHH
Confidence            456999999999999999999999999999977422  1111 1223567765555543

>3geu_A Intercellular adhesion protein R; TETR family, intercellular adhesion regulator, IDP00851, DNA repressor, transcription; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=86.01  E-value=0.4  Score=36.91  Aligned_cols=35  Identities=14%  Similarity=0.215  Sum_probs=27.5

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|++.
T Consensus         2 ~~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F   44 (189)
T 3geu_A            2 NAMKDKIIDNAITLFSEKGYDGTTLDDIAKSVNIKKASLYYHF   44 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHTTCCHHHHTTTC
T ss_pred             chHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHh
Confidence            4667777763    2 334   999999999999999999863

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=85.98  E-value=0.47  Score=34.91  Aligned_cols=25  Identities=12%  Similarity=0.206  Sum_probs=23.1

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4599999999999999999999975

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=85.97  E-value=0.74  Score=38.97  Aligned_cols=59  Identities=8%  Similarity=0.059  Sum_probs=43.3

Q ss_pred             HHHHHHHHH--HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHH
Q psy1898         104 IRLKIVEMA--AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEK  164 (230)
Q Consensus       104 ~R~rIV~l~--~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~  164 (230)
                      ...+|+..+  ..+.+.++||+.++++++||++.+++..+.|-+....+  .+.-.+++.-.+
T Consensus       153 ~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~~r--~~~~~LT~~G~~  213 (244)
T 2wte_A          153 EEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGK--DRKVELNELGLN  213 (244)
T ss_dssp             HHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT--TTEEEECHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC--ccEEEECHHHHH
Confidence            445666653  34699999999999999999999999999998854321  123455665554

>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=85.97  E-value=0.91  Score=33.74  Aligned_cols=54  Identities=19%  Similarity=0.192  Sum_probs=38.6

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIE  167 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~  167 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+.
T Consensus        42 ~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~   98 (144)
T 1lj9_A           42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYP   98 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHH
Confidence            35899999999999999999999999999977322  1111 112346776555544

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

Probab=85.95  E-value=1.4  Score=33.72  Aligned_cols=58  Identities=10%  Similarity=0.095  Sum_probs=40.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      ..+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+....
T Consensus        65 ~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~  125 (161)
T 3e6m_A           65 YGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEIS  125 (161)
T ss_dssp             HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHHHH
Confidence            346999999999999999999999999999977322  1111 122356776665554443

>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=85.91  E-value=0.93  Score=33.66  Aligned_cols=56  Identities=23%  Similarity=0.224  Sum_probs=39.9

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC--CCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~--~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...+  ..+ ...-.+|+.-.+.+...
T Consensus        46 ~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~~  104 (145)
T 2a61_A           46 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKV  104 (145)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHHHH
Confidence            469999999999999999999999999999773221  111 12235677665555433

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=85.85  E-value=0.47  Score=40.62  Aligned_cols=42  Identities=19%  Similarity=0.288  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      +|...|.-++..+.+|+|..+||..++++.+||..++.+...
T Consensus       112 Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~~  153 (286)
T 3n0r_A          112 IAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQA  153 (286)
T ss_dssp             HSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHHh
Confidence            555777666667779999999999999999999999988664

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

Probab=85.74  E-value=2.5  Score=32.96  Aligned_cols=54  Identities=22%  Similarity=0.190  Sum_probs=38.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC--CCC-CCCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~--~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.++||+.++++++||++.+++..+.|-+...+  ..+ ...-.+|+.-.+.+...
T Consensus        87 ~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~  143 (181)
T 2fbk_A           87 LRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHL  143 (181)
T ss_dssp             BCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence            8999999999999999999999999999773221  111 12345677666555443

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

Probab=85.71  E-value=0.99  Score=33.47  Aligned_cols=33  Identities=12%  Similarity=0.285  Sum_probs=30.4

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        51 ~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~   83 (146)
T 2fbh_A           51 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVR   83 (146)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCee
Confidence            358999999999999999999999999999773

>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=85.56  E-value=1.1  Score=33.06  Aligned_cols=32  Identities=9%  Similarity=0.139  Sum_probs=29.9

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.+..+||+.++++++||++.+++..+.|-+.
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~   81 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLY   81 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEE
Confidence            58999999999999999999999999999773

>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O 3jyv_O* 1ysh_E 1s1h_O

Probab=85.41  E-value=2.1  Score=33.67  Aligned_cols=90  Identities=18%  Similarity=0.265  Sum_probs=63.5

Q ss_pred             ChhHHHHHHHHHhcCCChhhhhhhhccccccc----ccCCccc-------CCCcCCHHHHHHHHHH------HHcCCCHH
Q psy1898          57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN----QLGGVFI-------NGRPLPNHIRLKIVEM------AAAGVRPC  119 (230)
Q Consensus        57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~~----~l~~~~~-------~g~~~s~~~R~rIV~l------~~~G~s~~  119 (230)
                      |+++...|++++..|++|++|.-.||-+||+-    ..|....       -.-.+|.|+...|-.+      ++....-.
T Consensus        30 ~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lrkHLe~n~kD~  109 (151)
T 3u5c_N           30 SESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDK  109 (151)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCSCHHHHSSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHHHCCCCHHHhhhHHhccCCCCCeeeecccHHHHHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHccccH
Confidence            58899999999999999999999999999884    2222111       2445888887765542      22333333


Q ss_pred             HHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         120 VISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       120 ~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +--..|-.-.+-|++..+-|+.+|.+.
T Consensus       110 ~sK~~L~liESkI~RL~rYYk~~~~LP  136 (151)
T 3u5c_N          110 DAKFRLILIESRIHRLARYYRTVAVLP  136 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcCC
Confidence            333445567888999999999988763

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=85.38  E-value=0.54  Score=37.03  Aligned_cols=40  Identities=20%  Similarity=0.255  Sum_probs=30.7

Q ss_pred             CCcCCHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898          97 GRPLPNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        97 g~~~s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +++-..+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus        17 ~r~r~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~t~Y~~F   64 (214)
T 2zb9_A           17 GRRPAEEVRAEVLHAVGELLLTEGTAQLTFERVARVSGVSKTTLYKWW   64 (214)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             CCCccHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCHHHHHHHC
Confidence            344455778888872    2 345   899999999999999999864

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

Probab=85.29  E-value=1.4  Score=33.98  Aligned_cols=55  Identities=9%  Similarity=0.067  Sum_probs=39.6

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+..
T Consensus        58 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  115 (168)
T 2nyx_A           58 GPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQ  115 (168)
T ss_dssp             CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            46999999999999999999999999999977321  1111 1223567765555443

>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=85.26  E-value=0.94  Score=33.79  Aligned_cols=33  Identities=21%  Similarity=0.373  Sum_probs=30.5

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        53 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~   85 (147)
T 1z91_A           53 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLIT   85 (147)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEE
Confidence            458999999999999999999999999999774

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

Probab=85.15  E-value=0.96  Score=34.14  Aligned_cols=56  Identities=16%  Similarity=0.178  Sum_probs=38.8

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+...
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~  112 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEAV  112 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHHH
Confidence            46999999999999999999999999999977422  1111 12234666655555443

>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=85.14  E-value=0.67  Score=36.82  Aligned_cols=33  Identities=12%  Similarity=0.148  Sum_probs=26.2

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      -.++-.+. +.|+|..++|+.+|||++||++|.+
T Consensus        13 ~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~   46 (192)
T 1y9q_A           13 ANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIER   46 (192)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34444444 3589999999999999999999964

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

Probab=85.07  E-value=0.79  Score=33.85  Aligned_cols=56  Identities=11%  Similarity=0.068  Sum_probs=39.9

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        49 ~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  107 (142)
T 2fbi_A           49 GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVSM  107 (142)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHHH
Confidence            46899999999999999999999999999977321  1111 11234677666555443

>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=84.95  E-value=0.99  Score=36.36  Aligned_cols=31  Identities=19%  Similarity=0.185  Sum_probs=29.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .|.++||+.||+|.+||++++++..+.|.+.
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~   55 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIE   55 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEE
Confidence            7999999999999999999999999999874

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=84.94  E-value=2.4  Score=29.52  Aligned_cols=44  Identities=14%  Similarity=0.083  Sum_probs=32.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .|+..+++....++.+...  ..+..+++..    +||       |.+||++++++.
T Consensus        19 ~~~~ys~e~k~~~v~~~~~--g~s~~~iA~~----~gI-------s~sTl~rW~k~~   62 (87)
T 2elh_A           19 PLRSLTPRDKIHAIQRIHD--GESKASVARD----IGV-------PESTLRGWCKNE   62 (87)
T ss_dssp             CCSSCCHHHHHHHHHHHHH--TCCHHHHHHH----HTC-------CHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHC--CCCHHHHHHH----HCc-------CHHHHHHHHHHH
Confidence            4667888887777777643  4777777664    565       999999999764

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=84.94  E-value=0.9  Score=35.36  Aligned_cols=37  Identities=14%  Similarity=0.272  Sum_probs=29.6

Q ss_pred             cCCHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhH
Q psy1898          99 PLPNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus        99 ~~s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kw  135 (230)
                      ..+.+.|.+|++.     .+.|   .|..+||+..|||++|+|+.
T Consensus         8 ~~~~~tr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~   52 (189)
T 3vp5_A            8 SLSDEKRNRVYDACLNEFQTHSFHEAKIMHIVKALDIPRGSFYQY   52 (189)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHCCcccccHHHHHHHhCCChHHHHHH
Confidence            3566788888873     2345   79999999999999999975

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

Probab=84.90  E-value=0.78  Score=35.00  Aligned_cols=56  Identities=14%  Similarity=0.183  Sum_probs=39.4

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        63 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~  121 (159)
T 3s2w_A           63 DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPDM  121 (159)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHHH
Confidence            46999999999999999999999999999977322  2111 11235677655555443

>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=84.85  E-value=2.5  Score=31.23  Aligned_cols=45  Identities=29%  Similarity=0.281  Sum_probs=35.6

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         155 PRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       155 pr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .+.++.+....++.+..+++..+..+++..    +||       |.+||+++++..
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~----~gv-------s~stl~~~~~~~   49 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARR----FNI-------PPSTLSTILKNK   49 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHH----HTC-------CHHHHHHHHHTH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHH----hCC-------CHHHHHHHHhch
Confidence            456789988888888877777777677764    465       999999999875

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=84.66  E-value=0.92  Score=41.77  Aligned_cols=41  Identities=10%  Similarity=0.024  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-|...+-    +++|..+||..||||+.||..+..+..
T Consensus       376 L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~RAl  420 (438)
T 1l9z_H          376 LSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL  420 (438)
T ss_pred             CCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55555555555454    689999999999999999999988754

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=84.65  E-value=0.7  Score=36.57  Aligned_cols=33  Identities=9%  Similarity=0.161  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.++..+...- |..++|+.+|||++||++|.+
T Consensus        10 ~~~rl~~~r~~~-tq~elA~~~Gis~~~i~~~e~   42 (189)
T 2fjr_A           10 VLDRICEAYGFS-QKIQLANHFDIASSSLSNRYT   42 (189)
T ss_dssp             HHHHHHHHHTCS-SHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhc-CHHHHHHHhCcCHHHHHHHHh
Confidence            344444444433 999999999999999999986

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=84.58  E-value=0.58  Score=40.02  Aligned_cols=45  Identities=13%  Similarity=0.262  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +.=..|++++..   +++..+||+.+|++++||+++++-..+.|-+..
T Consensus        30 ~Ral~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~   77 (275)
T 3mq0_A           30 RRAVRILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLAR   77 (275)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            333567776653   489999999999999999999999999998753

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=84.53  E-value=1.4  Score=35.81  Aligned_cols=44  Identities=18%  Similarity=0.096  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCC
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDD  214 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~  214 (230)
                      .+-.+.|.+++.++|..+..|+++.|    +       ||.+||+|-|..+++..
T Consensus        11 ~eR~~~i~~~l~~~~~~~~~~la~~~----~-------vs~~TiRrDl~eL~~~~   54 (190)
T 4a0z_A           11 DKRREAIRQQIDSNPFITDHELSDLF----Q-------VSIQTIRLDRTYLNIPE   54 (190)
T ss_dssp             HHHHHHHHHHHHHCTTCCHHHHHHHH----T-------SCHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHHHCCCEeHHHHHHHH----C-------CCHHHHHHHHHHhcCcc
Confidence            44567889999999999999999876    2       59999999999998864

>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=84.51  E-value=0.99  Score=33.99  Aligned_cols=56  Identities=14%  Similarity=0.179  Sum_probs=38.5

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      +.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+....
T Consensus        54 ~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  112 (150)
T 3fm5_A           54 GVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAK  112 (150)
T ss_dssp             CCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHHHH
Confidence            4799999999999999999999999999977422  1111 122356776665555443

>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=84.50  E-value=0.59  Score=39.02  Aligned_cols=41  Identities=17%  Similarity=0.305  Sum_probs=35.4

Q ss_pred             HHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|++++..   +++..+||+.++++++||++.++...+.|-+.
T Consensus         9 l~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~   52 (241)
T 2xrn_A            9 ASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVE   52 (241)
T ss_dssp             HHHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            467776653   48999999999999999999999999999874

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=84.47  E-value=1.5  Score=36.14  Aligned_cols=34  Identities=24%  Similarity=0.297  Sum_probs=30.2

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~  150 (230)
                      +..++|++||||++||..-+++-...|.+..  .+.
T Consensus        30 sE~~La~~lgVSRtpVREAL~~L~~~GlV~~~~~~~   65 (239)
T 2di3_A           30 SERALSETLGVSRSSLREALRVLEALGTISTATGSG   65 (239)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHTSEECCSTTS
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeecccC
Confidence            5679999999999999999999999998866  554

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=84.43  E-value=0.96  Score=38.15  Aligned_cols=83  Identities=8%  Similarity=0.069  Sum_probs=51.9

Q ss_pred             HHHHHHHH---cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCC-HHHH
Q psy1898         106 LKIVEMAA---AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIF-SWEI  181 (230)
Q Consensus       106 ~rIV~l~~---~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t-~~eI  181 (230)
                      .+|++++.   .+++..+||+.+|++++||++.++...+.|-+...+.  + .-.+.+...+.-.......+-.. +..+
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~~--~-~Y~lg~~~~~lg~~~~~~~~l~~~a~p~  102 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRAD--G-SYSLGPEMLRWVRLAGRTWAPPEEVVDI  102 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECTT--S-CEEECHHHHHHHHHHHHHHCCCHHHHHH
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCC--C-eEEecHHHHHHHHHHHccCCHHHHHHHH
Confidence            45665553   3699999999999999999999999999998753322  1 33455655443333333333222 3334


Q ss_pred             HHHHHHhhCC
Q psy1898         182 RDRLVKQDGI  191 (230)
Q Consensus       182 ~~~L~~~~Gi  191 (230)
                      .+.|.++.|.
T Consensus       103 l~~L~~~~~e  112 (260)
T 2o0y_A          103 MRQLSADTGE  112 (260)
T ss_dssp             HHHHHHHHTS
T ss_pred             HHHHHHhHCC
Confidence            4555554553

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=84.38  E-value=0.9  Score=34.95  Aligned_cols=38  Identities=21%  Similarity=0.192  Sum_probs=30.1

Q ss_pred             cCCHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898          99 PLPNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        99 ~~s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .-+.+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus        13 ~~~~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F   58 (206)
T 3kz9_A           13 LSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYF   58 (206)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHSCCSSCCHHHHHHHHTSCHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHc
Confidence            3456778888873     2345   899999999999999999863

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=84.38  E-value=3  Score=30.46  Aligned_cols=90  Identities=16%  Similarity=0.058  Sum_probs=57.0

Q ss_pred             HHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHH
Q psy1898         104 IRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSW  179 (230)
Q Consensus       104 ~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~  179 (230)
                      .-.+|+.++.    +..+..++|+.+++|+.++.+..++   +|.. +..       -+...-.+....++ .+++.+..
T Consensus         8 ~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~---~G~s-~~~-------~~~~~Rl~~A~~lL-~~~~~si~   75 (120)
T 3mkl_A            8 MRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLRE---EETS-YSQ-------LLTECRMQRALQLI-VIHGFSIK   75 (120)
T ss_dssp             HHHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHH---TTCC-HHH-------HHHHHHHHHHHHHH-TSTTCCHH
T ss_pred             HHHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHH---cCCC-HHH-------HHHHHHHHHHHHHH-HcCCCCHH
Confidence            3445555544    3489999999999999999988764   3431 110       00111122223333 56788888


Q ss_pred             HHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898         180 EIRDRLVKQDGICDKNSAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       180 eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                      +|+..    .|..      +.+...|.+++. |..|.
T Consensus        76 eIA~~----~Gf~------~~s~F~r~Fk~~~G~tP~  102 (120)
T 3mkl_A           76 RVAVS----CGYH------SVSYFIYVFRNYYGMTPT  102 (120)
T ss_dssp             HHHHH----TTCS------CHHHHHHHHHHHHSSCHH
T ss_pred             HHHHH----HCCC------CHHHHHHHHHHHHCcCHH
Confidence            87763    6874      889999988875 66665

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=84.34  E-value=0.78  Score=43.81  Aligned_cols=43  Identities=9%  Similarity=0.003  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+-    +|+|..+||+.||||..||..++.+...
T Consensus       550 ~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~  596 (613)
T 3iyd_F          550 GLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR  596 (613)
T ss_dssp             SSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            467777765555555    8999999999999999999999988653

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=84.31  E-value=0.76  Score=35.54  Aligned_cols=36  Identities=8%  Similarity=0.074  Sum_probs=28.1

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|+...
T Consensus         6 ~~~r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   49 (195)
T 2dg7_A            6 PGAEQRLKRAALELYSEHGYDNVTVTDIAERAGLTRRSYFRYFP   49 (195)
T ss_dssp             TTHHHHHHHHHHHHHHHSCGGGCCHHHHHHHTTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhcCccccCHHHHHHHhCCCHHHHHHHcC
Confidence            3567777762    3 345   8999999999999999998743

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=84.25  E-value=0.38  Score=35.01  Aligned_cols=25  Identities=20%  Similarity=0.316  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
T Consensus        22 ~~glsq~~lA~~~gis~~~is~~e~   46 (113)
T 2eby_A           22 PLDLKINELAELLHVHRNSVSALIN   46 (113)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4589999999999999999999974

>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=84.17  E-value=1  Score=30.82  Aligned_cols=43  Identities=14%  Similarity=0.302  Sum_probs=34.4

Q ss_pred             HHHHHHHHH-Hc-CCCHHHHhhhhc----cccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMA-AA-GVRPCVISRQLR----VSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~-~~-G~s~~~IAr~lg----VS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..|+..+ .. +.+..+|++.++    ++++||++.+++..+.|.+.
T Consensus        10 ~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~   58 (82)
T 1p6r_A           10 AELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALN   58 (82)
T ss_dssp             HHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeE
Confidence            344555544 33 599999999997    68999999999999999874

>3nrg_A TETR family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.56A {Chloroflexus aurantiacus}

Probab=84.11  E-value=1.2  Score=34.71  Aligned_cols=36  Identities=17%  Similarity=0.361  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus        11 ~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F   54 (217)
T 3nrg_A           11 PEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF   54 (217)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCTTGGGGTC
T ss_pred             hHHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCcHHHHHHHc
Confidence            56788888873     2445   899999999999999999853

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=84.06  E-value=0.67  Score=35.80  Aligned_cols=35  Identities=23%  Similarity=0.305  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhH
Q psy1898         101 PNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       101 s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kw  135 (230)
                      ..+.|.+|++.     .+.|   .|..+||+..|||++|+|+.
T Consensus         9 ~~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~agvs~~t~Y~~   51 (203)
T 3b81_A            9 FNNKRTELANKIWDIFIANGYENTTLAFIINKLGISKGALYHY   51 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHHcCcccCcHHHHHHHhCCCchhHHHH
Confidence            45678888873     2345   89999999999999999974

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=83.99  E-value=0.63  Score=35.84  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=23.5

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ...|+|..++|+.+|||+++|++|.+
T Consensus        78 ~~~glTq~elA~~lGis~s~is~~E~  103 (141)
T 3kxa_A           78 MKKGFTQSELATAAGLPQPYLSRIEN  103 (141)
T ss_dssp             HHTTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34699999999999999999999975

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=83.93  E-value=0.88  Score=32.16  Aligned_cols=25  Identities=8%  Similarity=0.131  Sum_probs=22.4

Q ss_pred             HcCCCHHHHhhhhccccch----hhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGC----VSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sT----V~kwik  137 (230)
                      ..|+|..++|+.+|||++|    |++|.+
T Consensus        12 ~~glsq~~lA~~~gis~~~~~~~is~~E~   40 (98)
T 3lfp_A           12 RAGISQEKLGVLAGIDEASASARMNQYEK   40 (98)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCcchhhhHHHHHHC
Confidence            4599999999999999999    888864

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

Probab=83.90  E-value=1  Score=33.92  Aligned_cols=41  Identities=15%  Similarity=0.242  Sum_probs=33.6

Q ss_pred             HHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-+.
T Consensus        50 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~   92 (153)
T 2pex_A           50 YLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVT   92 (153)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEe
Confidence            3444433 3 358999999999999999999999999999774

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=83.81  E-value=4.2  Score=28.98  Aligned_cols=83  Identities=11%  Similarity=0.014  Sum_probs=52.3

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCC-CCHHHHHHHHHHhhCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPG-IFSWEIRDRLVKQDGI  191 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~-~t~~eI~~~L~~~~Gi  191 (230)
                      .+..+..++|+.+++|++++++..+++-  |.. +.       .-+...-.+....++...+. ++..+|+..    .|.
T Consensus        16 ~~~~~~~~lA~~~~~s~~~l~r~fk~~~--G~s-~~-------~~~~~~Rl~~A~~lL~~~~~~~si~~IA~~----~Gf   81 (108)
T 3mn2_A           16 MRPITIEKLTALTGISSRGIFKAFQRSR--GYS-PM-------AFAKRVRLQHAHNLLSDGATPTTVTAAALS----CGF   81 (108)
T ss_dssp             TSCCCHHHHHHHHTCCHHHHHHHHHHHT--SSC-HH-------HHHHHHHHHHHHHHHHSSSSCCCHHHHHHH----TTC
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHh--CcC-HH-------HHHHHHHHHHHHHHHHcCCCCCCHHHHHHH----hCC
Confidence            3458999999999999999999877532  321 10       00011112233444544433 788887763    687


Q ss_pred             CCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898         192 CDKNSAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       192 ~~~~~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                      .      +.+...|..++. |..|.
T Consensus        82 ~------~~s~F~r~Fk~~~G~tP~  100 (108)
T 3mn2_A           82 S------NLGHFARDYRDMFGEKPS  100 (108)
T ss_dssp             C------CHHHHHHHHHHHHSSCHH
T ss_pred             C------CHHHHHHHHHHHHCcChH
Confidence            4      889999988764 55553

>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=83.80  E-value=1.4  Score=33.16  Aligned_cols=54  Identities=13%  Similarity=0.171  Sum_probs=38.4

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIE  167 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~  167 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+.
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  106 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFE  106 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHH
Confidence            35899999999999999999999999999977322  1111 122356666554443

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=83.53  E-value=0.44  Score=40.16  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH---cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         103 HIRLKIVEMAA---AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       103 ~~R~rIV~l~~---~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +.-.+|++++.   .+++..+||+.++++++||++.++...+.|-+.
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~   60 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVA   60 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44456776654   258999999999999999999999999999774

>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=83.50  E-value=1.6  Score=36.09  Aligned_cols=69  Identities=14%  Similarity=0.145  Sum_probs=52.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.+.=.+++..+.+..+.++||+.+++|.+||+.-+++.++.|.+.-.+    +.-.+|++-.+....+.+.
T Consensus        15 ~s~EdYLk~I~~L~~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~----~Gv~LTe~G~~~A~~i~~r   83 (200)
T 2p8t_A           15 YTVEDVLAVIFLLKEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ----RGHFLTLKGKEIRDKLLSM   83 (200)
T ss_dssp             CCHHHHHHHHHHTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC------CEEECHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC----CCeEECHHHHHHHHHHHHH
Confidence            44566666666665669999999999999999999999999999875332    3567788877766666553

>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=83.49  E-value=2.4  Score=33.54  Aligned_cols=56  Identities=11%  Similarity=0.051  Sum_probs=40.1

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+.++||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+...
T Consensus        56 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~  114 (189)
T 3nqo_A           56 EETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMVTC  114 (189)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHHH
Confidence            36999999999999999999999999999977321  1111 12235677655555443

>3hta_A EBRA repressor; TETR family, DNA binding protein, multidrug resistance, MULT binding protein, DNA-binding, transcription; 2.30A {Streptomyces lividans} PDB: 3hth_A* 3hti_A* 3htj_A* 3iuv_A

Probab=83.39  E-value=1.1  Score=35.78  Aligned_cols=40  Identities=15%  Similarity=0.235  Sum_probs=32.5

Q ss_pred             CCcCCHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898          97 GRPLPNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        97 g~~~s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ++.-..+.|.+|++.     .+.|   .|..+||+..|||++|+|...
T Consensus        22 ~r~~~~~~r~~Il~AA~~lf~~~G~~~~t~~~IA~~aGvs~~tlY~~F   69 (217)
T 3hta_A           22 PRRHDPERRQRIIDAAIRVVGQKGIAGLSHRTVAAEADVPLGSTTYHF   69 (217)
T ss_dssp             CGGGSHHHHHHHHHHHHHHHHHHTGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cCCCchhHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCcchhhhcC
Confidence            566677889999883     2345   899999999999999999864

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=83.34  E-value=1.1  Score=37.41  Aligned_cols=33  Identities=15%  Similarity=0.088  Sum_probs=29.8

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |..++|++|+||+.||.+-++...+.|.+...+
T Consensus        36 se~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   68 (243)
T 2wv0_A           36 SEREYAEQFGISRMTVRQALSNLVNEGLLYRLK   68 (243)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEeC
Confidence            789999999999999999999999999885443

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=83.15  E-value=0.99  Score=38.54  Aligned_cols=50  Identities=12%  Similarity=0.100  Sum_probs=37.5

Q ss_pred             cCCHHHHHHHHHHHHcC-------C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898          99 PLPNHIRLKIVEMAAAG-------V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-------~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ++..++...+......|       + |..++|++|+||+.||.+-++...+.|.+...
T Consensus        29 ~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   86 (272)
T 3eet_A           29 PAYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGR   86 (272)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CHHHHHHHHHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            33345555555555443       3 88999999999999999999999999976433

>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=83.06  E-value=0.85  Score=38.05  Aligned_cols=31  Identities=23%  Similarity=0.273  Sum_probs=28.5

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      |..++|++|+||+.||.+-++...+.|.+..
T Consensus        31 se~~La~~~~vSr~tvr~Al~~L~~~g~i~~   61 (239)
T 3bwg_A           31 VLETLMAQFEVSKSTITKSLELLEQKGAIFQ   61 (239)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            7899999999999999999999999997743

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=83.06  E-value=0.45  Score=39.04  Aligned_cols=24  Identities=13%  Similarity=0.329  Sum_probs=22.3

Q ss_pred             cCCCHHHHhhhhccccchhhhHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .|+|..++|+.+|||++||++|.+
T Consensus        29 ~g~t~~~lA~~~gis~~~i~~~~~   52 (236)
T 3bdn_A           29 LGLSQESVADKMGMGQSGVGALFN   52 (236)
T ss_dssp             TTCCSHHHHHHHTSCHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHc
Confidence            489999999999999999999975

>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=83.04  E-value=0.98  Score=34.89  Aligned_cols=43  Identities=19%  Similarity=0.228  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHc--CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA--GVRPCVISRQL-----RVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~--G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|..|++.+.+  ..|..+|...+     .||.+||||-++.+.+.|.+
T Consensus        19 ~qR~~Il~~l~~~~h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv   68 (145)
T 3eyy_A           19 PQRQLVLEAVDTLEHATPDDILGEVRKTASGINISTVYRTLELLEELGLV   68 (145)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcE
Confidence            678888876543  48888888877     69999999999999999966

>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=82.94  E-value=0.87  Score=31.14  Aligned_cols=22  Identities=14%  Similarity=0.111  Sum_probs=20.1

Q ss_pred             CCHHHHhhhhccccchhhhHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+..++|+.+|||++||++|.+
T Consensus        28 ~sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           28 MSMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             SCHHHHHHHHTCCHHHHHHHHT
T ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Confidence            3999999999999999999964

>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=82.94  E-value=1.1  Score=35.44  Aligned_cols=41  Identities=20%  Similarity=0.300  Sum_probs=34.0

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++..+ .+|+.++.+|.|.++||+.+++|..||...+++-+
T Consensus       154 ~Lt~rE-~~vl~~l~~g~s~~~Ia~~l~is~~TV~~hi~~i~  194 (215)
T 1a04_A          154 QLTPRE-RDILKLIAQGLPNKMIARRLDITESTVKVHVKHML  194 (215)
T ss_dssp             GSCHHH-HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            355544 36888889999999999999999999999888754

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=82.92  E-value=2.8  Score=31.89  Aligned_cols=54  Identities=11%  Similarity=0.123  Sum_probs=36.7

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC-CC-CCCCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IG-GSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~-~g-g~rpr~lt~~~~~~I~~l  169 (230)
                      ++..+||+.++++++||++.+++..+.|-++... .. +...-.+|++-.+.+.+.
T Consensus        53 ~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~~~~~~  108 (148)
T 4fx0_A           53 LTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRAALQKA  108 (148)
T ss_dssp             -CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC-----------CCBCHHHHHHHHHH
T ss_pred             cCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHHHHHHH
Confidence            7999999999999999999999999999773211 11 113346677766555444

>3q0w_A HTH-type transcriptional regulator EThr; TETR family, transcriptional repressor, transcription-transc inhibitor complex; HET: LL5; 1.60A {Mycobacterium tuberculosis} PDB: 3o8g_A* 3o8h_A* 3q0u_A* 3q0v_A* 3g1m_A* 3q3s_A* 3sdg_A* 3sfi_A* 1u9n_A* 1u9o_A* 3tp3_A 3qpl_A 3g1l_A* 1t56_A 3tp0_A*

Probab=82.87  E-value=1.1  Score=36.07  Aligned_cols=40  Identities=13%  Similarity=0.112  Sum_probs=29.6

Q ss_pred             CCcCCHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898          97 GRPLPNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        97 g~~~s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .++-+.+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus        38 ~~~~~~~~r~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~~tlY~~F   85 (236)
T 3q0w_A           38 ARPSGDDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYF   85 (236)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CCCChHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCcHHHHHHHC
Confidence            444566888888873    2 345   899999999999999999864

>2iu5_A DHAS, YCEG, HTH-type dhaklm operon transcriptional activator; synthase, TETR family; 1.6A {Lactococcus lactis subsp} SCOP: a.4.1.9 a.121.1.1

Probab=82.85  E-value=1  Score=34.89  Aligned_cols=36  Identities=6%  Similarity=0.035  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.+.|.+|++.    + +.|   .|.++||+..|||++|+|+..
T Consensus        11 ~~~~r~~Il~aa~~lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~F   54 (195)
T 2iu5_A           11 SIITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYF   54 (195)
T ss_dssp             TSHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             cHHHHHHHHHHHHHHHHhCCCCeeCHHHHHHHhCCCHHHHHHHc
Confidence            34677888773    2 345   899999999999999999853

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=82.75  E-value=0.61  Score=39.27  Aligned_cols=44  Identities=16%  Similarity=0.195  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +++.+|.. +..|  + |..++|++|+||+.||.+-++.-.+.|.+..
T Consensus        22 ~l~~~I~~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~   68 (248)
T 3f8m_A           22 ELDRMLDG-MRIGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER   68 (248)
T ss_dssp             HHHHHHHH-CCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHhC-CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            44555553 4445  4 7899999999999999999999999998755

>2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A

Probab=82.74  E-value=2.5  Score=29.49  Aligned_cols=52  Identities=13%  Similarity=0.070  Sum_probs=39.1

Q ss_pred             CHHHHHHHHHHHHhC-C--CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898         159 TPDVEKRIEEYKKTN-P--GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD  216 (230)
Q Consensus       159 t~~~~~~I~~l~~~~-P--~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~  216 (230)
                      +..+...|.+++.+. |  .++-.+|.+.|.+ .|+.     +|..||-.+=...++.++.
T Consensus        18 ~~~Ik~~Ik~lI~~Ed~~kPlSD~~I~~~L~~-~Gi~-----IaRRTVaKYRe~l~Ip~s~   72 (76)
T 2ahq_A           18 QGELMKLIKEIVENEDKRKPYSDQEIANILKE-KGFK-----VARRTVAKYREMLGIPSSR   72 (76)
T ss_dssp             HHHHHHHHHHHGGGCCSSSCCCHHHHHHHHTT-TSSC-----CCHHHHHHHHHHTC-----
T ss_pred             HHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH-cCCC-----ccHHHHHHHHHHcCCCchh
Confidence            456788888888753 3  3778899999987 7995     9999999999999998875

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

Probab=82.71  E-value=4.8  Score=31.78  Aligned_cols=69  Identities=17%  Similarity=0.201  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHc-CCCHHHHhhhh--------ccccchhhhHHHHHhhhCCCCcCC--CCCCC---CCCCCHHHHHHHHHH
Q psy1898         104 IRLKIVEMAAA-GVRPCVISRQL--------RVSHGCVSKILNRYQETGSIRPGV--IGGSK---PRVATPDVEKRIEEY  169 (230)
Q Consensus       104 ~R~rIV~l~~~-G~s~~~IAr~l--------gVS~sTV~kwikRy~e~G~v~p~~--~gg~r---pr~lt~~~~~~I~~l  169 (230)
                      ++.-|+.++.. .++.-+|++.+        ++|.++||.-+++..+.|-+....  .++++   --.+|+.-++.+..+
T Consensus         3 l~~~iL~lL~~~~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l~~~   82 (179)
T 1yg2_A            3 LPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEW   82 (179)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHH
T ss_pred             hHHHHHHHHhcCCCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHHHHH
Confidence            45566666554 48899999988        699999999999999999774321  11222   246788888888888


Q ss_pred             HHh
Q psy1898         170 KKT  172 (230)
Q Consensus       170 ~~~  172 (230)
                      +.+
T Consensus        83 ~~~   85 (179)
T 1yg2_A           83 FDQ   85 (179)
T ss_dssp             HHS
T ss_pred             HhC
Confidence            765

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=82.66  E-value=1.1  Score=36.01  Aligned_cols=41  Identities=12%  Similarity=0.226  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .++..+ .+|+.++.+|.|.++||+.+++|..||...+++-.
T Consensus       149 ~LT~rE-~~vL~~l~~g~s~~eIa~~l~is~~TV~~hi~~l~  189 (225)
T 3c3w_A          149 GLTDQE-RTLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLL  189 (225)
T ss_dssp             TSCHHH-HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHH-HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            356554 46888889999999999999999999999888754

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=82.61  E-value=0.96  Score=41.28  Aligned_cols=41  Identities=10%  Similarity=0.016  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-+...+-    +++|..+||..||||+.||..+..+..
T Consensus       361 L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVrqi~~rAl  405 (423)
T 2a6h_F          361 LSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKAL  405 (423)
T ss_dssp             SCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55566655555554    689999999999999999999988754

>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=82.58  E-value=1.1  Score=34.70  Aligned_cols=36  Identities=17%  Similarity=0.224  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus        12 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   55 (220)
T 3lhq_A           12 ALETRQHILDVALRLFSQQGVSATSLAEIANAAGVTRGAIYWHF   55 (220)
T ss_dssp             SHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCceeehhhc
Confidence            34667777762    2 345   899999999999999999863

>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_O 1ysh_E 3jyv_O* 1s1h_O

Probab=82.52  E-value=3.6  Score=32.45  Aligned_cols=90  Identities=18%  Similarity=0.245  Sum_probs=63.0

Q ss_pred             ChhHHHHHHHHHhcCCChhhhhhhhccccccc----ccCCccc-------CCCcCCHHHHHHHHHHH---Hc-CCCHHHH
Q psy1898          57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN----QLGGVFI-------NGRPLPNHIRLKIVEMA---AA-GVRPCVI  121 (230)
Q Consensus        57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~~----~l~~~~~-------~g~~~s~~~R~rIV~l~---~~-G~s~~~I  121 (230)
                      |+++...|+++|..|++|++|.-.||-+||+-    ..|...-       -.-.+|.|+...|-.+.   +. ....++.
T Consensus        32 ~eeVe~~I~klakkG~tpSqIG~iLRD~~GIp~Vk~vtG~kI~rILk~~glapeiPEDL~~LikKAv~lRkHLe~n~kD~  111 (153)
T 2xzm_O           32 PSTVVDLSVKLAKKGLTPSQIGVILRDQHGIPQVRFLTGQKILRILKKNGCAPQLPEDLYFLIKKALSIRKHLEKNRKDK  111 (153)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHSSCCSCHHHHHSSCHHHHHHHTTCCCSSCHHHHHHHHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHHHHHHCCCCHHHhhhHHhhcCCCCCeeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHcccch
Confidence            58899999999999999999999999999984    2222111       23457888876665422   11 1233344


Q ss_pred             h--hhhccccchhhhHHHHHhhhCCCC
Q psy1898         122 S--RQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       122 A--r~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      -  ..|-.-.+-|++..+-|+.+|.+-
T Consensus       112 ~sK~~L~LiESkI~RL~rYYk~~~~LP  138 (153)
T 2xzm_O          112 DSKYRLILVESRIHRLSRYYKLNQKLP  138 (153)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCcCC
Confidence            3  345567888999999999888764

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=82.49  E-value=1  Score=34.09  Aligned_cols=35  Identities=11%  Similarity=0.245  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEMA-----AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l~-----~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   49 (188)
T 3qkx_A            7 TDLAEQIFSATDRLMAREGLNQLSMLKLAKEANVAAGTIYLYF   49 (188)
T ss_dssp             HHHHHHHHHHHHHHHHHSCSTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHHc
Confidence            46677777632     345   999999999999999999763

>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=82.33  E-value=0.71  Score=36.27  Aligned_cols=31  Identities=23%  Similarity=0.372  Sum_probs=29.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.
T Consensus       165 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  195 (207)
T 2oz6_A          165 ITRQEIGRIVGCSREMVGRVLKSLEEQGLVH  195 (207)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            6889999999999999999999999999874

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

Probab=82.30  E-value=1.6  Score=32.89  Aligned_cols=65  Identities=8%  Similarity=0.064  Sum_probs=43.6

Q ss_pred             HHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         106 LKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       106 ~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      ..|+..+.  .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|+.-.+.+....
T Consensus        46 ~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~  115 (155)
T 3cdh_A           46 WRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAESLV  115 (155)
T ss_dssp             HHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHHHH
Confidence            34554443  35899999999999999999999999999977422  1111 122356776665555443

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=82.21  E-value=0.89  Score=35.25  Aligned_cols=34  Identities=21%  Similarity=0.271  Sum_probs=27.1

Q ss_pred             HHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.    + +.|   .|..+||+..|||++|+|...
T Consensus         9 ~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F   50 (193)
T 2dg8_A            9 QRRERILAATLDLIAEEGIARVSHRRIAQRAGVPLGSMTYHF   50 (193)
T ss_dssp             THHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCTHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCchhhheeC
Confidence            667777762    2 345   899999999999999999763

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=82.21  E-value=1.6  Score=32.11  Aligned_cols=40  Identities=33%  Similarity=0.401  Sum_probs=30.7

Q ss_pred             HHHHHHHHHhCC----CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNP----GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P----~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      ++.|.+++.++|    ..+..++++..    +       ||.+||.|+.++.|+.
T Consensus        19 e~~ia~yil~~~~~~~~~si~elA~~~----~-------vS~aTv~Rf~kkLGf~   62 (107)
T 3iwf_A           19 EKKIAQFILNYPHKVVNMTSQEIANQL----E-------TSSTSIIRLSKKVTPG   62 (107)
T ss_dssp             HHHHHHHHHHCHHHHTTCCHHHHHHHH----T-------SCHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHhCHHHHHHCCHHHHHHHH----C-------CCHHHHHHHHHHhCCC
Confidence            456666777776    57787777643    4       5999999999999986

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=82.21  E-value=1.9  Score=28.81  Aligned_cols=38  Identities=8%  Similarity=0.147  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         162 VEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       162 ~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .++.|.+++.++ +.++..+|++.|    |       +|.+||++.|+.+
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~l----g-------lsr~tv~~~l~~L   49 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKC----Q-------VPKKTLNQVLYRL   49 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHH----C-------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            355666666654 468898888765    4       4999999987764

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=82.17  E-value=1.5  Score=32.47  Aligned_cols=30  Identities=7%  Similarity=-0.046  Sum_probs=24.6

Q ss_pred             HHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         108 IVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       108 IV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +-.+.+ .|+|..++|+.+|||+++|++|.+
T Consensus        12 Lr~~R~~~glSq~eLA~~~gis~~~is~iE~   42 (112)
T 2wus_R           12 FRKKREERRITLLDASLFTNINPSKLKRIEE   42 (112)
T ss_dssp             HHHHHHTTTCCHHHHHHHSSCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            333443 489999999999999999999964

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

Probab=82.07  E-value=1.4  Score=32.85  Aligned_cols=65  Identities=11%  Similarity=0.128  Sum_probs=42.7

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      ..|+..+ ..+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+....
T Consensus        40 ~~iL~~l~~~~~~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  108 (144)
T 3f3x_A           40 FSILKATSEEPRSMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLEAN  108 (144)
T ss_dssp             HHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHHHHH
Confidence            3444433 333399999999999999999999999999977322  1111 112356776655554433

>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=81.94  E-value=1.2  Score=33.83  Aligned_cols=35  Identities=11%  Similarity=0.189  Sum_probs=27.8

Q ss_pred             HHHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++    ++ +.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   49 (194)
T 2g7s_A            7 QSKADDILQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHF   49 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             hhhHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHc
Confidence            467777776    22 345   899999999999999999863

>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=81.94  E-value=1.2  Score=34.92  Aligned_cols=36  Identities=25%  Similarity=0.200  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhH
Q psy1898         100 LPNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       100 ~s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kw  135 (230)
                      .+.+.|.+|++.    + +.|   .|..+||+..|||++|+|+.
T Consensus         6 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvsk~tlY~~   49 (203)
T 3cdl_A            6 LTDQKRESIVQAAIAEFGDRGFEITSMDRIAARAEVSKRTVYNH   49 (203)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHTT
T ss_pred             cchhHHHHHHHHHHHHHHHcCchhcCHHHHHHHhCCCHHHHHHH
Confidence            456788888873    2 345   89999999999999999985

>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=81.93  E-value=1.4  Score=31.62  Aligned_cols=86  Identities=16%  Similarity=0.113  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCC-CCCHHH
Q psy1898         102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNP-GIFSWE  180 (230)
Q Consensus       102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P-~~t~~e  180 (230)
                      .++=..|+.....|.+.++||..+++|.+++.+.++...+.|-+....  +  .-.+|+.-.+.+..+..-.- -....+
T Consensus         7 ~eIi~~IL~~i~~~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~--~--~~~LT~kG~~~l~~l~~~~~~l~~l~~   82 (95)
T 1r7j_A            7 LEIIQAILEACKSGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG--K--QYMLTKKGEELLEDIRKFNEMRKNMDQ   82 (95)
T ss_dssp             HHHHHHHHHHHTTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET--T--EEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC--C--eeEEChhHHHHHHHHHHHHHHHHHHHH
Confidence            355566676666679999999999999999999999999999885432  1  26788877765544432111 113445


Q ss_pred             HHHHHHHhhCC
Q psy1898         181 IRDRLVKQDGI  191 (230)
Q Consensus       181 I~~~L~~~~Gi  191 (230)
                      +.+.|.+..|+
T Consensus        83 ~e~~l~~~l~i   93 (95)
T 1r7j_A           83 LKEKINSVLSI   93 (95)
T ss_dssp             HHHHHHHHHC-
T ss_pred             HHHHHHHHcCC
Confidence            55555554454

>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=81.74  E-value=0.75  Score=35.22  Aligned_cols=21  Identities=14%  Similarity=0.044  Sum_probs=19.5

Q ss_pred             CCHHHHhhhhccccchhhhHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .|..+||+..|||++|+|+..
T Consensus        23 ~ti~~Ia~~agvs~~t~Y~~F   43 (194)
T 3bqz_B           23 TTTGEIVKLSESSKGNLYYHF   43 (194)
T ss_dssp             CCHHHHHHHTTCCHHHHHHHT
T ss_pred             CCHHHHHHHhCCCchhHHHhC
Confidence            899999999999999999863

>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=81.72  E-value=0.76  Score=36.15  Aligned_cols=31  Identities=19%  Similarity=0.261  Sum_probs=29.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.
T Consensus       168 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~  198 (210)
T 3ryp_A          168 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS  198 (210)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHCCcEE
Confidence            5789999999999999999999999999774

>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription regulation, TETR, DNA-binding transcription; 2.90A {Pseudomonas aeruginosa}

Probab=81.61  E-value=1.1  Score=35.29  Aligned_cols=37  Identities=19%  Similarity=0.187  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         101 PNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       101 s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.+.|.+|++.    + +.|   .|..+||+..|||++|+|+...
T Consensus         9 ~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2wui_A            9 SQKTRDGILDAAERVFLEKGVGTTAMADLADAAGVSRGAVYGHYK   53 (210)
T ss_dssp             CTHHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHHcCccccCHHHHHHHhCCCHHHHHHHcC
Confidence            45678888873    2 345   8999999999999999998743

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=81.61  E-value=3.3  Score=29.57  Aligned_cols=81  Identities=7%  Similarity=0.009  Sum_probs=50.7

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCC
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICD  193 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~  193 (230)
                      ...+..++|+.+++|++++.+..+++  .|.. +..       -+...-.+....++ .+++.+..+|+..    .|.. 
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~~--~G~s-~~~-------~~~~~Rl~~A~~lL-~~~~~si~~IA~~----~Gf~-   82 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQQ--LGIS-VLS-------WREDQRISQAKLLL-STTRMPIATVGRN----VGFD-   82 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHHH--HSSC-HHH-------HHHHHHHHHHHHHH-HHCCCCHHHHHHH----TTCC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH--HCcC-HHH-------HHHHHHHHHHHHHH-HcCCCCHHHHHHH----hCCC-
Confidence            35899999999999999999887753  2421 110       00111112223334 3456888877753    6885 


Q ss_pred             CCCCCCHhHHHHHHHcC-CCCCC
Q psy1898         194 KNSAPSVSSISRLLRGG-RRDDC  215 (230)
Q Consensus       194 ~~~~vS~sTV~R~Lr~~-g~~~~  215 (230)
                           +.+...|..++. |..|.
T Consensus        83 -----~~s~F~r~Fk~~~G~tP~  100 (107)
T 2k9s_A           83 -----DQLYFSRVFKKCTGASPS  100 (107)
T ss_dssp             -----CHHHHHHHHHHHHSSCHH
T ss_pred             -----CHHHHHHHHHHHHCcCHH
Confidence                 888988888875 55543

>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=81.57  E-value=0.88  Score=36.66  Aligned_cols=25  Identities=16%  Similarity=0.094  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++|+++|.+
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            4589999999999999999999964

>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=81.56  E-value=1.4  Score=34.46  Aligned_cols=36  Identities=22%  Similarity=0.275  Sum_probs=28.5

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|+...
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2xdn_A           10 QETRAQIIEAAERAFYKRGVARTTLADIAELAGVTRGAIYWHFN   53 (210)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCTTHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCcHHHHHHHHCCChHHHHHHhC
Confidence            4677888873    2 335   9999999999999999998743

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

Probab=81.56  E-value=1.3  Score=33.65  Aligned_cols=63  Identities=19%  Similarity=0.199  Sum_probs=42.2

Q ss_pred             HHHHHHH-H--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         106 LKIVEMA-A--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       106 ~rIV~l~-~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      ..|+..+ .  .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ...-.+|+.-.+.+..
T Consensus        50 ~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  118 (160)
T 3boq_A           50 FDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQ  118 (160)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHHH
Confidence            3455444 2  36999999999999999999999999999977422  1111 1223567765555443

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=81.42  E-value=0.81  Score=35.90  Aligned_cols=32  Identities=25%  Similarity=0.232  Sum_probs=29.6

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.-
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            68899999999999999999999999998753

>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=81.36  E-value=0.9  Score=34.75  Aligned_cols=33  Identities=18%  Similarity=0.243  Sum_probs=25.7

Q ss_pred             HHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         104 IRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       104 ~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .|.+|++    ++ +.|   .|..+||+..|||++|+|+.-
T Consensus         3 tr~~Il~aA~~lf~~~Gy~~~s~~~Ia~~agvskgtlY~~F   43 (179)
T 2eh3_A            3 TKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHF   43 (179)
T ss_dssp             HHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCCcHHHHHHc
Confidence            4666665    22 345   899999999999999999863

>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=81.14  E-value=1.3  Score=32.25  Aligned_cols=35  Identities=14%  Similarity=0.163  Sum_probs=31.2

Q ss_pred             HcCCCHHHHhhhhc----cccchhhhHHHHHhhhCCCCc
Q psy1898         113 AAGVRPCVISRQLR----VSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       113 ~~G~s~~~IAr~lg----VS~sTV~kwikRy~e~G~v~p  147 (230)
                      ..+.+..+||+.++    ++++||++.+++..+.|-+..
T Consensus        22 ~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r   60 (123)
T 1okr_A           22 KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDR   60 (123)
T ss_dssp             HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEE
Confidence            34699999999999    889999999999999998743

>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=81.07  E-value=1  Score=37.03  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=29.8

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      +-.++|++||||++||..=+++-...|.+...+
T Consensus        33 sE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~   65 (239)
T 1hw1_A           33 AERELSELIGVTRTTLREVLQRLARDGWLTIQH   65 (239)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEec
Confidence            789999999999999999999999999875444

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=81.07  E-value=0.31  Score=37.99  Aligned_cols=25  Identities=16%  Similarity=0.228  Sum_probs=0.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
T Consensus        12 ~~gltq~elA~~lgis~~~vs~~e~   36 (158)
T 2p5t_A           12 THDLTQLEFARIVGISRNSLSRYEN   36 (158)
T ss_dssp             -------------------------
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4589999999999999999999943

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=81.04  E-value=1.3  Score=34.05  Aligned_cols=36  Identities=19%  Similarity=0.138  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus        10 ~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   53 (202)
T 3lwj_A           10 NKERRQKILTCSLDLFIEKGYYNTSIRDIIALSEVGTGTFYNYF   53 (202)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCSCHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchhHHHHc
Confidence            34677777762     2345   899999999999999999853

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

Probab=81.03  E-value=0.89  Score=34.86  Aligned_cols=43  Identities=12%  Similarity=0.108  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHcC-CCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAAG-VRPCVISRQL-RVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~G-~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..|+..+..| .+..++++.+ +||.+|+++-+++..+.|.+.
T Consensus        27 W~l~IL~~L~~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~   71 (131)
T 4a5n_A           27 WKGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVH   71 (131)
T ss_dssp             SHHHHHHHHTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHhcCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEE
Confidence            355666655454 9999999999 999999999999999999874

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=80.99  E-value=0.84  Score=35.96  Aligned_cols=32  Identities=16%  Similarity=0.248  Sum_probs=29.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++..+||..+|+|+.||++.++++++.|.+.-
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            68899999999999999999999999998753

>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=80.96  E-value=1.4  Score=34.20  Aligned_cols=35  Identities=14%  Similarity=0.039  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F   49 (199)
T 2o7t_A            7 LKRREHIITTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNF   49 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHc
Confidence            3567777762    2 345   899999999999999999864

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=80.90  E-value=1.4  Score=34.10  Aligned_cols=37  Identities=19%  Similarity=0.194  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         100 LPNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       100 ~s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      -+.+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus        11 ~~~~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F   55 (212)
T 3knw_A           11 KSEAKRQHILDSGFHLVLRKGFVGVGLQEILKTSGVPKGSFYHYF   55 (212)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cchhhHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCChHHHHHHC
Confidence            455788888873    2 345   899999999999999999863

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=80.88  E-value=0.78  Score=36.56  Aligned_cols=31  Identities=23%  Similarity=0.425  Sum_probs=29.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.
T Consensus       179 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  209 (227)
T 3dkw_A          179 VAKQLVAGHLSIQPETFSRIMHRLGDEGIIH  209 (227)
T ss_dssp             SCTHHHHHHTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCcEE
Confidence            5789999999999999999999999999874

>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=80.82  E-value=1  Score=35.55  Aligned_cols=32  Identities=16%  Similarity=0.263  Sum_probs=30.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ++..+||+.++||+..|.++++.-++.|.+..
T Consensus        29 ~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s   60 (162)
T 3k69_A           29 VASRELAQSLHLNPVMIRNILSVLHKHGYLTG   60 (162)
T ss_dssp             BCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999998754

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=80.75  E-value=0.86  Score=36.00  Aligned_cols=31  Identities=26%  Similarity=0.401  Sum_probs=29.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.
T Consensus       164 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  194 (216)
T 4ev0_A          164 IRHHELAALAGTSRETVSRVLHALAEEGVVR  194 (216)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999885

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=80.73  E-value=1  Score=35.69  Aligned_cols=32  Identities=16%  Similarity=0.359  Sum_probs=30.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+..+||..+|+|+.||++.++++++.|.+.
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  200 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVK  200 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            47999999999999999999999999999875

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=80.63  E-value=1.4  Score=34.11  Aligned_cols=35  Identities=17%  Similarity=0.102  Sum_probs=28.1

Q ss_pred             HHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus        17 ~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F   59 (212)
T 1pb6_A           17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYF   59 (212)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHcCcchhhHHHHHHHHCCChhHHHHhC
Confidence            4677888872     2345   899999999999999999873

>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=80.62  E-value=0.93  Score=34.19  Aligned_cols=34  Identities=21%  Similarity=0.198  Sum_probs=27.0

Q ss_pred             HHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus         4 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   45 (170)
T 3egq_A            4 DQSVRIIEAALRLYMKKPPHEVSIEEIAREAKVSKSLIFYHF   45 (170)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhcCCccCcHHHHHHHhCCCchhHHHHc
Confidence            567777763    2 234   899999999999999999874

>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=80.57  E-value=0.97  Score=35.46  Aligned_cols=36  Identities=17%  Similarity=0.235  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +...|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~~tr~~Il~AA~~lf~~~G~~~~s~~~IA~~AGvs~gtlY~~F   50 (203)
T 2np5_A            7 SSTSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHF   50 (203)
T ss_dssp             --CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cchhHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCHHHHHHHc
Confidence            44567778773     2345   899999999999999999864

>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=80.56  E-value=0.87  Score=36.35  Aligned_cols=31  Identities=19%  Similarity=0.338  Sum_probs=29.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  218 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLH  218 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence            5889999999999999999999999999874

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=80.54  E-value=2.9  Score=28.51  Aligned_cols=36  Identities=19%  Similarity=0.053  Sum_probs=27.9

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.|..++.+++..+..||++.+    |       +|.+||++.|+.+
T Consensus         3 ~~Il~~L~~~~~~s~~eLa~~l----g-------vs~~tv~r~L~~L   38 (81)
T 2htj_A            3 NEILEFLNRHNGGKTAEIAEAL----A-------VTDYQARYYLLLL   38 (81)
T ss_dssp             HHHHHHHHHSCCCCHHHHHHHH----T-------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            4566777777779999998866    4       4999999987764

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

Probab=80.54  E-value=1.1  Score=34.55  Aligned_cols=56  Identities=13%  Similarity=0.153  Sum_probs=37.5

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      +.+..+||+.++++++||++.+++..+.|.+...  +..+ ...-.+|+.-.+.+....
T Consensus        62 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~  120 (168)
T 3u2r_A           62 GMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLKDLE  120 (168)
T ss_dssp             CEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHHHHH
Confidence            7999999999999999999999999999977422  1111 122356776665555444

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=80.50  E-value=1.4  Score=34.29  Aligned_cols=34  Identities=21%  Similarity=0.241  Sum_probs=27.1

Q ss_pred             HHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus         9 ~~r~~Il~aA~~lf~~~G~~~~t~~~Ia~~Agvs~gt~Y~yF   50 (204)
T 3anp_C            9 RRRERIFRAAMELFRNRGFQETTATEIAKAAHVSRGTFFNYY   50 (204)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCcccccHHHHHHHcCCchHHHHHHc
Confidence            567777762    2 345   899999999999999999864

>3bjb_A Probable transcriptional regulator, TETR family P; APC7331, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.50A {Rhodococcus SP}

Probab=80.50  E-value=1  Score=35.53  Aligned_cols=37  Identities=14%  Similarity=0.248  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         101 PNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       101 s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+.|.+|++.    + +.|   .|..+||+..|||++|+|+...
T Consensus        20 ~~~~r~~Il~AA~~lf~e~G~~~~s~~~IA~~AGVsk~tlY~~F~   64 (207)
T 3bjb_A           20 QRARHVRMLEAAIELATEKELARVQMHEVAKRAGVAIGTLYRYFP   64 (207)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            34677888872    2 345   8999999999999999998743

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=80.45  E-value=1.1  Score=34.11  Aligned_cols=35  Identities=14%  Similarity=0.173  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   49 (195)
T 3pas_A            7 DSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYY   49 (195)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHcChHhcCHHHHHHHhCCCchHHHHHc
Confidence            3567777762    2 334   999999999999999999863

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=80.43  E-value=1.5  Score=33.62  Aligned_cols=36  Identities=22%  Similarity=0.173  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus         6 ~~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~Agvs~~tly~~F   49 (194)
T 3dpj_A            6 QAQTRDQIVAAADELFYRQGFAQTSFVDISAAVGISRGNFYYHF   49 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hhhHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCChHHHHHHc
Confidence            35777888873     2345   899999999999999999864

>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=80.36  E-value=0.73  Score=34.16  Aligned_cols=40  Identities=20%  Similarity=0.223  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhCC----CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNP----GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P----~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      ++.|.+++.++|    ..+..++++.    .+       ||.+||.|+.++.|+.
T Consensus        23 e~~ia~yil~~~~~~~~~si~elA~~----~~-------vS~aTv~Rf~kklG~~   66 (111)
T 2o3f_A           23 ERKLADYILAHPHXAIESTVNEISAL----AN-------SSDAAVIRLCXSLGLK   66 (111)
T ss_dssp             HHHHHHHHHHCHHHHHTCCHHHHHHH----TT-------CCHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHChHHHHhcCHHHHHHH----HC-------CCHHHHHHHHHHcCCC
Confidence            456777777776    4777777764    44       5999999999999987

>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=80.36  E-value=0.65  Score=34.73  Aligned_cols=55  Identities=5%  Similarity=0.027  Sum_probs=38.3

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+...  +..+ ..--.+|++-.+.+..
T Consensus        49 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (140)
T 3hsr_A           49 EKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSP  106 (140)
T ss_dssp             CEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHH
Confidence            35899999999999999999999999999977322  1111 1223467765554443

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=80.30  E-value=0.34  Score=41.47  Aligned_cols=23  Identities=26%  Similarity=0.281  Sum_probs=0.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .|.++||+.+|||++||++.++.
T Consensus         6 ~ti~diA~~agVS~~TVSrvln~   28 (332)
T 2o20_A            6 TTIYDVARVAGVSMATVSRVVNG   28 (332)
T ss_dssp             -----------------------
T ss_pred             CcHHHHHHHHCCCHHHHHHHHcC
Confidence            58999999999999999999974

>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=80.20  E-value=1  Score=34.51  Aligned_cols=35  Identities=17%  Similarity=0.196  Sum_probs=27.5

Q ss_pred             HHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|.+|++.    + +.|   .|..+||+..|||++|+|+...
T Consensus         8 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   50 (206)
T 3dew_A            8 DCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFG   50 (206)
T ss_dssp             CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhcCCcccCcHHHHHHHhCCCHHHHHHHcC
Confidence            567777762    2 345   9999999999999999998743

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=80.12  E-value=12  Score=31.21  Aligned_cols=27  Identities=15%  Similarity=0.169  Sum_probs=24.0

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +...|++..++|+.+|||+++|++|++
T Consensus        40 r~~~gltQ~evA~~tGISqS~ISq~e~   66 (221)
T 2h8r_A           40 MQQHNIPQREVVDVTGLNQSHLSQHLN   66 (221)
T ss_dssp             HHHHTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            455699999999999999999999986

>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=80.10  E-value=0.91  Score=36.20  Aligned_cols=32  Identities=22%  Similarity=0.327  Sum_probs=29.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.-
T Consensus       168 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          168 LNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            78999999999999999999999999998753

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=80.04  E-value=1.5  Score=33.56  Aligned_cols=34  Identities=9%  Similarity=0.054  Sum_probs=26.8

Q ss_pred             HHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhH
Q psy1898         102 NHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       102 ~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kw  135 (230)
                      .+.|.+|++.    + +.|   .|..+||+..|||++|+|+.
T Consensus        13 ~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~   54 (203)
T 3f1b_A           13 AVREQQMLDAAVDVFSDRGFHETSMDAIAAKAEISKPMLYLY   54 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCcccccHHHHHHHhCCchHHHHHH
Confidence            3556777762    2 335   89999999999999999986

>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=80.02  E-value=1.1  Score=35.93  Aligned_cols=32  Identities=22%  Similarity=0.158  Sum_probs=29.8

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+..+||..+|+|+.||++.++++++.|.+.-
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            68999999999999999999999999998754

---

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	230
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	1e-48
d1k78a2	61	a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta	6e-32
d6paxa2	65	a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta	4e-30
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	1e-27

>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 =  153 bits (389), Expect = 1e-48
 Identities = 98/122 (80%), Positives = 118/122 (96%), Gaps = 1/122 (0%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
            VNQLGGVFINGRPLPN+IRLKIVEMAA G+RPCVISRQLRVSHGCVSKILNRYQETGSI
Sbjct: 3   RVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSI 62

Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
           RPGVIGGSKPR+ATP++E RIEEYK+++PG+FSWEIR++L++ +G+CD+++APSVS+ISR
Sbjct: 63  RPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAISR 121

Query: 206 LL 207
           L+
Sbjct: 122 LV 123

>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 =  108 bits (273), Expect = 6e-32
 Identities = 36/60 (60%), Positives = 50/60 (83%), Gaps = 1/60 (1%)

Query: 149 VIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR 208
           VIGGSKP+VATP V ++I EYK+ NP +F+WEIRDRL+  + +CD ++ PSVSSI+R++R
Sbjct: 1   VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA-ERVCDNDTVPSVSSINRIIR 59

>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 =  104 bits (262), Expect = 4e-30
 Identities = 35/59 (59%), Positives = 47/59 (79%), Gaps = 1/59 (1%)

Query: 151 GGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209
           GGSKPRVATP+V  +I +YK+  P IF+WEIRDRL+  +G+C  ++ PSVSSI+R+LR 
Sbjct: 1   GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLS-EGVCTNDNIPSVSSINRVLRN 58

>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 = 98.2 bits (245), Expect = 1e-27
 Identities = 50/63 (79%), Positives = 56/63 (88%)

Query: 86  GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
           GVNQLGGVF+NGRPLP+ +R +IVE+A  GVRPC ISRQLRVSHGCVSKIL RY ETGSI
Sbjct: 1   GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSI 60

Query: 146 RPG 148
           +PG
Sbjct: 61  KPG 63

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	230
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.96
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.8
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	99.58
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.35
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.3
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	98.81
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	98.25
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	97.98
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.86
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.82
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.79
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.65
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.57
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	96.51
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.47
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.27
d2p5ka1	63	Arginine repressor (ArgR), N-terminal DNA-binding	96.21
d1b4aa1	75	Arginine repressor (ArgR), N-terminal DNA-binding	96.21
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	96.2
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	96.09
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.0
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	95.98
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	95.69
d1aoya_	78	Arginine repressor (ArgR), N-terminal DNA-binding	95.66
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	95.62
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	95.4
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.39
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	95.39
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	95.3
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	95.23
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	95.16
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	95.09
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.09
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	94.97
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	94.89
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	94.78
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.63
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	94.62
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	94.6
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.59
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	94.54
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	94.42
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.38
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	94.37
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.27
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	94.27
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	94.24
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	94.2
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	93.93
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	93.89
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	93.86
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.81
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	93.65
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	93.65
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	93.42
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	93.34
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.22
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	93.14
d1iufa1	78	Ars-binding protein 1, ABP1 {Fission yeast (Schizo	93.12
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	92.98
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	92.97
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	92.72
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	92.63
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	92.5
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	92.43
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	92.42
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	92.33
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	92.31
d1y7ya1	69	Restriction-modification controller protein C.AhdI	92.3
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	92.19
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	92.04
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	92.01
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	91.87
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	91.82
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	91.4
d1zyba1	73	Probable transcription regulator BT4300, C-termina	91.39
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	91.37
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	91.34
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	91.21
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	91.16
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.81
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	90.79
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	90.67
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	90.6
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	90.42
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	90.37
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	90.24
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	90.12
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	90.05
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	90.01
d1tc3c_	51	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	89.89
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.85
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	89.71
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.44
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	89.4
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	89.33
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	89.18
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	89.03
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	88.89
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	88.82
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	88.19
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	88.14
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	88.02
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	87.97
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	87.94
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	87.9
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	87.79
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	87.72
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	87.65
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	87.56
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	87.39
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	87.35
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	87.07
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	87.03
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	86.99
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	86.82
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	86.68
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	86.66
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	86.5
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	86.46
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	86.35
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	86.18
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	86.04
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	85.67
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	85.26
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	85.16
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	85.08
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	85.08
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	85.08
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	85.05
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	84.29
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	84.22
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	84.14
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	84.03
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	83.97
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	83.58
d2esna1	89	Probable LysR-type transcriptional regulator PA047	83.34
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	83.26
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	83.01
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	82.95
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	82.8
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	82.2
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	81.97
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	81.91
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	81.89
d2ezla_	99	Ibeta subdomain of the mu end DNA-binding domain o	81.58
d1u78a2	50	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	81.34
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	81.31
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	81.21
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	80.97
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	80.9
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	80.6
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	80.26

>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=99.96  E-value=2.9e-30  Score=200.44  Aligned_cols=121  Identities=81%  Similarity=1.405  Sum_probs=116.1

Q ss_pred             cccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH
Q psy1898          86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR  165 (230)
Q Consensus        86 g~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~  165 (230)
                      ++|+||+.|.||+|||.|+|.+||+++++|++.++||++|+||++||++|+++|+++|.+.|+++++++|+.+++++.++
T Consensus         3 ~~n~~gg~~~~GrpLs~dlR~rIv~~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~~   82 (123)
T d1pdnc_           3 RVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENR   82 (123)
T ss_dssp             EECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHH
T ss_pred             CcccCCCcccCCcCCCHHHHHHHHHHHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999999988777899999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHH
Q psy1898         166 IEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLL  207 (230)
Q Consensus       166 I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~L  207 (230)
                      |.++++++|++|+|||+++|.. .|++..+..||+|||+|+|
T Consensus        83 I~~~~~~~P~~t~~El~~~L~~-egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          83 IEEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             HHHTTTTCTTCCHHHHHHHHHH-TSSSCSTTCCCHHHHHHHC
T ss_pred             HHHHHHhCCCccHHHHHHHHHH-cCCCCCCCCCChhhHhhcC
Confidence            9999999999999999999987 8998888899999999986

>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=99.80  E-value=3.7e-20  Score=126.32  Aligned_cols=62  Identities=79%  Similarity=1.320  Sum_probs=60.6

Q ss_pred             cccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898          86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus        86 g~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      |+|+||+.|.||+|||.|+|++||+++++|+|.++||++|+||++||+||+++|+|||+++|
T Consensus         1 ~~n~~gg~~~~GrPls~DLR~Riv~~~~~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~P   62 (63)
T d1k78a1           1 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKP   62 (63)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCC
T ss_pred             CcCCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCC
Confidence            68999999999999999999999999999999999999999999999999999999999976

>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=99.58  E-value=5.2e-16  Score=119.27  Aligned_cols=97  Identities=55%  Similarity=0.794  Sum_probs=76.4

Q ss_pred             CCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCCcc------------cCCCcCCHHHH
Q psy1898          40 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGGVF------------INGRPLPNHIR  105 (230)
Q Consensus        40 ~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~~~------------~~g~~~s~~~R  105 (230)
                      |+++|||||+|+||+|||.++|.+||+++.+|.+.++|+++|+||++|+  .+.++.            ..++..+.+..
T Consensus         1 ~~~~n~~gg~~~~GrpLs~dlR~rIv~~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~   80 (123)
T d1pdnc_           1 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIE   80 (123)
T ss_dssp             CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHH
T ss_pred             CcCcccCCCcccCCcCCCHHHHHHHHHHHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHH
Confidence            5789999999999999999999999999999999999999999999997  111111            12334667778


Q ss_pred             HHHHHHHHc--CCCHHHHhhhhc----------cccchhhhHH
Q psy1898         106 LKIVEMAAA--GVRPCVISRQLR----------VSHGCVSKIL  136 (230)
Q Consensus       106 ~rIV~l~~~--G~s~~~IAr~lg----------VS~sTV~kwi  136 (230)
                      ..|+.+.++  .++..+|+..|-          .|.+||++|+
T Consensus        81 ~~I~~~~~~~P~~t~~El~~~L~~egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          81 NRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             HHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC
T ss_pred             HHHHHHHHhCCCccHHHHHHHHHHcCCCCCCCCCChhhHhhcC
Confidence            888888776  488888988772          2677888773

>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=99.53  E-value=2.3e-15  Score=102.28  Aligned_cols=48  Identities=69%  Similarity=1.150  Sum_probs=46.6

Q ss_pred             CccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccc
Q psy1898          42 RMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQ   89 (230)
Q Consensus        42 ~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~   89 (230)
                      ++|||||.|+||+|||.++|.+|++++.+|.++++++++|+|||+|+.
T Consensus         1 ~~n~~gg~~~~GrPls~DLR~Riv~~~~~G~s~r~aA~rf~VS~s~v~   48 (63)
T d1k78a1           1 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVS   48 (63)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHH
T ss_pred             CcCCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHH
Confidence            589999999999999999999999999999999999999999999985

>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=99.35  E-value=2.3e-12  Score=85.49  Aligned_cols=60  Identities=58%  Similarity=1.105  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         150 IGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       150 ~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      .||.+|+..||+++.+|.++.+++|.+++|||++.|.+ .|+|+.+++||.|+|+|+|+..
T Consensus         2 IGGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~-egiC~~~nvPSvSsInRilR~k   61 (61)
T d1k78a2           2 IGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA-ERVCDNDTVPSVSSINRIIRTK   61 (61)
T ss_dssp             CCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHH-TTSSCTTTSCCHHHHHHHHHCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCcccHHHHHHHHHH-cCCCCCCCCCchHHHHHHhhcC
Confidence            46789999999999999999999999999999999998 9999999999999999999863

>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=99.30  E-value=4.7e-12  Score=84.93  Aligned_cols=59  Identities=59%  Similarity=1.088  Sum_probs=55.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         151 GGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       151 gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ||.+|++.||++..+|.++..++|.+++|||++.|.. .|+|+.+++||.|+|+|+|+.+
T Consensus         1 GGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~-egiC~~~~vPSvSsInRilR~~   59 (65)
T d6paxa2           1 GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLS-EGVCTNDNIPSVSSINRVLRNL   59 (65)
T ss_dssp             SCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHH-TTSSCTTTCCCHHHHHHHHHHH
T ss_pred             CCCCcCcCCHHHHHHHHHHHHhCCccchHHHHHHHHH-cCCCCCCCCCchHHHHHHHHHh
Confidence            4678999999999999999999999999999999998 9999999999999999999864

>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=98.81  E-value=1.7e-09  Score=77.50  Aligned_cols=70  Identities=14%  Similarity=0.269  Sum_probs=53.5

Q ss_pred             CcCCHHHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898          98 RPLPNHIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN  173 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~  173 (230)
                      +.||.++|.++|.++.+  |.|.++||+.||||.+||++|+++|+..+.....     .+.. .....+.|.++..+|
T Consensus         4 k~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~~~~~-----~~~~-~~~~~~ei~~L~~En   75 (89)
T d2jn6a1           4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGT-----TPSA-AVSEAEQIRQLKKEN   75 (89)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTCSC-----CCCH-HHHTHHHHHHHHHCG
T ss_pred             CCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHHhhcccccCC-----CCCc-chhHHHHHHHHHHHH
Confidence            46999999999998853  8999999999999999999999999877654321     1222 233455677776665

>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=98.25  E-value=4e-07  Score=57.46  Aligned_cols=40  Identities=10%  Similarity=0.160  Sum_probs=37.1

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.++.+..+.+..|+++|.+..+||+.||||++|+|+|+
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            3568889999999999999999999999999999999995

>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=97.98  E-value=2.7e-06  Score=52.17  Aligned_cols=33  Identities=24%  Similarity=0.438  Sum_probs=30.9

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.+|..|+.+|++..+||++|+|+++|||+.++
T Consensus         8 ~~~V~~L~~~G~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1           8 RDAVLNMWQQGLGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHh
Confidence            568889999999999999999999999999986

>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=97.86  E-value=7.3e-06  Score=55.05  Aligned_cols=42  Identities=21%  Similarity=0.351  Sum_probs=38.7

Q ss_pred             CCcCCHHHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHH
Q psy1898          97 GRPLPNHIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      -+.++.+.+.+|+.+++.|  ++..+||+.|||+++||+.|++.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            4679999999999999998  58899999999999999999986

>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=96.82  E-value=0.00051  Score=45.09  Aligned_cols=43  Identities=19%  Similarity=0.310  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.+.+|+.++.++  .|..++|+.|+||+.||++.++..++.|..
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            5677899888765  899999999999999999999999999953

>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=96.79  E-value=0.00081  Score=44.40  Aligned_cols=43  Identities=21%  Similarity=0.203  Sum_probs=37.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      .+|...|.-+...+-+|+|..+||+.+|+|.+||.+.+.|...
T Consensus        21 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             TSCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4677888877778889999999999999999999999987653

>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=96.65  E-value=0.0019  Score=39.98  Aligned_cols=45  Identities=18%  Similarity=0.237  Sum_probs=36.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         153 SKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       153 ~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +||++++++..+.+.+++...  .+..+|+..    +||       |.+||+|.|-..
T Consensus         1 GR~~~lt~~q~~~a~~l~~~G--~s~~~iA~~----~gV-------Sr~TiYry~pa~   45 (47)
T d1ijwc_           1 GRPRAINKHEQEQISRLLEKG--HPRQQLAII----FGI-------GVSTLYRYFPAS   45 (47)
T ss_dssp             CCCCSSCHHHHHHHHHHHHTT--CCHHHHHHH----HTC-------CHHHHHHHSCST
T ss_pred             CCCCcCCHHHHHHHHHHHHCC--CCHHHHHHH----HCc-------CHHHHHhhCCcc
Confidence            489999999999999999654  688877764    565       999999998443

>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=96.57  E-value=0.00046  Score=45.20  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=32.6

Q ss_pred             HHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         108 IVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       108 IV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      |+.+. +..+|..+||+.+|+|++||++.++...+.|.+
T Consensus         4 Il~~i~~~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV   42 (62)
T d2hoea1           4 ILKRIMKSPVSRVELAEELGLTKTTVGEIAKIFLEKGIV   42 (62)
T ss_dssp             SHHHHHHSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            44443 345999999999999999999999999999976

>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=96.51  E-value=0.0015  Score=42.96  Aligned_cols=41  Identities=22%  Similarity=0.288  Sum_probs=36.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus        19 Lp~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~   59 (68)
T d1or7a1          19 LPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAR   59 (68)
T ss_dssp             SCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            67778887878888999999999999999999999998765

>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=96.47  E-value=0.0005  Score=48.71  Aligned_cols=52  Identities=23%  Similarity=0.261  Sum_probs=45.5

Q ss_pred             cCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898          99 PLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      .++...|.+|+.++.+| ++.++||+.+++|++||++-++..++.|.+...+.
T Consensus        14 aL~d~~Rl~Il~~L~~~~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~   66 (94)
T d1r1ua_          14 ALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQ   66 (94)
T ss_dssp             HTCSHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HhCCHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEEE
Confidence            45668999999988776 99999999999999999999999999998865443

>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=96.27  E-value=0.00062  Score=48.52  Aligned_cols=51  Identities=18%  Similarity=0.204  Sum_probs=44.1

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         100 LPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      ++...|.+|+.++..| .+.++||+.+++|++||+.-++.-++.|.+...+.
T Consensus        20 L~~p~Rl~Il~~L~~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~   71 (98)
T d1r1ta_          20 LADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ   71 (98)
T ss_dssp             HCCHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             hCCHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE
Confidence            3447899999988765 99999999999999999999999999998865444

>d2p5ka1 a.4.5.3 (A:2-64) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.21  E-value=0.005  Score=40.35  Aligned_cols=45  Identities=22%  Similarity=0.138  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+.|..++.+++-.+..|+.+.|+. .|+.     ++.+||+|-|+..|+.
T Consensus         6 q~~I~~li~~~~i~tQ~eL~~~L~~-~G~~-----vTQaTlSRDL~eLg~v   50 (63)
T d2p5ka1           6 HIKIREIITSNEIETQDELVDMLKQ-DGYK-----VTQATVSRDIKELHLV   50 (63)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHH-TTCC-----CCHHHHHHHHHHHTCE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHH-cCCC-----eeHHHHHHHHHHhCCE
Confidence            4678899999999999999999988 7995     8999999999999875

>d1b4aa1 a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.21  E-value=0.0063  Score=41.22  Aligned_cols=45  Identities=22%  Similarity=0.164  Sum_probs=41.2

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      .+.|.+++.+++-.+..|+.+.|.. .|+.     |+.+||+|-|+..|+.
T Consensus         4 ~~~I~~li~~~~i~tQ~eL~~~L~~-~Gi~-----vTQaTlSRDL~eLg~v   48 (75)
T d1b4aa1           4 HIKIREIIMSNDIETQDELVDRLRE-AGFN-----VTQATVSRDIKEMQLV   48 (75)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHH-TTCC-----CCHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHH-cCCc-----eeHHHHHHHHHHhCCE
Confidence            4678899999999999999999988 7996     8999999999999986

>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=96.20  E-value=0.003  Score=45.64  Aligned_cols=43  Identities=19%  Similarity=0.079  Sum_probs=38.3

Q ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|...|.-++..+.+|+|..+||..+|||++||+.-+.|..
T Consensus        15 ~lLp~~qR~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~RA~   57 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTE   57 (106)
T ss_dssp             GGSCHHHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3478888988888899999999999999999999999988754

>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=96.09  E-value=0.0019  Score=41.90  Aligned_cols=39  Identities=13%  Similarity=0.135  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ..+|..|+.++. .+....++|+.||||++|+|+.+++|.
T Consensus        19 ~~Er~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmkky~   58 (60)
T d1umqa_          19 RVRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRS   58 (60)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHHHcC
Confidence            456777877665 578999999999999999999999885

>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=96.00  E-value=0.0038  Score=41.41  Aligned_cols=42  Identities=17%  Similarity=0.263  Sum_probs=36.0

Q ss_pred             HHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         105 RLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       105 R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +..|+.++.. | .|..+||+.+|+|.+||++.++...+.|.+.
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~   50 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQ   50 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            4567776654 4 9999999999999999999999999999763

>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=95.98  E-value=0.0034  Score=45.36  Aligned_cols=44  Identities=18%  Similarity=0.083  Sum_probs=38.6

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +.-+|...|.-++..+.+|+|..+||..+|||++||+.-+.|..
T Consensus        16 ~~LLpe~QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~   59 (106)
T d1xsva_          16 QSLLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTG   59 (106)
T ss_dssp             GGGSCHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34478888888888888999999999999999999999998855

>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=95.69  E-value=0.0052  Score=40.32  Aligned_cols=35  Identities=20%  Similarity=0.342  Sum_probs=31.6

Q ss_pred             HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|+.++.+|++..+||+.++||..||..-+.+-.
T Consensus        12 ~~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~   46 (67)
T d1a04a1          12 RDILKLIAQGLPNKMIARRLDITESTVKVHVKHML   46 (67)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            57888999999999999999999999999888744

>d1aoya_ a.4.5.3 (A:) Arginine repressor (ArgR), 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: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=95.66  E-value=0.014  Score=39.71  Aligned_cols=48  Identities=21%  Similarity=0.095  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +..+.|.+++.+++-.+..||.+.|.. .|+.    .|+.+||.|-|+..|+.
T Consensus         9 ~~l~~I~~li~~~~i~tQ~eL~~~L~~-~G~~----~vTQaTiSRDL~eLg~v   56 (78)
T d1aoya_           9 ELVKAFKALLKEEKFSSQGEIVAALQE-QGFD----NINQSKVSRMLTKFGAV   56 (78)
T ss_dssp             THHHHHHHHHHTCCCCSHHHHHHHHHH-HTCS----SCCHHHHHHHHHHHTCE
T ss_pred             HHHHHHHHHHHhCCcCCHHHHHHHHHH-cCCc----chhHHHHHHHHHHhCCE
Confidence            345678899999999999999999988 8882    27999999999999886

>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=95.62  E-value=0.0022  Score=46.32  Aligned_cols=52  Identities=21%  Similarity=0.211  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHH-HcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCC
Q psy1898         100 LPNHIRLKIVEMA-AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG  151 (230)
Q Consensus       100 ~s~~~R~rIV~l~-~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~g  151 (230)
                      ++...|.+|+..+ ..| .+.++||+.+++|.+||++-++..++.|.+...+.|
T Consensus        28 Ladp~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~G   81 (108)
T d1u2wa1          28 IADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEG   81 (108)
T ss_dssp             HHSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             hCCHHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEEEC
Confidence            4458899999765 555 899999999999999999999999999988665543

>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=95.40  E-value=0.012  Score=41.31  Aligned_cols=50  Identities=14%  Similarity=0.137  Sum_probs=45.6

Q ss_pred             CCCcCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898          96 NGRPLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus        96 ~g~~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.+..+...+..||.....| .|..|+++.+++|..-.++|.+.|.+.|.-
T Consensus        30 ~trRWva~RKaaVV~av~~Gl~S~~EAcrrY~LS~eEf~~W~~a~~~hGe~   80 (93)
T d2oa4a1          30 NTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGKD   80 (93)
T ss_dssp             CCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSS
T ss_pred             ccccccHHHHHHHHHHHHcCcCCHHHHHHHhCCCHHHHHHHHHHHHHHhHH
Confidence            46677889999999999988 999999999999999999999999998864

>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=95.39  E-value=0.0023  Score=50.45  Aligned_cols=47  Identities=28%  Similarity=0.298  Sum_probs=41.4

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         100 LPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ++...|.+|+.++..| ++..+||+.|++|++||++-++.-.+.|.+.
T Consensus        12 l~~~~R~~Il~~L~~~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~   59 (194)
T d2p4wa1          12 LGNETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEAGLIE   59 (194)
T ss_dssp             HHSHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3447899999987765 9999999999999999999999999999773

>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=95.39  E-value=0.0052  Score=40.61  Aligned_cols=43  Identities=9%  Similarity=0.154  Sum_probs=36.0

Q ss_pred             HHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      -+.+|+.++. . ..|..+||+.+|+|++||++.++...+.|.+.
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            3456776553 3 49999999999999999999999999999763

>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=95.30  E-value=0.0069  Score=39.61  Aligned_cols=36  Identities=14%  Similarity=0.132  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      .-.+|+.++.+|++.++||..+++|.+||...+++-
T Consensus         8 rE~~vl~l~~~G~s~~eIA~~L~is~~TV~~~~~~i   43 (67)
T d1fsea_           8 REREVFELLVQDKTTKEIASELFISEKTVRNHISNA   43 (67)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            345688889999999999999999999999888773

>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=95.23  E-value=0.014  Score=37.35  Aligned_cols=40  Identities=18%  Similarity=0.229  Sum_probs=32.2

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      +.++||+..|||.+||++.++.                +..++++.+++|.+..++
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~----------------~~~vs~~tr~rV~~~a~~   41 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK----------------TRFVAEETRNAVWAAIKE   41 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT----------------CSCCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC----------------CCccCHHHHHHHHHHHHH
Confidence            6789999999999999999862                123578888888877765

>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=95.16  E-value=0.013  Score=37.50  Aligned_cols=41  Identities=24%  Similarity=0.312  Sum_probs=33.0

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+.++||+..|||.+||++.++.                +..++++.+++|.+..++
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~----------------~~~Vs~~tr~rV~~aa~~   42 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNG----------------NPNVKPSTRKKVLETIER   42 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT----------------CTTSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCC----------------CCcCCHHHHHHHHHHHHH
Confidence            57899999999999999999851                123588888888877755

>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=95.09  E-value=0.011  Score=38.44  Aligned_cols=41  Identities=17%  Similarity=-0.027  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|. .-.+|+.++.+|.|.++||+.+++|..||...+++-.
T Consensus         4 ~Lt~-rE~~vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~   44 (65)
T d1l3la1           4 WLDP-KEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM   44 (65)
T ss_dssp             CCCH-HHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ccCH-HHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3443 3457888999999999999999999999998888743

>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=95.09  E-value=0.014  Score=37.79  Aligned_cols=43  Identities=21%  Similarity=0.342  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +.-.+|+..+.+ + .|.++||+.+|+|.+||++=++++.+.|.+
T Consensus         5 ~~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI   49 (63)
T d2cfxa1           5 QIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGII   49 (63)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            344567776654 3 999999999999999999999999999976

>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=94.97  E-value=0.0063  Score=42.89  Aligned_cols=49  Identities=18%  Similarity=0.180  Sum_probs=38.4

Q ss_pred             cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898          93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE  141 (230)
Q Consensus        93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e  141 (230)
                      |++++..+....|.+-|..--+|.+..++|+.+++|..+|++++++.+.
T Consensus        44 YiP~~~~~~~~~Rn~~I~~ef~G~n~~eLA~kY~lS~~~I~~Ii~~~rk   92 (94)
T d1rr7a_          44 YIPRGQALDSLIRDLRIWNDFNGRNVSELTTRYGVTFNTVYKAIRRMRR   92 (94)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHCCSSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             eeeccHHHHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            5555555566777555554448999999999999999999999998763

>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=94.89  E-value=0.017  Score=37.48  Aligned_cols=42  Identities=17%  Similarity=0.182  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHc--C-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898         103 HIRLKIVEMAAA--G-VRPCVISRQLRVSHGCVSKILNRYQETGS  144 (230)
Q Consensus       103 ~~R~rIV~l~~~--G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~  144 (230)
                      +.+.+|+.++.+  + ++..++|+.|+||+.||++-++.-++.|.
T Consensus         7 eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           7 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            445678876643  3 79999999999999999999999988885

>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=94.78  E-value=0.012  Score=38.95  Aligned_cols=36  Identities=11%  Similarity=0.161  Sum_probs=31.6

Q ss_pred             HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      -.+|+.++..|.+..+||..++||..||..-+.+-.
T Consensus        17 E~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~   52 (70)
T d1yioa1          17 EQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIM   52 (70)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            346778888999999999999999999999888754

>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=94.63  E-value=0.02  Score=36.57  Aligned_cols=41  Identities=24%  Similarity=0.306  Sum_probs=35.3

Q ss_pred             HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|+.++.+ + .|..+||+.+|+|.+||+.=+++..+.|.+.
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            467776554 4 8999999999999999999999999999764

>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=94.62  E-value=0.014  Score=37.56  Aligned_cols=22  Identities=27%  Similarity=0.265  Sum_probs=20.3

Q ss_pred             CCHHHHhhhhccccchhhhHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++.++||+..|||.+||++.++
T Consensus         1 vTl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4788999999999999999997

>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=94.60  E-value=0.019  Score=39.92  Aligned_cols=68  Identities=13%  Similarity=0.163  Sum_probs=49.0

Q ss_pred             HHHHHHHHHH-Hc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCC---CCCCHHHHHHHHHHH
Q psy1898         103 HIRLKIVEMA-AA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVEKRIEEYK  170 (230)
Q Consensus       103 ~~R~rIV~l~-~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rp---r~lt~~~~~~I~~l~  170 (230)
                      ..|..|+..+ .. ..+..+||+.++++++||++.+++..+.|-+........++   -.+|+.-++.+..+.
T Consensus        16 p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~   88 (100)
T d1ub9a_          16 PVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHHHHH
Confidence            5577888765 34 49999999999999999999999999999874322111222   357777666555443

>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=94.59  E-value=0.027  Score=35.85  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +=.+|+..+.. + .|..+||+.+++|.+||+.=+++..+.|.+.
T Consensus         4 ~D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           4 IDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            34577776665 3 8999999999999999999999999999764

>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=94.54  E-value=0.039  Score=37.80  Aligned_cols=41  Identities=17%  Similarity=0.143  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|. .-.+|+.++.+|++.++||..++||..||..-+++-.
T Consensus        22 ~LT~-rE~~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~   62 (87)
T d1p4wa_          22 RLSP-KESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM   62 (87)
T ss_dssp             SCCH-HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3453 3357888899999999999999999999998887643

>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=94.42  E-value=0.021  Score=36.77  Aligned_cols=41  Identities=17%  Similarity=0.136  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ...-+|.-|..+++..-+.+++|+.||||++|+++.+++|.
T Consensus        18 ~~~~Er~~I~~aL~~~gn~~~aA~~Lgisr~tL~rKlkk~g   58 (61)
T d1g2ha_          18 IGFYEAQVLKLFYAEYPSTRKLAQRLGVSHTAIANKLKQYG   58 (61)
T ss_dssp             CSHHHHHHHHHHHHHSCSHHHHHHHTTSCTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence            44466766777665544788999999999999999999874

>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=94.38  E-value=0.022  Score=36.74  Aligned_cols=34  Identities=18%  Similarity=0.190  Sum_probs=30.5

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG  148 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~  148 (230)
                      ..+..+||+.||||++||+.-+++..+.|-+.-.
T Consensus        21 ~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1          21 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEc
Confidence            4999999999999999999999999999987543

>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=94.37  E-value=0.012  Score=37.94  Aligned_cols=25  Identities=12%  Similarity=0.098  Sum_probs=22.9

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.|+|..++|+.+|||++||++|.+
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4599999999999999999999964

>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=94.27  E-value=0.029  Score=36.11  Aligned_cols=43  Identities=16%  Similarity=0.248  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         104 IRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       104 ~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .=.+|+..+.+ + .|..+||+.+|+|.+||+.=+++..+.|.+.
T Consensus         6 ~D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           6 LDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             HHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            34567776654 3 9999999999999999999999999999763

>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=94.27  E-value=0.016  Score=37.35  Aligned_cols=33  Identities=9%  Similarity=0.078  Sum_probs=26.6

Q ss_pred             HHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         105 RLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       105 R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..+|-.+. ..|++..++|+.+|||++||++|.+
T Consensus         5 ~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_           5 SERLKKRRIALKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHC
Confidence            34555544 4599999999999999999999954

>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=94.24  E-value=0.025  Score=36.33  Aligned_cols=41  Identities=17%  Similarity=0.213  Sum_probs=32.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT  172 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~  172 (230)
                      .+..+||+..|||++||++.++.                +..++++.++.|.+..++
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~~----------------~~~vs~~tr~rI~~~a~~   43 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVNQ----------------ASHVSAKTREKVEAAMAE   43 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHTT----------------CSSCCTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC----------------CCcCCHHHHHHHHHHHHH
Confidence            57899999999999999999851                123578888888877755

>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=94.20  E-value=0.027  Score=40.08  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|.+|+.++..| +|.++|++.+|||..||.|.-+
T Consensus        45 a~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~   80 (101)
T d1jhga_          45 GTRVRIIEELLRGEMSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHH
Confidence            6789999988888 8999999999999999988754

>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=93.93  E-value=0.017  Score=38.04  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=22.1

Q ss_pred             HcCCCHHHHhhhhccccchhhhHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..|+|..++|+.||||+.||++|.
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~yE   35 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYYR   35 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            359999999999999999999994

>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=93.89  E-value=0.063  Score=38.93  Aligned_cols=68  Identities=9%  Similarity=0.049  Sum_probs=47.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      ++..++|+.+|||..|+.-|.+    .|.+.|..+..+.-+..++++...|..... ..-..+..+|++.+..
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~   69 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEE----KGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL   69 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----TTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----cCCCCCCccCCcCcccchHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5688999999999999877654    688876544333567778887666653332 2346888888877653

>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=93.86  E-value=0.025  Score=39.15  Aligned_cols=38  Identities=11%  Similarity=0.107  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      -+|.-|..+++ .+....++|+.||||++|+++.+++|.
T Consensus        49 ~E~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~klk~~g   87 (89)
T d1etxa_          49 VEQPLLDMVMQYTRGNATRAALMMGINRGTLRKKLKKYG   87 (89)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHHHHhC
Confidence            45555666554 578999999999999999999999984

>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=93.81  E-value=0.12  Score=33.79  Aligned_cols=46  Identities=30%  Similarity=0.298  Sum_probs=38.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.+.++.++.-.|.+.++++|.....+|+..    +|+       +.|||+.+|++.
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~----fGv-------~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLRKGEIARR----FNI-------PPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHH----HTC-------CHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcchHHHHHHH----hCC-------ChhHHHHHHHHH
Confidence            4556899999999999999999888888763    676       999999999874

>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=93.65  E-value=0.069  Score=37.61  Aligned_cols=68  Identities=15%  Similarity=0.086  Sum_probs=47.9

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK  187 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~  187 (230)
                      .+..++|+.+|||+.|+.-|.+    .|.+.|..+..+.-+..++++...+..... .+-..+..+|++.|..
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~   71 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYDN----IELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDH   71 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH----TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHC
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----cCCcCCcccCCcccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            4789999999999999877754    688876544323467778887665543322 2346889999888753

>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=93.65  E-value=0.011  Score=45.95  Aligned_cols=46  Identities=15%  Similarity=0.247  Sum_probs=41.2

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         100 LPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       100 ~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ++...|.+|+.++..| +|..+||+.+|+|++||++-++.-.+.|.+
T Consensus        16 l~~p~R~~Il~~L~~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv   62 (190)
T d1ulya_          16 MLEDTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLV   62 (190)
T ss_dssp             HHSHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            3447899999988765 999999999999999999999999999976

>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=93.42  E-value=0.052  Score=35.98  Aligned_cols=45  Identities=16%  Similarity=0.209  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      +.=.+|++.+..   +++..+||+.++++++||++.++-..+.|-+..
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~   52 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            334567776542   489999999999999999999999999998753

>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=93.34  E-value=0.071  Score=34.44  Aligned_cols=39  Identities=26%  Similarity=0.380  Sum_probs=32.8

Q ss_pred             HHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         108 IVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       108 IV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      |..+..++  .+..+||+.|+|+++||..-+++..+.|-+.
T Consensus        14 I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~   54 (63)
T d2isya1          14 IYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLR   54 (63)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            33344443  8999999999999999999999999999774

>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=93.22  E-value=0.11  Score=37.92  Aligned_cols=66  Identities=18%  Similarity=0.238  Sum_probs=46.4

Q ss_pred             hHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHH
Q psy1898          59 HIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus        59 ~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +.+..+++.+      .++.+.+++++.                +.+.-.+.+... +++..+||+.+++|+++|++.++
T Consensus         6 ~~~~~~~~~~------~~~~~~~Gl~~~----------------~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~   63 (151)
T d1ku9a_           6 EAKKLIIELF------SELAKIHGLNKS----------------VGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLK   63 (151)
T ss_dssp             HHHHHHHHHH------HHHHHHTTCCHH----------------HHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHH------HHHHHHcCCCHH----------------HHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHH
Confidence            4566777777      666666653322                222222223333 48999999999999999999999


Q ss_pred             HHhhhCCCC
Q psy1898         138 RYQETGSIR  146 (230)
Q Consensus       138 Ry~e~G~v~  146 (230)
                      +..+.|.+.
T Consensus        64 ~L~~~GlV~   72 (151)
T d1ku9a_          64 KLEELGFVR   72 (151)
T ss_dssp             HHHHTTSEE
T ss_pred             HHHHCCCEE
Confidence            999999874

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.14  E-value=0.016  Score=41.24  Aligned_cols=34  Identities=29%  Similarity=0.402  Sum_probs=31.2

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ..+.+..+||+.++|+++||++.+++-.+.|-+.
T Consensus        32 ~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~   65 (109)
T d1sfxa_          32 RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEE
Confidence            3459999999999999999999999999999874

>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=92.98  E-value=0.027  Score=36.74  Aligned_cols=31  Identities=19%  Similarity=0.261  Sum_probs=29.2

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      +|..+||..+|+|+.||++.+++|++.|.+.
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~   60 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            7899999999999999999999999999774

>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=92.97  E-value=0.044  Score=35.67  Aligned_cols=35  Identities=17%  Similarity=0.265  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ++-.+|..+.+ .|+|..++|+.+||++++|++|.+
T Consensus         6 ~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1           6 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            34455555555 489999999999999999999964

>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=92.72  E-value=0.048  Score=36.41  Aligned_cols=36  Identities=6%  Similarity=0.039  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +++=.+|-.+.+ .|+|..++|+.+|||.+||++|.+
T Consensus         5 ~~iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~   41 (78)
T d1x57a1           5 LEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYES   41 (78)
T ss_dssp             CHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHc
Confidence            345556666655 489999999999999999999975

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=92.63  E-value=0.028  Score=37.64  Aligned_cols=34  Identities=21%  Similarity=0.153  Sum_probs=30.3

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      |..++|+.|+||+.||.+-++...+.|.+...+.
T Consensus        24 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   57 (78)
T d3bwga1          24 VLETLMAQFEVSKSTITKSLELLEQKGAIFQVRG   57 (78)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            7899999999999999999999999998765443

>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=92.50  E-value=0.022  Score=37.32  Aligned_cols=34  Identities=18%  Similarity=0.130  Sum_probs=30.4

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      ++..++|+.|+||+.||.+-+++..+.|.+...+
T Consensus        26 l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   59 (69)
T d2hs5a1          26 LSEPDICAALDVSRNTVREAFQILIEDRLVAHEL   59 (69)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            6789999999999999999999999999875443

>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=92.43  E-value=0.051  Score=37.24  Aligned_cols=32  Identities=16%  Similarity=0.197  Sum_probs=26.3

Q ss_pred             HHHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMAA-AGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+|..+.+ .|+|..++|+.+|||++||++|.+
T Consensus        14 ~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          14 YALNAVIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            34444444 599999999999999999999974

>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=92.42  E-value=0.03  Score=35.99  Aligned_cols=31  Identities=16%  Similarity=0.218  Sum_probs=25.4

Q ss_pred             HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      +|-.+. ..|++..++|+.+|||++|+++|.+
T Consensus         7 rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~   38 (66)
T d2r1jl1           7 RIRARRKKLKIRQAALGKMVGVSNVAISQWER   38 (66)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            344444 4599999999999999999999974

>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=92.33  E-value=0.027  Score=38.47  Aligned_cols=55  Identities=15%  Similarity=0.082  Sum_probs=39.9

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l  169 (230)
                      ++|.++||+.++++++||++++++..+.|.+...+-++..--.+|+.-.+.+.+.
T Consensus        21 ~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D~R~~~i~LT~~G~~~l~~~   75 (85)
T d3ctaa1          21 YLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTE   75 (85)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeecccccccceECHHHHHHHHHH
Confidence            4899999999999999999999999999987532211112235677666555443

>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=92.31  E-value=0.055  Score=37.13  Aligned_cols=38  Identities=11%  Similarity=-0.021  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      -.|.-|...++ .+....+.|+.|||+++|+++.+++|.
T Consensus        51 ~E~~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Klk~~g   89 (91)
T d1ntca_          51 LERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHCCCHHHHHHHHHHHC
Confidence            34555555544 567899999999999999999999985

>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=92.30  E-value=0.058  Score=34.92  Aligned_cols=32  Identities=13%  Similarity=0.177  Sum_probs=25.9

Q ss_pred             HHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+|-.+. +.|+|..++|+.+|||++|+++|.+
T Consensus        12 ~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          12 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHC
Confidence            4444444 4589999999999999999999963

>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=92.19  E-value=0.038  Score=36.89  Aligned_cols=32  Identities=19%  Similarity=0.208  Sum_probs=29.7

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .+|..+||..+|+|+.||.++++++++.|-+.
T Consensus        30 ~lt~~elA~~~g~sretvsr~l~~l~~~glI~   61 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRVLASLKRENILD   61 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            36899999999999999999999999999775

>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=92.04  E-value=0.2  Score=33.86  Aligned_cols=58  Identities=14%  Similarity=0.159  Sum_probs=40.3

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLV  186 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~  186 (230)
                      +.|+|..++|+.+|||.+++++|.+     |..           ..+......|...+.-.|.....++.+.+.
T Consensus        23 ~~gltq~~lA~~lgis~~~is~~E~-----g~~-----------~~s~~~l~~ia~~l~v~~~~~~~~~~~~~~   80 (87)
T d1lmb3_          23 ELGLSQESVADKMGMGQSGVGALFN-----GIN-----------ALNAYNAALLAKILKVSVEEFSPSIAREIY   80 (87)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT-----TSS-----------CCCHHHHHHHHHHHTSCGGGTCHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCccHHHHHHHHh-----ccC-----------CCcHHHHHHHHHHHCCCHHHHChhHHHHHH
Confidence            4599999999999999999999953     321           225666667777776666544444444443

>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=92.01  E-value=0.037  Score=38.96  Aligned_cols=40  Identities=15%  Similarity=0.274  Sum_probs=33.3

Q ss_pred             HHHHH-HHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         106 LKIVE-MAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       106 ~rIV~-l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      ..|+. ++. .| ++..+||+.++++++||++.+++..+.|-+
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV   66 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLV   66 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCE
Confidence            34443 433 45 899999999999999999999999999976

>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=91.87  E-value=0.057  Score=35.88  Aligned_cols=31  Identities=3%  Similarity=0.050  Sum_probs=29.3

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      .|..+||..+|+|+.||++.++++++.|.+.
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~   60 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999875

>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=91.82  E-value=0.053  Score=34.34  Aligned_cols=25  Identities=8%  Similarity=0.319  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++|+++|.+
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            4599999999999999999999964

>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=91.40  E-value=0.061  Score=34.62  Aligned_cols=26  Identities=15%  Similarity=0.189  Sum_probs=23.4

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      .+.|+|..++|+.+|||++||++|.+
T Consensus        11 ~~~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2          11 KEKGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            34699999999999999999999964

>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=91.39  E-value=0.061  Score=35.56  Aligned_cols=31  Identities=32%  Similarity=0.339  Sum_probs=29.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~  146 (230)
                      ++..+||..+|+|+.||++.++.+++.|-+.
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            6889999999999999999999999999874

>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=91.37  E-value=0.048  Score=35.04  Aligned_cols=25  Identities=16%  Similarity=0.198  Sum_probs=23.0

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++|+++|.+
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHHc
Confidence            5699999999999999999999963

>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=91.34  E-value=0.062  Score=35.82  Aligned_cols=33  Identities=21%  Similarity=0.155  Sum_probs=30.4

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      ..|..+||..+|+|+.||++.++.+++.|-+.-
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~   62 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYISR   62 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            478999999999999999999999999998853

>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=91.21  E-value=0.056  Score=37.88  Aligned_cols=34  Identities=21%  Similarity=0.179  Sum_probs=30.1

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI  150 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~  150 (230)
                      |.+++|++|+||+.||.+-+++-.+.|.+...+.
T Consensus        35 s~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1          35 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETT
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecC
Confidence            7899999999999999999999999998765443

>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=91.16  E-value=0.015  Score=38.42  Aligned_cols=21  Identities=5%  Similarity=-0.024  Sum_probs=19.0

Q ss_pred             CHHHHhhhhccccchhhhHHH
Q psy1898         117 RPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ...++|+.||||.+||..|++
T Consensus         4 nk~~lA~iFGVS~~TI~~W~~   24 (68)
T d1j9ia_           4 NKKQLADIFGASIRTIQNWQE   24 (68)
T ss_dssp             EHHHHHHHTTCCHHHHHHHTT
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            467999999999999999975

>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=90.81  E-value=0.12  Score=33.08  Aligned_cols=39  Identities=13%  Similarity=0.075  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.+..|..++.+++..+..|+++.|    |       ||.+||+|.+..+
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l----~-------vS~~ti~r~i~~L   43 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETL----G-------MSRAAINKHIQTL   43 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHH----T-------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            3455678888888899999998876    3       5999999987654

>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=90.79  E-value=0.12  Score=33.50  Aligned_cols=34  Identities=9%  Similarity=0.054  Sum_probs=26.8

Q ss_pred             HHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|++|++    ++ +.|   .|..+||+..|||++|+|+..
T Consensus         3 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   44 (73)
T d1t56a1           3 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYF   44 (73)
T ss_dssp             HHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHC
Confidence            45666776    22 334   999999999999999999874

>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=90.67  E-value=0.2  Score=31.81  Aligned_cols=40  Identities=18%  Similarity=0.121  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      ++.+..|...+++++..+..+|++.+    |       +|.+||++.+++.
T Consensus         4 D~~D~~IL~~L~~~~r~s~~eiA~~l----~-------ls~~~v~~Ri~rL   43 (63)
T d2cg4a1           4 DNLDRGILEALMGNARTAYAELAKQF----G-------VSPETIHVRVEKM   43 (63)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHH----T-------SCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            35567888889999999999998866    4       4999999998764

>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=90.60  E-value=0.31  Score=35.32  Aligned_cols=100  Identities=8%  Similarity=0.105  Sum_probs=59.3

Q ss_pred             CCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHH--HcCCCHHHHhhhhccccch
Q psy1898          54 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMA--AAGVRPCVISRQLRVSHGC  131 (230)
Q Consensus        54 ~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~--~~G~s~~~IAr~lgVS~sT  131 (230)
                      +|+.+.+-..++..+      ..+.+++...=-+..        ..++ .....|+..+  ..|.+..+||+.++++++|
T Consensus         2 ~p~~~dl~~~l~~~~------~~~~~~~~~~~~~~~--------~~lt-~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~   66 (141)
T d1lnwa_           2 YPVNPDLMPALMAVF------QHVRTRIQSELDCQR--------LDLT-PPDVHVLKLIDEQRGLNLQDLGRQMCRDKAL   66 (141)
T ss_dssp             CCCCTTHHHHHHHHH------HHHHHHHHHHHHHTT--------CCCC-HHHHHHHHHHHSSTTCBHHHHHHHTTCCHHH
T ss_pred             CCCChhHHHHHHHHH------HHHHHHHHHHHHhhc--------CCCC-HHHHHHHHHHHHCCCCCHHHHHHHHCccHhH
Confidence            577777777777766      555554431101111        0112 2233344433  3469999999999999999


Q ss_pred             hhhHHHHHhhhCCCC--cCCCCC-CCCCCCCHHHHHHHHH
Q psy1898         132 VSKILNRYQETGSIR--PGVIGG-SKPRVATPDVEKRIEE  168 (230)
Q Consensus       132 V~kwikRy~e~G~v~--p~~~gg-~rpr~lt~~~~~~I~~  168 (230)
                      |++.+++..+.|-+.  +.+..+ ...-.+|+.-.+.+..
T Consensus        67 vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          67 ITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            999999999999763  222211 1223567765544443

>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=90.42  E-value=0.048  Score=35.99  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=22.7

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            3589999999999999999999964

>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=90.37  E-value=0.097  Score=34.37  Aligned_cols=34  Identities=18%  Similarity=0.279  Sum_probs=27.5

Q ss_pred             HHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.     ...|   .|..+||+..|||++|+|+..
T Consensus         6 ~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~lY~~F   47 (77)
T d2gfna1           6 ERRRALADAVLALIAREGISAVTTRAVAEESGWSTGVLNHYF   47 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhCccccCHHHHHHHHCCCHHHHHHHC
Confidence            667777762     2345   899999999999999999874

>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=90.12  E-value=0.31  Score=30.97  Aligned_cols=39  Identities=18%  Similarity=0.182  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.+..|...+++|+..+..+|++.+    |       +|.+||++.+++.
T Consensus         5 ~~D~~IL~~L~~n~r~s~~~iA~~l----g-------is~~tv~~Ri~~L   43 (63)
T d2cfxa1           5 QIDLNIIEELKKDSRLSMRELGRKI----K-------LSPPSVTERVRQL   43 (63)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHH----T-------CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            4566788888899999999999876    4       4999999998754

>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=90.05  E-value=0.18  Score=32.19  Aligned_cols=41  Identities=10%  Similarity=0.030  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      ++...|.-|...+    ...++..+||+.||||+..|..+..+.-
T Consensus         9 L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al   53 (61)
T d1ku3a_           9 LSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL   53 (61)
T ss_dssp             SCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555554444444    3459999999999999999999987653

>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=90.01  E-value=0.086  Score=35.88  Aligned_cols=25  Identities=16%  Similarity=0.283  Sum_probs=23.2

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++||++|.+
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            4599999999999999999999986

>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=89.89  E-value=0.25  Score=29.98  Aligned_cols=44  Identities=23%  Similarity=0.287  Sum_probs=38.8

Q ss_pred             CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898          97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus        97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +..++.++|.++--|..-+.|.-++|+++.-|+-+|+++++.-.
T Consensus         3 ~~~L~~~e~aqlDVm~~L~~slhemaR~i~rSR~~ir~Yl~~Pl   46 (51)
T d1tc3c_           3 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             SCCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             chhhhHHHHHHHHHHHHhCCcHHHHHHHHHHhHHHHHHHhcChh
Confidence            56788899999888888899999999999999999999987533

>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=89.85  E-value=0.26  Score=31.00  Aligned_cols=39  Identities=21%  Similarity=0.202  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.+.+|...+++|+.++..+|++.+    |       +|.+||++.+++.
T Consensus         3 ~~D~kIl~~L~~n~r~s~~~lA~~~----g-------ls~~~v~~Ri~~L   41 (60)
T d1i1ga1           3 ERDKIILEILEKDARTPFTEIAKKL----G-------ISETAVRKRVKAL   41 (60)
T ss_dssp             SHHHHHHHHHHHCTTCCHHHHHHHH----T-------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            3567888889999999999999865    4       4999999988754

>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=89.71  E-value=0.15  Score=33.46  Aligned_cols=34  Identities=18%  Similarity=0.210  Sum_probs=27.5

Q ss_pred             HHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.     ...|   .|..+||+..|||++|+|+..
T Consensus         4 ~tre~Il~aa~~~~~~~G~~~~ti~~Ia~~agvs~~s~y~~F   45 (79)
T d2fbqa1           4 ETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHF   45 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhCcccccHHHHHHHHCcChhHHHHHC
Confidence            567777762     2334   999999999999999999884

>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=89.44  E-value=0.27  Score=30.80  Aligned_cols=39  Identities=21%  Similarity=0.196  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +.+.+|...+++|+..+..+|++.+    |       +|.+||++.+++.
T Consensus         3 ~~D~~Il~~L~~n~r~s~~eiA~~l----~-------ls~~~v~~Ri~~L   41 (60)
T d2cyya1           3 EIDKKIIKILQNDGKAPLREISKIT----G-------LAESTIHERIRKL   41 (60)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHH----C-------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence            4567888889999999999999876    4       4999999988765

>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=89.40  E-value=0.11  Score=33.48  Aligned_cols=33  Identities=18%  Similarity=0.206  Sum_probs=25.8

Q ss_pred             HHHHHHH----H-HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         104 IRLKIVE----M-AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       104 ~R~rIV~----l-~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .|.+|++    + .+.|   .|..+||+..|||++|+|...
T Consensus         2 ~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F   42 (71)
T d1jt6a1           2 LKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHF   42 (71)
T ss_dssp             HHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHC
Confidence            4566665    2 2334   999999999999999999875

>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=89.33  E-value=0.19  Score=32.36  Aligned_cols=36  Identities=19%  Similarity=0.187  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         101 PNHIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       101 s~~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.+.|.+|++.    + +.|   .|..+||++.|||++|+|+..
T Consensus         2 ~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F   45 (69)
T d2fq4a1           2 NIETQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWW   45 (69)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            34667777762    2 335   899999999999999999874

>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=89.18  E-value=0.15  Score=33.11  Aligned_cols=35  Identities=23%  Similarity=0.269  Sum_probs=27.9

Q ss_pred             HHHHHHHHH----H-HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVE----M-AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~----l-~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++    + ...|   .|..+||+..|||++|+|+..
T Consensus         4 e~tr~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F   46 (75)
T d3c07a1           4 EQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYF   46 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSTTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            466777776    2 2345   999999999999999999884

>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=89.03  E-value=0.36  Score=34.87  Aligned_cols=46  Identities=13%  Similarity=0.125  Sum_probs=33.8

Q ss_pred             CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898         158 ATPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG  210 (230)
Q Consensus       158 lt~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~  210 (230)
                      +|++ +..|.+.+.+.  ...++.+|.+.|.+ .+..     ++.+||||.|...
T Consensus        14 ~T~q-R~~Il~~L~~~~~~h~sa~ei~~~l~~-~~~~-----i~~aTVYR~L~~l   61 (134)
T d1mzba_          14 VTLP-RVKILQMLDSAEQRHMSAEDVYKALME-AGED-----VGLATVYRVLTQF   61 (134)
T ss_dssp             CCHH-HHHHHHHHHCC-CCSBCHHHHHHHHHH-TTCC-----CCHHHHHHHHHHH
T ss_pred             CCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHH-hCCC-----ccHHHHHHHHHHH
Confidence            3554 45566666543  36899999999987 6654     8999999998764

>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=88.89  E-value=0.13  Score=33.87  Aligned_cols=25  Identities=16%  Similarity=0.167  Sum_probs=22.8

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHH
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|+|..++|+.+|||++++++|.+
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            3599999999999999999999964

>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=88.82  E-value=0.14  Score=32.76  Aligned_cols=35  Identities=26%  Similarity=0.288  Sum_probs=27.4

Q ss_pred             HHHHHHHHH-----HHHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVE-----MAAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~-----l~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++     +.+.|   .|..+||+..|||++|+|+..
T Consensus         5 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~iY~~F   47 (68)
T d2id3a1           5 ARIREAVLLAAGDALAADGFDALDLGEIARRAGVGKTTVYRRW   47 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            356777776     23345   899999999999999999875

>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=88.19  E-value=0.24  Score=32.13  Aligned_cols=34  Identities=12%  Similarity=0.100  Sum_probs=26.7

Q ss_pred             HHHHHHHH----H-HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----M-AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l-~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..|.+|++    + .+.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~r~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F   48 (76)
T d2fd5a1           7 QTRARILGAATQALLERGAVEPSVGEVMGAAGLTVGGFYAHF   48 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTSCCHHHHHHHTTCCGGGGGGTC
T ss_pred             HHHHHHHHHHHHHHHHhCcccccHHHHHHHhCCCccchhhcC
Confidence            55667776    2 2344   999999999999999999874

>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=88.14  E-value=0.16  Score=32.87  Aligned_cols=34  Identities=18%  Similarity=0.188  Sum_probs=27.0

Q ss_pred             HHHHHHHHH----H-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM----A-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l----~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.    + +.|   .|..+||+..|||++|+|.+.
T Consensus         5 ~~r~~il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~y~~F   46 (71)
T d1ui5a1           5 QTRATIIGAAADLFDRRGYESTTLSEIVAHAGVTKGALYFHF   46 (71)
T ss_dssp             THHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHC
Confidence            566777762    2 334   899999999999999999884

>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=88.02  E-value=0.24  Score=32.50  Aligned_cols=34  Identities=15%  Similarity=0.086  Sum_probs=27.2

Q ss_pred             HHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus         7 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~y~~F   48 (78)
T d2o7ta1           7 KRREHIITTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNF   48 (78)
T ss_dssp             HHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHC
Confidence            567777762     2344   999999999999999999874

>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=87.97  E-value=0.087  Score=34.88  Aligned_cols=33  Identities=15%  Similarity=0.205  Sum_probs=29.7

Q ss_pred             CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898         117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV  149 (230)
Q Consensus       117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~  149 (230)
                      |.+++|+.|+||+.||.+-+++-.+.|.+...+
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEe
Confidence            789999999999999999999999999875443

>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=87.94  E-value=0.13  Score=30.70  Aligned_cols=31  Identities=16%  Similarity=0.238  Sum_probs=26.8

Q ss_pred             hhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898          58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVN   88 (230)
Q Consensus        58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~   88 (230)
                      .-.+.+|.+|..+|..+.+|+++|+++...+
T Consensus         5 ~Id~~~V~~L~~~G~gat~IAk~lgI~R~SV   35 (43)
T d1gdta1           5 KIDRDAVLNMWQQGLGASHISKTMNIARSTV   35 (43)
T ss_dssp             CSCHHHHHHHHHTTCCHHHHHHHHTCCHHHH
T ss_pred             ccCHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence            4567899999999999999999999877654

>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=87.90  E-value=0.21  Score=33.81  Aligned_cols=37  Identities=11%  Similarity=0.189  Sum_probs=30.3

Q ss_pred             cCCCCCChhHHHHHHHHHhc--CCChhhhhhhhcccccc
Q psy1898          51 INGRPLPNHIRLKIVEMAAA--GVRPCVISRQLRVSHGV   87 (230)
Q Consensus        51 ~~g~plp~~~r~~I~e~~~~--g~~~~~isr~lrvshg~   87 (230)
                      |+.+.-|.+||.++|+++..  |.+..++++.|+|+..+
T Consensus         1 M~rk~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~t   39 (89)
T d2jn6a1           1 MPTKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVT   39 (89)
T ss_dssp             CCCCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHH
Confidence            44445569999999999964  78999999999986555

>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=87.79  E-value=0.18  Score=32.56  Aligned_cols=34  Identities=21%  Similarity=0.175  Sum_probs=26.6

Q ss_pred             HHHHHHHH----HH-Hc---CCCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AA---GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~---G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++    ++ +.   +.|..+||+..|||++|+|++.
T Consensus         2 err~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~ly~~F   43 (72)
T d2g3ba1           2 ERRDAILKASATAIAQRGIRGLRVNDVAEVAGVSPGLLYYHF   43 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHC
Confidence            45666665    22 33   4999999999999999999985

>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=87.72  E-value=2  Score=30.49  Aligned_cols=67  Identities=18%  Similarity=0.213  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC--cCCCCCC-CCCCCCHHHHHHHHHH
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGS-KPRVATPDVEKRIEEY  169 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~--p~~~gg~-rpr~lt~~~~~~I~~l  169 (230)
                      ++..-.+.....+.+.++||+.++++++||++++++..+.|-+.  +.+..++ ..-.+|+.-.+.+...
T Consensus        36 q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~~  105 (138)
T d1jgsa_          36 QFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQC  105 (138)
T ss_dssp             HHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHHH
Confidence            33333333445579999999999999999999999999999773  2222221 2345677655554433

>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=87.65  E-value=0.2  Score=32.48  Aligned_cols=35  Identities=11%  Similarity=0.154  Sum_probs=27.0

Q ss_pred             HHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+.|.+|++.     .+.|   .|..+||+..|||++|+|+..
T Consensus         3 ~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~iY~~F   45 (74)
T d2g7sa1           3 QSKADDILQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHF   45 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCcchHHHHC
Confidence            3556677662     2334   999999999999999999873

>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=87.56  E-value=0.27  Score=31.72  Aligned_cols=34  Identities=18%  Similarity=0.064  Sum_probs=26.3

Q ss_pred             HHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..|.+|++    ++ ..|   .|..+||+..|||++|+|+..
T Consensus         4 ~rr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~y~~F   45 (72)
T d1pb6a1           4 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYF   45 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCChHHHHHHC
Confidence            34666665    33 334   999999999999999999884

>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=87.39  E-value=0.21  Score=31.52  Aligned_cols=49  Identities=24%  Similarity=0.362  Sum_probs=33.2

Q ss_pred             Chhhhhhhhcccccccc--cCCcccCCCcCCHHHHHHHHHHHHc-CCCHHHHhhhh
Q psy1898          73 RPCVISRQLRVSHGVNQ--LGGVFINGRPLPNHIRLKIVEMAAA-GVRPCVISRQL  125 (230)
Q Consensus        73 ~~~~isr~lrvshg~~~--l~~~~~~g~~~s~~~R~rIV~l~~~-G~s~~~IAr~l  125 (230)
                      +..||++..+||..++.  |.+    ....+.+.|.+|.+.+++ |..+..+|+.|
T Consensus         3 Ti~dvA~~agvS~~TVSr~Ln~----~~~Vs~~tr~rV~~aa~~lgY~pn~~A~~L   54 (57)
T d2hsga1           3 TIYDVAREASVSMATVSRVVNG----NPNVKPSTRKKVLETIERLGYRPNAVARGL   54 (57)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHTT----CTTSCHHHHHHHHHHHHHHTCCSCHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHhCC----CCcCCHHHHHHHHHHHHHHCcCCCHHHHHh
Confidence            45566666666666552  222    235789999999998876 88777777655

>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=87.35  E-value=0.3  Score=34.50  Aligned_cols=39  Identities=13%  Similarity=0.144  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         100 LPNHIRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       100 ~s~~~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      +++-.....+. +...|.|..+||+.+|+|+++|++.++-
T Consensus        14 L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~L   53 (114)
T d1r71a_          14 LTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTL   53 (114)
T ss_dssp             CCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGG
T ss_pred             CCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHHH
Confidence            44445555554 5567999999999999999999998864

>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=87.07  E-value=0.3  Score=31.44  Aligned_cols=34  Identities=6%  Similarity=0.094  Sum_probs=26.7

Q ss_pred             HHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..|.+|++    ++ +.|   .|..+||+..|||++|+|+..
T Consensus         6 ~t~~~I~~aa~~l~~~~G~~~~sv~~Ia~~agvs~~t~Y~~F   47 (71)
T d2iu5a1           6 ITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYF   47 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             HHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCccccHHHHHc
Confidence            56667776    22 335   899999999999999999874

>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=87.03  E-value=0.7  Score=32.37  Aligned_cols=55  Identities=13%  Similarity=0.003  Sum_probs=40.1

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCC-CCCCCCHHHHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGS-KPRVATPDVEKRIEEYK  170 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~-rpr~lt~~~~~~I~~l~  170 (230)
                      ++..+||+.++++++||++.+++..+.|-+...  +..++ .--.+|+.-++.+.+..
T Consensus        50 ~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~  107 (115)
T d2frha1          50 YYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLL  107 (115)
T ss_dssp             EEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHHHHH
Confidence            799999999999999999999999999976322  22221 22356777766665543

>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=86.99  E-value=0.22  Score=32.16  Aligned_cols=34  Identities=18%  Similarity=0.276  Sum_probs=25.9

Q ss_pred             HHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|.+|++    ++ ..|   .|..+||+..|||++|+|..-
T Consensus         2 etr~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~iy~~F   43 (73)
T d1sgma1           2 DSREKILHTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFF   43 (73)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCCSCHHHHST
T ss_pred             hHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHc
Confidence            35666666    22 334   999999999999999999763

>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=86.82  E-value=0.13  Score=32.45  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=20.5

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|++.
T Consensus        19 ~~s~~~Ia~~agvs~~tiy~~F   40 (62)
T d2vkva1          19 GLTTRKLAQKLGVEQPTLYWHV   40 (62)
T ss_dssp             HCCHHHHHHHHTSCHHHHHHHS
T ss_pred             cCCHHHHHHHhCCCHHHHHHHC
Confidence            4999999999999999999884

>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=86.68  E-value=0.13  Score=34.73  Aligned_cols=44  Identities=20%  Similarity=0.278  Sum_probs=32.2

Q ss_pred             CCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898         158 ATPDVEKRIEEYKKTNP----GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD  213 (230)
Q Consensus       158 lt~~~~~~I~~l~~~~P----~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~  213 (230)
                      +++. ++.|.+++.+||    ..+..++++.    .+       ||.+||.|+.++.|+.
T Consensus        16 Ls~~-e~~ia~yil~~~~~~~~~si~~lA~~----~~-------vS~sTi~Rf~kklG~~   63 (83)
T d2o3fa1          16 LPPS-ERKLADYILAHPHKAIESTVNEISAL----AN-------SSDAAVIRLCKSLGLK   63 (83)
T ss_dssp             SCHH-HHHHHHHHHHCHHHHHTCCHHHHHHH----TT-------CCHHHHHHHHHHTTCS
T ss_pred             CCHH-HHHHHHHHHcCHHHHHHccHHHHHHH----HC-------CCHHHHHHHHHHhCCC
Confidence            3444 346777777777    4677777653    44       5999999999999986

>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=86.66  E-value=0.37  Score=34.68  Aligned_cols=58  Identities=22%  Similarity=0.210  Sum_probs=41.0

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCC-CCCCCCCCHHHHHHHHHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIG-GSKPRVATPDVEKRIEEY  169 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~g-g~rpr~lt~~~~~~I~~l  169 (230)
                      ...+.+.++||+.++++++||++.+++..+.|-+..  .+.. +..--.+|+.-.+.+.++
T Consensus        41 ~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~  101 (139)
T d2a61a1          41 FEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKV  101 (139)
T ss_dssp             HHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHHH
Confidence            345799999999999999999999999999997631  1111 112335677665555444

>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=86.50  E-value=0.43  Score=33.90  Aligned_cols=21  Identities=5%  Similarity=-0.001  Sum_probs=19.5

Q ss_pred             CCHHHHhhhhccccchhhhHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .+..+||..+|||+.|+|+|.
T Consensus        37 ktqeqiAeelGisr~tLyrWr   57 (120)
T d2ao9a1          37 RTQDEMANELGINRTTLWEWR   57 (120)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH
T ss_pred             hhHHHHHHHhChhHHHHHHHh
Confidence            577799999999999999997

>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=86.46  E-value=0.27  Score=31.37  Aligned_cols=22  Identities=14%  Similarity=0.083  Sum_probs=20.4

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|+..
T Consensus        20 ~~si~~Ia~~agvs~~t~Y~~F   41 (70)
T d2gena1          20 ATTIEMIRDRSGASIGSLYHHF   41 (70)
T ss_dssp             TCCHHHHHHHHCCCHHHHHHHT
T ss_pred             cCCHHHHHHHHCcCHHHHHHHC
Confidence            4999999999999999999884

>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=86.35  E-value=0.19  Score=31.71  Aligned_cols=28  Identities=18%  Similarity=0.261  Sum_probs=22.8

Q ss_pred             CcCCHHHHHHHHHHHHc-CCCHHHHhhhh
Q psy1898          98 RPLPNHIRLKIVEMAAA-GVRPCVISRQL  125 (230)
Q Consensus        98 ~~~s~~~R~rIV~l~~~-G~s~~~IAr~l  125 (230)
                      ...+.+.|.+|.+..++ |..+..+|+.|
T Consensus        25 ~~vs~~tr~rV~~~a~~lgY~pn~~Ar~L   53 (57)
T d1qpza1          25 RFVAEETRNAVWAAIKELHYSPSAVARSL   53 (57)
T ss_dssp             SCCCHHHHHHHHHHHHHHTCCCCHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHCCCCCHHHHHH
Confidence            35788999999998876 88888888766

>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=86.18  E-value=0.23  Score=32.06  Aligned_cols=22  Identities=18%  Similarity=0.071  Sum_probs=20.6

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|.+.
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            4899999999999999999985

>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=86.04  E-value=0.33  Score=31.48  Aligned_cols=35  Identities=17%  Similarity=0.200  Sum_probs=27.6

Q ss_pred             HHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHHH
Q psy1898         103 HIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKILN  137 (230)
Q Consensus       103 ~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwik  137 (230)
                      ..|.+|++.     ...|   .|..+||+..|||++|+|+...
T Consensus         4 ~tr~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~Y~~F~   46 (73)
T d2fx0a1           4 QTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFN   46 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhCcccCcHHHHHHHHCcChhHHHHHCc
Confidence            567777762     2334   9999999999999999998753

>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=85.67  E-value=0.33  Score=31.50  Aligned_cols=35  Identities=20%  Similarity=0.278  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         102 NHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       102 ~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ...|.+|++.     ...|   .|..+||+..|||++|+|+..
T Consensus         4 ~~tr~~il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~F   46 (75)
T d2hyja1           4 QATRGRILGRAAEIASEEGLDGITIGRLAEELEMSKSGVHKHF   46 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCcHHHHHHHHCcCHHHHHHHC
Confidence            3567777762     2344   999999999999999999873

>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=85.26  E-value=0.29  Score=31.15  Aligned_cols=22  Identities=18%  Similarity=0.170  Sum_probs=19.9

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|...
T Consensus        19 ~~ti~~Ia~~agvs~~~iY~~F   40 (65)
T d2g7ga1          19 DFRMPDLARHLNVQVSSIYHHA   40 (65)
T ss_dssp             SCCHHHHHHHTTSCHHHHHTTS
T ss_pred             CCCHHHHHHHhCccccchhhcC
Confidence            5999999999999999999763

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.16  E-value=0.82  Score=28.90  Aligned_cols=36  Identities=14%  Similarity=0.043  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898         163 EKRIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG  209 (230)
Q Consensus       163 ~~~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~  209 (230)
                      ...|..++.+.+ .++..++++.|    +       ||..||+|-|..
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l----~-------VS~~TI~rdi~~   45 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEEL----S-------VSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHH----T-------SCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHH----C-------CCHHHHHHHHHH
Confidence            346667776665 47999999877    3       599999996654

>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=85.08  E-value=0.27  Score=33.05  Aligned_cols=25  Identities=16%  Similarity=0.123  Sum_probs=22.5

Q ss_pred             HHcCCCHHHHhhhhccccchhhhHH
Q psy1898         112 AAAGVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       112 ~~~G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +..+++..++|+..|||++|+++|.
T Consensus        22 ~R~~~t~~eLA~~~Gvs~~~ls~iE   46 (82)
T d2ofya1          22 ARGDMSMVTVAFDAGISVETLRKIE   46 (82)
T ss_dssp             HHTTSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHcCCHHHHHHHH
Confidence            3468999999999999999999996

>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=85.08  E-value=0.24  Score=32.33  Aligned_cols=34  Identities=21%  Similarity=0.269  Sum_probs=30.4

Q ss_pred             cC--CCHHHHhhhhcc-ccchhhhHHHHHhhhCCCCc
Q psy1898         114 AG--VRPCVISRQLRV-SHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       114 ~G--~s~~~IAr~lgV-S~sTV~kwikRy~e~G~v~p  147 (230)
                      .|  -|.++||+.||+ |++||+..++...+-|-+..
T Consensus        21 ~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1          21 TGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             HSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            46  788999999999 89999999999999998753

>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=85.08  E-value=0.27  Score=34.34  Aligned_cols=33  Identities=12%  Similarity=0.177  Sum_probs=29.6

Q ss_pred             CCCHHHHhhhhccc-cchhhhHHHHHhhhCCCCc
Q psy1898         115 GVRPCVISRQLRVS-HGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       115 G~s~~~IAr~lgVS-~sTV~kwikRy~e~G~v~p  147 (230)
                      .+|..+||..+|+| +.||++.++.+++.|.+..
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~   64 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY   64 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEE
Confidence            36899999999997 7999999999999998753

>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=85.05  E-value=0.37  Score=31.49  Aligned_cols=34  Identities=21%  Similarity=0.365  Sum_probs=26.9

Q ss_pred             HHHHHHHHHH-----HHcC---CCHHHHhhhhccccchhhhH
Q psy1898         102 NHIRLKIVEM-----AAAG---VRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       102 ~~~R~rIV~l-----~~~G---~s~~~IAr~lgVS~sTV~kw  135 (230)
                      .+.|.+|++.     .+.|   .|..+||+..|||++|+|+.
T Consensus         8 ~~~r~~il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~   49 (79)
T d2oi8a1           8 TQVRAEIKDHAWEQIATAGASALSLNAIAKRMGMSGPALYRY   49 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCCHHHHHHHTTCCHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCCCCchhhh
Confidence            4567777762     2334   89999999999999999976

>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=84.29  E-value=0.28  Score=34.67  Aligned_cols=64  Identities=16%  Similarity=0.018  Sum_probs=40.5

Q ss_pred             CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC-CCCCCCCCCCHHH---HHHHHHHHHhCCCCCHHHHHHHH
Q psy1898         116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGSKPRVATPDV---EKRIEEYKKTNPGIFSWEIRDRL  185 (230)
Q Consensus       116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~-~gg~rpr~lt~~~---~~~I~~l~~~~P~~t~~eI~~~L  185 (230)
                      .+..++|+.+|||+.|+.-|.    +.|.+.|.. +....-+..++.+   ...|..+.  +-+.+..+|++.+
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 YSIGEVSKLANVSIKALRYYD----KIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLK--YIGTPLEEMKKAQ   71 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHH----HTTSSCCSEECTTTCCEEEETGGGGHHHHHHHHH--HTTCCHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HcCCcccccccCCCCcccccHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence            367899999999999997775    468887743 2111234445544   33444443  3358888887754

>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=84.22  E-value=0.62  Score=31.98  Aligned_cols=35  Identities=11%  Similarity=0.164  Sum_probs=27.5

Q ss_pred             HHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898         104 IRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNR  138 (230)
Q Consensus       104 ~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikR  138 (230)
                      .....+. +.+.|++..+||+.+|.|++||++.++-
T Consensus         7 EeA~a~~~L~e~g~t~~~iA~~~Gks~~~V~~~LrL   42 (93)
T d1vz0a1           7 EEARGYQALLEMGLTQEEVARRVGKARSTVANALRL   42 (93)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHccchHHHHHHHHH
Confidence            3334443 4456899999999999999999999874

>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=84.14  E-value=0.28  Score=31.37  Aligned_cols=22  Identities=9%  Similarity=0.188  Sum_probs=20.5

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|+..
T Consensus        20 ~~ti~~Ia~~agvs~~~~Y~~F   41 (69)
T d2i10a1          20 GTSITDLTKALGINPPSLYAAF   41 (69)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHC
Confidence            4999999999999999999885

>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=84.03  E-value=0.55  Score=33.66  Aligned_cols=56  Identities=9%  Similarity=-0.046  Sum_probs=41.1

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCCC-CCCCCCCHHHHHHHHHHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGG-SKPRVATPDVEKRIEEYK  170 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~gg-~rpr~lt~~~~~~I~~l~  170 (230)
                      +++..+||+.++++++||++.+++..+.|-+..  .+..+ ..--.+|+.-++.+.++.
T Consensus        49 ~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~  107 (125)
T d1p4xa2          49 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLL  107 (125)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHH
T ss_pred             CccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHHH
Confidence            579999999999999999999999999997732  12211 122366777776666554

>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=83.97  E-value=0.44  Score=30.35  Aligned_cols=33  Identities=21%  Similarity=0.232  Sum_probs=25.7

Q ss_pred             HHHHHHH----H-HHcC---CCHHHHhhhhccccchhhhHH
Q psy1898         104 IRLKIVE----M-AAAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       104 ~R~rIV~----l-~~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      .|.+|++    + .+.|   .|..+||+..|||++|+|+..
T Consensus         3 tr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F   43 (68)
T d2d6ya1           3 TKARIFEAAVAEFARHGIAGARIDRIAAEARANKQLIYAYY   43 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCccccCHHHHHHHHCcchhHHHHHC
Confidence            4556665    2 2334   999999999999999999875

>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=83.58  E-value=0.46  Score=34.13  Aligned_cols=43  Identities=16%  Similarity=0.250  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898         103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI  145 (230)
Q Consensus       103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v  145 (230)
                      +++.-.+.....|.+.++||+.++++++||.+.+++..+.|-+
T Consensus        35 q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv   77 (137)
T d1z91a1          35 QYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLI   77 (137)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhccce
Confidence            4443333344567999999999999999999999999999976

>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=83.34  E-value=0.41  Score=32.27  Aligned_cols=51  Identities=14%  Similarity=0.104  Sum_probs=35.3

Q ss_pred             HHHcCCCHHHHhhhhccccchhhhHHHHHhhh-CC-CCcCCCCCCCCCCCCHHHHHH
Q psy1898         111 MAAAGVRPCVISRQLRVSHGCVSKILNRYQET-GS-IRPGVIGGSKPRVATPDVEKR  165 (230)
Q Consensus       111 l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~-G~-v~p~~~gg~rpr~lt~~~~~~  165 (230)
                      .++.| |.+.+|+.++||+++|++.+++.++. |. +-.+.   ++.-.+|+.-+..
T Consensus        17 v~~~g-s~t~AA~~l~isq~avs~~l~~lE~~~g~~Lf~R~---~~~~~lT~~g~~l   69 (89)
T d2esna1          17 LYRHR-NVGTAASELAISASAFSHALGRLRQGLDDELFLRQ---GNRMQPTQRAEHL   69 (89)
T ss_dssp             HHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEEE---TTEEEECHHHHHH
T ss_pred             HHHhC-CHHHHHHHHCCCCcHhhHHHHHHHhcCCceeEEEC---CCceeECHHHHHH
Confidence            44444 99999999999999999999999854 53 22221   2445556655433

>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=83.26  E-value=0.28  Score=31.86  Aligned_cols=22  Identities=14%  Similarity=0.170  Sum_probs=20.4

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|...
T Consensus        23 ~~ti~~Ia~~agvs~~~iY~~F   44 (75)
T d2id6a1          23 RATTDEIAEKAGVAKGLIFHYF   44 (75)
T ss_dssp             HCCHHHHHHHHTCCTHHHHHHH
T ss_pred             ccCHHHHHHHhCCCHHHHHHHC
Confidence            4999999999999999999875

>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=83.01  E-value=0.45  Score=30.60  Aligned_cols=22  Identities=5%  Similarity=-0.062  Sum_probs=20.1

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|...
T Consensus        24 ~~s~~~Ia~~agvs~~t~Y~~F   45 (74)
T d1v7ba1          24 TLSYDSLAEATGLSKSGLIYHF   45 (74)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHC
T ss_pred             ccCHHHHHHHhCcCcchHhhhC
Confidence            3999999999999999999873

>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=82.80  E-value=0.62  Score=30.16  Aligned_cols=26  Identities=12%  Similarity=0.116  Sum_probs=23.5

Q ss_pred             CCCHHHHhhhhccccchhhhHHHHHh
Q psy1898         115 GVRPCVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      .+|..+||+.||||+..|..+..+.-
T Consensus        25 ~~tl~eI~~~lgiSrerVrqie~~al   50 (68)
T d2p7vb1          25 DYTLEEVGKQFDVTRERIRQIEAKAL   50 (68)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            48999999999999999999988754

>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=82.20  E-value=1.4  Score=31.41  Aligned_cols=56  Identities=13%  Similarity=0.131  Sum_probs=39.9

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCCC-CCCCCCCHHHHHHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGG-SKPRVATPDVEKRIEEY  169 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~gg-~rpr~lt~~~~~~I~~l  169 (230)
                      .+.+..+||+.++++++||++.+++..+.|-+..  .+..+ ...-.+|+.-.+.+...
T Consensus        45 ~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~  103 (140)
T d2etha1          45 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEI  103 (140)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHHH
Confidence            4599999999999999999999999999997732  12111 12335666655554433

>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=81.97  E-value=0.51  Score=30.13  Aligned_cols=22  Identities=18%  Similarity=0.241  Sum_probs=20.0

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|+..
T Consensus        21 ~~ti~~Ia~~agvs~~~~y~~F   42 (72)
T d1vi0a1          21 QSQVSKIAKQAGVADGTIYLYF   42 (72)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHC
T ss_pred             cccHHHHHHHHCcCHHHHHHHC
Confidence            3999999999999999999873

>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=81.91  E-value=0.58  Score=30.61  Aligned_cols=34  Identities=18%  Similarity=0.149  Sum_probs=26.6

Q ss_pred             HHHHHHHH----HH-HcC---CCHHHHhhhhccccchhhhHH
Q psy1898         103 HIRLKIVE----MA-AAG---VRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       103 ~~R~rIV~----l~-~~G---~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      ..|.+|++    ++ ..|   .|..+||+..|||++|+|+..
T Consensus        11 ~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   52 (81)
T d1rkta1          11 KRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYF   52 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHC
Confidence            45667776    22 334   999999999999999999873

>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=81.89  E-value=0.64  Score=28.05  Aligned_cols=26  Identities=8%  Similarity=0.061  Sum_probs=23.3

Q ss_pred             cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898         114 AGVRPCVISRQLRVSHGCVSKILNRY  139 (230)
Q Consensus       114 ~G~s~~~IAr~lgVS~sTV~kwikRy  139 (230)
                      +..+..++|+.+++|+++++++.+++
T Consensus        18 ~~~tl~~lA~~~~~s~~~l~r~Fk~~   43 (54)
T d1bl0a1          18 SPLSLEKVSERSGYSKWHLQRMFKKE   43 (54)
T ss_dssp             SCCCCHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45999999999999999999998764

>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=81.58  E-value=0.65  Score=32.44  Aligned_cols=38  Identities=18%  Similarity=0.260  Sum_probs=27.4

Q ss_pred             HHHHHHHH----HHHcCCCH----HHHhhhhccccchhhhHHHHHh
Q psy1898         103 HIRLKIVE----MAAAGVRP----CVISRQLRVSHGCVSKILNRYQ  140 (230)
Q Consensus       103 ~~R~rIV~----l~~~G~s~----~~IAr~lgVS~sTV~kwikRy~  140 (230)
                      +.|..+|.    +..+|.+.    .++|.+++||.+|+++|..+-+
T Consensus        33 k~RL~~l~~V~~L~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~~V~   78 (99)
T d2ezla_          33 EKWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQ   78 (99)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCHHHHHHHHHHHC
Confidence            34444443    66678765    4578899999999999987543

>d1u78a2 a.4.1.2 (A:55-104) 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=81.34  E-value=2  Score=25.41  Aligned_cols=46  Identities=15%  Similarity=0.228  Sum_probs=34.6

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898         156 RVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGR  211 (230)
Q Consensus       156 r~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g  211 (230)
                      ..++-.+++-+.... .|...++.+|+.+|.    +.     +|..||-..+++.|
T Consensus         5 k~ls~rdernviraa-sns~kta~dir~el~----l~-----~sk~tiln~i~~~g   50 (50)
T d1u78a2           5 KALSVRDERNVIRAA-SNSCKTARDIRNELQ----LS-----ASKRTILNVIKRSG   50 (50)
T ss_dssp             CSSCHHHHHHHHHHH-HHCCCCHHHHHHHTT----CC-----SCHHHHHHHHHHTC
T ss_pred             cccchHHHHHHHHHH-hcchhhHHHHHHHHh----hh-----hHHHHHHHHHhhcC
Confidence            356667666666655 567899999998874    33     79999999998754

>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=81.31  E-value=0.49  Score=33.83  Aligned_cols=35  Identities=6%  Similarity=0.164  Sum_probs=31.3

Q ss_pred             HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898         113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP  147 (230)
Q Consensus       113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p  147 (230)
                      .+.+|..+||+.+++++..|.|+++.-+..|.+..
T Consensus        16 ~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s   50 (127)
T d1xd7a_          16 DEKTSSEIIADSVNTNPVVVRRMISLLKKADILTS   50 (127)
T ss_dssp             CSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccc
Confidence            34599999999999999999999999999997754

>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=81.21  E-value=0.53  Score=30.12  Aligned_cols=21  Identities=14%  Similarity=0.129  Sum_probs=19.5

Q ss_pred             CCCHHHHhhhhccccchhhhH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kw  135 (230)
                      +.|.++||++.|||++|+|+.
T Consensus        23 ~~t~~~Ia~~agvs~~slY~y   43 (72)
T d1zk8a1          23 EVTLASLAQTLGVRSPSLYNH   43 (72)
T ss_dssp             GCCHHHHHHHHTSCHHHHTTT
T ss_pred             cccHHHHHHHhCCCHHHHHHH
Confidence            399999999999999999976

>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=80.97  E-value=0.68  Score=29.21  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=20.2

Q ss_pred             CCCHHHHhhhhccccchhhhHH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKIL  136 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kwi  136 (230)
                      +.|..+||+..|||++|+|+..
T Consensus        21 ~~ti~~Ia~~agvs~~~iy~~F   42 (69)
T d2np5a1          21 GASVREVAKRAGVSIGAVQHHF   42 (69)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCHHHHHHHhCCCHHHHHHHC
Confidence            3999999999999999999873

>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=80.90  E-value=2.3  Score=28.60  Aligned_cols=39  Identities=15%  Similarity=0.108  Sum_probs=31.7

Q ss_pred             HHHHH-HcC--CCHHHHhhhhc--cccchhhhHHHHHhhhCCCC
Q psy1898         108 IVEMA-AAG--VRPCVISRQLR--VSHGCVSKILNRYQETGSIR  146 (230)
Q Consensus       108 IV~l~-~~G--~s~~~IAr~lg--VS~sTV~kwikRy~e~G~v~  146 (230)
                      ||+.+ +.|  .+.++||+.++  +|.+||+..++...+.|-+.
T Consensus        13 Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~   56 (87)
T d1stza1          13 IVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIY   56 (87)
T ss_dssp             HHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCccc
Confidence            44444 446  88999999966  58999999999999999874

>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=80.60  E-value=1.2  Score=29.85  Aligned_cols=57  Identities=12%  Similarity=0.099  Sum_probs=35.8

Q ss_pred             HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh-CC-CCcCCCCCCCCCCCCHHHHHHH
Q psy1898         107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET-GS-IRPGVIGGSKPRVATPDVEKRI  166 (230)
Q Consensus       107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~-G~-v~p~~~gg~rpr~lt~~~~~~I  166 (230)
                      +++..+.+-.|...+|+.+++|+++|++-+++..+. |. +..+.   ++.-.+|+.-...+
T Consensus         7 ~~f~~v~e~gs~~~AA~~L~isq~avs~~i~~LE~~lg~~Lf~R~---~~~~~lT~~G~~l~   65 (89)
T d1ixca1           7 KYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLERS---HRGIELTAAGHAFL   65 (89)
T ss_dssp             HHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC--------CCBCHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHhcCCceeeEec---CCccCccHhHHHHH
Confidence            344444443499999999999999999999998744 53 22222   23445566655333

>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=80.26  E-value=0.62  Score=29.60  Aligned_cols=21  Identities=10%  Similarity=0.061  Sum_probs=19.3

Q ss_pred             CCCHHHHhhhhccccchhhhH
Q psy1898         115 GVRPCVISRQLRVSHGCVSKI  135 (230)
Q Consensus       115 G~s~~~IAr~lgVS~sTV~kw  135 (230)
                      +.|..+||+..|||++++|+.
T Consensus        24 ~~si~~ia~~~gvs~~~~y~h   44 (68)
T d2g7la1          24 KVTMRRLAQELDTGPASLYVY   44 (68)
T ss_dssp             SCCHHHHHHHTTSCHHHHTTT
T ss_pred             cCCHHHHHHHHCcCHhHhhHH
Confidence            399999999999999999975